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https://f1000research.com/articles/13-34/v1	08 Jan 24	{ "type": "Research Article", "title": "Pelvic pain symptoms and endometriosis characteristics in relation to oxidative stress among adolescents and adults with and without surgically-confirmed endometriosis", "authors": [ "Amy L Shafrir", "Britani Wallace", "Ashley Laliberte", "Allison F Vitonis", "Christine B Sieberg", "Kathryn L Terry", "Stacey A Missmer", "Britani Wallace", "Ashley Laliberte", "Allison F Vitonis", "Christine B Sieberg", "Kathryn L Terry", "Stacey A Missmer" ], "abstract": "Background: While the majority of reproductive-aged females will experience pelvic pain during their lives, biological mechanisms underlying pelvic pain are not well understood. We investigated associations between pelvic pain symptoms and oxidative stress among people with and without surgically-confirmed endometriosis. Methods: Using an enzyme-linked immunosorbent assay, we measured 8-Hydroxy-2’-deoxyguanosine (8-OHdG) in urine samples and corrected for creatinine levels in 434 surgically-confirmed endometriosis participants compared to 605 participants never diagnosed with endometriosis. At enrollment, participants reported details of their pelvic pain symptoms. Linear regression was used to compute geometric mean (GM) creatinine-corrected 8-OHdG levels with 95% confidence intervals (CI) among all participants and those with and without endometriosis separately, adjusting for potential confounders. Interactions by surgically-confirmed endometriosis status were tested by Wald statistics. Results: No trends in 8-OHdG were observed among those with or without endometriosis for severity or frequency of dysmenorrhea, acyclic pelvic pain, dyspareunia or pain with bowel movements. Among endometriosis participants, lower 8-OHdG levels were observed for participants with any white, blue/black, or brown lesions (GM=76.7 versus 82.9 ng/mg; p=0.10), which was primarily driven by lower levels of 8-OHdG for any blue/black lesions (GM=72.8 versus 81.6 ng/mg; p=0.05). Conclusion: While no associations were observed between 8-OHdG and pelvic pain symptoms, future research is needed to assess how other pathways of oxidative damage, e.g. through proteins or lipids, may affect endometriosis-associated symptoms. Additionally, further research is needed to understand differences in oxidative stress among endometriosis lesion sub-phenotypes.", "keywords": [ "oxidative stress", "dysmenorrhea", "pelvic pain", "dyspareunia", "endometriosis", "endometriotic lesions" ], "content": "Introduction\n\nThe vast majority of reproductive-aged females will experience pelvic pain at some point in their lives. Upwards of 90% of females report experiencing dysmenorrhea1 and 15-20% report chronic pelvic pain.2 Pelvic pain can result in reduced quality of life, decreased work productivity, and substantial healthcare costs. While for some individuals, morbidity that may be causing their pelvic pain will be found, (e.g., endometriosis, uterine fibroids), others will struggle to find a gynecologic pathology that may explain their pain. At least 30% of individuals undergoing a laparoscopic surgery for chronic pelvic pain will have no visualized pathology.3 Among those with endometriosis, lesion location and revised American Society for Reproductive Medicine (rASRM) staging have not correlated with pelvic pain severity or pain remediation.4–6 Understanding the biological mechanisms underlying pelvic pain could help to advance treatment options to alleviate these life-impacting symptoms.\n\nWhile inflammatory pathways have been implicated in pelvic pain,7 less is known about the involvement of oxidative stress on pelvic pain symptoms. Normal cellular processes lead to the production of reactive oxygen species (ROS) that can cause tissue damage most notably to proteins, lipids, and DNA. Counteracting antioxidant mechanisms, such as neutralizing ROS, help to reduce the number of ROS in cells. Oxidative stress occurs when the balance between ROS and antioxidants begins to shift, due to either a decrease of antioxidant products or an increase in ROS. Higher levels of oxidative stress have been shown to be present in individuals with fibromyalgia, characterized by widespread pain, and to increase with increasing fibromyalgia pain severity.8 Additionally, oxidative stress is one of the factors implicated in the development and progression of diabetic peripheral neuropathy.9 Limited studies have assessed the association between pelvic pain symptoms and oxidative stress, with the majority observing an increase in oxidative stress and dysmenorrhea (period pain).10–15 However, most of the studies did not adjust for important potential confounders, such as age, body mass index, and cigarette smoking status, which affect oxidative stress levels, and did not assess associations between oxidative stress and pelvic pain symptoms other than dysmenorrhea.\n\nFurther, one of the challenges of studying oxidative stress is that oxidative products are difficult to measure. Free radicals have a very short half-life and thus markers of oxidative damage are often utilized to measure the extent of oxidative stress within an individual. While blood contains organic and inorganic metal content, which can be oxidized during sample collection and storage, urine contains far less organic and inorganic metal content and as such is less likely to have misclassification of in vivo oxidative stress levels due to collection and storage handling.16 8-Hydroxy-2′-deoxyguanosine (8-OHdG) also known as 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodG) is a widely used marker of DNA oxidative stress.16 After DNA repair due to oxidative stress, 8-OHdG is excreted in urine and has been shown to be a reliable marker of oxidative stress.17 Previous studies have noted associations between 8-OHdG and cancer, atherosclerosis, and diabetes pathogenesis.17 However, only one study has assessed pelvic pain symptoms and urinary 8-OHdG levels. This recent study among 188 female university students found no statistical association between dysmenorrhea and 8-OHdG levels.13\n\nTherefore, we sought to understand how oxidative stress measured by urinary 8-OHdG may be related to pelvic pain symptoms. In addition, we explored if these associations may be unique to individuals with endometriosis, a condition commonly found among those with chronic pelvic pain, or play a broader role in pelvic pain symptoms. We investigated the association between dysmenorrhea, acyclic pelvic pain and dyspareunia presence, severity and frequency, as well as pain with bowel movements, in relation to urinary 8-OHdG levels among females with and without surgically-confirmed endometriosis. Additionally, among those with endometriosis, we investigated the association between surgically visualized endometriotic lesion characteristics and urinary 8-OHdG levels.\n\n\nMethods\n\nThe Women’s Health Study: From Adolescence to Adulthood (A2A) cohort enrolled adolescents and adults oversampled for those surgically diagnosed with endometriosis from 2012 to 2018.18,19 Those with endometriosis (n=785) were enrolled from Brigham and Women’s Hospital (BWH) and Boston Children’s Hospital (BCH) and were eligible if they were 1) female; 2) aged 7-55 years; and 3) had a surgical diagnosis of endometriosis. Population and clinic sampled participants without any diagnosis of endometriosis (n=764) were recruited from the local Boston community through local advertisements, online postings, and word of mouth and from BWH and BCH clinics. These participants were eligible if they were females aged 7-55 years without any diagnosis of endometriosis. Those never diagnosed with endometriosis are referred to as “participants without endometriosis” in the manuscript. The study was approved by the BCH Institutional Review Board on behalf of both BCH and BWH (Approval number: P00004267; Approval date: 09/11/2012). Written informed consent was obtained from participants with both parental consent and participant assent for participants less than 18 years of age at enrollment.\n\nAt enrollment, participants completed an extensive baseline questionnaire to assess behavioral and reproductive factors, pain symptoms, quality of life, and medication use that expands upon the World Endometriosis Research Foundation (WERF) Endometriosis Phenome and Biobanking Harmonization Project (EPHect) standard clinical questionnaire.20 Survey data was managed with REDCap electronic data capture tools.21\n\nDetailed information was collected on the baseline questionnaire on the presence, severity, and frequency of dysmenorrhea (pain with periods), acyclic/general pelvic pain (pain not associated with menses), and dyspareunia (pain with sexual vaginal intercourse/penetration). Usual severity of dysmenorrhea was assessed categorically as none, mild (medication never or rarely needed), moderate (medication usually needed), and severe (medication and bed rest needed). Dysmenorrhea frequency within the past 12 months was assessed as never, occasionally, often, usually, and always. For acyclic pelvic pain, participants reported if they had experienced acyclic pelvic pain within the past three months. Among those with acyclic pelvic pain in the past three months, the 11-point numeric rating scale (NRS) was used to assess the acyclic pelvic pain severity during that timeframe, with 0=no pain and 10=worst pain imaginable. Acyclic pelvic pain frequency was assessed as less than monthly, monthly, weekly, and daily. Among participants aged 18 or older, participants reported if they had experienced dyspareunia in the last 12 months. Among those reporting dyspareunia, the 11-point NRS scale was used to assess severity while frequency of dyspareunia during or in the 24 hours after intercourse/penetration in the past 12 months was assessed as never, occasionally, often, usually, and always. Finally, participants reported if they had pain with bowel movements in the past 12 months. Those who reported pain rated the severity of their pain on the 11-point NRS scale.\n\nThe WERF EPHect surgical form was used to capture information on rASRM score, endometriosis subtype, and endometriosis lesion(s) color and location at the surgery closest to urine collection for endometriosis cases.22 We further categorized endometriosis lesions into colors that are normally observed earlier in the lesion progression (i.e. red, yellow, and clear lesions) and later in the lesion progression (i.e. blue, black/brown, and white lesions).\n\nUrine samples were collected at baseline in compliance with the WERF EPHect standardized fluids tools,23 with the exception that we did not require clean catch collection of urine samples. Participants completed a biospecimen questionnaire at the time of sample collection on which they reported date of last menstrual period, timing of last foods/beverages consumed, and recent medication and hormone use. All urine samples were aliquoted into cryovials and stored at -80oC until assayed.\n\n8-OHdG was measured in urine using the HT 8-oxo-dG ELISA Kit II (R&D Systems, Inc. Minneapolis, MN, USA) at the Clinical and Epidemiology Laboratory at Boston Children’s Hospital (BCH). Creatinine levels were also measured in the urine samples using an FDA-approved enzymatic assay method on the Roche Cobas 6000 system using Roche Diagnostics reagents (Indianapolis, IN) at the Clinical and Epidemiology Laboratory at BCH. Approximately 2-3 blinded quality control (QC) urine samples were distributed randomly within each batch. The coefficient of variation (CV) in blinded QC samples for 8-OHdG was 13% and for creatinine was 1.5%.\n\nInformation on covariates was collected on the baseline questionnaire and biospecimen form and included: age at urine collection (continuous), cigarette smoking history (never, former, current), age at menarche (continuous), menstrual cycle phase at time of urine collection (follicular, peri-ovulatory, luteal), hormonal medication use within 30 days from urine collection (yes, no), and pain medication use within 48 hours from urine collection (yes, no). Additionally, participants reported their menstrual period frequency in the past 12 months. We calculated body mass index (BMI) as kg/m2 based on self-reported weight and height. For women aged ≥20 years, BMI was categorized according to the World Health Organization Criteria: underweight (BMI < 18.5 kg/m2), normal weight (18.5-24.9 kg/m2), overweight (25-29.9 kg/m2), and obese (≥30 kg/m2). For those <20 years, the age- and sex-specific BMI Z-score was calculated and participants were categorized as underweight (Z-score ≤-2), normal weight (Z-score >-2 to <1), overweight (Z-score 1-2), and obese (Z-score >2). Participants were also asked to report their physical activity levels at baseline. Participants reported the average time per week they spent doing various activities (e.g. walking/hiking, jogging, running, lap swimming, playing various sports) in the past year. The 2011 Compendium of Physical Activities was then used to assign metabolic equivalent hours (MET-hours) per week to each of the activities.24 We multiplied the reported hours per week engaged in each activity by the appropriate MET score for that activity (e.g. 4 for walking, 8.3 for bicycling, 11.7 for running) and summed the values for the individual activities to create MET-h/wk of total activity. For those with surgically-confirmed endometriosis, information on age at first endometriosis symptoms, number of physicians seen until diagnosed, and time between first symptoms and surgical diagnosis also were reported on the baseline questionnaire.\n\nAlso at baseline, participants completed a semi-quantitative Food Frequency Questionnaire (FFQ), which included over 130 items on the consumption of a range of foods and beverages. The FFQ was utilized to calculate the Alternative Healthy Eating Index (AHEI) score for all participants. Details on this scoring method can be found elsewhere.25,26 Briefly, AHEI scoring is based on the consumption of fruit, vegetables, whole grains, sugar-sweetened beverages and fruit juices, nuts and legumes, red/processed meat, trans fat, long-chain (n-3) fats (EPA + DHA), polyunsaturated fat, sodium, and alcohol. Given the younger age of this cohort (37% <21 years old at baseline), we omitted alcohol from the AHEI calculation. The AHEI score is summed across all of the components and ranges from 0 to 100, with higher scores representing dietary patterns that are more aligned with healthy eating.\n\nOf the 1549 participants enrolled in the A2A cohort, 1209 provided a urine sample at baseline and all 549 endometriosis participants and 660 participants without endometriosis had 8-OHdG and creatinine measured in their baseline urine sample. Of these 1209 participants, we excluded participants who did not complete the questionnaire at baseline (5 endometriosis, 3 without endometriosis) or completed the questionnaire at baseline more than 60 days before/after their urine collection (105 endometriosis, 36 without endometriosis). We also excluded incident endometriosis participants (3 participants without endometriosis at enrollment diagnosed with endometriosis up to 3 years after enrollment) and those who were premenarchal or never cycled (5 endometriosis, 12 without endometriosis) for a final analytic sample size of 434 surgically diagnosed endometriosis participants and 606 participants without endometriosis. Dysmenorrhea analyses were restricted to participants who reported having menstrual periods in the past three months (264 endometriosis and 517 without endometriosis). Analyses of acyclic pelvic pain severity and frequency were restricted to participants who reported having acyclic pelvic pain in the past 3 months (268 endometriosis and 78 without endometriosis). Additionally, analyses of dyspareunia severity and frequency were restricted to participants age ≥18 who reported experiencing dyspareunia in the past 12 months (132 endometriosis and 136 without endometriosis). Analyses of endometriotic lesion characteristics were restricted to the 380 participants with a WERF EPHect surgical form completed at their most recent endometriosis surgery.\n\n8-OHdG and creatinine levels were log-transformed to improve normality. To adjust for differences in urine volume, we divided the 8-OHdG measurement by the creatinine measurement to calculate creatinine-corrected 8-OHdG levels (ng/mg). We then used the generalized extreme studentized deviate many-outlier detection approach to identify statistical outliers for creatinine-corrected 8-OHdG.27 For batch adjustment, levels of creatinine-corrected 8-OHdG were recalibrated to have a comparable distribution to an average batch according to the methods described by Rosner and colleagues.28\n\nAfter exclusions, we used linear regression to calculate geometric means (GM) and 95% confidence intervals (CI) for creatinine-corrected 8-OHdG levels, adjusting for age (continuous), hormone use within the 30 days prior to urine collection (yes, no), any pain medication use within 48 hours prior to urine collection (yes, no), Alternative Healthy Eating Index (quartiles), body mass index (underweight, normal weight, overweight, obese), and physical activity (quartiles of MET-hrs/week). Analyses were conducted among all participants and separately among those with and without endometriosis. Participants were excluded from analyses if they were missing the main pain symptom exposure variable. We calculated trend tests by modeling the categorical pain exposure variable as ordinal, adjusting for the same variables listed above. Pairwise comparisons between levels of categorical variables with three categories or more were performed using the Tukey adjustment for multiple testing. To evaluate if associations between pain symptoms and 8-OHdG levels differed between participants with and without endometriosis, we included an interaction term for endometriosis diagnosis status (endometriosis vs. no endometriosis) and each pain symptom in the linear regression models. The Wald statistic was used to calculate the two-sided p-value for interaction.\n\nIn sensitivity analyses, we restricted analyses to never smokers as cigarette smoking is known to have a significant effect on oxidative stress levels. Additionally, we excluded endometriosis participants who had an endometriosis-related surgery before they completed their baseline questionnaire and/or their baseline urine collection to remove the affects surgery may have had on oxidative stress levels and pain symptoms. All statistical analyses were performed using SAS version 9.4 (SAS Institute Inc., Cary, NC) and all p-values are two-sided.\n\n\nResults\n\nWe included 434 surgically confirmed endometriosis participants and 606 participants without endometriosis in our analyses. On average, baseline questionnaires were completed 6.8 days (standard deviation=17.5) prior to urine collection. At enrollment, those with endometriosis were younger (median age 18 vs. 24 years), and a higher proportion were overweight (25% vs. 20%) and identify as White race (91% vs. 71%) compared to those never diagnosed with endometriosis (Table 1). Additionally, participants without endometriosis were more likely to have had a period in the last three months (85% vs. 61%) compared to endometriosis participants, while endometriosis participants were more likely to have taken hormonal medications within 30 days of urine collection (87% vs. 54%) and pain medication within 48 hours of urine collection (23% vs. 18%) compared to those without endometriosis. Participants without endometriosis also reported higher physical activity and AHEI scores compared to endometriosis participants.\n\n1 Categories do not all add up to 434 participants with endometriosis and 606 without endometriosis due to missing values (BMI: no endometriosis=1; smoking: endometriosis=24, no endometriosis=16; age at menarche: no endometriosis=4; period in last 3 months: endometriosis=4; menstrual cycle phase: endometriosis=5, no endometriosis=8; hormone use: endometriosis=16, no endometriosis=5; physical activity: endometriosis=46, no endometriosis=77; Alternative Healthy Eating Index: endometriosis=51, no endometriosis=86).\n\n2 Participants without endometriosis did not have a surgical diagnosis of endometriosis.\n\n3 Geometric mean levels adjusted for age (continuous), hormone use within the 30 days prior to urine collection (yes, no), pain medication use within 48 hours prior to urine collection (yes, no), Alternative Healthy Eating Index (quartiles), body mass index (underweight, normal weight, overweight, obese), and physical activity (quartiles of MET-hrs/week).\n\n4 Participants in the Other/Unknown category included American Indian/Alaska Native (endometriosis: 1, no endometriosis: 0), Asian (endometriosis: 2, no endometriosis: 84), Native Hawaiian or Pacific Islander (endometriosis: 0, no endometriosis: 1), Multiracial (endometriosis: 13, no endometriosis: 32), other race (endometriosis: 14, no endometriosis: 11), unknown (endometriosis: 1, no endometriosis: 4).\n\n5 For women aged ≥20 years: underweight (BMI < 18.5 kg/m2), normal weight (BMI 18.5–24.9 kg/m2), overweight (BMI 25–29.9 kg/m2), or obese (BMI ≥ 30 kg/m2) according to World Health Organization criteria; For those <20 years, the age- and gender-specific BMI Z-score was calculated, and participants were categorized as underweight (Z-score ≤−2), normal weight (Z-score >−2 to <1), overweight (Z-score 1–2), or obese (Z-score >2).\n\n6 Due to the phrasing in the questionnaire, participants who self-reported having periods could have been on cyclic hormone therapy or having bleeding despite being on continuous hormones.\n\n7 Among participants with self-reported menstrual periods in the past 3 months, who were not on hormones and whose menstrual cycles were not long or irregular.\n\nFor pelvic pain symptoms, we observed no associations between 8-OHdG and dysmenorrhea (severity, frequency), acyclic pelvic pain (presence, frequency, or severity), dyspareunia (presence, frequency, or severity) as well as severity of pain with bowel movements (Table 2). Results between pain symptoms and 8-OHdG were similar when restricted to never cigarette smokers (Table 3). Additionally, results were similar when restricted to participants with urine collection and questionnaire completion before their baseline surgery (Table 4).\n\n1 All p-values are two-sided and were adjusted for age (continuous in years), hormone use within the prior 30 days of urine collection (yes, no), pain medication use within the prior 48 hours of urine collection (yes, no), Alternative Healthy Eating Index (quartiles), body mass index (underweight, normal weight, overweight, obese), and physical activity (quartiles of MET-hrs/week). P-values for interactions between endometriosis and comparison participants were calculated using the Wald statistic.\n\n2 Restricted to 264 endometriosis and 517 no endometriosis participants who reported having periods in the last 3 months. Due to the phrasing in the questionnaire, participants who reported having periods could have been on cyclic hormone therapy or having bleeding despite being on continuous hormones.\n\n3 Missing dysmenorrhea severity: 2 endometriosis and 8 no endometriosis participants.\n\n4 P-value for any difference between three dysmenorrhea severity groups.\n\n5 P-value for test of interaction for those with and without endometriosis.\n\n6 Restricted to participants who answered the baseline questionnaire from January 2014 onwards when this question was added and to participants who reported having periods in the last 3 months (183 endometriosis and 452 no endometriosis participants).\n\n7 Missing dysmenorrhea frequency: 4 endometriosis and 12 no endometriosis participants.\n\n8 P-value for linear test for trend modeling the exposure as ordinal.\n\n9 Missing presence of acyclic pelvic pain: 13 endometriosis and 15 no endometriosis participants.\n\n10 Among participants who reported acyclic pelvic pain in the past three months.\n\n11 Missing acyclic pelvic pain severity: 9 endometriosis and 7 no endometriosis participants.\n\n12 Missing acyclic pelvic pain frequency: 8 endometriosis and 1 no endometriosis participants.\n\n13 Among participants who had intercourse in the past 12 months (excluded 195 endometriosis and 17 no endometriosis aged <18 years, 3 endometriosis and 36 no endometriosis who declined to be asked dyspareunia questions, 57 endometriosis and 85 no endometriosis who had never had intercourse, 7 endometriosis and 14 no endometriosis had not had intercourse in the past 12 months, 5 endometriosis and 14 no endometriosis were missing information on dyspareunia).\n\n14 Among participants age ≥18 with dyspareunia in past 12 months.\n\n15 Missing dyspareunia severity: 2 endometriosis and 1 no endometriosis participants.\n\n16 Based on 0-10 numeric rating scale categorized as none/mild (0-3), moderate (4-6), severe (7-10).\n\n17 Missing severity of pain with bowel movements: 32 endometriosis and 18 no endometriosis participants.\n\n1 All p-values are two-sided and were adjusted for age (continuous in years), hormone use within the prior 30 days of urine collection (yes, no), pain medication use within the prior 48 hours of urine collection (yes, no), Alternative Healthy Eating Index (quartiles), body mass index (underweight, normal weight, overweight, obese), and physical activity (quartiles of MET-hrs/week). P-values for interactions between endometriosis and comparison participants were calculated using the Wald statistic.\n\n2 Restricted to 234 endometriosis and 473 comparison participants who reported having periods in the last 3 months. Due to the phrasing in the questionnaire, participants who reported having periods could have been on cyclic hormone therapy or having bleeding despite being on continuous hormones.\n\n3 P-value for any difference between three dysmenorrhea severity groups.\n\n4 P-value for test of interaction for those with and without endometriosis.\n\n5 Restricted to participants who answered the baseline questionnaire from January 2014 onwards when this question was added and to participants who reported having periods in the last 3 months (163 endometriosis and 417 comparison participants).\n\n6 Missing dysmenorrhea frequency: 2 endometriosis and 6 comparison participants.\n\n7 P-value for linear test for trend modeling the exposure as ordinal.\n\n8 Missing presence of acyclic pelvic pain: 5 endometriosis and 4 comparison participants.\n\n9 Among participants who reported acyclic pelvic pain in the past three months.\n\n10 Missing acyclic pelvic pain severity: 9 endometriosis and 6 comparison participants.\n\n11 Missing acyclic pelvic pain frequency: 8 endometriosis and 1 comparison participants.\n\n12 Among participants who had intercourse in the past 12 months (excluded 182 endometriosis and 17 comparison aged <18 years, 3 endometriosis and 32 comparison who declined to be asked dyspareunia questions, 57 endometriosis and 82 comparison who had never had intercourse, 7 endometriosis and 11 comparison had not had intercourse in the past 12 months, 1 endometriosis and 3 comparison were missing information on dyspareunia).\n\n13 Among participants age ≥18 with dyspareunia in past 12 months.\n\n14 Missing dyspareunia severity: 1 endometriosis and 1 comparison participants.\n\n15 Based on 0-10 numeric rating scale categorized as none/mild (0-3), moderate (4-6), severe (7-10).\n\n16 Missing severity of pain with bowel movements: 17 endometriosis and 6 comparison participants.\n\n1 All p-values are two-sided and were adjusted for age (continuous in years), hormone use within the prior 30 days of urine collection (yes, no), pain medication use within the prior 48 hours of urine collection (yes, no), Alternative Healthy Eating Index (quartiles), body mass index (underweight, normal weight, overweight, obese), and physical activity (quartiles of MET-hrs/week). P-values for interactions between endometriosis and comparison participants were calculated using the Wald statistic.\n\n2 Restricted to 197 endometriosis and 517 comparison participants who reported having periods in the last 3 months. Due to the phrasing in the questionnaire, participants who reported having periods could have been on cyclic hormone therapy or having bleeding despite being on continuous hormones.\n\n3 Missing dysmenorrhea severity: 2 endometriosis and 8 comparison participants.\n\n4 P-value for any difference between three dysmenorrhea severity groups.\n\n5 P-value for test of interaction for those with and without endometriosis.\n\n6 Restricted to participants who answered the baseline questionnaire from January 2014 onwards when this question was added and to participants who reported having periods in the last 3 months (132 endometriosis and 452 comparison participants).\n\n7 Missing dysmenorrhea frequency: 3 endometriosis and 12 comparison participants.\n\n8 P-value for linear test for trend modeling the exposure as ordinal.\n\n9 Missing presence of acyclic pelvic pain: 13 endometriosis and 15 comparison participants.\n\n10 Among participants who reported acyclic pelvic pain in the past three months.\n\n11 Missing acyclic pelvic pain severity: 6 endometriosis and 7 comparison participants.\n\n12 Missing acyclic pelvic pain frequency: 5 endometriosis and 1 comparison participants.\n\n13 Among participants who had intercourse in the past 12 months (excluded 129 endometriosis and 17 comparison aged <18 years, 3 endometriosis and 36 comparison who declined to be asked dyspareunia questions, 35 endometriosis and 85 comparison who had never had intercourse, 6 endometriosis and 14 comparison had not had intercourse in the past 12 months, 5 endometriosis and 14 comparison were missing information on dyspareunia).\n\n14 Among participants age ≥18 with dyspareunia in past 12 months.\n\n15 Missing dyspareunia severity: 1 endometriosis and 1 comparison participants.\n\n16 Based on 0-10 numeric rating scale categorized as none/mild (0-3), moderate (4-6), severe (7-10).\n\n17 Missing severity of pain with bowel movements: 18 endometriosis and 18 comparison participants.\n\nAmong the 380 endometriosis participants who had a WERF EPHect surgical form, the median time between surgery and urine collection was 13 days with an interquartile range of 0 days to 41 days. The vast majority of endometriosis participants had rASRM stage I/II disease (95%) and superficial peritoneal lesions only (96%; Table 5). There was a suggestion of lower 8-OHdG levels for participants with rASRM stage III/IV disease (GM=68.0; CI=55.4-83.5 ng/mg) compared to participants with rASRM stage I/II disease (GM=81.0; CI=77.3-84.9 ng/mg; p=0.10), although this was based on a small sample size of stage III/IV disease and thus limited power. These results remained similar when analyses were restricted to participants with urine collection prior to a baseline surgery (Table 6).\n\n1 Categories do not all add up to 434 cases due to missing values (age at first symptoms=10).\n\n2 All p-values are two-sided and were adjusted for age (continuous in years), hormone use within the prior 30 days of urine collection (yes, no), pain medication use within the prior 48 hours of urine collection (yes, no), Alternative Healthy Eating Index (quartiles), body mass index (underweight, normal weight, overweight, obese), and physical activity (quartiles of MET-hrs/week).\n\n3 Among endometriosis participants with a completed baseline WERF EPHect surgical form (N=380). Among the 380 endometriosis participants, 17 missing rASRM stage and 3 missing endometriosis subtype.\n\n1 Among endometriosis participants with a completed baseline WERF EPHect surgical form (N=298). Among the 298 endometriosis participants, 10 missing rASRM stage and 3 missing endometriosis subtype.\n\n2 All p-values are two-sided and were adjusted for age (continuous in years), hormone use within the prior 30 days of urine collection (yes, no), pain medication use within the prior 48 hours of urine collection (yes, no), Alternative Healthy Eating Index (quartiles), body mass index (underweight, normal weight, overweight, obese), and physical activity (quartiles of MET-hrs/week).\n\nFor superficial peritoneal endometriotic lesion color, the highest 8-OHdG levels were observed for participants with any yellow lesions compared to those without (GMyes=95.3; CI=77.6-116.9 ng/mg vs. GMno=78.9; CI=75.3-82.7 ng/mg; p=0.08; Table 5). Additionally, endometriosis participants with white, blue/black or brown lesions had lower 8-OHdG levels compared to participants without (GMyes=76.7; CI=72.0-81.8 ng/mg vs. GMno=82.9; CI=77.6-88.7 ng/mg; p=0.10). This difference appeared to be driven by lower 8-OHdG levels among participants with any blue/black lesions compared to those without (GMyes=72.8; CI=65.9-80.5 ng/mg vs. GMno=81.6; CI=77.2-85.9 ng/mg; p=0.05) and similarly low levels among participants with brown lesions (p=0.10). Results for brown lesions were attenuated when analyses were restricted to participants with urine collection before their baseline surgery; however, results for having any yellow lesions, any blue/black lesions, and any white, blue/black or brown lesions remained similar (Table 6). We did not observe any differences in 8-OHdG levels by lesion location.\n\n\nDiscussion\n\nIn this cross-sectional analysis among a predominately adolescent and young adult population, we observed that pelvic pain symptoms were not associated with urinary 8-OHdG levels among either participants with or without endometriosis. Among endometriosis participants, rASRM stage III/IV disease was associated with lower levels of urinary 8-OHdG compared to participants with stage I/II disease; however this finding was based on a small number of stage III/IV disease participants. Further, lower 8-OHdG levels were observed for participants with white, blue/black, or brown lesions, suggesting that the role of oxidative stress in endometriosis pathophysiology may differ by lesion type.\n\nThe majority of the previous studies on oxidative stress and pelvic pain symptoms have focused on dysmenorrhea with most observing an association between higher oxidative stress levels among those with dysmenorrhea.10–15 The largest study to date with 897 adolescents observed that the serum pro-oxidant/antioxidant balance was shifted more towards the pro-oxidant side among participants with primary dysmenorrhea compared to those without dysmenorrhea when adjusting for age and BMI.10 Conversely, Konishi et al. (2018) noted that severity of menstrual pain was not associated with urinary 8-OHdG levels among 188 female university students after adjusting for age and BMI. Similar to the results of Konishi et al. (2018), we observed that dysmenorrhea severity was not associated with 8-OHdG. Further, we observed that neither acyclic pelvic pain nor dyspareunia were associated with urinary 8-OHdG among participants with and without endometriosis. We may not have observed associations between 8-OHdG and pelvic pain symptoms in our study due to (1) assessing the DNA oxidative product of 8-OHdG given lipid or protein oxidation may have been more important for endometriosis-associated pelvic pain, (2) it may be that the interplay between oxidative stress and other molecules in the peritoneal cavity, such as inflammatory molecules, may be important for pelvic pain as opposed to oxidative stress on its own, or (3) the younger age of our study population (37% <21 years old) if associations between oxidative stress and pelvic pain are more apparent at older ages. Therefore, future research on other types of oxidative stress and the interplay between oxidative stress and the peritoneal microenvironment in relation to pelvic pain is needed.\n\nOxidative stress has been implicated in the onset and progression of endometriosis and higher levels of oxidative products have been observed in the peritoneal fluid of individuals with endometriosis compared to control participants.29 However, limited studies have assessed differences in oxidative stress levels among subsets of endometriosis patients and those that have, mainly focused on endometriosis patients presenting with infertility. In our study of mainly pain presenting endometriosis participants, we observed a suggestion of lower 8-OHdG levels for rASRM stage III/IV endometriosis compared to stage I/II; however, these results were based on a small sample of rASRM stage III/IV endometriosis participants. Contrary to our results, previous studies have observed increased oxidative stress with higher rASRM stage,11,14,30–32 while two small studies among infertile endometriosis patients observed no association between endometriosis stage and lipid oxidation.33,34 Differences between our results and the previous studies may be due to differences in the study populations with the younger, mostly pain presenting population in the A2A for which the association between oxidative stress and disease stage may be different from endometriosis patients who present with infertility. Additionally, differences between oxidative stress markers measured and biological sample types (e.g. blood, urine) utilized, as well as a lack of adjustment for potential confounders in the previous studies, may have led to differences between our results and previous studies. Finally, we noted that endometriosis participants with any white, blue/black or brown lesions had lower 8-OHdG levels compared to endometriosis participants with no white, blue/black or brown lesions, which appeared to be driven by the presence of blue/black lesions. To our knowledge, no other study has looked at lesion color and oxidative stress levels; therefore, these results warrant further exploration in other studies of endometriosis.\n\nThis study had some limitations including that we had only one marker of oxidative stress and thus may have missed associations between pelvic pain and protein and/or lipid oxidation. Additionally, some of the participants that have never been diagnosed with endometriosis within our study may have undiagnosed endometriosis; however, it is estimated that the community prevalence of undiagnosed endometriosis is <2%. Up to 10 years on since enrollment began in 2012, only four participants who at enrollment into our study had not been diagnosed with endometriosis, were subsequently diagnosed; the three participants who would have been eligible for these analyses were excluded. Effects of the characteristics of this small proportion of undiagnosed cases will be diluted among the true endometriosis-free participants. Further, as these analyses were cross-sectional, we cannot directly elucidate the cause and effect relationship between endometriosis lesion characteristics and 8-OHdG. Finally, the A2A population is predominately White, particularly among endometriosis participants; however, the population reflects the patients treated at the two participating hospitals and the general population of the people referred to those hospitals. Future research involving a more diverse population is needed.\n\nOur study also had several strengths. It is one of the largest studies to date to assess oxidative stress and pelvic pain symptoms, and it included a predominately young population including endometriosis participants who are more proximal to their endometriosis symptom onset compared to previous studies. Although we only included one measure of DNA damage due to oxidative stress, urinary measurement of 8-OHdG has been validated as a reliable biomarker of oxidative stress in previous studies; and in comparison to blood samples, is less affected by potential misclassification due to oxidative processes that occur during sample collection and storage. Finally, we assessed multiple dimensions of pelvic pain, including presence, severity and frequency, which provided a more nuanced assessment of the relationship between pelvic pain symptoms and oxidative stress.\n\n\nConclusions\n\nOur results suggest that urinary 8-OHdG is not associated with dysmenorrhea, acyclic pelvic pain, dyspareunia or pain with bowel movements; however, 8-OHdG did appear to be differentially associated with endometriotic lesion color. Further research into differences in oxidative stress levels between endometriosis lesion types may help to further efforts to understand biologically and clinically informative subgroups of endometriosis patients, who may have different underlying biological processes and thus may respond differently to treatments. Investigations of additional oxidative stress markers among a large population of endometriosis patients with a focus on diversity in endometriosis subtypes will help to advance not only a greater understand of endometriosis pathophysiology but may also help in the development of novel therapeutics for pelvic pain symptoms.", "appendix": "Data availability\n\nData are not publicly available due to information that could compromise research participants’ privacy and consent. However, experienced scientists who would like to inquire regarding use of data from this study to address specific hypotheses or replicate the analyses in this study may submit an application and research proposal. Data requests must be reviewed and approved by the BWH Institutional Review Broad (https://www.brighamandwomens.org/research/research-administration ). All inquiries should be directed to the A2A senior investigator and Boston Center for Endometriosis Scientific Director, Dr. Stacey Missmer (smissmer@hsph.harvard.edu). Data sharing will require a fully executed Data Usage Agreement.\n\n\nReferences\n\nArmour M, Parry K, Manohar N, et al.: The prevalence and academic impact of dysmenorrhea in 21,573 young women: a systematic review and meta-analysis. J. Womens Health. 2019; 28(8): 1161–1171. Publisher Full Text\n\nStanford EJ, Koziol J, Feng A: The prevalence of interstitial cystitis, endometriosis, adhesions, and vulvar pain in women with chronic pelvic pain. J. Minim. Invasive Gynecol. 2005; 12(1): 43–49. PubMed Abstract \| Publisher Full Text\n\nHoward F: The role of laparoscopy as a diagnostic tool in chronic pelvic pain. Best Pract. Res. Clin. Obstet. Gynaecol. 2000; 14(3): 467–494. 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PubMed Abstract \| Publisher Full Text\n\nCoxon L, Horne AW, Vincent K: Pathophysiology of endometriosis-associated pain: A review of pelvic and central nervous system mechanisms. Best Pract. Res. Clin. Obstet. Gynaecol. 2018 Aug 1 [cited 2020 Mar 2]; 51: 53–67. PubMed Abstract \| Publisher Full Text\n\nFatima G, Das SK, Mahdi AA: Some oxidative and antioxidative parameters and their relationship with clinical symptoms in women with fibromyalgia syndrome. Int. J. Rheum. Dis. 2017 Jan 1 [cited 2022 Nov 10]; 20(1): 39–45. PubMed Abstract \| Publisher Full Text\n\nHagen KM, Ousman SS: Aging and the immune response in diabetic peripheral neuropathy. J. Neuroimmunol. 2021 [cited 2022 Nov 10]; 355: 577574. Elsevier B.V. PubMed Abstract \| Publisher Full Text\n\nBahrami A, Bahrami-Taghanaki H, Khorasanchi Z, et al.: Menstrual problems in adolescence: relationship to serum vitamins A and E, and systemic inflammation. Arch. Gynecol. Obstet. 2020; 301(1): 189–197. PubMed Abstract \| Publisher Full Text\n\nAmreen S, Kumar P, Gupta P, et al.: Evaluation of oxidative stress and severity of endometriosis. J. Hum. Reprod. Sci. 2019; 12(1): 40–46. PubMed Abstract \| Publisher Full Text\n\nOrimadegun B, Awolude O, Agbedana E: Markers of lipid and protein peroxidation among Nigerian university students with dysmenorrhea. Niger. J. Clin. Pract. 2019; 22(2): 174–180. PubMed Abstract \| Publisher Full Text\n\nKonishi S, Yoshinaga J, Nishihama Y, et al.: Urinary 8-hydroxy-2′-deoxyguanosine (8-OHdG) concentrations and menstrual cycle characteristics in female university students. Int. J. Environ. Res. Public Health. 2018; 15(12): 1–8.\n\nSantulli P, Chouzenoux S, Fiorese M, et al.: Protein oxidative stress markers in peritoneal fluids of women with deep infiltrating endometriosis are increased. Hum. Reprod. 2015; 30(1): 49–60. PubMed Abstract \| Publisher Full Text\n\nSantanam N, Kavtaradze N, Murphy A, et al.: Antioxidant supplementation reduces endometriosis-related pelvic pain in humans. Transl. Res. 2013; 161(3): 189–195. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIl’yasova D, Scarbrough P, Spasojevic I: Urinary biomarkers of oxidative status. Clin. Chim. Acta. 2012; 413(19–20): 1446–1453. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWu LL, Chiou CC, Chang PY, et al.: Urinary 8-OHdG: A marker of oxidative stress to DNA and a risk factor for cancer, atherosclerosis and diabetics. Clin. Chim. Acta. 2004; 339(1–2): 1–9. Publisher Full Text\n\nDiVasta AD, Vitonis AF, Laufer MR, et al.: Spectrum of symptoms in women diagnosed with endometriosis during adolescence vs adulthood. Am. J. Obstet. Gynecol. 2018; 218(3): 324.e1–324.e11. PubMed Abstract \| Publisher Full Text Reference Source\n\nSasamoto N, Shafrir AL, Wallace BM, et al.: Trends in pelvic pain symptoms over 2 years of follow-up among adolescents and young adults with and without endometriosis. Pain. 2023 Mar 1 [cited 2023 Aug 4]; 164(3): 613–624. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVitonis AF, Vincent K, Rahmioglu N, et al.: World Endometriosis Research Foundation Endometriosis Phenome and biobanking harmonization project: II. Clinical and covariate phenotype data collection in endometriosis research. Fertil. Steril. 2014; 102(5): 1223–1232. Publisher Full Text Reference Source\n\nHarris PA, Taylor R, Thielke R, et al.: Research electronic data capture (REDCap)—A metadata-driven methodology and workflow process for providing translational research informatics support. J. Biomed. Inform. 2009 Apr; 42(2): 377–381. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBecker CM, Laufer MR, Stratton P, et al.: World Endometriosis Research Foundation Endometriosis Phenome and Biobanking Harmonisation Project: I. Surgical phenotype data collection in endometriosis research. Fertil. Steril. 2014 [cited 2020 Apr 8]; 102(5): 1213–1222. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRahmioglu N, Fassbender A, Vitonis AF, et al.: World Endometriosis Research Foundation Endometriosis Phenome and Biobanking Harmonization Project: III. Fluid biospecimen collection, processing, and storage in endometriosis research. Fertil. Steril. 2014; 102(5): 1233–1243. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nAinsworth BE, Haskell WL, Herrmann SD, et al.; 2011 compendium of physical activities: A second update of codes and MET values. Vol. 43, Medicine and Science in Sports and Exercise. Med. Sci. Sports Exerc. 2011 [cited 2022 Sep 19]; 43: p. 1575–81. PubMed Abstract \| Publisher Full Text\n\nChiuve SE, Fung TT, Rimm EB, et al.: Alternative dietary indices both strongly predict risk of chronic disease. J. Nutr. 2012 Jun 1; 142(6): 1009–1018. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nMcCullough ML, Willett WC: Evaluating adherence to recommended diets in adults: the Alternate Healthy Eating Index. Public Health Nutr. 2006 Feb [cited 2022 Sep 19]; 9(1a): 152–157. Publisher Full Text Reference Source\n\nRosner B: Percentage points for a generalized ESD many-outlier procedure. Technometrics. 1983; 25(2): 165–172. Publisher Full Text\n\nRosner BA, Cook N, Portman R, et al.: Determination of blood pressure percentiles in normal-weight children: some methodological issues. Am. J. Epidemiol. 2008; 167(6): 653–666. PubMed Abstract \| Publisher Full Text\n\nCarvalho LFP, Samadder AN, Agarwal A, et al.: Oxidative stress biomarkers in patients with endometriosis: Systematic review. Arch. Gynecol. Obstet. 2012; 286(4): 1033–1040. PubMed Abstract \| Publisher Full Text\n\nPolak G, Barczyński B, Kwaśniewski W, et al.: Low-density lipoproteins oxidation and endometriosis. Mediat. Inflamm. 2013; 2013: 1–4. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVerit FF, Erel O, Celik N: Serum paraoxonase-1 activity in women with endometriosis and its relationship with the stage of the disease. Hum. Reprod. 2008; 23(1): 100–104.\n\nPolak G, Wertel I, Barczyński B, et al.: Increased levels of oxidative stress markers in the peritoneal fluid of women with endometriosis. Eur. J. Obstet. Gynecol. Reprod. Biol. 2013; 168(2): 187–190. PubMed Abstract \| Publisher Full Text\n\nDo Amaral VF, Bydlowski SP, Peranovich TC, et al.: Lipid peroxidation in the peritoneal fluid of infertile women with peritoneal endometriosis. Eur. J. Obstet. Gynecol. Reprod. Biol. 2005 Mar 1 [cited 2022 Nov 17]; 119(1): 72–75. PubMed Abstract \| Publisher Full Text\n\nArumugam K, Dip YCY: Endometriosis and infertility: The role of exogenous lipid peroxides in the peritoneal fluid. Fertil. Steril. 1995 [cited 2022 Nov 17]; 63(1): 198–199. PubMed Abstract \| Publisher Full Text" }	[ { "id": "243123", "date": "11 Mar 2024", "name": "Sylvia Mechsner", "expertise": [ "Reviewer Expertise Gynecology", "Endometriosis" ], "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 investigated the correlation between pelvic pain symptoms and oxidative stress in individuals with and without surgically confirmed endometriosis. Although the research did not find any connections between 8-OHdG and pelvic pain symptoms, it offers valuable insight into the variations in oxidative stress among endometriosis lesion sub-phenotypes. The paper has an impressive sample size and is well structured and written. The use of only one marker for oxidative stress is a major limitation and may have resulted in missed associations. I have read this submission. I believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.\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": "251912", "date": "14 Mar 2024", "name": "Renata Voltolini Velho", "expertise": [ "Reviewer Expertise Endometriosis", "human 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\nPelvic pain symptoms and endometriosis characteristics in relation to oxidative stress among adolescents and adults with and without surgically-confirmed endometriosis\nAmy L Shafrir, Britani Wallace, Ashley Laliberte, Allison F Vitonis, Christine B Sieberg, Kathryn L Terry, Stacey A Missmer\nThe study examined the relationship between pelvic pain symptoms and oxidative stress in individuals with and without surgically confirmed endometriosis. Although no links were found between 8-OHdG and pelvic pain symptoms, the research provides valuable insight into the variations in oxidative stress among endometriosis lesion sub-phenotypes. The paper boasts an impressive sample size and is well-structured and written. However, the study's major limitation is that it only used one marker of oxidative stress, which may have resulted in missed associations. Is there any possibility to include other oxidative stress markers?\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/13-34
https://f1000research.com/articles/13-33/v1	08 Jan 24	{ "type": "Research Article", "title": "The impact of cyberbullying on loneliness and well-being among Malaysian adolescents: The mediation role of psychological distress", "authors": [ "Nadia Samsudin", "Nee Nee Chan", "Hashem Salarzadeh Jenatabadi", "Nee Nee Chan", "Hashem Salarzadeh Jenatabadi" ], "abstract": "Background: Cyberbullying is a distinct phenomenon characterised by the rapid dissemination of information, the permanence of content, and the availability of victims. Yet, there is a scarcity of studies in this field, and few studies have looked at the elements that contribute to cyberbullying behaviour. The aim of this study is to examine the relationship of cyberbullying with loneliness and well-being through psychological distress among adolescents in Malaysia. Methods: 386 teenagers with ages ranging from 12 to 18 were chosen using multistage cluster random sampling. To analyse the data, structural equation modeling was applied. Results: According to the study, cyberbullying has a positive relationship with psychological discomfort but a negative relationship with loneliness and general well-being. Additionally, psychological distress (depression, anxiety, and stress) mediates the relationship between cyberbullying and feelings of wellbeing and loneliness. Conclusions: The results ought to spark discussion about potential treatments to enhance teenage wellbeing and prevent emotional and mental health issues caused by social isolation.", "keywords": [ "cyberbullying", "psychological distress", "loneliness", "mediation analysis", "ICT" ], "content": "Introduction\n\nAs more powerful information technology is produced, the potential for cyberbullying and the misuse of information technology increases due to the immense power of virtual networks and Internet-based communication (Blinka et al., 2023). Researchers are debating its intrinsic susceptibility to various sorts of deviant misuse and inappropriate use more than before (Giumetti & Kowalski, 2022; Lee et al., 2021). Cyberbullying and other deviant behaviours online make use of information technology and social media platforms that are accessible online and are not limited by the parameters of time and location. Because there is no physical touch involved in virtual communication, it is difficult for young people to evaluate the dangers posed by their participation in online social media activities and to comprehend the scope of the damage they are causing (Alavi et al., 2022; Huang et al., 2021).\n\nThe correlation between cyberbullying and behavioural difficulties, social functioning, and psychological health (Hasan et al., 2023; Wright & Wachs, 2022) piques the curiosity of researchers, parents, educators, and the general public. Several studies have demonstrated that cyberbullying is significantly associated with distress (Fabris et al., 2022), loneliness or social isolation (Fang et al., 2022), low self-esteem (Gao et al., 2022) negative self-cognition (Li et al., 2022a), sleeping difficulties (Liu et al., 2021a), hopelessness (McField, Lawrence, & Okoli, 2023), maladaptive emotion regulation (Faura-Garcia et al., 2021), negative social comparison (Villanueva-Moya et al., 2022), resulting in severe consequences, particularly for the victims, including stress, anxiety, and depression (Alhujailli et al., 2020; Martínez-Monteagudo et al., 2020).\n\nRecent research on the link between cyberbullying and depression, both cross-sectional and longitudinal, suggests that cyberbullying is a positive predictor of depressed symptoms (Liu et al., 2020; Yang et al., 2022). Specifically, an increasing number of studies that are both cross-sectional and longitudinal (Cole et al., 2016) indicate that cyberbullying is strongly related with depression. In addition, the prospect of receiving threatening or unpleasant messages through their electronic devices anywhere and at any time of day (Slonje et al., 2013) makes victims believe that the repercussions of these crimes are irreparable, hence increasing their degree of despair. Cyberbullying may result in feelings of grief, emptiness, and/or impatience, as well as avoidance behaviours, which may be related to the phenomenon's special characteristics, such as anonymity and the quick dissemination of information on the Internet (Kowalski et al., 2014).\n\nLess studies have investigated the link between cyberbullying and low levels of subjective well-being, despite the fact that a significant number of studies have established a correlation between cyberbullying and elevated levels of depression (Chamizo-Nieto et al., 2023; Hellfeldt et al., 2020) and at the same time high levels of loneliness; thus, more research is required.\n\nIn recent years, as academics have explored the quality of life of individuals, there has been a growing interest in the study of happiness (Neira et al., 2018). The presence of well-being in one's life is a protective factor against the development of internalising symptoms like depression (Llorent et al., 2021) and psychosomatic conditions (Smith et al., 2018). It is common knowledge that happiness is an individual's perception of their own level of well-being (Li et al., 2022b). Several researchers have hypothesised that cybervictimisation has more harmful effects than traditional bullying (Eyuboglu et al., 2021; Ng et al., 2022) due to the anonymity of the attacker and the absence of monitoring (Graham, 2023). It entails personal life pleasure and positive interactions (Ford et al., 2015), which are essential for adolescents attempting to form an identity. Sadly, cyberbullying encounters can have a severe impact on psychological health, safety, and well-being (Lonergan et al., 2021), notably in adolescents, who are going through a period of rapid physical, psychological, and social development, all of which can contribute to feelings of anxiety, confusion, and emotional instability (Fomina et al., 2020). In this paper, we tested the premise that cyberbullying has a detrimental effect on mental health (well-being) in light of the severity of cybervictimisation's impacts on teenagers. The victim is put into a state of depression as a result of being subjected to digital threats, insults, and denigration. This depression prevents the victim from being able to enjoy any form of social engagement, whether it be online or offline, in a tranquil manner, because it produces dissatisfaction.\n\nIn addition, given that being a cybervictim is a bad experience that can lead to a decline in well-being and that depression can play a significant part in the dynamic that exists between being a cybervictim and one's overall state of well-being (DeSmet et al., 2019; Santos et al., 2021), it can be inferred that depression can impair well-being in adolescents, as mentioned previously. Some behaviours, such as cyberbullying, appear to increase when stressful circumstances are present. Stressful life events are a wide concept that includes negative social–environmental experiences encompassing multiple domains, such as mental states and social connections (Slavich & Immunity, 2019). Since adolescence is a life stage characterised by multiple physiological, psychosocial, and social–environmental changes (Castellví et al., 2020; Yu et al., 2020), stressful life events are widespread among teenagers (Chau et al., 2022).\n\nSeveral researchers believe that loneliness plays a significant role. To put it simply, it is one of the most pressing issues facing contemporary society (Lim et al., 2020). Jeste et al. (2020) believed that loneliness is a subjective feeling of distress induced by a disparity between the desire for and the sense of social ties. There are studies that show links between loneliness and the use of technical devices like mobile phones and computers (Liu et al., 2021b), as is evident when perusing the associated literature. Since adolescent technology use is so pervasive, investigating possible links between the two seems appropriate (O’reilly, 2020). Because of this, it's reasonable to assume that young people turn to online communication as a means of overcoming isolation. Besides that, many physical and behavioural diseases, including heart disease, depression, and cognitive impairment, have been related to loneliness (Freak-Poli et al., 2022; Tan et al., 2019). It is considered as a problem of the elderly. However, Wang et al. (2023) and MacDonald, Willemsen, Boomsma, and Schermer (2020) were able to demonstrate that loneliness is U-shaped across the lifetime, suggesting that it is most prevalent among individuals under the age of 25 and those over the age of 65. While the quality of social contacts protects older generations from loneliness, younger generations place a greater emphasis on their quantity (Schwartz-Mette et al., 2020). Intriguingly, the desire for contact with friends has a bigger impact on loneliness in both groups than actual contact (Verity et al., 2021).\n\nThe victims of cybercrime have been found to suffer from feelings of discontentment and disappointment, as well as difficulties in adjusting to their new environments (Şahin, 2012). It has been said that those who exhibit those kinds of actions have a greater propensity to experience feelings of loneliness (Brighi et al., 2019; Yurdakul & Ayhan, 2021). As a result, there is a strong connection between being a cyberbully or cybervictim and experiencing feelings of isolation. In addition, Shin and Kim (2022) and Méndez et al. (2020) believed that adolescents who are victims of cyberbullying spend a significant amount of time on the internet and on their mobile devices. It's possible that this is due to the fact that people who are predi28sposed to feelings of isolation make use of technologies like mobile phones and the internet as a way to cut themselves off from the rest of society. This lends credence to the idea that cybervictims experience feelings of isolation. Cybervictims do not behave aggressively and do not incite others to behave aggressively towards them. This implies that the high levels of loneliness experienced by cybervictims can be attributable to the negative experiences they have with their peers. [Cyber] victims are more likely to be isolated. According to the Zhou (2021) findings, when teenagers are excluded from their peer groups, this may result in a psychological trauma, which in turn leads to feelings of isolation. Cyberbullying includes activities such as labelling people with derogatory names and ostracising others on the internet (Ronis & Slaunwhite, 2019). The combination of being lonely and spending a lot of time online produces an atmosphere that is ripe for the development of cyberbullying practises.\n\nAccording to the conversations that came before, there has been an exponential increase in the number of researches on cyberbullying. In spite of the abundant and well-established evidence for researching risk factors that contribute to cyberbullying, relatively few studies have focused on depression, stress, and anxiety when investigating the factors that determine whether or not someone engages in cyberbullying. Yet, while studying the relationship between well-being and loneliness in relation to cyberbullying, the prior studies have not been able to come to a consistent set of conclusions. In addition, the potential mediating effects of internal stimuli (such as depression, stress, and anxiety towards cyberbullying) between well-being, loneliness, and cyberbullying have not been systematically tested within an integrated framework. This is despite the fact that these factors have been shown to have a strong relationship with each other.\n\nA serial multiple mediator model was constructed using the framework of structural equation modelling (SEM) and AMOS 21 in order to fully investigate the mechanism by which cyberbullying influences well-being and loneliness through indirect paths. This was done in order to gain a comprehensive understanding of how cyberbullying can have a negative impact on an individual's emotional state. In light of this, the purpose of the current investigation is to look into the following:\n\n1. The relationship of cyberbullying with a) Depression, b) Anxiety and c) Stress in among adolescents.\n\n2. The relationship of depression, anxiety, and stress with a) well-being and b) loneliness among adolescents.\n\n3. The relationship among cyberbullying, depression, anxiety, stress, well-being, and loneliness.\n\n4. The mediating roles of Depression, Anxiety and Stress between cyberbullying and loneliness\n\nThe proposed model is depicted in Figure 1.\n\n\nMethods\n\nThe survey was conducted with the University of Malaya Research Ethics Committee approval (Ref. no: UM.TNC2/UMREC_2492). The research methods were performed in accordance with the relevant guidelines and regulations.\n\nRespondents were provided with an explanation of the research purposed and informed consent was obtained from all respondents. We obtained written informed consent from the parents or legal guardians of all participants below the legal age of consent. This ethical requirement was met to ensure the protection of participants' rights and well-being.\n\nThere were a total of 386 Malaysian adolescents between the ages of 12 and 18 years old (the mean age was 15.73 years, and the standard deviation was 1.08 years). We used two different approaches to determine the most reliable and accurate number of participants based on the structure of our research model when determining the size of our sample. The first method that we used was based on the hypothesis presented by Hair et al. (2014). According to this theory, the required number of samples for the research should be proportional to the number of latent variables included in the investigation. This number should also take into account the number of indicators contained inside the latent variables, as detailed below:\n\n• There must be a minimum of one hundred respondents, there must be no more than five latent variables, and each variable must have at least three indicators.\n\n• There must be a minimum of 150 respondents, and there must be no more than seven latent variables, and each of these variables must have three indicators.\n\n• There must be a minimum of 300 participants, and certain latent variables must have no more than three indicators and no more than seven latent variables.\n\n• There must be a total of 500 respondents, and there are over seven latent variables, some of which have fewer than three indicators each.\n\nThe second way, the minimal sample size is predicted to be 10 times the most complex relationship in the study model by the PLS-SEM rule of thumb, which provides support for the sample size. The G*Power software's power analysis also revealed that a minimum sample size of 85 participants is necessary with an effect size of 0.15, an alpha value of 0.05, and a power of 0.80. As a result, if we use either of the two strategies mentioned above, we will require at least 100 participants for this study.\n\nPurposive sampling was used to recruit participants for the study through various social media platforms like Instagram, Tiktok, Facebook, Telegram, and Twitter. Only Malaysian who were fluent in English and between the ages of 12 and 18 were eligible to participate. Participants contributed to our investigation by filling out an English version of a questionnaire that was hosted on Google Forms. The participants gave their informed written consent, which covers the matters pertaining to anonymity and confidentiality, and it was received from them. There were 386 participants total, with 180 males and the remainder participants being females. It was made up of 150 Malay people, 168 Chinese people, and 68 Indian people. According to the findings, twenty individuals used the Internet for less than one hour per day, 188 used it for two to five hours per day, and 178 used it for more than six hours per day.\n\nThe level of cyberbullying was evaluated with the help of the Revised Adolescent Peer Relations Instrument (RAPRI), which was established by Griezel et al. (2012). It contains cyberbullying as well as cyber victims' goods, although for this particular study, just the cyberbullying materials were utilised. The RAPRI-Bully comprises of 5 items of bully visual and 8 items of bully text, all of which were scored on a Likert-type scale with 6 points, ranging from 1 (never) to 6 (always) (every day). Bullying through the use of video or photographs is referred to as “bully visual,” while bullying through the use of electronic communications such as emails, text messages, or instant chat messages is referred to as “bullying through the use of bully text.” For example, I used a mobile phone to forward a video to a student that I knew they wouldn't like (e.g., Sent a student an email with a message I knew would hurt their feelings). For measuring depression, anxiety, and stress we involved Depression Anxiety Stress Scales-21 (DASS-21) based on Lovibond and Lovibond (1995) theory. A total score on the DASS-21 can range anywhere from 0 to 63, with a subscale score ranging anywhere from 0 to 21, and an item score ranging anywhere from 0 (did not relate to me at all) to three (applied to me very much). The Warwick-Edinburg Mental Wellbeing Scale (WEMWBS) was used to evaluate an individual's positive mental well-being (positive functioning, happiness, and subjective wellbeing) over the course of the most recent two weeks (Tennant et al., 2007). The 14-item scale comprises five response categories, ranging from “None” (meaning “not at all ”) to “All the time” (meaning “always”). The final score ranges from 14 to 70 and indicates low to high levels of positive mental well-being based on the total of the respondents' ratings. The Pittsburgh Sleep Quality Index (PSQI) (Buysse, Reynolds III, Monk, Berman, & Kupfer, 1989) is a self-administered questionnaire that analyses a person's sleep quality over the course of the previous month. A modified version of the Likert scale developed by Russell et al. (1980) was utilised to assess levels of loneliness. This scale is comprised of four points that range from never to always. This index was used to assess the quality of the respondents' sleep. Subjective sleep quality, sleep latency, sleep duration, sleep efficiency, sleep disruption, usage of sleep medication, and daytime dysfunction are the seven components that make up the 19 different sections.\n\n\nResults\n\nThe descriptive statistics indicated that the mean and standard deviation for cyberbullying anxiety, depression, stress, well-being, and loneliness were respectively 2.78 and 0.98, 4.56 and 0.76, 4.03 and 0.98, 4.12 and 1.04, 4.01 and 0.83, and 4.89 and 1.11. Table 1 presents the correlation matrix for all of the study variables. There was a strong and positive correlation between cyberbullying and feelings of sadness, anxiety, and stress.\n\nThe results of this study show that the average variance extracted (AVE) values are higher than 0.50, which indicates that all of the measures have high-quality content and convergent validity. In addition, the validity is supported by the fact that all of the item loadings are higher than the cutoff value of 0.60. The item loadings range from 0.66 to 0.95. It would appear that the overall composite dependability of all latent variables is above 0.75 and sufficient. The values of the variables' Cronbach's alpha have been determined to be greater than the cutoff value of 0.70. The specifics of the discriminant validity are presented in Table 2. When the square roots of all AVE scores are greater than their corresponding inter-correlations, discriminant validity has been demonstrated. In light of the findings presented above, one can draw the conclusion that the measurement model displayed a degree of validity and reliability that is satisfactory.\n\nIt was discovered that the proposed model provided an excellent fit with the data. The model fit was perfect, including [χ2/df = 1.33, p < 0.05], [CFI = 0.93], [GFI = 0.91], [TLI = 0.96], and [RMSEA = 0.031]. It has been stated that there is a positive and significant association between cyberbullying and stress (beta = 0.39; p < 0.001), anxiety (beta = 0.53; p < 0.001), and depression (beta = 0.46; p < 0.001). It has been discovered that all three psychological indices—depression, anxiety, and stress—have a considerable favourable impact on feelings of loneliness, but a significant negative impact on feelings of overall well-being (see Table 3).\n\n\nDiscussion\n\nNumerous studies conducted over the past 20 years have demonstrated the high prevalence and harmful effects of cyberbullying among children, youth, and adolescents. Therefore, it is crucial to identify the elements that can lessen the negative effects that electronic aggression may have on its victims' mental health. It has become clear that resilience is a crucial process that can lessen the effects of various forms of trauma and victimisation. This study, however, is the first to examine the connections between psychological distress (from 13008) indices (stress, anxiety, and depression), loneliness, well-being, and bullying using a theoretical model that takes all factors into account at once. The prevalence of cyberbullying was the first pertinent result. In this study, almost 11% of teenagers reported having experienced cyberbullying in the previous year. The prevalence found in this study is consistent with the findings of earlier research conducted in Malaysia (Balakrishnan, 2015; Lee et al., 2023), despite the fact that prevalence estimates have varied significantly across studies. These statistics show that among teenagers, cyberbullying is a significant issue with a high prevalence.\n\nThe findings also demonstrated a substantial connection between cyberbullying and both well-being and loneliness. Therefore, experiencing cyberbullying increased the likelihood of disclosing depressive symptoms while also lowering happiness (Safaria & Suyono, 2020) and heightening loneliness. Cybervictimization may gradually damage the victim's self-esteem and cause feelings of loneliness and maladjustment, which may lead to increased depression and poorer mental health. Examples include receiving offensive or threatening messages, insulting comments, or rumours that make the victim look foolish. Cyberbullying has actually been linked to a higher likelihood of suicidal ideation (John et al., 2018).\n\nA systematic review (Gaffney et al., 2019) that reveals a high correlation between cyberbullying and internalising symptoms supports our findings, which demonstrate a favourable connection between cyberbullying and psychological distress (depression, anxiety, and stress). According to certain studies (Englander, 2021; Heiman and Olenik-Shemesh, 2016), being a victim can be a stressful situation for teenagers. Because they don't know who their assailants are and are always worried about being subjected to harassment, threats, and critical remarks, victims often feel helpless. This condition exacerbates emotional discomfort, which in turn can cause depression over time. Youths who feel good about themselves and are content with their circumstances are less likely to be victimised. The results of the correlational analysis reveal a substantial negative link, despite the fact that other studies (Cole et al., 2016) highlight how cyberbullying experiences are similar in adolescents and emerging adults insofar as they result in the same effects (such as anxiety, depression, etc.).\n\nIt was surprising to see a negative association between cyberbullying and loneliness. We anticipated a positive relationship, with cyberbullying serving as a (maladaptive) means to combat loneliness and generate responses from others. On the other hand, the more disconnected teenagers were from their peers, the less cyberbullying they reported experiencing. Not only is loneliness an unpleasant emotion, but it's also one that has a low arousal level in comparison to other negative emotions (Eres et al., 2021). Therefore, It is possible that being alone does not cause people to behave aggressively while they are online. It has been found that lonesomeness is more widespread among cybervictims than among cyberbullies, and that cyberbullying engagement is a consequence of loneliness rather than a cause of loneliness (Iorga et al., 2022). In a short-term longitudinal study, Wright and Wachs (2022) were able to demonstrate that cyberbullying decreased feelings of loneliness in boys at the second assessment point. Due to the cross-sectional design of the present study, the link might also be interpreted in the opposite direction: the more cyberbullying perpetrated, the less lonely the offenders felt, which would be consistent with the findings of Wright and Wachs (2022).\n\nRegarding the relationship between cyberbullying and wellbeing, the majority of previous studies have revealed unfavourable connections (Giumetti & Kowalski, 2022; Hellfeldt et al., 2020). We therefore anticipated a negative correlation but found the opposite: cyberbullying positively predicted well-being. Remarkably, the bivariate relationship between cyberbullying and well-being was not significant; cyberbullying positively predicted well-being only in the presence of other predictors, such as emotions of loneliness. Apparently, cyberbullying is only associated with improved well-being when contact limits and feelings of isolation are present. Experiencing release from a compelled condition of passivity by confronting others forcefully appears to have a weak association with well-being. It is important to keep in mind that the impact size is tiny and the standard error is relatively large, thus the relationship between cyberbullying and well-being is not substantial for all individuals (Chun et al., 2021). Surprisingly, among three mediators, anxiety was the strongest mediator between cyberbullying and both well-being and loneliness. The second one was depression. However, we found that stress is not a significant mediator in the relationship between cyberbullying and both well-being and loneliness.\n\nIn this study, it is necessary to address a few constraints. First, this study's conclusions were based on a cross-sectional design, which was incapable of establishing causal links between the research variables. Consequently, the bidirectional or causative relationships must be investigated further utilising longitudinal and experimental approaches. Second, the sample was comprised of junior teens from a particular region of Malaysia, limiting the generalizability of the findings. Hence, offline and online bullying may have larger detrimental consequences on the mental health of Malaysian teenagers. Consequently, the correlations between cyberbullying and depression, anxiety, stress, and the significance of loneliness and well-being may be larger in samples from collectivist cultures than from individualistic ones. Thus, it was suggested that future research duplicate our findings by gathering data from other cultural backgrounds (Malays, Chinese, and Indian). Thirdly, information about the frequency of assistance requests to private/public healthcare services relating to disordered eating behaviours will be useful in corroborating the findings of this study. Due to response bias, the use of self-reported metrics may influence the results to some extent. Future research should employ numerous informants (parents and instructors) and approaches, including experimentation, observation, and interviews.", "appendix": "Data availability\n\nAs the data involves potentially sensitive information, access is subject to approval. Interested readers or reviewers seeking access to the data can submit a request to the corresponding author, specifying the purpose of data usage and agreeing to adhere to confidentiality and ethical guidelines. Access will be granted based on the evaluation of each request to ensure the protection of participant privacy and data security.\n\n\nAcknowledgments\n\nThe authors extend their sincere gratitude to the participants for their invaluable cooperation in this research endeavor. 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Publisher Full Text" }	[ { "id": "253521", "date": "15 Apr 2024", "name": "Jason C McIntyre", "expertise": [ "Reviewer Expertise Social determinants of mental health", "Social identity", "loneliness", "psychosis", "discrimination." ], "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 examined the relationships between cyberbullying and various psychological constructs related to mental health using survey data and structural equation modelling. The research question is important and the data collection methods are mostly sound. However, in my opinion, there are major issues with the rationale, hypotheses, analyses, and interpretation. Of most concern, the paper seems to consistently confuse cyberbullying with cybervictimization. More specific feedback is below, which I hope the authors find helpful.\nIntroduction:\n\nIn the introduction, there were several speculative arguments not supported by evidence. For example, the below section is entirely speculative and does not include any empirical justification: “It’s possible that this is due to the fact that people who are predi28sposed to feelings of isolation make use of technologies like mobile phones and the internet as a way to cut themselves off from the rest of society. This lends credence to the idea that cybervictims experience feelings of isolation. Cybervictims do not behave aggressively and do not incite others to behave aggressively towards them. This implies that the high levels of loneliness experienced by cybervictims can be attributable to the negative experiences they have with their peers. [Cyber] victims are more likely to be isolated.”There are several arguments based on what past authors have “believed” or “said” rather than what they have “found”. Please ensure arguments refer to findings rather than other researchers beliefs or claims. There are several sentences that are not written in appropriate scientific style or have grammatical errors. E.g., “According to the conversations that came before, there has been an exponential increase in the number of researches on cyberbullying.” Several parts of the discussion seem to confound “cyberbullying” with “cybervistimisation”. It appears that the study is looking at the effects of being a cyberbully on psychological outcomes, but a lot of the cited research seems to be related to the consequences of being a victim of cyberbullying. A clearer justification is needed for why the mediator variables are likely to be mediators in the model. For example, there us overwhelming evidence that loneliness is causally linked to depression, yet the arrow is only pointing in one direction. The hypotheses are non-directional, despite the introduction implying clear directions of relationship (e.g., higher cyberbullying should be associated with lower wellbeing).\nResults:\nPlease report tests of normality and do appropriate tests for non-normal variables (e.g., Spearman’s rho vs Pearson’s r). Please indicate which correlation coefficients are significant. It would be helpful to include the SEM diagram and place the various direct and indirect coefficients into the figure to more clearly indicate the significant and non-significant paths. The description of the model is very brief and doesn’t detail the specific mediation pathways. Related to the above point, it is not clear what the phrase “has a favorable impact on loneliness” means. Please indicate whether effects are direct vs indirect, positive vs negative, significant vs non-significant.\nDiscussion: As in the introduction, the discussion confounds cybervictimization and cyberbullying throughout. It described the study as examining the impact of cyberbullying on wellbeing, which is not what was studied or measured. The discussion seems to be generally inconsistent with the method and 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? 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?\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? No", "responses": [] } ]	1	https://f1000research.com/articles/13-33
https://f1000research.com/articles/13-30/v1	08 Jan 24	{ "type": "Clinical Practice Article", "title": "Case Series: Management and outcomes of two cases of colonic perforation following colonoscopy", "authors": [ "Anis Belhadj", "Med Dheker Touati", "Mohamed Raouf Ben Othmane", "Firas Jaouad", "Mohamed Ridha Zayati", "Fahd Khefacha", "Ahmed Saidani", "Faouzi Chebbi", "Anis Belhadj", "Mohamed Raouf Ben Othmane", "Firas Jaouad", "Mohamed Ridha Zayati", "Fahd Khefacha", "Ahmed Saidani", "Faouzi Chebbi" ], "abstract": "Background Colonoscopy is a commonly utilized procedure in gastroenterology, but it carries risks of complications, with perforation being the most dreaded. The management of colonic perforation remains a topic of debate, as it can be effectively treated through surgical or non-surgical approaches. Our objective is to detail clinical presentations, diagnostic methods, and potential therapeutic options.\n\nCases For this study, we gathered clinical and radiological data from two cases of colonic perforation following colonoscopy. We examined clinical presentations, diagnostic methods employed, and the different therapeutic approaches used for each case. In both cases, patients exhibited symptoms of colonic perforation following colonoscopy. The first case was managed conservatively, with progressive clinical improvement. The second case showed signs of pneumoperitoneum, but no perforation was found during laparoscopic intervention. Both patients recovered well and experienced no complications during follow-up.\n\nConclusions Our study highlights the importance of understanding the risks associated with colonoscopy, particularly in patients with risk factors. It also underscores the diversity of available treatment approaches for iatrogenic colonic perforation, emphasizing the significance of a multidisciplinary approach in determining the optimal therapeutic strategy.", "keywords": [ "Colonic perforation", "Colonoscopy", "Iatrogenic Disease", "emergency", "management", "outcome" ], "content": "Introduction\n\nColonoscopy is one of the most frequently used complementary exploration methods in gastroenterology. While it is generally considered low-risk, complications can arise, among which perforation is the most feared, even in the absence of surgical intervention. The incidence of iatrogenic colonic perforation could be as low as 0.016% of all diagnostic colonoscopy procedure1 and could reach up to 5% in interventional colonoscopies.2,3\n\nThe most commonly observed radiological translation is that of pneumoperitoneum (PNP). However, cases of pneumoperitoneum occurring without perforation following a diagnostic colonoscopy have been reported.4 The management of colonic perforation remains a controversial issue, as it can be effectively handled through both surgical and non-surgical approaches.4,5\n\nIn this study, we present two cases of colonic perforation that occurred after colonoscopy, each with distinct manifestations and managed in different ways. The aim of our work is to detail the clinical presentations, diagnostic methods, and potential therapeutic options.\n\n\nCase presentations\n\nThe patient was a 44-year-old man of Arab descent who worked as a taxi driver and had no prior medical history of diabetes or hypertension. He was admitted to Mahmoud El Matri hospital in the gastroenterology department for a screening colonoscopy due to chronic constipation. The examination revealed moderate colon preparation using 4 liters of Polyethylene Glycol (PEG) administered orally over 4 hours before the colonoscopy. A 7 mm polyp was found in the left colon, which was surgically removed.\n\nOne day after the procedure, the patient experienced sudden, sharp, non-radiating abdominal pain. During the examination, the patient was afebrile and stable in terms of hemodynamics, respiration, and neurological status. Sensitivity was noted in the left flank without signs of peritonitis, while the rest of the abdomen was soft, depressible, and painless.\n\nBlood tests showed a mild biological inflammatory syndrome with a c-reactive protein (CRP) level of 39 mg/ml, and no leukocytosis, a hemoglobin level of 12 g/dl, and appropriate hemostasis. As a result, an abdominal computerized tomography (CT) scan with contrast injection was performed, revealing small retroperitoneal extra-digestive air bubbles adjacent to the middle third of the descending colon (Figure 1). Thickening of the surrounding peritoneal layers and an effusion were also observed.\n\nCT, computerized tomography.\n\nBased on the clinical and radiological findings, an immediate surgical intervention was deemed unnecessary. Instead, the patient was treated conservatively, with a strict fasting approach, total parenteral nutrition, and close clinical and biological monitoring. Additionally, the patient was placed on empiric antibiotic therapy consisting of cefotaxime 1 g * 3/day and Metronidazole 500 mg * 3/day, administered intravenously.\n\nSubsequent laboratory follow-up showed regression of the biological inflammatory response. An abdominal CT scan performed on the second day of treatment revealed a stable retroperitoneal aspect adjacent to the middle third of the left colon, with an associated localized peritoneal reaction (Figure 2).\n\nCT, computerized tomography.\n\nThe patient’s condition evolved with clinical and biological improvement, including sustained apyrexia, disappearance of abdominal pain, and a normal abdominal examination. An abdominal CT scan performed on the fifth day of treatment demonstrated partial regression of the retroperitoneal air bubbles, as well as persistent localized peritoneal reaction (Figure 3).\n\nCT, computerized tomography.\n\nOn the sixth day, a liquid diet via oral intake was gradually introduced and well tolerated. The patient was allowed to leave the hospital two days later.\n\nA follow-up after two months showed the absence of complications, a normal condition. Furthermore, a two-month follow-up CT scan confirmed the complete resolution of retroperitoneal air (Figure 4).\n\nCT, computerized tomography.\n\nThis case concerns a 55-year-old male patient of Arab descent with no significant medical history, who worked as a fishmonger. He was admitted to Mahmoud El Matri hospital in the gastroenterology department for a screening colonoscopy.\n\nAs per the information provided by the gastroenterology consultant, despite the colonic preparation being deemed satisfactory, the colonoscope could only be advanced up to a distance of 40 cm due to technical difficulties associated with an irreducible sigmoid loop, despite multiple attempts, leading to the termination of the procedure.\n\nIn the hours following the completion of the colonoscopy, the patient began experiencing abdominal pain accompanied by vomiting. The examination revealed an afebrile patient, eupneic, hemodynamically stable with a blood pressure of 130/70 mmHg and a heart rate of 89 bpm. Palpation of the abdomen indicated painful distension. An abdominal X-ray without prior preparation was performed, revealing bilateral pneumoperitoneum associated with aerocoly (Figure 5).\n\nGiven these clinical and radiological findings, a decision was made in favor of a laparoscopic surgical intervention to explore the abdominal cavity and investigate a potential colonic perforation. However, despite a meticulous and precise exploration of the entire abdominal cavity during the procedure, no perforation, leakage, or abdominal effusion was observed. The intervention concluded with the placement of an aspiration drainage in the cul-de-sac of Douglas.\n\nPostoperative recovery was uneventful, characterized by a reduction in abdominal pain and restoration of intestinal function. Liquid diet was gradually reintroduced, and following clinical and biological improvement, the patient was discharged from the hospital on the sixth day post-intervention. During a follow-up consultation one month later, the patient presented no complications.\n\n\nDiscussion\n\nThe case report presents two patients who underwent colonoscopies with potential colonic perforation complications. The strengths include detailed patient information, comprehensive clinical assessments, imaging diagnostics, and the demonstration of the effectiveness of conservative management in the first case. However, the second case lacks intraoperative photos, and the duration of monitoring is short for both cases.\n\nColonoscopy, a commonly performed procedure and the primary diagnostic tool for colorectal cancer, also plays a role in managing specific colorectal conditions, despite its relative safety, it does entail potential complications including colonic perforation, gastrointestinal bleeding, injury to intra-abdominal organs, and cardiopulmonary instability.6\n\nAlthough rare, Iatrogenic perforation carries a significant risk of morbidity and mortality.7 The optimal management approach involves a collaborative effort among endoscopists, radiologists, and surgeons, requiring their prompt availability.\n\nThe incidence of colonic perforation varies between diagnostic and therapeutic colonoscopies,8,9 with both sharing similar mechanisms such as mechanical injuries or barotrauma, but therapeutic colonoscopy presenting an additional potential risk of perforation,10 resulting in an incidence ranging from 0.03% to 0.8% for diagnostic colonoscopy and 0.15% to 3% for therapeutic colonoscopy.6\n\nDuring diagnostic procedures, iatrogenic perforations are most frequently observed in the sigmoid colon and the rectosigmoid junction. This occurs because of direct mechanical injury caused by the shearing forces exerted by the colonoscope’s shaft or tip during insertion.11,12 The risk of perforation can be further elevated by pericolic adhesions, which may result from previous gynecological surgeries or abdominal inflammation, as well as by severe diverticular disease. This increased risk is particularly notable when using large-caliber instruments13,14 with excessive force.\n\nIn the realm of interventional colonoscopies, researchers have highlighted several noteworthy risk factors for iatrogenic colonic perforation. These influential factors encompass polypectomies, especially for polyps exceeding 20 mm in size, pneumatic dilatation for the management of strictures linked to inflammatory bowel diseases, the application of argon plasma coagulation, along with endoscopic mucosal resection and endoscopic submucosal dissection for colorectal neoplasms. Moreover, patient-related variables, including age, female sex, malnutrition, multiple comorbidities, a history of inflammatory bowel disease, and prior colon surgery, as well as the experience level of the endoscopist, play significant roles in the risk profile. Furthermore, it’s worth noting that the use of flexible sigmoidoscopy has also been associated with an elevated risk of perforation.13\n\nThe risk of colonic perforation exists even in the absence of interventions, whether it occurs due to direct trauma to the colonic wall by the endoscope, shearing forces, or barotrauma. Regarding frequency, the sigmoid colon is the most commonly affected site in iatrogenic colonic perforation cases (53-64%), followed by the cecum (14-24%) and the ascending colon (24%), with notably lower incidences in the transverse colon, descending colon, and rectum.6 Colonic perforations can be categorized into three types: intraperitoneal (the most prevalent scenario), extraperitoneal, or a combination of both.6\n\nThe distribution of free air within distinct anatomical regions leads to the manifestation of symptoms and clinical signs, which depend on the type of perforation.13 Typically, colonic perforation presents with acute abdominal pain, sometimes accompanied by fever. It may also exhibit signs of peritonitis such as abdominal tenderness, guarding or rigidity, abdominal distension, or, in the case of extraperitoneal perforation, subcutaneous emphysema.13\n\nThe most common clinical feature of colonic perforation is the visualization of an extra-intestinal structure during the endoscopic examination.2 However, patients with colon perforation may present with symptoms and signs of peritonitis (primarily abdominal pain and tenderness) in the hours following the completion of colonoscopy, as seen in our third reported case. When perforation is suspected, an abdominal X-ray should be performed to rule out the presence of pneumoperitoneum. Other tests, such as computed tomography (CT) scanning and magnetic resonance imaging, are also highly useful for identifying the presence of free gas.13\n\nThe use of a water-soluble contrast enema is rarely performed to detect or confirm a concealed perforation. In practice, patients can be diagnosed and treated for colonic perforation based on generalized peritonitis, even in the absence of radiological evidence of perforation.\n\nWhile perforations usually occur during or within 24 hours of a colonoscopy, delayed perforations of the colon and rectum, as observed in our first case, have been reported. Therefore, physicians should consider colonic perforation if a patient presents with symptoms like fever, abdominal pain, or distension following the procedure, even if these symptoms manifest several days later. It is advisable to promptly and thoroughly assess and document any symptoms or signs indicative of iatrogenic perforation after an endoscopic procedure using a CT scan.14\n\nFollowing endoscopic resection, the presence of small gas bubbles may be observed, which do not necessarily indicate a genuine iatrogenic perforation.15 Hence, it is crucial to consider radiological findings alongside endoscopic and clinical assessments. Due to the intricate nature of managing iatrogenic perforations, it is essential to have a multidisciplinary team comprising the endoscopist, radiologist, and surgeon available. The post-treatment follow-up for an iatrogenic perforation is contingent upon its type, location, and the patient’s clinical status, necessitating nearly obligatory hospitalization.\n\nIndeed, the choice of treatment for iatrogenic perforation hinges on several factors, including the timing of diagnosis (whether intra- or post-procedure), the presence and nature of luminal contents (whether “clean” or not), the specific characteristics of the perforation (size and location), the patient’s overall health status, the expertise of the endoscopist, and the availability of closure devices. Therapeutic options encompass immediate endoscopic closure, a conservative approach, or surgical intervention. In cases where iatrogenic perforation is identified during the endoscopy, it is advisable, if feasible and reasonable, to complete the interventional procedure. Swift endoscopic closure, whenever possible, not only prevents peritonitis or mediastinitis but also reduces the necessity for surgical intervention.16–18 A variety of endoscopic clips have been applied according to the size of iatrogenic perforation.\n\nThe conservative approach entails the administration of intravenous antibiotics, withholding oral intake, continuous monitoring of hemodynamics, and maintaining close interdisciplinary follow-up.19 For malnourished patients or well-nourished individuals who won’t be able to eat for ≥ 7 days, parenteral nutrition is advised.20 If the conservative approach proves ineffective and the patient’s condition worsens, such as the development of septic or peritonitis symptoms, surgical intervention is strongly considered.21 Early surgery is typically preferred for patients with large perforations, generalized peritonitis, ongoing sepsis, deteriorating clinical conditions, or after percutaneous drainage has failed. The choice between laparoscopy and open surgery for managing iatrogenic perforations primarily depends on the perforation’s location and the surgeon’s judgment. Minimally invasive laparoscopic treatment has become the favored surgical approach for colonic iatrogenic perforations due to its superior outcomes compared to open surgery.7\n\n\nConclusions\n\nOur two cases have demonstrated two different scenarios in the management and clinical presentation of colonic perforation following colonoscopy. This article has provided a comprehensive overview of iatrogenic colonic perforation, covering its incidence, risk factors, clinical presentation, diagnostic methods, and treatment options. It emphasizes the importance of a multidisciplinary approach and the consideration of various factors when determining the appropriate course of treatment. The article also highlights the increasing preference for minimally invasive laparoscopic procedures in managing colonic iatrogenic perforations.\n\n\nConsent\n\nWritten informed consent for publication of their clinical details and clinical images was obtained from both patients.", "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\nRathgaber SW, Wick TM: Colonoscopy completion and complication rates in a community gastroenterology practice. Gastrointest. Endosc. 2006; 64(4): 556–562. PubMed Abstract \| Publisher Full Text\n\nRepici A, Pellicano R, Strangio G, et al.: Endoscopic mucosal resection for early colorectal neoplasia: pathologic basis, procedures, and outcomes. Dis. Colon Rectum. 2009; 52(8): 1502–1515. PubMed Abstract \| Publisher Full Text\n\nDamore LJ, Rantis PC, Vernava AM, et al.: Colonoscopic perforations: etiology, diagnosis, and management. Dis. Colon Rectum. 1996; 39: 1308–1314. Publisher Full Text\n\nKang HY, Kang HW, Kim SG, et al.: Incidence and management of colonoscopic perforations in Korea. Digestion. 1952; 78(4): 218–223. Publisher Full Text\n\nAvgerinos DV, Llaguna OH, Lo AY, et al.: Evolving management of colonoscopic perforations. J. Gastrointest. Surg. 2008; 12: 1783–1789. PubMed Abstract \| Publisher Full Text\n\nBasendowah MH, Futayni SA, Ismail RA, et al.: A Case of Post-Colonoscopy Cecal Perforation in a 78-Year-Old Man Responding to Conservative Management. Cureus. févr 2022; 14(2): e22364. PubMed Abstract \| Publisher Full Text\n\nMartínez-Pérez A, de’Angelis N, Brunetti F, et al.: Laparoscopic vs. open surgery for the treatment of iatrogenic colonoscopic perforations: a systematic review and meta-analysis. World J. Emerg. Surg. 2017; 12: 1–10. Publisher Full Text\n\nArora G, Mannalithara A, Singh G, et al.: Risk of perforation from a colonoscopy in adults: a large population-based study. Gastrointest. Endosc. mars 2009; 69(3 Pt 2): 654–664. PubMed Abstract \| Publisher Full Text\n\nRabeneck L, Paszat LF, Hilsden RJ, et al.: Bleeding and perforation after outpatient colonoscopy and their risk factors in usual clinical practice. Gastroenterology. déc 2008; 135(6): 1899–906, 1906.e1. PubMed Abstract \| Publisher Full Text\n\nLohsiriwat V, Sujarittanakarn S, Akaraviputh T, et al.: What are the risk factors of colonoscopic perforation? BMC Gastroenterol. 24 sept 2009; 9: 71. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLüning TH, Keemers-Gels ME, Barendregt WB, et al.: Colonoscopic perforations: a review of 30,366 patients. Surg. Endosc. juin 2007; 21(6): 994–997. PubMed Abstract \| Publisher Full Text\n\nHawkins AT, Sharp KW, Ford MM, et al.: Management of colonoscopic perforations: A systematic review. Am. J. Surg. avr 2018; 215(4): 712–718. PubMed Abstract \| Publisher Full Text\n\nde’Angelis N, Di Saverio S, Chiara O, et al.: 2017 WSES guidelines for the management of iatrogenic colonoscopy perforation. World J. Emerg. Surg. 2018; 13: 5. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPaspatis GA, Arvanitakis M, Dumonceau JM, et al.: Diagnosis and management of iatrogenic endoscopic perforations: European Society of Gastrointestinal Endoscopy (ESGE) Position Statement - Update 2020. Endoscopy. sept 2020; 52(9): 792–810. PubMed Abstract \| Publisher Full Text\n\nBaron TH, Wong Kee Song LM, Zielinski MD, et al.: A comprehensive approach to the management of acute endoscopic perforations (with videos). Gastrointest. Endosc. oct 2012; 76(4): 838–859. PubMed Abstract \| Publisher Full Text\n\nRaju GS, Fritscher-Ravens A, Rothstein RI, et al.: Endoscopic closure of colon perforation compared to surgery in a porcine model: a randomized controlled trial (with videos). Gastrointest. Endosc. août 2008; 68(2): 324–332. Publisher Full Text\n\nFritscher-Ravens A, Hampe J, Grange P, et al.: Clip closure versus endoscopic suturing versus thoracoscopic repair of an iatrogenic esophageal perforation: a randomized, comparative, long-term survival study in a porcine model (with videos). Gastrointest. Endosc. nov 2010; 72(5): 1020–1026. PubMed Abstract \| Publisher Full Text\n\nSchmidt A, Fuchs KH, Caca K, et al.: The Endoscopic Treatment of Iatrogenic Gastrointestinal Perforation. Dtsch. Arztebl. Int. 26 févr 2016; 113(8): 121–128. PubMed Abstract \| Publisher Full Text\n\nDi Leo M, Maselli R, Ferrara EC, et al.: Endoscopic Management of Benign Esophageal Ruptures and Leaks. Curr. Treat. Options Gastroenterol. juin 2017; 15(2): 268–284. PubMed Abstract \| Publisher Full Text\n\nWeimann A, Braga M, Carli F, et al.: ESPEN guideline: Clinical nutrition in surgery. Clin. Nutr. juin 2017; 36(3): 623–650. PubMed Abstract \| Publisher Full Text\n\nKnudson K, Raeburn CD, McIntyre RC, et al.: Management of duodenal and pancreaticobiliary perforations associated with periampullary endoscopic procedures. Am. J. Surg. déc 2008; 196(6): 975–982. discussion 981–982. PubMed Abstract \| Publisher Full Text" }	[ { "id": "260366", "date": "23 Apr 2024", "name": "Faming Zhang", "expertise": [ "Reviewer Expertise Microbiome and gastrointestinal intervention 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\nThis study addresses the management of iatrogenic colonic perforation, a challenging issue for clinicians. While the study has commendable intentions, it also presents some problems.\nREQUESTED REVISIONS: In the “Introduction” section, the coherence of the context needs to be further improved, particularly in the second paragraph.\nIn the “Case Presentations” section, the first case is a typical example of iatrogenic colonic perforation where conservative treatment proved effective. However, in the second case, the evidence of iatrogenic perforation needs to be more substantial.\nIn the “Discussion” section, the management of iatrogenic colonic perforation is an evolving field, with readers preferring more recent advancements rather than conventional topics. As seen in the citation, only two articles from the past five years have been referenced. The authors should conduct a more comprehensive discussion on iatrogenic colonic perforation, incorporating updated technologies such as colonic transendoscopic enteral tubing and the over-the-scope clip.\nThere are some details in the text that need further scrutiny and refinement. For instance, in the fifth paragraph on page eight, it mentions the third patient, whereas the case report only involves information about two patients.\n\nIs the background of the cases’ 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 conclusion balanced and justified on the basis of the findings? Partly", "responses": [] }, { "id": "327817", "date": "04 Nov 2024", "name": "Omorodion Omoruyi Irowa", "expertise": [ "Reviewer Expertise General Surgery", "Surgical endoscopy and Laparoscopy" ], "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\nCase 1 The abdominal examination section which was written as----- \"Sensitivity was noted in the left flank without signs of peritonitis, while the rest of the abdomen was soft, depressible, and painless.\" ---should be: Tenderness was noted in the left flank without signs of generalized peritonitis.\nProvide details on how the 7mm polyp was \"surgically removed\"\nThe first sentence in the sixth paragraph should be modified thus --- \"The patient’s symptoms resolved with clinical and biological improvement, including sustained apyrexia, disappearance of abdominal pain, and a normal abdominal examination\"\n\nCase 2 The abdominal X-ray was report as \"bilateral pneumoperitonium\". The report should have better been interpreted as pneumoperitoneum with air under both copula of the diaphragm and aerocoly. Note: The peritoneal cavity is one and air within it cannot be in two compartments\nMore details should be provided on the laparoscopic intervention especially in the face of dilated colon (aerocoly). How was the gut decompressed to allow for good exploration\nIn the Discussion section the authors should make it more robust by constant reference to the cases compared to the standard of care of colonic perforations\nThe conclusion is too sweeping and should be streamlined to the issue under discourse. The second sentence should be removed as this article is not a review of literature but a case report.\n\nIs the background of the cases’ 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 conclusion balanced and justified on the basis of the findings? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-30
https://f1000research.com/articles/13-29/v1	08 Jan 24	{ "type": "Study Protocol", "title": "Effectiveness of dynamic neuromuscular stabilization, neurodevelopmental techniques and proprioceptive neuromuscular facilitation on trunk and gait parameters in patients with subacute stroke: A three-arm parallel randomised clinical trial", "authors": [ "Swadha P Udhoji", "Raghuveer Raghumahanti", "Rakesh K Kovela", "Raghuveer Raghumahanti", "Rakesh K Kovela" ], "abstract": "Background Today, stroke is the principal cause of demise in both developed and developing countries. There are different techniques used to treat patients with sub-acute stroke. Trunk muscles play a key role, i.e. in keeping the spine and trunk in place. This stabilization requires moving the head and extremities freely and selectively. The aim of this study is to compare the effectiveness of dynamic neuromuscular stabilization (DNS), neurodevelopmental techniques (NDT) and proprioceptive neuromuscular facilitation (PNF) on trunk and gait parameters in the subacute phase of stroke. This study is intended to ascertain the efficacy of all three approaches individually and to compare the effectiveness of DNS, NDT and PNF on trunk and gait parameters. Furthermore, the findings of this study could be used to assist post-stroke survivors in their early recovery and improve their level of independence.\n\nMethods In this interventional study, participants will be divided into three groups, and in each group, 20 patients will be assigned randomly to each group using the sequentially numbered opaque sealed envelope method. Group A patients will be given DNS, Group B will be given NDT, and Group C will be given PNF. The patients will be given treatment for five days for four consecutive weeks. Outcome measures that will be used are trunk impairment scale (TIS), dynamic gait index (DGI) and gait parameters. Data will be collected before and after the 4-week treatment period.\n\nConclusions After the study, a conclusion will be drawn regarding which treatment technique is most suitable among all the three strategies for treating stroke patients if the hypothesis of the study is found valid. Clinical Trials Registry – India (CTRI) reference no. CTRI/2022/06/043037; date of registration 22/05/2022.", "keywords": [ "dynamic neuromuscular stabilization", "neurodevelopmental techniques", "proprioceptive neuromuscular facilitation", "subacute stroke", "trunk control", "balance", "gait parameters", "core stability" ], "content": "Introduction\n\nToday, stroke is the foremost cause of death in both developed and emerging countries.1 The World Health Organization currently defines stroke as being characterized by rapidly emerging neurological signs of localized (and global) deterioration of neurological function persisting over 24 hours or resulting in death, having no apparent cause beyond an internal circulatory source (defined in 1970 and still used).2 As per a recent analysis primarily based on cross-sectional studies, it is estimated that in India stroke incidence ranges between 105 and 152/100,000 people per year.3 Following an acute ischemic stroke (AIS), the blood brain barrier (BBB) passes through many hemodynamic phases. An increase in permeability (BBBP) could lead to unfavorable consequences like haemorrhagic transformation (HT) on the one hand or increased neoangiogenesis, enabling the entry of potential therapeutic agents on the other hand. Different hemodynamic phases and processes accompany stroke, leading to distinct pathological responses. These phases include hyperacute (less than six hours), acute (6–72 hours), subacute (more than 72 hours), and chronic phase (more than four weeks), with frequently divergent clinical outcomes that must be addressed.4 In cerebrovascular accident (CVA), there is decreased cerebral blood flow (CBF), which can impair neurological function, and lead to sparse oxygen distribution and glucose, starting the stroke pathophysiology cascade.5 After the stroke, if the clinical features last for two weeks, then it is called the acute stage or initial phase of stroke; if it lasts more than two weeks and the condition remains the same for up to six months, then it is called the sub-acute phase; if it lasts six months to years then it is called the chronic phase of stroke.6 An important predicting factor in the admitted patient is maintaining balance while sitting and performing the activity of daily living (ADLs) such as eating, toilet utilization, movement, self-hygiene, bathing, getting dressed, and bladder and bowel control.7 Changes in trunk position awareness and muscular weakening in stroke patients mostly impact balance problems.8 Trunk muscles play an important role, i.e., keeping the spine and trunk in place. This stabilization requires moving the head and extremities freely and selectively.7 Walking dysfunction is a significant problem for many subjects affected by stroke. This makes it difficult to carry out daily tasks.9 If not addressed early in the rehabilitation process, gait asymmetry can be prolonged and worsen gait impairment.10 Bobath, Brunnstrom, Coulter, Clayton, Fay, Kabat, Knott and Rood, Voss, and Kolar are some of the physiotherapeutic approaches available. As a result, stroke rehabilitation should be cost-effective and, on the contrary, stroke rehabilitation appears to be preferable to spontaneous recovery.11\n\nDynamic neuromuscular stabilization (DNS) is a new rehabilitation concept developed by Professor Pavel Kolar after being inspired by Vojta’s reflex locomotion.12\n\nPrinciples of DNS: The exact simultaneous contraction of the multiple muscles of the spine creates the integrated spinal stabilization system (ISSS), which includes the cervical extensors and flexors, diaphragm, transverses abdominis muscle, pelvic floor and multifidus. This concept is based on developmental kinesiology, which emphasizes the presence of star movement patterns at birth.12,13\n\nNDT-Bobath intervention is widely used to treat stroke. These are not the particular set of exercises, but the 24h × 7 days a week principle-oriented neuro rehabilitation, in which proper patterns and stimulation are made in a care-based manner, and the optimal usage of the patient’s brain neuroplasticity, avoidance of compensatory mechanisms, and the patient’s maximal independence in everyday activities.1,14\n\nAccording to Kabat, proprioceptive neuromuscular facilitation (PNF) is a technique which works based on the concept that increased voluntary responses are achieved when movement patterns are combined with other facilitative processes. In investigations of both subacute and chronic stroke, PNF intervention has been documented.7,15\n\nThere is a need to study and compare the utility of the external feedback-based approach, neurodevelopmental treatment (NDT) and proprioceptive neuromuscular facilitation (PNF) on trunk and gait function in stroke. This study tries to find the effect of an internal feedback-based approach (dynamic neuromuscular stabilization), which emphasizes the patient’s awareness of muscle activation by the intrinsic mechanism involving proprioception. The external feedback-based approaches, NDT and PNF utilize extrinsic feedback of the therapist to activate their muscles for improving the trunk and gait function in stroke. DNS assumes that core stability and basic extremity locomotion function are under central nervous system (CNS) control. It implies specific co-activation of the intrinsic muscles of the spine, which brings all joints in a functionally centrated position and provides a mechanical advantage for the best possible joint mobility throughout the range.\n\nThe aim of this study is to compare the effectiveness of DNS, NDT, PNF interventions on trunk control and gait parameters in the sub-acute stage in stroke patients.\n\n\nProtocol\n\nThis study is an interventional study with three arm parallel groups, randomized clinical trial; the study has been registered with the CTRI Clinical Trials Registry – India (CTRI) reference no. CTRI/2022/06/043037. Twenty patients will be assigned to each group (n = 60).\n\nThis study protocol adheres to the Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT) checklist (Figure 1).16 Patients will be selected from the inpatient department (IPD) of the Acharya Vinoba Bhave Rural Hospital, Sawangi, (Meghe), Wardha, Maharashtra and from the Ravi Nair Physiotherapy College (OPD) outpatient department for the study purpose. A printed form in the participant’s native language i.e. Marathi, Hindi and English for approval from participants with a signature will be taken by the principal investigator. Then, subjects will be assessed based on inclusion and exclusion criteria.17\n\nInclusion criteria\n\n• Both males and females between the ages of 40 and 65 years.\n\n• Subjects with sub-acute phase of stroke.\n\n• Those who have hemiparesis or hemiplegia as a result of a single stroke.\n\n• Those that can comprehend and follows instructions.\n\n• Patients who gave consent to be a part of the research.\n\nExclusion criteria\n\n• Those who have had a transient ischemic attack before.\n\n• Those who have a history of recurrent strokes.\n\n• Those who have a joint or muscular dysfunction that is not caused by a stroke.\n\n• Those who have a physician-determined unstable cardiovascular condition.\n\n• Patients who are enrolled in a different clinical trial.\n\nGroup A: DNS\n\nSubjects in this group will receive combined therapy of DNS and conventional physiotherapy, which will include trunk, pelvis and lower limb training. Conventional exercises include the active range of motion (ROM) exercises, stretching of the tightened muscles, mat exercises for stability, functional training for ADL.18 DNS includes a few developmental pattern exercises that involve the therapist positioning their thumbs on the chest area and encouraging regular breathing patterns while supporting the descent of the diaphragm to engage its stabilizing function. The DNS treatment is as follows: the protocol consists of 12 developmental pattern exercises that involve reflex-mediated diaphragm facilitation and the therapist using their thumb to hold its decent. This activates the core stabilizers by positioning the vertebral column, ribcage, pelvis, and scapula in position. For the first week, three developmental positions will be implemented to teach an appropriate breathing pattern and stabilization, and for the next three weeks, new three to four patterns from the DNS posters will be instructed. By the end of the fourth week, the participants will have to be able to successfully practice all the patterns illustrated on the DNS poster19: diaphragmatic breathing, three-month supine position with hips, knees and ankles at 90-degree flexion. Prone 3-month position with upper arms at a 90-degree angle to the trunk, support on elbows. Side lying, 5th-month position patient lying on the side, lower shoulder (support) and elbow will be flexed wrist in the neutral position. The lower limb is supported in a semi-flexed position at the knee, aligning the heel and hip with the ischial tuberosity. In seventh month of oblique sitting, the patient will be positioned on their side with their forearm, hand, hip, thigh, and ankle in alignment and the quadruped position.20 The patient will be placed on all fours, knees directly under the hips and hands and wrists directly under the shoulders. Patients in this group will undergo 45 minutes of trunk and pelvis and lower limb exercises followed by 10 minutes of relaxation period in-between the treatment and 15 minutes of conventional exercises excluding relaxation time for five days per week for four weeks.\n\nGroup B: NDT\n\nSubjects in this group will receive combined therapy of NDT and conventional physiotherapy which aim at trunk, pelvis and lower limb training. Conventional Exercises include the Active ROM exercises, stretching of the tightened muscles, MAT exercises for stability, functional training for ADL.18 A therapy program will be applied to the patients depending of the functional level in these will be: Latissimus dorsi muscle stretching, latissimus dorsi functional utilization and strengthening, performing to enhance the functional strength of abdominal and oblique muscles, arranging routines to assist in trunk extension, rotations, and counter-rotations (both to the right and left of the hips with an extended trunk, training the stabilizing muscles of the lumbar spine, and practicing functional reaching movements for the shoulders, both in front and to the sides.21 Participants in this group will perform 45 minutes of NDT with 15 minutes of conventional physiotherapy (Total one hour per day), five days a week for four weeks. Total one hour excluding the relaxation time of 10 minutes.\n\nGroup C: PNF\n\nIndividuals in this will undergo combined therapy of PNF and conventional physiotherapy, including trunk, pelvis, and lower limb training. For upper and lower extremity: D1 and D2 flexion and extension patterns using PNF principles. It will be progressed to active assisted motions, active resisted actions, and eventually active activities. And for trunk Rhythmic stabilization and alternating isometrics.22 Pelvic PNF Patterns of movement will be performed which are anterior elevation, posterior depression, posterior elevation and anterior depression by rhythmic initiation and repeated contraction of the hemiplegic side.23 The treatment will incorporate PNF elements, including positioning, manual contact, resistance and verbal commands. Study techniques such as rhythmic initiation, slow reversal, agonist reversals will be used.24 Patients in the group will undergo 45 minutes of pelvis, trunk and lower limb exercises on the involved side, followed by 10 minutes of relaxation and then 15 minutes of conventional exercise per day, a total of one hour excluding relaxation time. This will be for five days per week for four weeks.\n\nCriteria for discontinuing the interventions\n\nIf patient feels any discomfort during the treatment or because of the treatment, then health providers will be called immediately, the treatment will be discontinued, and the patient will be requested to withdraw his or her consent from the procedure if they no longer wish to proceed.\n\nRelevant concomitant care\n\nThe patient will be allowed to take physician prescribed drugs if there are any co-morbidities.\n\nOutcome measures will be taken on the first day and at the end of the four-week treatment. The assessor who is aware of the outcome measures and has similar experience to the physiotherapy resident conducting the study will take pre- and post-outcome measures using TIS, DGI and Gait parameters.\n\n• Trunk impairment scale helps measure motor impairment after a stroke. The TIS helps to determine dynamic sitting and static sitting balance and coordination of the trunk. It has three subscales for the evaluation of static, dynamic and coordination of the trunk. Intra-observer and inter-observer reliability is excellent, with a test/retest reliability coefficient (ICC) of 0.96 and inter-observer reliability coefficient of 0.99 for the TIS total score.\n\n• Dynamic gait index assesses the patient’s balance and fall risk. This instrument serves as a means to assess gait and balance, and the likelihood of experiencing a fall. On this scale, the capacity to keep one’s balance while walking in the presence of outside pressures is tested. The reliability is 0.97, and the validity is 0.83.\n\n• Gait parameters The primary variables to consider while evaluating walking are stride length, cadence, and gait velocity. The distance between two consecutive foot placements, or a stride, is equal to two step lengths. The number of steps taken over a certain period of time are measured by cadence. The 10-meter walk test evaluates walking speed over a short distance in meters per second.\n\nThis study design will involve three independent groups to investigate the efficacy of DNS, NDT, and PNF in trunk and lower limb, for trunk control, balance and gait parameters. Sixty subjects will be assigned to the study (20 participants in Group A, Group B and Group C).3 Six additional participants will be recruited in the event of dropout or a problem with data compilation, preserving the sample size. As a conservative estimate, we expect 66 subjects to complete the study (dropout rate = 25%).25\n\nWhere,\n\nZ α/2 is the level of significance at 5% i.e., 95 %.\n\nConfidence interval is = 1.96\n\nP = Prevalence of Stroke is = 2.6% = 0.0026\n\nd = Desired error of margin will be = 7% = 0.07\n\nA computer-generated number will be used for randomization, and patients will be assigned to three groups using the sequentially numbered opaque sealed envelope (SNOSE) method. Group A will receive DNS along with conventional exercises, Group B will be given NDT along with traditional exercises, and Group C will be given PNF along with conventional exercises targeting the trunk, pelvis and lower limbs. The principal investigator and the research coordinator will supervise the randomization of the participants. The study will be supervised by the postgraduate advisor, department head, principal, and research team advisor.\n\nFor the treatment, the assessor will be blinded. Unblinding can occur in an emergency where a participant’s medical care and safety are a concern. It will be done by the principal investigator, who has access to the data along with the permission of the ethical committee and the proper documentation for the reason for unblinding.\n\nThe evaluation data will be obtained pre-treatment with variable baseline characteristics. Research data will be placed in a secure database. Non-electronic documents, including signed informed consent forms and hard copies of evaluation forms, will be securely kept within the study setting under the supervision of principal investigator.\n\nSPSS version 27.0 will be used for conducting statistical analysis. The mean and SD will be subjected to normality test using Kolmogrov Smirnoff test. The outcomes of inferential statistics will be presented in a tabular format and subjected to testing at a 5% significance level (p<0.05). The variables – trunk impairment scale, dynamic gait index and gait parameters will be analyzed using a student’s paired t-test and Wilcoxon signed rank test to compare pre and post intervention results within the group. For the comparison of variables between the groups, a one-way ANOVA test, Kruskal Wallis test, and multiple comparison test will be used.\n\nA team committed to monitoring and combining the data will be established. The entire process will be supervised by clinicians and the departmental committee, which includes the guide, the head of the department, the principal, and members of the research guideline team. An auditing trial will be executed each month. Any deviance from the standard procedure will be recorded and will be addressed accordingly. The completed dataset will be made available to relevant authorities and uploaded to the institutional research website.\n\nResearch ethics approval\n\nThe study has been approved by the Institutional Ethics Committee of Datta Meghe Institute of Higher Education and Research (Deemed to be a University) DMIMS (DU)/IEC/2022/898 on 11th April 2022 for patients diagnosed with sub-acute stroke. The study is registered with the Clinical Trials Registry – India (CTRI) reference no. CTRI/2022/06/043037; date of registration 22/05/2022.\n\nConsent\n\nThe therapist will orient patients about the study and goals, and approaches before any patients are accepted. Written informed consent forms will be signed by the patients of subacute stroke before commencement of the study.\n\nConfidentiality\n\nThe study procedure will be explained to the patients and the principal investigator will obtain written informed consent. With the full guarantee of the patient’s confidentiality, agreement will be obtained from the patient if disclosure of certain information is necessary for the study.\n\nIt is unlikely that the participants will experience any negative effects from the assigned interventions. In the event that harm occurs, patients will be offered free in- or outpatient therapy as determined by an expert assessment at the completion of the four-week intervention.\n\nThe principal investigator will have the right to access the data. The principal investigator will store data in the DMIHER data repository after the study is finished, and the results are published.\n\nWe are planning to publish our findings in an indexed journal and to present the article at conference proceedings.\n\nThe study started in July 2022 and will be completed by December 2023.\n\n\nDiscussion\n\nWe intend to investigate the effects of the three approaches i.e. DNS, NDT, PNF on trunk control and gait parameters in individuals suffering from sub-acute stroke. The aim of this research is to ascertain the efficacy of these approaches and to compare these approaches in improving trunk control, balance and gait in stroke using TIS, DGI, and gait parameters as outcome measures. Trunk and pelvic control are vital for stability and locomotion in humans. Hemiplegic stroke impairs trunk function multi-directionally.\n\nA study was carried out by Raghuveer et al., in 2021 to ascertain the impact of NDT and DNS approaches on hemiplegics with impaired trunk strength, through diaphragm activation. A reflex-mediated diaphragmatic activation of core muscle, DNS, is done in patients with hemiplegia and was found to be more effective in functional improvement in the trunk than NDT.19 Similarly, Sharma et al., in 2020, co-activated the ISSS in all segments as a complete technique in treating any case and proved it is very effective in different neurological or musculoskeletal cases.12 Son and You et al., in 2017, demonstrated EMG research revealed that hemiparetic stroke victims had increased activation of the inner core TrA/IO muscles in DNS. DNS may have stimulated hemiparetic individuals’ underactive deep core TrA/IO muscles.26 In 2017 research was conducted to see the effect of strengthening the core combined with pelvic PNF in chronic stroke patients with trunk, balance, gait, and functional ability impairment. The patients were given strengthening of core combined with pelvic PNF and flexibility exercises of trunk muscles along with PNF. In chronic stroke patients, core stability exercises and pelvic PNF were more successful in reducing trunk dysfunction, balance, and gait.24 Kim et al. (2018) aimed to determine and achieve balance and walking competency of post-stroke patients when applying PNF for pelvic and lower extremity PNF using treadmills; they found a difference in the balance capability of post-stroke patients.27\n\nThere is a shortage in the literature comparing these three treatment approaches over trunk and gait parameters. There is a strong need to conduct a study to compare these approaches. Furthermore, the findings of this research could be used to assist post-stroke survivors in their early recovery and improve their level of independence.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nZenodo: Extended data for ‘Effectiveness of dynamic neuromuscular stabilization, neurodevelopmental techniques and proprioceptive neuromuscular facilitation on trunk and gait parameters in patients with subacute stroke: A three-arm parallel randomised clinical trial’, https://www.doi.org/10.5281/zenodo.10143795. 17\n\nZenodo: SPIRIT checklist for ‘Effectiveness of dynamic neuromuscular stabilization, neurodevelopmental techniques and proprioceptive neuromuscular facilitation on trunk and gait parameters in patients with subacute stroke: A three-arm parallel randomised clinical trial’, https://www.doi.org/10.5281/zenodo.10089270. 16\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 am grateful to Mr. Laxmikant Umate who helped with the sample size calculation for the study.\n\n\nReferences\n\nMikołajewska E: NDT-Bobath method in post-stroke rehabilitation in adults aged 42–55 years – Preliminary findings. Pol. Ann. Med. 2015 Sep 1; 22(2): 98–104. Publisher Full Text\n\nCoupland AP, Thapar A, Qureshi MI, et al.: The definition of stroke. J. R. Soc. Med. 2017 Jan 1 [cited 2023 Jul 3]; 110(1): 9–12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJones SP, Baqai K, Clegg A, et al.: Stroke in India: A systematic review of the incidence, prevalence, and case fatality. Int. J. Stroke. 2022; 17(2): 132–140. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBernardo-Castro S, Albino I, Barrera-Sandoval ÁM, et al.: Therapeutic nanoparticles for the different phases of ischemic stroke. Life. 2021; 11(6): 482. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKuriakose D, Xiao Z: Pathophysiology and treatment of stroke: present status and future perspectives. Int. J. Mol. Sci. 2020; 21(20): 7609. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlrabghi L, Alnemari R, Aloteebi R, et al.: Stroke types and management. Int. J. Community Med. Public Health. 2018; 5: 3715. Publisher Full Text\n\nChaturvedi P, Singh AK, Kulshreshtha D, et al.: Proprioceptive neuromuscular facilitation (PNF) vs. task specific training in acute stroke: the effects on neuroplasticity. MOJ Anat. Physiol. 2018 [cited 2022 Jan 27]; 5(2). Publisher Full Text Reference Source\n\nBohannon RW: Recovery and correlates of trunk muscle strength after stroke. Int. J. Rehabil. Res. 1995; 18(2): 162–167. PubMed Abstract \| Publisher Full Text Reference Source\n\nBeyaert C, Vasa R, Frykberg GE: Gait post-stroke: Pathophysiology and rehabilitation strategies. Spec. Issue Balance Gait. 2015 Nov 1; 45(4): 335–355. Publisher Full Text Reference Source\n\nBuckley C, Micó-Amigo ME, Dunne-Willows M, et al.: Gait asymmetry post-stroke: Determining valid and reliable methods using a single accelerometer located on the trunk. Sensors. 2019; 20(1): 37. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKhallaf ME: Effect of Task-Specific Training on Trunk Control and Balance in Patients with Subacute Stroke. de Carvalho M, editor. Neurol. Res. Int. 2020 Nov 18; 2020: 1–8. Publisher Full Text\n\nSharma K, Yadav A: Dynamic Neuromuscular Stabilization-A Narrative.\n\nRaghuveer R, Chitkara E, Raj P: Effectiveness of diaphragm activation using reflex mediated dynamic neuromuscular stabilization on trunk function in hemiplegia.2021.\n\nPathak A, Gyanpuri V, Dev P, et al.: The Bobath Concept (NDT) as rehabilitation in stroke patients: A systematic review. J. Fam. Med. Prim. Care. 2021; 10(11): 3983–3990. Publisher Full Text\n\nKrukowska J, Bugajski M, Sienkiewicz M, et al.: The influence of NDT-Bobath and PNF methods on the field support and total path length measure foot pressure (COP) in patients after stroke. Neurol. Neurochir. Pol. 2016; 50(6): 449–454. PubMed Abstract \| Publisher Full Text\n\nUdhoji SP: Spirit checklist for Effectiveness of dynamic neuromuscular stabilization, neurodevelopmental techniques and proprioceptive neuromuscular facilitation on trunk and gait parameters in patients with subacute stroke: A three-arm parallel randomised clinical trial. [Data]. Zenodo. 2023. Publisher Full Text\n\nUdhoji SP: Extended data for Effectiveness of dynamic neuromuscular stabilization, neurodevelopmental techniques and proprioceptive neuromuscular facilitation on trunk and gait parameters in patients with subacute stroke: A three-arm parallel randomised clinical trial. [Data]. Zenodo. 2023. Publisher Full Text\n\nMaček Z, Kolar M, Tučić M, et al.: Recommendations for physiotherapy intervention after stroke. Ann. Physiother. Clin. 2020; 2(1): 1011.\n\nRaghuveer R, Chitkara E, Raj P: Effectiveness of diaphragm activation using reflex mediated dynamic neuromuscular stabilisation on trunk function in hemiplegia. Med. Sci. 2021; 25(118): 3132–3139.\n\nKobesova A, Ulm R, Kolar P: Dynamic neuromuscular stabilization. Rehabil Spine Patient-Centered Approach. 3rd Ed.Los Angel USA: Wolters Kluwer; 2019.\n\nKılınç M, Avcu F, Onursal O, et al.: The effects of Bobath-based trunk exercises on trunk control, functional capacity, balance, and gait: a pilot randomized controlled trial. Top. Stroke Rehabil. 2016; 23(1): 50–58. PubMed Abstract \| Publisher Full Text\n\nChaturvedi P, Singh AK, Kulshreshtha D, et al.: Proprioceptive neuromuscular facilitation (PNF) vs. task specific training in acute stroke: the effects on neuroplasticity. MOJ Anat. Physiol. 2018; 5(1). Publisher Full Text\n\nChaturvedi P, Singh AK, Tiwari V, et al.: Post-stroke BDNF concentration changes following proprioceptive neuromuscular facilitation (PNF) exercises. J. Fam. Med. Prim. Care. 2020 Jul 30; 9(7): 3361–3369. Publisher Full Text Reference Source\n\nSharma V, Kaur J: Effect of core strengthening with pelvic proprioceptive neuromuscular facilitation on trunk, balance, gait, and function in chronic stroke. J. Exerc. Rehabil. 2017; 13(2): 200–205. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDaniel WW, Cross CL: Biostatistics: a foundation for analysis in the health sciences. Wiley; 2018.\n\nYoon HS, You JSH: Reflex-mediated dynamic neuromuscular stabilization in stroke patients: EMG processing and ultrasound imaging. Technol. Health Care. 2017; 25(S1): 99–106. PubMed Abstract \| Publisher Full Text\n\nKim CH, Kim YN: Effects of proprioceptive neuromuscular facilitation and treadmill training on the balance and walking ability of stroke patients. J. Korean Phys. Ther. 2018; 30(3): 79–83. Publisher Full Text" }	[ { "id": "308551", "date": "23 Aug 2024", "name": "Dr. Trapthi Kamath", "expertise": [ "Reviewer Expertise Physiotherapy" ], "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 study protocol presents a randomized clinical trial comparing the effectiveness of Dynamic Neuromuscular Stabilization (DNS), Neurodevelopmental Techniques (NDT), and Proprioceptive Neuromuscular Facilitation (PNF) on improving trunk control and gait parameters in patients with sub-acute stroke. It aims to provide insight into which of these rehabilitation methods is most effective in addressing motor dysfunctions commonly experienced by stroke survivors. Stroke is a leading cause of death and disability globally, with significant effects on neurological function, including motor control, balance, and gait. Rehabilitation approaches focus on improving these parameters to help patients regain independence in daily life activities. This study seeks to assess the comparative effectiveness of DNS, NDT, and PNF, focusing on their impact on trunk stability and gait function. The aim of the study to compare the effectiveness of DNS, NDT, and PNF interventions on trunk control and gait parameters in patients with sub-acute stroke. The Design includes Three-arm parallel randomised clinical trial with 60 participants, divided equally into three groups. Group A receives DNS and conventional physiotherapy, Group B receives NDT and conventional physiotherapy, and Group C receives PNF and conventional physiotherapy. Outcome Measures are Trunk Impairment Scale, Dynamic Gait Index and gait parameters. Data will be analysed using SPSS version 27.0.\nBlinding: The outcome assessor will be blinded to the group allocation to prevent bias in evaluation.\nStrengths: The use of randomization and blinding enhances the study’s credibility by minimizing potential biases. The focus on trunk control and gait function The study examines DNS, a newer technique gaining interest in the rehabilitation field Gold standard scales such as TIS and DGI for measuring trunk control and gait parameters ensures the validity of the results.\nWeaknesses: Limited Sample Size\nShort-Term Follow-Up This study includes a proper explanation of background, context showing an understanding existing research and its research gap. The study design is appropriate which aligns well with aim of the study. The study provides detailed protocols, data collection and set up, ethical considerations. The data base is very clear presented in usable and accessible format. I approve this article with suggestions to improve sample size and follow up time.\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": "316098", "date": "27 Aug 2024", "name": "Selvam Ramachandran", "expertise": [ "Reviewer Expertise Neurological Rehabilitation", "Health Professions Education" ], "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: Should indicate study protocol of three-arm parallel randomized clinical trial Introduction: Update the reference of citation no. 12 Study design and sample size: Please provide CTRI registration no. searchable in the CTRI registry. (not the reference no.) Study setting: Figure 1 shows the flow of participant recruitment and allotment to interventions. Please cite the SPIRIT checklist availability (Ref 16) Eligibility Criteria: The included population is 45-60yrs. The model demonstrating the activities in the supplementary material is a child. (Ref 17) Criteria for discontinuing interventions: It is not only the adverse events related to the care interventions, other events which could potentially affect the outcome of the interventions. Outcome Measures: Timeline: Can consider ongoing assessment at the end of 1st, 2nd and 3rd week in addition to outcome assessment at baseline and at end of 4th week. This will help the investigators to perform intention to treat analysis, in case of drop-outs Assessor: Describe who will assess the outcomes. Explain the phrase 'The assessor who is aware of the outcome measures and has similar experience to the physiotherapy resident conducting the study...' Sample Size Calculation: If the anticipated dropout rate is 25% of n=60, then 15 additional subjects will be required. Then total sample size would be 75 and not 66. Reference: Update the reference 12, 13\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/13-29
https://f1000research.com/articles/13-27/v1	08 Jan 24	{ "type": "Research Article", "title": "Identification of pathogenic-specific open reading frames in staphylococci species", "authors": [ "Fatima Naser Farhan", "Andrzej Zielezinski", "Wojciech M Karłowski", "Andrzej Zielezinski", "Wojciech M Karłowski" ], "abstract": "Background Bacteria within the Staphylococcus genus are notorious for causing a wide range of infections, and they possess genes that play a pivotal role in determining their pathogenicity. In this study, we characterized open reading frames (ORFs), which represent potential functional gene sequences, from selected staphylococcal genomes.\n\nMethods Our study involved the extraction, categorization, and annotation of ORFs using diverse analytical methods. This approach unveiled distinct ORFs in both pathogenic and non-pathogenic species, with some commonalities. To assess the conservation of these ORFs and their relevance to pathogenicity, we employed tblastn and Clustal Omega-Multiple Sequence Alignment (MSA) methods.\n\nResults Remarkably, we identified 23 ORFs that displayed high conservation among pathogenic staphylococci, with five of them extending beyond the Staphylococcus genus. These particular ORFs may encode products associated with RNA catabolism and could potentially function as regulatory small open reading frames (smORFs). Of particular interest, we found a single smORF situated within a conserved locus of the 50S ribosomal protein L1, present in 200 genomes, including 102 pathogenic strains.\n\nConclusions Our findings highlight the existence of ORFs with highly conserved elements, proposing the existence of 23 novel smORFs that may play a role in the pathogenicity of Staphylococcus species.", "keywords": [ "pathogenic Staphylococcus", "non-pathogenic Staphylococcus", "open reading frames", "comparative analysis", "bacteria", "pathogenicity" ], "content": "Introduction\n\nThe Staphylococcus genus consists of gram-positive cocci. The genus holds more than 40 species, grouped into pathogenic or non-pathogenic. Members of the pathogenic group are responsible for various infections such as nosocomial infections. However, non-pathogenic members are engaged in the food industry for the fermentation of cheese or meat. Scientists believe species habituate their pathogenic capabilities by possessing specific virulence factors acquired by horizontal gene transfer or mutations (Rosenstein & Götz, 2012).\n\nVirulence factors encompass adhesins, exoenzymes, toxins, and a heterogeneous assortment. While adhesins interpose the attachment to host cells, exoenzymes destroy host tissue, and heterogeneous groups compromise iron uptake systems. Lastly, toxins directly exert damaging effects on the host. However, detecting any or all these factors in the staphylococcal genome does not make it pathogenic. For example, the non-pathogenic S. carnosus TM300 has the virulence factor sortase A (strA) within its genome. The strA is essential for mediating attachment to the host tissue, indicating that the role of strA is not exclusive and depends on the contribution of the cognate substrate proteins to the infectious pathway (Götz, Bannerman & Schleifer, 2006). Physiological properties significantly influence the pathogenicity of staphylococci. These properties impact their interactions with other pathogens, their ability to persist within the infected host, their resistance to antibiotics and antimicrobial compounds, as well as their capacity to evade neutrophil-mediated killing (Rosenstein & Götz, 2012).\n\nPathogenic staphylococci species’ ability to quickly adapt to antibiotic treatment is considered an indispensable feature. Antibiotic resistance genes, acquired by mobile genetic elements (transposons or plasmids), serve as mediators for this resistance ability, enabling rapid spread through lateral gene transfer or spontaneous mutation. The increasing resistance of staphylococci left only a few antibiotics effective in treating infections and increased species’ virulence ability (Ventola, 2015). For example, S. aureus has developed different strategies to counteract the effect of antibiotics resulting in the emergence of a new strain known as Methicillin-resistant Staphylococcus aureus (MRSA). MRSA alone is responsible for 11,285 deaths per year in the US, killing more Americans yearly than HIV, Parkinson’s disease, emphysema, and homicide combined (Guo et al., 2020).\n\nA few studies have compared pathogenic and non-pathogenic staphylococci species. Such studies were usually limited to either the genomic aspect or performed on a small number of species. For instance, Rosenstein et al., (2009) analysed the genome of S. carnosus and compared a few features to S. aureus species. Heo and colleagues studied the genome of a few strains of S. epidiermidis, S. haemolyticus, and S. saprophyticus (Heo, Lee & Jeong, 2020). Although these species are opportunistic bacteria and involved in various infections, the study concluded that the genomes did not encode any virulence factors in S. aureus. Mannala et al. (2018) compared the genome of two highly virulent and low-virulent Staphylococcus aureus strains. Another study by Rosenstein & Götz (2012), defined the genomic information of pathogenic staphylococci species focusing on those derived from S. aureus strains. All previous studies highlighted similarities and dissimilarities between the genome of pathogenic and non-pathogenic staphylococci. Therefore, scrutiny of these analogies and diversity will enable us to understand the roots of their virulence ability and the followed infectious pathway.\n\nThe open reading frames are regions that either contain no stop codons or begin with a start codon and end with a termination codon. Each strand of the DNA sequence has three possible reading frames. Exploring bacterial ORFs provides an opportunity to discover novel functional genes (Cerqueira & Vasconcelos, 2020). Recently, biologists have been more concerned about the small ORFs (smORFs) (<50 amino acids) that manifest a vital role in several cellular regulatory activities, and more studies have focused on developing new approaches to annotate them (Mir et al., 2012). Intrinsic and extrinsic are the two in-silico methods for detecting ORFs. While the intrinsic pathway investigates ORFs coding potential, such as obvious ribosome binding site (RBS), the extrinsic technique hunts for conserved sequences among different species (Cerqueira & Vasconcelos, 2020). The latter is a potent approach for detecting smORFs (Warren et al., 2010; Wood et al., 2012; Cerqueira & Vasconcelos, 2020), considering that confirmed short-protein coding genes are without any marked RBS (Hemm et al., 2008). However, as of now, the number of annotated smORFs is considerably low.\n\nIn this study, we comparatively analysed ORFs extracted from ten selected staphylococci species, including five pathogenic and five non-pathogenic strains. Our objectives were to characterize the features of ORFs in pathogenic genomes, identify conserved ORFs specific to pathogenic staphylococci, and propose a novel approach for smORFs’ prediction and annotation. This study holds significance in addressing the need for comparative investigations of ORFs in pathogenic and non-pathogenic staphylococci genomes and contributes to the growing attention towards smORFs.\n\n\nMethods\n\nGenBank (Benson et al., 2010) and RefSeq (O’Leary et al., 2016) databases contain genome sequences of 98,079 staphylococci strains. We selected species whose pathogenicity is defined and confirmed for the comparative analysis. S. aureus Mu3 (Refseq assembly accession ID: GCA_000010445.1), S. lugdunensis HKU09-01 (GCA_000025085.1), S. haemolyticus JCSC1435 (GCA_000009865.1), S. saprophyticus ATCC 15305 (GCA_000010125.1), and S. schleiferi strain 1360-13 (GCA_001188855.1) represented the pathogenic species, while the non-pathogenic were S. carnosus TM300 (GCA_000009405.1), S. cohnii SNUDS-2 (GCA_001990205.1), S. warneri SG1 (GCA_000332735.1), S. nepalensis DSM 15150 (GCA_002902745.1) and S. pasteuri JS7 (GCA_002442915.1). We downloaded the genome sequence of these selected genomes from the NCBI FTP site (https://ftp.ncbi.nlm.nih.gov).\n\nWe employed version 6.6.0.0 of the EMBOSS getorf algorithm to extract open reading frames (ORFs) from the genomes specified in the previous section (Rice, Longden & Bleasby, 2000). The process involved running a Linux script with specific parameters for the EMBOSS getorf algorithm: ‘getorf -sequence genome.fa -find 1 -outseq genome_orf.txt.’ The optional qualifier -find [1] was utilized to determine the translation of ORF regions between the start and stop codons.\n\nThe identified ORFs were arranged according to size and any ORF shorter than 10 amino acids (aa) were discarded. Next, we identified shared ORFs within and between the two species groups. Eventually, we categorized these common ORFs into five groups based on their presence in the tested genomes: ORFs present in all tested genomes, ORFs present in all pathogenic genomes, ORFs present in all non-pathogenic genomes, ORFs present in some pathogenic genomes, and ORFs present in some non-pathogenic genomes (Underlying data: Appendix A–E) (Farhan et al., 2023). Figure 1 visualizes the ORFs filtration process (Farhan, 2023).\n\nThe functional annotation of ORFs followed two approaches: (i) a direct approach that utilized the annotated proteins files available in GenBank and RefSeq databases and (ii) an indirect approach based on the traditional BLASTp tool version 2.11.0 (Altschul et al., 1997). Following the direct approach, the sequence and coordinate of each ORF matched with its resembled annotated protein of the tested genomes — ORFs which failed in the direct annotation tested for the indirect annotation that utilized the BLASTp tool. The BLASTp tool parameters were adjusted to search in the non-redundant protein sequence database for homologous sequences to ORFs only in the Staphylococcus organism (taxid 1279), targeting a maximum of 100 species. Both identity level and query coverage should be higher than 85%.\n\nThe Blast2GO tool version 5.2.5 (Conesa et al., 2005) enables an efficient automatic functional annotation of protein sequences according to the gene ontology vocabulary. Gene ontology (GO) describes the biological framework of genes in three aspects: biological process, molecular function, and cellular component. The relationship between GO terms, when presented in graph-based terminology, the parent GO terms, refers to the node closer to the roots (Level = 2) of the graph and a child (Level ≥ 5) to that closer to the leaf nodes. Moreover, the algorithm performed the gene enrichment analysis and two-tailed Fisher exact test to identify the enriched biological processes in pathogenic tested genomes.\n\nThe DeepGOPlus algorithm (Version 1.0.2) was operated to predict the ORFs function, where their function was previously unknown (Kulmanov, Khan & Hoehndorf, 2018). The algorithm uses deep learning to learn features from query protein sequences besides cross-species protein-protein interaction networks. The resulting output was in the structure of GO terms, and the terms were presented in a graph chart using the QuickGO tool version 1.15 (Binns et al., 2009).\n\nA conserved sequence is an amino acid sequence in a protein (or a nucleotide base in DNA) that has remained unchanged throughout evolution to maintain a protein’s structure and function (Alberts et al., 2002). Testing the conservation level of unknown ORFs (unORFs) involved three stages: conservation within the Staphylococcus genus, conservation within pathogenic staphylococci species, and finally, extending the analysis beyond the Staphylococcus genus. We employed the tblastn algorithm version +2.11.0 (Altschul et al., 1997) to conduct the conservation test, gathering data based on identity level and query coverage (≥85). The student t-test provided by Python’s SciPy library was employed to assess the results’ significance.\n\nClustal Omega – a multiple sequence alignment (MSA) algorithm version 1.2.4 was used to align the sequences to assess the locus conservation assay (Sievers et al., 2011).\n\nBoth PathogenFinder 1.1 and NCBI Pathogen detection datasets (Cosentino et al., 2013; NCBI, 1988) facilitated entitling the species as either known to be pathogenic (1) or unknown pathogenicity (0). An ORF’s pathogenicity refers to the number of pathogenic genomes that own a homologous sequence. The pathogen frequency of an ORF was specified by dividing the pathogenicity of an ORF by the total number of genomes (Figure 2).\n\nThe Prodigal (Prokaryotic gene recognition and translation initiation site identification) algorithm (Version 2.6.3) pinpointed the ribosomal binding site (RBS) motifs in the S. aureus Mu3 genome (Hyatt et al., 2010) to verify whether the RBS motif preceded the ORF or not.\n\nTo explore the neighbouring genes for each ORF and outline its precise locus, the interval between all selected ORFs (selORFs) and genes of the S. aureus Mu3 genome was measured per their coordinates. We downloaded the annotated protein file for S. aureus Mu3 from Genbank FTP website.\n\n\nResults\n\nThe analysis started with extracting ORFs from 10 selected genomes (five pathogenic and five non-pathogenic) and any ORF smaller than 10 amino acids was excluded from the analysis. Subsequently, we categorized them into five groups based on their presence in the tested genomes (Table 1). The results revealed that six ORFs were common to all tested genomes across both groups. Among the found in some pathogenic tested genomes group, 1572 ORFs were present, and 15 unique ORFs were specific to all pathogenic genomes. Likewise, some non-pathogenic genomes exhibited 1567 identified ORFs; all non-pathogenic genomes contained 13 exclusively unique ORFs.\n\nTable 2 summarizes the results obtained from ORFs annotation via direct and indirect approaches. Interestingly, one ORF was identical to a part of the 30S ribosomal protein S9 sequence of all non-pathogenic tested genomes.\n\nOur methodology provided information about several hypothetical proteins whose functions were unknown. For example, the hypothetical protein in S. lugdunesis HKU09-01 overlapped with cell surface protein IsdA, indicating a role in transferring heme from haemoglobin to apo-IsdC. In S. aureus Mu3, the glycerophosphoryl diester phosphodiesterase homolog protein was identical to the unnamed protein product in S. haemolyticus JCSC1435. Parallel to results obtained from annotating ORFs of pathogenic tested genomes, the hypothetical protein of S. cohnii SNUDS-2 was identical to the YlbF/YmcA family competence regulator protein of S. nepalensis DSM 15150. In a nutshell, we detected 15 hypothetical proteins identical to known functional proteins shared between either some non-pathogenic or pathogenic species.\n\nBoth pathogenic and non-pathogenic groups have similar functional proteins, such as the 50S and 30S ribosomal proteins, translation initiation factors, acyl carrier proteins, ATP-binding proteins, transposase, and transcriptional regulators. Although both groups have 50S and 30S ribosomal proteins and transposase, they differ in counts and types. Eleven ORFs of pathogenic genomes overlapped with 28 proteins of either 30S or 50S ribosomal proteins, whereas 31 ORFs of non-pathogenic genomes overlapped with 65 ribosomal proteins. Sixty-one transposases were detected in pathogenic genomes, while only eight transposases in non-pathogenic genomes. The only family type familiar to both groups was the IS256 transposase family. According to the annotation results, 35 functions were unique to pathogenic genomes. In contrast, 38 processes were exclusive to non-pathogenic staphylococci.\n\nIn the context of exploring biological process GO terms (GO:0008150), our investigation revealed that multiple ORFs within both pathogenic and non-pathogenic tested genomes were associated with cellular process (GO:0009987) and metabolic process (GO:0008152) terms; however, they had several differences. The biological regulation (GO:0065007) GO term was dominant in the non-pathogenic compared to the pathogenic group (Figure 3A). The localization (GO:0051179), DNA integration (GO:0015074), DNA recombination (GO:0006310), cation transport (GO:0006812), and metal ion transport (GO:0030001) GO terms mapped solely to some ORFs from pathogenic tested genomes. In contrast, eight GO terms were exceptional to ORFs of non-pathogenic genomes (Figure 3B).\n\n(A) Biological process parent's GO terms. (B) Biological process child's GO terms. (C) Molecular function parent's GO terms. (D) Molecular function child's GO terms. (E) Cellular component parent's GO terms. (F) Cellular component child's GO terms.\n\nConcerning the molecular function (GO:0003674) GO term’s map, the transporter activity (GO:0005215) and sequence-specific DNA binding (GO:0043565) were exclusively associated with several ORFs of pathogenic tested genomes (Figure 3C). On the other hand, nucleotidyltransferase activity (GO:0016779) and RNA binding (GO:0003723) GO terms were unique to ORFs of non-pathogenic genomes (Figure 3D).\n\nWhen comparing the cellular process (GO:0005575) GO terms (Figure 3E), ORFs of pathogenic tested genomes were exclusively associated with the child GO term, large ribosomal subunit (GO:0015934) (Figure 3F). In contrast, ORFs of non-pathogenic tested genomes displayed specificity, aligning solely with the child GO term, small ribosomal subunit (GO:0015935).\n\nIn the enrichment analysis, biosynthetic (GO:0009058), cellular biosynthetic (GO:0044249), and organic substance biosynthetic (GO:1901576) processes were under-represented in the pathogenic compared to the non-pathogenic group with equal significant p-value (3.12E-05) and False Discovery Rate (FDR) value (0.0046016).\n\nUltimately, several functional characteristics distinguished ORFs of pathogenic tested genomes compared to ORFs of non-pathogenic genomes, and vice versa. We were left with many ORFs from both pathogenic and non-pathogenic species whose functions were unknown. These ORFs did not overlap with any annotated proteins, hits from the BLAST search were below the specified threshold, and they were not annotated to any GO term by the Blast2GO tool. We referred to these as unknown ORFs (unORFs).\n\nThe analysis revealed significant similarity between 816 unORFs from pathogenic tested genomes and over 49,000 sequences in various staphylococci species. This similarity was notably higher than observed among the 810 unORFs from non-pathogenic tested genomes, with a p-value of 5.59e-16 tested by U-Mann Whitney test, indicating substantial conservation (Figure 4A). Moreover, the identified unORFs from pathogenic genomes exhibited sensitivity to pathogenicity (p-value: 2.99e-43) (Figure 4B). Among these, 23 unORFs demonstrated exceptionally high conservation within pathogenic staphylococci genomes, displaying a pathogen frequency ≥ 0.98. We designated these as selected ORFs (selORFs). These selORFs, with an average size of 21 amino acids, exhibited specificity toward pathogenic staphylococci species (Underlying data: Appendix F) (Farhan et al., 2023).\n\n(A) Conservation of unORFs in pathogenic and non-pathogenic genomes within staphylococci species. (B) UnORFs of pathogenic tested genomes conservation within pathogenic and unknown pathogenicity staphylococci species. (C) Selected ORFs (selORFs) conservation outside the Staphylococcus genus.\n\nSubsequently, we explored the conservation level of the 23 selORFs beyond the Staphylococcus genus. Among them, selORF with ID AP009324.1_34709 and four other selORFs emerged in 293 genomes outside the staphylococci species (Figure 4C). Notably, most of these genomes (208 out of 293) belonged to the Bacillus genus.\n\nGene ontology and gene product\n\nDeepGoPlus predicted that our selORFs play a role in the mRNA catabolic process (GO:0006402) besides sharing functional similarities with the Pelota gene. However, the predicted GO term’s confidence level was between 0.3 and 0.4, considering algorithms find it challenging to find patterns in short sequences.\n\nFurther, the Prodigal algorithm indicated that neither of the selORFs was downstream of an RBS motif. Hence, we explored the neighbouring genes to test the hypothesis that our selORFs were likely non-coding RNA, translated on different frames, and probably engaged in regulatory functions.\n\nNeighbouring genes and anti-sense sequence\n\nRegulatory small proteins regulate their neighbouring genes or genes on the opposite strand. We measured the interval between selORFs and genes within the model genome (S. aureus Mu3). The mean distance between selORFs and genes on the forward strand was 19.203 (log2), a value comparable to the mean distance of selORFs on the reverse strand 19.0951 (log2). Based on these distances, we categorized the selORFs into two groups: (i) those with a zero distance and (ii) those with a non-zero distance. In the first category, selORFs exhibited overlaps with other genes on the same or opposite strands, occurring in various reading frames.\n\nNine selORFs demonstrated overlap with genes positioned on the same strand. Among these, five selORFs exhibited overlap with coding genes, including transposase, hypothetical protein, and serine protease genes. Conversely, four selORFs displayed overlap with non-coding rRNA genes, as indicated in Figure 5A. Interestingly, two distinct selORFs showed overlap with the same rRNA gene (SAHV_r0002), mirroring a similar occurrence with the transposase gene (SAHV_2363). Notably, the extent of overlap remained constrained, with the selORFs covering at most 13% of the gene size.\n\n(A) Distribution of SelORFs overlapped with genes within the model genome (S. aureus Mu3). (B) selORF to gene size ratio distribution.\n\nA total of 10 selORFs displayed overlap with genes situated on the opposite strand, with seven of these being coding genes and the remaining three being non-coding genes (Figure 5B). Within this set of 10 selORFs, eight exhibited overlaps with segments of individual genes on the opposite strand. Among these, three selORFs overlapped with tRNA-Val and rRNA non-coding genes. The remaining five selORFs demonstrated overlap with specific genes, namely hsdM (BAF77312.1), 50S ribosomal protein L1 (BAF77419.1), hypothetical protein (BAF77875.1), graD (BAF78358.1), and type I restriction enzyme EcoR124II M protein homolog (BAF78676.1). Furthermore, two selORFs displayed overlap with the 5′ and 3′ ends of distinct genes located on the opposite strand.\n\nWhen the distance between a selORF and a gene was not zero in the second group, the selORFs did not overlap with any genes within the tested genome. In total, seven selORFs fell into this group. Among these seven, only three displayed notable proximity to genes, with distances less than 5 log2 units. Specifically, selORFs identified by the IDs AP009324.1_3643 and AP009324.1_3911 were close to the rRNA genes on the same strand (SAHV_r0003 and SAHV_r0007, respectively). In contrast, the selORF AP009324.1_34650 was near the 30s ribosomal protein S12 gene (SAHV_0543) on the opposite strand.\n\nOf particular interest is the selORF previously mentioned (ID: AP009324.1_34709), which exhibited remarkable conservation in 102 of 200 pathogenic species. Most notably, this selORF stood out as the sole instance present in 100 non-Staphylococcus genomes, and it overlapped with the 50S ribosomal protein L1 on the opposite strand across these 200 genomes.\n\nNotably, the termination codon of selORF was positioned 305 nucleotides away from the start codon of the former ribosomal protein in 10 genomes, signifying a conserved genetic location for selORF. According to MSA, the amino acid sequence shared with our selORF within the 50S ribosomal protein L1 exhibited 100% identity across the adopted genomes. However, variations were observed in nucleotide sequences, attributed to differing frame translations. Aligning the investigated protein in each adopted genome yielded varying similarity scores compared to the S. aureus Mu3 50S ribosomal L1 protein (Figure 6A).\n\nFurthermore, we examined the specific selORF within genomes closely related to the Staphylococcus genus. According to NCBI taxonomy (Schoch, 2011), genomes such as Salinicoccus alkaliphilus DSM 16010 (NZ_FRCF01000009.1), Salinicoccus albus DSM 19776 strain YIM-Y21 (NZ_ARQJ01000028.1), Salinicoccus carnicancri Crm 50.SCCRM.1_10 (NZ_ANAM01000010.1), Nosocomiicoccus ampullae strain DSM 19163 (NZ_JACHHF010000004.1), and Nosocomiicoccus massiliensis isolate MGYG-HGUT-01449 (NZ_CABKSY010000018.1) were identified as closely related to the Staphylococcus genus. Interestingly, none of the 50S ribosomal protein L1 sequences in these analogous genomes matched the corresponding protein sequence in S. aureus Mu3 (Figure 6B). However, the MSA algorithm displayed that the region encompassing selORF exhibited similarity in amino acid and nucleotide sequences across all related genomes.\n\nThis selORF displayed significant conservation, particularly concerning the well-preserved 50S ribosomal protein L1 across multiple species. Despite its relatively small size (18 amino acids), the possibility of obtaining a functional protein remained notable within the Staphylococcus genus (0.0002964), as well as in Bacillus (0.0023744), all bacteria (0.00083889), and all organisms (0.0056284), based on data from the UniProt database.\n\n\nDiscussion\n\nBoth pathogenic and non-pathogenic staphylococci species occupy conserved proteins responsible for translation, replication, and survival (Rosenstein et al., 2009). Even though our results showed that both groups share the same fundamental functional proteins, each group developed genes that facilitate specific functions according to their adopted lifestyle. Results captured from the comparative analysis manifested their significance in various means by identifying functions of 15 hypothetical proteins, providing hints of the functional characteristics of each group, and highlighting a new methodology for spotting smORFs.\n\nAt this point, what distinguishes one group from another is still obscure, as there is a lack of studies comparing pathogenic to non-pathogenic species. Staphylococci species that are generally recognized as safe are known to be associated with food fermentation. Previous studies observed increased antioxidant activities in fermentation (Barrière, Leroy-Sétrin & Talon, 2001; Abubakar et al., 2012). Thiol reductase thioredoxin, oxidoreductase, and cytochrome aa3 quinol oxidase (restricted to non-pathogenic tested genomes) are enzymes required for the antioxidant pathway in bacteria. This feature of non-pathogenic species suggests it has been acquired as an adaptation to the fermentation’s environmental conditions (Rosenstein et al., 2009).\n\nABC transporter and heme IsdEF (iron-regulated surface determinant) transporter proteins (that were exclusive for pathogenic tested genomes) are required for the mechanism of heme obtaining in S. aureus (Nygaard et al., 2006; Zhu et al., 2008). Iron is a crucial metal for the life-sustaining of pathogenic bacteria and is vital for launching the infection process (Mazmanian et al., 2003; Kuroda et al., 2005). The IsdEF transporter is a surface lipoprotein that binds to heme and works beside the ABC transporter to transport heme into the cytoplasm of bacteria (Zhu et al., 2008). Another comparative study supports our findings as Rosenstein et al. (2010) also found iron uptake systems specific for pathogenic species.\n\nTransposons are mobile genetic elements of bacteria, which our analysis detected as exclusive for pathogenic Staphylococcus. They encode transposase enzymes, act on specific DNA sequences, and insert them into a new target DNA site. Moreover, transposons enhance the genomic diversification of staphylococci species, so the more transposons in the genome, the higher plasticity of the genome is (Baba et al., 2002; Loessner et al., 2002). Non-pathogenic staphylococci are considered relatively more stable due to the lack of transposons in their genomes; such findings emphasize the role of mobile elements in the pathogenicity of Staphylococcus (Rosenstein et al., 2009). The study outcome related to transposons strengthens several previous studies that suggested a role for transposase in spreading the antibiotic resistance gene among different species (Rowland & Dyke, 1989; Ito et al., 2003; Schwendener & Perreten, 2011; Zong, 2013; Harmer & Hall, 2015; Partridge et al., 2018; Guo et al., 2020). Indeed, such features led to the increasing pathogenicity of staphylococci species.\n\nBiosynthetic, cellular biosynthetic, and organic substance biosynthetic process GO terms were significantly under-represented in the pathogenic genomes tested. These terms are associated with the formation of substances required for metabolism. Cellular biosynthetic is involved in creating materials carried out by individual cells. However, the organic substance biosynthetic process is for any molecular entity containing carbon (Binns et al., 2009). As no article researches the biosynthetic process of any of the tested groups nor elaborates on the importance of such a process, the reason behind this underrepresentation still needs to be clarified. Nevertheless, localization, biological regulation, metal ion transport, and DNA recombination are typically expressed in pathogenic Staphylococcus genomes, as reported by several studies (Jin et al., 2014; Liu et al., 2018, 2020) and explains the annotation of these terms to ORFs of pathogenic tested genomes.\n\nThe infectious pathway of Staphylococcus is far more complicated and cannot be elucidated in one study. Thus, future studies are recommended with a larger sample size to test the expression level of each group’s uniquely annotated GO terms and deeply investigate their roles.\n\nThe importance of our findings emerges from the fact that smORFs have been ignored over the years, although several recent studies have shown their enormous potential (Hobbs, Astarita & Storz, 2010; Khitun, Ness & Slavoff, 2019; Cerqueira & Vasconcelos, 2020). The 23 selORFs features correspond to all smORFs properties. They are small (size <50 amino acids) and highly conservative. Some are nested within genes and predicted to be involved in regulatory function, mostly in the mRNA catabolic process. The mRNA catabolic process occurs in the ribosome during translation elongation and induces pathways of mRNA decay (Hayamizu et al., 2005). Translation stalling occurs when; (i) mRNA is damaged or truncated, (ii) in case of excessive mRNA secondary structure, or (iii) upon which there are insufficient amounts of amino acid or tRNA (Nielsen et al., 2011; Wencker et al., 2021), and stalling regulates the translation of downstream genes (Nakatogawa & Ito, 2002).\n\nBacteria have a wide range of regulatory mechanisms in their cellular stress response. Several shreds of evidence have proposed that smORFs have a role in cellular stress responses, such as antibiotics, host-infection, and nutrition hemostasis (Kültz, 2005; Hobbs, Astarita & Storz, 2010; Hobbs et al., 2012). The proposed mechanism by which smORFs affect cellular stress response is via both transcriptional and post-transcription regulation pathways. Sigma factor B (SigB) mediates the transcriptional response approach, while sRNA mediates the post-transcriptional regulatory mechanism (Novick, 2003).\n\nSigB contributes to the overall stress response in both staphylococci and bacilli. It regulates several gene transcription expressions, including those encoding virulence factors and biofilm formation in S. aureus (Wu, de Lencastre & Tomasz, 1996). SigB regulates the transcription of alternative frames and intergenic regions (IGRs) in bacteria, leading to harmful control genes in a collateral manner (Wu, de Lencastre & Tomasz, 1996; Bischoff et al., 2004; Miller et al., 2011). In a recent study, researchers identified three sigB-regulated genes within IGRs of S. aureus. Two of these genes contained smORFs encoding putative small proteins, whereas the third transcript was not preceded by a likely ribosomal binding site, suggesting it was a non-coding RNA. However, the transcript overlapped with the mntC gene by approximately 180 nucleotides, indicating a possible cis-acting anti-sense regulatory mechanism (Nielsen et al., 2011). Moreover, an unannotated smORF named gndA was found within the gnd gene. Researchers believed that the gndA is expressed in an alternative reading frame during heat shock in E. coli under the control of the Sig-B factor (Khitun, Ness & Slavoff, 2019).\n\nRNA III belongs to the trans-encoded base pairing small RNAs (sRNAs) (Geisinger et al., 2006). RNA III controls several genes’ expression profiles. It forms an imperfect duplex that targets specific mRNAs and represses their translation (Wadler & Vanderpool, 2007; Nielsen et al., 2011), so far most studied sRNAs in E. coli, B. subtilis, and S. aureus appear to be non-coding.\n\nIn line with these elaborations, the selORFs are hypothesised to be transcribed under the regulation of the Sig-B factor in certain conditions, thereby producing non-coding sRNAs, which negatively regulate the transcription of the adjacent gene (Pförtner et al., 2014; Rodriguez Ayala, Bartolini & Grau, 2020). However, this hypothesis first requires the exclusion of false-positive smORFs (Fuchs et al., 2021), then transcriptomics analysis of the verified selORFs in different environments, besides experimentally investigating Sig-B’s role in controlling their transcripts.\n\n\nAccession numbers\n\nGenome assembly database - RefSeq accessions: Staphylococcus aureus subsp. aureus Mu3 genome assembly ASM1044v1. https://identifiers.org/refseq.gcf:GCF_000010445.1\n\nGenome assembly database - RefSeq accessions: Staphylococcus lugdunensis HKU09-01 genome assembly ASM2508v1 https://identifiers.org/refseq.gcf:GCF_000025085.1\n\nGenome assembly database - RefSeq accessions: Staphylococcus haemolyticus JCSC1435 genome assembly ASM986v1. https://identifiers.org/refseq.gcf:GCF_000009865.1\n\nGenome assembly database - RefSeq accessions: Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 = NCTC 7292 genome assembly ASM1012v1. https://identifiers.org/refseq.gcf:GCF_000010125.1\n\nGenome assembly database - RefSeq accessions: Staphylococcus schleiferi genome assembly ASM118885v1 https://identifiers.org/refseq.gcf:GCF_001188855.1\n\nGenome assembly database - RefSeq accessions: Staphylococcus carnosus subsp. carnosus TM300 genome assembly ASM940v1. https://identifiers.org/refseq.gcf:GCF_000009405.1\n\nGenome assembly database - RefSeq accessions: Staphylococcus cohnii. Genome assembly ASM199020v1. https://identifiers.org/refseq.gcf:GCF_001990205.1\n\nGenome assembly database - RefSeq accessions: Staphylococcus warneri SG1 genome assembly ASM33273v1. https://identifiers.org/refseq.gcf:GCF_000332735.1\n\nGenome assembly database - RefSeq accessions: Staphylococcus nepalensis genome assembly ASM290274v1. https://identifiers.org/refseq.gcf:GCF_002902745.1\n\nGenome assembly database - RefSeq accessions: Staphylococcus pasteuri genome assembly ASM244291v1. https://identifiers.org/refseq.gcf:GCF_002442915.1\n\nNCBI Reference Sequence: Salinicoccus alkaliphilus DSM 16010, whole genome shotgun sequence. Accession number NZ_FRCF01000009.1; https://identifiers.org/refseq:NZ_FRCF01000009.1\n\nNCBI Reference Sequence: Salinicoccus albus DSM 19776 strain YIM-Y21 G343DRAFT_scaffold00006.6_C, whole genome shotgun sequence. Accession number NZ_ARQJ01000028.1; https://identifiers.org/refseq:NZ_ARQJ01000028.1\n\nNCBI Reference Sequence: Salinicoccus carnicancri Crm 50.SCCRM.1_10, whole genome shotgun sequence. Accession number NZ_ANAM01000010.1; https://identifiers.org/refseq:NZ_ANAM01000010.1\n\nNCBI Reference Sequence: Nosocomiicoccus ampullae strain DSM 19163 Ga0415238_04, whole genome shotgun sequence. Accession number NZ_JACHHF010000004.1; https://www.ncbi.nlm.nih.gov/nuccore/NZ_JACHHF010000004.1\n\nNCBI Reference Sequence: Nosocomiicoccus massiliensis isolate MGYG-HGUT-01449, whole genome shotgun sequence. Accession number NZ_CABKSY010000018.1; https://www.ncbi.nlm.nih.gov/nuccore/NZ_CABKSY010000018.1", "appendix": "Data availability\n\nFigshare: Underlying data for ‘Identification of pathogenic-specific open reading frames in staphylococci species’, https://doi.org/10.6084/m9.figshare.24588306.v1 (Farhan et al., 2023).\n\nThis project contains the following underlying data:\n\n• Appendix A: ORFs found in some pathogenic species dataset.\n\n• Appendix B: ORFs found in some nonpathogenic species dataset.\n\n• Appendix C: ORFs found in all tested genomes dataset.\n\n• Appendix D: ORFs found in all nonpathogenic tested genomes dataset.\n\n• Appendix E: ORFs found in all pathogenic tested genomes dataset.\n\n• Appendix F: Selected ORFs dataset\n\nFigshare: Analysis methodology - Open reading frames comparative analysis, https://doi.org/10.6084/m9.figshare.24588696.v1 (Farhan, 2023).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0)\n\n\nReferences\n\nAbubakar I, Gautret P, Brunette GW, et al.: Global perspectives for prevention of infectious diseases associated with mass gatherings. 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Publisher Full Text\n\nKuroda M, Yamashita A, Hirakawa H, et al.: Whole genome sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection. Proc. Natl. Acad. Sci. U. S. A. 2005; 102: 13272–13277. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLiu Q, Chen N, Chen H, et al.: RNA-Seq analysis of differentially expressed genes of Staphylococcus epidermidis isolated from postoperative endophthalmitis and the healthy conjunctiva. Sci. Rep. 2020; 10: 14234. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLiu J, Yang L, Hou Y, et al.: Transcriptomics Study on Staphylococcus aureus Biofilm Under Low Concentration of Ampicillin. Front. Microbiol. 2018; 9: 2413. Publisher Full Text\n\nLoessner I, Dietrich K, Dittrich D, et al.: Transposase-Dependent Formation of Circular IS 256 Derivatives in Staphylococcus epidermidis and Staphylococcus aureus. J. Bacteriol. 2002; 184: 4709–4714. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMannala GK, Koettnitz J, Mohamed W, et al.: Whole-genome comparison of high and low virulent Staphylococcus aureus isolates inducing implant-associated bone infections. Int. J. Med. Microbiol. 2018; 308: 505–513. PubMed Abstract \| Publisher Full Text\n\nMazmanian SK, Skaar EP, Gaspar AH, et al.: Passage of heme-iron across the envelope of Staphylococcus aureus. Science (New York, N.Y.) 2003; 299: 906–909. PubMed Abstract \| Publisher Full Text\n\nMiller M, Dreisbach A, Otto A, et al.: Mapping of interactions between human macrophages and Staphylococcus aureus reveals an involvement of MAP kinase signaling in the host defense. J. Proteome Res. 2011; 10: 4018–4032. PubMed Abstract \| Publisher Full Text\n\nMir K, Neuhaus K, Scherer S, et al.: Predicting Statistical Properties of Open Reading Frames in Bacterial Genomes. PLoS One. 2012; 7: e45103. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNakatogawa H, Ito K: The Ribosomal Exit Tunnel Functions as a Discriminating Gate. Cell. 2002; 108: 629–636. PubMed Abstract \| Publisher Full Text\n\nNational Center for Biotechnology Information (NCBI) [Internet]. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information; [ 1988] – [cited 2017 Apr 06]. https://www.ncbi.nlm.nih.gov/\n\nNielsen JS, Christiansen MHG, Bonde M, et al.: Searching for small σB-regulated genes in Staphylococcus aureus. Arch. Microbiol. 2011; 193: 23–34. PubMed Abstract \| Publisher Full Text\n\nNovick RP: Autoinduction and signal transduction in the regulation of staphylococcal virulence: Regulation of staphylococcus virulence. Mol. Microbiol. 2003; 48: 1429–1449. PubMed Abstract \| Publisher Full Text\n\nNygaard TK, Liu M, McClure MJ, et al.: Identification and characterization of the heme-binding proteins SeShp and SeHtsA of Streptococcus equi subspecies equi. BMC Microbiol. 2006; 6: 82. Publisher Full Text\n\nO’Leary NA, Wright MW, Brister JR, et al.: Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 2016; 44: D733–D745. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPartridge SR, Kwong SM, Firth N, et al.: Mobile Genetic Elements Associated with Antimicrobial Resistance. Clin. Microbiol. Rev. 2018; 31: e00088–e00017. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPförtner H, Burian MS, Michalik S, et al.: Activation of the alternative sigma factor SigB of Staphylococcus aureus following internalization by epithelial cells - an in vivo proteomics perspective. Int. J. Med. Microbiol. 2014; 304: 177–187. PubMed Abstract \| Publisher Full Text\n\nCerqueira FR, Vasconcelos ATR: OCCAM: prediction of small ORFs in bacterial genomes by means of a target-decoy database approach and machine learning techniques. Database (Oxford) 2020; 2020: baaa067. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRodriguez Ayala F, Bartolini M, Grau R: The Stress-Responsive Alternative Sigma Factor SigB of Bacillus subtilis and Its Relatives: An Old Friend With New Functions. Front. Microbiol. 2020; 11: 1761. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRosenstein R, Götz F: What Distinguishes Highly Pathogenic Staphylococci from Medium- and Non-pathogenic?Dobrindt U, Hacker JH, Svanborg C, editors. Between Pathogenicity and Commensalism. Current Topics in Microbiology and Immunology. Berlin, Heidelberg: Springer Berlin Heidelberg; 2012; pp. 33–89. PubMed Abstract \| Publisher Full Text\n\nRosenstein R, Nerz C, Biswas L, et al.: Genome Analysis of the Meat Starter Culture Bacterium Staphylococcus carnosus TM300. Appl. Environ. Microbiol. 2009; 75: 811–822. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRosenstein R, Götz F: Genomic differences between the food-grade Staphylococcus carnosus and pathogenic staphylococcal species.Int. J. Med. Microbiol.2010 Feb; 300(2-3): 104–108. PubMed Abstract \| Publisher Full Text\n\nRowland SJ, Dyke KG: Characterization of the staphylococcal beta-lactamase transposon Tn552. EMBO J. 1989; 8: 2761–2773. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSchoch C: NCBI Taxonomy. 2011 Apr 7 [Updated 2020 Feb 11]. Taxonomy Help. Bethesda (MD): National Center for Biotechnology Information (US); 2011. Reference Source\n\nSchwendener S, Perreten V: New Transposon Tn 6133 in Methicillin-Resistant Staphylococcus aureus ST398 Contains vga (E), a Novel Streptogramin A, Pleuromutilin, and Lincosamide Resistance Gene. Antimicrob. Agents Chemother. 2011; 55: 4900–4904. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSievers F, Wilm A, Dineen D, et al.: Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 2011; 7: 539. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVentola CL: The antibiotic resistance crisis: part 1: causes and threats. P T. 2015; 40: 277–283. PubMed Abstract\n\nWadler CS, Vanderpool CK: A dual function for a bacterial small RNA: SgrS performs base pairing-dependent regulation and encodes a functional polypeptide. Proc. Natl. Acad. Sci. U. S. A. 2007; 104: 20454–20459. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWarren AS, Archuleta J, Feng W-C, et al.: Missing genes in the annotation of prokaryotic genomes. BMC Bioinformatics. 2010; 11: 131. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWencker FDR, Marincola G, Schoenfelder SMK, et al.: Another layer of complexity in Staphylococcus aureus methionine biosynthesis control: unusual RNase III-driven T-box riboswitch cleavage determines met operon mRNA stability and decay. Nucleic Acids Res. 2021; 49: 2192–2212. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWood DE, Lin H, Levy-Moonshine A, et al.: Thousands of missed genes found in bacterial genomes and their analysis with COMBREX. Biol. Direct. 2012; 7: 37. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWu S, de Lencastre H , Tomasz A: Sigma-B, a putative operon encoding alternate sigma factor of Staphylococcus aureus RNA polymerase: molecular cloning and DNA sequencing. J. Bacteriol. 1996; 178: 6036–6042. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhu H, Xie G, Liu M, et al.: Pathway for Heme Uptake from Human Methemoglobin by the Iron-regulated Surface Determinants System of Staphylococcus aureus. J. Biol. Chem. 2008; 283: 18450–18460. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZong Z: Characterization of a complex context containing mecA but lacking genes encoding cassette chromosome recombinases in Staphylococcus haemolyticus. BMC Microbiol. 2013; 13: 64. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "288005", "date": "05 Aug 2024", "name": "Gisela Storz", "expertise": [ "Reviewer Expertise Small protein discovery and characterization." ], "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 presents a cataloging of open reading frames (ORFs) in Staphylococcus aureus species, focusing on five pathogenic and five non-pathogenic strains. Information about what genes contribute to pathogenesis is of interest, and improved annotation is needed in all organisms. However, I found both the bioinformatic analysis and the results presented limited.\nThe study presents too many lists and too much speculation in the absence of substantive insights.\nThe authors put too much emphasis on possible functions. Programs like Blast2GO and DeepGOPlus just provide predictions in the absence of other data. Additionally, gene overlap does not always predict function, nor do regulatory small proteins necessarily “regulate their neighbouring genes or genes on the opposite strand”. Similarly, the presence of a gene in the genome of a pathogenic organism does not guarantee a role in pathogenesis.\nInsufficient detail is provided for some of the analysis (thresholds, estimation of false positives and negatives, etc.). The lower size cut-off was 10 amino acids. Was there a top size cut-off?\nSome statements are unusually phrased. For example, Page 3: “toxins, and a heterogeneous assortment” (of what?) Page 3: “adhesins interpose the attachment” Page 3: “limited to either the genomic aspect” Page 3: “The open reading frames are regions that either contain no stop codons” Page 6: “Among the found” Page 11: “species occupy conserved proteins” (encode?)\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?\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": [] }, { "id": "321266", "date": "19 Sep 2024", "name": "Vishnu Raghuram", "expertise": [ "Reviewer Expertise Bacterial genomics", "phylogenetics" ], "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 study, the authors begin with 10 Staphylococcus genomes each from a different species, grouped them into pathogenic and non-pathogenic, and then identified ORFs of unknown function. The authors then attempt to provide insights into the distribution of these ORFs between the pathogenic and nonpathogenic groups as well as their potential pathogenic functions. This is an important line of research as a vast number of bacterial ORFs remain unannotated. However, selecting only one genome to represent an entire species significantly limits the scope of the study. Moreover, the study lacks sufficient detail in the methods which in turn makes it difficult to interpret the results. I have highlighted some examples below:\n\nMethods - Sequence data : How many genomes were available for each species and why were those specific accessions selected? Was it based on assembly quality? Or were those the only genome available for a given species? ORFs extraction: The criteria for ORF selection is not clear, in Figure 1: “ORF sequence → has another copy? → No → Discard” - the reason behind discarding ORFs is not mentioned. Is an ORF that is present in only one genome within a species group discarded? (and if so, why?). What is the AA identity cutoff for considering an ORF unique vs shared?\n\nConservation: “to conduct the conservation test, gathering data based on identity level and query coverage.....Clustal Omega…was used to align the sequences to assess the locus conservation assay” - I understand the authors used a t-test but it is not clear exactly what was compared to assess significance. It is also not explained what the ‘Locus conservation assay’ is.\n\nResults - Unknown ORFs’ conservation: “The analysis revealed significant similarity between 816 unORFs from pathogenic tested genomes and over 49,000 sequences in various staphylococci species” - are these referring to BLAST results? How are the authors handling redundant matches (matches to multiple highly similar/identical genomes) ?\n\nFigure 4: The source of the data that are plotted is not clear. The ‘Number of Genomes’ axis in the boxplots maxes out at 100, does that mean a single ORF can only be present in a maximum of 100 genomes? Or is this the number of species, as the authors mentioned earlier they are targeting a maximum of 100 species? In which case the axes labels must be changed.\nIn general, the figure legends do not have adequate descriptions of the plotted information, making them hard to interpret.\n\nWhile the discussion section re-summarizes the results and related studies, it lacks any synthesis of new ideas/insights from the results presented in this study. This section also makes certain assumptions that are not convincing due to the small starting dataset of 10 genomes, eg: “Transposons detected as exclusive for pathogenic Staphylococcus.”.\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?\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": [] } ]	1	https://f1000research.com/articles/13-27
https://f1000research.com/articles/13-26/v1	08 Jan 24	{ "type": "Case Report", "title": "Case Report: Management of Dadru Kushtha (Tinea Corporis) by Shamana Chikits", "authors": [ "Manisha Panda", "Sourabh Deshmukh", "Trupti Thakre", "Sourabh Deshmukh", "Trupti Thakre" ], "abstract": "Background Skin disorders are often seen as a result of a change in lifestyle, a lack of physical activity, and inadequate nutrition. Hygiene, emotional stress, and poor eating habits are also factors to consider. Kushta is the term used in Ayurveda to describe all skin disorders which is classified as Mahakushtha (major skin disorders) and Kshudrakushtha (minor skin disorders). Dadrukushta is a type of kshudrakushta that is commonly seen in clinical practice. In Ayurveda, the signs of dadrukushta are same as those of Tinea corporis, which is explained in modern science. Tinea corporis has a wide range of clinical symptoms that are mostly dependent on the infective organisms. By treating the condition with Ayurveda’s treatment therapy produces long term Outcomes.\n\nAim & Objectives Aim of this contemporary study was to assess how Ayurvedic modality shamana chikitsa works on Dadrukushta.\n\nCase A 27 year old male patient approached to Kayachikitsa OPD with complaints of blackish lesions with raised borders and itching over the chest and back (upper) region for 15 days having disturbed sleep which undergone treatment of shamanachikitsa (palliative care). Dadrukushta (Tinea corporis) can be dealt with shamana karma (palliative care) using internally Gandhakrasayan (Moringa ovalifolia prepared from sulphur), Panchtiktaghrita (Pancha means five, Tikta means bitter in taste. Tikta Rasapradhan Dravyas are collectively called as Panchatikta Dravyas. The five Dravyas are Azadirachta indica (Neem), Trichosanthes dioica (Patola), Solanum xanthocarpum (Kantakari), Tinofpora cordifolia (Guduchi) and Adhatoda vasica (Adulsa), fungiwin cream, Karanjataila (Pongamia pinnata oil tree), S-kin powder for local application for 45 days.\n\nResults The Gradation Score was 8 before treatment, after 45 days it was 0. The patient in this case study experienced relief in the symptoms.\n\nConclusions The patient obtained better results by Shamanachikitsa.", "keywords": [ "Dadrukushta", "Tinea corporis", "Shamana", "kshudrakushta", "skin disorders", "kushta" ], "content": "Introduction\n\nSkin is the biggest and heaviest organ in the body, spanning an average of 20 square feet. The most obvious function of the skin is to protect our internal organs from the environment, but it does so much more.1 Dermatophytes are fungi that invade and proliferate inside keratinized tissue (skin, hair, and nails).2 Trichophyton (which causes infections in the skin, hair, and nails), Epidermophyton (which causes infections on skin and nails), and Microsporum (which causes infections in the skin and nails) (which causes infections on skin and hair) are the three classes of dermatophytes. Based on their route of transmission, they have been classified as anthropophilic, zoophilic, or geophilic. Finally, depending on the people who have been affected.3 Incubation period is 1-3 weeks.4\n\nTinea corporis often manifests as a well-defined, strongly delineated, oval or circular, moderately erythematous, scaly patch or plaque with a raised leading edge.5 As the active boundary extends outward, the centre region becomes hypopigmented or brown and less scaly.6The margins are frequently circular and uneven. Multiple lesions gather to form polycyclic patterns.7 Ayurveda classifies all skin diseases as ‘Kushtha,’ which is further subdivided into two types: Mahakushtha (major skin disorders) and Kshudrakushtha (minor skin disorders). Dadru (Tinea corporis) is one of them.8 Acharya Charaka9 defines Dadru (Tinea corporis) as Kshudrakushtha (minor skin disorders), although Acharya Sushrut and Acharya Vagbhat define it as Mahakushtha.10 Vishamashana (incompatible food), vega vidharana (suppression of natural urges), diwaswapa (daytime sleeping), atilavana, atitikshnaahar (excessive salty or spicy food), contaminated food, drinking cold water immediately after physical work, or atapsevana (exposure to sunlight) are all factors that contribute to Kushta.11 Dadru’s principal lakshanas are Kandu (itching), Utsanna (elevated circular lesions), Mandala (circular patches), Raaga (erythema), and Pidakas (papule). Dadru samprapti is characterised by Pitta-kapha dosha vitiation and rasavaha and raktavaha strota dushti.12 Dadru is associated with Tinea/Fungal Infections because to comparable features. Tinea infections affect 5 persons out of every 1000.13 Tinea Cruris, often known as Jock Itch, is a fungal infection that affects the groin, perineum, and peri-anal region. It might appear unilaterally or bilaterally as a red, raised, and active border. The most prevalent organisms that cause ‘Tinea cruris’ are Trichophyton rubrum and Epidermophyton floccosum.14 The climate in India favours the acquisition and maintenance of mycotic infections. Dermatophyte infection is more frequent in people aged 16 to 45.15 Scalings in ‘Tinea cruris’ are varied, and vesiculation is uncommon. It frequently happens to individuals who are wearing garments made of synthetic materials, which tend to trap heat and humidity in the skin.16 It is treated in modern medicine using topical and systemic antifungal medications, as well as corticosteroids. Shodhan, Shaman, and Bahirparimarjan (topical) Chikitsa are Ayurvedic remedies for Dadru.17 In this case study, all these therapy techniques are applied.\n\nDadrukushta (Tinea corporis) is one of the kshudrakushta (minor skin disease) having lakshanas (symptoms) like Kandu (itiching), Atasipushpa like Pidika, Varna with Mandal (patches), Unnata Mandala (raised borders), Dirghapratana (macular rashes), Tamra Varna Pidika (copper coloured macular rashes).18 Due to vitiation of sapta dhatus (seven tissue) like three Doshas (bodily elements), Twak (skin), Rakta (blood), Mamsa (muscles) and Lasika (blood vessels) for manifestation of kushta.19 Dadrukushta is having management with shamanachikitsa (pacification).\n\n\nCase report\n\nA 27-year man working as a farmer, came with complaints of blackish lesions with raised borders and itching over the chest and back (upper) region for 15 days and having disturbed sleep because of itching. The patient was symptomless before 15 days, after that he started complaining of multiple blackish lesions with raised borders and itching over chest and back, gradually it increased and spread over chest and back (upper)region. The patient approached to MGACH & RC Salod (H) Wardha for Ayurvedic management after examination he was advised for Shamanachikitsa (palliative care). Patient had no significant past history. On examination vitals like blood pressure, temperature, heart rate and respiration rate were within normal limits.\n\nBefore 15 days, the patient was OK, but then he acquired round and reddish spots across his abdomen, accompanied by acute itching. He had received Allopathic treatment from a local practitioner for this but had not received satisfying results, so she came to MGAC Hospital for care.\n\nThere was no history of diabetes mellitus/insipidus, hypertension, bronchial asthma, or hypothyroidism. There was also no related family history. Except for the patient’s constipation, Ashthavidh pariksha was within normal limits. The patient was of madhyam akruti/medium body build andlocal examination revealed 4-5 circular erythematous, well-demarcated areas with vesicular eruption across the abdomen. There is no drainage from the lesion. The vital values were normal. Dadru (Tinea corporis) was identified based on clinical characteristics.\n\nAhar (diet) is mostly Mixed (Veg-Non veg),nidra (sleep) isdisturbed due to itching, patient has no bad Vyasan (habits), Occupation of the patient is farmer.\n\nAshtavidhaPariksha:\n\n1. Nadi/pulse – 74/min\n\n2. Mala/ bowel movement – Saam/bowel with undigested toxins\n\n3. Mutra/micturition – Samyak/proper\n\n4. Jivha/tongue – Saam/coated\n\n5. Shabda/speech – clear/Spashta\n\n6. Sparsha/temperature on touch – rough/khara\n\n7. Druka/eyes – Prakruta/normal with no pallor or icterus\n\n8. Akruti/body build – Madhyam/average\n\nAgni (digestive fire) = Agnimandya/poor\n\nBala/strength = Madhyam/average\n\nRaktadaaba (Blood pressure) = 130/80 mm/Hg.\n\n\n\n1. Inspection:\n\n• Size shape – annular lesions\n\n• Color – blackish lesions\n\n• Lesions – scaly patch\n\n2. Palpation:\n\n• Moisture – dryness\n\n• Temperature – warmth of the skin\n\n• Texture – rough\n\nBlood routine – Normal\n\nSamprapti Ghataka20\n\n• Dosha/bodily humors – Tridosha/dominance of three bodily humors\n\n• Dushya/elements affected by bodily humors – twaka, rakta, mamsa, lasika\n\n• Ama (undigested food particle) – Jatharagnijanya Ama/digestive fire related umdigested toxins\n\n• Agni (digestive fire) – Jatharagni\n\n• Srotas(inner transport system of the body) – Rasavaha, Raktavaha\n\n• Srotodushtiprakara/type of imbalance in inner transport system – Sanga/obstruction\n\n• Rogmarga(path of disease) – Bahya/external\n\n• Udhbhavasthana (site of location) – Amashaya/stomach\n\n• Vyaktasthana – twacha/skin\n\n• Rogaswabhava – chirakari/long-term\n\n• Sadhyasadhyaata – Sadhya/curable\n\nSamprapti: (pathogenesis)\n\n↓\n\nNidan (causative factor) sevana like Aharaja-Viharaja-Manasika (irregular food habits, Non Veg diet, consumption of alcohol), Ativyayam (excessive exercise), Atichinta (excess worry), Ratrijagarana (awakening at night).\n\n↓\n\nTridoshaPrakopa (Vitiation of all three elements)\n\n↓\n\nTwaka, Rakta, Mamsa, Lasika (Dushya)\n\n↓\n\nSthanasamshraya in Twacha (localized in skin)\n\n↓\n\nRukshapidika/dry lesion with kandu/itching\n\nDadruKushta/Tinea corporis\n\n\nMethods\n\nThe patient came to the OPD having the complaints of reddish patches. Written informed consent was taken from the patient before administration of conservative treatment and his detailed information was kept confidential.\n\nShamanachikitsa (Pacifying treatment) for 15 days comprising Gandhakrasayana, Panchatiktaghritawhich is to be given orally and fungiwin cream, Karanjataila and s-kin powder with Gomutra for localapplication (Table 1). After 15 days patient was called for followup. All medicines were continued except Gandhakrasayan, it was temporarily stopped for period of 7 days. After 7 days, the patient was asked to continue Gandhakrasayan for another 15 days with other medicines.\n\nAssessment criteria\n\nPatient evaluation was based on improvements in subjective criteria such as Kandu (Itching), Raaga (Erythema), Utsanna mandala (Elevated Circular Skin, Lesion), and Pidika (Eruption), as well as images of the lesion before, during, and after therapy. Raaga (Erythema) was present prior to therapy and persisted during the first follow up, however it was eliminated on days 15 and 45, respectively, following treatment completion. Thus, following therapy, there was total improvement in all indices. The same can be observed in the photos below, which were taken before, during, and after therapy.\n\nTinea corporis is a Dermatophyte that causes inflammatory and non-inflammatory lesions on glabrous skin.21After 15 days treatment, symptoms subsided in patient but there were still some annular lesions present. Hence Shamanachikitsa was continued with the gap of 7 days except Gandhakrasayan. After completion of Shamanachikitsa, the patient was assessed as per the gradation of Lakshana of Dadru like Utsanna Mandala, Pidikas and Kandu as shown in Table 2 which became grade 0 after 45 days of treatment as given in Table 3. Also, the patient was symptomatically improved (Figure 1).\n\n\nDiscussion\n\nIn the context of Ayurveda, kushtha is the term used to describe many types of skin illnesses, which encompass all main skin manifestations such as Tinea. The symptomatic manifestation of tinea corporis resembles that of “DadruKushtha” mentioned in Ayurvedic Samhita. This skin condition adversely affects one’s own quality of life. Ayurveda offers a viable medication for Tinea corporis.\n\nGandhak Rasayan’s mechanism of action: Gandhak rasayan is generally used to cure Kushtha roga. It is antimicrobial and anti-fungal in nature. It primarily affects Rakta Dhatu, causing Raktashodhana (purification of blood). Its antifungal property aids in the reduction of infection. It also performs the role of Rasayana. Its RaktaShodhaka, Vranaropak, Krumighna and Kushthagna properties reduce the Kandu, Pidika,Raaga and Daaha..22\n\nContents: Gandhak, Haritaki, Amalaki, Bibhitaki, Detoxified ghee, Ginger and Bhringraj. Mode of action: It is Raktashodhak, Vranaropak, Twachya, and Krumighna. It acts as a blood purifier and reduces Kandu/itching and Daha/burning sensation. Gandhaka Rasayana keeps three bodily humors, vata, pitta and kapha in equilibrium. It is a familiar, usually used formulation and specified in Kushtha.23\n\nGhrita is recommended in Kushtha Chiktsa in Samhitas. Vata -Pitta Shamaka and Tvachya (improves complexion) properties of Panchatikta Ghrita helps to alleviate Kushthaghna (skin disease).24\n\nKaranja oil is mentioned in Visarpa Chikitsa in BhaishajyaRatnavali. It consists of Krumighna (antifungal and antibacterial activities), Kandughana, Vranaropaka and Vranashodhaka properties.25Local application is beneficial for rapid absorption and reduction of kharata/dryness.26\n\nIngredients have antibacterial, antifungal, and antimicrobial characteristics, as well as Raktashodhaka (blood purification) and Vranaropak (wound healing) properties. While application of this powder Gomutra should be mixed which enhance its absorption property.27\n\nFungiwin contains Shuddha gandhak, Krishna jeerak, Avalguja etc which acts as a Krimighna, Rasayana Deepan, Pachan, Vishagna as well as Balya.it acts on all the Dhatus by acting on Dhatwagni. Hence help to formation of new cells in body. It also works as Antifungal with the gap of 7 days rejuvenation hence used in various skin diseases.\n\nDadru is Pitta-Kapha dominance according to Acharya Charak and Vagbhata, and Kaphapradhan according to Acharya Sushruta. Rasa and Rakta are both involved in the samprapti. Kushta is characterised in Samhita by repeated Shodhana and Shamana medications with Kushtaghna, Krumighna, and Kandughna characteristics. In addition, Bahiparimarjana Chikitsa (local application of medications) in the form of lepa and oil was recommended for improved results.28 In certain cases, the Ayurvedic therapy technique produces excellent outcomes. Pitta and Kapha are the most vitiated Doshas with Rasa and Rakta Dhatu, while Lasika and Tvak are Dushyas in Dadru.29‘Nidana Parivarjana’ is regarded as the initial stage in Dadru management. Untidiness of the body, sharing cloths (towels), and so on should be avoided depending on Nidana’s involvement.30 Dadru, in both its acute and chronic forms, causes physical and emotional distress in humans, as itching and other symptoms persist throughout the day.31 Ayurvedic medicine is a medical discipline that provides lasting cures by employing internal and external medicine. The qualities of Kushthaghna, Kandughna, and Krimighna might aid in the safe and successful treatment of Dadru patients.32 The skin is the index of a person’s mind; in daily life, people consume incompatible diets and dietary habits, which lead to many diseases, among which skin disorders are prominent, and Dadru is one of them. Dadru Kushtha is a very infectious Kaphapitta Pradhana Tridoshaja Aupasargika Roga. Dadru, while treatable, has a stubborn character. If the course of treatment is not carefully managed, remission and relapses are common; thus, treatment should be started as soon as feasible. Ayurvedic therapy focuses on avoiding etiological variables (Nidana Parivarjanam) and breaking down pathology (Samprapti Vighatana), which leads to Dhatu Samya.33\n\n\nConclusion\n\nTinea corporis is associated with DadruKushtha based on signs and symptoms. Chikitsa is planned in Kushtharoga, depending on the severity of Roga. ShamanaChikitsa is administered in Alpadoshaavastha (least severe). Dadru kushta is a kind of Kshudrakushta, according to Acharya Charak, and Mahakushtha according to Acharya Sushruta and Acharya Vagbhata. Tinea corporis or dermatophytosis may be involved. Because it is an infectious illness, personal hygiene is critical in its treatment. From this case study it can be concluded that use of Chikitsa upakramas described in Ayurveda like Shodhana (Nitya virechana with Gomutra siddha haritaki), Shamana (formulations like Arogyavardhini vati, Gandhak rasayan) and Bahiparimarjana (lepa of S-kin powder in gomutra and local application of Karanj oil) are effective in the management of Dudru kushta.\n\n\nConsent\n\nWritten informed consent for publication of their clinical details and/or 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\nMedical News Today UK: [cited 2020 Jan 27]. Reference Source\n\nWeitzman I, Summerbell RC: The dermatophytes. Clin. Microbiol. Rev. 1995 Apr; 8(2): 240–259. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSahoo AK, Mahajan R: Management of tinea corporis, tinea cruris, and tinea pedis: A comprehensive review. Indian Dermatol. Online J. 2016 Mar; 7(2): 77–86. PubMed Abstract \| Publisher Full Text\n\nLeung AK, Coenegrachts K: Common Problems in Ambulatory Pediatrics: Anticipatory Guidance and Behavioral Pediatrics. Nova Science; 2011.\n\nGupta AK, Chaudhry M, Elewski B: Tinea corporis, tinea cruris, tinea nigra, and piedra. Dermatol. Clin. 2003 Jul; 21(3): 395–400. v. PubMed Abstract \| Publisher Full Text\n\nKaushik N, Pujalte GG, Reese ST: Superficial Fungal Infections. Prim. Care. 2015 Dec; 42(4): 501–516. PubMed Abstract \| Publisher Full Text\n\nKelly BP: Superficial fungal infections. Pediatr. Rev. 2012 Apr; 33(4): e22–e37. PubMed Abstract \| Publisher Full Text\n\nSharma PV: Charaka Samhita of Agnivesha with English Translation. 1st Edition Reprint ed. Vol. 2. . Varanasi: Chaukhambha Orientalia; 2008; p. 183.\n\nSharma PV: Charaka Samhita of Agnivesa with English Translation. 1st Edition-Reprint ed. Vol. 2. . Varanasi: Chaukhambha Orientalia; 2008; p. 184.\n\nTrikamji J, Orientalia C, Samhita S: (Commentary of Dalhanacharya) and the Nyaya Chandrika, Varanasi. 5th edition. 2005; 37.\n\nRanajitaraya D: AshtangaSangraha of Sarvanga Sundari Vyakhyaya Samhita Sutrasthana- Prathama Bhaga, Shri. 3rd edition.Nagpur: Baidyanath Ayurveda Bhavana, pvt. Ltd; 1986; p. 137.\n\nRavidatta T, Vidyadhar S: ‘Charaksamhita’ Vol. 2 - Chikitsasthana ‘Kushtha chikitsitam Adhyaya’ 7/4-8 – Edition Chaukhamba Sanskrit Pratisthan, Delhi.2013; p. 181.\n\nVidyadhar S, Tripathi RD: Charak Samhita of Agnivesha revised by Charaka Redacted By Drudbala with vaidya manorama’ hindi commentary, Chaukambha Sanskrit pratishthan, Delhi reprint-chapter- 7 chikitsasthan shloka. Vol. 29-30. 2011; p. 185.\n\nUsha S: Tinea infections, unwanted guests. Express Pharma. 2010; 1.\n\nEl Gohary M, Van Zuuren EJ, Fedorowicz Z, et al.: Topical antifungal treatments for tinea cruris and tinea corporis. Cochrane Libr. 2014; 8: 7–9. Publisher Full Text\n\nSingh S, Beena PM: Profile of dermatophyte infections in Baroda. Indian J. Dermatol. Venereol. Leprol. 2003; 69(4): 281–283. PubMed Abstract\n\nGupta R: Textbook of Dermatology. 11th chapter – Fungal infections – Tinea cruris. First edition.New Delhi: Jaypee brothers; 2002; pp. 67–72. 81-8061-034-9.\n\nDr. Tripathi B : Charak Samhita Chikitsa Sthana, Choukhamba Surbharti PrakashanVaranasi.2005. p-305,7/23.\n\nVenkatesh P, Belavadi S: MANAGEMENT OF KITIBHA KUSHTA (PSORIASIS): A CASE STUDY. Int. J. Ayu. Pharm. Res. 2018 Aug.18 [cited 2023 Jun. 28]; 6(7). Reference Source\n\nVidyadhar S, Dutt TR: Agnivesha, Charak Samhita, Chikitsasthan 7/9, Delhi, Chaukambha Sanskrit Pratisthan.2019; p. 182.\n\nhttp\n\nChavhan MH, Wajpeyi SM: Management of dadru kushta (tinea corporis) through ayurveda-A case study. Int. J. Ayurvedic Med. 2020; 11: 120–123. Publisher Full Text\n\nGangadharshastri G: „Aayurvediya Aushadhigunadharmashastra‟- Part 2 – 30 Vaidyak Granth Bhandar Publication.2011; 271.\n\nThakre PP, Deshmukh S, Ade V: A Case Study on Plaque Psoriasis with Ayurvedic Management. Int. J. Ayurvedic Med. 2020; 11(2): 342–345. Publisher Full Text\n\nBramhashankar M: Bhaishajya Ratnavali, VolIII edition 1st, 57/26. New Delhi: Chaukhamba Sanskrit Bhavan; 2006; 145.\n\nSahu PJ, Singh AL, Kulkarni S, et al.: Study of Oral Tranexamic Acid, Topical Tranexamic Acid, and Modified Kligman’s Regimen in Treatment of Melasma. J. Cosmet. Dermatol. 2020; 19(6): 1456–1462. PubMed Abstract \| Publisher Full Text\n\nRajput Satyendra Singh H, et al.: Use of Karanj Oil (Pongamia glabra) In Topical Formulation. Res. J. Pharm., Biol. Chem. Sci. Jan. 2014; 5(3): 546.\n\nChavhan MH, Wajpeyi SM: Management of dadru kushta (tinea corporis) through ayurveda-A case study. Int. J. Ayurvedic Med. 2020; 11: 120–123. Publisher Full Text\n\nChaudhari VM, Kokate KK: Management of Dadru Kushtha with Ayurveda Intervention-A Case Study. J. Ayurveda Integr. Med. 2020 Jun 30; 5(03): 164–171.\n\nSharma UK: ROLE OF AYURVEDA IN MANAGEMENT OF DADRU KUSTH (FUNGAL INFECTION-TINEA): A CASE STUDY.\n\nJadhav PB, Wagh S: AYURVEDIC MANAGEMENT OF DADRU KUSTHA-A CASE REPORT.\n\nKumar A, Gwala BR, Meena HM, et al.: REVIEW OF DADRU KUSHTHA WSR TO FUNGAL DERMATOPHYTOSIS: A CONCEPTUAL STUDY.\n\nLunawat SR, Sabu NR: Ayurvedic Approach in Fungal Infections of Skin. WJPR. 2016; 5(4): 1757–1762." }	[ { "id": "245754", "date": "26 Feb 2024", "name": "Ghazala Javed", "expertise": [ "Reviewer Expertise Unani (Traditional ) medicine. Clinical Research in Unani 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\nThe case report lists management of Dadrukushta which is considered to be similar to Tines corporis. Somewhere it should be mentioned how the diagnosis of Tinea corporis was made?\n\nAlso, why 03 topical applications are being used? Do we have references in classical texts of Ayurveda to use them together? Is this the standard treatment plan for all cases of Dadrukushta?\nDiscussion should also mention limitations of this case study.\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": "11148", "date": "13 Apr 2024", "name": "Dr. Manisha Panda", "role": "Author Response", "response": "Respected reviewer, Diagnosis was made by signs and symptoms, gradations are also mentioned. So, kindly consider. Yes Ayurvedic references are present for topical lotions. Yours sincerely, Manisha Panda" }, { "c_id": "11149", "date": "13 Apr 2024", "name": "Dr. Manisha Panda", "role": "Author Response", "response": "Respected reviewer, Diagnosis was done by observing signs and symptoms similar to Tinea corporis. Ayurvedic references are followed for all medications. Yours Sincerely, Manisha Panda" } ] }, { "id": "265859", "date": "24 Apr 2024", "name": "Paradkar Hemant", "expertise": [ "Reviewer Expertise Ayurvedic Clinical research", "Ayurvedic Drug 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\nIntroduction: The introduction offers a comprehensive overview of Tinea corporis (Dadru kushtha) and its manifestations, including its clinical presentation, etiology, and conventional treatment approaches in both modern medicine and Ayurveda. However, enhancing its readability could be achieved by breaking down the text into smaller paragraphs or sections for better organization. History: In the history section, it's mentioned that the patient had received Allopathic treatment. It would be ideal to specify the treatment taken and its duration in detail to provide a clearer understanding of the patient's medical history.\nLab Investigations: While it's stated that the blood routine was normal, providing a detailed explanation of the investigations conducted along with their values would enhance clarity and understanding.\nTreatment Plan: It would be beneficial to justify the specific duration of treatment and explain the rationale behind the decision to temporarily stop Gandhakrasayan for 7 days before resuming it.\nObservation: The line “Hence Shamana chikitsa was continued with the gap of 7 days except Gandhakrasayan,” mentioned in the observation, seems to deviate from the treatment plan. Clarifying this discrepancy would improve coherence.\nAssessment Criteria: The outlined criteria for evaluating treatment effectiveness, including subjective parameters such as itching, erythema, and lesion characteristics, are clear. However, providing details on how these criteria were measured or assessed during follow-up visits would enhance transparency and reproducibility\nTherapeutic Approach: Elaborating on how each medication addresses Pitta-Kapha dosha imbalance and Dhatu involvement in Dadru Kushta would deepen understanding of the therapeutic approach and its mechanisms.\nExternal Applications: Including information on the time and duration for external applications would improve transparency and reproducibility, ensuring clarity in the therapeutic process.\nConclusion: If this is purely a case study of Shaman Chikitsa, concluding with Shodhan (Gomutra siddha Haritaki – nowhere mentioned in the manuscript) and Arogyavardhini (nowhere mentioned in the treatment plan) is not understandable. Perhaps providing a more coherent and focused conclusion would better summarize the findings of the study.\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? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly", "responses": [] }, { "id": "245763", "date": "11 Sep 2024", "name": "Manjunath M. Shenoy", "expertise": [ "Reviewer Expertise Dermatology with special interest in mYcology" ], "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 author/s, Happy to observe a case report on treatment of tinea corporis, however, please note my following comments. 1.Is this a novel treatment modality or is it a known form of treatment? 2. Having treated a lot of tinea corporis for many years, these lesions appear to be of more than 15 days duration. Please confirm the history once again. Is there any follow up to assess recurrence of the disease. This is important because tinea corporis is known for recurrence.\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? 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? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-26
https://f1000research.com/articles/13-24/v1	08 Jan 24	{ "type": "Research Article", "title": "Characterization of four digestates from different types of substrates used in biogas production in Northern Peru", "authors": [ "Jesús Rascón", "Lily del Pilar Juarez Contreras", "Euler Willan García Saldaña", "Wildor Gosgot Angeles", "Milton A. Huanes", "Luis Alberto Taramona Ruiz", "Miguel Ángel Barrena Gurbillon", "Lily del Pilar Juarez Contreras", "Euler Willan García Saldaña", "Wildor Gosgot Angeles", "Milton A. Huanes", "Luis Alberto Taramona Ruiz", "Miguel Ángel Barrena Gurbillon" ], "abstract": "Background Biol is one of the best-known digestates, which occurs during anaerobic digestion in biodigesters to generate biogas, using animal manure and vegetable waste. This digestate type is used in organic agriculture due to its easy application, contributing simultaneously to the circular economy and food security.\n\nMethods The objective of this study was to characterize four types of biol, generated in four anaerobic biodigesters for biogas production implemented in northern Peru fed with manure: i) pig manure; ii) cattle manure; iii) horse manure; iv) cattle manure with coffee processing water. All the biodigesters implemented had the same design but worked under different environmental conditions. Descriptive and multivalent statistics were applied to the data obtained for the parameters evaluated.\n\nResults The biols obtained had different nutritional compositions, depending on the type of substrate used. The biol from pig manure was characterized by high concentrations of bacteria, the one from cattle manure had low concentrations of nutrients in general, the one from horse manure was rich in salts, and the one from cattle manure with coffee processing water was rich in organic matter.\n\nConclusions These results showed that all the biols obtained can be used for organic agriculture. However, their selection will depend on the nutritional requirements of the type of crop and soil where the biols are to be applied.", "keywords": [ "Organic farming", "biol", "biodigesters", "nutritional composition", "manure" ], "content": "Introduction\n\nBiol is a liquid organic fertilizer obtained by anaerobic digestion of organic substrates, such as animal manure and plant waste, without oxygen (Hernández-Sarabia et al., 2021). It is a product with high economic profitability, and above all, it has the necessary nutrients for the correct development of plants or to improve soil quality (Fahrurrozi et al., 2016; Kilic, 2023). Organic fertilizers, such as biols, are used in organic agriculture to improve the quantity and quality of crop yields; stimulate microbiological activity by increasing soil organic matter; or replenish nutrients present in the soil, such as nitrogen (N), phosphorus (P), potassium (K) or calcium (Ca), and which are used by plants for their development (Zandvakili et al., 2019). These effects have been proven in crops such as cattle pastures and forages (Soares Filho et al., 2018), legumes (Limam et al., 2018) or lettuce (Fedeli et al., 2023). Another beneficial effect of biols is the improvement in soil structure, both biologically and physicochemically (Thomas & Singh, 2019). Organic fertilizers favor the presence of air in the soil, helping water infiltration and improving nutrient adsorption by roots, helping to optimize water retention. They also increase the defense capacity against pests and diseases, and reinforce resilience against extreme climatic changes that crops may suffer compared to when agrochemicals are used. In addition, organic fertilizers have a longer duration since organic matter decomposes slowly (Chew et al., 2019; Mącik et al., 2020).\n\nIn agricultural production, animal excreta and slurry are common as fertilizers (Muktamar et al., 2016; Phibunwatthanawong & Riddech, 2019). These manures are rich in nitrogen, not metabolized by animals, which is released into the environment as ammonium during decomposition (Lu et al., 2017). Although it is a way to reduce costs for many agricultural producers, using fresh manures can cause problems. Some problems are pollution of surface and groundwater by nitrates; air pollution by gases such as methane, one of the causes of global warming; and, in some cases, loss of fertility by salinization (Li et al., 2016; Wongsaroj et al., 2021). On the other hand, agroindustrial production generates a large amount of organic waste, especially plant waste or wastewater (Pandit et al., 2021; Rosemarin et al., 2020). For example, coffee production generates waste from fermentation and washing, such as coffee pulp and water (Serna-Jiménez et al., 2022). These by-products of the coffee production process are considered waste and tend to cause environmental problems related to the greenhouse effect, soil deterioration and air and water pollution (Schmidt Rivera et al., 2020). However, these by-products are renewable resources rich in carbohydrates and bioactive compounds (Chala et al., 2018; Villa Montoya et al., 2020).\n\nOne of the solutions to these problems is the establishment of anaerobic digestion systems or biodigesters for biogas generation, mainly using animal excreta and slurry together with plant waste as substrates (H. Wang et al., 2018; Y. Wang et al., 2021). These systems are based on anaerobic fermentation of the substrates added to the biodigester to generate biogas. The excreta of animals such as cattle, horses, pigs, sheep, or goats are the most commonly used substrates in this system. Some of these animals have modifications in their digestive system, such as a rumen or a large caecum, which allow them to digest cellulose thanks to the biome found inside them (Fujimori, 2021). Within this biome are mainly cellulolytic bacteria (cellulose decomposers), amylolytic bacteria (break down starches), proteolytic bacteria (break down proteins), and methanogenic bacteria (produce methane) (Froidurot & Julliand, 2022; Hua et al., 2022; Palangi & Lackner, 2022). Excreta containing a biome rich in different types of bacteria makes them suitable as inoculums to generate biogas, in addition to being the main substrate for anaerobic fermentation (Sequeda Barros et al., 2023). One of the most essential bacterial groups in biodigesters is the methanogenic bacteria, which produce methane. This gas is the main component of biogas, with concentrations between 50% and 70% of the total. As a result, biogas is an environmentally friendly fuel by closing the carbon cycle (Nwachukwu et al., 2022).\n\nAnother useful digestate, biol, is also produced in biodigesters for biogas production. Biol is a liquid organic fertilizer rich in nutrients (Barrena et al., 2019). One of the great benefits that biol has is its low concentration of bacteria, thus releasing fewer pathogens into the environment than fresh manures. Depending on the type of substrate used, they differ in their nutrient composition or concentrations of pathogens or bacteria (Risberg et al., 2017). However, one of their biggest problems is their concentration of nitrogenous compounds, as plants usually use only as much as they need. Excess nitrogenous compounds can affect soil fertility and impair crop production (Nkoa, 2014; Samoraj et al., 2022).\n\nEstablishing the nutritional composition and other parameters is an excellent way to know that using a biol will not harm a crop or soil. By establishing this composition, we can know two things. The first is to know if the biol, depending on the substrate used, meets the crop’s nutritional requirements, and the second is to know the amount of possible contaminants it may have (Chatzistathis et al., 2020). Some of the most commonly used substrates in biogas and biol production are excreta from cattle (Jafari-Sejahrood et al., 2019; Khayum et al., 2018), pig (Shen et al., 2019), alpaca (Fernandez-Lizama et al., 2019), goats (Hanafiah et al., 2017) or chickens (Matheri et al., 2017). These substrates can be mixed with other substrates, such as plant biomass (Martí-Herrero et al., 2019), organic waste from factories or households (Čater et al., 2015; Pavi et al., 2017), or even sewage (Guilera et al., 2020; Mohammed et al., 2017). Excreta, organic waste, and wastewater also have the function of inoculum, having a good content of fermenting bacteria (Wi et al., 2023). However, in some cases, formulated inoculums are added to enhance the anaerobic process, mainly when part of the substrate contains plant biomass rich in lignocellulose, which is difficult to decompose (Kainthola et al., 2019). All biols generated from the above substrates possess many nutrients and are generally safe for crops (Islam et al., 2019).\n\nIn northeastern Peru, agriculture is the Amazon department’s most important economic activity. The production of cattle, pigs, and horses stands out, as well as rice, cocoa, and coffee. With the growing demand for sustainable and environmentally friendly production, many small and large farms are adapting technologies to achieve this goal, with biodigesters for biogas and biol being the most viable for this purpose. However, more knowledge of the composition of the biols generated must be gained. Although there are several studies on the characterization of liquid organic fertilizers, there are no studies on the biols generated in biodigesters for biogas production. Determining the amount of nutrients present and their physical, chemical, or microbiological characterization is important. Mainly because nutritional requirements and specific conditions are needed depending on the crop type. To this must be added the type of substrate used. Therefore, the objective of the present work was to determine the microbiological, physicochemical, organic matter, and nutrient composition in four types of biol generated in different biodigesters for biogas production fed with four types of substrates. At the same time, it was determined which were the most important parameters at a general level, how they behaved, and which were the most influential ones in each biol.\n\n\nMethods\n\nFour different types of biols obtained from biodigesters for biogas production implemented in different districts of the Amazonas Department in northern Peru were studied. These biodigesters were fed with different substrates: pig manure (T1), cattle manure (T2), horse manure (T3), and cattle manure with coffee processing water (T4). The main design and operating parameters of the biodigesters are reported in Table 1.\n\nSpecifically, the biol obtained from pig manure (T1) was collected from a biodigester implemented at the military base in the district of Jazan (5°56′16.85″S 77°58′48.10″W, 1349 m.a.s.l.). The biol obtained from cattle manure (T2) was collected from a biodigester implemented in the experimental fields of the Universidad Nacional Toribio Rodríguez de Mendoza (UNTRM) in the district of Chachapoyas (6°14′0.33″S 77°51′5.54″W, 2305 m.a.s.l.). The biol obtained from horse manure (T3) was collected from a biodigester implemented in an experimental station of the UNTRM in the district of Florida-Pomacochas (5°49′19.02″S 77°57′40.23″W, 2253 m.a.s.l.). Finally, the biol obtained from the co-digestion of cattle manure and coffee processing water (T4) was collected from a biodigester implemented in a coffee farm in the district of Santa Rosa (6°26′48.53″S 77°28′29.45″W, 1845 m.a.s.l.).\n\nAll the biodigester samples were collected from the storage pond of each biodigester. Four samples were collected from the same biodigester for two weeks. Subsequently, the four samples from each biodigester were carefully mixed and stored at 4 °C before being analyzed in the laboratory.\n\nFour groups of parameters were analyzed in the laboratory: microbiological, physicochemical, organic matter, and nutrients. All analyses were performed twelve times for each biol and at the Soil and Water Research Laboratory of the UNTRM (Rascón, 2023).\n\nThe microbiological parameters analyzed were total coliforms (TC), fecal coliforms (FC), Escherichia coli (EC), Salmonella (SA), and Methanococcus (ME). All were determined by the Most Probable Number method, following the recommendations of APHA et al. (2017) for TC, CF, and EC; EPA (2006) for SA; and Acuña et al. (2008) for ME.\n\nThe physicochemical parameters analyzed were pH, electrical conductivity (EC) with a multiparametric equipment brand SI Analytics, model HandyLab 680; total solids (TS), by drying at 105°C in an oven brand MMMgruop, model Venticell; and sulfates (SULF) using a Thermo Scientific atomic absorption spectrophotometer, model Genesys 10S UV-Vis. All this follows the methodologies established by the APHA et al. (2017) and EPA (1978).\n\nThe chemical oxygen demand (COD) parameter was analyzed regarding organic matter. For COD, use was made of a HACH brand digester block, model DRB220, and a Thermo Scientific brand atomic absorption spectrophotometer, model Genesys 10S UV-Vis, following the methodology established by APHA et al. (2017).\n\nThe nutrients analyzed were total nitrogen (TN) using a semi-automatic Kjeldahl distiller Selcta brand, model PRO - NITRO S, following the methodology established by APHA et al. (2017); phosphorus (P) using a Thermo Scientific brand atomic absorption spectrophotometer, model Genesys 10S UV-Vis, using the modified Olsen method (Carter & Gregorich, 2007); Potassium (K), Calcium (Ca), Magnesium (Mg), Sodium (Na), Iron (Fe), Manganese (Mg), Zinc (Zn), Copper (Cu), Aluminum (Al) and Boron (B), by acid digestion, using an Agilent atomic emission spectrophotometer, model MP-AES 4100, following the methodology established by APHA et al. (2017).\n\nA descriptive statistics analysis (mean, standard deviation) of the composition of each of the four biols evaluated was performed. Subsequently, a principal component analysis (PCA) was applied, an ideal statistical method to reduce the dimensionality of a large data set (Van Der Maaten et al., 2009). PCA identifies the variance in correlated variables to generate a reduced set of uncorrelated variables known as principal components (PC). These PCs are weighted linear combinations of the original variables (Thioulouse et al., 2018). In this research, the PCA was determined using a correlation matrix. Eigenvalues were calculated to measure the importance of the components. Once the PCA was calculated, the number of components to be used was determined using the criterion of considering a sufficient number of components able to explain between 70% and 90% of the total variation of the original variables (Rencher, 2012). Finally, a biplot was used to interpret better the first two principal components (Jolliffe, 2002). The most important parameters were established through correlation by matrix multiplication between the matrix with the loading vectors of nutrients and PCs and the diagonal matrix constructed from the standard deviation of the principal components. After that, the most important parameters of the evaluated biols were those with a strong correlation, which bore greater than ±0.70 (Akoglu, 2018). Finally, to know the behavior of the parameters and determine which parameters were the most influential in each biol, a biplot with ellipses complemented with a Permutation-based Multivariate Non-Parametric Analysis of Variance (PERMANOVA) was used to confirm the dissimilarity between the biols found (Anderson & Walsh, 2013). All statistical analyses were performed at a significance level of P<0.05 with R statistical software version 4.3.0 (R Development Core Team, 2023).\n\n\nResults and Discussion\n\nAfter analyzing all the parameters of the biols for their characterization, it was found that about the microbiological parameters, the equine manure biol (T3) had shallow values of TC, FC, ECO, SA, and ME for the rest of the biols, indicating its innocuousness. However, the highest values of microbiological parameters were reported for the pig manure biol (T1) (Table 2).\n\nAs for the physicochemical parameters, the biols of horse manure (T3) and cattle manure with coffee processing water (T4) had an acid pH, while the biols of pig manure (T1) and cattle manure (T2) reported alkaline pH values. At the same time, the EC of the cattle manure biol (T2) and cattle manure biol with coffee processing water (T4) was low, indicating low concentrations of dissolved salts in the liquid medium, contrary to the horse manure biol (T3). TS and SULF, parameters of great importance in biols (Somers et al., 2020), were low in the swine manure biol but high in the horse manure biol (T3) (Table 2).\n\nOrganic matter, a parameter of great interest for improving soil structure and water holding capacity, and which is expressed in terms of DOC (Manasa et al., 2020), was very high in the cattle manure biol with coffee processing waters (T4), being approximately 5 to 10 times higher than in the other biols (Table 2).\n\nThe main nutrients analyzed, N-P-K, had very different concentrations depending on the biol. P concentrations were very high in the biol of cattle manure with coffee processing water (T4). In contrast, the concentration of TN was higher in the biols of horse manure (T3) and cattle manure with coffee processing water (T4). The concentration of K was high in the cattle manure biol (T3) but very low in the cattle manure biol with coffee processing water (T4). On the other hand, nutrients such as Ca, Mg, and Al had deficient concentrations in the swine manure biol (T1) but were very high in the horse manure biol (T3). As for Fe and Mn concentrations were high in the cattle manure biol with coffee processing water (T4) and low in the cattle manure biol (T2). Likewise, Zn and Cu concentrations were high in the cattle manure (T2) but low in the swine manure biol. Na concentrations were very high in the horse manure biol (T3), but very low in the cattle manure biol with coffee processing water (T4). Finally, it should be noted that B concentrations were only detected in the pig manure biol (T1) (Table 2).\n\nThe processing of biols through biogas production is considered a form of clean energy production, which contributes to the environment and nourishes plants (Holm-Nielsen et al., 2009). Therefore, it is important to know the physicochemical characteristics of a biol since it is possible to know its effectiveness for agricultural production (N. Wang et al., 2021). Before applying any biol, it is necessary to know its microbial load, especially pathogenic bacteria such as Escherichia coli or Salmonella, in order not to put at risk neither the development of plants nor food safety (Carraturo et al., 2022; Cathcart et al., 2022). Pig manure biol was the only one that presented values that put food safety at risk. This evidence shows that anaerobic digestion systems do not always eliminate the pathogens present in manure, so pasteurization would be necessary before use to reduce the levels of these pathogens (Ntinas et al., 2021; Proskynitopoulou et al., 2022).\n\nBiols from pig manure (T1) and cattle manure (T2) were slightly alkaline, with mean values of 7.58 and 7.76, respectively, while biols from horse manure (T3) and cattle manure with coffee processing water (T4) with mean values of 4.01 and 4.27 respectively. These results are ambiguous in finding acidic biols because it is normal to obtain biols with a pH range between 6 and 8 (Fagbohungbe et al., 2019; Samoraj et al., 2022). The reason for finding acidic pH is due to acidification within the biodigester (Sanchez- Beltrán et al., 2021), partly due to the higher amount of plant debris that may be in the horse manure or coffee processing waters, which are usually very acidic, as substrate (Getachew et al., 2023). However, biols with acidic pH are usually free of pathogenic microorganisms whose use would not imply risks to soil quality and, thus to crops and food safety (Parra-Orobio et al., 2021).\n\nThe concentrations of organic matter in swine, bovine, and equine manure biols are practically low, something to be expected, as it happens in most organic manures (Bhatt et al., 2019). The organic and nutritional composition of the characterized biols shows evident differences between them. However, it should be noted that the contractions of P, K, Ca, and Mg, as well as the concentrations of the rest of the micronutrients, are also low, being in organic form and needing a decomposition and mineralization process to be available to plants (Geisseler et al., 2021; Meena, 2019). It is understandable given that the substrates used are diverse and present a unique composition due to the particularities of the digestive systems of the animals from which they come, as well as the type of plant waste (Risberg et al., 2017). That said, it is considered that biols could be applied to all crops for agricultural production, as it contains essential nutrients that promote plant growth and yield (Shaji et al., 2021). Biols are frequently used for horticulture, in crops such as lettuce (Faran et al., 2023) or broccoli (Weimers et al., 2022), but it is also advisable to use it for pasture and forage production (Moreno Sandoval et al., 2022).\n\nAfter applying the principal component analysis (PCA), two principal components (PC) were selected that jointly explained 80% of the data variance. Fourteen parameters of great importance in the evaluated biols were identified (Table 3). The pH and B showed a strong negative correlation with PC1, while TS, SULF, K, Ca, Mg, Na, and Al had a strong positive correlation with PC1. On the other hand, Cu showed a strong negative correlation with PC2, while DOC, P, and Mn showed a strong positive correlation with PC2. It is important to highlight the microbiological parameters; although they did not show a strong correlation, they were close to a strong negative correlation, especially TC, FC, ECO, and ME.\n\nThe use of biol is highly recommended as it is a product that increases and stimulates growth and development in a large number of crops, such as potato, wheat, tomato or bell pepper, among others (De Corato et al., 2023; Garg et al., 2005). It is essential to know which are the most important parameters of the biol, since this will allow knowing how efficient the product is according to the type of crop and how it should be applied for agronomic purposes (Fernandez-Bayo et al., 2020). Nutrients in a biol must have balanced levels for proper crop development and good yields. The ideal levels will depend on each crop’s nutritional requirements and the type of soil where the biol is applied (Seelam et al., 2022).\n\nThe pH and B are found to be two critical parameters in biols, given their influence on plant nutrient availability and soil quality in general (Tadesse et al., 2022). The pH, which indicates acidity or alkalinity, can limit nutrient uptake and affect the soil microbiome if it is not in a suitable range, depending on the type of crop and soil in which the biol is applied (Ferrarezi et al., 2022). On the other hand, B is an essential micronutrient necessary for plant growth by participating in cell wall formation and nutrient transport. An adequate level of B can prevent soil deficiencies and improve crop quality and yield (Das & Purkait, 2020).\n\nTS parameters, SULF, K, Ca, Mg, Na and Al, are also critical for biols (Lee et al., 2023; Rizzo et al., 2020). STs provide organic matter and nutrients to the soil, improving its structure and water-holding capacity, so it is ideal for biols to have high concentrations of STs (Pandey et al., 2023). SULF, in a proper balance, provides sulfur, an essential nutrient, in a form that plants can absorb and utilize for growth and development (Afzal et al., 2020). Likewise, K, one of the essential macroelements for crops, plays a crucial role in crop growth and development, being essential for the regulation of water balance, fruit development, disease and stress resistance, and the transport of other essential nutrients, such as TN and P, within the plant (Johnson et al., 2022). Ca, Mg, and Na are also essential micronutrients for crops; the first two are necessary for forming cell walls and for the correct photosynthetic activity of plants (Martinez et al., 2020). Likewise, Na, necessary in small amounts, greatly influences the ionic balance by being part of the exchangeable cations in the soil (Cairo-Cairo & Diaz-Martin, 2019). However, excess Na can lead to soil salinization, reducing water availability and causing ionic toxicity, subjecting plants to osmotic stress (Ristorini et al., 2020). As for Al, although in itself it cannot be considered a nutrient, it has a significant influence on soil and plant health, especially in acid soils. Excess Al can be toxic to plants, altering nutrient uptake and damaging roots, reducing crop productivity (Shetty et al., 2021).\n\nOther important parameters for the evaluated biols are Cu, DOC, P, and Mn. Both Cu and Mn are essential micronutrients, which in adequate amounts control diseases in the case of Cu, which has fungicidal and bactericidal capabilities (Miller et al., 2022). In the case of Mn, it is involved in photosynthesis and several plant metabolic processes (Alejandro et al., 2020). P is another essential macronutrient, with N and K, which plays a fundamental role in plant growth and development, involved in photosynthesis, energy transfer, and DNA formation (Saravana Kumar et al., 2020). DOC is a way to measure the organic matter load of a biol, but not its quality, for which it is necessary to determine the contractions of micronutrients and macronutrients (Fernández-Domínguez et al., 2021). However, knowing the organic matter levels is essential when fertilizing a crop with a biol (García-López et al., 2023). As it decomposes, organic matter provides essential plant nutrients such as N, P, and K. At the same time, it improves soil quality by improving soil structure, promoting microbial activity, increasing the amount of organic carbon and enhancing soil biodiversity (Ji et al., 2023; Mahmood et al., 2020).\n\nThe PCA biplot allows us to evaluate how the parameters of the biols correlate with each other. For its elaboration, the first two PCs were used, which retain 79% of the variance of the data. The first thing we can highlight in the Biplot graph is the strong negative correlation between pH and Al. On the other hand, it can be seen that SULF, Mg, ST, Ca, K, Na, and EC have a strong positive correlation. P and Mn also have a strong positive correlation, as well as between all microbiological parameters and B (Figure 1).\n\nThe red circles highlight the variables and the area where the coincident vectors overlap in the biplot.\n\nTC: Total coliforms; FC: Fecal coliforms; ECO: Escherichia coli; SA: Salmonella; ME: Methanococcus; EC: Electrical conductivity; TS: Total solids; SULF: Sulfates, COD: Chemical oxygen demand; TN: Total nitrogen; P: Phosphorus; K: Potassium; Ca: Calcium; Mg: Magnesium; Na: Sodium; Fe: Iron; Mn: Manganese; Zn: Zinc; Cu: Cupper; Al: Aluminum; B: Boron.\n\nAgronomically, soil pH is a deterministic parameter that affects the availability and uptake of nutrients for plants (Liu et al., 2022). Having a pH less than 5 results in a higher concentration of Al, which is toxic to plants as it solubilizes into ionic forms (Al3+). Al3+ ions tend to displace essential cations such as Ca2+ and Mg2+ in the soil matrix, which react with water and release H+ ions, which increase soil acidity (Ahmed et al., 2022; Kar et al., 2021). This situation is unfavorable for plant development since the Al3+ ion inhibits root elongation and reduces nutrient absorption capacity (Vera-Villalobos et al., 2020). This behavior can be seen especially in the biols of equine manure (T3) bovine manure with coffee processing water (T4), which presented an acid pH and higher Al concentration.\n\nThe correlation observed between SULF, Mg, ST, Ca, K, Na, and EC reflects the diversity of sources and characteristics of these elements in the manures and plant material used as substrates in the different biodigesters. These nutrients and EC are related to soil salinity and biol quality (Jin et al., 2022; Manasa et al., 2020). An increase in any of these parameters in the biols to be applied can lead to an increase in soil salinity, adversely affecting plant health. This increase interferes with the absorption of water and nutrients, which reduces crop growth and yield, so the appropriate biol must be selected according to the type of crop and soil (Corwin, 2021). Among the biols evaluated, the one with the highest values for all these parameters was the equine manure biol, so its direct application can be a risk for soil salinity. One way to apply biols with high salt concentrations is to manage this salinity through different strategies, contributing to sustainable agriculture and reducing the risk of soil degradation. Some of the most common strategies are to favor soil leaching or to apply the biol in salinity-resistant crops (An et al., 2022).\n\nThe behavior between P and Mn is interesting from an agronomic point of view, as both nutrients are involved in plants’ photosynthetic, metabolic, and energetic processes (Taliman et al., 2019). P is a crucial component of adenosine triphosphate (ATP) energy molecules, which play a central role in cell energy transfer. On the other hand, Mn is an essential enzyme cofactor for oxygen release during photosynthesis and ATP generation (Chandra & Roychoudhury, 2020).\n\nThe last correlation observed between microbiological parameters (TC, FC, ECO, SA, and ME) and boron is intriguing from an agronomic perspective, given its impact on soil health, nutrient availability, and possible effects on soil fertility. The behavior found suggests that these bacteria’s activity influences B availability to plants. The bacteria evaluated decomposed organic matter in the biols, releasing organic compounds and nutrients, including B, previously bound to organic matter (Cuartero et al., 2021). At the same time, bacteria can mobilize nutrients in soils by mineralization and solubilization, thus being able to transform inorganic B compounds into soluble forms and facilitating their availability to plants (Diao et al., 2023; Ponomarev et al., 2022). We can verify this in the pig manure biol (T1), which presented a higher microbiological load in addition to being the only one with the presence of B.\n\nA biplot graph was made again, but in this case, ellipses were used to group the observations according to the type of biol. In the biplot with ellipses, it can be seen that the biols are dissimilar, so they are differentiated from each other. The PERMANOVA analysis confirms that the groups are significantly dissimilar (F = 516.22, P-Value = 0.001***). Regarding the parameters that most influence each biol, it was observed that nutrients did not influence the cattle manure biol (T2). The pig manure biol (T1) was significantly influenced by pH and bacterial parameters, emphasizing these in their nutritional composition. On the other hand, the horse manure biol (T3) was greatly influenced by SULF, ST, Mg, and Ca, emphasizing these in its nutritional composition. Finally, the biol of cattle manure with coffee processing water (T4) was strongly influenced by DOC, P, and Mn, highlighting these in their nutritional composition (Figure 2).\n\nTC: Total coliforms; FC: Fecal coliforms; ECO: Escherichia coli; SA: Salmonella; ME: Methanococcus; EC: Electrical conductivity; TS: Total solids; SULF: Sulfates, COD: Chemical oxygen demand; TN: Total nitrogen; P: Phosphorus; K: Potassium; Ca: Calcium; Mg: Magnesium; Na: Sodium; Fe: Iron; Mn: Manganese; Zn: Zinc; Cu: Cupper; Al: Aluminum; B: Boron.\n\nPM: Pig manure; CM: Cattle manure; HM: Horse manure; CM+CPW: Cattle manure with coffee processing water\n\nThe PCA analysis of the evaluated parameters reveals significant variability in the nutritional composition of the four biols. These results emphasize the importance of understanding the different and complex interactions between the origin of the substrates used to make the biols and the anaerobic digestion process (Ran et al., 2023). These nutritional differences imply that each biol is best suited to each crop type according to its nutritional requirements (Kovačić et al., 2022). It should be noted that biols may show intrinsic variability due to individual differences in animals, management practices, storage, or type of plant waste used for mixtures (Samoraj et al., 2022). This variability may result in biols with different nutrient profiles.\n\nFirstly, it was observed that no nutrient stood out in the cattle manure biol (T2). One reason for this was the initial composition of cattle manure. The diet or the health status of the animals influences their composition. It could be that the animals did not receive a nutritious diet or they were given some medication or vitamin supplement that unbalanced the nutrient composition of the manure, which was used for the elaboration of biol composition (Chozhavendhan et al., 2023; Manyi-Loh et al., 2019). Another reason would be that there was a natural decomposition process before being used for biol manufacture, degrading or volatilizing some nutrients (Bareha et al., 2021). This type of biol could be used in crops or soils that do not require a specific nutrient input.\n\nOn the other hand, the significant influence of pH and microbiological parameters in pig manure biol (T1) may be due to several factors, such as the type of diet pigs have and their digestive system (Shi et al., 2019). Pigs are monogastric animals, having only one stomach, unlike ruminant animals, which makes their manure rich in bacteria given the nature of their digestion (Li et al., 2020; Marchwińska & Gwiazdowska, 2022). At the same time, the health of these animals also plays a role. Healthy pigs tend to have a very diverse gut microbiome as they are omnivores, which can be reflected in the manure and, thus in the final biol (Froidurot & Julliand, 2022). Farmer management is also vital in the presence of bacteria such as Escherichia coli and Salmonella, which may indicate poor hygiene in the facilities where pigs are kept (L. Wang et al., 2021).\n\nIn contrast, horse manure biol (T3) strongly influenced SULF, ST, Mg, and Ca. Horses have a herbivorous diet, and their digestive system is adapted to process high-fiber plant material, possessing a large caecum and a functionally developed colon, which allows them to break down cellulose and other plant components (Altangerel et al., 2021). At the same time, these nutrients may not be absorbed by the intestinal flora of horses as they do not require large amounts (Joch et al., 2022). The mineral composition of forages and feeds fed to horses, which may vary according to soil type and related agricultural practices, should also be considered (Silva et al., 2022). This type of biol, rich in salts, may be ideal in soils deficient in this type of nutrients or crops requiring high concentrations of these nutrients (Symanczik et al., 2023).\n\nFinally, the cattle manure biol with coffee processing waters (T4), highlighted DOC, P, and Mn. As with the other biols, the initial composition of the manure used to make the biol is something to consider. Cows, ruminant animals, usually have excreta rich in organic matter, with grass and forage remains (Romero et al., 2022). However, it should be noted that the excreta was mixed with water from coffee processing, which gives an extra contribution to organic matter (Erazo & Agudelo-Escobar, 2023). At the same time, coffee, apart from being rich in organic compounds, is rich in minerals such as K, Mg, and P, contributing to their presence in the biol (Alemayehu et al., 2021; Shin et al., 2020). The high content of organic matter, phosphorus, and manganese in this biol could make it valuable for application in poorly fertile soils and low availability of these nutrients for plant growth.\n\n\nConclusions\n\nCharacterizing the microbiological, physicochemical, organic matter, and nutrient composition of any type of biol, including those that, besides manure, are added to agricultural wastes such as coffee processing waters, provides a valuable perspective on how and when they should be applied according to the type of crop or soil. The significant variability found in the composition of biols, depending on the type of substrate used for their preparation, is worth noting. The pig manure biol was rich in bacteria; the cattle manure biol did not stand out in any nutrient. At the same time, a large amount of salts characterized the horse manure biol, and finally, the cattle manure with coffee processing water was rich in organic matter and P. Therefore, the selection of each type of biol should be made carefully according to the crop’s nutritional requirements and the soil conditions. In addition, critical parameters such as pH, B, or P, among other nutrients, which play a fundamental role in the availability of nutrients for plants and soil quality, were evidenced. These findings support the usefulness of biols, particularly those incorporating agricultural wastes such as coffee processing waters, as versatile organic fertilizers that can improve soil fertility and stimulate crop growth, thus contributing significantly to sustainable agricultural practices and food security by producing high-quality food.", "appendix": "Data availability\n\nZenodo: Compositional data for four types of biol, https://doi.org/10.5281/zenodo.10065050 (Rascón, 2023).\n\nThis project contains the following underlying data:\n\n- Data_Digestates.xlsx (Compositional data for four types of biol)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nAll authors would like to thank Elder Chichipe Vela, Carlos Santa Cruz Guerrero, Edith Calderón Ordoñez, Lesvi Tatiana Cotrina Rioja, Homar Santillán Gómez, and especially to thank José Darvin Portocarrero Gómez and his family for all the logistical support for the development of this research.\n\n\nReferences\n\nAcuña PA, Ángel LS, Borray E, et al.: Aislamiento e identificación de microorganismos del género Methanococcus y Methanobacterium de cuatro fuentes de Bogotá D.C. 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PubMed Abstract \| Publisher Full Text\n\nSymanczik S, Lipp C, Mäder P, et al.: Limited effectiveness of selected bioeffectors combined with recycling phosphorus fertilizers for maize cultivation under Swiss farming conditions. Front. Plant Sci. 2023; 14(8): 1239393. Publisher Full Text\n\nTadesse A, Shanka D, Laekemariam F: Short-Term Integrated Application of Nitrogen, Phosphorus, Sulfur, and Boron Fertilizer and the Farmyard Manure Effect on the Yield and Yield Components of Common Bean (Phaseolus vulgaris L.) at Alle Special Woreda, Southern Ethiopia. Appl. Environ. Soil Sci. 2022; 2022: 1–12. Publisher Full Text\n\nTaliman NA, Dong Q, Echigo K, et al.: Effect of Phosphorus Fertilization on the Growth, Photosynthesis, Nitrogen Fixation, Mineral Accumulation, Seed Yield, and Seed Quality of a Soybean Low-Phytate Line. Plants. 2019; 8(5): 119. 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PubMed Abstract \| Publisher Full Text\n\nVilla Montoya AC, da Silva C , Mazareli R, et al.: Improving the hydrogen production from coffee waste through hydrothermal pretreatment, co-digestion and microbial consortium bioaugmentation. Biomass Bioenergy. 2020; 137(March): 105551. Publisher Full Text\n\nWang H, Xu J, Liu X, et al.: Study on the pollution status and control measures for the livestock and poultry breeding industry in northeastern China. Environ. Sci. Pollut. Res. 2018; 25(5): 4435–4445. PubMed Abstract \| Publisher Full Text\n\nWang L, Liu N, Gao Y, et al.: Surveillance and Reduction Control of Escherichia coli and Diarrheagenic E. coli During the Pig Slaughtering Process in China. Front. Vet. Sci. 2021; 8(October): 1–9. Publisher Full Text\n\nWang N, Huang D, Zhang C, et al.: Long-term characterization and resource potential evaluation of the digestate from food waste anaerobic digestion plants. Sci. Total Environ. 2021; 794: 148785. Publisher Full Text\n\nWang Y, Zhang Y, Li J, et al.: Biogas energy generated from livestock manure in China: Current situation and future trends.J. Environ. Manage.2021; 297(April): 113324. Publisher Full Text\n\nWeimers K, Bergstrand KJ, Hultberg M, et al.: Liquid Anaerobic Digestate as Sole Nutrient Source in Soilless Horticulture—Or Spiked With Mineral Nutrients for Improved Plant Growth. Front. Plant Sci. 2022; 13(March): 1–13. Publisher Full Text\n\nWi J, Lee S, Ahn H: Influence of Dairy Manure as Inoculum Source on Anaerobic Digestion of Swine Manure. Bioengineering. 2023; 10(4): 1–13. Publisher Full Text\n\nWongsaroj L, Chanabun R, Tunsakul N, et al.: First reported quantitative microbiota in different livestock manures used as organic fertilizers in the Northeast of Thailand. Sci. Rep. 2021; 11(1): 1–15. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZandvakili OR, Barker AV, Hashemi M, et al.: Comparisons of commercial organic and chemical fertilizer solutions on growth and composition of lettuce. J. Plant Nutr. 2019; 42(9): 990–1000. Publisher Full Text" }	[ { "id": "271747", "date": "14 Jun 2024", "name": "Rene Rietra", "expertise": [ "Reviewer Expertise soil chemistry", "nutrient uptake crops", "leaching", "circular fertilisers" ], "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 is about the analyses of 4 repeated sampling moments digestate samples from 4 digesters, resulting in 12 analyses per digester. The numbers are unclear. The authors have determined 22 parameters. Subsequently the authors do statistical analysis to find relations and differences between the samples from the four digesters.\nThe methods for analysis are unclear or very strange. It is stated that they use a modified Olsen method. That is a extraction method for soil analysis. They however also state that they use acid digestion, that suggest a semi-total destruction.\n\nThe content of the manuscript , 12 analysis per biol, is very small for a scientific manuscript. 12 analysis per bio, and 4 biols, is really not much. Therefore I think this manuscript just does not contain enough for a scientific manuscript. Also the discussion and conclusion is not scientifically interesting: digestate samples differ, and farmers should take this in account to have a balanced fertilisation. Yes, of course. But that is not science. That is the result of each manure or digestate measurement.\nEven if the measurements would be scientifically interesting, for example, because of the geographic circumstances, then the authors should make a comparison with literature. But that will be hard because the methods do not seem standard.\ndetailed remarks: -What is a biol? Is it a name, a local products name, a process? Why is it a type of digestate? -The number of samples, sampling moments, analysis is unclear. Four samples from the same biodigester for two weeks. But you have 12 analysis from each biol? -the four samples were mixed (?), -The methods for analysis are unclear: COD for organic matter? And why mention a AAS for a COD measurement? -modified Olsen methods for the analysis of a digestate? -the authors discuss the relevance of nutrients at page 8 and 9 that can be found in each textbook. -Have the methods and analysis been tested with other labs, with ring tests? What is the quality assurance?\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? 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? No\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "311801", "date": "10 Aug 2024", "name": "Jared Onyango Nyang'au", "expertise": [ "Reviewer Expertise Anaerobic digestion", "nutrient recovery", "analytical chemistry", "Biomass treatment for anaerobic digestion" ], "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 evaluated the properties of 4 digestates from digestates in Northern Peru. It evaluated microbiological, physiological,organic and nutrient composition. It could have been appropriate if number lines were used for easy reference during review.\nGeneral comments Title The title needs improvement. Characterization could be changed since the digestates are characterised and compared.\nAbstract The abstract should be rewritten. Briefly write an introduction that creates the context of the study, purpose, method, result, and conclusion. What problem will this study address? Key results should be quoted in the abstract.\nIntroduction\nWhat is Biol? Is it a commonly used term? If not, then just use a “digestate” What research gap does this study aim to address? It should be clearly defined in the introduction and relevant literature cited. For instance, are there issues with heavy metal or microbial contamination in Peru that need to be addressed? The key objective of the study is not well aligned well in the introduction. State the hypothesis to be tested. For instance do we expect variation in the digestates\nMethods\nThe information in paragraph 4 can be added to table 1. What was the digestion temperature of the substrates I suggest the feedstock composition to be changed to reflect the water added. Include how the sample preparation for microbiological analysis was done briefly. The methodology section needs to be rewritten. Some parts are incorrect, for instance, the method for analyzing Phosphorous. How can both AAS and UV-VIS be used to analyse P concurrently? Some key parameters such as ammonium-N, total carbon and volatile solids are missing in the method and results part Indicate how sample preparation was done for each of the parameter analysed. “Four samples were collected from the same biodigester for two weeks. Subsequently, the four samples from each biodigester were carefully mixed and stored at 4 °C before being analyzed in the laboratory”- Why was the samples collected within the time interval of 2 weeks, do we expect some variations over time based on the retention time.\nResults and discussion\nDigestates T3 and T4 have acidic pH, low than expected from digestates following anaerobic digestion. A low PH is indicative of inhibition of the AD process, therefore the process should have been stabilised first before sampling. There is a discussion on organic matter was it analysed? In Table 2, in the pH line remove “Unit”. Some information in paragraph 3,pg 7 is repeated Proper comparison of the 4 digestates is missing and also to literature Some of the discussions like pg 10-11 are not in the context of the study.\nConclusions Should be re-written and made concise Conclude on Key results and write key results. Where will the results be applied?. It should be clearly included in the conclusion.\nReferences The references are too many for this research article (129 in number). Use only relevant references.\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": [] }, { "id": "243505", "date": "29 Aug 2024", "name": "Olatunde Samuel Dahunsi", "expertise": [ "Reviewer Expertise Organic Agriculture", "Biomass and Bioenergy" ], "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 no issue evaluating this manuscript as it is a clearly designed and well-implemented research effort. The findings supports the use of biols from different animal wastes. Authors only need to ensure the following: 1. Correct English must be ensured throughout the manuscript 2. All tables must be presented in standard formats i.e., without internal grid lines\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/13-24
https://f1000research.com/articles/13-20/v1	08 Jan 24	{ "type": "Case Report", "title": "Case Report: The effect of bone morphogenetic proteins (BMP) in comparison with a xenograft in the management of mandibular bone defects", "authors": [ "Lutfallah Alhalabi", "Mazen Zenati", "Mazen Zenati" ], "abstract": "Background This study aims to compare the effect of Bone Morphogenetic Proteins (rhBMP), carried on a gelatin sponge scaffold in comparison with the Xenograft BioOss® in the management of mandibular bone defects.\n\nCase presentation The case is a 48-year-old woman who had 2 cysts in the mandibular bone, BMP2 was placed within the first hole with a gelatin sponge, and a BioOss® graft was placed within the second defect. The radiographic evaluation was conducted before and after surgery and 1, 3, and 6 months after the surgical work. Histological assessment was conducted after 6 months of the surgical work.\n\nResults The results of the radiographic evaluation found that there was no big difference between the healing in the holes filled with rhBMP2 with gelatin sponge and the healing in the holes filled with BioOss®.\n\nConclusion The use of a gelatin sponge impregnated with Bone Morphogenetic Proteins improves and accelerates the healing of bone defects and is comparable to the effectiveness of using a BioOss® graft.", "keywords": [ "Bone defects", "Bone Morphogenetic Proteins", "BioOss® graft", "hemostatic sponge", "Case Report." ], "content": "Introduction\n\nBone defects in the jaw are a common problem faced by oral and maxillofacial surgeons, especially when dental implants are needed within the bone. This deficiency is due to several reasons, the most important of which are periodontal tissue diseases, cysts, and severe surgical trauma during extraction.1\n\nSeveral techniques have been described to compensate for and speed up the healing of defective bone for the purpose of placing dental implants or avoiding fracture or deformation of the bone.2\n\nXenografts, such as inorganic bovine bone grafts, have been widely used to achieve three-dimensional healing of the maxillary bone in the field of repair of defects and alveolar resorption in several studies.3\n\nMany studies have examined the process of improving and accelerating bone healing by relying on many growth factors present in platelet-rich plasma, the most important of which are bone-forming proteins, in addition to the use of growth-directed membranes, which concluded that they can stimulate the mechanisms of chemotaxis, cell division, and cell differentiation, and the use of hemostatic sponges have been included in some studies as carriers of medicinal materials or a scaffold for osteoblasts.4\n\nIn a latest 2020 study, Vasyliev et al. investigated the effect of adding a low dose of 10 g/ml bone morphogenetic proteins to a Bio Oss® inorganic bovine bone graft to stimulate bone formation in rabbits.5\n\nTo date, obtaining the best material for the restoration of defective bony cavities in the jaws, in the fastest and best way to stimulate bone formation, and with the least possible complications and costs, is one of the most significant concerns of oral and maxillofacial surgeons worldwide.\n\nEsfahanizadeh et al. studied the efficacy of a Bio Oss® bone graft on bone defects and concluded that this graft supported bone morphogenesis in defects made in rabbit tibias.6\n\nTavakoli et al. found that applying hemostatic sponges to alveolar bone sockets after extraction accelerates hemostasis, collagen, and connective tissue formation, and alleviates post-extraction complications.7\n\nSohn et al. applied gelatin sponge to nine patients with lateral window maxillary sinus lifts to support the lifted mucosa and found new bone formation six months after the operation.8\n\nIn their comparative study of artificial bone grafts and gelatin sponges, Singh et al. indicated that sponges are not as effective as grafts and cannot be used alone as an alternative to grafting in bone defects.9\n\nKim et al. applied gelatin sponges loaded with bone-forming proteins to a bony defect of the radius of a rabbit and confirmed the effectiveness of this participation in bone regeneration.10\n\nAs for Fiorellini et al., the application of a gelatin sponge impregnated with bone morphogenetic protein showed great efficacy in preserving alveolar bone after extraction.11\n\nThis case report aims to compare the effectiveness of a gelatin sponge impregnated with bone-forming proteins with that of a Bio-Oss® bone graft in healing and managing bone defects.\n\n\nCase presentation\n\nA 48-year-old Syrian woman who is currently unemployed\n\nShe does not suffer from any systemic or psychological diseases, and her father suffered a myocardial infarction, she suffered from gum disease and lack of oral care, which led to the loss of most of her teeth\n\nShe had two cysts in the mandibular bone (Figure 1), and clinical examination showed pain and swelling in the jaw on both sides under the roots of the deviated teeth (Figure 1).\n\nDiagnostic radiographic examination revealed two root cysts on both sides of the lower jaw (Figure 2).\n\nSurgery was performed by extracting the roots of the remaining teeth and scraping the root cysts by using a bone shovel. Then, a gelatin sponge from ORCA® Foam, Item No: 7156411 impregnated with bone-forming protein rh-bmp2 was placed within the left bone defect, and a BioOss bovine graft was placed within the right bone defect (Figure 3).\n\nA radiographic image was taken immediately after the surgery (Figure 4).\n\nThen, radiological evaluation of the patient was conducted using cone-beam computed tomography (CBCT) images during the following observation periods (1, 3, and 6 months) as shown in, Figures 5, 6, 7.\n\nFor comparison between the results of the two subjects, the following radiological criteria were used:\n\n1- The vertical maximum diameter of the defect (mm).\n\n2- The vertical maximum diameter of the defect (mm).\n\n3- The total area of the defect (mm2).\n\n4- The radiographic bone density measurements in the center of the defect with Hounsfield units.\n\nThe results are shown in Table 1.\n\nAfter 6 months, a bone tissue biopsy was performed from the grafting area with a trephine bur of 2 mm in diameter and 5 mm in length. The cells were examined under a SKU: MI-4100LST microscope at 100× magnification (Figure 8).\n\nThe following criteria were adopted to compare the effects of the two materials on the bone healing of defects:\n\n1. The proportion of non-mineralized tissues\n\n2. The percentage of mineralized tissues\n\n3. Percentage of mature lamellar bone\n\n4. The percentage of young bone\n\n5. The percentage of remaining bone graft particles\n\nThe results are shown in Table 2.\n\n\nDiscussion\n\nThe aim of this case report was to compare the effect of the bone morphogenic protein rh-BMP carried on the gelatin sponge with the effect of foreign bone graft BioOss in healing and accelerating bony defects in the mandible, and to determine the ability of these proteins to compete with the BioOss bone graft, which has already proven its effectiveness in many previous studies.\n\nThe patient had two root cysts under the premolars, on the right and left sides of the lower jaw. After scraping the two cysts, a gelatin sponge impregnated with the bone morphogenic protein rh-BMP (10 g/ml) was placed within the left bony defect. A BioOss bone graft was placed in the right cavity. Healing was evaluated radiologically and histologically. The results were similar with a slight advantage in the healing of the defect, by the BioOss bone graft.\n\nThe radiological density of the new bone tissue formed within the bone defects was measured after (1, 3, and 6 months by measuring the Hounsfield units on digital radiographs after they were inserted into the computer program Digora for Windows 2.7.\n\nThe results of this study showed that the density after one month, three months and six months in the BMP2 group did not differ from the density in the BioOss defect.\n\nThe histological findings of the new bone tissue formed within the bone defects were measured after six months, and the results of this study showed that the percentages after six months in the BMP2 defect did not differ from the percentages in the BioOss defect.\n\nThe results of the report also converged with those of a radiographic study conducted by Kader et al. (2017),12 who studied 16 bone defects in the maxillary socket, which were divided into two groups (a group placed within the defects bmp2 on a scaffold of hemostatic collagen sponge for bleeding and a group placed within the defect bone graft defects). The results showed that there was no statistically significant difference between the two groups after radiographic examination after 6 months.\n\nThe results of this case agreed with those of a previous study Kim et al. (2013)10 which indicated that the use of a hemostatic gelatin sponge for bleeding as a carrier of bone morphogenetic proteins when a bone defect in the radius of rabbits improves bone healing and accelerates the healing of the defects.\n\nThis report also agreed with the study done by Esfahanizadeh et al. (2019),6 who studied the effectiveness of using a BioOss® bone graft within the bone defects made in the tibia of rabbits and concluded that this graft supported bone formation in some way.\n\nThe results of this research study also agreed with those of Singh et al. (2015)9 in their comparative study between artificial bone grafts and gelatin sponges, in which they showed that the effectiveness of the sponge is not equivalent to the effectiveness of grafts and cannot be used alone as an alternative to grafting in bone defects.\n\nThis case agreed with the results of a previous study (Carter et al., 2008)13 who concluded that mandibular bone defects can be successfully reconstructed using rhBMP-2-soaked sponges with and without bone marrow cells and allogenic bone.\n\nThe strength of this report lies in knowing the ability of bone-forming proteins to compete with foreign bone grafts in improving and accelerating bone healing. Also, this case was carried out on one patient and in the same jaw, which prevented the effect of the difference in the nature of healing between the upper and lower jaws or the effect of the difference in the nature of healing between people. Thus, the personal factor was neutralized.\n\nThe results of this case encourage us to repeat the comparison on several patients to increase the sample number and conclude better and scientifically more accurate results\n\n\nConclusions\n\nIt was concluded that the use of hemostatic sponges impregnated with BMP2 bone morphogenetic proteins in bone defects improved and accelerated the healing of bone defects both radiologically and histologically.\n\nIt was also concluded that the effectiveness of using this material was comparable to that resulting from the use of BioOss foreign bone graft in terms of radial density and good bone mineralization.\n\n\nConsent\n\nWritten informed consent was obtained from the patient for publication of this case report and any accompanying images.", "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\nKyriakidou E, O’Connor N, Malden NJ, et al.: Bone defects of the jaws: moving from reconstruction to regeneration. Dent. Update. 2014; 41(7): 613–622. Publisher Full Text\n\nKumar P, Vinitha B, Fathima G: Bone grafts in dentistry. J. Pharm. Bioallied Sci. 2013; 5(Suppl 1): S125–S127. PubMed Abstract \| Publisher Full Text\n\nMunhoz A, Ferreira JO, Yaedu RYF, et al.: Radiographic assessment of impacted mandibular third molar sockets filled with composite xenogenic bone graft. Dentomaxillofac. Radiol. 2006; 35(5): 371–375. Publisher Full Text\n\nBroggini N, Hofstetter W, Hunziker E, et al.: The influence of PRP on early bone formation in membrane protected defects. A histological and histomorphometric study in the rabbit calvaria. Clin. Implant. Dent. Relat. Res. 2011; 13(1): 1–12. PubMed Abstract \| Publisher Full Text\n\nVasilyev V, Kuznetsova S, Bukharova B, et al.: Osteoinductive potential of highly porous polylactide granules and Bio-Oss impregnated with low doses of BMP-2. IOP Conference Series: Earth and Environmental Science. IOP Publishing; 2020; Vol. 421(5): p. 052035. Publisher Full Text\n\nEsfahanizadeh N, Daneshparvar P, Takzaree N, et al.: Histologic Evaluation of the Bone Regeneration Capacities of Bio-Oss and MinerOss X in Rabbit Calvarial Defects. Int. J. Periodontics Restorative Dent. 2019; 39: e219–e227. PubMed Abstract \| Publisher Full Text\n\nTavakoli A, Sagart A: Evaluation of hemosponge in promoting dental socket healing after 3rd mandibular premolar extraction in a feline model. Braz. J. Oral Sci. 2015; 14(4): 330–333. Publisher Full Text\n\nSohn DS, Moon JW, Moon KN, et al.: New bone formation in the maxillary sinus using only absorbable gelatin sponge. J. Oral Maxillofac. Surg. 2010; 68(6): 1327–1333. Publisher Full Text\n\nSingh M, Bhate K, Kulkarni D, et al.: The effect of alloplastic bone graft and absorbable gelatin sponge in prevention of periodontal defects on the distal aspect of mandibular second molars, after surgical removal of impacted mandibular third molar: a comparative prospective study. J. Maxillofac. Oral Surg. 2015; 14(1): 101–106. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKim SG, Jeong JH, Che X, et al.: Reconstruction of radial bone defect using gelatin sponge and a BMP-2 combination graft. BMB Rep. 2013; 46(6): 328–333. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFiorellini JP, Howell TH, Cochran D, et al.: Randomized study evaluating recombinant human bone morphogenetic protein-2 for extraction socket augmentation. J. Periodontol. 2005; 76(4): 605–613. PubMed Abstract \| Publisher Full Text\n\nKader LA, Elbokle NN: RECOMBINANT HUMAN BONE MORPHOGENETIC PROTEIN-2 VERSUS AUTOGENOUS BONE GRAFT IN THE RECONSTRUCTION OF MAXILLARY ANTERIOR ALVEOLAR RIDGE DEFECTS. Egypt. Dent. J. 2017; 63(4-October (Oral Surgery)): 3077–3092. Publisher Full Text\n\nCarter TG, Brar PS, Tolas A, et al.: Off-label use of recombinant human bone morphogenetic protein-2 (rhBMP-2) for reconstruction of mandibular bone defects in humans. J. Oral Maxillofac. Surg. 2008; 66(7): 1417–1425. PubMed Abstract \| Publisher Full Text" }	[ { "id": "265422", "date": "09 May 2024", "name": "Dalia Rasheed Issa", "expertise": [ "Reviewer Expertise Periodontics", "implantology", "oral medicine", "craniofacial regeneration." ], "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 present case report entitled “Case report: the effect of bone morphogenetic proteins (BMP) in comparison with xenograft in the management of mandibular bone defects” This case report aimed to compare BMP-2 to xenograft for management of the mandibular bone defects. The study reveals several scientific issues and although the aim of this study could be good, there is a lack of important details. I unfortunately perceive it as \"not approved\". I hope these comments help the authors to improve this manuscript for future publication.\nIntroduction: -It should be more salient. -More references are needed to clarify the use of platelet concentrates and scaffolds. -The English should be revised and be in better way. -It is important to specify which BMP was used. Was it bone forming protein, bone morphogenetic protein in general, or bone morphogenetics protein-2. Also, it is better to use the abbreviation (BMP-2) if you choose to use it rather than using both at the same time.\nCase presentation: -Full clinical examination of the patient should be illustrated. -Presurgical therapy was not mentioned. It is not clear if it was performed or not. -The images' resolution should be better and illustration of each image is important. Moreover, it is better to present the measurements on the radiographic images. -The case presentation should thoroughly detail the methodology and BMP concentration should be presented in it. -The follow-up period is too short to evaluate the effect on bone formation. -The measurements, which consisted of two vertical dimensions, require further clarity and precision.\nDiscussion: -\"Foreign bone graft\" is not a scientific term. -Results from one case cannot provide sufficient comparison with other studies. -“Artificial bone graft\" is not a scientific term. -Results presented in \"reference 9\" are not consistent with those observed in this case report.\nConclusion: -“Good bone mineralization\" is not a scientific term.\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? Partly", "responses": [] }, { "id": "265415", "date": "29 May 2024", "name": "Mohammed Katib Alruwaili", "expertise": [ "Reviewer Expertise Periodontics", "bone grafts", "tissue engineering", "implant 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\nDear authors,\nThank you for your thorough and insightful study comparing the effects of Bone Morphogenetic Proteins (BMP) carried on a gelatin sponge scaffold with a Xenograft BioOss® in the management of mandibular bone defects. Your research contributes significantly to the field of oral and maxillofacial surgery by providing valuable insights into potential alternatives for bone defect management.\nHere are some points to consider for further refinement and clarification of your study:\nEnglish revision is needed. Title Clarity: The title effectively captures the essence of the study; however, specifying the type of bone defect (e.g., cystic defects) in the title could enhance clarity. Case Presentation: The case presentation provides detailed information about the patient, surgical procedures, and radiographic evaluations. However, including additional details on the patient's postoperative course, such as pain management and any complications, could enrich the case description. Radiographic and Histological Evaluation: The radiographic and histological evaluations are crucial components of the study. Providing more context on the radiographic assessment criteria and histological analysis methods would enhance the clarity of your findings. Discussion Strength: The discussion section effectively contextualizes the study findings within the existing literature and highlights the significance of the research. Consider discussing any limitations of the study and avenues for future research to further strengthen the discussion. Conclusion: The conclusion provides a clear summary of the study findings and implications. Consider emphasizing the clinical relevance of the findings and potential implications for patient care.\nOverall, your study provides valuable insights into the comparative effectiveness of BMPs and Xenograft BioOss® in mandibular bone defect management. Addressing the points mentioned above would further strengthen the clarity and impact of your research.\nThank you for your contribution to the field.\nBest regards,\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? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-20
https://f1000research.com/articles/13-19/v1	08 Jan 24	{ "type": "Research Article", "title": "The readiness of the Asian research ethics committees in responding to the COVID-19 pandemic: A multi-country survey", "authors": [ "Juntra Karbwang", "Cristina E. Torres", "Arthur M. Navarro", "Phanthipha Wongwai", "Edlyn B. Jimenez", "Yashashri Shetty", "Sudha Ramalingam", "Paresh Koli", "Lisa Amir", "Septi Dewi Rachmawati", "Monalisa Waworundeng", "Harnawan Rizki", "Asyraf Syahmi Mohd Noor", "Prakash Ghimire", "Pradip Gyanwali", "Subhanshi Sharma", "Namita Ghimire", "Chandanie Wanigatunge", "Kwanchanok Yimtae", "Cristina E. Torres", "Arthur M. Navarro", "Phanthipha Wongwai", "Edlyn B. Jimenez", "Yashashri Shetty", "Sudha Ramalingam", "Paresh Koli", "Lisa Amir", "Septi Dewi Rachmawati", "Monalisa Waworundeng", "Harnawan Rizki", "Asyraf Syahmi Mohd Noor", "Prakash Ghimire", "Pradip Gyanwali", "Subhanshi Sharma", "Namita Ghimire", "Chandanie Wanigatunge", "Kwanchanok Yimtae" ], "abstract": "Background COVID-19 is a highly challenging infectious disease. Research ethics committees (RECs) have challenges reviewing research on this new pandemic disease under a tight timeline and public pressure. This study aimed to assess RECs’ responses and review during the outbreak in seven Asian countries where the Strategic Initiative for Developing Capacity in Ethical Review (SIDCER) networks are active.\n\nMethods The online survey was conducted in seven Asian countries from April to August 2021. Two sets of online questionnaires were developed, one set for the chairs/secretaries and another set for the REC members. The REC profiles obtained from the REC members are descriptive in nature. Data from the chairs/secretaries were compared between the RECs with external quality assessment (SIDCER-Recognized RECs, SR-RECs) and non-external quality assessment (Non-SIDCER-Recognized RECs, NSR-RECs) and analyzed using a Chi-squared test.\n\nResults A total of 688 REC members and 197 REC chairs/secretaries participated in the survey. Most RECs have standard operating procedures (SOPs), and have experience in reviewing all types of protocols, but 18.1% had no experience reviewing COVID-19 protocols. Most REC members need specific training on reviewing COVID-19 protocols (93%). In response to the outbreak, RECs used online reviews, increased meeting frequency and single/central REC. All SR-RECs had a member composition as required by the World Health Organisation ethics guidelines, while some NSR-RECs lacked non-affiliated and/or layperson members. SR-RECs reviewed more COVID-related product development protocols and indicated challenges in reviewing risk/benefit and vulnerability (0.010), informed consent form (0.002), and privacy and confidentiality (P = 0.020) than NSR-RECs.\n\nConclusions Surveyed RECs had a general knowledge of REC operation and played a significant role in reviewing COVID-19-related product development protocols. Having active networks of RECs across regions to share updated information and resources could be one of the strategies to promote readiness for future public health emergencies.", "keywords": [ "COVID-19", "Pandemic", "IRB", "Institutional review board", "research ethics committee", "Strategic Initiative for Developing Capacity in Ethical Review", "SIDCER", "Network" ], "content": "Introduction\n\nCOVID-19 is a new, highly infectious disease that seriously challenges the research community.1,2 There are limited effective drugs and vaccines available and, to date, very limited specific treatment for mild COVID-19, which accounts for 80% of COVID-19 infected patients.3,4 Research on new treatments, prophylactics, and diagnostic products to address disease outbreaks is needed.3,5 Under the limited supply of effective drugs and vaccines, flattening the curve of the infection depends on adherence to the public health socio-behavioural interventions imposed by the state.6,7 Research on the effectiveness and acceptability of these non-pharmaceutical interventions is important to assist in making the decision about how to address the outbreak.8,9 While the researchers are finding solutions to end the epidemic, the institutional review boards (IRBs)/research ethics committees (RECs) are responsible for the oversight of research conduct to ensure that the researchers adhere to scientific principles and uphold the ethical principles of autonomy, beneficence, and justice and that they are responsive to the COVID-19 outbreak.10 Local IRBs/RECs have to encounter new challenges, some related to research approval of new investigational tools and approaches against the pandemic under a tight timeline and public pressure,1,2 and others related to delays in ongoing activities due to the diversion of human resources towards the pandemic response.11 Some local RECs in different countries may not be ready to address the challenges arising from the COVID-19 pandemic.12\n\nThe present study aimed to find the RECs’ responses and review practices during the COVID-19 outbreak in Asian countries, where Strategic Initiative for Developing Capacity in Ethical Review (SIDCER) networks are active in training and quality evaluation of RECs (www.SIDCER-FERCAP.org). This study describes how the local RECs in Asian countries faced and addressed the challenges in ethics review during the COVID-19 outbreak. Specifically, the study assessed RECs’ operational readiness and challenges to conduct the ethics review during the COVID-19 pandemic.\n\n\nMethods\n\nA multi-center cross-sectional, descriptive survey was conducted in seven countries by local team members of the Forum for Ethical Review Committees in the Asian and Western Pacific Region (FERCAP) network. The survey was carried out from April to August 2021. FERCAP conducted a common online survey of RECs in Asia among the RECs with external quality assessment (SIDCER recognized REC (SR-REC)) and no external quality assessment (Non-SIDCER recognized REC (NSR-REC)) to determine the response and review practices of RECs during the COVID-19 outbreak.\n\nTwo sets of questionnaires were developed using online Google forms, one set for the chairs/secretaries, and another set for the members. The questionnaires for the chairs/secretaries focused on REC profiles, activities during the COVID-19 outbreak, and identification of training needs among SR-RECs and NSR-RECs. The questionnaires to be completed by members gathered information on the REC’s membership profile, number of protocols reviewed, challenges encountered during COVID-19, training needs, and their knowledge and attitudes about reviewing COVID-19 related research. Knowledge and attitude questions were also prepared on five Likert scales. The initial draft questionnaire was pretested by sending it to focal persons in each country to determine if there was a common understanding of the questions and the expected response. Several meetings were held to discuss and share specific country issues related to the survey instrument and the target population, and the protocol was revised accordingly. No reliability test was done.\n\nThe study enrolled REC chairs/secretaries and members in seven countries: India, Indonesia, Malaysia, Nepal, Philippines, Sri Lanka, and Thailand. The current project utilized the resources and infrastructure of the existing networks (FERCAP and local ethics networks of each country). FERCAP gathered information from RECs that are network members and from other RECs who would agree to respond to the survey. FERCAP targeted a purposive sample of 500 REC members. The recruitment was conducted from April to August 2021.\n\nA round of meetings was held among the involved team members to finalize the protocol and share the protocol along with the set of questionnaires and informed consent forms in the online Google form. After getting the approval from the REC, the selected chair/secretaries and the members were sent the Google form for their response.\n\nThe study protocol was reviewed and approved by local RECs and some RECs granted exemption or subjected it to expedited review before the conduct of the survey in each country: Khon Kaen University Ethics Committee, Thailand, dated 31 March 2021 (HE641148); Republic of the Philippines, Department of health, Manila, Philippines, Single joint research ethics board, 1 June 2021 (SJREB-2021-40); Nepal Health Research Council, 24 March 2021 (190/2021P); Ethic Review committee Sri Lanka Medical Association, 21 May 2021 (ERC 21-010); Seth GS Medical College and KEM Hospital, Mumbai, India, 15 June 2021 (IEC (II)/OUT/427/2021); National Institute of Health (NIH), Malaysia, Medical research & Ethic Committee, 2 June 2021 (NMRR-21-969-59930 (IIR)); Faculty of Dentistry, University of Indonesia, Dental Research Ethics Committee, 5 April 2021 (01 Ethical exempted/FKGUI/IV/2021).13 Written informed consent was obtained through voluntary action by answering the Google form questionnaire in English. The answers from the REC chairs/secretaries were identifiable. However, in the case of REC members, answers were anonymous.\n\nThe collected data were analyzed to identify the common trends, significant challenges, and solutions. The information obtained from the REC members was described and presented in bar/pie/stacked charts. The data for the knowledge and attitude of REC members were presented in the stacked chart as a percentage of each value from the Likert scale; the data were also analyzed to obtain the means (SD) and interquartile range. The data from the chairs/secretaries were compared between SR-RECs and NSR-RECs presented in percentages and analyzed using the Chi-squared test in SPSS version 22.\n\n\nResults\n\nThe questionnaires were sent to 332 RECs, and the total responses from the chair/secretaries were 197 (59.3%), with 688 responses from the REC members (Table 1).\n\nFifty-one percent of the participants came from academic research institutions, followed by 33% from hospitals (Underlying data: Supplementary Figure 113). The majority of participants were medical doctors/dentists, followed by other medical professionals such as nurses, pharmacists, etc. (Underlying data: Supplementary Figure 213). There were equal numbers of social and biomedical scientists (7%), and a few laypersons and lawyers (6% and 3%, respectively).\n\nMost members reviewed only scientific/technical issues and less than 20% of members reviewed only Informed Consent Forms (ICFs); however, 8.9% claimed that they reviewed both technical and ICF issues (Underlying data: Supplementary Figure 313).\n\nAll of the countries have standard operating procedures (SOPs) but not all RECs in Sri Lanka had SOPs (Eight participants reported no SOPs) (Underlying data: Supplementary Figure 413). Within those RECs that reported having SOPs, there was a lack of some standard procedures. A total of 12.5% of participants indicated no SOP on structure and composition, 11.8% on initial review, 19.1% on post-approval process and documentation, 19.7% on standard assessment, 18.1% on agenda and minutes, 30.6% on serious adverse events (SAE) review, and 30.6% on archiving. A total of 31.8% of participants indicated that the list of international and national guidelines was missing.\n\nMost RECs had monthly board meetings (65.2%), followed by every two weeks (12.2%), and every week (7.6%) (except Sri Lanka), 9.1% quarterly, 2.5% every semester (except Sri Lanka), 1.0% annually (only in Malaysia and India). Only 2.3% had no REC meetings (only in Malaysia) (Underlying data: Supplementary Figure 513).\n\nGenerally, members from all countries (N = 678) have experience in reviewing all types of protocol (Underlying data: Supplementary Figure 613) but were most familiar with clinical research (79.9%) followed by public health (72.6%), socio-behavioural research (61.1%) and laboratory research (50.0%).\n\nOne hundred and twenty-four participants (18.1%) indicated that they had not been reviewing COVID-19 protocols. Generally, when reviewing COVID-19 protocols, members reviewed all elements required by international standards except advertisements, where half (50.6%) of the participants indicated that they had not reviewed this element (Underlying data: Supplementary Figure 713).\n\nFor those members who reviewed COVID-19 protocols (N = 503), several challenges were identified with the top three being the review of risk/benefit (46.1%), scientific design (35.6%), and vulnerability 34.6%. However, one-third (29.2%) of participants reported that they had no difficulty in reviewing COVID-19 protocols (Underlying data: Supplementary Figure 813).\n\nA total of 87.0% of participants (N = 684) indicated the need for training when reviewing COVID-19 protocols. The top three training needs (identified from 678 participants) were ethical issues relating to clinical research (60.9%), risk/benefit assessment (57.1%), and international guidelines and regulations (55.0%) (Underlying data: Supplementary Figure 913).\n\nRegarding the review of COVID-19 protocols, most of the participants conducted an online full board meeting (94.1%) and used a joint or central REC review in the case of a multi-centred study (92.1%). The participants also agreed that RECs need training in ethics review of COVID-19 protocols (93%). The participants considered that the majority of COVID-19 protocols were high risk and should be reviewed by the full board. The majority of participants recognized the issues of confidentiality and conflicts of interest (CoI) involving COVID-19 protocols (91.1%) and the importance of addressing these issues (Figure 1).\n\nFigure 1 demonstrates that more than 90% of the participants agreed that COVID-19 patients were vulnerable. They also agreed on the need for RECs to review and approve studies related to traditional medicine (82.2%), or unproven drugs, vaccines, and interventions for COVID-19 (85.1%). More than half of the participants thought that COVID-19 patients in hospitals should be allowed to participate in clinical trials. More than half of the participants were against employees of drug companies acting as principal investigators in Phase III clinical trials.\n\nThere were controversial opinions on three items with regard to COVID-19 studies1: The principal investigator can be any medical doctor,2 Any REC medical doctor can review technical issues, and3 Only COVID-19 patients should sign the ICFs (Figures 1 and 2).\n\nDuring the COVID-19 outbreak, similar measures were implemented in both SR-RECs and NSR-RECs surveyed such as masks, social distancing, community lockdown, travel restrictions, and limited access to institution facilities. The only difference between the SR-RECs and NSR-RECs was the limited access to institution facilities, which was found to be higher in SR-RECs (P = 0.03).\n\nSR-RECs complied with the member composition of RECs as required by the regulatory requirements and international guidelines, while some of the NSR-RECs lack non-affiliated and lay members. This aspect was significantly different between SR-RECs and NSR-RECs (P = 0.000 and 0.000, respectively) (Figure 3).\n\nBoth SR-RECs and NSR-RECs had adopted online meetings (80% and 66%, respectively). Some used online and face-to-face meetings (15% and 24%, respectively), and a few used face-to-face meetings only (5% and 10%, respectively).\n\nFigure 4 shows the workload of RECs, type of protocol reviewed, and post-approval review. More NSR-RECs reviewed less than 100 protocols during 2020 (P = 0.004) while more SR-RECs reviewed more than 500 protocols during 2020 (P < 0.004).\n\nBoth SR-RECs and NSR-RECs reviewed social and community, public health, and product development protocols. All countries reviewed COVID-19 protocols; however, some RECs did not review COVID-19 protocols (6 SR-RECs and 25 NSR-RECs). Significantly more SR-RECs reviewed COVID-19 protocols (P = 0.003) and product development protocols i.e. drug, vaccine, and diagnostic protocols (P = 0.000).\n\nBoth SR-RECs and NSR-RECs reviewed post-approval protocols. However, more SR-RECs reported having reviewed protocol violations (P = 0.001).\n\nAlthough both SR-RECs and NSR-RECs identified challenges in the review of the scientific methodology, ethical issue, ICF, CoI, and privacy and confidential issues (Figure 5), more SR-RECs identified challenges in the review of risk/benefit and vulnerability (0.010), ICF (0.002), and privacy and confidentiality issues (P = 0.020).\n\nSimilar training needs demanded by the chairs/secretaries of SR-RECs and NSR-RECs are shown in Figure 6. However, the need for training on specific ethical issues related to clinical trials was found to be significantly higher in SR-RECs when compared with NSR-RECs (P = 0.001).\n\n\nDiscussion\n\nThe results from the survey suggested that the RECs in Asian countries generally had satisfactory membership requirements including a multidisciplinary composition as required by international guidelines such as those provided by WHO,14 the Council for International Organizations of Medical Sciences (CIOMS),15 and The International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use (ICH) Good Clinical Practice (ICH GCP).16 The members of these RECs are typically composed of medical doctors/dentists, nurses, pharmacists, biomedical researchers, lawyers, bio-statisticians, social scientists, non-affiliated and laypersons. However, it was noted that some RECs lack laypersons and/or non-affiliated members.\n\nThe WHO guidelines emphasize the importance of including laypersons in RECs, as they play a vital role in representing the insights and perspectives of research participants. Additionally, the guidelines highlight the inclusion of non-affiliated members to enhance the independence of the committee. The absence of laypersons and/or non-affiliated members in some RECs may compromise their functionality and not align with the WHO guidelines and the European Medicines Agency (EMA) requirements, which mandate at least one lay and one non-affiliated member.14,17\n\nThe lack of explicit requirements for a layperson in some guidelines such as ICH GCP, may contribute to the absence of laypersons in certain committees. While the ICH GCP only calls for a “non-scientific member”, it is important to note that not all non-scientific members necessarily fulfil the role of a layperson who can effectively represent the perspectives of patients or research participants.14\n\nWhen comparing the composition of SR-RECs and NSR-RECs, it was found that SR-RECs comply better with international membership requirements by having laypersons and non-affiliated members. Including laypersons and non-affiliated members is crucial to ensure that the voices and perspectives of research participants are considered during the review process and that the decision-making process maintains independence.14\n\nThe Asian RECs adjusted well to the restrictions imposed by the government during the COVID-19 pandemic by utilizing online meeting platforms that also enabled them to prioritize the review of COVID-19 protocols by holding more frequent meetings as recommended by WHO as part of the pandemic response.18\n\nTo streamline the review process for multi-center COVID-19 protocols and other types of research, most of the REC members in this survey agreed to the use of a joint or single review system. Implementing a joint/single/central REC model was facilitated in Asia due to the harmonization of SOPs among 275 RECs certified under the SIDCER Recognition Program.19 This program fostered trust among SR RECs, enabling them to rely on using joint or single or central REC arrangements during the COVID-19 outbreak. This helped ensure the quality and timely review of multi-center clinical trials.18 It is worth noting that other countries faced challenges in the rapid review of multi-site COVID-19 protocols. South Africa, for example, encountered difficulties related to the operational readiness of their RECs.20 In the United States, using a single IRB has become mandatory for multi-center studies as part of the US Common Rule, aiming to ensure timely review of such studies.21\n\nOverall, the adoption of online platforms, more frequent meetings, and the practice of joint or single review systems have been effective strategies employed by Asian RECs to address the challenges posed by the COVID-19 pandemic and timely review of multi-center research protocols.\n\nIn general, the RECs in Asia can identify ethical issues in COVID-19 protocols. Most of the REC members classified the COVID-19 protocols as a high-risk type of research due to many uncertainties about the disease, and the vulnerability of the population in low- and middle-income countries. Despite recognizing the vulnerability of COVID-19 patients, REC members agreed that these patients should be included in clinical trials, demonstrating their familiarity with ethical principles outlined in guidelines such as the CIOMS ethical guidelines, which recommend the inclusion of vulnerable participants in health research unless there is a scientific justification for their exclusion.22–25\n\nMore than half of REC members disagreed that drug company employees should be principal investigator in Phase III clinical trials (Figure 2) indicating their recognition of CoI and the need to manage such conflict.26\n\nFurthermore, research on off-label use of herbal medicine such as andrographolide or repurposed drugs like hydroxychloroquine or ivermectin was common during the pandemic.27,28 In this survey, many REC Members agreed that the use of herbal medicine and off-label drugs should undergo clinical trials subject to REC review to gather evidence on their safety and efficacy for COVID-19. It was acknowledged that the dose and usage of these substances may differ from their established indications, which could lead to adverse side effects.29–31\n\nThe regular RECs training provided by the SIDCER network, which was established by the WHO special program in Tropical Disease Research (TDR) in 2001, has significantly contributed to the capacity-building of these RECs in Asia regardless of whether they were NSR-RECs or SR-RECs. The SIDCER network conducts regular research ethics training in FERCAP member countries in collaboration with local country fora in the Philippines, Indonesia, India, Sri Lanka, Malaysia, Nepal, Taiwan, and Thailand.19 This demonstrates the importance of active networks of RECs across regions for sharing information, resources, and expertise, and it serves as a strategy to enhance readiness for future public health emergencies.\n\nOverall, the efforts to strengthen REC capacity through training and networking have been instrumental in ensuring that ethical considerations are addressed effectively in COVID-19 research in Asia.\n\nThe important responsibilities of RECs are to scrutinize scientific soundness in research protocols that seek to generate new information and novel interventions to control the pandemic and ensure that the researchers uphold ethical principles to protect human participants.26\n\nIn addition to the initial review and approval of research protocols, RECs are responsible for monitoring researcher compliance with the approved protocols. This includes reviewing remote patient monitoring reports submitted by research teams and ensuring that researchers are updated about changes in prevention and treatment guidelines as new COVID-19 variants emerge. Post-approval review is essential to ensure the ongoing benefit and safety of research participants.\n\nWhile both SR-RECs and NSR-RECs reported conducting post-approval reviews, it was found that SR-RECs had more experience in reviewing protocol violations. This may be attributed to the fact that SR-RECs have undergone assessment regularly through the SIDCER Recognition Program, which includes evaluation of the REC’s post-approval monitoring process. This recognition process provides assurance that SR RECs have robust post-monitoring activities in place.\n\nAdditionally, SR-RECs often review more product development protocols, especially those supported by pharmaceutical companies. In these cases, there is typically better monitoring of GCP compliance as part of the sponsor’s responsibility; as a rule, the sponsor ensures that the investigators report all deviations/violations to the RECs for review.16\n\nAlthough both SR-RECs and NSR-RECs identified issues encountered with COVID-19, they still expressed the need for further training to effectively analyze and address the unique ethical challenges presented by COVID-19 protocols. The pandemic introduced specific ethical issues that were not encountered before32–35 and therefore additional training is crucial to ensure the scientific and ethical validity of research.\n\nCOVID-19 was a novel disease that spread rapidly and had severe health consequences, including death and serious health conditions. The uncertainty surrounding its origin, transmission, and evolution, combined with the limited availability of treatment and prevention options, posed significant challenges for the scientific community. Researchers and scientists were under pressure to conduct research and find rapid solutions to contain the spread of the virus and mitigate its impact.36,37 While the urgency of the situation called for expedited research, it was crucial that COVID-19 research adhered to scientific standards and ethical compliance.\n\nNew ethical challenges arose due to the public health emergency environment, where authorities imposed the movement restrictions. COVID-19 patients were quarantined at home or in hospitals, and some were in intensive care, making it more difficult to obtain informed consent using traditional practices.33,34,38,39 To adapt to these challenges, RECs faced the task of approving various forms of informed consent, including electronic consent, telephone consent, consent obtained through legally acceptable representatives, oral consent, waivers of signature, and other mechanisms that ensured consent was truly obtained, as required by the RECs.34,39\n\nTo navigate these challenges and ensure that research is conducted with scientific and ethical integrity, REC members require specific training. This training can cover various aspects, such as updates on evolving guidelines and regulations, and enhancing skills in analyzing complex study designs and methodologies.\n\nBy providing REC members with targeted training, they can gain the necessary knowledge and tools to effectively assess and address the ethical challenges specific to COVID-19 research. This training helps to promote consistency, rigor, and ethical compliance during the review process, ultimately safeguarding the rights, welfare, and well-being of research participants.\n\nThe REC members indicated that study design was one of the top challenges in reviewing COVID-19 protocols. In other studies, study design has also been raised as one of the challenges in COVID-19 reviews.33,34,40 Adaptive design has been introduced in many COVID-19 clinical trials to enhance the speed of product development. Although the advantages of the adaptive design have been accepted in many scientific communities, it was difficult for RECs to review them as risk/benefit ratio changed when methods, data analysis and products were modified during the course of a study.41,42 To address these challenges, REC members must familiarize themselves with different study designs, particularly adaptive design. By gaining knowledge and understanding of various study designs, RECs can be better prepared for future epidemics or public health emergencies where quick identification of new treatments is crucial to combat the disease outbreak.\n\nAlthough both SR-RECs and NSR-RECs identified several challenges in the review of protocols during the pandemic, SR-RECs are better equipped than NSR-RECs in reviewing COVID-19 and investigational medicinal product development protocols. One contributing factor is that SR-RECs have undergone assessment regularly through the SIDCER recognition program.19 The program evaluates various aspects of the REC’s review practice. The assessment includes the appropriateness of the composition of the REC, its operational procedures, and the thoroughness and completeness of the scientific and ethical review protocols. The program ensures that SR-RECs adhere to international ethical guidelines and the ICH GCP in their composition, operation and review processes. By undergoing this assessment, SR-RECs have proven their commitment to maintaining high scientific and ethical review standards. They have demonstrated their capability to effectively manage the review of COVID-19 and investigational product development studies comprehensively and rigorously. This recognition program helps enhance the capacity of SR-RECs and instills confidence in their ability to conduct ethical reviews of research protocols related to public health emergencies like COVID-19.\n\nMost of the participants who responded to the questionnaires were in the medical field and thus may not adequately represent the perspectives of the non-medical REC members. The number of participants was not equal for each country, as well as the SR-RECs and NSR-RECs. The questionnaires were in English thus some participants may not exactly understand the questions and skipped some questions.\n\n\nConclusions\n\nThe COVID-19 pandemic created an opportunity to highlight the importance of competent RECs that developed with the assistance of existing local research ethics networks under SIDCER-FERCAP in Asia. The Asian RECs responded to the challenges of the COVID-19 outbreak by adopting online platforms, more frequent meetings, and the use of joint or single review systems to ensure timely review.\n\nDuring the COVID-19 outbreak, RECs in countries with SIDCER networks generally had a basic understanding of REC operations and ethical principles when reviewing protocols related to the pandemic. However, specific training may have been necessary to enhance the quality of their reviews.\n\nThe SR-RECs played a significant role in reviewing COVID-19 protocols, including those related to product development. These RECs effectively managed the unique challenges posed by the pandemic while conducting ethics reviews.\n\nTo further strengthen the capacity for future public health emergencies, one strategy is to establish and maintain active networks of ethics committees across regions. These networks facilitate the exchange of new information, resources, and best practices among RECs. By sharing knowledge and collaborating, these RECs can enhance their preparedness and readiness to respond effectively to similar public health emergencies in the future. This collaborative approach promotes harmonized procedure, consistency and high-quality ethics review, ultimately protecting the rights and welfare of research participants.\n\n\nConsent\n\nImplied informed consent for publication of the participants’ details was obtained from the participants.", "appendix": "Data availability\n\nFigshare: Underlying data for ‘The readiness of the Asian research ethics committees in responding to the COVID-19 pandemic: A multi-country survey’, https://doi.org/10.6084/m9.figshare.24261226.v5. 13\n\nThis project contains the following underlying data:\n\n• Data file: TDR EC survey 2020 AUG 3 2022.xlsx\n\n- Sheet 1 “EC Member”: Survey responses of participants who are REC members.\n\n- Sheet2 “COVID Review”: Isolation and processing of the REC members’ survey responses regarding the operation of the members’ respective RECs with regards to COVID-19 protocols and the perception of EC members on ethical issues of COVID-19 research.\n\n- Sheet 3 “COVID Review Chart”: Reformatted data from the “COVID Review” sheet to display the processed data as stack bar charts.\n\n- Sheet 4 “Chair”: Survey responses of participants who are REC chairs/secretaries.\n\n- Sheet 5 “Affiliation”: Isolation and processing of the REC chairs/secretaries’ survey responses regarding the institution type/affiliation of their respective RECs in order to compare the affiliations of SR-RECs versus NSR-RECs.\n\n- Sheet 6 “Chair Composition”: Isolation and processing of the REC chairs/secretaries’ survey responses regarding the respondents’ role in their respective RECs in order to compare the compositions of SR-RECs versus NSR-RECs.\n\n- Sheet 7 “# Prot Rev”: Isolation and processing of the REC chairs/secretaries’ survey responses regarding the number of protocols reviewed by the respondents’ respective RECs in order to compare the number of protocols reviewed by SR-RECs versus NSR-RECs.\n\n- Sheet 8 “Issues”: Isolation and processing of the REC chairs/secretaries’ survey responses regarding the issues reviewed by the respondents’ respective RECs in order to compare the issues reviewed by SR-RECs versus NSR-RECs.\n\n- Sheet 9 “Training”: Isolation and processing of the REC chairs/secretaries’ survey responses regarding the training needs of the respondents’ respective RECs in order to compare the training needs of SR-RECs versus NSR-RECs.\n\n• Supplementary Figure 1: Participant Distribution.jpg\n\n• Supplementary Figure 2: The Roles-Expertise of Participants in REC.jpg\n\n• Supplementary Figure 3: Review Function of Participants in REC.jpg\n\n• Supplementary Figure 4: SOPs.jpg\n\n• Supplementary Figure 5: Frequency of REC Meeting.jpg\n\n• Supplementary Figure 6: Experience of Members in Reviewing Types of Protocols.jpg\n\n• Supplementary Figure 7: Elements Reviewed by REC when Reviewing COVID Protocols.jpg\n\n• Supplementary Figure 8: Challenges Identified by REC Members in Reviewing COVID-19 Protocols.jpg\n\n• Supplementary Figure 9: Training Needs when Reviewing COVID-19 Protocols.jpg\n\nFigshare: Extended data for ‘The readiness of the Asian research ethics committees in responding to the COVID-19 pandemic: A multi-country survey’, https://doi.org/10.6084/m9.figshare.24261226.v5. 13\n\nThis project contains the following extended data:\n\n• IRB Covid Survey Questionnaire.pdf\n\n• EC-IRB information version 2.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\nWe are grateful to Dr. Junjira Laothavorn for her assistance in the visualization of the data presentation. We sincerely appreciate her exceptional data visualisation skills, which have played a crucial role in transforming complex and raw data into visually appealing and informative graphical representations. We also would like to thank Dr. Panida Kongjam for her support in statistical analysis.\n\n\nReferences\n\nSisk BA, Baldwin K, Parsons M, et al.: Ethical, regulatory, and practical barriers to COVID-19 research: A stakeholder-informed inventory of concerns. PLoS One. 2022; 17(3): e0265252. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFord DE, Johnson A, Nichols JJ, et al.: Challenges and lessons learned for institutional review board procedures during the COVID-19 pandemic. J Clin Transl Sci. 2021 Mar 16; 5(1): e107. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWorld Health Organization (WHO): Clinical management of COVID-19: Living guideline. World Health Organization (WHO); 2023 [cited 2023 May 31]. 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International Ethical Guidelines for Health-related Research Involving Humans. 4th ed.Geneva: Council for International Organizations of Medical Sciences (CIOMS); 2016; pp. 71–73.\n\nGuideline 25: Conflicts Of Interest. International Ethical Guidelines for Health-related Research Involving Humans. 4th ed.Geneva: Council for International Organizations of Medical Sciences (CIOMS); 2016; pp. 95–98.\n\nNa-Bangchang K, Porasuphatana S, Karbwang J: Perspective: repurposed drugs for COVID-19. Arch Med Sci AMS. 2022; 18(5): 1378–1391. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nQuincho-Lopez A, Benites-Ibarra CA, Hilario-Gomez MM, et al.: Self-medication practices to prevent or manage COVID-19: A systematic review. PLoS One. 2021; 16(11): e0259317. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSchmith VD, Zhou JJ, Lohmer LRL: The Approved Dose of Ivermectin Alone is not the Ideal Dose for the Treatment of COVID-19. Clin Pharmacol Ther. 2020 Oct; 108(4): 762–765. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGras M, Gras-Champel V, Moragny J, et al.: Impact of the COVID-19 outbreak on the reporting of adverse drug reactions associated with self-medication. Ann Pharm Fr. 2021 Sep; 79(5): 522–529. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBaracaldo-Santamaría D, Pabón-Londoño S, Rojas-Rodriguez LC: Drug safety of frequently used drugs and substances for self-medication in COVID-19. Ther Adv Drug Saf. 2022; 13: 204209862210941. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBe B, Sa W, Jm B, et al.: Ethical Challenges in Clinical Research During the COVID-19 Pandemic. J Bioethical Inq 2020 Dec [cited 2023 May 30]; 17(4): 717–722. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBurgess T, Rennie S, Moodley K: Key ethical issues encountered during COVID-19 research: a thematic analysis of perspectives from South African research ethics committees. BMC Med Ethics. 2023 Feb 15; 24(1): 11. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFaust A, Sierawska A, Krüger K, et al.: Challenges and proposed solutions in making clinical research on COVID-19 ethical: a status quo analysis across German research ethics committees. BMC Med Ethics. 2021 Jul 19; 22(1): 96. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLumeng JC, Chavous TM, Lok AS, et al.: Opinion: A risk-benefit framework for human research during the COVID-19 pandemic. Proc Natl Acad Sci U S A. 2020 Nov 10; 117(45): 27749–27753. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGuideline 20: Research in Disasters and Disease Outbreaks. International Ethical Guidelines for Health-related Research Involving Humans. 4th ed.Geneva: Council for International Organizations of Medical Sciences (CIOMS); 2016; pp. 75–78.\n\nKasherman L, Madariaga A, Liu Q, et al.: Ethical frameworks in clinical research processes during COVID-19: a scoping review. BMJ Open. 2021 Jul 23; 11(7): e047076. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFoëx BA: The problem of informed consent in emergency medicine research. Emerg Med J EMJ. 2001 May; 18(3): 198–204. PubMed Abstract \| Publisher Full Text\n\nMcCarthy MS, McCarthy MW: Ethical challenges of prospective clinical trials during the COVID-19 pandemic. Expert Rev Anti Infect Ther. 2022 Apr; 20(4): 549–554. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHashmi SK, De Vol E, Hussain F: Pride and Prejudice during the COVID-19 Pandemic: The Misfortune of Inappropriate Clinical Trial Design. J Epidemiol Glob Health. 2021 Mar; 11(1): 15–19. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBranch-Elliman W, Elwy AR, Monach P: Bringing New Meaning to the Term “Adaptive Trial”: Challenges of Conducting Clinical Research During the Coronavirus Disease 2019 Pandemic and Implications for Implementation Science. Open Forum. Infect Dis. 2020 Nov; 7(11): ofaa490. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStallard N, Hampson L, Benda N, et al.: Efficient Adaptive Designs for Clinical Trials of Interventions for COVID-19. Stat Biopharm Res. 2020 Jul 29; 12(4): 483–497. PubMed Abstract \| Publisher Full Text" }	[ { "id": "298798", "date": "19 Aug 2024", "name": "Emma Cave", "expertise": [ "Reviewer Expertise I am a law academic who has been involved in related research in the UK. I am not an expert in empirical research methods and so the focus of this review is on the presentation of the results rather than its scientific validity." ], "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 interesting and important paper reports on two connected online surveys across 7 Asian countries in 2021. The research, which was itself subject to research ethics committee (REC) approval in each country, sought to capture the experiences, responses and challenges of RECs to COVID-related research protocols across 332 RECs. It offers a range of original insights and is significant in aiding understanding of the state of the REC approvals systems in Asia and of the research challenges that a global public health emergency can bring. The paper demonstrates the importance of RECs being operationally ready to play their important role in upholding ethical standards whilst facilitating scientifically robust and ethical research, and sets out some of the ways this goal can be achieved. The research is useful in planning for future pandemics and also in considering variation and similarities in composition, role and function of RECs across the different countries.\nPoints to consider\nThe survey was carried out in 2021, but in my opinion the article should be updated so that statements made about the current status of the disease are accurate to a 2024 audience. For example, the first two lines stating that the disease is ‘new’ and that there are limited vaccines available is of questionable accuracy in July 2024. The introduction should situate the research in relation to where we are now as well as where we were in 2021 when the survey was conducted. The introduction could usefully say what is novel about COVID from the perspective of ethics committees. This is mentioned on p 11, but the introduction could set out why the authors considered it to be different and therefore worthy of the survey. Was it the nature of the research (eg clinical, public health), the ethical issues it raises of conducting it (eg human challenge trials etc), the proliferation of new guidelines, the importance of timeliness (new expedited review processes), ways of conducting meetings (eg online) etc, or a range of these issues that prompted the research? For a global audience, it would also be useful for the Introduction to give a little more context on the ethics networks (SIDCER) and regulatory system/s across the 7 countries chosen and how consistent they are in approach. What are the key differences between an SR-REC and a NSR-REC? A conclusion is that the networks need to be strengthened so it would be useful to set out the baseline – what was the state of the networks when the survey was conducted? It would be helpful to say something about whether there was overlap in the data captured by the two surveys and how this was taken into account (eg to avoid double counting). Page 5 ‘most members reviewed on scientific/technical issues …and [some] members reviewed only Informed Consent forms’. Could the authors make clearer whether this is about apportionment of work within the ethics committees (eg some members focus on IC and some on technical issues), or a claim that the ethics committees only review technical issues and some only review IC. I thought the point about variation on SOPs was very interesting. Do the authors have a view as to whether standardisation would be beneficial and if so might it be worth commenting in the conclusions?\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?\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": "306967", "date": "19 Aug 2024", "name": "Paul Ndebele", "expertise": [ "Reviewer Expertise Research ethics" ], "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 assessed the readiness of RECs in selected Asian countries in responding to the covid-19 pandemic. 1. The introduction section is outdated. Covid-19 is no longer new and the RECs faced most of these challenges during the early days of the pandemic. The introduction should be recast to show that the authors were reflecting on the situation in 2020. 2. It is not clear how the respondents were invited. 3. It is not clear how informed consent was obtained.\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": [] } ]	1	https://f1000research.com/articles/13-19
https://f1000research.com/articles/12-784/v1	05 Jul 23	{ "type": "Case Study", "title": "The problematic space between art, ambition, and gameplay: The Medium and the issues concerning difficult subject matter and gameplay in games", "authors": [ "Katarzyna Marak", "Miłosz Markocki", "Krzysztof Chmielewski", "Dariusz Brzostek", "Krzysztof Chmielewski", "Dariusz Brzostek" ], "abstract": "This article identifies and examines a couple of selected issues regarding speculative digital games which endeavor to deal with serious subject matter. Due to the fact that speculative games are exceptionally well suited for symbolic representation of sensitive topics, they allow their creators to conceive ambitious projects that aspire to be great works of audiovisual art. However, because game texts belong to a very specific medium, it is not always possible to realize this ambition in the context of gameplay. For reasons of space and focus this article uses one particular game, The Medium (2021), to serve as the primary example of how the problems which occur in the process of combining specific, engaging gameplay with serious, sensitive subject matter, lead to situations in which a game can fail to fulfill the player’s expectations. By analyzing the structure, gameplay, and storytelling tools employed in The Medium, the article places emphasis on the significance of the possible tensions between the intention of the designers of the game experience and the experiences, ideas, and interpretations the players themselves bring to the game text.", "keywords": [ "digital game", "art", "The Medium", "eudaimonic gratification", "gameplay", "ludonarrative dissonance" ], "content": "Introduction\n\nAs games become ever more intricate, moving, and challenging, game studies have been moving away from looking at game texts as mere sequences of scripted choices contained in designed spaces; instead, in addition to examining the ludic profile of game texts, many analyses now tend to draw attention to “ideas of autonomy and control from both the player and designer perspectives” (Rothschild et al. 2013: 83) as well. This article adopts the position that examining a game text from a perspective that takes into consideration the story-related, agency-related, and design-related elements of that text allows for a more comprehensive and productive study of games.\n\nOf particular interest for this paper are the characteristics of fantasy, horror, and adventure games which aspire to portray, express, and convey ambitious themes, experiences, and stories; to this end, these game texts oftentimes include or rely on speculative elements, worlds, and scenarios, which allows them to move away from imitating reality, as well as the burden of the premise that “reality is objective and unambiguous” (Oziewicz 2017). For this reason, such games tend to be exceptional vehicles for symbolic representation of sensitive topics and excel at presenting allegorical figures and scenarios referring to trauma. There are numerous titles whose goal it is to present serious subject matter as a unique immersive experience. Non-mimetic games can concern diverse sensitive topics, including obsession, guilt, penance, impotence, bigotry, or dejection, as can be seen in games such as: Layers of Fear (2016), Hellblade: Senua’s Sacrifice (2017), Someday You’ll Return (2020), Silent Hill 2 (2001), Silent Hill 3 (2003), SOMA (2015), The Dark Pictures Anthology: House of Ashes (2021), or Scorn (2022). These are, of course, only a few to name in the context of a larger body of games employing supernatural of scientific speculative concepts or scenarios in order to offer “occasions to reflect on our condition as human beings and to reflect on what makes our life meaningful” (Cova et al. 2017: 349); the motivation to seek out narratives which elicit negative affective reactions (cf. Oliver & Bartsch 2010), i.e. eudaimonic motivations, leads the players to engage with texts which are able to provide them with satisfaction related to cognitive and emotional effort and experiences as they play the game: eudaimonic gratification.\n\nSpeculative games have at their disposal a whole range of reliable and effective cinematic and ludic tools. The employment of both makes it possible for the creators to include meaningful cultural details in their depicted worlds and build an atmosphere, as well as explore themes through visual design and mise-en-scène. The camera shots and shot composition help accentuate the most significant story elements, influencing the overall gameplay experience, similarly to game spaces, which contribute to the narrative and present challenges to the player. The complex, changeable nature of game characters, who can serve a function of a non-playable character, a protagonist, or an avatar, or even two of those at the same time, on the other hand, is inherent to the facilitation of ambiguity within a story framework.\n\nThis article aims at calling attention to the problems which occur and can be observed in some speculative games that attempt to combine specific, engaging gameplay with serious, sensitive subject matter, but are unsuccessful in doing so. To this end, this paper presents a case study of The Medium—a psychological horror video game developed and published by Bloober Team on January 28, 2021—and the ways in which it fails to fulfill the expectations of the player in the context of delivering eudaimonic gratification in being a game text, and not by reason of being a game text.\n\n\nMethods\n\nThis paper utilizes the method of case study as it is applied in cultural studies—an examination of “a typical cultural artifact and medium of modern culture, and [how] through studying its ‘story’or ‘biography’ one can learn a great deal about the ways in which culture works” (Du Gay et al. 2013: xxix). In the case of The Medium, this approach constitutes qualitative research of the particular type of digital game texts and the ludonarrative dissonance typical of those texts. Even if a case study will not provide any general conclusions regarding the dissonance and balance between the ludic and the narrative, it still can name at least some constitutive principles observable in a particular body of game texts.\n\nThe primary focus of this text concerns game texts featuring narratives revolving around sensitive topics and themes. Of particular interest to our research and observations is the interplay between the face-value narratives produced by such games as well as their symbolic vocabulary. Even more importantly, the games we consider are ambitious both in terms of concept and narrative at high aesthetic level. They touch upon a range of topics from child abuse, mental illness, to seeking and finding closure, or striving to reflect affective, social, and political realities in individualized, allegorical manner. Apart from the titles mentioned above, there are many more game texts of that type, including Among the Sleep (2014), The Beast Inside (2019), Blair Witch (2019), Detention (2017), The Dark Pictures Anthology: Little Hope (2020), Fran Bow (2015), Observer (2017), Perception (2017), Through The Woods (2016), Tell Me Why (2020). Some of these games fulfill their task of engaging the player in their story as much as in gameplay (Layers of Fear, Hellblade: Senua’s Sacrifice, Detention, or SOMA), while others fail in one or both of these goals (Someday You’ll Return, The Beast Inside, or Blair Witch).\n\nThe game The Medium was selected as a representative example of a story-driven speculative game dealing with serious subject matter, which tells dramatic and intriguing story, but offers the players rather awkward gameplay. The case study method is supplemented by data obtained from Steam platform. The players’ reviews on Steam were reviewed manually on Mar 6-10, 2023, in 3 different categories provided by Steam (positive, negative, mixed); no automatized tool was used. A total of 5,292 reviews (all Steam reviews for The Medium available on Mar 6, 2023) was read in whole in search for contents relevant to the article, with the utmost focus on the gameplay and mechanics. The purpose of the resulting analysis is the identification and overview of problems stemming from the necessity of translating a complex story into a satisfying gameplay experience. The Medium as a case study makes it possible to name the key issues resulting from the various restrictions placed on the player’s agency in relation to the narrative potential of the story, which are also present in some of the other similar story-driven speculative games.\n\nEthical approval and consent were not required for this study as the study is of low risk, with no intervention, no correspondence with the Steam users involved, and the use of anonymised data.\n\nThe events of The Medium take place in Poland. The story revolves around a young woman, Marianne, who is the player character and, seemingly, the center of the entire game narrative. Marianne happens to be a spirit medium, able to access the realm referred to as Spirit World, and capable of helping lost souls find rest. Alone and deprived of purpose after the death of her legal guardian, Jack Orkan, she is caught off guard by a phone call from a man who introduces himself as Thomas, and who claims to both understand her power and be able to explain its origin, as well as the nature of her recurring nightmares—on the condition Marianne meets him in person in the abandoned secluded Niwa Workers’ Resort. Upon her arrival, Marianne finds the building empty and in ruin, but full of traces, clues, and trapped souls connected to the appalling massacre that led to the closure of Niwa many years earlier. There is also another presence in Niwa, which Marianne later discovers to be the greatest threat in that place.\n\nThe two most noteworthy components of The Medium, informing its storytelling and its gameplay mechanics, are the concepts of splitting and superimposition, both involving the past and the present as well as the material and the spiritual. The depicted world does not merely include spirits and supernatural occurrences, but is in fact founded on the premise of reality consisting of two aspects meant to complement one another: the material world and the Spirit World. As a speculative game text, The Medium uses this idea to challenge “the materialist complacency that nothing exists beyond the phenomenal world” and expands its fictional reality beyond that which is tangible and explainable (Oziewicz 2017), offering the player emotional experiences, encounters, and knowledge that otherwise would be inaccessible to them. Marianne’s power to access the Spirit Word makes her quite literally the focal point of the story and the gameplay experience. The game emphasizes the juxtaposition and superimposition of the past and the present by means of splitting and switching the virtual environment, which affects the gameplay to a great extent; the story, however, uses this premise to a slightly different effect.\n\nIn the context of the overall narrative, the focus on the past seems to portray Marianne as a character as someone outside of her own timeline. In some ways, Marianne appears to exist outside of the present. Although the game itself opens with narration delivered by Marianne, concerning later events, the gameplay begins in Jack’s apartment, who at this point in time is already dead. His business, a funeral home, is also related to handling the dead, and is depicted as having become irrelevant after his death, as Marianne makes no mention of keeping it. Financial future is not the only thing Marianne fails to refer to. The player never learns of any friends, interests, present obligations or future plans she might have. At this point, there is also no mention of any other family members aside from Jack. It is only later in the game that Marianne, and therefore the player, finds out about her biological father, Thomas Rekowicz, and elder sister, Lilianne. Even more importantly, Marianne’s power is subsequently explained to be a family trait—it is no longer treated in the story as a bizarre ability setting her apart from others, but as a gift inherited from her father. However, none of this information she actually receives from living people with whom she could engage in conversation.\n\nThe story of Marianne’s family is revealed gradually as the game progresses through visions of the past, encounters with spirit remains of people either dead or gone, or through retrospective sequences revolving around those people. Once in Niwa, Marianne meets Sadness, a child spirit who is afraid but refuses her help. More importantly, Sadness mentions her connection to the monster roaming the ruins of Niwa, which occasionally pursues Marianne obsessively—the Maw. The player, watching Marianne’s visions eventually discovers that Sadness is in fact the child spirit of Lilianne, who came into existence after Lilianne was sexually abused by their father’s trusted friend, Richard Tarkowski. Marianne later realizes that she is Lilianne’s younger sister, whom Thomas Rekowicz sent away for her own safety after a fire that nearly killed both of them. Marianne’s visions also show more of Niwa’s past, which allows the player to understand that Thomas Rekowicz was a medium similar to Marianne; his special ability consisted in trapping a person’s mind in their body. He was hiding at Niwa, in Poland, with his family, when he was found and attacked by Henry Wilk, a Security Service agent. Although Thomas Rekowicz was able to neutralize Henry, the fire set by the latter constitutes the most grievous and catastrophic event in the entire story of the game, since it is at that moment when young Lilianne, terrified and hurting, is tricked by the growing darkness inside her. In exchange for saving her and her baby sister’s—Marianne’s—life, Lilianne sets the darkness which has been growing in her ever since Richard’s assault free into the world, where it takes the monstrous form of the Maw, which the player can recognize as the monstrosity haunting Niwa’s grounds, and the fiend responsible for the massacre that led to the resort’s closure. Marianne also learns that her father, having lost his connection to the Spirit World during his confrontation with Henry, devoted the rest of his life to confine the Maw by creating a special, magically reinforced bunker in which Lilianne spent the majority of her life. None of this knowledge is optional, as the information is not embedded in the world in form of narrative elements such as letters or journals, or expressed in the game environment; instead, it is scripted as cut-scenes, which turn the player from an actor into a captive spectator (cf. Calleja 2011). As a result, Marianne, together with the player, is suddenly burdened with both the knowledge of, and the emotional responsibility to be invested in, events she was (apart from the night of the fire) never a part of, and family members she had never met (in a meaningful way she would be aware of). She therefore appears to have no place she could occupy in the timeline of that story, unlike, for example, Heather Mason in Silent Hill 3, who also learns a great deal about her past self throughout the game in order to understand her role in her present. A related issue is Marianne’s lack of apparent dramatic need in the context of the fact that The Medium is regarded as a text of the horror genre. To make another comparison, Senua in Hellblade: Senua’s Sacrifice sets out to face Hela driven by a sense of guilt and the hope of Dillion’s resurrection; in Silent Hill 2 James Sunderland travels to Silent Hill in search for his wife, while the Artist in Layers of Fear rambles around his house because of the mad compulsion to complete the Painting. In contrast to the aforementioned characters, Marianne’s only motivation to go to Niwa is just a mysterious phone call made by a person claiming to be able to explain her nightmares. The dramatic need in horror games tends to require even greater suspension of disbelief than in other speculative games. However, the reason for Marianne to actually go to Niwa and stay there even after she realizes that the place is terribly dangerous is rather vague and inadequate; in consequence, affective identification with Marianne can become difficult, as she loses some credibility as a believable horror protagonist, and, as a result, she functions more as a blank canvas to encourage the players to focus more on the environmental storytelling rather than character-centric exploration.\n\nIn the context of The Medium as a narrative, there are far-reaching consequences of Marianne’s role and character arc within the framework of the game’s storytelling. Her dramatic need as a character becomes relevant only after the player is subjected to complete exposition through the sequences in which Marianne receives all the necessary visions, which means that each story fragment falls into place, leaving almost no potential questions or doubts. Thus, there are no Ingarden’s spots of indeterminacy or Iser’s textual gaps or blanks that would appear through the interaction with the player and need filling (Sandvoss 2007: 28). Since the game story advances itself (cf. Bateman 2021), there is little effort required from the player to ponder and create meaning along the way. This means that The Medium as a narrative does not allow for any ambiguity in its story; this is a very important point, as ambiguity tends to play\n\na major role in the emotional impact of the [independent story-based] games … By leaving space for the player to think and contemplate—unburdened by the requirements of completing functional challenges, the player is better able to emotionally invest, and subsequently receive a greater emotional return, in the diegesis (Cole et al. 2015),\n\nwith the core pleasure offered to the player being “the resolution of tension within the narrative, emotional exploration of ambiguities within the diegesis, or identification with characters” (Cole et al. 2015). Within the narrative of The Medium, there are few moments or places of ambiguity, apart from the very ending, which unfortunately in itself makes the resolution of tension impossible. Another aspect of the game which could potentially allow for ambiguity—but evidently does not—is the exceptional status of Spirit Marianne, or, in other words, Marianne’s Spirit Self. The Spirit Selves that the player encounters in the game are human spirits and monsters. Human spirits represent the given character as they were in the moment of their death, such as Spirit Jack, or in the moment of a severely traumatic experience. Sadness, the child spirit of Lilianne, is the most important among such characters, although the player is also introduced to the child spirits of Richard and Henry. Due to the fact that The Medium is a horror narrative, the monsters are the most visually striking Spirit Selves; the main antagonist, the Maw, is a humanoid creature born from Lilianne’s trauma, who indiscriminately destroys everything and kills anyone it can reach in both the material world and the Spirit World. The monstrous Spirit Self of Richard, meanwhile, known as the Childeater, is the result of Richard’s twisted obsession with little girls, which manifests itself in the form of a gargantuan lecherous, vaguely human-shaped entity with multiple arms and tentacles, which is a very direct manifestation of Richard’s tendencies; it does not seem to be able to affect the material world directly, only Richard’s behavior. Interestingly, in contrast to Sadness and Richard’s child Spirit Selves, Henry’s child Spirit Self seems to be the only child spirit not terrified of its monstrous Spirit Self. Instead, the child Spirit Self of Henry appears to be an extension of the Hound, a predatory monster living in Henry Wilk’s warped mind potentially since his childhood, whose canine shape crowned with an oversized human skull evidently points to associations with hunting, implying that the Hound may be always in control of adult Henry.\n\nOnly Marianne’s Spirit Self is the same in identity, appearance and personality as her material self. Therefore, Spirit Marianne is one of a kind, unlike any other character portrayed in the game as she is merely Marianne’s reflection in the Spirit World. She never speaks and she never does anything Marianne does not do in the material world; even in the sequences when Marianne needs to leave her physical body in order to find or access something in the Spirit World, her Spirit Self is indistinguishable from material Marianne as an avatar. She literally occupies the same space and time. This is an informed choice on the part of the creators, which makes sense from the point of view of actual gameplay, but it is important to note that other options were available. For example, it is possible to have two individual avatars at the center of the game narrative, as can be seen in Tell Me Why (2020), where the player switches between the twins who are the protagonists of the story. Similarly, it is possible to have a protagonist who is materially confined in specific locations of the game, and a separate playable character who exists on a different plane and is therefore unhindered by material obstacles, as can be seen respectively with Jodie and Aiden in Beyond: Two Souls (2013). The significance of the choice made by the creators of The Medium is best seen in the last cut-scene of the game, where a very different type of split screen is employed, and Marianne is never shown as two separate characters. Accordingly, Marianne’s Spirit Self is completely undeveloped as a character, in unlike Spirit Thomas, who is the Spirit Self of Thomas Rekowicz. Spirit Thomas is clearly an independent entity—ruthless, sarcastic, and more assertive than Thomas himself, bearing symbolic marks reflecting Thomas Rekowicz’s traumatic and violent life. In contrast, Spirit Marianne is not her own person–apart from the burns Marianne suffered in the fire as a baby, which in the Spirit World are expressed visually as fungal-like growth on her burned shoulder, there are no other indicators of her life experiences, as if Spirit Marianne barely existed outside of the context of the fire.\n\nThis also means that Marianne is the only character who never engages in any sort of internal dialogue with her own Spirit Self. Consequently, the player is unable to gain any additional insight into Marianne’s personality, feelings, or thoughts. What is more, Marianne’s death would be final, since the game earlier establishes that Marianne’s Spirit Self cannot survive for longer periods of time away from Marianne’s material body. As such, the character of Spirit Marianne is primarily a mere placeholder for material Marianne, being removed from the structure of character building within the game; taking into consideration the fact that having an independent Spirit Self is a dominant element of character building in The Medium, Marianne without an independent Spirit Self becomes the exception that proves the rule, making her even more unique. However, this uniqueness limits the potential for ambiguity in The Medium even further.\n\nStories in games are more than simply sequences of events, as their narratives emerge from game spaces, which sometimes incorporate elements of designed experiences (Rothschild et al. 2013: 83). Spacial mechanics of the narrative elements play an important part in shaping the gameful experience, as well as the player’s subjective appreciation of the game’s storytelling. It is narrative elements that make the game space meaningful, while the space itself allows for a specific arrangement of those elements, and the last and “most important element that needs positioning is the player” (Nitsche 2008: 44-45). It is the player who makes sense of the in-game events and situations, but the process itself—especially in speculative games—tends to be “evoked and directed by evocative narrative elements, formed by encounters or situations in the game that prime some form of comprehension” (Nitsche 2008: 44). The space of the game plays the central role in the meaning-making process, due to the fact that the player’s participation and their comprehension of the game world take place in a navigable, structured virtual space (Nitsche 2008: 159). The space in the game is both contextualized and motivated by the game’s fictional setting, and includes a variety of elements from objects and characters to lighting design. The design of the game space can be understood in terms of mise-en-scène; in case of game text, mise-en-scène blends the interactive and the narrative aspects of the game space (Pigulak 2022: 110). This role of mise-en-scène overlaps to a certain degree with the function of the narrative design, wherein it focuses the player’s attention on a specific object, part of the set design, or character; just like narrative design, mise-en-scène can be used to organize the space of the game, giving prominence to objects crucial to the narrative and interactivity of the game (Pigulak 2022: 110-111).\n\nInterestingly, The Medium makes heavy use of this function of mise-en-scène, but not in all of its locations. At the beginning of the game, just before Marianne receives her literal “call to adventure”, in the form of a phone call summoning her to the abandoned Niwa resort, the player has the opportunity to explore the place where she lives. The tenement apartment, which belongs to her deceased legal guardian, is full of his belongings and memorabilia related to his past1. The player, controlling Marianne, can pick up and examine numerous items around the apartment; Marianne’s comments regarding the objects she looks at reveal information about Jack’s past and the relationship she had with him. This sequence is probably the most detailed and oriented towards encouraging the player to explore the environment. However, once Marianne arrives at Niwa, there are few to no objects essential to the storyline concerning her family history.\n\nAnother important feature of game spaces are evocative spaces and elements, which tend to draw upon the player’s metagame knowledge and meta-genre knowledge. Relying on the already existing narrative-related experiences, the players infuse the evocative spaces and other elements with significance through reading and connecting them (Nitsche 2008: 44). Evocative spaces are also closely connected to environmental storytelling, which depends on using the virtual environment as a tool to convey the story, accentuating smaller stories expressed by the very world of the game (Markocki 2021: 72-73).\n\nThe Medium features detailed environmental storytelling concerning the Niwa massacre, but very few evocative spaces related to Marianne’s family history. There is not much in the game space for the player to infuse with significance, and practically no instances of pull narrative. Initial conversations with Sadness give the player no clues regarding her connection to Marianne. In a story focused on family trauma the player would expect appropriate evocative elements to be incorporated into the game world to stimulate the meaning-making process (Nitsche 2008: 44). However, The Medium lacks these crucial elements, which makes the comprehension of family history (i.e. the most critical part of The Medium’s story) difficult; instead, the aftermath of the Niwa massacre constitutes the foundation of the games environmental storytelling and artistic choices.\n\nThe sequences in the Spirit World demonstrate how it literally allows the past and present to coexist in the game—both in terms of gameplay and story—seeing as Marianne can interact with remnants that continue to exist but belong to the past inside her present timeline. It is also important to note that despite the visual (re)presentation, the material world and the Spirit World are not, in fact, two separate worlds; similarly to Silent Hill’s Otherworld, the Spirit World is rather a distinct version of the same depicted world occupying the same space within the same game world, which can be readily distinguished by the vastly different aesthetic design, interactable parts, and now traversable areas (Bizzocchi and Tannenbaum 2011) within the confines of the same virtual environment. Appropriately, the time and space in The Medium do not merge, but overlap, the past being always superimposed on the present. The primary location explored by the player, the abandoned Niwa resort, is both the most artistically polished game space, and the most saturated with details as far as the Spirit World is concerned. While the virtual environment of the Niwa resort in the material world offers the richest storytelling, including not only indices pointing to the murdered guests, but also to the previous everyday functioning of the resort as well as to the investigation carried out in it after the massacre, the Spirit World in that location introduces actual spirit entities and remnants of the past. The player can examine what remains of the Niwa resort, but they can actually interact with spirit entities and remnants to further explore the past.\n\nAs the game progresses, the story and the gameplay shift away from the Niwa massacre to Marianne’s family history. Consequently, the emphasis of the early gameplay is placed on clear objectives and actions required to achieve them—searching for the man who made the phone call to Marianne, helping the spirits of the massacre victims to move on, and unraveling the mystery of what had really happened at Niwa. However, as the narrative progresses, the Spirit World shifts from being a place of exploration to being a space of encounters and introspection. Marianne discovers that the man who called her, Thomas Rekowicz, and his daughter were the focal point of the events that led to the Niwa Massacre; she also discovers that they were her father and elder sister, respectively. By interacting with and talking to the Childeater or the Hound, who remained trapped on Niwa’s grounds, Marriane gathers evermore information, allowing the player to sort out the past events. The second part of the game is therefore more concerned with introspection and understanding Marianne’s origins and fate. This means that the nature of the challenges the player was expecting when they started the game, and responding to in the first part of the game, changes, altering from skill and dexterity based ones to cognitive and emotional ones (Cole et al. 2015). This can lead the player to shift their attention and engagement away from visual and ludic aspects of the game towards the story and the people it features, resulting in greater character attachment (Bopp et al. 2019), and to focus on eudaimonic gratification. However, in practice, the past ultimately eclipses the present, and the main character of the game is gradually overshadowed by other characters whose complex personalities and traumatic backstories demand increasingly more attention, judgment, and emotional responses from the player. As Marianne—together with the player—is relentlessly bombarded with more horrifying details and appalling secrets of the people who were strangers to her before she stepped into the resort but are now revealed to be somehow connected to her either through blood and love or through assault and hatred, the player learns nothing new about Marianne herself. At this point in the game, the story—and the narrative—is concerned with the past alone. Marianne has very little internal monologue that would shed light on how she is dealing with all the new information. If a comparison were to be made to a character in a similar situation, Heather Mason in Silent Hill 3 was also faced with discovering that there was much more to what she thought was her life, and had to quickly gain extensive intimate knowledge concerning the cruel, twisted history of family and her own birth before she had been, much like Marianne, taken away from a dangerous place by someone who wanted to protect her. There is much that Heather must understand and accept: the fact that she was previously another person, a young girl named Alessa, and that this girl was in so much pain due to the actions of her fanatical mother that her only wish was to die and thus escape her suffering. After the confrontation with the Memory of Alessa, Heather mentions how it is strange for her to refer to her former self as “Alessa”, since they are the same person, and adds: “‘You’ and I don’t think alike, after all … And it’s not that I don’t remember that sick room either …” (Silent Hill 3, 2003). In this way, Heather confirms what the player could previously only infer from her actions and spoken lines: the way she feels, what she thinks about her circumstances, and what her intentions will be as she continues her journey. In The Medium, Marianne does nothing of the sort, forcing the player to either guess or ignore her feelings and motivations. Such design strips her of subjectivity, rendering her experiences and feelings inconsequential. In practice, this means that for the player, who is in control of at least some of her actions, there is very little difference between Marianne as a character at the beginning of the game and halfway through the game.\n\nThis situation is, once again, consistent with the story told by The Medium; while the narrative of the game revolves around Marianne, the tragic story the creators attempted to convey concerns Thomas Rekowicz and his anguish over his powerlessness to protect his daughters. Marianne is more of a spectator than an actor in this drama. The push narrative continually provides the player with new information in order to sustain immersion in lieu of allowing them more agency; in these circumstances, Marianne continues to be the avatar, but never becomes the main character. Her role is limited to that of a high quality exploration tool. And even if this choice is fitting in regards to the narrative design of the game, it takes away from the game mechanics available to the player.\n\nThe Medium features an uneasy balance between its ludic and narrative elements, which continues to shift in favor of the narrative as the game progresses. The more justified the reasons for Marianne’s exploration of the depicted world, the fewer the tools that the game offers the player to influence the situations they participate in and their outcomes. This strategy does not seem to be directly aimed at player’s agency, or even constitute an attempt of subverting that agency, but rather is a logical outcome of adopting a particular hierarchy of narrative tools atypical to the genre. This seems to be confirmed by—among other things—the way the non-playable characters2 are structured, which conforms to the rules of quest design, but is used in a way more specific to gamebooks.\n\nAs a work of art The Medium is direct and explicit in its way of evoking an emotional response in the player. One of the most noticeable results of this is the fact that the characters encountered by the player in Niwa seem to be inspired by Propp’s structural units and the seven character functions (Propp 1968: 80). Despite the game’s tactful handling of its most sensitive moments, like the scene in which Thomas Rekowicz flips through Richard’s sketchbook which documents his abuse of Lilianne, or the way the game explains Henry’s childhood and twisted logic, it could still be argued that the characters themselves are presented very narrowly through the optics of their one specific role (Howard 2008: 71-72). The characters met by Marianne can be regarded in the context of those abstract functions, belonging to a limited catalog of archetypes (cf. Campbell 2008). For instance, the Maw can be regarded as a character which carries out the Villain function3, since it personifies the emotional rot and evil and continues to fight and pursue the Hero—who, in the case of The Medium, happens to Marianne. She is called by the Dispatcher (Thomas Rekowicz, who justifies her entire quest for exploration of and confrontation with the past of Niwa) to thwart the Villain and resolve the wronghoods. Naturally, this is an oversimplified take on the characters, not only due to the sheer fact that the syntagmatic analysis embedded in morphology of fairy tales was never meant to adequately explain the intricacies of interactive narratives incorporating ludic elements, but also due to the fact that a proper assigning of character functions in The Medium would require a more close examination of the distribution of those functions among multiple characters across different timelines (such as Spirit Thomas being a Hero in the past and the Helper in the Present) or one character being split into multiple characters who then serve different functions (as it is the case with Lilianne, whose character in the present may be interpreted as the Princess, but her child Spirit Self, Sadness, appears to play the role of the Donor to Marianne’s Hero, while the Maw, originating from Lilianne’s pain and the instinct to hurt the world that harmed her, constitutes the Villain that Marianne was summoned to defeat). In gameplay, on the other hand, The Medium’s directness manifests in its conspicuous linearity. The explicit nature of the storytelling entails the game’s reliance on push narrative and extremely tight narrative design, where the player’s movement and the amount of information they obtain is controlled very strictly. The use of horror convention, in which the game fantasy is realized through “cause-and-effect relationships suggested by the sequence of facts [that fantasy] details” (Govil-Pai 2006: 68), fulfills the function of a classic quest system, which results in the constant overlapping of the material world and the Spirit World. Consequently, the gameplay involves multiple timeline shifts to the point of obliterating the boundary between past and present, as mentioned previously. Even if the mid-game is structured like a typical Trial Narrative (van der Meer 2019), the use of classic cause-and-effect sequence (cf. Stepnowska 2017: 17-18) to represent the fantasy in the game means that between the linear delivery of new information and the rigid game progression the main questline of The Medium gradually becomes more and more like a railroad (cf. van der Meer 2019).\n\nAs a result, the sequences depicting the events of the past in which the player is in control of Spirit Thomas create an attractive break from this rigid progression. Due to his internal monologue and distinctive, cynical personality, Spirit Thomas may come across to many players as a more fleshed out, believable character, if not just more interesting in regards to his gameplay sections—even if he is available as a playable character only in a few selected sequences. The gameplay itself might also seem more satisfying whenever the player plays as Spirit Thomas, partially due to the novelty of locations within Richard’s mind and Henry’s mind—complete with new aesthetics, dangers and enemies—and partially because of the way in which the progress is rewarded with new information. It is also important to note that when the player takes control of Spirit Thomas, they already know the results and consequences of that character’s actions, even if those parts of the game create fully-fledged artistic experiences. It could be inferred that the sequences which employ Spirit Thomas as an avatar can be very satisfying immersive experiences for the specific type of players known as Immersion Seekers—including both subgroups—in accordance with the Gamer Motivation Model (Our Gamer Motivation Model, n.d.). In the context of the game’s plot, specifically the artistic arrangement of the order of exposition, the character of Spirit Thomas appears to be more coherent and credible; for the Fantasy players—again, in accordance with the Gamer Motivation Model—in turn, his role as avatar offers a new perspective on the gameplay and a welcome departure from the previous gameplay model.\n\nThere are many factors that both influence and, occasionally, constrain the player’s performance as they play the game. The traits of Marianne as a player character that are considerably distinct from the standard avatar characterization indicate the manner in which The Medium approaches the matter of the user experience design. From the designers’ perspective, the player gets immersed in the story rather than their own decisions, and Marianne’s essential function as the narrator of the game is continually reaffirmed by many elements included by game development. Additionally, the development solutions and animations of the main character clearly indicate which mechanics and visuals Bloober Team deemed to be crucial to conveying the story. For instance, Marianne may run into objects or even occasionally fail to bend her knees, but her animation of walking down the stairs is outstanding—which for a mid-budget production developed with Unreal Engine 4 is quite a development challenge—especially in moments crucial for building tension or ones constituting the metaphor of a rabbit hole. Both the cut-scene animations and the technical level design are, in this context, created with the utmost attention to detail, matching the standards of a work of art. In effect, The Medium delivers an impressive performance on its own while leaving little room for the players to perform. Even when the player has the chance to interact with the game world, they choose an item from a pop-up list when deciding on the possible interaction with a specific object (e.g. opening a lock). This solution might have been a standard one for story-centered games in the early 00s, but now prevails only in simple games (like hidden object or arcade games). This would place The Medium in the “wandering-through-story” category, as Jon Bannister calls it (Spigel 2005: 84), rather than one where the player shapes the story themselves. Of course, the above remarks by no means constitute a criticism of development solutions but are merely observations concerning the clearly well-defined priorities of the creative team.\n\nAs it is, the game tempo of The Medium is contingent on suspense and the player’s, and not the gameplay, progression. The puzzle quests themselves allow the player to tame the depicted world, but the lack of any progression of their difficulty level creates the impression that the given questline expresses itself like a walkthrough, providing the player with information essential to the actual gameplay. This further contributes to the impression that the focus of the game revolves around the game art, with history playing an important role, while playability and story—not so much. In terms of game design, as a result of its treatment of agency-expressing mechanics and their influence on the pacing of the story, The Medium appears to be an illustration of how not to pace a game.\n\nThe nature of this problem is also manifested in the fact that The Medium does not feature any actual boss battles, while there are sequences in the game which can be said to go against the player’s expectations in regards to the horror genre. An early example of this is the confrontation with the Childeater. This scene occurs after Marianne has learned what Richard did to Lilianne. Marianne and the Childeater trade some bitter words, accusations and excuses, all the while Marianne is held down by the Childeater’s slimy limbs. The audiovisual expressive vocabulary of the scene includes wide shots of Marianne restrained in the wheelchair, with more of the enemy’s tentacles slithering ominously behind her, juxtaposed with mid-shots and close-ups of Marianne’s face contorted in anger, hostility and disgust; the images are accompanied by unpleasant diegetic sounds and suspenseful music. This entire sequence, however, culminates in the following exchange:\n\nMarianne:\n\nThis man … Thomas … Who … What is he?\n\nChildeater:\n\nHe is the one who butchers the soul. The one who breaks it. But you … Yes, I know you … You can set me free … I can feel it. Please, do it.\n\nMarianne:\n\nYou don’t deserve it. You deserve nothing! Nothing, do you hear me?!\n\nChildeater:\n\nThen give it to me. Please … To not exist. That’s all I want.\n\nMarianne:\n\nSo be it. (The Medium, 2022)\n\nWith those words, Marianne opens her left fist, releasing a bright light which envelops the Childeater, herself, and eventually everything else, leaving the player looking at a blank screen, possibly pondering the Childeater’s final farewell: “Thank you, the girl from the red house” (The Medium, 2022). There is no confrontation, no satisfactory resolution from the gameplay point of view, despite the fact that the entire sequence is built up in a manner which the players can easily interpret as a prelude to a boss battle, based on their metagame knowledge.\n\nThe same issue comes into play later in the game, as The Medium offers no possible closure of the story- and gameplay-centered conflict introduced by the character of the Maw. From the ludic perspective, Marianne starts out with an objective and a series of quests: she is supposed to explore Niwa and grant the dead rest by sending their trapped spirits away. During this part of the game, the player becomes aware of a dangerous enemy—the Maw, a powerful hostile spirit entity that not only roams the Spirit World, where Marianne needs to regularly evade it by means of a couple of stealth mechanics, but also is able to partially exist in the material world. The ludic and aesthetic presentation and behavior of the Maw suggest to the player that they might at some point expect either a confrontation with that character—a final boss battle—or at least a final chase sequence, in which they could slip the Maw’s grasp once and for all. However, as Marianne’s work, represented in the gameplay as puzzles, is replaced with the preparation for what the player may presume to be her ultimate task—saving Lilianne—the player, by now emotionally invested, is denied more and more agency within gameplay, as well as, ultimately, a satisfying resolution of the story. Confronting the Maw—either by attacking it with the provided weapon or by stealing Lilianne away from its reach—is not an option available to the player. The lack of availability of interactivity thus translates into a lack of possibility of facing the main antagonist and only a number of lackluster interactions, which are few and far between. The Maw is supposed to be the primary antagonist, the evil haunting the site of the massacre, and the greatest threat to Marianne herself, seeing as it single-mindedly hunts her to take possession of her body. And yet, in the game whose scope (Bizzocchi and Tannenbaum 2011) can extend from ten to twelve hours, according to the official website, the total time of all interactions between Marianne and the Maw, taking into consideration every instance in which the two occupy a single location, spans only around eighteen to twenty-four minutes, depending on the player’s strategy and reflexes. Even taking into consideration the symbolic significance of the Maw, the gameplay does little to heighten, defuse, or resolve the tension between Marianne and the Maw in a meaningful manner that would be engaging to the player and fit the overall pacing of the story.\n\nThe aforementioned abrupt change of objective of the gameplay and the emphasis of the narrative creates another problem worth commenting on in this article. To better approach this matter it would be useful to consider two concepts related to aesthetic of reception: Eco’s Model Reader (Eco 1984) and Jauss’ horizon of expectations (Jauss 2005). Both of them can aid in examining the game tempo of The Medium—more specifically, the tension between the pacing imposed by the game and the pacing preferred by the player. Assuming that “every text is made of two components: the information provided by the author and that added by the Model Reader” (Eco 1984: 206), and taking into consideration that “the text postulates the presumptuous reader as one of its constitutive elements” (Eco 1984: 206), the gameplay is founded on the constant tension between the way the game progresses, telling its story through the narrative design the Model Player (Reader) would ideally follow and explore, and the preferences and expectations of the actual player, which contribute to that player’s horizon of expectations. This is a position unavoidable as far as the process of consuming any text of culture is concerned, seeing as\n\nthe new text evokes for the reader … the horizon of expectations and rules familiar from earlier texts, which are then varied, corrected, altered, or even just reproduced. Variation and correction determine the scope, whereas alteration and reproduction determine the borders of a genre-structure (Jauss 2005: 24).\n\nThe horizon of expectations emerges from what Jauss describes as the horizon of experience of the audience—in the case of a game text, the player; the horizon of experience consists of the entirety of the player’s previous experience gained from consuming other texts of culture, which builds their knowledge of conventions, structure, composition etc. that is then applied in the current process of gameplay. In case of games, this knowledge is particularly important due to the fact that a game “demands specific actions from the player for progression to occur”; this “contractual condition between game and player,” in Krzywinska’s words, differentiates the process of consuming a game text from the process of consuming texts of other media and, more importantly, profoundly affects the way in which the player expects the game to realize its potential and exert its effect (Krzywinska 2009: 270). In the case of a horror game, the player will have certain expectations regarding the manner in which the horror is going to be delivered, even if some of those expectations might be influenced by the expressive characteristics and narrative format of cinema, both of which tend to permeate the majority of the texts of the horror genre (Krzywinska 2009: 270). The same contractual condition, situated well within the player’s horizon of experience, will affect their playthrough of The Medium—while the game’s tense atmosphere, wide shots and particular camera angles, together with the overall aesthetics, will be readily accepted, if not welcome by the target audience, precisely due to their previous experience with other game texts of that genre, the same experience will surely render the lack of closure and confrontation as jarring and inadequate.\n\nThe horizon of experience is also a component of what Bourdieu refers to as cultural capital—in other words, the “familiarity with the internal logic of works that aesthetic enjoyment presupposes” (Bourdieu 1996: 2). In the particular case of games, the cultural capital of the player—which marks their horizon of expectations—is not limited to their familiarity with the genre, or other games belonging to it, but encompasses the knowledge of the world beyond the text itself: the history, geography, religion and politics, as well as the art of the country which is the point of reference for the game world. It is that knowledge which has the potential to shape the distinctive perception and interpretation of the signs, indices and symbols disseminated throughout game world, all of which in the case of The Medium refer to discernible aspects of Polish reality such as customs, the experience of the socialist era in Polish history, and religiousness. The same knowledge can invite the player to pursue passing references, indirect mentions, or intertextual connections included in the game, regardless of their actual function in the gameplay. Following and collecting cultural symbols which permeate the world of The Medium affects the pacing of the gameplay, which is then oriented more towards the search and scrutiny of cultural indices and signs that allow the player to embed the narrative and gameplay in the extratextual context than towards following the narrative design from one event to another. It is also likely that for the global player community the better part of the multitude of the signs and symbols mentioned above, largely inaccessible to people who lack the intimate knowledge of the genre, as well as of the Polish pop culture of the 80s and 90s, may be difficult to decipher and therefore bear little significance for their experience and interpretation of the game. The same signs and symbols can, however, constitute an important separate dialogue within the knowledge discourse between the creative team of Bloober Team and the reviewers, specifically the Polish ones.\n\nAnother issue worth discussing and one that is quite peculiar from the designers’ perspective is the manner in which The Medium uses the inertia of player choices. For the purpose of this article “inertia” will refer to the distance between the player making a decision on whether or not to take action, and the game world feedback concerning that particular decision, measured in the number of decision nodes between the decision itself and the feedback. Inertia is one of the factors influencing the gameplay tempo, and can signal the extent to which the game world is open and developed. The Medium features only a few nonlinear moments of exerting the player’s agency throughout the game, and the ones available affect only the immediate gameplay experience. And although it is inconsequential to discriminate between “superior” and “inferior” inertia, The Medium gameplay is paced by means of tools associated with cinematic texts rather than game texts, which means that the nature of inertia encountered in the game resembles much more the kind one would expect and appreciate in a film text. The game steers the player through its world through a cinematic narrative format and expressive apparatus, rather than engaging narrative design. This leads to an effect opposite of the one that would be normally desirable in the case of a game text—not only does it reinforce the impression that the puzzle quests are of no consequence in the context of the game as a narrative (the necessary hints are always nearby and do not require an extensive knowledge of the history of the Niwa resort or the personalities of the characters crucial to the story), but also it the changes the game tempo in favor of reactive elements at the cost of interactive ones. More specifically, the emphasis shifts from the operationalizable decisions of the player to the aesthetics, specifically the audiovisual representation. This shift increases the ludonarrative dissonance since the rate at which the story unfolds speeds up regardless of the player’s participation; at this point, the player is not so much making choices that would be rewarded with a noticeable change of the gameplay pace, as being pushed along by the plot.\n\nThis situation additionally affects the player’s perception of choices themselves, which by now appear binary as informed by the previously mentioned trial narrative structure. The Medium includes only one ending proper, without any flavors that would influence the experience of that ending (in contrast to, for example, the possible ending flavors of Silent Hill 2: “Leave”, “In Water,” and “Maria”). In contrast, there are at least five game-over scenarios, all of which put an end to the gameplay before the final resolution. Some of them include being captured by the Maw in the Spirit World or in the material world, or being overwhelmed by spirit moles; in both cases the player loses their avatar as the protagonist dies, thus failing the game. The game-over scenarios for the protagonist in The Medium are fairly typical for the horror game genre. Meanwhile, the other game-over scenarios concern a different avatar—Spirit Thomas. In the sequences where Marianne’s visions show her the past, the player relives fragments of Thomas Rekowicz’s life, which means they have the opportunity to control Spirit Thomas. The player can fail the game by getting Spirit Thomas killed in Henry’s or Richard’s mind, if they cannot avoid the dangers of those virtual environments. These moments, despite being only game-over scenarios, seem more relevant to the plot of the game, and can reinforce the positive negative experience. Unfortunately, none of the game-over scenarios constitute sufficient feedback in terms of gameplay; as a result the player knows they are limited to one, “correct” path, even if this was not the deliberate intention of the game development team.\n\nThe above issue is probably related to the emphasis on the artistic value of the final product. The visual aspect of level design in The Medium is artistic to a high degree, which corresponds with the game’s clear aspirations; the recreation of Hotel Orbis “Cracovia,” the clear inspirations drawn from Beksiński, as well as the impressive performance by Rosati and Dorociński, all confirm that The Medium appears to be primarily an art-driven experience, featuring a story that the player follows, instead of leading it (cf. Jenkins 2004). The game aesthetics (in a broad sense of the term cf. Schell (2008)) come together to create an impressive work of art at the cost of the game’s interactivity.\n\nLinear stories in speculative game texts are not uncommon. In well-balanced games the linear nature of the game’s main story is rarely an issue—the majority of the games mentioned in this article tend to rely on narratives that unfold in a more or less linear manner. Even if the game offers the player only one specific way to progress through it, and only one specific ending, the narrative experienced by the player is not a singular entity (Nitsche 2008: 45). The player needs to comprehend the game world and whatever occurrences or encounters which take (or have taken) place within it—the context and significance are determined by the player, contributing to the meaningfulness of the resulting experience. As Nitsche also points out, “[w]hile the reader of a novel is limited to the given text, the player of a game interacts with [the] evocative elements, cocreates them, and changes them. Whatever manifests itself in the shape of this comprehension is of a unique nature.” (Nitsche 2008: 44-45). In The Medium, meanwhile, one can readily observe the underlying drive to generate strong emotions through narrative elements rather than through interaction or particular game mechanics. The story of the game is meant to elicit complex negative emotions in order to exert its effect, a crucial part of which is the player’s appreciation of the sad narrative, involving “tender feelings and, more precisely, feelings of being moved” (Cova et al. 2017: 356). As such, the dominant narrative of The Medium, with its themes of loss, sacrifice, abuse, and anguish, aims at producing a specific “blend of cognitive activity … and affective states” (Cova et al. 2017: 356). As the player progresses through the game, experiencing and performing the unfolding story, they are meant to “reflect on meaningful questions” and experience “the feelings of being moved” (Cova et al. 2017: 356), thus achieving a sense of eudaimonic gratification associated with art—perhaps this is why the narrative in The Medium appears as decidedly linear. As a result of this ambitious premise, the game attempts to make meaning by engaging the player with emotionally powerful narrative moments, expressed in the form of aesthetically and visually captivating cut-scenes. The camera movements and angles used during those cut-scenes are meant to establish a poignant, distressing or sorrowful atmosphere, and, together with music, signal the significance of the events on screen in the context of the entire story of The Medium. A memorable example of this is one of the game’s most moving scenes, in which at the end of the game Marianne finds Spirit Thomas, the only remnant of her father, confined in the special bunker; the very first words of Spirit Thomas are those of concern:\n\nSpirit Thomas:\n\nIt’s you. You’re alive.\n\nMarianne:\n\nThomas?\n\nSpirit Thomas:\n\nIn a way. Yes.\n\nMarianne:\n\nWait, you’re the other one. The spirit. But the Hound … I thought you were gone.\n\nSpirit Thomas:\n\nGone? No. Trapped. (The Medium, 2022)\n\nThis scene actually constitutes the beginning of the game’s story as told by Marianne up to that point, both through cut-scenes and her narration throughout the game. The player can immediately realize that they are about to not only witness a conclusion to an important story element of the game, but also be subject to the full emotional impact of this particular narrative component of the game, which the story so far encouraged them to engage with. The meeting of Marianne and Spirit Thomas is a scene that is both satisfying to witness and sorrowful to experience, taking into consideration that the protagonist just missed the opportunity to meet Thomas Rekowicz by so little in the context of space and time in the game world. As such, Spirit Thomas, despite being evidently different from Thomas Rekowicz, takes on the role of a father figure for Marianne, who is the baby that had been left behind, and for the player, who is not only the actor, but also the spectator. Wide camera shots are replaced with mid-shots, and then close-ups, as the music swells at the very end, when Spirit Thomas assures Marianne that Thomas Rekowicz loved both his daughters very much. When eventually Spirit Thomas urges Marianne to flee, so that he can delay the Maw and guarantee her safety for at least a little while, Marianne is too emotionally attached to simply leave him behind:\n\nSpirit Thomas:\n\nIt’s coming. Time for you to go. I’ll hold it off for as long as I can.\n\nMarianne:\n\nI’m not leaving you!\n\nSpirit Thomas:\n\nYou can’t always save everyone, butterfly. Trust me, I know. And … I’m sorry. (The Medium, 2022)\n\nImmediately after this apology, Spirit Thomas pushes Marianne out of the Spirit World against her will, and away from himself so that he can stand between her and the Maw, presumably sacrificing himself for her. Thus, in such a relatively short but undeniably touching sequence—where last horizontally split shot shows a close-up of Marianne’s face in the material world, reflecting complex feelings as Spirit Thomas holds her hands and calls her “butterfly”, and a close-up of Spirit Thomas’s soft smile as he looks at her—The Medium elicits a whole range of complicated, predominantly negative affective reactions for the player to contemplate and attempt to reflect upon. This moment is evidently one of the few in which the creators seem to have shifted the emphasis from interactivity and agency to expression of powerful concepts and emotionally engaging experiences.\n\nAs the art overtakes the story’s place, one can deliberate on the moments in gameplay that benefit from this approach and the ones that lose some of its quality because of it. It is worth emphasizing that—very uncommonly for the genre—The Medium foregoes the importance of the narrative in favor of its art as an informed decision. The game director, Wojciech Piejko, stated openly that the team set out to design “the game like a movie, planning the best shots, the best camera angles” (Wales 2020). The decision to prioritize the cinematic aspects of the game results in decreasing The Medium’s potential as a meaningful interactive experience, sometimes even making it present itself more like an interactive fiction movie than a game text.\n\nIn games, there exists a necessity for “gateways between player and game system”, in the form of game interfaces (Nitsche 2008: 33). Players can interact with game spaces in two ways; one of them is movement through a space. Movement dominates the gameplay of The Medium, as Marianne traverses the space of Niwa in the material world and in the Spirit World, collecting clues and items. She then sometimes uses those items and navigates the two worlds separately, thus engaging in what Nitche refers to as “specialized manipulation of elements within [the] space” (Nitsche 2008: 33). In this way the player interacts with the game system and is rewarded with more pieces of the backstory, but such solution grants little satisfaction in terms of influencing the emerging narrative, or understanding Marianne’s motivations, since the backstory improves the player’s comprehension of the past–and even some of the present–events, but does not establish Marianne as a believable central character exploring those events.\n\nThis peculiar backstory of the game world, combined with the prevailing push narrative and limited ambiguity, leads to a very strained ending. Since everything is either shown, disclosed, or explained to Marianne directly, sometimes more than once (e.g. the origin of the Maw is suggested through echoes of the past in the Red House once, and then explained again twice by Spirit Thomas and later Lilianne herself), the game places little emphasis on the player’s interpretation of the information and active inference. There are simply not enough evocative narrative elements in the form of either situations, scenes or items that would “support and possibly guide the player’s comprehension” of the narrative; as Nitsche explains,\n\n[the] elements’ task is to improve a player’s experience and understanding of the game world. Players encounter and read these elements, comprehend the information in the context of a fictional world, and learn from them as they build contextual connections between elements (Nitsche 2008: 37).\n\nThe narrative of The Medium does not require the player to build any contextual connections. The story is instead pushed unto the player, and it seems to start and end without needing any player’s input. As a result, the gameplay merely supports the story, as it explores itself in front of the players, not because of their choices or actions. As Marianne arrives at the pier at the lake from her dreams, looking for her sister, the player has yet to make any significant connection, discovery, or choice of their own. Upon finding Lilianne, the sisters have a lengthy conversation, during which Lilianne fills in any of the gaps in Marianne’s—and the player’s—understanding of what had taken place in Niwa. During this cut-scene Lilianne, clearly depicted as exhausted and filled with anguish, gives Marianne a gun, asking the protagonist to free her from her agonizing existence by ending her life, since it is impossible for Marianne to send the Maw away as long as Lilianne lives:\n\nLilianne:\n\nIt all ends in me.\n\nMarianne:\n\nBut … No … NO!\n\nLilianne:\n\nYou can’t send a spirit away while the host is still alive. That’s why you couldn’t destroy the monster. That’s why Sadness didn’t want to go.\n\nMarianne:\n\nBut … You’re my sister!\n\nLilianne:\n\nThat’s why it has to be you. I— I’m not strong enough. It won’t let me. Only you can end this. Only you can fix what our father could not.\n\nMarianne:\n\nLilianne … I can’t. Please don’t make me do this.\n\nLilianne:\n\nI’m sorry. It’s the only way to destroy it. To prevent further bloodshed. (The Medium, 2022)\n\nAt this point, the Maw reaches the two sisters, proclaiming Marianne to be its perfect host; it continues to threaten her, dismissively referring to Lilianne as “old skin suit”, while Lilianne herself continues pleading with Marianne to “set her free”. The player can see Marianne putting the gun to her own head and threatening to kill herself, aware that the Maw needs her body to leave Niwa. The scene, from the moment of the Maw’s arrival, is shown in vertical split screen. This time, however, the single point of view depicts single subject; depending on the characters’ movements and the camera movements and angle, the players can see Marianne and other characters as they are in either the Spirit World, which this time occupies the dominant (left) part of the screen, or in the material world. The cut-scene constitutes the actual end of the game, never allowing the players to make the choice they would naturally expect at this point of gameplay, based on their metagame knowledge. Instead, in extreme close-up, Marianne opens her eyes, the screen goes blank, and the player can hear a single gunshot.\n\nIn this way, the game deprives Marianne—the main character of the story and the player’s character—not only of her present, but also of her future, regardless of her role as a player character (no choice is offered to the player) or as a character proper; she quite possibly ends her life in this moment, and if she lives, the game is not interested in her fate enough to inform the player of it. This radical artistic and design choice would fit a different audiovisual medium text, such as a film or a TV series, but falls flat in the case of a game. The Medium undoubtedly excels at creating what Jørgensen refers to as “positive discomfort” (Jørgensen 2019: 155). The game follows a script resembling very much that of a film matching the conceptual and aesthetic horror convention, enriched with attributes of interactivity. In a broader perspective of the pleasures of horror, it is worth considering the distancing factor in various artworks—be it literature, film, or game texts; according to Crowther, distance is what “momentarily invests the object with the character of representation rather than that of real physical existence” (Crowther 1993: 123). With this in mind, it is conceivable to reason that there is a purpose to the way Marianne is objectified by the game’s storytelling; the fact that her character is instrumental, inert in terms of agency (both her own and the one she would provide to the player as an avatar), and stripped of subjectivity facilitates the creation of an atmosphere of horror and tension without increasing the stakes concerning the game progress. Playing The Medium, the player can experience the “shudders and shocks”, as Crowther notes—or, in Burke’s words, “delightful horror, a sort of tranquillity tinged with terror” (Burke 1999: 123)—of a horror scenario “without running for the exit, because [they] know that the frightening phenomena are representations rather than realities” (Crowther 1993: 123). And yet digital games are unquestionably a medium that is known to permit “the sense of safety to be challenged both on the level of fiction and on the level of play”; this translates into their capacity for creating positive discomfort (Jørgensen 2016) which reaches beyond the representation and mirroring fright and unease, allowing for dissonance, impotence, and opposition as well. The players can experience discomfort in a game—either positive or negative—either as a sense of frustration stemming from being prevented from taking action they would deem as “right” or necessary, and instead “being the victim of the bad decisions made by nonplayer characters” (Jørgensen 2019: 159), or as a result of the sense of complicity (Isbister 2016: 8-10) caused by the “feeling that the events that unfold in the game happen because of the player’s choices” (Jørgensen 2019: 158). Regardless of whether it is the player’s agency or the very lack thereof that leads to the discomfort, the deliberate attempt to cause displeasure in the player is meant to inspire their reflection (Jørgensen 2016), contributing to the eudaimonic gratification they might seek. Positive discomfort is often employed in speculative games, especially in the horror genre, but the manner in which it is implemented in The Medium is far from optimal4.\n\nIn their research on the legitimacy of causing discomfort to the player, Gowler and Iacovides created a research tool taking into account various aspects of game design that participate in causing discomfort (Gowler and Iacovides 2019). In a similar manner, for the purpose of this article, 5,292 Steam user reviews have been examined5, all written by people who purchased the game. Among 719 unambiguously negative reviews, 80 mentioned the lack of agency, and 177 alluded to the ludonarrative dissonance. The users commented on the gameplay sophistication lagging behind the artistic aspect of the game, as they rated the game’s elements as graphically appealing, with a decent story and nearly non-existent gameplay, or claimed that it was easy to realize that the repetition of some elements is just a placeholder to create the illusion of a bigger gameplay.\n\nOf course, random individual comments do not reflect the reception of the game by the mass audience; however, a Steam review deemed by the community as one of the “most helpful” ones does summarize the majority of the problems of The Medium, describing it as a disappointing walking simulator-like experience, dressed up as a horror game, strongly emphasizing that it lacks game-like experience.\n\nThe leisurely paced endgame gameplay, intended to give the player time to appreciate the aesthetics of the game, might have been indeed, in the optics of game design, “enriched” with puzzle quests during the late stage of the game development. The players’ reception of the puzzles featured in The Medium appears to reflect a similar idea—the majority of reviews (1022) is rather neutral, pointing out their low difficulty level. Nonetheless, many reviews (677) emphasize the illusory nature of the choices involved in the puzzle solving, or even—according to some (410)—their pointlessness. Another Steam review labeled as “most helpful” highlights the frustration caused by the puzzle design, triggering the feeling of being treated by the game in a very condescending way by offering a single story with a single ending, forcing the player to push ahead in one direction only and, whenever the player stops in a location to solve a puzzle, by taking the players’ agency away, without offering the possibility to fail, assess one’s mistakes or discover the solution on their own.\n\nOn the other hand, the main struggle, namely gameplay sequences involving the Maw, is reduced to an obstacle quest with wasted potential—both in terms of the resolution of the narrative conflict and engaging gameplay. The game creators might have quite possibly aspired to introduce what Hopeametsä calls “positive negative experience” (Hopeametsä 2008: 191). This type of experience would be a good fit for a live game where the players are able to aim at a personalized in-game resolution; however, in a single player game, it clashes with conventional understanding of meaningful play Salen Tekinbaş and Zimmerman (2003). In fact, the common reading of the term “positive negative experience” as proposed by Montola (and referred to by Hopeametsä) implies the possibility of frustration—even one caused by game rules—being the catalyst of a personalized narrative experience.\n\nWhether the introduction of the positive negative experience does indeed meet the expectations of the target audience in the case of The Medium is a question worth considering. According to Montola, the players\n\nbelong to a subculture of gamers that is convinced of the value of non-fun games. They aim for intense experiences, regardless of their supposed emotional valence, and for them, the value of negative emotions is larger than just giving meaning to the subsequent positive twists (Montola 2010: 7).\n\nThe number of Steam reviews, both utterly positive and utterly negative might suggest that the positive negative experience employed in The Medium does resonate with some of the players, but antagonizes others. Additionally, the manner in which the Bloober Teams implemented the positive negative experience appears to support this assumption. The focus on the almost theatrical take on the artistic aspect of the game at the expense of the experience of agency and gameplay, even in spite of the possibility of frustrating the players, might not necessarily be a mistake of any kind, but simply compliance with the positive negative experience trend specific to aesthetic-centered games (cf. Umbelino and da Mota 2021).\n\n\nConclusion\n\nAs we include game texts among other works of art we need to take a closer look at their specific traits and affordances. There are game texts that aspire to touch upon serious sensitive subject matter; in their ambitious attempt to do this in a way specific to the game medium, they build upon works of art of other media, but make use of unique tools available only to their own medium. In the case of digital games the point of contact between the artist intention and the audience experience is just as important as in the case of any other work of art. This article has used as its case study The Medium, a game doubtlessly polished and well thought out as far as its artistic value is concerned. The creators of The Medium made it clear in interviews and other materials that they wanted their game to convey a certain important message. However, as Rothschild and colleagues point out, “the moment a game is available for an audience to play … control passes out of the hands of the designers of the experience and into the hands of those who take that experience and bring to it their own desires, ideas, and interpretations” (Rothschild et al. 2013: 84). This is a normal phenomenon regardless of whether or not the game’s content and form are balanced. In the case of The Medium, the players’ interpretation of the story told by the game does not seem to coincide exactly with the creators’ intentions, despite the fact that Marianne, as a character, is an active obstacle to bringing the player’s ideas and interpretations into the game, since, as the only character lacking a developed Spirit Self who could confront or advise her, she is an instrument of exploration of the game instead of being the subject of the player’s exploration. Piejko explains that\n\nthe team is striving to deliver something deeper too. “Playing as a medium will give you a very unique perspective that’s beyond the reach for ordinary people, and so the game’s statement is that there is no universal truth,” he explains, “there is always some grey area, and we think this topic is super-important right now when we are bombarded by media trying to shift our perspectives. “Sometimes if you crop a photo correctly it gives you a completely different message, so in The Medium we raise this topic, and the story is crafted so that the player will reveal more and more information which will change their perspective on what happened in the game and their opinion about the other characters.” (Wales 2020).\n\nDespite Piejko’s explanation concerning the lack of universal truth, it is actually difficult to identify how the gameplay is supposed to illustrate that premise. Regardless of different personal and visual perspectives included in the game, the information imparted on the players through push narrative is presented as reliable and is therefore implied to be objective—instead of, for instance, reading Thomas’ diary, the player actually re-enacts the given events as Marianne experiences them first-hand in her visions. At no point does Marianne—and, more importantly, the player—drastically change her opinion or a rigid attitude towards another character, or have to reevaluate a past event. Similarly, at no point does the player change their opinion of Marianne, since she continues to be a reliable narrator for the entire duration of the game (in contrast to, for instance, James Sunderland in Silent Hill 2, whom the player supports in his search for Mary, only to find out near the end of the game that it was James himself who killed her). The interpretation of the past is clear and presents all characters as either morally justified or morally despicable, with the only truly morally debatable choice—ending Lilianne’s suffering or condemning her to a desolate, tormented life—being still easily put into perspective within either rational, responsible context, or an emotional, misguided one. In the end, Piejsko’s description of the game seems to constitute a truism more than a statement in the postmodern era.\n\nNaturally, the control over the content and the message of the game, like any other work of art, does not belong to any single party since the meaning is made by all participants. The intention and expression of the artist(s) command neither more nor less respect than what the audience experiences. Therefore,\n\nthe element of “control” does not reside solely with the player (player choice, agency, and meaning construction) or with the game (designed experiences). Rather, control in a game play experience is an interplay of designed experiences and player projection that result in the player’s interpretation of the game’s narrative space (Rothschild et al. 2013: 83).\n\nIn case of a game text the importance of content of the game (the depicted world and the characters within, as well as their fate) and the message that is supposed to be conveyed matching the form (proper tools of the game medium and appropriate formal blocks) is particularly critical. This translates into the significance of matching the atmosphere and the subject matter of the game to the most compatible genre, which would meet the player’s expectations and fittingly shape the gameplay experience. Otherwise, the resulting work might constitute a moving story, but not a moving game. The Medium is an example of an aesthetically remarkable work of art involving choices either illusory or abandoned. The narrative structure itself does appear to match the serious subject matter and the genre to which the game belongs; however, the lack of intervals between the subsequent quests might not only fatigue the player, but also contribute to the impression of spectatorship taking precedence over exploration and interaction. The overabundance of puzzle quests, combined with the sustained illusion of some of them constituting important parts of Marianne’s journey, translates into a situation where the player is presented with gripping content, but not the relevant toolkit that would be represented by the game mechanics.\n\nThe most obvious manifestation of the illusory nature of agency in The Medium is perhaps the way in which Marianne finds out that her father was also a medium; the player does indeed look for and collect the necessary clues in order to unlock the relevant information—i.e. to learn Thomas Rekowicz’s backstory—but that search is so linear and unavoidable in the context of the questline that it is, in the end, exclusively reactive in nature. The interactive aspect of that activity consists in running into those clues; this might not be an actual error of development construction, taking into consideration Bateman’s idea of following Physical Trails of Breadcrumbs (Bateman 2021: 96-97); however, the pretense of non-linearity is negatively affected by the lack of partial rewards along the questline and the way Thomas’ backstory is presented in the scene meant to constitute the reward for the player’s efforts so far. This questline and the relevant gameplay are the part of the game in which the impression of being led by the story instead of actively uncovering it is particularly strong.\n\nDue to the fact that linearity and the impression of being led by the game story are highly subjective in nature, it is helpful to refer to opinions of the players. In addition to the qualitative content, they also provide quantitative perspectives on some of the matters discussed in this article. Even limiting the data to the comments available only on The Medium’s Steam page, 149 out of 5,292 Steam comments taken into consideration for the purpose of this text mention linearity, or even railroading, in regards to mechanics relevant to searching and using clues. As one of the players states, the only way they could fail a given quest would be if they “ate the hints.”\n\nThe Medium is undoubtedly a multi-layered work of art—specifically in the sense used by Kalinowski, which would classify it as a composite artwork (cf. Kalinowski 1981: 476). Many components of The Medium—or platforms—are positioned in a structural opposition to the gameplay; this takes away player’s agency, interferes with the natural pacing of the game, and renders the story- and mechanics-related decisions ostensibly illusory and irrelevant.\n\nIt is also worth mentioning that in October 2022 Bloober Team announced the upcoming adaptation of The Medium as a TV series. This change of medium might prove more than beneficial for the particular story the creators of the game set out to tell, especially taking into consideration the narrative and audiovisual tools which can be employed in a TV series to create an immersive experience. The Medium, being a beautifully crafted—and much needed in the audiovisual discourse—story is just the work of art that might achieve a much greater success in conveying its message and refining its symbolic aspects in the TV series format than as an interactive drama.\n\nThe aim of this article was to identify and examine selected problems that emerge at the intersection of art, ambition and gameplay design. The two most prominent issues visible in many serious speculative games, which are especially conspicuous in the game that served as the primary example for this text, include the collision of the creator’s intentions with the audience experience. This is naturally not exclusive to games, but the nature of games as a medium makes this problem more jarring, and the potential negative consequences for the player experience when the game text fails to meet the contractual condition and thus the player’s expectations—more far-reaching. There are many benefits to studying those problems in more detail, but one of the most substantial findings in the context of this particular article are the observations that can realistically contribute to better, more informed decisions concerning adopting game design solutions and tailoring game content to respective game genres. Keeping those conclusions in mind can lead to games maturing and evolving as a medium—both as a part of the entertainment industry and as a mode of expression in terms of art.", "appendix": "Data availability\n\nNo data are associated with this article. The article presents a case study and relies on close reading of the secondary texts. 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Proceedings of the Annual Symposium on Computer-Human Interaction in Play. 2019, October; pp. 325–337.\n\nGovil-Pai S: Principles of Computer Graphics: Theory and Practice Using OpenGL and Maya®. Germany: Springer US; 2006.\n\nHopeametsä H: 24 hours in a bomb shelter. Playground worlds. Helsinki: Ropecon; 2008; pp. 187–198.\n\nHoward J: Quests: design, theory, and history in games and narratives. AK Peters, Ltd.; 2008.\n\nIsbister K: How games move us: Emotion by design. MIT Press; 2016.\n\nJauss HR: Literary History as a Challenge to Literary Theory. Toward an Aesthetic of Reception. University of Minnesota Press; 2005.\n\nJørgensen K: The positive discomfort of spec ops: The line. Game studies. 2016; 16(2).\n\nJørgensen K: When Is It Enough? Uncomfortable Game Content and the Transgression of Player Taste. Transgression in Games and Play. 2019; pp. 153–167. Publisher Full Text\n\nKalinowski L: O możliwościach odczytywania dzieła sztuki. Tessera. Sztuka jako przedmiot badań. 1981; 106–120.\n\nKrzywinska T: Reanimating Lovecraft: The Ludic Paradox of Call of Cthulhu: Dark Corners of the Earth. Horror video games: essays on the fusion of fear and play. 2009; pp. 267–287.\n\nMarkocki M: Reactive games as an example of extensive use of evocative narrative elements in digital games: cases of Dwarf Fortress and RimWorld. Studia Humanistyczne AGH. 2021; 20(2): 71–83. Publisher Full Text\n\nMontola M: The positive negative experience in extreme role-playing. Proceedings of Nordic DiGRA 2010, Stockholm, Sweden, 16-17 August 2010. 2010; pp. 1–8.\n\nOliver MB, Bartsch A: Appreciation as audience response: Exploring entertainment gratifications beyond hedonism. Hum. Commun. Res. 2010; 36(1): 53–81. Publisher Full Text\n\nOur Gamer Motivation Model: Quantic Foundry. n.d. Retrieved November 12, 2022. Reference Source\n\nOwaku H: Silent Hill 2. PlayStation 2, Xbox, PlayStation 3, PC, Xbox 360. Konami.2001.\n\nOwaku H: Silent Hill 3. PlayStation 2, PC. Konami.2003.\n\nOziewicz M: Speculative fiction. Oxford Research Encyclopedia of Literature. 2017.\n\nPamięta-Borkowska J: Dysonans ludonarracyjny - co to takieg? Czyli polemika z tekstem sprzed 11 lat. 2019. March 2023. Reference Source\n\nPropp VI: Morphology of the Folktale. Vol. 9. . University of Texas Press; 1968.\n\nRothschild M, Ochsner A, Gray J: It’s all part of the game: the emergence of narrative and meaning in play. Ctrl-Alt-Play: Essays on control in video gaming. 2013; pp. 83–95.\n\nSandvoss C: The death of the reader. Fandom: Identities and communities in a mediated world. 2007; pp. 19–32.\n\nSpigel L: Tv’s Next Season? Cine. J. 2005; 45(1): 83–90. Publisher Full Text\n\nStepnowska T: Spory o istotę i granice światów przedstawionych fantastyki. Tekstowe światy fantastyki, pod red. Mariusza M. Lesia, Weroniki Łaszkiewicz i Piotra Stasiewicza. Wydawnictwo PRYMAT; 2017; pp. 11–21.\n\nSupermassive Games: The Dark Pictures Anthology: House of Ashes. PlayStation 4, PlayStation 5, Xbox One, Xbox Series X/S, PC. Bandai Namco Entertainment.2021.\n\nUmbelino MA, da Mota RR : Negativity in Play-How Negative Emotions create Meaningful Games. Anais Estendidos do XX Simpósio Brasileiro de Jogos e Entretenimento Digital. SBC; 2021, October; pp. 152–161.\n\nVan der Meer A: Structures of Choices in narratives in gamification and games. “UX Design”.2019. DOA Jenuary 2023. Reference Source\n\nWales M: Layers of Fear dev Bloober talks its Xbox Series X survival horror throwback The Medium. 2020. DOA September 2022. Reference Source\n\n\nFootnotes\n\n1 The flat at the beginning of the game is a perfect example of spatial past. The game takes place in the late nineties, and the virtual environment of the apartment is full of signs and indices referring to the specific time in Polish history; however, by being so peculiar they become practically invisible on the global scale symbolism–especially for players from outside the former Soviet bloc. Cultural capital of most of the Polish players includes familiarity with the legitimate local culture depicted in the socio-historical context of the apartment as the setting of the story, e.g. the icon of Black Madonna of Częstochowa, “Solidarity” banner and pins, soviet tea glass holders, or possible association with Wisława Szymborska’s poem “Cat in an Empty Apartment.”\n\n2 Whereas non-player character is a character not controlled by a player, a non-playable character is one that is not meant to be the player’s avatar, and lacks the necessary mechanics and skills of a playable character.\n\n3 Interestingly, the characters of the Maw and the Childeater function as complementary manifestations of the same function an antagonist may serve, even though in the context of the game story those are two different beings.\n\n4 Both the sub-optimal implementation of positive discomfort and the focus on game art in the mid-game increase the ludonarrative dissonance. In words of Pamięta-Borkowska, the very essence of ludonarrative dissonance–in the context of game development–lies in the unintentional nature of its occurrence (Pamięta-Borkowska 2019). Bloober Team might have actually knowingly allowed the emergence of this ludonarrative dissonance, but it is still worth to examine the benefit of this decision in the context of the end user experience.\n\n5 The number of reviews analyzed as of the time of writing the article." }	[ { "id": "198507", "date": "26 Sep 2023", "name": "Raine Koskimaa", "expertise": [ "Reviewer Expertise Game studies", "temporality in digital fictions", "reader-response 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\nThis article has merits in how it addresses the ludo-narrative dissonance in the case of a specific game (The Medium), and how the subject matter and genre expectations play a role in there. The case the authors are making is, that implementing a complex narrative concerning serious subject matter into playable game faces fundamental problems, which are related to the expectations raised by the horror game genre where The Medium belongs. In addition to the game analysis, there is a promise of looking also at \"the experiences, ideas, and interpretations the players themselves bring to the game text\", and this is supposed to take place through a data set of 5000+ reviews of the game available in the Steam platform.\nThe biggest problem with the draft as it is, is the imbalance between these two approaches. The game analysis is conducted in a detailed way, occupying majority of text, whereas the highly promising player review material is mentioned almost as a side thought. Furthermore, as a consequence of the game analysis emphasised, there are long passages basically just describing the game world, events and characters. These descriptions should be shortened significantly, but then, a couple of screenshots from the game (illustrating the split screen technique, for example) would be highly helpful.\nIt is problematic, that the argumentation is built upon what the players expect of the game belonging to horror genre (\"fails to fulfill the expectations of the player\"), but then most of the discussion seems to be based upon researcher experience. Researcher play is, of course, wholly acceptable method for doing game analysis, but with strong evaluative comments, the draft tends to go close to an elaborate piece of game review.\nAs there is the extensive work done with the Steam reviews, it would be highly recommendable to incorporate that material much more in the text. If it would be possible to base the argumentation explicitly on the Steam review findings, this would be a genuinely important contribution to game studies.\nBelow, I provide some more detailed questions and comments:\nThroughout the text, the authors emphasises the blankness of the main character as a handicap in design. This is, however, not automatically a design failure, as there are numerous examples of a blank character employed in an effective manner. In this case there would even be an explicit motivation for that, as Marianne is a medium, channeling various things. This is one of the main issues, where examples from the Steam reviews would be necessary, to substantiate the claim.\n“The Medium as a narrative does not allow for any ambiguity in its story” – Not any ambiguity? Still you claim that “Within the narrative of The Medium, there are few moments or places of ambiguity, apart from the very ending, which unfortunately in itself makes the resolution of tension impossible.” So some ambiquity, after all?\n“She [Marianne] literally occupies the same space and time.” – this is one of the places where the temporal structure of the game is highlighted, revealing problematic complexities: what does it mean that Marianne occupies “the same space and time”? The same as…? (Later on, “Appropriately, the time and space in The Medium do not merge, but overlap, the past being always superimposed on the present”). Without deep knowledge of the game, it seems that there are two distinct ontological levels (real life / spirit world), both of them with their own temporality (even though the spirit world is focusing on the past events, it seems to have a continuum of its own). Also, in what sense do time and space “not merge but overlap”? It is probably not the necessary to engage in a deep analysis of the temporality in The Medium for the purposes of the article, but it might be worth mentioning some of the temporal characteristics, as it is a feature of the game not typical of horror games.\n“Marianne without an independent Spirit Self becomes the exception that proves the rule, making her even more unique. However, this uniqueness limits the potential for ambiguity in The Medium even further” – This is unclear. If the player cannot gain insight into Marianne's personality, doesn't this leave room for ambiguity? “In The Medium, Marianne does nothing of the sort, forcing the player to either guess or ignore her feelings and motivations. Such design strips her of subjectivity, rendering her experiences and feelings inconsequential. In practice, this means that for the player, who is in control of at least some of her actions, there is very little difference between Marianne as a character at the beginning of the game and halfway through the game.” -- How does this differ from the \"iceberg\" technique of Hemingway and others, limiting the narration to the events taking place, and leaving all psychologizing for the reader to conceive? Wouldn't it rather be in line of the serious subject matter not to explain everything but leaving the implications for the player to ponder upon? Isn't this a major case of ambiguity (which there is supposedly not)?\n“This strategy does not seem to be directly aimed at player’s agency, or even constitute an attempt of subverting that agency, but rather is a logical outcome of adopting a particular hierarchy of narrative tools atypical to the genre.” -- I don't understand this. What are the \"narrative tools\" which are \"atypical to the genre\"?\n“This seems to be confirmed by—among other things—the way the non-playable characters are structured, which conforms to the rules of quest design, but is used in a way more specific to gamebooks.” – Please, elaborate!\n“also due to the fact that a proper assigning of character functions in The Medium would require a more close examination of the distribution of those functions among multiple characters across different timelines (such as Spirit Thomas being a Hero in the past and the Helper in the Present) or one character being split into multiple characters” -- This seems to be in direct contradiction with the previous claim that the characters \"are presented very narrowly through... one specific role\".\n“Whereas non-player character is a character not controlled by a player, a non-playable character is one that is not meant to be the player’s avatar, and lacks the necessary mechanics and skills of a playable character.” – I don’t get this.\nThe passage where Gamer Motivation Model is mentioned in relation to the Spirit Thomas, does not appear helpful for readers not familiar with the model (including a reference to two subgroups, which are not explained in any way). If this is considered so important that it cannot discarded, then the model should be briefly opened up here.\n“From the designers’ perspective, the player gets immersed in the story rather than their own decisions” -- What would it mean, if the case was that the players gets immersed in their own decisions?\n“Marianne’s essential function as the narrator of the game is continually reaffirmed by many elements included by game development.” -- Could you mention some examples of these elements here?\n“This further contributes to the impression that the focus of the game revolves around the game art, with history playing an important role, while playability and story—not so much.” -- Based on your own account, the story seems interesting and intricate enough.\nIn terms of game design, as a result of its treatment of agency-expressing mechanics and their influence on the pacing of the story, The Medium appears to be an illustration of how not to pace a game.” -- The pacing appears in several places, but it is not clearly explained -- does \"contigent on... the player's... progression\" simply mean, that there is no time limit, but the player may use as much time as she wishes for solving the puzzles (in Aarseth's term, transient time)? Or the opposite (intransient time)? If so, isn't this simply stating that you don't like games with in/transient time? In any case, this reads much more like a game review than analysis.\n“at this point, the player is not so much making choices that would be rewarded with a noticeable change of the gameplay pace, as being pushed along by the plot.” -- Why would a change in the gameplay pace be a reward? I have a feeling, that you are using the term \"pace\" in some idiosyncratic way I don't get.\n“This entire sequence, however, culminates in the following exchange: [excerpt from game dialogue]” -- There are parts cut out from the exchange, which contain quite obvious intertextual reference to the opening words of Lolita by Nabokov. It is not the aim of this paper to provide a full-fledged interpretation of the game, but this kind of allusion to a well-known work providing the perspective of a childmolester might still be worth mentioning here.\n“while the game’s tense atmosphere, wide shots and particular camera angles, together with the overall aesthetics, will be readily accepted, if not welcome by the target audience, precisely due to their previous experience with other game texts of that genre, the same experience will surely render the lack of closure and confrontation as jarring and inadequate.” -- This is exactly the kind of argument, which should be supported by the large empirical data you have collected from Steam.\n“The same signs and symbols can, however, constitute an important separate dialogue within the knowledge discourse between the creative team of Bloober Team and the reviewers, specifically the Polish ones.” -- What is this referring to? Has there been some public discussion between the designers and reviewers in Poland?\n“And although it is inconsequential to discriminate between “superior” and “inferior” inertia, The Medium gameplay is paced by means of tools associated with cinematic texts rather than game texts, which means that the nature of inertia encountered in the game resembles much more the kind one would expect and appreciate in a film text.” -- What do you mean by this distinction between superior and inferior inertia? What are the tools (associated with cinematic texts) that you refer to? What kind of inertia is appreciated in film texts? Please, be more specific.\n“Unfortunately, none of the game-over scenarios constitute sufficient feedback in terms of gameplay;” -- What do you mean by \"sufficient feedback in terms of gameplay\" in game-over scenarios?\n“The game aesthetics (in a broad sense of the term cf. Schell (2008)) come together to create an impressive work of art at the cost of the game’s interactivity” -- This is now very thoroughly described in the previous dozen pages, and it would be interesting to hear what the players (in Steam) are saying about this obvious imbalance.\n“This scene actually constitutes the beginning of the game’s story as told by Marianne up to that point,” -- This is unclear.\n“This moment is evidently one of the few in which the creators seem to have shifted the emphasis from interactivity and agency to expression of powerful concepts and emotionally engaging experiences.” -- I am puzzled. I thought the whole argument above has been, that the designers have sacrificed interactivity for engaging storytelling throughout the game?\n“This radical artistic and design choice would fit a different audiovisual medium text, such as a film or a TV series, but falls flat in the case of a game” – Again, is there support in the Steam materials for this claim?\n“the fact that her character is instrumental, inert in terms of agency (both her own and the one she would provide to the player as an avatar), and stripped of subjectivity facilitates the creation of an atmosphere of horror and tension without increasing the stakes concerning the game progress.” -- I don't understand this, what do you mean by “increasing the stakes concerning game progress”?\n“Positive discomfort is often employed in speculative games, especially in the horror genre, but the manner in which it is implemented in The Medium is far from optimal.” -- The argumentation in this whole paragraph would need much clarification; it is not clear now, what is exactly the reason for the \"less than optimal\" implementation of positive discomfort in The Medium. This seems to be the key passage in this article, so it would be crucial to clarify this paragraph.\nIt is a shame that the highly interesting Steam player review material is not properly presented and discussed. One would assume, that much more could be said about 700+ negative reviews, not to mention the even more interesting group of mixed reviews. It seems very strange, that such a big and important part of the research is this quickly mentioned in the article. I would suggest writing a whole chapter/section about the reviews, providing a proper qualitative analysis of it. And at the same time, the description of the game events could be much shortened, this way there could be a better balance between the game analysis and the review analysis.\n“According to Montola, the players ‘belong to a subculture of gamers that is convinced of the value of non-fun games…’” -- Which players? I assume Montola is writing about LARP players.\n“The focus on the almost theatrical take on the artistic aspect of the game at the expense of the experience of agency and gameplay, even in spite of the possibility of frustrating the players, might not necessarily be a mistake of any kind, but simply compliance with the positive negative experience trend specific to aesthetic-centered games” -- This is interesting, but would require more thorough discussion. It seems that there are two different phenomena discussed (and easily confused); the negative feelings caused by the serious, horrible subject matter, and negative feelings caused by the frustration with the design choices; these may come together in a meaningful way, but it is not clear here, if you want to say that it is the case in The Medium.\n“In the case of The Medium, the players’ interpretation of the story told by the game does not seem to coincide exactly with the creators’ intentions, despite the fact that Marianne, as a character, is an active obstacle to bringing the player’s ideas and interpretations into the game, since, as the only character lacking a developed Spirit Self who could confront or advise her, she is an instrument of exploration of the game instead of being the subject of the player’s exploration.” -- Is this based on the Steam reviews? Or purely on the researcher reading of the game?\n“At no point does Marianne—and, more importantly, the player—drastically change her opinion or a rigid attitude towards another character, or have to reevaluate a past event.” -- Earlier it is said, that there is no access to Marianne's mind in the game, so how is it possible to evaluate if she changes her opinions or not?\n“Similarly, at no point does the player change their opinion” -- Again, is the \"player\" here some sort of combination of the Steam reviewers, or the researcher-player?\n“Even limiting the data to the comments available only on The Medium’s Steam page, 149 out of 5,292 Steam comments taken into consideration for the purpose of this text mention linearity, or even railroading, in regards to mechanics relevant to searching and using clues. As one of the players states, the only way they could fail a given quest would be if they “ate the hints.”” -- This would be super important to look into in much more detail.\n“Many components of The Medium—or platforms—are positioned in a structural opposition to the gameplay” – What do you mean by “platforms“ here? Why is it added?\n“the game text fails to meet the contractual condition and thus the player’s expectations” -- This contractual condition would require elaboration earlier in the text\n“observations that can realistically contribute to better, more informed decisions concerning adopting game design solutions and tailoring game content to respective game genres.” -- And these observations are? It would be good to give a summary of them here in the Conclusions.\nIf the results of the game analysis would be based, or supported, by the findings in the reviews, then this would be a really strong article, with original contribution.\nConcepts to define: ludonarrative, pull & push narrative\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nIs the work clearly and accurately presented and does it cite the current literature? 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\n\nIs the case presented with sufficient detail to be useful for teaching or other practitioners? Yes", "responses": [ { "c_id": "10807", "date": "13 Apr 2024", "name": "Miłosz Markocki", "role": "Author Response", "response": "Thank you for your detailed review and the interesting suggestions. Your remarks were very helpful in improving our text. We have included as many suggestions as possible—however, the inclusion of some information would negatively affect the overall cohesion of the paper. One of such remarks is the one concerning space and temporality of the Spirit and material world, and the way they coexist in the game. The phrase we use (merge not overlap) has been chosen precisely for its semantics, i.e. the actual meaning of the verbs (“to merge” in the sense of joining things together to form one thing, and “to overlap” in the sense of parts of one thing covering parts of the other). The next remark we decided not to include was the question regarding ambiguity and the “iceberg” technique. To be on the safe side, we have made some adjustments concerning the nature of ambiguity in the text. However, we decided against mentioning the Hemingway’s “iceberg” technique. That technique allows the reader to recognize and judge the character’s motivation, based on the observation of the character’s actions; in contrast, The Medium relies on suspense in order to cast ambivalent light onto the characters. Whereas a literary text places the reader in the position of a spectator, removed from the events, actions, and their consequences, a game projects the player into the depicted world, making them both accountable for and complicit in those events. Therefore, limiting the insight into the character’s emotional state diminishes the player’s emotional investment in that character and restricts the space for cognitive attempts at interpreting the game plot as the story of Marianne’s character. As far as the questions regarding game pacing are concerned, for the purpose of the text we use the term “game pacing” as time between an action relevant to game mechanic, its in-game result and next repetition of decision making in regard to the same tool (it is not the same as the metrum of the game). The game pacing needs to be coherent in the context of the game genre and its quest structure. In our eyes it isn’t a matter of opinion, but well established patterns in game design. We have also decided against elaborating on the intertextual connections between The Medium and Nabokov’s Lolita. The literary and cultural allusions in games such as The Medium tend to be of largely fictional nature; they are meant to draw the player’s attention to the clear connotations with renowned texts of culture. In this context invoking Nabokov’s Lolita as an emblematic modern novel about a child predator allows the player to identify the theme of the game, just like the conversation between the child herself with her abuser points the audience to an archetypal (in the Euroamerican cultural framework, at least) pray-predator exchange known from Little Red Riding Hood. In this way the game facilitates the focus on key story elements, ones that are crucial from the point of view of the gameplay experience. We have also made appropriate adjustments in the text that further clarify the perspective of our analysis by mentioning the inclusion of the examination of letsplays. The aim of including letsplay videos was to avoid personal biases of the authors, and to help distinguish potential biases from the elements that are contingent more on the game text than on the scholar’s personal engagement with the game (Marak 2021: 217-218). In regards to Marianne changing—or not changing—her opinion we rely on the utterances included in the game as constitutive parts of the text itself. If a character does not say something explicitly, we do not attribute a particular attitude to them. Regarding the remarks and suggestions concerning the Steam reviews, we have made appropriate changes where necessary when it was possible to do so without compromising the coherence and cohesion of the respective passages. Sometimes, unfortunately, elaboration would require not only extensive quoting, but also introducing wider immediate context. Additionally, despite the excellent suggestion to focus more on the qualitative study of Steam reviews, the sheer number of them (as well as the fact that mixed reviews are unfortunately not recognized as a category on Steam). Lastly, as far as terminology is concerned, we have made appropriate adjustments, providing definitions of push and pull narrative. We have not elaborated on the concept of contractual condition, which is originally defined on page 11 of the PDF file, in order to avoid awkwardness in the passage." } ] }, { "id": "189933", "date": "10 Oct 2023", "name": "Mirosław Filiciak", "expertise": [ "Reviewer Expertise Media sudies", "game studies", "media archaeology", "cultural studies", "research on media practices and infrastructure" ], "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 touches on the interesting and perhaps still under-represented in the literature topic of speculative video games that touch on serious issues, suggesting that this medium is particularly predestined for this. This combination, however, does not always necessarily produce a satisfying result, as is shown in a meticulous, multi-faceted analysis of the game The Medium. I admit that at times perhaps all too detailed, as the length of a text devoted to essentially one game is somewhat overwhelming. For the most part, however, this material has been brought under control, and in addition to a close reading of the game, the authors also refer to analyses from the Steam platform.\nThe Authors elaborate well on the main theme, related to the illusory agency offered to players in the title under analysis. Also, reaching for reviews from the Steam platform is undoubtedly a good choice, which has allowed a very large sample to be collected (I was quite impressed to learn that these reviews were reviewed manually). A solid job has been done on the literature. What I found a little lacking in the conclusion was a broader view, moving further away from the example analysed and considering to what extent the tools and research insights developed can be applied to other games or their specific type. Despite these minor comments, my assessment of the whole is unequivocally positive.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\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? Yes\n\nIs the case presented with sufficient detail to be useful for teaching or other practitioners? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-784
https://f1000research.com/articles/12-1137/v1	12 Sep 23	{ "type": "Clinical Practice Article", "title": "Endovascular management of aortic aneurysm with severe neck angulation and/or iliac artery tortuosity using multiple stiff wire technique: a case series", "authors": [ "Taofan Taofan", "Suko Adiarto", "Iwan Dakota", "Suci Indriani", "Jonathan Edbert Afandy", "Achmad Hafiedz Azis Kartamihardja", "Sung-Gwon Kang", "Renan Sukmawan", "Suko Adiarto", "Iwan Dakota", "Suci Indriani", "Jonathan Edbert Afandy", "Achmad Hafiedz Azis Kartamihardja", "Sung-Gwon Kang", "Renan Sukmawan" ], "abstract": "Background: Suitable aortic neck is one of the essential components for thoracic endovascular aortic repair (TEVAR) and endovascular aortic repair (EVAR). Advanced techniques were developed to adjust and compromise the aneurysm neck angulation but with adding additional devices and complexity to the procedure. We proposed a simple technique to modify severe neck angulation and/or iliac artery tortuosity by using the multiple stiff wire (MSW) technique. Method: Two femoral accesses were required for the MSW technique. A guidewire with a support catheter was inserted through the right and left femoral arteries and positioned in the abdominal or thoracic aorta. Wire exchanges were done with extra stiff wire in both femoral accesses. It can be considered to add multiple stiff wires to align the torturous neck / iliac artery. Delivery of the stent graft main body can be done via one of the accesses. Result: Six patients with different aortic pathology were admitted to our hospital. Four patients undergo EVAR procedure and two patients undergo TEVAR procedure. All patients had aortic neck angulation problems with one patient having iliac artery tortuosity. MSW technique was performed on the patients with good results. Follow-up CTA after 3 months revealed a good stent position without stent migration and no endoleak was found in all but one patient. Conclusion: MSW technique is a simple and effective technique to modify aortic neck/artery angulation in TEVAR or EVAR procedure.", "keywords": [ "TEVAR", "EVAR", "neck angulation", "artery tortuosity", "multiple stiff wire technique" ], "content": "Introduction\n\nThe endovascular aortic repair (EVAR) technique has been developed for over 30 years since the first report by Parodi, et al.1 and recommended over open surgical repair by 2022 ACC/AHA Guideline for the Diagnosis and Management of Aortic Disease2 in descending thoracic aortic aneurysm (TAA), ruptured descending TAA, abdominal aortic aneurysm (AAA), and ruptured AAA. A suitable aortic neck is one of the essential components for EVAR and hostile neck anatomy has been related to early graft failure and long-term adverse events.3 Stent graft collapse, stent graft migration, type I endoleak, and late aneurysm rupture appear to be linked with severe neck angulation.4\n\nNowadays, advanced techniques were developed to adjust and compromise the aneurysm neck angulation such as kilt technique which involves aortic-cuff stent-graft implantation before aortic main-body stent-graft implantation, and endostapling technique to reinforce device seal and fixation.5,6 But, those techniques add additional devices and complexity to the procedure. We proposed a simple technique to modify severe neck angulation and/or iliac artery tortuosity by using the multiple stiff wire (MSW) technique with reports of application in six patients.\n\n\nMethods\n\nTwo femoral accesses were required for the MSW technique. Then, a guidewire with a support catheter was inserted through the right and left femoral arteries and positioned in the abdominal or thoracic aorta. Wire exchanges were done with 0.035″ × 260 cm Lunderquist Extra Stiff Wire (Cook Aortic Interventions, Bloomington, USA) in both femoral accesses. It can be considered to add multiple stiff wires to align the torturous neck/iliac artery. Delivery of the stent graft main body can be done via one of the accesses. After the main body deployment, the contralateral extra stiff wire can be withdrawn from the access then contralateral limb extension cannulation and deployment can be done as required.\n\n\nCase presentation\n\nAn 83-year-old woman was presented to the emergency department with abdominal pain that radiate into both lower limbs in the last hour. The patient had a history of hypertension and dyslipidemia. CT-Scan Angiography (CTA) revealed an abdominal aorta aneurysm from the inferior of superior mesentric artery until aortic bifurcation with length of 10.8 cm and maximum sac diameter of 7.4 cm and fusiform aneurysm of bilateral common iliac artery (CIA) with right diameter of 1.1 cm and left diameter of 1.5 cm. Infrarenal neck length is 22 mm with angulation of 85° (Figure 1A). The patient then prepared for EVAR procedure.\n\nA. Preoperative volume rendering computed tomography angiography (CTA); B. Initial aortography; C. Aortography showed reduction of the proximal neck angulation after insertion of the second stiff wire; D. Stent graft main body deployment; E. Final aortography; F. Follow up volume rendering CTA after three months.\n\nThe EVAR procedure was done with right and left femoral access that was gained with surgical cutdown technique. Initial aortography revealed a fusiform aneurysm at infrarenal abdominal aorta with short and tortuous neck (Figure 1B). The MSW technique with two stiff wires was done to align the tortuous proximal neck (Figure 1C). An Endurant II ETBF 23 mm × 13 mm × 145 mm stent graft main body (Medtronic, Santa Rosa, CA, USA) was deployed via right femoral artery (RFA) access (Figure 1D). The extra stiff wire from left femoral artery (LFA) was withdrawn and canulation for contralateral limb extension with guide wire was done. An Endurant II ETLW 16 mm × 13 mm × 93 mm stent graft extension (Medtronic, Santa Rosa, CA, USA) was inserted and deployed overlapped with the main body from the neo bifurcation to the left CIA. The right Endurant II ETLW stent graft extension sized 16 mm × 13 mm × 93 mm (Medtronic, Santa Rosa, CA, USA) was deployed from the right femoral artery overlapped with the main body. Evaluation aortography revealed type IA endoleak and left CIA wasn’t filled completely. A stent graft balloon catheter was inserted from the LFA and few intrastent post dilatation was done at infrarenal abdominal aorta and proximal of the CIA. Another evaluation aortography was done and eventually, there still was type IA endoleak. It was decided to add another Endurant II ETCF 25 mm × 25 mm × 49 mm stent graft extension (Medtronic, Santa Rosa, CA, USA) proximal from the main body. Final aortography revealed a good position of the stent grafts, both renal and iliac arteries were filled with contrast, and no sign of endoleak was found (Figure 1E).\n\nThe patient was discharged without any complaints. The follow-up CTA after 3 months revealed stent expansion of 19.3 mm at infrarenal aorta (maximum diameter was 60.2 mm), good stent position without stent migration and no endoleak was found (Figure 1F).\n\nA 55-year-old man presented to our hospital with stomach fullness and back pain in the past 2 weeks. The patient had a stomach massage before, but it didn’t relieve his symptoms. The patient denied history of hypertension and diabetes, but he was a smoker. CTA revealed a contained rupture of abdominal aortic aneurysm with intraluminal thrombus with a length of 10.32 cm and maximum sac diameter of 10.1 cm (maximum vascular diameter filled with contrast was 6.49 cm), Infrarenal neck length is 18.9 mm with angulation of 70.2° (Figure 2A). The patient then prepared for EVAR procedure.\n\nA. Preoperative volume rendering computed tomography angiography (CTA); B. Initial aortography with two stiff wire showed straightening of the proximal neck angulation; C. Stent graft main body deployment; D. Final aortography; E. Follow up volume rendering CTA after three months.\n\nThe EVAR procedure was done with puncture from right and left femoral access. The MSW technique was applied to this patient. Initial aortography revealed a contained rupture of aortic aneurysm at infrarenal abdominal aorta with enough length but tortuous neck (Figure 2B). A SEAL Bifurcated Stent Graft sized 28 × 50 mm (S&G Biotech, Yongin, Korea) main body was deployed via RFA (Figure 2C). The extra stiff wire from LFA was withdrawn and canulation for contralateral limb extension was done. SEAL Bifurcated Stent Graft extension 12(16) × 120 mm (S&G Biotech, Yongin, Korea) was inserted from left femoral artery access and deployed until the distal part was right above left internal iliac artery. The right stent graft extension with SEAL Bifurcated Stent Graft extension 12(16) × 120 mm (S&G Biotech, Yongin, Korea) was inserted from the RFA and deployed until the distal part was right above right internal iliac artery. Evaluation aortography revealed that contras filled the whole cover stent without endoleak, but the distal part of the right limb extension didn’t expand perfectly. After several post-dilatation was done with Reliant Stent Graft Balloon (Medtronic, Santa Rosa, CA, USA), the right limb extension expanded perfectly (Figure 2D). The EVAR procedure was done without any complications.\n\nThe patient was discharged without any complaints. Follow-up CTA after three months revealed stent expansion of 33.5 mm at infrarenal aorta (maximum diameter with thrombus was 69 mm), no stent migration, and no endoleak was found (Figure 2E).\n\nA 69-year-old man presented to our hospital with stomach fullness accompanied by nausea and vomiting in the last three months. The patient also had a complaint of a palpable non-pain lump in his stomach. He denied history of hypertension or diabetes, but he was an ex-smoker. There was a palpable pulsatile mass in the abdominal region. CTA revealed dissection of abdominal aorta aneurysm with a length of 6.99 cm and maximum sac diameter of 5.95 cm (maximum vascular diameter filled with contrast was 3.89 cm), infrarenal neck length is 5.00 mm with angulation of 75.4° (Figure 3A). The patient then prepared for EVAR procedure.\n\nA. Preoperative volume rendering computed tomography angiography (CTA); B. Initial aortography with two stiff wire showed straightening of the proximal neck angulation; C. Stent graft main body deployment; D. Final aortography.\n\nThe EVAR procedure was done with puncture from right and left femoral access. The MSW technique was applied to this patient. Initial aortography revealed an aortic aneurysm at infrarenal abdominal aorta until bilateral CIA with enough length but tortuous neck (Figure 3B). SEAL Bifurcated Stent Graft 24 × 50 mm main body (S&G Biotech, Yongin, Korea) was deployed via RFA (Figure 3C). The extra stiff wire from LFA was withdrawn and canulation for contralateral limb extension was done. SEAL NOVUS Flared Limb Stent Graft extension 12(20) × 120 mm (S&G Biotech, Yongin, Korea) was inserted from LFA access and deployed until the distal part was right above left internal iliac artery. The right stent graft extension with SEAL NOVUS Flared Limb Stent Graft extension 12(20) × 100 mm (S&G Biotech, Yongin, Korea) was inserted from the RFA and deployed until the distal part was right above right internal iliac artery. Post-dilatation was done with balloon catheter in left CIA. Evaluation aortography revealed that contras filled the whole cover stent without endoleak (Figure 3D). The EVAR procedure was done without any complications.\n\nThe patient was discharged without any complaint. Unfortunately, the patient declined the evaluation CTA because of patient’s malignancy related condition that was diagnosed after the EVAR procedure, but he didn’t have any complaint related to the aortic or vascular disease after 3 months follow-up.\n\nA 71-year-old man was referred to our outpatient clinic with a pulsatile mass in lower left abdomen. The patient had a stable condition. CTA revealed impending rupture of fusiform abdominal aorta aneurysm with a length of 9.11 cm and maximum sac diameter of 6.3 cm (maximum vascular diameter filled with contrast was 3.63 cm), infrarenal neck length is 2.27 mm with angulation of 50°. The access site was tortuous and heavily calcified (Figure 4A). The patient was prepared for elective EVAR and percutaneous transluminal angioplasty.\n\nA. Preoperative volume rendering computed tomography angiography (CTA); B. Initial aortography; C. After stent impalntation, arteriography revealed stenosis at left CIA; D. Iliac stent graft deployment; E. Final aortography; F. Follow up volume rendering CTA after three months.\n\nThe EVAR procedure was done with right and left femoral access that was gained with surgical cutdown technique. Initial aortography revealed a fusiform aneurysm at infrarenal abdominal aorta with stenosis at both CIAs (Figure 4B). Several plain balloon dilatations were done at both CIAs to facilitate the delivery of the stent graft main body. SEAL Novus stent graft main body sized 24 mm × 50 mm (S&G Biotech, Yongin, Korea) were deployed with SEAL bifurcated stent graft extension 12(18) × 100 mm (S&G Biotech, Yongin, Korea) until left CIA and SEAL bifurcated stent graft extension 12(16) × 100 mm (S&G Biotech, Yongin, Korea) until right CIA. Arteriography revealed there was still stenosis at left CIA (Figure 4C). It was decided to add another stent at left CIA, but there was dificulty to pass the lesion. MSW technique was used to align the left CIA using Radiofocus Extra Stiff Wire 0.035″ × 260 mm (Terumo, Somerset, NJ). Dynamic 10 × 56 mm stent graft (Biotronik, Berlin, Germany) was implanted at left CIA (Figure 4D). Final aortography revealed a good position of the stent-grafts, both renal arteries and iliac arteries were filled with contrast, and no sign of endoleak was found (Figure 4E).\n\nThe patient was discharged without any complaint. Follow-up CTA after 3 months revealed stent expansion of 23.0 mm at suprarenal aorta, 30.8 mm at infrarenal aorta (maximum diameter with thrombus was 59.1 mm), 28.8 mm at aortic bifurcation, 9.3 mm at right CIA, and 9.9 mm at left CIA, no stent migration, and no endoleak was found (Figure 4F).\n\nA 63-year-old man presented to our hospital with tearing chest pain that radiate to his back in the past 3 days. The patient had a history of hypertension and he was a smoker. CTA revealed an aortic aneurysm with extensive mural thrombus with aorta descendent’s maximum diameter of 53.5 mm, thoracoabdominal aorta maximum diameter of 92.5 mm, suprarenal aorta maximum diameter of 98.1 mm, infrarenal aorta maximum diameter of 51.8 mm, with angulation of 70.2°, and suspected rupture at peritoneal and thorax cavity (Figure 5A). The patient was than prepared for thoracic endovascular aortic repair (TEVAR) procedure.\n\nA. Preoperative volume rendering computed tomography angiography (CTA); B. Initial aortography with two stiff wires; C. Additional stiff wire was added to straighten the angulation; D. Stent graft deployment; E. Final aortography; F. Follow up volume rendering CTA after three months.\n\nThe TEVAR procedure was done with puncture from right and left femoral access. The MSW technique was applied to this patient. Initial aortography revealed an aortic aneurysm at descending thoracic aorta until abdominal aorta (Figure 5B). Additional stiff wire was added with a total of three stiff wires used to straighten the aorta (Figure 5C). SEAL Thoracic Stent Graft 36 × 200 mm (S&G Biotech, Yongin, Korea) was deployed at descending thoracic aorta (Figure 5D). Evaluation aortography revealed good stent position but there was type IV endoleak. Observation for 10 minutes was done, and another evaluation aortography revealed no more endoleak (Figure 5E). The TEVAR procedure was done without any complications.\n\nThe patient was discharged without any complaint. Follow-up CTA after 3 months revealed stent expansion of 18.2 mm at aorta descendent (maximum diameter with thrombus was 56 mm), stent expansion of 29.4 mm at thoracoabdominal aorta (maximum diameter with thrombus was 88.2 mm), no stent migration, and no endoleak was found (Figure 5F).\n\nA 45-year-old man presented to our hospital with lower abdominal pain radiating to epigastric in the past 3 months that getting worse in the past 3 days. The patient had undergone TEVAR with indication of Stanford A acute aortic dissection 2 years earlier. CTA revealed an impending rupture of pseudoaneurysm sized ±7 × 12 cm with leakage from the distal part of the previous TEVAR stent with 85.9° angulation of the aorta, distal from the previous stent (Figure 6A). The patient was then prepared for an extension TEVAR procedure.\n\nA. Preoperative volume rendering computed tomography angiography (CTA); B. Initial aortography; C. Two stiff wire was added to straighten the angulation; D. Stent graft deployment; E. Final aortography; F. Follow up volume rendering CTA after three months.\n\nThe procedure was done with puncture from right brachial, right and left femoral access. Initial aortography revealed dissection of the descending thoracic aorta with an entry tear from the distal of the previous TEVAR stent (Figure 6B). Wire snaring was done from the right brachial artery to the right femoral artery. Wire exchange was done with the 0.035″ × 300 cm Lunderquist Extra Stiff Wire (Cook Aortic Interventions, Bloomington, USA) and additional extra stiff wire was inserted from the left femoral artery (Figure 6C). SEAL Thoracic Stent Graft 36(32) × 130 mm (S&G Biotech, Yongin, Korea) was deployed at descending thoracic aorta until abdominal aorta, overlapped with the previous stent (Figure 6D). Evaluation aortography revealed good stent position without any endoleak (Figure 6E). The TEVAR procedure was done without any complications.\n\nThe patient was discharged without any complaint. Follow-up CTA after 3 months revealed stent expansion of 30.8 mm at aorta descendent (maximum diameter with thrombus was 98.7 mm), stent expansion of 33.9 mm at thoracoabdominal aorta (maximum diameter with thrombus was 114.3 mm), no stent migration, and no endoleak was found. There was an abdominal aortic aneurysm sized 47.33 mm at supra renal and 43.5 mm at infrarenal (Figure 6F). The patient didn’t have any complaints.\n\n\nDiscussion\n\nEVAR with severe neck angulation was associated with a significantly higher rate of type 1a endoleak until 2 years, neck-related secondary procedure until 3 years, migration rates until 1 year, aneurysm-related and all-cause mortality until 1 year, but not related to aneurysm sac increase and rupture.7 High-tortuosity neck in TEVAR also has its problem related to a significantly higher proportion of endoleaks, a potential risk factor for proximal stent-graft collapse or infolding, renal failure, stroke, longer operation time, and lower survival rate.8,9\n\nData from the ANCHOR trial showed that the use of Aptus Heli-FX EndoAnchor System (Medtronic, Santa Rosa, CA, USA) was associated with higher but not significant 2 years rate of freedom from type Ia endoleak, neck dilation, and sac enlargement compared to the control group.10 The Kilt technique appeared to significantly straighten neck angle without leaving additional death or re-intervention during 22 ± 15 months follow up and no newly developed endoleaks during 15.9 ± 16.4 months follow up.11 Although those techniques showed a good result to overcome the angulation of the aortic neck, they add additional complexity to the procedure, specialized devices, need special training for the operator, and also greater cost of the procedure. Several proposed simple novel techniques such as directional tip control technique, push-up technique, and using a large bore sheath to untwist tortuous iliac arteries seem promising but need further investigation.4,12,13\n\nOur MSW technique provides a simple solution to manage neck/artery angulation. It can be used in the thoracic aorta, thoracoabdominal aorta, abdominal aorta, or iliac artery. Our experience applying the technique in six different scenarios showed satisfactory results. There is no type I endoleak, stent migration, or enlargement of the aneurysm size found after follow-up CTA in all but one of our patients. The determination of how many stiff wires would be used in the procedure is based on operator judgment until the tortuosity of the vessel were straighten enough to facilitate stent graft deployment. It is important to always cover the stiff wire with a catheter, so the stiff wire didn’t contact directly with the vessel and the risk of dissection was reduced. We also recommend oversizing 20% of the main body stent graft to create an optimal seal between the stent graft and the aortic wall.\n\nFurther studies will be made for the MSW technique with a larger population and study design. Clear indications should be made with the straightening degree calculation of the technique.\n\n\nConclusion\n\nMSW technique is a simple and effective technique to modify aortic neck/artery angulation in TEVAR or EVAR procedure.\n\n\nConsent\n\nWritten informed consent has been obtained from the patients for publication of the case and accompanying images.", "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. CARE checklist for ‘Endovascular management of aortic aneurysm with severe neck angulation and/or iliac artery tortuosity using multiple stiff wire technique: a case series’. DOI: https://dx.doi.org/10.6084/m9.figshare.23925234.\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\nWe would like to thank the patients for allowing us to have their cases published.\n\n\nReferences\n\nParodi JC, Palmaz JC, Barone HD: Transfemoral intraluminal graft implantation for abdominal aortic aneurysms. Ann. Vasc. Surg. 1991; 5(6): 491–499. PubMed Abstract \| Publisher Full Text\n\nIsselbacher EM, Preventza O, Hamilton Black J, et al.: 2022 ACC/AHA Guideline for the Diagnosis and Management of Aortic Disease: A Report of the American Heart Association/American College of Cardiology Joint Committee on Clinical Practice Guidelines. Circulation. 2022 Dec 13; 146(24): e334–e482. Publisher Full Text\n\nde Vries JPPM : The Proximal Neck: The Remaining Barrier to a Complete EVAR World. Semin. Vasc. Surg. 2012; 25(4): 182–186. PubMed Abstract \| Publisher Full Text\n\nTakayama T, Phelan PJ, Matsumura JS: Directional tip control technique for optimal stent graft alignment in angulated proximal aortic landing zones. J. Vasc. Surg. Cases Innov. Tech. 2017; 3(2): 51–56. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJeon YS, Cho YK, Song MG, et al.: Clinical Outcomes of Endovascular Aneurysm Repair with the Kilt Technique for Abdominal Aortic Aneurysms with Hostile Aneurysm Neck Anatomy: A Korean Multicenter Retrospective Study. Cardiovasc. Intervent. Radiol. 2018; 41(4): 554–563. PubMed Abstract \| Publisher Full Text\n\nChaudhuri A, Kim HK, Valdivia AR: Improved Midterm Outcomes Using Standard Devices and EndoAnchors for Endovascular Repair of Abdominal Aortic Aneurysms with Hyperangulated Necks. Cardiovasc. Intervent. Radiol. 2020; 43(7): 971–980. PubMed Abstract \| Publisher Full Text\n\nBernardini G, Litterscheid S, Torsello GB, et al.: A meta-analysis of safety and efficacy of endovascular aneurysm repair in aneurysm patients with severe angulated infrarenal neck. PLoS One. 2022 [cited 2023 Jun 14]; 17(2): e0264327. Free Full Text Publisher Full Text \| PubMed Abstract \|\n\nChen CK, Liang IP, Chang HT, et al.: Impact on outcomes by measuring tortuosity with reporting standards for thoracic endovascular aortic repair. J. Vasc. Surg. 2014; 60(4): 937–944. PubMed Abstract \| Publisher Full Text\n\nUeda T, Fleischmann D, Dake MD, et al.: Incomplete Endograft Apposition to the Aortic Arch: Bird-Beak Configuration Increases Risk of Endoleak Formation after Thoracic Endovascular Aortic Repair1. Radiology. 2010; 255(2): 645–652. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMuhs BE, Jordan W, Ouriel K, et al.: Matched cohort comparison of endovascular abdominal aortic aneurysm repair with and without EndoAnchors. J. Vasc. Surg. 2018; 67(6): 1699–1707. PubMed Abstract \| Publisher Full Text\n\nKim TH, Jang HJ, Choi YJ, et al.: Kilt Technique as an Angle Modification Method for Endovascular Repair of Abdominal Aortic Aneurysm with Severe Neck Angle. Ann. Thorac. Cardiovasc. Surg. 2017; 23(2): 96–103. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDohi S, Yokoyama Y, Yamamoto T, et al.: Push-Up Technique and Anatomical Deployment With the Endurant Stent-Graft System for Severely Angulated Aneurysm Necks. J. Endovasc. Ther. 2017; 24(3): 435–439. PubMed Abstract \| Publisher Full Text\n\nChaudhuri A: Using a Large Bore Sheath to Untwist Tortuous Iliac Arteries at EVAR: A Simple and Effective Technique. Eur. J. Vasc. Endovasc. Surg. 2019; 57(3): 433. PubMed Abstract \| Publisher Full Text" }	[ { "id": "210037", "date": "12 Oct 2023", "name": "Apostolos Pitoulias", "expertise": [ "Reviewer Expertise vascular 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 is a quite interesting manuscript considering a simple and safe solution for the treatment of AAA with hostile neck anatomy and tortuous iliac arteries.\nConsidering the introduction, more information about the other aspects of hostile neck (reverse tapering, width, circumferential thrombus or calcification and length) should be included.\nConsidering the case presentations it would be great if you could also include intraoperative angulation measurements before and after the placement of the superstiff wires, in order to better evaluate the changes in the angulation of the neck. The same could also be applied for the iliac arteries. Also some more intraoperative data, such as operation-time, contrast agent volume and experience of the vascular surgeon, should be documented to better evaluate the safety, reproducibility, simplicity and effectiveness of the msw technique, especially since it is stated in the introduction and discussion that the kilt and endostapling techniques, although efficient and safe add more devices and complexity to the procedure.\n\nConsidering the discussion, it is lacking information about the tortuosity of the iliac arteries (although it is stated in the tile of the manuscript.)\nConsidering the Conclusion, the safety and reproducibility of the technique should be also included. Also here more information about the iliac tortuosity are required.\n\nFinally major linguistic revision is required.\n\nIs the background of the cases’ 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 conclusion balanced and justified on the basis of the findings? Partly", "responses": [ { "c_id": "10818", "date": "22 Mar 2024", "name": "Taofan Taofan", "role": "Author Response", "response": "Thank you for your insights regarding our manuscript. We've added some of your inputs into the updated manuscript: Considering the introduction 1) More information about the other aspects of hostile neck (reverse tapering, width, circumferential thrombus or calcification and length) should be included. \"...To be categorized as hostile, an AAA neck must have any of the following criteria: (1) >2 mm reverse taper within 1 cm below the renal arteries, (2) ≥60° angulation within 3 cm below renal arteries, (3) ≤10 mm neck length, (4) ≥50% circumference of neck thrombus, and (5) >3 mm focal bulging in the neck. 4 Severe neck angulations as one of the hostile neck features appear to be linked with stent graft collapse, stent graft migration, type I endoleak, and late aneurysm rupture. . 5 \" Considering the case presentations 2) Include intraoperative angulation measurements before and after the placement of the superstiff wires, in order to better evaluate the changes in the angulation of the neck. The same could also be applied for the iliac arteries. We've added intraoperative angulation measurements but unfortunately not all cases have the before - after image of the stiff wires placement. We hope that the measurement still can be compared to the CT Scan data. That also applies to the iliac arteries in case 4, we can't provide intraoperative Iliac Tortuosity Index change since it was calculated using centerline of flow a 3-dimensional imaging. 3) Some more intraoperative data, such as operation-time, contrast agent volume and experience of the vascular surgeon, should be documented to better evaluate the safety, reproducibility, simplicity and effectiveness of the msw technique, especially since it is stated in the introduction and discussion that the kilt and endostapling techniques, although efficient and safe add more devices and complexity to the procedure. We've added those data in every cases. \"...The procedure was done at the National Cardiovascular Center Harapan Kita, Jakarta, Indonesia with around 50 EVAR and TEVAR cases per year. Vascular intervention consultant cardiologist with an experience more than 10 years done this procedure assisted by vascular intervention fellow student.\" Considering the discussion 4) Information about the tortuosity of the iliac arteries. \"... Another problem in EVAR practice is the tortuosity of the iliac arteries which is associated with a significantly greater rate of limb occlusion (53% vs 12% P<0.03). Additional stenting is well accepted to address that complication. 13 However, kinking of the iliac limbs can also be an issue. 14\" Considering the Conclusion 5) The safety and reproducibility of the technique should be also included. Also here more information about the iliac tortuosity are required. \"MSW technique is a simple and effective technique to modify aortic neck angulation/iliac artery tortuosity in TEVAR or EVAR procedure. The technique is safe and reproducible although further research with larger sample sizes is needed to validate the results.\" Once again thank you so much for your time and effort to review our manuscript. Your review really helped us to top of our manuscript. Hope the updated version of the manuscript can be approved. Please let us know if further revision needed." } ] }, { "id": "221046", "date": "10 Nov 2023", "name": "Johanes Nugroho Ekoputranto", "expertise": [ "Reviewer Expertise Vascular" ], "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 titled \"Endovascular Management of Aortic Aneurysm with Severe Neck Angulation and/or Iliac Artery Tortuosity Using Multiple Stiff Wire Technique: A Case Series\" discusses a novel technique for addressing aortic neck angulation and iliac artery tortuosity in the context of endovascular aortic repair. The case series presents outcomes for six patients who underwent the procedure. The manuscript is well-structured, and the information provided is clear and detailed. However, there are some feedback.\nIt provides a comprehensive background on the importance of a suitable aortic neck in endovascular aortic repair and the associated challenges. The references cited are recent and relevant. The authors correctly acknowledge that existing techniques, such as the Kilt technique and EndoAnchor System, have shown promise in managing angulated aortic necks but also add complexity and cost to the procedures. The MSW technique is presented as a simpler and cost-effective alternative, which is supported by the successful outcomes in the cases presented.\n\nHowever, it would be beneficial to include specific statistics or data on the prevalence of aortic neck angulation and its clinical impact to underscore the significance of the problem. In the conclusion , it should reiterate the need for further research and larger sample sizes to validate the results.\nThe study could benefit from further elaboration and comparison of the MSW technique with other methods, emphasizing its potential advantages and limitations. It would also be helpful to discuss the long-term implication using the MSW technique.\n\nIn summary, the case reports and the discussion section collectively highlight the potential of the MSW technique in addressing aortic neck/artery angulation. The cases demonstrate its effectiveness, and the discussion section provides context and identifies the need for further research. The article continues to show promise, future studies and a more comprehensive discussion of the technique's advantages and limitations are necessary to strengthen its impact.\n\nIs the background of the cases’ history and progression described in sufficient detail? Partly\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 conclusion balanced and justified on the basis of the findings? Yes", "responses": [ { "c_id": "10817", "date": "22 Mar 2024", "name": "Taofan Taofan", "role": "Author Response", "response": "Thank you for your insights regarding our manuscript. We've added some of your inputs into the updated manuscript: 1) Specific statistics or data on the prevalence of aortic neck angulation and its clinical \"The prevalence of severe neck angulation in EVAR is noteworthy. A single-center study in Greece by Karathanos et al. found that 34 of 317 EVAR patients (10.7%) had a neck angle >60°. 9 EVAR with severe neck angulation compared to non-severe neck angulation was associated with a significantly higher rate of type 1a endoleak until 3 years (5.6% vs 2.6%; p< 0.00001; OR 2.57 95% CI 1.62–4.07), neck-related secondary procedure until 3 years (13.1% vs 9%; p<0.05; OR 1.42 95% CI 1.04–1.96), migration rates until 1 year (5.4% vs 4.0%; p< 0.05; OR 1.41 95% CI 1.03–1.94), aneurysm-related and all-cause mortality until 1 year (6.4% vs. 4.3%; p< 0.05; OR 1.51 95% CI 1.16–1.98), but not related to aneurysm sac increase and rupture. 10\" 2) In the conclusion , it should reiterate the need for further research and larger sample sizes to validate the results. \"....The technique is safe and reproducible although further research with larger sample sizes is needed to validate the results.\" Once again thank you so much for your time and effort to review our manuscript. Your review really helped us to top of our manuscript." } ] } ]	1	https://f1000research.com/articles/12-1137
https://f1000research.com/articles/12-1390/v1	20 Oct 23	{ "type": "Case Report", "title": "Case Report: Iatrogenic trauma of the bladder due to long-term unidentified intrauterine device malposition inside the bladder with rectovesical fistula", "authors": [ "Ahmad Agil", "Tjahjodjati Tjahjodjati", "Nur Atik", "Dedi Rachmadi", "Tengku Tania Zahrina", "Tjahjodjati Tjahjodjati", "Nur Atik", "Dedi Rachmadi", "Tengku Tania Zahrina" ], "abstract": "According to reports, there are 1.9–3.6 incidences of IUD migration and uterine perforation for every 1000 IUD insertions. It is important to note that bladder perforation caused by a misplaced IUD is uncommon and is thought to happen most frequently during insertion. Here, we describe a patient who presented with symptoms related to the migration of IUD to the bladder. It is feasible to draw the conclusion that the cystoscopy technique should be taken into consideration as a suitable therapy option for such injuries in this organ. When a problem cannot be effectively treated by cystoscopy alone, laparotomy should be considered.", "keywords": [ "intrauterine device", "cystoscopy", "vesicolithiasis", "iatrogenic bladder trauma" ], "content": "Introduction\n\nThe intrauterine device (IUD), a small T-shaped piece of plastic that is used as a form of contraception, has the potential to perforate the uterus and spread to the pelvic or abdominal organs. According to reports, there are 1.9–3.6 incidences of IUD migration and uterine perforation for every 1000 IUD insertions. It is important to note that bladder perforation caused by a misplaced IUD is uncommon and is thought to happen most frequently during insertion. According to the literature, there are three ways to remove an IUD that has migrated to the lower urinary tract: a laparoscopy, open surgery, or a cystoscopy.1\n\nAlthough potential causes of ectopic IUD have been proposed, no official study has been done on the topic due to the rarity of the occurrences.2 After parturition, a weak uterine wall combined with an ill-advised early implantation may cause the IUD to become entrenched in the uterine wall and eventually shift; ectopic displacement of the IUD may be caused by aberrant morphology and the uterus’ regular contractions; The material and shape of IUDs are continuously optimized and improved to lessen the side effects of IUD placement, but unsuitable material and shape may cause chronic incision to the uterine wall during uterine contraction, ultimately causing the IUD to shift and embed in the posterior wall of the bladder.\n\nProcedures carried out in or near the retroperitoneal abdominal space or pelvis has the potential to result in iatrogenic harm to the urinary tract, including the kidneys, ureters, bladder, and urethra. Discussions of these injuries are frequently directed toward specialists like urologists, obstetricians, gynecologists, and general surgeons whose procedures are most frequently implicated in iatrogenic urinary tract injuries.3\n\nIatrogenic bladder injury should be recognized as soon as it happens. According to a study by Adelman et al., of the 100 cases that were detected in studies during the past 10 years, more than 80% were discovered throughout the course of the treatment. In addition to being able to see the injured tissue directly, external bladder traumas may also be suspected if urine was discovered in the operating room, air was detected in the collection bag for the Foley catheter, or the Foley catheter itself was visible. Iatrogenic internal bladder injuries may cause new symptoms to appear such as abdominal bloating, trouble sustaining bladder distension with infused fluid, and the ability to see urine outside the bladder.4\n\nAlthough surgical repair of intraperitoneal bladder injuries is often accomplished by a laparotomy, little is known about minimally invasive therapies in this clinical situation. Improved view of the pelvic organs, earlier return to daily activities, reduced bleeding, postoperative pain, intraabdominal adhesions, danger of incisional hernias, and duration of hospital stay and incapacity are the advantages of the laparoscopic technique.5\n\nHere, we describe a patient who presented with symptoms related to the migration of IUD to the bladder.\n\n\nCase report\n\nThis study was performed at Hasan Sadikin General Hospital, Bandung, Indonesia in July 2022. Informed consent for the publication of this article was obtained from the patient.\n\nA 36-year-old woman presented with lower urinary tract obstruction symptoms. An abdominal CT scan revealed an encrustation of corpus alienum in the bladder, due to malposition of IUD copper T (Figure 1). The patient underwent cystoscopy + lithotripsy + IUD copper evacuation (Figure 2). Intraoperative findings revealed there was left posterolateral rectovesicula fistule. Clinically, no digestive remainders were found in the urine. CT scan examination also did not find any signs leading to rectovesicula fistule.\n\nThe patient had the IUD implanted for six years before the case. There was a history of pregnancy, but the patient underwent curettage due to abortion. During curettage, there was no IUD to be found on the uterus. The patient then was planned to undergo exploratory laparotomy and fistule repair in a joint procedure with digestive surgeon.\n\nMost authors agree that having an IUD placed by a gynecologist is crucial for preventing perforation. However, gynecologists also have been known to insert IUDs that migrate.6 In the present case, the IUD was inserted by a midwife. Additionally, the vaginal speculum used for IUD implantation can cause tissue injury and infection, which can result in adhesions that make the uterus more likely to be punctured.7\n\nMacroscopic hematuria, abdominal or suprapubic discomfort, the inability to urinate, and oliguria are all indications of bladder damage. These signs and symptoms typically occur within the first 48 hours following surgery for a thermal injury or up to 10–14 days later. Because of the aberrant spike in serum creatinine levels brought on by the substance’s reabsorption into the urine through the peritoneal membrane, biochemical profiles are used to diagnose this kind of damage.8 However, in our case, the signs and symptoms of vesicolithiasis were more dominant due to the encrustation of IUD in the bladder.\n\nCystoscopy and imaging, such as plain X-rays, computed tomography, and ultrasound, offer significant diagnostic assistance and are crucial in determining the appropriate surgical techniques and approaches.9 CT scan played an important role in identifying the ectopic IUD in our case, but failed to detect the rectovesica fistule.\n\nActinomyces infections, as is well known, can also cause perforation of the uterus. In the presence of an IUD, Actinomyces infection can frequently arise.10 Another noteworthy problem is the increased likelihood of IUD migration in women who give birth while their IUD is still in place. The uterus is more prone to perforation because of the hypoestrogenemia-induced shrinkage of the uterus and thinned uterine walls during the postpartum and breastfeeding periods.6\n\nCystoscopy and lithotripsy were used in our case to evacuate the IUD and demolish the calculus formed in the bladder. At first, there was no intention to close the injury as there was no manifestation of the trauma of the bladder wall due to primary closure. As the rectovesicula fistule was found intraoperatively, the laparotomy became mandatory.\n\nAbsorbable suture should be used for cystotomy repair, or surgical suture used to seal a bladder damage, to prevent producing a nidus that encourages the development of kidney stones. Additionally, it can be carried out using a single-layer or two-layer approach, interrupted or continuous.8 For two weeks, urinary diversion with a Foley catheter for continuous drainage should be kept up.11\n\nOnly a small number of case reports have described laparoscopic IUD evacuation surgery.12 Additionally, open surgery or laparoscopic partial cystectomies have been successful procedures for some individuals.13 One instance reported by Atakan et al. required a suprapubic cystotomy.14 These results imply that ectopic IUDs lodged in the bladder wall can be treated with both open and laparoscopic operations. However, there are further approaches that might be investigated.\n\nThis report contains some flaws. This case examined a patient whose IUD became stuck in the bladder wall and who also had a calculus that had been treated at one hospital. To compare open versus laparoscopic operations, the number of patients was insufficient. The decision between laparoscopy and open surgery should be made specifically for each instance because of the uniqueness of the problem, the large variety of IUDs on the market, and the conditions unique to each patient. The IUD develops a calculus when it comes into touch with urine, according to our observation.\n\n\nConclusions\n\nIUD migration to the bladder should be suspected if bladder stones are observed, especially in women who have given birth while wearing an IUD, urinary tract infections that are resistant to treatment, and symptoms including dyspareunia and vaginal discharge. The conclusion can be drawn that the cystoscopy technique should be taken into consideration as a suitable therapy option for such injuries in this organ. When there is a problem that cannot be effectively treated by cystoscopy alone, laparotomy should be considered.\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\nTan JH, Lip HTC, Ong WLK, et al.: Intrauterine contraceptive device embedded in bladder wall with calculus formation removed successfully with open surgery. Malaysian Fam. Physician Off. J. Acad. Fam. Physicians Malaysia. 2019; 14(2): 29. Academy of Family Physicians of Malaysia.\n\nChai W, Zhang W, Jia G, et al.: Vesical transmigration of an intrauterine contraceptive device: a rare case report and literature review. Medicine (Baltimore). 2017; 96(40): e8236. Wolters Kluwer Health. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEsparaz AM, Pearl JA, Herts BR, et al.: Iatrogenic urinary tract injuries: etiology, diagnosis, and management. Semin. Intervent. Radiol. United States. 2015 Jun; 32(2): 195–208. Publisher Full Text\n\nAdelman MR, Bardsley TR, Sharp HT: Urinary tract injuries in laparoscopic hysterectomy: a systematic review. J. Minim. Invasive Gynecol. 2014; 21(4): 558–566. Elsevier. PubMed Abstract \| Publisher Full Text\n\nAydin C, Mercimek MN: Laparoscopic management of bladder injury during total laparoscopic hysterectomy. Int. J. Clin. Pract. 2020; 74(6): e13507. Wiley Online Library. PubMed Abstract \| Publisher Full Text\n\nHoşscan MB, Koşar A, Gümüştaş Ü, et al.: Intravesical migration of intrauterine device resulting in pregnancy. Int. J. Urol. 2006; 13(3): 301–302. Wiley Online Library. PubMed Abstract \| Publisher Full Text\n\nHarrison-Woolrych M, Ashton J, Coulter D: Uterine perforation on intrauterine device insertion: is the incidence higher than previously reported? Contraception. 2003; 67(1): 53–56. Elsevier. PubMed Abstract \| Publisher Full Text\n\nArnold MR, Lu CD, Thomas BW, et al.: Advancing the Use of Laparoscopy in Trauma: Repair of Intraperitoneal Bladder Injuries. Am. Surg. 2019 Dec 1; 85(12): 1402–1404. SAGE Publications. PubMed Abstract \| Publisher Full Text\n\nBoortz HE, Margolis DJA, Ragavendra N, et al.: Migration of intrauterine devices: radiologic findings and implications for patient care. Radiographics. 2012; 32(2): 335–352. Radiological Society of North America. PubMed Abstract \| Publisher Full Text\n\nMarkovitch O, Klein Z, Gidoni Y, et al.: Extrauterine mislocated IUD: is surgical removal mandatory? Contraception. 2002; 66(2): 105–108. Elsevier. PubMed Abstract \| Publisher Full Text\n\nMinas V, Gul N, Aust T, et al.: Urinary tract injuries in laparoscopic gynaecological surgery; prevention, recognition and management. Obstet. Gynaecol. 2014 Jan 1; 16(1): 19–28. John Wiley & Sons, Ltd. Publisher Full Text\n\nSantos AP, Wetzel C, Siddiqui Z: Laparoscopic removal of migrated intrauterine device. BMJ Case Rep. 2017 Sep 27; 2017: bcr2017221342. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRahnemai-Azar AA, Apfel T, Naghshizadian R, et al.: Laparoscopic removal of migrated intrauterine device embedded in intestine. JSLS J Soc Laparoendosc Surg. 2014; 18(3): e2014.00122. Society of Laparoscopic & Robotic Surgeons. Publisher Full Text\n\nKaplan M, Ertrk E: Intravesical migration of intrauterine device resulting in stone formation. Urology. 2002; 60(5): 911. Elsevier." }	[ { "id": "220884", "date": "20 Nov 2023", "name": "Pande Made Wisnu Tirtayasa", "expertise": [ "Reviewer Expertise Urology", "kidney transplant", "pediatric urology", "biology molecular", "immunology" ], "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 title suggests that the patient also suffered from a rectovesical fistula. However, from the case explanation, no single examination led to the proof of a rectovesical fistula. Please consider adding additional statements/sentences that explain how the authors diagnose the rectovesical fistula and the management regarding it.\nIn general, this study has covered all requirements to be indexed as a case report study.\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": [] }, { "id": "218419", "date": "20 Nov 2023", "name": "Prahara Yuri", "expertise": [ "Reviewer Expertise Pediatric urology", "reconstruction", "endourology", "uro-andrology and laparoscopic urology" ], "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 submitting your valuable case in F1000 research. Some questions should be addressed:\nWhen did you performed the fistula repair procedure? And explain the patient's follow up?\n\nDid the IUD evacuation and fistula repair performed in different time or in the same time? Please explain why?\n\nWhat was the different of your case comparing to others?\n\nWhat were the possibility causes of IUD migration in your case?\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": [ { "c_id": "10607", "date": "22 Nov 2023", "name": "Ahmad Agil", "role": "Author Response", "response": "In this case, the only preoperative symptom that appears is urination that smells. Then, the preoperative CT scan results did not detect a fistula. We also did not predict that the patient's condition would be so severe that a fistula would occur. However, during the intraoperative procedure, we discovered a fistula. This is one of the unique things in our case. Best regards, Ahmad Agil" }, { "c_id": "10644", "date": "30 Nov 2023", "name": "Ahmad Agil", "role": "Author Response", "response": "1. After the treatment, a post-operation follow-up was completed. In the first follow-up, the patient was in good condition, had no dysuria or abdominal pain, and had clear urine. The patient was planned to be consulted by the digestive surgeon, but unfortunately, the patient was lost to follow-up. 2. IUD evacuation and fistula repair were not performed at the same time, because when consulted for digestive surgery the patient was advised to undergo colostomy diversion. However, the patient refused the action plan. 3. This case is a rare case where IUD malposition can cause complications including fistulas. This condition was also not detected during the previous examination because no significant symptoms were found. The patient only complained of dysuria and intermittent cloudy urination. 4. In this case the cause was not IUD migration but rather an error in placing the IUD during installation by the midwife. The patient said that after 1 year of installing the IUD it was found that the patient was pregnant and when checking, the IUD was not found during delivery." }, { "c_id": "10772", "date": "13 Apr 2024", "name": "Ahmad Agil", "role": "Author Response", "response": "Dear Dr. Prahara, I appreciate your willingness to offer a thorough review. In addition to addressing the questions you posed, I have incorporated enhancements to the article based on the feedback provided. Thank you once again. Best regards, Ahmad Agil" } ] } ]	1	https://f1000research.com/articles/12-1390
https://f1000research.com/articles/12-860/v1	20 Jul 23	{ "type": "Research Article", "title": "Development of a magneto-optical Kerr microscope using a 3D printer", "authors": [ "Koki Uebo", "Yuto Shiokawa", "Ryunosuke Takahashi", "Suguru Nakata", "Hiroki Wadati", "Koki Uebo", "Yuto Shiokawa", "Ryunosuke Takahashi", "Suguru Nakata" ], "abstract": "Background: Magneto-optical Kerr effect (MOKE) microscopes are powerful experimental tools to observe magnetic domains in magnetic materials. These devices are, however, typically large, unportable, and expensive (∼ several million yen), and therefore prevent many researchers in the field of materials science from easy access to study real-space images of magnetic domains. Methods: To overcome these issues, we utilize data from ”The OpenFlexure Project” developed by the University of Bath and the University of Cambridge. The purpose of this project is to make high-precision mechanical positioning of the studied sample available to anyone with a 3D printer, especially for use in microscopes. We built a low-cost and portable MOKE microscope device by a 3D printer. We redesigned the 3D modeling data of an ordinary optical microscope provided by The OpenFlexure project and incorporated additional elements such as optical polarizers and an electro-magnetic coil into the primarily designed microscope that did not originally have these elements. Results: We successfully observed magnetic domains and their real-space motions induced by magnetic fields using the palm-sized low-cost MOKE microscope, which costs approximately 20,000 yen in raw materials to construct. Conclusions: Our methodology to assemble a low-cost MOKE microscope will enable researchers working in the field of materials science to more easily observe magnetic domains without commercial equipment.", "keywords": [ "The OpenFlexure project", "Magneto-Optical Kerr microscope", "3D printing technology", "low-cost" ], "content": "Introduction\n\nIn recent years, the “provision of goods and services that meet diverse needs without disparity” in Society 5.0 and “production that does not waste resources” in the Sustainable Development Goals (SDGs) have been of importance in our society.1 In this respect, the 3D printing technology plays a key role in many occasions from manufacturing and construction to hobbies, in which one can create new objects from conceptions regardless of age, lifestyle, and occupation. In the field of science, 3D printing technology is being used to significantly reduce the cost of experimental equipment and to develop new optical elements such as optical choppers, filter brackets, and rails.2 It is, therefore, expected that researchers can conduct more experiments along this research direction with a finite budget since low-cost experimental equipment becomes available and experiments can be conducted without buying expensive equipment. One of the applications of 3D printing technology is to design and build microscopes with various external parameters such as magnetic fields. Combining optical systems and data processing methods with a 3D printed microscope, observations with the in-plane resolution of several hundred nanometers have recently been achieved.3,4 Furthermore, it has been reported that the sample stage can be moved several tens of nanometers.5,6 The mechanism of these sample stages was developed in the project called “The OpenFlexure Project”, in which the slight expansion and contraction of the plastic material is adjusted by a rubber band (O-ring). These recent technical developments enable the stage movement along any direction in three dimensions, which is often required for the practical use of optical microscopes. The 3D printed microscopes with nanometer scale in-plane resolution, depth resolution, and precision of stage movement are already easily available for end-users with a 3D printer.\n\nIn this article, we report the development of a 3D printed microscope to observe a real-space image of magnetic domains in magnetic materials by means of the magneto-optical Kerr effect (MOKE), i.e., a phenomenon that the polarization of the reflected light is rotated by a magnetic material in response to an applied linearly polarized light. To observe these magnetic domains, large and expensive equipment such as optical tables and polarizing microscopes have routinely been used since deflecting elements are required. However, by redesigning several components of the microscope originally designed by “The OpenFlexure Project” using 3D printing technology, we successfully made a compact and low-cost MOKE microscope without large-scale commercial equipment. The sample observed in this study is a magneto-optical (MO) sensor to demonstrate the feasibility of our new 3D-printed microscope in the present work. We choose the MO sensor particularly because a material with perpendicular magnetic anisotropy enables us to observe magnetic domains and their motions appearing on the surface of a magnetic sample with MOKE. We incorporated an electromagnet into the microscope to scrutinize the motions of magnetic domains caused by magnetic fields. Our 3D-printed microscope to observe magnetic domains can be applied for a range of materials including NiCo2O4 thin film samples,7–9 which are attracting attention towards next-generation electronic device applications.\n\n\nHardware design\n\nThe microscope device using 3D printing technology was fabricated based on a microscope device development project by the University of Bath and the University of Cambridge (The OpenFlexure Project). Figure 1 shows a 3D-printed MOKE microscope device that we have built in the present study. A key development of our study is to make it possible to build a portable MOKE microscope. The actuator gear is used for the X-Y stage movements. This gear makes the microscope portable because this gear does not require a large space. Specifically, the dimensions of the microscope are 105 × 105 × 160 mm3 and therefore considerably smaller than conventional microscopes. In the following, we will examine details of the 3D printed MOKE microscope and its applications to studies of magnetic materials. Firstly, we elaborate on optical paths, components, and the design of our MOKE microscope referring to the cost and performance of each optical element. Also, we describe actual measurements of magnetic domains and their motions caused by magnetic fields in a magnetic material to demonstrate the performance of our newly developed MOKE microscope.\n\n(a-c)(Left) Original 3D modeling data provided from “The OpenFlexure Project”. J. P. Sharkey et al., Rev. Sci. Instrum. 87, 025104 (2016); licensed under a Creative Commons Attribution (CC BY) license. (Right) Modified 3D modeling data of the counterpart components used in this study. The red frames indicate the main parts that we redesigned.\n\nThe optical path of the microscope can be seen in Figure 2. The light path from the light source to the sample is as follows: Light-emitting diode (LED) → Condenser Lens → Polarizer1 → Beam splitter → Tube Lens → Objective Lens → Sample. The light reflected from the sample reaches the camera through the following optical path: Sample → Objective Lens → Tube Lens → Beam splitter → Polarizer2 → Camera for imaging. This microscope employs the Köhler illumination method, in which the unevenness in the luminance of the light source does not appear on the illuminated surface.10 A vital development of this microscope is a polarizing element to observe magnetic domains using MOKE. Another distinctive feature of our design is the stage movement using O-rings and the ability to easily change the design of the device using 3D modeling data taken from OpenFlexure and edited with software Fusion360 (ver2.0.14569). Note that 3D modeling data edited in Fusion360 here can also be edited in other software available for free such as FreeCAD. To move the sample stage, one can rotate the actuator gear shown in Figure 1, making the O-ring expand and contract, which in turn moves the X-Y stage shown in Figure 1. Figure 1(a)-(c) show our upgrades of three components in our microscope. These revised components are important to make the MOKE microscope for practical use. We elaborate on these modifications in the following. The body (Figure 1(a)) was edited to sufficiently change the position of the sample stage along the Z-axis. We got rid of the black part indicated by a red rectangular shown in Figure 1(a) to insert the rods (Figure 1(b)) to rotate the polarizer1. With this modification, the distance from the objective lens to the sample can be adjusted when the objective lens with the different magnification is replaced. As shown in Figure 1(b), we added two rods to rotate the polarizing element because the MOKE microscope requires adjustment of the rotation angle of the polarizing element during measurements depending on the Kerr angles of magnetic materials, which in general differ from sample to sample. Figure 1(c) displays a component to install an electromagnet on top of the sample, enabling the application of a magnetic field perpendicular to the sample. To calibrate the magnitude of the magnetic field, a tesla meter (TM-801, KANETEC) was used. The measuring portion of the tesla meter instrument was placed at the position of the sample to be observed, and the instrument was calibrated after confirming that the sample was illuminated by light. We carefully measured the magnitude of the magnetic field at the position of the sample.\n\nThe reflective geometry is realized using a LED as a light source and a beam splitter. The electromagnet storage and polarizers are additional components to make an ordinary optical microscope into a MOKE microscope.\n\nWe refer to the cost and performance of each optical element used to assemble our microscope in Table 1. The total cost of filaments (ingredients of the 3D printing) and all the components to fabricate the MOKE microscope is 20,000 yen. This is an excellent cost performance in comparison with standard commercial MOKE microscopes. For instance, ZEISS Axio Imager costs >2,000,000 yen. Instead of purchasing such an expensive instrument, it is thus possible to access a MOKE microscope whose parameters can easily be improved with better optical elements such as objective lenses and tube lenses depending on the requirements of specific measurements.\n\nThe microscope fabricated in this study was used to image patterns of magnetic domains appearing on the surface of a magnetic sample. An electromagnet is placed above the sample, and the magnetic field is controlled by a DC power supply. Images were generated with a USB camera connected to a standard computer. The sample measured in this work is a MO sensor (Matesy GmbH: Magneto-optical sensors with mirror and DLC protection (type-A)), whose magnetic domains of the sample surface can be controlled by applying a magnetic field. The magnetic domain patterns were binarized with image analysis software (Igor 6.0 and ImageJ 1.53e). Such image analyses implemented in Igor can also be carried out in primitive programming languages such as Python. The camera properties such as brightness, vividness, exposure, and backlight correction were specified during imaging using free software called WebCamSetting 1.1.0.0. Specifically, the brightness and vividness were set to the minimum value 0 whereas the exposure and backlight correction were kept as default. This setting allows us to clearly observe MOKE images.\n\n\nMethods\n\nHere, we describe the methods of data acquisition and analysis. A USB camera is connected to the computer for the data acquisition and camera images were obtained using default camera settings. To binarize the images, we used the iterated binarization method in the Igor software. Since the ratio of dark and bright areas can be quantified with ImageJ, the data format was converted from image data to numerical values of ±1 to quantitatively obtain the Kerr intensity in Figure 3. Care was taken to record the data at the same areas of the sample surfaces while taking images with 10 different magnetic fields (±7.6, ±3.8, ±1.9, ±1.1 and ±0.76 mT) to evaluate magnetic field effects on the images.\n\nTo eliminate the background signals in the image data shown in Figure 3, the darkest image (1) (the single magnetic domain, mirroring the macroscopically saturated magnetization by a sufficient amount of magnetic field) is used as a representing background signal. Magnetic domain images at 10 different magnetic fields are subtracted from the image (1) with a software (ImageJ converts the image data into numerical values).\n\n\nResults\n\nThe data associated in this article are available in Underlying data.11 Figure 3 shows images of the magnetic domains of the MO sensor under magnetic fields varying from −7 mT to +7 mT using the electromagnet placed above the sample. These data were collected at room temperature and a white LED shown in Table 1 was used as a light source. The image is monochromatic dark when a sufficient amount of the field was applied (Figure 3 (1)). This is an expected behavior for ferromagnets when the total magnetization is saturated by the external field. Upon the application of a magnetic field, we clearly observed domains in the bright color (we characterized color as either bright or dark), which indicates that the magnetic domains along the other direction are induced by the field (Figure 3 (2)). It is also appreciable that the entire contrast of the image is drastically changed when the sign of the field is reversed (Figure 3 (2) and (3)). The image is dominated by domains in the bright color and is finally monochromatic bright when the substantial field was applied along the opposite direction to the initial field (Figure 3 (4) and (5)). In light of these real-space observations, we have analyzed the contrast of the images to estimate the magnetic field dependence of the net magnetization of the MO sensor. The Kerr intensity is defined as the differential areas of the respective domains within the scope and thereby represents the macroscopic magnetization of the sample. The magnetic field dependence of the Kerr intensity is consistent with the observations of the original images and reminiscent of the typical M- H curve of ferromagnets. Specifically, the coercive field inferred from the Kerr intensity is 2 mT, which quantitatively agrees with the experimental data of Faraday rotation provided by the company Matesy GmbH in Figure 3 (right), considering the relationship of 1 mT = 0.7958 kAm−1.\n\n\nConclusions\n\nIn conclusion, we have assembled a MOKE microscope using 3D printing technology. The total price is less than 2% of that of the standard commercial MOKE microscope, based on the comparisons we have made (for example, ZEISS Axio Imager costs >2,000,000 yen). To substantially reduce the size of the MOKE microscope, we utilized the 3D modeling provided by the OpenFlexure Project (and such an attempt to assemble a 3D printed MOKE microscope is for the first time to the best of our knowledge). The feasibility of our 3D-printed MOKE microscope is well confirmed by the measurements of the real-space images of the magnetic domains of the MO sensor under the magnetic fields and the analysis of the macroscopic magnetization estimated from these images.\n\nOn the experimental front, one can extend the maximum values of the magnetic field by replacing the electromagnet with the one which can tolerate higher electrical currents or superconducting magnets. The real-space resolution can be improved by increasing the magnification of the objective lens. These amplifications of the external parameters should be straightforward for end-users and can be achieved with reasonable costs compared to the price of conventional commercial MOKE microscopes. We thus believe that MOKE microscopes will be more easily available and customizable in the field of materials science along the direction we present in this work.", "appendix": "Data availability\n\nThe original 3D printing data from “The OpenFlexure Project” is available for download here: https://openflexure.org/projects/microscope/build.\n\nZenodo: koki-u/3d_microscope: Kerr microscope. https://doi.org/10.5281/zenodo.7950835. 11\n\nThis project contains the following underlying data:\n\n• Modified (3D print files).\n\n• Image (image files).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nHitachi-UTokyo Laboratory: Society 5.0 People-centric Super-smart Society. Springer; 2018.\n\nZhang C, Anzalone NC, Faria RP, et al.: Open-source 3d-printable optics equipment. PLoS One. 2013; 8(3): e59840. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGrant SD, Cairns GS, Wistuba J, et al.: Adapting the 3d-printed openflexure microscope enables computational super-resolution imaging. F1000Res. 2019; 8: 2003. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMatsui T, Fujiwara D: Optical sectioning robotic microscopy for everyone: the structured illumination microscope with the openflexure stages. Opt. Express. 2022; 39(13): 23216–23298.\n\nSharkey JP, Foo DCW, Kabla A, et al.: A one-piece 3d printed flexure translation stage for open-source microscopy. Rev. Sci. Instrum. 2016; 87(2): 025104. Publisher Full Text\n\nCollins JT, Knapper J, Stirling J, et al.: Robotic microscopy for everyone: the openflexure microscope. Biomed. Opt. Express. 2020; 11(5): 2447–2460. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDho J, Kim J: Magnetic domain structure of the ferrimagnetic (001) NiCo2O4 film with perpendicular magnetic anisotropy. Thin Solid Films. 2022; 756: 139361. Publisher Full Text\n\nTakahashi R, Tani Y, Abe H, et al.: Ultrafast demagnetization in NiCo2O4 thin films probed by time-resolved microscopy. Appl. Phys. Lett. 2021; 119(10): 102404. Publisher Full Text\n\nTakahashi R, Ohkochi T, Kan D, et al.: Optically induced magnetization switching in NiCo2O4 thin films using ultrafast lasers. ACS Appl. Electron. Mater. 2023; 5(2): 748–753. Publisher Full Text\n\nBell S, Morris K: An Introduction to Microscopy (English Edition). CRC Press; 2010. Publisher Full Text\n\nUebo K: kokiu/3d/_microscope: Kerr microscope (v1.0.0). [Data set]. Zenodo. 2023. Publisher Full Text" }	[ { "id": "189385", "date": "18 Aug 2023", "name": "Tatsunosuke Matsui", "expertise": [ "Reviewer Expertise My expertise is in development of novel optical materials and devices based on organic functional materials such as pi-conjugated materials and liquid crystals. I am also working on metamaterials", "plasmonics", "photonic crystals", "terahertz spectroscopy", "and optics in general." ], "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 shows development of an open-source, low-cost and compact 3D printed microscope for the observation of magnetic domains in magnetic materials by the magneto-optical Kerr effect (MOKE). Developments of such open-source and low-cost microscope are actively studied in recent years1. A lot of design files are freely available and the authors of the current manuscript utilized one of these 3D printable design developed by the OpenFlexure Project 2. In MOKE observation, polarizers have to be introduced to detect rotation of the polarization of the linearly polarized light reflected from a magnetic material under applied magnetic field. Therefore, they redesigned several components of the OpenFlexure microscope to attach electromagnet and polarizers, and they also made the data for the reproduction of them freely available. They also showed experimental results of the MOKE observation using commercially available magneto-optical (MO) sensor as a sample, which is sufficient to guaranty feasibility of their system.\nThe OpenFlexure microscope families are superior for their extremely high positioning precision with tens of nanometers based on flexure mechanism of the flexible plastics and low-cost stepper motors 3. Several groups have made contribution to the improvement of such OpenFlexure microscope for advanced scientific applications such as, the optical projection tomography (OPT)4, computational super-resolution imaging system based on the super-resolution radial fluctuation (SRRF) algorism5, and so on. The studies presented in the current manuscript successfully added new function to the OpenFlexure microscope, which may be useful for the researchers working in the field of materials science, especially in magnetic materials.\nWe are also one of such contributor and reported about a low-cost fabrication of the structured illumination microscope (SIM) for the optical sectioning based on the OpenFlexure stages6. I am confident that we are familiar with the basic working principle of the OpenFlexure microscope and are experienced in building 3D-printable microscopes, but I have poor experience on magnetic measurements. I can say that the authors present appropriate procedures for the reproduction of their work, but I think it will be more informative and helpful if they can provide detailed information about polarizer holder. The polarizers are key components in the MOKE observation and have to be rotated depending on the direction of axes of the magnetic material. The authors simply describe that the polarizers can be rotated in the current manuscript, but do not give detailed explanation how it can be done. My other concern is about uniformity of the LED illumination and the applied magnetic field in the field of view. I think it will be better if the authors can provide descriptions on these points.\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? Yes", "responses": [ { "c_id": "10787", "date": "14 Jun 2024", "name": "Hiroki Wadati", "role": "Author Response", "response": "1. This manuscript shows development of an open-source, low-cost and compact 3D printed microscope for the observation of magnetic domains in magnetic materials by the magneto-optical Kerr effect (MOKE). Developments of such open-source and low-cost microscope are actively studied in recent years1. A lot of design files are freely available and the authors of the current manuscript utilized one of these 3D printable design developed by the OpenFlexure Project 2. In MOKE observation, polarizers have to be introduced to detect rotation of the polarization of the linearly polarized light reflected from a magnetic material under applied magnetic field. Therefore, they redesigned several components of the OpenFlexure microscope to attach electromagnet and polarizers, and they also made the data for the reproduction of them freely available. They also showed experimental results of the MOKE observation using commercially available magneto-optical (MO) sensor as a sample, which is sufficient to guaranty feasibility of their system. Our Reply: We thank the reviewer for his careful reading of our manuscript and for considering our work worthy of publication. In the following, we answer his concerns one by one, and we point out the changes made in the manuscript to improve both the discussion and the figures following his suggestions. 2. The OpenFlexure microscope families are superior for their extremely high positioning precision with tens of nanometers based on flexure mechanism of the flexible plastics and low-cost stepper motors3. Several groups have made contribution to the improvement of such OpenFlexure microscope for advanced scientific applications such as, the optical projection tomography (OPT)4, computational super-resolution imaging system based on the super-resolution radial fluctuation (SRRF) algorism5, and so on. The studies presented in the current manuscript successfully added new function to the OpenFlexure microscope, which may be useful for the researchers working in the field of materials science, especially in magnetic materials. Our Reply: Thank you for highlighting the novelty of our present work in comparison with recent studies relevant to our study. Note that we found that Ref. 4 in the original manuscript was not properly cited and thus revised as follows: Opt. Express. 2022; 30 (13): 23208-23216. 3. We are also one of such contributor and reported about a low-cost fabrication of the structured illumination microscope (SIM) for the optical sectioning based on the OpenFlexure stages6. I am confident that we are familiar with the basic working principle of the OpenFlexure microscope and are experienced in building 3D-printable microscopes, but I have poor experience on magnetic measurements. I can say that the authors present appropriate procedures for the reproduction of their work, but I think it will be more informative and helpful if they can provide detailed information about polarizer holder. The polarizers are key components in the MOKE observation and have to be rotated depending on the direction of axes of the magnetic material. The authors simply describe that the polarizers can be rotated in the current manuscript, but do not give detailed explanation how it can be done. Our Reply: We totally agree that detailed information about the polarizer holder would be helpful for readers. To better understand our system, we have added the following sentence in the section on Hardware design: “The rod can be mechanically rotated by hand. The angle of the holder can vary from -75 to 75 degrees in the current setup.” 4. My other concern is about uniformity of the LED illumination and the applied magnetic field in the field of view. I think it will be better if the authors can provide descriptions on these points. Our Reply: To clarify the uniformity of the LED illumination, we rewrote the sentence as “This microscope employs the Köhler illumination method, where the illuminated light becomes collimated on the sample surface by using the three lenses. This ensures the uniformity of the LED illumination.” The in-plane component of the magnetic field was 0.1 mT or less, measured by a Tesla meter. Small non-uniformity causes no problem due to the observed small area (~0.5 × 0.5 mm). Moreover, the coercive field estimated from our Kerr intensity in response to the magnetic field is nearly identical to the Faraday rotation data provided by Matesy GmbH (Fig. 3), implying that the magnetic field is essentially homogeneous in our apparatus." } ] }, { "id": "215081", "date": "25 Oct 2023", "name": "Aurelio Hierro Rodriguez", "expertise": [ "Reviewer Expertise Nanomagnetism", "X-ray Transmission Microscopy", "Magneto-optics", "Magnetic Thin Films" ], "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 report on the development and implementation of a cheap 3D printed Kerr Microscope based on the main design of “The OpenFlexure Project”. The idea is very interesting and really brings the capability of performing Kerr Microscopy with small and cheap instruments. However, there are several and important flaws in the work, from its redaction to the discussion and conclusions, passing through the experimental details, that prevent us from recommending this manuscript for its publication. Here follows our indications and comments.\nAs a general first comment, the content is sometimes repetitive which makes the general reading difficult, thus the style should be improved.\nIn the introduction, current literature on 3D printing is referenced, however, no citations appear about other Kerr Microscope setups for information and comparison with current state of the art techniques. As this work is focused on Kerr Microscopy, it should be very important to have this framework well defined.\nAlso in the introduction, it is not clear for me what the authors mean with the sentence saying that the stage can be moved several tens of nanometers. Is this indicating the precision of the movement using the 3D printed stage actuators, or is the total displacement possible per axis? If it is the first case, then there is a clear problem as tens of nanometers is a very limited movement range for an optical microscope. Clarify.\nAlso in the introduction section, what is the meaning of depth resolution at the end of the first paragraph? Is that the depth of focus or the precision of the Z stage? If it is the first, then this strongly depends on the objective used and it is usually in the range of ~1 um.\nIn the second paragraph of the introduction, the application of the method to be discussed is focused towards a very specific material (NiCo2O4). If this work is devoted to present a general purpose and cheap Kerr Microscope, a wider discussion about systems where it could be used as a useful characterization tool should be cited and discussed briefly.\nIn the Hardware design section, a more thorough description of the polarization optics should be done as it is the key for a proper functioning of a Kerr Microscope. It would be great if comparison with in-plane magnetization sensitive microscopes would be done, as there are plenty of systems where in-plane magnetization is the main actor.\nAs a comment, in figure 1 caption, maybe it is not necessary to include the citation for the OpenFlexure Project as it is already in the main text. The caption should focus on the figure itself.\nThere is a typo in the description in the main text of figure 1(a): “by a red rectangular” should be “by a red rectangle”.\nThe maximum rotation of the analyser should be indicated in the description of panel b of figure 1 as this is important for the tuning of the microscope. Could it be possible to include a retarder waveplate in the design in addition to the analyser too as it exists in other KM for signal optimization? A comment about this would be helpful as this would indicate that the authors have reviewed current Kerr Microscope setups in detail.\nWe find the discussion about the electromagnet design very obscure. As it is a very important part of the microscope, it should be described with more detail indicating core material, remanent field, possible heating problems such as 3D printed plastic deformation? Also, stability of the microscope while utilization with the magnetic field on. Interference of the magnetic field with magnetic parts of the objective?\nJust a minor comment, probably, the price of the power supply for the electromagnet should be included in the total price of the microscope.\nIn the discussion about the domain imaging and analysis of the Magneto-optic sensor provided by Matesy Gmbh, we have a lot of doubts.\nFirst of all, why the authors binarize the data for its processing? The intensity of the signal recorded by the camera if it works in a linear manner is very important and can give useful information about the orientation of the magnetization within the system (vector sensitivity inherent to the MO effect). Here it is important also to indicate the dynamic range of the camera used as well as its relation with the smallest signal that the microscope can measure. A thorough discussion about this is mandatory as this work is describing a characterization technique.\nAnother important point here is the fact that the sample used for demonstrating the proof of concept does not really use the Kerr effect, but the Faraday effect which gives a huge signal when compared with polar Kerr for instance. The rotation indicated in figure 3 by the manufacturer of the sensor indicates a rotation of +/-8 degrees between saturations. This is very easy to measure and is adequate for an initial demonstration, but real samples measured using Kerr configuration will most probably show way smaller rotations of the polarization. In this regard, how are the low extinction ratio polarizers going to work? At this point we think that in order to demonstrate real capabilities of the proposed microscope, a real sample where Kerr effect is used for its characterization is mandatory, as is in this configuration where the microscope should work.\nFinally, two comments about figure 3. The external field units of the two loops (half-loops) presented should be the same, and the normalization protocol used for removing background and getting magnetic signal should be better clarified. As it is now, I understand that image 1 (-3.8 mT) is the one used for normalization, which shows stripes. If this is the image taken for normalization, why aren’t these stripes present always in all the images? A fully flat image should be taken to work as reference and then the microscope would be working in differential mode. Have the authors observed strong Faraday effects due to the objective optics in combination with the external field from the electromagnet? Please clarify this point.\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? 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": "10788", "date": "14 Jun 2024", "name": "Hiroki Wadati", "role": "Author Response", "response": "The authors report on the development and implementation of a cheap 3D printed Kerr Microscope based on the main design of “The OpenFlexure Project”. The idea is very interesting and really brings the capability of performing Kerr Microscopy with small and cheap instruments. However, there are several and important flaws in the work, from its redaction to the discussion and conclusions, passing through the experimental details, that prevent us from recommending this manuscript for its publication. Here follows our indications and comments. Our Reply: We thank the reviewers for their careful reading of our manuscript and for providing us with constructive comments. In the following, we answer their concerns one by one and point out the changes made in the manuscript to improve both the discussion and the figures following his suggestions. 1. As a general first comment, the content is sometimes repetitive which makes the general reading difficult, thus the style should be improved. Our Reply: We find that the OpenFlexure Project was mentioned several times in the introduction and Hardware Design sections. Therefore, we revised some sentences in these sections to avoid clutter. We also revised the English expressions throughout the text. 2. In the introduction, current literature on 3D printing is referenced, however, no citations appear about other Kerr Microscope setups for information and comparison with current state of the art techniques. As this work is focused on Kerr Microscopy, it should be very important to have this framework well defined. Our Reply: We added Refs. 12-14 to include the information on other Kerr Microscope setups for thin films of iron garnet, Pt/Co, and CoFeB. 3. Also in the introduction, it is not clear for me what the authors mean with the sentence saying that the stage can be moved several tens of nanometers. Is this indicating the precision of the movement using the 3D printed stage actuators, or is the total displacement possible per axis? If it is the first case, then there is a clear problem as tens of nanometers is a very limited movement range for an optical microscope. Clarify. Our Reply: The tens of nanometers indicated the precision of the movement. The movement range is a few millimeters. Now we wrote, Furthermore, it has been reported that the sample stage can be moved with the precision of several tens of nanometers. 4. Also in the introduction section, what is the meaning of depth resolution at the end of the first paragraph? Is that the depth of focus or the precision of the Z stage? If it is the first, then this strongly depends on the objective used and it is usually in the range of ~1 um. Our Reply: We would like to thank the referee for pointing this out. We removed “depth resolution” in the introduction to avoid confusion since the depth resolution is beyond our interest in the present study. 5. In the second paragraph of the introduction, the application of the method to be discussed is focused towards a very specific material (NiCo2O4). If this work is devoted to present a general purpose and cheap Kerr Microscope, a wider discussion about systems where it could be used as a useful characterization tool should be cited and discussed briefly. Our Reply: We added Refs. 12-14 to include the information on more general setups for observing magnetic domains of iron garnet, all-optical magnetization switching, and the creation of magnetic skyrmions. 6. In the Hardware design section, a more thorough description of the polarization optics should be done as it is the key for a proper functioning of a Kerr Microscope. It would be great if comparison with in-plane magnetization sensitive microscopes would be done, as there are plenty of systems where in-plane magnetization is the main actor. Our Reply: We chose THORLABS LPVISE2X2 with an extinction ratio of 100:1 or more in the visible light range. We also tried EDMUNDS 8.5\" x 5\" Linear Polarizing Film but did not succeed due to the lower polarization efficiency of 88%. We agree that there are a number of materials exhibiting in-plane magnetization. However, observations of magnetic domains of in-plane magnetism are beyond the scope of the present study, although this is indeed an interesting research direction in the future. 7. As a comment, in figure 1 caption, maybe it is not necessary to include the citation for the OpenFlexure Project as it is already in the main text. The caption should focus on the figure itself. Our Reply: We agree that the caption should explain a figure itself. We therefore replaced the detailed information of the original literature and “The Openflexture Project” with Ref. 5. in the figure caption. 8. There is a typo in the description in the main text of Figure 1(a): “by a red rectangular” should be “by a red rectangle”. Our Reply: We would like to thank the referee for pointing this out. We accordingly changed this part from “by a red rectangular” to “by a red rectangle.” 9. The maximum rotation of the analyser should be indicated in the description of panel b of figure 1 as this is important for the tuning of the microscope. Could it be possible to include a retarder waveplate in the design in addition to the analyser too as it exists in other KM for signal optimization? A comment about this would be helpful as this would indicate that the authors have reviewed current Kerr Microscope setups in detail. Our Reply: To be confirmed, the analyzer, which we call the polarizer 2 in the text, is not rotatable in the first place. We have added the following sentence in the caption for panel b of Figure 1: “Note that the angle of the rod for the polarizer 1 shown in panel b can vary from -75 to 75 degrees in the microscope.” 10. We find the discussion about the electromagnet design very obscure. As it is a very important part of the microscope, it should be described with more detail indicating core material, remanent field, possible heating problems such as 3D printed plastic deformation? Also, stability of the microscope while utilization with the magnetic field on. Interference of the magnetic field with magnetic parts of the objective? Just a minor comment, probably, the price of the power supply for the electromagnet should be included in the total price of the microscope. Our Reply: We included the information on the core material (iron) in Table 1. The relationship between the magnetic field (mT) and the current (A) is shown below, indicating no remnant field. So far, we have not observed any plastic deformations of the 3D printed objects due to thermal heating of the coil. Figure R1: Current evolution of the magnetic field of the coil we employed in the present study. (Please find the updated figure file in above hyperlink Figure R1) We included the information on the power supply as “DC power supply 6,000 Kungber stabilized power supply 0-30V, 0-5A” in Table 1. The total cost was changed from 20000 to 30000 yen. 11. First of all, why the authors binarize the data for its processing? The intensity of the signal recorded by the camera if it works in a linear manner is very important and can give useful information about the orientation of the magnetization within the system (vector sensitivity inherent to the MO effect). Here it is important also to indicate the dynamic range of the camera used as well as its relation with the smallest signal that the microscope can measure. A thorough discussion about this is mandatory as this work is describing a characterization technique. Our Reply: For the following reasons, analyses by binarization are well justified. (a) This thin film has high perpendicular magnetic anisotropy, so the magnetic domains of up and downward spins are distinct. (b) The width of the domain wall is much smaller than the spatial resolution of the optical microscope. Figure R2 shows the effect of binarization available with Zenodo of Ref.14. This operation makes the up and down magnetic domains created by strong perpendicular magnetic anisotropy more clearly visible. Domain walls are too small to be observed. Figure R2: (Left) Original data of magnetic domains in the MO sensor collected with B = -1.1 mT (Ref. 11). (Right) Binalized data, a part of which is shown in panel 2 of Figure 3 in the main text. Note that the black/white is inverted compared with the left figure for clarity. ((Please find the updated figure file in above hyperlink Figure R2) 12. Another important point here is the fact that the sample used for demonstrating the proof of concept does not really use the Kerr effect, but the Faraday effect which gives a huge signal when compared with polar Kerr for instance. The rotation indicated in figure 3 by the manufacturer of the sensor indicates a rotation of +/-8 degrees between saturations. This is very easy to measure and is adequate for an initial demonstration, but real samples measured using Kerr configuration will most probably show way smaller rotations of the polarization. In this regard, how are the low extinction ratio polarizers going to work? At this point we think that in order to demonstrate real capabilities of the proposed microscope, a real sample where Kerr effect is used for its characterization is mandatory, as is in this configuration where the microscope should work. Our Reply: The right side of Figure 3 is the Faraday effect (obtained by transmission) provided by the company Matesy GmbH to obtain the reference M-H curve. We are conducting microscopy measurements on this sample by using the reflective Kerr effect and have already observed magnetic domain images using this MO sensor as a real sample. Measurements on other samples are currently underway, and we would like to report on them in future publications. 13. Finally, two comments about figure 3. The external field units of the two loops (half-loops) presented should be the same, and the normalization protocol used for removing background and getting magnetic signal should be better clarified. As it is now, I understand that image 1 (-3.8 mT) is the one used for normalization, which shows stripes. If this is the image taken for normalization, why aren’t these stripes present always in all the images? A fully flat image should be taken to work as reference and then the microscope would be working in differential mode. Have the authors observed strong Faraday effects due to the objective optics in combination with the external field from the electromagnet? Please clarify this point. Our Reply: We apologize that the original statement was different from our analysis procedure and thereby misleading. We used the darkest image without stripes collected at -7.6 mT (not shown) as a background. This is certainly why these stripes are not present in normalized images. To make this point clearer, we wrote, “the darkest image at -7.6 mT is used as a representing background signal.” We changed the external field unit of the right loop from kAm-1 to mT by using the relationship of 1 mT = 0.7958 kAm-1. We confirmed that there are no Faraday effects of the objective lens. By considering the Verdet constant, this is much below 0.1 deg, much smaller than the Kerr rotation of the thin film." } ] } ]	1	https://f1000research.com/articles/12-860
https://f1000research.com/articles/9-492/v1	02 Jun 20	{ "type": "Research Article", "title": "Pesticide exposure and lung cancer risk: A case-control study in Nakhon Sawan, Thailand", "authors": [ "Teera Kangkhetkron", "Chudchawal Juntarawijit", "Teera Kangkhetkron" ], "abstract": "Background: Pesticide exposure might increase risk of lung cancer. The purpose of this study was to investigate the association between the historical use of pesticides commonly found in Thailand, and lung cancer. Methods: This case-control study compared a lifetime pesticide exposure of 233 lung cancer cases, and 458 healthy neighbours matched for gender, and age (±5 years). Data on demographic, pesticide exposure, and other related factors were collected using a face-to-face interview questionnaire. Associations between lung cancer and types of pesticides as well as individual pesticides were analysed using logistic regression adjusted for gender (male, female), age (≤54, 55-64, 65-74, ≥75), cigarette smoking (ever, never smoke), occupation (farmer, non-farmer), and exposure to air pollution (yes, no). Results: It was found that lung cancer was positively associated with lifetime use of herbicides, insecticides, and fungicides. Compared to people in the lowest quartile of number of days using the herbicides and insecticides, those in a higher quartile had an elevated risk of lung cancer, with odds ratio (OR) between 2.79 (95% confidence interval (CI) 1.12–6.95), and 28.43 (95% CI 11.11-72.76) (p < 0.001). For fungicides, only the most exposed group had a significant risk (OR = 4.97; 95% CI 1.49-16.56). For individual pesticides, those presenting a significant association with lung cancer were dieldrin (OR = 2.76; 95% CI 1.42-5.36), chlorpyrifos (OR = 3.98; 95 % CI 2.06-7.67), and carbofuran (OR = 2.58; 95% CI 1.48-4.51). Conclusions: The results showed that lung cancer among Thai people in Nakhon Sawan province is associated with previous pesticide use. This finding was consistent with previous studies in other parts of the world. Further study should focus on identifying more individual compounds that may cause lung cancer, as well as other types of cancer.", "keywords": [ "Lung cancer", "Pesticides exposure", "Herbicides", "Insecticides", "Fungicides" ], "content": "Introduction\n\nLung cancer is a common and deadly type of cancer. In 2018, there were 2.1 million people around the world diagnosed with lung cancer, and 1.8 million died of the disease1. In 2018, Thailand had 170,495 incidences, and 114,199 deaths of lung cancer2. Besides genetic factors3, a major risk factor of lung cancer is cigarette smoking4,5. However, lung cancer was also related to other risk factors, including asbestos, crystalline silica, radon, polyaromatic hydrocarbons, diesel engine exhaust particles, chromium, and nickel6,7. Recent studies have also linked cooking fumes to lung cancer8.\n\nPesticide exposure might also cause lung cancer9. The association between pesticides and lung cancer were presented around 50 years ago among grape farmers10. A large study in the United States found that lung cancer cases increase with the number of years working as a licensed pesticide applicator11. Another study in USA reported an increased risk of lung cancer among acetochlor herbicide users (RR = 1.74, 95% CI 1.07-2.84)12. In Pakistan, a study also found a strong association between pesticide exposure and lung cancer (OR = 5.1, 95% CI 3.1-8.3)13.\n\nSome studies can also link individual pesticides to lung cancer. In the USA, a study evaluated 50 pesticides and found that seven—dicamba, metolaclor, pendimethalin, carbofuran, chlorpyrifos, diazinon, and dieldrin—to be positively associated with lung cancer14. Another study also showed a significantly increased risk of lung cancer among applicators who had been exposed to dieldrin15. Jones et al.16 reported an increased lung cancer incidence among male pesticide applicators with the highest exposure category of diazinon (odds ratio (OR) = 1.6, 95% confidence interval (CI) 1.11-2.31). Other individual pesticides that had been associated with lung cancer were chlopyrifos17, diazinon18, pendimenthalin19 and carbofuran20.\n\nTo our knowledge, the association between lung cancer and pesticides has never been studied before among Thai people. The objective of this study was to investigate associations between pesticide exposure and lung cancer among people living in Nakhon Sawan province, Thailand. The results can be used for the prevention of lung cancer, and to support the global literature.\n\n\nMethods\n\nThis study is a population-based case-controlled study. Cases referred to people diagnosed with lung cancer during the period of January 1, 2014 to March 31, 2017, and having residence in Nakhon Sawan province, Thailand. Cases were selected from the database of Cancer Based Program (TCB) operated by Thai National Cancer Institute21. From 299 living cases registered during the study period, 229 cases (77%) were contacted in person, and participated in this study. Controls were neighbours who did not have lung cancer, but were of the same gender, and age (±5 years) as the cases. In each case, two controls were randomly selected by the interviewer. In this study, data from 458 controls were used as a comparison group.\n\nThe minimum sample size was determined to be 229 for cases and 558 for controls using Kelsey’s formula22 (unmatched population base case-control study). The assumptions used were as follows: proportion of case with pesticide exposure was 0.523, proportion of control with exposure was 0.424, and the ratio of case to control was 1:225.\n\nData on pesticide exposure and other risk factors were collected using a questionnaire previously used in a study on pesticide exposure and diabetes26. The questionnaire has two major parts (provided as Extended data in English)27. Part 1 is about demographic data. We collected data on gender, age, marital status, education, occupation, living duration in the community, distances between home and farmland, exposure to air pollution (i.e., cooking smoke, working in a factory with air pollution; asbestos, diesel engine exhaust, silica, wood dust, painting and welding exposure) and cigarette smoking. In Part 2, information on the historical use of pesticides were collected. In this study, pesticides were categorized into five groups: insecticides (organochlorine, organophosphate, carbamate, and pyrethoid), herbicides, fungicides, rodenticides, and molluscicides. For each groups of pesticides, we collected data on the numbers of years and days using pesticides. The data of lifetime pesticide exposure days were then computed by multiplying the total years of exposure by the number of days per year. This study also collected data on the use of 35 individual pesticides commonly found in Thailand.\n\nPesticide exposure data were collected by the researcher and two village health volunteers. Prior to data collection, all interviewers were trained on how to interview and properly use the questionnaire.\n\nCollected data were analysed using IBM SPSS Statistics (version 25) and OpenEpi (version 3.5.1). P values <0.05 were considered statistically significant. Demographic data was analysed using descriptive statistics. The associations were determined between lung cancer and groups of pesticides (herbicides, insecticides, fungicides, and molluscicides), between lung cancer and 17 individual compounds. Both crude and adjusted ORs with 95% confidence intervals (CIs) were presented. Adjusted ORs were analysed using multiple logistic regressions controlled for gender (male, female), age (≤54, 55–64, 65–74, and ≥75), cigarette smoking (ever, never smoke), occupation (farmer, non-farmer), and exposure to air pollution i.e., cooking smoke, and working in factory with air pollution (yes, no). In addition to the fundamental confounding factors, variables with statistically difference between cases and controls were included in a regression model.\n\nCumulative exposure days on groups of pesticides were categorized into quartiles (Q1-Q4; Q1 being the lowest exposure and Q4 the highest). The lung cancer risk was then predicted, using quartile 1 as a reference. For each specific pesticide, exposure data was categorized only to “ever used” and “never used”, but not the cumulative exposure days because number of subjects who reported using each pesticide was too small.\n\nThis study was approved by the Ethics Board of Naresuan University (project number 550/60). Written informed consent was obtained from each subject before the interviewing process.\n\n\nResults\n\nIn this study, most of study participants were male with a mean age of around 65. Both cases and controls have similar gender, age, marital status, education, occupation, period of residence, distances, pollution exposure, and cigarette smoking. More detailed demographic data among case and control groups were in Table 1 and in Underlying data28.\n\nN was 233 for case and 447 for control unless otherwise indicated.\n\nχ2 test for categorical data; t-test for continuous data with statistically significant (p<0.05).\n\n†Cooking smoke, working in factory with air pollution, etc.\n\nAfter adjusting for confounding factors, lung cancer was positively associated with historical exposure of study participants to herbicides, insecticides and fungicides (Table 2). The adjusted variables included in the analysis were gender (male, female), age (≤54, 55–64, 65–74, ≥75), cigarette smoking (ever smoke, never smoke), occupation (farmer, non-farmer), and exposure to air pollution, i.e., cooking smoke, and working in factories with air pollution (yes, no). Compared with people in the lowest quartile (Q1) of number of days using herbicides, those in Q2-Q4 days of using herbicides had an elevated risk of lung cancer with odds ratio (OR) between 6.32 (95% CI 2.57–15.53) for people with Q2 exposure, and 22.18 (95% CI 9.14–53.80) for Q4 exposure (p < 0.001). A similar association was also found for days of insecticide use and lung cancer (OR = 2.79 for Q2, and OR = 28.43 for Q4, p < 0.001). For fungicides, only the Q4 group had a significant risk (OR = 4.97; 95% CI 1.49–16.56). For individual compounds, lung cancer was statistically associated with a historical use dieldrin (OR = 2.76; 95% CI 1.42–5.36), chlorpyrifos (OR = 3.98; 95% CI 2.06–7.67), and carbofuran (OR = 2.58; 95% CI 1.48–4.51) (Table 3).\n\nLogistic regression adjusted for gender, age (≤54, 55–64, 65–74, and ≥75), cigarette smoking (ever smoke and never smoke), occupation (farmer and non–farmer), and pollution exposure (i.e., cooking smoke, and working in factory with air pollution).\n\nStatistically significant (p <0.05).\n\nP-values for linear trends were derived using a continuous variable with midpoint value of each category.\n\nLogistic regression adjusted for gender, age (≤ 54, 55–64, 65–74, and ≥ 75), cigarette smoking (ever smoke and never smoke), occupation (farmer and non-farmer), and exposure to air pollution (i.e., cooking smoke, and working in factory with air pollution).\n\n**Statistically significant (p < 0.05).\n\n\nDiscussion\n\nThe study results showed a positive association between lung cancer and the historical use of herbicides, insecticides, and fungicides (Table 3). The associations were closer for herbicides and insecticides, than for fungicides. For herbicides, compared to a group using the pesticides for less than 160 days (Q1), those in higher categories of days using herbicides all showed an elevated risk of lung cancer, with the highest among those using for more than 960 days (Q4) (OR = 22.18, 95% CI 9.14–53.80). A similar risk also presented among insecticide users. Lung cancer risk was found to increase in all categories of higher days using insecticides (Q2-Q4) with OR between 2.79 (95% CI 1.12–6.95) and 28.43 (95% CI 11.11–72.76). The highest category of years using insecticides (Q4) also showed a positive association with lung cancer (OR = 3.55; 95% CI 1.79–7.04). For fungicides, a significant association was found only among fungicide users at Q4 (>530 days) (OR = 4.97; 95% CI 1.49–16.56).\n\nThese results were consistent with literature indicating the potential carcinogenicity of pesticides29. In an experimental study, exposure to pesticides caused the production of reactive oxygen species (ROS), an oxygen-containing species containing an unpaired electron, such as superoxide, hydrogen peroxide, and hydroxyl radical, which are highly unstable and may cause DNA damage, protein damage, mutagenicity, necrosis, and apoptosis30. Pesticides may also increase the risk of cancer via other mechanisms including genotoxicity, tumour promotion, epigenetic effects, hormonal action and immunotoxicity31. In epidemiological study, evidence linked pesticide exposure to lung cancer are increasing, and the issue will be further discussed in the following section.\n\nFor individual pesticides, the study found lung cancer to be statistically associated with dieldrin (OR = 2.76; 95 % CI 1.42–5.36), chlorpyrifos (OR = 3.98; 95% CI 2.06–7.67), and carbofuran (OR = 2.58; 95% CI 1.48–4.51) (Table 3). Dieldrin is an extremely persistent organic pollutant linked to many health problems, e.g., Parkinson's disease, breast cancer, affecting the immunity system, the reproductive, and nervous systems32. In the USA, the Agricultural Health Study found seven pesticides including dicamba, metolaclor, pendimethalin, carbofuran, chlorpyrifos, diazinon, and dieldrin to be positively associated with lung cancer14. Further studies found dieldrin exposure to relate to the highest tertile of days use (RR = 5.30; 95% CI 1.50–18.60)33. In Thailand, 688 tons of dieldrin was used in 1981–1990, before it was banned on May 16, 1990.\n\nA study among pest control workers in Florida, USA found a long term exposure to organophosphate and carbamate insecticides to increase mortality risk of lung cancer (OR = 1.4; 95% CI 0.7–3.0) for subjects licensed from 10–19 year; OR = 2.1; 95% CI 0.8–5.5 for those licensed 20 year or more11. In the Agricultural Health Study, a dose response relationships was found between lung cancer and chlorpyrifos (RR = 2.18; 95% CI 1.31–3.64)17 and diazinon (RR = 3.46; 95% CI 1.57–7.65)18. Similar results were also replicated in later studies of the Agricultural Health Study cohort for chlorpyrifos (RR = 1.80; 95% CI 1.00–3.23), which are referring to applicators in the lowest category of exposure17. At this time, chlorpyrifos still not banned by Thai government. On the other hand, chlorpyrifos was the primary insecticide imported to Thailand (1,193,302 kilograms in 2013)34.\n\nFor carbofuran, it has demonstrated mutagenic properties in laboratory studies3. In the Agricultural Health Study, lung cancer risk of carbofuran for those with >109 days of lifetime exposure (RR = 3.05; 95% CI, 0.94–9.87) compared with those with < 109 lifetime exposure days35. In Thailand, a study reported 87 different commercial brands of insecticides which were used for 202 rice fields in Suphanburi Province (abamectin 40%, followed by chlorpyrifos 30%, and carbofuran 20%), 93 brands of plant hormones, and 56 brands of chemicals for the control of plant diseases36.\n\nThe major limitations of this case-control study were the recall bias where cases and controls can recall past exposure differently. Cases tend to memorize exposure better particularly when they know or are aware of exposure to cause their illness37. However, with limited available information on the issue in Thailand, we did not expected participants to aware of pesticides as causal factor for lung cancer. In addition, data on pesticide exposure were obtained solely from the interview questionnaire without any exposure measurement. However, this information bias usually occurs evenly across a case and control group, and only has a negative effect on the association38.\n\n\nConclusion\n\nThis study found that the occurrence of lung cancer among people in Nakhon Sawan province, Thailand is associated with pesticide use. Out of 17 individual pesticides investigated, dieldrin, chlorpyrifos, and carbofuran showed significant associations with lung cancer incidence. These results are consistent with the literature from other parts of the world. Further studies should focus on identifying more individual pesticides that could cause lung cancer, as well as other types of cancer.\n\n\nData availability\n\nFigshare: Pesticide and lung cancer. https://doi.org/10.6084/m9.figshare.12356270.v228.\n\nThis project contains the following underlying data:\n\nDataset_pesticide and lung cancer (SAV and CSV). (All underlying data gathered in this study.)\n\nData Dictionary (DOCX).\n\nFigshare: Questionnaire-pesticide and lung cancer Thailand. https://doi.org/10.6084/m9.figshare.12356384.v127.\n\nThis project contains the following extended data:\n\nQuestionnaire-pesticide and lung cancer Thailand (DOCX). (Study questionnaire in English.)\n\nData are available under the terms of the Creative Commons Zero “No right reserved” data waiver (CC0 1.0 Public domain dedication).", "appendix": "Acknowledgments\n\nFirst, our gratitude goes to the study participants, as without them, this study would not have been possible. We want to thank the village health volunteers for their help in data collection. We appreciate support by Dr. Adisorn Vatthanasak, chief of Nakhon Sawan Provincial Public Health Office. Thank you also to Mr. Kevin Mark Roebl of Naresuan University’s Writing Clinic for editing assistance.\n\n\nReferences\n\nBray F, Ferlay J, Soerjomataram I, et al.: Global cancer statistics 2018: GLOBOCAN estimates of incidence mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2018; 68(6): 394–424. PubMed Abstract \| Publisher Full Text\n\nInternational Agency for Research on Cancer: Thailand cancer statistics 2018: GLOBOCAN. World Health Organization, the Global Cancer Observatory-All Rights Reserved-May, 2019. Reference Source\n\nBrownson RC, Alavanja MC, Caporaso N, et al.: Family history of cancer and risk of lung cancer in lifetime non-smokers and long-term ex-smokers. Int J Epidemiol. 1997; 26(2): 256–263. PubMed Abstract \| Publisher Full Text\n\nParkin DM, Sasco AJ: Lung cancer: Worldwide variation in occurrence and proportion attributable to tobacco use. Lung Cancer J. 1993; 10(3–4): 266–286.\n\nHu J, Mao Y, Dryer D, et al.: Risk factors for lung cancer among Canadian women who have never smoked. Cancer Detect Prev. 2002; 26(2): 129–138. PubMed Abstract\n\nLeem JH, Kim HC, Ryu JS, et al.: Occupational Lung Cancer Surveillance in South Korea, 2006-2009. Safety Health Work. 2010; 1(2): 134–139. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKeller JE, Howe HL: Risk Factors for Lung Cancer Among Nonsmoking Illinois Residents. Environ Res. 1993; 60(1): 1–11. PubMed Abstract \| Publisher Full Text\n\nZhong L, Goldberg MS, Gao YT, et al.: Lung cancer and indoor air pollution arising from Chinese-style cooking among Nonsmoking women living in Shanghai, China. Epidemiology. 1999; 10(5): 488–494. PubMed Abstract\n\nAlavanja MCR, Bonner MR: Occupational pesticide exposures and cancer risk: a review. J Toxicol Environ Health B Crit Rev. 2012; 15(4): 238–263. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJungmann G: [Arsenic cancer in vintagers]. Landarzt. 1966; 42(28): 1244–1247. PubMed Abstract\n\nPesatori AC, Sontag JM, Lubin JH, et al.: Cohort mortality and nested case-control study of lung cancer among structural pest control workers in Florida (United States). Cancer Causes Control. 1994; 5(4): 310–318. PubMed Abstract \| Publisher Full Text\n\nLerro CC, Koutros S, Andreotti G, et al.: Use of acetochlor and cancer incidence in the Agricultural Health Study. Int J Cancer. 2015; 137(5): 1167–1175. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLuqman M, Javed MM, Daud S, et al.: Risk Factors for Lung Cancer in the Pakistani Population. Asian Pacific J Cancer Prev. 2014; 15(7): 3035–3039. PubMed Abstract \| Publisher Full Text\n\nAlavanja MC, Dosemeci M, Samanic C, et al.: Pesticides and lung cancer risk in the Agricultural Health Study cohort. Am J Epidemiol. 2004; 160(9): 876–885. PubMed Abstract \| Publisher Full Text\n\nPurdue MP, Hoppin JA, Blair A, et al.: Occupational exposure to organochlorine insecticides and cancer incidence in the Agricultural Health Study. Int J Cancer. 2007; 120(3): 642–649. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJones RR, Barone-Adesi F, Koutros S, et al.: Incidence of Solid Tumors Among Pesticide Applicators Exposed to the Organophhosphate Insecticide Diazinon in the Agricultural Health Study: An Updated Analysis. Occup Environ Med. 2015; 72(7): 496–503. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLee WJ, Blair A, Hoppin JA, et al.: Cancer incidence among pesticide applicators exposed to chlorpyrifos in the Agricultural Health Study. J Nati Cancer Inst. 2004; 96(23): 1781–1789. PubMed Abstract \| Publisher Full Text\n\nBeane Freeman LE, DeRoos AJ, Koutros S, et al.: Poultry and livestock exposure and cancer risk among farmers in the Agricultural Health Study. Cancer Causes Control. 2012; 23(5): 663–670. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHou L, Lee WJ, Rusiecki J, et al.: Pendimethalin Exposure and Cancer Incidence Among Pesticide Applicators. Epidemiology. 2006; 17(3): 302–307. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBonner MR, Lee WJ, Sandler DP, et al.: Occupational exposure to carbofuran and the incidence of cancer in the Agricultural Health Study. Environ Health Perspect. 2005; 113(3): 285–289. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNakhon Sawan Provincial Public Health Office: The report of cancer incidence cases in Thailand, Thai Cancer Based Online (TCB). Thai National Cancer Institute. 2018.\n\nKelsey JL, Whittemore AS, Evans AS, et al.: Methods in Observational Epidemiology. second edition. Oxford University Press. 1996; 444. Reference Source\n\nMazieres J, Pujol JL, Kalampalikis N, et al.: Perception of lung cancer among the general population and comparison with other cancers. J Thorac Oncol. 2015; 10(3): 420–425. PubMed Abstract \| Publisher Full Text\n\nDasgupta S, Meisner C, Wheeler D, et al.: Pesticide poisoning of farm workers-implications of blood test results from Vietnam. Int J Hyg Environ Health. 2007; 210(2): 121–132. PubMed Abstract \| Publisher Full Text\n\nWacholder S, McLaughlin JK, Silverman DT, et al.: Selection of Controls in Case-Control Studies: I. Principles. Am J Epidemiol. 1992; 135(9): 1019–1028. PubMed Abstract \| Publisher Full Text\n\nJuntarawijit C, Juntarawijit Y: Association between diabetes and pesticides: a case-control study among Thai farmers. Environ Health Prev Med. 2018; 23(1): 3. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJuntarawijit C: Questionnaire-pesticide and lung cancer Thailand. figshare. Dataset. 2020. http://www.doi.org/10.6084/m9.figshare.12356384.v1\n\nJuntarawijit C: Pesticide and lung cancer. figshare. Dataset. 2020. http://www.doi.org/10.6084/m9.figshare.12356270.v2\n\nParron T, Requena M, Hernandez AF, et al.: Environmental exposure to pesticides and cancer risk in multiple human organ systems. Toxicol Lett. 2014; 230(2): 157–165. PubMed Abstract \| Publisher Full Text\n\nAlavanja MC, Ross MK, Bonner MR: Increased Cancer Burden Among Pesticide Applicators and Others Due to Pesticide Exposure. CA Cancer J Clin. 2013; 63(2): 120–142. PubMed Abstract \| Publisher Full Text\n\nLyons G, Watterson A: A review of the role pesticides play in some cancer: children, farmers and pesticide users at risk. CHEM Trust report. 2010. Reference Source\n\nHelle RA, Marie VA, Thomas R, et al.: Effects of Currently Used Pesticides in Assays for Estrogenicity, Androgenicity, and Aromatase Activity in Vitro. Toxicol Appl Pharmacol. 2002; 179(1): 1–12. PubMed Abstract \| Publisher Full Text\n\nPurdue MP, Hoppin JA, Blair A, et al.: Occupational exposure to organochlorine insecticides and cancer incidence in the Agricultural Health Study. Int J Cancer. 2007; 120(3): 642–649. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTawatsin A, Thavara U, Siriyasatien P: Pesticides used in Thailand and toxic effects to human health. Med Res Archives. 2015. Publisher Full Text\n\nBonner MR, Lee WJ, Sandler DP, et al.: Occupational exposure to carbofuran and the incidence of cancer in the agricultural health study. Environ Health Perspect. 2005; 113(3): 285–289. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKaewboonchoo O, Kongtip P, Woskie S: Occupational Health and Safety for Agricultural workers in Thailand: Gaps and Recommendations, with a Focus on Pesticide Use. New Solut. 2015; 25(1): 102–120. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCoughlin SS: Recall bias in epidemiologic studies. 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PubMed Abstract \| Publisher Full Text" }	[ { "id": "65521", "date": "25 Jun 2020", "name": "Ann C Olsson", "expertise": [ "Reviewer Expertise Occupational cancer epidemiology", "lung cancer", "case-control studies", "cohort 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\nDear authors,\nI was pleased to review your paper that describes a case-control study in Thailand including 233 incident lung cancer cases and 458 controls focusing on exposures to pesticides. Please find enclosed my comments for your consideration. In the:\nIntroduction, first paragraph, I think you mean “Polycyclic aromatic hydrocarbons”? I would not call a paper from 1999 “Recent studies…..” because it’s >20 years old.\nMethods, first paragraph, it’s a case-control study, not a case-controlled study; it would be good to include a few more details such as any time limit for having resided in the province?; from where did the TCB receive cases?; were the diagnosis confirmed by some diagnostic tool? Please clarify if the 299 were contacted and 229 accepted, or if only 229 were contacted and accepted. I would be surprised if the latter, and wonder why the other were not contacted. We also wish to know the “participation rate” among the control subjects. Neighbours are not a random sample it’s a convenience sample. If you mean that the interviewer randomly selected control subjects among all neighbours you need to explain how this was done, e.g. within a distance from the house or “snowball” technique. Why do you adjust for farming (yes/no)? Please explain your rational. It does not make sense to me.\nQuestionnaire, the English questionnaire does not indicate that the number of days of pesticide use is per year, so it seems strange that lifetime exposure is calculated by multiplying years with days. Please also clarify if “exposure” refers to “personally mix or apply pesticides” only, or if it also includes working in the fields? Provide more details regarding the data collection e.g. were the interviewers employed for the study full-time, or were they students?, were there any quality control measures implemented, e.g. double interviews of a proportion of subjects, were the interviewers interviewing both cases and controls?\nResults, it is very strange that there is not difference between cases and controls regarding smoking, if you have an explanation for this please discuss it later.\nDiscussion, I don’t think that “the association were closer for herbicides and insecticides”, possibly “stronger” or “more pronounced”, and I prefer “more days” rather than “higher days”.\nAmong the limitations I think there is more to information bias, e.g. it is commonly difficult to assess exposure to specific chemicals because people don’t know the names or don’t recognize exposure. I must admit that I get suspicious that there are no missing in the data and no category for “don’t know” in the questionnaire. I would add potential selection bias to the discussion; although we don’t really know the participation rate among controls or how neighbours were selected, they are generally not an ideal control population.\n\nDisclaimer:\nWhere authors/reviewers are identified as personnel of the International Agency for Research on Cancer / World Health Organization, the authors/reviewers alone are responsible for the views expressed in this article and they do not necessarily represent the decisions, policy or views of the International Agency for Research on Cancer / World Health Organization\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?\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": [ { "c_id": "6164", "date": "22 Dec 2020", "name": "Chudchawal Juntarawijit", "role": "Author Response", "response": "Comment: Introduction, first paragraph, I think you mean “Polycyclic aromatic hydrocarbons”? I would not call a paper from 1999 “Recent studies…..” because it’s >20 years old. Response: The term was changed to polycyclic aromatic hydrocarbons. Comment: Methods, first paragraph, it’s a case-control study, not a case-controlled study; it would be good to include a few more details such as any time limit for having resided in the province?; from where did the TCB receive cases?; were the diagnosis confirmed by some diagnostic tool? Please clarify if the 299 were contacted and 229 accepted, or if only 229 were contacted and accepted. I would be surprised if the latter, and wonder why the other were not contacted. We also wish to know the “participation rate” among the control subjects. Neighbours are not a random sample it’s a convenience sample. If you mean that the interviewer randomly selected control subjects among all neighbours you need to explain how this was done, e.g. within a distance from the house or “snowball” technique. Why do you adjust for farming (yes/no)? Please explain your rational. It does not make sense to me. Response: The mistake was corrected and more information on residency, TCB, and diagnostic confirmation was added to the Methods. The information of the number of cases was clarified; and information on the participation rate was also provided. For the question, why did we adjust for farming? Actually, we tried to adjust for occupations since it is very likely that they will be exposed to pesticides differently. At first, there were several types of occupations, but due to the small number of participants in each category, the groups were limited to “farmer” and “none-farmer”. These two groups tended to have different risks of exposure to environmental pesticides, due to the nature of their work and physical health. Comment: Questionnaire, the English questionnaire does not indicate that the number of days of pesticide use is per year, so it seems strange that lifetime exposure is calculated by multiplying years with days. Please also clarify if “exposure” refers to “personally mix or apply pesticides” only, or if it also includes working in the fields? Provide more details regarding the data collection e.g. were the interviewers employed for the study full-time, or were they students?, were there any quality control measures implemented, e.g. double interviews of a proportion of subjects, were the interviewers interviewing both cases and controls? Response: More information was added and the mistakes were corrected. In this study, “exposure” refers to “personally mixed and/or applied pesticides” only, not working in the field. More information of interviewers was added to the methods. There were no other quality control measures implemented. Comment: Results, it is very strange that there is not difference between cases and controls regarding smoking, if you have an explanation for this please discuss it later. Response: Data on cigarette smoke was reanalyzed and the difference was observed using a new category. Comment: Discussion, I don’t think that “the association was closer for herbicides and insecticides”, possibly “stronger” or “more pronounced”, and I prefer “more days” rather than “higher days”. Response: The term “closer” was changed to “stronger” Comment: Among the limitations, I think there is more to information bias, e.g. it is commonly difficult to assess exposure to specific chemicals because people don’t know the names or don’t recognize exposure. I must admit that I get suspicious that there are no missing in the data and no category for “don’t know” in the questionnaire. I would add potential selection bias to the discussion; although we don’t really know the participation rate among controls or how neighbours were selected, they are generally not an ideal control population. Response: Yes, we agree that it was likely that some of participants could not recall or know the name of the pesticides used. If this type of bias occurs it would be equal between both the case and control groups, and minimize the association between exposure to pesticides and lung cancer. More information regarding bias was added to the Discussion section, and more information about the control group was added to the Methods. Those who could not recall or “don’t know” the name of the pesticides were categorized as “not used”." } ] }, { "id": "73264", "date": "30 Oct 2020", "name": "Matthew R Bonner", "expertise": [ "Reviewer Expertise Cancer epidemiology", "pesticides", "air pollution", "occupational and environmental 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\nThe manuscript reports the results of a case-control study designed to investigate exposure to pesticides and lung cancer. Cases and controls were recruited between January 1, 2014, and March 31, 2017, from Nakhon Sawan Province, Thailand. Controls were matched to cases on age and sex. Pesticide exposure was assessed with interviews with a structured questionnaire inquiring about days and years of pesticide use. Logistic regression, adjusting for potential confounders, was used to estimate the odds ratio and 95% confidence intervals. Pesticide classes (herbicides and organophosphate) and select specific pesticides were positively associated with lung cancer in this study. The authors conclude that “…lung cancer among Thai people in Nakhon Sawan province is associated with previous pesticide use.” Overall, the study seems to be designed well, but crucial information regarding several specific details are missing from the report. These details, and other concerns, are described below.\nComments:\nCrucial information about the lung cancer cases is missing. Specifically, were the cases comprised of 1st primary lung cancer or were lung cancer cases with a prior history of another cancer, including lung, eligible to participate in the study. Were the lung cancer cases’ diagnosis histologically confirmed? What was the stage and grade of these lung cancer cases? On average, how long after their diagnosis were lung cancer cases interviewed?\n\nWere potential controls excluded if they had a prior history of cancer?\n\nThe methods state that two neighbor controls were selected randomly. This implies that there a sampling frame of some sort. That sampling frame for random selection needs to be adequately described.\n\nThe controls were matched on age and sex to the cases. This necessitates a conditional logistic regression to account for the selection bias introduced by matching. Unconditional logistic regression is inappropriate for a matched case-control study. Breaking the matching and adjusting for the matching factors may not bias the odds ratios, but this should be confirmed by comparing ORs estimated with unconditional logistic regression and conditional logistic regression.\n\nIn table 2, there is striking qualitative confounding for the pesticide classes (yes vs. no). For instance, the crude OR organophosphates is 0.63 (95% CI = 0.46-0.87) while the adjusted OR is 1.77 (95% CI = 1.22-2.57). The use of unconditional logistic regression might explain this as the crude estimate for such a regression is inappropriate. That notwithstanding, a number of other variables were included in the regressions. Given this qualitative confounding, additional analyses to identify variables or combination of variables is driving this confounding is warranted.\n\nTobacco smoking is a recognized strong risk factor for lung cancer and a known potential confounder in studies of other exposures and lung cancer. As such, substantial efforts to mitigate confounder are often employed. In this study, smoking was a binary (ever vs. never) variable that may not adequately capture the interrelationship between pesticide use and lung cancer to control confounding. More detailed smoking information, if available, should be explored to determine the potential for residual confounding of the reported associations\n\nIn table 1, smoking is not associated with lung cancer. This suggests that selection forces in the recruitment of cases and controls are biasing the study results. It seems unusual that 61% of lung cancer cases were never smokers. Is this a typical feature of lung cancer in Thailand?\n\nThe results reported in tables 2 and 3 seem to be internally inconsistent. For instance, the ORs for organophosphates depicted in table 4 indicate a strong association with lung cancer with days of use (Q4 vs. Q1 OR = 28.43 (95% CI = 11.11-72.76); an extremely large magnitude. However, the ORs for specific organophosphate insecticides are much more modest, although the statistically significant associations with chlorpyfos and dielrin. A similar pattern is evident for herbicide as well. This lack of internal consistency really points to the methodological limitations as a likely explanation for the observed association.\n\nRecall bias was discussed as a limitation, but nothing is mentioned about other threats to internal validity. For instance, the potential for selection bias to arise from the recruitment strategies. As mentioned above, the lack of an association with smoking seems to indicate something is awry. In addition, exposure misclassification is undoubtedly present and should be discussed in the Discussion along with the other potential limitations.\n\nReferences 20 and 35 are the same report.\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?\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": "6165", "date": "22 Dec 2020", "name": "Chudchawal Juntarawijit", "role": "Author Response", "response": "Comment: 1. Crucial information about the lung cancer cases is missing. Specifically, were the cases comprised of 1st primary lung cancer or were lung cancer cases with a prior history of another cancer, including lung, eligible to participate in the study. Were the lung cancer cases’ diagnosis histologically confirmed? What was the stage and grade of these lung cancer cases? On average, how long after their diagnosis were lung cancer cases interviewed? Response: The cases comprised of 1st primary lung cancer. The cases were confirmed by Computerized Tomography scan (CT scan), Magnetic Resonance Imaging (MRI), ultrasound of the whole abdomen, and chest radiography or Chest X-ray (CXR), and histology of primary and metastasis. More information was added to Table 1, and provided in the Table below. On average, the patients were interviewed approximately1 year after they had been diagnosed with lung cancer. Table. More information on morphology and stage of the study cases. Morphology of lung cancer cases: Adenocarcinoma 114 (48.9) Small cell carcinoma 21 (9.0) squamous cell carcinoma 17 (7.3) Large cell carcinoma 9 (3.9) Neoplasm/ malignant 68 (29.2) Unspecified 4 (1.7) Stage IA, IB 14 (6.0) IIA, IIB 38 (16.3) IIIA, IIIB 57 (24.5) IV (Distant metastasis) 0 (0) Unknown/ unspecified 124 (53.2) Comment: 2. Were potential controls excluded if they had a prior history of cancer? Response: Yes, potential controls were excluded if they had a prior history of cancer. Comment: 3. The methods state that two neighbor controls were selected randomly. This implies that there a sampling frame of some sort. That sampling frame for random selection needs to be adequately described. Response: The control was, in fact, selected using convenience sampling. The information in the manuscript has been revised. Comment: 4. The controls were matched on age and sex to the cases. This necessitates a conditional logistic regression to account for the selection bias introduced by matching. Unconditional logistic regression is inappropriate for a matched case-control study. Breaking the matching and adjusting for the matching factors may not bias the odds ratios, but this should be confirmed by comparing ORs estimated with unconditional logistic regression and conditional logistic regression. Response: Matching of a few variables can be considered loose-matching, therefore, it is more appropriate to analyze using unconditional logistic regression. Kuo and team (2018) said that “There is a presumption that matched data need to be analyzed by matched methods. Conditional logistic regression has become a standard for matched case–control data to tackle the sparse data problem. The sparse data problem, however, may not be a concern for loose-matching data when the matching between cases and controls are not unique, and one case can be matched to other controls without substantially changing the association. Data matched on a few demographic variables are clearly loose-matching data, and we hypothesize that unconditional logistic regression is a proper method to perform.” (Kuo, Duan & Grady, 2018)* We gained interesting information by analyzing some of the data using Cox regression. The comparison between unconditional analysis and the Cox regression, yielded similar results. (see Table below). Comparing OR between Cox regression and logistic regression). Table. Comparing OR between Cox regression and logistic regression. Logistic regression Cox regression Endosulfan OR (cr ude) 1.61 (1.00–2.60) 2.01 (1.12-3.63) OR (adjusted) 1.60 (0.97–2.63) 1.81 (0.99-3.33) Dieldrin OR (crude) 2.45 (1.32–4.53) 3.28 (1.57-6.85) OR (adjusted) 2.56 (1.36–4.81) 3.62 (1.70-7.68) Chlorpyrifos OR (crude) 2.88 (1.74–4.76) 3.50 (1.91-6.41) OR (adjusted) 3.29 (1.93–5.61) 3.85 (2.05-7.22) Carbofuran OR (crude) 2.18 (1.37–3.45) 2.36 (1.43-3.89) OR (adjusted) 2.10 (1.28–3.42) 2.38 (1.41-4.01) *Kuo C-L, Duan Y and Grady J (2018) Unconditional or Conditional Logistic Regression Model for Age-Matched Case–Control Data? Front. Public Health 6:57. doi: 10.3389/fpubh.2018.00057 Comment: 5. In table 2, there is striking qualitative confounding for the pesticide classes (yes vs. no). For instance, the crude OR organophosphates is 0.63 (95% CI = 0.46-0.87) while the adjusted OR is 1.77 (95% CI = 1.22-2.57). The use of unconditional logistic regression might explain this as the crude estimate for such a regression is inappropriate. That notwithstanding, a number of other variables were included in the regressions. Given this qualitative confounding, additional analyses to identify variables or combination of variables is driving this confounding is warranted. Response: After re-categorizing the smoking variable, and correcting a mistake on the variable coding, the new analysis yielded more consistent results with crude OR at 1.35 (95%CI 0.98-1.86) and adjusted OR at 1.40 (95%CI 0.97-2.02). 6. Tobacco smoking is a recognized strong risk factor for lung cancer and a known potential confounder in studies of other exposures and lung cancer. As such, substantial efforts to mitigate confounder are often employed. In this study, smoking was a binary (ever vs. never) variable that may not adequately capture the interrelationship between pesticide use and lung cancer to control confounding. More detailed smoking information, if available, should be explored to determine the potential for residual confounding of the reported associations We actually collected data on the amount of cigarettes and smoking duration of the study participants, and then the information was used to compute number of cigarettes smoked by them in their life time. After grouping smoking status into “never smoked”, “smoked <109500 cigarettes”, and “smoked ≥109500 cigarettes”, a significant difference between case and control was found. The data was then used for the analysis of the odds ratio. Comment: 7. In table 1, smoking is not associated with lung cancer. This suggests that selection forces in the recruitment of cases and controls are biasing the study results. It seems unusual that 61% of lung cancer cases were never smokers. Is this a typical feature of lung cancer in Thailand? Response: Yes, 61% of the cases never smoked is acceptable. It was reported that smoking prevalence of Thai males decreased from 60% to 39%, and from 5% to 2.1% in females between 1991 and 2014 [1]. While a survey in 2017 reported a smoking prevalence of 20.7% of the total adult population over 15 years old [2]. It was interesting to note that in this study, 49.2% of the cases were adenocarcinoma lung cancer which has a limited relation to cigarette smoking, whereas squamous cell, and small cell lung carcinoma are highly related to smoking [3, 4]. [1] Jeon J, Sriplung H, Yeesoonsang S, Bilheem S, Rozek L, and et al. Temporal Trends and Geographic Patterns of Lung Cancer Incidence by Histology in Thailand, 1990 to 2014. Journal of Global Oncology 2018. [2] Tobacco Control Research and Knowledge Management Center (TRC). Annual Report of Thailand Tobacco Survey, 2018. Mahidol University. www.trc.or.th. 2018. [3] Wu K, Wong E, and Chaudhry S. Lung Cancer; Classification of invasive lung cancer. Clin Chest Med 2002; Mar; 23(1):65-81. [4] Limsila T, Mitacek EJ, Caplan LS, and Brunnemann KD. Histology and Smoking History of Lung Cancer Cases and Implications for Prevention in Thailand. Preventive Medicine 1994; 23:249-252. Comment: 8. The results reported in tables 2 and 3 seem to be internally inconsistent. For instance, the ORs for organophosphates depicted in table 4 indicate a strong association with lung cancer with days of use (Q4 vs. Q1 OR = 28.43 (95% CI = 11.11-72.76); an extremely large magnitude. However, the ORs for specific organophosphate insecticides are much more modest, although the statistically significant associations with chlorpyfos and dielrin. A similar pattern is evident for herbicide as well. This lack of internal consistency really points to the methodological limitations as a likely explanation for the observed association. Response: In this study, we actually collected data from 35 individual pesticides, but 17 of them were excluded due to small sample size (less than 5 in each cell). Therefore, the OR groups may be larger than the individual OR ones. Comment: 9. Recall bias was discussed as a limitation, but nothing is mentioned about other threats to internal validity. For instance, the potential for selection bias to arise from the recruitment strategies. As mentioned above, the lack of an association with smoking seems to indicate something is awry. In addition, exposure misclassification is undoubtedly present and should be discussed in the Discussion along with the other potential limitations. Response: The problems of selection bias and exposure misclassification has been further discussed in the manuscript as suggested. The problem of lack of association with smoking has already been solved. Comment: 10. References 20 and 35 are the same report. Rsponse: The error has been corrected." } ] } ]	1	https://f1000research.com/articles/9-492
https://f1000research.com/articles/12-740/v1	26 Jun 23	{ "type": "Research Article", "title": "Quality of life among patients with chronic heart failure in Nam Dinh Province, Vietnam", "authors": [ "Hoang Huy Ngo", "Ly Thi Hai Tran", "Nguyet Thi Nguyen", "Anh Thi Lan Mai", "Hoang Huy Ngo", "Ly Thi Hai Tran", "Nguyet Thi Nguyen" ], "abstract": "Background: This study aimed to assess the quality of life of patients with chronic heart failure (HF) to improve their treatment and care. Methods: This study was conducted to evaluate the quality of life of 89 patients suffering from chronic heart failure and was assessed using the Minnesota Living with Heart Failure Questionnaire (MLHFQ). In addition, the presence of depressive symptoms and perception of social support were also assessed by the Beck Depression Inventory-II (BDI-II) and the Multidimensional Scale of Perceived Social Support (MSPSS). Results: Of the 89 HF patients, 53.9% were female and 46.1% were male. The mean age of 89 patients was 62.28±13.26 years old, of which 64% were 60 years old and older. The mean time that patients lived with HF was 8.49±4.59 years. The overall Minnesota Living with Heart Failure Questionnaire mean score was high at 67.19±13.31 points. Regarding personal characteristics, the Minnesota Living with Heart Failure Questionnaire scores were significantly higher in women vs men, widowed/divorced vs being married patients, and patients living alone vs living with family detailed (67.52±11.80 vs 66.80±15.02; p=0.032), (67.58±11.62 vs 65.27±20.11; p=0.000), and (73.3±14.95 vs 66.50±13.04; p=0.014), respectively. Regarding heart failure associated features, the Minnesota Living with Heart Failure Questionnaire scores were significantly higher in patients living with longer heart failure, in more severity of Beck Depression Inventory-II, and lower levels of social support (all p-values of 0.000). Conclusions: The results of the study showed a poor quality of life in patients with chronic heart failure and raised concerns about improving the patients’ quality of life.", "keywords": [ "Heart failure", "patients", "quality of life", "Vietnam" ], "content": "Introduction\n\nIn addition to population aging and improvements in cardiovascular diagnosis and treatment, heart failure (HF) is a global clinical and public health problem that is increasing at an alarming rate worldwide.1 HF is associated with increased morbidity and mortality, places a significant burden on the health care system, and is one of the leading causes of hospitalization for adults and the elderly.2 Along with advances in disease diagnosis and treatment, assessing the quality of life (QoL), especially in chronic patients who have to live for many years with the same disease, is considered as one of the important activities in promotion of patient-centred care in which the patient’s views, experiences, and wishes are set forth, help with care decision-making, and ensures that the patient’s wishes are taken into account to guide better management of their condition.3,4\n\nStudies on QoL in patients with chronic HF reflect a common fact that the patients’ QoL was low.5,6 In recent years in Vietnam, as the role of nursing care has been increasingly confirmed, assessment of QoL in patients with chronic conditions, including heart failure, has begun to gain more attention. Beside progress in diagnosis and treatment of HF patients in Nam Dinh province, the patient’s QoL need to be concerned. This study was conducted to assess the QoL of patients with chronic HF in the Province, as baseline data for planning to improve the quality of care and healthcare provision.\n\n\nMethods\n\nThe descriptive study design was used and the sample size was conducted by using the sample size formular for descriptive study\n\nn: The appropriate sample size with probability α = 0.05 with Z1-α/2 = 1.96; p: Estimating the rate of good quality of live in patients with heart failure (p = 0.785); d: margin of error, d = 0.08. Substituting into the formula, the study sample size was 72. Finally, the sample size consisted of 89 HF patients who were conveniently selected from March 2022 to May 2022 at Nam Dinh Provincial Genereal Hospital, Vietnam.\n\nCriteria for selecting patients into the study included i) age from 18 years old and above, ii) diagnosed with HF, iii) be able to read and write with no matter affecting the ability to communicate, iv) agree to participate in the study. The exclusion criteria were i) patients in a severe condition requiring intensive care; ii) patients with other chronic diseases such as chronic kidney disease (CKD); cirrhosis; chronic obstructive pulmonary disease (COPD); diabetes mellitus; rheumatoid arthritis, etc., which affecting her/his quality of life; iii) patients was first diagnosed with heart failure. The data collection was conducted while the patients received treatment at the Cardiology Department.\n\nGeneral strategies we employed to address sources of bias in the proposed study\n\nStudy design: Choosing an appropriate study design and using appropriate control or comparison groups can help minimize biases. Randomizing the allocation of participants to different groups and implementing blinding (single-blind or double-blind) can help reduce selection and information bias. Sample size calculation: Conducting a sample size calculation before the study helps to ensure an adequate number of participants to achieve statistically meaningful results, which can reduce the impact of bias. Participant recruitment: Employing a systematic and unbiased approach to participant recruitment can help to minimize selection bias. This may involve using predefined inclusion and exclusion criteria and avoiding preferential selection of certain individuals. Data collection and measurement: Implementing standardized protocols and validated tools for data collection and measurement can help ensure consistency and accuracy, and reduce measurement bias.\n\nFor personal characteristics of the participated patients, age, gender, job, education, marital status, and living status and for features related to heart failure, stage of HF, feeling depressed, and social support were collected.\n\nBased on New York Heart Association (NYHA)7 classifications, heart failure patients are divided into four stages: NYHA I: Patients who have cardiac disease without any resulting limitations on physical activity. In NYHA II, patients had cardiac disease that slightly limited their physical activity. They were comfortable when at rest. In NYHA III patients, there was marked restriction in physical activity due to cardiac disease. They felt comfortable while resting. NYHA IV: Patients were unable to perform physical activity without discomfort owing to cardiac disease. Symptoms of anginal syndrome or cardiac insufficiency can manifest at rest.\n\nIn order to measure the QoL of HF patients, this study used the Minnesota Living with Heart Failure Questionnaire (MLHFQ), a commonly used tool to measure the HF patients’ QoL,8 the MLHFQ consists of 21 questions, each valued from 0 to 5, asked the patient how much the heart failure affected her/his life during the past 4 weeks, corresponding to from “No” to “Very much”. The total score ranged from 0 to 105 points, the overall MLHFQ score of each patient was calculated from the scores for all questions, the higher overall MLHFQ scores indicate the poorer QoL. The scores were classified into 3 levels9: < 24 points, 24 – 45 points and > 45 points correspond to high, moderate and poor levels of QoL, respectively.\n\nTo assess the presence and severity in depressive symptoms, the Beck Depression Inventory-II (BDI-II),10 the BDI-II consists of 21 self-reported items from 0 to 3 points and a range of scores from 0 to 63 points, classified into 4 levels11: 0–13 points, 14–19 points, 20–29 points and 30–63 points correspond to no depression, mild depression, moderate depression and severe depression, respectively.\n\nThe Multidimensional Scale of Perceived Social Support, a 12-item report of perceived adequacy of social support from three sources: family, friends, and significant other12 was also used in this study, each report has 7 choices from 1 corresponding to “Strongly disagree” to 7 corresponding to “Strongly agree” and the scores range from 12–84 points, divided into 3 levels13: 12–48 points, 49–68 points, 69–84 points correspond to low, moderate and high levels of social support, respectively.\n\nThis study was approved by Nam Dinh University Scientific and Human Research Ethics Committee (IRB-VN01012: No.469/GCN-HDĐD dated 03/3/2022). The purpose of the study was explained to patients who met the inclusion criteria. The study involved voluntary participation, anonymity was preserved, and the participants signed consent forms before participating. All patients were informed that they could refuse to participate or discontinue participation at any time.\n\nThe characteristics and features of the participants were described using frequency, percentage, mean, and standard deviation. ANOVA and T-tests were used if more than two means needed to be compared. Statistical significance was determined at a p-value of 0.05, and the data were analyzed using SPSS statistical software, version 25.\n\n\nResults\n\nThe mean age of 89 patients in the study was 62.28 ± 13.26 years (median: 65), the youngest was 33 years old and the oldest was 88 years old.24 The mean duration living with HF since the first HF diagnosis was 8.49 ± 4.59 years (median: 8), the shortest was 1 year and the longest was 21 years. All the 89 participants selected based on the criteria completed the study.\n\nThe overall Minnesota Living with Heart Failure Questionnaire (MLHFQ) mean score of 89 patients was 67.19 ± 13.31 points, the lowest score was 33 points and the highest score was 98 points. There were 89.9% of the total patients who had the overall MLHFQ score more than 45 points and no one had MLHFQ score less than 24 points. The scores of physical and emotional domains were 25.78 ± 5.98 points and 16.80 ± 4.19 points, respectively.\n\nThe majority of patients (64%) were over 60 years old and the proportions of male and female patients were 46.1% and 53.9%, respectively. More than half of participants (57.3%) were farmers. Regarding educational level, 42.7% of participants graduated from secondary school, no one had a university degree or higher. The percentages of patients living with a spouse and living with family were 83.1% and 89.9%, respectively.\n\nThe MLHFQ scores were higher (i.e. poorer QoL) in female patients compared with male patients (67.52 ± 11.80 points vs 66.80 ± 15.02 points; p-value of 0.032), divorced; single; widowed patients compared with married patients (67.58 ± 11.62 points vs 65.27 ± 20.11 points; p-value of 0.000), patients living alone compared with patients living with family (73.33 ± 14.95 points vs 66.50 ± 13.04 points; p-value of 0.014).\n\nThe number of patients lived with HF for 6-10 years, had NYHA-III, had severe depressive symptoms, and perceived low social support accounted for high percentages in the study sample which were 48.3%, 50.5%, 89.9%, and 86.5%, respectively.\n\nThe MLHFQ scores were higher (i.e. poorer QoL) in patients lived longer with HF, had more severe heart failure, had more severe depression, and had lower levels of social support in comparison with patients who had lower levels of corresponding features (all p-values of 0.000).\n\n\nDiscussion\n\nThe mean age of the HF patients in our study was 62.28 ± 13.26 years old. This age may be similar to or different from the age of HF patients in other studies regarding HF for example, it was 62.9 ± 14.6 years old in the study by Pressler et al. (2010)14; 64.4 ± 15.0 years old in the study by T.N.P. Do et al. (2019)15; 77.8 ± 5.9 years old in the study by Erceg et al. (2013)16; or 65.8 ± 12.9 years old in the study by Nesbitt et al. (2014).17 These age differences may be due to differences in the sample size, study time, and country. However, they reflect that population aging and heart failure tend to increase with age, especially at ≥ 60 years.18\n\nA systematic review and meta-analysis of 60 studies after the screening of 5423 studies showed a change in survival with chronic heart failure with an improvement in 5-year HF survival.19 In our study, the number of years patients had been living with HF was 8.49 ± 4.59 years. This number is not yet representative of the population of HF patients due to the small sample size and convenient sampling. However, it has contributed to the proof that patients with HF live longer thanks to the progress in HF diagnosis and treatment in the province and Vietnam. This is accompanied by a trend of increasing life expectancy, raising concerns about the quality of life of patients with HF, and a genuine need to improve the quality of life of HF patients.\n\nThe overall MLHFQ score of HF patients in our study was 67.19 ± 13.31 points (Table 1). A potential source of bias could be the sample size. The small sample size could limit the generalizability of our findings. Additionally, the use of self-reported surveys could lead to bias, as patients might overreport or underreport their symptoms. Finally, the researchers’ personal beliefs or interests could also influence the results, highlighting the need for transparency and ethical conduct in research. Evaluating and addressing these potential sources of bias is crucial to ensure the validity and reliability of the study, thus providing accurate information for healthcare providers to improve health outcomes for patients with chronic heart failure in Vietnam. According to the classification of Behlouli et al.,9 HF patients with MLHFQ scores > 45 points were considered to have poor QoL. In other words, although the study was the first to assess the QoL at a provincial hospital, it revealed a very low level of QoL, which needs to be addressed to improve accompanied advances in diagnosis and treatment. In comparison with the MLHFQ scores of HF patients in studies recently published, the MLHFQ score in our study was quite similar to the MLHFQ score of 74.16 ± 3.78 points in the study of Zhang et al. (2019) in China.20 Meanwhile, it was much higher (i.e., much poorer QoL) than the MLHFQ score of 35.8 ± 21.4 points in the study of Fonseca et al. (2021) in Europe.21 These differences might be explained by the study of Fonseca et al., which measured the QoL among HF patients in France, Germany, Italy, Spain, and the United Kingdom, where better care deliveries have been available and in contrast, Vietnam and China are populated countries where in general, people’s living conditions have been limited. They feel it is harder to live with HF’s condition. Regarding the classification of quality of life, in our study, the majority (89.9%) of patients had a poor QoL (MLHFQ score > 45 points, based on the classification of Behlouli et al.9), the remaining small number of patients (10.1%) had a moderate level of QoL. None had a high QoL (MLHFQ score < 24 points), which was also consistent with a common situation as mentioned in the study by Moradi et al. (2020)5 and in the study by Polikandrioti et al. (2019).6\n\nAs seen in Table 2, the female patients had poorer QoL (i.e., higher MLHFQ scores) than the male patients. Regarding the QoL of female and male patients, it is likely to see different results in different studies. For example, the study of Polikandrioti M et al.1 in 100 HF patients found no difference in the MLHFQ scores between male and female patients. In comparison, Fonseca A.F. et al.21 studied 804 HF patients. The results showed that the MLHFQ score of female patients (n = 223) was higher than that of male patients (n = 401) detailed (37.9 ± 20.9 points vs. 34.6 ± 21.6 points; p = 0.0481). In Vietnam, in terms of cultural traditions, the majority of women, besides working to earn, also have to shoulder a lot of responsibility, including raising children and housework, even for the logistics of family, relatives, and clan events. Their life becomes more complicated when having an illness, especially with chronic heart failure, resulting in feeling that their QoL is poor, which may be a reasonable explanation for the poorer QoL in female HF patients than in male patients HF patients in this study. Table 2 also shows that the group of patients in single, divorced, and widowed conditions had poorer QoL than those in the married group. The group of patients living alone had poorer QoL than those living with their families. Persons living in conditions of single, divorced, widowed, and alone, together with Vietnamese customs, are likely to be disadvantaged and vulnerable. Naturally, bearing the burden of chronic heart failure without supporting/sharing with a wife/husband or family members will make them feel complicated and worse about life. These findings should be considered when planning and delivering care to HF patients.\n\nAs shown in Table 3, patients with HF living with longer HF, more severe HF, more severe depression, and lower levels of social support had poorer QoL. Other studies, for example, the study of Audi,22 the study of Nesbitt et al.,17 and the study of Erceg et al.,16 also had similar results. It is reasonable for these results because heart failure tends to worsen over time with increasing severity of symptoms, which may initially have only a slight effect on patients’ activities, gradually reduce the patient’s independence in daily living activities, and seriously affect the patient’s life.23 These findings should be considered when planning care for HF patients, taking into account factors that worsen the patient’s QoL to improve the patient’s quality of life with appropriate support.\n\n\nConclusion\n\nThis study showed a poor QoL of the HF patients with the MLHFQ score of 67.19 ± 13.31 points and factors those made the HF patients’ QoL worse such as gender, marital and living status, HF duration, NYHA classification, depression, and social support. Health professionals need to understand and focus more on the quality of life (QoL) of patients with chronic heart failure to plan effective interventions and provide them with beneficial and holistic care.", "appendix": "Data availability\n\nHuy Ngo, Hoang; Thi Hai Tran, Ly; Thi Nguyen, Nguyet; Thi Lan Mai, Anh (2023). Quality of Life among Patients with Chronic Heart Failure in Nam Dinh Province, VietNam. figshare. Dataset. https://doi.org/10.6084/m9.figshare.22779302.v3. 24\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nPolikandrioti M, et al.: Factors associated with depression and anxiety of hospitalized patients with heart failure. Hell. J. Cardiol. 2015; 56(1): 26–35. PubMed Abstract\n\nZiaeian B, et al.: Epidemiology and aetiology of heart failure. Nat. Rev. Cardiol. 2016; 13(6): 368–378. 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PubMed Abstract \| Publisher Full Text\n\nWang YP, et al.: Assessment of depression in medical patients: a systematic review of the utility of the Beck Depression Inventory-II. Clinics. 2013; 68: 1274–1287. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZimet GD, et al.: The multidimensional scale of perceived social support. J. Pers. Assess. 1988; 52(1): 30–41. Publisher Full Text\n\nZimet GD, et al.: Psychometric characteristics of the multidimensional scale of perceived social support. J. Pers. Assess. 1990; 55(3-4): 610–617. Publisher Full Text\n\nPressler SJ, et al.: Cognitive deficits and health-related quality of life in chronic heart failure. J. Cardiovasc. Nurs. 2010; 25(3): 189–198. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDo TNP, et al.: Effect of the Optimize Heart Failure Care Program on clinical and patient outcomes - The pilot implementation in Vietnam. IJC Heart Vasc. 2019; 22: 169–173. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nErceg P, et al.: Health-related quality of life in elderly patients hospitalized with chronic heart failure. Clin. Interv. Aging. 2013; 8: 1539–1546.\n\nNesbitt T, et al.: Correlates of quality of life in rural patients with heart failure. Circ. Heart Fail. 2014; 7(6): 882–887. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLippi G, Sanchis-Gom F: Global epidemiology and future trends of heart failure. AME Med. J. 2020; 5(15): 1–6.\n\nJones NR, et al.: Survival of patients with chronic heart failure in the community: a systematic review and meta-analysis. Eur. J. Heart Fail. 2019; 21: 1306–1325. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhang R, et al.: Improvement in quality of life of Chinese chronic heart failure patients with neuropsychiatric complications over 12-months post-treatment with metoprolol. Medicine (Baltimore). 2019 Jan; 98(4): e14252. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFonseca AF, et al.: Burden and Quality of Life Among Female and Male Patients with Heart Failure in Europe: A Real-World Cross-Sectional Study. Patient Prefer. Adherence. 2021; 15: 1693–1706.\n\nAudi G, et al.: Factors affecting health related quality of life in hospitalized patients with heart failure. Cardiol. Res. Pract. 2017; 2017: 1–12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDunlay SM, et al.: Activities of daily living and outcomes in heart failure. Circ. Heart Fail. 2015; 8(2): 261–267. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHuy Ngo H, Thi Hai Tran L, Thi Nguyen N, et al.: Quality of Life among Patients with Chronic Heart Failure in Nam Dinh Province, VietNam. [Dataset]. figshare. 2023. Publisher Full Text" }	[ { "id": "208217", "date": "19 Apr 2024", "name": "Konstantinos Giakoumidakis", "expertise": [ "Reviewer Expertise Clinical Nursing", "Cardiovascular Nursing", "Chronic Diseases Management" ], "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, I would like to thank you for submitting your work to the journal. According to my evaluation, many concerns have been raised, so I have made the following comments:\nThe introduction is too short. Please give a more comprehensive introduction focusing on the definition of the problem, a brief relevant literature review, the aim of the study, and what new knowledge this study is expected to add to the existing body of knowledge. The study has a significantly small sample size that affects its representability, leading to a problematic ability to generalize the present study findings to a wide population of heart failure patients. Have the instruments used (MLHFQ, BDI-II, Multidimensional Scale of Perceived Social Support) been translated into Vietnamese and validated for the study population? The potential lack of instruments’ translation and validation is a significant weakness of the present study that negatively affects its reliability and validity. In addition, Cronbach’s alpha values for these instruments have not been given regarding the measurement of the tools’ internal consistency and reliability. The study sample consists of heart failure patients at any stage of the NYHA classification. This is a pivotal issue for lacking sample homogeneity, leading to results of low reliability. Why did you exclude from your study patients who were first diagnosed with heart failure? This criterion seems confusing. The study findings have a significant lack of novelty, and they are expectable. In my opinion, the study does not add new data to the existing body of knowledge.\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\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-740
https://f1000research.com/articles/11-4/v1	04 Jan 22	{ "type": "Case Report", "title": "Case Report: Anorexia as a new type of adverse reaction caused by the COVID-19 vaccination: a case report applying detailed personal care records", "authors": [ "Soichi Osozawa" ], "abstract": "Background: In Japan, more than 1,000 participants died shortly after receiving the coronavirus disease 2019 (COVID-19) vaccine, but the causal relation between the injection and death remains uncertain. Methods: Applying long-term personal vital care data for 28 months for an elderly patient, I investigated and evidenced adverse reactions after the first dose of the COVID-19 Pfizer vaccination. Results: The precise, detailed, and continuous data statistically clarified the long-term fevers associated with no meals or drinks. Interrupted time series analysis showed significant and fluctuating increases of body temperatures, pressures, and pulses, although solely long-term plots showed an abrupt and timely increase in these vital data after the vaccine. Conclusions: Anorexia was fatal, and newly reported in the present care records since the patient received the first dose of the COVID-19 vaccine.", "keywords": [ "case report", "COVID-19 vaccine", "adverse reactions", "before-after study", "statistic interrupted time analyses", "fever", "anorexia" ], "content": "Introduction\n\nAccording to the descriptions by the World Health Organization (2021):\n\n“Like any vaccine, coronavirus disease 2019 (COVID-19) vaccines can cause mild to moderate, short-term side effects, such as a low-grade fever or pain or redness at the injection site, fatigue, headache, chills, diarrhea, and allergic reaction. Most reactions to vaccines are mild and go away within a few days on their own. More serious or long-lasting side effects to vaccines are possible but extremely rare. Vaccines are continually monitored for as long as they are in use to detect rare adverse events and implement approaches to limit their occurrence.”\n\nTo date, except for anaphylactoid reactions, blood clots, myocarditis (Nassar et al., 2021) or pericarditis (Ashaari et al., 2021), and Guillain-Barré syndrome (McKean and Chircop, 2021; Kanabar and Wilkinson, 2021), adverse reactions to the COVID-19 vaccines are mild or moderate, occur shortly after vaccination and are not associated with more serious or lasting illness (Medicines & Healthcare products Regulatory Agency UK, 2021). Similarly, the reactions peaked within one day, although in rare cases lasted a week (Menni et al., 2021). The likelihood of accepting the vaccine were lower when the probability of serious adverse reactions such as paralysis was 1/100,000 in contrast to 1/million or 1/100 million (Kaplan and Milstein, 2021).\n\nThe present research, including a kind of “implementation research” (“an integrated concept that links research and practice to accelerate the development and delivery of public health approaches”; Theobald et al., 2018), is associated with evidence-based intervention but not a clinical study in sensu stricto associated with a clinical double-blind study, and so is presented as a case report. I applied the statistical concept of interrupted time series analysis for an elderly participant who received the first dose of the COVID-19 Pfizer vaccine on 2 June 2021. This analysis is usually applied to populations, but the concept is the same even for a single participant. In Japan, more than 1,000 participants died shortly after the injections of the COVID-19 vaccine until September 2021, but the causal relation between the injection and death remains uncertain (Ministry of Health, Labour and Welfare, Japan). I herein report previously unreported serious side effects, including unexpected adverse reactions, based on thoroughly monitored reliable long-term care records.\n\n\nCase report\n\nThe participant was diagnosed with dementia in 2015 and a femoral neck fracture on 1 March 2019, and when the fracture was almost repaired in a hospital, the participant moved to the Geriatric Health Services Facility, on 2 April 2019. This facility is staffed by with physicians, nurses, physical therapists, occupational therapists, nutritionists, and care workers.\n\nThe Japanese Government (Ministry of Health, Labour and Welfare) decided that healthcare workers and people over 65 years were the first to be vaccinated, and elderly participants were initially included as targeted persons. The participant was 90 years old and died on 25 August 2021, 28 weeks after the first vaccination. The second injection was planned on 25 June was cancelled due to the severe side effects that presented immediately after the first injection. The original nursing care level was 2 (partial assistant) but changed to level 5 (bedridden) on 20 July 2021.\n\nThe personal vital data and other related data were continuously monitored from April 2019 to August 2021 and included the day of the vaccine, 2 June 2021. The night shift care worker checked the digital data every hour for example, and the “Care Records” were precise and detailed. The records include timetable records of three meals (a meal, e.g., expressed as main dish 6/10, side dish 9/10, where 10/10 = complete meal, 0/10 = no meal), drinks (ml), body temperature, blood pressure, pulse, saturation of percutaneous oxygen (SpO2), urination, defecation, and physical and medical examinations. The data summary can be checked on a computer screen in the facility. Note that when fevered, the temperature is measured several times a day, and the last monitored temperature, not the maximum, appears on the PC screen as the default setting.\n\nContrasting the questionnaire survey among participants (Suehiro et al., 2021) and contrasting the multinational network cohort with electronic health records and health claims data (Li et al., 2021), the concept of the analysis is also applicable to a single participant. Because data from the million participants with mild to moderate and short-lasting side effects were privately measured and lacked long-term records, the present high-quality data, even for a single participant, are valid for scientific analyses.\n\n\nMethods\n\nThis research used a method of statistical analysis that involves tracking a long-term period before and after a point of intervention, in order to assess the intervention’s effects. According to Ferron and Rendina‐Gobioff (2005) and others, “the time series refers to the data over the period, while the interruption is the intervention, which is a controlled external influence or set of influences. The effects of the intervention are evaluated by changes in the level and slope of the time series and the statistical significance of the intervention parameters”. For this case report, the intervention is the COVID-19 Pfizer (Comirnaty) vaccination, given on 2 June 2021.\n\nI made a figure of vital data tracking a long-term period (28 months) produced by the Care Records for the patient (1,500 page hard copies in Japanese; Figure 1; made by Excel 2008 for Mac). I also made a figure of vital data tracking a short-term period (6 months) from the summery records (28 page hard copy in Japanese) produced by the care records for the patient (Figure 2; made by Excel 2021) for applying the interrupted time series analyses. Table 1 is a summary of the statistical analyses.\n\nThe COVID-19 vaccine was injected on 2 June 2021 (intervention), but the second injection planned on 25 June was cancelled. 5 pre-injection disorders are also shown.\n\nThe last one-week plots were omitted by body temperature disturbance. The regression line with the equation, coefficient of determination (R2), and level change by the interruption are shown.\n\nThe last one week of data were omitted by body temperature disturbance.\n\nFor body temperature for example, an interrupted time-series analysis approach was utilized. A linear regression model was fitted to describe the magnitude of change in temperatures in transitioning from one phase to another and the trend of temperatures at any specific time segment. Parameters of interest included: baseline error trend; immediate change in daily temperatures from the last observation in the pre-implementation phase to the first observation in the implementation phase; change in the slope of temperature trend from pre-implementation to implementation; immediate change in daily temperatures from the last observation in the implementation phase to the first observation in the post-implementation phase; temperature trend in the post-implementation phase; and estimated reduction in daily temperatures into the implementation phase (Elsaid et al., 2013).\n\nVital records covering 28 months (Figure 1) showed that body temperature, maximum and minimum pressures, and pulse drastically increased and violently fluctuated, and that both intake of meals and drinks and weight significantly decreased (ultimately no meal and drink; patient lost 1/4 body weight) after the COVID-19 vaccination, contrasting to the pre-injection “steady state” which had continued for more than two years with sporadic, short-termed disorders (detailed in Figure 1).\n\nVital records restricted to the last 6 months (180 days; Figure 2) show the pre-injection horizontal regression line, large + level change for temperature, pressures, and pulse, and – level change for meals and drinks, post-injection – regression line. The R2 value and other statistical parameters (Table 1) suggested that the injection strongly influenced and affected the vital system and induced a critical phase.\n\nTable 2 presents detailed care records for the period of June 2nd – June 14th, taken from the full care records (Osozawa, 2021). During this time, the patient’s temperature increased and remained increased until death. The patient also experienced hallucinations and decreased mental status, as well as decreased SpO2 levels. Another visual hallucination was observed on 17 June. The tongue coat was observed on 18 June. The final dinner (including breakfast and lunch) was on 2 June, the day of vaccination, after which the patient developed anorexia and did not eat, contrasting with the pre-vaccination time where the patient usually had full meals and drinks.\n\n\nDiscussion\n\nPre-injection disorders are shown on Figure 1, and they were short-term, recovered from, and of course unrelated to the vaccination.\n\nAbrupt and serious disorders that appeared just after the COVID-19 vaccination were clearly causally related to the vaccination (Figures 1 and 2; Table 1). Death was probably caused by these adverse reactions, especially by no meal or drink for nearly three months.\n\nThe fevers just after the injection in early June were likely a consequence of an adverse reaction to the vaccine (Table 2). The consequent fevers in mid-June and early August were potentially causally related (Figures 1 and 2; Table 1).\n\nCRP (C-reactive protein) increased from 0.11 mg/dl on 18 February 2021 (pre-injection) to 1.25 on 22 June and 1.12 on 9 July 2021 (post-vaccination; associated fever), and the leukocyte count decreased below the reference values. Thrombocytopenia frequently associated with critical thrombosis (Ministry of Health, Labour and Welfare; Fueyo-Rodriguez et al., 2021; Waraich and Williams, 2021; Sessa et al., 2021) was not found in the patient, but neutropenia reported by Charan et al. (2021) was probable. Increased CRP over 0.3 (< 0.3: normal level) suggested moderate class inflammation and might have been related to the following reported symptoms: fever flash on 2 June; leg pain on 3 June; nausea on 4 June; visual hallucinations (15 dancing girls are visible; deceased husband is visible) on 4 and 17 June; tongue coat on 18 June; and tongue swelling on 21 June. Fevers over 38°C tended to be associated with SpO2 95 (note that SpO2 was minimal at 94 on 6 June) and implied lung dysfunction and pneumonia. Polymyalgia rheumatica in early 2020 (see Osozawa, 2021) had a much higher CRP of 7.4 (c.f., Parperis and Constantinou, 2021), which later descended within the reference values and was unrelated to the present case. These disorders were possibly associated with cytokine release (or storm).\n\nSignificant increases in blood pressure and pulse to higher levels can be considered adverse reactions of injection (Figures 1 and 2; Table 1), presumably caused by inflammation. Inflammation was possibly associated with belching and nausea (and partial chills and fatigue; diarrhea was uncertain due to the dosage of magnesium oxide), which might have affected the appetite, reduced it, and led to anorexia. Note that the participant retained chewing and swallowing abilities as the dentists and physical therapists regularly checked and trained. Thus the anorexia nervosa triggered by the vaccination reduced the patient’s weight to 3/4 of the pre-vaccination weight.\n\nAnother concern was the dosage of the vaccine (0.3 ml/participant in a present case of the COVID-19 Pfizer (Comirnaty) vaccine). The amount is the same between men and women and Japanese and American individuals. The mean weight of an American woman was 77 kg in 2015-2016 (CNN), but the patient’s weight was only just over half of 77 kg at 40.5 kg (so the vaccine dosage should have been 0.15 ml). Therefore, I am concerned about the overdosage risk and its increased adverse reactions acting on the Japanese population. Centers for Disease Control and Prevention recently (November 2021) decided that the dose should be 0.1 ml/US children less than 11 years old.\n\n\nConclusion\n\nThe long-term vital records of this patient offered excellent data for adverse reactions to the COVID-19 Pfizer vaccine, including abnormally long-lasting fevers, high blood pressure, high pulse, and severe anorexia, ultimately leading to the patient’s death.\n\nWritten informed consent for publication of the patient’s clinical details was obtained from the patient’s family member. The personal care data are protected by the Personal Information Protection Law, Japan.\n\n\nData availability\n\nZenodo: Table S2: In Anorexia as a new type of adverse reaction caused by the COVID-19 vaccination: a case study applying detailed personal care records. https://doi.org/10.5281/zenodo.5778025 (Osozawa, 2021)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).", "appendix": "References\n\nAshaari S, Sohaib HA, Bolger K: A case report: symptomatic pericarditis post-COVID-19 vaccination. Eur. Heart J. - Case Rep. 2021; 5(10): 1–5. PubMed Abstract \| Publisher Full Text\n\nCharan J, et al.: Tocilizumab in COVID-19: a study of adverse drug events reported in the WHO database. Expert Opin. Drug Saf. 2021; 20: 1125–1136. PubMed Abstract \| Publisher Full Text\n\nElsaid K, Truong T, Monckeberg M, et al.: Impact of electronic chemotherapy order forms on prescribing errors at an urban medical center: results from an interrupted time-series analysis. Int. J. Qual. Health Care. 2013; 25: 656–663. PubMed Abstract \| Publisher Full Text\n\nFerron J, Rendina-Gobioff G: Interrupted Time Series Design, Encyclopedia of Statistics in Behavioral Science. Am. Cancer Soc. 2005; Publisher Full Text\n\nFueyo-Rodriguez O, Valente-Acosta B, Jimenez-Soto R, et al.: Secondary immune thrombocytopenia supposedly attributable to COVID-19 vaccination. BMJ Case Rep. 2021; 14: e242220. PubMed Abstract \| Publisher Full Text\n\nKanabar G, Wilkinson P: Guillain-Barré syndrome presenting with facial diplegia following COVID-19 vaccination in two patients. BMJ Case Rep. 2021; 14: e244527. PubMed Abstract \| Publisher Full Text\n\nKaplan RM, Milstein A: Influence of a COVID-19 vaccine’s effectiveness and safety profile on vaccination acceptance. PNAS. 2021; 118(10): e2021726118. PubMed Abstract \| Publisher Full Text\n\nLi X, Ostropolets A, Makadia R, et al.: Characterizing the background incidence rates of adverse events of special interest for covid-19 vaccines in eight countries: a multinational network cohort study. BMJ. 2021; 373. Publisher Full Text\n\nMenni C, Klaser K, May A, 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: 939–949. PubMed Abstract \| Publisher Full Text\n\nMcKean N, Chircop C: Guillain-Barré syndrome after COVID-19 vaccination. BMJ Case Rep. 2021; 14: e244125. PubMed Abstract \| Publisher Full Text\n\nNassar M, et al.: COVID-19 vaccine-induced myocarditis: Case report with literature review. Diabetes Metab. Syndr. Clin. Res. Rev. 2021; 15: 102205. PubMed Abstract \| Publisher Full Text\n\nOsozawa S: Table S2: In Anorexia as a new type of adverse reaction caused by the COVID-19 vaccination: a case study applying detailed personal care records [Data set]. Zenodo. 2021. Publisher Full Text\n\nParperis K, Constantinou M: Remitting seronegative symmetrical synovitis with pitting oedema following BNT162b2 mRNA COVID-19 vaccination. BMJ Case Rep. 2021; 14: e244479. PubMed Abstract \| Publisher Full Text\n\nSessa M, Kragholm K, Hviid A, et al.: Thromboembolic events in younger women exposed to Pfizer-BioNTech or Moderna COVID-19 vaccines. Expert Opin. Drug Saf. 2021; 20: 1451–1453. PubMed Abstract \| Publisher Full Text\n\nSuehiro M, et al.: Adverse events following COVID-19 virus vaccination in young Japanese population: The first cross-sectional study conducted by a questionnaire survey after the first injection. medRxiv preprint. 2021. Publisher Full Text\n\nTheobald S, Neal BN, Gyapong M, et al.: Implementation research: new imperatives and opportunities in global health. Lancet. 2018; 392: 2214–2228. Publisher Full Text\n\nWaraich A, Williams G: Haematuria, a widespread petechial rash, and headaches following the Oxford AstraZeneca ChAdOx1 nCoV-19 Vaccination. BMJ Case Rep. 2021; 14: e245440. PubMed Abstract \| Publisher Full Text" }	[ { "id": "226957", "date": "18 Dec 2023", "name": "Sankha Shubhra Chakrabarti", "expertise": [ "Reviewer Expertise Geriatric Pharmacovigilance", "Geriatric Neuropsychiatry" ], "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 read with interest the case report of COVID-19 vaccination resulting in a downwards progression of a previously healthy elderly ultimately culminating in death. There are some concerns which need to be addressed. 1. The author probably does not belong to the field of medical research and is not probably a clinical doctor either. Hence, the description of the case lacks some details. And some parts of it seem apparently lacking in medical details. I was deeply interested by the case because we have had similar experiences in our patients. I strongly suggest getting in touch with a medical co-author who would review the article and make it more acceptable. Just one example. \"long-term vital records of this patient offered excellent data for adverse reactions to the COVID-19 Pfizer vaccine, including abnormally long-lasting fevers, high blood pressure, high pulse, and severe anorexia, ultimately leading to the patient’s death\" This is not a justified statement. A single case report does not provide meaningful data. Further, long lasting fevers etc. are lay terms. More medically appropriate terms need to be used. Involving a medical co-author will also be meaningful as the author mentions \"The author had an existing relationship with the patient prior to the study.\"\n2. \"This case report was supported by funding from the Japan Society for the Promotion of Science,\" This is peculiar as the funding apparently is not for medical research. The author should modify the statement to acknowledge general funding support etc. but not keep it like this.\n3. Terminologies such as \"tongue coat\" visible etc. are not medically sound. The writing needs to be refined.\n4. References need to be provided for cytokine storm.\nThe report is valuable but needs to be almost completely rewritten along with a medical co-author.\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/11-4
https://f1000research.com/articles/12-448/v1	27 Apr 23	{ "type": "Research Article", "title": "The first released available genome of the common ice plant (Mesembryanthemum crystallinum L.) extended the research region on salt tolerance, C3-CAM photosynthetic conversion, and halophism", "authors": [ "Ryoma Sato", "Yuri Kondo", "Sakae Agarie", "Ryoma Sato", "Yuri Kondo" ], "abstract": "Background: The common ice plant (Mesembryanthemum crystallinum L.) is an annual herb belonging to the genus Mesembryanthemum of the family Aizoaceae, native to Southern Africa. Methods: We performed shotgun genome paired-end sequencing using the Illumina platform to determine the genome sequence of the ice plants. We assembled the whole genome sequences using the genome assembler “ALGA” and “Redundans”, then released them as available genomic information. Finally, we mainly estimated the potential genomic function by the homology search method. Results: A draft genome was generated with a total length of 286 Mb corresponding to 79.2% of the estimated genome size (361 Mb), consisting of 49,782 contigs. It encompassed 93.49% of the genes of terrestrial higher plants, 99.5% of the ice plant transcriptome, and 100% of known DNA sequences. In addition, 110.9 Mb (38.8%) of repetitive sequences and untranslated regions, 971 tRNA, and 100 miRNA loci were identified, and their effects on stress tolerance and photosynthesis were investigated. Molecular phylogenetic analysis based on ribosomal DNA among 26 kinds of plant species revealed genetic similarity between the ice plant and poplar, which have salt tolerance. Overall, 35,702 protein-coding regions were identified in the genome, of which 56.05% to 82.59% were annotated and submitted to domain searches and gene ontology (GO) analyses, which found that eighteen GO terms stood out among five plant species. These terms were related to biological defense, growth, reproduction, transcription, post-transcription, and intermembrane transportation, regarded as one of the fundamental results of using the utilized ice plant genome. Conclusions: The information that we characterized is useful for elucidation of the mechanism of growth promotion under salinity and reversible conversion of the photosynthetic type from C3 to Crassulacean Acid Metabolism (CAM).", "keywords": [ "common ice plant", "genome release", "halophilism", "salt-tolerance", "salinity", "photosynthesis" ], "content": "Introduction\n\nSoil salinity is one of the most detrimental abiotic stresses. Osmotic and ionic stresses can lead to decreased plant growth and economic damage, with estimates suggesting that it costs the global economy around $27.3 billion annually in lost crop yields (Qadir et al. 2014). Developing a wide range of strategies for adapting to and mitigating NaCl stress is required to address the negative impacts of salinity. Efficient resource management and crop improvement will help overcome the salinity-induced damages to agricultural production (Shrivastava and Kumar 2015). Mesembryanthemum crystallinum L. or the common ice plant is an annual plant of the family Aizoaceae, native to South Africa. This plant survives in the presence of a high salt concentration, even higher than that of seawater and can accelerate its growth under moderate salinity around 200 mM NaCl, wherein the growth and development of most crops are severely inhibited (halophilism; Agarie 2004). Also, it converts its photosynthetic mode from C3 to Crassulacean acid metabolism (CAM) under severe salt stress and drought stress (Adams et al. 1998). For the past half-century, the common ice plant has been frequently used as a model for elucidating the mechanisms of salt stress tolerance and photosynthetic conversion in response to salt and drought stresses.\n\nRecently, the molecular processes underlying these phenomena have been elucidated at the levels of transcription, post-transcription (Taybi and Cushman 1999; Zhang et al. 2021), translation, post-translation (Forsthoefel et al. 1995; Nimmo 2000), specific proteins (tonoplast and plasma-membrane H(+)-ATPases: Vera-Estrella et al. 1999; glucose 6-phosphate/phosphate translocator: Kore-eda et al. 2013; ions transporter and compatible solute synthase: Tran et al. 2020a), mitochondria, and chloroplasts (Tran et al. 2020b; Niewiadomska and Pilarska 2021). Also, high-throughput gene expression profiling has been conducted using expression sequence tags (ESTs) (Kore-eda et al. 2004), microarrays (Cushman et al. 2008), and next generation sequencing (NGS; Oh et al. 2015; Tsukagoshi et al. 2015; Chiang et al. 2016; Kong et al. 2020).\n\nIn these days, the comparative analysis of genome information focus on CAM related genes on the common ice plants has been reported (Shen et al. 2022), but this genome resource is not easy to use. The poor transparency of genome information causes the delayed elucidation of whole-genome functions of the common ice plants dominating not only photosynthetic conversion systems but also halophilism and salt tolerance. The genomic sequences include protein-coding regions and untranslated regions such as promoters and terminators. MicroRNAs (miRNAs) and long noncoding RNAs (lncRNAs) influence gene expression through affecting mRNA stability and translation efficiency (Hughes 2006). Information regarding the genome sequences’ biological functions facilitates a comprehensive understanding of the transcriptional regulatory mechanisms of gene expression. Disclosure to researchers around the world is essential for clarifying the responsibilities of the entire genome to NaCl and creating superior cultivars through genome editing and selective breeding.\n\nShort-read sequencing costs less than the long-read sequencing obtained using third and fourth NGS. Several software programs for de novo genome assembly for short reads have been developed. The algorithm for genome assembly (ALGA) is the newest assembler, based on an overlapping graphs model, which can generate more accurate results than conventional software using the de Bruijn graphs model (Swat et al. 2021). This achievement can be regarded as a model case of a genome study using NGS short reads, given its level of success.\n\nIn this study, we constructed the ice plant genome using easy-to-start applications such as ALGA to accelerate genome analysis. We investigated the characteristics of the genome, clarifying the repetitive sequences, tRNAs, and miRNAs (genomic regions and precursors), and identified gene regions using various software and web tools. This is the first report of whole-genome analysis of the common ice plant. Our results indicate the involvement of translated and untranslated regions in the regulatory processes of salt tolerance and photosynthetic conversion under stress in the ice plant.\n\n\nMethods\n\nAll the processes involved in this study were archived in protocol.io (Sato et al. 2023a) and were described in Figure S8 (Sato et al. 2023b).\n\nSeeds of the common ice plant (Mesembryanthemum crystallinum) were personally provided by Dr. John C. Cushman from the University of Nevada and stored under coolness and darkness until use. Originally, wild-type seeds were collected from the plants identified by Dr. Klaus Winter, an expert on the common ice plant, on a coastal cliff at the Mediterranean Sea shore close to Caesarea in Israel (around N32° 29′ 43.4″, E34° 53′ 22.8″) in 1978 (Winter et al. 1978). Three voucher specimens of M. crystallinum have been deposited in the Herbarium at the Royal Botanic Gardens Kew (55793.000, K000296094, and K000267571). In this study, our biological materials were recognized as the same plants as those specimens. Experiments, including collecting samples for this study, were conducted in compliance with relevant institutional, national, and international guidelines and laws. The seeds were aseptically sown on a medium for germination containing 4.6 g L-1 MS salt (mixed salts for Murashige-Skoog medium), 30 g L-1 sucrose, 1 mL-1 B5 vitamin (Gamborg et al. 1968), 1 g L-1 nicotinic acid, 1 g L-1 pyridoxine hydrochloride, 10 g L-1 thiamine hydrochlorides, and 100 g L-1 myo-inositol), 0.8% (w/w) agarose, and pH 5.7. The raising of seedlings was performed according to the methods published by Agarie et al. (2009). The two-week-old seedlings grown in a growth chamber under 12 h of light and 12 h of darkness at 25 °C were transferred to plastic pots filled with the growth medium soils composed of 50% peat moss, 30% cocopeat, and 20% perlite, specified for the ice plants (Japan Agricultural Cooperatives Ito-Shima, Fukuoka, Japan) and irrigated with a nutrient solution of 1.5 g L-1 OAT House No. 1 and 1.0 g L-1 No. 2 (OAT Agrio Co., Ltd., Tokyo, Japan) in a greenhouse at Kyushu University for five weeks. The plants were treated with the solution including 0.3% (w/w) NaCl for two weeks. Approximately 0.6 g of tissue from each leaf was collected, quickly frozen in liquid nitrogen, and stored at −80 °C.\n\nTotal genomic DNA was extracted from the leaf tissue and purified using MagExtractor™-Plant Genome Nucleic Acid Purification Kits (Toyobo Co., Ltd., Shiga, Japan), according to the manufacturer’s instructions. The DNA samples were fragmented by sonication and used to construct short insert paired-end libraries construction using NEBNext® Ultra™DNA Library Prep Kits for Illumina (New England Biolabs Ltd., Ipswich, MA, USA). Briefly, in the end-repair step, fragmented DNA was phosphorylated at the 5′ end and adenylated at the 3′ end. During the ligation step, full-length circulated adaptor sequences were ligated to the fragments. After adaptor cleavage, purification and size selection were performed. The indexed PCR products were taken to obtain the final sequencing libraries. The mean insert size for paired-end libraries was 300 bp. The paired-end (2×150 bp) sequencing was conducted on an Illumina NovaSeq 6000 platform (Illumina Inc., San Diego, CA, USA).\n\nThe mean insert size was calculated using REAPR (v1.0.18) (Hunt et al. 2013), and raw paired-end sequences were filtered based on the frequency of 21-mer sequences using the program Musket (v1.1) (Liu et al. 2013). The key parameter values were as follows: musket -omulti output -inorder pair1.fastq pair2.fastq. Sequence reads that appeared rarely or abnormally frequently were removed to obtain clean read data. In the corrected reads, unique and duplicate read numbers in the corrected reads were measured using fastqc (v0.11.9) (Simon 2010). The clean data were used for an estimate of genome size as follows. K-mers were counted and exported to histogram files using jellyfish (v2.3) (Marçais and Kingsford 2011) [key parameter: jellyfish histo reads.jf]. GenomeScope2.0 (Ranallo-Benavidez et al. 2020) corresponding key parameters were applied to calculate the genome sizes using k-mers lengths of 21 and 25.\n\nThe reads were assembled using ALGA (v1.0.3; Swat et al. 2021) with the default parameter --error-rate = 0.02. long DNA fragments 1 to 10 kb in length were combined, and gaps between them were filled with unknown bases (Ns) using Redundans (v0.14a; Pryszcz and Gabaldón 2016), a software program for scaffolding, with default parameter values. The genome coverage of reads was estimated using Mosdepth program (Pedersen and Quinlan 2018). The completeness of the assembled genome was evaluated based on the content of orthologs in higher plants, using the benchmarking universal single-copy orthologs (BUSCO) program (v5.0; Manni et al. 2021). The lineage dataset was embryophyta_odb10 (creation date: 2020-09-10, number of BUSCOs: 1614). We also searched for core genes in the genome sequences of nine other plant species: Kewa caespitosa, Pharnaceum exiguum, Macarthuria australis, Solanum chaucha, Populus trichocarpa, Arabidopsis thaliana, and Oryza sativa using BUSCO. The first three species belong to the same order, Caryophyllales, to which the ice plants belong. Genome information was obtained from the NCBI (see Note 1 “Address to genome information”, Sato et al. 2023b). The number of bases, sequences, sequences in several base number ranges, and maximum base length of the final draft genome sequences was calculated using gVolante (v2.0.0) (Nishimura et al. 2017). BLASTN (v2.2.31+; McGinnis and Madden 2004) was used to investigate the number of cDNA sequences identified by transcriptome (Lim et al. 2019), and registered DNA sequences (retrieved from NCBI, last accessed February 2022) were aligned to the final assembled genome sequence.\n\nThe 18S ribosomal genes were extracted using barrnap (v0.9; Seemann 2018) from the obtained genome sequences of the ice plant. As comparative objectives, 25 kinds of 18S ribosomal genes from general crops (Japanese radish [Raphanus sativus], Soybean [Glycine max], Japanese trefoil [Lotus japonicus], Barrelclover [Medicago truncatula], Adzuki bean [Vigna angularis], Banana [Musa acuminata], Barley [Hordeum vulgare], Sorghum [Sorghum bicolor], Bread wheat [Triticum aestivum], Maize [Zea mays], Apple [Malus domestica], Peach [Prunus persica], Coffee tree (Arabica var.) [Coffea arabica], Coffee tree (Robusta var.) [C. canephora], Clementine [Citrus clementina], Orange [C. sinensis], Poplar, Tobacco [Nicotiana tabacum], Tomato [Solanum lycopersicum], Eggplant [S. melongena], Potato [S. tuberosum] and Grape [Vitis vinifera]) were selected using the SILVA database (Release. 2020-08; Pruesse et al. 2007). After joining all ribosomal DNA sequences into one file, a molecular phylogenetic tree was created using implemented in NGPhylogeny.fr (Lemoine et al. 2019) (Released in 2019). SH-aLRT (Shimodaira-Hasegawa-approximate likelihood ratio test) (Shimodaira and Hasegawa 1999) was used to determine the molecular phylogenetic tree.\n\nRepetitive sequences were detected, and custom repeat libraries involving transposable elements and long terminal repeat-retro transposons were generated using RepeatModeler2 (v2.0.2; Flynn et al. 2020) and TEclass (v2.1.3; Abrusán et al. 2009). Known repeat sequences were detected and classified in the assembled genome sequence with reference to the Repbase library (Bao et al. 2015) and the custom repeat libraries, using RepeatMasker (v4.1.2-p1; Smit et al. 2013-2015). The capital letters in the genome sequences were replaced with small characters as soft masking.\n\nThe tRNA genes were identified in the draft common ice plant genome using tRNAscan-SE2.0 (v2.0.9) (Chan et al. 2021). The tRNA data of other nine plant species—Arabidopsis, rice, tomato, poplar, horseradish, potato, grape, soybean, and coffee tree (robusta species)—were obtained from the PlantRNA database (Cognat et al. 2013). The percentages of arbitrary tRNAs against the total tRNAs in the genome were calculated and compared to the ice plants’ values with those of the other species. Smirnov-Grubbs’ outlier tests were performed to select tRNAs more significantly involved. The test statistic T was calculated using the following equation:\n\nThe miRNA loci in the genome sequence were identified using the cmscan command in Infernal (v1.1.4; Nawrocki and Eddy 2013) using Rfam.\n\nThe BRAKER2 pipeline (v2.1.5; Brůna et al. 2021) was used for the prediction of genes in the common ice plant genome. Amino acid sequences were translated from the transcriptome profile reported by Lim et al. (2019) and used as additional reference data for the prediction of genes. BRAKER2 was used with the default parameters (–softmasking). The total sequences, total bases, total amino acids, and N50 were computed based on the resulting fasta-format files containing information about the genes, coding sequences, and amino acids using seqkit (v2.0.0; Shen et al. 2016) [key parameter: seqkit stats]. Protein BLAST searches (E-value < 1e-5) were conducted using DIAMOND (v2.0.13.151; Buchfink et al. 2021) against the NCBI-non-redundant protein sequences (retrieved from NCBI in March 2022), Uniprot-swissprot (retrieved in March 18), Ensemble TAIR10 (retrieved in March 2022), and NCBI poplar amino acid sequence databases (retrieved from NCBI in March 2022).\n\nThe protein domains in the genome were identified using the Pfam (v33.1) database (Mistry et al. 2021) with E-value < 1e-3, using HMMER (v3.1b2; Potter et al. 2018). The protein databases of rice, maize, and poplar from the NCBI (last accessed February 2022) were used in the domain for a detailed classification of the PKinase family, the iTAK (v18.12) web tool (Zheng et al. 2016; last accessed February 2022) was utilized. The ratio of families with a high ratio of genes to total genes in the ice plant was compared with that of the same families in the other plants. For statistical analysis, we used Smirnov-Grubbs’ outlier tests. The following equation was used to obtain the test statistic T:\n\nFinally, BLASTP was used to compare proteins generated from the ice plant genome and those from Arabidopsis, rice, maize, and poplar and renamed TAIR10 ID. These IDs were subjected to gene ontology (GO) enrichment analysis using DAVID (updated in 2022; accessed on March 24; Sherman et al. 2022) based on a modified Fisher exact probability test with E-value < 0.05.\n\n\nResults\n\nShort insert reads data (300 bp; Figure S1-(A), Sato et al. 2023b) with an estimated coverage of 50.92× and a ratio of unique to duplicate reads of about 1.63:1 was obtained by removing erroneous reads of raw paired-end data from the Illumina platform (BioProject: PRJDB13817; BioSample: SAMD00508673) (Table S1). The M. crystallinum genome size was estimated to be 366 to 369 Mb, with very low heterozygosity (about 0.010%) following an analysis of the frequency of 21 and 25-mers, using GenomeScope2.0 (Figure S1-(B) and (C), Sato et al. 2023b). The M. crystallinum final draft assembly included 286 Mb in 49,782 scaffolds with a scaffold N50 of 10,562 bp (Table S2). The BUSCO tool revealed 1,509 (93.49%) of 1,614 embryophyte library core genes, with 1,223 (75.77%) of these being ‘Complete’ matches in the genome. The completeness and contiguity of the genome were greater than the shotgun assembled M. australis and S. chaucha genomes (Figure S2: Sato et al. 2023b). Around 24,081 (99.5%) of the 24,204 transcripts from the transcriptome assembly of M. crystallinum leaves (Lim et al. 2019), and all 135 DNA sequences registered in the NCBI, were aligned to the assembled genome (Supplementary Dataset S1: Sato et al. 2023c).\n\nWe performed a phylogenic analysis using 18S ribosomal DNA (rDNA) among related species. The seven types of 18S rDNA were chosen from the ice plant genome sequence. Also, the other 25 plant species’ 18S rDNA sequences (see Phylogenetic tree creation among multiple plant species using 18S ribosomal DNA sequences in Methods) were retrieved from the ribosomal RNA database in SILVA and were aggregated with the ice plant 18S rDNAs. Based on these sequences, a molecular phylogenetic tree of 18S rDNA was constructed using PhyML+SMS/One Click in NGPhylogeny.fr (Figure S3, Sato et al. 2023b). The results showed that five species of 18S rDNAs were relatively closely related to poplar’s 18S rDNA.\n\nIn the 286.0 Mb M. crystallinum genome, 2,423 distinct repetitive sequences families, accounting for 110.9 Mb (38.8%) of the genome, were identified using custom repeat libraries and Repbase (Bao et al. 2015). This ratio was smaller than Shen et al.’s (2022) reported value (48.04%). In decreasing order of frequency, the annotated repetitive elements were unclassified 78.0 Mb (27.27%), retroelements 21.9 Mb (7.64%), long interspersed nuclear elements (LINE) 12.5 Mb (4.37%), long terminal repeats (LTR) 9.35 Mb (3.27%), and simple repeats 7.26 Mb (2.54%). Some retroelements were classified into subfamilies, including L1/CIN4 12.4 Mb (4.34%) and RTE/Bov-B 0.85 Mb (0.03%) in the LINE, and Ty1/Copia 4.90 Mb (1.71%) and Gypsy/DIRS1 4.35 Mb (1.52%) in the LTR (Table 1).\n\n(1) Retroelements: DNA sequences derived from viruses.\n\n(2) LINEs: Long interspersed nuclear elements.\n\n(3) LTR elements: Retrotransposons with long terminal repeat.\n\n(4) DNA transposons: DNA sequences moving through the genome.\n\nA total of 971 tRNAs, excluding pseudogenes, were detected in the assembled genome, and were sorted into several groups based on codon designation. The codon with the most abundant tRNA was isoleucine and the least was tryptophan (Figure S4, Sato et al. 2023b). The number of tRNAs was as follows: Arabidopsis 585, rice 505, poplar 505, tomato 723, horseradish 500, potato 736, grape 391, and soybean 700. Interspecific comparisons using the Smirnov-Grubbs outlier test and focusing on these eight species indicated that the abundance of isoleucine was significantly highest and that of tryptophan was significantly lower (P < 0.05; Figure 1 and Table S3, Sato et al. 2023b).\n\ntRNAs significant differently abundant from the other 8 species by Smirnov-Grabs outlier test, are shown in black, and the other tRNAs are shown in gray. Bars indicate ice plant, Arabidopsis, rice, tomato, poplar, horseradish, potato, grape, and soybean from the left of each series. Asterisks indicate statistical significance: * P < 0.05, n = 9.\n\nIn addition, miRNAs loci were identified from the genome with reference to the Rfam database, to obtain miRNA profiling independent of their expression levels. MiRNAs are 21 to 24 nt molecules that regulate post-transcriptional mRNA modification, playing important roles in plant growth and tolerance to environmental stress. 100 miRNA loci were identified and categorized into 25 families. The RNA family with the largest number of loci was MIR169 (25), followed by mir-399 (16), MIR159 (8), and mir-166 (7). mRNAs targeted by miRNA families were predicted (Table S4). For instance, MIR169 family miRNAs were presumed to bind to mRNAs encoding nuclear factor gamma subunit A (NF-YA) (Chiang et al. 2016). Overall, 13 types of 25 miRNA families were likely to target mRNAs encoding transcription factors: MYB33, MYB65, HD-ZIP, WRKY, AP2-like, NAC, ARFs, IAR3, ARF16, OsSPL14, SPL, GRF2, and HLH. The rest of the targeted mRNAs are anticipated to have functions in processes such as miRNA maturation, mRNA cleavage, or metal binding.\n\nGenes (34,223), coding sequences (35,702), and amino acid regions (35,702) were predicted from the soft-masked draft M. crystallinum scaffolds ab initio using a homology-based pipeline in BRAKER2 using transcriptome data (Table S4). The representative value on bases showed that coding sequence regions cover at least 10.6% (30.4 Mb) of the total genome sequence. In comparison to several databases on 25 plant species’ genes registered in PGDBj (Asamizu et al. 2014; last accessed in March 2022), the ice plants’ genes were as abundant as those of Sorghum bicolor and Arabidopsis lyrate. Additionally, summarized data indicated that the M. crystallinum gene number was 16 times larger than those of S. bicolor and A. lyrate, equivalent to about 27.6% of the number of genes of Triticum aestivum (bread wheat) and 3.31-fold greater than that of Pyropia yezoensis (bangia) (Figure S5, Sato et al. 2023b). Each translated protein sequence was used in a BLASTP search with the DIAMOND program (Buchfink et al. 2021) against four kinds of protein sequence databases. In order of the proportion of homologous amino acid sequences identified, they were NCBI-non-redundant (82.59%), poplar (70.65%), TAIR10 (65.39%), and Swiss-prot (56.05%; Table 2) (Supplementary Dataset S2: Sato et al. 2023d). To simplify gene ID conversion to GO terms, the results, including TAIR ID, were used in the functional estimation.\n\nA Pfam domain search based on the Pfam (Mistry et al. 2021) database identified 3,703 domains in 23,521 (97.1%) genes. The most frequently occurring domain was the protein kinase domain (PKinase), at 2.18%, followed by a domain of unknown function (DUF) 4238 (1.85%), reverse transcriptase (RVT)_1 (1.45%), PPR domain-containing protein (PPR)_2 (1.42%), and protein tyrosine and serine/threonine kinase (PK_Tyr_Ser-Thr) (1.18%) (Supplementary Dataset S3: Sato et al. 2023e). The PKinase family was further classified into 94 kinase families using iTAK (Zheng et al. 2016). The top 30 kinase families with the largest number of ice plant genes are shown in descending order in Figure 2. Compared to the other four plant species, the proportion of 12 families was significantly higher (P < 0.05), and eight families—DUF4238, RVT_1, RVT_2, RVT_3, Retrotrans_gag_2, zf_RVT, Retrotrans_gag_3, Retrotrans_gag—contained retroelement domains that could be attributed to a retrotransposable element (Figure 3). The annotated genes were assigned to GO classifications based on TAIR ID in three groups —biological process (BP), cellular component (CC), and molecular function (MF)—and were categorized into 403 GO terms using the gene functional classification tool in the DAVID web service. The proportion of genes assigned to 94 GO terms did not differ significantly among five plant species (P > 0.05; Figure S6 to S8, Sato et al. 2023b), indicating that they are essential to plant survival. These findings confirmed that the ice plant genome constructed in this study contained conserved genes to some extent. 18 GO terms were identified only from ice plants, although the number of genes was small (Table S6), involving virus resistance, pollen tube development, and fat biosynthesis (BP); cytoplasmic vesicle and “soluble NSF attachment protein receptor” (SNARE; CC); and O-acyltransferase for transferring fatty acids (MF).\n\nThe family with the highest number of genes is shown in black, and the other families are shown in white.\n\nThe top row for each family shows ice plant, Arabidopsis, rice, maize, and poplar. The independence of the proportion of genes belonging to a family in the ice plant is displayed using the Smirnov-Grubbs rejection test. Asterisks (*) indicate statistical significance: P < 0.05, n = 5. Independence is shown in red if the proportion is independently high in ice plant, in blue if it is low, and in gray if there is no difference.\n\n\nDiscussion\n\nM. crystallinum is utilized as a model plant for investigating halophilism, salt tolerance, and CAM photosynthesis. In this research, we have assembled the common ice plant’s genome sequence and elucidated the genome’s function in detail for the first time in this species. This genomic resource covers all protein-coding, non-transcribed, and untranslated regions. Our results of genomic functional analysis on M. crystallinum provide new insights into the molecular mechanisms underlying the plant’s adaptation to NaCl stress including conversion of the photosynthesis.\n\nThe total assembled genome length (286 Mb) was approximately 26% smaller than the genome size estimated using the experimental or bioinformatic method reported by Meyer et al. (1990; 390 Mb, de Rocher et al. (1990; 390 Mb), and Shen et al. (2022; 378 Mb). The genome size estimated using k-mer distribution analysis is likely to be smaller than that using experimental data, including flow cytometry, given the effects of repetitive sequences and other obscure nucleotide sequences (Bennett et al. 2003; Al-Qurainy et al. 2021). Barkla et al. (2018) have shown that the ploidy levels of the leaf increased throughout its development. Because polyploidy is becoming a concern when NGS is used for genome assembly (Kyriakidou et al. 2018), the endopolyploidy of ice plant leaves may increase the complexity of genome assembly. Experimental data is supposed to help to support the present results and determine the exact ice plant genome size.\n\nInterestingly, the phylogenic tree analysis indicated that the genome composition of the ice plant was similar to that of the poplar. Previous studies have reported poplar-derived genes for salt tolerance, including PtNF-YA9 (Lian et al. 2018), PtSAP13 (Li et al. 2019), and PtVP1.1 (Yang et al. 2015). These results suggest that the ice plant genome constructed in this study is a highly conserved sequence that can be used for phylogenetic relationship analysis.\n\nWe found that the repetitive M. crystallinum sequences occupy 110.9 Mb (38.8%) of the genome. Advances in genomics over several decades have revealed that repetitive sequences play essential roles in regulating gene expression in higher plants. Recent studies observed that the transposable elements, involving many repetitive sequences were highly expressed under heat, salt, and intense light stresses, in Arabidopsis, tomato, and mangrove species (Deneweth et al. 2022; Wang et al. 2022). These results suggested that it affected the expression levels of nearby genes for transcriptional factors, including DREB, NAC, MYB, AP2/ERF, NF-Y, and Abscisic acid 8′-hydroxylase. Further studies indicated that cis-regulatory motifs associated with C4 photosynthesis, rate-determined by the same enzyme up to at least 669, and the non-coding RNAs regulating methyltransferases expression levels are derived from transposable elements (Nosaka et al. 2012; Cao et al. 2016). Transposable element expression is suppressed by cytosine methylation in DNA sequences, chromatin remodeling, and degradation by small interfering RNA (siRNA; Ito 2013). These previous results suggested that the common ice plant has repetitive sequences with similar effects on gene expression regulation.\n\nTwo kinds of representative small non-coding RNAs were found in the ice plant genome—971 tRNAs and 100 miRNA loci—which are anticipated to be relevant to metabolic pathway and post-transcriptional modification. Generally, a tRNA recruits an amino acid corresponding to its codon, which means that the abundance of a specific tRNA is proportional to that of the relevant amino acid. Some studies have shown the effectiveness of amino acids in metabolism for environmental stress reduction. For example, 5-aminolevulinic acid, a key precursor in porphyrins biosynthesis, including chlorophyll and heme, can alleviate abiotic stresses, including salinity, drought, heat, cold, and UV-B (Tan et al. 2022). The Smirnov-Grabs outlier test revealed that the isoleucine-specific tRNA was present at a significantly higher proportion in the ice plant’s genome than in eight other plant species. It is the precursor of JA-Ile, the active molecule of the plant hormone jasmonic acid, which has been implicated in pathogen resistance in plants (Li et al. 2021). The least abundant coded tRNA was tryptophan, which serves as the melatonin precursor, a signaling molecule that regulates responses to abiotic stress, such as water shortage (Sadak and Ramadan 2021). These results suggest that the abundance of amino acids in the ice plant may differ from those in the other eight plants, indicating the possible presence of different stress tolerance mechanisms.\n\nSome miRNAs identified in the ice plant’s genome appeared to be key small molecules in the stability of mRNAs coding for epigenetic and transcription-related factors. NF-YA were targeted by 31 MIR169 loci known to integrally regulate gene expression by maintaining histone acetylation in soybeans (Lu et al. 2021), or binding to circadian rhythm-related elements, including the “CCAAT” motif in Arabidopsis (Wenkel et al. 2006; Zhao et al. 2016). Several miRNA-targeting transcription factors were associated with salt tolerance (HLH, SPL, HD-ZIP) (Shen et al. 2019; Wang et al. 2019, 2021) or CAM photosynthesis (WRKY, AP2, MYB, NAC) (Amin et al. 2019; Yuan et al. 2020; Shah et al. 2021). All target gene families were found in the protein family collection in the ice plant genome, except for SPL and lectin receptor kinase (see Supplementary Dataset S1, Sato et al. 2023c), indicating that an antagonistic relationship between miRNAs and mRNAs underlies the stress tolerance and photosynthetic conversion mechanisms of the ice plants. Additional miRNA sequence information is expected to provide more accurate data and form the basis for testing these assumptions.\n\nThe richest PKinase subfamily was “receptor-like kinase/Pelle, DUF26, SD-1, LRR-VIII and VWA, a moss-specific new RLK subfamily (RLK-Pelle_DLSV)”, containing primarily receptor-type kinases, which was consistent with the transcriptome profiling in a halophyte, Nitraria sibrica (Zhang et al. 2022). It has been assumed to be involved in cell wall biosynthesis, adhesion, and developmental regulation. For instance, WAK, the second most frequent PKinase in the ice plant genome, has been reported to control cell wall expansion, metal resistance, and pathogen resistance (Gish and Clark 2011). The common ice plants show halophilism or salt tolerance; a detailed study may help to shed light on the mechanism of this tolerance from the perspective of phosphorylation. In contrast to the rare PKinase, the richness of retrotransposon-derived domains (reverse transcriptase and gag genes), involved in RNA packaging and the replication cycle (Orozco-Arias et al. 2019), was apparent in the ice plant compared to the other plant species. A recent study suggested a human retrotransposon-derived imprinted gene, paternally expressed gene 10 (PEG10), mediates cellular proliferation and inhibits apoptosis (Golda et al. 2020). However, it remains unclear what effects these proteins have on the plants’ physiology. Our latest experiment demonstrated that the ice plant’s cell cycle-related genes were upregulated in the presence of 100 mM NaCl (Sato et al. 2022), possibly implying an impact of retrotransposon-derived proteins on the cell division of the ice plant’s cells. Lipases, transferases, and phosphatases were abundant, and transcription factors such as Myb, HLH, and AP2 were scarce in the genome of the common ice plant. Two reviews show these enzymes and transcription factors assume a key role in plants’ survival under salinity (Reyes-Pérez et al. 2019; Chaudhry et al. 2021), but it is not yet clear whether they interact with each other. Elucidation of these protein interactions by transcriptome and interactome analysis may provide crucial evidence about their unknown functions.\n\nFinally, comparing the gene functions among the genomes of five plant species —ice plant, Arabidopsis, rice, maize, and poplar—based on their gene counts, 18 gene functions were found only in the ice plant. Previous studies (12 reviews and 11 research articles) with sophisticated experimental backgrounds indicated that all gene functions were possibly associated with the mechanisms of halophilism, salt tolerance, and photosynthetic conversion. These gene functions were categorized as related to biological defense, growth, reproduction, transcription, post-transcription, and intermembrane transportation. Therefore, focusing on the homologous of the ice plant genes with these functions may provide critical insight into the salt-induced growth and photosynthetic systems.\n\n\nConclusion\n\nWe succeeded in assembling the M. crystallinum genome using Illumina PE reads, characterizing the genome, and identifying the potential gene, non-transcriptional and translational regions, and repetitive sequences. Furthermore, we made the ice plant genome available to all, which means the end of this plant’s genome information opacity temporarily. Our results revealed that salt tolerance increases with growth, and C3-CAM photosynthetic conversion in the presence of NaCl is probably controlled by both protein-coding genes and potential genomic factors, including transposable elements, tRNAs, miRNAs, and protein kinases. These findings provide new insights into the mechanisms of plant growth under environmental stresses and can be used to develop highly high salt-tolerant crops. We hope this study will be a good step stone to the developed genomic science of the common ice plant.", "appendix": "Data availability\n\nDDBJ BioProject: Mesembryanthemum crystallinum genome assembly and analysis. Accession number PRJDB13817, https://ddbj.nig.ac.jp/resource/bioproject/PRJDB13817.\n\nDDBJ BioSample: Mesembryanthemum crystallinum metadata. Accession number SAMD00508673, https://ddbj.nig.ac.jp/resource/biosample/SAMD00508673.\n\nDDBJ Sequence Read Archive (DRA): Raw data from Illumina Novaseq 6000. Accession numbers DRA015289 and DRR424237, https://ddbj.nig.ac.jp/resource/sra-submission/DRA015289 and https://ddbj.nig.ac.jp/resource/sra-run/DRR424237.\n\nThe assembled genome sequence and annotation information generated in this study are available at DDBJ (http://getentry.ddbj.nig.ac.jp/top-j.html), accession number BSSO01000001-BSSO01049782.\n\nProtocol.io: Methods in “The first released available genome of the common ice plant (Mesembryanthemum crystallinum L.) extended the research region on salt tolerance, C3-CAM photosynthetic conversion, and halophism” V.1. https://dx.doi.org/10.17504/protocols.io.6qpvr4qdogmk/v1\n\nfigshare: Supplementary_Information.pdf. https://doi.org/10.6084/m9.figshare.21788624 (Sato et al., 2023b)\n\nfigshare: Supplementary_Dataset_S1.xlsx. https://doi.org/10.6084/m9.figshare.21788666 (Sato et al., 2023c)\n\nfigshare: Supplementary_Dataset_S2.xlsx. https://doi.org/10.6084/m9.figshare.21788675 (Sato et al., 2023d)\n\nfigshare: Supplementary_Dataset_S3.xlsx. https://doi.org/10.6084/m9.figshare.21788681 (Sato et al., 2023e)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nComputations were partially performed on the NIG supercomputer at ROIS National Institute of Genetics (Mishima-shi, Shizuoka, Japan). 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PubMed Abstract \| Publisher Full Text" }	[ { "id": "178334", "date": "23 Jun 2023", "name": "Qijie Guan", "expertise": [ "Reviewer Expertise Bioinformatics", "C3 to CAM transition", "omics" ], "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 is of significant importance, and the authors have utilized the best genome assembly platform for shotgun sequencing. However, there are a few minor concerns that need to be addressed:\nIn the sample materials, it is mentioned that the ice plants were treated with 0.3% (w/w) NaCl for 5 weeks. Please double-check the unit, should it be w/v (weight/volume) instead of w/w (weight/weight)? Additionally, it would be helpful if the authors could provide information about the nutrient content in OAT1 House No.1 and No.2. Most importantly, the authors should clarify the CAM status of the ice plant before sampling.\n\nAlthough the author compared the ice plant genome against several other plant species, no CAM plants or C4 plants were included. It is recommended that the authors consider adding pineapple to the comparison.\n\nThe authors mentioned the release date of the SILVA database as 2020.08. It would be preferable if the authors could change the version of the database to its standard name, SILVA 138.1.\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": "9795", "date": "03 Jul 2023", "name": "Ryoma Sato", "role": "Author Response", "response": "Thank you for your suggestions. In the sample materials, it is mentioned that the ice plants were treated with 0.3% (w/w) NaCl for 5 weeks. Please double-check the unit, should it be w/v (weight/volume) instead of w/w (weight/weight)? In the sample materials, it is mentioned that the ice plants were treated with 0.3% (w/w) NaCl for 5 weeks. Please double-check the unit, should it be w/v (weight/volume) instead of w/w (weight/weight)? Yes, as you suggested, the notation should be w/v (weight/volume), but to adopt a more general notation, we have converted the concentration of NaCl from w/v to molar concentration as follows: < “Plant materials and growth conditions” in Methods > The plants were treated with the solution including 51 mM NaCl for two weeks. Additionally, it would be helpful if the authors could provide information about the nutrient content in OAT1 House No.1 and No.2. The expression on compositions of OAT House No. 1 and No. 2 have been changed as follows: < “Plant materials and growth conditions” in Methods > The plants were irrigated with a nutrient solution of 1.5 g L -1 OAT House No. 1, containing primary nutrients including 10% Nitrogen (1.5% as ammoniacal nitrogen and 8.2% as nitrate nitrogen), 8.0% water-soluble phosphoric acid, 27% water-soluble potassium, 4.0% water-soluble magnesium, 0.10% water-soluble manganese, 0.10% water-soluble boron, 0.18% iron, 2.0 × 10 -3% copper, 6.0 × 10 -3% zinc, and 2.0 × 10 -3% molybdenum, in addition to 1.0 g L -1 No. 2, comprising 11% nitrogen and 23% lime (OAT Agrio Co., Ltd., Tokyo, Japan) in a greenhouse at Kyushu University for five weeks. Most importantly, the authors should clarify the CAM status of the ice plant before sampling. In terms of CAM status, I think this is not necessary. The objective of this paper is to decode the genome sequence and we did not perform gene expression analysis, such as RNA-Seq analysis. Also, this is a genome analysis, so we used untreated plants. Therefore, we did not measure the internal pH of the ice plant's leaves. Although the author compared the ice plant genome against several other plant species, no CAM plants or C4 plants were included. It is recommended that the authors consider adding pineapple to the comparison. Thank you for your recommendation. The title of this paper includes the term “CAM”, but it did not mean that we will elucidate factors associated with CAM induction. The word “CAM” used in the introduction and elsewhere was to describe one of the characteristics of the common ice plant like the following six kinds of sentences. The information that we characterized is useful for elucidation of the mechanism of growth promotion under salinity and reversible conversion of the photosynthetic type from C3 to Crassulacean Acid Metabolism (CAM). Also, it converts its photosynthetic mode from C3 to Crassulacean Acid Metabolism (CAM) under severe salt stress and drought stress (Adams et al. 1998). These days, the comparative analysis of genome information focused on CAM-related genes in the common ice plants has been reported (Shen et al. 2022), but this genome resource is not easy to use. M. crystallinum is utilized as a model plant for investigating halophilism, salt tolerance, and CAM photosynthesis. Several miRNA-targeting transcription factors were associated with salt tolerance (HLH, SPL, HD-ZIP) (Shen et al. 2019; Wang et al. 2019; Wang et al. 2021) or CAM photosynthesis (WRKY, AP2, MYB, NAC) (Amin et al. 2019; Yuan et al. 2020; Shah et al. 2021). The first five sections, as explained earlier, contain the term “CAM” solely for the purpose of describing the physiological traits of the ice plant. The sixth section suggests that the discovery of miRNA could serve as a catalyst to advance research on salt tolerance and CAM. As such, the term CAM is seldom mentioned in this paper, and wherever the word is used, it is only for mere description or hinting at potential advancements in future research. Overall, the purpose of this study is to elucidate the characteristics of the ice plant's genome, so we did not focus on CAM this time. Instead, we are currently progressing with functional genomics analysis related to CAM and other traits using a full-length genome sequence with PacBio Sequel II and publicly available Hi-C data. Soon, we will submit a paper revealing the impact of the genome on the C3-CAM transition mechanism of the ice plant and the growth promotion mechanism under the presence of NaCl. The authors mentioned the release date of the SILVA database as 2020.08. It would be preferable if the authors could change the version of the database to its standard name, SILVA 138.1. Thank you for the suggestion. I changed the version number as follows: <” Phylogenetic tree creation among multiple plant species using 18S ribosomal DNA sequences” in Methods > …were selected using the SILVA 138.1 database (Release. 2020-08; Pruesse et al. 2007). The above is my reply. I appreciate your understanding and assistance in this matter despite your busy schedule." } ] } ]	1	https://f1000research.com/articles/12-448
https://f1000research.com/articles/11-627/v1	08 Jun 22	{ "type": "Research Article", "title": "Noise intensity and its impact on the perception and concentration level among forest harvesting workers in industrial forest plantation, North Sumatera, Indonesia", "authors": [ "Muhdi Muhdi", "Diana Sofia Hanafiah", "Asmarlaili Sahar", "Alex Angenano Telaumbanua", "Diana Sofia Hanafiah", "Asmarlaili Sahar", "Alex Angenano Telaumbanua" ], "abstract": "Background: Noise has the potential to affect the comfort and health of workers. The objective of this research was to find out the effect of noise caused by the timber harvesting process using chainsaws on the concentration of workers in an industrial forest plantation. Methods: This experimental study included 20 respondents which consisted of 10 chainsaw operators/helpers and 10 non-chainsaw operators. All respondents were exposed to the sound of a chainsaw in three different conditions (idle, half gas and racing conditions) with and without personal protective equipment (PPE). The sound intensity produced by the chainsaw and the noise received by the respondents were measured using a sound level meter. Respondents’ perception toward noise was recorded using a Likert scale. Respondents’ concentration level was assessed by giving 25 math-questions to be answered within 10 minutes. Wilcoxon sign rank test was used to analysed paired data. Results: The average sound intensity received by respondents’ left and right ears were lower than the average sound intensity produced by the chainsaw. The use of earmuffs leads to better perception towards noise when compared with the use of earplugs and the absence of any PPE. The Wilcoxon test result showed that noise did not have significant impact on the concentration level of chainsaw operators, whilst the contrary result is true for non-chainsaw operators. Conclusions: The research indicated that although the noise produced by the chainsaw machine was considered noisy for both chainsaw operators and non-chainsaw operator, it did not have a significant effect on the concentration level of chainsaw operators and only affected the non-chainsaw operators. Therefore, given that the non-chainsaw operators were still affected by the noise, noise control measures are still needed to ensure occupational safety and health for the workers.", "keywords": [ "Chainsaw", "forest harvesting", "industrial forest plantation", "noise" ], "content": "Introduction\n\nThe timber harvesting process is considered a strenuous activity due to the overall forest harvesting processes, facilities, and infrastructure as well as natural factors such as topography and climate, which are complex entities that must be well-directed and well organized.1,2 In addition, forestry workers are at high-risk for accident and health problems. Accidents may happen due to several factors, such as carelessness of workers, inadequate skill or lack of occupational experience to operate heavy equipment, and low awareness towards occupational health and safety aspect.3,4\n\nDespite technological advances that have resulted in a diverse range of timber harvesting machinery,5 chainsaws are still widely used in forest operation due to their multifunctional use and low financial investment.6 On the other hand, the use of chainsaws has been linked to the high accident rates in professional and non-professional work.7,8\n\nChainsaw operators are undoubtly exposed to some threats such as noise, hand-arm vibrations (HAVs), exhaust gases, and timber dust.9,10 According to Nugroho,11 chainsaws are more dangerous than ordinary saws in many ways. A rotating chain can cause serious injury and noise produced by the machine could interfere with hearing in communication. In fact, continuous exposures to noise can cause health problems and discomfort at work, ranging from physiological and psychological disorders, balance disorders, communication difficulties, to hearing loss.12 Physiological disorders that may occur in response to noise are raised blood pressure and heart rate, reduced hearing acuity, earaches, nausea, impaired muscle control, and others.13 A study also found that noise (up to 85 dBA) could induce stress in some people.14 It is also widely known that exposure to noise that exceed the allowed threshold could pose the operator to the risk of hearing loss.15 Together, noise and its subsequent effects on health and safety aspect could lead to the decrease in employees’ work performance.12 In addition, noise can also cause mental disturbances such as increased irritability, anxiety and impaired concentration which could lead to safety hazard.16 Therefore, the noise that exceeds the allowed threshold and lasts for a long time must be controlled or prevented so as not to interfere with human life.\n\nThe purpose of noise control is to prevent workers from being exposed to these occupational hazards. This can be done by several methods, ranging from the use of personal protective equipment and implementation of rotational shiftwork, to the substitution or elimination of the noise source.17 Protective strategies also include identification of noise problems in workplace and determination of noise levels received by employees.15 According to Chandra,18 the main tool for measuring noise levels is using a sound level meter. This tool works to measure noise in the range of 30 to 130 decibels (dB) with frequencies between 20 to 20,000 Hertz (Hz). The result of this measurements are then compared with the threshold value. In Indonesia, to protect the safety and health of workers, the government has also issued various policies related to the threshold value of noise standard (including Decree of the Minister of Manpower No. Kep-51/MEN/1999 on Physical Threshold Values at Work Sites). The government has also adopted the logging work standards formulated by the International Labour Organization.19\n\nGiven that noise plays a significant role in determining occupational safety and health, research on the noise intensity and its control efforts, as well as its impact on the perception and concentration of workers in a workplace with significant noise become mandatory. This research was conducted to measure workers’ perception of noise generated by chainsaws in logging activities, and to analyze the impact of the noise on the concentration level of workers in an industrial forest plantation. The result of this study is important in order to reduce noise exposure by continuing to innovate, improve technology, remodify, and other aspects needed in an industrial forest plantation.\n\n\nMethods\n\nAll procedures in this study were approved by the Health Research Ethics Committee at the Faculty of Medicine, Universitas Sumatera Utara, Medan, North Sumatra, Indonesia (14th March 2021). Written informed consent was obtained from each respondent following the explanation about the nature of the study.\n\nThe population in this study was all workers at PT. Toba Pulp Lestari, North Sumatera, Indonesia. The sampling technique used in this study was non probability sampling using a saturated sampling method. Inclusion criteria for this study were (1) chainsaw operator or non-chainsaw operator who has worked for at least a year, (2) allowed by the supervisor to participate in the study, (3) right-handed. Left-handed workers were excluded from the study. To maintain work productivity, respondents were chosen from different compartments/team (one respondent/team). A total of 20 workers were recruited as respondents, which comprised of 10 chainsaw operators and 10 non-chainsaw operators.\n\nThe study conducted was an experimental study with pre- and post-test group design. Respondents were grouped into chainsaw operator group and non-chainsaw operator group. Each group consisted of 10 workers. All respondents in each group were exposed to the sound of a real chainsaw in three different conditions, namely idle (gas trigger was not pulled), half gas (gas trigger was half pulled) and racing (gas trigger was fully pulled). During the exposure, sound intensity measurement was done in the chainsaw machine and workers’ left and right ear with three replication with a span of 30 seconds. The procedures took place in an outdoor setting at the timber harvesting site.\n\nAfter that, respondents’ perception toward the noise produced by the chainsaw was measured three times in each condition (idle, half gas, racing) by using Likert scale. First measurement was done without the use of any personal protective equipment. In the second measurement, respondents were asked to use the earmuff. Lastly, in the third measurement, the respondents were asked to use the earplug. So that in total, for the measurement of respondents’ perception toward noise, each respondent was exposed to the noise of chainsaw nine times (3 times during idle condition, 3 times during half gas, and 3 times during racing condition).\n\nRespondents’ concentration level was later assessed using a designated questionnaire (detailed below) after the exposure of the sound of chainsaw in idle and racing conditions only. The measurements in each condition were done three times; without the use of any personal protective equipment, after using earmuff, and after using earplug. In this step, the respondent was exposed to the noise six times (3 times during idle conditions, and 3 times during racing conditions).\n\nSince all measurements were done in outdoor setting, there were potential source of bias, such as the present of noise coming from other chainsaws or machinery used in the work setting. In order to minimize this bias, we decided to do the research during resting time (12.00-13.00 Western Indonesian Time), so that there were no other concurrent activities that may distract or produced extra noise that may affect the measurements. According to previous study, during this range of time, healthy individual also showed acceptable levels of cognitive performance. This may reduce the effect of circadian rhythm variations in each respondents while performing the test, especially while measuring the concentration level.\n\nInterviews were conducted to gather information about respondents’ age, working experience expressed in years, and whether they were frequently exposed to noise outside working environment. The structured-interview was done by AAT at the logging site in PT. Toba Pulp Lestari for approximately 5 minutes. The interview guide was developed by the authors to include all necessary data and no prior testing was done.39 The data were recorded in a dummy table that has been prepared prior to the interview. No audio/video were recorded.\n\nSound intensity was measured in decibels (dB) using a sound level meter (Danoplus SLM-25, Danoplus, China) for ten minutes. Measurements were made on the chainsaw machine (Husqvarna 365, Husqvarna AB, Stockholm) and respondents’ right and left ear. The respondents were asked to stand up and place the chainsaw according to their usual working state. Sound intensity measurement on the chainsaw machine was done by placing the sound level meter approximately 5-10 cm from the chainsaw. Meanwhile, measurements in the right and left ear were done by placing sound level meters (one on the right ear, and one in left ear) in direct contact with the ear. All three measurements were done at the same time using different sound level meter.\n\nThe measurement was carried out in idle (the saw was on and the gas trigger was not pulled), half gas (gas trigger was half full) and racing (gas trigger was fully pulled) conditions. The measurements were repeated three times in each condition with a span of 30 seconds. This procedure was done to determine the amount of sound intensity produced by the chainsaw machine and the one received by the respondents.\n\nRespondents’ perception toward noise produced by the chainsaw machine was measured using a Likert scale, ranging from 1 (very noisy) to 5 (very quiet). The measurement was carried out after the respondents were exposed to the sound of chainsaw in three different conditions (idle, half gas and racing). Measurement in each condition was carried out three times: without using personal protective equipment/PPE, using earmuffs (Peltor X4A, Peltor, Poland) and using earplugs (E-A-R Ultrafit 340-4002, E-A-RTM, US). Respondents were then asked to describe the sound according to the Likert scale. A mean value ranging from 4.20 to 5.00 was considered as very quiet, 3.40 to 4.20 was considered as not noisy, 2.60 to 3.40 was considered as quite noisy, 1.80 to 2.60 was considered as noisy, meanwhile 1.00 to 1.80 was considered as very noisy.\n\nThe concentration levels of each respondent were measured using a questionnaire which comprised of 25 math-questions that must be filled within 10 minutes.20 The measurements were done after the respondents were exposed to the sound of chainsaw in 4 different conditions (chainsaw idle without personal protective equipment, chainsaw idle with personal protective equipment, chainsaw racing without personal protective equipment and chainsaw racing with personal protective equipment) for five minutes, so a total of four measurements were done and compared.\n\nSaphiro-Wilk normality test was used to ascertain the distribution of the data. Data that were not normally distributed would be analysed using non parametric test. Wilcoxon sign rank test was used to compare repeated measurements, including the sound intensity measured in respondents’ left and right ear during idle, half gas, and racing conditions, and the concentration level of each respondent without and with personal protective equipment in idle and racing conditions. The results were considered as significant if the p-value was below 0.05. All statistical analyses were performed using the Statistical Package for the Social Sciences (SPSS, RRID:SCR_016479), version 21 (IBM® Inc., USA).\n\n\nResults and discussion\n\nWorkers in a timber harvesting site, consisting of 20 respondents (10 chainsaw operators and 10 non-chainsaw operators) were recruited in this study.38 Non-chainsaw operators were recruited from field foremen and heavy equipment operators working at logging site of PT. Toba Pulp Lestari Tbk, Aek Nauli Sector, and the truck driver who was in charge of transporting the harvested timber to the timber processing site. The characteristics of respondents based on age and work experience are shown in Table 1.\n\nBased on Table 1, majority of the saw operators were of productive age with work experience that varies from 1 year of work to the longest of 13 years of work. The respondent’s work experience expressed in years also indicates how long the workers have been exposed to noise as a consequence of their daily job up until the research began.\n\nFrom interviews conducted, it was found that more than half (60%) of chainsaw operators included in this study listen to music or watch television at a high volume outside their working environment. This finding suggest that frequent exposure to noise at work may cause hearing impairment among the chainsaw operators so that they need to listen to music or television at higher volume. This fact should be a concern for company to carry out regular inspections of the operator’s hearing organs to avoid permanent hearing loss.\n\nIn a previous study done by Yovi et al.,21 chainsaw-operators had frequent direct interaction with the chainsaw with an average of 4 hours working duration. It must be taken into account that while working, the operators had to carry a chainsaw with the weight of 20 kg for approximately 2.4 to 3 hours. This suggests that workers not only suffered from the load but also from the vibration of the chainsaw. Noise produced by the chainsaw is also known to influence both operator’s workload and concentration. It was found that the mean workload during on and off (not carry-idle) differed significantly. These findings were also in accordance with a previous study on the physical strain experienced by the chainsaw operator in a forrest felling operation in Turkey. The results showed that the mean heart rate of chainsaw operators increased from 70.5 beats/minute during resting (pre-work resting heart rate) to 122.8 beats/minute while working. The average physical workload, measured as relative heart rate at work (%HRR) was 44.79, while the ratio of working heart rate to resting heart rate was 1.74. The average ratio of working heart rate to 50% level was 0.97. In addition, the chainsaw operator had a mean estimated maximum aerobic capacity of 43.34 milliliters per kilogram for every minute. According to those values, the works of chainsaw operations falls between heavy workload categories.22 Altogether, these findings emphasized the importance of using personal protective equipment to reduce the noise.\n\nThe sound intensities measured in the chainsaw and respondents’ left and right ear are shown in Figure 1.\n\nResults are shown as the means of the sound intensity.\n\nResults showed that the sound intensity received by the left ear and right ear were generally lower than those produced by the chainsaw (Figure 1). This is probably due to external factors including distance from the source of noise (machine) to the operator’s ear, in addition to wind and surrounding materials/environment which also reduces sound received by the ear. Meanwhile, a factor that may contributes to the difference in sound intensity received by the left ear and right ear is the hand preference of the respondent; in this study, all respondents were right-handed. In addition, the intensity of sound received by the left ear is greater than the right ear due to the distance between the sound source (chainsaw) which is closer to the left ear compared to the right ear. In this study, no detailed measurements were made of the value of the reduction in noise levels due to these external factors. This is due to the limitations of the available measuring tools.\n\nBased on the Wilcoxon test result, it can be concluded that there was no significant difference in the sound intensity received by respondents’ left and right ear during idle, half gas, and racing condition (p<0.05).\n\nThe measurement of both sound intensity produced by the chainsaw and the intensity received by the ear at the time of timber harvesting is useful to determine how much time is allowed for working based on the ISO (International Standard Organization), OSHA (Occupational Safety and Health Association), and Indonesian standards (Table 2).\n\nTotal effective working time of chainsaw operators at PT Toba Pulp Lestari Tbk is about 8 hours a day. From the results, when the chainsaw was turned on in idle conditions, the average sound intensity reaching the respondent’s ears was 82.11 dB (Figure 1). Referring to Table 1, it can be concluded that in idle conditions, respondents could operate the chainsaw safely for 8 hours because the sound intensity produced by the chainsaw was still below the threshold set by the ISO (International Standard Organization), OSHA (Occupational Safety and Health Association) and Indonesian standard. Meanwhile, when the chainsaw is turned on at half gas mode, the average sound intensity received by the respondent’s ears is 96.47 dB (Figure 1), which means that the chainsaw can be operated safely for only one hour according to ISO standards or for 4 hours and 2 hours according to OSHA and Indonesian standards, respectively. Furthermore, when the chainsaw was turned on in racing conditions, the average sound intensity received by the respondent’s ears was 106.95 dB (Figure 1), which means that the chainsaw can be operated safely without causing any hearing impairment for 0.25 hour according to ISO standards, 1 hour according to OSHA, or 0.5 hour according to the Indonesian standard. This is in accordance with the specifications of the chainsaw machine used in the study, where the average sound produced by the machine is about 125 dB and the intensity of the sound received by the ear is about 108 dB.\n\nDuring harvesting and felling activities, chainsaw operators are exposed to the noise produced by the chainsaw for approximately 4 hours every day, which means that their exposure to noise exceeds the permitted time limit set by the ISO, OSHA, and Indonesian standards.\n\nA study done by Rukat et al.23 showed that the impact of vibration and noise emitted from a chainsaw depends on several factors including the type of the drive (electric vs combustion); even with same or similar power, chainsaw with different type of drive may generates noise and vibrations with different magnitude. Chainsaw with combustion engine showed a higher sound level pressure compared to electric chainsaw. The greatest difference in the sound level pressure between the two chainsaws tested on that study was noted in the octave band with the center of frequency of 125 Hz, where the value for the combustion chainsaw is greater by 19.8 dB than electric chainsaw. The findings might be due to the chainsaw designs that differ significantly, such as in the characteristics of the drive, rotational speed, and the phenomena happened in each of the driving unit operating at the maximum speed and full load.\n\nChainsaw machines cause significant noise due to the movement and friction of the components of the combustion engine which causes changes in air frequency and pressure, in addition to the movement of the chain which rotates at a high speed and rubs against the blades. Everyone’s perception of an object can be different, which may be positive or negative. The difference in perception can occur in chainsaw operators and non-chainsaw operators to the noise they receive.\n\nFigures 2 to 4 show the different perceptions of chainsaw operators and non-chainsaw operators on chainsaw noise without using PPE, using earmuffs and earplugs, in idle, half gas, and racing conditions, respectively. Without using PPE, chainsaw operators consider the noise produced by the chainsaw in idle mode as “quite noisy”, while the non-chainsaw operators consider it as “very noisy”. After using earmuffs, both chainsaw operators and non-chainsaw operators consider the noise as “noisy”. Both chainsaw and non-chainsaw operators consider the noise as “quite noisy” after using earplugs (Figure 2).\n\nDuring half gas condition without the use of PPE, both chainsaw operator and non-chainsaw operator consider the noise as “noisy”. After using earmuffs, the perception of the chainsaw operators was improved to “not noisy” while the perception of non-chainsaw operators slightly improved to “quite noisy”. Then when using earplug both chainsaw operators and non-chainsaw operators considered the noise as “noisy” (Figure 3).\n\nWhen the chainsaw was in racing condition without the use of PPE, the chainsaw operators and non-chainsaw operators considered the noise as “very noisy”. After using the earmuffs, the perception of the chainsaw operator turned to “quite noisy” while the perception of the non-chainsaw operators was slightly improved to “noisy” and after using the earplugs the perception of the chainsaw operators and the non-chainsaw operator was turned to “very noisy” (Figure 4). This result was contrary with the statement from the foreman who said that the chainsaw operators did not find the machines noisy or feel disturbed because they were already accustomed to the sound of the chainsaw.\n\nBased on Figures 2–4, there are differences in the perception of chainsaw operators and non-chainsaw operators. However, both chainsaw operators and non-chainsaw operators have the same perception trend: the higher the sound intensity, the more it considered as noisy; and the more disturbed the respondents were because the disturbance due to sounds are influenced by several factors, including loudness perception.24\n\nThe difference in the perception when using earplugs and earmuffs occurs because the earmuff reduction power is stronger than the earplugs. Earmuffs can reduce noise pressure around 25-40 dB, while earplugs can reduce noise pressure around 8-30 dB.25 It depends on whether or not the respondent loosens the earplugs.26 Similar study results from Yovi and Suryaningsih27 showed that the chainsaw operators and non-chainsaw operators have a significantly different perception on the chainsaw sounds in each chainsaw mode (idle, half-gas, racing) and when using or not using ear protectors. This difference might rise because different respondents may react differently to the same stimulus/circumtances.\n\nUnlike earplug which is inserted to the ear canal, earmuffs are designed to be worn over the ears. This allows the earmuffs to be worn even when there is an infection in the ear and can be provided in one size. Due to their size, earmuffs will not easily be lost, and their use can be monitored because of its visibility from a distance.28 These ear protectors are usually used for protection up to 110 dB.25 The disadvantage is that they can be uncomfortable for prolonged use in hot environments and interferes with the use of other protective equipment, such as goggles.28 Meanwhile earplugs, being small and lightweight, tend to be more comfortable and easy to combine with other protective equipment such as hats and goggles, but because it needs to be inserted to the ear canal, it is more difficult to monitor the use of earplugs compared to earmuff and requires special fitting instructions.28 This type of ear protection device is usually used for protection up to 100 dB.15\n\nIt was also found that at the research site, all chainsaw operators did not use earmuffs or earplugs as personal protective equipment because it was not provided by the contractor and respondents did not know about personal protective equipment such as earmuffs or earplugs. Based on the results of interviews with all chainsaw operator respondents, in terms of the comfort of wearing earmuffs and earplugs, respondents considered earmuffs as more comfortable to use than earplugs because it offers higher noise reduction. In fact, chainsaw operators are actually willing to use PPE such as earmuffs or earplugs if it was provided by the contractor.\n\nRespondents’ concentration was assessed by ignoring pre-existing conditions that might affect the concentration levels, such as respondent’s chronotype, sleep deprivation, or any substance/drug intake (e.g caffeine).29 Wilcoxon test result on the concentration level of the respondents before and after wearing PPE in idle and racing conditions are shown in Table 3.\n\nThe use of PPE, which aimed to reduce the noise received by the respondents, did not show a significant effect on the concentration level of chainsaw-operators, both in idle and racing conditions. Wilcoxon test result shows that the concentration level of chainsaw-operators remain statistically the same before and after using PPE (p>0.05). Thus it can be concluded that the chainsaw operators were not bothered by the noise of the chainsaw or were used to the noise, and in this research, it does not give significant effects to the level of concentration of chainsaw operators in both conditions. Meanwhile Baiquni30 stated that most of the operators do not feel any disturbance due to noise to themselves so that this can be used as a guide that the operator is immune to noise.\n\nBased on the results of interviews with the cutting foreman, the majority of chainsaw operators do not feel the chainsaw is noisy when turned on. This is contrary to the results of interviews which show that chainsaw operators did actually feel the chainsaw was noisy when turned on in the racing conditions, therefore, in this study, chainsaw operators were exposed to the noise in idle and racing condition, both with PPE and without PPE. The result does not show a significant differences because although they considered the condition as noisy, chainsaw operators does not experience impaired concentration power when the chainsaw is turned on. This is contrary with the non-chainsaw operators who cannot concentrate when noise exists (p<0.05).\n\nWilcoxon test results shows that noise did interfere with the concentration level of non-chainsaw operators when the chainsaw was turned on in the idle and racing conditions. The concentration level of non-chainsaw operators differ significantly before and after using PPE (p<0.05). This result indicated that the noise is disturbing to the non-chainsaw operators, probably because they were not accustomed to the noise, and the use of PPE helped them to concentrate.\n\nNoise, which includes sound produced by human activities, has been intensively studied for its detrimental effects on human comfort, health, and productivity.31 Physical workload combined with noise intensity that exceeds 85 dB(A) for 8 hours of work could lead to fatigue symptomps such reduced concentration, physical exhaustion, dizziness and others.32,33 Yovi et al.27 stated that noisy environmental conditions can cause the operator to feel tired and lose their concentration easily. Therefore, one strategy to control noise exposure is for the company to provide replacement workers when the noise exposure has exceeds the allowed time limit and provide them with the necessary PPE.\n\nOther strategies, ranging from engineering approaches that aim to reduce the noise by adding protective equipment to the machines, to substitution or elimination of the noise source, may be applied to control noise exposure in the industrial forest plantation. Companies may consider to substitute their machinery with ones that produce less noise. From the literature, it was found that the water-cooled engine (more cylinder four-stroke one) is less noisy than the air-cooled one-cylinder two-stroke combustion engine (low weight). According to Neri et al.,34 there are differences in noise levels between Li-ion batteries and electric chainsaws. The study showed that Li-Ion battery powered chainsaw emitted lower noise and vibrations compared to wired chainsaw; but in general, these two chainsaws were better then the endothermic chainsaw in terms of both noise and vibrations they emitted. Thefore, the use of battery-powered chainsaws may decrease the exposure to noise and onset of hand-arm vibrations when compared with the use of combustion chainsaws.35\n\nA study done by Wojtkoviak et al.36 showed that lubricating the chainsaw’s cutting system with oil may help to reduce the noise generated by the chainsaw; even when they have similar cutting elements and used under identical condition. The noise reduction varies with different types of oil; the use of vegetable oil as lubricant resulted in the lowest noise emission. Skarzynski and Lipinski37 found that a higher noise level is generated during cross-cutting with the upper side of the guide bar and that kerf height affects significantly the level of emitted noise.\n\nSince the study was done in outdoor setting, limitations of this study mainly come from inability to control external factors, such as wind that may reduces the sound intensity received by respondents. Other than noise, there are also several factors that may affect concentration level of respondents, which were overlooked in the study. These factors include chronotype of each respondent, sleep adequacy, consumption of drugs or other substance.\n\n\nConclusions\n\nThe noise did not show significant effects on the power concentration of the chainsaw operators. Thus it can be concluded that the chainsaw operators do not feel disturbed by chainsaw noise or are accustomed to the noise. However, the noise produced by the chainsaw disturbs the concentration of the non-chainsaw workers. Therefore, noise control measures are still needed to ensure occupational safety for the workers, especially the non-chainsaw workers.\n\n\nData availability\n\nZenodo: Noise Intensity and Its Impact on The Perception and Concentration Level Among Forest Harvesting Workers in Industrial Forest Plantation, North Sumatera, Indonesia. https://doi.org/10.5281/zenodo.6423524.38\n\nThis project contains the following underlying data:\n\n• Raw data of noise intensity; raw data of perception dan concentration of workers.xlsx (raw data of noise intensity and raw data of perception and concentration scores of workers)\n\nZenodo: Noise Intensity and Its Impact on The Perception and Concentration Level Among Forest Harvesting Workers in Industrial Forest Plantation, North Sumatera, Indonesia. https://doi.org/10.5281/zenodo.6579109.39\n\n• Blank informed consent form (English); Blank informed consent form [english].pdf\n\n• Interview Guide; Interview Guide.pdf\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0)", "appendix": "Acknowledgements\n\nWe thank Rector of Universitas Sumatera Utara and PT Toba Pulp Lestari for facilitating this research.\n\n\nReferences\n\nPurwoko A, Muhdi HAS: Residual stand damages caused by conventional and reduced impact timber harvesting in the natural forest. 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Environmental Pollution. 2016; 218: 1162–1169. Publisher Full Text\n\nNugroho A: Measurement of Mechanical Vibration and Chain Saw Noise. Bogor Agricultural University;2005.\n\nKholik HM, Krishna DA: Analysis of noise level of production equipment on employee performance. Jurnal Teknik Industri. 2012; 13(2): 194. Publisher Full Text\n\nRachmatiah I: Health and Safety at Work Environment. Yogyakarta:Gadjah Mada University Press;2015.\n\nFithri P, Annnisa IQ: Analysis of Work Environment Noise Intensity in the Utilities Area of PLTD and Boiler Units (Case Study of PT. Pertamina RU II Dumai). Jurnal Sains, Teknologi dan Industri. 2015; 12(2): 278–285.\n\nRimantho D, Cahyadi B: Noise analysis of employees in the work environment in several types of companies. Jurnal Teknologi. 2015 Jan 31; 7: 21–27.\n\nSuryaningsih: Effects of Chainsaw Noise on Perception and Concentration Power. Bogor Agricultural University;2011.\n\nWang X, Orelaja OA, Ibrahim DS, et al.: Evaluation of noise risk level and its consequences on technical operators of tobacco processing equipment in a cigarette producing company in Nigeria. Scientific African 2020; 8: e00344. Publisher Full Text\n\nChandra B: Introduction to Environmental Health. Jakarta:EGC Medical Book Publishers;2007.\n\nSafety and Health in Forestry Work: The Annals of the American Academy of Political and Social Science. Vol. 108.International Labour Organization;1998; 206–210.\n\nYovi EY: Noise, Worker Perception, and Worker Concentration in Timber Harvesting Activity. Jurnal Manajemen Hutan Tropika. 2011; XVII(2): 56–62.Reference Source\n\nYovi EY, Yamad Y: Addressing occupational ergonomics issues in indonesian forestry: Laborers, operators, or equivalent workers. Croatian Journal of Forest Engineering. 2019; 40(2): 351–363. Publisher Full Text\n\nÇalişkan E, Çaǧlar S: An assessment of physiological workload of forest workers in felling operations. African Journal of Biotechnology. 2010; 9(35): 5651–5658.\n\nRukat W, Barczewski R, Jakubek B, et al.: The comparison of vibro-acoustic impact of chainsaws with electric and combustion drives. MATEC Web of Conferences. 2018; 182: 1–7. Publisher Full Text\n\nSkagerstrand Å, Köbler S, Stenfelt S: Loudness and annoyance of disturbing sounds–perception by normal hearing subjects. International Journal of Audiology. 2017; 56(10): 775–783. PubMed Abstract \| Publisher Full Text\n\nCahyadi B, Timang GA: Mapping of noise levels made by drilling machines on project x using contour zone method. IOP Conference Series: Materials Science and Engineering. 2019; 528(1): 012066. Publisher Full Text\n\nZiayi Ghahnavieh N, Pourabdian S, Forouharmajd F: Protective earphones and human hearing system response to the received sound frequency signals. Journal of Low Frequency Noise Vibration and Active Control. 2018; 37(4): 1030–1036. Publisher Full Text\n\nYovi EY; Suryaningsih: Noise, Worker Perception, and Worker Concentration in Timber Harvesting Activity.2011; XVII(2): 56–62.Reference Source\n\nMarkowitz S, Sataloff R, Sataloff J:Hearing protection devices.Sataloff R, Sataloff J, editors. Occupational hearing loss. 3rd ed.Taylor & Francis;2006; p. 463–70.\n\nValdez P: Circadian rhythms in attention. Yale Journal of Biology and Medicine. 2019; 92(1): 81–92. PubMed Abstract\n\nBaiquni K: Study on Noise Aspects at the Stamping Shop Unit, Karawang, Plant PT Toyota Motor Manufacturing Indonesia. Bogor Agricultural University.\n\nMarques G, Pitarma R: A Real-Time Noise Monitoring System Based on Internet of Things for Enhanced Acoustic Comfort and Occupational Health. IEEE Access. 2020; 8: 139741–139755. Publisher Full Text\n\nIhsan T, Afriani N, Edwin T, et al.: Effect of Occupational Noise Exposure to Work-Fatigue of Indonesian Crumb Rubber Plants. IOP Conference Series: Materials Science and Engineering. 2021; 1041(1): 012038. Publisher Full Text\n\nTabraiz S, Ahmad S, Shehzadi I, et al.: Study of physio-psychological effects on traffic wardens due to traffic noise pollution; exposure-effect relation. Journal of Environmental Health Science and Engineering. 2015; 13(1): 1–8.\n\nNeri F, Laschi A, Foderi C, et al.: Determining noise and vibration exposure in conifer cross-cutting operations by using Li-Ion batteries and electric chainsaws. Forests. 2018; 9(8): 1–13. Publisher Full Text\n\nColantoni A, Mazzocchi F, Cossio F, et al.: Comparisons between battery chainsaws and internal combustion engine chainsaws: Performance and safety. Contemporary Engineering Sciences. 2016; 9(27): 1315–1337. Publisher Full Text\n\nWojtkowiak R, Kromulski J, Dubowski A: Measurements of noise resulting from cutting chain movements on a chain-saw bar, lubricated with different oils. Acta Scientiarum Polonorum Silvarum Colendarum Ratio et Industria Lignaria. 2007; 6(1): 85–93.Reference Source\n\nSkarzynski J, Lipinski R: Effect of kerf height on noise emission level in the internal combustion chain saw Stihl MS 211 and the electric chain saw Stihl E 180C during cross cutting of wood.2013; 62(62): 55–62.\n\nMuhdi HDS, Sahar A, Telaumbanua AA: Noise Intensity and Its Impact on The Perception and Concentration Level Among Forest Harvesting Workers in Industrial Forest Plantation, North Sumatera, Indonesia. [Data]2022 Apr 8 [cited 2022 Apr 8]. Publisher Full Text\n\nMuhdi HDS, Sahar A, Telaumbanua AA: Noise Intensity and Its Impact on The Perception and Concentration Level Among Forest Harvesting Workers in Industrial Forest Plantation, North Sumatera, Indonesia. [Data]2022 May 25 [cited 2022 May 31].Reference Source" }	[ { "id": "174078", "date": "01 Jun 2023", "name": "Vasiliki Dimou", "expertise": [ "Reviewer Expertise Forest Products Harvesting and Forest Ergonomics" ], "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 very much for giving me the opportunity to evaluate this article. The purpose of the article is interesting and very practical. The authors describe the exposure of the forest harvesting workers in an industrial forest plantation to the noise in three different conditions (idle, half gas and racing conditions).\nThe work is clearly and accurately presented and it cites the current literature but be careful in p. 4: \"The interview guide was developed by the authors to include all necessary data and no prior testing was done39\"- Maybe the number of the bibliographic reference is 20 and not 39?\n\nThe study design is appropriate and the work is technically sound, but be careful in p. 5 \"...chainsaw in 4 different conditions (chainsaw idle without personal protective equipment, chainsaw idle with personal protective equipment, chainsaw racing without personal protective equipment and chainsaw racing with personal protective equipment) for five minutes, so a total of four measurements were done and compared…\" - I wonder if the correct one is six measurements instead of four measurements, given that 'personal equipment' includes 2 conditions 'earmuffs and earplugs'?\n\nIn the context of replication and comparison it would be good to show the main technical characteristics of the Husqarna 365 chainsaw in a table (p.4) (Engine Size/Power Hp/ Max rpm/Capacity/Weight empty.\n\nIn addition I would suggest that the questionnaire (25 math-questions) be listed in an appendix.\n\nThe conclusions are drawn adequately supported by the results. But be careful in p.7: \"...while the non-chainsaw operators consider it as “very noisy”...\" - I wonder if the correct one is ‘quite noisy’?\n\nAfter using earmuffs, both chainsaw operators and non-chainsaw operators consider the noise as “noisy”...\" - I wonder if the correct one is ‘’not noisy’’?\n\nI would suggest that after a description of the Likert scale, the corresponding limits should be included in parentheses e.g. ‘not noisy’ (3.40-4.20).\n\nIn fig. 1 the unit of measurement is missing, I assume it is dB?\n\nIn fig. 2-4, for better comparison, the axes ‘Perception of workers’ should contain the entire Likert scale, i.e. 0-5.\n\np.4: \"...The structured-interview was done by AAT at the logging site...\" - It must be mentioned, at least for the first time, written in full in parentheses (Associate of Accounting Technicians).\n\np.5-6: \"...In a previous study...Altogether, these findings emphasized the importance of using personal protective equipment to reduce the noise.\" - These references are better suited to the introduction than here. At this point literature references on noise would be interesting.\n\np.6: \"...Based on the Wilcoxon test result, it can be concluded that there was no significant difference in the sound intensity received by respondents’ left and right ear during idle, half gas, and racing condition (p<0.05).\" - Shouldn’t the right and left ear noise difference be treated numerically, because sound level is a logarithmic quantity? For example, it is stated that for sound levels that differ by 3 dB, the stronger one has twice the intensity of the weaker one, that is, the level of 85 dB is twice as loud as that of 82 dB, while two 85 dB sounds added have a level of 88 dB and not 170 dB.\n\nLogarithmic measurements of sound intensity must be converted into numerical measurements of sound intensity using: ex =y, where x the results in logarithmic measurements of sound intensity. So with the new numerical measurements of sound intensity ‘y’, the Wilcoxon test must be done again.\n\np.6: \"...Referring to Table 1, it can be concluded that in idle conditions,...\" - Is Table 2 likely to be the correct one?\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "9780", "date": "14 Jul 2023", "name": "Muhdi Muhdi", "role": "Author Response", "response": "Thank you very much for reviewing our manuscript. We have revised the manuscript according to your comments and suggestions. Thank you for kindly." } ] }, { "id": "170754", "date": "05 Jun 2023", "name": "Mohamad Siarudin", "expertise": [ "Reviewer Expertise Forest management", "forest product technology", "agroforestry", "carbon accounting" ], "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 your interesting article. This article seems good in originality and clear in the problem addressed. It provides information on how the noise intensity affects the perception and concentration of the forest harvesting workers. However, I have some concerns on different sections of the manuscript.\nIntroduction\nWell organized. Clear research objective, however, I would suggest including the safety aspect of sound intensity in the objective and conclusion.\nMethod\nYou mention that the sampling method was a saturated sampling technique. Does it mean that all of the population was included in the survey? How many populations? Please mention it.\n\nPlease add a brief reason for the “right-handed” respondent criteria.\n\nI found redundancies in describing idle, gas, and racing.\nResult\nPlease avoid using a single sentence in one paragraph (please also recheck throughout the paper).\n\nFigure 1: It would be nice if you can show the deviation standard (among 3 replications) in the figure.\n\nPlease check your referring (Table 1? Should be Table 2?) in the Sound intensity subsection, paragraph 4th.\n\nI would suggest more references to enrich the discussion of the findings in the sound intensity subsection.\n\nFigure 2-4: the use of scale in the Y-axis is not clear and is not described in the method. In the description, you use categorical data: very noisy, noisy, quite noisy. Please make it clear and consistent in the methods, figure, and discussion.\n\nWhy does the perception between Figure 2 (idle), 3 (half-gas), and 4 (racing) tend to decrease in scale? In my understanding, the sound should tend to increase.\nConclusion\nThe conclusion seems to answer the objective of the study, which focuses on the concentration of the workers. However, this study also covers the safety aspect of sound intensity by comparing it to several standards, as well as the perception of the workers (that appears in the title). In my opinion, this safety aspect is interesting and could be included in the study objective and 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? 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": "9781", "date": "14 Jul 2023", "name": "Muhdi Muhdi", "role": "Author Response", "response": "Thank you very much for reviewing our manuscript. We have revised the manuscript according to your comments and suggestions. Thank you for kindly." } ] } ]	1	https://f1000research.com/articles/11-627
https://f1000research.com/articles/13-14/v1	03 Jan 24	{ "type": "Software Tool Article", "title": "COverlap: a Fiji toolset for the 3D co-localization of two fluorescent nuclear markers in confocal images", "authors": [ "Mélodie Ambroset", "Bruno Bontempi", "Jean-Luc Morel", "Mélodie Ambroset", "Bruno Bontempi" ], "abstract": "With the increasing complexity and throughput of microscopy experiments, it has become essential for biologists to navigate computational means of analysis to produce automated and reproducible workflows. Bioimage analysis workflows being largely underreported in method sections of articles, it is however quite difficult to find practical examples of documented scripts to support beginner programmers in biology. Here, we introduce COverlap, a Fiji toolset composed of four macros, for the 3D segmentation and co-localization of fluorescent nuclear markers in confocal images. The toolset accepts batches of multichannel z-stack images, segments objects in two channels of interest, and outputs object counts and labels, as well as co-localization results based on the physical overlap of objects. The first macro is a preparatory step that produces maximum intensity projections of images for visualization purposes. The second macro assists users in selecting batch-suitable segmentation parameters by testing them on small portions of the images. The third macro performs automated segmentation and co-localization analysis, and saves the parameters used, the results table, the 3D regions of interest (ROIs) of co-localizing objects, and two types of verification images with segmentation and co-localization masks for each image of the batch. The fourth macro allows users to review the verification images displaying segmentation masks and the location of co-localization events, and to perform corrections such as ROI adjustment, z-stack reslicing, and volume estimation correction in an automatically documented manner. To illustrate how COverlap operates, we present an experiment in which we identified rare endothelial proliferation events in adult rat brain slices on more than 350 large tiled z-stacks. We conclude by discussing the reproducibility and generalizability of the toolset, its limitations for different datasets, and its potential use as a template that is adaptable to other types of analyses.", "keywords": [ "3D segmentation", "co-localization", "confocal microscopy", "angiogenesis", "bioimage analysis", "endothelial cell proliferation", "ImageJ", "Fiji toolset" ], "content": "Introduction\n\nIn recent years, the complexity of bioimage analysis workflows has significantly increased because of the extraordinary volume of data generated from microscopy experiments.1 Although a plethora of user-friendly bioimage analysis methods and tools are now available to life scientists,2 there is no single turnkey solution, owing to the variety of existing imaging problems.3 Additionally, performing complex analysis workflows without computational skills has become increasingly challenging or even impossible.4 In cell biology, computer vision has the dual advantage of automating the analysis process and enabling complete data extraction from images.5 Perhaps just as importantly, the creation of macros or scripts for quantifying images addresses the need to report reproducible bioimage analysis workflows, because code and its documentation serve as traceable entities that can be conveniently reviewed and reused as necessary.4,6 Despite the availability of excellent teaching materials for life scientists wanting to learn programming,7–9 there seems to be a lack of practical and accessible published examples (such as Refs. 10–13) that can inspire programming novices.\n\nWe introduce COverlap, a Fiji toolset consisting of four macros designed to segment and detect the co-occurrence of two nuclear markers in confocal multichannel z-stack images. A testing step on small subsamples of images first facilitates the selection of batch-suitable parameters for the segmentation workflow, which consists of image enhancement processes (normalization, filtering, and background subtraction), followed by thresholding and connected component analysis to identify and count objects in two image channels. The toolset combines pre-existing plugins to perform a fully automated segmentation and co-localization analysis based on the percentage of volume overlap between objects. Finally, the toolset provides support for the visualization, manual review, and annotation of results while giving users the opportunity to implement a documented set of corrections without having to perform the entire analysis again.\n\nAfter providing a detailed description of the toolset’s requirements, installation procedure, and operation, we present an experiment in which we used COverlap to detect newly formed endothelial cells in the anterior cingulate cortex (ACC) of adult rats, a cerebral region involved in the long-term storage of memories. This area being widely spread in the brain, and endothelial proliferation events quite rare outside of development, aging, disease, or injury,14,15 this experiment required the acquisition of a substantial number of x20 multichannel tiled z-stack images spanning the region of interest on several 50 μm-thick coronal brain sections per animal. To reveal endothelial proliferation, we labeled newly synthesized DNA in the nuclei of proliferating cells using an EdU (5-Ethynyl-2-deoxyuridine) assay, performed immunofluorescence staining of ERG, a transcription factor specific to endothelial nuclei in the brain, and used COverlap to detect their co-occurrence. The toolset organization, with a clear separation of interactive from automated steps, greatly facilitated the analysis of more than 350 multidimensional images, while the automated recording of all parameters and results ensured the reproducibility of the experiment.\n\nWe conclude this article by addressing how the object segmentation and co-localization analysis components of the workflow were selected and how they may not be applicable to all comparable analysis challenges. We then discuss how COverlap can be flexibly used either as a parameterizable solution for non-programmers with a compatible experiment or as an adaptable template, which we believe exemplifies good practices in reporting a bioimage analysis workflow.\n\n\nMethods\n\nOur toolset is written in the ImageJ macro language and is designed to be installed in Fiji16 as a set of clickable action buttons that trigger four individual macros. The version of Fiji used to write and run this toolset was 1.54f. The toolset relies on classical segmentation algorithms (filtering, background subtraction, thresholding, watershed) to extract objects from images and on a user-defined minimum volume overlap ratio to quantify co-localizing objects.\n\nThe toolset can be installed by downloading the COverlap_Toolset.ijm file on GitHub and placing it in the macros/toolsets/directory of Fiji. Additionally, the toolset requires the installation of plugins MorphoLibJ17 and 3D ImageJ Suite.18 Users must enable the following update sites in Fiji: IJPB-plugins, 3D ImageJ Suite, Java8, and ImageScience. The GitHub README.md file19 provides a detailed tutorial for the installation and use of COverlap.\n\nThe toolset requires z-stack multichannel (up to four, minimum two) images, where the two channels ideally contain nuclear or blob-like markers. The toolset was tested by using .tif and .nd files but could be tested with other types of files that the Bio-formats Importer can open.\n\nTo run, the toolset requires an Image folder containing the experiment and an initially empty Results folder. Two types of Image folder and naming organization are possible (Figure 1): either a master folder contains one subfolder per image (such as is required for .nd files where a given subfolder contains the .nd file and one .tif image per channel), or a single folder contains all the images. In the former case, the name of each subfolder needs to include: the identifier of the sample (such as unique identifying code) and the name of the region analyzed (such as “ACC” for anterior cingulate cortex or “PC” for parietal cortex). In the latter case, the name of the image must include this information.\n\nThe toolset was run on a workstation with an Intel® Core™ i9-10900 CPU @ 2.80GHz, 128 GB of RAM, and Windows 10 64-bit.\n\nCOverlap comprises four macros that can be individually triggered by four action buttons. Each macro performs a specific step (Figure 2):\n\n1. A preliminary creation of maximum intensity projection (MIP) for each image.\n\n2. A testing step that allows testing of the workflow on small portions of images to select the best parameters for filtering, background subtraction, and thresholding for a given batch.\n\n3. The manual drawing of regions of interest (ROIs) for all images in the batch followed by automatic segmentation and 3D co-localization of the two nuclear markers.\n\n4. A review step, where results and segmentations/co-localization masks can be verified, and corrections applied if needed (ROI adjustment, z-stack reslicing, and volume estimation correction), with appropriate documentation of any such correction.\n\nRed bubbles: Macros. Blue: Manual steps. Grey: automated steps. Green: output elements.\n\nThe first macro of this toolset allows for the creation of an MIP for each image of the batch and saves it as a TIFF file in the corresponding image folder.\n\nThe MIPs generated in this preliminary step will be used as a visualization tool, both as a support for drawing the ROI during the parameter-testing phase (Macro 2) and the batch analysis (Macro 3), and for the creation of verification images on which the positions of co-localization events found during the batch analysis are displayed on the MIP, making it easy for users to locate them and appreciate their distribution (Macros 4).\n\nA click on the “1” icon of the toolset launches the first macro, and users are invited to specify the folder organization of their images (Figure 1), a substring (sequence of characters) contained in the file name of all the images, and the extension of images that need to be retrieved from the folder. If no substring is specified, then all images of the specified extension type are processed. Users can then pick a different Lookup Table (LUT) for each channel they want to be part of the MIP or the option “None” for non-existing channels or channels they do not wish to project. An option for disabling the automatic display of all channels as a composite image is also available.\n\nThe second macro allows users to test various segmentation parameters (filtering, object minimum size, background subtraction, and threshold) on small portions of images.\n\nUsers are invited to point to their Images and Results folders and to specify the names of their target markers and the channel on which they are located. Users can also indicate the names of one and up to two ROIs. These region names should be included in the names of the images that contain them for the macro to properly use their respective associated parameters. If incorrectly spelled or no regions are specified, the left-column parameters will be used for all images. The point of this feature is to allow for region-specific thresholds to be chosen, for example, in cases where different brain regions whose contents are systematically different were imaged. Notably, the current implementation of the macro only works with one ROI per image.\n\nAs done previously, users must also provide a substring contained in all image file names, as well as their extension, for the macro to retrieve them in the image folder. These parameters can be saved for retrieval during the subsequent steps of the toolset or later use of the macro.\n\nThe macro then displays a list of paths on which users are invited to click to open an MIP from the batch. Once an MIP is opened, users fill in various segmentation parameters in the interface. After they select a representative portion of the image and add it to the ROI Manager, the macro will crop the original image around this test ROI and perform the segmentation test for both channels automatically.\n\nThe segmentation of the two nuclear markers of interest performed by this second macro consists of the same steps as those that will be performed during the batch analysis with the third macro (Figure 3). Both macros duplicate the working channels and close the original image to preserve its integrity. Each subsequent step of the segmentation is sequentially performed on each duplicated channel.\n\nContrast enhancement is first performed on each slice of the z-stack, by way of the histogram stretching method (also called normalization, Process > Enhance contrast… in ImageJ), where pixel values of the image are recalculated so their range is linearly “stretched” to be equal to the maximum range for the data type (for example 0-65535 for 16-bit images), with 0.35% pixels allowed to become saturated (to prevent a few outlying pixels from causing the histogram-stretch to not work as intended). Each channel is then cropped around the ROI previously drawn by the user and subsequently converted to an 8-bit image by linearly scaling from min-max to 0-255, where min and max values are the “Display range” in Image > Show Info or the values displayed in the Image > Adjust > Brightness > Contrast tool.\n\nImage enhancement processes are then applied: first, denoising is achieved using a 3D median filter18 (Plugins > 3D Suite > Filters > 3D Fast Filters) chosen for its edge-preserving qualities, followed by a 3D Gaussian filter (Process > Filters > Gaussian Blur 3D) to further smooth images. 3D filtering takes into account possible voxel anisotropy: if the voxels are non-cubic, the ratio between the x and y parameters and the z parameters should approximate that of the ratio between the x and y dimensions and the z dimension of the voxel. The rolling ball background subtraction is then performed (Process > Background subtraction) on each slice of the stack in order to get rid of uneven background fluorescence, which would prevent a global thresholding from working. As a rule of thumb, the selected radius of the rolling ball must be at least as large as the radius of the largest object to be detected in the image. Setting parameters to 0 for any of the enhancement processes will result in the macro skipping this particular step.\n\nThe images are then ready for segmentation. The images are processed using the users’ numerical threshold parameter for each channel and the Plugins > 3D Suite > Segmentation > 3D Simple Segmentation. The plugin is based on connected-component analysis, which clusters voxels above an intensity threshold based on their connectivity (here, using an algorithm where all 26 neighboring voxels, including diagonally, are considered connected) and assigns a value to each cluster (see Chapters 2 and 9 of Ref. 20). This method generates a labeled image where each segmented object is attributed to a gray level and has the advantage of including a minimum size filter that allows the exclusion of smaller particles that are out of the nucleus of interest size range.\n\nUsers have the option to apply a watershed algorithm to segmented images using the Plugins > 3D Suite > Segmentation > 3D Watershed Split plugin, chosen for its ability to split merged objects based on the local maxima of their Euclidean distance map (i.e., the farthest points from the boundaries of objects, corresponding to their centers). The watershed radius should be approximately the radius of the objects of interest in a given channel.\n\nUsers can optionally exclude objects that touch the edges of the ROI. For this, the labeled image is binarized (objects appear in white and the background in black), and the ROI is drawn in white as a two-pixel line on each slice of the z-stack. The image is then converted back into a labeled image, where the ROI and any object that it touches are labeled as a single object. The largest object in the image is then removed, thereby removing the drawn ROI and the touching objects. Users should be advised that this algorithm cannot function properly if the image contains a very large object that comprises more voxels than the object composed of the ROI and the objects it touches. However, this is unlikely in the case of images used for nuclei segmentation and co-localization. The ROI should also be drawn in a single line, so that its border is continuous: any hollow in the ROI created with the “Alt” key will result in the object exclusion feature not functioning. As this feature is mostly useful to avoid detecting spurious co-localization events on the edge of the ROI due to partially segmented objects, we also advise users to disable it during Macro 2 to save processing time.\n\nThe result of this automated segmentation test can then be visualized. For both channels, users can compare the original (contrast-enhanced) image, the enhanced (filtered/background subtracted) image, and the composite visualization image displaying the test ROI and the outline of the segmented nuclei (green LUT) on the original image (red LUT). Users can browse the z-stack and toggle the segmentation outline on and off to assess whether their marker of interest has been properly segmented using the chosen parameters.\n\nParameters can be repeatedly tested until a suitable set is reached without having to reopen the image each time, and users can switch to another image without exiting the macro to test these parameters on a different sample. When a given set of parameters is deemed applicable to the majority of images in the batch, a “Save parameters” box can be ticked before running the test, which generates a file that the third macro retrieves to fill in the graphical user interface (GUI) for parameters automatically. Users can then proceed to batch analysis using the Macro 3.\n\nThe third macro performs segmentation and co-localization analysis on the entire batch of images. Users indicate the batch folder containing all the images and MIPs generated with Macro 1 (or image subfolders where each holds an original image and its MIP), as well as a separate output folder (which may contain saved parameters from Macro 2) to store the results, ROIs, and verification images.\n\nUsers are prompted to check the targets, channels, and regions parameters that are retrieved from the file saved in Macro 2 and modify them if needed. Similarly, the macro retrieves the segmentation parameters saved in Macro 2 to fill the GUI, and users can check and modify them as needed. If the “Save parameters” box is ticked, the previously saved parameters are overwritten. In any case, when the analysis is started, all the detection parameters used for the batch, as well as the date and time of processing, are saved in the Results folder.\n\nThe macro then opens each MIP in turn, and users are prompted to draw one ROI per image, on which the analysis will be performed. As this process may take a long time, proportional to the number of images in the batch and the complexity of the region to be drawn, we advise that users plan ahead and divide their batch into several smaller, more manageable batches if they have a limited amount of time to dedicate to ROI drawing. If users wish to use the edge-exclusion option (see Macro 2), the ROI edges must be continuous (as opposed to having holes drawn in with the Alt key). Users can skip drawing an ROI on images that they do not wish to analyze, as the macro will later ignore images without a matching ROI. Once all the images have been read, the segmentation and co-localization analyses are performed. Alternatively, users can place an already created set of ROIs in the Results folder and uncheck the “Ask for ROI” option in the segmentation GUI. Each ROI must be named after its corresponding image (after the following example “ImageName_ROI.zip”). This technique can also be used in cases where ROIs have already been drawn once, and the analysis must be run again.\n\nFor each image, both channels are first segmented using the same process as that described for Macro 2, before the object-based co-localization analysis is performed.\n\nOur method initially defines objects that possess overlapping voxels as co-localized and allows the setting of a minimum percentage of voxels (relative to the total number of voxels in the object, i.e., a minimum volume overlap ratio) that need to be overlapping to be considered as co-localization. For two labeled images obtained from two channels A and B, the MultiColoc plugin of the 3D Suite computes all co-localizations (i.e., all intersections of voxels) between every possible A-B pair of objects. The macro then selects only pairs of objects for which, for at least one of the two objects, the volume overlap ratio meets or exceeds the overlap threshold set in the parameters. If the threshold is set at 50%, only pairs comprising at least one object for which at least 50% of its total volume overlaps the other object will be retained. Notably, this method allows multiple co-localizations to be preserved for a single object.\n\nDepending on the hardware specifications, especially for large batches and/or large images, the analysis can take a long time. The progress is displayed in the Log window (image being processed/total number of images), while the macro runs in the background (images are not displayed). Each time an image is processed, the Results folder is updated, such that if the macro is interrupted before its completion, the results for images that have been successfully analyzed are not lost. Specifically, for each image analyzed, the results table is updated, a.zip file containing a set with the 3D ROIs of each co-localizing object is saved, and two types of verification images are created.\n\nThe results table summarizes, for each analyzed sample: the parent folder it belonged to (which can be named after a relevant group or batch name), the sample’s name, its target region, its number of z-slices, the area of the drawn ROI, the total area and the volume analyzed, the number of segmented objects for channels A and B, the number of objects A co-localizing in B, the number of objects B co-localizing in A for a given overlap threshold, and the date and time of processing.\n\nThe first type of verification image is a .jpg image based on the MIP from Macro 1, which displays the outline of the analyzed ROI, as well as enlarged outlines around the found co-localization events. Its purpose is to facilitate the localization of these events for users, who can also obtain a general idea of their distribution in the analyzed ROI. The other type of verification image is a .tif image comprised of a z-stack with four binary channels: two (red and green) channels corresponding to each marker segmentation, one (blue) to the co-localization events detected by the macro, and one (grey) to the overlap of objects that were excluded by the co-localization threshold. The first three channels of this image are displayed as a composite, such that any detected co-localization will conveniently appear in white, through the superposition of the three red, green, and blue LUTs. The purpose of this image is to enable users to verify both the segmentation and the co-localization analysis in the analyzed volume: major segmentation problems (such as an inappropriate threshold resulting in noisy segmentation) and spurious co-localization events should be apparent in this image. Users can also review the initially hidden fourth channel to assess the appropriateness of their overlap threshold.\n\nIn addition to these verification images, a set of 3D ROIs for co-localizing objects is also saved for each image containing co-localization events. Using the 3D Manager plugin,18 users can perform additional measurements on co-localized objects, such as intensity measurements on the original image and measurement of volume or other geometric properties.\n\nOnce the analysis is completed, a message is displayed in the Log window, and the text file containing the detection parameters is appended with the date and time of completion of the analysis. Users can then proceed to the review step at any time they deem convenient.\n\nThe fourth macro allows users to review their analyzed images and perform corrections, such as trimming of the ROI (e.g., to exclude an air bubble trapped in the mounting medium between the slide and coverslip), reslicing of the z-stack (to exclude out-of-focus slices), changing the overlap threshold for co-localizations, or correcting the volume estimation.\n\nAfter inputting their Images and Results folders, users indicate the name of the targets and their respective channels, as well as the original overlap threshold with which the images have been analyzed. The macro then retrieves and displays the list of verification images from the Results folder. Users are invited to open a composite image from the list to review it. They can open the corresponding MIP visualization image at the same time to check where the detected co-localization events are located, but must close it before the next step. When they are ready to perform corrections, users click on the OK button and are presented with a list of corrections that may be applied to the image. If they confirm that they wish to perform corrections, the “Correction Options” GUI is displayed.\n\nUsers can perform several actions:\n\n• They can reshape the ROI to exclude parts of it, such as a bubble, tear in the tissue, or part of the ROI that is too close to the edge of the sample. Note that if users have failed to encompass everything they wished to analyze in the original ROI, this cannot be fixed at this point, and the image should be reprocessed using Macro 3.\n\n• They can reslice the z-stack by excluding the slices at the beginning and/or end of the stack. This is useful when the initial z-stack comprises out-of-focus slices that either generate spurious segmentation or are devoid of objects.\n\n• They can review overlapping objects: those above the chosen overlap threshold that are detected as co-localized appear on channel 3, and those under the threshold are located on channel 4. Users can change the overlap threshold if they are not satisfied (we advise, however, that this should be performed on all images).\n\nOnce the options are set, the macro performs all the above-mentioned corrections. Objects are quantified again with these new parameters, from the corrected composite image directly, without having to reopen the original image, and co-localizations are analyzed again for these objects. An important feature of this correction step is that it corrects the estimated analyzed volume.\n\nWhile the initially calculated volume corresponds to the area of the ROI multiplied by the number of z-slices multiplied by the size of the z-step, this algorithm wraps, for each slice, a convex hull selection around all detected cells regardless of the channel and uses the sum of these selections’ areas multiplied by the size of the z-step in place of the original formula. This allows users to base the analysis only on the volume that has objects in it and is especially useful when the biological sample is not perfectly flat on the microscope slide and does not fill the totality of the ROI in the first and/or last few slices of the z-stack (Figure 4). Users can ignore this option and rely on the “cookie-cutter” ROI-based volume estimation, which is also provided and considers the new ROI shape and the new number of slices (e.g., in the case of a very sparse labeling or if the exact same ROI is being used for all images).\n\nFollowing corrections, new files are saved in the Results folder, containing the mention “Adjusted” in their name: the new ROI if it has been modified, the new visualization images (Composite and MIP) showing the corrected analysis, and the new set of 3D ROIs for co-localizing events that users can later review or use for measurements.\n\nOne advantage of this review step is that while the whole process may take time for large batches of images, users do not have to review all images at once and can use the macro any number of times to review parts of the batch. Because the macro appends, retrieves, and displays the original Results file, users can easily know where they left off the previous time and continue their review work at a later time.\n\n\nUse cases\n\nThere are two ways immunohistochemical analysis can help reveal the presence of an angiogenic phenomenon in situ. The first is by showing changes in the architecture of the capillary network, such as an increase in the number of branches or the length of its segments.21 The second is by detecting endothelial cell proliferation, which is necessary for the creation of new blood vessels. In this example, we used COverlap to identify proliferating endothelial cells in the ACC of rats that performed a memory task versus control animals. The goal of the experiment was to examine the survival kinetic of proliferating endothelial cells at various delays after the encoding of an associative olfactory memory.\n\nIn accordance with the principles of the European community, the experimental protocols were validated by the local ethics committee (CEEA-50, APAFIS n°20108), the animal welfare committee of IMS (Integration from Material to System lab, UMR5218 CNRS/Université de Bordeaux, Talence, France, agreement n°A-33-522-5) and the French Ministry of Research.\n\n48 two-months old male Sprague-Dawley rats (Janvier Labs, Saint Berthevin, France) were attributed an identifying number and acclimated for one week before being randomly allocated to experimental and control groups (controlling that no weight difference existed between groups) and moved from group-housing to single-housing according to protocol recommendations22). Animals were given unrestricted access to water and food pellets (A04, Safe). Animals were handled daily for at least 5 days after the first week of acclimation to minimize experimenter-induced stress. To reduce potential stress and neophobic responses, animals were then habituated to consume powdered chow (A04, Safe) from cups for 3 days before the experiment.22 The general health of animals as well as food and water intake were monitored daily and scored throughout the experiment. The experiment was conducted during the light period (7 a.m to 7 p.m., 100 lux) of the light-dark cycle.\n\nFour groups of rats (3-6 months old), each divided into one experimental and one control group of six animals each, performed the initial phases of the Social Transmission of Food Preference task (as described in Ref. 22) in which rodents learn about the safety of a new food by smelling it on a conspecific’s breath. Group sizes were determined according to the protocol article.22 Rats were intraperitoneally injected three times with the proliferation marker 5-Ethynyl-2’-deoxyuridine (EdU, CAS 61135-33-9, Boc Sciences, 60 mg/mL in saline solution with 9 g/L NaCl; 60 mg/kg of body weight per injection): once immediately after the encoding phase of the memory (morning), once in the evening, and once the following morning (injections were repeated to maximize chances of detecting endothelial proliferation linked to memory encoding). Depending on groups, rats were euthanized 1, 3, 6, or 30 days after the last injection of EdU to assess cell proliferation and survival at various post-encoding delays. The euthanasia protocol consisted of a lethal intraperitoneal injection of sodium pentobarbital (EXAGON®, 200 mg/kg of weight) and lidocaine (LUROCAÏNE®, 20 mg/kg).\n\nRats were perfused intracardiacally at a slow rate (13 mL/min) to preserve the cerebrovascular endothelium, with 300 mL of heparinized saline solution (2.5 mL/L heparin (5000 UI/mL, Choay, Cheplapharm, France), 9 g/L NaCl, in 18 MΩ water), followed by 350 mL of cold fixative solution (40 g/L paraformaldehyde (Merck, 158127) in phosphate buffer (PB, containing 4.8 g/L monosodium phosphate (Merck, S0751) and 22.72 g/L disodium phosphate (Merck, S0876) in 18 MΩ water)). After extraction, the brains were left overnight in the fixative solution at 4°C before being sliced into 50 μm-thick sections with a vibratome. According to local regulations, bodies were placed in leak-proof sealed bags in a dedicated freezer before retrieval by a biological waste disposal company.\n\nFour histology batches were generated, in which the different experimental conditions (post-encoding Delay (1, 3, 6, 30 days) × Group (Experimental, Control)) were evenly represented in each batch. All subsequent steps of the experiment (immunohistochemistry, image acquisition and analysis) were performed blind to the experimental group of animals (Experimental or Control). Eight brain slices per animal, with four spanning the ACC (a brain region involved in associative olfactive memory consolidation) and four spanning the parietal cortex (PC, not involved in this consolidation process) were stained for nuclei (DAPI), blood vessels (Tomato lectin), proliferating nuclei (EdU), and endothelial nuclei (ERG transcription factor). The detailed immunofluorescence protocol is available in the associated Zenodo repository.23\n\nUsing a spinning-disk confocal microscope, we acquired one multichannel z-stack mosaic per slice, covering either the ACC or one side of the PC. Out of the possible 384 (Delay (4) × Group (2) × Animals (6) × Brain region (2) × Brain slices (4)), we acquired a total of 360 images, because some slices were either too damaged or inadequately mounted on the slide. Image acquisition specifications are available in the Zenodo repository23 where we filled Rebecca Senft’s Microscopy Checklist24 and provided a link to FPBase25 to display the spectra viewer for our experiment.\n\nIn the parameters GUI of Macro 1 (Figure 5A), we indicated that our Image folder contained one subfolder per image, in which a file always named “Scan1.nd” was stored with its three corresponding .tif channel images. An example of a resulting MIP with the three chosen LUTs is shown in Figure 5B. Although only the first two channels (ERG and EdU labeling) were used for quantification, we chose to include the third channel with the Lectin staining on MIPs to facilitate the visualization of the vascular network.\n\nWe used Macro 2 to determine the best set of parameters for the segmentation of ERG+ and EdU+ nuclei. Due to slight batch-dependent differences in background fluorescence, we chose different thresholds for a given batch but kept the minimum size, filtering, and background subtraction parameters consistent across batches (Figure 6A). This was made possible by the fact that our experimental conditions were evenly distributed among batches, and we advise against such a choice if it introduces a potential bias in the experimental results. Here, we assume that despite our efforts to perform the staining and imaging protocol in an identical manner for all batches, a number of slight variations may have occurred that could explain this difference, such as the percentage of error during pipetting, temperature variations during heat-induced antibody retrieval, or duration of mounting medium curing (7-10 days before the first day of imaging for one batch).\n\nWe performed multiple rounds of testing on multiple images. For each image, various small representative ROIs were selected to test the segmentation parameters. The output of such a test is presented in Figure 6B: toggling the outline on and off and examining the filtered image output helped us determine the optimal parameters for the segmentation of our targets. When we found the best compromise for the majority of images in a given batch, we ticked the “Save parameters” box before starting the last test. The parameters selected for each batch are listed in Table 1.\n\nWe launched Macro 3 separately for each batch with their set of segmentation parameters determined with Macro 2 (Table 1) and with an overlap threshold set at 30%, chosen to reliably exclude false positives while still accounting for size and shape differences between EdU and ERG labeling.\n\nWe drew an ROI for only 359 of the 360 images because the MIP inspection revealed a problem with the tile-stitching of one image in Batch 3. The processing time, number of images, and data size for each batch are listed in Table 2. One GB of images required a mean 3:35 minutes of processing time, which corresponded to a mean of 11:19 min per image.\n\nAll 359 verification images were inspected using the Macro 4. We filled the corrections GUI (Figure 7A) for each image requiring adjustments and chose to perform volume estimate correction (Figure 4) for all images regardless. Example of adjusted verification images (.jpg MIP and .tif composite files) produced by this correction step are shown in Figure 7B.\n\nThe “Comment” section was particularly useful to report problems with images. We also systematically used it to describe the reason for a ROI modification. We tried to be consistent in our qualification of identical issues or justifications across images in order to classify them after the batch was fully reviewed (e.g. using “Sparse” to describe sparsely labeled ERG or “Removed corpus callosum” for a ROI modification).\n\nDISCARDED IMAGES\n\nThe review revealed that two animals presented a complete absence of EdU labeling, indicative of injection issues since other animals in the same histology batch were normally labeled; all acquired images for these animals (four of the ACC and two of the PC each) were excluded from further analysis.\n\nOf the 347 remaining images, 15, all from the PC region, were also discarded upon first inspection: one because of an error in which the same slice had been acquired twice, and the others because the tissue was too damaged and/or improperly mounted to produce accurate segmentation. In general, tissue from the PC was more damaged than that from the ACC.\n\nInspection of the appended results file revealed that due to the rather weak labeling of ERG, some of the remaining 332 images were annotated as “Sparsely labeled” in the optional comments section. We chose to set a density of object/mm3 threshold to exclude sparsely labeled images in a reproducible way and excluded 31 (23 CP, 9 ACC) images for which the density of labeled ERG cells was less than 3500 ERG objects per mm3.\n\nCORRECTIONS PERFORMED\n\nOf the 301 z-stacks left, 292 (97%) were resliced to exclude out-of-focus optical slices, indicating that the range of the z-stack acquisition was consistently too generous. This type of information is crucial for planning future experiments, in which care will be taken to acquire a shorter range in z.\n\nEighteen (≈6%) ROIs were adjusted to exclude air bubbles in the mounting medium (6), damaged or torn tissue (5, as illustrated in Figure 7B), or part of the corpus callosum that was unduly encompassed in the initial ROI drawing (7).\n\nThe co-localization overlap threshold was deemed satisfactory and maintained at 30% for all images.\n\nEXPERIMENTAL RESULTS\n\nFor the two targets (number of ERG+ and number of EdU+ objects) and for the two possible types of co-localization events (number of ERG+ objects in EdU+ objects and number of EdU+ objects in ERG+ objects), we calculated the density of objects per mm3 of analyzed tissue (using the corrected volume estimate) for all valid slices, and averaged them to obtain a mean density per region for each animal. The results are shown in Figure 8.\n\nIndividual data points correspond to mean of slices per animal.\n\nWe performed Šídák’s multiple comparison test using GraphPad Prism for each brain region to determine whether, for each post-encoding delay, the experimental and control groups had significantly different object densities. None of the comparisons revealed significant differences between the groups (Table 3).\n\n\nDiscussion\n\nWhile every component of a bioimage analysis workflow is crucial, every choice made to select one option over another contributes to making the analysis overly tailored to the specific problem that it attempts to solve. For both segmentation and co-localization analysis, we briefly discuss such choices as well as some possible alternatives. We then suggest that the code can also be used as a template or source of inspiration, and the inadequate parts adjusted to suit the different requirements of other datasets.\n\nNormalization is a critical choice and may not be appropriate for all types of analysis. First, care must be taken that the relative intensity distribution is nearly identical for all images in the experiment. Second, it should be noted that while normalization may be convenient for visualization and segmentation purposes, it represents a loss of information (in our case, 0.35% of pixels are allowed to become saturated) and may alter results if further processing steps are based on absolute gray values.26 Here, normalization facilitates nuclei segmentation despite varying illumination along the depth of the samples.26 Likewise, users may not want to downscale images acquired with a higher bit-depth to 8-bit, as this also results in a loss of information. In our case, however, it allows us to work with lighter images, which speeds up processing without compromising segmentation quality. Additionally, the narrower range of gray values simplifies the testing and selection of a suitable intensity threshold.\n\nWe have included three steps in the workflow that are classically used to enhance images for the purpose of segmentation (see Chapter 3 in Ref. 20): two spatial nonlinear (median) and linear (Gaussian) filters to denoise images and smooth out irrelevant details, and Fiji’s rolling ball algorithm (based on Ref. 27) to eliminate background fluorescence. Taking advantage of the parameter GUI, a step can be omitted by setting its parameter to zero, making it possible to apply each step alone or in combination with one or two other steps. Although users can choose the parameters, the order in which the steps are performed cannot be modified without modifying the code. If this workflow proves ineffective in enhancing more complex images, users may want to consider alternative denoising techniques (reviewed in Refs. 28, 29) and illumination correction methods.30–32\n\nNucleus segmentation in 3D presents a much greater challenge than in 2D33 but provides several advantages. In contrast to segmenting the MIP of the stack, it prevents false positives that can occur in the co-localization analysis when nuclei are located atop one another in z. Compared to limiting the analysis to a single z-plane, it maximizes the quantity of information analyzed by allowing the segmentation of at least two layers of nuclei along the z-axis (Figure 9). This has the added benefit of preserving the three-dimensional geometry of the nuclei and better describing their spatial relationship in situ.\n\nWe implemented the 3D Simple Segmentation of the 3D Suite,18 which consists of thresholding pre-processed images, performing connected component analysis, and filtering out objects by size. When necessary, the 3D watershed algorithm of the 3D Suite was applied to separate the touching objects. To avoid excluding touching nuclei that the watershed algorithm might not have separated, we solely implemented the minimum size and excluded the maximum-size filter. We employed a numerical threshold, as suggested by the plugin’s interface, which we empirically found performed satisfactorily on our preprocessed images. Nevertheless, if an automatic threshold is preferred, minor modifications to the code would permit it, because the plugin can operate on a previously obtained binary mask by setting the threshold at 1. If both numerical and automatic thresholds fail to consistently extract objects, users can attempt to implement the iterative thresholding algorithm of the 3D Suite.18\n\nOur segmentation method would certainly exhibit limitations for densely packed or overlapping nuclei that represent a difficult segmentation case, even for more advanced tools.33 In our experiment, EdU+ nuclei were sparsely distributed and often appeared in doublets which the watershed algorithm was able to properly split when they were touching. In addition, the endothelial nuclei were sufficiently spaced to be segmented satisfactorily. However, owing to the elongated shape of ERG+ objects, we abstained from applying the watershed algorithm to prevent their over-segmentation. We recognize that our result for the density of ERG+ objects might be slightly underestimated because some touching objects were counted as a single entity. While this does not hinder the co-localization analysis, it makes the density of EdU+ in ERG+ objects a more dependable indicator than the density of ERG+ in EdU+, because co-localizing EdU+ objects are still expected to exceed the overlap threshold, while touching ERG+ objects counted as a single object may not.\n\nDeep learning (DL) methods have revolutionized the field of bioimage analysis and are quickly becoming the gold standard for classification, denoising or segmentation.34 For the latter, some DL solutions are now accessible to biologists with limited computational skills (listed in recent reviews33,35,36), but most are difficult to set up and use, especially for 3D segmentation.33 Moreover, user-friendly platforms such as deepImageJ37 rely on pretrained models, which are currently not widely available in 3D. Training new models from scratch requires extensive computing power in the case of 3D data as well as large annotated datasets that are time-consuming and difficult to produce.38 While we wager that these challenges will soon be overcome given the rapid expansion of the field, we chose to use a classical method that does not have such heavy hardware or annotation requirements.\n\nTwo types of strategies are used to assess co-localization. Pixel-based approaches consider the image as a whole and evaluate the correlation between the signal intensities of two channels. Their main drawback is that they are not informative about the location of co-localization events. Conversely, object-based approaches rely on segmentation and allow quantification of the degree of co-localization between objects. Several reviews39–41 can inform users on the various metrics and tools associated with different types of co-localization analysis, and Cordelières and Zhang13 offer a guideline decision tree to help determine which type is most suited to a particular experiment.\n\nIn object-based methods, segmented objects can be described by two types of centers: the centroid or geometrical center, which relates to the shape of the object, and the intensity center or center of mass, which considers the distribution of fluorescence intensities within the object. When objects have sizes close to the optical resolution, their centers are commonly used to assess co-localization, such as is possible with the popular Fiji plugin JACoP.42 For example, two objects can be considered co-localized if the distance between their centers is smaller than the optical resolution (distance between centers approach).40 Another approach makes it possible to deal with size heterogeneity when resolution-limited objects in channel A co-localize with larger objects in channel B: in this case, one can quantify the number of centers from A that fall inside the volume of objects in B (centers-particles coincidence approach).43\n\nReducing objects larger than the optical resolution to the coordinates of their centers may lead to underestimation of the co-localization events and does not preserve information about the geometry or intensity of objects or the extent of co-localization. A more straightforward approach in this case is to compute the overlap (physical or intensity-based) between the objects. DiAna,44 another comprehensive Fiji plugin, uses physical overlap to assess co-localization and offers several segmentation algorithms as well as various measurements of the properties of objects (such as volume or mean intensity) and distances between them. Despite its extensive functionalities, this plugin is not fully macro recordable in Fiji, making it suboptimal for automating our batch analysis and the creation of verification images.\n\nTherefore, we used the MultiColoc plugin of the 3D Suite18 in our workflow. A notable advantage of this plugin is that it allows multiple co-localizations to be preserved for a single object (e.g., several subcellular components per cell). Similar to Zhang and Cordelières,12 who used the volume overlap method in their demonstration, we implemented an overlap threshold. Owing to the filtering and segmentation process, the labels can be slightly dilated compared with real objects. With an appropriately set overlap threshold, false positives for objects that are in close proximity but that slightly overlap owing to label expansion can be excluded. Contrary to Zhang and Corderlières’s workflow, ours does not assume that objects in one channel are consistently smaller than those in the other, and all pairs of objects where at least one meets the volume overlap criteria are counted as co-localized.\n\nThe co-localization metric extracted by our workflow is the number of co-localizing objects (for A in B and B in A). We used it to compute densities of co-localizing objects per volume of tissue analyzed, but users can also take advantage of the object quantification for each channel to compare the ratio of co-localizing objects over the total number of objects instead. Overall, we designed our workflow to be as conservative as possible to suit various measurement requirements without having to perform the entire analysis again. 3D ROIs for co-localizing objects are saved for users to perform measurements as needed, using the 3D Manager and the original image. In addition, while the composite image is primarily a visualization tool, it is also two clicks (or lines of code) away from being split into binary masks and turned again into label images by the 3D Manager, for each channel and the co-localized and discarded overlapping objects. Thus, the possibility of performing any kind of supplementary measurement on the properties of objects or their relationships is preserved.\n\nWith COverlap, we have focused our efforts on several points that contribute to creating a reproducible bioimage analysis workflow.\n\nFirst, we strived to make our workflow user-friendly. We kept it contained in a single software (or “collection”45) to simplify its use and enhance its accessibility,2 used GUIs whenever possible to collect user input, and wrote detailed documentation to support its implementation. We also provided the code itself, which we organized and commented to improve its readability.\n\nSecond, we attempted to make the organization of the workflow time efficient. We attempted to divide it into its interactive and automated steps by isolating the parameter testing and reviewing phases from the batch analysis. This ensures that no manual input alters the reproducibility of the main analysis and allows users to perform other tasks while it runs. It also gives users the freedom to organize the time they allocate to the testing and reviewing steps as they need.\n\nThird, we aimed to achieve traceability and transparency. We attempted to produce reproducible results by automatically recording all parameters used for a given analysis. We also implemented a method for users to review the analysis and perform corrections in an automatically documented (and optionally user-commented) fashion. The conservative manner of recording results, ROIs, and visualization images also provides a measure of scalability to the toolset: not only can users verify results again at any time after they have been obtained, but they can also reuse the produced files to perform new measurements (such as measuring intensities on the original image, or performing spatial statistics on the segmented objects) without having to perform the whole analysis again.\n\nFinally, we sought to impart flexibility to this toolset. At a lower level, by making it fairly parameterizable for absolute non-coders who would want to try it in a compatible experiment. For example, the toolset may be used to assess the proliferation of other cell types with nuclear markers, such as Olig2 for oligodendrocytes and their precursors,46 or to investigate neuronal activation with markers for NeuN (RBFOX3) and the transcription factor c-Fos. At a higher level, by offering the code as a modifiable template or even as a skeleton, where one (and especially scripting beginners) can reuse the general organization of the code or alter specific functions to suit their needs, such as implementing a different segmentation style or type of co-localization analysis.\n\n\nSoftware availability\n\nSource code is available from: https://github.com/mambroset/COverlap-a-Fiji-co-localization-toolset\n\nArchived source code available from: https://zenodo.org/doi/10.5281/zenodo.1016114119\n\nLicense: GPL 3.0\n\nFiji (RRID:SCR_002285)16 and the MorphoLibJ17 and 3D ImageJ Suite (RRID:SCR_024534)18 plugins necessary to run the toolset are freely available through the provided links. To install these plugins, users must enable the following update sites in Fiji: IJPB-plugins, 3D ImageJ Suite, Java8 and ImageScience.\n\nAny question that holds a potential interest for other users can be posted on the image.sc forum and linked to the username of the author @Melow.\n\nFigures were made with Adobe Illustrator (RRID:SCR_010279), and Draw.io (RRID:SCR_022939) for the diagrams in Figure 1, Figure 2, and Figure 3. Data were formatted with Microsoft Excel 2019 (RRID:SCR_016137) and statistical analysis was performed using GraphPad Prism 9 (RRID:SCR_002798).", "appendix": "Data availability\n\nBecause of the very large size of our dataset, we provided only a sample of it with one image per brain region (ACC and PC) on Zenodo 23 for testing and demonstration purposes, along with the full immunohistochemistry protocol and the image acquisition specifications file. The full dataset is available upon request to the authors.\n\nZenodo: COverlap: a Fiji co-localization toolset (Supplementary material)\n\nhttps://doi.org/10.5281/zenodo.10205178 23\n\nThis project contains the following underlying data:\n\n- Testing Files.zip (a sample dataset that allows testing of the toolset)\n\n- protocol-IHC_DAPI405_Lectin488_EdU555_ERG633.xlsx (the detailed immunohistochemistry protocol to stain ERG, EdU and Lectin on rat brain slices)\n\n- ImageAcquisition_Specs.docx (Microscopy Checklist 24 detailing all image acquisition settings and link to the experiment’s associated spectra viewer 25 )\n\n- ARRIVE_Checklist.pdf (the ARRIVE guidelines 2.0 author checklist)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nMicroscopy was performed at the Bordeaux Imaging Center, a service unit of the CNRS-INSERM and Bordeaux University, member of the national infrastructure France BioImaging supported by the French National Research Agency (ANR-10-INBS-04). The help of Dr. Magali Mondin and Dr. Fabrice Cordelières as well as the technical support of Dr. Anne Hambucken are acknowledged.\n\n\nReferences\n\nLevet F, Uhlmann V, Jug F: Editorial: Methods and Tools for Bioimage Analysis. Front. Comp. Sci. 2022 May 30; 4: 931939. Publisher Full Text\n\nHaase R, Fazeli E, Legland D, et al.: A Hitchhiker’s guide through the bio-image analysis software universe. FEBS Lett. 2022; 596(19): 2472–2485. PubMed Abstract \| Publisher Full Text\n\nMeijering E, Carpenter AE, Peng H, et al.: Imagining the future of bioimage analysis. Nat. Biotechnol. 2016 Dec; 34(12): 1250–1255. PubMed Abstract \| Publisher Full Text\n\nSladoje N, Miura K: Introduction.Miura K, Sladoje N, editors. Bioimage Data Analysis Workflows – Advanced Components and Methods. Cham: Springer International Publishing; 2022 [cited 2023 Aug 24]; pp. 1–5. (Learning Materials in Biosciences). Publisher Full Text\n\nDanuser G: Computer Vision in Cell Biology. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLucas AM, Ryder PV, Li B, et al.: Open-source deep-learning software for bioimage segmentation. Mol. Biol. Cell. 2021 Apr 19; 32(9): 823–829. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGómez-de-Mariscal E, García-López-de-Haro C, Ouyang W, et al.: DeepImageJ: A user-friendly environment to run deep learning models in ImageJ. Nat. Methods. 2021 Oct; 18(10): 1192–1195. PubMed Abstract \| Publisher Full Text\n\nLaine RF, Arganda-Carreras I, Henriques R, et al.: Avoiding a replication crisis in deep-learning-based bioimage analysis. Nat. Methods. 2021 Oct; 18(10): 1136–1144. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCordelières FP, Bolte S: Chapter 21 - Experimenters’ guide to colocalization studies: Finding a way through indicators and quantifiers, in practice.Waters JC, Wittman T, editors. Methods in Cell Biology. Academic Press; 2014; pp. 395–408. Reference Source\n\nBolte S, Cordelières FP: A guided tour into subcellular colocalization analysis in light microscopy. J. Microsc. 2006 Dec; 224(3): 213–232. PubMed Abstract \| Publisher Full Text\n\nMascalchi P, Cordelières FP: Which Elements to Build Co-localization Workflows? From Metrology to Analysis.Rebollo E, Bosch M, editors. Computer Optimized Microscopy. New York, NY: Springer New York; 2019 [cited 2023 Feb 14]; pp. 177–213. (Methods in Molecular Biology; vol. 2040). Publisher Full Text\n\nCordelièresa FP, Bolte S: JACoP v2.0: improving the user experience with co-localization studies. ImageJ User Dev. Conf. Novemb. 2009. 2006; 224(3): 213–232.\n\nLachmanovich E, Shvartsman DE, Malka Y, et al.: Co-localization analysis of complex formation among membrane proteins by computerized fluorescence microscopy: application to immunofluorescence co-patching studies. J. Microsc. 2003 Nov; 212(Pt 2): 122–131. PubMed Abstract \| Publisher Full Text\n\nGilles JF, Dos Santos M, Boudier T, et al.: DiAna, an ImageJ tool for object-based 3D co-localization and distance analysis. Methods. 2017; 115: 55–64. PubMed Abstract \| Publisher Full Text\n\nMiura K, Paul-Gilloteaux P, Tosi S, et al.: Workflows and Components of Bioimage Analysis.Miura K, Sladoje N, editors. Bioimage Data Analysis Workflows. Cham: Springer International Publishing; 2020 [cited 2023 Sep 12]; pp. 1–7. (Learning Materials in Biosciences). Publisher Full Text\n\nSteadman PE, Xia F, Ahmed M, et al.: Disruption of Oligodendrogenesis Impairs Memory Consolidation in Adult Mice. Neuron. 2020 Jan; 105(1): 150–164.e6. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "253715", "date": "02 Apr 2024", "name": "Thomas Boudier", "expertise": [ "Reviewer Expertise Image processing", "Image analysis" ], "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 is well written and easy to follow. The methods and procedures are well detailed, maybe too detailed. The solution proposed clearly is of interest for biologists interested in co-localization analysis of nuclear structures.\nHowever, the solution is presented as generic but no results are presented to prove the genericity of the procedure. The segmentation part is extremely image and problem dependent and, as stated in the discussion, may not be applicable to other problems. It is also not very clear how are handled multiple channels co-localization, the original images can have more than two channels but only two are analysed for co-localisation ?\nI then suggest the authors to redefine their article as a applied co-localisation and segmentation solution for neurobiology studies, involving large images, sparse nuclei and limited number of markers. They should present their problem first, review available solutions (only presented in discussion) and why they are not fully adapted to their problems.\nComments :\nThe abstract is a bit long, the description of the 4 macros can be omitted there. The requirements for folder names is a bit unclear, an example could be given. The naming of the Rois is also not very clear. Minimal systems requirements should not be the system used by the authors, change the section name or provide a proper minimal system requirement. Figure 2 can be split in two parts (macros 1,2,3 then 4). The conversion to 8-bits should not, as admitted by authors, be put as a common rule and should be used exceptionally. The \"remove touch edges\" section can be shortened. Table 3 could be removed. Figure 9 can be improved.\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? Partly", "responses": [] }, { "id": "265543", "date": "14 May 2024", "name": "Jean-Karim Heriche", "expertise": [ "Reviewer Expertise image and data analysis" ], "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 set of tools aimed at the detection of colocalization of two nuclear markers in fluorescence confocal microscopy images. The colocalization detection workflow is implemented as macros for the Fiji platform and usage is illustrated on the quantification of proliferating endothelial cells in rat brain slices through the detection of colocalization of a nuclear marker of endothelial cells and a nuclear marker of cell proliferation.\nThe paper is well-written and easy to follow and the procedures described with enough details to make it possible for readers to replicate the approach. Running the macros is also relatively easy as each step provides instructions to guide the user. There is however room for improvement:\nWhile the described tools can be useful, the approach is image- and problem-specific and these limitations should be made clearer from the beginning. For example I was unable to read tif images using the one subfolder per image mode where each channel is in a separate file (similar to the example data without the nd file), is this not supported? Related to this, as co-localization analysis isn’t new and there are other ImageJ/Fiji plugins for the task, it would be of interest to know what motivated the development of another plugin and where possible have some performance comparison. The user experience could be improved:\n\n- There is no indication of progress during long tasks. Some sort of progress indicator would be useful.\n\n- What input should be populated by default should be carefully reviewed. Could they be interfering with the loading of new data? Also, I believe one should always want to save parameters as it’s easy to overlook the checkbox and have to go back. An option to save and reload previous settings would also be useful (including ROI selection).\n\n- While the guidance is useful for beginners, once one knows how to use the tools, the “Action Required” windows get in the way. Some settings to disable them would be good.\n\n- While a GUI platform is useful for visual exploration of the effect of parameter choices, it’s not particularly well suited to scale up to batch analyses. In particular, the manual selection of ROIs for all images would be tedious for large batches. For smaller images, the default could be to select the whole image. Data availability on request is not acceptable. Image data must be made available for example using a public repository, ideally one that also collects a minimum of metadata such as the BioImage Archive [Ref-1] which would make the data more findable independently 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? 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": "265535", "date": "16 May 2024", "name": "Bijie Bai", "expertise": [ "Reviewer Expertise Biomedical imaging and deep learning" ], "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 presents COverlap, a Fiji toolset designed for automated 3D segmentation and co-localization of fluorescent nuclear markers in confocal microscopy images. The presented plugin comprises four macros, streamlining the process of visualization, parameter testing, image segmentation, and statistical analysis. The paper includes detailed instructions of the toolbox, open-sourced code, as well as analysis using real experimental data for demonstration. Overall, this is a solid and well-documented work, which will be particular helpful in bioimage analysis for those who are beginners in programming. The emergence of tools like these is encouraging and vital for the advancement of biological research. I recommend the acceptance of this paper, provided the following comments are addressed:\n- Despite the paper itself is self-contained, comparison with other existing works especially those similar and already implemented as Fiji plug-ins (e.g., Stauffer W, et. al.,2018 (Ref 1)) would help readers and users to better understand the contributions and advantages of this work. - While the toolset has shown robust performance with the dataset used in this study, its performance and adaptability to other types of datasets or different staining and imaging techniques were not extensively tested. Further testing or discussion on its performance across various application scenarios should be added, such as confocal microscopes from different manufacturers, other cell and tissue types, and other staining methods or biomarkers. - It would also be beneficial to discuss or test the generalizability of the toolset to non-confocal microscopic imaging techniques such as STED, FLIM, and Light-sheet microscopes. Additionally, how would the toolset support the case where there is only one single along z-axis, like those obtained from a wide-field fluorescence microscope? - An in-depth discussion on the major design considerations of the toolset would be enlightening. For example, why the number of image channels are limited to 2 to 4? Why are certain types of filtering selected? Despite efforts to support beginners, the complexity of the tasks automated by the toolset may still pose a challenge to biologists. To reduce the learning curve, it would be beneficial for the authors to provide default settings or recommended configurations tailored to representative application cases. This approach would help users more effectively harness the toolset and achieve reliable results without extensive adjustments of the many tuning knobs available. - Considering the processing demands of large datasets, would author add parallel feature and/or GPU support for future versions? What are the advantages of the presented toolset compared to many emerging AI-based segmentation and analysis tools?\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": [] } ]	1	https://f1000research.com/articles/13-14
https://f1000research.com/articles/13-13/v1	03 Jan 24	{ "type": "Case Report", "title": "Case Report: The importance of initial assessment in acute pulmonary embolism", "authors": [ "Meity Ardiana", "Dwi Fachrul Octafian Hidayat", "Louisa Fadjri Kusuma Wardhani", "Putu Dwipa Krisna Devi", "Badai Bhatara Tiksnadi", "Dwi Fachrul Octafian Hidayat", "Louisa Fadjri Kusuma Wardhani", "Putu Dwipa Krisna Devi", "Badai Bhatara Tiksnadi" ], "abstract": "Background: Pulmonary embolism (PE) remains the third most frequent cardiovascular disease worldwide and is associated with high mortality rates. We presented a case of PE with a history of tibial surgery and showed the role of Computed Tomography Pulmonary Angiography (CTPA) in early diagnosis and management of PE. Case presentation: A 23-year-old man was referred to our hospital with sudden dyspnea followed by sharp chest pain, haemoptysis, pre-syncope, diaphoresis, and weaknesses. He had a history of tibial surgery and immobilization one month before admission. His vital sign was unstable, with blood pressure of 110/60 mmHg (supported by Norepinefrin 0.5 mcg/kg/minutes), heart rate of 120 beats/minute, respiratory rate of 24 times/minute, and oxygen saturation of 99% (oxygen mask 6 lpm). An electrocardiogram showed sinus tachycardia with McGinn-White sign. A chest X-ray showed Palla sign. An echocardiogram showed reduced right ventricular systolic function with McConneal sign. CTPA was performed due to the moderate-high risk PE with the presence of hyperattenuating and partial filling defect. Streptokinase was then administered, followed by adequate anticoagulation using rivaroxaban for three months. The clinical and CTPA evaluation showed a good result. Conclusions: Initial assessment using PE’s scoring system will help clinicians determine the needs of CTPA. CTPA has a sensitivity of 53-100% and a specificity of 83-100% for the diagnosis of PE. This makes CTPA mandatory in high-risk PE, thus speeding up the initial treatment, which correlates with clinical outcomes.", "keywords": [ "Pulmonary embolism", "PE", "high-risk pulmonary embolism", "VTE", "Case Report" ], "content": "Background\n\nPulmonary Embolism (PE), as a part of Venous Thromboembolism (VTE), remains the third most frequent cardiovascular disease worldwide.1 An annual incidence rate for PE ranges from 39-115 per 100,000 populations. The incidence rate per year is 1.5 per 1000 persons.2,3 PE is associated with more than 370,000 deaths in European countries, in which 34% died suddenly or within a few hours of the acute events.3 PE commonly occurs as a fatal event with or without hemodynamic instability in the acute cardiac unit. The mortality rate of PE is around 50-58% in hemodynamic instability patients and 8-15% in hemodynamics stable patients.2 As it is a life-threatening condition, rapid and specific diagnostic tools are needed.1–3\n\nComputed Tomography Pulmonary Angiography (CTPA) has been proposed as a standard imaging modality to diagnose PE. CTPA has the advantages of availability, excellent accuracy, strong validation in prospective management outcomes, low rates of inconclusive results, short acquisition time, and allowing more comprehensive assessment of the clot burden in Pulmonary Arteries (PAs). These make CTPA the suitable diagnostic tool in the Acute Cardiac Care Setting.2,3 We presented a case of pulmonary embolism with a history of tibial surgery and showed the role of CTPA in early diagnosis and management of pulmonary embolism.\n\n\nCase presentation\n\nA 23-year-old Javanese man, working as a content editor, was referred to our emergency room (ER) with a suspected pulmonary embolism. His chief complaint was sudden shortness of breath one hour before hospital admission. The symptoms were accompanied by sharp chest pain in the lower right posterior area and blood coughing. He also had a history of pre-syncope, diaphoresis, and weaknesses for the past week. The medical history revealed right tibial surgery with plate implantation one-month prior to his admission. He injured himself during mountain climbing and suffered an open tibial fracture. He had been taking full bed rest ever since. Based on the clinical feature, we used PE’s risk assessment to better diagnose the involvement of PE. The Geneva score of 9 and Wells’ score of 7 showed a moderate-high risk for PE (Tables 1 and 2). Thus CTPA was planned.\n\nDVT, Deep Vein Thrombosis; PE, Pulmonary Embolism.\n\nDVT, Deep Vein Thrombosis; PE, Pulmonary Embolism.\n\nUpon admission in the referrer hospital, his vital signs showed blood pressure 80/60 mmHg, heart rate 140 beats/minute, respiration rate 28 times/minute, and oxygen saturation of 90% (free air). He was alert but seemed weak and cyanotic. Adequate oxygenation support, fluid administration, and inotropes were administered to stabilize him before referred to our hospital. It took 12 hours from first medical contact until he came to our hospital.\n\nThe vital sign in our hospital showed unstable hemodynamics supported by Norepinefrin 0.5 mcg/kg/minutes with a blood pressure of 110/60 mmHg, heart rate 120 beats/minute, respiratory rate 24 times/minute, and oxygen saturation of 99% (oxygen mask 6 lpm). Physical examination showed loud P2, tachycardia, and cold-wet perfusion.\n\nThe electrocardiogram revealed sinus tachycardia with normal frontal and horizontal axis, S waves in the lead I, deep Q waves in lead III, and T inversion in the lead III (McGinn-White sign), as shown in Figure 1(A).\n\nWe performed laboratory examination, which resulted in increased D-dimer (20.770 ng/mL) with both troponin (50 ng/mL) and creatinine serum (1.0 mg/dL) within normal limit. The chest X-ray (CXR) examination showed enlarged right descending pulmonary artery (Palla sign), as shown in Figure 1(B).\n\nEchocardiography examination at the previous hospital revealed decreased Right Ventricular (RV) function with preserved left ventricular function (Figure 2A). There was an akinetic segment at the basal–mid-right ventricle, whereas other segments were normokinetic (McConnel Sign), as shown in Video 1 and Figure 2B. Upon arrival at our ER, a CT Angiography examination was performed. It showed an hyperattenuating and partial filling defect, which supported a typical pulmonary embolism finding (Figure 3; Video 2).\n\nRV, Right Ventricle; RA, Right Atrium; LV, Left Ventricle; LA, Left Atrium.\n\nBased on CTPA findings, supported by clinical and other examinations, Pulmonary Embolism was assessed with Pulmonary Embolism Severity Index (PESI) Score of 83 points (Class II, low risk 1.7-3.5% 30-days mortality rate) (Table 3). He then received thrombolytic therapy with intravenous streptokinase 250,000 IU loading dose for 30 minutes, followed by streptokinase 100,000 IU for 24 hours. Afterwards, the patient was given anticoagulation with rivaroxaban 15 mg twice a day for 21 days and other supportive therapy. His symptoms were improved with reduction of chest pain and shortness of breath after 14 days admission. Follow-up therapy was given at discharge with rivaroxaban 15 mg once a day for three months.\n\nBP, Blood Pressure.\n\nThe patient was monitored in the outpatient clinic. The patient had no complaints with normal physical examination results. After three months of anticoagulation treatment, CTPA was evaluated to assess the treatment efficacy. No residual pulmonary embolism or infarction was found (Video 3).\n\n\nDiscussion\n\nPulmonary embolism is associated with a high mortality rate in the acute phase. Most patients die within the first few hours of the events, so early diagnosis helps provide better outcomes.3 However, clinical features and baseline findings often cannot unequivocally rule out PE, whereas follow-up examination (CTPA) is not cost-effective. This causes a follow-up examination to be carried out only in intermediate-high risk PE.2,3\n\nPE is suspected in patients with shortness of breath, sharp chest pain, pre-syncope or syncope, and haemoptysis. Syncope may occur as a feature of hemodynamic instability and RV dysfunction. Assessment of risk factors such as history of injury and surgery is also necessary to support the suspicion of PE since orthopaedic procedures have the highest incidence of developing a PE (0,7-30% chance). A tibial fracture is associated as a strong risk factor for PE (OR >10) with an incidence of 0.21%. These are related to positioning during surgery and immobility that contributes to an increase in venous stasis. The Electrocardiogram (ECG) and CXR are often nonspecific, but tachycardia is followed by S1Q3T3 pattern (McGinn-White sign; Prominent S wave in the lead I, Q wave in the lead III, and T inversion in the lead III) is a strong predictor of PE. These patterns appear in 15-25% PE. We found patients with clinical, ECG, and CXR supporting moderate-high risk PE with hemodynamic instability (Wells’ score 7 and Geneva score 9).2–5\n\nMost patients will not survive within the first hours of the event. The consequences of a false-positive or false-negative diagnosis can be rapidly fatal in terms of PE; therefore, a prompt diagnosis leads to a better treatment and outcome.6 The use of scoring systems guides the need for additional modalities. CT examination has good sensitivity and specificity in diagnosing PE. A meta-analysis showed that CTPA has a sensitivity of 53-100% and specificity of 83%-100%.7 Unfortunately, it is often not yet available in some regional hospitals. As in this case, the patient was then referred to our hospital on a supportive clinical basis. However, fast and accurate results through a CTPA examination can help diagnose patients and determine the next management step.\n\nFollowing an acute embolic event, the patient is at risk for fatal circulatory collapse due to right-sided heart failure and subsequent embolism. Assessment of hemodynamics, RV failure, and increased Pulmonary Arteries (PA) pressure as part of acute pulmonary hypertension (PHT) needs to be done carefully. Early recognition of acute right ventricular failure is an important sign that requires immediate treatment. The presence of acute embolic obstruction that significantly affects the pulmonary circulation could increases pulmonary vascular resistance (PVR), resulting in acute PHT. The clinical impact of an embolism depends not only on the size of the embolus but also on its cardiopulmonary status. The RV compensates for the obstruction of RV outflow by increasing RV contraction. This resulted in increased myocardial oxygen demand and decreased RV efficiency. Pericardial constraint and RV dilatation lead to bowing the intraventricular septum into the Left Ventricle (LV), causing a decrease in LV preload. This is the underlying cause of circulatory collapse and cardiogenic shock. Echocardiography is a diagnostic modality that can monitor right ventricular strain or right ventricular failure. Echo provides visualization of RV clots, RV dilatation and hypokinesis, straightening, leftward bowing, paradoxical motion of the interventricular septum, decreased LV volume, tricuspid regurgitation, McConneal, and PA dilatation. The presence of RV hypertrophy (wall thickening > 5-6 mm) helps in differentiating acute, subacute, and chronic massive PE.1,2,6\n\nCTPA is mandatory in cases of high-risk PE. CTPA also has the ability to assess morphological abnormalities that indicate RV failure when it is found1 RV dilatation (RV cavity size is larger than the LV) with or without contrast reflux into the hepatic veins2; pulmonary embolism index more than 60%3; Deviation of the intraventricular septum to the LV. CTPA has a sensitivity of 53-100% and a specificity of 83-100%. Acute PE conditions can be in the form of partial or total obstruction, which causes the appearance of1 widening of the affected arteries due to impaired filling of the arterial lumen by total obstruction2; The picture of a partial filling defect surrounded by contrast material due to a central partial occlusion, among which can be “polo mint sign” (long-axis view) and “railway track” (longitudinal view)3; Peripheral intraluminal filling defect that forms acute angles to the arterial wall due to eccentric partial obstruction.1,2,6\n\nThe echocardiogram findings of McConneal signs and decreased RV systolic function showed right heart failure. The CTPA findings of hyperattenuating and partial filling defect, as shown in Figure 3, supported the involvement of PE as a cause of hemodynamic instability in this patient. Pulmonary embolism blocks pulmonary blood flow, resulting in right heart failure. Acute right heart failure due to lack of systemic output is the leading cause of death in high-risk PE. Initial therapy for pulmonary embolism focuses on restoring circulation through the pulmonary vessels and subsequently preventing the pulmonary embolism recurrence. Experimental studies indicate that aggressive volume expansion is not beneficial and worsens right ventricular function because of mechanical overstretch or reflex mechanisms that decrease contractility. However, light fluid administration (500 ml) can increase the cardiac index in PE patients, lower cardiac index, and normal blood pressure.3,8\n\nThrombolytic therapy in acute PE aims to restore pulmonary perfusion more rapidly to reduce pulmonary arterial pressure and resistance, resulting in improved right ventricular function. The administration of fibrinolytic shows good outcome if performed within onset of 6-14 hours. As the patient came with hemodynamic instability, we administered streptokinase 250,000 IU intravenous loading dose within 2 hours, followed by 100,000 IU intravenously for 24 hours. Approximately >90% of patients respond to thrombolytics within 36 hours. Maximum profit will appear within 48 hours.3\n\nIn patients with acute PE, anticoagulation is recommended to prevent death and symptom recurrence. The duration of anticoagulation is at least three months. The anticoagulation options lie between parenteral and oral therapies. Newer oral anticoagulants (NOACs) such as dabigatran, edoxaban, rivaroxaban, or apixaban could be an alternative therapy. The use of NOACs is non-inferior and safer than vitamin K-antagonists. Rivaroxaban can be started 1-2 days after administration of UFH, LMWH, or fondaparinux. Rivaroxaban is given 15 mg twice daily for three weeks, then 20 mg once for the following months.3,9\n\n\nConclusions\n\nThe patient presented with moderate-high risk PE and was supported by clinical, ECG, Chest X-Ray, and echocardiography suggestive of PE. The use of PE’s risk assessment will help determine the needs of CTPA. CTPA has the advantages of availability, excellent accuracy, strong validation in prospective management outcomes, low rates of inconclusive results, short acquisition time, and allowing more comprehensive assessment of the clot burden in PAs. These make CTPA the suitable diagnostic tool in the Acute Cardiac Care Setting. Utilization of CTPA for the immediate diagnosis of pulmonary embolism patients helps determine the patient management accurately. Adequate therapy can reduce the risk of mortality and morbidity from pulmonary embolism.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nConsent\n\nWritten informed consent for publication of their clinical details and clinical images and videos was obtained from the patient.\n\n\nWidgets\n\n1 video file.\n\nhttps://doi.org/10.6084/m9.figshare.20341371.v1.10\n\n1 video file.\n\nhttps://doi.org/10.6084/m9.figshare.20342835.v1.11\n\n1 video file.\n\nhttps://doi.org/10.6084/m9.figshare.20342874.v1.12", "appendix": "References\n\nWittram C, Maher MM, Yoo AJ, et al.: CT angiography of pulmonary embolism: Diagnostic criteria and causes of misdiagnosis. Radiographics. 2004; 24(5): 1219–1238. PubMed Abstract \| Publisher Full Text\n\nGhaye B, Ghuysen A, Bruyere P-J, et al.: Can CTT PPullmonary Angiography Allow Assessment of Severity and Prognosis in Patients Presenting with Pulmonary Embolism? What the Radiologist Needs to Know. Radiographics. 2006; 26: 23–39. PubMed Abstract \| Publisher Full Text\n\nKonstantinides SV, Meyer G, Bueno H, et al.: 2019 ESC Guidelines for the diagnosis and management of acute pulmonary embolism developed in collaboration with the European respiratory society (ERS). Eur. Heart J. 2019; 00: 1–61.\n\nClemente V: A case of pulmonary embolism after abdominal surgery. Ital. J. Emerg. Med. 2017: 1–4.\n\nKim HJ, Walcott-Sapp S, Leggett K, et al.: Detection of pulmonary embolism in the postoperative orthopedic patient using spiral CT scans. HSS J. 2010; 6(1): 95–98. PubMed Abstract \| Publisher Full Text\n\nWittram C, Kalra MK, Maher MM, et al.: Acute and chronic pulmonary emboli: Angiography-CT correlation. Am. J. Roentgenol. 2006; 186: S421–S429. Publisher Full Text\n\nRathbun S, Raskob G, Whitsett T: Sensitivity and specificity of helical computed tomography in the diagnosis of pulmonary embolism: a systematic review. Ann. Intern. Med. 2000; 132: 227–232. PubMed Abstract \| Publisher Full Text\n\nSociety TRC: Pulmonary embolism, part I: Epidemiology, risk factors and risk stratification, pathophysiology, pulmonary embolism.2013; 18: 129–138.\n\nSakuragi T, Sakao Y, Furukawa K, et al.: Successful management of acute pulmonary embolism after surgery for lung cancer. Eur. J. Cardiothorac. Surg. 2003; 24(4): 580–587. PubMed Abstract \| Publisher Full Text\n\nArdiana M, Hidayat DFO, Wardhani LFK, et al.: Video 1. An echocardiogram showed reduced right ventricular (RV) systolic function and McConneal sign. f1000research.com. Media. 2022. Publisher Full Text\n\nArdiana M, Hidayat DFO, Wardhani LFK, et al.: Video 2. The Computed Tomography Pulmonary Angiography (CTPA) examination performed in the emergency room. f1000research.com. Media. 2022. Publisher Full Text\n\nArdiana M, Octafian Hidayat DF, Wardhani LFK, et al.: Video 3. The Computed Tomography Pulmonary Angiography (CTPA) evaluation performed in the outpatient clinic. f1000research.com. Media. 2022. Publisher Full Text" }	[ { "id": "284679", "date": "21 Jun 2024", "name": "Luca Valerio", "expertise": [ "Reviewer Expertise Clinical management and epidemiology of pulmonary embolism in particular and venous thromboembolism in general." ], "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 case report on a case of acute pulmonary embolism with a focus on the initial assessment, risk stratification, and risk-based management. It is very well written and presents a balanced mix of typical and atypical features. The typical features make the case interesting for the young physician, while the atypical ones will interest the experienced physician.\n\nThe typical features include the antecedent risk factor - orthopaedic surgery, the vital signs, and the symptoms. While it is uncommon for chest pain, hemoptysis, and pre-syncope to co-occur, these are all typical signs and it is interesting to find them in the same patient. The atypical features include the relatively young age.\n\nThere is one major problem throughout the article that needs to be corrected. In pulmonary embolism, \"high-risk probability of PE\" and \"high-risk PE\" are two completely different things (note the words \"probabality\" and \"of\"). The first refers to the result of the assessment of the pre-test (or clinical) probability that a patient has PE at all before the gold standard test (CTPA or ventilation/perfusion scan) has been performed, and is used to decide whether to perform CTPA, because this may return false positive and may also unnecessarily expose patients to radiation. In contrast, \"high-risk PE\" refers to the assessment of risk of early (in-hospital or 30-days) death that occurs AFTER (or: at the same time as) a diagnosis has been made (using CTPA or ventilation/perfusion scan) based on a series of clinical, laboratory, and echocardiographic parameters, and is used to decide how to manage the patient (to sum up, low-risk patients can go home immediately, intermediate-risk patients may require only medium- or intensive-care monitoring, high-risk patients may require systemyc thrombolysis and intensive care monitoring). There is confusion between these two points in the Abstract and the Discussion. But to the PE clinician \"high risk of PE\" and \"high-risk PE\" mean, and should mean, two totally different things belonging to two separate stages of the management process. I detail below where the wording needs to be adapted to prevent this potentially dangerous misunderstanding.\n\nThere is also a very important missing point: an explicit statement of the risk stratification class. This must be made as clear as possible, because it guides the management of acute PE according to all current guidelines. In particular, it should be stated very explicitly that this patient was eligible for intravenous thrombolysis (which was indeed performed) because its risk class was high (high-risk PE) according to the European (ESC) guidelines, or, alternatively, massive according to the US guidelines. This point is of utmost importance, as this is the key element for the decision-making in acute PE.\n\nRecommendations\nABSTRACT 1) even among clinicians working with patients with pulmonary embolism and devoting their career to clinical research in pulmonary embolism and, to the best of my experience, in most countries, it is very uncommon to refer to the S1Q3T3 pattern in the electrocardiogram as \"McGinn-White Sign\". It is much more common to refer to it as, indeed, \"S1Q3T3 sign\". I therefore suggest that the Authors write \"S1Q3T3 pattern (McGinn-White sign)\" instead of \"McGinn-White sign\"; that is, the eponymic form should be enclosed between parentheses after the more traditional one. For instance, the way the sign is described in the Case Presentation is entirely understandable. If the word limit for the Abstract is reached, just write \"S1S3T3 pattern\" without eponymic. 2) similarly, \"Palla's sign\" is relatively uncommon and I suggest to instead write \"enlarged right pulmonary artery (Palla's sign)\". Again, much better in the Case presentation. If the word limit for the Abstract is reached, just write \"enlarged right pulmonary artery\". 3) the exact spelling of the echocardiographic sign the Authors refer to is \"McConnell sign\" rather than \"McConneal sign\" (see for instance (Konstantinides SV.et.al., 2020 ref 2 ). Please correct. 4) This sentence cannot be correct: \"CTPA was performed due to the moderate-high risk PE\". The sentence suggests that, \"because of\" (\"due to\") a moderate-high risk PE, a CTPA was performed; that is, that it was known that the patient had a moderate-high risk PE before the CTPA was even performed. But it is impossible for a diagnosis of PE to be posed without imaging (CTPA or ventilation/perfusion scan). Therefore, the Authors must have meant either \"due to the moderate-high risk pre-test risk of PE\" or \"A CTPA showed hyperattenuating and partial filling defect, confirming a moderate-high risk PE\". In the latter case, \"moderate-high\" would refer to the PE risk stratification and would not be correct (in the European guidelines, the naming \"intermediate-high\" is used; in the US guidelines, the naming \"submassive\" is used). In the case presentation, a correct sentence is used: \"(...) Wells' score of 7 showed a moderate-high risk for PE\" (the \"for\" makes all of the difference!), revealing that the sentence in the Abstract fell in the first of the cases I described. Please correct accordingly. 5) \"adequate anticoagulation\" does not describe exactly what is adequate in this context. It would be more informative to write \"therapeutic\" anticoagulation (as opposed to prophylactic or sub-therapeutic).\n\nKEYWORDS 6) I suggest that the keyword \"Risk stratification\" is added.\n\nINTRODUCTION 7) For the sentence in the Introduction, a more recent and direct reference for the numbers of deaths in Europe is Barco S.et.al., 2020 ref 1 which should replace ref. 3. However, current reference 3 may be kept for the first sentence of the Discussion (\"...helps provide better outcomes (3)\"). 8) It is not entirely correct to write \"Computed Tomography Pulmonary Angiography (CTPA) has been proposed as a standard imaging modality to diagnose PE.\" because CTPA has not merely been proposed: it is in fact the current recommended standard, and has been for a long time now (over 20 years). This formulation may be misleading to younger doctors. I suggest the Authors write \"Computed Tomography Pulmonary Angiography (CTPA) is the current standard imaging modality to diagnose PE.\"\n\nCASE PRESENTATION 9) The sentence \"we used PE’s risk assessment to better diagnose the involvement of PE.\" is linguistically very unclear (one does not \"diagnose\" an \"involvement\" in medicine, but only a disease; also, one does not diagnose \"better\" or \"worse\" - one either diagnoses or does not diagnoses). I think that the Authors should write clearly what they did: \"We assessed the pre-test probability of PE based on the patient's clinical presentation\". This sentence describes exactly the meaning and purpose of scores such as the Geneva score, the Wells score, or the Leiden score: establishing the probability a patient has a PE based solely on clinical and laboratory parameters and not on the diagnostic test CTPA (pre-test probability) in order to assess whether it is meaningful to perform a CTPA to diagnose PE. 10) \"referring hospital\" would be more common word usage than \"referrer hospital\". 11) please correct \"before referred to our hospital\" into either \"before he was referred to our hospital\" or \"before referral to our hospital\". 12) I believe it should be Norepinephrine rather than Norepinefrin - unless the latter is a commercial name for the active ingredient/active principle? 13) For the sake of conciseness, the Authors may write \"Laboratory testing revealeed incraed D-dimer (...)\" instead of \"We performed laboratory examination, which resulted in (...)\". 14) The numbers between brackets here are quite crowded: \"(Class II, low risk 1.7-3.5% 30-days mortality rate)\". It may be clearer if rewritten as \"(Class II, low risk; 30-days mortality rate 1.7 to 3.5%)\".\nDISCUSSION 15) The sentences \"However, clinical features and baseline findings often cannot unequivocally rule out PE, whereas follow-up examination (CTPA) is not cost-effective. This causes a follow-up examination to be carried out only in intermediate-high risk PE.2,3\" does not seem to be correct. CTPA is not a \"follow-up examination\" in PE: it is the gold standard for diagnosis! In medicine, the wording \"follow-up\" is reserved for the long-term (chronic) monitoring of patients who have already a diagnosis and are currently stable; it is not used in acute/emergency medicine. The sentences may be misleading, as they suggest to the reader that CTPA is only performed in intermediate-high risk PE. This is absolutely not the case - even low-risk PE must have been diagnosed before it can be assessed as being low risk, and this must absolutely have occurred with either CTPA or ventilation/perfusion scan. I checked references 2 and 3 at the end of the second sentence, and I think there is a misunderstanding: CTPA should be carried out only in patients with a \"intermediato to high pre-test probability of PE\", NOT in patients with \"intermediate-high risk PE\" (the latter means that one already knows that the patients has PE because the CTPA has already been carried out, and that the patient has a high probability of DYING from PE, not of HAVING PE). I think rewriting the two sentences as follows would solve the issue: \"However, clinical features and baseline findings often cannot unequivocally rule out PE, whereas CTPA, that can diagnose a PE, is not cost-effective in all patients, as it may lead to false positives and unnecessarily expose them to radiation. This causes the CTPA to be considered appropriate only in patients with a intermediate to high clinical risk of having a PE (2, 3).\". In addition, please refer the reader, for maximum clarity, to a discussion of the latest guidelines where this point is examined explicitly, such as ref 1 (in addition to existing references 2 and 3). Note that the following paragraph is written in a perfectly correct way - the point is the SUSPICION of PE.\n\n16) \"Tachycardia is followed by S1Q3T3 pattern (...) is a strong predictor of PE\": first, please remove the \"is\" (probably a type); second, it is not entirely true that this pattern is a strong predictor of PE; it is not very specific; to the best of my knowledge, less than 30% (I just noticed that you indeed write 25-30% in the next sentence, confirming what I thought). In biostatistics, usually, only positive predictive values above 90% justify the wordisng \"strong prediction\". I would rather write \"strongly suggests PE\". 17) \"We found patients with (...)\" supposedly refers to the patient described in this report; then, it would better be written as \"In the patient we described in this Report, clinical signs, ECG and CXR findings all supported a moderate to high pre-test risk of PE (...)\" (note that, once again, it would be wrong to write \"moderate-high risk PE\", because this wording would refer to the risk of early death). 18) \"Most patients will not survive within the first hours of the event.\": this is quite misleading, as the overall case fatality of PE does not go beyond 5%, and that hardly qualifies as \"most patients\". Only the subset of patients assessed as high-risk have a higher fatality. Please correct into \"Patients with a high-risk PE may not survive beyond the first hours of the event\". 19) Please correct \"McConneal\" into \"McConnell sign\".\n\n20) In tthe sentence \"Following an acute embolic event, the patient is at risk for fatal circulatory collapse due to right-sided heart failure and subsequent embolism.\", please remove \"subsequent embolism\", because this is simply plainly wrong - the pulmonary embolism itself (the one already there) causes right-sided heart failure, and not a new, \"subsequent\" embolism following the right-sided heart failure. Please add a sentence detailing that therefore, once PE has been diagnosed, the risk of death from right-sided heart failure must be assessed based on several clinical and imaging parameters, so that the patient is assigned to a formal class that in turn determines; for the appropriate word use read and cite the 2019 ESC guidelines (Konstantinides SV.et.al., 2020 ref 2 ) and/or, for a shorter practical example, Gallo A.et.al.,2019 ref 3 21) \"CTPA is mandatory in cases of high-risk PE. \": once again, this is very misleading, because \"high-risk PE\" means \"PE with high risk of death\" and not \"high pre-test probability of having PE\". Please write \"CTPA is mandatory in patients with a high pre-test probability of PE\" or \"CTPA is mandatory in patients with a high clinical probability of PE\".\n\n22) There is duplication of information and some kind of circularity in the DIscussion, because there are two separate paragraphs both on the diagnostic value of CTPA: the paragraph suarting with \"most patients will not survive within the first hours (...)\" and again the paragraph starting with \"CTPA is manadatory in cases of high-risk PE\". Note how they both report the same piece of information on the sensitivity and specificity of CTPA! Please merge the two paragraphs into a single paragraph that should precede the paragraph on the death risk stratification (which is the one starting with \"Following an acute embolic event\"). This is the most obvious and logical order: first, discuss the problem of diagnosis (pre-test probability to decide whether to perform CTPA); then, discuss the problem of risk of death/prognosis assessment. 23) The two sentences \"Pulmonary embolism blocks pulmonary blood flow, resulting in right heart failure. Acute right heart failure due to lack of systemic output is the leading cause of death in high-risk PE.\" repeats for the second or third time what has already been said. This paragraph should re-focus on the current case and discuss treatment. Please remove the two sentences.\n\nCONCLUSIONS 24) Once again, correct \"moderate-high risk PE and was supported by clinical (...)\" into \"moderate to high pre-test probability of PE as suppored by (...)\". 25) Correct \"The use of PE’s risk assessment will help determine the needs of CTPA\" into \"The assessment of clinical (pre-test) probability of PE helps to decide on the need of CTPA\". 26) Correct \"in the Acute Cardiac Care Setting\" into the more general and appropriate \"in case of suspicion of PE in the acute setting\". 27) Correct \"Utilization of CTPA for the immediate diagnosis of pulmonary embolism patients helps determine the patient management accurately. Adequate therapy can reduce the risk of mortality and morbidity from pulmonary embolism.\" into \"If a PE is diagnosed, CTPA also supports the subsequent assessment of the risk of early death from PE, guiding the choice of adequate therapy and ultimately reducing the risk of mortality and morbidity from PE\".\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? 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? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-13
https://f1000research.com/articles/13-7/v1	03 Jan 24	{ "type": "Research Article", "title": "From classroom to global goals: A bibliometric analysis of Universitas Indonesia’s student projects addressing Sustainable Development Goals (SDG) 3", "authors": [ "Dita Garnita", "Rahmi Rahmi", "Hideo Joho", "Abdul Kadir", "Dita Garnita", "Hideo Joho", "Abdul Kadir" ], "abstract": "The Sustainable Development Goals (SDGs) represent a vital contribution to both developed and developing nations. It is imperative to assess SDG-related activities to discern the impact of such initiatives across various domains, including health and education. While current bibliometric analyses on SDGs predominantly encompass peer-reviewed articles, it is paramount to acknowledge that SDGs are universally pertinent and necessitate universal engagement. Consequently, there is a compelling need to broaden the bibliometric scope concerning SDGs, surpassing the realm of peer-reviewed papers. This research introduces a pioneering examination of SDG-associated academic undertakings, encompassing undergraduate, master’s, and doctoral research projects on an expansive scale. The evaluative framework stems from a decade’s culminating research endeavours published by Universitas Indonesia (UI). The emphasis of this study was directed towards Good Health and Well-being (SDG 3), given its intricate set of indicators. Furthermore, there remains a paucity of research probing the influence of libraries in the context of SDG 3 indicators within the Indonesian milieu. Through a bibliometric approach, we employed a descriptive analysis to scrutinize the publications’ breadth and evolution. Science mapping facilitated an exploration of inter-topic relationships and spotlighted prominent research themes. The diverse range of research predilections unearthed through our analysis underscores the significance of integrating student research projects into the bibliometric discourse on SDGs. This inquiry aims to heighten recognition of the extensive scholarly contributions by students and ideally will galvanize a younger demographic to immerse themselves in SDG-aligned research pursuits.", "keywords": [ "bibliometric analysis", "final student project", "good health and well-being", "sustainable development goals" ], "content": "Background\n\nBibliometric analysis applies mathematical and statistical methods to books, journals, and other publications (Roemer & Borchardt, 2015). This type of analysis uses quantitative methods to measure, track, and analyse scientific literature (Roemer & Borchardt, 2015). It allows us to identify developments in a given field, influential authors or researchers, and the most productive journals by subject (Grace, Florence & Florence, 2019). Along with the development of a more active role for librarians in research activities and scientific communication, bibliometric analysis is increasingly being applied in various libraries worldwide. The results can contribute to the development of library collections (Belter & Kaske, 2016). However, the focus of bibliometric activities in academic libraries has changed from collection development to research evaluation by researchers, research groups, departments, and universities (Corrall et al., 2013).\n\nResearch evaluation through bibliometric analysis can use several indicators to measure development and trends in scientific activity by evaluating a scientific discipline, institution, journal, or other scientific entity (Anninos, 2014). Herrera-Calderon et al. (2021) explained that the results of bibliometric research can be used to create new knowledge and assist in decision-making. Furthermore, Donthu et al. (2021) described two types of bibliometric analysis techniques: descriptive analysis and science mapping. In addition, network analysis can be utilized to enrich a bibliometric analysis. The descriptive analysis technique aims to determine the contributions that research publications make to specific fields; for example, measurements related to publications (number of publications, number of authors, or productivity per year), citations (number of and average citations), as well as related publications and citations (number of publications cited, h-index, and collaboration index). Meanwhile, science mapping aims to determine the relationships between publications, among others, by analysing citations (citation analysis, co-citation analysis, and bibliographic coupling), words (co-word analysis), and authors (co-authorship analysis).\n\nThe application of bibliometric analysis in academic libraries has several benefits, including increasing librarians’ competence, expanding libraries’ role and involvement in decision-making in universities, and increasing the influence and reputation of libraries at universities. Case studies conducted in Sweden, Nigeria, Australia, New Zealand, Ireland, and the United Kingdom suggest that academic libraries offer bibliometric analysis services to provide useful information for evaluating the university’s research performance. Libraries are suitable for conducting this type of evaluation because they have a collection of repositories and publication databases that can act as data sources for analysing university publication outputs (Åström & Hansson, 2013; Corrall et al., 2013; Grace et al., 2019).\n\nIn libraries and higher education institutions in Indonesia, bibliometric analysis is applied to analyze the use of collections, investigate the development of research on specific topics, and help with the analysis of teaching curriculum needs in library science study programs (Tupan, 2016; Aulia & Rusli, 2020; Amalia & Prasetyawan, 2021). Bibliometric analysis is also used to evaluate the suitability of the contributions of researchers’ publications to a particular vision and mission and the university’s leading research topics (Maryatun & Handayani, 2022). In addition to evaluating individual researchers’ performances, bibliometric analysis can assess the university’s overall research performance. Research is a component considered in university accreditation and ranking in Indonesia (Filiana et al., 2020; Times Higher Education, 2022; UI GreenMetric WUR, 2022).\n\nLibraries’ role in supporting scientific research and communication also involves supporting the 2030 United Nations (UN) agenda. The UN agenda consists of 17 Sustainable Development Goals (SDGs), which provide an integrated framework for economic development and environmental and social factors (Tbaishat, 2021). These goals are targets for countries worldwide to achieve by 2030. In higher education, the issue of sustainable development has been consistently considered necessary over the past decade. In addition to facilities and campus life, sustainable development must be integrated into education and research in universities (Shiel et al., 2020). Thus, access to information through libraries can increase the achievement of the SDGs (Tbaishat, 2021).\n\nAs a university library, the Universitas Indonesia (UI) Library has collections, services, and library staff that support the implementation of teaching, research, and community service. The UI library has printed and digital displays, including textbooks, reference books, scientific journals, proceedings, ancient manuscripts, and multimedia collections. The UI Library also has a collection of research from the UI academic community (the UIANA collection), including undergraduate theses, master’s theses, dissertations, final assignments, research reports, and inaugural speeches. To help users access the collection, the UI Library has a reference service (referral service) with several programs, including information literacy training, literature searches via links and emails, guidance on the use of reference sources, E-resources delivery services for UI professors, and document similarity checking (Perpustakaan UI, 2022). UI academicians can also ask for help from a reference librarian in the health, social, and humanities or science and technology clusters to find the literature they need for their research.\n\nScientific research results from the UI can contribute to the achievement of SDGs. Research results from the UI can also be used as a source of data for Voluntary National Review (VNR) activity, which measures SDG indicator achievements in relation to those 17 objectives. According to the Universitas Indonesia Research Portal, there are 4165 research outputs related to the health sciences cluster or SDG 3 (good health and well-being) – the most compared to other SDGs (Perpustakaan UI, 2022). According to data from SciVal, in 2018–2021, 14.4% of the research conducted at the UI was in the fields of health and medicine (medicine, pharmacology, toxicology, and pharmaceuticals), indicating that this field is the leading research field at the UI (SciVal.com, 2021). These data can help the UI earn a good SDG rating in university rankings, such as THE Impact Ranking and UI GreenMetric. Unfortunately, the scientific works listed on scholar. UI.ac.id do not include those created by UI students, such as undergraduate theses, master’s theses, and dissertations. Therefore, UI students’ research performance should be evaluated according to the SDGs, especially SDG 3.\n\nSeveral previous studies have used the bibliometric method to examine SDG 3, which relates to good health and well-being. For SDG 3, three major themes were identified: access to universal healthcare, maternal health, and global health. In addition to research on SDG 3, some studies consider specific indicators, including access to health services in rural areas through telemedicine and psychological well-being (suicide death rate) (Da Costa et al., 2020; Palozzi et al., 2020). These three studies used data from the Scopus database.\n\nIn Indonesia, several studies have also been conducted in relation to SDG 3; for example, access to health services, especially the mapping of hospitals’ online registration system, and infectious diseases such as tuberculosis and dengue haemorrhagic fever, have been investigated (Dimisyqiyani et al., 2020; Maula et al., 2018; Sebba et al., 2017). However, the number of publications remains lower than those of other ASEAN countries, such as Thailand, Singapore, Malaysia, and Vietnam. The three abovementioned studies used the Scopus and PubMed databases as data sources. In addition, this finding indicates that SDG 3 has an important role in the health system in various countries.\n\nMeanwhile, research on libraries’ role in relation to the SDGs, especially SDG 3 indicators, has not been widely performed in Indonesia. Previous research has tended to discuss library programs and librarians’ role in achieving the SDGs (Fatmawati, 2018; Rufaidah & Iskak, 2019; Suprapto & Qosyim, 2022). This study shows that libraries could contribute to achieving SDGs, especially SDG 4 (quality education), by increasing literacy culture. Libraries could implement information literacy workshops, literacy guidance, technology training, information dissemination, and mobile library programs in villages. Librarians need to improve their professional and social competencies, including skills in information technology, media literacy, and information literacy. According to this perspective, research on SDG 3 (good health and well-being), especially studies using the bibliometric method, has been widely conducted. Unfortunately, most existing studies only examined journal articles found through Scopus. This study uses UI students’ final projects as a data source.\n\n\nMethods\n\nThis quantitative study has a non-experimental, or observational, cross-sectional design. This study used secondary data derived from the metadata of the UI Library collection, especially the undergraduate theses, master’s theses, and dissertations of students from the Faculty of Medicine (FK), Faculty of Dentistry (FKG), Faculty of Public Health (FKM), Faculty of Nursing (FIK), and Faculty of Pharmacy (FF) published from 2011–2020 (Rahmi, 2023). The bibliometric analysis performed in this study adopted the analytical steps of Bradford’s Law regarding the distribution of scientific papers, namely (1) the number of published final assignments, (2) the viewing of sources by faculty, study program, and type of work to identify those that produce the most publications; and (3) the creation of groups based on the topics discussed.\n\nThe UI Library Automation and Digital Archive (LONTAR) automation system obtained secondary data in collection metadata. Data were downloaded in March 2022. The data analysis continued until May 2022.\n\nThe population used in this research consisted of UI Health Sciences students (Faculty of Medicine, Faculty of Dentistry, Faculty of Public Health, Faculty of Nursing, and Faculty of Pharmacy) who submitted final projects that were published in 2011–2020 and stored in the thesis and dissertation collection of the Universitas Indonesia Library published in 2011–2020 because their final projects are related to SDG 3, Good Health and Well-being. Moreover, the data included in the sample had to meet both inclusion and exclusion criteria. Inclusion criteria consist of the final project for the UI Library collection completed by a UI Health Sciences student (Faculty of Medicine, Faculty of Dentistry, Faculty of Public Health, Faculty of Nursing, and Faculty of Pharmacy); published in the years 2011–2020; and in the form of an undergraduate thesis, master’s thesis, or dissertation. The exclusion criteria are missing data (incomplete); duplication of data; or final work submitted for a specialist or professional program.\n\nIn total, there were 13,603 final projects produced by UI Health Sciences students, 10,443 of which were published in the years 2011–2020; 5476 were undergraduate theses, master’s theses, or dissertations, and 2674 of these had missing data (incomplete), duplicated data, or were in the form of specialist and professional program final works.\n\nSecondary data were collected by downloading the metadata from the UI Library’s final project collection of undergraduate theses, master’s theses, and dissertations published in 2011–2020 by UI Health Sciences students through the UI library’s LONTAR automation system. The data included the authors’ names, counsellors’ names, titles (Indonesian and English), faculty, year of publication, type of work, abstract, study program, subject topic, and keywords.\n\nResearchers collected data by searching the back-office automation system LONTAR UI Library. The search strategy was: 1. A search in the LONTAR back office was carried out in the “Processing > Add Data” menu; 2. A keyword search was done in “264b Publisher Name”; 3. The keywords used were the names of the faculties with collections of final assignments related to SDG 3, including “Faculty of Medicine”, “Faculty of Dentistry”, “Faculty of Public Health”, “Faculty of Nursing”, and “Faculty of Pharmacy”; 4. The type of collection searched was the final project collection, including “UI—Undergraduate Thesis (Open)”, “UI—Undergraduate Thesis (Membership)”, “UI—Master Thesis (Open)”, “UI—Master Thesis (Membership)”, “UI—Dissertation (Open)”, “UI—Dissertation (Membership)”, and “Download”; and 5. After the search results appeared, the data were downloaded in Microsoft Excel (.xlsx) file using Excel version 365.\n\nData processing consisted of data cleaning and data coding. Data cleaning was done by removing missing data (for example, work lacking a title, topic subject), eliminating duplicated data, and correcting writing errors (for example, the year “2104” was updated to “2014”). After the data cleaning process, 3059 final assignments remained, which were then put into categories (coded) according to the 13 targets of SDG 3. The categories used to code the data were: 1. Maternal Health; 2. Baby and Toddler Health; 3. Infectious Diseases; 4. Non-Communicable Diseases and Mental Health; 5. Drug and Alcohol Abuse; 6. Traffic Accidents; 7. Access to Reproductive Health Services; 8. Access to Universal Healthcare; 9. Hazardous Chemicals and Pollution; 10. Tobacco Control (Cigarettes); 11. Drug and Vaccine Development; 12. Health Personnel (HR); and 13. Health Risk Management.\n\nTwo “raters” performed the data coding process to improve its reliability: an undergraduate Library Science student and an undergraduate Public Health student. The level of agreement between them serves as an indicator of the quality of the categorisation. Cohen’s Kappa was used to assess the level of agreement between the two raters. The following is an interpretation of the Kappa values (Warrens, 2015).\n\n0.00–0.20 = Low agreement\n\n0.21–0.40 = Sufficient agreement\n\n0.41–0.60 = Moderate agreement\n\n0.61–0.80 = Substantive agreement\n\n0.81–1.00 = Almost perfect agreement\n\nCohen’s Kappa was measured using GNU PSPP version 1.5.3 software. The Kappa value deter-mined in the test was 0.52, so the raters showed a moderate level of agreement.\n\nData analysis was performed through descriptive analysis, science mapping, and multivariate analysis.\n\nThe descriptive analysis was conducted to visualise the distribution of the variables studied, including the faculty, publication year, type of work, subject topic, and SDG 3 target. The descriptive analysis was performed using IBM SPSS Statistics Standard 28.0 software and Tableau Public version 2022.1.2.\n\nScience mapping was performed to visualise the co-occurrence network of the relationships between topic subjects in the selected work (Ding et al., 2014). VOSviewer software version 1.6.18 was used.\n\nMultivariate analysis was performed using a multinomial logistic regression with predictive models. Multinomial logistic regression was used because the dependent variable in this study (SDG 3) was categorical (13 categories). This type of analysis allows a model consisting of several independent variables that are considered the best to predict the occurrence of the dependent variable to be created (Field, 2018). The multivariate analysis was performed using IBM SPSS Statistics Standard 28.0 software.\n\n\nResults\n\nThe Technical Implementation Unit (UPT) of the UI Library was established on 5th March, 1983, according to the Decree of the Minister of Education and Culture No. 0130/O/1983 regarding the Organization and Work Procedures of Universitas Indonesia Article 4 and Article 131-136, which explains the functions, duties, and organisation of the UI Library UPT. In 1987, the UI Library, formerly the UPT Central Library, moved to a new building on the UI Depok Campus. The Central Library then served to coordinate 12 faculty libraries (Perpustakaan UI, 2018).\n\nIn 2011, the UI Library moved into a new building dubbed “The Crystal of Knowledge”. This building was constructed according to one of the points of the UI’s strategic plan at the time: integration into the field of facilities. The process of integrating collections into the UI Library UPT started in March 2012. The Central Library, Faculty of Humanities Library, Faculty of Engineering Library, Faculty of Mathematics and Natural Sciences Library, Faculty of Nursing Library, and Faculty of Law Library followed. Several other faculties still retain separate libraries but have moved some of their collections to new buildings, namely, the Faculty of Computer Science Library, Faculty of Psychology Library, Faculty of Social and Political Sciences Library, Faculty of Public Health Library, and Faculty of Economic Library (Perpustakaan UI, 2018).\n\nThe UI library aims to collect, select, organise, and provide access to various information and knowledge resources for UI Citizens. Therefore, the UI Library collects and preserves library materials that are intellectual works. In addition, the UI Library follows developments in and adopts information and communication technology to improve its services. This is reflected in the vision of the UI Library for 2015–2019. Specifically, “In 2019, Universitas Indonesia Library will become a reference for national and regional university libraries sourced from the intellectual works of UI Citizens, and quality e-resources owned and supported by modern facilities owned by Universitas Indonesia.” The UI Library’s mission is (Perpustakaan UI, 2015): (1) to provide quality access for UI residents and the public to information and knowledge resources, with excellent service based on information and communication technology; (2) to support the research conducted by UI Citizens by providing information and knowledge resources based on information and communication technology; (3) to provide community services for the utilisation of information and knowledge resources mainly via UIANA collections based on information and communication technology at the national and regional scales; and (4) to build entrepreneurship by offering empowering information resources and knowledge based on information technology.\n\nTo help realise its vision, the UI Library has support services, collections, and facilities. UI Library Services are grouped into circulation services, reference services, and information technology services. Circulation services include membership activation, borrowing and returning printed books, and a free library certificate (SKBP). Reference services consist of information literacy training, literature searching, guidance on the use of reference sources, e-resource delivery services (EDS), document similarity checking, library utilisation studies, manuscript services, broadcast information, special collection services and journals, and research tools services. Finally, information technology services consist of website access and management services, access to e-resources, and LONTAR development (Perpustakaan UI, 2022).\n\nIn addition to these services, the UI Library has various collections to meet users’ information needs. At the end of 2021, the UI Library collections included 3,626,797 titles (3,761,309 total copies). The collections include e-resource collections (88.9%), UIANA collections (5.1%), textbooks (4.4%), printed magazines and journals (1.1%), reference books (0 4%), multimedia collections (0.1%), and ancient manuscripts and classic books (0.1%) (Perpustakaan UI, 2022).\n\nAs the data above show, after e-resources (e-books, proceedings, e-journals, online videos, and other electronic resources owned and subscribed to by UI), one of the largest collections in the UI Library is the UIANA collection. The UIANA collection is grey literature consisting of undergraduate theses, master’s theses, dissertations, non-seminar papers, research reports, proceedings, and other scientific works from the UI Academic Civitas (Tyasmara & Susetyo-Salim, 2018). This collection can be accessed in both printed and digital forms.\n\nDistribution of final project publications by year of publication\n\nThe analysis results presented in Table 1 show the project distribution by publication year. Most of the UI students’ final project publications that were related to SDG 3, Good Health and Well-being, were published in 2019 (23.1%), 2020 (14.7%), and 2018 (13.1%). The number of publications from year to year tended to increase, as shown in Table 2. The average growth rate of the number of publications per year, from 2011–2020, was 29%.\n\nDistribution of final project publications by faculty\n\nAs the data analysis presented in Table 2 shows, most of the UI students’ final assignments related to SDG 3 came from the Faculty of Public Health (35.9%) and the Faculty of Medicine (26.8%). Final project publications from other faculties included the Faculty of Nursing (19.2%), the Faculty of Pharmacy (13.9%), and the Faculty of Dentistry (4.2%). In terms of the growth rate in the number of publications, the Faculty of Dentistry has had the highest average annual growth rate (84%), followed by the Faculty of Medicine (57%), the Faculty of Public Health (50%), the Faculty of Nursing (48%), and the Faculty of Pharmacy (43%).\n\nDistribution of final project publications by study program\n\nBased on the results of the data analysis presented in Table 2 most of the publications of the UI students’ final assignments related to SDG 3 came from students completing the Doctoral Education Bachelor Program (14.17%), Master of Public Health Sciences (11.18%), and Bachelor of Pharmacy (10, 7%). As Table 2 shows, the epidemiology master’s degree program has the highest average publication growth rate per year (168%), followed by the medical science doctoral degree (141%) and the medical education master’s degree (119%) programs.\n\nDistribution of final project publications by type of work\n\nThe analysis results presented in Table 3 show the distribution by type of work. Most of UI students’ published final assignments related to SDG 3 were undergraduate theses (54%). Master’s theses accounted for 42% of the total, while dissertations accounted for as much as 4%. The number of publications almost always increased yearly for each type of work. Nevertheless, the highest average growth rate in the number of publications per year was in the dissertation collection—as much as 207%.\n\nThe topics for UI student thesis publications were chosen by the librarian based on the Library of Congress subject heading. The results of the analysis presented in Figure 1 show that the most common subjects are industrial safety (appearing in 49 publications), breastfeeding (38 publications), industrial hygiene (27 publications), nursing care (25 publications), and tuberculosis (25 publications). In terms of development, the number of subjects studied most frequently changed from year to year. This is demonstrated in Figure 2. In 2011, the most commonly studied subjects were Bacillus thuringiensis, diabetes mellitus, and Dengue haemorrhagic fever, while in 2020, the most frequently researched subjects were nursing care, health education, and reproductive health.\n\nSDG 3, Good Health and Well-being, has 13 targets, which are shown in Table 4. Of these 13 targets, most of the UI students’ final project publications had topics related to Target 4, Non-Communicable Diseases and Mental Health (18%), followed by Target 11, Drug and Vaccine Development (17.8%), and Target 13, Health Risk Management (13.2%). Meanwhile, topics related to Target 6 (Traffic Accidents), Target 5 (Abuse of Narcotics and Alcohol), Target 7 (Access to Reproductive Health Services), and Target 10 (Tobacco/Cigarette Control) appear less frequently in UI students’ final assignments. In addition, 14.2% of publications in the “Other” category are not directly related to SDG 3 targets, including topics related to forensics, diagnostics, nutrition, health promotion, and others.\n\nIn terms of the growth rate of publications, as Table 5 shows, Target 1 (Maternal Health) has undergone the greatest average annual growth (152%), followed by Target 2 (Infant and Toddler Health) and Target 8 (Universal Healthcare Access). The analysis results presented in Table 6 show which topics have been most frequently studied in each faculty and program. Target 4 (Non-Communicable Diseases and Mental Health) and Target 11 (Development of Drugs and Vaccines) are the most frequently studied topics in all faculties. Table 7 shows the distribution of final project publications related to SDG 3 based on the type of work.\n\nFigure 3 shows the results of the word co-occurrence analysis of the topic subject (index keywords) and keywords (author keywords) of UI students’ final project publications related to SDG 3 that were published in 2011–2020. The analysis results led to the following 17 clusters: Cluster 1 – Health Services and Performance of Health Workers; Cluster 2 – Diabetes Prevention and Management; Cluster 3 – HIV/AIDS; Cluster 4 – Non-Communicable Diseases and Mental Health; Cluster 5 – Occupational Health and Safety; Cluster 6 – Dental Health and Mental Health; Cluster 7 – Maternal and Child Health; Cluster 8 – Youth Health; Cluster 9 – Child Development; Cluster 10 – Respiratory Tract Infections; Cluster 11 – Adolescent Reproductive Health; Cluster 12 – Infectious Diseases; Cluster 13 – Maternal Health; Cluster 14 – Health Promotion; Cluster 15 – Drug Abuse; Food Hygiene and Sanitation; Cluster 16 – Cancer; and Cluster 17 – Risk Management.\n\nEach cluster associated with SDG 3 targets has links to the following targets:\n\nCluster 1: Target 8, Target 12\n\nCluster 2: Target 4, Target 11\n\nCluster 3: Target 3, Target 7\n\nCluster 4: Target 4, Target 11\n\nCluster 5: Target 13\n\nCluster 6: Target 4, Target 11, Target 14\n\nCluster 7: Target 1, Target 2\n\nCluster 8: Target 7, Target 11, Target 14\n\nCluster 9: Target 2, Target 14\n\nCluster 10: Target 3, Target 9\n\nCluster 11: Target 7\n\nCluster 12: Target 3, Target 11\n\nCluster 13: Target 1, Target 11\n\nCluster 14: Target 10, Target 14\n\nCluster 15: Target 5; Target 14\n\nCluster 16: Target 4, Target 11\n\nCluster 17: Target 13\n\nThe results of the statistical test that are presented in Table 8 show p-values below the significance level (α) of 0.05, which means that there are significant relationships between the faculty, publication year, and type of work and the topic of UI students’ final project publications in the field of good health and well-being. The coefficient of determination (R2) value of 0.562 indicates that the above factors can explain 56.2% of the variation in the dependent variable, the topic of UI students’ final project publications related to good health and well-being. Other factors can explain the rest of the variation.\n\nA multinomial logistic regression analysis was used to find the variables with the most influence on UI students’ final project publications related to SDG 3. Table 9 presents the regression analysis results, where “Other Topics” was used to compare the relationships between the 13 topics related to SDG 3 and the year of publication, faculty, and work variables. Meanwhile, the Faculty of Pharmacy (FF) and dissertation were used as the comparison groups for the faculty and type of work variables.\n\nTable 9 presents the regression coefficient (B) and odds ratio (OR) values. These analysis results reveal which topics are more common in a particular faculty compared to other faculties: The greater the B and OR values in a group, the greater the frequency of topic discussion compared to other groups. For example, the group with the largest B and OR scores for maternal health is the Faculty of Public Health (FKM), suggesting that maternal health is most frequently studied by FKM students. The same was found for infant and toddler health, infectious diseases, traffic accidents, access to reproductive health services, hazardous chemicals and pollution, health personnel (HR), and health risk management.\n\nMeanwhile, the Faculty of Pharmacy (FF) excels in the topic of drug and vaccine development, compared with other faculties. Faculty of Nursing (FIK) students have mostly researched non-communicable diseases and mental health, narcotics and alcohol abuse, and tobacco control (cigarettes) compared with other faculties. The complete results are presented in Table 9.\n\nIn terms of publication year, the analysis results presented in Table 9 show whether a topic tends to be studied more or less frequently throughout the year. A positive B value for publication year indicates a directly proportional relationship between the frequency of discussion and the year.\n\nConversely, a negative B value indicates that the frequency of discussion is inversely proportional to the year. This information affirms that non-communicable diseases and mental health, narcotics and alcohol abuse, access to universal health services, hazardous chemicals and pollution, tobacco control (cigarettes), and drug and vaccine development tend to be researched more frequently as the year progresses, while the remaining topics (maternal health, infant and toddler health, infectious diseases, traffic accidents, access to reproductive health services, health personnel, and health risk management) tend to be less and less researched.\n\nIn terms of the type of work, several topics are studied more by doctoral students (S-3) than undergraduate (S-1) or master’s (S-2) students, including narcotics and alcohol abuse, access to health services, reproduction, and the development of drugs and vaccines, maternal health, infant and toddler health, non-communicable diseases and mental health, access to universal health services, tobacco control (cigarettes), and health personnel (HR) were most commonly studied by master’s students. For undergraduate students, the most frequently studied topics included infectious diseases, traffic accidents, hazardous chemicals and pollution, and health risk management.\n\nThe prediction model for UI students’ final project publications related to good health and well-being involved the analysis of the relationship between the subject of publication and the SDG 3 target discussed in the publication. This analysis was conducted using a simple linear regression method to determine the relationships between two or more variables and was intended to predict the value of the dependent variable (SDG 3 target) via the independent variable (publication subject). The dependent variable in a linear regression must be numerical, so the SDG 3 targets were assigned numbers 1–14.\n\nAs the statistical test results presented in Table 10 show, the p-value was smaller than the significance level (α) of 0.05, which indicates a significant relationship between the publication subject and UI students’ final project publication topics related to good health and well-being. Furthermore, the correlation value (R) of 0.977 indicates a strong, positive relationship, and the coefficient of determination (R2) of 0.954 indicates that the subject can explain 95.4% of the variation in the dependent variable, namely the Topic of Publication of UI Students’ Final Projects Related to Good Health and Well-being.\n\nThe regression equation model cannot be displayed in Table 10 because 2261 topic subjects were used as independent variables. The model was applied as a topic predictor, as shown in Figure 2. These predictors allow librarians to enter the subject of publication to find the SDG 3 target that is associated with the topic. For example, Figure 4 shows that a final project with the subject “abortion” was coded “1” for the SDG 3 target “maternal health”.\n\n\nDiscussion\n\nThis study used secondary data from the UI Library collection, acquired through the LONTAR system. During data processing, information bias can occur, especially during the categorisation process based on the 13 SDG 3 targets. Meanwhile, of the 5476 documents that met the inclusion criteria, 2802 (51%) had missing or duplicated data or were in the form of final works of specialist and professional programs. The number of missing data points may have caused selection bias in this study.\n\nIn total, the final project publications (undergraduate theses, master’s theses, and dissertations) of UI students from 2011–2020 and related to good health and well-being accounted for 2674 titles or 1.8% of all undergraduate theses, master theses, and dissertations in the UI Library. Of the five faculties that belong to the health sciences cluster, the Faculty of Public Health (FKM), the Faculty of Medicine (FK), and the Faculty of Nursing (FIK) have published the most. This may be because the number of students in these three faculties (9% of the total UI students) exceeds the number of students in the Faculty of Dentistry (FKG) and the Faculty of Pharmacy (FF) (only 3% of the total UI students). In addition, the FK, FKM, and FIK have more study programs than the FKG and FF.\n\nThe publication year data shows that the number of publications significantly increased in 2019, to almost double that of the previous year, with the average growth rate per year reaching 29% (see Figure 5). This shows that research interest in good health and well-being as an SDG did not gain much traction until 2019. A similar, significant upward trend was reported in the Punnakitikashem and Hallinger (2019) study on sustainable health management, which showed that the number of publications almost doubled in 2013 compared to the previous year. These trends suggest that research on good health and well-being could be researched more and more frequently in the years to come.\n\nHowever, the number of final project publications produced in 2020 was less than that in 2019. This is due to librarians’ decreased productivity in processing the final project collection during the implementation of the work-from-home (WFH) system during the COVID-19 pandemic. One of the reasons for this decline in productivity was inadequate equipment and internet network access. This increased the number of final assignments by UI students published in 2020 that have not been processed. To overcome this and given the control of COVID-19 cases, the UI Library implemented a full work-from-office (WFO) system in 2022. In addition, the UI Library plans to recruit student staff (Wiradha) to assist with the processing of final project publications.\n\nMost of the publications were theses. Meanwhile, dissertations only accounted for 3.5% (94 titles) of all publications. Dissertations were only included from about 52.6% of the estimated number of doctoral program graduates from the health sciences cluster in 2011–2020. Therefore, the UI Library needs to increase the acceptance of scientific works from doctoral programs. The UI library could work with the UI Directorate of Education (Dirpen) to form regulations that require students of all levels to upload their final assignments to the UI Library and disseminate this policy to all faculties at UI.\n\nThe analysis results show that the 30 topics studied were dominated by those related to access to universal health services (nursing care, public health, national health insurance, hospital administration, medical care, and health insurance), non-communicable diseases (diabetes mellitus, obesity, blood pressure, and fatigue), infectious diseases (tuberculosis, malaria, and Escherichia coli), maternal and child health (breastfeeding, child development, anaemia, and nutrition), and health risk management (industrial safety, industrial hygiene, and occupational health and safety).\n\nAccess to universal health care was in the top five most-discussed topics every year from 2017 to 2020. This aligns with the findings that Ghanbari et al. (2021) reported that researchers’ interest in studying universal health service access has increased continuously from 2009 to 2019. In addition, Sweileh (2020) shows that universal health service access was the most frequently studied SDG 3 target from 2015–2019. Therefore, continuing to increase interest in researching this topic, especially in developing countries, will be useful to understand the challenges and obstacles inhibiting the achievement of universal health service access and the improvement of global health overall (Ghanbari et al., 2021).\n\nRegarding SDG 3 targets, UI students most often studied Target 4, Non-Communicable Diseases and Mental Health. This aligns with the results of basic health research showing that the prevalence of non-communicable diseases, such as diabetes mellitus (1.5%) and heart disease (1.5%), in Indonesia is higher than the incidence of infectious diseases, such as pulmonary tuberculosis (0.42%) and hepatitis (0.39%). As far as mental health issue was concerned, the prevalence of severe mental health disorder was cited at 1.7% of Indonesian community (Hartini et al., 2018).\n\nMeanwhile, topics that have not been widely researched include Target 6 (Traffic Accidents), Target 5 (Abuse of Narcotics and Alcohol), and Target 10 (Tobacco Control). This also conforms to Sweileh’s results (2020) showing that these topics, especially drug and alcohol abuse, were not studied much compared with other topics according to the listings in the Scopus database from 2015–2019. The stigma against narcotics users can make researching the topic challenging. Narcotics abuse can increase the risk of other health problems, such as HIV/AIDS and hepatitis (Sweileh, 2020). Librarians must be competent in educating users about alternative research and sampling methods for hard-to-reach communities. In addition, librarians need insight into appropriate secondary data sources for research related to SDG 3.\n\nThe word co-occurrence analysis using the VosViewer software identified the five words with the most links to other topics: “knowledge”, “teenager”, “hypertension”, “industrial safety”, and “attitude” (see Figure 6).\n\nThe words “knowledge” and “attitude” indicate that publications related to SDG 3 mostly focus on promotive and preventative efforts. It has been proved that promotive efforts can support the enabling factor to increase self-determination and control among people regarding their health while prevention efforts focus on avoiding the increase of risk factors towards disease, therefore for early detection can be done in reducing the incident and damage related to people’s health (Helfer et al., 2020). Furthermore, the words associated with “knowledge” and “attitude” indicate that pregnant and lactating women, children, and adolescents are the most frequently studied populations. The health problems studied in the adolescent population have been quite diverse but are dominated by non-communicable diseases and mental health. The number of studies on non-communicable diseases is also indicated by the term “hypertension”, which is one of the words that is most frequently related to other topics. Hypertension is a risk factor for various non-communicable diseases, including diabetes mellitus. In addition to these topics, industrial safety is also widely studied. This topic is also related to health risk management and occupational safety and health. Its presence in this analysis indicates that, in addition to the populations of pregnant women, breastfeeding women, children, and adolescents, UI students study industry and the workplace broadly.\n\nPublication year\n\nThe results of the multivariate analysis show a significant relationship between the year of publication and the topic chosen. Non-communicable diseases and mental health, drug and alcohol abuse, access to universal health services, hazardous chemicals and pollution, tobacco control (cigarettes), and drug and vaccine development have tended to be researched more frequently over the years, while the remaining topics (maternal health, infant and toddler health, infectious diseases, traffic accidents, access to reproductive health services, health personnel, and health risk management) have tended to be researched progressively less. Librarians can consider this information when selecting collection procurement activities. Collections related to topics that tend to be researched more frequently each year can be prioritised, adopting one of the benefits of bibliometrics: assistance with decision-making in developing collections (Grace et al., 2019).\n\nFaculty\n\nThe results of the multivariate analysis showed a significant relationship between faculty and publication topic. Among topics related to SDG 3, FKM students generated more publications on related topics than other faculties, except for drug and vaccine development, which was mainly covered by FF students, and non-communicable diseases and mental health, abuse of narcotics and alcohol, and tobacco control (cigarettes), which were mainly covered by FIK students. These topics were also researched by FK and FKG students. However, students in those faculties also studied topics that were not directly related to SDG 3, such as anatomy, physiology, forensics, and dental and bone health.\n\nType of work\n\nThe results of the multivariate analysis showed a significant relationship between the type of work and the topic chosen. Several topics were identified as being studied more frequently by postgraduate students (S-2 and S-3) than undergraduate students (S-1), including narcotics and alcohol abuse, access to reproductive health services, the development of drugs and vaccines, maternal health, infant and toddler health, non-communicable diseases and mental health, access to universal health services, tobacco control (cigarettes), and health personnel (HR). Other topics (infectious diseases, traffic accidents, hazardous chemicals and pollution, and health risk management) have been mainly studied by undergraduate students. One of the UI Library’s services to which the results of this analysis can be applied is the Lecturer and Postgraduate Special Reading Room Service. In this service, one librarian can consult with a user on their literature search. In addition, librarians can use the results of this analysis to provide information to meet users’ needs, especially those in postgraduate programs.\n\nSubject\n\nThe results of the multivariate analysis show a significant relationship between the subject and the topic chosen. In addition, using the linear regression analysis that examined the relationship between the subject and the topic of publication, a linear regression model could be made to predict the topic of publication based on the subject. This offers another of the benefits of bibliometrics, namely that, according to Zipf’s Law, the analysis of the occurrence of words in documents can contribute to identifying index makers (Latief, 2014). The US National Library of Medicine (NLM) has implemented word occurrence analysis to aid in indexing. The NLM uses an algorithm with a text ranking approach to implement automatic medical subject heading (MeSH) indexing.\n\n\nConclusions\n\nThe development of the publication of UI students’ final assignments for 2011–2020 related to good health and well-being as a Sustainable Development Goal shows that SDG 3 has attracted significant research interest since 2019. Naturally, non-communicable diseases and mental health have been the most frequently studied topics. However, over time, other topics have begun to interest UI students, particularly access to universal health services.\n\nThe publication cluster mapping shows that UI student research related to SDG 3 has mostly focused on the promotive and preventative aspects of health problems. The most frequently studied subjects have been pregnant and breastfeeding women, children, adolescents, and industry or workplaces.\n\nHowever, many topics related to SDG 3 have not yet been widely studied by UI students, including traffic accidents, the abuse of narcotics and alcohol, and tobacco control. Therefore, by utilising data from the bibliometric analysis of the main research themes in each faculty, libraries can formulate collection promotion strategies related to SDG 3 topics and identify the collection topics to prioritise. The creation of a publication topic prediction model can also inspire librarians to develop a system that supports automatic subject indexing.\n\nBased on these results, the researcher offers the following suggestions. First, UI libraries need to coordinate with related units at the UI (the Directorate of Education and the Directorate of Information Systems and Technology) to create systems and policies that require students at all levels to upload their final assignment publications to the UI Library, especially students in doctoral programs and from faculties whose collection rate remains low. Second, UI Library collection metadata can be studied via bibliometric analysis to support collection development activities and library reference services. Therefore, librarians’ subject indexing activities must be accurate. After the subject indexing process, validation must also be performed to ensure data accuracy.", "appendix": "Data availability\n\nZenodo: bibliometricdata_sdgs3. https://doi.org/10.5281/zenodo.10336832 (Rahmi, 2023).\n\nThe project contains the following underlying data:\n\n- bibliometricdata_sdgs3.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\nThe authors are grateful to two student assistants from the Faculty of Public Health Sciences and the Faculty of Humanities for their significant contributions to the data labelling process. Due to confidentiality agreements, their names cannot be explicitly mentioned.\n\n\nReferences\n\nAmalia FA, Prasetyawan YY: Kajian Pemanfaatan Koleksi Jurnal Internasional UPT Perpustakaan Universitas Diponegoro melalui Perspektif Bibliometrik pada Tesis Sekolah Pascasarjana tahun 2018–2019 [Study of upt diponegoro university library utilization of international journal collections through a bibliometric perspective in postgraduate school thesis 2018-2019]. Jurnal Ilmu Perpustakaan dan Informasi. 2021; 6: 117–136.\n\nAnninos LN: Research performance evaluation: Some critical thoughts on standard bibliometric indicators. Stud. High. Educ. 2014; 39: 1542–1561. Publisher Full Text\n\nÅström F, Hansson J: How implementation of bibliometric practice affects the role of academic libraries. J. Librariansh. Inf. Sci. 2013; 45: 316–322. Publisher Full Text\n\nAulia ES, Rusli RP: Manfaat Kajian Bibliometrik Sebagai Penunjang Analisis Kebutuhan Kurikulum Program Studi Ilmu Perpustakaan dan Informasi [The benefits of bibliometric studies as a support for analyzing the curriculum needs of the library and information science study program]. Inov. Kurikulum. 2020; 17: 59–68. Publisher Full Text\n\nBelter CW, Kaske NK: Using bibliometrics to demonstrate the value of library journal collections. C&RL. 2016; 77: 410–422. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCorrall S, Kennan MA, Afzal W: Bibliometrics and research data management services: Emerging trends in library support for research. Libr. Trends. 2013; 61: 636–674. Publisher Full Text\n\nDa Costa BFC, Ramalho A, Gonçalves-Pinho M, et al.: Suicide mortality rate as a sustainable development goal (SDG): A bibliometric analysis. Psychiatry Q. 2020; 93: 15–26. PubMed Abstract \| Publisher Full Text\n\nDimisyqiyani E, Sedianingsih RAS, Azizah N: Analisis bibliometrik dan pemetaan sistem registrasi on line di rumah sakit [Bibliometric analysis and mapping of the online registration system in hospitals]. Int. J. Appl. Bus. Econ. Res. 2020; 4: 22–34.\n\nDing Y, Rousseau R, Wolfram D: Measuring scholarly impact: Methods and practice. Springer International Publishing; 2014. Reference Source\n\nDonthu N, Kumar S, Mukherjee D, et al.: How to conduct a bibliometric analysis: An overview and guidelines. J. Bus. Res. 2021; 133: 285–296. Publisher Full Text\n\nFatmawati E: Multi-Kompetensi Perpustakaan dalam Mendukung Pembangunan Nasional [Multi-competence of libraries in supporting national development]. Jurnal Perpustakaan Pertanian. 2018; 27: 1–6. Publisher Full Text\n\nField A: Discovering statistics using IBM SPSS Statistics. SAGE Publications; 2018. Reference Source\n\nFiliana A, Prabawati AG, Rini MNA, et al.: Perancangan Data Warehouse Perguruan Tinggi untuk Kinerja Penelitian dan Pengabdian kepada Masyarakat [Higher education data warehouse design for research performance and community service]. Jurnal Teknik Informatika dan Sistem Informasi. 2020; 6: 174–183. Publisher Full Text Reference Source\n\nGhanbari MK, Behzadifar M, Doshmangir L, et al.: Mapping research trends of universal health coverage from 1990 to 2019: Bibliometric analysis. JMIR Public Health Surveill. 2021; 7: e24569. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGrace A, Florence ON, Florence IA: Need and justification for the implementation of bibliometrics studies in library and information science schools curriculum in higher institutions in Nigeria. UNIZIK Journal of Research in Library and Information Science. 2019; 4: 110–117.\n\nHartini N, Fardana NA, Ariana AD, et al.: Stigma toward people with mental health problems in Indonesia. Psychol. Res. Behav. Manag. 2018; 11: 535–541. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHelfer T, Faeh D, Luijckx E, et al.: The Connection between Health Promotion, Prevention, and Psychosocial Health: An Innovative Action Model. Open Public Health J. 2020; 13(1): 850–855. Publisher Full Text\n\nHerrera-Calderon O, Yuli-Posadas RÁ, Peña-Rojas G, et al.: A bibliometric analysis of the scientific production related to “zero hunger” as a sustainable development goal: Trends of the pacific alliance towards 2030. Agriculture & Food Security. 2021; 10: 1–15. Publisher Full Text\n\nLatief KA: Bibliometrics dan Hukum-hukumnya: Sebuah pengantar. Dimensi metodologis ilmu sosial dan humaniora. Pustaka Larasan. 2014. Reference Source\n\nMaryatun M, Handayani W: Analisis Bibliometrik Penelitian Tugas Akhir Mahasiswa di Faculty Ekonomika dan Bisnis Universitas Gadjah Mada [Bibliometric Analysis of Student Final Project Research at the Faculty of Economics and Business, Gadjah Mada University]. Media Pustakawan. 2022; 29: 65–80. Publisher Full Text Reference Source\n\nMaula AW, Fuad A, Utarini A: Ten-years trend of dengue research in Indonesia and South-east Asian countries: A bibliometric analysis. Glob. Health Action. 2018; 11: 1504398. Publisher Full Text\n\nNworie J, Magnus U: Library collection, nature, types and uses in academic libraries. Library Use Companion and Study Skills. 2017; pp. 24–32. Reference Source\n\nPalozzi G, Schettini I, Chirico A: Enhancing the sustainable goal of access to healthcare: Findings from a literature review on telemedicine employment in rural areas. Sustainability. 2020; 12. Publisher Full Text\n\nPerpustakaan UI: Rencana Strategis Perpustakaan Universitas Indonesia Tahun 2015–2019 [University of Indonesia Library Strategic Plan for 2015–2019]. Perpustakaan UI; 2015.\n\nPerpustakaan UI: Profil perpustakaan UI. Universitas Indonesia Library; 2018. Reference Source\n\nPerpustakaan UI: Laporan Kinerja UPT Perpustakaan UI Triwulan I Tahun 2022 [UI Library UPT Performance Report for Quarter I of 2022]. Universitas Indonesia; 2022.\n\nPunnakitikashem P, Hallinger P: Bibliometric review of the knowledge base on healthcare management for sustainability, 1994–2018. Sustainability. 2019; 12: 205. Publisher Full Text\n\nRahmi R: bibliometricdata_sdgs3. [Data set]. Zenodo. 2023. Publisher Full Text\n\nRoemer RC, Borchardt R: Meaningful metrics: A 21st-century librarian’s guide to bibliometrics, altmetrics, and research impact. Association of College and Research Libraries; 2015. Reference Source\n\nRufaidah VW, Iskak PI: Peran pusat perpustakaan dan penyebaran teknologi pertanian (pustaka) kementan dalam tujuan pembangunan berkelanjutan [The role of the central library and dissemination of agricultural technology (library) of the Ministry of Agriculture in the goal of sustainable development]. Journal of Documentation and Information Science. 2019; 3: 45–56.\n\nSciVal.com: Publications by subject area Universitas Indonesia 2018 to 2021. Elsevier; 2021. Reference Source\n\nSebba AK, Fitriana V, Cahyadin.: Tuberculosis research in ASEAN countries: A bibliometric analysis. Berita Kedokteran Masyarakat. 2017; 33. Publisher Full Text\n\nShiel C, Smith N, Cantarello E: Aligning campus strategy with the SDGs: An institutional case study.Filho WL, et al., editors. Universities as living labs for sustainable development. Springer; 2020; pp. 11–27. Publisher Full Text\n\nSuprapto N, Qosyim A: Mobile library in Indonesian villages: A form of sustainable development goal in education (SDG 4). Libr. Philos. Pract. 2022; 1–12.\n\nSweileh WM: Bibliometric analysis of scientific publications on “sustainable development goals” with emphasis on “good health and well-being” goal (2015–2019). Glob. Health. 2020; 16(68): 68. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTbaishat D: Jordanian public libraries in relation to achieving SDGs: Shoman Library in action. Public Library Quarterly. 2021; 40: 125–143. Publisher Full Text\n\nTimes Higher Education: THE impact rankings methodology 2022 version 1.3. THE World Universities; 2022. Reference Source\n\nTupan T: Peta perkembangan penelitian pemanfaatan repositori institusi menuju Open Access: Studi bibliometrik dengan VOSViewer [Map of the development of institutional repository utilization research towards open access: A bibliometric study with VOSViewer]. Khizanah Al-Hikmah: Jurnal Ilmu Perpustakaan, Informasi, dan Kearsipan. 2016; 4: 104–117. Publisher Full Text\n\nTyasmara NC, Susetyo-Salim TA: Access policy of UIANA Collection in the Library Universitas Indonesia. Adv. Sci. Lett. 2018; 24: 5012–5014. Publisher Full Text\n\nUI GreenMetric WUR: Guideline UI GreenMetric world university rankings 2022: Collective actions for transforming sustainable universities in the post-pandemic time. Universitas Indonesia; 2022. Reference Source\n\nWarrens MJ: Five ways to look at Cohen’s kappa. Journal of Psychology & Psychotherapy. 2015; 05(1). Publisher Full Text" }	[ { "id": "262171", "date": "12 Jun 2024", "name": "Carlos Vílchez-Román", "expertise": [ "Reviewer Expertise Bibliometric and scientometric 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\nYour Report\nPlease provide a full report, expanding on your answers to the questions above. In particular, if you answered “no” or “partly” to any of the questions, please give constructive and specific details as to how the authors can address any criticisms. Please indicate clearly which points must be addressed to make the article scientifically sound. (50 words min.)\nThe study examines the relationship between Universitas Indonesia (UI)'s undergraduate and postgraduate students' academic output and the 13 sustainable development goal (SDG)3 targets: good health and well-being. The authors provide a detailed description of the results using univariate and multivariate statistics. However, three primary issues require a significant revision: breadth of literature review, alignment between research question and design, and results discussion confronting Indonesian health indicators.\nBreadth of literature review The authors conducted an extensive literature review of bibliometric studies that explored the relationship between research output and SDG. Therefore, the revision of the Introduction could be enriched if the authors examined three state-of-the-art papers that also discuss the alignment between academic output and development agendas [1-3]. [1] Yegros-Yegros, A. et al. (2020). Exploring why global health need are unmet by research efforts: the potential influences of geography, industry and publication incentives. [2] Ciarli, T., Ed. (2022). Changing directions: Steering science, technology and innovation towards the SDGs. [3] Kumar, A. et al. (2024). Priorities of health research in India: evidence of misalignment between research outputs and disease burden.\nAlignment between research question and design/analytical strategy The authors conducted a detailed descriptive analysis, but it needs to be clarified which research question is guiding this study. In other words, it is unknown which is the knowledge gap they identified and tried to provide an answer.\nIt is important to remember that the research problem, usually (but not necessarily) expressed as a question, precedes the research objective. Once the authors elaborate on the research question, they should explain why they selected the multinomial regression analysis to explore the relationships among the selected variables.\nResults discussion confronting Indonesian health indicators. According to the abstract, \"This research introduces a pioneering examination of SDG-associated academic undertakings, encompassing undergraduate, master's, and doctoral research projects on an expansive scale\". That explains the initial approach to the results discussion.\nHowever, the analyses focused on SDG 3, so it is pretty surprising that they did not discuss the results considering the most severe diseases in Indonesia. In this sense, the authors should emphasize the discussion of their results confronting Indonesia's health indicators for the primary causes of death [4]: cardiovascular disease (35%), cancer (12%), chronic respiratory disease (6, and diabetes (6%). Ref [4]\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": "349720", "date": "27 Dec 2024", "name": "Jian Dai", "expertise": [ "Reviewer Expertise educational 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\nThis paper performs a bibliometric analysis of Universitas Indonesia's student projects addressing SDG 3. The study is valuable, but there are still some issues that need improvement.\n1. The Background section needs to be reorganized. The authors should first indicate the research background and motivation, rather than introducing the bibliometric analysis methods first.\n2. The Kappa value is 0.52, so how do you deal with those inconsistent coding results? This process needs to be detailed.\n3. The limitations of this study need to be discussed.\nI hope the authors find my suggestions helpful.\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/13-7
https://f1000research.com/articles/11-167/v1	10 Feb 22	{ "type": "Research Article", "title": "Perceived stress, sources of stress and coping strategies among undergraduate medical students of Nepal: a cross-sectional study", "authors": [ "Ujjawal Paudel", "Anima Parajuli", "Rashmi Shrestha", "Shivanee Kumari", "Saroj Adhikari Yadav", "Kedar Marahatta", "Ujjawal Paudel", "Anima Parajuli", "Rashmi Shrestha", "Shivanee Kumari", "Kedar Marahatta" ], "abstract": "Background: Medical students are subjected to various stressors throughout their training, which has a considerable impact on their physical and mental health. Some students have positive ways of coping, while others take to maladaptive coping measures. This study aims to assess severity, sources of stress, and coping strategies among medical students of a non-Western low-income country from South Asia. Methods: A self-administered questionnaire-based cross-sectional study was carried out. Demographic variables were collected and stress level was assessed using PSS 14 (Perceived Stress Scale 14). The sources of stress were assessed using MSSQ (Medical Student Stressor Questionnaire) and coping strategies were evaluated using the Brief-Coping Orientation to Problems Experienced 28. Results: The response rate was 95%. The mean PSS score was 27.85. Overall, 55% of students were stressed (male 52%, female 60%), the difference among gender was not significant. Basic science students perceived higher levels of stress than clinical clerkship students. Academic related stressors caused higher stress, whereas other variables caused moderate stress. The major stressors were examinations, inadequate time to study, poor marks, extensive amount of learning content, and the need to performing well in the exam. The five most common coping strategies used were active coping, acceptance, planning, self-distraction, and instrumental support. The least common coping mechanism was substance use. All MSSQ domains positively correlated with the total PSS score. Students with higher PSS scores were likely to use behavioral disengagement, venting, and self-blame as the primary coping strategies. Conclusions: Stress level among the medical students is high and mainly in relation to academia. Inadequate guidance from teachers contributed significantly. Stressed students were likely to use maladaptive coping strategies. Strategies to enhance teacher-student communication and adaptive coping measures should be implemented. Further studies should be done to evaluate the effects of stress on the academic outcomes of students.", "keywords": [ "stress", "coping stress", "medical students", "medical education", "mental health." ], "content": "Introduction\n\nStress is a state of mental or emotional strain or tension resulting from adverse or demanding circumstances.1 Medical students are subjected to various kinds of stressors throughout their training. A systematic review by Liselotte et al. showed overall psychological distress consistently higher in medical students than in the general population.2\n\nStudies that have examined sources of stress among medical students generally point to three key areas: academic pressures, social issues, and financial problems.3 The sources of stress and the various ways in which students cope with them are of vital importance as they can have a considerable impact on their physical and mental health.4 Some students have positive ways of coping with stressors like positive reframing, planning, and recreational activities like sports and music,5 while others may opt for maladaptive coping measures like substance abuse.6 Similarly, a study among medical students in North India, which is quite similar to Nepal, showed significant stress among medical students. Worrying about the future was rated the highest by the final year students, faculty shortcomings and insufficient feedback were rated highest by the second-year students, and financial concerns the highest by the first-year students.7 Previous studies investigating the link between stress and academic performance in medical students have shown a negative correlation between the high level of stress and academic performance.8\n\nOnly a few studies have been done in medical schools in Nepal regarding the psychological distress among medical students. A study was done in Manipal College of Medical Science, Pokhara, Nepal, using the General Health Questionnaire (GHQ). It showed a prevalence of psychological morbidity among medical students of 20.9%.9 The most common causes of stress identified by the students were quality of food in mess, dissatisfaction with lecture classes, and vastness of academic curriculum, and frequency of examinations.9 Another study done in Universal College of Medical Sciences, Bhairahawa, Nepal showed that stress during exams and preparation phase stood out as the stressful period among medical students.10 A high prevalence of depression, anxiety, and burnout was found among medical students and residents in another study in Nepal, the academic-related factors being the main stressor identified in the study.11\n\nThere has been no study on psychological stress among medical students in Patan Academy of Health Sciences (PAHS), a medical school adopting innovative teaching-learning approaches. Therefore, we wanted to identify the severity of stress, recognize the sources of stress and explore the coping strategies used, among undergraduate medical students of PAHS, Kathmandu, Nepal.\n\n\nMethods\n\nThis is a cross-sectional study done in 15 November 2019 to 14 December 2019 among undergraduate medical students of PAHS, a government medical school of a non-Western low-income country, Nepal. PAHS has adopted several new and innovative approaches in the teaching and learning of medicine like problem-based learning in the first two years of integrated basic science study, and the clinical presentation curriculum in third to final years of clinical clerkship.\n\nThe study is based on self-administered questionnaires. Written informed consent was obtained from the participants. All medical students of the four batches (two basic sciences and two clinical clerkship) currently in School of Medicine of PAHS were included in this study with their informed consent. Consenting students were asked to fill out the questionnaire together in class. Students not giving consent and students among the researcher team, were excluded from the study. A total of 231 students from four batches were available to be included in this study.\n\nPrevious estimates of the prevalence of stress among medical students in Nepal from similar tools are not available. Thus, we assumed a prevalence of 50% and took a 10% margin of error and a 5% level of significance. After adding a 10% non-response rate, the sample size came out to be 106. Two-stage stratified random sampling was done based on the year of study and gender followed by the lottery method for each strata this reduced the number of students included from the maximum 231 to 106. Of the 106, 101 completed the questionnaire and gave consent. Students were asked to complete a set of questionnaires consisting of four parts: Demographics, Medical Student Stressor Questionnaire (MSSQ),12 Perceived Stress Scale (PSS),13 and Brief-COPE (Coping Orientation to Problems Experienced).14 Ethical approval was taken from the institutional research committee of the Patan Academy of Health Sciences [Ref no: std1506111071] and research was carried out per relevant guidelines and regulations.15\n\nDemographic questionnaire\n\nDemographics questionnaire was developed. It comprised of questions about age, gender, address, year of study, do they stay in PAHS hostel or not, etc. These questionnaires were compiled in Microsoft Word (Microsoft Office Professional Plus 2019 version 2112) and discussed in the research group and reviewed by the research advisors to establish content validity. Finalized questionnaire were distributed among all respondents.\n\nPerceived Stress Scale questionnaire\n\nPerceived stress was measured using the PSS-14.13 PSS-14 is a pretested and pre-validated questionnaire. This questionnaire comprises 14 questions with responses varying for each item ranging from never, almost never, sometimes, fairly often, and very often (labeled as 0-4 respectively) based on the occurrence during one month prior to the survey. It is designed to assess the degree to which participants evaluate the stress levels in their lives over the previous month.13 PSS-14 scores were obtained by reversing the scores on positive items, i.e., 0 = 4, 1 = 3, 2 = 2, and so on, and then summing across all 14 items. The scale yields a single score where high scores meant higher levels of stress and lower scores meant lower levels of stress. The PSS-14 has a range of scores from 0 to 56. A cut-off value of 28 (i.e., 50%) was used, and the scores were labeled as stressed and not stressed when above or below this cut-off value, respectively. This cut-off value was selected from a similar study done in Pakistan.5\n\nMedical Student Stress questionnaire\n\nThe MSSQ was used to assess sources of stress and their severity.12,16 MSSQ as well is a pretested and pre-validated questionnaire. It comprises 40 questions. Respondents were asked to rate this set of forty items or stressors using a scale of 0 to 4 where 0 = causing no stress at all, 1 = causing mild stress, 2 = causing moderate stress, 3 = causing high stress, and 4 = causing severe stress. Examples of stressors are examinations, heavy workload, lack of time to review what has been learned, etc.\n\nThe MSSQ grouped stressors in six domains based on an underlying theme.12 The six domains are: 1. Academic Related stressors (ARS), 2. Intrapersonal and interpersonal Related Stressors (IRS), 3. Teaching and Learning-related stressors (TLRS), 4. Social Related Stressors (SRS). 5. Drive and desire Related Stressors (DRS), and 6. Group Activities Related Stressors (GARS).12 Total scores in individual domains were calculated by using weighted means. Stressors with scores of 0 – 1.00, 1.01 – 2.00, 2.01 – 3.00, and 3.01 – 4.00 were graded as mild, moderate, high, and severe respectively.\n\nBrief-COPE questionnaire\n\nThe Brief-COPE-28 scale, a pretested pre-validated questionnaire, was used to assess coping strategies used by students in response to their stress.14 It contains 28 items and is rated on a four-point Likert scale; 1 = I haven't been doing this at all, 2 = I've been doing this a little bit, 3 = I've been doing this a medium amount, 4 = I've been doing this a lot. In total, this scale covers 14 dimensions. These are grouped into maladaptive coping strategies denial, self-distraction, behavioral disengagement, venting, self-blame, and substance use and adaptive coping strategies active coping, instrumental support, planning, acceptance, emotional support, humor, positive reframing, and religion.14\n\nA total of 106 students were randomly selected from the sample using two-stage stratified random sampling based on the year of study and gender followed by the lottery method for each strata. The selected students were given questionnaires with written instructions. Informed consent was taken from all the participants in written form. The questionnaire was distributed amongst students and the researchers collected the completed questionnaires.\n\nData were entered into Microsoft Excel (Microsoft Corporation, 2018, Microsoft Excel)(RRID: SCR_016137). It was analyzed using Statistical Package for Social Sciences (SPSS) 13.0 (SPSS Inc. Released 2005. SPSS for Windows, Version 13.0. Chicago) (RRID: SCR_002865). The mean score of perceived stress was calculated. The number and percentage of stressed cases were calculated according to demographic variables. Six different domains of MSSQ, i.e. ARS, IRS, TLRS, SRS, DRS and GARS, were calculated. Descriptive statistics were used to measure the severity of stressors. Spearman’s correlation was applied to test the correlation between perceived stress (PSS score) and coping strategies among students. The p-value<0.05 was considered significant.\n\n\nResults\n\nOut of 106 students, one didn’t give consent for the study and four didn’t complete the questionnaire. 101(95%) of respondents filled and submitted the questionnaire which was used for further analysis. The demographic characteristics of students are shown in Table 1. Since four of the students did not fill in the address on the questionnaire, they were omitted from the analysis of this question and the remaining 97 were used to analyze the address.29\n\nThe medical students at PAHS are from two different backgrounds: an academic science background where they must complete two years of study, and from a paramedic background where they must complete three years of study. The academic background of the students is taken in account for this study as shown in Table 1.\n\nAs shown in Table 2, among 101 students, 55 of them were stressed (when using a cut-off score of 28), while 46 of them were not stressed. Thus, the prevalence of stress in our study was found to be 55%. Female students were more stressed compared to their male counterparts (60% vs 52%) but the difference was not statistically significant (p < 0.05).\n\nSimilarly, there was less stress in senior years. However, the difference among different years was not significant (p > 0.05). But, as shown in Table 2, on regrouping students by the phase of study, students in basic science years were significantly more stressed compared to students in clinical clerkship (66.7% vs 42%, with p-value 0.017, i.e. < 0.05).\n\nIn total, 33 (52.4%) students staying at the PAHS hostel were stressed, while only 22 (57.9%) students not staying in the hostel were stressed. Despite this the difference was not statistically significant (p = 0.10). There was also no significant difference in the presence of stress among students from within or outside Kathmandu Valley (p > 0.05).\n\nThe mean and standard deviation of stressors score are shown in Table 3 below.\n\nARS scores were significant amongst both male and female students as seen in Table 3. SRS was higher among males while other stressors were higher among females. Apart from IRS scores, other stressors were higher in those students staying outside the hostel. However, none of these differences were statistically significant.\n\nThe top ten stressors with their mean values are presented in Table 4. Eight of the top ten stressors are ARS. The most common stressors are test examinations, lack of time to review what has been learned, getting poor marks, an extensive amount of content to be learned, and the need to do well (self-expectation).\n\nARS scores (2.22 vs. 2.14) and GRS scores (1.82 vs. 1.61) were higher in basic science students but other domains were higher in clinical clerkship. Stressors were highest in basic science first-year students while lowest in clinical clerkship second-year students. However, the differences were not statistically significant.\n\nThe five most common coping strategies used by students during the event of stress were active coping, acceptance, planning, self-distraction, and instrumental support. The least common coping mechanism was substance use. The mean scores of coping mechanisms used by students are presented in Table 5.\n\nThere were significant differences in coping strategies used according to gender, phase of the study i.e. basic science or clinical clerkship (p < 0.05), location of accommodation i.e. hostel or outside hostel (p < 0.05), and stress. Male students appear to cope with stress by substance/alcohol use (p < 0.05). The strategies that were significant among different groups of respondents are presented in Table 6.\n\n* Student’s Independent Sample T-Test.\n\n** One-Way ANOVA.\n\n\nDiscussion\n\nWe found that 55% of the medical students demonstrated stress above the cut-off value. The prevalence of stress is more among the initial first two years (basic science years) compared to the latter part of the clinical years (66.7% vs. 42.0%). Students reported academic and related stressors as the major sources of stress. In addition, the primary coping strategies used by students during stressful events were active coping, acceptance, planning, self-distraction, and instrumental support. Male students were also using alcohol and substances higher than females (p < 0.01) to cope with a stressful situation.\n\nA similar study from Pakistan, which also used PSS to evaluate stress, reported a higher mean PSS score when compared to our study (30.84, SD = 7.01 vs. 27.85 SD = 6.25).5 In a similar study in Manipal, which used GHQ to assess stress, psychological morbidity was 20.9% and it was higher among basic science students.9 A study from Agha Khan University reported that over 90% of the students felt stressed at one time or another during their course.17 Another study from India reported that 73% of the students had perceived stress at one time or another during their medical training.18 Saipanish reported that 61.4% of students in Thai Medical School had experienced some degree of stress as measured by the Thai stress test.19 The amount and severity of stress experienced by medical students appears to vary according to their curriculum, settings of medical schools, and more importantly, the type of psychometric tests used.\n\nIn this study female students perceived a higher level of stress as compared to male students however, the difference was not statistically significant. Similarly another study by Cohen et al. in the USA showed no significant difference in stress between male and female students.13 However, a similar study in Pakistan reported significantly higher stress among female students compared to their male counterparts.5\n\nMore students in basic science years were stressed as compared to clinical years (66.7% vs. 42.0%) which was statistically significant (p = 0.017). It might be because they have adapted to the system and setting of PAHS. A study done at Manipal, another Nepali medical school, showed the highest level of stress in the first-year basic science students. At PAHS, stress levels decreased with the increase in the year of study. At Manipal, however, there was less stress in the second year of basic science but higher stress in the clinical years of study.9 Similar results were reported in studies from Pakistan, Thailand, and India.13,17,18 We do not have tools to evaluate this discrepancy, but a plausible explanation might be different academic settings between these institutions.\n\nA study that evaluated the correlation between stress and academic performance in the first two years of medical school showed a negative correlation between stress and academic performance.8 Though we did not evaluate academic performance in our study, we expect it might be similar here as well.\n\nThe mean score of MSSQ at our institution was 1.88 (moderate stress) whereas it was 3.9 (severe stress) at Taibah University, Saudi Arabia.20 The major source of high stress among the students in our studies was ARS, which was similar to a study done in Xavier University School of Medicine, Netherlands, that showed high ARS and GRS.21 In Saudi Arabia, ARS and IRS were high.20 Though the overall TLRS and IRS score caused moderate stress, lack of guidance from teachers and verbal abuse from teachers caused high stress in PAHS. The major stressors at the Pakistani Medical School were also of the academic and psychosocial domains.5\n\nOur study showed that academic stress is higher among basic science students. However, other studies done in Pakistan, Saudi Arabia, Netherlands, and Manipal have shown that academic stress is higher in the students in their clinical years.3,4,9,20\n\nThis study shows test examinations, lack of time to review what has been learned, and, a large amount of content as main academic stressors. This was similar to a study done in Manipal, where the most common causes of stress were dissatisfaction with lecture classes, the vastness of the academic curriculum, and the frequency of examinations.9 A study conducted in the United Arab Emirates (UAE) also showed that the major stressors among the students were the frequency of examinations, time management, and academic workload.22\n\nCoping strategies are behavioral and psychological efforts that apply to master, tolerate, reduce, or minimize stressful events.23 The primary coping strategies used by students during stressful events were active coping, acceptance, planning, self-distraction, and instrumental support. Students from Manipal also used similar coping strategies along with positive reframing and emotional support.9 Similar studies from UAE, India, Netherlands, and UK also showed similar results.21–25 Although the coping strategies were different among males and females, the only significant difference in strategy was substance use, which was higher in males (p < 0.01): a finding similar to a study in Glasgow University, UK.25 In India, another statistically significant difference was observed, females used meditation as a coping strategy.24\n\nWe saw that stressed students used venting and self-blame, similar to the study done in Manipal.9 The medical students from Brazil who were stressed used escape-avoidance tactics more than non-stressed students.26 Pakistani post graduate students who were using maladaptive coping styles were more likely to be stressed.27 However, it is not clear whether there is a cause-effect relation between avoidant coping strategies and stress.\n\nSubstance use was the least used coping mechanism by students, which may have been under-reported despite confidentiality and anonymity of the response was assured. There were low incidences of alcohol/substance use in Manipal as well as in Pakistan, which may be due to the social stigmata associated with alcohol use in these societies.9,27 But studies from the UK suggest the use of alcohol, tobacco, and drugs as common strategies.28,29 The cultural variation between the two societies may have contributed to the difference.\n\nAll stressor domains of MSSQ and total MSSQ positively correlated with the PSS score, which was significant, except for DRS, as shown in Table 3. It suggests that students with more stressors in (most of the domains) MSSQ are also likely to perceive more stress. The correlation was moderate between total PSS score and ARS, GRS, and total MSSQ while it was weak within total PSS, IRS, SRS, DRS, and TLRS.\n\nOur study also showed that students with high stress were likely to have maladaptive coping strategies. The correlation was moderate. Though the difference was not statistically significant, the total PSS scores negatively correlated with adaptive coping strategies. This indicates that students might have decreased stress due to adaptive coping.\n\nOur findings may not be generalisable to other medical schools in Nepal since PAHS has a unique teaching-learning strategy. The cross-sectional design of our study is another limitation since associations could not be calculated. Prospective studies are necessary to study the associations between stressors and the incidence of stress. Since we did not evaluate the level of stress with academic performance, we cannot comment on the association between the two. The questionnaires were used as it is in the English language, potentially causing issues with students as this may not be their first language. The systematic translation, cultural validation, and adaptation in the local language of Nepalese medical students was not done.\n\n\nConclusion\n\nStress level among PAHS students was high and mainly academic. Further studies should be done to evaluate the effects of stress on the academic outcomes of students. The stress level was highest among the first-year students. This has a strong implication to provide a support mechanism for the first-year students. Strategies to enhance teacher-student communication could be implemented. Since stressed students were more likely to use maladaptive coping strategies like behavioral disengagement, substance use, venting, denial, and self-blame, measures should be taken to support students to adopt a more positive and healthy coping approach.\n\n\nData availability\n\nFigshare: Underlying data of “Perceived Stress, Sources of Stress and Coping Strategies among Undergraduate Medical Students of Nepal”. https://doi.org/10.6084/m9.figshare.c.5757833.v1.29\n\nThe project contains the following underlying data:\n\n- Raw data of Stress.xlsx\n\nFigshare: Underlying data of “Perceived Stress, Sources of Stress and Coping Strategies among Undergraduate Medical Students of Nepal”. https://doi.org/10.6084/m9.figshare.c.5757833.v1.29\n\nThe project contains the following extended data:\n\n- Questionnaire of Stress.docx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nEthics approval and consent to participate\n\nThis study was approved by the Institutional Review Committee (Ethical Committee) of Patan Academy of Health Sciences (PAHS), Kathmandu, Nepal with ref no: std1506111071. Written informed consent was obtained from all participants.\n\n\nConsent for publication\n\nWritten informed consent was obtained from the participants.\n\n\nAuthors' contributions\n\nUP, AP, RS, and SK first planned conception and designed this research. UP, AP, RS, and SK did the data collection. All six authors, UP, AP, RS, SK, SAY, and KM worked for data analysis and interpretation. UP, AP, RS, and SK wrote the first draft of the manuscript. SAY and KM did further revision and editing of the manuscript. All six authors, SAY, SP, UP, AP, RS, SK, and KM critically revised the article. And final approval of the version to be published was also done by all six authors.", "appendix": "Acknowledgments\n\nWe would like to acknowledge the faculties of the Department of Community Health Science for helping us and mentoring throughout the conduct of this research. A sincere thanks go to Prof. (Associate) Shital Bhandary for his supervision and guidance on data analysis. We would like to acknowledge all our participants with much appreciation for giving their valuable time for filling up the questionnaires.\n\n\nReferences\n\nStress [Def. 1]: Oxford Dictionary Online.n.d. Retrieved August 30, 2015. Reference Source\n\nDyrbye LN, Thomas MR, Shanafelt TD: Systematic Review of Depression, Anxiety, and Other Indicators of Psychological Distress Among U.S. and Canadian Medical Students. Acad. Med. 2006; 81: 354–373. PubMed Abstract \| Publisher Full Text\n\nVitaliano PP, Russo J, Carr JE, et al.: Medical school pressures and their relationship to anxiety. J. Nerv. Ment. Dis. 1984; 172: 730–736. Publisher Full Text\n\nSilver HK, Glicken AD: Medical student abuse. Incidence, severity, and significance. JAMA 1990; 263: 527–532. Publisher Full Text\n\nShah M, Hasan S, Malik S: Sreeramareddy CT: Perceived stress, sources and severity of stress among medical undergraduates in a Pakistani medical school. BMC Med. Educ. 2010 [cited 2015 Feb 10]; 10(1): 2. PubMed Abstract \| Publisher Full Text Reference Source\n\nGuthrie EA, Black D, Shaw CM, et al.: Embarking upon a medical career: psychological morbidity in first-year medical students. Med. Educ. 1995; 29: 337–341. PubMed Abstract \| Publisher Full Text\n\nGarg K, Agarwal M, Dalal PK: Stress among medical students: A cross-sectional study from a North Indian Medical University. Indian J. Psychiatry 2017 Oct-Dec; 59(4): 502–504. PubMed Abstract \| , PubMed Abstract \| Publisher Full Text\n\nStewart SM, Lam TH, Betson CL, et al.: A prospective analysis of stress and academic performance in the first two years of medical school. Med. Educ. 1999 Apr; 33(4): 243–250. Publisher Full Text\n\nSreeramareddy CT, Shankar PR, Binu VS, et al.: Psychological morbidity, sources of stress and coping strategies among undergraduate medical students of Nepal. BMC Med. Educ. 2007; 7: 26. PubMed Abstract \| Publisher Full Text\n\nBali H, Rai V, Khanduri N, et al.: Perceived Stress and Stressors among Medical and Dental Students of Bhairhawa, Nepal: A Descriptive Cross-sectional Study. JNMA J. Nepal Med. Assoc. 2020 Jun 30; 58(226): 383–389. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPokhrel NB, Khadayat R, Tulachan P: Depression, anxiety, and burnout among medical students and residents of a medical school in Nepal: a cross-sectional study. BMC Psychiatry 2020 Jun 15; 20(1): 298. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYusoff MSB: A Confirmatory Factor Analysis Study on the Medical Student Stressor Questionnaire among Malaysian medical students. Educ Med J. 2011; 3(1): e44–e53. Publisher Full Text\n\nCohen S, Kamarck T, Mermelstein R: A global measure of perceived stress. J. Health Soc. Behav. 1983; 24: 385–396. Publisher Full Text\n\nCarver CS: You want to measure coping but your protocol too long: consider the Brief COPE. Int. J. Behav. Med. 1997; 4(1): 92–100. PubMed Abstract \| Publisher Full Text\n\nInstitutional Review Committee (IRC) of Patan Academy of Health Sciences (PAHS). Reference Source\n\nYusoff MSB: A multicenter study on validity of the Medical Student Stressor Questionnaire (MSSQ). Intern. Med. J. 2011; 18(1): 14–18.\n\nShaikh BT, Kahloon A, Kazmi M, et al.: Students, stress and coping strategies: a case of Pakistani medical school. Educ. Health (Abingdon) 2004; 17: 346–353. PubMed Abstract \| Publisher Full Text\n\nSupe AN: A study of stress in medical students at Seth G.S. Medical College. J. Postgrad. Med. 1998; 44: 1–6. PubMed Abstract\n\nSaipanish R: Stress among medical students in a Thai medical school. Med. Teach. 2003 Sep; 25(5): 502–506. PubMed Abstract \| Publisher Full Text\n\nKholoud AH: Prevalence of Stressors among Female Medical Students Taibah University. Journal of Taibah University 2010 [cited 2015 August 26]; 5(2): A8. Publisher Full Text Reference Source\n\nShankar PR, Balasubramanium R, Ramireddy R, et al.: Stress and Coping Strategies among Premedical and Undergraduate Basic Science Medical Students in a Caribbean Medical School. Education in medicine 2014 December; 6(4). Publisher Full Text Reference Source\n\nGomathi KG, Ahmed S, Sreedharan J: Causes of stress and coping strategies adopted by undergraduate health professions students in a university in the United Arab Emirates. Sultan Qaboos Univ. Med. J. 2013; 13: 437–441. PubMed Abstract\n\nCoping Strategies: California: MacArthur Research Network on Socioeconomic Status and Health.1998 [cited 30th August 2015]. Reference Source\n\nPratap SS, Acharya A, Deepak RS: Study on stress among undergraduate students of a medical college in coastal Andhra Pradesh. JEMDS. 2013 April; 2(13): 2043–2049. Publisher Full Text\n\nMofat KJ, McConnachie A, Ross S, et al.: First-year medical student stress and coping in a problem-based learning medical curriculum. Med. Educ. 2004 May; 38(5): 482–491. PubMed Abstract \| Publisher Full Text\n\nBassols AMS, et al.: Stress and coping in a sample of medical students. Arch. Clin. Psychiatry. 2015; 42(1): 1–5. Publisher Full Text\n\nKasi PM: Studying the association between postgraduate trainees’ work hours, stress and the use of maladaptive coping strategies. J. Ayub. Med. Coll. 2007; 19(3).\n\nAshton CH, Kamali F: Personality, lifestyles, alcohol and drug consumption in a sample of British medical students. Med. Educ. 1995; 29: 187–192. PubMed Abstract \| Publisher Full Text\n\nChapman JEG, Yu K, White PD: A follow-up survey of alcohol consumption and knowledge in medical students. Alcohol Alcohol. 2001 Nov-Dec; 36(6): 540–543. PubMed Abstract \| Publisher Full Text\n\nCohen S, Williamson G: Perceived stress in a probability sample of the United States. The Social Psychology of Health: Claremont Symposium on Applied Social Psychology Newbury Park, CA: Sage Spacapam S, Oskamp S.1988; 31–67.\n\nAdhikari Yadav S: Underlying data of “Perceived Stress, Sources of Stress and Coping Strategies among Undergraduate Medical Students of Nepal”.2021. Publisher Full Text" }	[ { "id": "147808", "date": "26 Aug 2022", "name": "Bijit Biswas", "expertise": [ "Reviewer Expertise Chronic Disease Epidemiology", "Mental Health", "Occupational Health" ], "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 was aimed at assessing severity, sources of stress, and coping strategies among medical students of a non-Western low-income country in South Asia. The article has several major issues, especially in the methodology.\nAbstract\nIn the abstract please avoid terms like \"non-Western low-income country from South Asia\", be specific (i.e, Nepal)\n\nPlease add statistical findings in the abstract (i.e, correlation coefficient with p values) along with text to enrich it.\nIntroduction:\n\nAvoid 2-3 sentence paragraphs\n\nNo previous study is not a sufficient rationale. Kindly state other causes.\n\nMethods:\nWhy was 50% prevalence assumed for sample size calculation? If no prior study on this topic in Nepal author may cite other studies conducted in the sub-continent or region for sample size calculation.\n\nKindly elaborate on 2 stages of stratified random sampling used in the study. preferably add a flowchart.\n\nIf 106 was the minimum sample size then how could statistical tests be done in a lower sample (i.e, 101)?\n\nReport validity and reliability measures used for the tools used in the study (i.e, Cronbach's alpha).\n\nWas the questionnaire administered in English or the local language? If local language authors had to prevalidate translation before using them for the study.\n\nStatistical analysis portion did not state the exact tests used for the study in some cases (i.e, ANOVA)\n\nResults, Discussion, and Conclusion seem ok.\nReferences did not follow any particular style (i.e, Vancouver)\nThe article cited very old references (>10 years) which might not be relevant now.\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?\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": "10196", "date": "13 Sep 2023", "name": "Saroj Adhikari Yadav", "role": "Author Response", "response": "Dear Reviewer, We extend our sincere gratitude for your meticulous review of our manuscript. Your insightful feedback, alongside the contributions from fellow reviewers and our esteemed mentors, has been instrumental in enhancing the quality of our work. Addressing your suggestions, we have diligently incorporated the following revisions into the abstract: In response to your recommendation, we have included the specific name of the country in the abstract, thereby providing a more comprehensive contextualization of our study. We have pruned the abstract to exclude insignificant findings, ensuring that it now succinctly encapsulates the essence of our research. The logical merging of smaller paragraphs has been executed, enhancing the abstract's coherence and flow. We have redefined the rationale, offering readers a clearer understanding of the motivations behind our study. Furthermore, we have elaborated on the two stages of stratified random sampling, with the aim of facilitating easier comprehension for our readers. The administration of the questionnaire in English has been more comprehensively explained, providing essential context to our methodology. We have ensured that the appropriate statistical analysis methods employed are adequately mentioned. Regarding the prevalence assumption and sample size, we appreciate your consideration of the statistical norms of using 50% as a baseline, and the 10% non-response rate was added while calculating a sample size of 106. Following a thorough review of the biostatistical recommendations, we have decided to retain these aspects as they are. Once again, we would like to express our gratitude for your invaluable input, which has undoubtedly enriched our research. Your dedication to the peer review process is greatly appreciated. Best regards, Dr. Adhikari Yadav" } ] }, { "id": "168111", "date": "15 May 2023", "name": "Alicia Fournier", "expertise": [ "Reviewer Expertise Stress", "Emotion regulation", "Quality of life at work", "Interoception" ], "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 objective of this paper was to identify the perceived intensity of stress and its sources among medical students in Nepal and to identify coping strategies used to deal with this stress. This exploratory cross-sectional study was conducted on 101 Nepalese students and provides new information on the origin of perceived stress.\nAlthough it is important to take care of the health of medical students, this study remains too descriptive. The authors could have used moderation analyses to study the effects of coping strategies on the stressor/perceived stress factor relationship.\nRegarding the introduction, the authors do not sufficiently develop the innovative aspect of their study. For example, the authors highlight an innovative approach to teaching and learning in the school where the study was conducted. The authors should develop this approach and compare their results with schools in Nepal where there is no such teaching.\nAlso, the authors should further develop what the first cycle is. Throughout the paper, I did not understand the difference between students in basic sciences and those in clinical placement. It was only thanks to the first line of the discussion that I understood the difference. Additionally, mixing early and late cycle students in the analyses is not relevant. Stress factors are not the same, so wouldn't it be beneficial for the authors to compare these two groups of students throughout the paper? Furthermore, Table 1 confuses me: what is the context of the study? Are they all medical students or are there also paramedical students?\nMoreover, the statistical analyses are not sufficiently developed and well reported. For example, the analyses carried out to compare the participants are only mentioned in a table note. The authors should mention this in the statistical section. Additionally, they do not explain why they performed t-tests in some cases and ANOVAs in others. The result section needs to be rewritten. This part remains too vague and difficult to understand. There is a lack of a guiding thread so that the reader doesn't get lost. Descriptive tables of all variables are also missing.\nI also draw the authors' attention to the choice of the 28 cutoff for the PSS-14. I would like to remind them that this tool is not a diagnostic tool and that it would be preferable to use it as a continuous score. The cutoff of 28 is an arbitrary score used in papers but remains unvalidated. The authors should be cautious in their interpretation.\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? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "10198", "date": "13 Sep 2023", "name": "Saroj Adhikari Yadav", "role": "Author Response", "response": "Dear Reviewer, Thank you for your comprehensive review and invaluable feedback on our manuscript. We greatly appreciate your time and insights, which have been instrumental in refining our work. We are pleased to inform you that we have diligently addressed your suggestions and made the required edits to enhance the manuscript's quality and clarity. Here's a brief overview of how we incorporated your valuable input: Statistical Analysis: We have provided a more detailed explanation of the statistical analyses used in the methods section, including the rationale for choosing specific tests. Additionally, we've included a table summarizing the descriptive statistics of all variables. Introduction: We have expanded on the innovative aspects of our study, particularly the unique teaching and learning approach at the school where the research was conducted. We've also clarified the distinctions between students in basic sciences and those in clinical placement. Comparison of Student Groups: We now focus our analyses on early and late-cycle students, recognizing the differences in stress factors. This change will provide more meaningful insights. Your further recommendations can be meaningful for us when we plan our next research project. PSS-14 Cutoff: We acknowledge your concern regarding the PSS-14 cutoff and have revised our interpretation accordingly, emphasizing its use as a continuous score, though 50% cutoff is used in other similar articles as well and is a norm in biostat. These revisions, guided by your feedback, and our mentors' suggestions, have significantly improved the manuscript. We remain committed to ensuring that our research meets the highest standards, and your feedback has been invaluable in achieving this goal. We look forward to your continued evaluation and input as we work towards producing a more robust and insightful contribution to the field. Once again, thank you for your dedication to improving our research. Your efforts are sincerely appreciated. Warm regards, -Dr Adhikari Yadav" } ] } ]	1	https://f1000research.com/articles/11-167
https://f1000research.com/articles/13-2/v1	03 Jan 24	{ "type": "Systematic Review", "title": "The effectiveness of using escitalopram in pediatric generalized anxiety disorder and the methods to predict the treatment response: A systematic review and meta-analysis", "authors": [ "Mohammad J. J. Taha", "Warda A. Alrubasy", "Shams Khalid Sameer", "Bassam Essam", "Mohammad T. Abuawwad", "Ahmed M. Z. Hassan", "Mohamed R. Darwish", "Yousef E. Ahmed", "Mohamed A. Shebl", "Marwah E. Krikar", "Aliaa E. Gadallah", "Khalil AbdelKhalek", "Abdulqadir J. Nashwan", "Mohammad J. J. Taha", "Warda A. Alrubasy", "Shams Khalid Sameer", "Bassam Essam", "Mohammad T. Abuawwad", "Ahmed M. Z. Hassan", "Mohamed R. Darwish", "Yousef E. Ahmed", "Mohamed A. Shebl", "Marwah E. Krikar", "Aliaa E. Gadallah", "Khalil AbdelKhalek" ], "abstract": "Background Generalized Anxiety Disorder (GAD) affects approximately 10–15% of children and adolescents. Selective Serotonin Reuptake Inhibitors (SSRIs) are among the main treatment options. Escitalopram, an SSRI for adult anxiety, is being studied for pediatric use. Predicting the treatment response could optimize interventions. This systematic review aimed to understand the safety and efficacy of escitalopram in the treatment of pediatric GAD and to determine potential treatment response indicators.\n\nMethods Searches for randomized controlled trials (RCTs) on escitalopram’s effectiveness in pediatric GAD were conducted across six databases. Two reviewers selected the trials, extracted data, and evaluated the trial quality independently. A third reviewer resolved the discrepancies. Outcomes were presented as mean differences (MDs) with 95% confidence intervals (CIs), while the Cochrane risk of bias tool was used to gauge evidence quality.\n\nResults Five RCTs including 401 patients were analyzed. Escitalopram showed a greater reduction in The Pediatric Anxiety Rating Scale PARS score than placebo (MD -6.1, 95% CI [-8.75 to -3.44] (P = 0.09, I2 = 65%)). Multiple methods have been used to predict escitalopram treatment responses, such as reaction time changes, executive functions, and Amygdala Functional Connectivity, including the CYP2C19 metabolizer phenotype. The data indicated that neuroimaging was the most effective predictor of the treatment response.\n\nConclusion Escitalopram notably reduced PARS scores in pediatric patients with GAD. Neuroimaging, as a biomarker, is a valuable predictor of treatment response and provides insights into the neurological aspects of anxiety disorders, offering the potential for groundbreaking treatment advancements.", "keywords": [ "Generalized Anxiety Disorder", "Pediatrics", "Escitalopram", "Systematic review", "Meta-analysis" ], "content": "Introduction\n\nGeneralized Anxiety Disorder (GAD) is among the most prevalent mental health problems in children and adolescents, affecting an estimated 10%–15%.1 It is characterized by excessive uncontrollable worrying and anxiety that could affect the affected child’s or adolescent’s relationships, situations, and day-to-day performance. Moreover, evidence shows a stronger association between anxiety disorders and suicidal ideation in these age groups than in the unaffected groups.2 Despite all the aforementioned risks and the awareness of mental health that is constantly being raised among youth, a large proportion of young people with severe mental disorders have failed to seek and receive mental health care.3 Furthermore, little guidance in the diagnostic systems for the assessment of anxiety disorders to identify those in need of treatment makes the treatment of GAD challenging. In recent years, there has been a significant increase in the depth of understanding of the neurochemistry and functional neuroanatomy behind pediatric anxiety disorders, since data from functional neuroimaging suggest that pediatric patients with anxiety have functional abnormalities in the connections in the brain between the amygdala, medial prefrontal cortex, insula, ventrolateral prefrontal cortex, and dorsolateral prefrontal cortex.4 Selective serotonin reuptake inhibitors (SSRIs) are among the main treatment modalities used to treat pediatric anxiety, and are believed to improve the neurochemical and neuroanatomical changes that occur in GAD.5 Despite the availability of several other drug classes, SSRIs are considered the first-line management for pediatric anxiety.5,6 Evidence to detect the efficacy and safety of SSRIs in pediatrics with a generalized anxiety disorder is still growing. Escitalopram is an SSRI often used to treat anxiety in adults. The exact mechanism of escitalopram is not fully understood, but it is believed that escitalopram increases serotonin levels in the brain by blocking presynaptic neuronal uptake. This leads to the improvement and relief of anxiety symptoms.7 However, the use, efficacy, and safety of escitalopram for pediatric anxiety are still under investigation. Additionally, the prediction of an escitalopram treatment response could significantly improve clinical intervention because it can improve patient outcomes by lowering the risk of adverse reactions as well as by eliminating the need for repeated iterations of trial-and-error testing, which minimizes costs and saves time.8 There is a shortage in the amount of data that helps clinicians assess which patients will respond to escitalopram treatment. In this study, we aimed to address the knowledge gap regarding the efficacy and safety of escitalopram in the treatment of pediatric generalized anxiety disorder and identify the potential predictors of escitalopram treatment response.\n\n\nMethods\n\nThis study was submitted to PROSPERO (CRD42023395315). For context, search strategy, methods, outcomes, discussion, and conclusions, we adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) recommendations. Because all included data had previously been published, no ethical approval was required.\n\nThe following databases were searched from inception to February 4, 2023: PubMed, Scopus, Google Scholar, ClinicalTrials.gov, Web of Science, and the Cochrane Library. The search process was done for all databases on February 4 and again once the filtration process was completed to ensure that no new papers were missed. Moreover, manual searches were performed for important publications and references indicated in the included studies. Studies included in the analysis were limited to those conducted with human participants only. The search terms used are listed in Table 1.\n\nWe considered all randomized controlled trials of non-adult (age<18 years) (pediatric, adolescent, and child) patients with generalized anxiety disorder who were prescribed escitalopram and compared with placebo. At the title and abstract levels, two authors independently reviewed all the studies (B.E, M. R, and A.Z). Papers that met the criteria for inclusion in the title and abstract review or that could not be disqualified based on the information in the abstract were reviewed at the full-text level by two authors independently (S.K, W. A, A. Z, M.R., B. E and A.J). Conflicts in full-text review were resolved in a discussion and by a third reviewer (K.A).\n\nTo prevent bias, each publication was extracted separately by two randomized authors, and any disagreements were resolved by a third reviewer. The study design, participant country, participant age, escitalopram information, control information, outcomes, prediction methods and side effects were among the characteristics extracted from the studies. Every process followed the suggested techniques.9,10\n\nUsing standards modified from the Cochrane Collaboration guidelines, we evaluated the study quality based on the following criteria: (a) selection bias (random sequence generation and allocation concealment), (b) performance bias, (c) detection bias, (d) attrition bias, (e) reporting bias, and (f) other sources of potential bias, such as pharmaceutical and biotechnology sponsorship. Three or more components with a high risk of bias were of low quality, whereas four or more elements with a low risk of bias were of high quality.\n\nAccording to Egger et al.,11,12 publication bias assessment is unreliable for <10 pooled studies. Therefore, in the present review, we could not assess publication bias using the Egger’s test for funnel plot asymmetry.\n\nWe performed a sensitivity analysis to ensure that none of the included studies affected the results, and to examine whether the overall effect size was statistically robust. Heterogeneity was assessed by visual inspection of the forest plots and measured using I-square and Chi-square tests. The Chi-square test measures the existence of significant heterogeneity, whereas the I-square quantifies the magnitude of heterogeneity in the effect size. Heterogeneity was assessed and interpreted according to the recommendations of the Cochrane Handbook of Systematic Reviews.\n\n\nResults\n\nA PRISMA diagram (Figure 1) shows the details of the database search and screening processes. Following the retrieval of studies from the initial database search, 124 duplicate records were found and removed using EndNote X9 Software. The titles and abstracts of 305 records were screened against our eligibility criteria, yielding 55 records that warranted further full-text screening. Notably, the manual search did not yield any relevant studies. Fifty records were excluded; among these 50, three trials matched our eligibility criteria, but their results were not posted.13–15 The reasons for exclusion are provided in Figure 1. Finally, five studies were included in this paper. Three studies were fit for quantitative and qualitative analyses, while the other two papers were analyzed qualitatively. For quantitative analysis, the main outcome was the PARS score, while for qualitative analysis, the main outcome was the side effects. Finally, a total of 5 studies were included in the qualitative and quantitative synthesis of our review.\n\nThe outcome reporting bias was low risk in two of the included papers and high risk in three papers,16 which was evaluated as having a high risk of bias because the study did not report the effect of COVID-19 on anxiety and PARS scores in the results section despite mentioning it in the protocol, while in Refs. 16, 17 the change in γ-aminobutyric acid concentrations in the anterior cingulate was mentioned in the protocol and was not reported. The risk of bias (ROB) for all studies is illustrated in Figures 2 and 3. This study included 401 pediatric patients with GAD (a mean age of 13.5 years old). The baseline characteristics of patients are presented in Tables 2 and 3.\n\nThe overall standardized mean difference between the escitalopram and placebo groups regarding the improvement in anxiety symptoms favored escitalopram (MD-4.53, 95% Confidence Interval (CI) [-7.75, -1.31, P=0.00001], and the pooled studies were heterogonous (Heterogeneity: Chi2 = 2.83, I2= 99%) (Figure 4). To resolve heterogeneity, we conducted a sensitivity analysis in multiple scenarios, excluding one study in each scenario. Heterogeneity was best resolved by excluding AbbiVie (P=0.09, I2=65%). After removing the AbbiVie study from the meta-analysis model, the overall mean difference was still in favor of escitalopram over the placebo (Mean Difference (MD) -6.1, 95% CI [-8.75 to -3.44]; see (Figure 5)). According to the average baseline PARS score in the studies, the reduction was estimated to be nearly 35%.\n\nMany factors were reported to predict the treatment response to escitalopram in pediatric patients (see Table 4).\n\nAccording to Lu, et al.18 escitalopram showed a significant treatment-by-time interaction that significantly increased many connections in the brain, including functional amygdala-VLPFC connectivity, BLA-VLPFC connectivity, and left SFA and PCC, compared to placebo in adolescents with GAD.\n\nMoreover, Escitalopram’s influence on behavioral performance was investigated by Lu et al.,19 who discovered that patients using the drug had significantly faster reaction times than controls for all emotional stimulus types. The reaction times of the patients who received placebo showed no changes. They also examined amygdala-based functional connectivity during emotion processing and discovered that escitalopram reduced connectivity between the right amygdala and vmPFC and subgenual ACC during emotion processing from baseline to week 2, while enhancing connectivity between the left amygdala and right angular gyrus.\n\nEscitalopram was found to be superior to placebo in terms of response rate on the PARS, Clinical Global Impression of Severity (CGI-S), and Children’s Global Assessment Scale (CGAS). Escitalopram and placebo, however, had similar outcomes in terms of remission rates.16\n\nRegarding side effects and vital signs, Strawn reported that there were no significant differences between escitalopram and placebo. Despite their rarity, SAE, CSSRS, self-injurious behaviors, and suicide were the most serious events reported after escitalopram was prescribed to patients.17\n\n\nDiscussion\n\nThe main aim of this study was to investigate the overall effect of escitalopram in minors (age: <18 years) with generalized anxiety disorder and to summarize the elements that can be used to predict the treatment response to escitalopram in these patients. The most obvious finding of this study was based on the overall mean difference of the included studies, suggesting that escitalopram is superior to placebo in the treatment of GAD in pediatric and adolescent patients. As it is known that escitalopram is recommended for treatment of major depressive disorder (MDD), generalized anxiety disorder, panic disorder, and social anxiety disorder (SAD) in adults, its use in minors is still under study. The first randomized control trial assessing the effect of escitalopram versus placebo was conducted by Strawn et al., which took into consideration the results of the previous meta-analysis on the use of other SSRI with GAD in youth.\n\nThe results of our study were similar to those of the study conducted by Isolan et al., in which all the patients showed significant improvement during escitalopram treatment.21\n\nTwo previous meta-analyses have been conducted on the effect of other SSRIs in pediatric anxiety, and (have concluded) the significance of the statistical and clinical improvement of anxiety symptoms; however, to the best of our knowledge, this is the first systematic review and meta-analysis that exclusively summarizes the effect and treatment response prediction of escitalopram in pediatric GAD.22,23\n\nFive eligible studies involving 401 patients with GAD were analyzed. The largest study yielded different outcomes; escitalopram’s advantage over the placebo was a marginal (-1) reduction in PARS, compared to the other studies (-5 in Ref. 17; -8 in Ref. 18), which accounts for the heterogeneity of the analysis. Unfortunately, this study did not publish the participants’ PARS scores, either at baseline or post-treatment with escitalopram, making it difficult to conduct a comparison and discover the cause of the heterogeneity. However, the results of this study indicate that escitalopram is superior to the placebo.\n\nThe PARS is built upon a checklist of 50 anxiety symptoms (covering SAD, SoP, and GAD) and 7 global items that are administered to the child and parent(s) together. Each of these global items is rated on a six-point (0–5) scale and reflects the number of presenting symptoms, their frequency, the severity of the feelings of anxiety, the severity of physical symptoms of anxiety, overall avoidance of anxiety-provoking situations, and anxiety-related interference with functioning at and outside of the home.24 According to a study conducted by Caporino et al., a 35% reduction in the PARS score from the baseline is considered a treatment response, which is similar to the results of our study (average baseline was 17 and the MD was -6.25 Similar results were found in a previous meta-analysis conducted by Baldwin et al. on the effect of escitalopram on social anxiety disorder and found that escitalopram was associated with a 33% mean decrease from the baseline.26\n\nTreatment prediction in patients receiving escitalopram was performed using different methods to predict treatment response and avoid the trial-and-error mechanism that is usually performed in the treatment of anxiety spectrum disorders. SSRIs treatment outcome prediction was performed to understand the variability in response to different drugs among different patients, and the results were described as clinically useful. In our paper, prediction for escitalopram was done by four different methods, according to Strawn et al., anxiety patients who were identified as intermediate metabolizers of CYP2C19 are predicted to have a greater response in treatment as opposed to rapid metabolizers, this is attributed to higher plasma concentrations of the drug in intermediate metabolizers. The CYP2C19 enzyme is the main metabolizer of escitalopram, thereby altering the drug activity according to its levels in different individuals, which depends mainly on the genetic factor, as the CYP2C19 gene has high polymorphism, with over 30 alleles.27\n\nMoreover, similar results were found in a study discussing the variability of CYP2C19 in treatment outcomes among children treated with escitalopram.6\n\nIn addition, results in adults were also similar; according to a retrospective study discussing the effect of CYP2C19 on treatment with SSRI in adults, intermediate metabolizers were associated with generally higher efficacy of SSRIs, and the study also showed that these patients were more susceptible to adverse effects of escitalopram treatment.28\n\nThe second method reported is the role of functional neuroimaging (fMRI) in treatment prediction, and according to two papers conducted by Lu, et al., functional connectivity of the amygdala plays the main role. This could be explained by the fact that the amygdala has an intimate relationship with anxiety, as this brain center plays a crucial role in processing emotional stimuli such as fear and threat emotions. Most neurostructural studies on pediatric anxiety disorders suggest functional amygdala dysconnectivity as a biomarker for GAD.29 A higher connectivity between the amygdala and right angular gyrus in patients receiving escitalopram was demonstrated by Lu et al., which serves as a factor for the prediction of improvement in anxiety symptoms at the 8th week. Functional brain activity in different brain regions was also found to be a treatment predictor for SSRIs in a study conducted by Preuss et al.; SSRI responders were observed to have a higher activity of the posterior cingulate gyrus, medial prefrontal cortex, and the thalamus during emotional response. Baseline amygdala-vmPFC connectivity and escitalopram-induced increase in amygdala-angular gyrus connectivity at week 2 predicted the magnitude of subsequent improvement in anxiety symptoms.30\n\nThe use of amygdala connectivity has also been studied by Lu et al., but this time in conjunction with exposure to emotional stimuli. Functional MRI showed a change in functional connectivity between the left amygdala and the ventrolateral prefrontal cortex (VLPFC) from baseline to the 2nd week of treatment during emotional response, which predicted the improvement in treatment response in the 8th week, which could be useful in identifying escitalopram responders upon treatment initiation. The use of functional brain activity in different brain regions as a treatment predictor for SSRIs has been reported in several studies.30–33\n\nFurthermore, a study predicting escitalopram treatment response was performed by Harris et al., who explained that the change in functional connectivity between pretreatment and early treatment (second week) yielded significant results in the prediction of drug response.34\n\nThis suggests that pretreatment and early treatment of amygdala connectivity could be used as an acute finding that helps predict which patients are more likely to respond to treatment as early as two weeks after starting the treatment course.\n\nAdditionally, it is worth mentioning that these changes described in the amygdala during emotional processing may show some contrast in anxious adults since a study reported that the magnitude of treatment response by venlafaxine was predicted by lower amygdala activity at the baseline.35\n\nThe final method was the use of executive functions (EFs) as a predictor of treatment response, which is defined as a set of general-purpose control processes that are responsible for regulating behaviors and thoughts. It is linked to the prefrontal cortex, which is responsible for managing the dynamics of cognition and actions.36 Assessment of the various EF subfields in pediatric patients with GAD at baseline can predict their response to treatment, as in the study conducted by Baumel et al. found that youths who had significant impairment in planning, organization, and task completion at baseline showed greater improvement, while those with significant baseline impairment in emotional control and working memory showed less improvement. The improvement in executive functions is considered very important and goes beyond treatment prediction, as executive function deficits in patients with generalized anxiety may exhibit poor inhibition, set-switching deficits, impairment of working memory, difficulties in planning, and task completion, all of which can affect their academic performance and interpersonal relations.20,37 In addition, assessment of EF at baseline in anxious patients may be of great benefit for decision-making as some treatment options depend on certain executive functions; for example, anxiety and cognitive behavioral therapy CBT both require involvement of the executive functions as both require formation of future scenarios; anxiety formats a negative scenario while CBT formats a positive scenario, as such EF deficits may affect the CBT utility.38 Figure 6 illustrates the take-home message from this paper.\n\n\nConclusion\n\nReturning to the aim posed at the beginning of this study, escitalopram was shown to be effective in the treatment of GAD in pediatric and adolescent patients, and biomarkers such as functional connectivity, executive functions, and CYP2C19 enzyme activity were used to predict treatment response. This could help in decision-making and reduction of the repeated iterations of trial-and-error testing, which minimizes costs and saves time.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nPRISMA checklist for “The effectiveness of using escitalopram in pediatric generalized anxiety disorder and the methods to predict the treatment response: A systematic review and meta-analysis” https://doi.org/10.6084/m9.figshare.24660633.v1. 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\nBeesdo K, Knappe S, Pine DS: Anxiety and anxiety disorders in children and adolescents: developmental issues and implications for DSM-V. Psychiatr. Clin. 2009; 32(3): 483–524. Publisher Full Text\n\nGale CK, Millichamp J: Generalised anxiety disorder in children and adolescents. BMJ Clinical Evidence. 2016; 2016.\n\nMerikangas KR, et al.: Service utilization for lifetime mental disorders in US adolescents: results of the National Comorbidity Survey–Adolescent Supplement (NCS-A). J. Am. Acad. Child Adolesc. Psychiatry. 2011; 50(1): 32–45. Publisher Full Text\n\nStrawn JR, et al.: Neurobiology of pediatric anxiety disorders. Curr. Behav. Neurosci. Rep. 2014; 1: 154–160. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBushnell GA, et al.: Treating pediatric anxiety: Initial use of SSRIs and other anti-anxiety prescription medications. J. Clin. Psychiatry. 2018; 79(1): 16m11415. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAldrich SL, et al.: Influence of CYP2C19 metabolizer status on escitalopram/citalopram tolerability and response in youth with anxiety and depressive disorders. Front. Pharmacol. 2019; 10: 99. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLandy K, Rosani A, Estevez R: Escitalopram.2020.\n\nLequerré T, et al.: Predictors of treatment response in rheumatoid arthritis. Joint Bone Spine. 2019; 86(2): 151–158. Publisher Full Text\n\nCochrane Handbook for Systematic Reviews of Interventions. Wiley;\n\nWan X, et al.: Estimating the sample mean and standard deviation from the sample size, median, range and/or interquartile range. BMC Med. Res. Methodol. 14: 135. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEgger M, et al.: Bias in meta-analysis detected by a simple, graphical test. BMJ. 1997; 315(7109): 629–634. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTerrin N, et al.: Adjusting for publication bias in the presence of heterogeneity. Stat. Med. 2003; 22(13): 2113–2126. Publisher Full Text\n\nClinicalTrials.Gov: Acute and Long-Term Antidepressant Treatment Success in Adolescents With Anxiety (AtLAS-A) - Tabular View - ClinicalTrials.Gov. Accessed 6 Apr. 2023. Reference Source\n\nMD, J.S.P.-G.E.T.f.P.A.A.t.I.S.a.E.P.C.t.r., NCT04623099: 14 Feb. 2022. Reference SourceReference SourceReference Source\n\nStrawn JR, et al.: 2.9 A Multicenter Double-Blind, Placebo-Controlled Trial of Escitalopram in Children and Adolescents With Generalized Anxiety Disorder. J. Am. Acad. Child Adolesc. Psychiatry. Oct. 2022; 61(10): S185. Publisher Full Text Reference Source\n\nAbbVie: A Randomized, M., Double-Blind, Flexibly-Dosed, Efficacy and Safety Study of Escitalopram in the Treatment of Children and Adolescents With Generalized Anxiety Disorder. Clinical trial registration, study/NCT03924323.21 Oct. 2022. Reference SourceReference SourceReference Source\n\nStrawn JR, et al.: Escitalopram in adolescents with generalized anxiety disorder: a double-blind, randomized, placebo-controlled study. J. Clin. Psychiatry. 2020; 81(5): 6584. Publisher Full Text\n\nLu L, et al.: Acute neurofunctional effects of escitalopram in pediatric anxiety: a double-blind, placebo-controlled trial. J. Am. Acad. Child Adolesc. Psychiatry. 2021; 60(10): 1309–1318. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLu L, et al.: Acute neurofunctional effects of escitalopram during emotional processing in pediatric anxiety: a double-blind, placebo-controlled trial. Neuropsychopharmacology. 2022; 47(5): 1081–1087. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBaumel WT, et al.: Executive Functioning in Pediatric Anxiety and Its Relationship to Selective Serotonin Reuptake Inhibitor Treatment Response: A Double-Blind, Placebo-Controlled Trial. J. Child Adolesc. Psychopharmacol. 2022; 32(4): 215–223. Publisher Full Text\n\nIsolan L, et al.: An open-label trial of escitalopram in children and adolescents with social anxiety disorder. J. Child Adolesc. Psychopharmacol. 2007; 17(6): 751–760. PubMed Abstract \| Publisher Full Text\n\nWehry AM, et al.: Assessment and treatment of anxiety disorders in children and adolescents. Curr. Psychiatry Rep. 2015; 17: 1–11.\n\nStrawn JR, et al.: The impact of antidepressant dose and class on treatment response in pediatric anxiety disorders: a meta-analysis. J. Am. Acad. Child Adolesc. Psychiatry. 2018; 57(4): 235–244.e2. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGroup, R.U.o.P.P.A.S: The pediatric anxiety rating scale (PARS): Development and psychometric properties. J. Am. Acad. Child Adolesc. Psychiatry. 2002; 41(9): 1061–1069.\n\nCaporino NE, et al.: Defining treatment response and remission in child anxiety: signal detection analysis using the pediatric anxiety rating scale. J. Am. Acad. Child Adolesc. Psychiatry. 2013; 52(1): 57–67. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBaldwin DS, et al.: Efficacy of escitalopram in the treatment of social anxiety disorder: A meta-analysis versus placebo. Eur. Neuropsychopharmacol. 2016; 26(6): 1062–1069. Publisher Full Text\n\nHicks JK, et al.: Clinical Pharmacogenetics Implementation Consortium (CPIC) guideline for CYP2D6 and CYP2C19 genotypes and dosing of selective serotonin reuptake inhibitors. Clin. Pharmacol. Ther. 2015; 98(2): 127–134. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCampos AI, et al.: Impact of CYP2C19 metaboliser status on SSRI response: a retrospective study of 9500 participants of the Australian Genetics of Depression Study. Pharmacogenomics J. 2022; 22(2): 130–135. Publisher Full Text\n\nMakovac E, et al.: Amygdala functional connectivity as a longitudinal biomarker of symptom changes in generalized anxiety. Soc. Cogn. Affect. Neurosci. 2016; 11(11): 1719–1728. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPreuss A, et al.: SSRI treatment response prediction in depression based on brain activation by emotional stimuli. Front. Psych. 2020; 11: 538393. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWeber-Goericke F, Muehlhan M: A quantitative meta-analysis of fMRI studies investigating emotional processing in excessive worriers: application of activation likelihood estimation analysis. J. Affect. Disord. 2019; 243: 348–359. PubMed Abstract \| Publisher Full Text\n\nKujawa A, et al.: Prefrontal reactivity to social signals of threat as a predictor of treatment response in anxious youth. Neuropsychopharmacology. 2016; 41(8): 1983–1990. Publisher Full Text\n\nBurkhouse KL, et al.: Neural correlates of explicit and implicit emotion processing in relation to treatment response in pediatric anxiety. J. Child Psychol. Psychiatry. 2017; 58(5): 546–554. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHarris JK, et al.: Predicting escitalopram treatment response from pre-treatment and early response resting state fMRI in a multi-site sample: A CAN-BIND-1 report. NeuroImage: Clinical. 2022; 35: 103120. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStrawn JR, et al.: 2.9 A Multicenter Double-Blind, Placebo-Controlled Trial of Escitalopram in Children and Adolescents With Generalized Anxiety Disorder. J. Am. Acad. Child Adolesc. Psychiatry. Oct. 2022; 61(10): S185. Publisher Full Text\n\nNCT04623099: Pharmacogenetically-Guided Escitalopram Treatment for Pediatric Anxiety: Aiming to Improve Safety and Efficacy (PrEcISE).Nov. 2020. Publisher Full Text Reference SourceReference Source\n\nAcute and Long-Term Antidepressant Treatment Success in Adolescents With Anxiety (AtLAS-A) - Tabular View - ClinicalTrials.Gov. http\n\nAbuawwad M: PRISMA 2020 checklist GAD. [dataset]. figshare. 2023. Publisher Full Text" }	[ { "id": "340513", "date": "23 Nov 2024", "name": "Andrea Fagiolini", "expertise": [ "Reviewer Expertise I am a Professor of Psychiatry", "and my research is primarily concerned with the pharmacological treatment of mood", "anxiety", "and psychotic disorders." ], "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 looks at how well escitalopram works for generalized anxiety disorder (GAD) in people who have not been studied much before. Here are my questions and suggestions:\n1) While the manuscript mentions side effects, the discussion is limited. A more detailed exploration of adverse effects (e.g., suicidal ideation, somatic symptoms) and how they compare between escitalopram and placebo would enhance the clinical relevance of the paper. 2) The significant heterogeneity (I² = 65%) in the primary analysis, is partly resolved through sensitivity analyses. Nevertheless, a more detailed discussion of the sources of heterogeneity (e.g., methodological differences between studies, sample characteristics) would be helpful. 3) The Risk of Bias (ROB) figures indicate that several included studies are subject to a considerable degree of bias in specific domains. Although this is acknowledged, a more detailed discussion of the potential impact of this factor on the results would be beneficial. 4) The number of participants included in the meta-analysis, 401, is relatively modest for a meta-analysis of this nature. This limitation should be more strongly emphasized, particularly in relation to the generalizability of the findings. 5) Although predictors such as CYP2C19 polymorphisms and amygdala connectivity are mentioned, the practical clinical applicability of these findings is not fully discussed. For instance: a) What are the financial and logistical implications of integrating these predictors into clinical practice? b) It would be beneficial to ascertain whether these predictors are currently accessible in routine 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/13-2
https://f1000research.com/articles/11-514/v1	12 May 22	{ "type": "Opinion Article", "title": "Lessons from COVID-19 for GCR governance: a research agenda", "authors": [ "Jochem Rietveld", "Tom Hobson", "Shahar Avin", "Lalitha Sundaram", "Lara Mani", "Tom Hobson", "Shahar Avin", "Lalitha Sundaram", "Lara Mani" ], "abstract": "The Lessons from Covid-19 Research Agenda offers a structure to study the COVID-19 pandemic and the pandemic response from a Global Catastrophic Risk (GCR) perspective. The agenda sets out the aims of our study, which is to investigate the key decisions and actions (or failures to decide or to act) that significantly altered the course of the pandemic, with the aim of improving disaster preparedness and response in the future. It also asks how we can transfer these lessons to other areas of (potential) global catastrophic risk management such as extreme climate change, radical loss of biodiversity and the governance of extreme risks posed by new technologies.\nOur study aims to identify key moments- ‘inflection points’- that significantly shaped the catastrophic trajectory of COVID-19. To that end this Research Agenda has identified four broad clusters where such inflection points are likely to exist: pandemic preparedness, early action, vaccines and non-pharmaceutical interventions. The aim is to drill down into each of these clusters to ascertain whether and how the course of the pandemic might have gone differently, both at the national and the global level, using counterfactual analysis. Four aspects are used to assess candidate inflection points within each cluster: 1. the information available at the time; 2. the decision-making processes used; 3. the capacity and ability to implement different courses of action, and 4. the communication of information and decisions to different publics. The Research Agenda identifies crucial questions in each cluster for all four aspects that should enable the identification of the key lessons from COVID-19 and the pandemic response.", "keywords": [ "COVID-19", "Corona", "pandemic", "pandemic response", "global catastrophic risks", "GCR", "counterfactual analysis" ], "content": "Introduction: the COVID-19 pandemic and preparing for future GCRs\n\nAs of March 2022, the coronavirus disease 2019 (COVID-19) pandemic has resulted in the registered deaths of at least 6 million people (McPhillips 2022), though the actual death toll may be higher still, close to 17 million, according to the Economist (The Economist 2021).1 The pandemic has caused disruption to global supply chains, hampered humanitarian responses and hindered healthcare provision. Across the globe, it has impacted billions of lives and, in many instances, exposed inadequacies in societies, processes and institutions. The pandemic presents a grim set of lessons about how we handle global threats that, as humanity, we should learn, internalise and implement.\n\nThe ‘COVID-19 Lessons’ project at the Centre for the Study of Existential Risk looks into the lessons that can be learned from the COVID-19 pandemic and from the global response, specifically with a focus on improving our ability to handle future Global Catastrophic Risks (GCRs). It focuses on identifying and investigating the most impactful decisions and actions (or failures to decide or to act) that significantly altered the course of the pandemic, with the aim of improving disaster preparedness and response in the future. It also asks how we can transfer these lessons to other areas of risk management to help us address global challenges of potential catastrophic impact such as future pandemics, extreme climate change, radical loss of biodiversity and the governance of extreme risks posed by novel technologies.\n\nThere is, at present, no agreed definition of a GCR, with most definitions relating to global death tolls in the millions or billions (Bostrom and Ćirković 2011, Avin et al. 2018, Turchin and Denkenberger 2018) and some looking further to catastrophic impacts in terms of economic loss or suffering (e.g. Blong 2021). Depending on the definition used, COVID-19’s impact is either too small to count as a GCR, or just large enough to count on the smaller end of the scale, with the attention of the field still dedicated to scenarios that kill hundreds of millions or billions of lives. Nonetheless, the (fortunate) rarity of GCR events means GCR scholarship relies on smaller catastrophes for empirical evidence to understand higher-impact scenarios. The COVID-19 pandemic and, especially, the global response to it, now represents one of the most relevant sources of information for the study of GCRs. It bears more structural similarities to the GCR scenarios that humanity is likely to face in coming decades than with historic pandemics (e.g. the 1918 influenza pandemic or the black death), past large-scale industrial disasters (e.g. Fukushima or Chernobyl), or large-scale natural disasters (e.g. the Toba eruption). While the specific mechanisms by which the pandemic spread globally and killed are familiar, the failures to prevent or mitigate it are numerous and highly relevant to GCR research and policy.\n\nIt should be noted that, among the range of potential GCR scenarios that humanity currently faces, pandemics are conspicuous because of how well prepared for them we are - at least in principle. We already possess a complex of national and international organisations dedicated to monitoring and responding to health threats, and there are existing infrastructures for research and development, along with robust pathways for investment. Healthcare spending and the infrastructural capacity and resilience of national health services do vary greatly by region and country, yet taken overall, the funding, knowledge and infrastructure that can be brought to bear on a pandemic outbreak significantly exceeds that which is presently available for addressing alternate GCR scenarios, such as environmental protection or asteroid deflection.\n\nThe crucial question is how we can ensure that the lessons from COVID-19 not only reach the desks of policymakers, but actually leads to lasting and effective policy and cultural change: that we come out of this pandemic safer and more resilient against a wide range of global risks, and that these lessons guide the actions of present and future generations. Global catastrophes of this magnitude are, fortunately, rare, but so are the windows of opportunity to truly change humanity’s attitude towards them.\n\nBefore we can draw lessons that are relevant for prevention and mitigation across a wide range of GCRs, it stands to reason that we first need to understand the decisions and actions that were instrumental in making COVID-19 a global disaster. Crucially, it is also necessary to gain some understanding of how existing (or novel) knowledge and governance mechanisms or changes in decision making could have plausibly prevented this outcome.\n\nEfforts to understand different elements of the COVID-19 pandemic are already well underway. Governments, public health experts and planners are attempting to understand topics as diverse as the origins of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogen (the virus that causes COVID-19) and the effectiveness of social distancing measures and other non-pharmaceutical interventions. This project’s focus is on understanding what the COVID-19 pandemic tells us about the nature of global-scale, systemic risks and to draw out the lessons that can be learned about how to better prepare for such risks in the future.\n\nThe project explores the ways that the pandemic could have gone differently. Through a detailed review of secondary literature and a series of expert interviews, we are working to identify key decision and action junctures, or “inflection points”, in the history (and prehistory) of COVID-19 to ask:\n\n1. What were the decisions and actions that shaped the course of the pandemic? Who were the decision makers and in what context were they operating?\n\n2. Were these particular decisions or actions inevitable? What other options were available?\n\n3. If things could have been different, how? What would have been the (likely) outcomes of choosing or acting differently?\n\n4. What changes in policy, preparedness or implementation would have made it possible for different, and better, responses to this type of global risk?\n\nThese counterfactuals make it possible to compare the actual course of the pandemic with possible and perhaps better courses.\n\nCounterfactuals are “contrary to facts”, i.e. conditionals that identify a “possible” or “alternative” world in which the antecedent did not actually occur (Levy 2008). They are useful in that they allow us to think of a world where different decisions—such as different public health interventions—were adopted. This method is not without its difficulties, as “we cannot rerun history” (Sato 2021, p65). There are, however, various ways to increase the validity of counterfactual analysis, such as through maximising clarity and plausibility of the conducted analysis, which is what we are aiming for. Utilising both quantitative analysis on the basis of forecasting—and qualitative analysis—on the basis of expert elicitation and the analysis of documents—our research will explore what impact different decisions could have made in terms of lives lost and the humanitarian and social costs of the pandemic. These insights can provide vital lessons for decision-makers, now and in the future.\n\nIn our research to date, we have identified four broad types of issues that we believe had the most significant impact on the course of the pandemic, and which largely determined the observed death tolls. These four clusters are Pandemic Preparedness, Early Action, Vaccines and Non-Pharmaceutical Interventions.\n\nThe clusters are each structured as follows: (1) they assess what information was available to experts and decision-makers relevant to each cluster when COVID-19 broke out; (2) they assess decision-making processes, analysing what decisions were made, when, and how and if other decisions, potentially at different points in time, could have resulted in better outcomes in terms of the pandemic trajectory; (3) they assess implementation and infrastructure, i.e. what infrastructure and capacities relevant to the clusters at hand were available? Was this infrastructure up to the task to effectively address the pandemic? Regarding implementation, were decisions taken relevant to the particular clusters adequately implemented? If not, why was implementation lacking and how can this be improved in future responses? Where was there room for implementation improvement and how would this have potentially positively altered the trajectory of the pandemic? Finally, (4) they assess communication aspects relevant to the different clusters, as communication is key in navigating any crisis. For each of these four aspects, we indicate our current knowledge base and invite interested parties to share their insights with us.\n\nBelow, we provide a short overview of each cluster, giving some illustrative examples of each and offering some initial suggestions as to how counterfactually these issues or events could have been responded to differently, and the impact this could have had.\n\nMost importantly, each cluster concludes with a set of “open questions''. These questions are efforts to bring together what we do know with an agenda for further research and a call for collaboration with other interested parties. We believe that working together to answer these questions can play a major part in supporting lasting and effective policy and cultural change so that we come out of this pandemic safer and more resilient against a wide range of global risks, and that these lessons are passed on to present and future generations.\n\nWhile this document lays out an agenda for what we envision to be crucially important research to attain these goals, we also intend that it might form a useful reference document to a range of different readers: providing an overview of current knowledge relating to the COVID-19 pandemic and international responses to it.\n\n\nCluster #1: pandemic preparedness\n\nThe first cluster of our research agenda looks into pandemic preparedness. The World Health Organization (WHO) defines pandemic preparedness as “a continuous process of planning, exercising, revising and translating into action national and sub-national pandemic preparedness and response plans” (WHO 2022a). The organisation sees pandemic preparedness as an integral part of preparedness to threats to human health caused by any emergency, which includes disease outbreaks, but also occurrences of natural disasters or chemical incidents (WHO 2022a). As pandemic preparedness is a continuous process, this makes pandemic plans living documents, which are to be “reviewed regularly and revised if necessary, for example based on the lessons learnt from outbreaks or a pandemic, or from a simulation exercise” (WHO 2022a). This cluster asks what role pandemic preparedness had to play in the period leading up to the COVID-19 pandemic, where preparedness shortcomings emerged, as well as how notions of preparedness have started to evolve since the outbreak.\n\n\n\n1. What information was available to policy makers and experts about preparations they should make for future pandemics? What information was available about the likelihood and severity of future pandemics?\n\n2. What information did pandemic exercises deliver? Was this information followed up on?\n\n3. What information was available regarding different pandemic preparedness options (e.g. tabletop simulations, large-scale exercises, stockpiles, surveillance, etc.)? What information was available about the likely cost and efficacy of these options? What information was available about how best to utilise such tools?\n\n4. What was the size and structure of the research community focusing on understanding and preparing for future pandemics? What were its key findings and focus areas for research? What were its pathways to deliver findings and recommendations to policy makers?\n\nAlthough the knowledge base surrounding pandemics and pandemic preparedness was substantial (Madhav et al. 2017), it can be argued that decision makers did not do enough with this information in preparing their countries for the eventuality of a pandemic. Part of the problem is that not all countries seem to have conducted pandemic preparedness exercises, and that those who did, did not always prepare for the “right” type of pandemic (there was a general bias towards preparing for pandemic influenza). It has also been noted that some countries organised their exercises in ways that were so theoretical in nature that they turned out to have little bearing on the outbreak of an actual pandemic. This was laid painfully bare by COVID-19 (Salden 2020).\n\nIn addition to the knowledge that could have been garnered from pandemic exercises, there was a wealth of information on preparedness that had been accumulated from responses to previous outbreaks, such as those of severe acute respiratory syndrome (SARS), H1N1, Middle East respiratory syndrome (MERS) and Ebola. These outbreaks were invariably evaluated by high level panels, which then produced reports providing decision-makers with detailed information on what measures they should take to be better prepared for the next pandemic (IISD 2016). Our initial research suggests that decision makers in government and elsewhere frequently acted inadequately in response to this type of information and that this contributed to a lack of preparedness when SARS-CoV-2 was discovered in late 2019.\n\nFinally, while many countries had developed pandemic preparedness plans in recent decades, there are a number of ways that the effectiveness and adequacy of these plans might be questioned. For instance, following the 2009 H1N1 pandemic, many European countries revised their national pandemic plans to prepare for future influenza pandemics and to strengthen implementation of the International Health Regulations (IHR 2005) (WHO 2022b). The revised plans considered the national and global experiences from the 2009 pandemic, and in some countries, they were used to form the basis of the initial national response to COVID-19 (UK Department of Health & Social Care 2020). Yet, some of these plans cautioned against measures that have become commonplace in the COVID-19 pandemic response, such as mask-wearing and border closures (Blanco-Jimenez 2021). We suggest that it is important to understand the causes of this disparity and investigate national and regional variations in planning.\n\nOur current knowledge base on this information-aspect is moderate, so we invite people who could provide further insights into the role of information in pandemic preparedness to share their insights with us.\n\n\n\n1. Did decision makers decide to organise pandemic exercises? If so, why and how? Why did they run them in particular ways? Who participated in such exercises, and who did not?\n\n2. Was information resulting from pandemic exercises followed up on? If yes, how? If not, why not?\n\n3. What other pandemic preparedness actions were considered? Why were they pursued, or not pursued, in different countries at different times?\n\nWHO ran a number of initiatives that sought to prepare member states for pandemic influenza, such as the Pandemic Influenza Preparedness (PIP) Framework (2011) though, notably, not for other types of pandemics (WHO 2022c). Similarly, many countries ran pandemic scenario exercises in the years leading up to the COVID-19 outbreak; however, these were also largely focused on how to respond to pandemic influenza, and our initial research suggests that this may have been to the detriment of their preparedness for other types of viruses. Even instances where an influenza preparedness plan may have provided the right kind of guidance for the COVID-19 pandemic, the specific content of these plans and the actions that governments took based on their recommendations, should still be considered as important elements of the global pandemic response.\n\nIt is possible that these preparedness plans and exercises, focusing on influenza pandemics, may have framed the expectations of decision makers. Hence, officials may have been caught off guard by the outbreak of a coronavirus pandemic. In the case of the UK, it has now emerged that the government based its early response on pandemic influenza scenarios, even though exercises had been conducted on coronaviruses (Booth 2021a). In the early weeks of the pandemic, there was a considerable degree of uncertainty about the transmissibility and lethality of COVID-19 compared with influenza, which complicated assessments of the novel virus. Here, tapping into the knowledge delivered by conducted coronavirus pandemic exercises—as opposed to pandemic influenza scenarios—would have been appropriate and therefore constitutes a missed opportunity. By now, a consensus exists that all SARS-CoV-2 variants encountered by March 2022 are causing significantly more morbidity and mortality than recent influenza strains. It can be assumed that this is due to a combination of higher transmissibility and lethality leading to an overall larger burden of disease despite significantly higher lethality for example of some Highly Pathogenic Avian Influenza (HPAI) strains which have in recent decades not been able to transmit more than sporadically to humans (Hammers 2022).\n\nAnother issue has been the disjuncture between the highly theoretical way in which some pandemic exercises were set up and the very real events and consequences of an actually occurring pandemic. A useful illustration of this is provided by the Netherlands, which, in 2019, organised an exercise to simulate the outbreak of an influenza epidemic. This exercise focused largely on communication and on coordinating management responsiveness within healthcare systems, leaving little room to consider some of the concrete dilemmas, policy trade-offs and pressures that a real pandemic would bring about.\n\nPractitioners who participated in the simulation later reflected that the exercise was totally incomparable to the actual pandemic of COVID-19, and that at the time of the exercise they saw it as a merely theoretical exercise. One of them noted that a crisis exercise does not have a “face”, whereas the actual pandemic very much did: healthcare practitioners saw exhausted colleagues, overwhelmed hospital managers, and patients who were short on breath (Salden 2020). One of the participants, a governor of a number of regional hospitals, reflected amidst the first COVID-19 wave in Spring 2020: the exercise was “very useful, but no one thought this [outbreak] was ever going to happen” (Salden 2020). In the same vein, the international Independent Panel for Pandemic Preparedness & Response (2021, 20) (hereafter: the Independent Panel) also noted the need “for preparedness assessment to place more focus on the way the system functions in actual conditions of pandemic stress.”2\n\nAs noted, information resulting from pandemic exercises was not always adequately followed up on. Preliminary information seems to suggest that the UK ran a large number of exercises but did not implement key recommendations from them, such as the need for PPE stockpiles and better contact tracing systems (Booth 2021b). This may have been the result of a lack of political prioritisation, which appears to have been an issue in many countries. In the United States, for example, pandemic preparedness was made a priority under the Obama administrations, but under the Trump administration, the position of pandemic adviser was downgraded, and the relevant official was no longer able to convene the cabinet (Tracy 2020). The impact of shifts in political prioritisation is also demonstrated by the decision of California’s administration, under the leadership of Brown, to sell off or destroy the stockpiles of ventilators and PPE that had been built up under the Schwarzenegger administration (Marinucci 2020).\n\nOur current knowledge base on this aspect is high, but we do invite people who could provide further insights into the role of decision-making in pandemic preparedness to share their insights with us.\n\n\n\n1. What did the pandemic exercises look like? How were exercises structured and why?\n\n2. Did pandemic exercises result in new infrastructure/capacities? (PPE, vaccine development capacities, investment in R&D). If yes, how? If not, why not?\n\nPandemic preparedness exercises were conducted in many countries (WHO 2018), but many of these exercises seem to have inadequately prepared countries for a real pandemic, or at least, for the current coronavirus pandemic. An important part of the problem, as noted above, is that exercises were often inadequately followed up on, which means that they did not deliver significant new health capacities and infrastructure, such as stockpiles of PPE, vaccine development capabilities, scalable ICU capacity, and track and trace systems.\n\nA related problem, that exacerbated the failure of many countries to act upon the lessons learned from their preparedness exercises, was the more generalised underfunding of pandemic preparedness. The Independent Panel (2021, p. 56) highlighted this lack of funding for pandemic response, while also noting that in some places, periods of adequate funding and capacity building were followed by budget cuts and capacity reduction. Whether these cycles were influenced by generalised issues of political prioritisation or by shifting attitudes towards the costs and benefits of maintaining large buffers of residual capacity for health emergencies, the consequences of the cuts appear stark in many countries. The aforementioned example of California demonstrates clearly how these reductions in capacity occurred in the years preceding the COVID-19 pandemic. The UK’s pandemic influenza stockpile is another example. It was estimated at GBP 831 million in 2013, but declined by 40% over six years (Davies et al. 2020).\n\nPreliminary evidence suggests that some countries were better prepared, and these countries tended to be those that had previous recent experience with large-scale outbreaks, such as Southeast Asian countries (with SARS) and West African countries (with Ebola) (Ahanhanzo et al. 2020; Nuki et al. 2020). These countries acted swiftly in introducing measures to control and monitor the spread of SARS-CoV-2. In many cases, it appears that they had—as a result of their more recent experience of viral outbreaks—also developed a public health infrastructure that was better able to respond to the outbreak of a pandemic (Independent Panel 2021). It should be noted, however, that pandemics necessarily entail different phases and that countries’ early performance in the COVID-19 response is not necessarily a predictor of later performance in pandemic response (Frieden 2021).\n\nOur current knowledge base on this aspect is limited, so we invite people who could provide further insights into the role of infrastructure/implementation in pandemic preparedness to share their insights with us.\n\n\n\n1. Did decision-makers communicate the importance of preparedness? If so, how? If not, why not?\n\n2. Did decision-makers aim to create awareness among the general public about pandemic risk and societal resilience against this risk? If so, how? If not, why not?\n\nPublic communication has an important role to play in pandemic preparedness, informing the public about the risk of pandemics and preparing it for eventual outbreaks. Information provision and communication with regards to pandemic risks could also run through the education system, creating basic health awareness among children, including teaching them the basic tools of staying safe during a pandemic. The Disaster Risk Reduction (DRR) literature has demonstrated the importance of the role of education in disaster preparedness (Johnston et al. 1999, Ronan and Johnston 2003, Shaw et al. 2004, Paton et al. 2008). Preliminary information seems to suggest that there were generally few awareness raising campaigns from governments about the risk of pandemics and the importance of preparedness towards their publics. It is important to assess the extent to which societal and political awareness could have helped in the (early) response to COVID-19. If public communication and awareness turns out to be a significant aiding factor, the question becomes: how can we sustain pandemic communication and awareness after the current COVID-19 outbreak? Potential lessons can be learnt from countries with previous pandemic experience that built up pandemic public communication systems before the outbreak of COVID-19.\n\nOur current knowledge base on this aspect is high, but we invite people who could provide further insights into the role of communication in pandemic preparedness to share their insights with us.\n\nOn a final note, it is important to acknowledge that “pandemic preparedness” has a very different meaning today compared to pre-Covid times. In the face of the very real COVID-19 pandemic, many more elements have now been added to the “preparedness toolbox”. We recognise how the term “pandemic preparedness” has shifted over time and are interested in evaluating the pandemic response through both understandings (pre- and post-Covid) of the term.\n\nThe following is a (non-exhaustive) list of some of the key “open questions” that we have identified to date for this cluster of issues. These are indicative of the ongoing research agenda guiding this phase of our project, and we would be particularly keen to speak with practitioners and experts that can shed further light on answers to some or all of these questions:\n\n1. What constitutes a successful pandemic plan and an effective pandemic preparedness training exercise?\n\n2. How much funding is required to successfully realise these plans and exercises nationally and regionally? And how might this figure differ across states with different levels of wealth and different institutional capacities?\n\n3. How can global, regional, and national actors work together to ensure that relevant capacity to achieve exercises is built across the globe and that key recommendations flowing from exercises are actually being implemented?\n\nIn other words, we aim to answer the following overarching questions:\n\nWhat kind of pandemic preparedness—in terms of knowledge, institutional capacity, resources, and training—would actually serve to make sure that the world was better prepared for the next pandemic?\n\nWhat can we learn from the successes and failures of various efforts to prepare for a global pandemic that will allow us to better prepare for other categories of Global Catastrophic Risk, such as those associated with climate change, the loss of biodiversity, and the rise of potentially disruptive technologies?\n\n\nCluster #2: early action\n\nThis cluster focuses on the early action phase in the pandemic response. We define the “early action phase” as the initial months of the COVID-19 pandemic from December 2019 until the summer/early autumn of 2020.3 This period encompasses the initial detection of the virus in China, early outbreaks on every inhabited continent, and the end of what came to be known as the “first wave” of infections, and the end of a first round of “lockdown” restrictions in many countries.\n\nIn the very early phases of disease outbreak, a rapid containment strategy may still be feasible. The WHO defines rapid containment as effectively “stopping the development of a pandemic when it is initially detected before the virus spreads more widely” (WHO nd.). Once the virus spreads more widely, however—across countries and continents—countries are forced to respond to community level outbreaks and will usually consider a wide range of public health measures to contain, suppress, or eliminate these outbreaks. Our “early action phase” considers both of these phases.\n\n\n\n1. What information was available about SARS-CoV-2 in the early days and weeks immediately following its discovery?\n\n2. What assumptions were prevalent in the expert community about the virus and its transmissibility and lethality in the early days? How were these communicated to decision-makers?\n\n3. What information was available about the effectiveness of various containment measures in the early days? What models were used, and how were they presented to decision-makers? What were the main arguments from experts against various forms of early containment?\n\n4. What information-gathering approaches were used in the early days? What other approaches were available, and why were they not pursued?\n\n5. What information-sharing infrastructure existed on the eve of the pandemic? What information-sharing infrastructure was stood up during the early days? Who was included and who was excluded from such networks?\n\nLittle was known about COVID-19 when the first few cases of the novel disease emerged. There was ongoing uncertainty in the first few weeks about the prevalence and precise mechanisms of human-to-human transmission and the extent of asymptomatic spread (Parry 2020; WHO 2020).\n\nRegarding the effectiveness of containment measures, decision-makers had to take clues from what was implemented—effectively or otherwise—in countries that experienced the earliest outbreaks, as well as from modelling of related diseases and historic knowledge concerning respiratory viruses and the spread of disease. There was, however, considerable uncertainty at the time, and there were competing interpretations and recommendations coming from a range of actors across the scientific community. It was against this background of uncertainty that decision makers had to chart a course of action and shape the early pandemic response.\n\nOur current knowledge base on this aspect is medium, so we invite people who could provide further insights into the role of information in early action to share their insights with us.\n\n\n\n1. Which containment measures did decision makers choose and how did they come to these decisions?\n\nDuring any crisis, effective decision making in the early response is vital. Unfortunately, this element was not always present in the early response to the COVID-19 pandemic. While we acknowledge that decision making efficacy will always be easier to adjudge with the benefit of hindsight—and the limited information, higher uncertainty and the existing bounds of infrastructural capacity will shape decision-making processes—our research to date suggest a number of instances where robust decision making may have significantly altered the trajectory of the pandemic.\n\nWhen considering the possibility of early containment for example, China could have banned commercial flights leaving the country earlier, while other countries could have closed their borders sooner. While these types of intervention may have seemed drastic or even draconian at the time, it is now clear that avoiding such decisions may have led to the longer-term imposition of both border closures and disruption to international travel.\n\nIt should also be queried why WHO did not apply the precautionary principle in its decision-making (or if it did, then what other considerations were factored in that took precedence). The precautionary principle entails assuming that human-to-human transmission is taking place in an outbreak of a novel pathogen unless evidence to the contrary emerges (Independent Panel 2021).\n\nThe costs of applying the precautionary principle would arguably have been far lower than the cost of choosing to delay action or prioritising the continuation of trade, travel or business; thus, insufficiently preparing for and mitigating against an outbreak that would prove to be as serious as the COVID-19 pandemic (Independent Panel 2021).\n\nDespite this, China and other Asian countries did take early containment measures internally, including the imposition of lockdowns, the disinfection and shutting down of wet markets and bans on domestic travel (Graham-Harrison 2020). Many other countries, including the majority of European states, tended to react slowly, adopting a wait-and-see approach and appearing rather unprepared for the COVID-19 pandemic (Lawler 2020). This once again demonstrates the interaction and interdependence of robust decision making with various aspects of pandemic preparedness. On the one hand, gaps emerged in what processes were ready to be deployed, what institutional capacity existed, while at the same time, mistakes were made in implementing plans and setbacks occurred in deploying processes that had been prepared.\n\nBesides individual country approaches, there was a lack of international leadership early on in the pandemic. The G7 and G20, United Nations (UN), and WHO all fell short in taking effective and timely measures and providing global and regional leadership at the time it was most needed (Wilson & Pilling 2020; AlQershi 2020). Coordinated measures at the highest levels could have made it easier for countries to take tough measures themselves and explain these to their citizens. Unfortunately, global and regional measures either did not come, came late or were insufficient. Leadership rivalry and contradictory approaches carried the day, whereas cooperative leadership and joint efforts were mostly lacking (Wright 2021; OECD 2020). It is understandable that there is a strong temptation for countries to adopt a “my country first”-approach during crises, but when it comes to global challenges with systemic effects, this appears to have been a self-defeating strategy in the medium-to-long term, not least in the face of a pathogen that spreads without consideration of national borders.\n\nOur current knowledge base on this aspect is medium, so we invite people who could provide further insights into the role of decision-making in the early response to share their insights with us.\n\n\n\n1. Did countries have the infrastructure/capacities to close borders, enforce lockdowns etc.?\n\n2. Did countries have the capacity to support individuals in isolation?\n\n3. Did countries have the capacity to enact targeted containment through testing and tracing?\n\nWhen analysing the early response, it is important to assess whether countries possessed the relevant infrastructural capacity to implement public health decisions and containment measures. Did countries have the infrastructural capacity and organisational capabilities to close their borders, enforce lockdowns, and track and eliminate infection chains? Were there sufficient policy and legal capacities and clarity to enact such measures rapidly? Much has been reported about the challenges and dilemmas of low-income countries to implement lockdowns, given high dependence on daytime wages in the informal sector (Piper 2020). Equally, not all countries have had the capacity (economic or indeed political) to support individuals in isolation, which is an important tool to curb infections.\n\nOur current knowledge base on this aspect is limited, so we invite people who could provide further insights into the role of infrastructure/implementation in the early response to share their insights with us.\n\n\n\n1. How did decision-makers communicate early action measures to their publics?\n\n2. What kind of communication approach was required in this early phase?\n\nFinally, there were communication inconsistencies and mistakes early on in the pandemic. These occurred at all levels, but the frequency and severity of poor communication and mixed messaging from senior levels of the political executive (in a number of states) seems particularly important to note. A seemingly minor but very telling example is how some leaders accidentally shook hands with other officials after publicly announcing people should stop doing so themselves, while others even boasted about the practice, in clear defiance of warnings from the scientific community (BBC 2020a; Mason 2020).\n\nMore serious examples came from, amongst others, Brazil and the USA. President Jair Bolsonaro directly contradicted the advice provided by the Brazilian Governments’ Health Ministry by urging the Brazilian public not to comply with social distancing and other public health measures (Human Rights Watch 2020). In the USA, there was a considerable flow of misinformation emanating from the Trump administration with regards to the pandemic and measures to contain it (Sauer et al. 2021). There were a number of examples of effective public communication by national leaders as well. Particularly notable examples include Germany’s Angela Merkel, New Zealand’s Jacinda Ardern and The Netherlands’ Mark Rutte, who communicated factually, cautiously and reassuringly in the early days of the pandemic (Wilson 2020; Delahunty 2020; Brassey and Kruyt 2020). Singapore has also been commended for its effective and transparent communication strategy (Sagar 2020).\n\nResearch has shown that reliable and speedy communication is crucial in navigating complex crises, such as pandemics. US researchers found that “communication should be rapid and accurate, while building credibility and trust and showcasing empathy—all with a unified voice” (Sauer et al. 2021, p65). Public communication in the early months of the pandemic was especially important as it coincided with the rollout of early—and often unprecedented (at least in Europe/Northern America)—public health measures, such as social distancing, test and trace systems, and the prohibition of mass gatherings. The imposition of these measures, and ultimately their effectiveness, was largely dependent on public acceptance and cooperation. While most modelling for these so called non-pharmaceutical interventions clearly stated an acceptable degree of non-compliance within their efficacy predictions, effective public communication was required to successfully convince the public that they were necessary.\n\nAs much was still unknown about COVID-19 in the early pandemic, public communication necessarily included some discussion of uncertainty. According to Igoe (2021), there are two sources of uncertainty in science communication: uncertainty deriving from changes in knowledge, and uncertainty occurring when leaders and public figures contest or debate scientific findings in public (Igoe 2021). It appears, from our research to date, that both categories of uncertainty were present in the early action phase of the pandemic response. Firstly, as new information became available, experts frequently had to revise and retract earlier public health advice or revisit their previous epidemiological models. At the same time, political leaders and public figures often sought to emphasise certain aspects of uncertainty, or to question particular scientific claims, in order to advocate for different political or economic prioritisations. Both these factors may have convoluted the clarity of public messaging, leading to public confusion at times in various countries (Han et al. 2020). Where the uncertainty resulting from the rapidly shifting knowledge base concerning COVID-19 was not well-communicated, it may also have contributed to an undermining of trust in the scientists themselves.\n\nFinally, alert level systems were introduced early on to communicate the risk of COVID-19. The UK unveiled a five-level, colour-coded alert system in May 2020, which ranks the current threat level from COVID-19 (Sabbagh 2020). Colour-coded maps have also been widely used to accompany travel advice for different countries and regions (European Centre for Disease Prevention and Control 2022).\n\nOur current knowledge base on this aspect is medium, so we invite people who could provide further insights into the role of communication in the early response to share their insights with us.\n\nThe following is a (non-exhaustive) list of some of the key “open questions” that we have identified to date for this cluster of issues. These are indicative of the ongoing research agenda guiding this phase of our project, and we would be particularly keen to speak with practitioners and experts that can shed further light on answers to some or all of these questions:\n\n1. How can policy makers, practitioners and scientific advisers determine the most effective containment measures when much is unknown?\n\n2. Why were borders not closed earlier and how much of a difference would this have made?\n\n3. What is needed to achieve border closures and other effective containment measures as early as necessary during future pandemics? Why was coherent action and effective leadership lacking by the world’s global and regional institutions, such as the G7 and G20, the UN, WHO, the EU and other regional organisations?\n\n4. How can public communication be improved in the next pandemic and/or other crises?\n\nAgain, we restate here that we are working towards answering two basic questions in relation to the early action phase:\n\nWhat kind of early responses—including containment, knowledge-sharing and communications—to the discovery of the COVID-19 outbreak would have significantly altered the trajectory of the pandemic, and significantly reduced the global loss of life, injury and harm?\n\nWhat can we learn from the successes and failures of various early response efforts to contain or otherwise mitigate the COVID-19 pandemic to better prepare us to respond effectively to other categories of Global Catastrophic Risk; such as those associated with climate change, the loss of biodiversity, and the rise of potentially disruptive technologies?\n\n\nCluster #3: vaccines\n\nVaccines were developed at extraordinary speed and are likely to be remembered as one of a few success stories of the pandemic response. While 2020 saw the introduction of lockdowns, masks, and social distancing, to many, vaccines represented the only viable and sustainable way out of the COVID-19 crisis. Before the development of antiviral medicine such as molnupiravir and Paxlovid, it was believed that vaccines were the only medical means to protect people against the virus (Aripaka 2021). Alongside non-pharmaceutical interventions such as social distancing etc., a number of experts believed that mass vaccination programs would be able to, at least theoretically, end the pandemic. Current data regarding vaccine rollouts and the continual emergence of vaccine-evading variants, however, suggest this is no longer a realistic scenario (Charumilind et al. 2021).\n\nIn the early months of the pandemic, multiple companies developed vaccines based on the genome sequence that was released in January 2020. The vaccines were developed at a remarkable speed and moved quickly through the various development, clinical trial, and authorization-for-use phases (Ball 2020). The mRNA vaccines particularly received much attention, as this new generation of vaccines can be developed very quickly and thus proved very promising both from a scientific and public health point of view (Ball 2020). In December 2020, the worldwide vaccination campaign truly started with the first people being vaccinated in the United Kingdom. Since then, billions of people have been vaccinated in a global vaccination campaign (BBC 2020b; Bloomberg 2022).\n\nFor all the successes of the global effort to develop, manufacture and distribute vaccines for COVID-19, there do, however, remain a significant number of challenges and substantial gaps in the provision of these. The most significant among these remains the need to deliver and effectively distribute vaccinations to the populations of countries in the Global South. At the same time, even the vast scale of the vaccination programs rolled out in Europe and North America has failed to eliminate the spread of the virus; indeed, December and January of 2021/22 have borne witness to rising infection rates in a number of high-vaccination countries.\n\nCommitments such as those made by the G7 to donate vaccines to the Global South are still in their implementation phase (Reuters 2021; Gye 2021). Meanwhile, as of late September 2021, the WHO-led COVID-19 Vaccines Global Access (COVAX) was forecasting to deliver 1.45 billion vaccines through its scheme by the end of the year, compared with the 2 billion it forecast to deliver earlier in the year (Horner 2021). The aforementioned tendency of some countries to prioritise purchasing additional vaccine doses for their own citizens, as opposed to distributing these to other countries has posed an important political challenge to vaccine equity around the world. Many countries in the Global North are now administering vaccine boosters (and indeed, even discussing an additional fourth booster dose) while many health care workers in the Global South are still waiting for their first dose (Maxmen 2021). Another problem is mis- and disinformation surrounding vaccines, which has arguably led to a less successful vaccine rollout than desired (Loomba et al. 2021).\n\nA final challenge that has come to light is that vaccinations offer reduced protection against new variants of SARS-CoV-2, such as the Delta and Omicron variants, when compared to earlier strains of the virus. Still, many researchers hold that it is currently our best tool in the fight against the virus and the respiratory disease it causes (Mancini and Burn-Murdoch 2021).\n\n\n\n1. What did early prognoses of vaccine discovery/development look like?\n\n2. How was information about vaccine efficacy and safety collected? How was it communicated to decision makers, medical professionals, and the public?\n\n3. What information was available about the logistical challenge of “getting shots into arms”, and what solutions were offered by experts and by local practitioners? How was information about the successes and challenges of vaccine rollout fed back into further planning and rollout cycles?\n\n4. Where does vaccine misinformation originate, how does it spread, and how much of an effect does it have on vaccine uptake? What actions were taken to counter vaccine misinformation, and were they effective?\n\n5. What did proposals for rapid vaccine development, approval and global rollout look like, as discussed in the relevant policy and research communities, on the eve of the pandemic? How did these differ from the paths taken during COVID-19?\n\nThe development, manufacturing and distribution of COVID-19 vaccines represents a complex process where multiple strands of information, expertise and knowledge intersect. For example, it is necessary to bear in mind there was a background of scientific expertise and technological capability that resulted from the prior years and decades of vaccine R&D (particularly that concerning mRNA vaccines) that made rapid vaccine development after the COVID-19 outbreak possible (Dolgin 2021). Shorter term factors, such as early predictions of how likely a successful vaccine development was, and how long it was likely to take, should also be considered. This information formed the basis of which decision-makers took early decisions surrounding vaccine investment and advance purchase agreements (a strategy to provide upfront financing for COVID-19 vaccines to accelerate their development and availability) (Medicines Law & Policy 2021).\n\nInformation about the various available vaccines, such as expected effectiveness and potential side-effects, informed decision-making on vaccine eligibility, while waning effectiveness gave rise to the booster-debate. Vaccine mis- and disinformation has proven a great obstacle in ensuring maximum vaccine uptake and has received increasing attention, including in public communication efforts as discussed below.\n\nOur current knowledge base on this aspect is high, but we still invite people who could provide further insights into the role of information with regards to vaccines—especially on matters of manufacturing and distribution logistics—to share their insights with us.\n\n\n\n1. What decisions were made with regards to national vaccination plans? How and why did countries decide to enter into advance purchase agreements? How were vaccination strategies, e.g. age group and risk group prioritisation, decided?\n\n2. How were decisions about global distribution of vaccines made? How were decisions to join or not join COVAX made?\n\n3. How did vaccine developers decide on production targets? How did vaccine developers choose which countries to supply first?\n\nA wide range of decisions had to be made with regards to vaccines, including about early investment and advance purchase agreements, vaccine eligibility and vaccination strategies. More recently, debates have arisen over what rights (of travel, of social mixing, for example) should be associated with vaccination status. On the global level, vaccine inequity has led to calls for more vaccine donations to the Global South. Pledges that have been made so far, such as the G7-pledge, which is still in the implementation phase, have been criticised by campaigners as “too small, too slow and too narrow” (Wintour 2021; Financial Times 2021). The prospect of mandatory licensing, which might be expected to enable local production in a greater number of countries, is still insufficiently clear. One of the points of interest is the role of scientific experts in vaccine decision-making, as well as what underpins the varying vaccination strategies in different countries.\n\nOur current knowledge base on this aspect is limited, so we invite people who could provide further insights into the role of decision-making with regards to vaccines to share their insights with us.\n\n\n\n1. Were countries able to roll out vaccines as planned? What were the most common implementation hurdles?\n\n2. What were common challenges in vaccine approval, production, and logistics (transport, storage, and point-of-care delivery)?\n\nThere were significant logistical challenges associated with the implementation of vaccination campaigns. Countries had to set up an entire infrastructure ranging from vaccine storage and transportation to vaccine administration at local sites. The challenges were compounded by the strict storage requirements of some of the vaccines, such as the Pfizer vaccine which initially needed to be stored at −70C, requiring a cold supply chain (Pfizer 2021). The empirical analysis will assess whether countries had the capacities to effectively roll out vaccines and what some of the most common implementation hurdles were.\n\nOur current knowledge base on this aspect is medium, so we invite people who could provide further insights into the role of infrastructure/implementation with regard to vaccines to share their insights with us.\n\nCommunication about vaccines is a crucial pillar in the vaccination effort, to ensure the availability of reliable information about vaccines and thus, it is hoped, increase public confidence in the vaccination campaign. As with most communication, and scientific communication in particular, vaccine communication is multifaceted, as it aims to convey information with regards to the effectiveness and safety of different types of vaccines, practical information (who is eligible? Where can one get the vaccine? etc.), and it aims to address mis- and disinformation. The issues raised above with regard to uncertainty and the communication of uncertainty are only amplified. The latter can only effectively be done with an understanding of where these types of false information come from, through reaching out to sceptics and marginalised groups, and through rebuilding trust from the bottom up, such as through trusted community leaders (US Centers for Disease Control and Prevention 2022).\n\nOur current knowledge base on this aspect is high, but we still invite people who could provide further insights into the role of communication with regards to vaccines to share their insights with us.\n\nThe following is a (non-exhaustive) list of some of the key “open questions” that we have identified to date for this cluster of issues. These are indicative of the ongoing research agenda guiding this phase of our project, and we would be particularly keen to speak with practitioners and experts that can shed further light on answers to some or all of these questions:\n\n1. How have different countries approached vaccine development, approval, purchase, distribution, and communication?\n\n2. Which strategies led to high vaccination rates?\n\n3. What actions impacted other countries’ ability to obtain or distribute vaccines?\n\n4. Which vaccination strategies should be followed, now and in the future? How can we best define vaccine equity and how can it be ensured around the world?\n\nEchoing prior sections of this Research Agenda, we restate here that we aim to answer two fundamental questions in relation to vaccines:\n\nWhat would an adequate—or even, an ideal—vaccine infrastructure look like, and what strategy for the development, testing, manufacture, and distribution of COVID-19 vaccines would have most significantly altered the trajectory of the pandemic, and significantly reduced the global loss of life, injury, and harm?\n\nWhat can we learn from the successes and failures of national, regional, and global efforts to develop, test, manufacture and distribute COVID-19 vaccinations to better prepare us to respond effectively to other categories of Global Catastrophic Risk?\n\n\nCluster #4: non-pharmaceutical interventions\n\nNon-pharmaceutical interventions (NPIs) are, as defined by the US Centers for Disease Control and Prevention (2020), “actions, apart from getting vaccinated and taking medicine, that people and communities can take to help slow the spread of illnesses like pandemic influenza (flu) (…), also known as community mitigation strategies.” NPIs have been a key instrument in the pandemic response. While they were part of the early response (cluster 2), cluster 4 looks into the use of NPIs during the stage where the virus was widely circulating, so beyond the early action stage. During this period, new information regarding the effectiveness of these measures came in, while compliance with measures became more uneven across the world. This was due to phenomena such as lockdown fatigue and the politicisation of adhering to measures such as mask wearing in certain countries. Other factors, such as populations that are largely reliant on day-labour or non-provision of social goods such as sickness pay, have also influenced the ability and willingness of populations to adhere to these measures. In a number of instances, civil society and grassroots organisations have become involved in cases of low state capacity, aiding communities during the pandemic and fostering broader community resilience.\n\n\n\n1. What information was available about the effectiveness of NPIs on the eve of the pandemic?\n\n2. What information was collected during the pandemic on the effectiveness of NPIs?\n\n3. What information was collected during the pandemic on factors affecting compliance with NPIs?\n\nWhile on the one hand it is important to assess what information became available about the effectiveness of NPIs during the pandemic, it is also needed to zoom in further on what made these NPIs work. For instance, is financial support necessary to make lockdowns and quarantining effective? And what informs lockdown fatigue and how can countries best address this challenge? How did information on these factors subsequently shape decision making?\n\nModels have been built to estimate how many people would have come into contact with SARS-CoV-2 in the absence of public health measures, including NPIs, and they can therefore give us an indication of how effective these measures were and continue to be. Obviously, there is uncertainty in these models. Yet, they provide us with useful insights in terms of counterfactuals and the effectiveness of adopted measures against COVID-19.\n\nOur current knowledge base on this aspect is medium, so we invite people who could provide further insights into the role of information with regard to NPIs to share their insights with us.\n\n\n\n1. Which NPIs did decision-makers opt for? Why?\n\n2. What would an ideal timeline with regards to NPIs have looked like?\n\n3. What local/civil society decisions were made and how did they affect the pandemic response?\n\n4. What was the role of experts in NPI decision making?\n\nAs noted in the early action cluster, at the start of the COVID-19 pandemic, various NPIs were introduced in many countries, such as social distancing, the ban of mass gatherings, the closure of schools and offices, and eventually, the introduction of full-scale lockdowns. These measures have been generally quite effective in slowing the spread of SARS-CoV-2, as has been demonstrated by various studies and models (Thu et al. 2021; Future of Humanity Institute 2022). Decision-making on NPIs has generally been contested and hotly debated. Early on in the pandemic, public consensus carried the day in many countries; though this was far from universal. Even in countries where NPI measures were widely accepted and adhered to in the early months of the pandemic, measures such as the cancellation of public events and mask wearing became increasingly contested as the pandemic dragged on, lockdown fatigue set in, and the financial impacts became increasingly clear and difficult to bear.\n\nMask-wearing has become a political issue in various countries, such as in the United States, where it acts as a fault line between Democrats and Republicans (Aratani 2020). The role of scientific experts in decision-making processes is also a crucial factor, as many countries institutionalised scientific advisory bodies that provided governments with needed scientific and public health expertise in the pandemic response (Colman et al. 2021). However, the relationship between politicians and scientific experts is a complex one. Politicians generally face a variety of political and societal pressures that in some cases can go directly against the advice of scientific experts, which then potentially adversely affects pandemic decision making. At the same time, experts do not always agree, and there can be contestation between experts and expertise coming from different specialisms. It is important to further elucidate these dynamics to better understand public decisions taken in the context of the COVID-19 pandemic.\n\nIn many countries, local civil-society initiatives were set up to help with the pandemic response, supporting people to self-isolate, making masks etc. In some cases, these initiatives were set up in a context of low state capacity, filling important provision gaps. Women-led grassroots groups have often been at the forefront of these initiatives, improving hand washing facilities, setting up community kitchens, and raising awareness about COVID-19, to mention just a few examples (Sverdlik 2021). It will be important to understand what differences these local, societal responses made in the unfolding of the pandemic.\n\nOur current knowledge base on this aspect is medium, so we invite people who could provide further insights into the role of decision-making with regard to NPIs to share their insights with us.\n\n\n\n1. What factors contributed to countries’ ability or inability to implement NPIs? Was implementation and enforcement uniform across society? If not, why not?\n\n2. What aspects of infrastructure or details of implementation contributed to public compliance with NPIs?\n\n3. How did local civil-society and community groups organise and deliver support for NPIs? Did they rely on any pre-existing infrastructure, either state-provided or grassroots?\n\nThe ability of states to implement NPIs, which relates to their “implementation capacity”, has also played a role in their ability to control the spread of the virus. Especially large states, such as the USA, Brazil, and Russia, found it difficult to control the spread of SARS-CoV-2, partly because of their big populations and high population density in their main cities (Wong and Li 2020). While some of these states are believed to have ‘high state capacity’, the spread of SARS-CoV-2 was at times so fast that health systems in these countries collapsed or came close to collapsing, as happened to New York City in Spring 2020 (Armstrong et al. 2020). Developing countries, on the other hand, have often lacked the capacity to roll out public health measures in the way that other countries could. This often has to do with years of underinvestment in public health, limited fiscal space, and limited state capacity in general (UN 2022; Serikbayeva et al. 2021). This reflects the uneven impact the pandemic has had globally, which has also been visible on the national level in, for instance, its disproportionate impact on minority groups, such as on BAME communities in the UK (UK House of Commons Women and Equalities Committee 2020).\n\nThis brings us to the issue of compliance with NPIs. Compliance with NPI measures varied between countries and regions even in the early months of the pandemic, however, this compliance also decreased to various extents as the COVID-19 pandemic dragged on (Six et al. 2021, Liu et al. 2021). There is some evidence to suggest that compliance may correlate with public fear of the virus. The logic here is that when SARS-CoV-2 was “new”, people tended to fear it, and complied to a large extent with NPIs. Inversely, when the novelty of the virus dissipated, people became gradually less afraid, and compliance decreased accordingly (Harper et al. 2021). Compliance also became less steady through politicisation of some of the public health measures, such as mask wearing and bans on mass gatherings. Especially in Western countries, some of the public health measures were increasingly seen as incompatible with liberal democratic freedoms and resistance against them grew steadily.\n\nAs a final point, we have seen innovation with regards to NPIs. Masks soon became a staple of the pandemic response, and allowed for, for instance, safe(r) travel by public transport. Old and trusted test and trace systems were revived through the development of contact tracing apps. “Work from home orders” also worked surprisingly well, particularly in the developed world, due to developments in delivery infrastructures and videoconferencing, and would not have been imaginable on this scale 20 years ago. Other innovations were “hybrid” and “intelligent lockdowns”, which involved closing some public and private places while keeping others open, all on the basis of live monitoring of the public health situation (de Haas et al. 2020; Tullis 2020; de Voogd 2020). This allowed the avoidance of stark trade-offs between full-scale lockdowns and full societal openness. More recently, vaccine passports have been introduced to allow reopening of many societies (European Commission 2022).\n\nOur current knowledge base on this aspect is moderate, so we invite people who could provide further insights into the role of infrastructure/implementation with regard to NPIs to share their insights with us.\n\n\n\n1. How were NPIs communicated to the public?\n\n2. How did experts and governments communicate in response to resistance to NPIs, e.g. objections to wearing masks or lockdown resistance?\n\n3. What new forms of communication emerge during the pandemic, at the local, national and international level? What new information needs were these new forms addressing, and how well did they perform?\n\nPublic communication on NPIs was mostly conducted through press conferences. These kept the general public informed about the applicable measures and provided their rationale. As was the case with vaccines, there was a need to address mis- and disinformation as well. The UK ran the TV-campaign “Stop the Spread” with the WHO in May and June 2020 to raise awareness of the volume of misinformation around COVID-19 and to encourage people to double check information (WHO 2021). As noted, the task of communication evolved over the course of the pandemic, from crisis communication to a sustained effort that responded to changes in the epidemiological situation, and to emerging issues, such as mis- and disinformation and NPI fatigue surrounding masks and lockdowns.\n\nDuring the later phases of the pandemic, public communication also faced new challenges: it effectively had to convince the public that countries were still in “crisis mode” amidst growing lockdown fatigue and increasing doubts and resistance against public health measures. It is important to acknowledge and explore the relationship between the nature of certain NPIs and the types of societies they are introduced in, as this relationship touches on various important issues, including compliance, public trust, and the ability of politicians and policymakers to control the spread of SARS-CoV-2.\n\nOur current knowledge base on this aspect is medium, so we invite people who could provide further insights into the role of communication with regard to NPIs to share their insights with us.\n\nThe following is a (non-exhaustive) list of some of the key “open questions” that we have identified to date for this cluster of issues. These are indicative of the ongoing research agenda guiding this phase of our project, and we would be particularly keen to speak with practitioners and experts that can shed further light on answers to some or all of these questions:\n\n1. Which models are most useful in determining the effectiveness of NPIs and assessing counterfactuals and how can these inform present and future pandemic responses?\n\n2. How can one best analyse decision-making processes in the context of the pandemic and the role of scientific experts therein?\n\n3. What are the determinants of compliance with NPIs and how can people best be motivated to comply with measures aimed to control the spread of SARS-CoV-2? To what extent can (non-medical) innovation and technology guide us out of the pandemic?\n\n4. And what does the role of technology and innovation in the pandemic response tell us about their (potential) role in other crises, such as those involving climate change and the loss of biodiversity?\n\nOnce again, our aim here is to answer to overarching questions in relation to NPIs:\n\nWhat types of NPIs, accompanied by what provision of resources and which communication strategies, would have most significantly altered the trajectory of the pandemic, and significantly reduced the global loss of life, injury, and harm?\n\nWhat can we learn from the successes and failures of national, regional, and global efforts to mitigate or control the COVID-19 pandemic through NPIs in order to better prepare us to respond effectively to other categories of Global Catastrophic Risk?\n\n\nConclusion: lessons from COVID-19 research agenda, the way forward\n\nThe “Lessons from COVID-19” project aims to analyse responses to the COVID-19 pandemic. It aims to draw broader lessons not only for future pandemics, but also for other global catastrophic risks (GCRs), such as extreme climate change and possible catastrophic accidents involving novel technologies. The project will identify and assess key inflection points during the pandemic, when decisions or the lack thereof significantly altered the course of the pandemic, and moved the death toll up or down. Counterfactual analysis will be employed to get a sense of how the trajectory of the pandemic could have been changed for the better based on a different set of interventions in the pandemic response.\n\nBased on our initial survey of secondary sources, a set of early-stage interviews, and our preliminary observations more broadly, efforts to contain the pandemic seem to have effectively failed in the first few months after the outbreak of COVID-19, especially when set against a background of notionally high information availability and preparedness (as compared with other GCRs). In particular, January and February 2020 were lost months, in which early action was lacking in many parts of the world and the opportunity to contain the virus was missed. Complacency and a “wait-and-see” approach gave COVID-19 the chance to transform from an outbreak of concern to a pandemic that could no longer be stopped in its tracks. On top of that, few countries truly had pandemic preparedness in order, a key factor that needs to be addressed to ensure more timely and effective pandemic responses in the future.\n\nThis research agenda has formulated key questions with regards to the pandemic response, based on four broad “clusters”, ranging from pandemic preparedness to non-pharmaceutical interventions. Key questions focus on the usefulness and effectiveness of pandemic preparedness plans, the lack of early action and containment measures, vaccine strategies and vaccine equity and the role of science and technology in managing catastrophic crises, such as the COVID-19 pandemic. Crucially, we focus on the decision making around these themes.\n\nWe are interested in forging partnerships and collaborations with organisations, experts, and individuals that have expertise in pandemic risk and/or are/were involved with the pandemic response. We believe national and international partnerships are key to learning the right lessons from a pandemic that has affected us all and in translating these lessons into public policies that will better prepare us for present and future pandemics, and catastrophic and existential risks more broadly.\n\n\nData availability\n\nThere are no data associated with this article.", "appendix": "Acknowledgements\n\nWe would like to express our thanks to Jess Whittlestone and Sean Ó hÉigeartaigh for helping secure funding for the project, and for early involvement in the research. We are also grateful to Akaraseth Puranasamriddhi for his research contributions to our project. Finally, we thank Charlotte Hammer for her insights shared through an interview and written comments that directly benefited our research agenda.\n\n\nReferences\n\nAdam D: The pandemic’s true death toll: millions more than official counts. Nature. 2022 January 18. 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Views from scientists on government advisory boards during the COVID-19 pandemic: a qualitative interview study in five European countries. BMJ. 2021; 6(9). Publisher Full Text Reference Source\n\nde Haas M , Faber R, Hamersma M: How COVID-19 and the Dutch ‘intelligent lockdown’ change activities, work and travel behaviour: Evidence from longitudinal data in the Netherlands. Transp. Res. Interdiscip. Perspect. 2020; 6(July): 100111–100150. Publisher Full Text\n\nDolgin E: The tangled history of mRNA vaccines. Nature. 2021 September 14; 597: 318–324. PubMed Abstract \| Publisher Full Text Reference Source\n\nHammers C: Interviewed by Jochem Rietveld, March 2022.2022.\n\nHan E, Tan MMJ, Turk E, et al.: Lessons learnt from easing COVID-19 restrictions: an analysis of countries and regions in Asia Pacific and Europe. Lancet. 2020; 396(10261): 1525–1534. Publisher Full Text\n\nHarper C, Satchell L, Fido D, et al.: Functional Fear Predicts Public Health Compliance in the COVID-19 Pandemic. 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PubMed Abstract \| Publisher Full Text\n\nMadhav N, Oppenheim B, Gallivan M, et al.: Pandemics: Risks, Impacts, and Mitigation. Disease Control Priorities: Improving Health and Reducing Poverty. Jamison D, Gelband H, Horton S, et al., editors. 3rd edition.Washington (DC): The International Bank for Reconstruction and Development; 2017.\n\nParry J: China coronavirus: cases surge as official admits human to human transmission. BMJ. 2020; 368: m236. Publisher Full Text PubMed Abstract \| Reference Source\n\nPaton D, Smith L, Daly M, et al.: Risk perception and volcanic hazard mitigation: Individual and social perspectives. J. Volcanol. Geotherm. Res. 2008; 172(January): 179–188. Publisher Full Text\n\nRonan K, Johnston D: Hazard education for youth: a quasi-experimental investigation. Risk Anal. 2003; 23(5): 1009–1020. Publisher Full Text\n\nSato S: Counterfactual Analysis. Research Methods in the Social Sciences: An A-Z of key concepts. Morin J-F, Olsson C, Atikcan EÖ, editors. Oxford: Oxford University Press; 2021.\n\nSauer M, Truelove S, Gerste A, et al.: A Failure to Communicate? How Public Messaging Has Strained the COVID-19 Response in the United States. Health Security. 2021; 19(1): 65–74. PubMed Abstract \| Publisher Full Text\n\nSerikbayeva B, Abdulla K, Oskenbayev Y: State Capacity in Responding to COVID-19. Int. J. Public Adm. 2021; 44(11-12): 920–930. Publisher Full Text\n\nShaw R, Shiwaku K, Kobayashi H, et al.: Linking experience, education, perception and earthquake preparedness. Disaster Prevention and Management: An International Journal. 2004; 13(1): 39–49. Publisher Full Text\n\nSix F, de Vadder S , Glavina M, et al.: What drives compliance with COVID-19 measures over time? Explaining changing impacts with Goal Framing Theory. Regul. Gov. 2021. PubMed Abstract \| Publisher Full Text\n\nThu TP, Bao PN, Ngoc H, et al.: Effect of the social distancing measures on the spread of COVID-19 in 10 highly infected countries. Sci. Total Environ. 2021; 742(Nov): 140430. PubMed Abstract \| Publisher Full Text\n\nTurchin A, Denkenberger D: Global catastrophic and existential risks communication scale. Futures. 2018; 102(September): 27–38. Publisher Full Text\n\nWong D, Li Y: Spreading of COVID-19: Density matters. PLoS One. 2020; 15(12): e0242398. PubMed Abstract \| Publisher Full Text\n\n\nFootnotes\n\n1 There are inherent difficulties with estimating COVID-19 death tolls. For a comprehensive and thorough discussion of this challenge, see Adam (2022).\n\n2 The Independent Panel for Pandemic Preparedness & Response was formed following a request from the World Health Assembly to the Director-General of WHO in May 2020 to initiate “an impartial, independent, and comprehensive review of the international health response to COVID-19 and of experiences gained and lessons learned from that, and to make recommendations to improve capacities for the future” (Independent Panel 2021, 8). The Panel initiated its work in September 2020 and reported in May 2021. For more information on the Panel’s work, see https://theindependentpanel.org/.\n\n3 We acknowledge this is a contested boundary. It is still a useful cut-off point though as the summer/early autumn of 2020 represented a transition period in which many countries had experienced a first wave- often followed by a period in which the pandemic receded to some extent. As more information on the effectiveness of the various public health measures became steadily available during this period of time, countries transited from the early action phase to a sustained pandemic management phase." }	[ { "id": "156391", "date": "04 Jan 2023", "name": "Stephen Hanney", "expertise": [ "Reviewer Expertise The organisation and impact of health research and health research systems." ], "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 generally well-written, ambitious opinion paper provides a research agenda or structure to study the response to the COVID-19 pandemic, and learn lessons from a Global Catastrophic Risk (GCR) perspective. Using this structure it outlines the team’s current knowledge base on a series of issues, and asks if readers can provide insights on specific points.\nThe excellent aims of the study, for which this paper provides the research agenda, include investigating key decisions (or failures to decide) that altered the course of the pandemic, and then using the lessons to improve pandemic preparedness in future. The study also seeks to ask how the lessons could be transferred to other areas of potential GCR management such as extreme climate change and radical loss of biodiversity. The study aims to identify the key moments, or “inflection points”, through examining what are called four broad clusters: pandemic preparedness, early action (from December 2019 to summer/early autumn 2020), vaccines and non-pharmaceutical interventions (NPIs). Four aspects are listed that are common across all four clusters and can be used to assess the possible inflection points in each cluster. These aspects are: information, decision making, infrastructure/implementation and communications.\nThe research agenda identifies different and specific key questions for each of the four aspects in turn, in each of the four clusters. The paper provides some text addressing the questions and at the end of each aspect indicates whether the team’s knowledge base is high, moderate or low but, irrespective of that, invites readers to provide further insights. Additionally, at the end of each cluster there is a concluding section listing some of the open questions that, the authors say, “are indicative of the ongoing research agenda guiding this phase of our project”. They say they would particularly like to speak to experts and practitioners who can shed light on those questions.\nThe many strengths of the paper suggest that the research agenda is likely to provide a sound basis for a substantial analysis of key parts of the pandemic, and the identification of useful lessons. For example, the first main section is on Cluster #1, pandemic preparedness, and it starts with the important observation from a World Health Organization (WHO) report that pandemic preparedness should be defined as “a continuous process”. Using this as the definition helps focus the analysis on where the shortcomings emerged, and how notions of preparedness have now started to evolve.\nThere are, however, considerable challenges facing the task of constructing and presenting a research agenda in this field. An enormous number of studies have already been conducted on diverse aspects of the COVID-19 pandemic, and thousands of papers have already been published. Therefore, constructing a new research agenda that adequately reflects, incorporates and builds on the existing state of knowledge requires considerable effort and thought. As noted, the authors ingeniously attempt to alleviate this challenge, and indeed bolster the pool of evidence for them to analyse, by inviting readers at the various points to share their own insights. In this way the authors are themselves, at times, indicating that they are aware that some arguments should be supported by additional evidence from the published literature, and that they are actively seeking such evidence for their ongoing study.\nBeing invited to review this paper some six months after its publication in May 2022, itself presents challenges and opportunities because some of the inevitably large number of suggestions about further insights that could be made, and the additional evidence, come from the stream of publications that continued through that six months. In particular, there were other comprehensive studies that attempted to provide lessons from the pandemic based on wide-ranging analysis. Some of these drew on and collated evidence from hundreds of earlier publications (The Lancet Commission, 2022; Hanney et al, 2022). While, of course, these collations published after May 2022 could not have been included in the paper under review, many of the insights in them are drawn from analysis of earlier publications. Having acknowledged this point, the overlaps mean it is not helpful for this review to be divided into insights that had been available before May 2022, and those now available. Instead, from here on this review will be divided into two main parts (with one common reference list):\nA) Suggestions made as a reviewer of points where possible amendments should be seriously considered in future editions of the paper.\nB) Comments made as a reader in response to the authors’ requests for additional insights to consider for possible inclusion in the study, and possibly in any future editions of the paper, as the authors see fit. Many of these comments are based on analysis included in the two recent collations of evidence described above, and cite papers whose contributions are usually described at greater length in one or both of those two collations. (It might be worth noting, however, that along with much excellent analysis, there are some points in the report of the Lancet Commission 2022 on lessons for the future from the COVID-19 pandemic that do not seem consistent with the evidence published elsewhere).\nA) Suggestions as a reviewer of points where possible amendments should seriously be considered in future editions of the paper.\nIntroduction, and repeated elsewhere. As noted, one of the aims of the paper is to identify lessons that could be transferred to other areas of potential GCR management such as extreme climate change and radical loss of biodiversity. This is a laudable aim, but I think the paper would benefit from a somewhat further explanation of how “extreme climate change” and “radical loss of biodiversity” are sufficiently parallel to the rapid emergence of the pandemic to allow many lessons to be drawn. The authors themselves claim that January and February 2020 “were lost months, in which early action was lacking in many parts of the world and the opportunity to contain the virus was missed” (pp.17/18). That seems correct, but also underlines a key difference of timescale with the other GCRs above where the crises seem to be building up over many years. Perhaps this distinction could also additionally be considered as a possible limitation towards the end of the article?\n\nIntroduction. While the Introduction generally sets the paper up well, I think it might be easier for the reader to absorb the key point that the clusters will be used to organise the rest of paper if some of the points were presented slightly differently here. In the Introduction there is a numbered list of four questions that the study is asking about the decisions taken in the pandemic and counterfactuals about what could have been done differently. Then there is a very brief paragraph in which the four clusters of issues to be studied are included in a brief sentence with no numbering of the points. Then the four aspects to be considered in each cluster are described, with numbers attached to each one. However, the remainder of the full paper is organised according to the clusters, with each one of the subsequent main sections headed with the number and name of the relevant cluster. Therefore, perhaps it would be helpful in the Introduction if it was the clusters that were presented more prominently and in a numbered list.\n\nCluster #1: pandemic preparedness/Cluster #2: early action. In Cluster #2 the paper highlights decision making in the early phase in China and other Asian countries. Below, however, I outline how there were also important examples of early action in Australia and New Zealand, and these might suggest it could be better to consider referring (alternatively or also) to WHO’s Western Pacific Region as the location for examples of early action? Useful evidence from Australia about early action is linked to pandemic preparedness and research. Coordinated research preparedness had occurred through the 13 organizations who were members of the Australian Partnership for Preparedness Research on Infectious Disease Emergencies (APPRISE) that was created in 2016. It responded to COVID-19 by activating a pre-planned research platform as early as 13th January 2020 (National Health and Medical Research Council, 2020). In New South Wales (NSW) the government’s response built on previous pandemic planning and as early as 21st January 2020 NSW Health opened its Public Health Emergency Operations Centre. This was ready if, and when, necessary, “to coordinate case finding, contact tracing, outbreak control, communications, and other preventive actions” (McAnulty & Ward, 2020). There was also effective early action in New Zealand shortly after the first cases were reported, although in this instance it was not so much a result of earlier pandemic preparedness (Geoghegan et al, 2021). There are also wider accounts of evidence from Australasia and countries such as Germany that analyse the valuable role of health research systems in working closely with politicians in developing and using evidence for early and effective action, including to introduce NPIs (Hanney et al, 2022 - see especially pp. 23-28). (This issue is further discussed in point 5 below).\n\nCluster #3: Vaccines. On pp.12/13 the paper rightly refers to the remarkable speed of the vaccine development by multiple companies, particularly for the mRNA vaccines, and how this technology was based on many years of prior work by expert scientists. While all this is correct and relevant, I think the years of work by scientists at Oxford University should also be featured as their rapid COVID vaccine development was similarly based on their earlier work that had led to the development of a vaccine platform that was available when COVID-19 arrived. According to Sarah Gilbert, lead developer of the vaccine, the team had been “thinking about an appropriate response to Disease X; how could we mobilise and focus our resources to go more quickly than we had ever gone before. And then Disease X arrived” (Lane, 2020; Gilbert & Green, 2021).\n\nCluster #4: NPIs (p.14-17) in relation to Cluster #2: early action (p.9-11). The paper states “cluster 4 looks into the use of NPIs during the stage where the virus was widely circulating, so beyond the early action stage”. The paper also acknowledges NPIs were part of the early action, but, as noted, above, the effective early introductions of NPIs in Australia and New Zealand etc had considerable success, and while selected NPIs (such as border controls) were continued after the early phase, the virus was still not widely circulating in those countries. Therefore perhaps in that context, and to enhance understanding about the effective use of NPIs, it would be valuable to consider going further and applying some of the Cluster #4 questions about NPIs specifically to evidence from those countries. Examples include the actions by the NSW Health that brought researchers in to the department to co-produce evidence on NPIs and other policies (Campbell et al, 2021). Similarly, in New Zealand, the experts played a key role in informing action, and research teams with links to the Ministry of Health produced valuable evidence about how highly effective the NPIs had been, and also could potentially provide useful evidence in relation to the following question in Cluster #4, Decision-making: “What would an ideal timeline with regards to NPIs have looked like” (Jefferies et al, 2020; Geoghegan et al, 2021). (However, fuller relaxation of NPIs in both countries was followed in 2022 by a large increase in cases, but the high level of vaccination achieved by then meant the cumulative death rate in each country, while considerably increased, was still much lower than in most other countries).\n\nB) Comments made as a reader in response to the authors’ requests for additional insights to consider for possible inclusion in the study, and possibly in any future editions of the paper, as the authors see fit.\nIn terms of how far preparedness helped countries respond well to the pandemic, various insights might come from comparing the pandemic performance of countries with the data published in the Global Health Security (GHS) Index in October 2019 about the countries' potential level of health security preparedness (GHS Index, 2019). While the GHS Index went much wider than just pandemic preparedness, and found no country was completely prepared for a major health emergency, various authors raised questions about why the countries ranked first and second on the GHS Index, ie the US and the UK, had a much higher death rate from COVID-19 than many other countries (Nuzzo et al, 2020; Tworek et al, 2020; Farrar, 2021; Hanney et al, 2022; The Lancet Commission, 2022).\n\nThe Cluster #2: early action, Information section starts with the question: “What information was available about SARS-CoV-2 in the early days and weeks immediately following its discovery?” A range of important insights about this can be found in the early chapters of the authoritative account by Jeremy Farrar, with Anjana Ahuja, called Spike: The Virus vs The People. The Inside Story (Farrar, 2021).\n\nIn the Cluster #2: early action, Decisions section, particularly where the role of WHO is discussed, further insights might come from drawing on the Lancet Commission Report’s sections on the early response and WHO shortcomings (pp.10-12) (The Lancet Commission, 2022), and the WHO’s response to the report’s criticisms (WHO, 2022).\n\nThere are insights about the unique research infrastructure existing in the UK at the start of 2020 that, while not specifically related to pandemic preparedness per se, might be relevant for several of the clusters. It is widely agreed that it was the research infrastructure of the National Institute for Health Research (NIHR), embedded across the National Health Service (NHS), that facilitated the Randomised Evaluation of COVID-19 Therapy (RECOVER) trial’s rapid recruitment and globally leading progress to identify existing drugs that were, or were not, effective therapies for treating COVID-19 (Lane & Fauci, 2020; Pessoa-Amorim et al, 2021; Hanney et al, 2022).\n\nFor the Cluster #2: early action, Communications section, additional analyses not only concur with the examples of effectiveness already identified in paper, including the role Germany’s Angela Merkel and New Zealand’s Jacinda Ardern, but also provide further insights. Additional examples of effectiveness are reported from jurisdictions such as Senegal, South Korea and the Canadian province of British, along with an attempt to list common features found in many examples of effective pandemic communication that might be useful if more widely adopted (Tworek et al, 2020).\n\nFor Cluster #3: vaccines, there are many additional studies available that can provide further insights on some of the questions asked in the paper. In the information section, one question relates to the nature of proposals being considered in research communities prior to the pandemic for rapid vaccine development, and what actually happened. Here, previous analysis proposed that research on innovations such as drugs and vaccines could be accelerated through approaches including increasing resources, working in parallel, starting or working at risk and improving processes (Hanney et al, 2015). Rapid analysis of the work on developing COVID-19 vaccines suggested examples of all of these approaches could be seen (Hanney et al, 2020). This paper also considered which of the factors it might be possible to replicate in future on a regular basis, and which factors, such as the extreme concentration of resources and avoidance of the usual queues for decisions, might only be possible in a pandemic-type situation. In addition to the improved processes noted above through new vaccine platforms, there were striking examples of working in parallel, and crucially including early manufacture in that (Lurie et al, 2020) along with provision of greatly increased resources, in particular with Operation Warp Speed in the US which combined enormous financial resources with the logistical expertise provided through the Department of Defense (Slaoui & Hepburn, 2020; Koehlmoos et al, 2022). In the Decision making section, the Lancet Commission provides further insights on questions about how decisions were made about the global distribution of vaccines and the COVID-19 Vaccines Global Access Facility (COVAX) (The Lancet Commission, 2022).\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? Yes", "responses": [ { "c_id": "10802", "date": "17 Jan 2024", "name": "Jochem Rietveld", "role": "Author Response", "response": "First of all, we’d like to express our sincere thanks for the time and effort invested in writing this review. This is very much appreciated. Our response will now proceed in a point-by-point format A) 1. The difference in timescales has now been acknowledged in the introduction. A note has also been added that this may limit crosscutting insights from the pandemic to some other risk areas that seem to operate on different timescales. 2. The clusters have now been numbered in the introduction, while the four aspects have been given letters instead of numbers, to clarify the article’s structure. 3. We have now included a mention of the early interventions of Australia and New Zealand in the early action cluster (cluster 2). 4. The work of the Oxford team that developed a platform to prepare for the arrival of ‘disease X’ has now been acknowledged in the vaccine cluster (cluster 3) 5. The success of Australia and New Zealand in preventing widespread circulation of the virus through the effective use of NPIs has now been added to the NPI cluster (cluster 4). This includes a note that this makes them particularly interesting cases in this cluster. B) While no immediate in-text edits have been made in response to the points made under B), we very much welcome these additional insights offered by the reviewer and see these as important starting points for the implementation of our research agenda." } ] }, { "id": "203305", "date": "22 Sep 2023", "name": "Ortwin Renn", "expertise": [ "Reviewer Expertise Sociology and Risk Governamnce" ], "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\nReview The article provides a metanalysis of the management and governance approaches to deal with the Covid-19 crisis worldwide. The paper defines four broad clusters: pandemic preparedness, early action (from December 2019 to summer/early autumn 2020), vaccines and non-pharmaceutical interventions (NPIs). Within each of these cluster the paper addresses four crucial aspects: information, decision making, infrastructure/implementation and communications. The main objective for this review is to learn from the experiences with COVID 19 in order to be better prepared for other global catastrophic risks.\nThe paper summarizes what the authors re-construct as major policy responses during the four phases of the crisis. It also lists potential drivers and reasons for good or bad performance and suggests some lessons for how to improve emergency preparedness and governance for future pandemics but also for other major disasters.\nEach section of the paper ends with a subjective assessment of what the authors believe is their level of knowledge and a series of question for other professionals to ship in their own evidence and knowledge. The lessons for other disasters categories are not explicitly articulated but left open for further input.\nIn my view, the endeavor to collect and categorize the experiences from managing and governing the pandemics is extremely ambitious but certainly worth while pursuing. The main challenges here are:\nVery different performance profiles in different countries (In terms of policies, institutional responsibilities, compliance rates, death toll, health system performance, etc.)\n\nMajor differences in vulnerability (age distribution, spatial density, status of health systems)\n\nLarge variety of institutional and legal systems in the countries affected by the pandemic,\n\nDifferent roles of private and public institutions in different countries\n\nLarge variation in individual compliance, protective actions, and behavioral responses.\nIn light of these challenges, I find it almost impossible to draw general conclusions about what deficits were encountered and what went wrong on a global perspective. One might cluster countries with similar political culture and institutional settings or select particularly interesting examples such as US, Brazil, New Zealand, Korea, Sweden, Italy and Tanzania.\nA second problem with the paper is the reliance on expert judgement rather than empirical evidence. I am fully aware that there is an abundance of empirical evidence that is hard to digest and ever harder to summarize. This may be an interesting case for using AI systems. Even if other investigators have been asked to contribute, it is unclear whether the authors like to collect more evidence or more expert judgements. It would be good to specify what input in what from the authors expect from the rest of the community. The references in the paper right now represent only a small fraction even of the comparative empirical research and would need to be substantially enhanced if the claim for a comprehensive review is sustained. Alternatively, the authors could systematically collect professional judgments but, in this case, it would be good to use a more organized method such as Delphi or Consensus Conferencing.\nFinally, I would be skeptical about the potential to draw conclusions from the pandemic for other applications of global catastrophes. Other than the normal generalities (be better prepared, have emergency management teams ready before disaster strikes, engage in effective communication, etc.) many of the mentioned global disasters such as global climate change or being hit by a large meteorite, require management and governance responses that differ al lot from the context of pandemics. Unless the authors provide some good evidence or arguments that show the transferability of lessons from COVID to be meaningfully applied to other disasters, I am not convinced.\nOverall, I endorse the experiment to organize a collective effort to synthesize the experiences from the COVID crisis and start a mutual learning process by asking for input from the scientific and policy communities worldwide. However, I would suggest a far more structured approach, a clearer distinction between countries and political cultures, and more specific set of questions and input categories for potential contributors and a more differentiated perspective when applying insights from the pandemic to other disaster areas.\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? No\n\nAre arguments sufficiently supported by evidence from the published literature? No\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Partly", "responses": [ { "c_id": "10803", "date": "17 Jan 2024", "name": "Jochem Rietveld", "role": "Author Response", "response": "First of all, we’d like to express our sincere thanks for the time and effort invested in writing this review. This is very much appreciated. Our response will now proceed in a point-by-point format Re- input from the rest of the community: We agree further specification in this area would be helpful. With your suggestions in mind, we have added a paragraph to the introduction in which we outline two main routes for implementation of our research agenda: an ‘expert judgments route’ through use of the Delphi method and/or a ‘empirical data route’ through systematic data collection by a collective of researchers. Re-very different performance profiles in different countries: We recognise this challenge. We hope and expect to find patterns in response and challenges experienced by many countries. These patterns and challenges can be illustrated by using country examples. We do not aim to provide any conclusive accounts about specific countries or clusters of countries. While there is significant merit in such an approach, this is beyond the scope of our endeavour. However, if there is an interest among researchers in taking the above approach, we would of course encourage them to do so Re- management and governance responses vis-a-vis different global disasters: We recognise that specific global disasters will require tailored management and governance responses. It is clear that certain lessons from the COVID-19 pandemic will be limited in scope and may only be transferable to future pandemics of a similar viral agent. One can think of the patterns of spread of SARS-CoV-2 and the lessons that have been learnt in mitigating against this spread, through, for instance, social distancing and mask wearing. These are lessons that have little relevance for, say, meeting the challenge of climate change and rapid AI development and deployment. We believe, however, that there are also transferable lessons to be identified and learnt. The reviewer has a point when he calls these the usual ‘generalities, such as ‘be prepared, communicate effectively’ etc. However, while these ‘generalities’ may have been highlighted in the academic literature and national and international and policy circles for years, including before the COVID-19 pandemic, it is evident that the pandemic has exposed that these insights have been insufficiently implemented in policy practice, both at the national, regional, and global level. The pandemic has also offered a significant case to assess how all the insights in governance, communication, and leadership have played out in practice. This has led to new insights and perspectives, as well as the revision of ‘established wisdoms’ in public health, such as those held around dominant ways of viral spread. Misinformation and disinformation, while not new, have had an outsized influence on the pandemic response on a scale not seen in crises in recent years and governments struggled to deal with this challenge. Overall the pandemic has demonstrated that while many of the ‘usual generalities’ such as ‘be prepared’ and ‘communicate effectively’ continue to hold, these also require to be continuously updated and redefined in the face of new developments and challenges." } ] } ]	1	https://f1000research.com/articles/11-514
https://f1000research.com/articles/12-512/v1	18 May 23	{ "type": "Review", "title": "Making science public: a review of journalists’ use of Open Science research", "authors": [ "Alice Fleerackers", "Natascha Chtena", "Stephen Pinfield", "Juan Pablo Alperin", "Germana Barata", "Monique Oliveira", "Isabella Peters", "Stephen Pinfield", "Juan Pablo Alperin", "Germana Barata", "Monique Oliveira", "Isabella Peters" ], "abstract": "Science journalists are uniquely positioned to increase the societal impact of open science by contextualizing and communicating research findings in ways that highlight their relevance and implications for non-specialist audiences. Through engagement with and coverage of open research outputs, journalists can help align the ideals of openness, transparency, and accountability with the wider public sphere and its democratic potential. Yet, it is unclear to what degree journalists use open research outputs in their reporting, what factors motivate or constrain this use, and how the recent surge in openly available research seen during the COVID-19 pandemic has affected the relationship between open science and science journalism. This literature review thus examines journalists’ use of open research outputs, specifically open access publications and preprints. We focus on literature published from 2018 onwards—particularly literature relating to the COVID-19 pandemic—but also include seminal articles outside the search dates. We find that, despite journalists’ potential to act as critical brokers of open access knowledge, their use of open research outputs is hampered by an overreliance on traditional criteria for evaluating scientific quality; concerns about the trustworthiness of open research outputs; and challenges using and verifying the findings. We also find that, while the COVID-19 pandemic encouraged journalists to explore open research outputs such as preprints, the extent to which these explorations will become established journalistic practices remains unclear. Furthermore, we note that current research is overwhelmingly authored and focused on the Global North, and the United States specifically. Finally, given the dearth of research in this area, we conclude with recommendations for future research that attend to issues of equity and diversity, and more explicitly examine the intersections of open science and science journalism.", "keywords": [ "Open science", "journalism", "COVID-19" ], "content": "Introduction\n\nOpen science (OS) is a global movement aiming to “make scientific research from all fields accessible to everyone” (UNESCO, 2023). It encapsulates a range of practices that seek to provide free and unrestricted access to research findings (i.e., publishing research papers in publicly available venues) but also to the research process itself (e.g., sharing software, code, protocols, or datasets used in research). Collectively, these practices are united by a vision of a scientific system that is more collaborative, equitable, sustainable, and beneficial—to scientists as well as the wider societies within which they work (ibid.). In line with this vision, an increasing number of scholarly publications are made freely available to the public each year (Piwowar et al., 2018, 2019). Adding to this growth in open access (OA) journal publications is the increasingly common practice of making research freely available ahead of peer review in the form of preprints (Puebla et al., 2021). The scholarly community’s use of open research outputs has further accelerated during the COVID-19 pandemic, with an unprecedented number of OA publications and preprints becoming available (Fraser et al., 2021; Waltman et al., 2021).\n\nHowever, making research outputs openly available does not automatically make them accessible to a public audience. Academic publications are written for peer researchers and academics rather than the general public and use specialized language and rhetorical features meant for communication with and within certain communities (Fahnestock, 1986). They are written according to the conventions and norms of the disciplines within which they are produced and can be very difficult for ‘lay’ readers to understand. Thus, realistically, open licensing only expands access to academic and practitioner audiences who have the educational or professional background to read research. For the public to truly engage with and benefit from open outputs, it is necessary to provide not only “technical” or “material” access to research but also “conceptual access” that enables them to understand and use the findings (Kelly & Autry, 2013).\n\nScience journalists are ideally positioned to provide such conceptual access because they can critique, contextualize, and communicate findings from open research outputs in ways that highlight their relevance and implications for non-specialist audiences. That is, science journalists can help align the ideals of OS “with the realities of complex, specialized genres of writing to provide better, more ‘open,’ access to research” (Kelly & Autry, 2013, p. 1). Yet, it is unclear to what degree journalists use the resources and outputs emerging as a result of the adoption of OS in their reporting, what factors motivate or constrain this use, and how the recent surge in openly available research seen during the COVID-19 pandemic has affected the relationship between OS and science journalism (SJ) (Schultz, 2023).\n\nTo examine these gaps, we conducted a review of a review of peer-reviewed publications, preprints, editorials, commentaries, and blog posts, exploring the intersections of SJ and OS, with a focus on journalists’ use of openly available research outputs (i.e., OA publications and preprints). We focused on these two forms of OS because journalists tend to report on study results, rather than the methods, protocols, or datasets used to conduct the research (Matthias et al., 2019). Using relevant keywords, we searched Google Scholar for literature published since 2018—particularly literature relating to the COVID-19 pandemic—but also included seminal articles (i.e., those frequently mentioned by other sources) outside the search dates. Although Google Scholar indexes literature from many languages, the search algorithm is highly biased towards English-language publications (Rovira et al., 2021); as such, this language bias is a limitation of our review. We extracted, grouped, and abstracted results and arguments using an adapted qualitative meta summary approach (Sandelowski & Barroso, 2007) to provide a narrative synthesis of the key findings. We found very little scholarship that explicitly examines how OS practices, values, or concepts interface with journalistic ones, nor how journalists engage with open research outputs. Therefore, this review mainly covers research and theoretical contributions that discuss the intersections of OS and SJ tangentially or as a secondary concern, rather than a primary focus. Journalists’ use of open data and open code, while relevant to this discussion, is outside the scope of this paper and will be discussed in future work.\n\nOur findings show that although science journalists are ideally positioned to facilitate public access to research, their potential to do so is hampered by an overreliance on traditional criteria for evaluating scientific quality; concerns about the trustworthiness of open research outputs; and challenges identifying, using, and verifying the findings. We also found that, although the COVID-19 pandemic encouraged journalists to explore OA outputs such as preprints, the extent to which these explorations will become established journalistic practices remains unclear. Additionally, most of the literature reviewed is authored and focused on the Global North, and the United States specifically. In general, more perspectives from and on the Global South are needed, as are empirical studies to be used as an evidentiary base. We conclude with recommendations for future research that is empirically and theoretically grounded, attends to issues of equity and diversity, and more explicitly examines the intersections of OS and SJ.\n\n\nThe argument for OS-based journalism\n\nPhilosopher of science Kevin Elliott is one of few scholars who has explicitly examined the intersection of OS and SJ. In 2019, he proposed that “bringing open science and science journalism into conversation with each other” (Elliott, 2019, p. 5) could lead to more critical science media coverage that helps audiences better understand the value judgments that shape scientific work. Such critical coverage would move beyond simply reporting research findings to illuminating the process of science itself. In doing so, it could address value judgments inherent in all research—such as the choice of research questions or methods, and the impacts of those choices for the results and their interpretations—but could also focus on those specific to the OS movement, such as the factors that motivate researchers to post articles ahead of peer review (i.e., preprints) or publish in OA journals (Elliott, 2019). It could also emphasize personally or societally relevant aspects of research findings (Elliott, 2022), which sometimes differ from those seen as scientifically relevant (Elliott & Resnik, 2019). Besançon et al. (2021) have similarly argued that high quality, critical journalism is essential for communicating and contextualizing research knowledge with public audiences. The authors view OS practices as both facilitating and complicating journalists’ work by providing a “wealth of available information” that would otherwise not be accessible. Finally, Arbuckle (2019) has highlighted that science journalists sometimes also provide material access to research, as they help bring findings that are not openly available to a wider public audience.\n\nThese OS-specific arguments echo broader conceptualizations of SJ as acting as a bridge between science and society that enables citizens to engage with research knowledge. For example, Ampollini and Bucchi (2020) argue that media coverage of research integrity issues could connect researchers with citizens, media, policy makers, and other research stakeholders in important discussions about the nature of science. More broadly, health and science journalists have been conceptualized as “brokers” of research knowledge (Gesualdo et al., 2020; Pentzold et al., 2021; Yanovitzky & Weber, 2019) who can communicate, critique, and contextualize science and thus make it more “conceptually” accessible (Kelly & Autry, 2013) and transparent in ways that are “societally-relevant” (Elliott & Resnik, 2019). Applied to the OS context, the knowledge broker framework (Yanovitzky & Weber, 2019) suggests that journalists have the potential to facilitate broader engagement with open research outputs by: 1) fostering public awareness of the OS and OA movements, 2) rendering open outputs (conceptually) accessible to nonacademic audiences, 3) engaging a wider public with debates around openness that are taking place within academia, 4) linking those debates to wider social issues or policies with public relevance, and 5) mobilizing open research findings to hold those in power to account when policies or decisions do not align with the available evidence. Such brokerage functions may enable journalists to build trust in science, as providing clear and understandable descriptions of OS practices involved in research can boost public credibility judgments of the findings (Song et al., 2022). Similarly, although health and science journalists fulfill some traditional journalistic roles—such as watchdog (holding powerful scientific or pharmaceutical institutions to account) and agenda setter (driving attention to new trends, issues, and findings in research)—they also play additional roles such as the civic educator, using their skills to teach audiences about the nature of scientific research and its limits and risks (Fahy & Nisbet, 2011).\n\nThese roles and functions, while not always consistently performed in practice, could enable science journalists to contribute to OS by making “scientific knowledge openly available, accessible and reusable for everyone, to increase scientific collaborations and sharing of information for the benefits of science and society, and to open the processes of scientific knowledge creation, evaluation, and communication to societal actors beyond the traditional scientific community” (UNESCO, 2021, p. 6). That is, science journalists are ideally positioned to contribute to the “science communication” pillar of OS proposed in the influential UNESCO recommendations by brokering open research knowledge to public audiences. However, although scholars have highlighted this potential for journalists to contribute to the OS movement, very few studies have empirically examined journalists’ perceptions or use of open research outputs.\n\n\nJournalists’ pre-pandemic use of Open Access publications and preprints\n\nJournalists have often been accused of “uncritically accepting sources’ designation of what is important and worthy of notice” (Dunwoody, 2021, p. 20). This tendency—identified in journalists working across multiple beats—is likely to be more common among those who cover research-heavy topics, such as science and health, for two reasons. First, the complex, jargon-laden, and hyper-specialized nature of scientific work (Baram-Tsabari et al., 2020; Ordway, 2022) means that journalists often rely heavily on the judgements of the scientists they interview to critique, contextualize, and verify new research findings (Conrad, 1999; Hansen, 1994; Sebbah et al., 2022). Second, the mutual dependence of journalists on scientists (i.e., as sources of evidence and information) and scientists on journalists (i.e., as sources of public exposure and support) can encourage these groups to adopt one another’s norms and values (Moorhead et al., 2022)—a phenomenon known as the medialization of science (Peters et al., 2008; Weingart, 2012). Of course, tensions between journalistic and scientific values do arise (Sponholz, 2010; Wihbey & Ward, 2016) and the impact of medialization may be more limited than previously theorized (Lehmkuhl et al., forthcoming). Yet, medialization’s influence can be seen in media coverage of scholarly communications topics, such as peer review or research integrity, which mirror academic discourses and primarily present perspectives of scientists and scientific institutions (Ampollini & Bucchi, 2020). While we found no English-language research investigating media coverage of the OA movement, it is likely that a similar trend exists.\n\nJournalists’ internalization of scientific values may also influence how, or even whether, they use OA publications. What journalists consider ‘credible’ or ‘newsworthy’ often hinges on the perceptions of the scientists they interview (Dunwoody, 2021). This may be one reason why some journalists preferentially cover research published in journals that are viewed as ‘prestigious’ or ‘reputable’ in the eyes of the academy, such as Nature, Science, JAMA, or Proceedings for the National Academy of Science (Dumas-Mallet et al., 2017; Hansen, 1994; Lehmkuhl & Promies, 2020; MacLaughlin et al., 2018; Moorhead et al., 2021; Olvera-Lobo & Lopez, 2015; Rosen et al., 2016; Schäfer, 2011; St Lewis, 2011). The influence of journal reputation (itself often conflated with a journal’s Impact Factor; Morales et al., 2021) on journalists’ selection practices is so strong that it has been proposed as a core aspect of the science-specific news value of scientific relevance, reflecting the “Importance of an event for the scientific progress” (Badenschier & Wormer, 2012, p. 73). Many of these journals have traditionally been closed access and now operate under a hybrid OA model (i.e., researchers can choose to publish their work OA for a fee).\n\nImportantly, these high-impact journals also tend to have more resources to invest in science public relations (PR) efforts than other journals, enabling them to publish press releases and other press materials, circulate newsletters, and reach out to journalists to encourage them to cover newly released studies (Nelkin, 1995). PR materials such as press releases have been termed “information subsidies” (Granado, 2011) because they offer journalists the quotes, information, and context needed to craft science news stories with minimal time and effort. These same journals have also invested heavily in science news agencies, such as EurekAlert! and AlphaGalileo, which notify thousands of journalists worldwide about soon-to-be published research. These notifications provide journalists with early access to research under the condition that they adhere to an embargo (i.e., hold off on any media coverage until after a set date). Given increasing demands of science journalists’ time (Massarani et al., 2021a), it is no surprise that PR efforts are consistently associated with increased coverage (Comfort et al., 2022; Lehmkuhl & Promies, 2020; MacLaughlin et al., 2018). Science journalists’ heavy reliance on these information subsidies is thus an additional factor encouraging coverage of top, historically closed-access journals. It also encourages journalists to prioritize English-language, international research, rather than studies that may be more locally relevant (Granado, 2011).\n\nIn addition, some US journalists report considering the Impact Factor of the journal when deciding which studies to cover (Rosen et al., 2016; Schultz, 2023). Indeed, both the percentage of studies that receive news coverage and the number of news stories that are published per study tend to increase with the Impact Factor of the journal they were published in (Dumas-Mallet et al., 2017). Although relying on heuristics like the Impact Factor may be a pragmatic practice for busy journalists, the concept of scientific relevance on which they are based is highly problematic. It tends to privilege research produced in English in the Global North (especially the US and UK) and published in major international journals (Granado, 2011; Olvera-Lobo & Lopez, 2015) resulting in a lack of coverage of locally relevant research in the Global South (Nguyen & Tran, 2019). It also does not bode well for OA journals, many of which do not (yet) have an Impact Factor because they are not indexed in Clarivate’s Web of Science database (Bergan, 2020) or, as newer journals, may not yet be established as ‘reputable’ sources in the eyes of scientists or the journalists who report on their work. Indeed, exploratory research suggests that some journalists are “more suspicious of open access journals, believing they lacked a credible review process” (Van Witsen & Takahashi, 2021, p. 10).\n\nAt the same time, journalists report that journal paywalls are a major barrier preventing their use of research (Arbuckle, 2019; Boss et al., 2022; Gesualdo et al., 2020; Hinnant et al., 2017; Ordway, 2022), which may motivate them to rely on OA publications instead. This hypothesis is partially supported by existing evidence. Some studies suggest that OA publications receive more news coverage, on average, than their non-OA counterparts (e.g., Taylor, 2020), while others find no evidence of such an “altmetric attention advantage” in news coverage (e.g., Alhoori et al., 2015). These seemingly conflicting findings may, in part, be explained by the alternative strategies journalists have developed for accessing paywalled research articles, such as obtaining copies direct from authors (De Dobbelaer et al., 2018; Schultz, 2023), using subscription databases to which their institutions have access (Boss et al., 2022), and relying on free summaries or abstracts rather than complete papers (Bray, 2019). Some journalists may also be temporarily granted access to paywalled research as part of journals’ publicity efforts through the embargo system, as evidenced by the positive correlation between the promotion of research articles via embargo emails and their subsequent media coverage (Lemke et al., 2022). This advance warning is meant to provide the time needed to interview sources, do background research, and, in theory, provide more nuanced and thorough coverage of the research (Oransky, 2013). In practice, however, embargoes enable journals to restrict the flow of scientific information and to control media coverage of science by signaling which studies should be covered, by whom, and when (Kiernan, 2003; Oransky, 2022).\n\nIt is also possible that the type of OA plays a role in whether or not a research article is used by journalists. Specifically, Schultz (2021) found that journalists preferentially cover articles from subscription journals that have been made OA at the expense of the authors (i.e., hybrid OA) or have been deposited in a publicly accessible form in an institutional repository (i.e., green OA), rather than those published in fully open journals (i.e., gold or diamond OA). While more research is needed, it is possible that journalists avoid using gold and diamond OA because of their suspicion of OA journals but have no such qualms about covering open research articles that have been published in closed (and thus ‘reputable’) journals. Indeed, a recent survey study by Schultz (2023) found that, while science journalists are generally positive about OA, they are more willing to cite papers from hybrid rather than gold OA journals. However, as discussed above, it is also possible that hybrid and closed access journals have more resources to invest in publishing press releases and other forms of science PR and are thus more successful in garnering media coverage (Lehmkuhl & Promies, 2020; MacLaughlin et al., 2018).\n\nFinally, the ability to circumvent paywalls is not distributed equally among all journalists. Many of the access strategies discussed above—such as requesting articles from authors or using databases—tend to require time and resources that some journalists simply do not have. This is particularly likely for journalists based in the Global South (Nguyen & Tran, 2019), those working for digital, rather than print, publications (Manninen, 2017), those without subject-specific training (Leask et al., 2010), and journalists with less advanced information literacy skills, such as students or inexperienced reporters (Boss et al., 2022).\n\nWhile journal reputation, science PR, and access barriers are important factors in journalists’ engagement with OA publications, their use of preprints is strongly connected to perceptions and beliefs about peer review. Research suggests that journalistic discourses surrounding peer review tend to mirror those found in academic debates (Ampollini & Bucchi, 2020), portraying peer review as a “guarantee of good science” and the “cornerstone of maintaining the quality” of research (Ampollini & Bucchi, 2020, p. 466; Sebbah et al., 2022). As such, many journalists may be weary of OS initiatives that challenge traditional notions of peer review, such as preprints. For example, Dunwoody (2021) argues that journalists’ reliance on interviews with scientific experts means that those experts can “easily sell the argument that journalists must respect the scientific process and, for example, must wait for peer review to take place before embarking on a wider dissemination of research results” (p. 20; also, Oransky, 2022). Indeed, many science journalists “assume that peer review assures quality control of the science” (Conrad, 1999, p. 286; also Forsyth et al., 2012) and professional journalism organizations have been known to discourage the use of unreviewed science (Associated Press, 2020; Fox, 2018). This is particularly true for controversial topics that are newsworthy—that is, on those issues that have the potential to generate the most misinformation or confusion among the public (Science Media Centre, n.d.).\n\nMany of these controversial, newsworthy research topics are found in the life sciences, an umbrella term encompassing many health- and medicine-related research fields. These fields are unique in their historically low levels of preprint use (Puebla et al., 2021), high levels of press release promotion (Lemke et al., 2021; Orduña Malea & Costas, forthcoming), and correspondingly large volumes of media coverage (Banshal et al., 2019; Ginosar et al., 2022; Joubert et al., 2022). With potential to directly influence health policy, medical practice, and public wellbeing, the risks associated with posting and promoting preprints are also arguably greater in health-related fields than in other research areas (Bonnechère, 2020; Chung, 2020; Maslove, 2018), raising additional concern about the use of health-related preprints in journalism. UK’s Science Media Centre Director Fiona Fox (2018) emphasized these risks in an open letter on her blog titled “the preprint dilemma: good for science, bad for the public?” In it, she urged scholars, academic publishers, and science communicators to consider the wider impacts of preprint use, particularly within the controversial, newsworthy research areas on which the SMC focuses.\n\nMany of Fox’s concerns—and those of the scholars who would come after her—centered on the ways in which preprints can disrupt the system of “checks and balances” that she saw as essential for supporting accurate, trustworthy science media coverage. This system, which is still largely in place today, relies heavily on the peer review process as a quality control mechanism and embargo system as a source of story ideas (as discussed above). While embargoes are controversial (Altman, 1996; Oransky, 2013), Fox (2018) argued that they offer journalists the time needed to more thoroughly vet and communicate the research they cover—time they would otherwise not have in a “24-hour rolling news” cycle that privileges newness and originality over accuracy and rigor. In a world with preprints as news sources, Fox (2018) feared that embargoes would no longer be possible—and that the resulting damage would be irreparable. “The critical point is this,” she wrote, “once these findings have been reported in one or two national newspapers they cannot be unreported.”\n\nFox’s letter was quickly followed by an opinion piece in Nature, in which SMC senior press manager Tom Sheldon (2018a) amplified Fox’s concerns to more than 3 million online monthly readers (“Announcement: A new iPad app for Nature readers,” 2012; see also Sheldon, 2018b). This pivotal moment brought fears about preprint coverage into the mainstream scholarly discourse, but also sparked some of the first arguments in defense of preprint-based news coverage. In a series of comments responding to Sheldon’s (2018a) article, scholars and OS advocates highlighted the limitations of relying on peer review as a quality control mechanism (Tennant et al., 2018), arguing that media coverage of preprints and peer reviewed articles posed similar risks to public wellbeing (Sarabipour, 2018). Underpinning the responses to Sheldon’s piece was a belief that “the tension between supporting preprints and good journalism is a false dichotomy” (Sarabipour, 2018); that the benefits of preprints for science outweighed any potential risks for the public (Sarabipour, 2018; Sarabipour et al., 2018); and that, rather than suppressing preprint-based journalism, scholars and journalists could work together to support accurate and engaging science media coverage (Fraser & Polka, 2018; Sarabipour et al., 2018).\n\nThe body of scholarship summarized above advanced important arguments about the potential risks and benefits of preprint-based media coverage and provided some of the first anecdotal evidence that journalists occasionally covered preprints before the pandemic. For example, Sheldon (2018a) reported that journalists had started “trawling” preprint servers for potential story ideas and argued that this practice had the potential to put news audiences at risk. Similarly, Sarabipour (2018) argued that “Responsible journalists already report on preprints with the help of real-time commentary from scientists on Twitter and elsewhere”, citing a story in The Atlantic by journalist Ed Yong (2016) that featured tweets about a bioRxiv preprint by Sender et al. (2016) as an example. Molldrem et al. (2021) have also noted that arXiv preprints have at least occasionally been (mis)used by journalists before the pandemic, as evidenced by widespread coverage of a problematic study of cold fusion posted to the server in 2013. While each of these examples is anecdotal on its own, collectively they provide preliminary evidence that at least some journalists occasionally covered preprints before the pandemic, and that social media may have helped them to do so.\n\n\nJournalists’ use of Open Access publications and preprints during the COVID-19 pandemic\n\nSurprisingly, we found almost no research examining journalists’ engagement with OA publications during the pandemic. One exception is a survey study of US-based science journalists examining how COVID-19 had changed their knowledge or perceptions of OA, which in this case was defined as including both OA publications and preprints (Schultz, 2023). The study found that most journalists had been familiar with OA before the pandemic, although COVID-19 may have increased their knowledge of certain forms of OA, such as green OA. While this study provides some of the first insights into how journalists perceive the OA movement and how the pandemic has changed these perceptions, the generalizability of the findings is limited by the small and nonrandom nature of the sample. More research is needed to better understand whether or how the pandemic has shifted journalists’ perceptions of, and willingness to use, OA publications, particularly beyond the US context.\n\nSimilarly, our review of the literature suggested that scholars have yet to explicitly examine media coverage of OA versus closed access publications during the COVID-19 pandemic. Scholars have compared social media attention to open and closed access COVID-19 publications (e.g., Torres Salinas et al., 2020), as well as journalistic coverage of preprints (discussed in the next section). Yet, none to our knowledge have focused on articles published in OA journals or available through green OA. It is possible that the lack of research is due to the methodological and data quality-related challenges of tracking media coverage of research (Fleerackers et al., 2022), as well as disciplinary norms for studying science journalism. With a few exceptions (Matthias et al., 2020; van Schalkwyk & Dudek, 2022), SJ and communication scholars tend to identify science news stories using topic-related keyword searches, rather than by searching for coverage of specific research outputs (Fleerackers et al., 2022; Hansen, 2009). It is also possible that the lack of interest in this topic is linked to the fact that almost all COVID-19 research was made OA during the early pandemic period, even if only temporarily (Besançon et al., 2021; Engebretson, 2020). We discuss the urgent need for more studies in our Recommendations for future work.\n\nThe onset of the COVID-19 pandemic delivered exactly the type of widespread coverage of preprints in controversial, health-related fields that Fox and Sheldon feared, bringing new urgency to what had been a mostly theoretical debate back in 2018 (Molldrem et al., 2021). The early months of the crisis saw a sharp increase in the volume of available COVID-19-related preprints (Else, 2020; Horbach, 2020; Watson, 2022) and an “Increased permeability between scholarly circles, the news media, and the lay public” (Molldrem et al., 2021, p. 1470), with preprint servers such as medRxiv and bioRxiv becoming key disseminators of pandemic research (Vergoulis et al., 2021). Given the lack of peer reviewed evidence about the virus available at the time, COVID-19-related preprints became a key source of information for journalists (Fraser et al., 2021; Majumder & Mandl, 2020). While much of the resulting media coverage was helpful or benign, flawed and controversial preprints also made headlines (see Majumder & Mandl, 2020; Molldrem et al., 2021; Scheirer, 2020; van Schalkwyk et al., 2020, for reviews of these cases). Concerns about misinformation—similar to those discussed back in 2018—resurfaced, with scholars arguing that “conversations surrounding individual non–peer-reviewed preprints has made it difficult to extract meaningful signals about reliable, cumulative scientific evidence from the noise of sometimes short-lived findings” (Brossard & Scheufele, 2022, p. 614) and warning that “uncontrolled and potentially misleading information will reach the general public, directly or via the media, leading to incorrect, sometimes fatal, responses to the pandemic” (Chirico et al., 2020, p. 300).\n\nDespite these fears, COVID-19-related preprints appear to have stood up relatively well to the scrutiny of peer review (Kodvanj et al., 2022; Nelson et al., 2022; Otridge et al., 2022; Zeraatkar et al., 2022), although a minority do appear to have changed in important ways between initial posting and journal publication (Brierley et al., 2022) or been retracted (Abritis et al., 2021; Santos-d’Amorim et al., 2021). Scholars have proposed that the use of OS practices such as open data could help prevent misleading coverage of preprint research and improve the quality of SJ overall (Breznau et al., 2020). Others have argued that journalism could similarly mitigate the potential risk of misinformation by identifying and providing early, critical coverage of the preprints that are most likely to cause considerable damage to the public (Stollorz, 2021). This dual role of journalism—as both a cause and antidote for the spread of preprint-based misinformation—aligns with recent proposals that communicating OS outputs to public audiences can be both enriching (i.e., if it improves public perceptions, awareness, and knowledge of science) and misleading (i.e., if research outputs are not communicated with care) (Ho et al., 2021; Vignoli & Rörden, 2019).\n\nSome evidence suggests that news coverage of COVID-19-related preprints outstripped preprints on other subjects, at least during the early months of the pandemic. In the US, UK, Brazil, Germany, and South Africa, journalists from diverse media outlets drew on COVID-19-related preprints as sources of coverage (Fleerackers et al., 2022; Massarani et al., 2021a; Massarani & Neves, 2022; Simons & Schniedermann, forthcoming; van Schalkwyk & Dudek, 2022). A widely cited study by Fraser et al. (2021) found that more than a quarter of COVID-19-related preprints posted to bioRxiv and medRxiv during the first ten months of COVID-19 were mentioned in at least one media story, while only about 1% of those on other topics received media coverage. Besançon et al. (2021) found that COVID-19-related preprints posted to arXiv, medRxiv, and bioRxiv between January and July 2020 each received more coverage in blogs and news stories than non-COVID-19-related preprints posted to arXiv during the same time period. Similarly, coverage of preprints in German news outlets was relatively low before the pandemic, but surged in 2020 and 2021 (Simons & Schniedermann, forthcoming). Some journalists describe this widespread adoption of preprints as a “paradigm shift” that is likely to persist post-pandemic (Fleerackers et al., 2022). Scholars have made similar claims that preprints represent a long-term “cultural shift” in journalism (Fraser et al., 2021, p. 18; Stollorz, 2021; van Schalkwyk & Dudek, 2022).\n\nHowever, other studies have found that preprints were less influential within COVID-19 journalism than the dominant discourse suggests. For example, a small study found no significant difference in the amount of media coverage received by medRxiv preprints and peer reviewed publications about COVID-19-related therapies that were posted between February 1 and May 10, 2020 (Jung et al., 2021). Kousha and Thelwall (2020) found that the five COVID-19-related research articles that received the most media coverage were all peer reviewed publications. Similarly, journalists from around the world have reported that they drew primarily on peer-reviewed publications and interviews with local scientists for their pandemic coverage, with preprints acting as a more secondary information source (Massarani et al., 2021b). This finding is supported by comments from some of the journalists interviewed by Fleerackers et al. (2022), who claimed that they “doubt [ed] that arXiv is the place a lot of medical reporters are going to eagerly pull reporting from” (p. 11) post-pandemic. In addition, although journalists feel positive about open research in general—even more now than before the pandemic—they remain more skeptical of preprints than OA journal publications (Schultz, 2023). More broadly, researchers have yet to compare pre-pandemic and pandemic levels of preprint news coverage. Moreover, it is possible that the volume of preprint-coverage varies across geographies, media outlets, and individual journalists. For example, Massarani et al. (2021a) found that journalists in the Asia/Pacific region were among the most likely to use preprints, whereas those in African and Middle Eastern countries were among the least likely.\n\nRegardless of how the volume of preprint news coverage has changed as a result of COVID-19, preprint-based journalism seen during the pandemic appears to be qualitatively different from “normal” SJ (Fleerackers et al., 2022). While transparency and accuracy are key tenets of ethical, high quality journalism (Kovach & Rosenstiel, 2021; SPJ Code of Ethics - Society of Professional Journalists, n.d.), journalists do not consistently uphold these standards when covering preprints, with between 42-61% of preprint-based media stories failing to disclose the unreviewed nature of the preprints they reported (Fleerackers et al., 2021; Oliveira et al., 2021; van Schalkwyk & Dudek, 2022). A study of the German media landscape before and after the pandemic found similar results, with descriptions of preprints becoming more tentative during the pandemic—even for stories that were unrelated to COVID-19 (Simons & Schniedermann, forthcoming). The lack of consistency in reporting can be problematic, given that “the framing of a reporter’s coverage … can sensationalize and distort preliminary findings, particularly when there is uncertainty, disagreement, and confusion among experts” (Molldrem et al., 2021, p. 1476). To prevent such distortions, scholars have argued that journalists should adopt more standardized procedures for covering preprints, such as drawing on outside expertise to vet the results and labeling results as “under review” or “preprint research” (Ginsparg, 2021; Dunwoody, as quoted in Hamilton, 2020). Interestingly, although many journalists reported adopting both of these novel practices to cover preprints during the pandemic (Fleerackers et al., 2022; Massarani et al., 2021c; Schultz, 2023), they are also skeptical of the effectiveness of these measures. Specifically, journalists feel they lack the expertise (not to mention time) to verify preprint research and believe audience members are unlikely to know the term ‘preprint’ or understand how peer review works (Fleerackers et al., 2022). While results are mixed, a growing body of research suggests that public understanding of preprints is, indeed, limited—at least in the US (Ratcliff et al., 2023; Wingen et al., 2022).\n\n\nRecommendations for future work\n\nIn reviewing the literature discussed in the preceding sections, we have identified several gaps and directions for future research, which we outline below.\n\nSomewhat surprisingly, we have not been able to identify any studies that examine how and to what extent journalists have used OA publications during the COVID-19 pandemic. While a few studies have looked at journalists’ perceptions and use of pandemic-related preprints, other types of open research outputs—including but not limited to OA publications—have been largely overlooked in the research literature. More broadly, few studies so far have examined how journalists perceive the OA movement and its relevance to their work, how they view OA journals and articles, and whether the pandemic has changed these attitudes and to what extent. In addition, research is needed to understand whether engagement with OA research and exposure to the OS values associated with it might push science journalists to reflect on their own values, practices, roles, or norms. Very little is known about how journalists find and access closed access publications, and whether access barriers are greater for certain kinds of journalists, such as freelancers, generalists, and journalists based in the Global South.\n\nIt has been suggested that the COVID-19 pandemic constitutes a professional paradigm shift in terms of journalistic and media coverage of preprints; however, we don’t have a clear sense of how often and for what purposes journalists covered preprints pre-pandemic. There is a particular need for studies examining journalists’ use of preprints before the COVID-19 outbreak and during other recent pandemics and outbreaks (e.g., Ebola, Zika). Longitudinal research is also needed in order to highlight changes in preprint coverage over time, identify patterns and shifts in attitudes or behavior, and assess the impact of COVID-19 on journalistic practices and norms.\n\nIn a similar vein, much has been written about the potential of preprints to elicit public confusion and misinformation, yet only a handful of case studies have examined the flow of misinformation from preprints to media and public discourse. How much preprint coverage actually contributed to pandemic misinformation remains unknown—which is crucial to understand in preparation for future public health crises. Evidence in this regard would also help inform the current debate on the benefits and pitfalls of preprints, which at this point remains largely speculative. More broadly, it is unclear how audiences understand and respond to the descriptions of preprints they encounter in the news and how journalists can best communicate the unreviewed nature of preprint knowledge without losing audience trust in science or in journalism. (Ratcliff et al., 2023).\n\nFinally, our review suggests that research examining journalists’ use of open research outputs beyond the Global North is sorely needed. As Rao (2019) has identified, journalists and audiences in the Global South are uniquely affected by “gender, race, sexuality, caste, and various other forms of exclusions [that] play out in multiple arenas” (p. 702). Our understanding of OS-based journalism will remain incomplete unless we examine how such exclusions shape the nature of the news in these countries, which house the majority of the world’s population yet are so often overlooked in journalism scholarship (Wright et al., 2019). As this literature review largely focused on English-language literature, conducting a review of contributions published in other languages would be an important first step towards filling this gap. For example, Brazilian initiatives such as SciELO and the Bori Agency have launched PR efforts to increase the public visibility of OA publications (Packer, 2014; Righetti et al., 2022). In addition, discussions on how bridging OA and science communication could promote reflections on issues related to science, society, and democracy have gained strength in Brazil (Barata, 2022). Yet, these initiatives and discourses have not been well-represented in international databases and metrics (Barata, 2019).\n\nMore broadly, we lack research examining how journalists’ use of open research outputs depends on aspects of their identity and professional context (e.g., their gender, education, status as a freelancer/staff member, nature of the media outlet(s) they work for). Such research is needed given the increasing diversification and expansion of (science) journalism professionals, formats, and practices (Ginosar et al., 2022; Schapals, 2022) and growing awareness that journalists’ experiences are not universal but rather shaped by the intersections of their identities, contexts, and backgrounds (Jackson, 2022; Massarani et al., 2021a; Mesmer, 2022).\n\n\nConclusion\n\nOpen science seeks to make science accessible to all, including non-experts, decision-makers, and the public at large. However, OS cannot fulfill its democratic potential “if those who are unfamiliar with the research world do not know how to seek […] openly available research, and have difficulty parsing the meaning once they do” (Arbuckle, 2019, p. 6). Communicating open scientific findings and processes with everyone in an understandable and accessible language is, therefore, essential for increasing the societal impact of OS. For this reason, open science needs science journalism. Yet, despite the potential for SJ to contribute to the OS movement by making open research knowledge more conceptually accessible, little is known about journalists’ use of open outputs or adherence to OS values. Through a narrative synthesis of the scant scholarship that has examined the intersection of OS and SJ, this review simultaneously took a first step towards filling this gap and revealed the many additional questions that remain unanswered. As OA publications, preprints, and other forms of OS become increasingly mainstream among researchers, addressing these known unknowns is essential: for scientists, journalists, and the publics they serve.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nAcknowledgements\n\nWe would like to thank Esteban Morales for contributing thoughtful suggestions for improving this manuscript.\n\n\nReferences\n\nAbout us\|Science Media Centre: n.d.. Retrieved January 13, 2022. 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PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "174170", "date": "06 Jun 2023", "name": "Cameron Neylon", "expertise": [ "Reviewer Expertise Open science", "research evaluation", "scholarly publishing" ], "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 timely and important review of the relationship between open access and dissemination practices and science journalism during the COVID-19 pandemic. It is particularly valuable in identifying gaps in the literature with respect to preprints, journalism and their risks and benefits.\nMy expertise is not in studies of science journalism so additional expertise may be required to ensure the comprehensive coverage of the review. From the perspective of open science practices the review covers the core aspects of importance. I would find it helpful to have a table or dataset that categorizes or lists the identified outputs as well as the relevant search terms but this is a minor issue.\nMinor point: Introduction paragraph 4 \"...a review of a review of...\" is presumably a duplication? If not then maybe rephrasing will help.\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": "10753", "date": "10 Jan 2024", "name": "Natascha Chtena", "role": "Author Response", "response": "Thank you for taking the time to read our paper and for your valuable feedback. Comment 1: I would find it helpful to have a table or dataset that categorizes or lists the identified outputs as well as the relevant search terms but this is a minor issue. Thank you for this suggestion. All of the reviewed outputs are already included in the bibliography and we have not included specific search terms because we do not wish to imply that the search was systematic. We also employed a snowball search approach to identify relevant works by using the bibliography or reference list of already identified papers. As such, while we see the value of this suggestion for a systematic review or meta-analysis, we do not feel it is appropriate or necessary here. Comment 2: Introduction paragraph 4 \"...a review of a review of...\" is presumably a duplication? If not then maybe rephrasing will help. It was indeed a duplication and has now been corrected. Thank you for catching that." } ] }, { "id": "201145", "date": "31 Oct 2023", "name": "Ivan Oransky", "expertise": [ "Reviewer Expertise Science and medical journalism", "research integrity", "publishing" ], "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\nThank you for the opportunity to review this paper. I found it an insightful look at a young field of study: how journalists make use of open research. With that in mind, I have some comments, many of which are not necessarily specific suggestions for consideration as much as points the authors may want to consider in this work and efforts moving forward.\nI am comfortable with the employed search strategy for a literature review like this, but would recommend a comment that limiting searches to the literature indexed by Google Scholar will exclude a great deal of grey literature as well as writing by journalists -- who are unlikely to publish in the peer-reviewed literature.\nThe manuscript does a good job of exploring just how big a barrier paywalls are, including the nuances such as articles about COVID-19 being largely available at various periods. But it is also worth noting that large publishers often make their entire libraries available to specialist reporters through organizations such as AHCJ and NASW. Eg https://m.healthjournalism.org/journal-access\nI found myself wondering whether the subjects and research approaches in preprints and OA journals markedly different from those in paywalled papers. Would that be another factor in what journalists decided to cover?\nRe: \"It also does not bode well for OA journals, many of which do not (yet) have an Impact Factor because they are not indexed in Clarivate’s Web of Science database (Bergan, 2020) or, as newer journals, may not yet be established as ‘reputable’ sources in the eyes of scientists or the journalists who report on their work.\" What about paywalled journals that switch (these are mentioned in passing), or the large number of OA journals that do now have IFs? Perhaps this sentence might be moved to where Schultz (2021) is discussed.\nI would like to see a bit more discussion of the watchdog role journalists can plan in holding OA work itself accountable. It's mentioned in the antidote/mitigate section but there seems to be more to say.\nRe: \"For example, a small study found no significant difference in the amount of media coverage received by medRxiv preprints and peer reviewed publications about COVID-19-related therapies that were posted between February 1 and May 10, 2020 (Jung et al., 2021),\" it strikes me that \"no significant difference\" is probably still a change from before the pandemic. I might draw a more direct line between this and the fact that medRxiv did not exist until just a few months before the pandemic. Comparisons to previous pandemics and outbreaks are definitely important but may be challenging.\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": "10754", "date": "10 Jan 2024", "name": "Natascha Chtena", "role": "Author Response", "response": "Thank you for taking the time to read our paper and for providing valuable comments for its improvement. Comment 1: I am comfortable with the employed search strategy for a literature review like this, but would recommend a comment that limiting searches to the literature indexed by Google Scholar will exclude a great deal of grey literature as well as writing by journalists -- who are unlikely to publish in the peer-reviewed literature. As suggested, we have added a sentence noting the limitations of Google Scholar in relation to grey literature: Although Google Scholar indexes literature from many languages, the search algorithm is highly biased towards English-language publications (Rovira et al., 2021); as such this language bias is a limitation of our review. In addition, relying on Google Scholar likely excluded relevant grey literature, such as policy papers, reports, working papers, and writing by journalists. Comment 2: The manuscript does a good job of exploring just how big a barrier paywalls are, including the nuances such as articles about COVID-19 being largely available at various periods. But it is also worth noting that large publishers often make their entire libraries available to specialist reporters through organizations such as AHCJ and NASW. Eg https://m.healthjournalism.org/journal-access Thank you. We have added a sentence noting the access major publishers provide to specialist reporters, with the caveat that these types of partnerships are not universal: These seemingly conflicting findings may, in part, be explained by the alternative strategies journalists have developed for accessing paywalled research articles, such as obtaining copies direct from authors (De Dobbelaer et al., 2018; Schultz, 2023), using subscription databases to which their institutions have access (Boss et al., 2022), and relying on free summaries or abstracts rather than complete papers (Bray, 2019). In addition, some major publishers make their libraries available to journalists who are members of specialized organizations, such as the Association of Health Care Journalists and the National Association of Science Writers (both based in the US). However, these privileges are not universal. Associations based in other countries, such as RedeComCiência (Brazilian Network of Journalists and Science Communicators), do not have the same partnerships in place, exacerbating asymmetries between the Global North and South. Comment 3: I found myself wondering whether the subjects and research approaches in preprints and OA journals markedly different from those in paywalled papers. Would that be another factor in what journalists decided to cover? It could be that research available as a preprint or an OA journal article differs from research published in a closed access journal, but we don’t feel there is a strong enough body of evidence to substantiate this claim. In fact, there is evidence that most preprints get published (Abdil & Blekhman, 2019; Fraser et al., 2020) and that those that do are relatively similar to the final journal article (e.g., Brierley et al., 2022). In addition, many preprint servers do not accept non-traditional outputs, and they also screen for format/layout, meaning that they won't accept submissions that don't follow the traditional scholarly article structure (Malički et al., 2020). That is, they won't accept things that are \"markedly different\" from journal articles. We also are not aware of any research suggesting any established differences between OA journals and paywalled ones, as the boundaries have become so blurry in recent years. Abdill, R. J., & Blekhman, R. (2019). Tracking the popularity and outcomes of all bioRxiv preprints. eLife, 8, e45133. https://doi.org/10.7554/eLife.45133 Brierley, L., Nanni, F., Polka, J. K., Dey, G., Pálfy, M., Fraser, N., & Coates, J. A. (2022). Tracking changes between preprint posting and journal publication during a pandemic. PLOS BIOLOGY, 20(2), e3001285. https://doi.org/10.1371/journal.pbio.3001285 Fraser, N., Momeni, F., Mayr, P., & Peters, I. (2020). The relationship between bioRxiv preprints, citations and altmetrics. Quantitative Science Studies, 1(2), 618–638. https://doi.org/10.1162/qss_a_00043 Malički, M., Jerončić, A., ter Riet, G., Bouter, L. M., Ioannidis, J. P. A., Goodman, S. N., & Aalbersberg, Ij. J. (2020). Preprint servers’ policies, submission requirements, and transparency in reporting and research integrity recommendations. JAMA, 324(18), 1901–1903. https://doi.org/10.1001/jama.2020.17195 Comment 4: \"It also does not bode well for OA journals, many of which do not (yet) have an Impact Factor because they are not indexed in Clarivate’s Web of Science database (Bergan, 2020) or, as newer journals, may not yet be established as ‘reputable’ sources in the eyes of scientists or the journalists who report on their work.\" What about paywalled journals that switch (these are mentioned in passing), or the large number of OA journals that do now have IFs? Perhaps this sentence might be moved to where Schultz (2021) is discussed. Per your suggestion, we have updated this section to provide a more nuanced discussion of OA journals and IFs: It also does not bode well for some OA journals, which do not (yet) have an Impact Factor because they are not indexed in Clarivate’s Web of Science database (Bergan, 2020) or, as newer journals, may not yet be established as ‘reputable’ sources in the eyes of scientists or the journalists who report on their work. Of course, these same reservations may apply to some closed access journals as well, and may not be relevant to major OA journals with high Impact Factors and recognized brands, such as PLOS Medicine or Nature Communications. Still, exploratory research suggests that some journalists are “more suspicious of open access journals, believing they lacked a credible review process” (Van Witsen & Takahashi, 2021, p. 10). Comment 5: I would like to see a bit more discussion of the watchdog role journalists can plan in holding OA work itself accountable. It's mentioned in the antidote/mitigate section but there seems to be more to say. We have expanded on this in the section “The argument for OS-based journalism”: Similarly, although health and science journalists fulfill some traditional journalistic roles—such as watchdog (holding powerful scientific or pharmaceutical institutions to account) and agenda setter (driving attention to new trends, issues, and findings in research)—they also play additional roles such as the civic educator, using their skills to teach audiences about the nature of scientific research and its limits and risks (Fahy & Nisbet, 2011). These roles and functions, while not always consistently performed in practice, are important for ensuring that the growing trend towards openness in science supports the interests of society and the integrity of the scholarly record. For example, science journalists have published nuanced, critical coverage of recent OS-related controversies, such as the use of predatory practices among major OA publishers (Brainard, 2023; Kolata, 2017), flawed preprint studies (Miller, 2022; Bartlett, 2023), and the high cost of article processing charges associated with OA publishing (Ansede, 2023). Similarly, Retraction Watch—a blog and database founded and managed by science and health journalists—maintains a running list of retracted COVID-19 articles, including OA articles and preprints, and regularly features news about problematic research practices, including fraud, plagiarism, and predatory publishing in both closed and open science. Science journalists’ ability to call attention to pernicious aspects of OS, while simultaneously helping publics take advantage of its benefits, makes them ideally positioned to help make “scientific knowledge openly available, accessible and reusable for everyone, to increase scientific collaborations and sharing of information for the benefits of science and society, and to open the processes of scientific knowledge creation, evaluation, and communication to societal actors beyond the traditional scientific community” (UNESCO, 2021, p. 6). Comment 6: Re: \"It also does not bode well for OA journals, many of which do not (yet) have an Impact Factor because they are not indexed in Clarivate’s Web of Science database (Bergan, 2020) or, as newer journals, may not yet be established as ‘reputable’ sources in the eyes of scientists or the journalists who report on their work.\" What about paywalled journals that switch (these are mentioned in passing), or the large number of OA journals that do now have IFs? Perhaps this sentence might be moved to where Schultz (2021) is discussed. Jung et al. (2021) found that preprints were covered in a median of 1.5 news stories while peer reviewed publications were covered in a median of 1 news story. However, we are hesitant to draw attention to this difference given it was non significant (p value of 0.70) and the sample was very small (n=106), focused on a narrow topic, and likely not representative of coverage of other COVID-19 or medRxiv preprints. However, we have addressed your concern about distinguishing the effects of the launch of medRxiv on preprint coverage from the effects of the onset of the pandemic by adapting the following sections. We cite research that was not yet published when we conducted our initial review: Similarly, coverage of preprints in German news outlets was relatively low before the pandemic, but surged in 2020 and 2021 (Simons & Schniedermann, 2023). Finally, a study found that preprints were featured in less than 2% of media coverage of research before the pandemic, but that this proportion surged to almost 4% after the onset of COVID-19 (Fleerackers et al., 2023). Moreover, this surge appeared to be driven entirely by COVID-19 preprints, as the launch of the medical preprint server medRxiv in 2019 had little or no effect on rates of preprint coverage. Some journalists describe this widespread adoption of COVID-19 preprints as a “paradigm shift” that is likely to persist post-pandemic (Fleerackers et al., 2022). Scholars have made similar claims that the recent coverage of preprints represents a long-term “cultural shift” in journalism (Fraser et al., 2021, p. 18; Stollorz, 2021; van Schalkwyk & Dudek, 2022). In addition, although journalists feel positive about open research in general—even more now than before the pandemic—they remain more skeptical of preprints than OA journal publications (Schultz, 2023). Moreover, it is possible that the volume of preprint-coverage varies across geographies, media outlets, and individual journalists. For example, Massarani et al. (2021a) found that journalists in the Asia/Pacific region were among the most likely to use preprints, whereas those in African and Middle Eastern countries were among the least likely. In addition, Fleerackers et al. (2023) found little or no change in the coverage of non-COVID-19 preprints during the pandemic period, suggesting that journalists’ embrace of COVID-19 preprints may not extend to preprints on other topics, nor those posted during less urgent crisis contexts." } ] }, { "id": "214228", "date": "31 Oct 2023", "name": "Alyssa Arbuckle", "expertise": [ "Reviewer Expertise Open access", "open scholarship", "scholarly communication" ], "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 examines the intersection of open scholarship and science journalism. The authors suggest that this is an understudied area, despite the critical importance of open access research to journalism and vice versa. They provide a thorough literature review of the research that is available on science journalists’ use of open access research. Notably, the authors dig into the actual usage of preprints by science journalists during the COVID-19 pandemic, which had become a hot button topic for those working in the field.\nI would be interested to see one of the arguments of this article fleshed out slightly; that is, for the authors to interrogate the value of specialist language more deeply. It is a truism of academic research that it is obscure and opaque to anyone outside a specific discipline (and sometimes sub-discipline). Indeed, this is one of the areas where science journalists and other knowledge brokers come into play: as translators for a broader, more generalized readership. But it is important, too, to not lose sight of the value of shorthand. As Laura Mandell writes in Breaking the Book: Print Humanities in the Digital Age, shorthand allows for an expedited exchange of ideas between specialists without having to include all of the detailed context and history of each theory or concept being explored and built upon. Translation and comprehension are necessary, of course; but there is value to the complexity and detail of research, too. How does this tension affect the production, circulation, and uptake of open access research?\nI also found the point about science journalists relying on prestige markers such as the Impact Factor an angle that would be well worth digging more deeply into. Prestige and open access publishing are often critiqued within the context of hiring, review, or tenure and promotion. What does it mean that science journalists and hiring and promotion committees are depending on the same arbitrary and easily gamed metrics?\nOverall, this article provides an important summation of the current state of play regarding science journalism and open scholarship. It highlights that for open access research to reach its full impact, it must be findable, legible, and reusable; science journalism is one of the mechanisms to reach such a goal. The article closes with recommendations for future work, all of which would be well worth pursuing. I will look forward to reading more from the lead author and her co-authors 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": [ { "c_id": "10755", "date": "10 Jan 2024", "name": "Natascha Chtena", "role": "Author Response", "response": "Thank you for taking the time to read our paper and for providing valuable comments for its improvement. Comment 1: I would be interested to see one of the arguments of this article fleshed out slightly; that is, for the authors to interrogate the value of specialist language more deeply. It is a truism of academic research that it is obscure and opaque to anyone outside a specific discipline (and sometimes sub-discipline). Indeed, this is one of the areas where science journalists and other knowledge brokers come into play: as translators for a broader, more generalized readership. But it is important, too, to not lose sight of the value of shorthand. As Laura Mandell writes in Breaking the Book: Print Humanities in the Digital Age, shorthand allows for an expedited exchange of ideas between specialists without having to include all of the detailed context and history of each theory or concept being explored and built upon. Translation and comprehension are necessary, of course; but there is value to the complexity and detail of research, too. How does this tension affect the production, circulation, and uptake of open access research? Thank you for this suggestion. We have revised the second paragraph of the Introduction to highlight the value and utility of specialist language when used among experts: Academic publications are written for peer researchers and academics rather than the general public and use the jargon, rhetorical features, and communication norms and conventions of the disciplines within which they are produced (Fahnestock, 1986). Such specialist language can enhance understanding within these disciplinary communities, contributing to more economical, precise communication that supports collaboration among experts (Hirst, 2003). However, it can be very difficult for ‘lay’ readers to understand. Hirst, R. (2003). Scientific jargon, good and bad. Journal of Technical Writing and Communication, 33(3), 201–229. https://doi.org/10.2190/J8JJ-4YD0-4R00-G5N0 Comment 2: I also found the point about science journalists relying on prestige markers such as the Impact Factor an angle that would be well worth digging more deeply into. Prestige and open access publishing are often critiqued within the context of hiring, review, or tenure and promotion. What does it mean that science journalists and hiring and promotion committees are depending on the same arbitrary and easily gamed metrics? We have added a sentence noting the problematic use of the IF within RPT processes: Although relying on heuristics like the Impact Factor may be a pragmatic practice for busy journalists, the concept of scientific relevance on which they are based is problematic for several reasons. First, the Impact Factor of a journal is not a valid marker of an individual paper’s quality and significance, although it is often used as one (e.g., within faculty review, promotion, and tenure decisions; McKiernan et al., 2019 ). In addition, the metric also tends to privilege research produced in English in the Global North (especially the US and UK) and published in major international journals ( Granado, 2011; Olvera-Lobo & Lopez, 2015) resulting in a lack of coverage of locally relevant research in the Global South ( Nguyen & Tran, 2019)." } ] }, { "id": "214232", "date": "31 Oct 2023", "name": "Moumita Koley", "expertise": [ "Reviewer Expertise Open science", "research evaluation", "open access" ], "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 timely and relevant article, especially since open science is an essential discussion in the scholarly community. The UNESCO Open Science recommendations highlight the importance of the accessibility of science to the broader public. As mentioned in the article, it is, however, not always possible for the general public to understand highly specialized scientific articles, and science journalism can be really beneficial in bringing complex knowledge in a simpler form to people. In this regard, the accessibility of scholarly articles to journalists is an important consideration and enabler as well. So, how open access is enabling better science journalism needs to be understood. However, as a scholar who studies open science from a different perspective, my knowledge of science journalism and related literature is not adequate to evaluate the quality of the literature review provided here. Also, I assume that this article is a review of literature addressing science journalism and open science, not \"a review of a review of...\".\nThis article presents a review of literature that mainly addresses the questions of open access rather than the broader concept of open science. Open science is a much broader concept where open access is an element. So unless the literature addresses the use of other elements, such as open data, code, etc., by the science journalists, in a more accurate sense, this article tracks mostly the use of open-access research by journalists. Using open science and open access interchangeably does not help the cause of open science as a broad concept.\nSince 'Altmetrics' is becoming increasingly popular in assessing the impact of research, especially on society, reporting any study by journalists' impact on the altmetric scores will be an interesting observation.\n\nThe method and value of science is deeply rooted in the peer-review process. As indicated by the cold fusion reporting through preprint and the recent controversy of widespread coverage of the LK-99 as the potential superconductor (not mentioned in the present article), indicates the problematic nature of covering preprint by SJs. Also, how the newer trend of peer-reviewed preprints are used by the SJs and how these newer model of publications can be used to remove confusion regarding the quality of preprints could be an exciting addition to this article.\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? Partly", "responses": [ { "c_id": "10756", "date": "10 Jan 2024", "name": "Natascha Chtena", "role": "Author Response", "response": "Thank you for taking the time to read our paper and for providing valuable comments for its improvement. Comment 1: This article presents a review of literature that mainly addresses the questions of open access rather than the broader concept of open science. Open science is a much broader concept where open access is an element. So unless the literature addresses the use of other elements, such as open data, code, etc., by the science journalists, in a more accurate sense, this article tracks mostly the use of open-access research by journalists. Using open science and open access interchangeably does not help the cause of open science as a broad concept. To clarify our focus on OA journal publications and preprints, we have changed the title to: Making science public: A review of journalists’ use of open access research In addition, we have reframed the abstract to focus more specifically on OA journal articles and preprints, not OS broadly defined. At the same time, we feel it is important to contextualize journalists’ engagement with OA and preprints within the wider OS movement, given that OA/preprints are a part of OS and should be considered with the wider motivations and goals of openness in mind. We have taken care not to use the terms OS and OA interchangeably, referring to OA pubs and preprints as ‘open research outputs’ and OS when discussing the movement as a whole. Comment 2: Since 'Altmetrics' is becoming increasingly popular in assessing the impact of research, especially on society, reporting any study by journalists' impact on the altmetric scores will be an interesting observation. Altmetrics continue to be displayed on journal websites, but we are not aware of evidence that suggests that they are being used for research assessment. However, we agree that journalism can affect the altmetric scores of a paper, which appears to be tied to the type of access journalists have to the work. We mentioned this in our original manuscript but have provided additional references to strengthen the claim as follows: Some studies suggest that OA publications receive more news coverage, on average, than their non-OA counterparts (e.g., Taylor, 2020; Wang et al., 2015; Torres-Salinas et al., 2020), while others find no evidence of such an “altmetric attention advantage” in news coverage (e.g., Alhoori et al., 2015). In addition, the last two sentences of the paragraph link access to embargoed copied with higher media coverage, which would also lead to higher citations. Comment 3: The method and value of science is deeply rooted in the peer-review process. As indicated by the cold fusion reporting through preprint and the recent controversy of widespread coverage of the LK-99 as the potential superconductor (not mentioned in the present article), indicates the problematic nature of covering preprint by SJs. Also, how the newer trend of peer-reviewed preprints are used by the SJs and how these newer model of publications can be used to remove confusion regarding the quality of preprints could be an exciting addition to this article. We agree that journalists’ perception and use of peer-reviewed preprints is an exciting avenue for future research and have noted this in our recommendations for future work: Longitudinal research is also needed in order to highlight changes in preprint coverage over time, identify patterns and shifts in attitudes or behavior, and assess the impact of COVID-19 on journalistic practices and norms. Examining changes in journalists’ use of preprints beyond the pandemic is especially important as preprints, themselves, continue to evolve. For example, as more and more preprint review services come online (Henriques et al., 2023), future research could examine how journalists perceive and use preprints that have been peer reviewed outside of the traditional journal publishing system." } ] }, { "id": "214223", "date": "08 Nov 2023", "name": "Henrik Karlstrøm", "expertise": [ "Reviewer Expertise Scientific publishing", "metascience", "bibliometrics" ], "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\nGiven that increased public engagement with scientific research is an impetus of the Open Science movement itself, the research question of this paper is highly relevant. The authors do a good job of establishing the ways in which brokerage between science and journalism can improve public understanding of the scientific process. I find the paper well-structured, well-argued and discussing a topic of potentially high import.\nThe paper is quite limited in scope. The authors note that there are few empirical investigations of science journalists' engagement with OS literature, and state that \"this review mainly covers research and theoretical contributions that discuss the intersections of OS and SJ tangentially or as a secondary concern, rather than a primary focus\". It is good that the authors acknowledge the limitations of reviewing a literature that is only tangentially concerned with the question at hand. You can only work with what is available, of course, and the authors do note that an empirical investigation of journalists' use of code and data is planned in the future. However, this limitation to conceptual discussions obviously affects the scope of the findings claimed by the paper.\nGiven the lack of empirical data, the authors are correct to call this a review of existing literature. There is a discrepancy between how this is framed in the abstract and in the key recommendations. The abstract states: \"We find that, despite journalists’ potential to act as critical brokers of open access knowledge, their use of open research outputs is hampered by an overreliance on traditional criteria for evaluatingscientific quality; concerns about the trustworthiness of open research outputs; and challenges using and verifying the findings.\" However, these are not really findings, given that the literature reviewed does not directly address these questions. A better framing would have been to focus on the gaps identified in the literature, as these are amply demonstrated in the paper.\nOverall, this is a useful overview of the literature that exists at the crossroads of science journalism, open science and COVID research. It constitutes a taking stock of the current situation and a roadmap for further investigation into the factors that shape decisions by non-scientists who are trying to navigate the somewhat insular world of academic publishing.\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": "10757", "date": "10 Jan 2024", "name": "Natascha Chtena", "role": "Author Response", "response": "Thank you for taking the time to read our paper and for providing valuable comments for its improvement. To streamline the abstract with our recommendations for future work, we have revised the abstract to further highlight the gaps identified in the literature: Science journalists are uniquely positioned to increase the societal impact of open research outputs by contextualizing and communicating findings in ways that highlight their relevance for non-specialist audiences. Yet, it is unclear to what degree journalists use open research outputs, such as open access publications and preprints, in their reporting; what factors motivate or constrain this use; and how the recent surge in openly available research seen during the COVID-19 pandemic has affected this. This article examines these questions through a review of relevant literature published from 2018 onwards, particularly literature relating to the COVID-19 pandemic. We find that research that explicitly examines journalists’ engagement with open access publications or preprints is scarce, with existing literature mostly addressing the topic tangentially or as a secondary concern, rather than a primary focus. Still, the limited body of evidence points to several factors that may hamper journalists’ use of these outputs and thus warrant further exploration. These include an overreliance on traditional criteria for evaluating scientific quality; concerns about the trustworthiness of open research outputs; and challenges using and verifying the findings. We also find that, while the COVID-19 pandemic encouraged journalists to explore open research outputs such as preprints, the extent to which these explorations will become established journalistic practices remains unclear. Furthermore, we note that current research is overwhelmingly authored and focused on the Global North, and the United States specifically. We conclude with recommendations for future research that attend to issues of equity and diversity, and more explicitly examine the intersections of open access and science journalism." } ] } ]	1	https://f1000research.com/articles/12-512
https://f1000research.com/articles/12-1610/v1	29 Dec 23	{ "type": "Study Protocol", "title": "A novel questionnaire to perform teletriage of dental emergencies in children: A before-and-after study nested within a randomized clinical trial", "authors": [ "Ana Paula Dornellas", "João Vitor Marques", "Isabelle Aníbal Oliveira dos Santos", "Marcelo Ramos", "Júlia Mulder", "Ana Estela Haddad", "João Vitor Marques", "Isabelle Aníbal Oliveira dos Santos", "Marcelo Ramos", "Júlia Mulder", "Ana Estela Haddad" ], "abstract": "Background: This will be a before-and-after study nested within a randomized clinical trial. Its objective will be to analyze the effectiveness of a teleconsultation and validate a questionnaire for performing teletriage in dental urgency/emergency situations in children aged 3 to 13, whose parents will have signed a free and informed consent form, and who have had full access to the internet. Methods: The Questionnaire for Teletriage of Emergencies and Urgencies in Pediatric Dentistry (QuesT-Odontoped)—will be validated by applying it to 140 randomized child parents/guardians. After validation, another 260 children seeking emergency dental care in the municipality of Carangola, Minas Gerais, Brazil, will receive a remote consultation, be randomized, and then allocated into two groups: G1, teleconsultation, and G2, teleconsultation and face-to-face consultation (immediately after the former) with a blinded evaluator, involving anamnesis and conventional clinical examination. The G2 sample will be used in the before-after study. Both groups will be followed-up for 7 and 14 days using pain and quality-of-life scales, applied at baseline and after each follow-up period. Clinical follow-up will be carried out after 12 and 24 months to assess the outcome of the tooth that had been indicated for treatment in the teletriage. The Mann-Whitney test will be used to assess pain; Student's t test or the Mann-Whitney test will be used to assess quality of life and the number of missing teeth after 24 months; and Poisson's regression analysis will be used to assess the influence of other variables. The significance level will be set at 5%. Conclusions: In conclusion, this study expects to confirm the hypothesis that remote urgency consultation (teletriage), through a validated questionnaire, will be able to define the planning of the clinical situation, reducing the chance of displacements and progression of infection, helping to eliminate patient pain and discomfort.", "keywords": [ "Teletriage", "Teledentistry", "Remote consultations", "Pediatric dentistry", "Primary teeth", "Urgencies", "Emergencies" ], "content": "Introduction\n\nPediatric patients often have difficulty communicating their pain experience. It is not uncommon for parents to become aware of the problem and seek dental care only when the pain is intense and prolonged.1 Pain symptoms—whether intense, prolonged, spontaneous or nocturnal—may suggest changes in the pulp-dentin complex. Dentoalveolar trauma is common in this population, and requires immediate communication between patients and dentists, which is essential for the decision-making process involved in providing the patient with the needed first aid.2 In some cases, the prognosis will depend on prompt and appropriate intervention. However, dental emergency services are not available full-time in all geographic regions of a country. In Brazil, the social isolation measures adopted by the government as a result of the COVID-19 pandemic impacted the supply and demand of dental services, and any significant delay in adopting adequate measures for cases of dental emergencies/urgencies could compromise the final results and affect the patient’s quality of life.3\n\nWithin the scope of the Unified Health System (SUS), urgencies represent an important opportunity to identify the individuals and locations that are most vulnerable. Ordinance GM/MS no. 2048 of November 5, 2002, of the Ministry of Health4 provides that healthcare units should carry out patient reception and risk classification screening, and that this process should be conducted by a college graduate health professional, specifically trained for conducting these procedures. The regulation also recommends that pre-established protocols must be used in order to assess the degree of urgency of each patient. Today, however, the organization of dental emergency services is still based on the rationale of order of patient arrival, contrary to the hierarchization principle adopted by the SUS,5 according to which the level of care required for each case must be identified, so that access to the required services can be ensured according to their complexity. In addition, patients rely on urgent care as a gateway to the system. The Ministry of Health sought to standardize patient reception in emergency services, and standardize the care process across the country6 by means of a risk classification system. By doing so, it sought to improve the work process and enhance the effectiveness of healthcare services, provided in a humanized and patient-centered fashion, with the goal of ensuring more favorable outcomes. To this end, patient reception carried out by using a risk classification system and protocol ensures proper development of work processes, and improves the resolution capacity of health services. In addition, this system and protocol ensure prioritization of the more severe clinical cases, and an appointment scheduling based on patient demands.7 Studies in the literature have used questionnaires to diagnose dental problems in children, such as caries lesions, dental calculus, gingivitis, dental fractures, and malocclusions.8,9 However, to the best of our knowledge, none have proposed a model questionnaire for dental urgency cases, providing guidance for the proper referral of these patients.\n\nFaced with the COVID-19 pandemic, each country has adopted different policies to resume its dental care services. The United Kingdom, for instance, chose to select cases through teledentistry, and to see only those patients requiring urgent treatment.10 In Brazil, Resolution 226 of June 4, 2020,11 and Ordinance No. 526 of June 24, 202012 of the Ministry of Health have regulated teleconsultation, telemonitoring, and teletriage procedures for dentists working in primary care. In this respect, teledentistry is a method of proven capability to provide healthcare to underserved population groups, or to those unable to attend a face-to-face consultation.13‒16 Teledentistry may also be a viable alternative for assessing deferrable and non-deferrable urgency cases, by conducting a screening process based on available information and communication technologies, e. g. video calls or text messages containing photos.17‒21 The World Health Organization (WHO)22 recommended that its member-countries make use of telehealth as a strategy to improve the quality of services provided, even before the pandemic.23\n\nIt is known that teledentistry has been considered a practical and economically viable strategy to provide healthcare to underserved populations, including the socially disadvantaged, those living in remote locations or rural areas, or those who simply do not have access to routine dental care.24‒28 In this context, teletriage has been associated with streamlined patient referral, shorter waiting lines, and improved ordering of care priorities. Based on an accurate assessment provided by remote screening, patients can receive proper primary support in an appropriate and customized fashion, and be directed to telecare or to the dental office itself, when needed, thus minimizing unnecessary displacements and contamination risks.29 However, consistent scientific evidence is still lacking on the advantages of teletriage in dentistry; therefore, further investigation into the possibilities of using telecommunication tools in the planning of health actions is warranted, particularly for the sake of municipalities that do not have the human resources to provide specialized care, and general populations that do not have access to a specialist.\n\nThe foremost aim of this study will be to analyze the effectiveness of teletriage and of an urgency/emergency risk classification system for children, compared to face-to-face consultation for these patients. Secondarily, other key issues will be investigated, as follows:\n\n1 - validation of a questionnaire for dental urgency screening in children;\n\n2 - assessment of the level of agreement among diagnoses and risk ratings assigned to cases screened in person versus remotely;\n\n3 - proposal and testing of an oral health protocol for patient reception and risk classification for children seeking an urgency/emergency dental care service.\n\n\nProtocol\n\nThe design of this study (both before-and-after study as well as the randomized clinical trial) was approved by the Research Ethics Committee, School of Dentistry, University of São Paulo (approval no. 46974821.9.0000.0075), on June 1st, 2021. It was also submitted to The Brazilian Clinical Trials Registry, code RBR-523hrsx. The research protocol was written following SPIRIT (Standard Protocol Items: Recommendations for Interventional Trials) guidelines.30\n\nThe study will be divided into the following stages: (1) questionnaire validation, (2) randomized clinical trial, and (3) before-and-after study, each with their own methodology.\n\nTeam and participants\n\nThe allocation sequence was generated by an external professional (Dentist, PhD);\n\nThe participants enrollment and their assignment to interventions will be carried out by the main researcher (APD).\n\nQuestionnaire validation\n\nThe inclusion of the research participants in this stage will be made upon a digital acceptance of a free and informed digital consent form (FICF), which will be digitally signed by the person in charge of the child (parents/guardians) and uploaded through a digital link, for this remote part of the study. This form presents the research objectives clearly, as well as the guidelines that will be provided to patients. Permission to disclose data will be part of this document, and shall ensure confidentiality of participant identity. All the participants will be informed that their participation in the study is voluntary and the participants will be informed that their anonymised data will be published.\n\nBefore-and-after study nested within a randomized clinical trial\n\nFor this stage, inclusion of participants in the study groups will also take place upon a digital acceptance of a free and informed digital consent form (FICF), uploaded through a digital link, and parents or guardians must mark the tick – box to consent for the remote part of the study, on behalf of the child. The parents/guardians of participants assigned to the face-to-face consultation group (G2) will also be required to sign a FICF.\n\nIn both stages (questionnaire validation and before-and-after study nested within a randomized clinical trial), in addition to the parent/guardian consent, the study will consider the age and level of understanding of the participants in the sample, whose agreement to participate will be obtained by reading a specific document, or verbally for those who cannot read and/or access the link provided. The form of acceptance will depend on the child’s maturity level, which may only be verbal, which does not necessarily require a signature, according to the Ethic Committee guidelines and approval. Children belonging to G2 (in person) and with sufficient understanding will be invited to fill out, in person, the same free and informed agreement form (FIAF) that had been sent to their parent/guardian online in stage 1, totaling two filled-out forms for G2 (Figure 1). In this case, parents/guardians are also required to fill out an informed agreement.\n\nG1, teleconsultation; G2, teleconsultation plus face-to-face consultation.\n\nThe data collected will be stored using specific procedures to ensure the secrecy and confidentiality of the participants’ information. The access to the final trial dataset will be exclusive to the main researcher and the project supervisor. Only remote consultation platforms that have robust security standards, and that meet the regulations of the General Data Protection Law (LGPD) will be used to store the data. In addition, the research subjects will have the right to leave the study at any time, with no detriment to their care.\n\nQuestionnaire validation\n\nThe parents/guardians of children with dental pain who seek care at the University of São Paulo School of Dentistry or the University of São Paulo Health Superintendence (SAU) will receive the contact information for one of the researchers, complete with a telephone number, and information about the requirements for having a remote consultation. The questionnaire will be applied to 140 participants, and reapplied to 14 randomized participants (Figure 2). Randomization, in blocks of four participants, will be performed using freely available statistical software (MedCalc® 15.11, MedCalc Software, Ostend, Belgium), and the sequence generated will be distributed in sealed brown envelopes. The envelope will only be opened after the patient accepts the FICF or FIAF at the time of the teleconsultation performed via Video For Health (V4H) platform, a service dedicated to digital health with a video call management functionality and aligned with the LGPD in Brazil.\n\nBefore-and-after study nested within a randomized clinical trial\n\nThe present research project will consist of a randomized, controlled, noninferiority, and blinded (examiners) clinical study, with 260 children aged 3 to 13 years in dental urgency situations. All of the participants investigated will be users of Basic Health Units, hospitals or dental clinics, residing in the municipality of Carangola, MG, Brazil. A link providing access to the Telehealth and Teledentistry Center from the University of São Paulo School of Dentistry (Nutes/FOUSP) platform will be sent to each patient after said patient makes the first contact through WhatsApp, a messaging app. All patients will be previously evaluated by a previously trained researcher in a teleconsultation (“before”), and then randomized and divided into two groups: G1, comprising 130 patients seen via a teleconsultation, and G2, comprising 130 patients seen via a teleconsultation and also in person (Figure 3). The face-to-face evaluation (“after”) will be performed by two researchers who will be blinded to the result of the teleconsultation, who will perform anamnesis and clinical examination using a specific dental record, and who will answer whether or not the patient’s case is an urgent situation at the end of the evaluation. The dental condition motivating inclusion of the patient in the study will be treated by the researcher, and any other patient needs will be seen to by referring them to the health unit where they were registered.\n\nG1, teleconsultation; G2, teleconsultation plus face-to-face consultation.\n\nPatients in G1 and G2 will be followed up for seven and 14 days using specific instruments to assess the absence or presence of pain (Wong-Baker scale)31 and quality of life, according to the child’s age (Child Perceptions Questionnaire, CPQ,32 or Early Childhood Oral Health Impact Scale, ECOHIS).33 In the case of urgencies involving teeth, a 12- and 24-month follow-up of the tooth reported in the teletriage will be carried out. The clinical criteria used to determine treatment success will be no fistula or exudate, no abscess, no painful symptoms, and no pathological mobility (Figure 4).\n\nG1, teleconsultation; G2, teleconsultation plus face-to-face consultation.\n\nThe inclusion criteria will be the same for the two stages of patient selection in the study.\n\nInclusion criteria\n\na) children aged 3 to 13 years, with dental pain, whose parents seek urgent care at the Dental School of the University of São Paulo in São Paulo, or at the public network in the city of Carangola, in the state of Minas Gerais.\n\nb) patients with a sufficiently good internet connection to allow a synchronous consultation.\n\nExclusion criteria\n\nThe exclusion criteria will be the same for the two stages of patient selection of the study:\n\na) patients who fail to attend the face-to-face consultation, when assigned to G2;\n\nb) patients with internet access difficulties.\n\nQuestionnaire validation stage\n\nThe parents/guardians of children with dental pain who seek care at the University of São Paulo School of Dentistry or at the University of São Paulo Health Superintendence (SAU) will receive the contact information for one of the researchers, complete with a telephone number, and information about the requirements for having a remote consultation.\n\nBefore-and-after study nested within a randomized clinical trial\n\nWhen arriving at a Basic Health Unit, a hospital or a dental clinic outside opening hours, the parents/guardians of children with dental pain will find a poster outside containing the contact information for one of the researchers, complete with her/his telephone number, the ethics committee approval number, and the requirements for having a remote consultation.\n\nQuestionnaire validation\n\nThe questionnaire will be applied to 140 participants, and reapplied to 14 randomized participants. Randomization, in blocks of four participants, will be performed using statistical software (MedCalc® 15.11, MedCalc Software, Ostend, Belgium), and the sequence generated will be distributed in sealed brown envelopes.\n\nBefore-and-after study nested within a randomized clinical trial\n\nRandomization, in blocks of four patients, to assign them to one of the treatment groups, will be performed using statistical software (MedCalc® 15.11, MedCalc Software, Ostend, Belgium), and the sequence generated will be distributed in sealed brown envelopes. The envelopes must be opened immediately after the start of the teleconsultation.\n\nThe examiners/researchers (authors on the paper and two dental practitioners based at the clinics) will be trained by the author responsible for the project (APD) to carry out the research prior to the first stage. This will involve a four hour training program for urgency situations of dental origin in children, and a 4-hour calibration program for questionnaire application.\n\nPrior to the beginning of the study, the researcher will explain the study and how teledentistry will be used within the Family Health Units to the entire team.\n\nThe synchronous teletriage will be carried out using the teleconsultation-dedicated NuTes-FOUSP platform that complies with the LGPD, as well as a questionnaire containing objective questions to ascertain whether or not the situation in question is a case of a dental urgency. The time required to apply the questionnaire will depend on how long it takes to obtain the answers from the patients’ parents/guardians.\n\nIn the clinical stage of the study, the time of the face-to-face dental consultation, to be performed immediately after the synchronous consultation shall not exceed one hour.\n\nThe clinical situations listed below will be considered dental urgencies (ADA, 2020)2:\n\n• irreversible pulpitis;\n\n• pericoronitis;\n\n• abscess or localized bacterial infection, resulting in localized pain and swelling;\n\n• tooth fracture, resulting in pain or causing soft tissue trauma.\n\n• dental trauma, involving avulsion and/or luxation;\n\n• a missing or fractured restoration, or one causing gingival irritation and requiring a provisional restoration;\n\n• extensive caries or a defective restoration that is causing pain;\n\n• pain that requires replacing the provisional filling of an endodontic access opening;\n\n• perforated or ulcerated oral mucosa, requiring trimming or adjustment of a wire or orthodontic appliance.\n\nThe clinical situations listed below will not be considered dental urgencies:\n\n• initial or follow-up dental examination;\n\n• routine radiography;\n\n• dental prophylaxis;\n\n• routine periodontal therapy;\n\n• orthodontic procedure other than that needed to treat an acute problem (e.g., pain, infection, trauma);\n\n• extraction of an asymptomatic tooth;\n\n• restorative dentistry procedure, including treatment of an asymptomatic carious lesion;\n\n• aesthetic dental procedure\n\nQuestionnaire validation\n\nThe risks involved in this study are those inherent in virtual environments, electronic media, or non-face-to-face activities, considering the limitations of the technologies used or those of researchers in ensuring data confidentiality and preventing data violation.\n\nBefore-and-after study nested within a randomized clinical trial\n\nIn addition to the risks mentioned above, there are other risks inherent in any pediatric dental treatment, including those related to the possible failure of the proposed dental treatment. Additional risks are those related to data collection, such as possible discomfort felt during the remote and/or face-to-face consultation, during the assessment, examination, and therapeutic procedures themselves, and possible annoyance and/or emotional or social stress occasionally felt by the patient and/or by parent/guardian when answering questions related to the child’s health.\n\nTo reduce these risks, the procedures will be monitored by the researcher, who will be prepared to provide all the assistance needed. In the event of personal injury caused directly by any procedure or treatment proposed in this study, the child will be entitled to free dental treatment.\n\nThe data will be collected at different timepoints, as shown in Table 1.\n\nG1, teleconsultation; G2, teleconsultation plus face-to-face consultation.\n\nSample for questionnaire validation\n\nThe guidelines of the European Statistical System stipulate that the development and validation of instruments must follow five steps: (1) conceptualization, (2) questionnaire design, (3) questionnaire testing, (4) revision, and (5) data collection.34 Considering that the questionnaire conceptualization and design have already been completed, our considerations will begin from the questionnaire testing step. The first step involved in instrument testing is evaluation by a panel of experts (content validation). There is a controversy in the literature regarding the recommended size for this panel, ranging from five to twenty members,35,36 depending on their experience and qualifications. Subsequently, data collection will be carried out by applying the questionnaire (criterion validity). To this end, a sample size of at least 10 participants is recommended for each item37; therefore, the minimum sample size of the present study will be 140 subjects. In order for the instrument to be considered reliable (test and retest), it must be able to produce similar results when applied to the same individual at different times, and by different interviewers. For this purpose, a sample size corresponding to 10% of the total “N” (i.e., 14 patients in the current version of the questionnaire) should be used.\n\nSample size calculation for the RCT\n\nPrimary outcome: the presence of dental pain in children and adolescents, considering independent samples (in this case, there is no pairing of individuals, and the interventions will be assigned to different individuals). The possibility of dropouts during the follow-up period was taken into account.\n\nIn performing the sample size calculation for independent samples, the proportion of dental pain observed in children and adolescents will be considered as 32.7%,38 and the minimum, clinically relevant proportion difference will be 15%. Thus, considering a two-tailed test, a significance level of 0.05, and a power of 0.80, the calculation will yield a total number of 236 patients. Owing to the possibility of participant dropout during the follow-up period, 10% of this number will be added to the final sample, bringing the total number of patients required per experimental group to 130 (G Power, version 3.1.9.4).\n\nSample size calculation for the before-and-after study\n\nBefore-and-after studies are considered observational studies, and use a preliminary diagnostic test to decide whether or not to treat a series of examined patients. These patients are submitted to another diagnostic method, and the treatment decision can then be revised. Since this before-and-after study is nested within a randomized controlled trial (RCT), the sample size calculation will take into account the primary outcome of the RCT and the two experimental groups. However, only the group evaluated using both methods (teletriage + face-to-face consultation) will be eligible for this study. Therefore, the before-and-after study sample will consist of 130 patients.\n\nOutcomes\n\nPrimary outcome: the presence of dental pain in children and adolescents, considering independent samples.\n\nSecondary outcome: quality of life (questionnaires according to age group) and tooth loss.\n\nQuestionnaire validation\n\nThe kappa coefficient (k) and content validity index (CVI) will be used to quantify the degree of agreement among experts during content validation. In order to assess the reliability of the instrument, the test and retest results will be evaluated using the intra-examiner agreement test (kappa test, k), which is the appropriate statistical procedure to assess the reliability of categorical and nominal variables. The criterion validity will be analyzed by comparing the results of the teleconsultation with those of the face-to-face consultation using the chi-square test (χ2). The significance level will be set at 5%, and the data will be analyzed using Jamovi and RStudio software.\n\nRandomized clinical trial\n\nPrimary outcome: pain (Wong-Baker scale); secondary outcomes: quality of life (questionnaires according to age group) and missing teeth.\n\nThe primary outcome of the randomized clinical study will be any change in pain score observed at the 7-day and 14-day follow-up timepoints compared to baseline. This outcome comprises an ordinal qualitative variable; therefore, comparison between the teleconsultation and face-to-face consultation groups will be performed using the Mann-Whitney test.\n\nOther secondary outcomes will be evaluated, such as the impact of treatments on oral health-related quality of life, and the number of missing teeth after the 24-month follow-up period. Differences between the groups regarding the final and initial scores of the questionnaires on oral health-related quality of life, as well as the number of missing teeth, will be compared using Student’s t test or the Mann-Whitney test, depending on the type of data distribution (normal or non-normal). In addition, Poisson’s regression analysis will be performed to assess the influence of other variables on the results. The significance level will be set at 5%, and the data will be analyzed using Jamovi and RStudio software.\n\nBefore-after study nested within an RCT\n\nDescriptive analyses regarding diagnosis for needing urgent treatment will be performed using the teletriage questionnaire, alone and in combination with the face-to-face consultation. The possible treatment decision outcomes for these analyses, and for both the remote and the face-to-face examination, will be (i) the need for urgent treatment or (ii) the possibility of elective treatment. The frequency of change in the treatment decision will be calculated considering that the change can be (i) from urgent to elective treatment or (ii) from elective to urgent treatment. Explanatory variables related to the children, such as sex, age (randomization strata), and caries experience may be used in the analyses. The primary outcome in this study will be any change in treatment decision after the face-to-face consultation. Prevalence ratio (PR) values and respective 95% confidence intervals (95% CI) will be calculated, and univariate and multiple regression analyses will be performed. The significance level will be set at 5%, and the data will be analyzed using Jamovi and RStudio software.\n\nThe study is in the phase of inclusion of patients; and the questionnaire is in the validation stage. Completion of this project is scheduled for the second half of 2024.\n\nThe results of this study will be presented at scientific meetings and published in peer-reviewed medical journals.\n\n\nConclusions\n\nThe hypothesis of the present study is that the synchronous remote urgent consultation (or teleconsultation) performed using a validated questionnaire will be able to determine the appropriate screening decision for the clinical situation in which the patient finds him/herself.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nWinters J, Cameron AC, Widmer RP: Pulp therapy for primary and immature permanent teeth. Handbook of Pediatric Dentistry. 2013; pp. 103–122. Publisher Full Text\n\nAmerican Dental Association (ADA): What Constitutes a Dental Emergency?2020. Reference Source\n\nGlendor U, Andersson L: Public health aspects of oral diseases and disorders: dental trauma. Quintessence. 2007; 203–211.\n\nBrasil: Ministério da Saúde. Portaria 2048 de 5 de novembro de 2002. Aprova o Regulamento Técnico dos Sistemas Estaduais de Urgência e Emergência. Diário Oficial da União, Brasília, DF.7 nov 2002.\n\nBRASIL: Ministério da Saúde. Portaria n. 1600, de 7 de julho de 2011. Reformula a Política Nacional de Atenção às Urgências e institui a Rede de Atenção às Urgências no Sistema Único de Saúde (SUS). Brasília.2011 [citado 2017 out. 7]. Reference Source\n\nPagliotto LF, Souza PB, Thomazini JO, et al.: Classificação de risco em uma unidade de urgência e emergência do interior paulista Cuidarte Enferm. 2016; 10(2): 148–155.\n\nCampos TS, Arboit EL, Mistura C, et al.: Acolhimento e classificação de risco: percepção de profissionais de saúde e usuários. Rev. Bras. Promoç. Saúde. 2020; 33: 1–11. Publisher Full Text\n\nLeão J, Porter S: Telediagnosis of Oral Disease. Braz. Dent. J. 1999; 10(1): 47–53. PubMed Abstract\n\nEwers R, Schicho K, Wagner A, et al.: Seven years of clinical experience with teleconsultation in craniomaxillofacial surgery. J. Oral Maxillofac. Surg. 2005; 63: 1447–1454. PubMed Abstract \| Publisher Full Text\n\nMallineni SK, Innes NP, Raggio DP, et al.: Coronavirus disease (COVID-19): Characteristics in children and considerations for dentists providing their care. Int. J. Paediatr. Dent. 2020 May; 30(3): 245–250. Epub 2020 Apr 16. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBRASIL: Conselho Federal de Odontologia. CFO. Resolução 226 de 04 de junho de 2020. Dispõe sobre o exercício da Odontologia a distância, mediado por tecnologias, e dá outras providências.Reference Source\n\nBRASIL: Ministério da Saúde. Portaria GM/MS No 526, de 24 de junho 2020. Inclui, altera e exclui procedimentos da Tabela de Procedimentos, Medicamentos, Órteses, Próteses e Materiais Especiais do SUS. Diário Oficial da União. Brasília: Ministério da Saúde.02 jul 2020.\n\nHaddad AE, Skelton-Macedo MC: Teleodontologia na formação dos profissionais de saúde.Mathias I, Monteiro A, (Org). Gold book: Inovação tecnológica em educação e saúde Rio de Janeiro: EdUERJ; 2012 [Cited May 25, 2017]. Reference Source\n\nArtese F: Covid-19: The aftermath for orthodontics. Dental Press J. Orthod. 2020 Mar; 25(2): 7–8. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGasparoni A, Kanellis MJ: Covid-19 and dental emergencies: reflections on teledentistry. Braz. Dent. Sci. 2020; 23(2): 4. Publisher Full Text\n\nGhai S: Teledentistry during COVID-19 pandemic. Diabetes Metab. Syndr. 2020 Sep-Oct; 14(5): 933–935. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAsociación Latinoamericana de Odontopediatría: Teleodontologia: Aplicação em Odontopediatria durante a pandemia COVID-19. Rev. Odontopediatr. Latinoam. 2020; 10(2). Publisher Full Text Reference Source\n\nBavaresco CS, Hauser L, Haddad AE, et al.: impact of teleconsultations on the conduct of oral health teams in the telehealth brazil networks programme. Braz. Oral Res. 2020; 34: 1–9. Publisher Full Text Reference Source\n\nCaprioglio A, Pizzetti GB, Zecca PA, et al.: Management of orthodontic emergencies during 2019-NCOV. Prog. Orthod. 2020 Apr 7; 21(1): 10. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDave M, Seoudi N, Coulthard P: Urgent dental care for patients during the COVID-19 pandemic. Lancet. 2020; 395(10232): 1257. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGuo H, Zhou Y, Liu X, et al.: The impact of the COVID-19 epidemic on the utilization of emergency dental services. J. Dent. Sci. 2020 Mar; 15: 564–567. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nResolution WHA58.28 eHealth: 2005. Reference Source\n\nCarrer FCA, et al.: Teleodontologia e SUS: uma importante ferramenta para a retomada da Atenção Primária à Saúde no contexto da pandemia de COVID-19. Scielo Preprints. 2020. Publisher Full Text Reference Source\n\nBerndt J, Leone P, King G: Using teledentistry to provide interceptive orthodontic services to disadvantaged children. Am. J. Orthod. Dentofac. Orthop. 2008 Nov; 134(5): 700–706. PubMed Abstract \| Publisher Full Text\n\nKopycka-Kedzierawski DT, Billings RJ: Teledentistry in inner-city child-care centres. J. Telemed. Telecare. 2006; 12(4): 176–181. PubMed Abstract \| Publisher Full Text\n\nFricton J, Chen H: Using teledentistry to improve access to dental care for the underserved. Dent. Clin. N. Am. 2009 Jul; 53(3): 537–548. PubMed Abstract \| Publisher Full Text\n\nKhurshid A: Effectiveness of preventive oral health care in Hispanic children living near US-Mexico border. Int. J. Public Health. 2010 Aug; 55(4): 291–298. PubMed Abstract \| Publisher Full Text\n\nHaddad A, da Silva D , Monteiro A, et al.: Follow up of the Legislation Advancement Along the Implementation of the Brazilian Telehealth Programme. J. Int. Soc. Telemed. eHealth. 2016; 4: 1–7. Reference Source\n\nWheeler SQ, Windt JH: Telephone triage: theory, practice and protocol development. San Anselmo, CA: TeleTriage Systems Publishers; 2013.\n\nCalvert M, Kyte D, Mercieca-Bebber R, et al.: Guidelines for inclusion of patient-reported outcomes in clinical trial protocols: the SPIRIT-PRO extension. JAMA. 2018; 319(5): 483–494. Publisher Full Text\n\nWong DL, Baker CM: Smiling faces as anchor for pain intensity scales. Pain. 2001; 89(2-3): 295–297. Publisher Full Text\n\nBarbosa Tde S, Gavião MB: Quality of life and oral health in children - Part II: Brazilian version of the Child Perceptions Questionnaire. Cien. Saude Colet. 2011; 16(7): 3267–3276. PubMed Abstract\n\nMartins-Júnior PA, Vieira-Andrade RG, Corrêa-Faria P, et al.: Impact of early childhood caries on the oral health-related quality of life of preschool children and their parents. Caries Res. 2013; 47(3): 211–218. Publisher Full Text\n\nBrancato GS, Macchia M, Murgia M, et al.: Handbook of recommended practices for questionnaire development and testing in the European statistical system. European Statistical System; 2006.\n\nLynn MR: Determination and quantification of content validity. Nurs. Res. 1986; 35(6): 382–385. PubMed Abstract\n\nHaynes SN, Richard D, Kubany ES: Content validity in psychological assessment: A functional approach to concepts and methods. Psychol. Assess. 1995; 7(3): 238–247. Publisher Full Text\n\nDe Vet HCW, Terwee CB, Mokkink LB, et al.: Measurement in medicine: a practical guide. Cambridge University Press; 2011.\n\nPentapati KC, Yeturu SK, Siddiq H: Global and regional estimates of dental pain among children and adolescents-systematic review and meta-analysis. Eur. Arch. Paediatr. Dent. 2021; 22(1): 1–12. Publisher Full Text" }	[ { "id": "265384", "date": "15 May 2024", "name": "Shimaa Kotb", "expertise": [ "Reviewer Expertise Oral medicine", "oral pathology", "periodontology", "dental implants .dental surgery", "Dental 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\nBreif Description of Article: Teledentistry article show the importance of the remote delivery of clinical care through electronic communications. Dental’s virtual consultation is a convenient way to connect with patients from the comfort of their homes to show support and interest in their oral health state . Strength: Article is interesting, Informative, Discuss helpful effective tools in planning the treatment and screening patients easily without time consuming, Effective method for reassurance patient in emergency situation and in alleviate the sever pain. Weakness: 1.Need more research in the future on this issue with large sample size. 2. Some References need to be updated Summary: Teledentistry, a promising tool, is still not widely used in dentistry. Teledentistry enables remote assessment, allowing for efficient screening and triage of patients. Teledentistry could be as effective as face-to-face technology for oral screening, particularly in school-based programs, caries assessment, referrals, and teleconsultations, especially during emergencies. Decision : Accepted with minor correction (related to the update 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? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] }, { "id": "278729", "date": "04 Jun 2024", "name": "Alexandre Baudet", "expertise": [ "Reviewer Expertise Dentistry", "Public health", "Infection prevention and control", "Antibiotic stewardship", "Antibiotic resistance" ], "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 study protocol presents the rationale and describes the methodology used to analyze the effectiveness of a teleconsultation and validate a questionnaire for performing teletriage in dental urgency/emergency situations in children aged 3 to 13 in Brazil. A before-and-after study nested within a randomized clinical trial will be carried out with 130 children in the group G1: teleconsultation only (control group) and 130 children in the group G2: teleconsultation plus face-to-face consultation (before-after group). The dental pain and the quality of life assessed with questionnaires according to age group will be the main outcomes with a following time of 24 months. The paper is well-structured and easy to follow. One comment for the authors to consider: figure 3 is unclear and not in accordance with the text, it should highlight that G1 = teleconsultation only (control group), G2 = teleconsultation (before) plus face-to-face consultation (after); actually G1 is indicated as before period and G2 as after period.\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/12-1610
https://f1000research.com/articles/12-1608/v1	29 Dec 23	{ "type": "Study Protocol", "title": "Comparison of tranexamic acid plus intramuscular oxytocin with intramuscular oxytocin alone for prophylaxis of primary postpartum haemorrhage in vaginal delivery", "authors": [ "Sukanya Singh", "Surekha Tayade", "Surekha Tayade" ], "abstract": "In contemporary obstetrics, postpartum hemorrhage is one of the primary causes of maternal mortality. Postpartum hemorrhage is defined as blood loss of more than 500 mL within the first 24 hours of birth. The term, late postpartum hemorrhage is used when the bleeding lasts more than 24 hours. Due to the physiological changes that occur during pregnancy, the body may sustain a 500 mL blood loss without experiencing any severe negative consequences. However, even a modest amount of blood loss might be harmful in cases of comorbidities like anemia. However, even a modest amount of blood loss might be harmful in cases of comorbidities like anemia. Postpartum hemorrhage poses a double threat because it decreases the mother's strength and immunity, leaving her more vulnerable to puerperal illnesses. Second, the loss of blood could be fatal. Maternal death occurs gradually as a result of constant trickle-like blood loss. There are predictors which may help us in scrutinizing patients to be labeled as high risk for postpartum hemorrhage, however, there are no formulized criteria for postpartum hemorrhage. The active management of the third stage of labor is a management protocol made to prevent as well as manage this potentially life-threatening condition. It has significantly led to a reduction in maternal mortality rates. However, with more permutation - combinations of medical management and using different pharmacological agents we can devise a better algorithm for further deduction in the mortality rates. Here we propose to randomly allocate and administer an additional drug, tranexamic acid, in addition to uterotonics prophylactically given during the active management of the third stage of labor in vaginal deliveries. In doing so we compare the differences between groups in which only oxytocin was given and in which oxytocin plus tranexamic acid was given.", "keywords": [ "postpartum hemorrhage", "prevention", "tranexamic acid", "vaginal delivery", "maternal mortality" ], "content": "Introduction\n\nThe most common and serious consequence for mothers after giving birth is postpartum haemorrhage (PPH). Worldwide, pregnancy and childbirth-related factors account for the deaths of nearly five lakh women annually. Severe anaemia, the need for a blood transfusion, hospitalisation, and infection are some of the most common outcomes of PPH. Goal 5 of the Millennium Development Plan calls for a 75 percent drop in the maternal mortality rate by 2015, which equates to an annual drop of 5.5 percent.\n\nIn medical literature, PPH is elaborated as postpartum haemorrhage of 500 mL or greater blood loss.1 Bleeding from or into the genital tract after delivery and before the end of puerperium is clinically defined as the quantity of bleeding that negatively affects the patient's overall state as demonstrated by rising pulse rate and lowering blood pressure.\n\nThere are two main categories:\n\n• Primary: blood loss on the first day within 24 hrs after a baby's birth.\n\n• Secondary: late or delayed haemorrhage is bleeding occurring post-24h but before the end of the puerperium.\n\nMost cases of PPH may be traced back to uterine atony. Polyhydramnios, macrosomia, preeclampsia, preeclamptic pregnancies, protracted or augmented labour, numerous pregnancies, prior caesarean section, and a history of preeclampsia are all additional risk factors.2,3 However, most patients with PPH had low-risk pregnancies and can't pinpoint any specific causes for their condition.4,5 The prevalence of PPH was 9.2 percent among a sample of 1620 rural Indian women. Women with PPH did not vary from women without PPH in terms of maternal or socio-demographic variables.6 Therefore, preventing PPH in all women is crucial.7–10\n\nThe first line of defence in the treatment of PPH is oxytocin. Ergometrine and carboprost and misoprostol administered intramuscularly and intravenously are two more methods. The well-established uterotonics, notably oxytocin, may be supplemented by the biochemical haemostatic impact of pro-haemostatic medicines like Tranexamic acid (TXA).11 TXA may be given in a diverse range of healthcare settings, is cost-effective, and can minimise PPH and related morbidity and death in areas where tertiary obstetric care is unavailable. TXA has the potential to contribute to the objective of decreasing maternal mortality by lowering the likelihood of hysterectomy, the danger of severe anaemia, and blood transfusion requirements.\n\nRationale: A step closer to achieving the Millennium Development Goals for maternal health care during childbirth is by reducing the rates of maternal mortality and morbidity and by treating PPH. Uterotonics are advised for all pregnancies in order to reduce the risk of preeclampsia during the third stage of labour. Most preventative measures are carried out within the crucial window of placental expulsion for PPH prevention. The only portion of active management of third stage of labour which has proven to reduce the risk of postpartum haemorrhage is postpartum treatment with uterotonics, and more specifically oxytocin.12–16 According to a recent systematic review and mathematical model, the preventative or therapeutic use of TXA for PPH might save about 22,000 fatalities annually throughout the world (assuming a 30 percent effect size). By using this study, we can infer valuable information which will help obstetricians if additional use of tranexamic acid along with intramuscular oxytocin should be used prophylactically for prevention of primary PPH.\n\nThe study is aimed to estimate if the prophylactic administration of tranexamic acid along with intramuscular oxytocin is linked to improvement in Primary Postpartum Haemorrhage, mortality and morbidity and the negative effects linked to its uses in vaginal delivery.\n\nPrimary objectives\n\n1. To determine the efficacy of tranexamic acid as an add therapy to intramuscular oxytocin in reducing blood loss in vaginal delivery.\n\n2. To compare the two groups of tranexamic acid plus intramuscular oxytocin in one arm versus intramuscular oxytocin in another arm.\n\nSecondary objectives:\n\n1. To determine need for blood transfusion.\n\n2. To determine need for additional uterotonics.\n\n3. To determine the side effects.\n\n\nProtocol\n\nStudy setting: Jawaharlal Nehru Medical College and Acharya Vinoba Bhave Rural Hospital.\n\nEligibility criteria: Inclusion Criteria:\n\n1. Scheduled or unscheduled vaginal delivery of all age groups and parity\n\n2. Singleton or twin gestation\n\nExclusion criteria:\n\nSevere surgical and medical complications\n\n• Past allergy with tranexamic acid\n\n• Thrombi-embolic disorders history.\n\n• Antenatal conditions such as abnormal placenta\n\n• Placenta abruption, Placenta-previa, severe preeclampsia, adherent placenta, macrosomia, multiple pregnancies, polyhydramnios,\n\nGynaecological or Fibroid uterus disorders that can complicates the pregnancy.\n\nInterventions description:\n\nAfter receiving institutional ethics committee permission, we began the research. Women who meet the eligibility requirements will be educated about the study's purpose and requested to sign an informed consent form in the Marathi language before being enrolled. Demographic characteristics, obstetric history and medical history will be noted.\n\nIn this study, 55 subjects would be administered Intramuscular Oxytocin 10 units, during of birth of new-born’s anterior shoulder (control group) and 55 women would be administered Oxytocin 10 units, along-with Injection Tranexamic acid, 1g diluted in 100mL solution of lactated ringers (LR), intravenously during the birth of a new-born’s anterior shoulder (experimental group). The subjects would be unaware about the allocation as the allocation would be randomised. The amount of blood loss would be accessed. The blood loss will be estimated by using Brass v drape and the amount of blood suctioned by suction machine. Pre delivery and post-delivery haemoglobin, morbidity and mortality and side effects will be compared in both groups.\n\nOutcomes:\n\nPrimary outcome measures\n\n1. Different groups as per blood loss:\n\n• Women receiving only oxytocin\n\n• Women receiving oxytocin and tranexamic acid\n\nSecondary outcome measures\n\n2. Difference in Post-delivery (up to 6 hours) in the same two groups of:\n\n• Haemoglobin/haematocrit\n\n• Additional uterotonics requirement\n\n• Blood transfusion requirement\n\n3. Side effects related to drug used.\n\nParticipant timeline: Patients visiting Acharya Vinoba Bhave Rural Hospital for vaginal delivery during two years.\n\nSample size:\n\nThe SPSS 16.0 application is used for necessary statistical analysis. Age, weight, blood loss, and labours will all be measured to determine their respective means and standard deviations. For determining whether there is a statistically significant difference among the two groups in terms of the continuous variables used to measure blood loss and labour time, an unpaired t-test will be performed. The chi-square test will be used for comparing two groups statistically for higher blood loss (>500ml) and a drop in haemoglobin of >10%. The significance level selected must correspond to a probability value of p≤0.05.\n\nThe major factor will be the frequency with which each group has a decrease in haemoglobin of more than 10% and how those percentages compare to one another. Due to the small sample size, we recommend using an alpha error of 0.01. The sample size formula is as follows:\n\nCochran formula for sample size:\n\nWhere,\n\n2α/22: Significance Level = 1.96 (5% i.e., 95% confidence interval)\n\np = incidence of PPH = 7% = 0.07\n\nE = Error of Margin desired = 7% = 0.07\n\nRecruitment:\n\nThe term patients visiting Acharya Vinoba Bhave Rural Hospital for vaginal delivery as per our inclusion criteria will be encouraged to participate in the study. Patients will be explained about the drug and its intervention during normal delivery.\n\nAllocation by computer-generated random numbers. Allocation concealment mechanism is not applicable. The participants will enrol willingly after fulfilling the inclusion criteria. The allocations will be done the principal investigator with. Guidance from study supervisor. Blinding of the trial participants will be done.\n\nThe amount of blood loss would be accessed. The blood loss will be estimated by using Brass v drape and the amount of blood suctioned by suction machine. The data collection will be one time intervention hence patient compliance and follow up will not be an issue.\n\nPre delivery and post-delivery haemoglobin, morbidity and mortality and side effects will be compared in both groups in tabulated format. Range checks for data values will be assessed by the principle investigation. A self-administered questionnaire will be filled by the patient at the time of discharge.\n\nThe study's output will result in articles that are published in indexed journals.\n\nThe investigations and data collections are yet to begin.\n\n\nDiscussion\n\nWhen dealing with patients who are experiencing life-threatening bleeding, time is of the importance. Common cause of maternal death is bleeding after giving birth. Every six minutes, a mother dies from postpartum bleeding somewhere in the globe.17 Postpartum haemorrhage is a prominent cause of maternal mortality worldwide, especially in high-income nations, despite the fact that most of the fatalities happen in low- and middle-income regions. FDPs, especially D-dimers, a biomarker of fibrinolysis, are increased in women with postpartum haemorrhage.18,19 By inhibiting plasmin's enzymatic action on fibrin, tranexamic acid provides an alternative approach of maintaining haemostasis; nonetheless, postpartum haemorrhage can still be treated with current pharmacological and surgical techniques. Women with postpartum haemorrhage might benefit from tranexamic acid because of its ability to lessen bleeding after surgery. There are two major reasons why tranexamic acid is so crucial. To begin, PPH is the primary reason of mortality for new mothers. More than half of all haemorrhage-related maternal fatalities happen within eight hours after giving delivery.20 Many women who may have benefitted from therapy will perish in the meantime. Second, administering tranexamic acid as soon as possible maximises its efficacy.\n\nSince tranexamic acid is inexpensive, heat stable, and commercially accessible in large quantities, it should be kept on hand at all times at obstetric emergency care facilities.\n\nFor the therapy of postpartum haemorrhage, tranexamic acid must be utilised in addition to all standard medical (uterotonics), surgical and non-surgical therapies. Some infusion solutions, such as those containing carbohydrates, electrolytes, dextran amino and acids, may be combined with it; however, solutions containing blood for transfusion, penicillin, or mannitol should not. Women who have had a previous thromboembolic event, are hypersensitive to tranexamic acid, have current intravascular clotting, or have a history of coagulopathy are not eligible for anti-fibrinolytic medication.\n\nMost women in high-income nations give birth in hospitals or have access to ambulance services, allowing medical professionals to quickly treat postpartum haemorrhage with intravenous tranexamic acid. About 40% of women in poor and middle-income nations give birth at home due to no or limited means of transportation. Medical professionals are present for most deliveries, but they aren't trained to provide IV medications. Women often lose consciousness during the lengthy hospital transport that follows. Medics should learn how to inject oxytocin subcutaneously and intravenously. This therapy has the potential to save lives in the community, meaning more women will have access to it sooner. Since tranexamic acid has a broad therapeutic index, it may be administered intravenously after an initial intramuscular injection.\n\nWomen are more likely to survive postpartum haemorrhage now than ever before because of advancements in urgent obstetric care, particularly using tranexamic acid as first-line treatment. Moreover, postpartum haemorrhage is becoming increasingly common.21–23 The number of women who suffer from the psychological and bodily aftereffects of PPH as a result will rise accordingly. Risk aspects for maternal morbidity after PPH and strategies for reducing these risks require more study.24\n\nICE approval received from the Datta Meghe Institute of Higher Education & Research (Ref No. DMIHER (DU)/IEC/2023/798)\n\nDate: 21/03/2023", "appendix": "Data availability\n\nCurrently no data is associated with this article as this is a study protocol.\n\nZenodo: SPRIT checklist for ‘Comparison of Tranexamic Acid plus Intramuscular Oxytocin with Intramuscular Oxytocin alone for prophylaxis of Primary Postpartum Haemorrhage in vaginal delivery’, DOI.: https://doi.org/10.5281/zenodo.8206239\n\nLicense: Creative Commons Attribution 1.0 Generic\n\n\nAcknowledgements\n\nWe acknowledge the support of the statistician for the valuable feedback.\n\n\nReferences\n\nWorld Health Organization: Managing complications in pregnancy and childbirth. Geneva: World Organization; 2000.\n\nKramer MS, Berg C, Abenhaim H, et al.: Incidence, risk factors, and temporal trends in severe postpartum hemorrhage. Am. J. Obstet. Gynecol. 2013; 209(449): 449.e1–449.e7. Publisher Full Text\n\nBateman BT, Berman MF, Riley LE, et al.: The epidemiology of postpartum hemorrhage in a large, nationwide sample of deliveries. Anesth. Analg. 2010; 110: 1368–1373. PubMed Abstract \| Publisher Full Text\n\nMathai M, Gülmezoglu AM, Hill S: Saving womens lives: Evidence-based recommendations for the prevention of postpartum haemorrhage. Bull. World Health Organ. 2007; 85: 322–323. PubMed Abstract\n\nMcCormick ML, Sanghvi HCG, Kinzie B, et al.: Preventing postpartum hemorrhage in low-resource settings. Int. J. Gynaecol. Obstet. Off. Organ. Int. Fed. Gynaecol. Obstet. 2002; 77: 267–275. Publisher Full Text\n\nGeller SE, Goudar SS, Adams MG, et al.: Factors associated with acute postpartum haemorrhage in low-risk women delivering in rural India. Int. J. Gynecol. Obstet. 2008; 101(1): 94–99. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGoffinet F, Mercier F, Teyssier V, et al.: Postpartum haemorrhage: recommendations for clinical practice by the CNGOF (December 2004). Gynecol. Obstet. Fertil. 2005; 33: 268–274. PubMed Abstract \| Publisher Full Text\n\nAmerican College of Obstetricians and Gynecologists: Clinical Management Guidelines for Obstetrician-Gynecologists Number 76, October 2006: postpartum hemorrhage. Obstet. Gynecol. 2006; 108: 1039–1047.\n\nRoyal College of Obstetricians and Gynaecologists: Prevention and management of postpartum haemorrhage. Guidelines no 52. London: RCOG; 2009.\n\nWorld Health Organization: Recommendations for the prevention and treatment of postpartum haemorrhage. WHO; 2012.\n\nBegley CM, Gyte GML, Devane D, et al.: Active versus expectant management for women in the third stage of labour. Cochrane Database Syst. Rev. 2015; 3: CD007412. PubMed Abstract \| Publisher Full Text\n\nWesthoff G, Cotter AM, Tolosa JE: Prophylactic oxytocin for the third stage of labour to prevent postpartum haemorrhage. Cochrane Database Syst. Rev. 2013; 10: CD001808. Publisher Full Text\n\nDeneux-Tharaux C, Sentilhes L, Maillard F, et al.: Effect of routine controlled cord traction as part of the active management of the third stage of labour on postpartum haemorrhage: multicentre randomised controlled trial (TRACOR). BMJ. 2013; 346: f1541. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGülmezoglu AM, Lumbiganon P, Landoulsi S, et al.: Active management of the third stage of labour with and without controlled cord traction: a randomised, controlled, non-inferiority trial. Lancet. 2012; 379: 1721–1727. PubMed Abstract \| Publisher Full Text\n\nLalonde A, Daviss BA, Acosta A, et al.: Postpartum hemorrhage today: ICM/FIGO initiative 2004–2006. Int. J. Gynaecol. Obstet. Off. Organ Int. Fed. Gynaecol. Obstet. 2006; 94: 243–253. PubMed Abstract \| Publisher Full Text\n\nHofmeyr GJ, Abdel-Aleem H, Abdel-Aleem MA: Uterine massage for preventing postpartum haemorrhage. Cochrane Database Syst. Rev. 2013; 2016: CD006431. Publisher Full Text\n\nSay L, Chou D, Gemmill A, et al.: Global causes of maternal death: a WHO systematic analysis. Lancet Glob. Health. 2014; 2: e323–e333. Publisher Full Text\n\nBonnar J, Davidson JF, Pidgeon CF, et al.: Fibrin degradation products in normal and abnormal preg- nancy and parturition. Br. Med. J. 1969; 3: 137–140. Publisher Full Text\n\nDucloy-Bouthors AS, Duhamel A, Kipnis E, et al.: Postpartum haemorrhage related early increase in D-dimers is inhibited by tranexamic acid: haemostasis parameters of a randomized controlled open labelled trial. Br. J. Anaesth. 2016; 116: 641–648. PubMed Abstract \| Publisher Full Text\n\nBrenner A, Ker K, Shakur-Still H, et al.: Tranexamic acid for post-partum haemorrhage: What, who and when.Best Pract. Res. Clin. Obstet. Gynaecol.2019; 61: 66–74. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKramer MS, Berg C, Abenhaim H, et al.: Incidence, risk factors, and temporal trends in severe postpartum hemorrhage. Am. J. Obstet. Gynecol. 2013; 209: 449.e1–449.e7. PubMed Abstract \| Publisher Full Text\n\nFord JB, Roberts CL, Simpson JM, et al.: Increased postpartum hemorrhage rates in Australia. Int. J. Gynecol. Obstet. 2007; 98: 237–243. Publisher Full Text\n\nLutomski J, Byrne B, Devane D, et al.: Increasing trends in atonic postpartum haemorrhage in Ireland: an 11-year population-based cohort study. BJOG An. Int. J. Obstet. Gynaecol. 2012; 119: 306–314. Publisher Full Text\n\nCarroll M, Daly D, Begley CM: The prevalence of women's emotional and physical health problems following a postpartum haemorrhage: a systematic review. BMC Pregnancy Childbirth. 2016; 16: 261. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "240831", "date": "13 Mar 2024", "name": "Ritu Singh", "expertise": [ "Reviewer Expertise I am a obstetric and gynecologist", "a minimal invasive surgeon." ], "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. Rationale of the study is clearly explained 2. Study design - not mentioned 3.Method details- a. Not mentioned - how authors will see efficacy of the drugs? b. Authors are going to do haemoglobin test in both group within 6 hours? We will do haemoglobin routinely the next day of delivery. Is it a hospital policy of the author to do haemoglobin within 6 hour or she will do it specifically in their study participants? c. You are using it in active management, if PPH occurs what will you do - not mentioned. d. In eligibility criteria not mentioned- is she taking term patient or preterm. e. Will you be going to take all the patients visiting to hospital? She has written Principal investigator will do allocation - will she be available 24 x7 in the hospital? f. How allocation and blinding will be done - not mentioned clearly g. Self-administered questionaries - not mentioned\n4. Aims, objective and outcome measures are not aligned a. In Aims written- linked to improvement in PPH - how you are going to do it b. In the Aim section of the author -it is written- “linked to improvement in Primary Postpartum Haemorrhage, mortality and morbidity and the negative effects linked to its uses in vaginal delivery’’. Is author going to see mortality also, it is not mentioned in material methods c. What negative effects - not mentioned. d. Primary objectives are ‘’ 1. To determine the efficacy of tranexamic acid as an add therapy to intramuscular oxytocin in reducing blood loss in vaginal delivery.2. To compare the two groups of tranexamic acid plus intramuscular oxytocin in one arm versus intramuscular oxytocin in another arm’’ In this way the author will see efficacy – what parameters she will include not mentioned in material methods. How she will compare the two groups not mentioned. e. Secondary objective- what side affects you are going to observe - not mentioned. There are many side effects of any drug, what side effects the author is going to see, they have to specify it. f. Are you going to use suction cannula also. (as you have mentioned suction machine) Is it not a con founding factor, as suction cannula is itself is used in PPH management.\n5.In Abstract- a. Author sentence is “The term, late postpartum haemorrhage is used when the bleeding lasts more than 24 hours.’’\n\nIt should be- The term, late postpartum haemorrhage is used when the bleeding occurs after 24 hours till puerperium. b. 'However, even a modest amount of blood loss might be harmful in cases of comorbidities like anaemia.’ This sentence is written twice\n6. In Introduction-a it is not consequences - it is a complication. b. Reference-not mentioned in 1st paragraph. c. \"Bleeding from or into the genital tract after delivery and before the end of puerperium is clinically defined as the quantity of bleeding that negatively affects the patient's overall state as demonstrated by rising pulse rate and lowering blood pressure.\"- sentence not correct d. Preeclampsia and preeclamptic pregnancies are same e It is not numerous - it is multiple pregnancies f. Prevalence 9.2 percent - reference? g. In introduction- Last paragraph is “The first line of defence in the treatment of PPH is oxytocin. Ergometrine and carboprost and misoprostol administered intramuscularly and intravenously are two more methods.” In this sentence there are not only two more,’ ergometrine, carboprost, misoprostol ' are 3 drugs. It should be –are other methods- not two more methods h. In rationale- reference for systemic review\n7. In Discussion Have to write points relevant to your study, no other details. 8. Need gross editing\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": [] } ]	1	https://f1000research.com/articles/12-1608
https://f1000research.com/articles/12-1607/v1	29 Dec 23	{ "type": "Study Protocol", "title": "Effect of Yogasana and Pranayama on cardiopulmonary functions on sawmill, sugar cane and bidi workers in the rural sector", "authors": [ "Milind Abhimanyu Nisargandha", "Shweta Dadarao Parwe", "Vaishali Vasant Kuchewar", "Chhaya Anil Saraf", "Milind Abhimanyu Nisargandha", "Vaishali Vasant Kuchewar", "Chhaya Anil Saraf" ], "abstract": "Background The rural sector is an essential component of the country’s economy, and the economy is based on the large number of workers involved in various activities such as agriculture, forestry, and small and large-scale industries. People work in different industries like sawmills, sugarcane and Bidi factories for their livelihoods. These workers, among other factory workers, are frequently exposed to hazardous working conditions that can have a negative impact on their health. These workers are at high risk of developing respiratory and cardiovascular diseases due to prolonged exposure to dust, smoke and other harmful substances. This study aimed to evaluate the effect of yoga and pranayama on cardiopulmonary function in the sawmill, sugar cane and Bidi workers in the rural sectors.\n\nMethods 348 workers will be randomly assigned to the Yogasana and Pranayama group or the control group. The intervention of the Yogasana and Pranayama group will be planned for a 20-week program, while the control group will be continuing their as-usual activities. Cardiopulmonary function will be assessed for baseline parameters, and after the intervention has been completed similar parameters will be recorded.\n\nConclusions It could be concluded that the Yogasana and Pranayama may be effective for improving the cardiopulmonary function in sawmill, sugar cane, and Bidi workers in rural sectors.\n\nRegistration\nCTRI/2023/07/055733.", "keywords": [ "Bidi Workers", "Cardiopulmonary Functions", "Sawmill Workers", "Sugar Cane", "Workers", "Praṇayama", "Yogasana." ], "content": "Introduction\n\nThe likelihood of developing cardiopulmonary disease is increased due to high exposure to dust and pollution, which occurs with many people working in the industrial area.1 This high level of impact of exposure in the sawmill, sugar cane and Bidi workers leads to respiratory disorders. Yogasana and pranayama is an essential yogic practice that changes cardiopulmonary and autonomic variables.2 Yoga reduces stress and autonomic function, and the Yogic breathing practice was reported to benefit cardiovascular and autonomic variables.3 This cardiopulmonary risk is more associated with the people working in the industries.4 In India, in most markets, people work in many small- (sawmill, Bidi company) and large-scale industries (sugarcane). The majority of the people who work in these factories are from poor socio-economical backgrounds.5 While working, they are directly or indirectly exposed to dust and pollution in their workplace. In India, Maharashtra state is one of the major sugar, sawmills and Bidi producers. In the Wardha districts, Samudrapur Tehsil is where people’s primary income source is rolling the Bidi. Many of these workers are exposed to snuff powders while working for long durations. These people are regularly exposed to the risk of inhalation directly.\n\nThis study aims to investigate the effect of Yogasana and Pranayama on the cardiopulmonary functions of the workers in the rural sector who are engaged in sawmills, sugar cane, and Bidi industry work. These industries expose workers to high levels of air pollution, which can harm their health, mainly their cardiopulmonary function.6–8 This study seeks to determine whether the practice of Yogasana and Pranayama can mitigate the adverse effect of industrial air pollution on the workers’ cardiopulmonary function.9,10 The study is essential as it can provide insight into the potential of Yogasana and Pranayama as a preventive measure against the adverse health effects of exposure to industrial air pollution in the workplace.11\n\nSugar cane workers are highly exposed to wood dust (Bhusa) while working near the boiler to generate steam. This high exposure to dust and air pollution by sugar cane workers leads to cardiopulmonary diseases such as asthma, cardiovascular diseases, respiratory diseases and due to this leads to deaths were reported12 in a few studies over the last decade.13,14\n\nAnother study assessed the ventilator function of persons exposed to sawdust with rhinitis symptoms.15 A total of 500 sawmill workers in Ibadan were studied to evaluate occupation-induced lung damage due to exposure to sawdust. Occupational-related problems were measured through a structured questionnaire. The study was conducted on 500 workers at University College Hospital (UCH) Ibadan and served as age and sex-matched with control. Findings reported that respiratory symptoms are common in the sawmill workers and 4.1% workers suffered airway obstruction.16\n\nIn a study published on Bidi workers where raw tobacco dust is a known sensitizing agent,17 there was evidence of alveolitis in the manufacturing industry of tobacco. Some workers in tobacco manufacturing sectors were found to experience respiratory-related symptoms and lung fibrosis.18\n\nAnother study was conducted to determine the rice husk dust effect on pulmonary function in the rice mill workers. In this study the population was 150 male rice mill workers from 6 different rice mills with 50 as control of similar age, sex ethnic group, and agriculture work background. Out of which 28 rice mill workers suffered with obstructive diseases, whereas eight suffered from restrictive pulmonary impairment.19\n\nThe study conducted by Patil SN in 2008 conducted pulmonary function tests on sugar cane workers. The workers exposed to sugar cane dust were compared with normal healthy adults as a control group. In this study, they found dysfunction in high duct exposure in sugarcane workers in a specific region of Western Maharashtra, India.20\n\nRhinitis is one of the common clinical conditions found in occupational-related disorders. It affects the respiratory upper airway and also involves the lower respiratory tract along with considerable airflow limitation.21 Exposure of sawdust leads to symptoms related to rhinitis.22\n\nClip pipe workers are also exposed to high-concentration airborne mold spores. A few cases were reported in Finland, where they suffered from allergic alveolitis. In this study, they compared the immunological and clinical effects of continuous mould spore exposure, where eight non-smoking workers, six on-chip pipes, and two on-bark pipes were evaluated, and chronic bronchitis symptoms were reported due to exposure to wood dust.23,24\n\nExposure to this pollution is related to an enhanced risk of cardiopulmonary morbidity.25 Most of the studies on the subject are related to the urban population. This study will compare sawmills, sugar cane, and Bidi workers’ occupational hazards and incidences of respiratory symptoms. Recently, from 2001 there are no published studies on the comparison of these three groups regarding cardiopulmonary risks treated with the intervention of Yogasana in the Indian scenario. This paucity of data and the risk of cardiopulmonary problems observed in the factory workers can be resolved through the investigation of our study.\n\nYogasana and Pranayama is an ancient traditional Yogic practice from Ayurveda for reducing stress and improve autonomic function. Yogasana (postural exercise) and Pranayama (breathing exercise) were reported to produce a positive effect on cardiovascular and autonomic function variables.26 Cardiopulmonary risk is more highly associated with people working in the industrial area.27 They are highly exposed to dust and air pollution in the environment where they work. Keeping this view in mind, the aim of the study is to evaluate the effect of Yogasana and Pranayama on cardiopulmonary function in sawmills, sugar cane, and Bidi workers in rural sectors.\n\n\n\n1. To evaluate the effect of cardiopulmonary function in sawmill, sugar cane, and Bidi workers.\n\n2. To evaluate the effect of Yogasana and Pranayama on autonomic function test in sawmill, sugar cane, and Bidi workers.\n\n3. To compare the effect of Yogasana among the sawmill, sugar cane, and Bidi workers.\n\n\nMethods\n\nThis will be parallel group, single blind, randomized control trial.\n\nThe study will be conducted in the Department of Physiology, Jawaharlal Nehru Medical College Sawangi (M) Wardha and Mahatma Gandhi Ayurved College and Hospital and Research Centre Salod (H) Wardha.\n\nSelection of the subjects will be done from outdoor patients (OPD) and indoor patients (IPD) of the Medicine Department, Jawaharlal Nehru Medical College Sawangi (M) Wardha and Department of Panchakarma, Mahatma Gandhi Ayurved College Hospital, and Research Centre Salod (H) Wardha. Also, subjects will be selected at their respective mills by organizing camps in the factory.\n\nIn this study, 348 subjects will be required according to the sample size calculation. The inclusion criteria will be: 1) sawmill, sugar cane, and Bidi workers aged between 25 and 40 years; 2) minimum exposure (i.e., employed in the industry) of 5 years and above; 3) those who have respiratory symptoms like breathlessness and cough. The exclusion criteria will be: 1) sawmill, sugar cane, and Bidi workers not exposed for more than 5 years; 2) Bidi workers who are BidiBidi smokers (confounder); 3) sawmill, sugar cane, and Bidi workers with hypertension (HTN), metabolic disorders, and congenital anomalies in cardio-respiration; 4) those who are addicted to alcohol. The allocation sequence was generated used computer-generated random numbers. The allocation concealment mechanism was a central telephone method.\n\nA sample of 348 has been calculated using Epi Info statistical software version 7.2.\n\nTo calculate the sample size for this study, several factors need to be considered, including the level of significance, power of the study, and effect size.\n\nAssuming a level of significance of 0.05, a power of 0.80, and a moderate effect size of 0.5, the sample size can be calculated using the following formula:\n\nWhere:\n\n• n = sample size\n\n• Zα/2 = the critical value of the standard normal distribution at 0.05 level of significance (1.96)\n\n• Zβ = the critical value of the standard normal distribution at 0.80 power (0.84)\n\n• SD = standard deviation of the population (assumed to be 10 based on previous studies)\n\n• d = effect size (0.5)\n\nPlugging in these values, we get:\n\nTherefore, a sample size of at least 87 participants per group would be needed for this study. However, it is important to note that the sample size may need to be adjusted based on the specific population being studied and any potential confounding variables smoking history, family history of diabetic, hypertension.\n\nInterventions\n\nTo improve adherence\n\nWe will motivate the participants by showing them videos of different exercises to build confidence among them for improvement. Every day we will send a reminder and motivational video on the WhatsApp group.\n\nConcomitant care\n\nIf they are on bronchodilator or any other medication, subjects will not be included in this study, as this may change the results of the study.\n\nBlinding (masking)\n\nNo unblinding is permitted in this study.\n\nThe pulmonary function test (PFT) will be carried out through the Med Spiro PC based digital spirometer used for determining the peak expiratory flow rate, peak inspiratory flow rate, vital capacity, and maximum voluntary ventilation. Subjects will be given instruction on how to perform the pulmonary function test in this study, the intervention will be given as Yogasana and Pranayama with the help of a yoga teacher. The trained Yoga teacher will teach the experimental groups specific Asana like Halasana (plough), Akarna-dhanurasana (reverse bow posture), Ardh-matsyendrasana (half spine twist), Ushtrasana (camel), Bhujangasana (cobra), and Surya namaskar (sun salute) for their flexibility, physical strength and to improve their endurance. They will be required to do these exercises every day for 60 minutes after the 20-minute physical training or practicing different Yogasana. They will also be trained in the Pranayama for breathing exercise i.e., alternate nostril breathing, Kapalbhati, Bhastrika, and Bhramari Pranayama for improve their lung efficiency. This practice will be given to the subjects every day for up to 20 weeks under the supervision of a Yoga teacher. After the 20 weeks of training, their parameters will be assessed again. The study is expected to take 18-24 months.\n\nData management\n\nAfter data collection, all data entry will be performed by a trained data operator, who will code the patients’ name, OPD and IPD number, and these will be safely stored with a password on the excel sheets.\n\nStatistics\n\nAnalysis of the population and missing data\n\nData will be maintained with a hard copy on file. If data are missing, it will be optioned from hard copy. Dropout or follow up can be separately recorded in the entry registers.\n\nHarms\n\nIn this study there are no drugs, hence no adverse effects are predicted. However, overstretching may cause muscle pain, and in osteoporosis patients fractures may happen. Some patients may also experience asthma attacks due to the exertion.\n\nData access\n\nData will be access via a separate excel sheet and it will be password-protected.\n\nThis trail is registered under the Clinical Trail Registry India and the registration number for this trail is CTRI/2023/07/055733.\n\nParticipants who meet the eligibility criteria will be randomized into the internal group ABC and control group D. They will be randomly divided into four groups, Group A, Group B, and Group C, and the control group D. In each group, there will be 87 subjects included. All the baseline parameters will be recorded at the time of recruitment in the hospital. A lung function test will be carried out for determining the relatively affected cardiopulmonary status among the workers of the sawmill, sugar factory, and Bidi rolling workers.\n\nParticipants, research assistants and the clinicians will be unaware of which group the subjects will be assigned to in this study. The blinded group codes will be kept absolutely confidential during the trial to observe for any improvement in any specific group due to the intervention.\n\nBaseline parameters will be assessed in the participants: complete blood count (CBC), measuring the pulse with a pulse meter, blood pressure with digital sphygmomanometer, lipid profile, BMI, hip waist ratio, and computerized spirometer recoded force vital capacity (FVC), force expiratory volume for 1 second in percentages (FEV1 %), peak expiratory flow rate (PEFR), peak inspiratory flow rate (PIFR).\n\nAfter 20 weeks of the intervention of Yogasana and Pranayama, the same parameters will be assessed again.\n\nThe subjects will be withdrawn from the study if they are not able to complete the training, if they start any bronchodilators or other medication than alters pulmonary function value, or if any problems emerge with them like asthma attack or, while performing Yogasana, severe pain. They will be noted along with their dropout criteria. They will be allowed to continue Yogasana and Pranayama if they feel comfortable.\n\nWe will observe for any significant changes in the groups after 20 weeks of the intervention.\n\nIn this study, the PICO model will be incorporated. The population is sawmill, sugar cane, and Bidi workers; the intervention is Yogasana and Pranayama; the comparison will be among the different groups of sawmill, sugar cane, and Bidi workers with a control group; and the outcome of the study will be the benefits of Yogasana and Pranayama.\n\nThe predicted timeline for this study is presented in Table 1.\n\n\nDiscussion\n\nWe expect to find that practising Yogasana and Pranayama positively affects the cardiopulmonary function of the sawmill, sugar cane, and Bidi workers in the rural sector. We expect the workers will show significant improvement in lung capacity, oxygen saturation level, and heart rate variability after regular practice of Yogasana and Pranayama.\n\nIn this study, we expect to find that regular practice of Yogasana and Pranayama may lead to a positive effect on the cardiopulmonary function of sawmills, sugar cane, and Bidi workers in the rural sector. The workers who will be doing regular practice of Yogasana and Pranayama may improve their lung function, blood pressure, and decrease their heart rate compared to those who did not.\n\nPranayama is a form of breathing exercise that originated in ancient India and is now practised worldwide. It involves controlling the breath to improve physical, mental, and emotional health.28 A previous study suggests that some of the benefits of practising Pranayama for reduce stress and anxiety.29 The Pranayama may calm the mind and reduce stress and anxiety levels. It may also promote relaxation and a sense of well-being.30\n\nWe expect the study will suggest that deep breathing is used in Pranayama, which may be helps to increase the lung’s capacity and oxygen intake. This will have the potential to improve overall respiratory health. Pranayama may improve the movement of oxygen and blood throughout the body, which can strengthen the immune system and overall wellness. Pranayama can aid in the integration of the sympathetic and parasympathetic nervous systems, which can improve overall health and well-being. Pranayama can also help to improve digestive issues such as constipation, bloating, and indigestion.31 A few other studies suggest that Pranayama can help to improve mental clarity and focus, which can improve productivity and performance.32–34\n\nIn this study, we will not consider the socio-economical background and lifestyle factors of the participants, which may influence the results. This study did not collect information on factors such as dust exposure, occasional consumption of alcohol, and diet, which may affect the cardiopulmonary function of the participants. Therefore, the study findings should be interpreted in the context of the limitations mentioned above.\n\nIn terms of generalizability, the study findings may apply to similar populations of sawmill, sugar cane, and Bidi workers in rural sectors. However, the findings cannot be generalizable to other populations such as urban workers or individuals with different occupational exposures, therefore, the study findings should be considered in the context of the specific population in rural sectors.\n\nThe work will be presented conferences and published in an indexed journal.\n\nNot yet started, it will start in September 2023.\n\nThe study is approved by the Datta Meghe Institute of Medical Sciences Institutional Ethical Clearance Committee (protocol no: DMIMS (DU)/IEC/2021/664) after due consultation and gatekeepers’ consent and presentation. The I.E.C. letter was provided by ICE DMIMSU (DU) on 18.12.2021 Wardha, Maharashtra, India.\n\nRe- regd no: ECR/440/Inst/MH/2013/RR-2019.\n\n\nConsent\n\nInformed written consent will be obtained for the purpose of the study from all the participants. Anonymity and confidentiality will be explained to them before the study begins, and they will voluntary sign the consent form. The informed consent agreement will include that the participants can withdraw his or her name from the study at any point if they no longer feel comfortable.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nSPIRIT checklist for ‘Effect of Yogasana and Pranayama on cardiopulmonary functions on sawmill, sugar cane and bidi workers in the rural sector’ https://doi.org/10.5281/zenodo.8010744.\n\n\nAcknowledgements\n\nWe would like to express our sincere gratitude to all those who have contributed to the drafting of this protocol. First and foremost, we would like to thank our co-authors for their invaluable insights and contributions to the writing the manuscript of protocol. We extend our appreciation to the faculty members of the Department of Physiology SIMATS who provided constructive feedback and helped to improve the quality of the protocol. We also acknowledge the Physiology Faculty team at JNMC for their support.\n\n\nReferences\n\nD’Amato G, Liccardi G, D’Amato M, et al.: Environmental risk factors and allergic bronchial asthma. Clin. Htmlent. Glyphamp. Asciiamp. Exp. Allergy. 2005 Sep [cited 2023 Aug 13]; 35(9): 1113–1124. Publisher Full Text\n\nNivethitha L, Mooventhan A, Manjunath NK: Effects of Various Prāṇāyāma on Cardiovascular and Autonomic Variables. Anc. Sci. Life. 2016; 36(2): 72–77. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWenger MA, Bagchi BK: Studies of autonomic functions in practitioners of yoga in India. Behav. Sci. 1961 [cited 2023 Aug 11]; 6(4): 312–323. PubMed Abstract \| Publisher Full Text\n\nKivimaki M: Work stress and risk of cardiovascular mortality: prospective cohort study of industrial employees. BMJ. 2002 Oct 19 [cited 2023 Aug 11]; 325(7369): 857–857. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlemseged EA, Takele AK, Zele Y, et al.: Assessment of Chronic Respiratory Health Symptoms and Associated Factors Among Flour Mill Factory Workers in Addis Ababa, Ethiopia, 2019: A Cross-Sectional Study. J. Asthma Allergy. 2020 Dec 31 [cited 2023 Aug 11]; 13: 483–492. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBerglund B, Brunekreef B, Knöppe H, et al.: Effects of Indoor Air Pollution on Human Health. Indoor Air. 1992 [cited 2023 May 2]; 2(1): 2–25. Publisher Full Text\n\nEnvironmental factors in cardiovascular disease\|Nature Reviews Cardiology.[cited 2023 May 2]. Reference Source\n\nThe mechanisms of air pollution and particulate matter in cardiovascular diseases\|SpringerLink.[cited 2023 May 2]. Publisher Full Text\n\nBaklouti S, Fekih-Romdhane F, Guelmami N, et al.: The effect of web-based Hatha yoga on psychological distress and sleep quality in older adults: A randomized controlled trial. Complement. Ther. Clin. Pract. 2023 Feb 1 [cited 2023 May 2]; 50: 101715. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nRani DS: Yoga: Its Origin, History and Development.2(5).\n\nYang N: A Critical Review of Yoga Interventions and Anxiety: Characteristics, Components, and Effects. Pepperdine University; 2022. [PhD Thesis].\n\nKumari S, Kumbhar-Patkar V, Patil Y: Measuring the Impact of Technology Trends and Forecasts in Sugar Industry Towards Sustainable Health-Care Services. Indian J. Public Health Res. Dev. 2017 Oct 1; 8: 939. Publisher Full Text\n\nAlves F: Por que morrem os cortadores de cana? Saúde E Soc. 2006; 15(3): 90–98. Publisher Full Text\n\nRibeiro H: Sugar cane burning in Brazil: respiratory health effects. Rev Saúde Pública. 2008; 42: 370–376. PubMed Abstract \| Publisher Full Text\n\nDunga JA, Alkali NH, Adamu YM, et al.: FEV1, FVC, FEV1/FVVC as predictors of rhinitis among saw mill workers in north central Nigeria. Niger. J. Med. 2016; 25(2): 152–158. PubMed Abstract \| Publisher Full Text\n\nIge OM, Onadeko OB: Respiratory symptoms and ventilatory function of the sawmillers in Ibadan, Nigeria. Afr. J. Med. Med. Sci. 2000; 29(2): 101–104.\n\nJäppinen P, Haahtela T, Liira J: Chip pile workers and mould exposure A preliminary clinical and hygienic survey. Allergy. 1987; 42(7): 545–548. PubMed Abstract \| Publisher Full Text\n\nHuuskonen MS, Husman K, Järvisalo J, et al.: Extrinsic allergic alveolitis in the tobacco industry. Occup. Environ. Med. 1984; 41(1): 77–83. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSingh SK, Nishith SD, Tandon GS, et al.: Some observations of pulmonary function tests in rice mill workers. Indian J. Physiol. Pharmacol. 1988; 32(2): 152–157. PubMed Abstract\n\nPatil SN, Somade PM, Joshi AG: Pulmonary function tests in sugar factory workers of Western Maharashtra (India). J. Basic Clin. Physiol. Pharmacol. 2008; 19(2): 159–166. PubMed Abstract\n\nParwe SD, Ingle AS, Nisargandha MA, et al.: Healthcare Workers Novel Coronavirus (NCOVID 19) life-threatening situation during the pandemic. Int. J. Res. Pharm. Sci. 2020; 11: 1222–1225. Publisher Full Text\n\nChandra K, Arora VK: Occupational Lung Diseases in Sewage Workers: A Systematic Review.2018; 19: 2.\n\nHurrass J, Heinzow B, Aurbach U, et al.: Medical diagnostics for indoor mold exposure. Int. J. Hyg. Environ. Health. 2017; 220(2): 305–328. Publisher Full Text\n\nAlwis KU: Occupational exposure to wood dust.1998.\n\nPope CA III, Burnett RT, Thun MJ, et al.: Lung Cancer, Cardiopulmonary Mortality, and Long-term Exposure to Fine Particulate Air Pollution. JAMA. 2002 Mar 6 [cited 2023 Aug 12]; 287(9): 1132–1141. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChoudhary S, Chawla VK: EFFECT OF YOGA AND PHYSICAL EXERCISE ON RESTING CARDIO-VASCULAR AND CARDIO-VASCULAR AUTONOMIC FUNCTION PARAMETERS: A COMPARISON. Int. J. Basic Appl. Physiol. 2021; 10(1): 48.\n\nKivimäki M, Leino-Arjas P, Luukkonen R, et al.: Work stress and risk of cardiovascular mortality: prospective cohort study of industrial employees. BMJ. 2002; 325(7369): 857. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNisargandha MA, Parwe SD: Does Obesity Lead to Sciatic Pain: A Comparative Study. Int. J. Curr. Res. Rev. 2020; 12: 120–125. Publisher Full Text\n\nThe effect of pranayama on test anxiety and test performance - PubMed.[cited 2023 Aug 12]. Reference Source\n\nYoga Breathing, Meditation, and Longevity - Brown - 2009 - Annals of the New York Academy of Sciences - Wiley Online Library.[cited 2023 Aug 12]. Publisher Full Text\n\nRanjita R, Hankey A, Nagendra HR, et al.: Yoga-based pulmonary rehabilitation for the management of dyspnea in coal miners with chronic obstructive pulmonary disease: A randomized controlled trial. J. Ayurveda Integr. Med. 2016 Jul 1 [cited 2023 May 30]; 7(3): 158–166. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nPhysiological Effects of Yogic Practices and Transcendental Meditation in Health and Disease - PMC.[cited 2023 May 30]. Reference Source\n\nDrigas A, Mitsea E: Breathing: A Powerfull Tool for Physical & Neuropsychological Regulation. The Role of Mobile Apps. Tech. Soc. Sci. J. 2022; 28: 135–158. Publisher Full Text Reference Source\n\nThapa A, Oliya R, Das R, et al.: Integrating Yogic Practices to Conventional Medicine in Preventing and Treating Medical Disorders.2022 Apr 27; 5: 036." }	[ { "id": "251343", "date": "21 May 2024", "name": "Gopal Nambi", "expertise": [ "Reviewer Expertise Rehabilitation" ], "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 title of the study is not clear and self-explanatory. Abstract:\nPlease include background of the study. Mention the study design, study duration and study setting. Mention the character of the study participants. Mention the intervention provided to the participants in short. The outcome measures used in the study are not sufficient. Mention the statistical tests used for the study. Present the reports with 95%CI with upper and lower limits for all outcome variables. The conclusion of the study is not clear; it should be drawn on the basis of study reports.\nManuscript:\nPlease elaborate the introduction part as it is not scientifically written. Provide a reference for Pranayama and yogasana for saw mill and bedi workers. Mention the application procedure, merits, and demerits of Pranayama and yogasana for saw mill and bedi workers. The need for the study is not mentioned clearly in recent references. Mention the gaps monitored by the researcher in the previous studies. Include the clinical significance of the study for the researchers, clinicians and patients. Mention the study design, study duration and study setting. Include the ethical approval and clinical trial registration number. Follow the CONSORT guidelines to present the study. Mention the character of the study participants. Mention the randomization and allocation procedure in clear. Mention the blinding procedure in detail. Include the diagnostic criteria of the disease and its ICD classification. Mention who has diagnosed the participants and their qualifications and experience. Mention the outcome variables with their reliability and validity. Include the figures for the intervention program, for study replication. Mention the intervention parameters of study interventions. Include the sample size calculation with a suitable reference. The samples included in the study are not sufficient to generalize the results. The statistical tests included are not apt for this study. Mention how the covariables are controlled and how the homogeneity is measured. Mention the treatment compliance rate, dropout rate and adverse effects. Present the reports with 95%CI with upper and lower limits for all outcome variables. Include the MCID score and effect size of all the variables. Summarize the discussion part. Include the mechanism behind the changes in the outcome variables with these intervention modalities in these patients. The conclusion of the study is not clear; it should be drawn based on study reports. Include the real-time limitations faced by the researcher. Include the future recommendations of the study.\n\nIs the rationale for, and objectives of, the study clearly described? No\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? No", "responses": [ { "c_id": "13021", "date": "30 Dec 2024", "name": "Shweta Parwe", "role": "Author Response", "response": "Dear sir/ madam, This brings to your attention that this is a stduy protocol, not an original article. Your suggestion of the study is appreciated, as this is the study protocol. The study is yet to be completed; after completion, the study will provide all data; hence, it could not be corrected as suggested by the reviewer. Thank you very much for your kind attentions Dr shweta Parwe" } ] }, { "id": "240553", "date": "05 Jun 2024", "name": "Maheshkumar Kuppusamy", "expertise": [ "Reviewer Expertise Good for policy making" ], "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 could provide more background information on the specific occupational hazards and exposures faced by sawmill, sugar cane, and Bidi workers, and their potential impact on respiratory and cardiovascular health.\n\n2. Discuss the prevalence and burden of respiratory and cardiovascular diseases in these occupational groups, both in the local context and globally, if relevant data is available.\n\n3. Highlight the importance of implementing preventive and therapeutic interventions to mitigate the health risks associated with these occupations.\n\n4. Explain why Yogasana and Pranayama were chosen as the interventions of interest, and provide a brief overview of the existing evidence supporting their potential benefits for respiratory and cardiovascular health.\n\n5. Clearly state the gaps in the current literature that this study aims to address, particularly in the context of occupational health in rural sectors.\n\n6. Consider the broader implications of the study for promoting holistic health and wellness in occupational settings, and the potential for integrating traditional practices like Yogasana and Pranayama into workplace wellness programs.\n\n7. Regarding sample size, it would be better to explain the sample size calculation in a clear narrative rather than just providing the formula. Describe the parameters used (effect size, power, significance level, etc.) and justify the chosen values based on previous similar studies or relevant guidelines.\n\n8. In the methods section, provide more details on the pulmonary function tests (PFTs) that will be conducted. Cite the specific guidelines or standards that will be followed for conducting and interpreting the PFTs, such as the American Thoracic Society (ATS) or European Respiratory Society (ERS) guidelines.\n\n9. The statistical analysis section needs more elaboration. Specify the statistical tests that will be used for different types of data (e.g., t-tests, ANOVA, regression analyses) and the assumptions that will be checked. Describe how you will handle missing data and any planned subgroup or sensitivity analyses.\n\n10. Discuss the potential limitations of the study, such as the relatively small sample size, the possibility of selection bias, lack of long-term follow-up, and the inability to control for all potential confounding factors (e.g., lifestyle, environmental exposures).\n\n11. Elaborate on the expected outcomes and potential implications of the study findings. How might the results contribute to our understanding of the effects of Yogasana and Pranayama on cardiopulmonary function in occupational settings? Discuss the potential for implementing these interventions as preventive or therapeutic measures in high-risk occupational groups.\n\n12. Consider adding a section on the ethical considerations and informed consent process for the study, as this is an essential aspect of any research involving human participants.\n\n13. Provide more details on the data management plan, including procedures for data entry, storage, and quality control measures to ensure data integrity and accuracy.\n\n14. Discuss the potential for generalizability of the study findings to other occupational groups or settings beyond the specific population studied (sawmill, sugar cane, and Bidi workers).\n\n15. Discuss the potential mechanisms by which Yogasana and Pranayama may improve cardiopulmonary function, drawing from existing literature and theoretical frameworks.\n\n16. Compare and contrast the findings of this study with those of previous studies that have investigated the effects of Yogasana, Pranayama, or similar interventions on respiratory and cardiovascular health.\n\n17. Explore the potential implications of the study findings for occupational health policies and practices, particularly in the context of the rural sectors where the study population is based.\n\n18. Discuss the feasibility and potential challenges of implementing Yogasana and Pranayama interventions in occupational settings, considering factors such as time constraints, worker compliance, and workplace infrastructure.\n\n19. Highlight the strengths and limitations of the study design, and discuss how these might have influenced the observed results.\n\n20. Suggest future research directions based on the findings of this study, such as investigating the long-term effects of Yogasana and Pranayama, exploring the effectiveness of different intervention durations or intensities, or examining the potential for combining these interventions with other preventive or therapeutic measures.\n\n21. Discuss the potential impact of the study findings on the overall health and well-being of the target population, beyond just respiratory and cardiovascular outcomes\n22.\n\nConsider including a brief section on the potential impact of the study, highlighting how the findings could contribute to improving occupational health and safety or informing policies and interventions in this area.\n23. Reference 1, 2 3, 6 13, 18, 24, are very old. Replce with New references like\n\nfor ref 2, you can cite following references, Kuppusamy M, et. Al., 2018 (Ref 1) Shobana R, et.al., 2022 (Ref 2)\nAlong with Reference 28, add following references remove Ref 29, and cite more appropriate citations like Jagadeesan T, et. al., 2022 (Ref 3) Malarvizhi M, et.al., 2019 (Ref 4)\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/12-1607
https://f1000research.com/articles/12-1606/v1	29 Dec 23	{ "type": "Case Report", "title": "Case Report: Unusual pulmonary involvement in a patient with Costello syndrome", "authors": [ "Hamida Kwas", "Majdoub Fehri Sabrine", "Znegui Tasnim", "Majdoub Fehri Sabrine", "Znegui Tasnim" ], "abstract": "Costello syndrome (CS) is a rare disease with intellectual disability, characterized by failure to thrive, short stature, joint laxity, loose soft skin, and distinctive facial features. This disease is caused by heterozygous germline mutations in the HRAS proto-oncogene. Cardiac and neurological abnormalities are the most common. Cardiovascular manifestations include valvular pulmonary stenosis, arrhythmia and hypertrophic cardiomyopathy. Neurological manifestations are dominated by hydrocephalus, seizures, and tethered spinal cord. Respiratory system manifestations have been reported in people with CS, but a full description of the different lung involvement and respiratory symptoms in these patients is not available. We report the case of a 19-year-old non-smoking man, followed for a Costello syndrome since the age of 8 months, who complained of exertional dyspnea and chest pain for over 18 months. The chest CT scan showed bullous emphysema of the left lung with a giant bulla in the left upper lobe measured than 20 cm long axis responsible for passive atelectasis. Pulmonary function tests revealed a severe non-reversible obstructive ventilatory defect. Faced with the worsening of his dyspnea despite treatment with bronchodilators and recurrent respiratory infections, it was decided to surgically remove the the giant emphysematous bulla. After bullectomy, a clinical and functional respiratory improvement was noted.", "keywords": [ "Costello syndrome", "lung emphysema", "giant pulmonary bulla", "lung function bullectomy" ], "content": "Introduction\n\nCostello syndrome (CS) is a rare genetic disorder that involves delayed physical and mental development. Infants with Costello syndrome are characterized by stunted growth, short stature, joint laxity, loose soft skin, facial dysmorphism, intellectual deficit and heart defects.1 Costello syndrome (CS) estimated number of patients worldwide is 300.2 Cardiac and neurological abnormalities are the most common. Respiratory system manifestations have been reported in people with CS, but a full description of the different lung involvement and respiratory symptoms in these patients is not available.3 We report a case of Costello syndrome with significant bullous emphysema complicated by exertional dyspnea and recurrent respiratory infections.\n\n\nCase report\n\nThe patient was a 19-year-old male. He is the second born male of two unrelated Tunisian parents. Prenatal history was remarkable for hypertension and coronary artery disease. The mother has no pathological history. He was delivered at 39 weeks gestation via vaginal vertex delivery. At birth he had he had breathing difficulties that were well controlled by oxygen therapy for 3 days. The patient is unemployed, nonsmoker and never treated for pulmonary tuberculosis. He had been followed for a Costello syndrome since a young age. The patient has a heart defect with a stenosis of the left pulmonary artery, for which he had surgery at the age of 8 months, and neurological impairment leading to moderate mental retardation. The patient had for 18 months before his admission a chest pain and exertional dyspnea.\n\nOn admission, physical examination revealed the patient had short stature (weight = 54 kg and height = 159 cm) and loose skin (cutis laxa). His facial features were coarses, with a wide forehead, epicanthal folds, low-set ears and thick lips. Examination of the respiratory system revealed absent breath sound in the left hemithorax. Pulse oximetry was 94%. The chest X-ray (Figure 1) revealed a left clearness without a vascular framework evoking a great-abundance spontaneous pneumothorax or a giant emphysema bulla. The chest CT scan (Figures 2 and 3) showed bullous emphysema of the left lung. The giant bulla was in the left upper lobe measured than 20 cm long axis responsible for passive atelectasis. Pulmonary function tests revealed a severe non-reversible obstructive ventilatory defect with a forced expiratory volume in one second (FEV1) = 0,760 L (25% predicted) and a forced vital capacity (FVC) = 0,960 L (26% predicted) and FEV1/FVC = 41.27%. Thus, the patient was maintained under oxygen (oxygen (2 l/min) with a long-acting inhaled bronchodilator (Formoterol: 12 μg twice daily).\n\nFaced with the worsening of his dyspnea despite medical treatment and recurrent respiratory infections one month after hospital discharge, it was decided to surgically remove the giant emphysematous bulla. Bullectomy was performed using the video-assisted thoracoscopic surgery approach. Intraoperatively, we saw multiple bullaes in the upper, middle, and lower lobe. The giant bulla was removed and pleural symphysis was performed. Soon After the operation, the chest pain disappeared with a marked improvement in his dyspnea.\n\n\nDiscussion\n\nThroughout history, Costello syndrome has been an extremely rare congenital anomaly syndrome that has attracted a lot of interest from doctors and scientists. Since the seminal work of Costello in 1971, scientific research on the Costello syndrome has increased largely.4\n\nThis syndrome is characterized by a mental retardation, learning disability, a high birth weight, an absolute or relative macrocephaly, neonatal feeding problems, short stature, curly hair, broad forehead, broad nose, large mouth and thick lips, cutis laxa, papilloma and various defects of internal organs.5,6\n\nPatients with this syndrome have a high incidence of cardiac involvement, including cardiac hypertrophy, congenital heart defect, and arhythmia.7 Complex pulmonary and airway co-morbidities are present in an important proportion of neonates and infants caring CS.7 wheezing and bronchial hypersecretion are frequently observed in children with CS. Involvement of the bronchial tree, particularly bronchomalacia and tracheomalacia, have been reported. These abnormalities can be serious and require a tracheotomy.8 Obstructive sleep apnea syndrome has been shown to be common in these patients, often accompanied by upper airway narrowing.9\n\nSeventy eight percent of CS patients experience respiratory complications as newborns.3 Transient respiratory distress and combined upper and lower airway anomalies are common in neonatal presentations.3 The origin of respiratory airway obstruction is not specifically identified. However, patients with CS generally present common diagnostic described by a combined involvement of the upper and lower respiratory tract with airway malacia being commonly diagnosed.10\n\nCostello syndrome is caused by heterozygous germline mutations of HRAS. These mutations are responsible for the production of an abnormally active H-Ras protein. Among these mutations, the most common is p.Gly12Ser, which is found in approximately 80% of patients.11 The high risk of malignant tumors occurs with patients present this mutation.12 Other rare mutations have been reported, particularly in patients with severe disease phenotypes. These are p.Gly12Cys, p.Gly12Asp, p.Gly12Glu and p.Gly12Val mutations which were found in patients with a severe form of CS progressing early to death.10\n\nStudies related to histopathological aspects of the respiratory tract in CS patients have demonstrated some congenital anomalies, as an example we mention: dysplasia of the pulmonary vasculature, lymphatics, airways, and alveoli. Besides, other histological results have been reported like: fibromuscular dysplasia of arteries, lung fibrosis, and different pulmonary infiltrates. Other histologic findings reported abnormal connective tissue in pleura, septal connective tissue, vessel, and alveolar walls.10 The involvement of elastic fibers in cutis laxa is widely distributed, affecting organs such as the skin, alveoli, aorta, and intestine.13\n\nOther abnormalities of the lung parenchyma have been described in patients with CS such as the deposition of atypical fragmented elastic fibres in the alveolar walls, abnormal collagen fibers in the pleura as well as the development of endogenous lipid pneumonia.14\n\nHowever, pulmonary emphysema is an exceptional disorder not described in the literature. It can be explained by the deposition of atypical elastic fibers in the alveolar walls. This pulmonary manifestation plays a decisive role in prognosis.\n\nThere is no specific treatment for Costello syndrome. The patient may benefit from symptomatic treatment, during the first months of life, such as: enteral or nasogastric tube nutrition, treatment of papilloma, speech therapy, occupational therapy, psychomotricity and physiotherapy for joint and postural anomalies.12\n\n\nConclusion\n\nPatients with Costello syndrome share characteristic findings affecting multiple organ systems. Pulmonary emphysema is an exceptional disorder that has not been described in these patients. This type of pulmonary abnormalities can be complicated by pneumothorax, secondary to the rupture of the emphysema bubbles, which can be life-threatening. Thus, the search for pulmonary involvement by performing a chest CT scan and an evaluation of respiratory function should be considered in patients with Costello syndrome.\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\nGripp KW, Morse LA, Axelrad M, et al.: Costello syndrome: clinical phenotype, genotype, and management guidelines. Am. J. Med. Genet. A. 2019; 179: 1725–1744. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPierpont ME, Magoulas PL, Adi S, et al.: Cardio-facio cutaneous syndrome: clinical features, diagnosis, and management guidelines. Pediatrics. 2014; 134: e1149–e1162. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGomez-Ospina N, Kuo C, Ananth AL, et al.: Respiratory System Involvement in Costello Syndrome. Am. J. Med. Genet. A. 2016 Jul; 170(7): 1849–1857. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAbe Y, Aoki Y, Kuriyama S, et al.: Prevalence and clinical features of Costello syndrome and cardio-facio-cutaneous syndrome in Japan: findings from a nationwide epidemiological survey. Am. J. Med. Genet. A. 2012; 158A(5): 1083–1094. PubMed Abstract \| Publisher Full Text\n\nHennekam RC: Costello syndrome: an overview. Am. J. Med. Genet. C Semin. Med. Genet. 2003; 117C(1): 42–48. PubMed Abstract \| Publisher Full Text\n\nKerr B: The Clinical Phenotype of Costello Syndrome. Monogr. Hum. Genet. 2009; 17: 83–93. Publisher Full Text\n\nGripp KW, Morse LA, Axelrad M, et al.: Costello syndrome: Clinical phenotype, genotype, and management guidelines. Am. J. Med. Genet. A. 2019; 179(9): 1725–1744. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLo IF, Brewer C, Shannon N, et al.: Severe neonatal manifestations of Costello syndrome. J. Med. Genet. 2008; 45(3): 167–171. PubMed Abstract\n\nMarca GD, Vasta I, Scarano E, et al.: Obstructive sleep apnea in Costello syndrome. Am. J. Med. Genet. A. 2006; 140A(3): 257–262. PubMed Abstract \| Publisher Full Text\n\nGomez-Ospina N, Kuo C, Ananth AL, et al.: Respiratory system involvement in Costello syndrome. Am. J. Med. Genet. A. 2016; 170(7): 1849–1857. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBurkitt-Wright EM, Bradley L, Shorto J, et al.: Neonatal lethal Costello syndrome and unusual dinucleotide deletion/insertion mutations in HRAS predicting p.Gly12Val. Am. J. Med. Genet. A. 2012; 158A(5): 1102–1110. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTajir M, Fergelot P: Costello syndrome: report of a case. Pan Afr. Med. J. 2012; 12: 64. PubMed Abstract\n\nMori M, Yamagata T, Mori Y, et al.: Elastic fiber degeneration in Costello syndrome. Am. J. Med. Genet. 1996; 61(4): 304–309. PubMed Abstract \| Publisher Full Text\n\nWaldburg N, Buehling F, Evert M, et al.: Pulmonary infiltrates in Costello Syndrome. Eur. Respir. J. 2004; 23(5): 783–785. PubMed Abstract \| Publisher Full Text" }	[ { "id": "250021", "date": "08 Apr 2024", "name": "Agnès Hamzaoui", "expertise": [ "Reviewer Expertise children respiratory 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 case reported is very rare, and no association between Costello Syndrome and Emphysema was previously described. At the opposite, lung fibrosis was reported. Moreover the patient is aged 19 and doing well while the majority of Costello patients with respiratory involvement die at a young age. Finally, this case is interesting as a reminder of a very infrequent disease, and an exceptional cause of emphysema. English needs some improvement.\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": "11440", "date": "29 Apr 2024", "name": "Hamida Kwas", "role": "Author Response", "response": "The case reported in our article is very rare and no association between Costello syndrome and emphysema has been previously described in the literature. Other respiratory abnormalities have been described in some patients with CS such as dysplasia of the pulmonary vasculature, lymphatics, airways, lung fibrosis, and various pulmonary infiltrates. Our patient is 19 years old and has been doing well to this day. Despite respiratory involvements, some patients live several years and even die in adulthood (Kerr et al., Genotype-phenotype correlation in Costello syndrome: HRAS mutation analysis in 43 cases. J Med Genet. 2006;43:401–405 ; Waldburg et al.,Pulmonary infiltrates in Costello Syndrome. Eur Respir J. 2004;23:783–785)." } ] }, { "id": "249997", "date": "06 May 2024", "name": "Nazario Foschi", "expertise": [ "Reviewer Expertise Oncology", "Rare Disease", "Urogynaecology", "Urothelial cancers" ], "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 your presentation of this unusual presentation. 1. As a rare syndrome, Costello has a low number of presentations and small literature, as of today. 2. Having gained new knowledge acquisitions as new therapeutic regimens and prolonged follow up protocols have been introduced, life expectancy of this population is increasing, and this need specific controls and clinical and diagnostic evaluations. 3. Cardio-thoracic evaluation should be performed periodically to promote early diagnosis of unusual condition and expected cardiologic evolutions. Moreover, this report is relevant as periodically this population should be screened for malignancies with the possible use of invasive manoeuvres. Thoracic and lung involvement could represent another issue to face with particularly if any kind of anaesthesia is planned.\nYou should add in discussion this topic as cancerogenesis in this population need a specific attention and multidisciplinary evaluation. As reported in one of the largest case series on this topic reporting surgical and endoscopic data of costello patients needing procedures all along childhood with different levels of invasiveness and presurgical screening. [Ref-1]\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": [] } ]	1	https://f1000research.com/articles/12-1606
https://f1000research.com/articles/10-1121/v1	08 Nov 21	{ "type": "Research Article", "title": "The utilization of new products formulated from water coconut, palm sap sugar, and fungus to increase nutritional feed quality, feed efficiency, growth, and carcass of gurami sago (Osphronemus goramy Lacepède, 1801) juvenile", "authors": [ "Azrita Undefined", "Hafrijal Syandri", "Netti Aryani", "Ainul Mardiah", "Indra Suharman", "Azrita Undefined", "Netti Aryani", "Ainul Mardiah", "Indra Suharman" ], "abstract": "Background: Giant gourami (Osphronemus goramy Lacepede, 1801) has become popular aquaculture in Indonesia. However, information on the feed used is minimal. This study analyzed the change in feeding nutrition, fish growth, feed efficiency, and body-carcass using product formulated from water coconut, palm sap sugar, and fungus. Methods: A total of 2,000 ml coconut water and 1,000 ml of palm sap sugar solution were formulated. Each product formulated was added with 6 g of Aspergillus niger (called product P1), 6 g of Rhizopus oligosporus (called product P2), and 6 g of Saccharomyces cerevisiae (called product P3). Commercial feeds supplemented with P1, P2, and P3 products are designated P1, P2, and P3 diets. Commercial feed added to freshwater is called the P4 diet (placebo). Their dosage is 300 ml/kg of feed. Gurami sago juveniles (initial weight 50±2.5 g and length 13.2±0.4 cm) were stocked in triplicate nets (2×1×1 m) in a freshwater concrete pond with a stocking density of 30 fish/net, an initial feeding rate of 3% per day until study termination. Results: Our results support our hypothesis that different product formulations have a significant effect (p<0.05) on growth performance and feed efficiency. At the same time, supplementing commercial feed with varying formula products has a significant impact (p<0.05) on the fatty acid composition of the diets and carcass body of gurami sago. Conclusion: Diet P2 contains a higher concentration of fatty acids to increase body weight, feed efficiency, and the best carcass fatty acid composition than other experiments for sago gurami reared in freshwater concrete ponds.", "keywords": [ "Aquaculture", "fatty acids profile", "coconut water", "palm sap sugar", "giant gourami", "growth performance", "feed efficiency" ], "content": "Introduction\n\nIn Indonesia, giant gourami (Osphronemus goramy Lacepede, 1801) is one of the most important freshwater fish species because it has a high market price1–4. However, the giant gurami contributes less to the total production of freshwater aquaculture than tilapia, African catfish, and Pangasius catfish5. For this reason, the Ministry of Maritime Affairs and Fisheries of the Republic of Indonesia drives fish farmers to increase the annual production of giant gurami from various local strains, namely Tambago, Palapa, Bastar, Galunggung, Blusafir, and Sago4,6–8.\n\nEfforts have been made to increase the production of giant gurami globally using aquaculture activities such as different feeding rates in floating cages9, differences of stocking density in concrete freshwater ponds4, and increased variety in the aquaculture systems, such as in an earthen freshwater pond, concrete freshwater pond and floating cages7,8,10. These aquaculture operations use commercial pellet fish feed, but the feed conversion ratio is higher, ranging between 1.43 and 1.65 . Conversely, the feed efficiency ratio is still low. In this context, between 30 to 40% of fish feed is released as a waste load to water bodies4,8,11. This is a particular problem, as the cost of fish feed is a significant challenge for aquaculture operations12–18.\n\nDifferent strategies have been developed to improve aquafeed nutrition, including enriching feed with fish oil9,19, soybean oil20, iodine and selenium21, EPA and DHA22, and the use of probiotics23. The goal is to make the diet rich in nutrients such as amino acids, fatty acids, minerals, and vitamins because the animal cannot synthesize them in sufficient quantities to meet their needs17,24,25.\n\nCurrently, it is essential to evaluate the supplementation of feed with natural ingredients that are cost-effective and sustainable from plant resources, without compromising the growth of cultured fish and aquafeed quality. Among these ingredients are coconut water and palm sap sugar; both contain health-friendly nutrients such as minerals, amino acids, enzymes, organic acids, fatty acids, vitamins, and phenolic compounds26–28. Water coconut has been used successfully to treat diseases in humans, such as throat infections, tapeworms, gonorrhea, digestive problems, influenza, lice, giardia, bronchitis, and cholera29–31. Palm sap sugar is also claimed to have health benefits due to its low glycemic index and possesses antioxidants, vitamins, and minerals32–34. On the other hand, some researchers have reported that fungi also improves aquafeed's nutritional value15,35,36. Based on previous research, supplementation of commercial feed with product formulas consisting of coconut water, palm sugar, and fermented with various fungi (Aspergillus niger, Rhizopus oligosporus, and Saccharomyces cerevisiae) is very important to evaluate. In addition, fish has a dominant function on consumer health because it is rich in amino acids, fatty acids, vitamins, and minerals19,21,25. Therefore, we also analyzed gurami sago's health lipid indices by analyzing several carcass fatty acids types.\n\nWe hypothesized that commercial feed supplemented with various formulated products could improve the nutritional quality of the feed and carcass, feed efficiency, and juvenile gurami sago growth rate. The current study evaluated the fatty acid composition and proximate composition of commercial pellet fish feed supplemented with various formulation products and their effect on growth performance, feed use efficiency, and fatty acid composition in the carcass of gurami sago juvenile.\n\n\nMethods\n\nThe study conducted by Hafrijal Syandri and his colleagues under the project entitled Optimization of New Formula Products Based on Local Materials To Strengthen Food Independence In The Aquaculture Sector In The New Normal Era of Coronavirus disease (Covid-19). The Ministry of Education, Culture, Research, and Technology of the Republic of Indonesia funded this research under grant number:170/E4.1/AK.04.PT/2021. The Ethics Committee for Research and Community Service at Bung Hatta University has approved this research (110/LPPM/Hatta/III-2021 which followed the ARRIVE guidelines. Approval was given to collect and rear juvenile gurami sago in the Aquaculture Laboratory, Faculty Fisheries, and Marine Science Universitas Bung Hatta. All efforts have been made to relieve the suffering of experimental animals. Therefore, gurami sago didn't suffer for this study, and they were still in good condition when they returned to the pond after research was completed. Where some fish were euthanized, this was carried out by piercing part of the fish's brain. Gurami sago fish were not classified as a protected animal according to Indonesian legislation.\n\nA total of 300 g of palm sap sugar (Arenga pinnate M.), purchased from local palm sugar farmers, was cooked in 3,000 ml freshwater at 60 °C for 15 minutes, and then cooled for 20 minutes in an open space. Next, we mixed 6,000 ml of mature coconut water (Cocos nucifera L.) with 3,000 ml of the palm sap sugar solution. The total product formulated is 9,000 ml and was divided into three containers of 3,000 ml. The first part added 6 g of Aspergillus niger (called P1), the second part added 6 g of Rhizopus oligosporus (called P2), and the third part added 6 g of Saccharomyces cerevisiae (called P3). Each portion (3,000 ml) was fermented for 48 hours in a plastic jerry can with a capacity of 5 liters. The aeration process was carried out continuously using Aerasi Fujimac MAC-40K-40L/min made in Japan.\n\nFloating commercial feed (781-2 PT. Japfa Comfeed Indonesia Ltd) was 2 mm with a proximate composition (dry weight %) of 10.66% moisture content, 30.10% crude protein, 4.09% crude fat, and 45.35% carbohydrate total with 2.5% ash, and 9.18% crude fiber. The feed is supplemented with the products P1, P2, P3, up to 300 ml/1 kg of feed. Commercial feed with only added freshwater (P4) was used as a control. These are referred to as P1, P2, P3 and P4 feeds. The products P1, P2, P3, and P4 were each sprayed evenly to 1 kg of the commercial feed, and then dried in the open air for 30 minutes. After that, we gave feed to the experimental fish.\n\nA total of 360 juvenile gurami sago of local strains were obtained from the Aquaculture Laboratory Faculty of Fisheries and Marine Science at Universitas Bung Hatta Padang of Indonesia. Exclusion criteria were if fish were found to be in poor health or would not eat the commercial food initially provided. Gurami sago juveniles were acclimatized for 30 days before the experiment, which commenced during January 2021. Juvenile fish were placed in the concrete freshwater pond 24-m3 (6×4×1 m) with a capacity of 5,600 L. During the acclimation, juveniles were fed commercial feed (781-2 PT. Japfa Comfeed Indonesia Ltd) with 30.10% crude protein content, 4.09% crude fat, 2.5% crude ash, and 9.18% crude fiber). Feeding was done three times daily (09.00 AM, 1.00 PM and 5.00 PM), and fish were fed the equivalent of 3% of their body weight per day.\n\nThe 360 juvenile gurami sago weighed on average 50±2.5 g and had an average length of 13.2±0.4 cm, and had not previously been used in earlier research. The juveniles' weight was measured using AD-600i scales with 0.001 g accuracy (ACIS model number AD-600i , China) and its use was approved by the Indonesian Directorate of Metrology, and body length was measured using a meter ruler with 1 mm accuracy. The fish were distributed in 12 nets framed with size 2-m3 (2×1×1 m) PVC pipe (1200 L capacity) placed inside two freshwater concrete ponds of size 18-m3 (6×2×1.5 m). The experimental groups were P1, P2, P3, and one control group (P4) with three replications each (12 total). Each net contained 30 fish. Fish were randomized to groups using a lottery method by Hafrijal Syandri and Azrita undefined. The water temperature varied between 27 °C and 30 °C (mean 28.5 °C). The dissolved oxygen (DO) level ranged from 5.8 to 6.2 mg L-1 (mean 5.72). The pH varied between 6.5 and 6.8 (mean 6.67). Temperature, DO level, and pH measurements were recorded weekly throughout the experiment. The water samples were collected at 10.00 AM at depth of 20 cm from each concrete pond for the determination of the water temperature, dissolved oxygen, and pH. Water temperature was measured using a thermometer (Celcius scale). An oxygen meter (YSI model 52, Yellow Spring Instrument Co, Yellow Spring, OH, USA) was used in-situ, pH values were determined with a pH meter (Digital Mini- pH meter, 0-14pH, IQ Scientific, Cemo- Science Thailand).\n\nFish were given a feed of 2 mm floating type pellets supplemented with product formulations P1, P2, P3, and control (P4) three times a day at 9.00 AM, 1.00 PM, and 6.00 PM. Fish were hand-fed at a 3% body weight rate per day until study termination, which was after rearing them for 90 days from February to April 2021. Fish samples were collected every 30 days to evaluate length and weight, and fish were fasted for 24 hours before sampling to empty the intestinal contents. Nine fish per net were randomly sampled every 30 days and euthanized with tricaine methanesulfonate (MS 222, Sigma Aldrich Co, USA MO, 50 mg L-1), then length and weight were measured. The amount of MS 222 used is 2,000 mg at each measurement of the sample (0, 30, 60, and 90 days).\n\nThis study used standard methods from the Association of Authorized Analytical Chemists37 to analyze the proximate composition of experimental diets and fish carcasses. One fish (mean weight 100 g) from each experiment replicates (P1, P2, P3), and control (P4) were collected from the rearing nets. We then euthanized the 12 fish by injecting their brains to examine the carcasses. Samples of the diet and wet fish were dried at 135 °C for two hours. The crude protein was analyzed using an automatically processed Kjeldahl (Buchi 430/323) using a Kjeltec methods (6.25), automatic Kjeldahl system (Buchi/430/323) model 1625, Moline IL USA. The fat content was analyzed using a Soxhlet Apparatus with the Soxhlet system 1046 (Foss, Hoganas Sweden). The ash content was analyzed using a muffle furnace (600 °C for four hours). We have calculated the total carbohydrates by subtracting the sum of % crude protein, % crude fat, % crude ash, and % moisture contents from 100%37. The proximate compositions of diets and carcasses were calculated by P.T. Saraswanti Indo Genetech Bogor Indonesia (SIG Laboratory, Accredited Testing Laboratory-LP-184-IDN).\n\nDiets and carcasses were analyzed using a fatty acid composition by the gas chromatography-mass spectrometry (GC-MS) method. The total lipid extraction was carried out according to modified Folch et al. (1957) as described by Rajion, 198538 using a chloroform: methanol (2.1. v/v) solvent system. Transmethylation was performed using 14% methanolic boron trifluoride. Diets and carcasses were analyzed for fatty acids composition by PT. Saraswanti Indo Genetech Bogor Indonesia (SIG Laboratory, Accredited Testing Laboratory-LP-184-IDN).\n\nNine fish sampled from each net were weighed and accounted for separately during the final sampling. Weight gain (WG, %), specific growth rate (SGR, %/day), feed conversion ratio (FCR), and feed conversion efficiency (FCE) were analyzed based on formulas9,10,39:\n\n\n\n\n\n\n\n\n\nThe nutritional quality of lipids AI and TI was calculated based on the equations40.\n\n\n\n\n\nWhere\n\nAI = Atherogenic index\n\nTI = Trombogenic index\n\nC12:0 = lauric acid\n\nC14:0 = myristic acid\n\nC16:0 = palmitic acid\n\nC18:0 = stearic acid\n\nΣMUFA = sum concentrations of all monosaturated fatty acid\n\nΣn-6 = sum concentrations of n-6 polyansaturated fatty acid\n\nΣn-3 = sum concentrations of n-3 polyunsaturated fatty acid\n\nSPSS 16.0 software package (SPSS; Chicago IL) was used for data analysis. Levine's test was used for determining homogeneity of data. One-way ANOVA was used for the determined treatment effect, followed by a post hoc Duncan's multiple range test41. Data are reported as mean value ± standard deviation for each treatment42. Microsoft Office Professional Plus 2019 was used for plotting the figures.\n\n\nResults\n\nNo samples were excluded from analysis. Figure 1 shows the growth performance of gurami sago at 30, 60, and 90 days for all groups during the experimental phase. No death was observed with any diets, so survival remained at 100% for all treatments during the 90 days of experimentation. Juvenile gurami sago fed feed P2 presented significantly higher growth performance with increased weight gain percent, lower feed conversion ratio (FCR), and improved feed conversion efficiency (FCE), compared to animals fed feed P1, P3, and P4 (Table 1). On the other hand, the P2 diet also led to a significant increase in fat and carbohydrates but not a significance difference in protein (Table 2).\n\na b c d – significant differences in rows. Analytical replicates n = 3\n\na b c d - significant differences in rows. Analytical replicates n = 3\n\nThe fat content differed significantly among the four diets. Diet P2 showed substantially higher protein and fat contents than diets P1, P3, and P4. Carbohydrate content was similar in diets P1, P2, and P3 but significantly higher than diet P4. The energy content differed considerably among the four diets (Table 3).\n\na b c d - significant differences in rows, Analytical replicates n= 3\n\nCF 781-2 – commercial pellet feed\n\nThe four diets demonstrate a high level of saturated fatty acids (SFAs), with palmitic acid (C16:0) and stearic acid (C18:0) as the abounding. The concentration of monosaturated fatty acids (MUFAs) was similar in diets P1, P2, and P3 and very low in diet P4, with the highest values recorded for oleic acid (C18:1 n-9) in all diets. We did not detect myristoleic acid (C14-1 n-9) or heptadecenoic acid (C17:1 n-8) in the P4 died and initial feed compositions. Regarding polyunsaturated fatty acids (PUFAs), diet P2 had the highest value, with linolenic acid (C18:3 n-3) dominant. Additionally, we recorded EPA (C20:5 n-3) and DHA (C22:6 n-3) in diets P1, P2, and P3, whereas, in diet P4, they were not detected (Table 4).\n\na b c d - significant differences in rows\n\nValues are % total fatty acid expressed as mean ± SE. of three separate determinations.\n\nn.d = Unidentified fatty acids, SFA= Saturated fatty acids; MUFA= Monounsaturated fatty acids; PUFA= Polyunsaturated fatty acid; FA= Fatty acids\n\nGurami fish fed diets P1, P2, P3, and P4 showed high levels of saturated fatty acids (SFA) in their body carcasses, with palmitic acid (C16:0) and stearic acid (C18:0) being the most abundant. The oleic acid (C18:1 n-9) in all body carcasses of gurami sago fish contained higher values. For gurami sago fed P1 diet, their carcasses also had the highest palmitoleic acid content (C16:1) compared to other feeds. Polyunsaturated fatty acids (PUFA) had the highest value in animal carcasses fed the P2 diet. For the four carcasses, linolenic acid (C18:2n-6) was dominant. We noted that EPA and AA levels were lacking in all four carcass bodies, whereas DHA was high (Table 5).\n\na b c d - significant differences in rows\n\nValues are % total fatty acid expressed as mean ± SD. of three separate determinations.\n\nn.d= Unidentified fatty acids, SFA= Saturated fatty acids; MUFA= Monounsaturated fatty acids; PUFA= Polyunsaturated fatty acid; FA= Fatty acids\n\nInitial commercial pellet feed\n\n\nDiscussion\n\nCommercial feed equipped with formulated products directly impacts the growth performance; in this study, the highest increases in final body weight (g), body weight gain (%), and the highest specific growth rate (%/day) were shown in the P2 diet at 147.74±1.02 g, 193.99±4.46%, and 1.15±0.01, respectively. In this experiment, supplementing the feed with formula products caused the feed protein level to decrease from 30% (initial composition) to 19.36±0.41% and 21.27±0.12% of all the diets experimental. Considering this result, the moisture of the feed increased from 10.66% to between 35.60% and 37.28%. However, while this does not cause a difference in body protein levels, it does affect the bodyweight of livestock. In this context, the experimental phase did not significantly affect the carcass protein of the body. Although the protein content is not different for each diet, there was a difference between the gurami sago's final growth and feed conversion ratio. We calculated that the FCR at diet P2 was 1.36, while at P4, it was 1.55. However, commercial fish feed resulted in a higher FCR when fish were cultured in earthen freshwater ponds (FCR = 1.87) than concrete freshwater ponds (FCR = 1.45)4,8. On the other hand, the weight gain and growth of the animal decreased with increasing fiber content in the diet43. The P4 diet has a high fiber content because it does not contain formulated products; as a result, the growth and feed conversion efficiency on the P4 diet are lower than other diets.\n\nFurthermore, carbohydrate levels in all experimental diets are lower than the initial composition; nevertheless, they did not decrease the growth of the gurami sago. This species belongs to the group of herbivorous fish10. Herbivorous and omnivorous fishes can increase amylase activity higher than carnivorous fish44. However, the poor overall growth of organisms is caused by low carbohydrate digestibility45. Several scientists have reported that fish growth and feed efficiency can increase by providing feeds supplemented with varying levels of carbohydrates46–48, regardless of the content of feed protein, fat, crude fiber, and carbohydrates in the experimental diet. We recommend using products formulated from natural sources of coconut water, palm sugar, and fungus in commercial fish feeds, thereby increasing the production value of the net yield and bringing more significant financial benefits.\n\nThe aquaculture industry needs to use rich nutritional feed, i.e., high in protein, fatty acids, minerals, and vitamins16,17,49,50. Therefore, increasing feeding nutrition and maximizing digestive enzyme activity in farmed fish can be done by providing raw feed ingredients fermented15,51–53. In this context, the new approach we are developing to improve feed quality, feed efficiency, and growth rate in gurami sago is to supplement commercial feed with formulated P1, P2, and P3 products. This strategy has been successful in increasing the nutrient quality of commercial feed. Fish feed supplemented with P2 products had the highest total fat content with 35.99% SFA, 31.33% MUFA, and 32.66% PUFA. In contrast, the P4 diet had the lowest total fat content, having 24.59% SFA, 21.79% MUFA, and 22.78% PUFA, respectively.\n\nThis study showed that the commercial fish feed equipped with products P1, P2, and P3 contained more complete fatty acids than the diet P4; the feeds' fat content was 3.47%, 3.68%, 3.49%, and 3.09%, respectively. Diet P4 did not contain linolenic acid (C18:3 n-3), EPA (C20:5n-3), and DHA (C22:6n-3). Accordingly, the commercial feed must be supplied with linolenic acid, EPA, and DHA because these are crucial to meet physiological needs, production performance, and health for fish22,54–56. In this experiment, EPA + DHA levels were 2.65%, 3.11%, and 2.72% of P1, P2, and P3 diets, while in the P4 diet (control), EPA + DHA was not recorded. For Atlantic salmon (Salmo salar L.) juveniles, the EPA and DHA levels in their diet are recommended to range from 0.50 to 1.0%57,58. Regardless of not recordeding EPA and DHA in the P4 diet however, freshwater fish, including gurami sago, are estimated to be able to synthesize unsaturated fatty acids (HUFAs), such as C20 and C22, from C18 PUFAs in the feeds through series reactions of chain elongation and desaturation. Thus, adequate amounts of C18:3-n3 and C18:2n-6 would meet their EFA requirements. The amount of DHA and EPA varies significantly between the P1, P2, and P3 diets, while DHA/EPA ratios in the diet have increased due to supplementing with formulation products. In this context, the differences in the DHA/EPA ratio in each experimental diet are due to differences in the use of fermenters, namely Aspergillus niger, Rhizopus oligosporus, and Saccharomyces cerevisiae. Other researchers state that to develop better feed formulations, the calculated ratio of DHA/EPA in the diet must be precise59. For example, the DHA/EPA ratios in the diet for maximum growth of Golden pompano, Trochinotus ovatus juvenile was 1.4617, 1.30 for gilthead seabream, Sparus aurata60, 0.53 for Atlantic salmon, Salmo salar in freshwater58 and 1.02 for Nile tilapia, Oreochromis niloticus61.\n\nThis study has estimated that the DHA/EPA ratios of 1.70 in the P2 diet can optimally increase the fish growth rate and feed efficiency. However, farmed fish's growth rate and feed efficiency depend on physiological, environmental, and farming factors62. The Aspergillus niger, Rhizopus oligosporus, and Saccharomyces cerevisiae used successfully in this experiment are also reported by other scientists to ferment fish feed raw materials such as corn-cob, soybean meal, and sunflower cake63,64. Furthermore, Rhizopus oligosporus is the main microorganism used in the fermentation process because it produces a wide range of enzymes, such as carbohydrase, proteases, lipases, and phosphatase65–67. Nevertheless, coconut water also plays a vital role in enriching the nutritional of feed in this experiment because coconut water contains minerals, amino acids, enzymes, organic acids, fatty acids, vitamins, and a few phenolic compounds26–28. Moreover, palm sap sugar also has an essential role in increased feed quality because palm sap sugar contains minerals, vitamins, and antioxidants33–34.\n\nMany freshwater fish species have low values of PUFA and higher levels of MUFA and PUFA19,67–69; however, the gurami sago found a high level of PUFA and a lower presence of MUFA. Some of the fatty acids in the animal body are affected by diet. Palmitic acid (C16:0) in the group SFA is most abundant in all treatments, however lower in the P4 group, with the highest body carcass level attained in diets P2 and P3 were 24.03%, and 23.04%, respectively. The C:16 and C18:2 n-6 fatty acids accumulate in giant gurami-fed high fat content diets, as demonstrated for common carp (Cyprinus carpio)70 and Atlantic salmon (Salmo solar)69. In experiments carried out with Oreochromis niloticus fed diets, rich lipids, linolenic and oleic acids have been accumulating in significant concentrations19,70,71. Other fish species such as Silver barb (Puntius gonionotous)72 and Asian red-tailed catfish (Hemibagrus wyckioides)73 can synthesize 20C PUFA of n-3 and n-6 series from 18C PUFA by desaturation and elongation. This capacity highlights the essential role of 20C PUFA in this group, serving as potential precursors of prostanoids. This potent ability has been observed in other freshwater fish, such as the zebrafish (Danio rerio)74.\n\nIn the present study, eicosatrienoic acid (C20:2 n-6) was not detected in all experiment diets; however, this fatty acid was present in the body carcass of giant gurami in all treatments ranging from 0.27% to 0.42% of total fatty acids composition. This data showed that this fatty acid type has an essential role in this species. The gurami sago fish synthesized it from other precursors ranging from 0.095% and 0.097% of total body lipids composition. In addition, AA, EPA, and DHA fatty acids, which were restricted in the diets, remained in the experimental fish in different proportions between feeds; this difference is due to the variation of added product formulation to each diet.\n\nThe results of our study show that the giant gurami sago strain is a strain capable of preserving its normal PUFA levels (C18:2 n-6, C18:3 n-3, C20:2 n-6, C20:4 n-6, C20:5 n -3 and C22:6 n-3). However, these fatty acids were at very low or undetectable levels in the diets, like eicosadienoic acid type. This fact demonstrates that gurami sago, similar to other freshwater fish species, such as Oreochromis niloticus61 and Cyprinus carpio21, can elongate and desaturate fatty acids from precursors present in the diet, including 18C:0 fatty acids and possibly from linoleic fatty acid in large quantities from the diets.\n\nIn the present study, the atherogenic index (AI) ranged from 1.68 and 2.19, and the thrombogenic index (TI) between 0.43 and 0.72 in all diets. This finding is related to a significant discrepancy of SFA values between experimental diets. AI and TI indexes are directly related to the levels of C14:0, C16:0, and C18:0, all of which are thrombogenic promoters19. AI and TI levels in gurami sago fed feed P1, P2, and P3 diets were lower than P4 (control); AI and TI indices show potential to stimulate platelet aggregation. The smaller the AI and TI values, the greater the protective potential of coronary artery disease75. The AI and TI values that the Food and Agriculture Organization and the World Health Organization76 recommend for human health range from 0.4 to 0.5. Although the AI and TI values of the gurami sago were higher than 0.5, we have hypothesized that consuming gurami sago meat does not harm consumers' health. In aquaculture, AI and TI indices, among others, depend upon levels of fish oil supplement in the diet19, different sources of oils in diet9,55, the effect of fish farming activities and handling methods after harvest77. In addition, feed quality used, age, gender, species, and environmental conditions also affect AI and TI values67,68,78,79.\n\n\nConclusion\n\nThis study shows that feed products made from natural and sustainable sources of coconut water, palm sap sugar, and fungus combined with commercial feeds can enhance nutrient-rich diets in gurami sago. The main factor that improved was the fatty acid composition of the PUFA group (i.e., linolenic acid, DHA, and EPA). The increase is related to growth rate, feed conversion ratio, and feed conversion efficiency. The P2 formulation was optimal for feed quality, fish growth, feed efficiency, and carcass fatty acids. This feed also contributes to improving the nutritional quality of giant gourami lipids, which is beneficial to consumers' health. These findings provide basic knowledge about efforts to improve the quality of nutrient-rich feeds and the basis for efficient use of feeds in future fish farming operations.\n\n\nData availability statement\n\nfigshare: The utilization of new products formulated from water coconut, palm sap sugar, and fungus to increase nutritional feed quality, feed efficiency, growth, and carcass of gurami sago (Osphronemus goramy Lacepède, 1801) juvenile. https://doi.org/10.6084/m9.figshare.1664107380\n\nThis project contains the following underlying data:\n\n- Table 1a. Raw data growth for 0, 30, 60, 90 days.\n\n- Table 1b. Raw Data growth performance, FCR, FCE_90 days_giant gurami\n\n- Table 2. Raw data proximate composition carcass of gurami sago after 90-days\n\n- Table 3. Raw data proximate composition of diets\n\n- Table 4. Raw data Composition of fatty acids and total lipid in the diets enriched\n\n- Table 5. Raw data Composition of fatty acids of the carcass\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).", "appendix": "References\n\nArifin OZ, Prakoso VA, Subagja J, et al.: Effects of stocking density on survival, food intake and growth of giant gourami (Osphronemus goramy) larvae reared in a recirculating aquaculture system. Aquaculture. 2019; 509: 159–166. Publisher Full Text\n\nSlembrouck J, Arifin OZ, Pouil S, et al.: Seasonal variation of giant gourami (Osphronemus goramy) spawning activity and egg production in aquaculture ponds. Aquaculture. 2020; 527: 735450. Publisher Full Text\n\nAryani N, Suharman I, Azrita A, et al.: Diversity and distribution of fish fauna of upstream and downstream areas at Koto Panjang Reservoir, Riau Province, Indonesia [version 2; peer review: 2 approved]. F1000Res. 2019; 8: 1435. 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Reference Source\n\nFAO/WHO: Fat and Oils in Human Nutrition: Report of a Joint Expert Consultation. FAO/WHO, Rome, Italy. 1994. Reference Source\n\nŚimat V, Bogdanovic T, Poljak V, et al.: Changes in fatty acid composition, atherogenic and thrombogenic health lipid indices and lipid stability of bogue (Boops boops Linnaeus, 1758) during storage on ice: Effect of fish farming activities. J Food Compos Anal. 2015; 40: 120–125. Publisher Full Text\n\nErken N, Özden Ö: Proximate composition and mineral contents in aqua cultured sea bass (Dicentrarchus labrax), sea bream (Sparus aurata) analyzed by ICP-MS. Food Chem. 2007; 102(3): 721–725. Publisher Full Text\n\nLuzia LA, Sampaio GR, Castellucci CMN, et al.: The influence of season on the lipid profiles of five commercially important species of Brazilian fish. Food Chem. 2003; 83(1): 93–97. Publisher Full Text\n\nSyandri H, Aryani N, Azrita A, et al.: The utilization of new products formulated from water coconut, palm sup sugar, and fungus to increase nutritional feed quality, feed efficiency, growth, and carcass of gurami sago (Osphronemus goramy Lacepède, 1801) juvenile. figshare. Dataset. 2021. http://www.doi.org/10.6084/m9.figshare.16641073.v2" }	[ { "id": "118909", "date": "28 Jan 2022", "name": "Nurul Huda", "expertise": [ "Reviewer Expertise Food Science." ], "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\nThere is a need to highlight improvement in the quality of commercial fish pellet by using local natural source ingredients.\nAbstract\nMethods: authors need to mention the percentage of palm sap sugar solution (10%?).\nResults: authors need to mention numerical results of growth performance, chemical compositions and fatty acid profiles of the treated fish.\nConclusion: authors need to highlight the ability of diet P1 to increase body weight, feed efficiency, and fatty acid profiles.\nIntroduction\nAuthors need to provide justification of choosing the Sago local strains as the treated fish.\n‘We hypothesized that commercial feed supplemented with various formulated products’. As the authors used local water coconut and palm sap sugar as ingredients on their product formulation, they should state that this was the feed used in the hypothesis.\n\nMethods\nChange 3,000 ml to 3 litres and 9,000 ml to 9 litres\nChange the cooked term to heated.\nIt is suggested not to spell out the producer name or brand of commercial feed used during the study.\nDoes 2 mm of commercial feed refer to the length of the individual pellet?\nNeed to mention whether the preparation of experiment diets was only conducted before the feeding trial? If yes, Authors need to mention the storage condition for the formulated diets during 90 days of feeding trial.\nNo need to re-mention the details proximate composition of commercial pellets.\nNeed to mention the reason behind the changes of feeding time from 5:00 PM (during acclimation) to 6:00 PM (during experiment).\nNeed to mention the objective and detail procedures for the fish brain injection. What kind of tools were used?\nNeed to mention the necessary drying of diet and fish sample at 135 °C for two hours: is it for moisture content analysis? If yes, the authors need to cite suitable reference for this method as normally moisture content analysis conducted at 105 °C for the whole night or after the constant weight of the samples reached.\nSuggested not the spell out the name of commercial lab used for the chemical analysis of diet and fish sample. Maybe can state as analysis was conducted in accredited lab.\nResults\nCheck the statistical analysis of result presentation. Normally \"a\" notification refers to the highest value of the results data. This comment applied to all statistical analysis result presentation. E.g. in table 1 the authors write:\nFinal body weight (g) 132±2.08a 147.74±1.02b 118.74±1.22c 109.73±1.89d\nThis should be written with ‘a’ as highest or lowest: therefore\nFinal body weight (g) 132±2.08b 147.74±1.02a 118.74±1.22c 109.73±1.89d (a = highest) OR Final body weight (g) 132±2.08c 147.74±1.02d 118.74±1.22b 109.73±1.89a (a = lowest)\nTable 3. Statement (% dry weight basis) normally refers to the presentation of proximate composition at 0.00% of moisture content. Authors need to delete the above mentioned statement of change to % wet basis. The current data presentation refers to the % wet basis of proximate composition.\nDiscussion:\nAuthors need to discuss the increase of carbohydrate content of sample P1, P2 and P3 then P4 which was probably contributed by the addition of palm sap sugar solution.\nRelocate the following to Conclusion or Recommendations: \"We recommend using products formulated from natural sources of coconut water, palm sugar, and fungus in commercial fish feeds, thereby increasing the production value of the net yield and bringing more significant financial benefits”.\nAuthors need to discuss the mechanism behind the production or increasing content of linolenic acid, EPA , and DHA in diets P1, P2 and P3. Are there previous reports or proven ability for the fungus used to produce or to convert mentioned fatty acid from palm sap sugar solution and or coconut water?\nConclusion\nNeed to highlight the growth performances of treated fish rather than the fatty acid compositions.\nNeed to highlight the term of local natural source ingredients.\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": "9323", "date": "29 Dec 2023", "name": "Hafrijal Syandri", "role": "Author Response", "response": "We have responded to article comments from Prof. Nurul Huda, Faculty of Food Science and Nutrition, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia. Abstract part Background: Giant gourami (Osphronemus goramy Lacepede, 1801) has become popular aquaculture in Indonesia. However, information on the feed used is minimal. This study analyzed the change in feeding nutrition, fish growth, feed efficiency, and body carcass using product formulated from water coconut, palm sap sugar, and fungus Methods: A total of 2 litres of coconut water and 1 litres of palm sap sugar solution (10%) were formulated. Each product formulated was added with 6 g of Aspergillus niger (called product P1), 6 g of Rhizopus oligosporus (called product P2), and 6 g of Saccharomyces cerevisiae (called product P3). Commercial feeds supplemented with P1, P2, and P3 products are designated P1, P2, and P3 diets. Commercial feed added to freshwater is called the P4 diet (placebo). Their dosage is 300 ml/kg of feed. Gurami sago juveniles (initial weight 50±2.5 g and length 13.2±0.4 cm) were stocked in triplicate nets (2×1×1 m) in a freshwater concrete pond with a stocking density of 30 fish/net, an initial feeding rate of 3% per day until study termination. Results: Our results support our hypothesis that different product formulations have a significant effect (p<0.05) on growth performance. The weight gain and feed conversion efficiency in the P1, P2, P3, and P4 diets were 167.24%, 193.99%, 134,22%, 115.98%, and 0.65, 0.73, 0.65, and 0.64, respectively. At the same time, supplementing commercial feed with varying formula products has a significant impact (p<0.05) on the fatty acid composition of the diets and carcass body of gurami sago. Lipid content in fish carcasses fed P1, P2, P3, and P4 diets were 2.90%, 4.42%, 2.98%, and 2.76%, respectively. Conclusion: Diet P2 contains a higher concentration of fatty acids to increase body weight, feed efficiency, and the best carcass fatty acid composition than other experiments for sago gurami reared in freshwater concrete ponds. Methods part Change 3,000 ml to 3 litres and 9,000 ml to 9 litres. Comment: We are agreed to change 3,000 ml to 3 litres and 9,000 ml to 9 litres It is suggested not to spell out the producer name or brand of commercial feed used during the study. Comment: There are several types of feeds produced by manufacturers. Therefore we have to mention the manufacturers and brands of commercial feeds. Does 2 mm of commercial feed refer to the length of the individual pellet? Comment: The size 2 mm is the diameter of the individual pellet feed. Need to mention whether the preparation of experimental diets was only conducted before the feeding trial? If yes, the Authors need to mention the storage condition for the formulated diets during 90 days of the feeding trial. Comment: The addition of different formula products to the experimental diet was carried out every day before being given to the experimental fish. We need to mention the reason behind the changes in feeding time from 5:00 PM (during acclimation) to 6:00 PM (during the experiment). Comment: We wrote that 6:00 PM was a mistake; it should have been 5:00 PM according to the acclimatization schedule. Need to mention the objective and detail procedures for the fish brain injection. What kind of tools were used? Comment: Before the fish was euthanized, it was soaked in fresh water at a temperature of 10°C for five minutes. The goal is for the fish to be calmer and pierce their brain easier.The tools used are a large animal syringe (9G x 1 inch). Need to mention the necessary drying of diet and fish sample at 135 °C for two hours: is it for moisture content analysis? If yes, the authors need to cite suitable reference for this method as normally moisture content analysis conducted at 105 °C for the whole night or after the constant weight of the samples reached. Comment: The water content analysis should be carried out at a temperature of 1050 C. Result part Check the statistical analysis of the result presentation. Usually \"a\" notification refers to the highest value of the results data. This comment applied to all statistical analysis result presentations. e.g. in table 1, the authors write. Comment: We will consider for other manuscripts. Table 3. Statement (% dry weight basis) normally refers to the presentation of proximate composition at 0.00% of moisture content. Comment: We agreed to change to % wet basis because the writing moisture data (Table 3) Conclusion part: Need to highlight the growth performances of treated fish rather than the fatty acid compositions. Comment: we have written at the conclusion, i.e., the increase is related to growth rate, feed conversion ratio, and feed conversion efficiency. The P2 formulation was optimal for feed quality, fish growth, feed efficiency, and carcass fatty acids." } ] }, { "id": "145759", "date": "16 Nov 2023", "name": "Norazmi-Lokman Nor Hakim", "expertise": [ "Reviewer Expertise aquaculture" ], "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\nLanguage: Editing for the language is required throughout the manuscript due to too many mistakes or inappropriate use of some terms that might lead to confusion or misunderstanding. For example: abstract: 'Commercial feed added to freshwater is called the P4 diet (placebo).' For some readers, this might mean the commercial feed is added to the freshwater which will lead to the question.... why? Why do you add the feed into freshwater? Though I think what the authors meant here is that they spray freshwater on the commercial pellet as a placebo (control treatment). I recommend the authors to send this manuscript for proofreading to avoid confusion among readers.\nTitle: I feel the title needs to be simplified to really capture the research. For example: What new products? is it the fermented product? Basically this research is about feeding the guramis with commercial feed enriched with coconut-based products that were fermented using different types of fungus. Just some suggestions: 'Efficacy of feed enriched with fermented coconut products on gurami sago growth and carcass composition' or 'Fermented coconut product enriched feed influence gurami sago growth and carcass composition'. Just some suggestions. Feel free to change or come up with a new simplified title.\n\nIntroduction:\nWater coconut or coconut water?\n'Based on previous research, supplementation of commercial feed with product formulas consisting of coconut water, palm sugar, and fermented with various fungi (Aspergillus niger, Rhizopus oligosporus, and Saccharomyces cerevisiae) is very important to evaluate'... please give example of which literature or which previous research. I think the authors should add 1-2 more sentences on the application of fermented product as supplementation in aquaculture. Has it been tried before in other species?\nMethods:\nFor me, the main problem in the methodology is the way the experiments were conducted in concrete ponds where the fish were reared together and are only separated by using nets. Since the fermented products were sprayed onto the pellets and were left out to dry for just 30 mins before being fed to the fish, there is a high possibility that leaching of the sprayed products might occur (they leached into the rearing water during feeding). The fermented product might be lost in the water or accidentally exposed to other fish (since they were reared in the same water and just separated by nets). The authors need to explain and elaborate more or discuss this matter in the discussion section too.\n\nAlso, what is the amount of feed intake for each treatment? Yes you did feed them 3% of their body weight per day, but that is the amount given, what about the actual amount the fish really ate? Did they finish all the food? Were there any leftovers? Did the fish accept the fermented pellet well?\nWas the fatty acid profile analysis conducted after the food is dried? Did the author try to analyze wet pellets? (pellets that have been dried and then fed to fish making them wet) this might help to detect whether there was leaching occurred.\nAll these issues need to be addressed by the authors or the result might be biased.\nLast subtopic in the method section... Data Analysis\nResults.\nWhat statistical analysis did the authors use to analyze the growth performance? There were no error bars or any information on the result of the statistical analysis here in the graph. I suggest the authors run repeated measures ANOVA to analyze the growth performance since the data taken was at 4-time points. This will ensure that the growth performance differences between and within each treatment at each time point can be detected. It will make the analysis more robust.\nDiscussion\n\nThe discussion section did not discuss the mechanism of how the fermented products work on the fish and how they change or make the fatty acid profile of each treatment differs from one another. The discussion was focused mainly on the different nutritional content of the pellets and how it affects fish. Now the authors are using the same commercial pellet and it was sprayed with different fermented products. How does this affect the fatty acid profile and proximate analysis (of certain nutrients)? For example, what are the nutrients in the coconut water and palm salp sugar that influence the fiber content of the pellet? What is the function of the fungus then? Also, did the fermentation process have any effect? This was not discussed.\nConclusion\nThe conclusion section needs to be rewritten. Which feed is the best for gurami sago?\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": "10662", "date": "29 Dec 2023", "name": "Hafrijal Syandri", "role": "Author Response", "response": "The author will revise the title in the new version with the efficacy of feed enriched with fermented coconut water products on growth and carcass composition of gurami sago (Osphronemus goramy Lacepède, 1801) juvenile. In the introduction part, the authors added this sentence on the new version: On the other hand, the supplementation of commercial feed with a formulated product consisting of coconut water, palm sugar, and fermented various fungi (Aspergillus niger, Rhizopus oligosporus, and Saccharomyces cerevisiae) has never been tested on fish. Therefore, it is crucial to analyze the efficacy of feed enriched with fermented coconut water products on juvenile sago gurami's growth and carcass composition (Osphronemus goramy Lacepède, 1801) in this study. Additionally, we examined the health lipid index of gurami sago by evaluating various types of fatty acids in the carcass. In the methods after the sentence, The products P1, P2, P3, and P4 were each sprayed evenly on 1 kg of the commercial feed and then dried in the open air for 30 minutes. The feed is given gradually so that the experimental fish eat all of it. This aims to prevent the leaching of sprayed fermentation products so that these products do not dissolve into the rearing water during feeding. Fish were hand-fed at a 3% body weight rate per day until study termination, which was after rearing them for 90 days from February to April 2021. Each experimental fish received well-fermented pellets so that they finished all the feed given. In this study, the author did not analyze commercial wet pellet feed. The author will complete an analysis of the growth performance of juvenile sago gourami fish at each growth measurement point (0, 30, 60, and 90 days) related to Figure 1 using the ANOVA test. In the new version, The author will discuss the nutritional content of coconut water and palm sugar and how they contribute to the nutritional content of fish feed. The author will also discuss the fermentation process's effect on feed's nutritional content. We will revise the conclusions to state the most optimal feed for the growth of gorami sago fish. The author will revise the use of English in this article for the new version." } ] } ]	1	https://f1000research.com/articles/10-1121
https://f1000research.com/articles/8-1193/v1	26 Jul 19	{ "type": "Opinion Article", "title": "Moral injury and the four pillars of bioethics", "authors": [ "Thomas F Heston", "Joshuel A Pahang", "Joshuel A Pahang" ], "abstract": "Health care providers experience moral injury when their internal ethics are violated. The routine and direct exposure to ethical violations makes clinicians particularly vulnerable to harm. The fundamental ethics in health care typically fall into the four broad categories of patient autonomy, beneficence, nonmaleficence, and social justice. Patients have a moral right to determine their own goals of medical care, that is, they have autonomy. When this principle is violated, moral injury occurs. Beneficence is the desire to help people, so when the delivery of proper medical care is obstructed for any reason, moral injury is the result. Nonmaleficence, meaning do no harm, has been a primary principle of medical ethics throughout recorded history. Yet today, even the most advanced and safest medical treatments all are associated with unavoidable, harmful side-effects. When an inevitable side-effect occurs, not only is the patient harmed, the clinician also suffers a moral injury. Social injustice results when patients experience suboptimal treatment due to their race, gender, religion, or other demographic variables. While moral injury occurs routinely in medical care and cannot be entirely eliminated, clinicians can decrease the prevalence of injury by advocating for the ethical treatment of patients, not only at the bedside, but also by addressing the ethics of political influence, governmental mandates, and administrative burdens on the delivery of optimal medical care. Although clinicians can strengthen their resistance to moral injury by deepening their own spiritual foundation, that is not enough. Improvements in the ethics of the healthcare system as a whole are necessary in order to improve medical care and decrease moral injury.", "keywords": [ "moral injury", "burnout", "bioethics" ], "content": "Introduction\n\nMoral injury occurs when a person experiences an immoral event that disrupts their fundamental moral integrity. Injuries can be self-inflicted by intentionally doing something wrong or come about as collateral damage through observation of a real or perceived action that violates an internal sense of right and wrong. Those suffering from moral injury have a disruption of their sense of morality, with consequences impacting their capacity to behave in a moral manner. The injury reduces their capacity to think of themselves as a moral, good person (Yan, 2016).\n\nThe term moral injury was introduced initially to describe the reaction of military veterans to the participation in or observation of profound ethical transgressions occurring during wartime (Shay & Munroe, 1999). The diagnosis of moral injury in veterans relies on the presence of three factors: a betrayal of what is right, which is carried out by someone who holds legitimate authority (e.g. a leader), and occurs in a high stakes situation (Shay, 2014). The diagnosis of moral injury, however, has not been limited to those exposed to the atrocities of war. It has also been evaluated in refugees, health care workers, and adolescents transitioning to adults (Chaplo et al., 2019). In these diverse groups, while moral injury is recognized as a distinct entity from other psychological conditions, such as post-traumatic stress disorder, the diagnosis relies on poorly defined, generalized criteria, which is very similar to that used for combat veterans. While symptom scales have been developed for military personnel, adolescents, and refugees, no specific diagnostic criteria exist for health care workers (Chaplo et al., 2019; Koenig et al., 2018; Nickerson et al., 2018).\n\nThe optimal treatment of moral injury, just like the diagnosis of moral injury, remains unclear. Proposals to treat moral injury in medical professionals include participation in support groups, building up personal character, and personal reflection by keeping a diary. The inclusion of standard treatments for post-traumatic stress disorder in veterans suffering from moral injury has also been proposed.\n\nA maxim of medicine is that a correct diagnosis is half the cure. In the case of moral injury as it specifically applies to medical professionals, we propose that a violation of the four pillars of bioethics forms the foundation of the diagnosis. We propose a framework for moral injury in health care based upon the four pillars of bioethics (Beauchamp, 2006). These pillars are patient autonomy, beneficence, nonmaleficence, and social justice. They serve as an effective foundation for evaluating moral behavior in medicine. Our framework clarifies the meaning of moral injury in medicine. When a physician, nurse, or other health care provider participates in, or witnesses a violation of, one or more of these core principles, moral injury occurs. Treatment strategies focused on repairing the breach of these principles of morality in health care may be the best way to heal the injury. Improving the recognition of and reflection upon the moral stressors that clinicians encounter in their practice may prevent moral injury from progressing further. This framework will help more clearly define moral injury in medical professionals, allowing the development of treatment specific to those working in health care.\n\n\nPatient autonomy\n\nThe principle of respect for autonomy holds that each person with capacity has the right to make their own decisions, and providers have a moral obligation to respect this right. In the clinician-patient relationship, patient autonomy can be especially vulnerable. This principle is often at the forefront of ethical concerns in health care (Entwistle et al., 2010); (Stammers, 2015).\n\nCompromising patient autonomy can result in moral injury, regardless of whether or not the perceived event is a true violation. For example, children presenting to the emergency department may openly voice a desire to not get an injection or an intravenous line. Although it is recognized that the decision of the legal caregiver overrides that of a young child, the perception of compromised autonomy can result in moral injury. Although the reason for the injection or intravenous line is medically indicated, the action nevertheless is against the will of the child. Logically, we know children will cry and object to many medical treatments. Still, whenever possible, it is recommended to obtain consent from both the child and the parent. Consent to treatment requires permission from the legal representative of the child, and if possible, assent from the child as well (Tait & Hutchinson, 2018). The accumulation of such experiences that challenge the clinician’s duty to respect patient autonomy may eventually lead to moral injury.\n\n\nNonmaleficence\n\nThe principle of nonmaleficence is captured by the Latin maxim, primum non nocere: “above all, do no harm.” It has been estimated that medical error is the third leading cause of death in the United States (Makary & Daniel, 2016). While the potential to reduce these errors is debated, common preventable harms include medication adverse events, central line infections, and thromboembolisms (Nabhan et al., 2012). With increasing ability to treat patients comes increasing opportunity to harm patients as systems become more complex. Most clinicians are very aware and regularly reminded of these statistics, however, the seemingly futile efforts to try and reduce the incidence of these harms is troublesome and can contribute to moral injury. Bureaucratic and administrative interference, well intended or not, can hamper efforts by physicians and nurses to decrease harm, leading to moral injury and a sense of powerlessness.\n\n\nBeneficence\n\nWith the many opportunities to harm a patient in mind, we must also remember that patients come to clinicians in search of improvement or restoration of their health, which leads to the principle of beneficence. The commitment to helping others is the driving force amongst health care workers and to accomplish this goal there must be a net benefit over harm (Gillon, 1994). Decisions on diagnostic pathways, treatment plans and societal policies all must balance the benefit versus harms, and these balances also must be made in context of the patient’s values.\n\nBeneficence, when compromised, creates numerous conflicts in medicine that can result in moral injury. When the cost of proper medical care exceeds the ability of an individual patient to pay, beneficence can be compromised. Pharmaceutical pricing is a common cause of this moral compromise. For example, many patients with atrial fibrillation will benefit from changing their warfarin prescription to a newer, direct oral anticoagulant such as apixaban. However, the up-front price of the newer medication prohibits them from changing, even though the total financial cost of the newer medication is estimated to be lower due to fewer medical complications (Gupta et al., 2018). Beyond the financial impact, the negative impact upon the patient’s health can be devastating. Compromising the principle of beneficence occurs when the patient is unable to take the best medication because of financial limitations. Although the medical complications from the older medication will ultimately cost more money, the hard reality is that patients will take the cheaper medication because they cannot afford the up-front costs of the newer, better medication.\n\n\nSocial justice\n\nThe final pillar of bioethics is social justice. Justice demands that limited resources be distributed fairly, and that patients not be discriminated against due to any number of demographic variables such as race, religion, gender identity, sexual orientation, age, or cultural background. Moral injury occurs when these ideals conflict with the hard reality of medical care where discrimination does occur, primarily along socioeconomic lines.\n\nThese complex socioeconomic disparities cause moral injury because clinicians know what their patients need and find the economic barriers to needed care to be illogical, unnecessary, and capricious. They know that not getting that nursing home bed placement will result in a bad outcome, often at a much higher cost. They know that not getting a patient with a substance use disorder necessary treatment will ultimately cost more to society, although the health care plan may save money. They have seen first-hand the elderly family member decide they would rather die than leave a large medical bill for their surviving relatives. Witnessing these events on a regular basis doesn’t cause burnout, it causes moral injury.\n\nMedical professionals working in medical systems and countries that rely on privately funded insurance may also experience a constant violation of the principle of social justice. For example, one study comparing a population with universal medical insurance found disparities in the care given to racial and ethnic minorities to be greatly decreased or even eliminated (Chaudhary et al., 2018). A similar study found that universal medical insurance ameliorated socioeconomic disparities in mortality (Veugelers & Yip, 2003). Medical professionals working in private medical insurance systems who know about and trust such research studies may experience a persistent low-grade violation of their bioethics. This, over time, may progress to symptomatic moral injury. The primary means of addressing such issues would be meaningful involvement in improving the larger health care system.\n\n\nConclusion\n\nMoral injury occurs when there is a disruption in an individual’s sense of personal morality and capacity to behave in a just manner. It is a common occurrence in medicine because of ongoing violations of bioethics that have become an intrinsic part of the healthcare system. The prevention of moral injury is accomplished by decreasing violations of the four pillars of bioethics whenever possible. Patients deserve autonomy, and we can give this to them. Although we cannot always help our patients as much as we would like, we can always help them in at least some way. We can be vigilant when taking measures to increase patient safety and decrease harm. With a firm understanding of the basic principles of bioethics, medical professionals can become more adept at identifying and reflecting upon moral violations in the workplace. This recognition helps prevent recurrent moral injury, decreases burnout, and can help to heal previous injuries.\n\n\nData availability\n\nNo data are associated with this article.", "appendix": "Grant information\n\nThe author(s) declared that no grants were involved in supporting this work.\n\n\nReferences\n\nBeauchamp TL: The ‘four principles’ approach to health care ethics. In: Ashcroft, R.E., Dawson, A., Draper, H., and McMillan, J. R. eds. Principles of health care ethics. Chichester, UK: John Wiley & Sons, Ltd. 2006; 3–10. Publisher Full Text\n\nChaplo SD, Kerig PK, Wainryb C: Development and validation of the moral injury scales for youth. J Trauma Stress. 2019; 32(3): 448–458. PubMed Abstract \| Publisher Full Text\n\nChaudhary MA, Sharma M, Scully RE, et al.: Universal insurance and an equal access healthcare system eliminate disparities for Black patients after traumatic injury. Surgery. 2018; 163(4): 651–656. PubMed Abstract \| Publisher Full Text\n\nEntwistle VA, Carter SM, Cribb A, et al.: Supporting patient autonomy: the importance of clinician-patient relationships. J Gen Intern Med. 2010; 25(7): 741–745. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGillon R: Medical ethics: four principles plus attention to scope. BMJ. 1994; 309(6948): 184–188. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGupta K, Trocio J, Keshishian A, et al.: Real-World Comparative Effectiveness, Safety, and Health Care Costs of Oral Anticoagulants in Nonvalvular Atrial Fibrillation Patients in the U.S. Department of Defense Population. J Manag Care Spec Pharm. 2018; 24(11): 1116–1127. PubMed Abstract \| Publisher Full Text\n\nKoenig HG, Ames D, Youssef NA, et al.: The Moral Injury Symptom Scale-Military Version. J Relig Health. 2018; 57(1): 249–265. PubMed Abstract \| Publisher Full Text\n\nMakary MA, Daniel M: Medical error-the third leading cause of death in the US. BMJ. 2016; 353: i2139. PubMed Abstract \| Publisher Full Text\n\nNabhan M, Elraiyah T, Brown DR, et al.: What is preventable harm in healthcare? A systematic review of definitions. BMC Health Serv Res. 2012; 12: 128. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNickerson A, Hoffman J, Schick M, et al.: A Longitudinal Investigation of Moral Injury Appraisals Amongst Treatment-Seeking Refugees. Front Psychiatry. 2018; 9: 667. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShay J: Moral injury. Psychoanalytic Psychology. 2014; 31(2): 182–191. Publisher Full Text\n\nShay J, Munroe J: Group and milieu therapy for veterans with complex posttraumatic stress disorder. In: Saigh, P. A. and Bremner, J. D. eds. Posttraumatic stress disorder: A comprehensive text. Boston: Allyn and Bacon, 1999; 391–413. Reference Source\n\nStammers T: The evolution of autonomy. New Bioeth. 2015; 21(2): 155–163. PubMed Abstract \| Publisher Full Text\n\nTait AR, Hutchinson RJ: Informed Consent Training in Pediatrics-Are We Doing Enough? JAMA Pediatr. 2018; 172(3): 211–212. PubMed Abstract \| Publisher Full Text\n\nVeugelers PJ, Yip AM: Socioeconomic disparities in health care use: Does universal coverage reduce inequalities in health? J Epidemiol Community Health. 2003; 57(6): 424–428. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYan GW: The invisible wound: moral injury and its impact on the health of operation enduring freedom/operation iraqi freedom veterans. Mil Med. 2016; 181(5): 451–458. PubMed Abstract \| Publisher Full Text" }	[ { "id": "51660", "date": "26 Jul 2019", "name": "Lindsay B Carey", "expertise": [ "Reviewer Expertise Bioethics", "Moral Injury" ], "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 innovative and valuable consideration/discussion of moral injury (MI) in light of the key bioethical principles - both of which are used to justify the political issue of employee burnout within the clinical context.\nGiven the current literature however, Shay's definition of MI (considered valuable but now too simplistic) which is used as the basis for this article, is no longer the dominant definition of moral injury since (for example) the work of Litz et al. (2009)1, or Jinkerson (2016)2, or Carey & Hodgson (2017).3 It is important to note, that since Shay's definition, there have been at least 17 different definitions of Moral Injury (refer Hodgson & Carey, 20173) and currently the most comprehensive synthesized version is that of Carey & Hodgson, 2018; Frontiers in Psychiatry4 which needs to be noted by the authors of this article, indicating that there are other MI definitions but few utilize a holistic bio-psycho-social-spiritual paradigm to define or consider MI.\n\nMost of the statements within the article are sufficiently supported; however, I think it important to cite Beauchamp and Childress (2013)5 with regard to biomedical ethics and the bioethical principles (not just Beauchamp).\nFurther, it can be argued that the real issue of MI within the medical/clinical context (in light of the more complex definitions of MI) should actually be due to a clinician suffering \"a trauma related syndrome caused by the physical, psychological, social and spiritual impact of grievous moral transgressions, or violations, of an individual's deeply-held moral beliefs and/or ethical standards due to: (i) an individual perpetrating, failing to prevent, bearing witness to, or learning about inhumane acts which result in the pain, suffering or death of others, and which fundamentally challenges the moral integrity of an individual, organization or community, and/or (ii) the subsequent experience and feelings of utter betrayal of what is right caused by trusted individuals who hold legitimate authority\" (Carey & Hodgson, 2018).\nIt other words it can be argued that as a result of breaches of fundamental bioethical principles that \"...grievous moral transgressions, or violations, of an individual's deeply-held moral beliefs and/or ethical standards\" will occur, resulting in a moral injury (Carey & Hodgson, 2018, p. 2). Then it should be explained that \"A moral injury can eventuate as a result of one or two types of occurrences, namely when (i) an individual perpetrates, fails to prevent, bears witness to, or learns about inhumane acts which result in the pain, suffering or death of others, and which fundamentally challenges the moral integrity of an individual, organization or community, and/or (ii) the subsequent moral injury experience and feelings of utter betrayal of what is right, caused by trusted individuals who hold legitimate authority\" (Carey & Hodgson, 2018, p.2).\n\nTo shift too far from such a definition/explanation would mean that it is not really a complex 'moral injury' at all - but rather a 'superficial' incident that conflicts with professional bioethics. Put simply, the more advanced / complex definitions of moral injury should be utilised and will actually co-align a lot easier with the bioethical principles.\nThe conclusions are somewhat justified on the basis of the presented arguments; however, it is somewhat of an assumption to conclude that ....a firm understanding of bioethics ....will prevent recurrent MI! This is doubtful - indeed t'would be like saying that a better understanding of bioethics will prevent the effects of witnessing a trauma related incident (e.g., a murder). Highly improbable!\nThere is also no evidence provided to indicate/justify that a better recognition of the connection between bioethics and MI will decrease burnout! Indeed one can speculate that better recognition might actually increase one's stress, and increase the chances of subsequent burnout! (Not decrease burnout!). The most one could argue (in the absence of solid evidence) would be that \"a better understanding of the effects of breaching bioethical principles within the work place, and the possible correlation with experiencing a moral injury, may explain feelings of recurrent burnout\"... but it certainly would NOT prevent MI nor unlikely to prevent injuries. The conclusion needs to be edited as well as adding a note for empirical research to be undertaken with regard to MI and clinician burnout in the clinical context.\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Partly\n\nAre all factual statements correct and adequately supported by citations? Partly\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": [ { "c_id": "4781", "date": "13 Aug 2019", "name": "Thomas F Heston", "role": "Author Response", "response": "I appreciate the comments from the reviewer and in general agree. In other groups outside of health care providers, moral injury is becoming more precisely defined. However, the definition and implications of moral injury in health care professionals currently remains vague. With this perspective paper, we aim to stimulate investigation into the relationship between a violation of well established bioethical principles and moral injury. We remain convinced that moral injury, both minor and large, regularly affects medical professionals, and that there most likely is a strong relationship to the four pillars of bioethics. Nevertheless, more research and investigation clearly is indicated. Again, the comments from the reviewer are thorough and greatly appreciated." }, { "c_id": "4782", "date": "29 Jul 2019", "name": "Lindsay B Carey", "role": "Reviewer Response", "response": "Dear Article Authors,I concur with your \"aim to stimulate investigation into the relationship between a violation of well established bioethical principles and moral injury\" and \"that moral injury.... regularly affects medical professionals, and that there most likely is a strong relationship between (breaches of) the four pillars of bioethics\" and moral injury - Indeed this seems logical and most viable. However my concern is that, currently your understanding of MI \"remains vague\" and this is understandable because some researchers and even yourselves, have based their understanding of MI on a basic definition. Except for those who wish MI to remain vague/basic for their own purposes, the research regarding MI, demonstrates that MI is far more complex than originally conceived. I think it is important to note that on the one hand you opt for a simple definition of MI, yet one of your own article statements aligns with more complex definitions: \"When a physician, nurse, or other health care provider participates in, or witnesses a violation of, one or more of these core principles, moral injury occurs\". I am simply suggesting: (1) the correlation between violations of bioethical principles and a MI or a potential moral injury event (PMIE), seems logical and would unquestionably affect clinician morale, however any correlation between bioethical principles and MI requires a more complex definition of MI. (2) There is no need for another definition of MI specific to clinicians - this would simply muddy the waters - there are already several comprehensive definitions (Litz et al, Jinkerson and a combination of Shays and others by Carey & Hodgson) as already noted in my earlier review - which are all based on empirical research/case studies. If there is no correlation with these more complex definitions, then perhaps it is not moral injury to which you are referring, but something entirely different.To be sure however, I support your argument/logic about bioethical principles regularly being breached in the health care context which could result in a moral injury for clinicians, however MI is complex and therefore requires a more comprehensive definition - which in my view would actually support your investigation into the relationship between a violation of well established bioethical principles and moral injury." }, { "c_id": "10189", "date": "17 Nov 2023", "name": "Thomas F Heston", "role": "Author Response", "response": "Thank you again for your time and effort in helping improve this article. I apologize for the delayed response, which was unavoidable due to severe, prolonged illness. I believe this article remains relevant. I have attempted to fully address all of the issues raised. Thank you- the article is significantly improved. I am hopeful this meets your approval so that it can be indexed, as this remains an important topic." } ] }, { "id": "65320", "date": "13 Jul 2020", "name": "Jan Helge Solbakk", "expertise": [ "Reviewer Expertise Bioethics" ], "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 very short and well written paper. But the paper would have benefited from further substantiation by relating the concept of moral injury to the concepts of moral failure, moral residue and moral distress.\nHere are some references the authors are advised to consult:\nLisa Tessman, Moral distress in health care: when is it fitting? Medicine, Health Care and Philosophy (2020) 23:165–177 https://doi.org/10.1007/s11019-020-09942-7.1\n\nBoudreau, Tyler. 2011. The morally injured. The Massachusetts Review 52(3/4): 746–754.2\n\nCampbell, Stephen, Connie Ulrich, and Christine Grady. 2016. A broader understanding of moral distress. The American Journal of Bioethics 16(12): 2–9.3\n\nTessman, Lisa. 2015. Moral failure: On the impossible demands of morality. New York: Oxford University Press.4\n\nWilliams, Bernard. 1973. Ethical consistency. In Problems of the self, ed. B. Williams, 166–186. Cambridge: Cambridge University Press.5\nIn addition, I advice the authors to consult the literature on adverse events in health care that are impossible to predict or prevent and which may cause moral distress, burnout and moral injury. That is, the fact that less than 50% of all adverse events in health care are possible to predict and prevent (of which a significant minority causes permanent disability, 7%, or death, 7%), is a painful reminder of the prevalence of unavoidable normative ignorance in health care and the importance of learning to live through moral failure caused by such events. For this, see e.g:\nRafter, N., Hickey, A., Condell, S. et al. (2015). Adverse events in health care: learning from mistakes. QJM: An International Journal of Medicine, 108, 4: 273–277, and De Vries, E.N., Ramrattan, M.A., Smorenburg, S.M. et al. (2008). The incidence and nature of in- hospital adverse events: a systematic review. Qual Saf Health Care,17: 216-223.6\nFinally, the authors are advised to focus more on the problem of moral failure and injury among health care workers. In the present version of the paper the main focus is on the patient's experience of moral injury.\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Partly\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": [ { "c_id": "10190", "date": "17 Nov 2023", "name": "Thomas F Heston", "role": "Author Response", "response": "Thank you again for your time and effort in helping improve this article. I apologize for the delayed response, which was unavoidable due to a severe, prolonged illness. I believe this article remains relevant. I have attempted to fully address all of the issues raised about the different aspects of moral compromise, not just moral injury. You have made me think more deeply about this issue and I appreciate that. I am hopeful this revised version meets your approval so that it can be indexed, as this remains an important topic. As a clinician, I see a lot of focus on clinical trials and \"evidence-based medicine\" but the effect of these technological advances on our shared morality is only rarely discussed. This is an important topic. Thanks again." } ] } ]	1	https://f1000research.com/articles/8-1193
https://f1000research.com/articles/9-1275/v1	27 Oct 20	{ "type": "Software Tool Article", "title": "DeepCLEM: automated registration for correlative light and electron microscopy using deep learning", "authors": [ "Rick Seifert", "Sebastian M. Markert", "Sebastian Britz", "Veronika Perschin", "Christoph Erbacher", "Christian Stigloher", "Philip Kollmannsberger", "Rick Seifert", "Sebastian M. Markert", "Sebastian Britz", "Veronika Perschin", "Christoph Erbacher", "Christian Stigloher" ], "abstract": "In correlative light and electron microscopy (CLEM), the fluorescent images must be registered to the EM images with high precision. Due to the different contrast of EM and fluorescence images, automated correlation-based alignment is not directly possible, and registration is often done by hand using a fluorescent chromatin stain, or semi-automatically with fiducial markers. We introduce “DeepCLEM”, a fully automated CLEM registration workflow. A convolutional neural network predicts the fluorescent signal from the EM images, which is then automatically registered to the experimentally measured chromatin signal from the sample using correlation-based alignment. The complete workflow is available as a FIJI macro and could in principle be adapted for other imaging modalities as well as for 3D stacks.", "keywords": [ "Correlative Microscopy", "Image Registration", "In-silico labeling", "Deep Learning" ], "content": "Introduction\n\nCorrelative Light and Electron Microscopy (CLEM) combines the high resolution of electron microscopy (EM) with the molecular specificity of fluorescence microscopy. In super-resolution array tomography (srAT) for example, serial sections are imaged first under the fluorescence microscope using super-resolution techniques such as structured illumination microscopy (SIM), and then in the electron microscope1. With this technique, it is possible to identify and assign molecular identities to subcellular structures such as electrical synapses1,2 or microdomains in bacterial membranes3 that cannot be resolved by EM due to insufficient contrast.\n\nTo visualize and interpret the results of CLEM, the fluorescent images must be registered to the EM images with high accuracy and precision. Due to the different contrasts of EM and fluorescence images, automated correlation-based image alignment, as used e.g. for aligning EM serial sections4, is not directly possible. Registration is often done by hand using a fluorescent chromatin stain2, or semi-automatically with fiducial markers using tools such as eC-CLEM5. Further improvement and automation of the registration process is of great interest to make CLEM scalable to larger datasets.\n\nDeep Learning using convolutional neural networks (CNNs) has become a powerful tool for various tasks in microscopy, including denoising and deconvolution as well as classification and segmentation, reviewed in 6 and 7. One interesting application of CNNs is the prediction of fluorescent labels from transmitted light images of cells, also called “in silico labeling”8,9.\n\nWe show here that this approach can be used to predict the fluorescent chromatin stain in electron microscopy images of cell nuclei. The predicted “in silico” chromatin images are sufficiently similar to real experimental chromatin images acquired with SIM to use them for automated correlation-based registration of CLEM images. Based on this observation, we developed “DeepCLEM”, a fully automated CLEM registration workflow implemented in FIJI10 and based on CNNs.\n\n\nMethods\n\nWe used previously acquired imaging data of Caenorhabditis elegans and of human skin samples from healthy subjects. Sample preparation as well as the acquisition of the imaging data has been previously described in detail1,2,11. Briefly, C. elegans worms were cryo-immobilized via high-pressure freezing and subsequently processed by freeze substitution. All samples were embedded in methacrylate resin and sectioned at 100 nm. Ribbons of consecutive sections were attached to glass slides and labeled with fluorophores. Live Hoechst 33342 was used to stain chromatin and immunolabeling was used to visualize molecular identities. The sections were then imaged with SIM super-resolution microscopy. Next, they were processed for electron microscopy by heavy metal contrasting and carbon coating. The regions of interest previously imaged with SIM were then imaged again on the same sections with scanning electron microscopy, resulting in pairs of images that needed to be correlated.\n\nTo prepare ground truth for network training, we manually registered the chromatin channel to the EM images as described in 2. We selected 30 subimages and super-imposed them in the software Inkscape. By reducing the opacity of the chromatin images, they could be manually resized, rotated and dragged until the Hoechst signal coincided with the electron-dense heterochromatin puncta in the underlying EM images.\n\nWe implemented DeepCLEM as a Fiji10 plugin, using CSBDeep12 for network prediction. Preprocessing of the images as well as network training were performed in Python using scikit-image13 and TensorFlow14. First, a neural network trained on manually registered image pairs predicts the fluorescent chromatin signal from previously unseen EM images (Figure 1A). This \"virtual\" fluorescent chromatin image is then automatically registered to the experimentally measured chromatin signal from the sample using correlation-based alignment in FIJI (Figure 1B). The transformation parameters from this automated alignment are finally used to register the other SIM images that contain the signals of interest to the EM image (Figure 1C).\n\nFrom the EM image (A), a CNN predicts the chromatin channel (B), to which the SIM image (C) is registered (D). The same transform is applied to the channel of interest (E) to obtain a CLEM overlay (F).\n\nDeepCLEM requires FIJI10 with CSBDeep12 to run. The paths to the images and model file are entered in a user dialog (Figure 2). After running DeepCLEM, the correlated images and a .XML file containing the transform parameters are written to the output directory. The workflow is summarized in Figure 1; instructions for installing and running DeepCLEM and for training custom networks are included in the repository.\n\n\nResults\n\nWe trained DeepCLEM on correlative EM and SIM images of C. elegans and on human skin tissue and compared prediction and registration results for different network architectures and preprocessing routines. A generative adversarial network (pix2pix) showed promising results in some images from the skin dataset, but overall performance was best using the ProjectionCARE network from CSBDeep12.\n\nEM images had large differences in contrast even when acquired in the same laboratory. We compared different preprocessing routines, including normalization and histogram equalization, and found that histogram equalization alone resulted in the best performance on our data. The best combination of preprocessing steps for optimizing contrast may however depend on the data.\n\n\nDiscussion\n\nWe developed “DeepCLEM”, a fully automated CLEM registration workflow implemented in Fiji10 based on prediction of the chromatin stain from EM images using CNNs. Our registration workflow can easily be included in existing CLEM routines or adapted for other imaging modalities as well as for 3D stacks.\n\nWhile we found that \"DeepCLEM\" performs well under various conditions, it has some limitations: using chromatin staining for correlation requires the presence of nuclei in the field of view. This limitation could be overcome by using e.g. propidium iodide to label the overall structure of the tissue.\n\n\nData availability\n\nSource code, pretrained networks and example data as well as documentation are available online at:\n\nhttps://github.com/CIA-CCTB/Deep_CLEM.\n\n\nSoftware availability\n\nSource code available from: https://github.com/CIA-CCTB/Deep_CLEM.\n\nArchived source code at time of publication: https://doi.org/10.5281/zenodo.409524715\n\nLicense: MIT License.", "appendix": "Acknowledgements\n\nThis publication was supported by COST Action NEUBIAS (CA15124), funded by COST (European Cooperation in Science and Technology).\n\n\nReferences\n\nMarkert SM, Britz S, Proppert S, et al.: Filling the gap: adding super-resolution to array tomography for correlated ultrastructural and molecular identification of electrical synapses at the C. elegans connectome. Neurophotonics. 2016; 3(4): 041802. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMarkert SM, Bauer V, Muenz TS, et al.: 3D subcellular localization with superresolution array tomography on ultrathin sections of various species. Methods Cell Biol. 2017; 140: 21–47. PubMed Abstract \| Publisher Full Text\n\nGarcía-Fernández E, Koch G, Wagner RM, et al.: Membrane Microdomain Disassembly Inhibits MRSA Antibiotic Resistance. Cell. 2017; 171(6): 1354–1367.e20. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCardona A, Saalfeld S, Schindelin J, et al.: TrakEM2 Software for Neural Circuit Reconstruction. PLoS One. 2012; 7(6): e38011. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPaul-Gilloteaux P, Heiligenstein X, Belle M, et al.: eC-CLEM: flexible multidimensional registration software for correlative microscopies. Nat Methods. 2017; 14(2): 102–103. PubMed Abstract \| Publisher Full Text\n\nvon Chamier L, Laine RF, Henriques R: Artificial intelligence for microscopy: what you should know. Biochem Soc Trans. 2019; 47(4): 1029–1040. PubMed Abstract \| Publisher Full Text\n\nBelthangady C, Royer LA: Applications, promises, and pitfalls of deep learning for fluorescence image reconstruction. Nat Methods. 2019; 16(12): 1215–1225. PubMed Abstract \| Publisher Full Text\n\nChristiansen EM, Yang SJ, Ando DM, et al.: In Silico Labeling: Predicting Fluorescent Labels in Unlabeled Images. Cell. 2018; 173(3): 792–803.e19. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGuo SM, Yeh LH, Folkesson J, et al.: Revealing architectural order with quantitative label-free imaging and deep learning. eLife. 2020; 9: e55502. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSchindelin J, Arganda-Carreras I, Frise E, et al.: Fiji: an open-source platform for biological-image analysis. Nat Methods. 2012; 9(7): 676–682. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nÜçeyler N, Kafke W, Riediger N, et al.: Elevated proinflammatory cytokine expression in affected skin in small fiber neuropathy. Neurology. 2010; 74(22): 1806–1813. PubMed Abstract \| Publisher Full Text\n\nWeigert M, Schmidt U, Boothe T, et al.: Content-aware image restoration: pushing the limits of fluorescence microscopy. Nat Methods. 2018; 15(12): 1090–1097. PubMed Abstract \| Publisher Full Text\n\nVirtanen P, Gommers R, Oliphant TE, et al.: SciPy 1.0: fundamental algorithms for scientific computing in Python. Nat Methods. 2020; 17(3): 261–272. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAbadi M, Agarwal A, Barham P, et al.: TensorFlow: Large-Scale Machine Learning on Heterogeneous Distributed Systems. arXiv: 160304467 [cs]. 2016. Reference Source\n\nSeifert R: CIA-CCTB/Deep_CLEM: First release of DeepCLEM (Version v1.0). Zenodo. 2020. http://www.doi.org/10.5281/zenodo.4095247" }	[ { "id": "77801", "date": "04 Feb 2021", "name": "Martin L. Jones", "expertise": [ "Reviewer Expertise Image Analysis", "CLEM", "Machine Learning", "Electron microscopy" ], "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 present an automated method, deployed as a Fiji plugin, for registering 2D CLEM data. This is demonstrated on a \"super resolution Array Tomography\" (srAT) dataset, building on their previous method development work, where the sample is sliced into 100nm sections prior to imaging in SIM and SEM. The DeepCLEM plugin generates synthetic fluorescence data from the EM images that are aligned to the real fluorescence signal to perform the registration.\n\nThis type of effort is crucial in harnessing the huge potential of correlative multimodal imaging as cross-modal registration is a significant bottleneck in many cases. The method of imaging both LM and EM on the processed and cut sections is perhaps not as widespread as other methods, such as, e.g. whole cell confocal imaging followed by resin-embedding, followed by EM imaging. The method used in this paper avoids the familiar CLEM registration problems of non-linear warping induced by the EM sample preparation and mismatched axial resolutions. This constrains the registration task to a \"similarity\" type transform rather than affine or non-rigid as is required in some other CLEM registration tasks.\nThe open source plugin is easy to install and runs as described on the test data provided.\nA few points that I think should be addressed:\nIn the abstract and introduction, it is mentioned that \"registration is often done by hand using a fluorescent chromatin stain\" - this seems overly specific, in general CLEM alignment might make use of many different markers or features. Focusing on the specific stains is appropriate later when describing the specific use-case presented, but the authors might inadvertently deter potential users wanting to use different stains that could feasibly be trained for in the deep learning step.\n\nThe abstract refers to a Fiji Macro, but the code appears to be a python/jython script that is to be installed as a plugin. Is there an additional .ijm IJ1 macro available, or is this a typo?\n\nAlthough it is common to call this type of method \"automated\", there is a front-loaded training step for the deep learning element. It isn't clear whether the trained model from the author's data would be sufficiently generalised to other datasets, or whether an amount of training will commonly be required for each different dataset.\n\nI believe the preferred capitalisation is \"Fiji\" and not \"FIJI\"\n\nec-CLEM is mentioned and the text implies that it is only used with fiducials, but it can also be used for aligning using the fluorescence and EM data directly via manual landmark placement on intrinsic structures and/or stains. ec-CLEM also has an \"autofinder\" functionality that seems like it should be mentioned as potentially the nearest functionality in an existing tool. It would be useful to see a comparison, or an explanation as to how DeepCLEM differs if a direct comparison isn't possible.\n\nFor the manual registration section, it would be better practice to use a more reproducible method, such as ec-CLEM or Fiji landmark-based registration (as opposed to the stated method using inkscape) since these methods retain a record of the steps and transforms. Although, in the context of the paper this is a means-to-an-end for acquiring training data for demonstration purposes, it would be preferable if the advice to potential users of the plugin were to err on the side of reproducible methods for their own training.\n\nIn \"Implementation\" it would be useful to state a bit more detail about the training, for example training/validation split and suitable data quantities for users to train their own model.\n\nIf the goal is to enable non-computational researchers to perform the whole workflow, the GitHub README and Jupyter notebooks should have a bit more description, in particular with regards to training, a process that is quite alien with unfamiliar jargon for non-specialists.\n\nThe text mentions \"correlation based alignment in Fiji\" - looking in the source code this is specifically the \"Register Virtual Stack Slices\" plugin, this should be mentioned in the text as it is a major computational step in the workflow. Also, the use of \"similarity\" as opposed to rigid, affine etc should be specified in the text since other CLEM practitioners may be more familiar with other alternatives.\n\nAn important point that is missing is some kind of quantification of the quality of the registration compared to a gold-standard produced manually. Understanding this is likely to be very important for researchers who might be considering using this tool. If possible, to maximise usability, some sort of \"confidence\" metric would be very useful for the user, but I appreciate this is probably non-trivial!\n\nThe authors propose extensions to their method for dealing with situations where nuclei are not present in the images. It would be useful if the authors could provide a brief focused description of the scope of the tool as it is currently configured, so that potential users can quickly assess whether it's suitable for their task or what they might need to do to extend it. For example, the GitHub repo suggests the image must have a minimum of 3 nucleoli - this should be mentioned in the body of the paper as well.\n\nRelated to the above, the title and abstract make no specific mention of the method being based on imaging both LM and EM in the cut sections as opposed to a perhaps more common workflow such as confocal on whole cells followed by EM data on sections or block face. To avoid potential confusion, this constraint should be made more clear in the abstract.\n\nThe abstract and discussion mention adaptations to apply to other modalities and 3D stacks. Given the srAT-based application it is not obvious what these adaptations would be, so an elaboration on this point would be useful\nOverall, the tool itself works as described on the data type provided, but I think there is a risk that users might be tempted to stretch beyond the current scope of the tool, so this scope should be made more clear in the text.\n\nIs the rationale for developing the new software tool clearly explained? Yes\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? Partly\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": [ { "c_id": "8575", "date": "16 Aug 2022", "name": "Philip Kollmannsberger", "role": "Author Response", "response": "R: In the abstract and introduction, it is mentioned that \"registration is often done by hand using a fluorescent chromatin stain\" - this seems overly specific, in general CLEM alignment might make use of many different markers or features. Focusing on the specific stains is appropriate later when describing the specific use-case presented, but the authors might inadvertently deter potential users wanting to use different stains that could feasibly be trained for in the deep learning step. A: We removed the mention of a specific stain in the abstract to reflect the general applicability of the method. R: The abstract refers to a Fiji Macro, but the code appears to be a python/jython script that is to be installed as a plugin. Is there an additional .ijm IJ1 macro available, or is this a typo? A: The code is a Jython script with graphical user interface to be run within Fiji. From the user's perspective, it is indeed a plugin. We changed “macro” to “plugin”, as suggested. R: Although it is common to call this type of method \"automated\", there is a front-loaded training step for the deep learning element. It isn't clear whether the trained model from the author's data would be sufficiently generalised to other datasets, or whether an amount of training will commonly be required for each different dataset. A: The trained network can be applied to different datasets if they have similar contrast, usually from the same microscope or sample type. Otherwise, (re-)training of the network is necessary. We now make this clearer in the manuscript and include a description of the training workflow. R: I believe the preferred capitalisation is \"Fiji\" and not \"FIJI\" A: Thank you, we corrected this. R: ec-CLEM is mentioned and the text implies that it is only used with fiducials, but it can also be used for aligning using the fluorescence and EM data directly via manual landmark placement on intrinsic structures and/or stains. ec-CLEM also has an \"autofinder\" functionality that seems like it should be mentioned as potentially the nearest functionality in an existing tool. It would be useful to see a comparison, or an explanation as to how DeepCLEM differs if a direct comparison isn't possible. A: We now refer to ec-CLEM autofinder which is similar in terms of functionality. It is based on finding corresponding features in both modalities, e.g., using wavelet-based spot detection or the centers of segmented regions, and then performing registration of these automatically detected landmarks. We did not perform a direct quantitative comparison. If suitable corresponding spots can be found (e.g. beads), the performance on the same images using the same registration algorithm should be comparable. In cases where spot finding or similar methods in ec-CLEM do not perform well because the images are too dissimilar or if there are no fiducial markers, then transferring the EM image to fluorescence using DeepCLEM could be used to generate input data for point-based registration in ec-CLEM. R: For the manual registration section, it would be better practice to use a more reproducible method, such as ec-CLEM or Fiji landmark-based registration (as opposed to the stated method using inkscape) since these methods retain a record of the steps and transforms. Although, in the context of the paper this is a means-to-an-end for acquiring training data for demonstration purposes, it would be preferable if the advice to potential users of the plugin were to err on the side of reproducible methods for their own training. A: We agree that these methods are more reproducible and added an additional note to the paragraph on manual registration to encourage users to use such reproducible methods. Since we already had created the training data, we did, however, not repeat the alignment. For assessing the performance (see below), we instead artificially displaced the two channels - in this case, the steps and transforms are also known exactly. R: In \"Implementation\" it would be useful to state a bit more detail about the training, for example training/validation split and suitable data quantities for users to train their own model. A: We now include more detail about the training workflow in the implementation section and compared the performance for different amounts of training images. R: If the goal is to enable non-computational researchers to perform the whole workflow, the GitHub README and Jupyter notebooks should have a bit more description, in particular with regards to training, a process that is quite alien with unfamiliar jargon for non-specialists. A: We extended both the description of the training parameters as well as the documentation of the entire workflow, including training in the Jupyter notebook. R: The text mentions \"correlation based alignment in Fiji\" - looking in the source code this is specifically the \"Register Virtual Stack Slices\" plugin, this should be mentioned in the text as it is a major computational step in the workflow. Also, the use of \"similarity\" as opposed to rigid, affine etc should be specified in the text since other CLEM practitioners may be more familiar with other alternatives. A: The text now explicitly mentions the use of the \"Register Virtual Stack Slices\" plugin and the \"similarity\" transform in our work, but in principle, our workflow should also work with other means of correlation-based registration. R: An important point that is missing is some kind of quantification of the quality of the registration compared to a gold-standard produced manually. Understanding this is likely to be very important for researchers who might be considering using this tool. If possible, to maximise usability, some sort of \"confidence\" metric would be very useful for the user, but I appreciate this is probably non-trivial! A: We now performed quantification of the quality of the registration using the manually aligned ground truth data as a reference where the best solution is already known. We observed that in most cases, the registration either works and has a very small error or is completely off by several 100 nm, which should be easy to spot. If a few images from an experiment are manually aligned and included in the training set, the registration of the remaining images improves significantly (Table 1). Instead of providing a confidence metric, which would indeed be non-trivial, we recommend visual inspection using the overlay. Possible ways to implement a confidence metric would be to output a confidence level for the neural network prediction, and to check the quality of the alignment using a correlation metric between fluorescent and predicted image. R: The authors propose extensions to their method for dealing with situations where nuclei are not present in the images. It would be useful if the authors could provide a brief focused description of the scope of the tool as it is currently configured, so that potential users can quickly assess whether it's suitable for their task or what they might need to do to extend it. For example, the GitHub repo suggests the image must have a minimum of 3 nucleoli - this should be mentioned in the body of the paper as well. A: We added more detail regarding the scope and limitations of this tool and its current requirements to the abstract, introduction, and discussion section, including the need for at least three heterochromatin patches if chromatin staining is used for registration. R: Related to the above, the title and abstract make no specific mention of the method being based on imaging both LM and EM in the cut sections as opposed to a perhaps more common workflow such as confocal on whole cells followed by EM data on sections or block face. To avoid potential confusion, this constraint should be made more clear in the abstract. The abstract and discussion mention adaptations to apply to other modalities and 3D stacks. Given the srAT-based application it is not obvious what these adaptations would be, so an elaboration on this point would be useful A: The way it is currently configured, DeepCLEM can in principle be used to register any CLEM data where corresponding 2D slices are available in both modalities, whether they were acquired on the same cut sections (srAT) or prior and post sectioning. The examples we provide however are restricted to srAT. We now state this in the text." } ] }, { "id": "77401", "date": "08 Feb 2021", "name": "Reinhard Rachel", "expertise": [ "Reviewer Expertise TEM", "STEM", "tomography", "CLEM", "microbiology", "cell biology" ], "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 by Seifert et al. (Univ. Würzburg, Germany) provides a convenient software tool (a macro name DeepCLEM) for linking fluorescent light microscopy images (here: structured illumination microscopy) to the information seen in electron micrographs (in this particular case: FE-SEM), obtained from serial sections on slides. In a first glance, this short paper describes the development and application of a flexible and easy to handle software tool to a program which is open to many microscopy researchers, ImageJ / Fiji, in form of a macro, which can easily be added to any Fiji installation. Thus, it appears that this tool can be used by many groups aiming to analyze biological samples using correleative light and electron microscopy (CLEM). A few questions arise when reading the manuscript - which do not modify the overall positive impression of this study.\n\nThe group uses Hoechst 33342 for staining and the biological objects are visualized by SIM - would it be sufficient to visualize the objects by 'standard' wide-field fluorescent microscopy, which is present in almost all biological laboratories, while SIM requires access to instruments which are not available everywhere?\n\nWhat kind of knowledge is necessary to perform the 'prediction of fluorescent signals from EM images', i.e. generating the \"virtual\" fluorescent images? Does this macro work as provided, i.e. 'fully automatically'? Is any user intervention needed? - the authors trained their macro on their datasets. Is it likely that this macro \"as trained in the author's lab\" also works on images from other labs? or is it necessary to go through a training phase? if so: workflow?\n\nHistogram equalization of EM images - was this done with routines implemented in Fiji?\n\nCan the authors at least provide one set of parallel results obtained using DeepCLEM vs. ec-CLEM? or at least comment on this?\nWith comments on my points listed above, and according improvements in the manuscript, this can be indexed - thus, approved with reservations.\n\nIs the rationale for developing the new software tool clearly explained? No\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? Partly\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": [ { "c_id": "8576", "date": "16 Aug 2022", "name": "Philip Kollmannsberger", "role": "Author Response", "response": "R: The group uses Hoechst 33342 for staining and the biological objects are visualized by SIM - would it be sufficient to visualize the objects by 'standard' wide-field fluorescent microscopy, which is present in almost all biological laboratories, while SIM requires access to instruments which are not available everywhere? A: If the structures used for alignment (e.g., chromatin) can be resolved and the WF images can be manually aligned, it is also possible to obtain a prediction and do automated alignment, although the achievable quality of the registration is obviously limited by the resolution of the fluorescence channel. We now added this in the discussion of the scope and limitations of the tool. R: What kind of knowledge is necessary to perform the 'prediction of fluorescent signals from EM images', i.e. generating the \"virtual\" fluorescent images? Does this macro work as provided, i.e. 'fully automatically'? Is any user intervention needed? A: Using a trained network for prediction and alignment can be done fully automatically in Fiji, only the paths of the images and network must be provided in the user dialog. For retraining, some knowledge (e.g., setting up a python environment) is necessary. We now added a more detailed description of the training workflow. Currently, the training process should probably be performed by some more experienced person while using the trained network does not require any special knowledge. R: The authors trained their macro on their datasets. Is it likely that this macro \"as trained in the author's lab\" also works on images from other labs? or is it necessary to go through a training phase? if so: workflow? A: It may be possible to use the provided network trained on our data on images from other labs directly, however in most cases re-training is required. We now describe the required workflow in more detail and perform a quantitative comparison of registration quality where images from an experiment were either included in the training set or not. R: Histogram equalization of EM images - was this done with routines implemented in Fiji? A: We used the standard histogram equalization implemented in Fiji. We added this detail to the method description. R: Can the authors at least provide one set of parallel results obtained using DeepCLEM vs. ec-CLEM? or at least comment on this? A: We now comment on ec-CLEM and its “autofinder” functionality which is closest to our tool in terms of functionality. While ec-CLEM autofinder uses spot finding or centers of segmented regions as points of interest to perform registration on, we predict the image of the other modality and then use correlation-based alignment." } ] } ]	1	https://f1000research.com/articles/9-1275
https://f1000research.com/articles/11-1408/v1	30 Nov 22	{ "type": "Research Article", "title": "Morphometric study of the lumbar vertebrae in dried anatomical collections", "authors": [ "Sharad Ashish", "P. Kalluraya", "Mangala M. Pai", "B.V. Murlimanju", "Y. Rao", "Latha V. Prabhu", "Amit Agrawal", "Sharad Ashish", "P. Kalluraya", "B.V. Murlimanju", "Y. Rao", "Latha V. Prabhu", "Amit Agrawal" ], "abstract": "Background: The objective of this anatomical study was to perform the morphometry of dried lumbar vertebrae in human cadavers. Methods: This study utilized 200 adult human cadaveric dried lumbar vertebrae. The digital Vernier calipers was used to perform the measurements. The height, antero-posterior length, transverse length of the body of the vertebrae, interpedicular distance at the lateral ends, lamina length, height and thickness, superior and inferior articular facet height and width, mid sagittal and transverse diameter of vertebral foramen, height, width and thickness of the pars inter-articularis were measured. Results: The vertebral body’s anteroposterior length was more at the lower border than at the superior border (p < 0.01). The length of lamina was higher over the right in comparison to the left (p < 0.001). The height of lamina, width of inferior articular facet, diameter of lateral recess and thickness of pars inter-articularis were greater for the left sided specimens (p < 0.01). The statistical significance was not observed for the comparison of the remaining parameters (p > 0.05). Conclusion: This anatomical study offered several dimensions of lumbar vertebrae, which are essential in the surgical practice. The implants at the lumbar vertebrae need to be manufactured based on the anatomical dimensions of that particular sample population.", "keywords": [ "Lumbar Vertebrae", "Pars Interarticularis", "Skeletal Fixation" ], "content": "Introduction\n\nIn Latin language, ‘lumbus’ means ‘lion’, hence lumbar vertebrae are compared to a lion. They are very flexible and offer stability to the vertebral column. There are few studies available, which offer the morphometric data of the lumbar vertebrae, however there are not many studies available about the dimensions of pars inter-articularis in the anatomical collections. In the radiographs of the lumbar vertebrae, the pars inter-articularis resembles the neck of a Scottish dog. Since the surgical techniques of the vertebral column involve the utilization of bony anatomical landmarks, the morphometric data of the various parts of the vertebrae are essential. The accurate anatomical dimensional knowledge is important to understand the etiopathogenesis of the lower backache. The bony landmarks like the pars inter-articularis, transverse process, superior and inferior articular facets are particularly important during the internal fixation of the lumbar spine. The pars interarticularis are important parts of lumbar vertebrae, which help during the surgical instrumentation.1 The anatomical studies help in understanding the detail complex morphometry of the vertebral column.2,3 In this context, the objective of this anatomical study was to perform the morphometry of dried lumbar vertebrae of the human cadavers in sample Indian population.\n\n\nMethods\n\nThis descriptive anatomical study included 200 adult cadaveric dry lumbar vertebrae. The sample size was calculated by referring the article by Singh et al..4\n\nThe formula applied was\n\nZ1-α/2= Z value at ‘α’ level of significance\n\nZ1-β = Z value at (1-β) % power\n\nσ= anticipated population standard deviation of the outcome variable (or) common assumed standard deviation between the two groups\n\nd= clinically significant difference\n\nThe protocol of this present research is available online at https://www.protocols.io/view/morphometric-study-of-the-lumbar-vertebrae-in-drie-cjqhumt6. The age and gender of the specimens was not taken into consideration. Congenitally deformed lumbar vertebrae were excluded from the present study. Measurements of this study are performed by the digital Vernier calipers. The data are expressed in millimeters and tabulated as mean ± standard deviation. The details of the measurements performed in this investigation are represented in Figure 1 and Table 1. The SPSS software (version 26) was utilized to perform the statistical analysis.\n\nThe ethics committee of our institution has approved this research (Institutional Ethics Committee, Kasturba Medical College, Mangalore, IEC KMC MLR: 02/2022/60, dated 17.02.2022). Since this is a study from the cadaveric dried bones, the consent from the participants is not applicable. This was waived by our institutional ethics committee. This present research is following the guidelines of the international ethical standards. Since this is a cross sectional study from the dried lumbar vertebrae of the donated cadavers and did not reveal the identity of the body donor, the written informed consent was not taken from the body donor’s family for the use and publication of this research.\n\n\nResults\n\nThe anatomical data obtained in this study are given in Tables 2 and 3. The vertebral body anteroposterior dimension was more at its lower border than at the upper (p < 0.01). The length of lamina was higher over the right side (p < 0.001). The height of lamina, width of inferior articular facet, diameter of lateral recess and thickness of pars inter-articularis were greater for the left side (p < 0.01). The remaining parameters, which were compared on the right and left sides did not reveal the difference with respect to the statistical significance (p > 0.05).\n\n* p<0.01\n\n* p<0.05-significant; p<0.01-moderately significant; p<0.001-highly significant\n\n\nDiscussion\n\nIf the significant part of vertebral body is involved in a disease, there will be neurological deficits and instability of the back. Internal fixation of vertebral column is the best management available for the traumatic spine injury, lumbar canal stenosis, spondylolisthesis and malignant tumors. The internal fixation offers better stabilization and decreases the duration of the morbidity. The spinal surgery is also performed in prolapsed intervertebral disc and conditions like scoliosis. It was reported that, this is among the hardest surgeries to perform as it is prone for the postoperative complications.5 Krag et al.6 performed the morphometry of the vertebrae in cadavers, both manually and radiologically. Characterizing the morphology of the spine among populations, would allow personalizing the conditions under which each individual should be exposed. The morphometric data of the vertebrae are not only useful in the field of neurosurgery, but are also essential to the specialties like neurology and orthopedics. Dimensions of the cervical and thoracic spine were already determined in our collections, few years ago.7 This present study was the continuation of this and here we determined the parameters in the lumbar vertebrae. The morphometrical data of various parts of lumbar vertebrae, procured from this study can be considered as the reference data for our study population.\n\n\nImplications and limitations\n\nThere are not many studies being performed about the morphometry of pars inter-articularis. It offers structural support to the vertebral column and considered as the main support. Pars inter-articularis is a dense cortical bone and is exposed in the posterior approaches. There are morphometrical studies, which are performed by using the radiological methods like utilizing the radiographs and computed tomogram scans.8 The vertebral column robusticity increased significantly over the time affecting the dimensions of the vertebral body as well.8 According to Kapoor et al.9, the inter-pedicular distance was 18.5 mm at the first lumbar vertebra, 21.5 mm at the lower lumbar vertebrae. Aly and Amin10 reported that the interpedicular distance in the lumbar vertebrae varies from 17 to 43.4 mm and this increases towards inferior region. Nayak et al.11 opined that the dimensions of vertebral foramen are higher in the atypical lumbar vertebrae than in the typical. The height of body of vertebrae was 171 cm in males and 158.2 cm in females.8\n\nIn the present study, we could not segregate the vertebrae with respect to their number, age and gender. This can be considered as a limitation of this anatomical research. Since it was just a cross sectional anatomical investigation from the dried vertebrae, the specimens from the same cadaver could not be determined as these are random collections. More studies with larger cohort and validated methods of accurate geometric measurements will be helpful in studying this complex anatomy.\n\n\nConclusion\n\nWe report the measurements of parts of the vertebrae of the lumbar region in sample Indian population. It is believed that, these data will help the operating neurosurgeons and spine surgeons during the surgeries like laminectomy and decompression. They are also essential in planning the accurate sizes of the plates and screws in the internal fixation. The implants have to be manufactured depending on the anatomical dimensions of that particular sample population.", "appendix": "Data availability\n\nFigshare. LUMBAR VERTEBRAE MORPHOMETRIC DATA.xlsx. DOI: https://doi.org/10.6084/m9.figshare.21307917.v1 12\n\nThis project contains the following data:\n\n- This descriptive anatomical study included 200 adult cadaveric dry lumbar vertebrae. The sample size was as per the previous study by Singh et. al. The age and gender of the specimens was not taken into consideration. Congenitally deformed lumbar vertebrae were excluded from the present study. Measurements of this study are performed by the digital Vernier calipers. The data are expressed in millimeters and tabulated as mean ± standard deviation. The details of the measurements performed in this investigation are represented in Fig. 1 and Table 1. The SPSS software (version 26) was utilized to perform the statistical analysis.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC BY 4.0).\n\n\nReferences\n\nRivkin MA, Okun JF, Yocom SS: Novel free-hand T1 pedicle screw method: Review of 44 consecutive cases. J Neurosci Rural Pract. 2014; 5: 349–354. PubMed Abstract \| Publisher Full Text\n\nBerry JL, Moran JM, Berg WS, et al.: A morphometric study of human lumbar and selected thoracic vertebrae. Spine. 1987; 12: 362–367. PubMed Abstract \| Publisher Full Text\n\nPanjabi MM, Goel V, Oxland T, et al.: Human lumbar vertebrae. Quantitative three-dimensional anatomy. Spine. 1992; 17: 299–306. Publisher Full Text\n\nSingh R, Srivastva SK, Prasath CS, et al.: Morphometric measurements of cadaveric thoracic spine in Indian population and its clinical applications. Asian Spine J. 2011; 5: 20–34. PubMed Abstract \| Publisher Full Text\n\nKwan MK, Chiu CK, Gani SMA, et al.: Accuracy and safety of pedicle screw placement in adolescent idiopathic scoliosis patients: a review of 2020 screws using computed tomography assessment. Spine. 2017; 42: 326–335.\n\nKrag MH, Weaver DL, Beynnon BD, et al.: Morphometry of the thoracic and lumbar spine related to transpedicular screw placement for surgical spinal fixation. Spine. 1988; 13: 27–32. PubMed Abstract \| Publisher Full Text\n\nPrameela MD, Prabhu LV, Murlimanju BV, et al.: Anatomical dimensions of the typical cervical vertebrae and their clinical implications. Eur. J. Anat. 2020; 24: 9–15.\n\nGleinert-Rożek MŁ, Kosiński A, Kaczyńska A, et al.: Metric analysis of the lumbar region of human vertebral column. Folia Morphol. (Warsz). 2020; 79: 655–661. PubMed Abstract \| Publisher Full Text\n\nKapoor Y, Anil S, Krishnaiah M, et al.: Morphometry of the Lumbar Vertebrae and its Clinical Significance. Scholars Journal of Applied Medical Sciences. 2014; 2: 1045–1052.\n\nAly T, Amin O: Geometrical dimensions and morphological study of the lumbar spinal canal in the normal Egyptian population. Orthopedics. 2013; 36: e229–e234. PubMed Abstract \| Publisher Full Text\n\nNayak G, Panda SK, Chinara PK: Morphometry of lumbar spine- a holistic comparative study between typical and atypical lumbar vertebrae. International Journal of Anatomy, Radiology and Surgery. 2020; 9: AO04-AO07.\n\nPai M: LUMBAR VERTEBRAE MORPHOMETRIC DATA.xlsx. figshare. Dataset.2022. Publisher Full Text" }	[ { "id": "156968", "date": "23 Dec 2022", "name": "Srinivasa Rao Sirasanagandla", "expertise": [ "Reviewer Expertise Natural products", "osteoporosis", "cardiovascular research and Bisphenol A associated toxicity and morphological variations." ], "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 present study provides the morphometric data of the lumbar vertebrae in dried anatomical collections in the Indian population. The authors presented the manuscript in a detailed manner, along with protocol, and data availability files. However, I have the following comments for the authors to make the article more effective and scientifically sound.\nIntroduction\nAuthors should cite some of the recent articles dealing with the morphometry of lumbar vertebrae.\n\nMethods\nIt should be stated how many observers were involved in the data collection.\n\nThis section should explain how the authors avoided observational bias.\n\nThe time of the study's conduct needs to be mentioned.\n\nIf possible, provide more information about the lumbar vertebrae, such as whether they are typical or atypical.\n\nThe statistical test used in the study is missing, though it is mentioned in the data availability file.\n\nIn Tables 2 and 3, the statistical tests used need to be mentioned in the caption.\n\nIn Table 2, p value representation for AP length needs to be double-checked.\n\nDiscussion\nThe heading \"Implications\" in this section may not be appropriate as it deals only with the review of the literature.\n\nIncluding information about how the current study's findings differ from those of previous studies will make the paper more interesting.\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": "9277", "date": "03 Feb 2023", "name": "Mangala Pai", "role": "Author Response", "response": "Reviewer comment - Introduction - Authors should cite some of the recent articles dealing with the morphometry of lumbar vertebrae. Author Reply: Two more recent references are added in this revised version. Julin M, Saukkonen J, Oura P, et al.: Association between vertebral dimensions and lumbar modic changes. Spine (Phila Pa 1976). 2021; 46(46): E415–E425. PubMed Abstract \| Publisher Full Text Kot A, Polak J, Klepinowski T, et al.: Morphometric analysis of the lumbar vertebrae and intervertebral discs in relation to abdominal aorta: CT-based study. Surg Radiol Anat. 2022; 44: 431–441. PubMed Abstract \| Publisher Full Text Reviewer comment - Methods: It should be stated how many observers were involved in the data collection. Author Reply: All the measurements were performed by one among the authors of this manuscript. Reviewer comment - Methods: This section should explain how the authors avoided observational bias. Author Reply: The same author performed the measurements to prevent the inter-observer error. Three measurements were performed and the average of it was taken to prevent the intra-observer error. Reviewer comment - Methods: The time of the study's conduct needs to be mentioned. Author Reply: The study duration was 6 months from 16.02.2022 to 16.08.2022. Reviewer comment - Methods: If possible, provide more information about the lumbar vertebrae, such as whether they are typical or atypical. Author Reply: The present study did not segregate the vertebrae into typical or atypical, because of the random collections of the dried vertebrae. We could not number the vertebrae with respect to the lumbar region. Reviewer comment - Methods: The statistical test used in the study is missing, though it is mentioned in the data availability file. Author Reply: The paired ‘t’ test was applied to compare the parameters between the right and left sides. Reviewer comment - Methods: In Tables 2 and 3, the statistical tests used need to be mentioned in the caption. Author Reply: It was already given in the footnote of the table; now, in this revised version, this is also added in the caption. Reviewer comment - Methods: In Table 2, p value representation for AP length needs to be double-checked. Author Reply: The AP length was rechecked and it is correct as the dimension was statistically significant and more for the inferior border." }, { "c_id": "9851", "date": "29 Nov 2023", "name": "Mangala Pai", "role": "Author Response", "response": "In this revised version, we have removed the headings ‘implications’ and ‘limitations’. The sentence about difference of this study from the previous report is added." } ] } ]	1	https://f1000research.com/articles/11-1408
https://f1000research.com/articles/12-1415/v1	27 Oct 23	{ "type": "Research Article", "title": "A systematic review of trends in photobiomodulation in dentistry between 2018 and 2022: advances and investigative agenda", "authors": [ "David Yeret Rodriguez Salazar", "Jimmy Alain Málaga Rivera", "José Edinson Laynes Effio", "Alejandro Valencia-Arias", "Jimmy Alain Málaga Rivera", "José Edinson Laynes Effio", "Alejandro Valencia-Arias" ], "abstract": "Background Photobiomodulation (PBM) involves laser therapy utilized in medical sciences to modulate biological processes acting as a palliative and immune response-enhancing treatment. This study conducts a comprehensive bibliometric analysis to explore current trends in PBM-related scientific production, encompassing publications, citations, impact, keywords and clusters. Additionally, it aims to predict future research trends in this domain.\n\nMethods The data for this quantitative and qualitative bibliometric analysis were obtained from 608 scientific documents retrieved in November 2022, with 123 sourced from Web of Science and 485 from Scopus, Utilizing Excel, the data was processed in Excel to extract essencial information. Productivity and impact were evaluated for eligibility, and VOSviewer aided in determining associativity for the bibliometric analysis.\n\nResults The findings of this study demostrate that the scientific production related to PBM adheres to a growth power law, exhibiting characteristics of both exponential and linear phases. Notably, recent research trends emphasize critical concepts such as laser therapy, orthodontics, and dental pulp stem cells. Particularly significant is the burgeoning interest in utilizing PBM within dentistry as a complementary alternative to existing protocols.\n\nConclusions PBM stands as a promising laser therapy within medical applications. Through a detailed bibliometric analysis, this study underscores the increasing significance of PBM, especially within the realm of dental treatments. These insights offer a glimpse into the evolving landscape of PBM research and provide valuable guidance for potential future directions of study.", "keywords": [ "photomodulation", "PBM", "wavelength", "light amplification", "Laser Therapy", "Medical sciences", "Dentistry", "Dentistry", "Esthetic Dentistry" ], "content": "Introduction\n\nThe main reason for seeking health care is pain, and currently, as an alternative treatment, laser light, known as PBM, has been established as an important noninvasive therapy.1,2 PBM stimulates the healing and regenerative process, modifies certain harmful processes,3 ameliorates inflammation and pain, and activates the immune response against pathogens.3–5\n\nRegarding analgesic therapy, PBM has actions at the levels of local and systemic pathways, favouring vasodilation, improving lymphatic drainage, generating axonal depolarization, and reducing vasoactive amines (prostaglandins - leukotrienes) and cytokines.6\n\nThe subjective experience of pain7 is associated with a delay in the wound healing process, which is affected by various causes, such as stress, psychological state and type of wound closure, among others.8,9 PBM has an effect on the scarring process, but the parameters used must be taken into account to achieve an optimal dose that ensures the desired effect.10\n\nPBM, as a clinically noninvasive therapy, has been shown to exert beneficial effects in neurosensory recovery, in the restoration of functional disability,11,12 in the treatment of musculoskeletal injuries, in degenerative diseases13 and in the healing process, both in regenerative medicine and dentistry12; however, to date, its use in dentistry has been limited.13\n\nIn dentistry, PBM is used to generate, at the cellular level, an increase in differentiation and replication in alveolar bone and to biostimulate and regenerate soft tissues.14 Correct wound healing and reducing the intensity and duration of postoperative pain consequently improve prognoses and result in periodontal treatment efficacy and patient comfort.15\n\nAdditionally, regarding periodontal surgery, there are still controversies regarding the effect of PBM with respect to wound healing and reducing postoperative pain.16–18\n\nTherefore, the main objective of this article is to investigate the trends in the application of PBM between 2018 and 2022 using a bibliometric analysis of publications retrieved from Scopus and Web of Science. Specifically, this systematic review aims to:\n\n‐ Analyze the trends in the use of PBM in dentistry between 2018 and 2022.\n\n‐ Identify the key areas of application for PBM in dental practice.\n\n‐ Evaluate the effects of PBM on wound healing and postoperative pain reduction in dentistry.\n\n‐ Explore controversies and gaps in the current literature regarding the use of PBM in dentistry.\n\nAmong the conclusions, the main trends in the use of PBM are based on the biostimulation and regeneration of soft tissue and hard tissue, with a consequent decrease in inflammatory mediators, thus producing analgesia.\n\n\nMethods\n\nTo address the research objective, an exploratory bibliometric analysis was conducted to assess scientific activity in this field.19 Additionally, the study was carried out following the parameters established by the PRISMA statement for conducting literature reviews.20,21\n\nBoth inclusion and exclusion criteria were established for the study selection process. Inclusion criteria encompassed all articles that, in the main scientific metadata, such as title and keywords, include terms such as oral health and PBM, as well as their respective synonyms, validated by thesauri such as that of UNESCO.\n\nRegarding the exclusion criteria, we followed two consecutive phases in accordance with the PRISMA statement. The first phase involved screening, which entailed the omission or exclusion of articles that exhibited indexing errors, as such publications do not allow the quantitative analysis of the main research metadata. Likewise, all records with themes that are different from the objective of the review are excluded.\n\nThe second phase of exclusion, referred to as eligibility, involved eliminating all publications, that, having passed the first phase of exclusion, that show evidence of insufficient methodological rigor are eliminated.\n\nTo obtain publications for the bibliometric analysis, the two main databases in terms of scientific coverage, rigor in evaluation processes, thematic diversity and obtaining metadata22 were selected as sources of information: Scopus and Web of Science.\n\nThe selected studies will be grouped into thematic categories based on their approaches and findings. This will facilitate a qualitative synthesis of findings related to the application of PBM in dentistry between 2018 and 2022. Furthermore, we will consider variability among the studies and explore potential subgroups for more detailed analyses.\n\nOnce the source of information for the literature review process had been defined, a search strategy was devised for the specific search interface of each database considering the inclusion criteria, resulting in two specialized search queries. In Scopus, we implemented the following search strategy:\n\n(TITLE ((dent* OR “oral health” OR bucal) AND (photobiomodulation* OR photomodulation* OR pbm OR wavelength OR “light amplification”))) OR (KEY ((dent OR “oral health” OR bucal) AND (photobiomodulation* OR photomodulation* OR pbm OR wavelength OR “light amplification”))).\n\nThe search strategy for Web of Science mirrored that of Scopus in terms of terminology and metadata but adapted to the distinct search interface, resulting in the following search strategy:\n\n(TI= ((dent OR “oral health” OR bucal) AND (photobiomodulation* OR photomodulation* OR pbm OR wavelength OR “light amplification”))) OR (AK= ((dent OR “oral health” OR bucal) AND (photobiomodulation* OR photomodulation* OR pbm OR wavelength OR “light amplification*”))).\n\nThe search strategies retrieved a total of 608 scientific documents, with 123 sourced from Web of Science and 485 from Scopus. These documents were stored and processed in Microsoft Excel®, during which all duplicate documents were eliminated. The two exclusion phases defined in the eligibility criteria were then applied. Additionally, bibliometric indicators, enabling the evaluation of productivity and impact of authors, journals, and countries23 were extracted. The free access software VOSviewer was utilized to visualize associativity, scientific cooperation factors and thematic relationships.\n\nFinally, in accordance with the international PRISMA statement for literature review processes, we provide a flow diagram illustrating the methodological design in Figure 1.\n\nAs evidenced, publications are identified using search strategies in the two selected databases, and all identified duplicate articles were eliminated. Subsequently, two phases of exclusion, i.e., screening and eligibility, were applied. Ultimately, 498 documents were included in the bibliometric analysis.\n\n\nResults\n\nThe indicator “publications per year” reflects the number of new works published within a specific timeframe in a particular research field. Figure 2, we illustrate the number of studies published from 1987 to 2022, revealing an exponential growth of 99%. Notably, the years 2019 and 2020 saw the highest number of publications. Particularly, the year 2020 stood out with the most publications on PBM, reaching 67; some of these publications explored how laser therapy induces a photobiomodulatory effect in cells and tissues, contributing to improvements in reparative processes.24\n\nThe year 2019 had the second highest scientific productivity on the subject, with a total of 63 publications; some of the articles investigated the way in which low-energy PBM therapy favours cell therapy by improving cell sheet transplantation.25\n\nThe next indicator analysed is the number of publications by author. Figure 3 shows the 10 authors with the highest number of publications in the research field. Fried D, with a total of 24 publications, has investigated the development of clinical probes with the ability to acquire transillumination and infrared reflectance images with short wavelengths and the diagnosis of lesions on the occlusal tooth surfaces, among other lines of study.26\n\nAwazu K stands as the second most productive author in this research field, boasting 18 publications. His works delve into less invasive procedures utilizing pulsed nanosecond lasers, aiming to reduce tissue damage and enhance dental caries treatment.27 Additionally, he has conducted research on the effects of lasers with a wavelength of 6.2 μm, specifically their absorption capabilities for dental caries without causing harm to dental tissue.28\n\nFurthermore, Yoshikawa K has contributed with 16 publications, followed by Gutknecht N, Ishii K, Yamamoto K, and Yasuo K, each boasting 15 publications. Marques MM follows closely with 13 publications, succeeded by Moreira MS with 12 publications and Fekrazad R with nine publications.\n\nThe indicator “publications per journal” signifies the number of publications within the field of study attributed to a scientific journal. In Figure 4, we present the top ten journals with the highest number of publications. Leading the productivity chart is the journal “Progress In Biomedical Optics And Imaging - Proceedings Of SPIE”, boasting 53 publications on PBM. Studies within this journal delve into various aspects, including the dehydration dynamics of fluorosis lesions, revealing its similarity to caries lesions.29 Furthermore, these studies demonstrate the efficacy of SWIR light at 1950 nm, showcasing an exceptionally high demineralization contrast and its optimal use in assessing lesion activity on tooth surfaces.30\n\nNext, “Lasers in Medical Science” had 45 publications. Among the published studies, the efficacy of the Fenton reagent in the bleaching process was investigated, as well as its ability to improve the performance of bleaching agents when combined with light.31 Additionally, a study explored the positive bioenergetic effects of PBM on the mitochondria of osteoblasts among dental pulp stem cells in humans.32\n\nThis indicator represents the trends for countries in terms of publications pertaining to PBM. Figure 5 presents the ten countries with the highest level of productivity in the field of research. The first is the United States, with 110 publications, including one that shows how biophotonic approaches can reduce the burden of microorganisms, decontaminate surfaces and tissues, and avoid the spread of viruses through minimally invasive techniques33 and one that investigate the clinical efficacy and safety of photon energy transfer during PBM dosing.34\n\nBrazil has 69 publications on the subject. In these studies, authors demonstrate how PBM utilizing light-emitting diode (LEDs) can be effectively combined with biomaterials to promote bone formation, control pain, and the manage the inflammatory process.35 Additionally, these studies identify that irradiation strategies employing red LEDs proved to be effective in reducing concentrations of nitric oxide (NO) and reactive oxygen species (ROS), while also stimulating the viability of human dental pulp fibroblasts exposed to lipopolysaccharides.36\n\nThis indicator gauges the impact authors have made by considering the number of citations linked to their research work. Figure 6 showcases the top ten authors with the highest number of citations in the research field. At the forefront is Fried D with an impressive 508 citations for his 24 publications. Notably, Fried D holds the title for the author with the most significant scientific impact, making him a pivotal reference in the research field (see Figure 3). One of his most cited articles, focusing on the nature of light scattering concerning dental enamel and dentin through a comparison of scattering data using Monte Carlo scattering simulators with angular resolution,37 has been cited in 327 publications.\n\nFeatherstone J has garnered an impressive 357 citations for his contributions across five publications on PBM. His analysis delves into the measurements of the inhibition of dental caries subsequent to enamel irradiation. Particularly, Featherstone’s research reveals that enamel conditioned with a laser exhibits a more resistant surface to acid dissolution compared to untreated enamel.38\n\nThis review of scientific literature on PBM enabled the identification of the ten journals currently boasting the greatest scientific impact based on the number of citations, as depicted in Figure 7. “Photomedicine And Laser Surgery”, amassing a total of 457 citations and holding the mantle of the most productive journal in this domain. Publications within this journal extensively analyze the bacterial efficacy of antimicrobial photodynamic therapy as a complement to scraping and radicular smoothing in periodontal disease.39\n\n“Dental Materials” stands out with an impressive 453 citations. The publications in this esteemed journal predominantly explore the enhancement of aesthetic and biological properties through the addition of titanium in composites. However, the research underscores the necessity for improvements in their microstructure and properties to meet the demands of future dental implant applications.40 Moreover, a separate study within the journal investigates the impact of a 2% quaternary ammonium cavity disinfectant, emphasizing its non-cytotoxic effects on fibroblasts. Additionally, the study sheds light on how this disinfectant’s anti-inflammatory properties can stimulate the healing and repair of dental tissues.41\n\nIn Figure 8, we observe the ten countries showcasing the highest number of citations linked to publications in the research field of PBM. Leading the pack is the United States, boasting a remarkable 1677 citations and solidifying its position as the country with the most significant impact and productivity in this domain. Notably, several publications from the United States delve into the profound impact of PBM therapy on the gene expression of postnatal dental pulp stem cells, measuring pivotal inflammatory and mineralization processes within tissues.42\n\nIllustrated in Figure 8, we observe the impact per country based on citations associated with their research publications. Notably, Brazil emerges with approximately 667 citations, establishing itself as the second most productive country in this realm (refer to Figure 5). Brazil’s publications focus on the treatment of opportunistic oral diseases associated with COVID-19 utilizing PBM and antimicrobial photodynamic therapy, resulting in noteworthy effectiveness by eliminating associated symptoms and alleviating pain.43\n\nShifting our focus to the evolution of conceptual literature on PBM, we analyze its progression. Figure 9 sheds light on the most significant keywords in research for each year. In the investigations of 1994, the concept of “dentine” (or dentin) took center stage, particularly exploring techniques to measure caries in secondary dentin.44 Remarkably, this concept has retained its importance in the literature, being the most investigated term in both 2006 and 2012.\n\nIn 2014, the research field saw phototherapy at its core. For instance, a study by Ref. 13 meticulously analyzed the benefits of low-level laser therapy emphasizing its role in healing, inflammation reduction and pain management. Furthermore, as posited by Ref. 45, a single dose of LED irradiation can effectively biomodulate oxidative stress in dental pulp cells.\n\nAs we progress to the years 2019, 2020, 2021 and 2022, \"low-level laser therapy\" emerges as the most investigated topic. Research in this domain demonstrated the positive impact of PBM in individuals with dental implants.46 However, it also shed light on a limitation concerning the efficacy of PBM in postoperative implant patients. Consequently, the authors recommend further exploration through randomized controlled trials to scrutinize various variables.47\n\n\nDiscussion and conclusions\n\nThis bibliometric study facilitated an in-depth analysis of keywords associations within the scientific production on PBM. Figure 10 delineates the principal thematic cluster highlighted in green. Within this cluster, “Optical Coherence Tomography” (OCT) emerges as the central theme interlinked with other vital terms such as “Enamel”, “SWIR Imaging\" (spiral images), “Er:YAG Laser,” “Biofilm,” and”Endodontics”. OCT s prominence stems from its ability to generate images within a depth range of 2 and 3 mm, allowing for a structural characterization at the enamel and dentin levels. This aids in determining the extent and progression of structural issues, pivotal for accurate diagnoses and treatment planning (Clarkson, 2014). Notably, OCT in the realm of endodontics has demonstrated superior results compared to computed microtomography, especially in visualizing empty spaces concerning apical filling.48 Furthermore, it has shed light on PBM’s potential application in cell regeneration within endodontic treatments.49\n\nThe orange thematic cluster “Diode Laser” stands out as the second most relevant in the study of PBM. It is intricately associated with keywords like “Photodynamic Therapy,” “Nd:YAG Laser,” and “Disinfection.” Photodynamic therapy, an alternative antibacterial therapeutic modality, has underscored the efficacy of diode lasers in enhancing periodontal clinical parameters after implementing a comprehensive oral disinfection protocol in nonsurgical procedures.50 These lasers have showcased bactericidal prowess and promising outcomes in the treatment of infectious diseases.51 Blue and blue–violet diode lasers have gained widespread application in dentistry, serving as effective devices in clinical treatments across dental surgery, endodontics, oral surgery, orthodontics, periodontics, and dental aesthetics. Moreover, they find utility in disinfection and PBM.52\n\nWithin the red cluster themed around “Dental Implant”, vital keywords like “Osseointegration,” “Dental Pulp Stem Cells,” “Bone Regeneration,” “Wound Healing,” “Periodontology,” “Tooth Extraction,” and “Periodontitis” hold prominence. A majority of findings within this cluster are associated with favorable alterations in cell proliferation, particularly highlighting the potential of growth factors in fibroblasts and osteoblasts.53 Studies exploring stem cells from dental pulp suggest a positive response to phototherapy.54 TPBM has emerged as a subject of research, showcasing its potential in generating anti-inflammatory and analgesic effects during the bone repair process within dentistry.55\n\nIn the purple cluster, focusing on “Phototherapy”, key terms such as “Dental Pulp,” “Stem cells,” “Tissue Engineering,” “PBMT,” and “Dental Implant” hold significance. These terms are associated with studies encompassing a spectrum of investigations, ranging from complementary therapies to regenerative endodontic treatments,56 as well as the regeneration of dental tissues and stem cells.57–59\n\nFigure 11 presents a network highlighting coauthorship or associativity among authors contributing to the scientific production on PBM. The dominant cluster, depicted in red, features notable authors like Moreira M, Marques M, Pedroni A, Sarra G, Diniz I and Abe G. Their contributions have shed light on how PBM can be effectively employed in cell biology, owing to its cell therapy and tissue engineering properties.60\n\nWithin the green cluster, notable authors such as Gutknecht N, Al - Karadaghi T, and Hilgers R are featured. Their research has demonstrated that dual wavelength lasers neither induce harmful thermal changes nor negatively impact sterilization of the root canal or the removal of the smear layer during endodontic treatment.61\n\nMoving to the clusters’ delineation, the yellow cluster comprises De Freitas P, De Paula Eduardo C and Aranha A, while the purple cluster involves Martins M, Grecca F and Kopper P. Finally, the blue cluster highlights the contributions of authors Fernandes K, Bussadori S and Mesquita - Ferrari R, who have significantly enriched the body of knowledge surrounding PBM.\n\nConcerning the keyword analysis of the scientific activity associated with PBM, Figure 12 employs a Cartesian plane to juxtapose the frequency of keyword usage with the average year of use. This representation delineates four quadrants, each offering distinct insights. Quadrant I encompasses the most frequent used and current keywords, Quadrant II features the least frequent yet most current keywords, Quadrant III encompasses both the least frequent and the least current keywords, and Quadrant IV comprises the most frequently used keywords, although they appear less frequently in the current scientific literature.\n\nIn Quadrant IV, the most frequently occurring yet less current words are positioned indicating diminishing relevance in the research field. Here, we find two significant concepts: “Dentistry,” crucial for demonstrating the utility of fibre tips in various dental laser applications,62 and “Laser” and “Dentin”, where authors emphasize a less invasive technique for selective removing dental caries through laser due to its absorption by organic matter.63\n\nQuadrant III comprises less frequent and less current concepts in the scientific literature. These concepts are likely to lose prominence in future PBM research: “Osseointegration,” “Phototherapy,” “Optical Coherence Tomography,” “Wavelength,” “Dental Caries,” and “Dental Implants.”\n\nQuadrant II holds the most current keywords but with lower research frequency, signifying emerging trends: “Dental Pulp Stem Cells,” “Dental Pulp,” “Photodynamic Therapy,” “Diode laser,” “Caries detection,” “Stem cells,” and “Periodontology.” Additional concepts encompass “Orthodontics,” where authors have evaluated the outcomes of periodontal laser therapy in controlling inflammation after orthodontic tooth movement,64 and “Laser therapy,” demonstrating that PBM via laser irradiation enhances bone integration.65\n\nQuadrant I houses the most frequent and current concepts, considered to be growing concepts and highly relevant within the scientific community. This quadrant exclusively features the keyword “low-level laser therapy,” proven to yield a higher success rate in pulpotomy procedures for primary molars.66\n\nThe discerned trends in keywords through this bibliometric analysis enable the determination of the research agenda. This agenda serves as a foundational input for future researchers, encouraging them to delve into recent and pertinent topics, thereby ensuring the scientific community is nourished with cutting-edge information (Figure 13).\n\nThe primary themes arising from PBM are presently significant, encompassing concepts like lasers and the overarching analysis of dentistry. These have been extensively explored over a substantial timeframe, contributing to a wealth of information within the scientific realm.\n\nHowever, among these key concepts, some have recently emerged in research but have now become foundational. This indicates their potential to assume central positions in the forthcoming landscape of PBM research. Notable among these are low-level laser therapies or low-level light therapies, as elaborated earlier, and diode lasers, which have gained prominence as widely used technologies in dentistry in recent years.\n\nAnother emergent concept steering future research is orthodontics, intimately connected to laser therapies, forming a pivotal axis within PBM as expounded earlier, and in association with endodontic treatment.\n\nAs depicted in Figure 13, not all key concepts hold equal significance for future research. For instance, enamel analysis, a subject addressed in the mid-1990s with a surge in 2015, has since witnessed a decline in related studies, indicating a diminishing trend post-2019. Similarly concepts like caries detection, pulsed nanosecond lasers, and minimal interventions lack substantia elaboration from authors, thereby diminishing their relevance in future research directions.\n\nIn conclusion, research in PBM has undergone exponential growth in recent years, showing a pronounced inclination towards low-level laser therapy and the utilization of emerging technologies such as laser diodes in dentistry. This evolution is evident in the thematic progression, shifting from initial focal points like “dentine” and “caries” to broader and intricate treatments, particularly in areas like tissue regeneration and cell therapy involving dental pulp stem cells. Additionally, several burgeoning research terms such as “diode laser,” “caries detection,” “orthodontics,” and “low-level laser therapy” have emerged and are anticipated to assume pivotal roles in future PBM studies.\n\nHence, the research agenda for PBM is characterized by the integration of diverse study areas, melding technologies like optical coherence tomography (OCT) with the analysis of dental tissues like enamel and dentin. Concurrently, a decline in the relevance of previously pivotal topics such as “osseointegration,” “phototherapy,” and “dental implants” has been observed, indicating a shift in research priorities. This bibliometric review serves as an invaluable compass for prospective researchers and professionals keen on PBM, offering a clear vision of emerging trends and most pertinent subjects in this dynamically evolving field.", "appendix": "Data availability\n\nZenodo. Trends in Photobiomodulation in Dentistry between 2018 and 2022: Advances and Investigative Agenda. DOI: https://doi.org/10.5281/zenodo.8411713. 67\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nZenodo. Trends in Photobiomodulation in Dentistry between 2018 and 2022: Advances and Investigative Agenda. PRISMA checklist. DOI: https://doi.org/10.5281/zenodo.8411713. 67\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nYadav A, Gupta A: Noninvasive red and near-infrared wavelength-induced photobiomodulation: Promoting impaired cutaneous wound healing. Photodermatol. Photoimmunol. Photomed. 2017; 33: 4–13. PubMed Abstract \| Publisher Full Text\n\nConvissar RA, Ross G: Photobiomodulation lasers in dentistry. Semin. Orthod. 2020; 26: 102–106. 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PubMed Abstract \| Publisher Full Text\n\nDaood U, Yiu CKY: Transdentinal cytotoxicity and macrophage phenotype of a novel quaternary ammonium silane cavity disinfectant. Dent. Mater. 2019; 35: 206–216. Publisher Full Text\n\nda Rocha EA , Alvarez MMP, Pelosine AM, et al.: Laser photobiomodulation 808 nm: Effects on gene expression in inflammatory and osteogenic biomarkers in human dental pulp stem cells. Front. Pharmacol. 2022; 12: 782095. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBerlingieri G, Alvares CMA, Serrano RV, et al.: Phototherapies for COVID-19-associated opportunistic oral infections. Photodiagn. Photodyn. Ther. 2022; 37: 102678. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDijkman GEHM, de Vries J , Arends J: Secondary caries in dentine around composites: A wavelength-independent microradiographical study. Caries Res. 1994; 28: 87–93. PubMed Abstract \| Publisher Full Text\n\nMontoro LA, Turrioni APS, Basso FG, et al.: Infrared LED irradiation photobiomodulation of oxidative stress in human dental pulp cells. Int. Endod. J. 2014; 47: 747–755. PubMed Abstract \| Publisher Full Text\n\nVande A, Sanyal P, Nilesh K: Effectiveness of the photobiomodulation therapy using low-level laser around dental implants: A systematic review and meta-analysis. Dent. Med. Probl. 2022; 59: 281–289. PubMed Abstract \| Publisher Full Text\n\nQu C, Luo F, Hong G, et al.: Effects of photobiomodulation therapy on implant stability and postoperative recovery: A systematic review and meta-analysis. Br. J. Oral Maxillofac. Surg. 2022; 60: e712–e721. PubMed Abstract \| Publisher Full Text\n\nSuassuna FCM, Maia AMA, Melo DP, et al.: Comparison of microtomography and optical coherence tomography on apical endodontic filling analysis. Dentomaxillofac. Radiol. 2018; 47: 20170174. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlnagar AM, Mahmoud M, Gutknecht N, et al.: Effect of photobiomodulation therapy on regenerative endodontic procedures: A scoping review. Lasers Dent. Sci. 2019; 3: 227–234. Publisher Full Text\n\nFreire AEN, Carrera TMI, de Oliveira GJPL , et al.: Comparison between antimicrobial photodynamic therapy and low-level laser therapy on non-surgical periodontal treatment: A Clinical Study. Photodiagn. Photodyn. Ther. 2020; 31: 101756. PubMed Abstract \| Publisher Full Text\n\nMahmoudi H, Bahador A, Pourhajibagher M, et al.: Antimicrobial photodynamic therapy: An effective alternative approach to control bacterial infections. J. Lasers Med. Sci. 2018; 9: 154–160. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFornaini C, Fekrazad R, Rocca J-P, et al.: Use of blue and blue-violet lasers in dentistry: A narrative review. J. Lasers Med. Sci. 2021; 12: e31. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNadershah M, Abdel-Alim HM, Bayoumi AM, et al.: Photobiomodulation therapy for myofascial pain in temporomandibular joint dysfunction: A double-blinded randomized clinical trial. J. Maxillofac. Oral Surg. 2020; 19: 93–97. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPereira LO, Longo JPF, Azevedo RB: Laser irradiation did not increase the proliferation or the differentiation of stem cells from normal and inflamed dental pulp. Arch. Oral Biol. 2012; 57: 1079–1085. Publisher Full Text\n\nLopes CCA, Limirio JPJO, Zanatta LSA, et al.: Effectiveness of photobiomodulation therapy on human bone healing in dentistry: A systematic review. Photobiomodul. Photomed. Laser Surg. 2022; 40: 440–453. PubMed Abstract \| Publisher Full Text\n\nZaccara IM, Mestieri LB, Pilar EFS, et al.: Photobiomodulation therapy improves human dental pulp stem cell viability and migration in vitro associated to upregulation of histone acetylation. Lasers Med. Sci. 2020; 35: 741–749. PubMed Abstract \| Publisher Full Text\n\nMarques MM, de Cara SPHM , Abe GL, et al.: Effects of photobiomodulation therapy in dentoalveolar-derived mesenchymal stem cells: A review of literature. Lasers Dent. Sci. 2017; 1: 1–7. Publisher Full Text\n\nKim HB, Baik KY, Seonwoo H, et al.: Effects of pulsing of light on the dentinogenesis of dental pulp stem cells in vitro. Sci. Rep. 2018; 8: 2057. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKim HB, Baik KY, Choung P-H, et al.: Pulse frequency dependency of photobiomodulation on the bioenergetic functions of human dental pulp stem cells. Sci. Rep. 2017; 7: 15927. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPedroni ACF, Diniz IMA, Abe GL, et al.: Photobiomodulation therapy and vitamin C on longevity of cell sheets of human dental pulp stem cells. J. Cell. Physiol. 2018; 233: 7026–7035. PubMed Abstract \| Publisher Full Text\n\nAl-Karadaghi TS, Gutknecht N, Jawad HA, et al.: Evaluation of temperature elevation during root canal treatment with dual wavelength laser: 2780 nm Er,Cr:YSGG and 940 nm diode. Photomed. Laser Surg. 2015; 33: 460–466. PubMed Abstract \| Publisher Full Text\n\nStock K, Hibst R: Smart fiber tips for dental laser applications. Med. Laser Appl. 2008; 23: 6–13. Publisher Full Text\n\nIshii K, Saiki M, Yasuo K, et al.: Selective removal of carious dentin using a nanosecond pulsed laser with a wavelength of 6.02 μm. Biophotonics: Photonic Solutions for Better Health Care. Brussels, Belgium: SPIE; 2010; pp. 630–633.\n\nJohnson TM, Bice RW, Gilbert WA: Orthodontic treatment of periodontally compromised teeth after laser periodontal therapy: A case report. Photobiomodul. Photomed. Laser Surg. 2021; 39: 528–534. PubMed Abstract \| Publisher Full Text\n\nBlay A, Blay CC, Tunchel S, et al.: Effects of a low-intensity laser on dental implant osseointegration: Removal torque and resonance frequency analysis in Rabbits. J. Oral Implantol. 2016; 42: 316–320. PubMed Abstract \| Publisher Full Text\n\nEbrahimi M, Changiz S, Makarem A, et al.: Clinical and radiographic effectiveness of mineral trioxide aggregate (MTA) partial pulpotomy with low power or high power diode laser irradiation in deciduous molars: A randomized clinical trial. Lasers Med. Sci. 2022; 37: 2293–2303. PubMed Abstract \| Publisher Full Text\n\nSalazar DYR, Rivera JAM, Effio JEL, et al.: Trends in Photobiomodulation in Dentistry between 2018 and 2022: Advances and Investigative Agenda. [Data set]. Zenodo. 2023. Publisher Full Text" }	[ { "id": "219905", "date": "03 Nov 2023", "name": "Herney Andres Garcia-Perdomo", "expertise": [ "Reviewer Expertise Evidence synthesis", "clinical epidemiology", "education", "urologic 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\nDear Authors\nCongratulations on this important effort to analyze the trends in the use of PBM in dentistry between 2018 and 2022.\nI would like to comment about specific points, and I hope these will improve the quality of your manuscript.\n\nThis is not a systematic review, this is a bibliometric analysis or study. Therefore, please change any description throughout the manuscript.\n\nThe final part of the introduction must describe the main objective of the study. Consequently, please, state only the main one.\n\nDelete any conclusion from the introduction section.\n\nDescribe in the limitation section that the bibliometric analysis was limited to Scopus.\n\nDelete the methodological design section. It is already described in the methods section\n\nDelete that this is a quantitative and qualitative bibliometric analysis. Leave it as: bibliometric study or analysis.\n\nFigures do not see correctly. Add high-quality images\n\nAdd a strengths and limitations section.\n\nAs this is not a systematic review, the way to write is not associated with PRISMA, I suggest deleting it.\nHope this will help you to improve the quality of your important article.\nThank you.\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": [ { "c_id": "10677", "date": "28 Dec 2023", "name": "JHOANY ALEJANDRO VALENCIA ARIAS", "role": "Author Response", "response": "We appreciate the review of our manuscript titled \" Trends in photobiomodulation in dentistry between 2018 and 2022: advances and investigative agenda \" by the reviewers. We value the detailed and constructive feedback they have provided. We would like to inform you that we are in the process of preparing detailed responses to each reviewer, and we will be sending them separately in response to their valuable insights. We are committed to addressing each of the points raised and improving the quality and clarity of our work based on the received feedback. Comments of Reviewer 1 This is not a systematic review, this is a bibliometric analysis or study. Therefore, please change any description throughout the manuscript. The final part of the introduction must describe the main objective of the study. Consequently, please, state only the main one. Delete any conclusion from the introduction section. Describe in the limitation section that the bibliometric analysis was limited to Scopus. Delete the methodological design section. It is already described in the methods section. Delete that this is a quantitative and qualitative bibliometric analysis. Leave it as: bibliometric study or analysis. Figures do not see correctly. Add high-quality images. Add a strengths and limitations section. As this is not a systematic review, the way to write is not associated with PRISMA, I suggest deleting it. Response to Reviewer 1 We appreciate your meticulous review of our manuscript. Following your feedback, we have clarified the study's nature as a bibliometric analysis rather than a systematic review, and we've revised the introduction to succinctly state the primary objective. Any conclusions in the introduction have been removed, and the limitations section now specifies that the bibliometric analysis was confined to Scopus and Web of Science. The redundant methodological design section has been deleted, and we've adjusted the description to label the study as a bibliometric analysis without the quantitative and qualitative distinction. Figures have been replaced with higher-quality images, and we've incorporated specific sections on strengths and limitations. Lastly, any association with PRISMA has been removed, aligning with the study's nature. We value your insightful comments, which have significantly enhanced the clarity and quality of our article." } ] }, { "id": "219907", "date": "09 Nov 2023", "name": "Brenda Yuliana Herrera Serna", "expertise": [ "Reviewer Expertise Epidemiological and evidence analysis 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\nThe authors are thanked for synthesising evidence of a development that should have wider application. The major concern is with respect to methodology. They announce a literature review but combine elements of what is intended to be a systematic review. Something in the middle is a scoping review.\n\nIn effect, the methodology reflects the characteristics of an analysis that would not meet the specifications of a full systematic review. To adhere to a bibliometric analysis it is suggested to extend the search to more than two databases including, among others, grey literature.\nI suggest reviewing the PRISMA indications for scoping and for protocol. I understand the intention of the bibliometric analysis, but they may still be useful. http://www.prisma-statement.org/Extensions/ScopingReviews\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? 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": "10678", "date": "28 Dec 2023", "name": "JHOANY ALEJANDRO VALENCIA ARIAS", "role": "Author Response", "response": "We appreciate the review of our manuscript titled \" Trends in photobiomodulation in dentistry between 2018 and 2022: advances and investigative agenda \" by the reviewers. We value the detailed and constructive feedback they have provided. We would like to inform you that we are in the process of preparing detailed responses to each reviewer, and we will be sending them separately in response to their valuable insights. We are committed to addressing each of the points raised and improving the quality and clarity of our work based on the received feedback. Comments of Reviewer 2 The authors are thanked for synthesising evidence of a development that should have wider application. The major concern is with respect to methodology. They announce a literature review but combine elements of what is intended to be a systematic review. Something in the middle is a scoping review. In effect, the methodology reflects the characteristics of an analysis that would not meet the specifications of a full systematic review. To adhere to a bibliometric analysis it is suggested to extend the search to more than two databases including, among others, grey literature. I suggest reviewing the PRISMA indications for scoping and for protocol. I understand the intention of the bibliometric analysis, but they may still be useful. http://www.prisma- statement.org/Extensions/ScopingReviews Response to Reviewer 2 We extend our gratitude to the reviewer for acknowledging our efforts in synthesizing evidence for a development with broader applications. The concern regarding the methodology has been duly acknowledged. The comment rightly identified the amalgamation of elements that, despite being declared as a literature review, appeared more aligned with a scoping review, indicating a deviation from the intended systematic approach. In response, we adjusted the methodology to ensure closer alignment with the specifications of a comprehensive systematic review. However, expanding the search to include more than two databases, as suggested, was not feasible, as detailed in the discussion. Such an expansion would have significantly altered all obtained results. It's important to note that all text based on the PRISMA protocol has been removed, as highlighted in the discussion. The suggestion to review the PRISMA indications for scoping and protocols was carefully considered, and our approach was reassessed accordingly." } ] }, { "id": "219906", "date": "16 Nov 2023", "name": "Idalia Rodríguez Delgado", "expertise": [ "Reviewer Expertise Odontology" ], "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 part of the advances in dentistry, laser therapy is currently being used to improve the results of different types of dental treatments, hence the importance of having an analysis of the uses of Photobiomodulation (PBM).\nBelow are some observations that were found in the article, with the purpose that these contributions serve for a better quality of the article.\nDuring the development of the writing, it is observed that a bibliometric analysis was carried out in two databases and although they mention that they used the PRISMA declaration for the exclusion criteria, it is suggested that this criterion be eliminated since it does not comply with the entire PRISMA protocol.\nIn the introduction at the end only place the general objective or purpose of the study and eliminate the conclusions only place them at the end of the article.\nIt is recommended to improve the quality of some of figures, since they are not clearly visible, it is suggested to include others with better quality of definition.\nCongratulations the authors of this article that demonstrates current trends in dentistry, hoping that these recommendations will be useful to improve the quality of their writing.\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? Yes", "responses": [ { "c_id": "10679", "date": "28 Dec 2023", "name": "JHOANY ALEJANDRO VALENCIA ARIAS", "role": "Author Response", "response": "We appreciate the review of our manuscript titled \" Trends in photobiomodulation in dentistry between 2018 and 2022: advances and investigative agenda \" by the reviewers. We value the detailed and constructive feedback they have provided. We would like to inform you that we are in the process of preparing detailed responses to each reviewer, and we will be sending them separately in response to their valuable insights. We are committed to addressing each of the points raised and improving the quality and clarity of our work based on the received feedback. Comments of Reviewer 3 During the development of the writing, it is observed that a bibliometric analysis was carried out in two databases and although they mention that they used the PRISMA declaration for the exclusion criteria, it is suggested that this criterion be eliminated since it does not comply with the entire PRISMA protocol. In the introduction at the end only place the general objective or purpose of the study and eliminate the conclusions only place them at the end of the article. It is recommended to improve the quality of some of figures, since they are not clearly visible, it is suggested to include others with better quality of definition. Response to Reviewer 3 Thank you for your thoughtful feedback on our manuscript. We appreciate your keen observations and have taken them into careful consideration. Regarding the bibliometric analysis, we acknowledge the limitations of conducting it in only two databases. However, due to resource constraints and the nature of our study, expanding the database coverage might not be feasible. We have revised the manuscript to eliminate the mention of using the PRISMA declaration for exclusion criteria, recognizing that our approach does not fully adhere to the complete PRISMA protocol. In the introduction, we have now revised it to conclude with only the general objective or purpose of the study, as suggested. Additionally, we have moved the conclusions to the end of the article to enhance the overall structure. We appreciate your comment on the figures and have endeavored to improve their quality. High-definition images have been included to enhance visibility and clarity. Once again, we thank you for your valuable insights, which have undoubtedly contributed to the refinement of our manuscript." } ] } ]	1	https://f1000research.com/articles/12-1415
https://f1000research.com/articles/11-1532/v1	19 Dec 22	{ "type": "Research Article", "title": "Advanced materials foresight: research and innovation indicators related to advanced and smart nanomaterials", "authors": [ "Lucian Farcal", "Amalia Munoz Pineiro", "Juan Riego Sintes", "Hubert Rauscher", "Kirsten Rasmussen", "Amalia Munoz Pineiro", "Juan Riego Sintes", "Kirsten Rasmussen" ], "abstract": "Background: Advanced materials are most likely to bring future economic, environmental and social benefits. At the same time, they may pose challenges regarding their safety and sustainability along the entire lifecycle. This needs to be timely addressed by the stakeholders (industry, research, policy, funding and regulatory bodies). As part of a larger foresight project, this study aimed to identify areas of scientific research and technological development related to advanced materials, in particular advanced nanomaterials and the sub-group of smart nanomaterials. The study identified and collected data to build relevant research and innovation indicators and analyse trends, impact and other implications. Methods: This study consisted of an iterative process including a documentation phase followed by the identification, description and development of a set of core research and innovation indicators regarding scientific publications, EU projects and patents. The data was extracted mainly from SCOPUS, CORDIS and PATSTAT databases using a predefined search string that included representative keywords. The trends, distributions and other aspects reflected in the final version of the indicators were analysed, e.g. the number of items in a period of time, geographical distribution, organisations involved, categories of journals, funding programmes, costs and technology areas. Results: Generally, for smart nanomaterials the data used represent around 3.5% of the advanced nanomaterials data, while for each field analysed, they represent 4.4% for publications, 13% for projects and 1.1% for patents. The study shows current trends for advanced nanomaterials at a top-level information that can be further extended with sub-indicators. Generally, the results indicated a significant growth in research into advanced nanomaterials, including smart nanomaterials, in the last decade, leading to an increased availability of information. Conclusion: These indicators identify trends regarding scientific and technological achievements and represent an important element when examining possible impacts on society and policy implications associated to these areas.", "keywords": [ "Foresight", "indicators", "advanced materials", "advanced nanomaterials", "smart nanomaterials" ], "content": "Abbreviations\n\nAdMa: Advanced materials\n\nCLP: Classification, Labelling and Packaging of substances and mixtures (EU Regulation (EC) No 1272/2008)\n\nCSS: Chemicals strategy for sustainability\n\nCORDIS: Community Research and Development Information Service (by the European Commission)\n\nEC: European Commission\n\nEU: European Union\n\nFAIR: Findable, accessible, interoperable and reusable\n\nFP: Framework programme\n\nIPC: International Patent Classification\n\nKPI: Key Performance Indicator\n\nNM – Nanomaterial\n\nOECD: Organisation for Economic Co-operation and Development\n\nOECD WPMN – OECD’s Working Party on Manufactured Nanomaterials\n\nPATSTAT: The European Patents Office’s database on bibliographical and legal event patent data from leading industrialised and developing countries\n\nREACH: Registration, Evaluation, Authorisation and Restriction of Chemicals (Regulation (EC) No 1907/2006)\n\nREFIT: European Commission's regulatory fitness and performance programme\n\nR&I: Research and innovation\n\nSeTA: Semantic Text Analyser\n\nSCOPUS: Elsevier's abstract and citation database\n\nSSbD: Safe and sustainable by design\n\nSSIA: Safer and Sustainable Innovation Approach\n\nSNM: Smart nanomaterial\n\nTIM: Tools for Innovation Monitoring\n\nUSPTO: United States Patent and Trademark Office\n\n\nIntroduction\n\nThe European Union (EU) has adopted interconnected legislation to avoid trade barriers and ensure free movement of goods and people within the EU. The European Commission (EC) continuously evaluates whether EU legislation is meeting the needs of citizens and business through the European Commission's regulatory fitness and performance (REFIT) programme.1 REFIT checks regulatory fitness and performance, aiming to ensure that EU legislation delivers results for citizens and businesses effectively, efficiently and at minimum cost, striving to make existing EU laws simpler and less burdensome to apply.\n\nAmong other things, EU legislation aims to ensure that chemicals placed on the market and the products in which they are incorporated, can be produced and used safely for humans and the environment. Safety of chemicals is addressed, among others, by two core pieces of legislation: the Regulations on Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH)2 and on Classification, Labelling and Packaging of substances and mixtures (CLP).3 A vision for the chemicals of the future is to ensure that they are inherently safe and sustainable.4 The latter requires, among others conditions, that they fit into a circular economy,5 which is a concept aimed at minimising waste, reusing and recycling products, saving resources and preserving the environment. For the sake of regulatory preparedness, legislators desire to be able to predict the entry into the market of chemicals with tailor-made properties in order to understand if they would have any associated needs for updating the legislation and/or guidance related to safety and/or sustainability.\n\nIn order to achieve the goals set out in the Commission’s European Green Deal,6 the Commission published a Chemicals Strategy for Sustainability (CSS) towards a toxic-free environment.4 It is part of the EU’s zero pollution ambition,7 which is a key commitment of the European Green Deal, which is also driving a New Industrial Strategy for Europe8 that promotes responsible design and development of chemicals, materials and products. Safe and sustainable chemicals and materials9,10 can help to reach these policy goals.11 The Green Deal includes an action for boosting the investment and innovative capacity for production and use of chemicals that throughout their life cycle are safe and sustainable by design (SSbD).\n\nOne tool for predicting which chemicals enter the market is a foresight study.12 Foresight studies explore the future of scientific and technological achievements and their potential impacts on society. They aim to identify the areas of scientific research and technological development that are most likely to bring about change and drive future economic, environmental and social benefits. Among others, foresight builds on indicators. An indicator is a quantitative or a qualitative measure derived from a series of observed facts that can reveal relative positions, e.g. at given regular intervals, and it can point to the direction of change across different units and through time.13,14\n\nAccording to the Commission’s 2021 Strategic Foresight Report,15 the EU is a strong player in terms of knowledge and innovation, providing almost 20% of the world’s total research and development, publications and patenting activity. The EU has e.g. the largest share of worldwide patent applications in advanced manufacturing technologies and the Internet of Things for mobility.16 The EU is a technological champion in advanced manufacturing and materials, with its industry delivering many critical enablers to global production lines, as well as a leader in future smart and sustainable mobility and low-carbon technologies.15,17\n\nThrough its financial instruments and research and innovation programmes the EC supports research into and development of advanced materials for applications, for example in energy, construction, mobility, health, agriculture and the electronics sectors to deliver the green transition.4,8 Regarding smart nanomaterials e.g. “It is expected that future research activities in the European Union will investigate whether the current approach to safe-by-design covers the dynamic features of smart nanomaterials too and, if not, how to adapt it and provide manufacturers and regulators with the appropriate tools for its implementation.”.18 Figure 1 illustrates how policy can steer the development of advanced materials towards safer alternatives and the associated tools required.\n\nThus, advanced materials are important drivers for the Green and Digital Transition, support the EU industrial recovery and can provide many economic, environmental and social benefits. However, as any other result of innovation, they may pose challenges (e.g. to ensure that they are safe and sustainable along their entire life cycle) that need to be timely addressed by regulators, in collaboration with other stakeholders. Some foresight regarding the kind of materials and areas of development of advanced materials seems appropriate as an initial step to anticipate those possible challenges. This should help both regulators and producers to be prepared to address them so that future advanced materials can deliver their maximum positive impacts to society.\n\nIn order to monitor progress, the EC intends to establish, in close cooperation with stakeholders, Key Performance Indicators (KPIs) to enable the measurement of the industrial transition towards the production of safe and sustainable chemicals as envisioned in the CSS.4\n\nAdvanced materials (AdMa)19–23 generally mean materials that have novel or enhanced properties that improve performance in comparison to other materials already on the market (or the products and processes in which they are used for) and represent a broad class of materials that include semiconductors, biomaterials and nanomaterials. They can boost the transition to greener technologies, as they have improved characteristics and enhanced performance (which may include reduced environmental impacts), thus contributing to a more sustainable future.24 The advanced materials “are associated with progressive technologies with the perspective to derive direct or indirect benefits in the form of highly specialised outcomes for multidisciplinary areas”.25 The new or enhanced properties (e.g. specific or improved performance) of AdMa are often determined by a combination of their chemical composition, physical properties, specific structures and higher complexity, often involving specific production processes.21 Often today's advanced materials become tomorrow's standard materials, i.e. over time the currently new or improved properties and the resulting enhanced performance will become a common feature.\n\nIn the context of the OECD’s Working Party on Manufactured Nanomaterials (WPMN)26 Steering Group on AdMa, they are understood as”materials that are rationally designed to have new or enhanced properties, and/or have targeted or enhanced structural features with the objective to achieve specific or improved functional performance. This includes both new emerging manufactured materials, and materials that are manufactured from traditional materials. This also includes materials from innovative manufacturing processes, such as bottom-up approaches, that enable the creation of targeted structures from starting materials. It is acknowledged that what are considered to be AdMa will change with time”.21\n\nMany sectors and applications rely on AdMa as the key to providing better solutions, including applications in safety and sustainability such as healthcare & medicine, construction, energy, transportation, home & personal care, packaging, agriculture, textiles, electronic appliances.27,28 The “Materials 2030 Manifesto” presents nine selected innovation markets and considers the European Green Deal and other policies that aim to create new value-chains.\n\nIt was proposed29 that categorisation, or classification, of AdMa is possible taking into consideration:\n\n• Functionality: active materials (smart, responsive, multifunctional, adaptive);\n\n• Structure: structural materials (structured, multistructural, artificially structured);\n\n• Manufacturing: advanced processes (controlled assembly of structures);\n\n• Composition: composites, nanomaterials and bio-based materials.\n\nSince the term advanced material is not univocally defined, the study mentioned above also aimed to characterise the use of the term 'advanced material' to obtain a reasonable distinction of advanced materials from other types of materials. Also, a set of criteria was described that could be applied to assess the ‘relevancy of advanced materials’. The proposed relevance assessment should allow the prioritisation of measures, e.g. with regards to the chemical safety. The four dimensions proposed for the relevance assessment includes: scientific (e.g. novelty of properties or the novelty of scale or combination of properties that advanced materials may have), economic and technical (e.g. their potential impact on technology development), hazard and risk (e.g. effect thresholds of different endpoints by exposure levels) and regulatory dimension (e.g. requirements for the generation and assessment of information on hazards and exposures as well as for the assessment of risks, coverage by the current legislation definitions and scope). In addition, a first description of identified advanced material clusters was performed. The outcomes of this analysis were presented in factsheets for each material,30 which provide an overview of the characteristic properties of the identified advanced materials along with notes on the application range and potential risks and their regulatory status, as far as it can be anticipated.\n\nSmart materials are materials that change their critical (functional) properties during use and activate specific functions upon exposure to external stimuli, which may come from their surroundings, for example a change in temperature, pH, light or contact with enzymes, to produce a dynamic and at times reversible change.31 Examples include sensors and targeted delivery systems (or carriers), which are already used in medical products, cosmetics and electronics, and furthermore R&D (research and development) applications are under development for e.g. agriculture, food, and packaging.32 An overview of the different types of smart materials available is provided in the ‘Smart Materials Books Series’ published by the Royal Society of Chemistry33 since 2012. Currently it is a collection of forty-three (43) books, including ten book titles referring to nanomaterials.\n\nThe aim of this project, as part of a larger foresight study, is to identify areas of scientific research and technological development related to advanced materials, in particular advanced nanomaterials and the sub-group smart nanomaterials that are most likely to bring changes and drive economic, environmental and social development and benefits for the future. It should lead to insights into trends of future applications and support the anticipation of possible regulatory challenges. It should be noted that several players (e.g. industry, policy makers, funding bodies, researchers) could equally benefit from these outcomes.\n\nThis study identifies and collects data in order to firstly build relevant indicators, and secondly to use the indicators to analyse the trends, impact and other implications, see Figure 2. This study addresses the objectives below sequentially:\n\n(1) Identify and analyse key research and innovation indicators;\n\n(2) Identifying trends and their drivers by analysing scientific publications, projects and patents on advanced nanomaterials, in an attempt to look into the future of scientific and technological achievements for advanced nanomaterials;\n\n(3) Examine possible impacts on society and policy implications associated to advanced nanomaterials.\n\nIn order to achieve these objectives, several key questions need to be answered, e.g. what are the current trends related to the development of advanced nanomaterials, which are the dominant sectors, organisations and countries that develop advanced materials, or what are the (current or future) policy actions that aim to resolve the upcoming challenges related to the advanced nanomaterials?\n\n\nMethods\n\nIn order to achieve the goals of the study, a methodology for creating indicators was established. As a starting point, the study analysed relevant policy documents, especially those related to the European Green Deal6 and its priorities, in order to identify some of the already defined directions towards safe and sustainable advanced materials. The study then examined and analysed research and innovation trends (e.g. publications, projects and patents) in these areas in relation to the European policies or legislation.\n\nThe methodology applied to establish research and innovation indicators related to advanced (nano) materials is described below. It consists of an iterative process that involves a background analysis of policy documents in the context of the topics covered by the study (e.g. advanced materials, advanced nanomaterials and smart nanomaterials) and a preliminary collection of information. Once the context is established, the methodology includes the identification and definition of indicators and further indicators development that involves data collection and analysis, by defining first the keywords for data search and the use of several tools for data extraction and analysis from databases. The methodology presented can be applied to any (sub) group of materials, for example smart nanomaterials, multicomponent nanomaterials, etc. by defining first an appropriate set of keywords to be included in the search strings.\n\nFollowing the analysis of relevant policy and technical documents, a list of keywords and the desired indicators were created. This was an iterative process that aimed to identify, describe and collect data that is used to analyse trends and perspectives for advanced nanomaterials.\n\nBesides the analysis of specific technical reports on advanced materials (as shown in the introduction section), the methodology consisted also of identification and analysis of several policy documents, foremost the European Green Deal policy documents (e.g. EC Communications regarding the EU Green Deal, the new Industrial Strategy for Europe, the new Circular Economy Action Plan, the Farm to Fork Strategy and the Chemicals Strategy for Sustainability). This preparatory phase generated a preliminary list of keywords. Therefore, the set of European Green Deal policy documents,4–8,34,35 described in the introduction, were consulted and analysed in order to refine the objectives of the study, as well as to support the keywords definition for developing indicators, as shown below. The analysis was performed, first by extraction of terms (words) and their frequency used in these policy documents, using KNIME, a free and open-source tool.36 The terms related to the materials, sectors, safety and sustainability or regulation and policy (about 190 terms) were then selected and used to further refine and enrich the set of keywords for the R&I indicators data collection. The analysis included also the ranking of these terms based on their frequency in the policy documents (data not shown).\n\nThis background analysis was complemented with the application of open access tool Semantic Text Analyser (SeTA) “the information retrieval tool for policy makers”.37 SeTA applies advanced text analysis techniques to large document collections (e.g. from EUR-Lex, CORDIS, Data.europa.eu, Publications Office of the European Union), helping policy analysts to understand the concepts (defined by keywords, expressions and terms which are similar or related at the semantic level) expressed in thousands of documents and to visualise the relationships between these concepts and their development over time.38 For the current study, the tool was useful for automatically analysing the occurrence of several terms, such as advanced nanomaterials (see Figure 3 generated using SeTA tool), advanced materials or smart materials, which are already indexed in the SeTA database. Please note that some terms e.g. new materials, biomaterials, functional materials, innovative materials, novel materials, nanostructured materials, composite materials, nanotechnology, nanostructured and composites, were common to all three areas mentioned above. These results were used to further refine the list keywords to be used for the indicators.\n\nThe size of the dots reflect the number of documents found by the tool e.g. advanced nanomaterials (blue dot) = 56 documents, biomaterials (orange dot) = 4761 documents, composites (green dot) = 17373 documents.\n\nIn this step a preliminary list of indicators was prepared starting from terms identified by analysing the policy documents as described above. Subsequently, further analyses of their relevance and adequacy to the current study were carried out for the selection of provisional indicators that fit the purpose of the study. Their relevance to the advanced nanomaterials areas, as well as their ability to capture temporal, sectorial and/or geographical trends were considered, as briefly described in the following.\n\nAfter the preliminary analysis, the fields (i.e. publications, projects, patents) to be searched in the study were defined and linked to advanced nanomaterials, including also a focus on smart nanomaterials.\n\nThen an initial list of core indicators relevant for the current study was defined which resulted from the investigation of research and innovation resources within the selected fields of scientific publications, EU projects and patents (Figure 4). This was an iterative step, in which a brief description regarding the indicators’ title, relevance, data and possible sub-indicators was developed. The proposed sub-indicators focused on yearly trends, geographical distribution, organisations involved, journal categories for publications, costs of projects, keywords, etc.\n\nIn this step the extraction of data from public databases (SCOPUS, CORDIS, PATSTAT and Data.europa.eu) using automatic data mining tools and analysis were performed using Tools for Innovation Monitoring (TIM). TIM is a tool developed by the EC’ Joint Research Centre (JRC) that regularly downloads the documents included in the above databases for further text mining. During the data mining process that extracts documents based on user-defined keywords combined in a search string, both the list of keywords and the search strings used for data collection were also refined. The collection of data, namely the number of publications, projects, etc. was done only by using the automatic tool TIM and based on the search strings mentioned later. No other manual (reviewers) screening was performed. For the indicators’ data, the screening did not include reports.\n\nKeywords definition\n\nThe keywords definition was based on an i) analysis of scientific/technical reports on advanced and smart (nano) materials, ii) analysis of policy documents, as well as iii) the use of automatic tools for text analysis, as described above.\n\nA set of keywords were defined in order to build comprehensive search strings and further use them to extract the data from the database. The sets of keywords cover the description of advanced (nano) materials (mainly functional and structural descriptors), including few very specific descriptors for smart nanomaterials, see Table 1.\n\n\n\n• active\n\n• adaptive\n\n• advanced\n\n• artificially structured\n\n• biobased\n\n• biomaterial\n\n• biomimetic\n\n• complex\n\n• composite\n\n• functional\n\n• hybrid\n\n• innovative\n\n• intelligent\n\n• multicomponent (multi-component)\n\n• multifunctional\n\n• multistructural\n\n• responsive\n\n• smart\n\n• stimuli responsive\n\n• structural\n\n• structured\n\n\n\n• intelligent\n\n• smart\n\n• stimuli responsive\n\n\n\n• nanoform\n\n• nanomaterial\n\nThe strings used for the searches were created in a way that the data extracted includes a combination between nanomaterials-related terms and the “advanced” descriptors are shown in Table 1. Additional filters were applied, depending on the specificity of the indicator and data required (e.g. data only on publications, projects or patents), timelines (e.g. data only between 2011 and 2020 for publications) or type of applications. The Boolean operators AND, OR and NOT were used to combine them. The final strings applied for each case are shown in the results section, together with the analysis performed.\n\nFor nanomaterials-related terms, several options were tested during the study iterations. For example, the addition of other nano-related descriptors generated very large datasets (e.g. the addition of terms like “nano” or “nanoparticle” resulted in more than 400 000 results for publications, while the search using “nano” generated more than 800 000 results because the use of wildcard ‘’ generated data on all possible combinations of nano, and therefore gave less specific results. Most likely, the different options have an impact both on the amount and relevance of the data collected, and thus also on the specificity of the indicators. Finally, in order to generate a highly relevant set of results, which is representative for the topic covered by the study only the terms “nanoform” and “nanomaterial” were used in the final search string. In addition, by default TIM applies a stemming39 process to the search terms entered by the user, in order to widen the set of matched documents (e.g. the term “technology” will match both “technology” and “technologies”).\n\nFurthermore, a set of keywords to cover the uses of these types of advanced materials were defined. Without being complete, this list, which is based on the examples of applications described previously30 with further additions, intends to allow the analysis and extraction of a representative set of data for the areas and sectors which use the advanced nanomaterials.\n\nFinally, the selection of keywords followed an iterative approach in which a set of recent policy documents and scientific literature were consulted.18,29,30-35\n\nData extraction and analysis\n\nBased on the keywords, the search strings were defined for each individual indicator and used in the search engine for data extraction. The main tool used for data extraction was the TIM Technology Editor40 that facilitates the access to data related to science and innovation and allows to create and visualise datasets about specific technological issues, that otherwise would have been carried out into the specific databases and manually combined. The search was performed in the fields title, abstract, author keywords and automatic keywords39 of the documents, the automatic keywords were generated by TIM, which attributed a variable number of words (10-15) to each document. In our study TIM brought together datasets (exported as.xlsx files) from different sources regarding patents, scientific publications and EU grants: 1) peer-reviewed scientific publications from SCOPUS, 2) worldwide patent applications from PATSTAT and 3) projects funded by the EU's framework programmes for research and innovation (FP5 to Horizon 2020 [H2020]) from CORDIS, the EC’s Community Research and Development Information Service. For the latter, additional data files with detailed information on FP5, FP6, FP7 and H2020 projects were extracted directly from the European data portal and used for analysis, especially regarding the costs of the projects, and the data sources used were SCOPUS, CORDIS, PATSTAT and Data.europa.eu. The exact strings applied are listed in Table 2, therefore included a general search (in all 3 databases connected to TIM and also a separate search, publications, projects or patents. For the purpose of reproducibility, an alternative to the TIM Technology Editor used in this study users can access “TIM Open Access”, a version of TIM without restrictions and that allows its users to perform searches and analysis on Open Access data. Therefore, it currently offers access to publications from Semantic Scholar, worldwide patent applications from PATSTAT, and projects EU funded projects from CORDIS. In addition, the same searches can be done in each of the databases separately, the results would then need to be combined manually. TIM facilitates the extraction of all together and the visualisation. Except Scopus, all are open access.\n\nThe first string is the general final string, and the subsequent entries show the extension of each string for the three cases of publications, projects and patents.\n\nData retrieved:\n\n* 2-Feb-2022;\n\n 21-Jun-2022;\n\n* 23-Jun-2022;\n\n‡ subgroup of advanced nanomaterials.\n\nThe creation of the final version of the indicators followed the above process and workflow (Figure 5) including some iterative refinement steps. First the collection of data using TIM was performed based on keywords related to advanced (including smart) nanomaterials description as well as keywords related to the application of these materials. The resulting data was analysed by looking at various aspects, like trends, distributions, and finally, the indicators were developed, including selecting how to visualise and report. The analysis included several aspects (e.g. for publications) and included indicators such as yearly distributions, categories of journals, author keywords or geographical distribution; for EU funded projects the analysis included aspects such as yearly distribution, value of projects, geographical distribution (e.g. countries, organisations); for patents the analysis looked into the yearly distribution, technology sub-areas or geographical distribution.\n\nThe figures included in the Results section were created with Microsoft Excel, while the maps were created with MapChart using the data extracted with the method presented above.\n\n\nResults\n\nThe final search strings in TIM for “advanced nanomaterials” and for “smart nanomaterials” (see Table 2) and the data generated (from 1996 until the end of 2021) (Figure 6) were used as a starting point for the detailed analyses and to create the indicators for the three major areas screened in this study, i.e. scientific publications, EU funded projects and patents (Table 3). Additional fields (e.g. timeframes, classes or topics) were added to these basic search strings, depending on the specificity of the analysis and the desired indicator. Generally, ‘node size’ data from TIM datasets was used for the analysis that represent the number of results (e.g. number of documents) for that specific indicator.\n\nPlease note that the scale of the y-axis, number of items, is different for advanced nanomaterials and smart nanomaterials.\n\n\n\n• Distribution of publications to different categories of journals\n\n• Organisations involved in publications\n\n• Geographical distribution of publications\n\n• Distribution of publications per sector and type of applications\n\n• Trends in the keywords used in publications\n\n\n\n• Distribution of projects between the framework programmes and funding schemes\n\n• Costs of EU projects\n\n• Distribution of projects among EU member states\n\n• Organisations involved in EU projects\n\n\n\n• Distribution of patents to categories and technology areas\n\n• Geographical distribution of patents\n\n• Technology areas for the patents\n\nIn this section, the results for advanced nanomaterials, including smart nanomaterials (ca. 3.5% of the identified items for advanced nanomaterials), are analysed. In some cases, a specific evaluation of smart nanomaterials data was also included.\n\nFigure 6 depicts the total number of documents per year for EU projects, patents and publications (articles, reviews, book chapters and conference proceedings) for advanced nanomaterials and smart nanomaterials (bottom); the extraction was performed with TIM and the search strings are indicated in Table 2.\n\nAs seen from Figure 6 (top) for advanced materials there is a steady increase in publications from 2001 (63 articles) to 2021 (more than 6200 articles), and with the rise in shared knowledge also the number of reviews increases. The book chapters appear from 2008 onwards and fluctuate a bit; they represent 5% of the total publications. The annual number of conference documents have remained at a fairly stable level; relatively they represent 7% of the total number of documents. The patents steadily increase from 6 in 2001 to around 500 in 2019 and then seem to fall again; this decrease may reflect the time needed to grant patents. The EU projects represent the number of projects that the EU has (co) funded via its research programmes and the year that the project started; the number of projects increases constantly until 2011 followed by a stable number of projects per year with an average of ~40 projects/year. A detailed analysis of the data collected for the three areas is presented in the sections below.\n\nThe information extracted from SCOPUS using TIM covers data for the period 2012 until 2021 and includes peer-reviewed articles (70 %), reviews (18%), book chapters (6%) and conference proceedings (6%) addressing advanced nanomaterials; the percentages is the relative distribution of the publication categories. However, for simplicity, in most of the indicators below, we have merged this data in one item called ‘Publications’, unless otherwise stated. Overall, in this period there are 45,687 publications on advanced nanomaterials, of which 2,041 (4.4%) refer to smart nanomaterials. The final search string used for this search is shown in Table 2.\n\nThe extracted publications were analysed with regards to annual number of publications, see Figure 7. As expected, a significant increase in number of yearly publications was seen both for advanced materials (2012 = 1943 publications to 2021 = 7569 publications, i.e. an increase of 390 %) as well as for the sub-field smart nanomaterials (2012 = 67 publications to 2021 = 415 publications i.e. an increase of >600%).\n\nThe pie chart shows the percentage of different types of publications on advanced nanomaterials.\n\nWhen comparing with the publications on nanomaterials (data not shown), the trend is similar for the period analysed. The total number of publications on advanced nanomaterials (45,687) represent 56% of the total number of publications on nanomaterials (81,653)1. Interestingly, this percentage increased constantly from 47% in 2012 to 58-59% after 2018. For the relative occurrence of the types of publications (articles, books, etc.), there are no significant differences between nanomaterials and advanced nanomaterials.\n\nAnalysing how the publications on advanced nanomaterials are distributed over different categories of journals reveals the following pattern, see Figure 8., which shows the top thirty categories of journals ranked according to the number of publications and including the time distribution from 2012 to 2021. Material science and engineering are very well represented over the whole period, reflecting research into developing advanced nanomaterials and into understanding the properties and possible uses of them. Also, chemistry and surface chemistry are well represented, indicating that possibly the greater reactivity of nanosized materials is a sought-after property, this is supported by the appearance of Catalysis among these journal categories. These first categories are followed by journals from the biotechnology and bioengineering areas. Interestingly there are categories of journals (e.g. Pollution, Process Chemistry and Technology) in which the publications were listed more recently only (2021), while for other categories (e.g. Metals and Alloys, Biochemistry, Genetics and Molecular Biology, or Surfaces and Interfaces) there are no publications listed in the last years two years analysed (2020-2021).\n\nAn analysis of the most frequently used keywords is presented in Figure 9. It can be observed that most of the frequent terms refer to the material type (e.g. nanomaterials, nanoparticles, nanocomposites, carbon nanotube, graphene, polymer), to the functionality or specific property (e.g. drug delivery, stimulus response, self assembly, bio sensor, controlled release, mesoporous silica) or more general terms such as nanomedicine, nano technology, smart/smart material.\n\nThe box size reflects the frequency of use of the keywords.\n\nThe worldwide geographical distribution of publications on advanced nanomaterials for the top 24 countries and the EU (Figure 10) shows that China is the country that has the highest number of publications (16,693), followed by the USA (8,793). The region of the EU is in between with 12,213 publications. In addition to the bar chart, the map inset of the EU illustrates the level of publications on advanced nanomaterials by the EU member states.\n\nThe map shows the distribution of publications on advanced nanomaterials in EU countries in the period 2012-2021.\n\nThe data on projects funded under the European framework programmes (FP5, FP6, FP7 and Horizon 2020) covering the period 1998 to 2021 was extracted from the CORDIS database using TIM, and 563 projects on advanced nanomaterials were identified, of which 77 (13.6%) are related to smart nanomaterials. The search string used is shown in Table 2, while the distribution of projects per year and framework programmes are illustrated in Figure 11 and Figure 12.\n\nTo be noted that the duration of the framework programmes go from five years to seven years between FP6 and FP7.\n\nA significant increase in both number of projects and available funding is observed in the period 1999 (FP5) to 2020 (Horizon 2020). Furthermore, also the number of funded projects studying smart nanomaterials has increased from an average of 1 project per year in FP5 to 7 projects per year in Horizon 2020. As seen from Figure 11 the number of EU-funded projects has remained rather constant in the period 2011 to 2021. However, the project funding increased from €464 million under FP7 (2007 to 2013) to €589 million under H2020 (2014 to 2020), or in other words from €66.3 million/year to €84.1 million/year; see Figure 12.\n\nRegarding the geographical distribution among EU member states (Figure 13) it can be seen that 26 of the 27 EU member states participate to the projects, and that the large member states participate to more projects than the smaller ones, and that the old member states are more frequently involved in projects than the newer member states. Regarding the institutions organisations participating in the EU funded projects (Figure 14), the old member states (including the former member, the UK which has 7 of the top-25 institutions) are represented, whereas none of the newer member states have yet institutions among the 25 most frequent ones.\n\nThe data on patents was extracted from PATSTAT using TIM and 3,428 existing patents on advanced nanomaterials were identified, of which 37 (1%) are related to smart nanomaterials. The search string used to extract the patents is shown in Table 2.\n\nWhen analysing the number of patents awarded for advanced nanomaterials per year in the period 2011 to 2021 (Figure 15) there is a significant increase between 2011 and 2018 and a slight decrease in 2019-2020, which may just reflect the time that it takes to grant a patent. The first patent on smart nanomaterials was granted in 2007, and until 2013 at a maximum 1 patent per year was granted in this area, in 2014 two patents were granted, and afterwards 5 or more patents were granted each year. The small, but increasing, number of patents for smart nanomaterials may indicate that in the future, as this technology matures, more patents will be applied for and granted. The EC workshop ‘Safe and Sustainable Smart Nanomaterials’32 discussed a number of example areas in which smart nanomaterials are under development, for example agriculture41–46 and medical applications.47–49 These applications are still at the experimental research phase, but for agricultural applications they are clearly moving towards being the new way of dosing, in a timely manner and exactly needed amounts, essential nutrients and fertiliser as well as chemicals protecting plants against stressors. For medical applications smart nanomaterials are perceived for example as a future way of delivering medicine within the body to the precise location where it is needed. It is challenging to develop such applications into fully functional ones and time is required to go from identifying the concept to being able to patent it.\n\nAccording to the International Patent Classification (IPC)50 and USPTO Classification,51 there are several areas of technology to which patents on advanced nanomaterials, including smart nanomaterials, pertain (Table 4).\n\n* Category according to the United States Patent and Trademark Office (USPTO): Y = general tagging of new technological developments; general tagging of cross-sectional technologies spanning over several sections of the IPC.\n\nAn analysis (not illustrated) of the technology areas of patents on ‘advanced nanomaterials’ versus the first year of using that technology area showed that in the period 1996 to 2021 the technology areas grew from 14 (in 1996) to 100 (in 2020), which is an indication of the uptake of advanced nanomaterials across innovative industrial applications. In the period of 1996 to 1999 the same 14 technology areas were considered, and more technology areas were used, adding between 495 patents (technology area applied since year 2000) and 20 patents (technology area applied since year 2007) to the number of patents granted. The indicators below (Figure 16) shows the most frequent technology sub-areas to which the patents were assigned, as well as the geographical distribution of patents on advanced nanomaterials (Figure 17).\n\nThe map shows the distribution of patent applications for advanced nanomaterials in EU countries.\n\n\nDiscussion\n\nCurrent trends related to the advanced nanomaterials\n\nThe presented analysis aimed to build indicators for advanced materials allowing to identify areas of growth. Figure 18 below illustrates the top level of information extracted by the analysis. Based on trend analysis of publications, projects and patents, and applying a set of keywords identified through iterative analysis of policy documents, we gained an overview of the overall number of publications and their yearly distribution within each category (see Table 2), as well as their geographical distribution (see Figure 10). For publications, we identified the most frequently involved countries worldwide (Figure 10). For the EU, we identified the number of publications on advanced nanomaterials per EU member state, the participation of each EU member state for projects (see Figure 13), as well as the top 25 organisations participating in EU projects (see Figure 14) related to advanced nanomaterials, which include organisations based in Switzerland (which is associated to the EU research programme) and the UK (which was deeply involved before Brexit in 2020). For publications only and the categories of journals in which they appeared see Figure 8. For the projects, the analysis focussed on the EU, and we elucidated information on the framework programmes and the costs of the projects (Figure 12). The analysis of the patents provided information on the technology areas in which new patents were granted.\n\nAccording to the ‘Science, research and innovation performance of the EU 2020’,16 the EU accounts for about one fifth of the world’s R&D, publications and patents. As illustrated by the outcomes of the analysis of scientific publications, projects and patents on advanced nanomaterials, there has been a significant growth in research into advanced nanomaterials, including smart nanomaterials, in the period of 2012 to 2021 leading to an increased availability of information; see e.g. Figure 7 ‘Scientific publications’ cover peer-reviewed articles, reviews, book chapters and conference proceedings. EU’s funding schemes have increasingly supported research into advanced nanomaterials, including smart nanomaterials, see e.g. Figure 11; this in turn has contributed to increasing the number of scientific publications originating from within the EU. Also, the number of patents granted per year has increased significantly in the 10-year period analysed as shown in Figure 15.\n\nBased on the information presented above it is evident that in the period 2011 to 2021 the number of scientific publications and patents have increased significantly, whereas the increase in the number of EU-funded projects has been less notable. However, the project funding increased from €464 million under FP7 (2007 to 2013) to €589 million under H2020 (2014 to 2020), or in other words from €66.3 million/year to €84.1 million/year (see Figure 12). Hence, on average each project would be bigger under H2020 than under FP7.\n\nRelevancy of indicators\n\nThese indicators would lead to identification of trends of future scientific and technological achievements in the area of advanced nanomaterials, which in turn would be one information element when examining possible impacts on society and policy implications associated to these areas. For example, taken collectively this information reflects that the new technology is maturing and evolving from being a new research field to becoming applied science, and products containing the technology are becoming available also to the general public. However, the indicators in general but also those proposed here should be seen as a dynamic tool, as the input data may change every day (e.g. when new articles are published) but also regarding the keywords applied in the search queries to select the input data. The keywords used in this study are considered as representative terms for the area of advanced nanomaterials and the indicators proposed reflect the search string applied. As new descriptions will be available for advanced nanomaterials, they can be added to the list or other terms can be withdrawn from the string.\n\nIn addition, more detailed analyses can be performed in order to look closer at and analyse, for example the distribution of advanced nanomaterials per sectors (agriculture, construction, electronics, energy, environment, medicine, biotechnology, etc.), specific applications and use of advanced nanomaterials (fertilisers, paintings, cosmetics, packaging, textiles, bioelectronics, sensors, batteries, solar cells, water treatment, biomarkers, coatings, drug carriers, tissue engineering, 3D printing, optics, etc.), most visible types of advanced nanomaterials (frequently used, characterised, etc.), new (smart) materials and applications that are at R&D stage and may soon be placed on the market, production and consumption patterns, online searching trends by the general public, economic and social impacts, or educational and training programmes related to the area of advanced (nano) materials.\n\nAs mentioned, such indicators would need periodical updating of the input data and their timelines in order to maintain their relevance. As the description or definition of advanced materials might change over time, any indicator needs to be a dynamic tool being able to capture new developments in this area.\n\nThe methodology used in the study by Giese et al. 202029 for identifying publications containing keywords on advanced materials included searching with a set of keywords in the Web of Science Core Collection52 and extracting the data published between 2000 and 2018. The following terms were identified and used for characterising materials regarding their functionality, structure and manufacturing processes:\n\n• Functionality: “active materials”, “smart materials”, “functional materials”, “multifunctional materials” and “adaptive materials”;\n\n• Structure: “structural materials”, “structured materials”, “multistructural materials” and “artificially structured materials”;\n\n• Manufacturing: “advanced manufacturing” and “advanced processing”.\n\nIn our study, the starting point is the above-mentioned terms, which have been further refined and adapted, e.g. we have used keywords related to the ‘functionality’ and ‘structure’, applying them in the same search string. This approach has led to extraction of data (publications, projects and patents) that contain all possible combinations of the two characteristics (function and structure) of the advanced (nano) materials.\n\nOften, advanced materials are at the nanoscale or have one or more nanoscale entities as components of their structure, for example ‘nanohybrids’.18,53 In the case of nanostructured advanced materials, the assembly method is also reported54 to play a role in determining their unique properties. In particular, smart nanomaterials both present more complex structures than conventional nanomaterials and are designed to have higher dynamism by actively transforming in response to external stimuli.\n\nThe Smart Nanomaterials Industry Analysis by BIS Research55 forecasts the market to grow at a significant Compound Annual Growth Rate (CAGR) of 33% on the basis of value during the forecast period from 2019 to 2029. According to this study, North America dominated the global smart nanomaterials market with a share of 37% in 2019 and the key players were identified to be, in alphabetical order, Abbott, ANP Co. Ltd., Akzo Nobel N.V., Bayer AG, BASF SE, Clariant, Donaldson Company Inc., JM Material Technology Inc., Nanologica, Nanogate, NanoBeauty, OPTINANOPRO, The Nano Gard L.L.C., and Yosemite Technologies Co. Ltd.\n\nThe EU policies related to the Green Deal6 (Figure 19), bring various opportunities to stakeholders (e.g. researchers, industry), but at the same time the policies come with major challenges regarding their implementation, e.g. upcoming updates (or new) of legislation, funding within the Horizon Europe Framework Programme (2021-2027) and beyond, and, in general, the alignment between legislation, industry and consumers. All these players will be influenced in one way or another by the implementation of the European Green Deal policy and its related actions (e.g. chemicals sustainability strategy, farm to fork, the industrial strategy and the circular economy action plan).\n\nThe Chemicals Strategy for Sustainability Towards a Toxic-Free Environment is presented in an EC Communication4 that in its Annex proposes more than 80 key actions related to the implementation of the Chemicals Strategy for Sustainability. The actions are grouped in five main categories: i) innovating for safe and sustainable EU chemicals, ii) Stronger EU legal framework to address pressing environmental and health concerns, iii) Simplification and consolidation of the legal framework, iv) Providing a comprehensive and transparent knowledge base on chemicals and v) Provide a model inspiring chemicals management globally. In the coming years the actions will dominate the work on the EU chemicals policy, with a strong emphasis on updating the legislation towards a “stronger EU legal framework”. According to the EC Communication, “the measures presented in this action plan, including legislative proposals and targeted amendments to REACH, will all need to be carried out in line with the better regulation principles and subject to evaluations and impact assessments as appropriate”. One of these actions refer directly to nanomaterials (i.e. “Review of the definition of nanomaterial” which resulted in the adoption of the new definition56), while the majority refer to chemicals in general and their safety and sustainability.\n\n\nConclusions\n\nThe study established and tested the methodology for creating a set of research and innovation indicators in the area of advanced materials, with a focus on advanced nanomaterials and smart nanomaterials (Figure 20):\n\n• The methodology used a set of predefined keywords for data search and used several tools and databases for data extraction. The keywords are an essential element in establishing the indicators, as any modification will influence the input data used for the indicator. However, the authors consider that the set of keywords used in this study are representative and the results offer a good view on the analysed area. The methodology is reproducible provided the availability of access to the data extraction and databases mentioned in the study.\n\n• The study developed a first set of indicators, in order to understand the level of complexity and data needed for such exercise and also to be used as a starting point for developing additional indicators or sub-indicators.\n\n• Regarding the results, there is clearly an important growth both in scientific publications, patents and EU funding. Asia, led by China, is a very important player within the area of advanced materials (e.g. publishing and patents).\n\nThe numbers represent the total items analysed for advanced nanomaterials, while the total number of items analysed for smart nanomaterials are given in the brackets.\n\nSeveral EU initiatives57–62 are actively promoting ontology development, as well as the standardisation of documentation of data for advanced materials, including nanomaterials. The outcomes of such projects should further support the development of the classification of advanced materials as well as the progress of data interoperability and knowledge sharing. A clearer classification and description of advanced materials will also help building and refining indicators and similar tools for monitoring the development and impact in this area.\n\nIndicators for identification and monitoring AdMa could feed into other initiatives, such as the Early4AdMa system63 and can generally contribute to implementing a ‘Safer and Sustainable Innovation Approach’ (SSIA), currently developed by the OECD and being extended to integrate the safe and sustainable by design concept,64 or support the risk screening for such materials, e.g.65 Monitoring the area of AdMa could – with appropriate indicators to be developed – also provide timely insights into whether, how fast and how efficiently policy ambitions and action plans are turned into reality.\n\nAs a next step, the indicators can be further extended and developed (additional or more specific sub-indicators, identify new technologies or materials), while a dashboard that integrates all the indicators could be designed.", "appendix": "Data availability\n\nThe underlying data used for this publication were collected using the methodology presented above from the open sources databases (SCOPUS, CORDIS, PATSTAT and Data.europa.eu) using open access data mining tools TIM Technology Editor 40 and Semantic Text Analyzer (SeTA). 37 No files were compiled but were temporarily exported from TIM (Microsoft Excel format) in order to generate the charts presented in the Results section. The additional analyses are performed directly in TIM and in order to reproduce the study, the data should be collected and analysed in TIM using the method presented above (e.g. by using the search string presented in Table 2).\n\n\nAcknowledgments\n\nThe content of this publication is purely those of the authors and does not necessarily reflect the position or opinion of the European Commission.\n\nThe authors thank to our former colleagues at JRC, Agnieszka Mech, Stefania Gottardo (currently Centro Euro-Mediterraneo sui Cambiamenti Climatici (CMCC), Risk Assessment and Adaptation Strategies Division, Italy) and Paula Jantunen (currently Sweco Finland Oy), for their contributions to the initial discussions at the very early stage of this study.\n\n\nReferences\n\nEC: REFIT - making EU law simpler, less costly and future proof.2020. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWIPO: International Patent Classification (IPC).Reference Source\n\nUSPTO: The United States Patent and Trademark Office.Reference Source\n\nClarivate: Web of Science.Reference Source\n\nAich N, Plazas-Tuttle J, Lead JR, et al.: A critical review of nanohybrids: synthesis, applications and environmental implications. Environ. Chem. 2014; 11(6): 609. Publisher Full Text\n\nJortner J, Rao CNR: Nanostructured advanced materials. Perspectives and directions. Pure Appl. Chem. 2002; 74(9): 1491–1506. Publisher Full Text\n\nB. I. S. Research: Global Smart Nanomaterials Market – Analysis and Forecast, 2019-2029.2020. Reference Source\n\nEC: Commission Recommendation of 10 June 2022 on the definition of nanomaterial 2022/C 229/01 (OJ C 229, 14.6.2022, p. 1–5).2022. Reference Source\n\nEMMC: The European Materials Modelling Council.Reference Source\n\neNanoMapper: eNanoMapper ontology - BioPortal.Reference Source\n\nOntocommons: Ontology-driven data documentation for industry commons.Reference Source\n\nVIMMP: The Virtual Materials Marketplace.Reference Source\n\nNanoCommons: The European Nanotechnology Community Informatics Platform.Reference Source\n\nJeliazkova N, et al.: Towards FAIR nanosafety data. Nat. Nanotechnol. 2021; 16(6): 644–654. PubMed Abstract \| Publisher Full Text\n\nOomen A, et al.: Towards Safe and Sustainable Advanced (Nano)materials: A proposal for an early awareness and action system for advanced materials (Early4AdMa).2022. Publisher Full Text\n\nOECD: Sustainability and Safe and Sustainable by Design: Working Descriptions for the Safer Innovation Approach (ENV/CBC/MONO(2022)30).2022. Reference Source\n\nArvidsson R, Peters G, Hansen SF, et al.: Prospective environmental risk screening of seven advanced materials based on production volumes and aquatic ecotoxicity. NanoImpact. 2022; 25: 100393. PubMed Abstract \| Publisher Full Text\n\n\nFootnotes\n\n1 Search string (data retrieved: 13 July 2022): topic:(nanoform OR nanomaterial) AND class:(conf OR boch OR review OR article) AND emm_year:[2012 TO 2021]" }	[ { "id": "158446", "date": "11 Jan 2023", "name": "Steffi Friedrichs", "expertise": [ "Reviewer Expertise nanotechnology", "chemistry", "materials", "sustainability", "innovation analysis and managament (incl. EU projects)", "standardisation", "policy analysis", "policy development", "statistical analyses (incl. text-mining)" ], "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 is a well-written piece of a timely study into the keywords related to the field of advanced materials and nanomaterials (i.e. including 'smart' nanomaterials'). The paper furthermore represents and excellent example of how policymaking could and should be connected to and supported by scientific evidence.\nIn the following points of mild 'criticism', I would like to encourage an improvement of the paper over and beyond its readily publishable nature.\nA bit of more generous punctuation or rephrasing could support better readability: - 'The EU has e.g. the largest share of worldwide patent applications in advanced manufacturing technologies and the Internet of Things for mobility.' - this sentence worked in spoken language, but not in written form. the same is tru here: 'Regarding smart nanomaterials e.g. “It is expected that future research activities in the European Union will investigate whether the current approach to safe-by-design covers the dynamic features of smart nanomaterials too and, if not, how to adapt it and provide manufacturers and regulators with the appropriate tools for its implementation.”' detailed list of typos / errors:\na space missing in the caption of Figure 9 in the brackets of the first sentence under the header ‘Advanced and smart (nano)materials’: ‘or the products and processes in which they are used for’ (delete either ‘in’ or ‘for’.\n\nThe figures could be improved, and their captions made clearer:\nFigure 1: it is not correct that 'advanced materials' necessarily lies on a direct line between 'European Green Deal' and 'tools and data', because the latter's sub-sections are directly related to each other. A triangular arrangement of the green, blue and red clusters may be more appropriate. Moreover, the caption should be more detailed (i.e. describe what the small hexagons around the big central ones are). Figure 2: the caption needs to be more detailed: what do the numbers (1) - (2) - (3) describe. The figure should take more care to making sure that the elements of a list are of comparable nature (i.e. 'consumers' and 'environment' in a list of 'policy', 'legislation', 'funding') Figure 8: there needs to be a note explaining, which sort of categorisation was used (i.e. where it comes from). Most importantly, many journals are assigned to more than one category; it needs to be stated that the statistics were correct for this. Figures 11 and 12: the data on Projects is the most wobbly, when it comes to key-word analyses, because projects are based on their underlying proposal text, which are written for an entirely different purpose than publications and patents are written for: proposals aim to leverage funding during a stringent evaluation process and on a limited number of pages. There are a number of limitations and biases that should be taken into account when using text-mined data from projects; these include:\nThe statistics used here capture winning proposals only. the terms used in a proposal (and thus) project text are likely to mimic/copy those used in the call text (where projects are bound to call text); this was one of the finding in our text-mining analyses for the NanoFabNet Project (https://acumenist.com/mapping-the-scientific-landscapes-of-nanofabrication-sustainability/) [NOTE: we were alerted to this 'bias' by finding that the keywords found in 'open call'-projects (e.g. Marie Curie) seemed to correspond more closely to those of publications, while the keywords used in 'call-text-bound'-calls seemed to be lagging behind in the use of keywords (because they keywords would first need to be included in the next multiannual framework, before they are used in successful proposals)]. similar to the previous bullet, the amount of funding for a specific area depends mostly on how much money had been earmarked for a specific scientific field by the EU.\n\nFigure 13: it does not seem appropriate to exclude the UK from the visualised result for the simple reason that UK-institutes are included in Figure 14. The same underlying selection should be applied to both figures so as to render them comparable. Figure 15: there should be a note explaining the drop of patents at 2020 and 2021; this is an artefact that is to do with the handling and publication of patents through the relevant databases; since this artefact does not apply to publications or projects, it needs to be explained to keep the data comparable.\n\nSpecific comment/suggestion: - should 'actuator' not be one of the key-words (see table 1)\n\nComment regarding the conclusions: Tt would be desirable to draw more possibilities/recommendations from the conclusions. The text makes a link between the KPIs that the EC wants to develop and the CSS, but how will the analysis and results presented in this paper contribute to this? The paper says 'These indicators would lead to identification of trends of future scientific and technological achievements in the area of advanced nanomaterials, which in turn would be one information element when examining possible impacts on society and policy implications associated to these areas.' and it would be interesting to read more about 'how exactly' this can be achieved.\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": [ { "c_id": "9418", "date": "29 Mar 2023", "name": "Lucian Farcal", "role": "Author Response", "response": "Thank you very much for reviewing the paper and for the useful suggestions on both the content and formatting, that we hope are reflected in the second version of the article (to be uploaded). 1. The document was proofread once again and the text refined, as indicated and as needed, in order to improve its readability. Please note that some sentences indicated are ad verbatim citations of other papers, and we have thus not changed. 2. Typos were corrected. 3. Figures: Figure 1: the format was changed as suggested. The caption was completed with an additional explanation regarding the second layer of hexagons. Figure 2: the caption was extended with an explanation on the numbers (they are linked to the study objectives). Regarding the elements included together in the right-side box, in order to distinguish between them, they were represented in different colours. However, for this schematic representation of the objectives, the comparability between the main impacted areas was not considered essential, but rather their identification. Figure 8: the categorisation used is based on the categories defined by the SCOPUS database (see Scopus Subject Areas), from where the original data was extracted. Indeed, one journal (and its publications) may be assigned to more than one category. This is now mentioned in the text under Methods (under ‘Data extraction and analysis’ section) as well as in the Results, in the text related to Figure 8. Figures 11 and 12: we are indeed aware of the limitations of automatic data mining methods generally for such purposes and also in this particular case: Indeed, the indicator represents only funded (winning) projects, as mentioned in the text. The tool used for data mining, TIM, uses the public information displayed in CORDIS and that is listed under the ‘Fact Sheet’ of the projects (title and abstract). The full proposal, generally, is not publicly available and cannot be searched. It would be interesting to look also in the Reporting or Results sections of the projects in order to cover not only the proposed text, but also the outcomes. For the latter, some results should appear in the publication statistics. However, such detailed analysis was not under the scope and was not performed in this study. Additional details on the search methodology were included in the text (under “Data extraction and analysis”) Figure 13: this figure is based on TIM’s automatic filter for EU countries and aimed to reflect the situation at the moment when the data was extracted (2022), for EU. In addition, the analysis looked in more detail, in order to show also the contribution of former EU countries (such as UK) or associated countries in the Horizon FPs (such as Switzerland), etc., through their organisations involved in the projects. A more general indicator (including all European countries or worldwide, not only EU) may be used to show this data. Figure 15: short additional text was added to the text related to this figure. (In general, the indicators are indeed a dynamic tool for which the data may change frequently, as the new resources are published and made available online). 4. Specific comment/suggestion: Thank you for the suggestions. For this study, it will not be possible to add it to the current list, as the addition of a new keyword will influence the whole set of indicators, thus necessitating a full repetition of the study. It should also be noted that one of the aims was to create a first list of keywords relevant for advanced materials, which can be refined based on the feedback received and can be used in any other context. Hence, the list of keywords can be updated in the next phases of the study. For example, the addition of ‘actuator’ to the search list, would add e.g. nine new (9) publications (only for 2019), six new (6) patents to the overall data and no new projects." } ] }, { "id": "183340", "date": "05 Sep 2023", "name": "Ander Reizabal", "expertise": [ "Reviewer Expertise Materials science", "smart materials" ], "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 undertakes the pivotal task of discerning the landscape of scientific research and technological advancements within the realm of advanced materials, with a specific emphasis on advanced nanomaterials, particularly the sub-category of smart nanomaterials. Its primary objective revolves around the systematic collection and meticulous analysis of data to construct relevant research and innovation indicators, thereby providing profound insights into prevailing trends, impacts, and other significant facets within this dynamically evolving field. To ensure clarity and transparency, this paper expounds upon the methodologies employed, encompassing an iterative process that involves documentation, the establishment of core research and innovation indicators, and the utilization of prominent databases, including SCOPUS, CORDIS, and PATSTAT.\nHowever, as we embark on this scholarly journey, it is essential to address some critical aspects and potential refinements within the study's foundations and methodologies:\nMethodology Foundations:\nObjective Clarity: While the study's intent is to provide an objective representation of reality through data analysis, the introductory section contains repeated expressions and sentences that may not align with the desired objectivity. Enhancing the clarity of the introduction will effectively communicate the transparency and objectivity of the authors.\n\nDefinition of Advanced Materials: The definition provided for \"advanced materials\" is broad and subjective, leaving room for interpretation. Defining what constitutes an \"advance\" in materials science is vital to avoid ambiguity.\n\nKeyword Selection: The selection of keywords, as illustrated in Figure 3 and the related text, warrants meticulous consideration. Each chosen term should be critically evaluated for its relevance and significance within the context of advanced materials. The rationale behind their selection should be clearly elucidated.\n\nRelevance of Keywords: The mere presence of a keyword in a paper does not necessarily imply a substantive connection to the topic. The study should explore methods to determine the relevance and significance of each keyword in the context of the research.\n\nSources of Innovation: It is important to acknowledge that reviews and books often compile existing research rather than presenting novel findings. This could potentially result in the duplication of research efforts. Additionally, the mere inclusion of a keyword in a project or conference presentation may not indicate innovation; it should be considered in the context of project outcomes.\nNon-Methodology Points for Discussion and Inclusion:\nComprehensive Data: Figures such as 10, 13, 14, 15, 16, and 17 provide valuable insights but could benefit from a broader perspective. Incorporating data related to the overall growth in relevant fields can provide context and enhance the interpretation of specific trends.\n\nGrant Outcomes: Exploring data on the success rates and outcomes of grants related to advanced materials could be enlightening for stakeholders. Identifying which grants have led to tangible advancements or commercial products would be particularly valuable.\nDiscussion and Conclusions:\nMaturity of Technology: The statement regarding technology maturation evolving from a research field to applied science requires a more robust foundation. The study should elaborate on the evidence supporting this assertion.\n\nKeyword Representation: The claim that the chosen set of keywords is representative and provides a comprehensive view of the analyzed area needs substantiation. Discussing the methodology's robustness and its ability to yield a comprehensive representation would enhance confidence in the study's results.\nIn conclusion, this study marks an important step toward understanding the landscape of advanced materials, but careful consideration and refinement of its foundations, methodologies, and interpretations will enhance its relevance and credibility within the field of materials science research.\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?\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? No", "responses": [ { "c_id": "10793", "date": "23 Jan 2024", "name": "Lucian Farcal", "role": "Author Response", "response": "Thank you very much for reviewing the paper and for the suggestions, which we have addressed in the second version of the article. Several sections were refined in order to reflect the comments received, e.g.: The Introduction, including the ‘study objectives’ was refined. The Methodology section was further refined to bring more clarity, especially related to the data collection and analysis. The Results section was refined. The data shown has not been modified. Methodology Foundations: 1. Objective Clarity The introduction section starts with the EU and international context of the study by referring to the EU policy context and ongoing activities in this area at international level (e.g. OECD) or as part of different research projects. These activities proposed already a set of definitions and classifications for advanced materials which were used as a base for the study and further extraction of data for the indicators. As such, the introduction aimed to list the essential policy and technical aspects needed in this context. In this context (and as part of a larger foresight study) the objectives were designed to address a first set of aspects related to research and innovation in this area, reflected in research projects, publications and patents. 2. Definition of Advanced Materials Defining the advanced materials was outside the scope of this study, therefore the authors exploit existing resources. The starting point of the study were currently agreed definitions by the scientific community, of advanced materials. These generated a set of representative terms, used later as keywords for extracting data. However, we fully agree that defining what is ‘advanced material’, is crucial for such a study and the authors tried to cover these aspects in the introduction and further in the Discussion section. Perhaps it is important to clarify also that the study did not intend to address specific components of advanced materials (that could be included in future and extended indicators). 3. Keyword Selection Figure 3 was generated automatically with an online tool (Semantic Text Analyser - SeTA) that applies advanced text analysis techniques to large document collections, methodology detailed in the JRC Technical Report (Reference 38). SeTA was used as complementary tool for the selection of representative keywords, for the refinement and validation of previous background analysis. 4. Relevance of Keywords The authors agree that additional methods may exist and can be applied for increasing the relevance and specificity of data extracted. The methodology was developed in an iterative manner, with the aim of identifying a set of ‘representative keywords’, without the intention of being complete. The authors consider that the keywords used are highly significant (considering the definitions used), while the relevance is adequate but indeed, both aspects can be further refined e.g. in case more specific sub-indicators will be developed. Acknowledging that the reviewer’s observation (The mere presence of a keyword in a paper does not necessarily imply a substantive connection to the topic.) is fully correct, we note that the study extracts statistical data, and hence will give an overall impression of where the field is going and that individual papers could be off the mark or undetected. 5. Sources of Innovation For the core indicators presented, the authors preferred not to discriminate between the types of publications. We agree that additional, more specific, sub-indicators can be created using only a sub-set of data (e.g. categories of data shown in Figure 6). Such aspects were not within the scope of the current study, which intended to cover more general indicators. Non-Methodology Points for Discussion and Inclusion: 1. Comprehensive Data We thank the reviewer for sharing this idea. This would generate more complex, composite indicators, which could be one of the follow-ups of this study that aimed to generate a set of simple indicators using the tree main databases mentioned in the Methodology. 2. Grant Outcomes We recognise the importance of this aspect and note that it could be further explored in a follow-up study, as it could not be addressed in the current study. Discussion and Conclusions: We thank the reviewer for this positive feedback. Discussion section has been refined." } ] } ]	1	https://f1000research.com/articles/11-1532
https://f1000research.com/articles/12-310/v1	21 Mar 23	{ "type": "Research Article", "title": "How an international research funder’s forum developed guiding principles to ensure value and reduce waste in research", "authors": [ "Matthew Westmore", "Michael Bowdery", "Anne Cody", "Kelly Dunham", "Dorota Goble", "Barbara van der Linden", "Evelyn Whitlock", "Elaine Williams", "Cristina Lujan Barroso", "Michael Bowdery", "Anne Cody", "Kelly Dunham", "Dorota Goble", "Barbara van der Linden", "Evelyn Whitlock", "Elaine Williams", "Cristina Lujan Barroso" ], "abstract": "Background: When health-related research funding agencies choose to fund research, they balance a number of competing issues: costs, stakeholder views and potential benefits. The REWARD Alliance, and the related Lancet-REWARD Campaign, question whether those decisions are yielding all the value they could. Methods: A group of health-related research funding agencies, organisations that represent health-related research funding agencies and those that inform and set health-related-research funding policy from around the world have come together since 2016 to share, learn, collaborate and influence emerging practice. This group meets under the name of the Ensuring Value in Research Funders’ Forum (EViR Funders’ Forum). The EViR Funders’ Forum worked together to develop a set of ten Guiding Principles, that if funders adhered to would reduce research waste and ensure value in research. Results: The EViR Funders’ Forum has previously agreed and published a Consensus Statement. The Forum has agreed on a set of ten Guiding Principles to help health-research funders to maximise the value of research by ensuring that: research priorities are justifiable; the design, conduct and analysis of research minimise bias; regulation and management are proportionate to risks; methods and findings are accessible in full; and findings are appropriately and effectively disseminated and used. Conclusions: When setting research funding policy, we must balance multiple stakeholders’ needs and expectations. When funders do this well, they maximise the probability of benefits to society from the research they support - when funders do this badly, they passively allow or actively contribute to research waste. These challenges must be resolved by funders either working together or in conjunction with other actors in the research ecosystem.", "keywords": [ "research funding", "funding agency", "funding policy", "transparency", "waste", "value in research", "international forum" ], "content": "Introduction\n\nThe impact of health-related research, and the difference research makes for patients and the public, is the main focus of research funding agencies. It is the reason health-related research maintains the support of our health, public health and social care services and society more generally. But it is also essential to consider and acknowledge how funders deliver research systems and whether there are opportunities to enhance the efficiency and effectiveness of funding organisations.\n\nResearch funding agencies’ (RFAs) practice improvements are often set in the context of current global debates, specifically focusing on the purpose, accountability, and quality of research. These include issues raised about research integrity (World Conference on Research Integrity, https://wcrif.org/); the “crisis” of reproducibility in research (Ioannidis, 2016); avoidable waste across the research enterprise (Chalmers and Glasziou, 2009, Lancet Series Research: increasing value, reducing waste (https://www.thelancet.com/series/research)); the impact, openness and transparency of specific health-related research activities (AllTrials, All Trials Campaign, http://www.alltrials.net/, Chalmers, Glasziou and Godlee, 2013); and the rise (and threat) of populism vis-a-vis science (Grant, 2017). Mostly these are well-meaning attempts to improve science; in some cases, they are biased attempts to undermine public confidence (Ignore the public at your peril, Times Higher Education (THE), https://www.timeshighereducation.com/news/ignore-public-at-your-peril).\n\nHealth-related research funding is provided through a range of sources such as the commercial sector, public resources (e.g. taxation or government borrowing) and philanthropic funding agencies, whose source funding comes from charitable activity such as raising donations or through a charitable trust. RFAs have mandated (e.g. through legislation) as well as internally developed policies and procedures that guide how they decide what research to fund and how funded research should be conducted and communicated. Research funders operate within a specific context, what the World Health Organisation would describe as an “integrated health research system” (Pang et al. 2003). Although RFAs operate within different integrated research systems, defined by geographic, political, scientific and societal contexts, funding organisations share similar challenges. Whilst research funders can influence the environment in which they operate, they are one part of the wider research ecosystem.\n\nOver the last 20 years, there have been a growing number of initiatives to improve health-related research practices across the spectrum of activities required to support research development, conduct and communication. These initiatives are often related to specific sectors of the research system (e.g. regulators or journal editors) or specific issues in the research process. Examples include the James Lind Alliance (https://www.jla.nihr.ac.uk/), public involvement in research identification and prioritisation, research integrity, evidence synthesis methodology such as Cochrane’s innovative methods development and evidence synthesis for pre-clinical research via SYRCLE.\n\nThe Research Waste and Rewarding Diligence Alliance (REWARD) is a significant initiative in the world-wide efforts for quality improvement in research. The REWARD Alliance came from an initial paper on avoidable research waste in research in 2009 (Chalmers and Glasziou, 2009), which was later followed up with a series (Lancet Series Research: increasing value, reducing waste, (https://www.thelancet.com/series/research)), detailing expert consensus recommendations for all sectors of the research ecosystem. Both the REWARD Alliance and the 2014 Lancet series recommended aligned and collective action by different stakeholder groups – one such group suggested was research funders. The formation of the Ensuring Value in Research (EViR) Funders’ Forum, whilst not formally part of the REWARD Alliance, was strongly influenced by the work of the REWARD Alliance.\n\nThis paper sets out ten Guiding Principles, and a conceptual model, developed by the EViR Funders’ Forum in an attempt to contextualise and address these issues for funders. It will be of interest to RFAs considering their own policies and practice and researchers seeking to understand funders’ perspectives on these issues.\n\n\nMethods\n\nTo address the challenges facing health-related research, a group of health-related research funders, organisations that represent health-related research funders and those that inform and set funding policy from around the world, have come together to discuss these challenges, to share learnings, and to explore the potential for collaboration. The group started planning the Forum in 2016; the first meeting was held in January 2017. The group meets under the name of the Ensuring Value in Research Funders’ Collaboration and Development Forum (EViR Funders’ Forum, for short) (Chinnery et al. 2018).\n\nThe Forum’s focus is on health-related research for two reasons: firstly, the initial members are health-related research funders; secondly, the debates on research waste and integrity, whilst relevant to all areas of research, are more established and have greater resonance given the implications, risks and opportunities associated with health-related research.\n\nThe National Institute for Health Research (NIHR) in the UK, the Patient-Centered Outcomes Research Institute (PCORI) in the US and the Netherlands Organisation for Health Research and Development (ZonMw) in the Netherlands planned and co-hosted the initial meetings. This steering group has grown since. Since its inception, the Forum has met twelve times, typically hosted by a different health-related funding organisation, or lately online due to travel restrictions:\n\n1. London, England. NIHR – January 2017\n\n2. The Hague, Netherlands. ZonMw – June 2017\n\n3. Washington D.C., USA. PCORI – November 2017\n\n4. Cardiff, Wales. Health Care Research Wales (HCRW) – May 2018\n\n5. Canberra, Australia. National Health and Medical Research Council (NHMRC) – November 2018\n\n6. Dublin, Ireland. Health Research Board (HRB) – March 2019\n\n7. Washington, DC., USA. PCORI – September 2019\n\n8. Berlin, Germany. REWARD-EQUATOR Conference 2020\n\n9. Virtual – September 2020\n\n10. Virtual – October 2021\n\n11. Virtual – March 2022\n\n12. Virtual – October 2022\n\nThrough meetings, webinars (added in 2018), and surveys of current practice, the EViR Funders’ Forum has interacted with 53 organisations that either fund health-related research, represent funders or are active contributors to this agenda. Figure 1 lists the organisations from whom at least one individual attended at least one meeting, webinar or responded to electronic surveys.\n\nThe Forum operates an open invitation policy whereby any public or philanthropic health-related research funding organisations, organisations that represent funders, or organisations that set health-related research funding policy, regardless of location, context, funding type, size or where on the research continuum (from basic discovery through to public health) may participate. The Forum also welcomes other non-funding related organisations to discuss the wider research system and specific topics of conversation. By encouraging diversity across a wide range of contexts, experiences and practices, the Forum provides a greater learning environment to start to address some of the uncertainties currently facing the whole research ecosystem. These practices also contribute to the broader purpose and aim of the EViR Funders’ Forum - to share experiences and to learn on what funders can do to maximise the probability of impact within and across respective research funding parameters.\n\nThe initial activities of the EViR Funders’ Forum focused on developing a Consensus Statement and a set of Guiding Principles to serve as the backbone of our collaboration (Chinnery et al. 2018). Surveys and sharing current practices through the surveys and open discussions were carried out to obtain and increase wider perspectives from other funding organisations.\n\n\nResults\n\nThe development of the EViR Consensus Statement (see Figure 2) was an important step to ensure commitment, common purpose and shared understanding from funding organisations (Chinnery et al. 2018).\n\nFollowing the Consensus Statement, the Funders’ Forum began to develop the EViR Guiding Principles. These principles are an extension of the Consensus Statement to help guide funders to ensure their work delivers the greatest value. The NIHR’s Adding Value in Research Framework (AViR, https://www.nihr.ac.uk/about-us/our-contribution-to-research/how-we-are-improving-research/adding-value-in-research.htm) was used to help shape the Guiding Principles. The NIHRs AViR Framework was initiated in response to the research waste, research integrity and research transparency literature [https://www.nihr.ac.uk/about-us/our-contribution-to-research/how-we-are-improving-research/adding-value-in-research.htm, and as a result of Lancet avoidable waste series (2014)]. The Guiding Principles were iterated and agreed by consensus during the first three EViR Funders’ Forum meetings. The ten Principles are published on the EViR website (https://evir.org/our-principles/) and reproduced in Table 1.\n\nBeyond statements of intent and guiding principles, funders must consider how well their policies and practices align and support their mission of funding research that is credible and beneficial to the public. The ten Guiding Principles provide the practical link between the conceptual domains in the Consensus Statement to the actual policies, procedures and activities delivered by funders. The resulting conceptual model underpinning work of the EViR Funders’ Forum is shown in Figure 3.\n\nMany funders will describe the outcomes they are trying to achieve as impact. The EViR Funders’ Forum has deliberately not defined impact, as this is a much broader topic whose importance will be specific to an individual funder and context. However, the Forum does recognise that the probability of positive impact (benefit) should be enhanced through the application of these principles and practices designed to maximise value (see Figure 4). The model also draws on a tacit understanding that impacts are in relation to benefits accrued to society rather than impacts in relation to surrogate outcomes, such as academic publications and their related metrics. This would also include the impact research has on research itself; for example, by changing research agendas, opening up new avenues of exploration that could lead to further benefits, and closing down others that could not.\n\nFunders are seeking to maximise the benefits their research delivers and ensure these are relative to the research costs incurred. Cost is interpreted broadly to include tangible costs such as time and money and intangible costs such as opportunity costs, political support, public support, participant and stakeholder experience and enthusiasm, patient and public participation.\n\nTo maximise the probability of benefit (impact) relative to the tangible and intangible costs incurred, funders’ policies and procedures should aim to ensure the research they support is:\n\n- Relevant to the intended end user of the research (e.g. patients and clinicians for clinical research; the next research community in the translational pathway for earlier phase research).\n\n- High quality and with minimal bias.\n\n- Transparent and open. This should also apply to funders’ activities.\n\nThese high-level aims are achieved by ensuring that:\n\n- Research priorities are justifiable.\n\n- Design, conduct and analysis are robust and appropriate.\n\n- Regulation and management are proportionate to risks.\n\n- Complete information on research methods and findings are publicly accessible and in usable formats.\n\n- Findings are appropriately and effectively disseminated.\n\nAn integrated conceptual model, as outlined in Figure 1, allows funding organisations to think coherently and comprehensively about their research practices to identify key areas for improvement. Policies and practices can be investigated and evaluated to determine their alignment with all or some of the Guiding Principles outlined in this paper. Conducting performance audits of specific policies can then help to guide quality improvement across a range of funders and within different contexts (e.g. Boutron et al. 2016, Nasser et al. 2017, Whitlock et al. 2018, Cody et al. 2021). The Forum is currently piloting an audit tool for members to track their performance against the conceptual model and Guiding Principles.\n\n\nDiscussion\n\nFor funders of health-related research, this work provides a logic model of the indicators of a high value research funder. The Guiding Principles are an aspiration we work to, rather than a checklist or a target to be achieved. As research policy and practice evolve, the interpretation of each Principle will accrue additional facets. For example, what constitutes a robust research design will change over time as new methods become available, and the ways in which research protocols and findings can be shared continue to increase. As such, the Guiding Principles give structure and focus to continual improvement strategies, first with policies and procedures and then with monitoring and measurement.\n\nDespite the increased attention since the original paper on avoidable waste in research, Chalmers and Glasziou lamented that “research waste is still a scandal” but also recognised that the establishment of the EViR Funders’ Forum is “… perhaps the most notable and potentially influential development …” in addressing avoidable waste in research (Glasziou and Chalmers, 2018).\n\nThe Forum has used the Guiding Principles to share their experience, learn from each other and collaborate to move its collective understanding forward. Diverse topics have been discussed against the framework of the Guiding Principles: for example, data sharing, automation, priority setting, novel decision-making processes, and transparency.\n\nLonger-term working groups have focussed on implications for preclinical research (Ritskes-Hoitinga et al. 2018); stakeholder engagement; dissemination and implementation; systematic reviews ahead of new primary research; and self-audit against the Guiding Principles as a whole.\n\nTo date, funders in the Forum have used the Guiding Principles as a tool for internal measurement, process improvement, and strategy development. The Research Quality Committee of the National Health and Medical Research Council in Australia (NHMRC 2019) used the Guiding Principles to inform the process of developing its recently released Research Quality Strategy, the aim of which is to ensure the highest quality and value of NHMRC-funded research. The Health Research Council of New Zealand has shared the Guiding Principles with its statutory Research Committees with responsibility to provide advice to Council on the assignment of funds, and shared information in New Zealand Health Research Strategy cross-agency discussions with a view to increasing awareness and enhancing engagement in ensuring value in research. The National Institute for Health and Care Research in the UK has fully incorporated all ten Guiding Principles into its own Adding Value in Research Framework and is developing new areas of work to deliver on them.\n\nFunders in the Forum have also applied the Guiding Principles to standards/requirements for researchers seeking funding. The Scar Free Foundation now requires applicants for funding to embed the EViR Guiding Principles in the study design, management and dissemination of their research. Several funders now require researchers to demonstrate that there is a need for the proposed study that is informed by a systematic review or other robust evaluation of the available evidence (Italian Ministry of Health, NIHR, NHMRC, PCORI, HCRW, HRB and the Stroke Association). While NIHR and PCORI had this requirement prior to the formation of the Funders’ Forum, others have been prompted by their participation in the Forum.\n\nOne of the authors (MR-H) has led a linked project to highlight ways to apply the Guiding Principles to pre-clinical research by adding pertinent examples. In 2020, a pre-clinical working group was established which will focus on furthering the implementation of the Guiding Principles for pre-clinical research as well.\n\nIt is important that funders understand current practice internationally and evaluate progress in improving research systems. The Guiding Principles provide a framework for this discussion. Some principles lend themselves to simple quantitative measures (e.g. percentage of studies registered, Knowles 2020), while others are more complex and qualitative. Even those that may at first appear more straightforward need to be seen in context: for example, whilst regulated clinical trials are required by law to be registered, the same does not apply to other types of health research and practice varies between health services research, biomedical research, and population health research. Funders and the wider community will need to develop methods for monitoring and tracking these process measures. In doing so, it is important to remember that these will inevitably only be indicators. These indicators are useful because they are largely within our collective influence within medium term time frames. However, they should not be confused with the end aim; namely, maximising the benefits to society from research, which is the end state of a complex system.\n\nThere are also implications for research-on-research or meta-research. Research-on-research uses a range of research methods to investigate the process of research or of funders’ policies and guidance with the aim of improving the planning, conduct and sharing of research as well as its governance and oversite, including how funding decisions are made. The concepts in this paper are grounded in the research-on-research literature but it is fragmented and often descriptive. More research is required under each guiding principle. The Guiding Principles may provide the framework for a research-on-research agenda that can provide evidence regarding funders’ policies and practice. This is already beginning to happen; the NIHR has a long running research-on-research programme that has used the concepts and issues discussed here as an organising framework for its research agenda (NIHR research on research (RoR), https://www.southampton.ac.uk/netscc/research/index.page).\n\nThis work highlights how funders are placing greater emphasis on research practices and by doing so contribute to the improvements of the research they fund. The Funders’ Forum and its Guiding Principles will continue to translate into funder policies and procedures, and to ensure value in research.\n\n\nConclusions\n\nA research funder’s policies and procedures are aimed at ensuring the relevance, quality and transparency of the research process. When RFAs do this well, they will maximise the probability of benefits to society from the research they support - when they do this badly, they passively allow or actively contribute to research waste. This requires continuous, committed, concerted and collaborative effort. The funders within the EViR Funders’ Forum do just that – they work together to effect change within our own organisations and within the wider global research system.\n\nWe hope other organisations want to be involved in the Forum, so if you would like any further information about our work, or if your organisation is interested in joining the Forum, please contact evirfundersforum@gmail.com.", "appendix": "Data availability\n\nFull agendas of the EViR Funders’ Forum meetings, redacted only to remove personal data, are available in the public domain on https://evir.org/events-and-outputs/events/. Due to data protection concerns, minutes of the meetings are available on request, please contact the EViR secretariat (evirfundersforum@gmail.com) for more information.\n\n\nAcknowledgments\n\nThe authors would like to thank Merel Ritskes-Hoitinga (Utrecht University, The Netherlands, j.ritskes-hoitinga@uu.nl) for her work leading the link and understanding of the Guiding Principles to preclinical research.\n\n\nReferences\n\nBoutron I, Ravaud P, Graham I, et al.: Increasing value and reducing waste in biomedical research: Who's listening? Lancet. 2016; 387(10027): 1573–1586.\n\nChalmers I, Glasziou P: Avoidable waste in the production and reporting of research evidence. Lancet. 2009; 374(9683): 86–89. PubMed Abstract \| Publisher Full Text\n\nCody A, Hiney M, Clarke P, et al.: Funders’ responsibility to ensure value in research: a self-audit by the Health Research Board Ireland [version 2; peer review: 2 approved]. HRB Open Res. 2021; 4: 35. Publisher Full Text\n\nGlasziou P, Chalmers I: Research waste is still a scandal—an essay by Paul Glasziou and Iain Chalmers. BMJ. 2018;k4645. Publisher Full Text\n\nChalmers I, Glasziou P, Godlee F: All trials must be registered and the results published. BMJ. 2013; 346(jan09 2): f105–f105. Publisher Full Text\n\nChinnery F, Dunham K, van der Linden B , et al.: Ensuring value in health-related research. Lancet. 2018; 391(10123): 836–837. Publisher Full Text\n\nIoannidis J: Why Most Clinical Research Is Not Useful. PLoS Med. 2016; 13(6): e1002049. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKnowles RL, Ha KP, Mueller J, et al.: Challenges for funders in monitoring compliance with policies on clinical trials registration and reporting: analysis of funding and registry data in the UK. BMJ Open. 2020; 10: e035283. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNasser M, Clarke M, Chalmers I, et al.: What are funders doing to minimise waste in research? 2017.\n\nNHMRC’s Research Quality Strategy: Canberra: National Health and Medical Research Council; 2019. 978-1-86496-024-2.\n\nPang T, Hanney S, Bhutta Z, et al.: Knowledge for better health: a conceptual framework and foundation for health research systems. Bull. World Health Organ. 2003; 81: 815–820. PubMed Abstract\n\nRitskes-Hoitinga M, Westmore M, Goble D, et al.: The guiding principles of the ensuring value in research funders’ forum can also ensure value in preclinical research.NMHRC REWARD conference on research translation. 27-28 November 2018, Sydney.\n\nWhitlock E, Dunham K, Bowen K, et al.: PCORI Methodology Standards in Practice: Use of systematic reviews to support proposals for new research. 7th Annual NHMRC Symposium on Research Translation, Sydney, Australia, 27-28 November 2018. 2018." }	[ { "id": "167144", "date": "24 Mar 2023", "name": "Till Bruckner", "expertise": [ "Reviewer Expertise Clinical trial registration and reporting", "meta-research", "regulatory science" ], "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 provides a narrative overview of the creation and evolution of the EViR Funders’ Forum and its development of a Consensus Statement and Guiding Principles to help health research funders to maximise the value of research. It is a valuable addition to the literature because it describes an innovative platform that allows and enables diverse funders from different countries to jointly discuss how to address issues of common concern.\nOne arguable shortcoming of the paper is that it fails to explore the more ‘political’ (in the broadest sense) aspects of funders’ engagement with the issues of research waste and research quality. Funders may face considerable barriers to acting decisively to maximise the value of research. For instance, openly acknowledging that funders may not be making optimal use of public money could invite criticism from political decision-makers and taxpayers and threaten their budgets. Another barrier is that funders often seem determined to maintain positive relationships – including long-standing personal relationships – with the research community, which disincentivises the imposition of sanctions.\nFor example, the world’s largest medical research funder, the National Institutes of Health (NIH), has continued to award new funding to grantees that had violated NIH’s own policies and thereby generated research waste (https://www.statnews.com/pharmalot/2022/10/14/clinical-trials-nih-transparency/). In general, there often seems to be a gap between funders’ publicly stated aspirations and their subsequent translation into practice. In this context, it is excellent that the authors cite Knowles et al., who focuses on the thorny issue of implementation.\nHowever, given space constraints, omission of these more ‘political’ aspects from the scope of the article is defensible, especially given that the Consensus Statement and Guiding Principles provide a useful starting point for further debate about funders’ upstream aspirations. The Forum’s experiences gained during the ongoing piloting of an audit tool might provide a good starting point for a future, separate publication that focuses on the downstream challenges of implementation.\nIn sum, this paper is a valuable addition to the literature. I look forward to future publications documenting the Forum’s further development and experiences over time.\nTill Bruckner TranspariMED Bristol, UK, 23 March 2023\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": [] }, { "id": "168745", "date": "19 Apr 2023", "name": "Hans Lund", "expertise": [ "Reviewer Expertise Evidence-Based approaches to clinical practice", "to research (for example: evidence-based research) and to teaching. Meta-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 authors and the organisation behind should be praised for their initiative and for promoting a better and more transparent approach to funding health research.\nI suggest the authors to consider the following comments and questions:\nMaybe explain a little more in details how figure 2, table 1, figure 3, and figure 4 were developed. How many participated in the process? What were the diversity of the group for example geographically, experience with funding or as applicant? How was consensus achieved? and alike.\n\nThe authors mentioned the importance of meta-research both as inspiration for the Consensus Statement, Guiding Principles, the conceptual model and their definition of value in research, and in the Discussion. As it can be very difficult to find funding calls including meta-research, and even big difficulties in finding funding support for meta-research in open calls, it would have been good if the need of research evaluating researchers and research practice, evaluating research ethic committees practice, funders practice and scientific journal practice was highlighted in the Guiding Principles.\n\nThe authors should maybe consider an alternative definition of value in research or valuable research (see Figure 4): For science to be of value it needs to be both scientific valid and relevant. Thus, valuable research could be defined as the product of scientific validity and the societal relevance of the study in relation to the costs (Valuable Research = Validity x Relevance / Costs). Validity deals with how research is designed and carried out to reduce bias, including whether research is answering a research gap. Relevance deals with the importance of the research for society in general and the needs of the intended end users specifically. In this context, end users can be defined as those who will either use the results of the research and/or be affected by the results. Costs in the equation includes the resources used in conducting the study and the risks study participants are taking.\n\nOn page 8 the authors refers to Figure 1, but maybe they should have referred to Figure 3?\n\nOne way to improve the use of means for health research is by carrying out different forms of research priority setting processed. The results from such processes can inform the researchers when arguing for a new study, but it could also be an important source of prioritisation of funding calls. The authors should consider to include this in the Discussion. A recent study indicates that such processes lacks both systematicity and transparency and may be of relevance for the discussion in the present paper. (See: Lund et al. 2022)1.\nThe paper is a very important contribution to diminish waste in research, and by providing suggestions for how funding decisions could be made it is possible to have more relevant and important studies supported in the future. Thanks for this brilliant initiative.\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": "10792", "date": "31 May 2024", "name": "Cristina Lujan", "role": "Author Response", "response": "Dear Professor Hans Lund, We would like to thank you for reviewing our paper and responding so positively to this work. We are particularly grateful for your insightful comments, which we fully agree with, even if some we were unable to amend the paper directly. Please find our responses below: Comment 1. All artefacts were developed and approved through the forum meetings. Final versions were ratified by the steering group and presented back to the full list of individuals and organisations that attended the meetings. Whilst different members of the Forum joined at different times, and different members were active in the discussion to a greater or lesser extent, the diversity of input is reflected in Figure 1. Comment 2. The authors thank the review for this insightful comment. It is noted and the authors agree. This point was discussed at a number of meetings but it did not become part of the agreed guiding principles and so it would not be appropriate to change the agreed principles to incorporate this point. However, in the recent EViR Strategic Workplan this has been acknowledged as a priority area (https://evir.org/events-and-resources/resources/evir-strategic-workplan-expanding-our-vision/) and work is currently ongoing with experts in the field. Comment 3. This is an interesting view that clearly has merit. The definition of value we used was purposefully centred on real world impact or outcomes and was inspired by Michael Porter's definition of healthcare value in http://www.nejm.org/doi/full/10.1056/NEJMp1011024?viewType=Print& The reason for choosing a definition firmly related to real world impact was to ensure that our focus was on real world benefits rather than outputs or process issues like scientific validity and relevance. This allowed a diverse group of funders, from across the world, with different political, social and scientific contexts, from pre-clinical and early phases to health service research, to align under the idea that we are all interested in delivering benefits to society rather than just good science. As well as creating a sense of alliance, to be candid, this prevented us from discussing different views and definitions of research impact, and meant we could focus on the task at hand, which was to develop useful guidance to change funder practices. That said, the reviewer's points are entirely correct, which is why we structured our framework (figure 3) under the headings of relevance, quality (akin to validity), and openness. It could be interpreted that we were saying value = (relevance x quality x openness) / costs, which aligns with the reviewer's thinking. We did not articulate it that way in the agreed version, so while we don't disagree with the reviewer, it would not be appropriate to change the text now. Comment 4. We agree, and the manuscript has been updated. Comment 5. We agree with this point. Unfortunately, the journal prevented us from including further details on why each guiding principle is important and some practical examples of how to delivery them because we had already placed this material on our website. We can not add this to the paper but the reviewer may be reassured that we agree and have included this on our website - Applying the principles - EViR" } ] } ]	1	https://f1000research.com/articles/12-310
https://f1000research.com/articles/12-145/v1	08 Feb 23	{ "type": "Research Article", "title": "Analysis of the effect of wind speed in increasing the COVID-19 cases in Jakarta", "authors": [ "Dewi Susanna", "Yoerdy Agusmal Saputra", "Sandeep Poddar", "Yoerdy Agusmal Saputra", "Sandeep Poddar" ], "abstract": "Background: COVID-19 remains a public health problem around the world. It is possible the climate could affect the transmission of COVID-19. Wind is one of the climate factors besides temperature, humidity, and rainfall. This study aimed to describe spatial patterns and find the correlation of wind speed (maximum and average) with the pattern of COVID-19 cases in Jakarta, Indonesia. Methods: The design of this study was an ecological study based on time and place to integrate geographic information systems and tested using statistical techniques. The data used were wind speed and weekly COVID-19 cases from March to September 2020. These records were obtained from the special coronavirus website of Jakarta Provincial Health Office and the Indonesian Meteorology, Climatology and Geophysics Agency. The data were analyzed by correlation, graphic/time trend, and spatial analysis. Results: The wind speed (maximum and mean) from March to September 2020 tended to fluctuate between 1.43 and 6.07 m/s. The correlation test results between the average wind speed and COVID-19 cases in Jakarta showed a strong positive correlation (r = 0.542; p value = 0.002). Conclusions: The spatial overlay map of wind speed (maximum and mean) with COVID-19 cases showed that villages with high wind speeds, especially coastal areas, tended to show an earlier increase in cases. The higher wind speed allowed an increase in the distribution of the COVID-19 virus in the air in people who did not apply health protocols properly.", "keywords": [ "COVID-19", "SAR-CoV-2", "maximum wind speed", "average wind speed", "spatial–temporal analysis" ], "content": "Introduction\n\nSeveral nations are currently experiencing a significant increase in coronavirus (COVID-19) cases, including Indonesia (https://worldometers.info/coronavirus/). A total of 34,874,744 confirmed cases with 1,097,497 deaths (case fatality rate (CFR) 3.1%) were reported in 216 countries based on data from the World Health Organization (https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200831-weekly-epi-update-3.pdf?sfvrsn=d7032a2a_4). In Indonesia, the number of people who have been infected and the number who have died are approximately 287,008 and 10,740 (CFR 3.7%), respectively, with the most predominant regions being Jakarta (73,700), East Java (43,536), and Central Java (22,440) (https://covid19.go.id/peta-sebaran).\n\nBased on various studies worldwide, the SARS-CoV-2 virus that is responsible for COVID-19 is described as highly contagious. Saliva droplets produced by asymptomatic carriers appear to be the possible transmission media. In addition, specific observations using highly sensitive laser beams indicated that loud speech tends to emit countless droplets of oral fluid per second. In a closed and stagnant air environment, the drops finally disappear from the viewing window within the range of eight to14 minutes. Based on these findings, regular speech shows a high probability of transmitting the airborne virus in confined spaces.1 Therefore, aerosol transfer appears to be the most significant method of SARS-CoV-2 spread compared with other media.1–3 Furthermore, recent studies have shown that the virus remains active in airborne particles beyond three hours.4,5\n\nAlthough related studies are minimal, the wind is perceived as a critical climatic factor for virus transmission.6 Previous research studied four meteorological parameters (temperature, dew point, humidity, and wind speed). The number of coronavirus cases in Turkey demonstrated the function of wind speed in promoting the spread. The parameter with the highest correlation was generated by wind speed in 14 days and therefore showed that extensive wind speeds led to increased virus cases.7\n\nConversely, higher wind speeds in external settings contribute to dilution and droplet removal, resulting in a decline in airborne concentration (https://apps.who.int/iris/bitstream/handle/10665/70863/WHO_CDS_CSR_GAR_2003.11_eng.pdf?sequence=1&isAllowed=y).8 Previous research from Brazil that examined the association between weather and COVID-19 spread in tropical climates countries showed that wind speed was negatively correlated (p < 0.01). Therefore, the variable also serves as a potential consideration in suppressing disease transmission.9\n\nBased on the description above, it can be assumed that wind speed is a major influencing factor of COVID-19 spread. Therefore, it was crucial to comprehend the effects of wind speed on the virus, as Jakarta appeared to be the pandemic's epicenter. Consequently, this research successfully investigated the relationship between wind speed and the weekly occurrence of COVID-19 in the Special Capital Region of Jakarta.\n\n\nMethods\n\nA step by step description of the protocols can be obtained at: dx.doi.org/10.17504/protocols.io.ewov1odzylr2/v1\n\nA quantitative method was applied with an ecological design that provides real-time and location analysis, using geographic information systems and the data were tested using statistical techniques.\n\nThe secondary data comprised daily reports of COVID-19 infection and wind speed (maximum and mean) in Jakarta from the pandemic inception, specifically between March and September 2020. These records were obtained from the website of the Jakarta Provincial Health Office (https://corona.jakarta.go.id/id/data-pemantauan) and the website of the Indonesian Meteorology, Climatology and Geophysics Agency (https://dataonline.bmkg.go.id/akses_data). Subsequently, the general information was converted into 31-weeks documentation. Furthermore, a basic map of Jakarta with neighboring community boundaries was obtained using the GADM Map and Data site (https://gadm.org/maps/IDN/jakartaraya.html). Coordinates for the weather monitoring stations were accessed online (https://www.gps-latitude-longitude.com/). The Jakarta province comprising 261 urban villages served as the research location.\n\nUnivariate analysis was conducted to determine individual variable distribution, including maximum and average wind speed (m/s), as well as the number of COVID-19 cases. This process is descriptive and quantitative, where the data exist in statistical distribution tables, line graphs, and thematic maps based on the research objectives. Subsequently, the bivariate analysis involved Pearson's product-moment correlation test to evaluate the relationship between independent (wind speed factor) and dependent variables (COVID-19). Specifically, the method stated the possible existence (p < 0.05), closeness (r), and direction of the relationship. In addition, the strengths of the association were qualitatively divided into four categories, where r = 0.00–0.25 was absence/weak relationship, r = 0.26–0.50 was moderate, r = 0.51–0.75 was strong and r = 0.76–1.00 was very strong/perfect.(10) The correlation value also determined the direction of the relationship as a positive (+) or negative (−) pattern. This value (r) was evaluated by the conditions, where r = 0 was no linear relationship, r = −1 was perfect negative linear and r = 1 was perfect positive linear.10 Furthermore, the univariate and bivariate analyses were conducted at the Computer Laboratory using SPSS 21 software (RRID:SCR_002865).\n\nSpatial analysis was performed to observe the relationship pattern between the two variables. Based on a selected community, an interpolation process was employed to create an overlay map of COVID-19 cases and climate parameters. The Jakarta grid map interpolation was used to estimate the magnitude of climate variables outside the measurement points (weather stations) by applying the following steps. Firstly, a grid map of five weather monitoring stations was created. The interpolation was performed by entering the point values or coordinate attribute data (longitude and latitude) into the climate variable attribute table. The coordinate points were joined in the climate variable map. Secondly, the independent variable vector data were digitized by inputting the spatial data on climate variables into a base map, then processing and selecting a color symbol (singleband pseudocolor) with color ramp blues. Consequently, a digital category of high and low climate variables was formed depending on the data magnitude. Thirdly, the dependent variable vector data were digitized by entering spatial data on COVID-19 rates into the base map, depending on the community, followed by processing and selecting a point symbol (centroid). A digital category of large and small cases was generated based on the disease data. Fourthly, the two vector maps were interpolated with the plugin interpolation menu. Therefore, an interpolated raster plot was obtained and used to analyze or predict the climate variable values in each community. The resulting color gradations and point symbols did not show any ratio but only reported ordinal values, including high-low climate variations and number of virus cases. This color gradation ranged from dark blue to white, indicating high to low wind speeds (maximum and mean). Subsequently, the colors were created digitally using a singleband pseudocolor with ramp blues colors from Quantum Geographic Information System (QGIS) software (RRID:SCR_018507) with a natural grouping of five classes, where very dark blue = very high, dark blue = high, blue = medium, light blue = and white = very low. The dot symbol (centroid) varied from large to small, representing the virus spread. Similarly, the point symbol size was digitally generated using a simple marker or a standard symbol from the QGIS software with a linear classification between 0 and 17.\n\nThe spatially analyzed data were further processed with overlayed thematic graphics and maps to show the relationship pattern based on time and location. The spatial analysis was associated with the statistical correlation results generated using the QGIS software version 3.0 at the Computer Laboratory of the Faculty of Public Health, University of Indonesia.\n\n\nResults\n\nThe wind speed (maximum and mean) from March to September 2020 tended to fluctuate between 1.43 and 6.07 m/s. This variable appeared minimal during the last week of each month (fourth, fifth, fourth, fourth, and fifth weeks of March, April, May, June, and July, respectively). However, it showed a higher performance in the middle of each month (second, second, second, third, third, and third weeks of March, May, June, July, August, and September, respectively).\n\nFurthermore, the maximum and minimum wind speed values of 6.07 and 4.5m/s occurred during the first, ninth, and 15th weeks, respectively. Meanwhile, the optimal and minimum average wind speeds of 2.75 and 1.43 m/s were obtained in the 29th and fourth weeks, respectively.\n\nThe Pearson product-moment correlation test was applied in the statistical analysis of the relationship to show the occurrence (p < 0.05), direction (positive/direct or negative/opposite), and closeness (r). The Jakarta data from March to September 2020 were processed. The correlation test results between the average wind speed and COVID-19 cases showed a strong relationship strength and a positive pattern (p = 0.002, r = 0.542). These conditions indicated that higher average wind speeds increased the possibility of COVID-19 occurrence. However, no significant relationship existed between the maximum wind speed and the virus occurrence.\n\nFigure 1 shows that wind speeds possibly generated a pattern similar to the COVID-19 cases. The reverse form of the maximum wind speed with COVID-19 cases occurred in the second to fourth, eighth, 15th, 17th, 19th, 22nd, 23rd, 27th, 28th, 30th, and 31st weeks, while for average wind speed, the pattern was observed at weeks three, four, seven, nine, 13, 14, 16, 17, 19–22 and 27–29.\n\nThe spatial analysis was created by overlaying a map of COVID-19 cases with a plot of the sunlight duration to obtain the interpolation from the weather monitoring stations. Color gradations and dot symbols represent this interval and the virus occurrence. In addition, the interpolated values were used to predict a relationship between sunlight duration and COVID-19 in each village around the research location.\n\nApart from generating a high-low comparison of sun exposure to the number of COVID-19 cases, the virus transmission pattern from March to September 2020 was also ascertained. There were incomplete data, including the records per village, that commenced from March 25, 2020. This circumstance tended to influence the distribution pattern in March, causing a uniform condition to be a low category.\n\nIn each month, the spatial pattern of maximum wind speed tended to fluctuate, including the maximum high wind speed dominating the central and northern parts of the capital city in the first two months (March and April). Subsequently, the flow expanded to the northeast and northwest regions, comprising Tanjung Priok, Koja, Kebon Bawang, Lagoa, Kali Baru, North Rawabadak, South Rawabadak, Warakas, Papanggo, North Tugu, West Semper, Cilincing, and East Semper communities. The maximum moderate wind speed consistently occurred in the southeastern part that included most of the urban villages in East Jakarta. In contrast, low maximum wind speeds were reported in the southwest part relating to the urban villages in South Jakarta.\n\nBased on the spatial map overlaying the maximum wind speed and COVID-19 cases, urban villages with high maximum wind speeds tended to demonstrate faster virus transmission than areas with moderate and low maximum wind speeds. A relatively high spike in cases in July circulated across the villages of Lagoa (101) and Kebon Bawang (10), and in August at Lagoa (144), Cilincing (131), South Rawabadak (105), and West Semper (109), compared with other neighboring villages. However, a small number of villages with moderate and low maximum wind speeds also showed an increase in July at West Cempaka Putih (101), and in August at Johar Baru village (127), and West Cempaka Putih (106), as illustrated in Figure 2.\n\nThe spatial pattern of the average wind speed in each month appeared relatively similar, including the high average wind speed dominating the northeast and northwest regions of the city. This area covered Kebon Bawang, Tanjung Priok, Koja, Lagoa, Kali Baru, North Rawabadak, South Rawabadak, Warakas, Papanggo, North Tugu, West Semper, Cilincing, Kramat, Tegal Alur, Pengadungan, Kali Deres, and Samanan. Furthermore, the average wind speed consistently occurred in the areas with high and low average wind speed convergence, including Kapuk Muara, Kapuk, Rawa Buaya, Duri Kosambi, Sunter Agung, Sunter Jaya, West Kelapa Gading, East Kelapa Gading, and Pegangsaan Dua. The low average wind speeds also remained constant in the central and southern parts, including central, south, and east Jakarta.\n\nBased on the spatial overlay map of the average wind speed and COVID-19 cases, villages with high average wind speeds experienced an increase of cases faster compared with areas with medium and low average wind speeds. A relatively high spike also occurred in July at Kebon Bawang (101) and Lagoa (101), and in August at Lagoa (144), Cilincing (131), West Semper (109), and South Rawabadak (105), compared with other adjacent villages. However, a smaller number of villages with medium and low average wind speeds also showed an increase in July at West Cempaka Putih (101), and in August at West Pademangan (158), Johar Baru (127), and West Cempaka Putih (106), as represented in Figure 3.\n\n\nDiscussion\n\nBased on the correlation analysis between the average wind speed and COVID-19 cases in Jakarta, a significant correction between strong and unidirectional associations was reported, indicating that higher average wind speeds accelerated the virus transmission. This outcome matched several previous studies,7,11–16 where the wind speed was also known to increase the airborne SARS-CoV-2 spread.12 Droplets released during normal speech tend to survive in the air between eight and 14 minutes, similar to confined environments.1 Recent studies have also shown that the virus can remain infectious in airborne particles beyond three hours.4,5 Therefore, aerosol transmission appears to be the main channel, compared with other media.1–3 Under these circumstances, the wind speed variable plays a significant role in promoting the spread,7 and with wind speeds in Jakarta ranging from 1.43 to 6.07 m/s, the surviving airborne virus quickly spreads.12\n\nIn this context, higher wind speeds adversely impact individuals who do not correctly apply health protocols (avoiding crowds, not keeping close distances, and not wearing/removing masks).7 Therefore, the transmission of impure cases is influenced by the rate of wind speed spreading the virus. Furthermore, government policies also play an essential role in influencing the disease rates, in the form of implementing health protocols (washing hands,17 wearing masks,17 physical distancing18), staying at home,19 working from home,20,21 and large-scale social restrictions/enforcement of restrictions on community activities (Pembatasan Sosial Berskala Besar/Pemberlakuan Pembatasan Kegiatan Masyarakat).22–24\n\nBased on a weekly graphical analysis of Jakarta, the fluctuations in wind speed tended towards the pattern of COVID-19 cases. The variable results were also consistent with similar outcomes of the correlation test in Jakarta, indicating a significant relationship with strong and positive patterns. This also indicated that higher average wind speeds triggered extensive COVID-19 spread.\n\nThe spatial relationship between wind speed and COVID-19 cases in Jakarta from March to September 2020 showed that urban villages that had high wind speeds tended to experience a faster transmission than other areas with medium and low values. However, a smaller number of villages with moderate and low wind speeds also showed increased cases. This result was possibly influenced by determining the source location of the COVID-19 cases using the domicile/residential address in the last 14 days, despite the possible occurrence of the infection while conducting external activities. Therefore, the spatial pattern of COVID-19 cases in Jakarta did not match the actual spatial pattern from the infection origin.25 In addition, other factors, including community non-compliance in implementing health protocols and Pembatasan Sosial Berskala Besar (PSBB) or large-scale social restrictions policies, led to transmissions outside the home (https://www.liputan6.com/news/read/4368373/survei-bps-55-persen-masyarakattak-patuhi-protokol-kesehatan-karena-tidak-ada-sanksi). The previous survey proved that approximately 26.46% of the community did not correctly implement health protocols outside the home (https://www.bps.go.id/publication/2020/09/28/f376dc33cfcdeec4a514f09c/perilaku-masyarakat-di-masa-pandemi-covid-19.html). Therefore, strict health protocols (washing hands, wearing masks, physical distancing), implementation of maximum capacity, and operating hours rules in places with open-air conditions and crowds, particularly tourist attractions in areas with high wind speeds, including coastal areas, are among several considerations for policymakers.\n\nThe majority of the previous studies employed case and wind speed data on similar days, although the reporting record did not represent the infection date, as the symptoms typically manifested after days of transmission. The time required for tracking and testing was equally essential, causing difficulty in determining the actual infection date. Therefore, to minimize possible bias, daily case and wind speed data were converted to a weekly form, based on a mean incubation period (symptom appearance) of between five and six days, with a maximum of 14 days.25\n\nThis study is expected to consider certain limitations that may have influenced the overall results. No analysis was conducted using time lags, and, therefore, it was not possible to determine the most significant relationship between the wind speed and the COVID-19 case variables between week one (t) and subsequent intervals ((t+1), (t+2), and so on). In addition, the unavailability of variable data in smaller regions, neighborhood/community associations (Rukun Tetangga/Rukun Warga), produced indefinite distribution patterns. However, other risk factors, including population size, density, mobility and immunity, community behavior (washing hands, wearing masks, and physical distancing), and the nature of the virus were not included in this research. In addition, the limited period of data collection (seven months) possibly influenced the analysis. Furthermore, a comparative analysis of the relationship between wind speed variables and case variables was performed per week, every 14 days, and monthly, indicating that the time frames were closely related. Therefore, further studies are expected to consider the abovementioned factors and generate significant improvements. Low wind speeds are associated with a high concentration of air pollutants, and therefore may promote a longer permanence of viral particles in polluted air of cities, thus favoring an indirect means of diffusion of the novel coronavirus (SARS-CoV-2).26 Since this research did not include concentration of pollutants, therefore, it is suggested that future research should involve pollution levels in the area of the study to achieve comprehensive results.\n\n\nConclusions\n\nBased on the overall results, environments with high average wind speeds tend to demonstrate an increased number of COVID-19 cases, particularly in coastal regions. This factor also accelerates airborne SARS-CoV-2 spread among people that do not correctly apply the prescribed health protocols. Therefore, the impure cases are triggered by the rate of the wind-speed-based transmission. Consequently, strict health protocols (washing hands, wearing masks, physical distancing), applying maximum capacity, and regulating work hours in places with open-air conditions and crowd potentials, especially tourist attractions in areas with high wind speeds, including coastal regions, serve as a basis for consideration in policymaking.\n\n\nEthical approval\n\nThis research was approved by the Research and Community Engagement Ethical Committee, Faculty of Public Health, Universitas Indonesia, No. 210/UN2.F10. D11/PPM.00.02/2021.", "appendix": "Data availability\n\nDryad. Wind Speed Data. https://doi:10.5061/dryad.41ns1rnj9 27\n\nThis project contains the following underlying data:\n\n- Wind_speed_data1.csv\n\n- README_wind_sd.md\n\nSpecial Capital Region of Jakarta Provincial Health Office COVID-19. https://corona.jakarta.go.id/id/data-pemantauan 28\n\n- Data on Covid-19 cases\n\nMeteorology, Climatology, and Geophysics Agency. https://dataonline.bmkg.go.id/akses_data 29\n\n- Wind speed data\n\nGADM Map and Data. https://gadm.org/maps/IDN/jakartaraya.html 30\n\n- The base map for the Special Capital Region of Jakarta\n\nLongitude and Latitude/GPS coordinates. https://www.gps-latitude-longitude.com/ 31\n\n- Coordinates of the weather monitoring station\n\n\nAcknowledgments\n\nThe authors are grateful to the Directorate Research and Development Universitas Indonesia through PUTI Grant for financial support.\n\n\nReferences\n\nStadnytskyi V, Bax CE, Bax A, et al.: The airborne lifetime of small speech droplets and their potential importance in SARS-CoV-2 transmission. Proc. Natl. Acad. Sci. U. S. A. 2020 Jun 2 [cited 2021 Jul 22]; 117(22): 11875–11877. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMorawska L, Milton DK: It Is Time to Address Airborne Transmission of Coronavirus Disease 2019 (COVID-19). Clin. Infect. Dis. 2020 Nov 1 [cited 2021 Jul 22]; 71(9): 2311–2313. PubMed Abstract \| Publisher Full Text\n\nZhang R, Li Y, Zhang AL, et al.: Identifying airborne transmission as the dominant route for the spread of COVID-19. Proc. Natl. Acad. Sci. U. S. A. 2020 Jun 30 [cited 2021 Jul 22]; 117(26): 14857–14863. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVan Doremalen N, Bushmaker T, Morris DH, et al.: Aerosol and Surface Stability of SARS-CoV-2 as Compared with SARS-CoV-1. N. Engl. J. Med. 2020 Apr 16; 382(16): 1564–1567. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSmither SJ, Eastaugh LS, Findlay JS, et al.: Experimental aerosol survival of SARS-CoV-2 in artificial saliva and tissue culture media at medium and high humidity.2020 Jun 4 [cited 2021 Jul 22]; 9(1): 1415–1417. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShe J, Jiang J, Ye L, et al.: 2019 novel coronavirus of pneumonia in Wuhan, China: Emerging attack and management strategies. Clin. Transl. Med. 2020 Jan 20 [cited 2020 Aug 5]; 9(1): 19. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nŞahin M: Impact of weather on COVID-19 pandemic in Turkey. Sci. Total Environ. 2020 Aug 1 [cited 2020 Jul 29]; 728: 138810. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nCai QC, Lu J, Xu QF, et al.: Influence of Meteorological Factors and Air Pollution on The Outbreak of Severe Acute Respiratory Syndrome. Public Health. 2007 Apr 1 [cited 2020 Aug 5]; 121(4): 258–265. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nRosario DKA, Mutz YS, Bernardes PC, et al.: Relationship between COVID-19 and weather: Case study in a tropical country. Int. J. Hyg. Environ. Health. 2020 Aug 1 [cited 2020 Jul 29]; 229: 113587. Publisher Full Text Reference Source\n\nHastono SP: Statistik Kesehatan. Jakarta:Rajawali Pers;2011.\n\nCoşkun H, Yıldırım N, Gündüz S: The Spread of COVID-19 Virus Through Population Density and Wind in Turkey Cities. Sci. Total Environ. 2021 Jan 10 [cited 2021 Apr 25]; 751: 141663. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nSarkodie SA, Owusu PA: Impact of meteorological factors on COVID-19 pandemic: Evidence from top 20 countries with confirmed cases. Environ. Res. 2020 Dec 1 [cited 2021 Aug 16]; 191: 110101–110107. Publisher Full Text Reference Source\n\nHassan MS, Bhuiyan MAH, Tareq F, et al.: Relationship between COVID-19 infection rates and air pollution, geo-meteorological, and social parameters. Environ. Monit. Assess. 2021 Jan 1 [cited 2021 Aug 17]; 193(1): 1–20. Publisher Full Text Reference Source\n\nArefin MA, Nabi MN, Islam MT, et al.: Influences of weather-related parameters on the spread of Covid-19 pandemic – The scenario of Bangladesh. Urban Clim. 2021 Jul 1 [cited 2021 Aug 16]; 38: 100903–100914. Publisher Full Text Reference Source\n\nSangkham S, Thongtip S, Vongruang P: Influence of air pollution and meteorological factors on the spread of COVID-19 in the Bangkok Metropolitan Region and air quality during the outbreak. Environ. Res. 2021 Jun 1 [cited 2021 Aug 16]; 197: 111104–11. Publisher Full Text \| Free Full Text\n\nHridoy A-EE, Mohiman MA, Tusher SMSH, et al.: Impact of meteorological parameters on COVID-19 transmission in Bangladesh: a spatiotemporal approach. Theor. Appl. Climatol. 2021 Feb 3 [cited 2021 Aug 16]; 144(1): 273–285. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChen X, Ran L, Liu Q, et al.: Hand Hygiene, Mask-Wearing Behaviors and Its Associated Factors During The COVID-19 Epidemic: A Cross-Sectional Study Among Primary School Students in Wuhan, China. Int. J. Environ. Res. Public Health. 2020; 17(8). Publisher Full Text\n\nMacIntyre CR: Case Isolation, Contact Tracing, and Physical Distancing are Pillars of COVID-19 Pandemic Control, Not Optional Choices. Lancet Infect. Dis. 2020 Jun 16 [cited 2020 Aug 11]; 20: 1105–1106. Publisher Full Text\n\nFowler JH, Hill SJ, Levin R, et al.: Stay-at-home orders associate with subsequent decreases in COVID-19 cases and fatalities in the United States. PLoS One. 2021 Jun 1 [cited 2021 Sep 9]; 16(6): e0248849–e0248815. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChiba A: The effectiveness of mobility control, shortening of restaurants’ opening hours, and working from home on control of COVID-19 spread in Japan. Health Place. 2021 Jul 1 [cited 2021 Sep 10]; 70(102622): 102614–102622. Publisher Full Text Reference Source\n\nOkuyan CB, Begen MA: Working from home during the COVID-19 pandemic, its effects on health, and recommendations: The pandemic and beyond. Perspect. Psychiatr. Care. 2021 May 18 [cited 2021 Sep 10]; 58: 173–179. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDaghriri T, Ozmen O: Quantifying the effects of social distancing on the spread of COVID-19. Int. J. Environ. Res. Public Health. 2021 May 23 [cited 2021 Sep 10]; 18(11): 1–17. Publisher Full Text Reference Source\n\nWellenius GA, Vispute S, Espinosa V, et al.: Impacts of social distancing policies on mobility and COVID-19 case growth in the US. Nat. Commun. 2021 May 25 [cited 2021 Sep 10]; 12(1): 1–7. Publisher Full Text Reference Source\n\nYogadhita GY, Donna B, Ariani M, et al.: Dampak pembatasan sosial berskala besar di komunitas terhadap kunjungan pasien COVID-19 di rumah sakit. J Kebijak Kesehat Indones JKKI. 2021 Mar 31 [cited 2021 Sep 10]; 10(1): 8–16.Reference Source\n\nKementerian Kesehatan Republik Indonesia:Pedoman pencegahan dan pengendalian coronavirus disease (COVID-19).Aziza L, Aqmarina A, Ihsan M, editors. Kementerian Kesehatan RI. Jakarta:Kementerian Kesehatan RI; 5th ed.2020. 1–214 p.Reference Source\n\nCoccia M: How do low wind speeds and high levels of air pollution support the spread of COVID-19? Atmos. Pollut. Res. 2021; 12(1): 437–445. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDryad: Wind Speed Data.Publisher Full Text\n\nSpecial Capital Region of Jakarta Provincial Health Office COVID-19. http\n\nMeteorology, Climatology, and Geophysics Agency.Reference Source\n\nGADM Map and Data.Reference Source\n\nLongitude and Latitude/GPS coordinates. http" }	[ { "id": "164423", "date": "24 Mar 2023", "name": "Edmund I. Yamba", "expertise": [ "Reviewer Expertise Main research area is Biometeorology and Bioclimatology with current focus on weather and climate driven infectious diseases", "extreme heat and human health", "air pollution and respiratory infections", "weather and climate extreme impacts", "tropical climate variability", "climate modelling and Urban Heat Island (UHI) warming" ], "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 study, the authors examined the effect of wind speed on COVID-19 outcome in Jakarta, Indonesia. Using maximum and mean wind speed data from the Indonesian Meteorology, Climatology and Geophysics Agency; and weekly COVID-19 cases from the special coronavirus website of Jakarta Provincial Health Office, they established the link between wind speed and COVID-19 cases via correlation, graphic/time trend, and spatial analysis. Their results showed that high wind speeds were associated with an increased number of COVID-19 cases, particularly in coastal regions. Hence, the authors concluded that wind speed plays a role in the transmission of COVID-19, especially the coastal areas of Jakarta.\nThis study is significant and offers valuable insights into the relationship between wind speed and the transmission of the COVID-19 virus in Jakarta. The findings have practical implications for the implementation of health protocols in areas with high wind speed to mitigate the spread of the virus. The presentation of the study is clear, engaging and comprehensible. Nonetheless, the manuscript requires revision to enhance its quality. Below are my comments regarding areas that need improvement.\n1. The title vs the content presented: Based on my interpretation, it appears that the authors seek to establish the association between wind speed and COVID-19 cases in Jakarta, without delving into causality, as evidenced by their utilization of Pearson's correlation analysis. The use of the term \"effect\" in the title implies a notion of causality. Nevertheless, the research work put forth does not explicitly establish causality, but rather investigates the existence of a relationship through inferences. It is recommended that the authors reconsider the phrasing of the title to reflect the content of their study. For example, something like “The relationship between wind speed and COVID-19 infections in Jakarta”.\n2. Introduction/novelty: Despite the work's overall satisfactory and engaging presentation, the authors have not explicitly addressed the existing research gaps and their contributions to filling them. Previous studies have established the relationship between wind speed and the spread of COVID-19, which raises questions about the motivation behind the authors' replication of this work in Jakarta. Specifically, what were the compelling research questions that drove this inquiry and how were they answered? Hence, the originality or novelty of the work appears to be limited, and the authors should strive to enhance it. One suggestion for improvement could be to extend beyond the typical approach of establishing correlations between weather variables and COVID-19, which is prevalent in most existing literature. Merely identifying a correlation between two variables is insufficient to determine the causative relationship between them. Therefore, panel estimation techniques, for example, could be explored by the authors to investigate the causal aspect further.\n3. Data collection: The authors conducted a study that involved the collection of daily wind speed and COVID-19 case data spanning March to September 2020, which was then converted into weekly data for 31 weeks. The rationale for the conversion remains unclear, and it would be beneficial if the authors could elucidate their reasons for doing so and how this approach facilitated more effective analysis. Additionally, it is essential to understand how gaps in the data were managed as the quality of the data used is fundamental to the reliability of the results obtained. The authors reported that the study was conducted in Jakarta province, consisting of 261 urban villages. However, it is not evident whether the data used were obtained from each of these villages and aggregated for the province. If this was the case, it would be useful to know whether data were available for each village. It is recommended that the authors provide more comprehensive details regarding the availability and quality of the data used in their analysis to enhance the reliability of their findings.\n4. Statistical data analysis: The authors employed Pearson's product-moment correlation test to assess the association between wind speed (independent variable) and COVID-19 cases (dependent variable). However, it is important to note that Pearson's correlation test necessitates the use of normally distributed data. As the daily COVID-19 and wind speed data were not normally distributed, the utilization of Pearson's approach may prove problematic. Therefore, it is imperative that the authors examine the normality of the daily or weekly data used to inform their selection of the appropriate correlation test. In this context, Spearman's correlation test may be suitable since it does not rely on the approximate normality of the data. Furthermore, the authors categorized the strengths of the correlation between wind speed and COVID-19 into four groups: absence/weak relationship (r = 0.00–0.25), moderate (r = 0.26–0.50), strong (r = 0.51–0.75), and very strong/perfect (r = 0.76–1.00). It is necessary to elucidate the scientific rationale for this division and the guidelines employed. This will enhance the clarity and reliability of the authors' findings and recommendations.\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": [ { "c_id": "9715", "date": "29 Nov 2023", "name": "Dewi Susanna", "role": "Author Response", "response": "Dear Dr. Edmund I. Yamba Department of Meteorology and Climate Science, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana Thank you very much for the valuable comments. Here, we tried to respond your comments as follow: The title vs the content presented: Based on your interpretation, it appears that the authors seek to establish the association between wind speed and COVID-19 cases in Jakarta, without delving into causality, as evidenced by their utilization of Pearson's correlation analysis. The use of the term \"effect\" in the title implies a notion of causality. Nevertheless, the research work put forth does not explicitly establish causality, but rather investigates the existence of a relationship through inferences. It is recommended that the authors reconsider the phrasing of the title to reflect the content of their study. For example, something like “The relationship between wind speed and COVID-19 infections in Jakarta”. Response: Thank you for the proper title. The title of the article has been revised to \"The relationship between wind speed and COVID-19 infections in Jakarta\" Introduction/novelty: Despite the work's overall satisfactory and engaging presentation, the authors have not explicitly addressed the existing research gaps and their contributions to filling them. Previous studies have established the relationship between wind speed and the spread of COVID-19, which raises questions about the motivation behind the authors' replication of this work in Jakarta. Specifically, what were the compelling research questions that drove this inquiry and how were they answered? Hence, the originality or novelty of the work appears to be limited, and the authors should strive to enhance it. One suggestion for improvement could be to extend beyond the typical approach of establishing correlations between weather variables and COVID-19, which is prevalent in most existing literature. Merely identifying a correlation between two variables is insufficient to determine the causative relationship between them. Therefore, panel estimation techniques, for example, could be explored by the authors to investigate the causal aspect further. Responses: The previous research gaps and the researcher's contribution in filling the previous research gaps (novelty) have been added in the introduction section: “In several countries, researchers have found that high wind speeds play a role in the increase of COVID-19 cases.7–12 This is because SARS-CoV-2 can survive in the air, so wind speeds accelerate the spread of the virus by carrying droplets to various destinations.7 In the internal environment, higher wind speeds decrease the viral load indoors, which can prevent SARS outbreaks.14 Other researchers have found that high wind speeds can actually suppress the spread of COVID-19 cases.15–17 This study considers some of the limitations of previous studies by examining the potential of wind speed in influencing the spread of cases based on regional characteristics7,9–12,15,17 because environmental conditions between regions are different.18 In addition, daily COVID-19 case data were converted into weekly cases to adjust for the incubation period of COVID-19 (5-6 days) and the uncertain time interval between the first day of infection and the day of sampling.19 As well as the potential spread of cases based on regional characteristics in DKI Jakarta, especially in coastal areas”. Data collection: The authors conducted a study that involved the collection of daily wind speed and COVID-19 case data spanning March to September 2020, which was then converted into weekly data for 31 weeks. The rationale for the conversion remains unclear, and it would be beneficial if the authors could elucidate their reasons for doing so and how this approach facilitated more effective analysis. Additionally, it is essential to understand how gaps in the data were managed as the quality of the data used is fundamental to the reliability of the results obtained. The authors reported that the study was conducted in Jakarta province, consisting of 261 urban villages. However, it is not evident whether the data used were obtained from each of these villages and aggregated for the province. If this was the case, it would be useful to know whether data were available for each village. It is recommended that the authors provide more comprehensive details regarding the availability and quality of the data used in their analysis to enhance the reliability of their findings. Responses: The reason for converting daily covid-19 case data into weekly covid-19 case data has been added to the data collection section: The conversion of daily cases to weekly cases is related to several considerations, such as the incubation period of COVID-19, which lasts for 5–6 days on average, and the uncertain time interval between the first day of infection and the day of sampling.19 An explanation of how to obtain covid-19 case data in 261 villages has been adjusted in the data collection section: These data were obtained from case reports of hospitals, health centers, and laboratories recorded per urban village by the Jakarta Provincial Health Office and can be accessed on the Jakarta Provincial Health Office website (https://corona.jakarta.go.id/id/data-pemantauan) and reports of two weather monitoring stations (Kemayoran station and Tanjung Priok station) in Jakarta, which can be accessed on the website of the Meteorology, Climatology, and Geophysics Agency (https://dataonline.bmkg.go.id/akses_data). Statistical data analysis: The authors employed Pearson's product-moment correlation test to assess the association between wind speed (independent variable) and COVID-19 cases (dependent variable). However, it is important to note that Pearson's correlation test necessitates the use of normally distributed data. As the daily COVID-19 and wind speed data were not normally distributed, the utilization of Pearson's approach may prove problematic. Therefore, it is imperative that the authors examine the normality of the daily or weekly data used to inform their selection of the appropriate correlation test. In this context, Spearman's correlation test may be suitable since it does not rely on the approximate normality of the data. Furthermore, the authors categorized the strengths of the correlation between wind speed and COVID-19 into four groups: absence/weak relationship (r = 0.00–0.25), moderate (r = 0.26–0.50), strong (r = 0.51–0.75), and very strong/perfect (r = 0.76–1.00). It is necessary to elucidate the scientific rationale for this division and the guidelines employed. This will enhance the clarity and reliability of the authors' findings and recommendations. Responses: An explanation of the use of the pearson-product moment test has been added to the statistical data analysis section: Before the correlation test is applied, the data normality test is conducted first. The results of the normality analysis show that the maximum wind speed variable is normally distributed, while the average wind speed and COVID-19 cases are not normally distributed. From these results, variables that are not normally distributed are then transformed by the square root (x) to obtain normality. This step is taken to fulfil the requirements for multiple linear regression analysis (normality assumption). The source of the correlation strength categorization has been provided and the reason for categorizing the correlation strength has been added: In addition, the strengths of the association were qualitatively divided into four categories, where r = 0.00–0.25 was absence/weak relationship, r = 0.26–0.50 was moderate, r = 0.51–0.75 was strong and r = 0.76–1.00 was very strong/perfect.20 This categorization aims to determine how strongly the independent variables (maximum wind speed and average wind speed) correlate with the dependent variable (COVID-19 cases). It is also used to discuss the results of the analysis in the discussion section. Thank you for all the input so this article became more comprehensives and understandable for the readers." } ] } ]	1	https://f1000research.com/articles/12-145
https://f1000research.com/articles/12-1578/v2	28 Dec 23	{ "type": "Data Note", "title": "A guide to selecting high-performing antibodies for Rab1A and Rab1B for use in Western Blot, immunoprecipitation and immunofluorescence", "authors": [ "Vera Ruíz Moleón", "Maryam Fotouhi", "Riham Ayoubi", "Sara González Bolívar", "Kathleen Southern", "Peter S. McPherson", "Carl Laflamme", "NeuroSGC/YCharOS/EDDU collaborative group", "ABIF consortium", "Vera Ruíz Moleón", "Maryam Fotouhi", "Riham Ayoubi", "Sara González Bolívar", "Kathleen Southern", "Peter S. McPherson" ], "abstract": "Rab1 is a highly conserved small GTPase that exists in humans as two isoforms: Rab1A and Rab1B, sharing 92% sequence identity. These proteins regulate vesicle trafficking between the endoplasmic reticulum (ER) and Golgi and within the Golgi stacks. Rab1A and Rab1B may be oncogenes, as they are frequently dysregulated in various human cancers. Moreover, they contribute to the progression of Parkinson’s disease. The availability of high-quality antibodies specific for Rab1A or Rab1B is essential to understand the distinct functions of these Rab1 proteins in both health and diseaseand to enhance the reproducibility of research involving these proteins. In this study, we characterized seven antibodies targeting Rab1A and five antibodies targeting Rab1B for Western Blot, immunoprecipitation, and immunofluorescence using a standardized experimental protocol based on comparing read-outs in knockout cell lines and isogenic parental controls. These studies are part of a much larger, collaborative initiative seeking to address the antibody reproducibility issue by characterizing commercially available antibodies for human proteins and publishing the results openly as a valuable resource for the scientific community. While uses of antibodies and protocols vary between laboratories, we encourage readers to use this report as a guide to select the most appropriate antibodies for their specific needs.", "keywords": [ "Uniprot ID P62820 (Rab1A) and Q9H0U4 (Rab1B)", "RAB1A and RAB1B", "Rab1A and Rab1B", "antibody characterization", "antibody validation", "Western Blot", "immunoprecipitation", "immunofluorescence" ], "content": "Introduction\n\nMultiple steps in membrane trafficking are coordinated by Rab proteins, a family of small guanosine triphosphatases (GTPase).1 Rab GTPases undergo a dynamic cycle, alternating between an active GTP-bound state, catalyzed by guanine exchange factors (GEF), and an inactive GDP-bound state, achieved through GTP hydrolysis, stimulated by a GTPase-activating protein (GAP).1–3 When activated, Rab proteins partake in crosstalk through shared effector proteins or through Rab activators to ensure vesicle traffic is spatiotemporally regulated.1 Homologous to YTP1 in yeast, the Rab1 human proteins play key roles in regulating ER-Golgi and intra-Golgi transport. They exist as two isoforms in humans, Rab1A and Rab1B. While Rab1A and Rab1B share 92% amino acid identity, understanding their specific roles in membrane trafficking is a matter of ongoing investigation.4–6 Rab1B has been proposed to function in the initial stages of the secretory pathways, serving to assemble and disassemble machinery required for vesicle fission and fusion,4 whereas Rab1A exhibits unique functions such as its involvement in cell adhesion and migration, and plays a role in facilitating autophagosome formation, an early step in the autophagy pathway7,8\n\nElevated expression of RAB1A and RAB1B genes have implications in various cancer types, including colorectal cancer,9 hepatocellular cancer,10 gliomas,11 tongue carcinomas, prostate cancer12 for RAB1A and colorectal cancer,13 hepatocellular cancer,14 and prostate cancer12 for RAB1B. Rab1A in human cancer is highly studied in comparison to Rab1B as abnormal expression of Rab1A activates mTORC1 signalling, promoting tumour growth, invasion and ultimately cancer progression.9 Rab1 proteins are also involved in the pathogenesis of Parkinson’s disease, characterized by accumulation of α-synuclein. Inhibition of ER-Golgi traffic has been reported to trigger α-synuclein aggregation, suggesting that an increase in production of Rab1 proteins can potentially rescue this α-synuclein toxic phenotype.15 Further research is required to understand the role of Rab1A and Rab1B in various diseased states and their potential as therapeutic targets to slow the progression of cancer and neurodegeneration. In-depth mechanistic investigations would significantly benefit from the accessibility of high-performing antibodies, which can help elucidate the underlying processes and pathways involving Rab1A and Rab1B. An editorial by Biddle et al. can provide valuable insights on how to interpret the antibody characterization data found in this article.16\n\nThis research is part of a broader collaborative initiative in which academics, funders and commercial antibody manufacturers are working together to address antibody reproducibility issues by characterizing commercial antibodies for human proteins using standardized protocols, and openly sharing the data.17–19 Here, twelve commercially available antibodies that target either Rab1A or Rab1B were tested in Western Blot, immunoprecipitation and immunofluorescence applications using a knockout-based validation approach. This article serves as a valuable guide to help researchers select high-quality antibodies for their specific needs, facilitating the biochemical and cellular assessment of Rab1A and Rab1B properties and function.\n\n\nResults and discussion\n\nOur standard protocol involves comparing readouts from wild-type (WT) and knockout (KO) cells.20,21 The first step was to identify a cell line(s) that expresses sufficient endogenous levels of a given protein to generate a measurable signal. To this end, we examined the DepMap transcriptomics database to identify all cell lines that express the Rab1 isoforms at levels greater than 2.5 log2 (transcripts per million “TPM” + 1), which we have found to be a suitable cut-off (Cancer Dependency Map Portal, RRID:SCR_017655). Commercially available HAP1 cells express Rab1A and Rab1B transcripts at RNA levels above the average range of cancer cells analyzed. Parental and RAB1A and RAB1B KO HAP1 cells were obtained from Horizon Discovery (Table 1).\n\nFor Western Blot experiments, we resolved proteins from WT and RAB1A and RAB1B KO cell extracts and probed them side-by-side with all antibodies in parallel (Figure 1).21 Figure 1 indicates which antibodies are intended for Rab1A (A) or Rab1B (B). In the results, it was observed that Rab1A antibodies, namely ab302545*, NBP3-11042, NBP3-11043, 13075* and 11671-1-AP immunodetected their target, Rab1A protein as a ~23 kDa band in the HAP1 WT lysate while the levels of Rab1A increased by ~2-3 fold in the lysates of Rab1B KO cells. Similarly, Rab1B antibodies 17824-1-AP and PA5-77240 detect Rab1B at ~23 kDa in the HAP1 WT lysate, and revealed a similar ~2-3 fold increase in Rab1B protein level in the Rab1A KO lysate. These results demonstrated that a compensatory mechanism exists to ensure that overall Rab1 protein levels remain balanced.\n\nLysates of HAP1 (WT and RAB1A and RAB1B KO) were prepared and 30 μg of protein were processed for Western Blot with the indicated Rab1A and Rab1B antibodies. Figure 1A represents the findings from the Western Blot experiments for antibodies intended to bind to Rab1A while Figure 1B represents the Western Blots for antibodies intended to bind Rab1B. The Ponceau stained transfers of each Blot are presented to show equal loading of WT and KO lysates and protein transfer efficiency from the acrylamide gels to the nitrocellulose membrane. Antibody dilutions were chosen according to the recommendations of the antibody supplier. Exceptions were given for antibodies ab302545*, NBP3-11042, 13075, 11671-1-AP, PA5-104066, 17824-1-AP, PA5-104067 and PA5-77240, which were titrated to the corresponding dilutions found below, as the signals were too weak when following the supplier’s recommendations. Antibody dilution used: ab302545 at 1/200, NBP3-11042* at 1/500, NBP3-11043* at 1/500, 13075** at 1/200, 11671-1-AP at 1/500, PA5-44578 at 1/500, PA5-104066 at 1/500, NBP3-18251 at 1/200, 17824-1-AP at 1/500, MA5-31880* at 1/500, PA5-104067 at 1/200, PA5-77240 at 1/200. Predicted band size: 22 kDa. Monoclonal antibody, Recombinant antibody.\n\nAs per our standard procedure, we next used the antibodies to immunoprecipitateRab1A and Rab1B from HAP1 cell extracts. The performance of each antibody was evaluated by detecting the Rab1A and Rab1B protein in extracts, in the immunodepleted extracts and in the immunoprecipitates using an antibdy that was validated by Western Blot (Figure 2).21\n\nHAP1 lysates were prepared, and IP was performed using 2.0 μg of the indicated Rab1A and Rab1B antibodies pre-coupled to Dynabeads protein A or protein G. Samples were washed and processed for Western Blot with the indicated Rab1A and Rab1B antibodies. Figure 2A represents the IP results for antibodies intended to immunodetect Rab1A while Figure 2B represents the results for antibodies intended to immunodetect Rab1B. For Rab1A Western Blots (A), ab302545* was used at 1/200. For Rab1B Western Blots (B), 17824-1-AP was used at 1/500. The Ponceau stained transfers of each Blot are shown. SM=4% starting material; UB=4% unbound fraction; IP=immunoprecipitate; LC=antibody light chain. Monoclonal antibody, Recombinant antibody.\n\nFor immunofluorescence, antibodies were screened using a mosaic strategy, as per our standard procedure. First, the HAP1 WT and RAB1A KO cells were plated together in the same tissue culture wells, using different colour fluorescent dyes to distinguish the two cell lines, and the seven Rab1A antibodies were tested. Then, HAP1 WT and RAB1B KO cells were plated together using the same strategy, and the five Rab1B antibodies were tested. Cells were imaged in the same field of view to reduce staining, imaging and image analysis bias (Figure 3). Quantification of immunofluorescence intensity hundreds of WT and KO cells was performedfor each antibody tested. The images presented in Figure 3 are representative of the results of this analysis.\n\nHAP1 WT were labelled with a green fluorescence dye, and HAP1 RAB1A and RAB1B KO cells were labelled with a far-red fluorescent dye. Figure 3A represents WT cells plated together RAB1A KO, while Figure 3B represents WT cells plated with RAB1B KO cells. WT/KO cells are plated to a 1:1 ratio in a 96-well plate with optically clear flat-bottom. In panel (A), WT and RAB1A KO cells were stained with the antibodies intended to target Rab1A, and the corresponding Alexa-fluor 555 coupled secondary antibody including DAPI. In panel (B), WT and RAB1B KO cells were stained with the antibodies intended to target Rab1B, and the corresponding Alexa-fluor 555 coupled secondary antibody including DAPI. Acquisition of the blue (nucleus-DAPI), green (identification of WT cells), red (antibody staining) and far-red (identification of KO cells) channels was performed. Representative images of the merged blue and red (grayscale) channels are shown. WT and KO cells are outlined with green and magenta dashed line, respectively. When the concentration was not indicated by the supplier, we tested antibodies at 1/100 or 1/500, which was the case for antibodies NBP3-11042, NBP3-11043, PA5-44578, PA5-104066, NBP3-18251 and 17824-1-AP. At these concentrations, the signal from each antibody was in the range of detection of the microscope used. Antibody dilution used: ab302545* at 1/100, NBP3-11042* at 1/100, NBP3-11043* at 1/100, 13075** at 1/800, 11671-1-AP at 1/700, PA5-44578 at 1/500, PA5-104066 at 1/100, NBP3-18251 at 1/100, 17824-1-AP at 1/50, MA5-31880* at 1/1000, PA5-104067 at 1/1000, PA5-77240 at 1/50. Bars = 10 μm. Monoclonal antibody, Recombinant antibody.\n\nIn conclusion, we have screened seven Rab1A and Rab1B commercial antibodies by Western Blot, immunoprecipitation and immunofluorescence. Several high-quality antibodies that selectively detect either Rab1A or Rab1B under the standardized experimental conditions were identified in each of the tested applications. In our efforts to address the antibody reliability and reproducibility challenges in scientific research, the authors recommend the antibodies that demonstrated to be underperforming be removed from the commercial antibody market. However, the authors do not engage in result analysis or offer explicit antibody recommendations. A limitation of this study is the use of universal protocols - any conclusions remain relevant within the confines of the experimental setup and cell line used in this study. Our primary aim is to deliver top-tier data to the scientific community, grounded in Open Science principles. This empowers experts to interpret the characterization data independently, enabling them to make informed choices regarding the most suitable antibodies for their specific experimental needs.\n\nThe underlying data for this study can be found on Zenodo, an open access repository for which YCharOS has its own community.22,23\n\n\nMethods\n\nAll Rab1A and Rab1B antibodies are listed in Table 2, together with their corresponding Research Resource Identifiers, or RRID, to ensure the antibodies are cited properly.24 Peroxidase-conjugated goat anti-rabbit and anti-mouse antibodies are from Thermo Fisher Scientific (cat. number 65-6120 and 62-6520). Alexa-555-conjugated goat anti-rabbit and anti-mouse secondary antibodies are from Thermo Fisher Scientific (cat. number A21429 and A21424).\n\n Monoclonal antibody,\n\n** Recombinant antibody\n\nBoth HAP1 WT and RAB1A and RAB1B KO cell lines used are listed in Table 1, together with their corresponding RRID, to ensure the cell lines are cited properly.25 Cells were cultured in DMEM high-glucose (GE Healthcare cat. number SH30081.01) containing 10% fetal bovine serum (Wisent, cat. number 080450), 2 mM L-glutamate (Wisent cat. number 609065), 100 IU penicillin and 100 μg/mL streptomycin (Wisent cat. number 450201).\n\nWestern Blots were performed as described in our standard operating procedure. HAP1 WT and the HAP1 RAB1A and RAB1B KO lines (listed in Table 1) were collected in RIPA buffer (25 mM Tris-HCl pH 7.6, 150 mM NaCl, 1% NP-40, 1% sodium deoxycholate, 0.1% SDS) from Thermo Fisher Scientific (cat. number 89901) supplemented with 1× protease inhibitor cocktail mix (MilliporeSigma, cat. number P8340). Lysates were sonicated briefly and incubated for 30 min on ice. Lysates were spun at ~110,000 × g for 15 min at 4°C and equal protein aliquots of the supernatants were analyzed by SDS-PAGE and Western Blot. BLUelf prestained protein ladder from GeneDireX (cat. number PM008-0500) was used.\n\nWestern Blots were performed with a precast midi 10% Bis-Tris polyacrylamide gels from Thermo Fisher Scientific (cat. number WG1201BOX) ran with MES SDS buffer (Thermo Fisher Scientific, cat. number NP000202), loaded in LDS sample buffer (Thermo Fisher Scientific, cat. number NP0008) with 1× sample reducing agent (Thermo Fisher Scientific, cat. number NP0009) and transferred on nitrocellulose membranes. Proteins on the Blots were visualized with Ponceau S staining (Thermo Fisher Scientific, cat. number BP103-10) which is scanned to show together with individual Western Blot. Blots were blocked with 5% milk for 1 hr, and antibodies were incubated overnight at 4°C with 5% milk in TBS with 0.1% Tween 20 (TBST) (Cell Signalling Technology, cat. number 9997). Following three washes with TBST, the peroxidase conjugated secondary antibody was incubated at a dilution of ~0.2 μg/mL in TBST with 5% milk for 1 hr at room temperature followed by three washes with TBST. Membranes were incubated with Pierce ECL from Thermo Fisher Scientific (cat. number 32106) or Clarity Western ECL Substrate from Bio-Rad (cat. number 1705061) prior to detection with the iBright™ CL1500 Imaging System from Thermo Fisher Scientific (cat. number A44240). Membranes incubated with primary antibodies NBP3-11043, 13075*, PA5-44578, PA5-104066, NBP3-18251 and PA5-104067 were developed with Clarity Western ECL Substrate, and the remaining antibodies with Pierce ECL.\n\nImmunoprecipitation was performed as described in our standard operating procedure. Antibody-bead conjugates were prepared by adding 2 μg or 10 μL of antibody NBP3-18251 (unknown concentration) to 500 μL of Pierce IP Lysis Buffer from Thermo Fisher Scientific (cat. number 87788) in a 1.5 mL microcentrifuge tube, together with 30 μL of Dynabeads protein A - (for rabbit antibodies) or protein G - (for mouse antibodies) from Thermo Fisher Scientific (cat. number 10002D and 10004D, respectively). Tubes were rocked for ~1 hr at 4°C followed by two washes to remove unbound antibodies.\n\nHAP1 WT were collected in Pierce IP buffer (25 mM Tris-HCl pH 7.4, 150 mM NaCl, 1 mM EDTA, 1% NP-40 and 5% glycerol) supplemented with protease inhibitor. Lysates were rocked for 30 min at 4°C and spun at 110,000 × g for 15 min at 4°C. 0.5 mL aliquots at 2.0 mg/mL of lysate were incubated with an antibody-bead conjugate for ~1 hr at 4°C. The unbound fractions were collected, and beads were subsequently washed three times with 1.0 mL of IP lysis buffer and processed for SDS-PAGE and Western Blot on a precast midi 10% Bis-Tris polyacrylamide gels. Prot-A: HRP (MilliporeSigma, cat. number P8651) was used as a secondary detection system at a concentration of 0.3 μg/mL.\n\nImmunofluorescence was performed as described in our standard operating procedure.21 HAP1 WT and the HAP1 RAB1A and RAB1B KO cell lines were labelled with a green and a far-red fluorescence dye, respectively. The fluorescent dyes used are from Thermo Fisher Scientific (cat. number C2925 and C34565). The nuclei were labelled with DAPI (Thermo Fisher Scientific, cat. number D3571) fluorescent stain. WT and KO cells were plated in a 96-well plate with optically clear flat-bottom (Perkin Elmer, cat. number 6055300) as a mosaic and incubated for 24 hrs in a cell culture incubator at 37°C, 5% CO2. Cells were fixed in 4% paraformaldehyde (PFA) (Beantown chemical, cat. number 140770-10 ml) in phosphate buffered saline (PBS) (Wisent, cat. number 311-010-CL) for 15 min at room temperature and washed 3 times with PBS. Cells were permeabilized in PBS with 0.1% Triton X-100 (Thermo Fisher Scientific, cat. number BP151-500) for 10 min at room temperature and blocked with PBS with 5% bovine serum albumin (BSA) (Wisent, cat. number 800-095), 5% goat serum (Gibco, cat. number 16210-064) and 0.01% Triton X-100 for 30 min at room temperature. Cells were incubated with IF buffer (PBS, 5% BSA, 0.01% Triton X-100) containing the primary Rab1A and Rab1B antibodies overnight at 4°C. Cells were then washed 3 × 10 min each with IF buffer and incubated with corresponding Alexa Fluor 555-conjugated secondary antibodies in IF buffer at a dilution of 1.0 μg/mL for 1 hr at room temperature with DAPI. Cells were washed 3 × 10 min with IF buffer and once with PBS.\n\nImages were acquired on an ImageXpress micro widefield high-content microscopy system (Molecular Devices), using a 20x NA 0.95 water objective lens and scientific CMOS camera (16- bit, 1.97 mm field of view), equipped with 395, 475, 555 and 635 nm solid state LED lights (Lumencor Aura III light engine) and bandpass emission filters (432/36 nm, 520/35 nm, 600/37 nm and 692/40 nm) to excite and capture fluorescence emission for DAPI, CellTrackerTM Green, Alexa fluor 555 and CellTrackerTM Red, respectively. Images had pixel sizes of 0.68 × 0.68 microns. Exposure time was set with maximal (relevant) pixel intensity ~80% of dynamic range and verified on multiple wells before acquisition. Since the IF staining varied depending on the primary antibody used, the exposure time was set using the most intensely stained well as reference. Frequently, the focal plane varied slightly within a single field of view. To remedy this issue, a stack of three images per channel was acquired at a z-interval of 4 microns per field and best focus projections were generated during the acquisition (MetaXpress v6.7.1, Molecular Devices). Segmentation was carried out on the projections of CellTrackerTM channels using CellPose v1.0 on green (WT) and far-red (KO) channels, using as parameters the ‘cyto’ model to detect whole cells, and using an estimated diameter tested for each cell type, between 15 and 20 microns.26 Masks were used to generate cell outlines for intensity quantification. Figures were assembled with Adobe Photoshop (version 24.1.2) to adjust contrast then assembled with Adobe Illustrator (version 27.3.1).", "appendix": "Data availability\n\nZenodo: Antibody Characterization Report for Rab1A and Rab1B, https://doi.org/10.5281/zenodo.8356353. 22\n\nZenodo: Dataset for the Rab1A and Rab1B antibody screening study, https://doi.org/10.5281/zenodo.8400619. 23\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 thank the NeuroSGC/YCharOS/EDDU collaborative group for their important contribution to the creation of an open scientific ecosystem of antibody manufacturers and knockout cell line suppliers, for the development of community-agreed protocols, and for their shared ideas, resources and collaboration. We would also like to thank the Advanced BioImaging Facility (ABIF) consortium for their image analysis pipeline development and conduction (RRID:SCR_017697). Members of each group can be found below.\n\nNeuroSGC/YCharOS/EDDU collaborative group: Thomas M. Durcan, Aled M. Edwards, Chetan Raina and Wolfgang Reintsch.\n\nABIF consortium: Claire M. Brown and Joel Ryan.\n\nThank you to the Structural Genomics Consortium, a registered charity (no. 1097737), for supporting this project. The Structural Genomics Consortium receives funding from Bayer AG, Boehringer Ingelheim, Bristol-Myers Squibb, Genentech, Genome Canada through Ontario Genomics Institute (grant no. OGI-196), the EU and EFPIA through the Innovative Medicines Initiative 2 Joint Undertaking (EUbOPEN grant no. 875510), Janssen, Merck KGaA (also known as EMD in Canada and the United States), Pfizer and Takeda.\n\nAn earlier version of this of this article can be found on Zenodo (doi: 10.5281/zenodo.8356353).\n\n\nReferences\n\nStenmark H: Rab GTPases as coordinators of vesicle traffic. Nat. Rev. Mol. Cell Biol. 2009; 10(8): 513–525. Publisher Full Text\n\nBarr F, Lambright DG: Rab GEFs and GAPs. Curr. Opin. Cell Biol. 2010; 22(4): 461–470. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLi G, Marlin MC: Rab family of GTPases. Methods Mol. Biol. 2015; 1298: 1–15. Publisher Full Text\n\nPlutner H, Cox AD, Pind S, et al.: Rab1b regulates vesicular transport between the endoplasmic reticulum and successive Golgi compartments. J. Cell Biol. 1991; 115(1): 31–43. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPlutner H, Schwaninger R, Pind S, et al.: Synthetic peptides of the Rab effector domain inhibit vesicular transport through the secretory pathway. EMBO J. 1990; 9(8): 2375–2383. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYang J, Zhou X, Zhang R, et al.: Differences in IFNβ secretion upon Rab1 inactivation in cells exposed to distinct innate immune stimuli. Cell. Mol. Immunol. 2021; 18(6): 1590–1592. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGyurkovska V, Murtazina R, Zhao SF, et al.: Dual function of Rab1A in secretion and autophagy: hypervariable domain dependence. Life Sci. Alliance. 2023; 6(5): e202201810. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang C, Yoo Y, Fan H, et al.: Regulation of Integrin β 1 recycling to lipid rafts by Rab1a to promote cell migration. J. Biol. Chem. 2010; 285(38): 29398–29405. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nThomas JD, Zhang YJ, Wei YH, et al.: Rab1A is an mTORC1 activator and a colorectal oncogene. Cancer Cell. 2014; 26(5): 754–769. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nXu BH, Li XX, Yang Y, et al.: Aberrant amino acid signaling promotes growth and metastasis of hepatocellular carcinomas through Rab1A-dependent activation of mTORC1 by Rab1A. Oncotarget. 2015; 6(25): 20813–20828. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBao ZS, Li MY, Wang JY, et al.: Prognostic value of a nine-gene signature in glioma patients based on mRNA expression profiling. CNS Neurosci. Ther. 2014; 20(2): 112–118. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAbd Elmageed ZY, Yang Y, Thomas R, et al.: Neoplastic reprogramming of patient-derived adipose stem cells by prostate cancer cell-associated exosomes. Stem Cells. 2014; 32(4): 983–997. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhai H, Song B, Xu X, et al.: Inhibition of autophagy and tumor growth in colon cancer by miR-502. Oncogene. 2013; 32(12): 1570–1579. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHe H, Dai F, Yu L, et al.: Identification and characterization of nine novel human small GTPases showing variable expressions in liver cancer tissues. Gene Expr. 2002; 10(5-6): 231–242. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCooper AA, Gitler AD, Cashikar A, et al.: Alpha-synuclein blocks ER-Golgi traffic and Rab1 rescues neuron loss in Parkinson’s models. Science. 2006; 313(5785): 324–328. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBiddle MS, Virk HS: YCharOS open antibody characterisation data: Lessons learned and progress made. F1000Res. 2023; 12(12): 1344. Publisher Full Text\n\nAyoubi R, Ryan J, Biddle MS, et al.: Scaling of an antibody validation procedure enables quantification of antibody performance in major research applications. bioRxiv. 2023.\n\nCarter AJ, Kraemer O, Zwick M, et al.: Target 2035: probing the human proteome. Drug Discov. Today. 2019; 24(11): 2111–2115.\n\nLicciardello MP, Workman P: The era of high-quality chemical probes. RSC Med. Chem. 2022; 13(12): 1446–1459.\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: 8. Publisher Full Text\n\nAlshafie W, Fotouhi M, Shlaifer I, et al.: Identification of highly specific antibodies for Serine/threonine-protein kinase TBK1 for use in immunoblot, immunoprecipitation and immunofluorescence. F1000Res. 2022; 11: 977. Publisher Full Text\n\nMoleon VR, Fotouhi M, Ryan J, et al.: Antibody Characterization Report for Rab-1A and Rab-1B. Zenodo. 2023. Publisher Full Text\n\nSouthern K: Dataset for the Rab-1A and Rab-1B antibody screening study. Zenodo. 2023. Publisher Full Text\n\nBandrowski A, Pairish M, Eckmann P, et al.: The Antibody Registry: ten years of registering antibodies. Nucleic Acids Res. 2023; 51(D1): D358–D367. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBairoch A: The Cellosaurus, a Cell-Line Knowledge Resource. J. Biomol. Tech. 2018; 29(2): 25–38. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStringer C, Wang T, Michaelos M, et al.: Cellpose: a generalist algorithm for cellular segmentation. Nat. Methods. 2021; 18(1): 100–106. PubMed Abstract \| Publisher Full Text" }	[ { "id": "246962", "date": "26 Feb 2024", "name": "Shinsuke Niwa", "expertise": [ "Reviewer Expertise cell biology" ], "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. It would be helpful to have a table describing which antibodies are useful and reliable and which are not for each application.\n\n2. A limitation of this study is that the authors analyzed only the human cell line HAP1 and not widely used cells such as Hela cells and 293 cells.\n3. While \"the authors recommend the antibodies that demonstrated to be underperforming be removed from the commercial antibody market\", one cannot conclude usefulness of these antibodies in cell lines derived from other species such as mouse, hamster (CHO cells) and rat.\n\nIs the rationale for creating the dataset(s) clearly described? Partly\n\nAre the protocols appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and materials provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes", "responses": [] }, { "id": "253285", "date": "28 Mar 2024", "name": "Claudia Fallini", "expertise": [ "Reviewer Expertise Cell biology and neuroscience" ], "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 report, Moleon and colleagues characterize several antibodies directed against the human Rab1A or Rab1B proteins. Rab1 proteins are small GTP-binding proteins that participate in vesicle trafficking, among other cellular functions. Interest in these proteins also stems from their potential role as oncogenes, as several cancer types have been shown to upregulate Rab1A or Rab1B. The authors carefully characterized 7 Rab1A and 5 Rab1B antibodies by western blot, immunoprecipitation, and immunofluorescence assays using KO and isogenic parental cell lines. The results are clearly presented, and the methods detailed enough to allow replication. Overall, there are no specific concerns in my view. Only few minor typos were identified such as missing spaces in the abstract (\"diseaseand\") and on page 5 (\"immunoprecipitateRab1A\", \"antibdy\", and \"performedfor\").\n\nIs the rationale for creating the dataset(s) clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and materials provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes", "responses": [] } ]	2	https://f1000research.com/articles/12-1578
https://f1000research.com/articles/12-435/v1	24 Apr 23	{ "type": "Review", "title": "Emerging pneumococcal serotypes in Iraq: scope for improved vaccine development", "authors": [ "Haider N. Dawood", "Ali H. Al-Jumaili", "Ahmed H. Radhi", "Delan Ikram", "Ali Al-Jabban", "Haider N. Dawood", "Ali H. Al-Jumaili", "Ahmed H. Radhi", "Ali Al-Jabban" ], "abstract": "Abstract: Pneumococcal disease is a global public health concern as it affects the young, aged and the immunocompromised. The development of pneumococcal vaccines and their incorporation in the immunization programs has helped to reduce the global burden of disease. However, serotype replacement and the emergence of non-vaccine serotypes as well as the persistence of a few vaccine serotypes underscores the need for development of new and effective vaccines against such pneumococcal serotypes. In the Middle East, places of religious mass gatherings are a hotspot for disease transmission in addition to the global risk factors. Therefore, the periodic surveillance of pneumococcal serotypes circulating in the region to determine the effectiveness of existing prevention strategies and develop improved vaccines is warranted. Currently, there is a lack of serotype prevalence data for Iraq due to inadequate surveillance in the region. Thus, this review aims to determine the pneumococcal serotypes circulating in Iraq by drawing inferences from the global pneumococcal serotype prevalence data as well as recently published literature from neighboring countries to refine existing vaccination strategies and help in the development and introduction of improved pneumococcal vaccines in the country.", "keywords": [ "Iraq", "Pneumococcal disease", "Pneumococcal serotypes", "Pneumococcal vaccines", "Serotype replacement" ], "content": "Introduction\n\nStreptococcus pneumoniae, the causative agent of pneumococcal disease, is responsible for devastating morbidity and mortality among children, adolescents, and adults especially below five years and above 60 years of age, particularly the immunocompromised population, patients with chronic diseases, and smokers.1,2 It is a commensal microbe that normally colonizes the upper respiratory mucosa of humans, which in turn facilitates its transmission.3 However, several bacterial and host factors promote pathogen invasion into sterile body sites, thereby causing severe invasive pneumococcal disease (IPD) manifestations, such as septicemia, meningitis, and bacteremic pneumonia.3,4 As a public health prevention strategy, the World Health Organization (WHO) has recommended the global inclusion of pneumococcal conjugate vaccines (PCVs) into routine infant immunization programs.5 Currently, 148 countries have adopted this strategy, which has significantly reduced the burden of pneumococcal disease among children (<5 years) from 14.5 million episodes and 826,000 deaths in the pre-PCV period (2000) to 9.18 million cases and 318,000 deaths in 2015.6–8 In addition, the pneumococcal polysaccharide vaccine (PPSV) was developed to prevent IPD among the elderly (≥65 years) and high-risk populations (≥2 years).9 However, an increase in the emergence of nonvaccine serotypes (NVTs) or serotype replacement has been observed due to the vaccine’s selection pressure.10–13\n\nThis review aims to revise and shed light on the S. pneumoniae serotypes circulating in Iraq. Due to the lack of adequate surveillance in the region, limited serotype prevalence data are available for Iraq. Therefore, we draw inferences for Iraq by reviewing recently published data from neighboring countries in the Eastern Mediterranean region (EMR) and across the globe. We hope that this review will aid readers (researchers and policymakers) in making informed decisions regarding the development and introduction of improved pneumococcal vaccines.\n\n\nS. pneumoniae serotypes\n\nPneumococci possess several virulence factors, of which the polysaccharide capsule is the most important, as it is an essential armor against phagocytosis and aids colonization by overcoming its mucus-mediated clearance.14,15 The capsule is also the target antigen for the development of multivalent vaccines against this pathogen. Pneumococcal serotypes are differentiated based on antigenic differences and the chemical composition of these capsular polysaccharides.14 A serogroup includes serotypes that have common serological properties (i.e., cross-reactive antibodies).16\n\nWhile most pneumococcal capsules are generally anionic, the capsule of serotype 1 exists as a zwitterion and those of serotypes 7A, 7F, 14, 33A, 33F, and 37 have been reported to be uncharged.16 The capsule of serotype 14 is less soluble than other pneumococcal polysaccharide capsules.16 The capsule strands are normally linked to the bacterial surface via covalent linkages to the peptidoglycan, except in the case of serotype 3, where noncovalent interactions with phosphatidylglycerol have been reported.17 It has been suggested that the release of the capsular polysaccharide of serotype 3 strains reduces antibody-mediated protection and is responsible for the reduced efficacy of the currently available PCV against serotype 3.18\n\nSerotype distribution varies temporally and geographically and is also influenced by age, the presence of antimicrobial resistance genes, as well as disease syndrome and severity.5 The establishment of this commensal nasopharyngeal flora occurs within the first year of birth.19 Nasopharyngeal carriage determines disease development as well as pathogen dissemination. Infants and young children have higher carriage rates (27–85%) than adults (~10%).5,14 It has been reported that a carriage rate of 30–40% is maintained till the age of 9 years, progressively declining thereafter.14 In fact, the low carriage rates among adults indicates immunological protection upon previous exposure.14,19 Variations in carriage rates have been noted to depend upon the local epidemiology, with higher rates noted in socioeconomically weaker countries and in impoverished communities with low vaccination rates.5,14\n\nCurrently, more than 100 serotypes of S. pneumoniae are known, of which only about 23 cause 80–90% of invasive disease where the pathogen migrates to sterile sites within the body.1,20–22 Young children (<5 years) and adolescents/adults are colonized by different pneumococcal serotypes.14 Between 2004 and 2009, the most prevalent global serotypes among children <5 years were reported to be 19A, 19F, 14, and 6A, while those most commonly circulating among adults (>16 years) were serotypes 19A, 3, 6A, and 7F.23 Additionally, a few serotypes show a propensity towards specific organ systems. Serotypes 6, 10, and 23 are frequently isolated from the meninges during meningitis, while serotypes 1 and 3 favor lung colonization during pneumonia.22\n\nThe capsular serotype determines the duration of nasopharyngeal carriage, as well as its invasive potential.14,24,25 Serotypes with poor immunogenicity often colonize for longer durations.14,19 In most published reports, serotypes 1, 4, 5, 7F, 8, 12F, 14, 18C, and 19A showed high invasive potential, while 6A, 6B, 11A, 15B/C, and 23F were less invasive and showed a higher colonization frequency.14,24–31 The serotypes causing acute otitis media in children (<18 years) globally were reported to be 3, 6A, 6B, 9V, 14, 19A, 19F, and 23F.32 Among adults, serotypes 1 and 19A predominantly caused invasive pneumococcal pneumonia, and serotype 14 was responsible for nonbacteremic pneumonia incidents during the post-PCV (PCV7) introduction phase.33,34 For bacteremic pneumonia, serotypes 1, 7F, and 8 were associated with a lower risk of death, while infections with serotypes 3, 6A, 6B, 9N, and 19F resulted in increased mortality.35 Serotype 1 is one of the most frequently isolated pathogen during IPD incidents, but rarely colonizes the nasopharynx.36 It is mostly recovered from young adults without any comorbidities and has the potential to cause disease outbreaks and epidemics.36 Among pediatric patients, serotype 1 was often reported to be associated with empyema complications post-pneumococcal infection in the period prior to PCV use, while serotypes 3, 7F, 14, and 19A have emerged post-PCV7 introduction.14,37–41 Sirotnak et al. reported that S. pneumoniae serotype 1 also induced peritonitis among female children in the UK.42 The mucoid serotype 3 has a thicker capsule, greater virulence, and higher mortality rate than other strains and is the second most common isolate in adult IPD cases.43–45 It is associated with severe clinical manifestations, such as empyema, cardiotoxicity, bacteremia and meningitis, with a fatality rate of 30–47%.17 Moreover, it resists antibody-mediated clearance, as the antibody titers required to confer protection are not elicited by the current conjugate vaccine.17,18 Prior to PCV introduction, serotype 14 was reported to be the most common cause of pneumococcal-associated hemolytic uremic syndrome among children, which shifted to serotypes 1, 3, 7F, and 19A in the post-PCV7 era, with serotype 3 being the most predominant.14,46–49 Among adults, the following serotypes have been reported to be associated with an elevated risk of: empyema (serotypes 1, 3, 5, 7F, 8, 19A), necrotizing pneumonia (serotype 3), septic shock (serotypes 3, 19A), meningitis (serotypes 10A, 15B, 19F, 23F), reduced quality-adjusted life-years (serotypes 15B, 3, 10A, 9N, 19F, 11A, 31), and increased case-fatality rates (serotypes 3, 6B, 9N, 11A, 16F, 19F, 19A).50 Among vaccinated children <5 years, serotypes 1, 7F, and 12F showed a higher invasive potential than serotype 19A.51 Further, the NVTs 8, 12F, 24F, and 33F were at the upper end of the invasiveness spectrum in this cohort.51\n\nThe serotypes 19A, 6A, 19F, 6B, 15A, 9V, and 14 have been reported to exhibit erythromycin resistance, while 19A, 19F, 35B, 6A, 6B, 23A, 9V, 15A, and 14 demonstrated penicillin resistance.23 Serotype 19A strains have been reported to be multidrug resistant and are prevalent globally.52,53\n\n\nPneumococcal vaccines and serotype replacement\n\nThe first PCV offered protection against 7 pneumococcal serotypes (PCV7: 4, 6B, 9V, 14, 18C, 19F, 23F) and was licensed in 2000.54 Currently, 26 countries use the 10-valent (PCV10: PCV7 + 1, 5, 7F) formulation and 114 countries use the 13-valent (PCV13: PCV10 + 3, 6A, 19A) formulation, while 7 countries use both.5,8,54 In India, an alternate 10-valent formulation, Pneumosil® (Serum Institute of India), has been adopted. In the USA, two new polyvalent conjugate vaccines, PCV15 (PCV13 + 22F, 33F) and PCV20 (PCV15 + 8, 10A, 11A, 12F, 15B), are now available for use in adults ≥18 years.55 Merck Sharp & Dohme’s (MSD’s) (PCV13 + 2, 8, 9N, 10A, 11A, 12F, 15B, 17F, 20, 22F, 33F) and Affinivax’s (PCV13 + 2, 8, 9N, 10A, 11A, 12F, 15B, 17F, 20B, 22F, 33F) 24-valent vaccine formulations are under clinical trials.56 Additionally, a 23-valent pneumococcal polysaccharide vaccine (PPSV23: 1, 2, 3, 4, 5, 6B, 7F, 8, 9N, 9V, 10A, 11A, 12F, 14, 15B, 17F, 18C, 19A, 19F, 20, 22F, 23F, 33F) was licensed in 1983 for use in the elderly and high-risk populations.54 Furthermore, Inventprise plans to develop a vaccine to target important emerging serotypes such as 2, 16F, 24F and 35B while Vaxcyte has also announced a 30-valent preclinical PCV to target newly emerging IPD strains and antibiotic resistance.56 Table 1 lists the different pneumococcal vaccines and the serotypes they cover.\n\nThe impact of PCVs in reducing pneumococcal colonization and invasive disease by vaccine serotypes in vaccinated children, as well as herd protection among the unvaccinated population, is well documented.57–60 Although pneumococcal vaccines have had a tremendous impact on the global pneumococcal disease burden, serotype replacement (i.e., the replacement of the vaccine serotypes [VTs] with nonvaccine serotypes) has slightly dulled the overall benefits of immunization.11\n\nAlterations in the serotype prevalence among pneumococcal populations can originate from both serotype replacement as well as serotype (capsular) switching.61 Serotype replacement refers to the expansion of NVTs within the population.62,63 On the other hand, serotype switching, or capsular switching, is the change in a serotype from a single clone that occurs due to alterations in the cps locus which is responsible for capsular polysaccharide synthesis.61 These 2 events are not mutually exclusive, as capsular switch variants often expand within the population.61,62\n\n\nGlobal pneumococcal serotype prevalence\n\nIn the period preceding worldwide PCV introduction, the most commonly circulating pneumococcal serotypes in children (<5 years) were reported to be 1, 5, 6A, 6B, 14, 19F, and 23F, which accounted for 58–66% of global IPD cases.21 During this period, PCV7-related serotypes were responsible for 49–82% of global childhood IPD episodes.21 Upon PCV7 implementation, the percentage of IPD cases caused by PCV7 serotypes reduced to approximately 14.8% and to 12.5% after the introduction of the higher-valent PCVs (i.e., PCV10/13).64,65 The PCV10-specific serotypes 1, 5, and 7F accounted for 16.3% of overall childhood IPD cases in regions where PCV7 had been introduced, while the figure was 9.2% in post-PCV10/13 implementation settings.64 Following the introduction of PCV7 and PCV10/13, the most common PCV13 serotypes were 19A, 3, and 6A.45,64 Serotype 19A was the most prevalent (21.8% cases) among pediatric IPD cases in the post-PCV7 period, and was responsible for 14.2% of incidents in regions with higher-valent vaccine introduction.64 The global increase in the prevalence of serotype 19A in the PCV13 period is a cause of concern, as it indicates reduced vaccine efficacy against this serotype.45 Furthermore, this serotype is also globally associated with high multidrug resistance (MDR) potential. Wantuch and Avci also highlight PCV13's reduced effectiveness against serotype 3 prevalence, which has remained nearly constant in the pre-(1999–2000) and post-PCV (2010–2011) periods.45\n\nGlobally, about 29.4% and 42% of childhood IPD cases were caused by non-PCV13 serotypes in post-PCV7 and post-PCV10/13 administration settings, respectively. Serotype 22F was the most prevalent (5% of childhood IPD episodes) in regions where PCV10/13 had been introduced, followed by 12F, 33F, 24F, and 15C (~4% episodes each). Serotypes 15B, 23B, 10A, and 38 were responsible for 3.4–3.7% of cases globally. However, several variations in the prevalence of these serotypes were observed across different regions. In several regions, except in the EMR, serotypes 22F, 12F, and 33F were responsible for 4–16% of childhood IPD cases. Serotype 24F was prevalent in the Western Pacific region and Europe (but not North America). Serotype 38 was more prevalent in North America and 12F, 15C, and 10A in Europe.64 In Japan, a nationwide surveillance study was conducted between 2012 and 2014 among pediatric (2 months–16 years) patients that revealed the emergence of IPD due to NVTs 24F and 15A post-approval of PCV13 use in routine vaccination.66 Ubukata et al. found that the prevalence of 9 (10A, 12F, 15A, 15B, 15C, 22F, 24F, 33F, and 35B) and 5 serotypes (12F, 15C, 22F, 23A, and 35B) increased significantly among children and adults, respectively, during the PCV13 period. Notably, a rapid increase was observed in 15A and 35B.67 The NVT 24F was recently reported to be a cause of concurrent bacteremia among 22-month-old twins who had been fully vaccinated with PCV13, with the last dose administered 6 months prior to hospitalization.68 This serotype also showed a high invasive potential (pneumococcal meningitis) post-PCV13 implementation in France in the pediatric population along with serotype 12F.69,70\n\n\nPneumococcal serotype prevalence in the Eastern Mediterranean Region\n\nThe EMR has a substantial burden of lower respiratory tract infections, with pneumococci contributing maximally to the mortality rate (16.6 per 100,000).71 In 2015, this region reported 37,100 pneumococcal deaths and 968,000 pneumococcal disease cases.7 High-income countries within the region have introduced PCV into their National Immunization Programs (NIPs), and several low-income countries have received support from Gavi, the Vaccine Alliance, for the same.71 Several middle-income countries have now introduced PCV, except for a few countries such as Iran, Jordan and Egypt.8 Currently, a majority of EMR countries have incorporated PCV13 use, while Morocco, Pakistan, and Tunisia use the 10-valent Synflorix® vaccine.8\n\nThe Gulf countries of the Middle East exhibit a high pneumococcal disease burden, with risk factors similar to those existing globally, such as age-related risks, chronic disease-related risks, as well as risks arising due to immunodeficiencies, smoking, and alcoholism.72,73 Additionally, religious mass gatherings occurring within this region act as hotspots for pathogen dissemination among pilgrims (especially those with comorbidities) during Hajj, Umrah, and Arba’een.74–77 Thus, the active surveillance of pneumococcal serotypes prevalent within this region would help determine the effectiveness of the adopted immunization strategies and aid in developing novel measures to control disease transmission and outbreaks. Currently, the EMR has a vaccination coverage of 52% for 3 doses of PCV.78 Further, it has been reported that the predominant MDR pneumococcal strains in the Arab League belong to serotypes 19F, 23F, 6B, and 19A.79–81\n\nPneumococcal vaccines have not yet been included in the NIP of Iran and are only recommended for high-risk groups. Recently, a systematic review and meta-analysis of published reports between 2010 and 2017 showed that the overall prevalence of invasive S. pneumoniae infections is very low (2.5%) among Iranian children.82 However, as the included studies covered only 3 geographical regions within the country, this study was not fully representative of the whole population and could not entirely estimate the overall S. pneumoniae prevalence. Among children (<5 years) in Tehran, serotype 23F was reported to be the most invasive circulating serotype, followed by 19F, 19A, and 9V. Serotype 19A was significantly associated with penicillin resistance.83\n\nAnother systematic literature review on pneumococcal serotype distribution conducted among clinical and carrier Iranian patients between January 2000 and August 2019 revealed that 23F was the most commonly circulating serotype in Iran and was associated with IPD. Other serotypes that caused IPD included 19F, 19A, 6A/B, 9V, and 11A. Among carrier patients, 6A/B, 19F, 14, 17F, and 20 were the most frequent.84\n\nA study conducted between February 2015 and September 2015 and between July 2018 and March 2019 collected approximately 40 samples during each period from patients (1 month to 72 years of age) in Tehran.85 About 38 of these samples were derived from invasive infections, of which 42% occurred in children ≤5 years. The pneumococcal serotypes in the samples were determined to be 23F, 14, 3, 19F, 19A, 6A, 6B, 9V, and 18C, of which the first 5 were the most common (in decreasing order). This is consistent with serotype prevalence data for other Asian countries.86,87 The common serotypes isolated from invasive infections were 23F, 19A, and 14, while 3, 19F, and 23F were commonly associated with noninvasive disease. Among pediatric patients ≤5 years, the most prominent serotypes were 19A, 3, 23F, and 14, while 23F was predominant in adults ≥64 years. In the former age group, serotype 19A was observed in 35.2% of IPD cases, while serotypes 3, 23F, and 14 were predominantly non-IPD related. Overall, serotype 23F was frequently associated with penicillin resistance and was also predominant among MDR strains. A significant rise in serotype 19A MDR isolates was noticed among invasive infections in the second period of sample collection, possibly due to antibiotic selection pressure.85\n\nIraq incorporated the use of PCV into the NIP in 2017. However, there are insufficient serotype surveillance data for Iraq. Most publications on S. pneumoniae in this region focus on its antimicrobial resistance, but do not identify the serotype of the isolate. Between June 2018 and May 2020, 41.6% of patients were confirmed to have pneumococcal meningitis in Iraq based on cerebrospinal fluid samples.88 The age of patients ranged from 1 to 40 years, with a majority (83.7%) being under 5 years and 58.4% being less than a year old. The overall annual incidence rate (IR) of laboratory-confirmed pneumococcal meningitis in Iraq was 0.62/100,000, with a maximum IR of 1.56 in Karbala (site of Arba’een pilgrimage), 0.65 in Karkh, 0.58 in Al-Rusafa, 0.3 in Kirkuk, and a minimum of 0.09 in Maysan. However, as all Iraqi governorates were not covered in this study, the overall incidence rate for pneumococcal meningitis was likely underestimated. In a recent report, a nonvaccine S. pneumoniae serotype, 33C, was isolated from a hospitalized child with nephrotic syndrome and sepsis, which can be fatal.89\n\nThere are several publications that study the impact of PCV vaccinations, serotype prevalence, and pneumococcal drug resistance among the people of Kuwait.90–93 The 7-valent PCV was introduced to the pediatric population in 2007 and was replaced with the higher-valent (PCV13) formulation in 2010.93 In the period following PCV7's introduction (2006–2011), a majority (46%) of clinical pneumococcal isolates were derived from the adult population >50 years, where 27% of cases were found to be invasive. Although a lower percentage (23%) of isolates were obtained from pediatric (≤5 years) samples, IPD was responsible for nearly half (49%) of the cases in this age group.90 The common serotypes circulating among children (≤5 years) during this period were 19F, 19A, 6A, 8, and 15B (invasive) and 19F and 23F (noninvasive).90 Serotypes 14, 3, 1, 19F, and 8 were associated with invasive disease and 19F, 23F, 6B, 14, and 19A with noninvasive events among the adult population >50 years.90 In comparison to the pre-PCV (10.33 isolates/year) and post-PCV7 (7.75 isolates/year) periods, PCV7-related serotypes showed a greater decline after PCV13 introduction, falling to 1.4 isolates/year.92 An increased incidence of cases due to non-PCV7 serotypes 1, 6A, and 3 (which are included in PCV13) was reported post-PCV7 vaccine introduction.90 After the introduction of the 13-valent vaccine, the 6 additional serotypes included in PCV13 showed a reduced frequency of occurrence (3.12 isolates/year) as compared to the pre-PCV (4 isolates/year) and post-PCV7 (7.5 isolates/year) periods, while the nonvaccine serotypes increased (13.25 isolates/year post-PCV7 and 11.52 isolates/year post-PCV13 introduction as compared to 6.33 isolates/year in the pre-PCV phase).92\n\nIn Lebanon, the private sector introduced PCV7 in 2006, followed by PCV10 and PCV13 in 2010. The universal introduction of the vaccine by the government was done in 2015. The Lebanese Inter-Hospital Pneumococcal Surveillance Program was a 6-year (October 2005–December 2011) program wherein 257 samples were isolated from patients with IPD affected mostly by pneumonia (46.5%), bacteremia (21.5%), and meningitis (17.2%).94 The case-fatality rate was estimated to be 13.4%. Among affected patients, 33.1% were >60 years and 24.1% under 2 years. About 17.4% were penicillin resistant, with serotype 19F being the most common, followed by 6 and 14; 10.9% were MDR strains (19F and 14). IPD caused by vaccine serotypes was 41.4% for PCV7, 53.9% for PCV10, and 67.2% for PCV13. The most prevalent serotypes, overall, were those covered by PCVs: 19F, 6, 3, 14, 1, and 19A. In children <2 years, the most common serotypes/groups were 14, 19F, and 6. Serotype 3 was, surprisingly, the highest in those aged >60 years. The NVTs (not part of PCV7, 10, or 13) isolated were 22F, 33F, 11 A/D, 9N, 10A, 12F, 8, 15A, 15 B/C, 16F, 23A, 29A, 35B, and 38.\n\nThe NVT 24F has been reported to be an emerging serotype among patients with IPD (mostly [87.5%] <6 years of age with unknown pneumococcal vaccination status) in Lebanon, with 4 cases noted in 2019.95 The genome sequencing of this serotype, isolated from samples collected between 2013 and 2019, showed that it is highly virulent and antimicrobial resistant.95 The prevalence of this NVT among IPD cases in children has also been reported in the European and Western Pacific regions.64,68,70,96,97\n\nDuring a surveillance study conducted between September 2007 and August 2008 in Casablanca, serotypes 19F, 14, 23F, 6B, and 19A were found to be prevalent among pediatric (<5 years) IPD patients.81 Recently, a report was published on early neonatal respiratory distress, revealing meningitis caused by serotype 17F via vertical transmission.98\n\nPCV7 was incorporated into the Saudi Arabian NIP in 2008 and was replaced with the 13-valent vaccine in 2010.99 Between 2005 and 2010, serotypes 23F, 19F, 6B, 5, and 1 were commonly associated with invasive episodes among children <5 years.99 This period showed a notable decline in the PCV7 serotype 18C and a significant rise in the PCV13 serotype 19A.99 About 66% and 62% of isolates were reported to be penicillin and erythromycin resistant, respectively.99 Similarly, between 2009 and 2012, the serotypes 23F, 6B, 19F, 18C, 4, 14, and 19A (in decreasing order) were reported to cause IPD among patients <15 years of age.100 In this study, all pneumococcal isolates were found to be resistant to cotrimoxazole, while 77% and 36% were observed to be erythromycin and penicillin resistant, respectively. Penicillin resistance was higher among serotypes 23F, 6B, and 19F.100 In the post-PCV13 introduction phase (January 2012 to December 2014), serotypes commonly isolated from the Eastern province of Saudi Arabia included 11A, 19A, 17F, 23F, 3 and 19F.101 The previously rare but most prevalent serotype in this study, 11A (part of PPSV23), exhibited maximum penicillin resistance. Overall, 67.9% of isolates were resistant to both penicillin and macrolides, 17% to only penicillin and 5.6% to only macrolides.101 These reports indicate that there is widespread drug resistance among pneumococcal isolates in Saudi Arabia. Of the pneumococcal isolates collected from 24 Saudi Arabian hospitals between January and December 2009, 33% were resistant to penicillin G, 26% to erythromycin, and 11% to ceftriaxone.102\n\nIn Oman, PCV7 was introduced in 2008, followed by the implementation of PCV10 in 2010, and PCV13 in 2012, in response to global reports on the emerging MDR serotype 19A. Among adults, PPSV23 use was implemented for high-risk patients.103 IPD afflicted 45.5% of adult patients (≥51 years) in the period following PCV13 incorporation (2014–2016), with a maximum case-fatality rate of 21.7%.104 In comparison, 26.5% of the affected population was ≤5 years, where the case-fatality rate was 14.2%.104 Of note, 28% of the population was between 6 and 50 years, with a mortality rate of 8.1%. The major clinical presentations of IPD were pneumonia (52.3%), meningitis and septicemia (17.4% each). The most prevalent serotypes among all age groups were reported to be 12, 15, 19F, 3, 19A, and 22, while serotypes 1, 7F, 17F, 18C, and 9N/L had moderate prevalence. Serotypes 12, 19F, 23A, and 16F were commonly isolated from pediatric patients ≤5 years, whereas serotypes 3, 15, 19A, 19F, 22, 12, and 11 were common in adults (≥51 years). The most common serotypes in the 6–50 years’ age bracket were 1, 12, 15, and 7F. About 40.9% of these isolates were found to be resistant to penicillin.\n\n\nConclusions\n\nThe reduction in the occurrence of vaccine-type serotypes since the introduction of PCVs points towards the might of vaccines in combating deadly infectious diseases. However, growing antibiotic resistance, serotype switching and replacement, and the persistence of a few vaccine serotypes (especially serotypes 3 and 19A) indicates that both vaccine-type and nonvaccine-type pneumococcal serotypes still remain a global public health concern. Thus, there is an ever-increasing need to combat IPD via effective, new-generation vaccines that utilize effective immune mechanisms, especially in the case of serotype 3, which can evade the immune system. Limited serotype prevalence data are available for Iraq due to lack of facilities for laboratory studies. In addition, issues such as vaccine inaccessibility in the public sector, war and conflict situation, displacement camps and climate change characterized by high temperature, dust storms, drought and increased desertification are additional challenges for a successful pneumococcal vaccination program in the country. Thus, in Iraq and its neighboring countries in the EMR, improving surveillance would help provide the essential disease burden data required for refining vaccination strategies and improving outcomes. The active surveillance of NVT 33C, recently isolated from Iraqi children with nephrotic syndrome and sepsis, is essential to understand the degree of spread of the pathogen among Iraqi communities. In the PCV13 era, the emergence of serotype 24F in many regions of the world as one with maximum invasive potential and multidrug resistance warrants its periodic surveillance, as well as its inclusion in the next generation of pneumococcal vaccines. Improved polyvalency of vaccines, such as those under development by Inventprise and Vaxcyte, would help combat nonvaccine serotypes. Such an expanded coverage by the newer generation of vaccines is theoretically expected to reduce IPD cases caused by emerging non-PCV13 serotypes. In conjunction, continuous studies on molecular epidemiology of the pathogen within the EMR region would also help monitor antibiotic resistance patterns. We hope that this review guides policymakers and researchers to make informed decisions pertaining to the development and introduction of improved pneumococcal vaccines in Iraq.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nAcknowledgements\n\nWe would like to thank Adivitiya, Rosario Vivek and Dr. Rituraj Mohanty from IQVIA, India for writing assistance and providing insights.\n\n\nReferences\n\nChen H, Matsumoto H, Horita N, et al.: Prognostic factors for mortality in invasive pneumococcal disease in adult: a system review and meta-analysis. Sci. Rep. 2021; 11(1): 11865. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nG. B. D. Lower Respiratory Infections Collaborators: Estimates of the global, regional, and national morbidity, mortality, and aetiologies of lower respiratory infections in 195 countries, 1990-2016: a systematic analysis for the Global Burden of Disease Study 2016. Lancet Infect. 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Publisher Full Text\n\nMokaddas E, Albert MJ: Impact of pneumococcal conjugate vaccines on burden of invasive pneumococcal disease and serotype distribution of Streptococcus pneumoniae isolates: an overview from Kuwait. Vaccine. 2012; 30 Suppl 6: G37–G40. PubMed Abstract \| Publisher Full Text\n\nMokaddas E, Albert MJ: Serotype distribution and penicillin-non-susceptibility of Streptococcus pneumoniae causing invasive diseases in Kuwait: A 10-year study of impact of pneumococcal conjugate vaccines. Expert Rev. Vaccines. 2016; 15(10): 1337–1345. PubMed Abstract \| Publisher Full Text\n\nMokaddas EM, Shibl AM, Elgouhary A, et al.: Effect of the introduction of pneumococcal conjugate vaccines on serotype prevalence in Kuwait and Saudi Arabia. Vaccine. 2018; 36(43): 6442–6448. PubMed Abstract \| Publisher Full Text\n\nMokaddas E, Syed S, Albert MJ: The 13-valent pneumococcal conjugate vaccine (PCV13) does not appear to provide much protection on combined invasive disease due to the six PCV13 non-PCV7 serotypes 1, 3, 5, 6A, 7F, and 19A in Kuwait during 2010-2019. Hum. Vaccin. Immunother. 2021; 17(11): 4661–4666. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHanna-Wakim R, Chehab H, Mahfouz I, et al.: Epidemiologic characteristics, serotypes, and antimicrobial susceptibilities of invasive Streptococcus pneumoniae isolates in a nationwide surveillance study in Lebanon. Vaccine. 2012; 30 Suppl 6: G11–G17. PubMed Abstract \| Publisher Full Text\n\nReslan L, Finianos M, Bitar I, et al.: The Emergence of Invasive Streptococcus pneumoniae Serotype 24F in Lebanon: Complete Genome Sequencing Reveals High Virulence and Antimicrobial Resistance Characteristics. Front. Microbiol. 2021; 12: 637813. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMunoz-Almagro C, Ciruela P, Esteva C, et al.: Serotypes and clones causing invasive pneumococcal disease before the use of new conjugate vaccines in Catalonia, Spain. J. Infect. 2011; 63(2): 151–162. PubMed Abstract \| Publisher Full Text\n\nJanoir C, Lepoutre A, Gutmann L, et al.: Insight Into Resistance Phenotypes of Emergent Non 13-valent Pneumococcal Conjugate Vaccine Type Pneumococci Isolated From Invasive Disease After 13-valent Pneumococcal Conjugate Vaccine Implementation in France. Open Forum. Infect. Dis. 2016; 3(1): ofw020. Publisher Full Text\n\nNzoyikorera N, Lehlimi M, Diawara I, et al.: Early neonatal respiratory distress revealing meningitis caused by Streptococcus pneumoniae serotype 17F: a case report. Afr. Health Sci. 2021; 21(4): 1711–1714. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShibl AM, Memish ZA, Al-Kattan KM: Antibiotic resistance and serotype distribution of invasive pneumococcal diseases before and after introduction of pneumococcal conjugate vaccine in the Kingdom of Saudi Arabia (KSA). Vaccine. 2012; 30 Suppl 6: G32–G36. PubMed Abstract \| Publisher Full Text\n\nal-Sherikh YA, Gowda LK, Ali MMM, et al.: Distribution of serotypes and antibiotic susceptibility patterns among invasive pneumococcal diseases in Saudi Arabia. Ann. Lab. Med. 2014; 34(3): 210–215. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlnimr AM, Farhat M: Phenotypic and molecular study of pneumococci causing respiratory tract infections. A 3-year prospective cohort. Saudi Med. J. 2017; 38(4): 350–358. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShibl AM, Memish ZA, Kambal AM, et al.: National surveillance of antimicrobial resistance among Gram-positive bacteria in Saudi Arabia. J. Chemother. 2014; 26(1): 13–18. Publisher Full Text\n\nBizri AR, Althaqafi A, Kaabi N, et al.: The Burden of Invasive Vaccine-Preventable Diseases in Adults in the Middle East and North Africa (MENA) Region. Infect. Dis. Ther. 2021; 10(2): 663–685. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAl-Jardani A, Al Rashdi A, Al Jaaidi A, et al.: Serotype distribution and antibiotic resistance among invasive Streptococcus pneumoniae from Oman post 13-valent vaccine introduction. Int. J. Infect. Dis. 2019; 85: 135–140. PubMed Abstract \| Publisher Full Text" }	[ { "id": "174929", "date": "15 Jun 2023", "name": "Godfrey M. Bigogo", "expertise": [ "Reviewer Expertise Epidemiology of 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 authors sought to describe the Streptococcus pneumoniae serotype landscape in Iraq where there is inadequate surveillance for this pathogen. Published data from Iraq's neighbors is extensively used. Citations are properly done for all data used in the article. Two suggestions for the authors to consider:\nI would strengthen the conclusion by stating that the serotypes in Iraq are likely to be similar to those circulating in the neighboring countries due to similarities including ecological conditions, cultural practices (like mass gatherings during worship).\n\nIs burden data available for any of Iraq's neighbors (Iran, Kuwait, Saudi Arabia etc.). If so, how does that compare with Iraq's IPD incidence of 0.62/100,000?\nMinor issue: The opening statement in the Introduction could be rewritten as follows; \"....for devastating morbidity and mortality among children below five years of age, adolescents, adults above 60 years of age, the immunocompromised population...\".\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? Partly", "responses": [ { "c_id": "10789", "date": "17 Jan 2024", "name": "Delan Ikram", "role": "Author Response", "response": "1. I would strengthen the conclusion by stating that the serotypes in Iraq are likely to be similar to those circulating in the neighboring countries due to similarities including ecological conditions, cultural practices (like mass gatherings during worship). Author Response: Thank you for your kind comment. This statement has been added to the conclusions section (Page 15): “Pneumococcal serotypes in Iraq are likely to be similar to those circulating in the neighboring countries due to similarities including ecological conditions and cultural practices like mass gatherings during worship. Additionally, based on a comment by the second reviewer we have also added the following statement: “However, serotype replacement and capsule switching are regulated by selection pressure unique to the population.” 2. Is burden data available for any of Iraq's neighbors (Iran, Kuwait, Saudi Arabia etc.). If so, how does that compare with Iraq's IPD incidence of 0.62/100,000? Author Response: The authors would like to thank the reviewer for this comment. As per the available literature, the prevalence of invasive S. pneumoniae infections was found to be low (2.5%) among children in Iran (Avarvand et al., 2021). This data is already available in the section on Iran (Page 12). In Saudi Arabia, the incidence of confirmed IPD cases was estimated to be 2.5−21.6 per 100,000 children (<5years) (Almazrou et al., 2016). This has now been added to the section on Saudi Arabia (Page 14) as: “A multicenter, prospective study conducted between June 2007 and January 2009 estimated the incidence of confirmed IPD cases to be 2.5−21.6 per 100,000 children <5 years.” Its reference has been added to the end of the reference list as per journal guidelines. Further we have also added a statement to Page 8: “However, inadequate surveillance as well as inconsistent reporting methods are associated with an underestimation of pneumococcal diseases burden in the Gulf countries (Mokaddas et al., 2018)”. 3. Minor issue: The opening statement in the Introduction could be rewritten as follows; \"....for devastating morbidity and mortality among children below five years of age, adolescents, adults above 60 years of age, the immunocompromised population...\". Author Response: Thank you for your suggestion. The opening statement in the Introduction (Page 2) has now been modified as follows: “Streptococcus pneumoniae, the causative agent of pneumococcal disease, is responsible for devastating morbidity and mortality among children <5 years of age, adolescents, adults >60 years of age, the immunocompromised population, patients with chronic diseases, and smokers.”" } ] }, { "id": "208951", "date": "16 Oct 2023", "name": "Karthik Subramanian", "expertise": [ "Reviewer Expertise Pneumococcal infections", "host-pathogen interactions", "bacterial pathogenesis" ], "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 review aims to summarize the emerging pneumococcal serotypes in Iraq and the middle eastern region to determine the effectiveness of the vaccines and help policy makers in Iraq to make informed decisions regarding introduction of improved vaccines. I believe this review is important and timely not just for the eastern Mediterranean region, but also has global relevance since it is a place of mass religious gatherings and pneumococcus is widely known for its horizontal gene transfer and global spread of resistant clones. In my opinion the authors can summarize the data and present it in a way that makes it easily comprehensible for readers rather than simply presenting the data on serotype prevalence. Below are my specific comments.\nMost of the data presented in this review is drawn from systematic reviews. Since the inferences drawn in the review rely on these systematic reviews, it is important to assess the QC of these reviews such as clinical heterogeneity, statistical heterogeneity as well as models used for meta analysis. In some cases, the authors refer to systematic reviews from very few geographical regions of a country - e.g. Iran. How reliable are these studies? The reliability of the data presented is heavily dependent on the QC of these meta analyses. Therefore the authors need to ensure that they only present data from robust systematic reviews.\n\nSection on pneumococcal serotypes - I suggest that the authors tabulate the pneumococcal serotypes associated with colonization vs. invasive disease along with the supporting references.\n\nMany times the authors list some serotypes as frequently associated with carriage and IPD. This does not make sense. For e.g. page 6, under data from Iran, 19F is classified into both IPD and carrier populations. Similarly, serotype 23F is listed under both carriage and IPD.\n\nFor the data on countries from EMR region, age-wise stratification of serotype prevalence and correlation with antibiotic resistance profile is needed.\n\nThe authors need to refrain from claiming that they can draw inference for Iraq from neighboring countries since although regions are located geographically closer, serotype replacement and capsule switching are regulated by selection pressure unique to the population. Even in this review there are unique serotypes associated with Iraq such as NVT 33C that is not found elsewhere in the region.\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": "10790", "date": "17 Jan 2024", "name": "Delan Ikram", "role": "Author Response", "response": "1. Most of the data presented in this review is drawn from systematic reviews. Since the inferences drawn in the review rely on these systematic reviews, it is important to assess the QC of these reviews such as clinical heterogeneity, statistical heterogeneity as well as models used for meta analysis. In some cases, the authors refer to systematic reviews from very few geographical regions of a country - e.g. Iran. How reliable are these studies? The reliability of the data presented is heavily dependent on the QC of these meta analyses. Therefore the authors need to ensure that they only present data from robust systematic reviews. Author Response: Thank you for your comment. As suggested, we have assessed the articles (systematic reviews/meta-analysis) which were used in the manuscript. All studies included in this review were found to be reliable. Heterogeneity was assessed in each study and further analysis was performed accordingly. Sensitivity analysis and subgroup analysis were performed even if there was marginal heterogeneity. Quality assessment was performed for most studies included in systematic reviews and score was acceptable in each review. Regarding the systematic review and meta-analysis conducted among Iranian children from three geographical regions of the country, the study was found to be robust with a good quality score of 8 and no publication bias (as assessed via a funnel plot). So, overall, all systematic reviews are reliable in terms of heterogeneity and analysis. We have also added this statement to the Introduction section (Page 3). Our assessment has also been briefly compiled below (we had made a table but since we are not able to upload that via the journal portal we have copy-pasted the column information below): Study: Avarvand et al., 2021 Number of studies included: 7 studies I2/Heterogeneity: There was a significant heterogeneity among the studies (P<0.001; I2 = 98.26%). Mitigation: 1. Random effect model to mitigate heterogeneity impact 2. Subgroup analysis e.g., for geographical regions and detection methods for prevalence 3. Sensitivity analyses were performed by removing one study at a time to evaluate the impact of each study on the summary results and between-study heterogeneity Interpretation in terms of significant heterogenous (Yes/No): This SLR included good quality papers and heterogeneity was assessed via I2 test (P<0.001; I2 = 98.26%) so random effect model was used along with subgroup and sensitivity analysis. Publication bias was also assessed by funnel plot, which was symmetric, showed no evidence of publication bias and confirmed by the results of Begg’s rank correlation (z = 0.30, P = 0.76) and Egger’s regression result (t = 0.32, P = 0.76). Study: Weinberger et al., 2010 Number of studies included: 9 studies I2/Heterogeneity: 1. For Pneumonia risk estimation: All of the serotypes exhibited low levels of heterogeneity among studies based on the I2 values, with the exception of serotypes 9V and 23F, which exhibited moderate levels of heterogeneity. 2. Foe meningitis risk estimation: Overall, substantial heterogeneity among studies was not there. Mitigation: 1. Random effect model and fixed effect model both were used to compare impact of heterogeneity 2. Logistic regression Interpretation in terms of significant heterogenous (Yes/No): No significant heterogeneity so considered Study: Ballsells at al., 2018 Number of studies included:13 datasets (9 included data provided by collaborators and 4 from published studies) I2/Heterogeneity: Heterogeneity for each serotype included in the meta-analyses using the I2 where values of less than 25% indicate low heterogeneity, of 25% to 50% as moderate and above 50% as considerable heterogeneity. Heterogeneity was negligible to moderate for serotypes with a higher or lower invasive disease potential than 19A, except for 12F, 15A, 15BC. Sensitivity analyses did not influence the heterogeneity for these meta estimates. Mitigation: Random effect model for meta-analysis was used as substantial heterogeneity in the included studies was anticipated. Sensitivity analyses were conducted to explore the effect of differences across datasets on overall meta-estimates by restricting analysis to datasets with the following characteristics: a) ≥70% PCV coverage, b) low prevalence of HIV, c) industrialized country settings, d) case counts from years subsequent to introduction of a higher valent PCV (10/13), e) implementation of PCV10 or PCV13 Interpretation in terms of significant heterogenous (Yes/No): Less heterogeneity so considered Study: Chen et al., 2021 Number of studies included: 26 studies I2/Heterogeneity: Heterogeneity evaluated using I2 statistics was interpreted as follows: I2= 0%, no heterogeneity; I2> 0% but < 25%, minimal heterogeneity; I2≥ 25% but < 50%, mild heterogeneity; I2≥ 50% but < 75%, moderate heterogeneity; and I2≥ 75%, strong heterogeneity. Mitigation: For outcome of mortality: • Age >64 vs <65 years: I2 32.2% • State of septic shock at admission vs no septic shock: I2 0% • non-community-acquired infection vs community-acquired infection: I2 10.1% • Underlying chronic diseases: I2 72.9% Interpretation in terms of significant heterogenous (Yes/No): Acceptable quality and heterogeneity of studies so considered Study: Chamkhaleh et al., 2020 Number of studies included: 8 studies I2/Heterogeneity: NA Mitigation: NA Interpretation in terms of significant heterogenous (Yes/No): Acceptable quality of studies so considered Study: Johnson et al., 2010 Number of studies included: 160 studies I2/Heterogeneity: Homogenous data: In Africa, ten serotypes had an ICC (Intraclass correlation) <0.2, thus the meta-estimates for these ten serotypes are particularly sensitive to the addition or removal of serotype data in this region. Asia and LAC also had a large number of serotypes with ICC<0.2 (six and five serotypes, respectively). By contrast, in Oceania, only serotype 14 had an ICC<0.2, indicating relative homogeneity in the reported serotype proportion data for this region. Mitigation: Marginal random-effects meta-analysis Interpretation in terms of significant heterogenous (Yes/No): No heterogeneity with 160 studies data so considered Study: Balsells et al., 2017 Number of studies included: 68 studies I2/Heterogeneity: Datasets were heterogenous Mitigation: Random effects model (DerSimonian-Laird method). Heterogeneity was addressed by analyzing the most comparable data and case definitions. Analysis was stratified by PCV vaccine formulation and used data for children of the same age (<5 years) whenever possible. Sensitivity analysis was performed. Interpretation in terms of significant heterogenous (Yes/No): Though data was heterogenous but was having good amount of data and analyzing comparable data only so considered. 2. Section on pneumococcal serotypes - I suggest that the authors tabulate the pneumococcal serotypes associated with colonization vs. invasive disease along with the supporting references. Author Response: The authors would like to thank the reviewer for this suggestion. We have created Table 1 (Page 5) which provides the “Colonization or invasive potential of S. pneumoniae serotypes”. As per journal guidelines all tables have been shared in a separate document. 3. Many times the authors list some serotypes as frequently associated with carriage and IPD. This does not make sense. For e.g. page 6, under data from Iran, 19F is classified into both IPD and carrier populations. Similarly, serotype 23F is listed under both carriage and IPD. Author Response: Thank you for your comment. Both serotypes 19F and 23F cause invasive disease but are also common in carriage (Sandgren et al., 2004). This can be clearly visualized in the newly created tables 1 and 3 of the revised manuscript. The ability of pneumococcal serotypes to colonize or cause invasive disease may be influenced by both host-derived as well pathogen-derived factors. As per published literature, both serotypes 19F and 23F have a low invasive potential and are primarily found in carriers (Burgess et al., 2008). These serotypes are known to be associated with an impaired antibody response following invasive pneumococcal disease (Littorin et al., 2018; Soininen et al., 2001). Further, in addition to the capsular serotype, the clonal type may also determine the disease causative potential of pneumococcal serotypes as published by Sandgren et al. (2004) who reported that clones belonging to the same serotype showed different abilities to cause invasive disease. 4. For the data on countries from EMR region, age-wise stratification of serotype prevalence and correlation with antibiotic resistance profile is needed. Author Response: Thank you for your suggestion. We have incorporated Table 3 into the manuscript (Pages 9−11) which provides an “Age-wise stratification and antibiotic resistance among S. pneumoniae isolates in the Eastern Mediterranean Region”. As per journal guidelines all tables have been shared in a separate document. 5. The authors need to refrain from claiming that they can draw inference for Iraq from neighboring countries since although regions are located geographically closer, serotype replacement and capsule switching are regulated by selection pressure unique to the population. Even in this review there are unique serotypes associated with Iraq such as NVT 33C that is not found elsewhere in the region. Author Response: The authors would like to thank the reviewer for this suggestion. We have removed this statement from the abstract and from the Introduction section (Page 3, paragraph 2) and modified the paragraph to ensure readability." } ] } ]	1	https://f1000research.com/articles/12-435
https://f1000research.com/articles/12-1604/v1	28 Dec 23	{ "type": "Research Article", "title": "Iron deficiency anemia in H.pylori pediatric patients and the role of IL-1β", "authors": [ "Selvi Nafianti", "Iskandar Japardi", "Iqbal Pahlevi Adeputra Nasution", "Oke Rina Ramayani", "Rosita Juwita Sembiring", "Dina Keumala Sari", "Supriatmo Supriatmo", "Sulaiman Yusuf", "Iskandar Japardi", "Iqbal Pahlevi Adeputra Nasution", "Oke Rina Ramayani", "Rosita Juwita Sembiring", "Dina Keumala Sari", "Supriatmo Supriatmo", "Sulaiman Yusuf" ], "abstract": "Background Helicobacter pylori infection has long been recognized to be the cause of iron deficiency anemia (IDA). However, the data in this study shows that only some of children infected with Helicobacter pylori developed an IDA. The objective was to analyze the correlation between IL-1β levels with the incidence of IDA in children with Helicobacter pylori infection.\n\nMethods The study was a cross-sectional in which subjects with Helicobacter pylori infection were examined for IL-1β levels along with the incidence of IDA. The study was carried out for one full year period, started from January 2022 to January 2023, at the H. Adam Malik Hospital in Medan and its affiliation. The subjects in this study were pediatric patients who experienced abdominal pain and range between the ages of 2-18 years old. The entire samples were taken by using consecutive sampling. Subjects’ blood sampling were extracted for IL-1β examination (ELISA) and diagnostic tests of Iron Deficiency Anemia, while the diagnosis of H. pylori infection was done by endoscopy (CLO)\n\nResults The subjects consisted of 52 children in which 26 of them have Helicobacter pylori (+) and of those 26 children, 23 had IDA (prevalence ratio 11.5 (95% CI 3.015-43.864). There were indications that patients with H. pylori infection (+) is 11.5 times more likely to develop IDA. The cut-off point for IL-1β levels based on the freqtableuency of IDA in children with H. pylori infection is ≤ 1.3 pg/mL The sensitivity and specificity value of IL-1β levels in predicting IDA was 87% and 66.7% respectively. The positive and negative predictive value was 95.2% and 40% (respectively) with the accuracy level of 84.6 %.\n\nConclusion There is a significant correlation between Helicobacter pylori infection and IDA. Interleukin-1β levels were significantly higher in children infected with H. pylori (+) in comparison to H. pylori (-).", "keywords": [ "H.pylori", "Iron Deficiency Anemia", "IL-1β Levels" ], "content": "Introduction\n\nThe incidence of IDA and H. pylori infection are believed to be associated, indicating a substantial improvement in IDA with successful H. pylori eradication. One meta-analysis study revealed that combination therapy for H. pylori elimination with administration of iron was more potent in treating IDA.1 While, other meta-analyses indicated different results, where the accrual of Hb levels following H. pylori eradication was not significant and IDA refractory events after H. pylori eradication were still found, especially in severe cases.2\n\nThe inflammatory process has a crucial impact in the occurrence of IDA with H. pylori infection. Gastric mucous membrane layer inflammation is influenced by Interleukin (IL)-1β. The surge of IL-1β production in the antrum and corpus then stimulates parietal cells to inhibit gastric acid secretion and increase the transcription of other proinflammatory cytokines such as interferon-α, IL-6, and IL-8.3 Multi center studies (Brazil, Chile and England) in adolescents show that H. pylori infection can lead to decreased iron absorption in children by inducing IL-1B increase.4\n\nOnly few H. pylori-infected children experience IDA. One of the pro-inflammatory cytokines, particularly IL-1β, increased significantly in this infection and is associated with impaired iron absorption. Therefore, the correlation between IL-1β levels and the incidence of IDA in H. pylori infection needs a further study.\n\n\nMethods\n\nThis research was conducted in the period between January 2022 to January 2023. The subjects for this study were children who experienced recurrent abdominal pain, nausea and vomiting. The selections of subjects begin with determining the target population, the accessible population, the method of selection, sample size, as well as determining the inclusion and exclusion criteria. The study has received the necessary approval from the University Sumatera Utara Ethics Commission (No: 1185/KEP/USU/2021).\n\nMeasurement of serum IL-1β levels was carried out using the ELISA method. The examination uses a quantitative sandwich enzyme immuno-assay technique. Previously, a monoclonal antibody specific for IL-1β was coated on the microplate. Standard, sample, control and conjugate were introduced into the well with a pipette and the presence of IL-1β would be paired by immobilized antibody with a monoclonal enzyme-linked antibody specific for IL-1β. The color intensity formed would be proportional to the amount of bounded IL1B.\n\nEndoscopic examination was necessary to support the occurrence of Helicobacter Pylori infection showing a hyperemic appearance of the gastrointestinal mucosa, which is also supported by CLO examination. Preparation for the CLO examination by screening the patient who was not taking antibiotics, PPI (proton pump inhibitor) and bismuth 2 weeks prior the procedure.\n\nStudy subjects had to meet the following inclusion criteria: pediatric patients aged 2-18 years who experienced recurrent abdominal pain, nausea and vomiting; the patient’s parents/guardians’ writtenconsent to be included as a research subject; recently not getting antibiotics, bismuth, H2 antagonists, proton pump inhibitors, and any immunomodulators in the last four weeks; patients who have not taken iron supplements in the last 3 months; in good nutritional status and no history of gastrointestinal surgery. The exclusion criteria were patients with malignancy, immunosuppression and worm infections.\n\nTo analyze the correlation between subject characteristics and the presence of H. pylori infection, the Chi square test (if the nominal data is 2 values), the Kruskall Wallis test (the nominal data is more than 2 values), the independent T test (for interval/ratio data) were used. The Mann Whitney test was used to determine the correlation between IL-1β laboratory characteristics and the presence of H. pylori infection. Chi square test was a bivariate test used to find the presence of H. pylori infection and IDA. For IL-1β levels, the cut-off value was sought and plotted onto the ROC curve to gain sensitivity, specificity, positive and negative predictive values.\n\n\nResults\n\nThe population study were 52 children who experienced recurrent abdominal pain, nausea and vomiting and consisting of 26 H. pylori (+) and 26 H. pylori (-) patients. All children involved in this study met the inclusion criteria. Table 1 contained complete subject characteristic.\n\nTable 2 shows the analysis results of the corellation between H. pylori infection and IDA.\n\n* Chi square, IDA = Iron Deficiency Anemia.\n\nOf the 26 children with H. pylori (+), there were 23 (88.5%) with IDA. Meanwhile, out of 26 children without H. pylori, only 2 (7.7%) had IDA. The analysis using the Chi Square test demonstrated a significant correlation between H. pylori infection and iron deficiency anemia (p<0.001). The Prevalence Ratio value obtained was 11.5 (95% CI 3.015 – 43.864) meaning that H. pylori-infected (+) children would be 11.5 times more probable to have iron deficiency anemia than children with H. pylori (-). The analysis with ROC curve (Figure 1) demonstrated that the AUC area of IL-1β levels in predicting IDA H. pylori-infected children was 87% with p=0.041 and 95% CI 65.7%-100%. This shows that IL-1β levels can be used to predict IDA in H. pylori (+) children.\n\nAs seen on the line chart in Figure 2, the cut-off value of IL-1β levels in predicting IDA in H. pylori (+) children is 1.3 pg/mL. Table 3 displays the accuracy values which include sensitivity, specificity, positive predictive value (PPV), negative predictive values (NPV) and the accuracy of IL-1β levels in predicting IDA in H. pylori (+) children.\n\nThe sensitivity value of IL-1β levels in predicting IDA was 87%, the specificity value was 66.7%, the positive predictive value (PPV) was 95.2%, the negative predictive values (NPV) was 40% and the accuracy level was 84.6%.\n\n\nDiscussion\n\nMost studies reveal that persistent H. pylori infection in the mucosa of the gaster can cause iron deficiency anemia or IDA, especially in the population of children and adolescents. The cause of H. pylori infection-associated IDA is still indefinite, where in general the majority of pediatric patients with IDA associated with H. pylori infection do not display any signs of blood loss as a result of gastrointestinal hemorrhagic lesions. In general, in developing countries with low socioeconomic levels, it is often difficult to maintain an adequate iron balance where intake of iron-rich foods with high iron bioavailability from animals is rare or nonexistent. Lack of vitamin C intake combine with frequent consumption of tea and a diet high in phytates and polyphenols are risk factors for IDA.5 Iron deficiency in children will also affect learning ability, lack of ability memory, lack of concentration, failure in education and affect children’s cognitive and motor development.6,7 Our study is the first study of the association between IL-1β and the incidence of IDA in children with abdominal pain due to H. pylori. This study showed a corellation between H. pylori infection and IDA (p<0.001) 95% CI 3.015-43.865) (Table 2).\n\nRecurrent abdominal pain (RAP) is a frequent incident in children, characterized by symptoms of 3 or more episodes of pain over a 3-month period that interferes with normal daily activities.8,9 The occurrence of RAP caused by H. pylori is inconclusive, despite the fact that several studies have reported that CagA+ strains might be causing recurrent abdominal pain in H. pylori-infected children. Cytotoxin-Associated Gene A (CagA) is one of the primary virulence factors in H. pylori infection.10 This study shows that abdominal pain in the H. pylori (+) infection group is more dominant than H. pylori (-) around 65.4% (Table 1). Another possible cause of abdominal pain in children with H. pylori (+) is the gastric mucosa inflammation. Interleukin-1β cooperates with other inflammatory cytokines to stimulate neutrophils in the mucosa of the gaster, causing inflammation.\n\nInflammation that occurs in H. pylori infection depends on bacterial virulence factors and the immune response of the host. The occurrence of H. pylori infection results in inflammation that persists in the gastric mucosa and is chronic, the host immune system, both innate and adaptive immunity plays a crucial role in the pathogenesis of gastroduodenal disorders in response to the inflammatory process against infection by H. pylori. This situation is mediated by a series of pro (IL-1β, IL-6 and IL-8) and anti (IL-1RN and IL-10) inflammatory cytokines.11\n\nInterleukin 1β (IL-1β) is involved in various cellular activities, such as the inflammatory response and gastric acid secretion. The inflammatory response of H. pylori infection help activaties neutrophils and lymphocytes which cause epithelial damage by cytokines release. The correlation between cytokines with its nflammation degree and neutrophil activity is positive, where the cytokine level is proportional to the degree of inflammation and also the neutrophil activity.12\n\nInterleukin-1β is a proinflammatory cytokine that acts as an acute phase response and is associated with disease onset. These cytokines can be detected in various medical conditions, including H. pylori infection. During inflammation and infection IL-1β is released and causes inflammatory response which affects chronic diseases as well as H. pylori infection.13 This study found significant differences in Interleukin-1β levels in H .pylori (+) compared to H. pylori (-) with p<0.001. This proves that IL-1β is crucial in the severity of H. pylori infection and has clinical aspects for H. pylori-infected patients’ management to prevent gastric malignancy in the future.\n\nOur study showed the correlation between H. pylori infection and IDA (p<0.001) 95%CI 3.015-43.865). This can be assessed from the ROC curve analysis (Figure 1) where the AUC area obtained from IL-1β levels can predict IDA in H. pylori (+) children that is equal to 87% with p=0.041 and 95% CI 65.7%-100%.\n\nIn the study, we found that the cut-off value of IL-1β levels for predicting IDA in children with H. pylori (+) was 1.3 pg/mL with a sensitivity value of 87% and a specificity value of 66.7% (Figure 2 and Table 3). The cut off value of 1.3 pg/mL is important because this value portrays the accuracy of IL-1B in predicting IDA in infection caused by H. pylori.\n\nThe pathophysiology infection caused by H. pylori initiates an inflammatory response through a process of mediator release, such as cytokines which interacts between immunocompetent/hematopoietic cells and between the immune system/neuroendocrine system. Interleukin-1β (IL-1β) induces the release of other interleukins such as IL-8 and the combination of the two cytokines affects neutrophil activation in the gastric mucosa of H. pylori-infected patients.14\n\nIn addition, IL-1β can reduce gastric acidity by suppressing gastric acid secretion, through regulation of H+/K+ATPase expression and suppressing gastrin release, which in turn suppresses Sonic Hedgehog gene, causing gastric atrophy.15 If the above situation does not get an immediate treatment, it will eventually lead to stomach cancer. This decrease in gastric secretion can also cause disturbances of iron metabolism, where gastric acid is important for iron absorption by converting ferric iron into ferrous iron which is more easily absorbed.\n\n\nConclusions\n\nThis research found a significant correlation between Helicobacter pylori infection and iron deficiency anemia, even though the mechanism is not fully comprehensive. H. pylori-infected children had significantly different IL-1β levels compared to H. pylori (-), demonstrating that IL-1β is crucial in determining how severe an infection is and that treatment of infection with IL-1β could help prevent future gastric cancer.", "appendix": "Data availability\n\nOpen Science Framework: Iron Deficiency Anemia in H. pylori Pediatric Patients and the Role of IL-1β, https://doi.org/10.17605/OSF.IO/7WK6A. 16\n\nThis project contains the following underlying data:\n\n- Revised Database Selvi Nafianti.xlsx (questionnaire response and laboratory measurement data)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nHuang X, Qu X, Yan W, et al.: Iron deficiency anaemia can be improved after eradication of Helicobacter pylori. Postgrad. Med. J. 2010 May; 86(1015): 272–278. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGheibi S, Farrokh-Eslamlou H, Noroozi M: Refractory iron deficiency anemia and Helicobacter Pylori Infection in pediatrics: A review. Iranian Journal of Pediatric Hematology Oncology. 2015; 5: 50–64. PubMed Abstract\n\nChen ST, Ni YH, Li CC, et al.: Hepcidin correlates with interleukin-1β and interleukin-6 but not iron deficiency in children with Helicobacter pylori infection. Pediatr. Neonatol. 2018 Dec 1; 59(6): 611–617. Publisher Full Text\n\nQueiroz DMM, Rocha AMC, Crabtree JE: Unintended consequences of Helicobacter pylori infection in children in developing countries: Iron deficiency, diarrhea and growth retardation. Gut Microbes. 2013; 4: 494–504. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTahir E, Ayotte P, Little M, et al.: Anemia, iron status, and associated protective and risk factors among children and adolescents aged 3 to 19 years old from four First Nations communities in Quebec. Can. J. Public Health. 2020 Oct 1; 111(5): 682–693. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYoon SH, Kim DS, Yu ST, et al.: The usefulness of soluble transferrin receptor in the diagnosis and treatment of iron deficiency anemia in children. Korean J. Pediatr. 2015 Jan 15; 58(1): 15–19. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHammoodi MS, Al-Ani MH: Coexistence of iron deficiency anemia with Helicobacter pylori infection among children aged 6 to 12 years in Erbil city. Med. J. Tikrit Univ. 2019; 25(2): 121–130. Publisher Full Text\n\nAlimohammadi H, Fouladi N, Salehzadeh F, et al.: Childhood recurrent abdominal pain and Helicobacter pylori infection, Islamic Republic of Iran اإلسالميةإيرانمجهوريةيفالبوابيةةَّ بامللويوالعدوىالطفولةمرحلةيفاملتكررالبطنياألمل. East Mediterr. Health J. 2016; 22: 860–864. PubMed Abstract \| Publisher Full Text\n\nHassan Z, Ahmed R, Hussain S, et al.: Helicobacter pylori infection in children with recurrent abdominal pain. Prof. Med. J. 2022 Apr 30; 29(05): 681–685. Publisher Full Text Reference Source\n\nCharlotte OIL, Bénédicte ANL, Arnaud MO, et al.: Role of Helicobacter pylori Infection in Recurrent Abdominal Pain of the Child in Brazzaville. Open J. Pediatr. 2020; 10(04): 587–599. Publisher Full Text\n\nVianna JS, Almeida da Silva PE, Bastos RI: Genes de patogenicidade de Helicobacter pylori, polimorfismos de citocinas e fatores ambientais afetam o desenvolvimento de doenças gástricas: uma visão geral. Revista de Epidemiologia e Controle de Infecção. 2016 Oct 4; 6(4). Publisher Full Text\n\nSun X, Cai H, Li Z, et al.: Association between IL-1β polymorphisms and gastritis risk. Medicine (United States). 2017 Feb 1; 96(5): e6001. Publisher Full Text\n\nDi Iorio A, Ferrucci L, Sparvieri E, et al.: Serum IL-1β levels in health and disease: A population-based study. “The InCHIANTI study.”. Cytokine. 2003 Jun 21; 22(6): 198–205. Publisher Full Text\n\nEl-Omar EM: The importance of interleukin 1B in Helicobacter pylori associated disease. Gut. 2001; 48: 743–747. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHong JB, Zuo W, Wang AJ, et al.: Helicobacter pylori Infection Synergistic with IL-1β Gene Polymorphisms Potentially Contributes to the Carcinogenesis of Gastric Cancer. Int. J. Med. Sci. 2016 Apr 8 [cited 2023 Aug 15]; 13(4): 298–303. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNafianti S, Japardi I, Nasution IPA, et al.: Iron Deficiency Anemia in H.pylori Pediatric Patients and the Role of Il-1β. [Dataset]. OSF. 2023. Publisher Full Text" }	[ { "id": "257446", "date": "02 Apr 2024", "name": "Fernando Javier Barreyro", "expertise": [ "Reviewer Expertise Gastroenterology" ], "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 by Niafanti et al explored the correlation between IL-1β levels with the incidence of IDA in pediatric population with Helicobacter pylori infection in Indonesia. The authors used a monocenter cross-sectional study taking data from children who consulted of recurrent abdominal pain, nausea and vomiting who underwent upper endoscopy from 2022 to 2023. The authors observed an association between IL-1β and the incidence of IDA in children with abdominal pain due to H. pylori. The results are reported in a clear and well-organized manner. The data have been gathered appropriately and were interpreted adequately. Still, there are some issues that should be addressed in order to increase the overall quality of this work.\nMajor comments:\nSample calculation based on preliminary data on H. pylori related IDA is necessary. Otherwise, this evidence should be presented as exploratory. Celiac disease should be in the exclusion criteria list. All the patients must have a duodenal biopsy, and at least aTTG-IgA test.\n\nMinor comments\n\nIn method section, is not clear why the authors describe Kruskal Wallis test (non-parametric test for ordinal or continuous variable) as a 2x2 test for more than 2 values. Chi square test fits OK for this analysis. Please revised and describe the statistical methods by variable type: categorical, and ordinal or continuous by distribution. Statistical software must be added Endoscopic gastric mucosa grading (eg. Kyoto), and histological gastric mucosa findings should be described (eg. Updated Sidney or OLGA, OLGIM) Typing polishing should be done all over the manuscript, e.g.: “The cut-off point for IL-1β levels based on the frequency of IDA in children with H. pylori infection is ≤ 1.3 pg/mL” for “The cut-off point for IL-1β levels based on IDA incidence in children with H. pylori infection is ≤ 1.3 pg/mL”\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?\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? Yes", "responses": [] }, { "id": "298625", "date": "08 Jul 2024", "name": "Yuliasih Yuliasih", "expertise": [ "Reviewer Expertise Internal medicine and 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\nThe title and topic raised in this article are interesting, however, the execution of the research and writing in several parts of the manuscript are still inadequate and still need to be corrected and confirmed. The most important parts to improve are the title, method and data presentation. While the title states the role of IL-1β, the manuscript does not explain how this conclusion can be reached. There was only a correlation assay in the group with H. pylori (+). In addition, it is important to present the IDA status of each patient and their IL-1β levels. Last but not least, table 3 shows the majority of IL-1β levels were low (≤1.3 pg/mL) in patients with H. pylori (+). This suggests that IL-1β may not be the key cytokine in this inflammatory process.\nDetailed other comments: - Adjust the abstract if new results are displayed. - The background is still not strong enough, you can add more reasoning and urgency to this research. Especially the reasons for choosing this cytokine among other cytokines. Please also readjust the introduction to the title, if the title is updated. - CLO/endoscopy results also need to be displayed. - Exclusion and inclusion criteria need to be clarified again. - How the patient is diagnosed also needs to be mentioned in the manuscript. - Nutritional status and socioeconomic criteria can be subjective, please clarify. - It looks like come data in figure 1, 2, and table 3 are redundant. It would be better if it was displayed compactly, and other more important data was displayed. - Improve the discussion because it does not support your results and lacks continuity to create a conclusion.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [] } ]	1	https://f1000research.com/articles/12-1604
https://f1000research.com/articles/11-561/v1	23 May 22	{ "type": "Research Article", "title": "Misconceptions about COVID-19 vaccine among adults in Saudi Arabia and their associated factors: A cross-sectional study conducted in 2021", "authors": [ "Fatma I. Albeladi", "Eman A. Kubbara", "Marwan A. Bakarman", "Turki Al Amri", "Rasha Eid", "Najla Alyazidi", "Ameera Alkhamesi", "Atheer Alasslany", "Fatma I. Albeladi", "Marwan A. Bakarman", "Turki Al Amri", "Rasha Eid", "Najla Alyazidi", "Ameera Alkhamesi", "Atheer Alasslany" ], "abstract": "Background: It is of utmost importance for the elements that influence public compliance with vaccination against COVID-19 to be assessed, including misconceptions, rumors, and conspiracy theories. Hence, in this study, we aimed to estimate the distribution of the most common misconceptions regarding COVID-19 vaccines and their predictors in Saudi Arabia.\n\nMethods: We distributed an online questionnaire to participants aged 18 years or older. The survey included two sections. The first section comprised questions related to participants’ demographic characteristics, level of education, and their sources of information about COVID-19. The second section assessed participants' perceptions regarding 11 of the most common misconceptions regarding COVID-19 vaccines, rated using a 5-point Likert scale. Using ordinal logistic regression, we conducted an evaluation of the relationships among different predictors including age, sex, educational level, and sources of information, as well as acceptance of misconceptions about vaccination.\n\nResults: The most widely accepted misconception was that the COVID-19 vaccine had severe side effects, with 34.8% of participants believing this misinformation. Factors that were significantly associated with acceptance or non- acceptance of misconceptions were: 1) sex, with female respondents in this survey accepting rumors significantly more often than male respondents (p<0.001); 2) educational level, especially secondary school, was associated with a significantly lower acceptance of misconceptions (p=0.001). In total, 60.5% of participants used social media as their primary source of information, which was also a significant positive predictor of acceptance of misconceptions (p=0.034).\n\nConclusion: It is of critical importance to increase assurance regarding the safety of COVID-19 vaccines, the issue most likely to involve misconceptions, and to address the elements that affect belief in rumors among the population.", "keywords": [ "COVID-19", "vaccination", "vaccine hesitancy", "acceptance", "misconceptions", "rumors", "misinformation", "predictors." ], "content": "Introduction\n\nCOVID-19 has transformed the world since its emergence in December 2019, leading to a very large number of infected cases and deaths in 213 countries, as of 23 December 2020.1 The earliest cases likely occurred in October or November 2019, according to molecular clock inference studies.2 Vaccination has led to the eradication or reduction of many infectious diseases, including smallpox, rubella, polio, and measles.3 Thus, to combat SARS-CoV-2, the virus that causes COVID-19, and prevent its continued spread globally, numerous vaccines have been developed. However, acceptance of these vaccines has faced challenges in the form of hesitancy, non-acceptance, and belief in conspiracy theories. Vaccine skepticism has been highlighted as a worldwide health threat.4\n\nThe first COVID-19 vaccine human trial started in March 2020. Several other trials began shortly after that, and by September of the same year, eight vaccines had either progressed to phase ІІІ clinical trials or had been approved for use. However, many people remain skeptical about the vaccines. A study performed in several countries of Europe revealed that 7.8% of respondents are unwilling to be vaccinated.5 Several vaccine candidates have been developed using different approaches, such as viral vectors, RNA, and single proteins. Some vaccines have been approved for use in multiple countries, such as the in United States and Saudi Arabia.6 In December 2020, the Ministry of Health developed a mobile application in Saudi Arabia, known as Sehaty, and vaccination centers were established in various regions across the country.7 Vaccines that were initially approved for use in susceptible groups later became accessible to all populations.8 Subsequently, the COVAX initiative for global access to COVID-19 vaccines was initiated by the World Health Organization and numerous countries to speed the production of vaccines against the disease and provide unbiased access to vaccines internationally.9 The effective final price of a new vaccine may vary depending on various factors that the manufacturers may consider when it comes to pricing, which is also an essential factor when considering vaccine hesitancy.10 Vaccines should have at least 50% efficacy against the virus to effectively fight the spread of infection.11 To reach sufficient immunity, a large proportion of the population should be vaccinated, and this mostly depends on public acceptance or rejection of vaccination.11\n\nMany factors contribute to compliance with vaccination against COVID-19, including male sex, older age, and fear of infection. Also, being married can boost the likelihood of receiving the vaccine. A recent study revealed that approximately 68% of Saudi respondents planned to receive the COVID-19 vaccine and 7% were hesitant. The study also found that compliance with vaccination was higher among well-educated respondents, non-Saudis, and government employees.12 A study done in 2020 revealed that a high percentage of individuals reported that they would receive the COVID-19 vaccine if it became accessible.13 Vaccine hesitancy has been demonstrated even among health care workers, especially nurses.14 However, a recent study in Vietnam revealed contradictory results, with a high acceptance rate (76.1%) among health care workers.15\n\nIn wealthy countries like the United States, so called anti-vaxxers are widely opposed to vaccination owing to a belief in the correlation of vaccines with autism and other adverse effects. The anti-vaccination movement has led to measles outbreaks in some parts of the country, highlighting the danger of misconceptions and false beliefs in preventive health care delivery.16 Other essential predictors of vaccine hesitancy are complacency owing to underestimation of the risk of a contracting a disease. Confidence in vaccination is related to vaccine safety, efficacy, and trust in the health system, as well as convenience, which involves the affordability and availability of vaccines.17 A recent survey in Bangladesh found significant rates of refusal of the COVID-19 vaccine in groups such as older people, day laborers, and those who were skeptical of the country’s health policy.18\n\nIn countries like the United States, the most vaccine-hesitant individuals are those with lower income levels and no health insurance. These individuals are also more likely to be women and Black.19 Various factors have been identified that explain why some people avoid being vaccinated, including concerns about safety and effectiveness.20 It has been revealed that a small percentage of the population has anti-vaccination beliefs, and a larger portion can be considered vaccine-skeptical.21\n\nVaccine hesitancy or refusal could be partly related to the dissemination of incorrect information on social media; 30%–60% of information on social media platforms tends to be anti-vaccination, and over 50% of the information on websites that discuss vaccination is false or inaccurate.22\n\nIn this study, we aimed to assess the most widely accepted misconceptions among adults in Saudi Arabia regarding vaccination against COVID-19 and to investigate the predictors that can increase or decrease acceptance or refusal of vaccination among the general public.\n\n\nMethods\n\nThis study was approved by the Unit of Biomedical Ethics Research Committee at King Abdulaziz University, Saudi Arabia (Reference No. 254-21). Participation in the survey was voluntary, and informed consent were electronically provided by all respondents to the online survey. All collected data were treated with confidentiality.\n\nWe administered an online cross-sectional survey in Saudi Arabia between 21st April and 28th December in 2021. All adult male or female individuals (citizens and residents) aged 18 years or older at the time of the survey and living in the Kingdom of Saudi Arabia during the study period were eligible to participate. Data were collected using a Google Forms-based questionnaire, and invitations were distributed via social media or e-mail.\n\nThe sample size was calculated using the formula: (n=Z2p (1-p)/m2, where: n=1.9620.5(1-0.5)/0.052=384.1), the minimum number of participants that should be accepted in the survey was 384, the number was increased to 1131 respondents.\n\nThe questionnaire began with information about the study purpose and an explanation of the confidentiality of personal information. Informed consent was obtained from all respondents before they could proceed with the questionnaire; participants were informed that they could withdraw at any time.\n\nWe conducted a pilot study among 10% of the study population (n=113) to test the applicability of the questionnaire and accessibility for the study sample. This step helped in determination of the required organization and administration procedures for the study and revealed the difficulties in design and language that could arise in the survey. The questions were in Arabic, which was the official language of all participants. The survey was translated into English and then back-translated into Arabic to ensure that the meaning was not changed. A copy of the survey can be found in Extended data.\n\nThis study was conducted to assess the main misconceptions among the public and their predictors regarding vaccination against COVID-19. Respondents’ perceptions toward different misconceptions were evaluated using a 5-point Likert scale, where 5 indicated “strongly agree” and 1 indicated “strongly disagree.”\n\nThe survey consists of two parts. The first section included questions on participants’ sociodemographic characteristics, including sex, age, profession, education level, and their sources of information regarding COVID-19. The second section addressed 11 misconceptions derived from the literature, the community, social media, and websites. Respondents were asked to use a 4-point categorized scale to report the extent to which they agreed or disagreed with each of the 11 points (1=strongly disagree and 4=strongly disagree). The 11 misconceptions discussed were as follows. 1) I do not believe in the safety of the COVID-19 vaccines. 2) My genetic material will be affected by COVID-19 vaccines. 3) A device will be implanted in my body via the COVID-19 vaccines. 4) The COVID-19 vaccines have serious side effects, such as causing severe allergy. 5) Fertility is decreased in women who received a COVID-19 vaccine. 6) I have been infected with COVID-19, so vaccination is unnecessary. 7) Once I am vaccinated, I don’t have to wear a face mask. 8) A COVID-19 vaccine will change my test results to positive. 9) I am unlikely to have complications from COVID-19, so it is not necessary for me to be vaccinated. 10) You can get COVID-19 from the vaccine. 11) If I am vaccinated, I am more likely to get another disease.\n\nIBM SPSS software 28.0 was used for the analysis (IBM Corp., Armonk, NY, USA). We calculated the number and proportion of each predictor (age, sex, education level, and sources of information). The relationship between different predictors and acceptance of misconceptions was estimated using ordinal logistic regression. Log odds were estimated at 95% confidence intervals (CIs), and p-values less than 0.05 were considered significant. Visualization of the data was carried out using Tableau 2021.4.\n\n\nResults\n\nTable 1 shows participants’ sociodemographic characteristics. A total of 1131 respondents were included, with 60.5% women and 39.5% men. Most respondents (37.4%) were in the age group 18–30 years, followed by the age groups 31–40 years (34.7%), 41–50 years (19.6%), and 51–60 years (7.2%); only 1.1% of participants were in age group 61–70 years. In total, 50.1% of respondents were employed, followed by students (25.7%) and homemakers (14.3%). Most participants had a university-level education (68.7%); 20.4% completed secondary school, 9.0 % of respondents had an education level above university, and 1.9% had education levels below secondary school.\n\nTable 2 shows that 60.5% of participants obtained their information regarding COVID-19 from social media platforms like WhatsApp, Facebook, and Twitter. This was followed by traditional media, such as newspapers and television. In total, 21.0% and 9.0% of respondents relied on websites found using the Google search engine, 4% relied on scientific journals, and 0.8% obtained their information from YouTube.\n\nTable 3 and Figure 1 show that the most widely accepted misconception among participants was that the COVID-19 vaccines have serious effects like causing allergy, with 34.8% of respondents either agreeing or strongly agreeing with this false information. This was followed by not believing in the safety of COVID-19 vaccines, accepted by 34.2% of participants; and the belief that COVID-19 can be contracted from the vaccine, with 24.4% of respondents either agreeing or strongly agreeing with this misconception; 23.1% of participants accepted the misinformation that COVID-19 vaccines change lab test results to positive, and 22.3% believed that they would develop another disease if they were vaccinated. Furthermore, 19.9% of respondents believed that they were unlikely to have COVID-19 complications so it was not necessary to be vaccinated; another 17.2% believed that once vaccinated, use of a face mask was unnecessary; 17% accepted the rumor that previous infection with COVID-19 meant that vaccination was unnecessary; 12.5% of respondents agreed or strongly agreed with the misconception that their genetic material can be affected by COVID-19 vaccines; and 11.6% believed that COVID-19 vaccines cause infertility among women. Finally, 7.7% of respondents either agreed or strongly agreed with the misinformation that COVID-19 vaccines contain a tracking device.\n\nThe most common source of information among respondents was social media, with 70.5% of male respondents and 53.9% of female respondents obtaining their information about COVID-19 from this source. The age group that most commonly used social media to obtain information regarding COVID-19 was 18–30 years (71.6%). Students also commonly used social media (70.1%) to find relevant information. Regarding educational level, social media was used most by respondents with a university degree (65.6%).\n\nTable 4 shows the results of ordinal logistic regression, conducted to analyze the relationship among predictors including sex, age, profession, educational level, and acceptance of misconceptions. Sex was a significant positive predictor of acceptance of misconceptions (p<0.001). The log odds of accepting misconceptions were 0.368 points higher, on average, for female than male respondents. Age was not a significant predictor of accepting misconceptions. However, the age group 18–30 years generally had the lowest rates of accepting misconceptions compared with other groups, although the difference was not significant.\n\nRegarding the profession of respondents, being a pensioner was associated with a decrease (−0.581) in the log odds of accepting misconceptions in comparison with other professions, although the association was not significant (p=0.130). A secondary school education level was a significant negative predictor of acceptance of misconceptions (p=0.001). The log odds of accepting misconceptions was lower (−0.420), on average, for secondary or high school educational levels. Furthermore, having an education above university level was associated with decreased log odds of acceptance of misconceptions, although the association was not significant. An education level below secondary school was a positive non-significant predictor of acceptance of misconceptions. Finally, using Google, traditional media like newspapers or television, and social media to obtain information about COVID-19 were all significant positive predictors of acceptance of misconceptions (p=0.013, p=0.037, p=0.034, respectively).\n\n\nDiscussion\n\nVaccination against COVID-19 is of paramount importance as new mutations of SARS-CoV-2 continue to emerge, which can increase the spread and severity of the disease.23,24 Vaccination against COVID-19 faces many challenges and obstacles owing to a lack of acceptance or reluctance to receive the vaccine among the general public for reasons related to doubts about safety, efficacy, the health care system, or distrust of policymakers.25 A global survey conducted in 19 countries involving more than 13,000 participants exploring compliance with COVID-19 vaccination showed differing proportions of acceptance, with a high rate (88.6%) in China. In contrast, 59%–75% was found in Western countries and rates as low as 54.8% were identified in Russia.4 Saudi Arabia has a higher vaccination acceptance rate (64.7%), similar to many Western countries.26\n\nDespite the relatively high rates of compliance with COVID-19 vaccination in some countries, there is still a proportion of the population with vaccination hesitancy, which could be partly explained by the dissemination of some misconceptions and rumors that are likely to affect vaccine acceptance among the general public. In our study, misconceptions and rumors about the COVID-19 vaccine, which were distributed on social media or websites, were collected and scrutinized to better understand the factors that might affect their spread and acceptance.\n\nWe investigated 11 misconceptions, including the presence of a tracking device in vaccines. Only 7.7% of respondents either agreed (n=54, 4.8%) or strongly agreed (n=33, 2.9%) with this rumor. This percentage is small compared with those in other surveys conducted in many countries throughout the Middle East; in one survey, 27.7% of participants reported that they believed that the vaccines contain microchips that can be used to control people.27\n\nAnother misconception was that COVID-19 vaccines can cause infertility in women. In our survey, 11.6% of respondents either agreed (n=84, 7.4%) or strongly agreed (n=48, 4.2%) with this misinformation. This percentage is lower than results of the above survey in which 23.4% of respondents reported that they believed COVID-19 vaccines can lead to sterility and the inability to conceive.27 The smaller percentages of the abovementioned misconceptions found in our survey can be attributed to the considerable efforts made by Saudi health authorities to increase awareness about COVID-19 vaccination among citizens and residents.\n\nThe notion that COVID-19 vaccines have serious side effects like severe allergy was accepted by 34.8% of respondents who either agreed (n=297, 24.7%) or strongly agreed (n=114, 10.1%) with this rumor. This proportion is relatively high compared with other misconceptions examined in this study. One of the most likely reasons for acceptance of this misconception may be false news reports regarding the death of one participant in the COVID-19 Oxford vaccine clinical trial owing to disease complications and other false reports regarding complications caused by the vaccine.28 Elhadi and colleagues reported that nearly one-third of study participants had concerns about serious complications owing to the vaccine.29 Another survey conducted in countries throughout Latin America and the Caribbean confirmed these results, with a high percentage of the population feeling anxious regarding the vaccine’s adverse effects, especially in Venezuela (92.7%).30 It is essential to consider the central part played by the media in disseminating such false information. As an example, the number of YouTube videos focused on the adverse effects of COVID-19 vaccines increased threefold from July to December 2020, with cumulative views increasing from 11.7% to 27.2%.31 This was also proven in our survey, where we found that different sources of information, including Google searches and use of traditional media like newspapers or television as well as social media, were positive predictors of acceptance of misconceptions.\n\nDoubts regarding the safety of COVID-19 vaccines were reported by 34.2% of respondents who agreed (n=249, 22.0%) or strongly agreed (n=138, 12%) shared these misconceptions. However, 65.8% of participants disagreed with this misconception, compared with the results of a survey conducted in Jordan where 56.8% of workers in medical fields believed that the vaccines are safe and 31.9% of non-medical workers shared this belief.32\n\nIn the abovementioned survey, Abdelkarim Aloweidi and colleagues reported that 8.7% of medical workers and 17.3% of non-medical workers believed the rumor that COVID-19 vaccines can affect genetic material. These results are roughly similar to ours, where 12.5% of respondents either agreed (n=78, 6.9%) or strongly agreed (n=63, 5.6%) with this misconception. The lower proportion among those in the medical field compared with other disciplines is owing to greater knowledge about the vaccines’ mechanisms of action. Another misconception reported in the same survey was that there is an increased risk of contracting another disease after vaccination against COVID-19. The survey results showed that 7.7% of respondents in the medical field and 10.6% of non-medical workers believed this theory. In comparison, we found that 22.3% of respondents agreed (n=168, 14.9%) or completely agreed (n=84, 7.4%) with this misconception, which is higher than in that previous study.\n\nThe belief that it is not necessary to receive a COVID-19 vaccine because one feels they are unlikely to develop any complications from the disease is also common in some populations. In our sample, 19.9% of respondents either agreed (n=132, 11.7%) or strongly agreed (n=93, 8.2%) with this misconception. This is supported by the results of a survey among nurses in Hong Kong, where 27.9% of respondents agreed that vaccination was unnecessary for this reason.33 Comparable results were also found in China, with 29.2% of participants unwilling to be vaccinated because they thought they were healthy and had a low probability of complications from COVID-19 infection.34\n\nAnother incorrect theory explored in our survey was that previous infection with COVID-19 meant that there was no need to be vaccinated. It has been shown that some patients who contract COVID-19 infection may not produce long-lasting antibodies against the virus, making them vulnerable to reinfection,35 which makes vaccination necessary, even with a previous infection. Another false belief was that the COVID-19 vaccine could lead to infertility; in our survey, 11.6% of respondents either agreed or strongly agreed with this rumor. Another a recent study proved that such claims were incorrect.36\n\nWe investigated the relationship regarding acceptance of misconceptions with predictors including sex, age, educational level, occupation, and sources of information. We found sex to be a strong positive predictor of acceptance of misconceptions (p=0<001). Our results showed that, on average, women had greater acceptance of misconceptions than men. This result has been confirmed in surveys conducted among Jordanian students where male students had a greater intent to be vaccinated. This may be attributed to men perceiving the disease as being more dangerous than women.37 This finding was also reported in a study in the United States, in which women were less accepting of COVID-19 vaccination than men.38 A greater tendency to accept vaccination among men than women might be partly explained by a greater non-acceptance of rumors than women. Another survey conducted in Saudi Arabia supported this result, showing that men have greater compliance with vaccination than women, although the difference was not significant.39\n\nAll professions in this survey were found to be negative predictors of the acceptance of misconceptions, but the associations were not significant. Pensioners were more likely to disagree with misconceptions compared with other professions, but the association was not significant. However, contradictory results were reported in a survey conducted in Qatar; retired participants were reported to be more hesitant to be vaccinated.40 In our study, pensioners, followed by students, were more likely to disagree with misconceptions compared with other occupations, although the association regarding students was also not significant. This result is supported by a study where Jordanian students in health school accepted the COVID-19 vaccines more than did other groups.41\n\nThe age group 18–30 years showed the greatest association with negative prediction of accepting misconceptions, but the association was not significant. This contradicts another survey where participants who believed in conspiracy theories were slightly younger than those who did not believe conspiracy theories.42 Our findings are supported by those of a study conducted in the United Kingdom, in which vaccine-hesitant individuals were more likely to be under age 65 years.5 Another survey conducted by Tamam El-Elimat and colleagues showed that younger individuals tended to accept vaccination more than other age groups.43\n\nEducation level is an essential predictor of the acceptance of misconceptions. Our results indicated that the educational levels secondary school and university or above were associated with decreased acceptance of rumors, and the association was significant at the secondary school level (p=0.001). Our survey also showed that having less than a secondary school education is a positive predictor of accepting misinformation; however, the association was not significant. Our finding is supported by a study in the United States, which concluded that low literacy levels were associated with reluctance to be immunized.44 However, our findings were in contrast to those of a study showing that well-educated people have lower rates of accepting vaccination.45 However, such rejection can be attributed to other factors because misconceptions and rumors are not the only factors affecting vaccination hesitancy.\n\nMost of our respondents (60.5%) reported using social media platforms like Facebook, Whatsapp, and Twitter as their main source of information in relation to COVID-19. Another survey reported that only 16% of their study population used Facebook as a source of information, and 16% obtained their information from traditional media sources.46 A strong significant association was found in our survey between the source of information and acceptance of misconceptions whereas other studies have indicated that 30%–60% of the information on social media platforms has an anti-vaccine tendency and over 50% of the information on vaccine-related websites is false or inaccurate.22 This may contribute to the spread of false information regarding COVID-19 vaccines among the population.\n\nIt must be noted that this study has some limitations as it aimed mainly to assess the distribution of acceptance of misconceptions among participants and the factors that can increase or decrease this acceptance, but it didn’t measure the willingness to be vaccinated among the same respondents, more surveys are needed to assess the correlation between distribution of misconceptions and willingness to be vaccinated.\n\n\nConclusions\n\nThe results of our study showed that the most accepted misconception among respondents in Saudi Arabia was that COVID-19 vaccines have serious side effects like causing allergy, followed by the rumor that COVID-19 vaccines are unsafe. This should raise a red flag for policymakers to address the spread of misinformation by increasing awareness among the public using the most popular platforms, namely, social media, and implementing additional measures aimed at reducing the spread of COVID-19 vaccine-related misinformation and rumors.\n\n\nData availability\n\nDryad: Misconceptions about COVID-19 vaccine among adults in Saudi Arabia and their associated factor, https://doi.org/10.5061/dryad.2jm63xsr9.47\n\nThis project contains the following underlying data:\n\n- Misconceptions.csv\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nZenodo: Misconceptions about COVID-19 vaccine among adults in Saudi Arabia and their associated factor, https://doi.org/10.5281/zenodo.6385577.48\n\nThis project contains the following extended data:\n\n- Figure_files.doc\n\n- Table_file.doc\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).", "appendix": "Acknowledgments\n\nWe thank Edanz for editing a draft of this manuscript.\n\n\nReferences\n\nAfolabi AA, Ilesanmi OS: Dealing with vaccine hesitancy in Africa: the prospective COVID-19 vaccine context. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAbila DB, Dei-Tumi SD, Humura F, et al.: We need to start thinking about promoting the demand, uptake, and equitable distribution of COVID-19 vaccines NOW!. Public Heal. Pract. 2020 Nov [cited 2021 Aug 1]; 1: 100063. 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 1 [cited 2021 Aug 1]; 93(7): 4280–4291. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAbedin M, Islam MA, Rahman FN, et al.: Willingness to vaccinate against COVID-19 among Bangladeshi adults: Understanding the strategies to optimize vaccination coverage. PLoS One. 2021 [cited 2021 Aug 1]; 16(4): e0250495. Publisher Full Text \| Free Full Text\n\nNguyen KH, Srivastav A, Razzaghi H, et al.: COVID-19 Vaccination Intent, Perceptions, and Reasons for Not Vaccinating Among Groups Prioritized for Early Vaccination — United States, September and December 2020. Morb. Mortal. Wkly Rep. 2021 Feb 12 [cited 2021 Aug 1]; 70(6): 217–222. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMcKee C, Bohannon K: Exploring the Reasons Behind Parental Refusal of Vaccines. J. Pediatr. Pharmacol. Ther. JPPT. 2016 Mar 1 [cited 2021 Aug 1]; 21(2): 104–109. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYin F, Wu Z, Xia X, et al.: Unfolding the Determinants of COVID-19 Vaccine Acceptance in China. J. Med. Internet Res. 2021 Jan 1 [cited 2022 Apr 26]; 23(1): e26089. PubMed Abstract \| Publisher Full Text\n\nKwok SWH, Vadde SK, Wang G: Tweet Topics and Sentiments Relating to COVID-19 Vaccination Among Australian Twitter Users: Machine Learning Analysis. J. Med. Internet Res. 2021 May [cited 2021 Jun 4]; 23(5): e26953. Publisher Full Text \| Free Full Text\n\nMaitra A, Sarkar MC, Raheja H, et al.: Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility. J. Biosci. 2020 Dec 1 [cited 2021 Jul 8]; 45(1) Publisher Full Text \| Free Full Text\n\nCosar B, Karagulleoglu ZY, Unal S, et al.: The most recent SARS-COV-2 mutations and their subsequent viral variants. Cytokine Growth Factor Rev. 2021 Jul [cited 2021 Aug 1]; 63: 10–22. Publisher Full Text \| Free Full Text\n\nRutten LJF, Zhu X, Leppin AL, et al.: Evidence-Based Strategies for Clinical Organizations to Address COVID-19 Vaccine Hesitancy. Mayo Clin. Proc. 2021 Mar 1 [cited 2021 Aug 1]; 96(3): 699–707. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAl-Mohaithef M, Padhi BK: Determinants of COVID-19 Vaccine Acceptance in Saudi Arabia: A Web-Based National Survey. J. Multidiscip. Healthc. 2020 [cited 2021 Aug 6]; Volume 13: 1657–1663. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSallam M, Dababseh D, Eid H, et al.: High rates of covid-19 vaccine hesitancy and its association with conspiracy beliefs: A study in jordan and kuwait among other arab countries. Vaccines. 2021 Jan 1 [cited 2021 Jul 2]; 9(1): 1–16. Publisher Full Text \| Free Full Text\n\nHakim MS: SARS-CoV-2, Covid-19, and the debunking of conspiracy theories. Rev. Med. Virol. 2021 [cited 2021 Jul 8]; 31: e2222. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nElhadi M, Alsoufi A, Alhadi A, et al.: Knowledge, attitude, and acceptance of healthcare workers and the public regarding the COVID-19 vaccine: a cross-sectional study. BMC Public Health. 2021 Dec 1 [cited 2021 Aug 1]; 21(1): 955. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nUrrunaga-Pastor D, Bendezu-Quispe G, Herrera-Añazco P, et al.: Cross-sectional analysis of COVID-19 vaccine intention, perceptions and hesitancy across Latin America and the Caribbean. Travel Med. Infect. Dis. 2021 May 1 [cited 2021 Aug 4]; 41: 102059. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBasch CE, Basch CH, Hillyer GC, et al.: YouTube Videos and Informed Decision-Making About COVID-19 Vaccination: Successive Sampling Study. JMIR Public Heal. Surveill. 2021 May 1 [cited 2021 Aug 4]; 7(5) Publisher Full Text \| Free Full Text\n\nAloweidi A, Bsisu I, Suleiman A, et al.: Hesitancy towards COVID-19 Vaccines: An Analytical Cross–Sectional Study. Int. J. Environ. Res. Public Health. 2021 May 2 [cited 2021 Aug 6]; 18(10): 5111. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang K, Wong ELY, Ho KF, et al.: Intention of nurses to accept coronavirus disease 2019 vaccination and change of intention to accept seasonal influenza vaccination during the coronavirus disease 2019 pandemic: A cross-sectional survey. Vaccine. 2020 Oct 21 [cited 2022 Apr 26]; 38(45): 7049–56. PubMed Abstract \| Publisher Full Text\n\nGan L, Chen Y, Hu P, et al.: Willingness to Receive SARS-CoV-2 Vaccination and Associated Factors among Chinese Adults: A Cross Sectional Survey. Int. J. Environ. Res. Public Health. 2021 Feb 2 [cited 2022 Apr 26]; 18(4): 1–11. Publisher Full Text Reference Source\n\nVarghese PM, Tsolaki AG, Yasmin H, et al.: Host-pathogen interaction in COVID-19: Pathogenesis, potential therapeutics and vaccination strategies. Immunobiology. 2020 Nov 1 [cited 2022 Apr 26]; 225(6): 152008. PubMed Abstract \| Publisher Full Text\n\nMarkert UR, Szekeres-Bartho J, Schleußner E: Adverse effects on female fertility from vaccination against COVID-19 unlikely. J. Reprod. Immunol. 2021 Nov 1 [cited 2022 Jan 14]; 148: 103428. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSallam M, Dababseh D, Yaseen A, et al.Conspiracy Beliefs Are Associated with Lower Knowledge and Higher Anxiety Levels Regarding COVID-19 among Students at the University of Jordan.2020 Jul 2 [cited 2021 Jul 8]; 17(14): 1–15. Reference Source\n\nMalik AA, McFadden SAM, Elharake J, et al.: Determinants of COVID-19 vaccine acceptance in the US. EClinicalMedicine. 2020 Sep 1 [cited 2022 Apr 26]; 26: 100495. PubMed Abstract \| Publisher Full Text Reference Source\n\nAlobaidi S: Predictors of Intent to Receive the COVID-19 Vaccination Among the Population in the Kingdom of Saudi Arabia: A Survey Study. J. Multidiscip. Healthc. 2021 [cited 2022 Apr 26]; Volume 14: 1119–1128. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlabdulla M, Reagu SM, Al-Khal A, et al.: COVID-19 vaccine hesitancy and attitudes in Qatar: A national cross-sectional survey of a migrant-majority population. Influenza Other Respir. Viruses. 2021 May 1 [cited 2022 Apr 26]; 15(3): 361–70. PubMed Abstract \| Publisher Full Text\n\nSallam M, Dababseh D, Eid H, et al.: Low COVID-19 Vaccine Acceptance Is Correlated with Conspiracy Beliefs among University Students in Jordan. Int. J. Environ. Res. Public Health. 2021 Mar 2 [cited 2022 Apr 26]; 18(5): 1–14. Publisher Full Text \| Free Full Text\n\nEarnshaw VA, Eaton LA, Kalichman SC, et al.: COVID-19 conspiracy beliefs, health behaviors, and policy support. Transl. Behav. Med. 2020 Oct 8 [cited 2022 Apr 26]; 10(4): 850–856. PubMed Abstract \| Publisher Full Text Reference Source\n\nEl-Elimat T, AbuAlSamen MM, Almomani BA, et al.: Acceptance and attitudes toward COVID-19 vaccines: A cross-sectional study from Jordan. PLoS One. 2021 Apr 1 [cited 2022 Apr 26]; 16(4): e0250555. PubMed Abstract \| Publisher Full Text\n\nKhubchandani J, Sharma S, Price JH, et al.: COVID-19 Vaccination Hesitancy in the United States: A Rapid National Assessment. J. Community Health. 2021 Apr 1 [cited 2021 Aug 4]; 46(2): 270–277. Publisher Full Text \| Free Full Text\n\nCerda AA, García LY: Hesitation and Refusal Factors in Individuals’ Decision-Making Processes Regarding a Coronavirus Disease 2019 Vaccination. Front Public Heal. 2021 Apr 21 [cited 2021 Aug 4]; 9. Publisher Full Text \| Free Full Text\n\nDi Gennaro F , Murri R, Segala FV, et al.: Attitudes towards Anti-SARS-CoV2 Vaccination among Healthcare Workers: Results from a National Survey in Italy. Viruses. 2021 Mar 1 [cited 2021 Aug 4]; 13(3). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAdam E: Misconceptions about COVID-19 vaccine among adults in Saudi Arabia and their associated factor, Dryad, 2022. Dataset. Publisher Full Text\n\nAdam E: Misconceptions about COVID-19 vaccine among adults in Saudi Arabia and their associated factor. Zenodo. 2022. Publisher Full Text" }	[ { "id": "182219", "date": "18 Jul 2023", "name": "Jessica Carter", "expertise": [ "Reviewer Expertise Public Health", "Social Determinants of Health", "Behaviour Change and Health Promotion", "Prevention Science", "Vaccine Hesitancy." ], "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\nThank you for the opportunity to review this interesting and important study. Overall, this research is sound and offers a clear outline of methods, results and the implications of these.\n\nAreas of suggestion are minor but would improve readability and replicability:\nIntroduction: much of the detail here, particularly information on the vaccine development, could be reduced. The data given from studies outside of Saudi Arabia could also be shortened and/or made clearer why these are applicable to your study's population. The inclusion of definitions of vaccine hesitancy and refusal, and \"misconception\", would be useful.\n\nMethods: rationale for the choice of 11 statements would be valuable. This may be relevant to include in Introduction as supporting content around dis/misinformation and vaccine hesitancy. Perhaps also worth explaining the reason not to measure COVID-19 vaccine acceptance/willingness to be.\n\nMethods: this section notes a 4-point scale but Abstract notes a 5-point. Please ensure all references to the scale are consistent and correct.\n\nGeneral: language is wordy at points, particularly in the Abstract and Introduction. Consider revising these sections for greater clarity and conciseness.\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": "199319", "date": "30 Aug 2023", "name": "Muhammad Chutiyami", "expertise": [ "Reviewer Expertise Infectious diseases", "immunization", "community health nursing" ], "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 opportunity to review the manuscript. Below are some minor comments to improve the manuscript;\nThere is a need for a clearer justification of the 11 items to assess misconception. The current information under survey items; ‘second section addressed 11 misconceptions derived from the literature, the community, social media, and websites’ is verge. At a minimum, you can cite some of the literature sources. You could also acknowledge the lack of validation of the questionnaire as a limitation. Also, acknowledge the limitation that the data used was collected in 2021, and that it is possible those misconceptions have changed currently.\nPlease indicate the source of the sample size formula.\nIn your logistic regression analysis (Table 4), it is important to add the reference category under each variable e.g. male, 61-70 years, etc. This will ease the interpretation of the table.\nIn the discussion (5th paragraph), it is important to reflect more on the vaccine's actual severe/long-term side effects, which may influence those misconceptions, rather than accepting all severe side-effects as misconceptions.\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/11-561
https://f1000research.com/articles/11-1290/v1	10 Nov 22	{ "type": "Study Protocol", "title": "Management of evidence and conflict of interest in guidelines on early childhood allergy prevention and child nutrition: study protocol of a systematic synthesis of guidelines and explorative network analysis", "authors": [ "Katharina Sieferle", "Corinna Schaefer", "Eva Maria Bitzer", "Katharina Sieferle", "Corinna Schaefer" ], "abstract": "Background: With the rising prevalence of allergic diseases in children, prevention of childhood allergies becomes an important public health issue. Recently, a paradigm shift is taking place in the approach to preventing allergies, and clinical practice guidelines (CPG) and food-based dietary guidelines (FBDG) play an important role in providing practitioners with the latest evidence and reliable guidance. However, concern about the methodological quality of the development of FBDGs and CPGs, including limitations in the systematic reviews, lack of transparency and unmanaged conflicts of interest (COI), reduce the trust in these guidelines. Methods: We aim to synthesize the available guidance on early childhood allergy prevention (ECAP) through a systematic search for national and international CPGs and FBDGs concerning ECAP and child nutrition (CN) and to assess the quality of the guidelines and management of COI. Additionally, we will analyse the content and the evidence base of the recommendation statements. We aim to quantify the COI in guideline panellists and explore possible associations between COI and recommendations. Through a social network analysis, we expect to elucidate ties between panellists, researchers, institutions, industry and other sponsors. Guidelines are an important tool to inform healthcare practitioners with the newest evidence, but quality and reliability have to be high. This study will help identify potential for further improvement in the development of guidelines and the management of COI. If the social network analysis proves feasible and reveals more information on COI in comparison to disclosed COI from the previous analyses, the methodology can be developed further to identify undisclosed COIs in panellists. Ethics and dissemination: This research does not require ethical approval because no human subjects are involved. Results will be published in international peer-reviewed open access journals and via presentations at scientific conferences.", "keywords": [ "Early childhood allergy prevention", "clinical practice guideline", "food-based dietary guideline", "conflict of interest" ], "content": "Introduction\n\nThe prevalence and impact of allergic diseases, including food allergies, eczema, contact dermatitis as well as hay fever and asthma is continuously rising, especially in children.1 Asthma and other allergic diseases reduce the quality of life and their economic burden is high.1,2 Therefore prevention of childhood allergies is an important public health concern.1 Prevention of food allergies previously concentrated on avoidance of the potential allergen during pregnancy, breast-feeding and infancy, but based on the “dual-allergen-exposure hypothesis”3 a gradual paradigm shift is taking place in the approach to preventing allergies - from avoidance to early and sustained exposure. According to this hypothesis, exposure to food allergens through the skin can lead to allergic sensitization whereas early consumption of the food protein can induce oral tolerance.3 The hypothesis has been investigated in numerous trials with different objectives. Although the preventive effect of early introduction of peanuts and chicken eggs on food allergies has been confirmed in different systematic reviews,4,5 there still remains uncertainty with respect to the definition of populations at risk and the preparation of food (e.g. boiled, pasteurised or raw egg). With regard to the prevention of eczema and asthma the findings are inconclusive6–8 and additional studies are needed. Thus, despite extensive and ongoing research on early childhood allergy prevention (ECAP), the pieces of the puzzle revealed so far do not provide a comprehensive picture and several pieces are still missing.\n\nIn fields with rapidly evolving evidence such as ECAP, clinical practice guidelines (CPG) and food-based dietary guidelines (FBDG) play an important role in providing practitioners in allergy prevention and child nutrition (CN) with reliable guidance. FBDGs and CPGs are statements including recommendations intended to optimize health behaviour and patient care, which are ideally informed by systematic reviews of existing evidence and an assessment of the benefits and harm of alternative care options.9,10 It should be noted that making guideline recommendations always involves judgement: regarding the strengths and limitations of the evidence, the balance of benefits and harm and ethical or legal considerations.11 Thus, guidelines, though based on a systematic review, are far from “objective”. With respect to the prevention of food allergies the review of Perkin et al.,12 illustrates that guidelines interpret the evidence differently and come to diverging recommendation statements: While some institutions frame their statements according to the PICO-scheme of the underlying trials, i.e. the LEAP trial regarding the introduction of peanuts,13 others assume the evidence can be extrapolated to a variety of food allergens beyond peanut and chicken eggs and advocate for their early introduction.\n\nEven if our understanding of the impact of FBDGs and CPGs on preventive practice and public health outcomes is limited, they have the potential to enhance translation of research into practice, improve healthcare quality and safety9,14 and shape the professional and public discussion on health and nutrition.15\n\nThere is considerable concern from physicians, consumer groups and other stakeholders about the methodological quality of the development of FBDGs and CPGs, including limitations in the systematic reviews that serve as the evidence base for CPGs, lack of transparency and unmanaged conflicts of interest.16–20 Diverging recommendations across guidelines might decrease the confidence in guidelines in general, if the reasoning leading to a recommendation statement is not transparent and no information regarding the developmental process of the guideline is provided.9,21 Organizations such as the U.S. Institute of Medicine and the Guidelines International Network (G-I-N) have therefore developed recommendations to define trustworthy guidelines.14\n\nWhen assessed for their overall quality using the Appraisal of Guidelines for Research and Evaluation (AGREE II) tool, CPGs on for example the management of pediatric Type 2 Diabetes Mellitus and the management of fever in children only achieved insufficient scores in the domain ‘Rigor of development’, showing that the methodology of guideline development can still be improved.22,23 However, to date there has been no systematic investigation of whether CPGs and FBDGs on ECAP comply with methodological standards in guideline development.\n\nConflicts of interest (COI) have also been identified as causing differences in recommendations16,19,24 and in turn COI were suggested to be one of the most relevant factors impairing the public’s trust in nutrition guidelines.25 In the context of guideline development COI can be understood as “circumstances that create a risk that professional judgements or actions regarding a primary interest will be unduly influenced by a secondary interest”.26,27 Secondary interests can be divided into material interests, which include actions leading to direct financial gain, and non-material interests, which can include the pursuit of professional status and recognition, competition with other professionals, support of friends or colleagues, and access to or remaining in a group or network. COI can also be divided into direct financial COI, which arise from financial relationships with persons or organizations, including fees for lectures, investments or shares in products or services or study sponsorship, and into indirect COI. In addition to non-material COI, indirect COI also include intellectual COI, which refer to the increased risk of maintaining a specific point of view due to one’s own academic activities.28\n\nIt has to be assumed that industry sponsorship is prevalent in ECAP29–31 and with the paradigm shift in allergy prevention, commercial interest might even be increasing with regard to “baby food add-ins” which claim to contain adequate doses of allergens to facilitate introduction and induce oral tolerance.12 Therefore, vested interests could be fostered as well. Standards for disclosure and management of COIs in guideline development have been set by the Guidelines International Network in 2015.28 These recommendations include issues such as trying not to include members in the guideline development panel if they have (direct financial or indirect) COI, using standardized forms for the disclosure of interests, making disclosures of interests publicly available and easily accessible and others.28 However, it has been shown that many guideline authors have potentially relevant undisclosed COI and COI management is often inadequate.28,32,33 It is not yet known, to what extent policies and standards for management and disclosure of COI have been adopted for the development of guidelines on ECAP and whether this point is also acknowledged in FBDGs.33–35 It is also not clear, whether COI in guideline development are associated with the content of the recommendations and with the prevalence of intervention- and industry-friendly recommendations.\n\nThis study aims to synthesise national and international guidelines on ECAP and child nutrition and to systematically assess their methodological quality. We aim to investigate the management of conflicts of interest in these guidelines and the possible association of the COI with the guideline recommendations. We will also use the data to explore and visualize the networks of guideline panellists in the field of ECAP and child nutrition.\n\n\nMethods\n\nThe methods for the search strategy, selection and data collection processes will be reported based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines on the conduct of systematic reviews.36 This protocol is reported in line with the PRISMA-P guidelines.48\n\nThe study consists of three consecutive tasks:\n\n1. Assess the quality of the guideline development process and the management of evidence and COI of CPGs and FBDGs on ECAP and CN and provide a content analysis of the recommendation statements and an analysis of the evidence base of the recommendation statements.\n\n2. Quantify the amount of COI in guideline panel members and explore the association between the role of the panellist and COI and between COI and the recommendation statements.\n\n3. Explore the merits of social network analysis as a tool to elucidate ties between guideline panel members, ECAP and CN researchers, and research sponsors.\n\nSearch strategy\n\nOnly a small percentage of guidelines is published in databases like MEDLINE, Embase etc. Therefore we will conduct the systematic search for national and international CPGs and FBDGs concerning ECAP and CN according to established recommendations for guideline retrieval37 including the following databases and websites: Guideline International Networks database on clinical guidelines (GIN), Turning Research into Practice (TRIP), ECRI Guidelines Trust and the Alliance for the implementation of Clinical Practice Guidelines (AiCPG) – the successor of the National Guideline Clearinghouse, the Association of the Scientific Medical Societies in Germany (AWMF), WHO, the National Institute for Health and Care Excellence (NICE), as well as national and international clinical specialty societies. MEDLINE will be searched using the CADTH filter for guidelines.38 Furthermore, we aim to identify (supra) national institutions that report on dietary and/or clinical guidelines. For institutions reporting on FBDGs we will use the Food and Agriculture Organization of the United Nations (FAO) directory of FBDGs, that provides links to more than 100 guidelines from all over the world, summary information in English as well as additional resources.39 Figure 1 describes the search strategy.\n\nLegend: FAO=Food and Agriculture Organization of the United Nations, WHO=World Health Organization, WP2=Work package 2, FBDG=Food-based Dietary Guideline, CPG=Clinical Practice Guideline, ECAP=Early Childhood Allergy Prevention, CN=Child Nutrition.\n\nThese websites and databases do not have the same extensive search possibilities as bibliographic databases (like MEDLINE), but the following search filters will be applied if available: only fully published guidelines (no guidelines in development, withdrawn, etc.), publication year from 2010, publication in English or German. The search will be restricted to publications dating from 2010 up to now in order to capture the earliest guidelines that could have addressed the ongoing evidence shift as well as all recent guidelines.\n\nEligibility criteria\n\nScreening of the retrieved publications will be done by two members of the study group. Disagreements will be resolved by discussion. Publications will be eligible for inclusion if they meet the following criteria:\n\n• Population: Infants (up to one year) or pregnant women or breastfeeding women (with or without increased risk for the development of allergies or asthma)\n\n• Intervention: Primary prevention of immediate or IgE-mediated allergies, atopic eczema or asthma\n\n• Comparator: not applicable\n\n• Outcome: New cases of immediate or IgE-mediated allergies, atopic eczema or asthma\n\n• Time frame: dating from 2010, only guidelines that were valid at the time of search and the most recent updates\n\n• Publication types: We will include full guidelines and possible addenda, consensus statements, as well as position papers which address health professionals\n\n• Language: English or German\n\nData extraction and quality assessment\n\nData of included guidelines will be extracted by the first author and cross-checked by another author. Data will be entered into a relational database using MS Access which facilitates data export for quantitative analysis. The following data will be extracted from each guideline: Guideline editor, leading scientific societies, sponsorship, contact and person responsible, composition of guideline panel (name, academic title, institution, area of expertise or profession, their tasks in relation to the preparation of the guideline), independence of the coordinators and lead authors, declaration and assessment of COI, report of any potential sources of COI (explanation of potential conflicts of interest, assessment of conflicts of interest, and managing conflicts of interest), direct COI (e.g. financial, personal, institutional benefits), indirect COI (e.g. clinical, academic, personal interest, membership or function in expert association, clinical activities, publications, author or co-authorship, research projects, conducting clinical trials, leading participation in educational institutes, personal relationships with a representative of a company in the healthcare industry), imposed abstentions because of COI and external review of the guideline draft and for each relevant recommendation statement the topic of recommendation, recommendation statement in plain text, level of evidence and grade of recommendation will be assessed.\n\nFurthermore, we will extract data regarding the evidence base of the relevant recommendation statements including information on authors, publication type (in case of primary studies: study type, risk of bias), country and sponsorship for each cited study.\n\nBesides the management and disclosure of COI, a balanced and varied composition of the guideline panel and of stakeholders involved in the guideline development is important to prevent single persons or professions from having a disproportionate influence on the recommendations. We will therefore also assess the composition of the guideline panels and stakeholders involved in the development of the included guidelines.\n\nTo determine the methodological stringency of guideline development, AGREE II will be employed. The methodological quality of each included guideline will be independently assessed by two authors. AGREE II consists of 23 items covering the following 6 domains: scope and purpose, stakeholder involvement, stringency of development, clarity of presentation, applicability and editorial independence. Additionally, 2 overall assessment items are included: The quality of the overall guideline rated on a scale from 1-7 and the decision as to whether the guideline would be recommended for use in practice. The AGREE II overall assessment of the guideline indicates the general quality of the guideline. It “requires the user to make a judgement as to the quality of the guideline, taking into account the criteria considered in the assessment process” [40 S.10]. Each item of the AGREE II instrument is scored on a 7-point scale (1=strongly disagree to 7=strongly agree). Quality scores of each domain will be calculated, by adding up the scores of the individual items in the domain and by scaling the obtained score as a percentage of the maximum possible score for that domain:\n\nThe six domain-scores are independent and shall not be aggregated into a single quality score.40 Discrepancies in scorings will be resolved by discussion between the two authors (KS, EMB).\n\nSynthesis of results and analysis\n\nThe basic information of all included guidelines will be summarized narratively. Subsequently, guidelines will be categorized according to indications (e.g. food allergies, asthma, atopic eczema) to allow for content-related analysis within each group. Particular emphasis will be put on the respective comparisons of clinical practice guidelines regarding the prevention of food allergies in contrast to FBDG. First, we will compare the evidence base of recommendations. To this end, included publication types and number of citations will be analysed. In addition, the publications will be compared to the studies that have been included in a living systematic review of a neighbouring project within the HELICAP research group.41 To complete the synthesis of guidelines, we will compare the recommendations issued by the different guidelines regarding the topic and tenor of each statement as well as the assigned level of evidence, and the respective grade of recommendation.\n\nThe second part of the analysis will be dedicated to the disclosure and management of COI. We will investigate what kind of and how often particular COI are disclosed, what measures are taken to manage COI and we want to explore whether associations exist between topics and COI. If possible, the analysis will be carried out on the level of recommendation statements, otherwise information will be summarized per guideline. Then this analysis will be repeated, this time using the guideline authors as a unit of analysis. In order to capture relevant research activities of guideline panellists a co-author analysis will also be carried out: Authors and co-authors of studies that have been included in the living systematic review of our neighbouring project within HELICAP will be matched to a list of guideline panellists.41\n\nIn the third part of the analysis we will visualize collaboration networks between guideline panellists, researchers and research sponsors using a social network analysis.42 Authors, institutions, and sponsors will be understood as “actors” and connections between them such as affiliations or joint publications will inform the “ties” between them.42 Different metrics of density and centrality indices will be employed to represent relationships and patterns of interaction.43 The strength of ties between two actors will be determined according to different indicators, e.g. the number of joint publications of two researchers or the funding a scientist received from a particular company within a particular time period.43 These indicators are designed to identify core-actors (opinion-leaders), subgroups with closer relationships (cluster or cliques) as well as actors who serve as “bridges” and connect otherwise separated actors and clusters within a network.44–46 Moreover, in a small pilot study, e.g. for German guideline authors, we will investigate the impact of additional information, e.g. congress programs or entries in study registries, on the shape of the networks.\n\nFor content-related analysis MAXQDA 2020, a software used in qualitative studies, will be employed. All statistical analysis will be conducted using SPSS Statistics 27. The network analysis will be carried out with Ucinet 6.47\n\nPatient and public involvement\n\nPatients and/or the public were not involved in the design, conduct or reporting of this research.\n\n\nDiscussion\n\nAllergy prevention in early childhood is a topic that warrants collaborative public health action as it affects the daily routine of parents in the areas of nutrition and environmental exposure. It involves different areas of medical expertise, and it requires policies for example regarding the reduction of air pollution and the development of a healthy environment. To our knowledge, this will be the first study synthesizing the internationally available guidance on the primary prevention of IgE-mediated allergies, atopic eczema and asthma in early childhood. The findings will facilitate an integrated perspective on this topic and can help promote a collaborative discussion.\n\nThere is evidence that often COI are not disclosed adequately,32 therefore we want to assess the number of COI disclosed in guidelines on ECAP. Assuming, that guideline authors disclose possible COI and that the respective guidelines report these disclosures adequately, we will also be able to provide a comprehensive overview of existing COI in the field of ECAP. In addition, we will determine whether there are associations between the COI and the content of the guideline recommendations. To do this, we will evaluate the COI of guideline panel members in guidelines with conflicting recommendations.\n\nOn the one hand potential for further improvement in the management of COI in guidelines will be identified and on the other hand transparency and the reliability of the guidelines can be increased. Furthermore, we expect a new understanding of research networks in ECAP and possible sources of COI as relationships between the actors of a network become evident. For example, if a researcher receives regular funding from one sponsor, we have to assume a high risk of a financial COI or if two researchers seem to collaborate closely based on joint publications, we have to assume a high risk of indirect COI. If the social network analysis proves feasible and reveals more information on COI in comparison to disclosed COI from the previous analyses, the methodology will be developed further.\n\nAccording to the ethic committee of the Chamber of Physicians Baden-Württemberg this research does not require an ethical approval because no human subjects are involved. Findings from this study will be published upon finalization in internationally peer-reviewed journals with focus on public health, allergy prevention and evidence-based medicine. The project consortium also establishes a plan to coordinate the participation of subprojects in national and international conferences of medical associations, e.g. European Academy of Allergy and Clinical Immunology, and German Society for Social Medicine and Prevention. When we publish our results, we do not mention any real names, so no conclusions can be drawn about individual persons.\n\nAt submission of this protocol the systematic search and screening of search results has been completed. The quality assessment of the guidelines through AGREE II has been finalized and the data extraction on management and disclosure of conflicts of interests is underway.", "appendix": "Data availability\n\nNo underlying data are associated with this article.\n\nFigshare: PRISMA-P checklist for “Management of evidence and conflict of interest in guidelines on early childhood allergy prevention and child nutrition: study protocol of a systematic synthesis of guidelines and explorative network analysis”. https://doi.org/10.6084/m9.figshare.21501462.v1. 48\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nPawankar R: Allergic diseases and asthma: a global public health concern and a call to action. World Allergy Organ J. 2014; 7(1): 12. [published Online First: 19 June 2014]. PubMed Abstract \| Publisher Full Text\n\nPawankar R, Canonica GW, Holgate ST, et al., editors. 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Publisher Full Text\n\nBorgatti S, Everett M, Freeman LC: Ucinet 6 for Windows: Software for social network analysis. User's guide. Harvard, MA:Analytic Technologies;2012.\n\nSieferle K:PRISMA-P checklist HELICAP WP1 (COI). figshare. [Dataset]. Journal Contribution. 2022. Publisher Full Text" }	[ { "id": "202322", "date": "12 Sep 2023", "name": "Paxton Loke", "expertise": [ "Reviewer Expertise Food allergy" ], "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 study proposal in particular the conflict of interest aspect. Below are a few comments for clarification.\nThe search strategy in Figure 1 did not include Asia or Asian countries. Please comment on why these countries are excluded.\n\nPlease comment on including German publications and not any other languages besides English.\n\nPopulation: Please comment on the rationale of including only infants up to one year and whether or not this may be overly restrictive.\n\nWill the definition of IgE-mediated allergies, atopic eczema or asthma be included in the final publication?\n\nRegarding Task 3: Please comment on whether or not there will be any bias and how this will be addressed. For example, it is possible that authors may collaborate to harness different expertise for a common goal, and this may not necessary be a conflict of interest.\n\nMinor comment in Introduction: suggest deleting “only” from this sentence “…children only achieved insufficient scores…”\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": [ { "c_id": "10800", "date": "17 Jan 2024", "name": "Katharina Sieferle", "role": "Author Response", "response": "The search strategy in Figure 1 did not include Asia or Asian countries. Please comment on why these countries are excluded. -> This was originally decided due to feasibility reasons, expecting most English-speaking guidelines to originate from the included countries. After additional consideration, we have decided not to exclude Asian countries or other countries, and to instead include all available guidelines in English. The search strategy has been updated and a new figure 1 has been included. Please comment on including German publications and not any other languages besides English. -> We included German guidelines because this study is part of a German research group on Public Health, making the German perspective especially relevant. Besides German, only guidelines in English were included, due to feasibility and limited resources. Population: Please comment on the rationale of including only infants up to one year and whether or not this may be overly restrictive. -> The topic of interest of the research group is allergy prevention in early childhood and infancy. The first year of life is an important time for allergy prevention, since many allergy prevention measures concern the duration of breastfeeding and (timing of) introduction of complementary feeding, which typically is recommended to take place in the first year of life. To be included in our analysis, guidelines do not need to exclusively address children under 1 year of life but should make recommendations on the first year of life, or on interventions in the mother during pregnancy and breastfeeding. We therefore think this will not be too restrictive. The text was revised in the manuscript to make this clearer. Will the definition of IgE-mediated allergies, atopic eczema or asthma be included in the final publication? -> So far, we had not included a definition, but upon your question have now included further references, on which we have based our understanding of allergic diseases, in the study protocol. Regarding Task 3: Please comment on whether or not there will be any bias and how this will be addressed. For example, it is possible that authors may collaborate to harness different expertise for a common goal, and this may not necessary be a conflict of interest. -> We are not sure if we understood this comment correctly. Ideally, a guideline panel should encourage authors from different areas of expertise that are relevant to the subject area of the guideline, as well as patients or citizens to collaborate. A diverse guideline panel facilitates the consideration of different perspectives and helps avoid possible distortions caused by secondary interests. Conflicts that might arise from different expertise belong to the category of intellectual conflicts of interest, which we don’t see as severe. We are primarily interested in direct financial and personal interests, to what extent they occur and if they occur, how they are managed. We hope this answered your question? Minor comment in Introduction: suggest deleting “only” from this sentence “…children only achieved insufficient scores…” -> Thank you for the suggestion, the text was changed accordingly." } ] }, { "id": "206646", "date": "15 Sep 2023", "name": "Nina Veetnisha Gunnarsson", "expertise": [ "Reviewer Expertise Allergy", "food allergy" ], "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 very innovative and interesting systematic review and synthesis of child allergy guidelines.\nWhat is meant with immediate allergies? Clarify.\n\nIn figure 1, why were these countries included specifically and not others?\n\nPopulation: infants up to one year? Rational behind this?\n\nA replication of the study may be difficult, as there are many different analysis and tasks.\n\nTime frame: from 2010, rational behind this choice?\n\nPublication types: additional type of texts such as position papers, consensus statements etc, is this needed, and if, why?\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": [ { "c_id": "10801", "date": "17 Jan 2024", "name": "Katharina Sieferle", "role": "Author Response", "response": "1. What is meant with immediate allergies? Clarify. We have originally used the phrase immediate allergies and IgE-mediated allergies in the study protocol, both meaning type I hypersensitivity reactions. We have decided to now only use IgE-mediated allergies to prevent any possible confusion or misunderstanding. 2. In figure 1, why were these countries included specifically and not others? This was originally decided due to feasibility reasons, expecting most English-speaking guidelines to originate from the included countries. After additional consideration, we have decided not to exclude other countries, and to instead include all available guidelines in English. The search strategy has been updated and a new figure 1 has been included. 3. Population: infants up to one year? Rational behind this? The topic of interest of the research group is allergy prevention in early childhood and infancy. The first year of life is an important time for allergy prevention, since many allergy prevention measures concern the duration of breastfeeding and (timing of) introduction of complementary feeding, which typically is recommended to take place in the first year of life. To be included in our analysis, guidelines do not need to exclusively address children under 1 year of life but should make recommendations on the first year of life, or on interventions in the mother during pregnancy. The text was changed in the manuscript to make this clearer. 4. A replication of the study may be difficult, as there are many different analysis and tasks. This study is part of a German research group and is divided into three tasks. This study protocol covers the whole study with all included tasks. However, all tasks will be conducted and analyzed individually, making replication of the tasks easier. 5. Time frame: from 2010, rational behind this choice? Even though as early as 2008 avoidance of common allergens to prevent allergies was no longer recommended, there was a lack of evidence on allergy prevention measures (Greer et al. 2008). The LEAP study was published in 2015, leading to a further evidence shift towards an early introduction of common allergens (Du Toit et al. 2015). With guidelines from 2010 to 2019, we aim to be able to see this resulting shift in recommendations and underlying evidence. Additionally, only valid guidelines should be included in the analysis. Many guideline-developing organizations have set timeframes for guidelines to be valid for after publication. Guidelines older than 2010 should therefore definitely not be valid anymore at the time of search. We have included a more comprehensive rationale in the text. 6. Publication types: additional type of texts such as position papers, consensus statements etc, is this needed, and if, why? Thank you for this question/suggestion. After additional consideration, we have decided to only include Clinical Practice Guidelines and Food-based Dietary Guidelines that make recommendations on Early Childhood Allergy Prevention, to compare these two publication types. Eligibility criteria were changed accordingly in the manuscript." } ] } ]	1	https://f1000research.com/articles/11-1290
https://f1000research.com/articles/11-1015/v1	07 Sep 22	{ "type": "Research Article", "title": "Alterations in cerebral glucose metabolism measured by FDG PET in subjects performing a meditation practice based on clitoral stimulation", "authors": [ "Andrew B. Newberg", "Nancy A. Wintering", "Chloe Hriso", "Faezeh Vedaei", "Feroze B. Mohamed", "Sara E. Gottfried", "Reneita Ross", "Nancy A. Wintering", "Chloe Hriso", "Faezeh Vedaei", "Feroze B. Mohamed", "Sara E. Gottfried", "Reneita Ross" ], "abstract": "Background: The relationship between sexuality, or the libido, and spirituality or religion has long been debated in psychiatry. Recent studies have explored the neurophysiology of both sexual experiences and spiritual practices such as meditation or prayer. In the present study, we report changes in cerebral glucose metabolism in a unique meditation practice augmented by clitoral stimulation called, Orgasmic Meditation, in which a spiritual state is described to be attained by both male and female participants engaged in the practice as a pair. Methods: Male (N=20) and female (N=20) subjects had an intravenous catheter connected to a bag of normal saline inserted prior to the practice. During the practice, men stimulated their partner’s clitoris for exactly 15 minutes (he received no sexual stimulation). Midway through the practice, researchers injected 18F-fluorodeoxyglucose so the scan would reflect cerebral metabolism during the practice. Positron emission tomography (PET) imaging was performed approximately 30 minutes later. Results: In the female participants, the meditation state showed significant decreases in the left inferior frontal, inferior parietal, insula, middle temporal, and orbitofrontal regions as well as in the right angular gyrus, anterior cingulate and parahippocampus compared to a neutral state (p<0.01). Male subjects had significant decreases in the left middle frontal, paracentral, precentral, and postcentral regions as well as the right middle frontal and paracentral regions during meditation (p<0.01). Men also had significantly increased metabolism in the cerebellum and right postcentral and superior temporal regions (p<0.01). Conclusions: These findings represent a distinct pattern of brain activity, for both men and women, that is a hybrid between that of other meditation practices and sexual stimulation. Such findings have potential psychotherapeutic implications and may deepen our understanding of the relationship between spiritual and sexual experience.", "keywords": [ "FDG PET", "Brain", "Meditation", "Spirituality", "Cerebral Glucose Metabolism", "Clitoris", "Stimulation" ], "content": "Introduction\n\nOver the past 25 years, a variety of meditative and spiritual practices have been studied by our group and others with functional neuroimaging techniques. We have previously performed a number of functional neuroimaging scans as part of a larger program studying the effects of various meditative practices that have been previously published.1–5 This research has led to a greater understanding of the brain structures and networks involved in various meditative practices. A number of structures appear to be associated with meditative and spiritual practices including the frontal and parietal lobes, and limbic structures, along with larger networks such as the default mode network (DMN) and the salience network. Other previous studies have shown how various meditation practices can affect brain processes related to emotion, cognition, and sensory experience.6 However, additional research is required to further assess various types of meditative and spiritual practices, and their effects within the brain.\n\nFor the present study, we explored the neurophysiological effects of a unique meditation method called Orgasmic Meditation (OM). This practice involves female clitoral stimulation with a partner as a central focus (for this study a separate male partner was selected by each female subject as described in the methods section). An important point to consider initially is whether this practice can be appropriately classified as a form of meditation. For example, the definition of “meditation” given by Merriam-Webster’s dictionary is: “to engage in mental exercise (such as concentration on one's breathing or repetition of a mantra) for the purpose of reaching a heightened level of spiritual awareness”. While the definition on Wikipedia is: “Meditation is a practice where an individual uses a technique – such as mindfulness, or focusing the mind on a particular object, thought, or activity – to train attention and awareness, and achieve a mentally clear and emotionally calm and stable state”. Based upon the description of the practitioners, the OM practice appears to meet these basic definitional criteria by using a specific physiological process, in this case, clitoral stimulation, as a focus for the mind.\n\nIn a broader context, mindfulness is being attentive to what is – to the sensations in the body, to emotions, to thoughts – in the context of whatever the practitioner is doing. Thus, applying the principle of mindfulness to virtually any physical practice or process can turn that practice into a form of meditation. For example, walking meditation could be considered simply walking, breathing meditation simply breathing, and mindful eating simply eating. If one accepts that these other physical activities could be forms of meditation, then it is reasonable to conclude that a practice based upon what would normally be considered sexual stimulation can also be a form of meditation. Of course, there is certainly the potential concern that any effect of OM is more based on the sexual stimulation itself rather than on the meditative focus. However, there are traditional Hindu, Taoist, and Buddhist practices dating back thousands of years that use sexual stimulation in a similar manner. Ultimately, meditation is defined by those performing the practice, and any study that targets meditation has to assume that the practitioners are doing the specific practice and doing it the way they describe it.\n\nAccording to OM practitioners, both the female and male participants are actively engaged in the practice and, hence, there is a specific effect to the male subject as well as the female subject. A recent study of the OM practice indicated that partners had improved health measures such as an increased sense of closeness.7 Thus, it seems appropriate to explore the neurophysiological mechanism of action of the OM practice. One of the main advantages of studying this practice is that it is well characterized and can be performed for 15 minutes with an additional several minutes of preliminaries before starting and a brief concluding component (see below in methods for additional details). While this practice is called, OM, the goal is not specifically to achieve orgasm or climax but has the purpose of achieving a meditative state. For the purposes of this study, subjects performed the meditation in the same manner following the standard practice methods closely.\n\nSince the overall goal of this study was to determine the neurophysiological correlates specifically during the practice, it was a challenge to determine the most appropriate technique for evaluating this practice. Furthermore, we were interested in observing neurophysiological changes in both the female and male subjects in order to determine the similarities and differences between them. Functional magnetic resonance imaging (fMRI) was not possible for studying the changes that occur during the practice since logistically, the two participants could not be in the scanner at the same time. In addition, the practice involves a moderate amount of motion that would adversely affect image acquisition, and hence, quality. We have previously used both positron emission tomography (PET) and single photon emission computed tomography (SPECT) to study meditation practices, particularly those that involve specific body positions or movements.8 For the present study, we selected the use of 18F fluorodeoxyglucose (FDG) PET to specifically evaluate cerebral glucose metabolism. In order to perform this study, we placed an intravenous (IV) catheter into the arm of both the male and female participants prior to performing the OM practice. A bag of normal saline was connected to the IV and was placed on the other side of a screen to maximize privacy of the participants during the practice. We wanted to ensure that we were obtaining the cerebral metabolism associated not only when the subjects were clearly engaged in the practice, but also during the peak part of the practice. By injecting the subjects at the mid-point of the practice, we could effectively capture changes in cerebral glucose metabolism during the last half, or most intense part of the practice. We compared the cerebral glucose metabolism between the OM state and a “neutral” state. In the neutral state, the participants were located in the same room, positioned as they would be during the actual OM practice, and performing a sensory stimulation task by stroking the leg instead of the clitoris. Thus, the study was designed to match all aspects of the OM and neutral conditions with the exception of the clitoral stimulation during the meditation practice. The order of these two conditions were randomized and were done on two separate days. We should note that we previously published initial fMRI imaging data on the same participants as in this PET study.9 Both the PET and MRI scans were performed on the same day, but as mentioned above, the MRI data were acquired immediately following the practice whereas the PET data acquisition was designed to help assess changes specifically during the practice. However, we found a number of significant changes in the brain regions of both the male and female participants (see below) and hence we hoped to compare those results to the changes in cerebral glucose metabolism observed during the OM practice.\n\nBased on the current literature regarding meditation techniques, and the study design, we hypothesized that several brain regions would be particularly involved with OM. The regions that have been observed to be affected during other meditation studies include the limbic areas and insula associated with emotional processing, frontal regions and the anterior cingulate involved with attention, and posterior regions involved with the DMN (also see below). In our prior studies, in addition to those of others, we have found alterations in frontal lobe function during the practice of concentrative meditation techniques.1,2,10 Specifically, activity in the frontal lobe is typically increased during practices that involve focused attention and decreased during practices that are associated with a sense of flow or sense of surrender.1,11,12 Since the male subjects performing OM do report a subjective feeling of flow or “losing oneself” during the practice, we might expect reduced frontal lobe function. With regard to the female subjects, we might also expect a reduction in frontal lobe function since they are more passive as recipients of the stimulation, rather than performing an attentional task. The parietal lobe is another brain region affected by intense meditation practices typically showing decreased activity associated with subjects who describe a loss of the sense of self or a feeling of self-transcendence.1,13–15 We predicted that there would be decreased parietal lobe activity associated with this meditation as well since practitioners describe similar experiences.\n\nIt is also important to consider potential brain changes associated more specifically with clitoral stimulation. Several PET and fMRI studies have explored the effect of manual clitoral stimulation, particularly during sexual orgasm, on the brain. The results have shown a blend of findings that depended on the specific results of the stimulation (e.g., for sensory reception, pleasure, orgasm). For example, a 15O H2O PET study found significant increases in cerebral blood flow in the sensory cortex and the inferior parietal lobe during clitoral stimulation compared to rest.16 Proceeding to orgasm was associated with significant reductions in the regional cerebral blood flow (rCBF) of the left lateral orbitofrontal cortex, inferior temporal gyrus and anterior temporal pole. In both men and women, during sexual arousal, usually through visual stimulation, activation has been reported in several frontal lobe structures, as well as the thalamus, cingulate cortex, insula, and amygdala.17–20 During orgasm in men and women, activation has further been reported in the cerebellum, anterior cingulate gyrus, and dopaminergic pathways.21 This distinction between sexual arousal and actual orgasm or climax is important with respect to OM since the majority of times, such a climax is not attained. In fact, in our study, none of the women reported achieving actual climax during the practice.\n\nThus, we hypothesized that the practice of OM would appear to be neurophysiologically closer to meditation-based practices rather than sexual arousal or orgasm. However, given its approach, and the use of clitoral stimulation to enhance the meditative state, we hypothesized that the pattern of brain activity associated with OM would be unique and contain elements of both sexual stimulation and meditation, as well as elements that distinguish it from sexual experience and currently studied meditative practices such as mindfulness, loving-kindness meditation, or yoga. Therefore, we hypothesized that for women, there would be decreased activity in the parietal regions as well as the frontal lobe regions due to the meditative elements. We also might expect increased metabolism in the limbic areas, basal ganglia, and thalamus primarily due to sexual stimulation. In men, since there is no direct sexual stimulation at all, and participants report a subjective feeling similar to that of flow experiences, we expected that there would be decreased metabolism in the frontal lobe regions along with possibly increased metabolism in the limbic areas (due to some sexual arousal). We also expected that there might be alterations in the structures of the DMN including the parietal regions mentioned above and also the posterior cingulate cortex. Finally, since this is a paired practice, we expected the potential for changes in the social areas of the brain of both male and female participants, including the insula, angular gyrus, and supramarginal gyrus. The goal of the study was ascertaining whether the pattern of cerebral metabolism associated with this unique form of meditation was distinct in comparison to sexual stimulation alone and also other meditation-based practices.\n\n\nMethods\n\nSubjects were recruited by the Marcus Institute of Integrative Health at Thomas Jefferson University Hospital, and data from the concomitantly acquired fMRI scans from these same subjects were previously published including information on their demographics.9 Written informed consent, approved along with the protocol (IRB#11D.412; approved on 12 September 2019) by the Institutional Review Board of Thomas Jefferson University, was obtained from all subjects by the principal investigator prior to undergoing study procedures (typically on the day of the initial scanning). All procedures performed involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards. Blank consent forms, information sheets and case report forms can be found as Underlying data.22\n\nSubjects were healthy individuals who were included if they been performing the OM practice for at least one year on a regular basis (two to three times per month). Subjects were recruited between September 2019 and June 2020. During that time, all patients provided consent and underwent the various aspects of the study including PET imaging so that all data was collected during this period. A total of 20 female subjects were chosen first and they then selected their male partner who they had done the practice with before and who subsequently had to agree to participating. The number of 20 pairs was selected based on prior power calculations associated with changes in brain imaging associated with other meditation-based practices by our research group. Married individuals had to perform the practice with their spouse. Subjects were excluded by the principal investigator if they: (1) had any physical, psychological, or brain-related disorders that may affect cerebral metabolism; (2) were taking medications that could alter cerebral glucose metabolism; and (3) could not lie still in the scanner. Women of childbearing age were not included if they were pregnant or breastfeeding.\n\nThe FDG PET was performed using standard of care imaging procedures at the Marcus Institute of Integrative Health. There were two test subjects for each session, a female subject and a male subject, who performed the OM practice as a pair in a closed room in the imaging facility. A physical screen was placed in the room for added privacy during the tracer injection. Both subjects had an IV catheter inserted prior to performing the practice and had an IV bag of saline placed on a moveable pole with an IV line connected to the catheter. The man was clothed throughout the practice and did not receive any direct sexual stimulation. The woman was clothed in a manner to allow her genitalia to be exposed during the practice. The room was prepared according to the standard practice methods. A blanket and pillows were placed on the floor to provide comfort and support during the practice. The female participants then laid down on the pillows with the male subject seated by her right side. The man performed stimulation of the clitoris for 15 minutes using a sterile glove and lubricant as needed. There was no risk of pregnancy or sexually transmitted diseases since there was no actual penetration or sexual intercourse. Prior to beginning the meditation, the two participants verbally informed each other that the practice is about to begin. They set a timer for 15 minutes and began the practice. A similar timer was also set by the research team. Halfway through the 15-minute practice, the principal investigator and research technologist quietly entered the room behind the screen in order to inject the tracer for the PET scans over a one-minute period, and then left the room so that the subjects could complete the practice with minimal disturbance.\n\nFor the PET scan, 148 to 296 MBq of FDG was injected via a manual bolus. When the practice was completed, the subjects rested for approximately 15 minutes and then were escorted into the scanner fully clothed. The female participant was scanned first, followed by the male subject, for every scanning session. PET and corresponding MRI images were simultaneously obtained on a 3T Siemens mMR PET-MRI scanner (Siemens Medical Solutions USA, Inc., Malvern, PA) over approximately 30 minutes.\n\nA neutral, comparison state was also performed to account for the specific elements of the practice without clitoral stimulation component or the actual meditation process. Thus, subjects had the IV catheters and line placed, following which they entered the meditation room and were positioned in the same fashion as during the actual OM practice. Instead of stroking the clitoris, the male participant was asked to stroke the female participant’s upper leg to account for motor activity in the man and the sensory response in the woman. Each pair performed this neutral condition for the same 15-minute time period as the OM practice and were injected half way through. After the 15-minute neutral condition, the subjects rested for approximately 15 additional minutes and then were brought into the scanner. Importantly, we randomized the ordering of the meditation and neutral conditions so that half the pairs did the meditation first and half did the meditation second. Also, none of the participants reported achieving orgasm during the practice.\n\nAll PET/MRI acquisitions included a Dixon sequence used for the derivation of standard MR attenuation correction maps by separating water, fat, and bone signal and automatically applying the calculated attenuation correction. Image reconstruction was performed using a Poisson ordered-subsets expectation maximization algorithm with four iterations and 21 subsets. This image processing producing an image with a matrix size of 344 x 344 pixels and a voxel size of 1 x 1 x 2 mm.\n\nIt should be noted that we did not use arterial sampling to measure absolute cerebral glucose metabolism, but rather evaluated relative activity in the selected regions. There are two main reasons that this was not used for the current study. Practically, it would not have been feasible to perform arterial sampling while preserving the integrity of the OM practice. Physical access to the subjects and movement of the subjects during the practice would make such measurements impossible to acquire. Also, this is an approach required when it is expected that different states would be associated with absolute changes in cerebral glucose metabolism. We did not expect this for the current study. In part, this is not likely since the subjects function as their own control and the practice is expected to result in different patterns of cerebral metabolism that would require normalization to whole brain activity anyway, which is taken into account in our current analysis. Thus, we were able to successfully observe relative changes in brain structures within subjects and between the two conditions.\n\nThe 18F-FDG PET brain images were pre-processed using SPM12 (Wellcome Department of Cognitive Neurology, Institute of Neurology, London, UK) running on MATLAB (RRID:SCR 001622) 2020b (MathWorks Inc., Sherborn, MA). The processing steps are as follows: 1) Segmentation of the anatomical (T1-weighted) MRI data into gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF) tissue compartments and creation of a skull-stripped version of the original anatomical scan used for PET-MRI co-registration. 2) PET-MRI co-registration: Using rigid-body transformations the spatial orientation of the PET and MRI images from the same subject were aligned. 3) Partial volume effect correction (PVEc) of PET images: voxel-based correction was applied using the Müller-Gärtner (MG) method provided by the PETPVE12 toolbox.23–25 4) Glucose Intensity normalization: The whole brain (grey and white matter) PET signal was used as a reference region to standardize the regional PET signal to standard uptake value ratio (SUVR) allowing for the direct inter-subject comparison of preprocessed PET data. 5) Normalization: deformations produced from the SPM12 segmentation implemented in step 1 were applied to the PVEc PET images to transform the functional data into the standard Montreal Neurological Image (MNI) space. 6) Smoothing: A 6-mm full-width at half maximum (FWHM) Gaussian kernel was used to smooth the final PVEc PET images.\n\nStatistical analysis was performed using statistical module in the Data Processing & Analysis for Brain Imaging (DPABI V5.1_201201 (RRID:SCR_010501))26 running on MATLAB R2020b (The Math Works, Inc., Natick, MA, United States). Voxel-wise two-sample t-tests were conducted to obtain the brain metabolism differences between each two groups. The resulting statistical maps were corrected for multiple comparisons to a significant level of p < 0.01 using Gaussian Random Field (GRF) theory correction with 25 voxels as the minimum cluster size. The clusters showing significant group differences between the OM and neutral states were selected as regions of interest (ROIs) and the average of SUVR was extracted over the mask of each ROI. Pearson’s correlation analysis was conducted to estimate the correlation between the intensity of experience scores and SUVR measurements for the whole group and then for the just male and female subject groups separately. The Benjamini-Hochberg false discovery rate (FDR) based on the selected ROIs was used in post-hoc fashion to reduce the risk of committing a type I error. Finally, we performed an exploratory analysis to assess whether there might be any correlations (Pearson correlation) between changes in metabolism in brain areas between two subjects in a given pair. The latter correlations might provide an interesting focus for future studies of practices that engage subjects in pairs or larger groups to ascertain whether there is some concordance or “resonance” between the brain of people doing a practice together.\n\nWe asked all subjects to rate the quality of their OM experience by answering the following questions, which were also presented in our earlier article9: Q1: “How similar was the process you completed to what you have typically known Orgasmic Meditation to be? (on a scale from 0, not at all, to 10, identical/indistinguishable)”; Q2: “How intense was the practice you just had? (on a scale from 0, not at all intense, to 10, the most intense OM experience you ever had; 5 would be your average experience)”.\n\n\nResults\n\nThe demographic information for the participants are given in Table 1,22 including mean age, experience, and the subjective scores that the participants provided regarding the intensity of the meditation experience. This was the same group for which we presented fMRI data in a previous report.9 We asked subjects to provide a description of how they would characterize the subjective experience of the OM practice. Several common statements included from the women: “I feel connected to my partner, connected to myself, and a feeling of joy and love in the world”. Men also reported a sense of “flow and connectedness with the partner” as well as a “greater sense of connection with the world”. The male subjects also had a strong sense of tactile or sensory awareness with their partner through the stimulation process. Both men and women frequently described a feeling of oneness, relaxation and joy during the practice, as well as a sensation of “energy” or “electricity” throughout their body.\n\nFor the entire group, the OM practice during the study was rated as a mean of 9.7±0.6 (out of 10) in comparison with their usual meditation experience. The intensity of the experience during the OM practice was rated as 6.6±1.4 (out of 10) for the entire group and the breakdown by men and women is given below.\n\nRegarding the PET analysis, there were significant differences between the neutral and OM conditions for the group as a whole, and for the male and female subjects separately. Overall, there were many more regions with decreased metabolism during OM than increased metabolism. In the group as a whole, during OM there were mostly decreases in several frontal, temporal and parietal regions with increases only in the left cerebellum and right inferior and superior temporal lobes (p < 0.01, GRF corrected, cluster size > 25 voxels). The regions identified by the two-sample t-test are shown in Figure 1 and Table 2. In the female subjects only, there were decreases in metabolism during OM in several frontal, temporal, and parietal regions as well as the left insula, left precuneus, right angular gyrus, and right parahippocampus during OM. There was an increase in the right inferior frontal region only. The regions found to have significant changes in the female subject group are shown in Figure 2 and Table 3. In male participants, there were increases in the left and right cerebellum and right superior temporal gyrus during OM and decreases in several frontal, temporal and parietal regions. The regions found to have significant changes in the male subject group are shown in Figure 3 and Table 4. The unthresholded statistical maps between the meditation and neutral conditions can be accessed as a NeuroVault collection: https://identifiers.org/neurovault.collection:12567.27\n\nTwo-sample t-test, p < 0.01, GRF-corrected, cluster size > 25 voxels. OM, Orgasmic Meditation; GRF, Gaussian Random Field.\n\nTwo-sample t-test, p < 0.01, GRF-corrected, cluster size > 25 voxels. The regions are based on AAL atlas. Negative peak intensity values reflect decreased metabolism during OM and positive values reflect increases. X, Y, Z coordinates of primary peak locations in the space of MNI. The voxel T threshold for voxel p threshold 0.01 is: 1.75. OM, Orgasmic Meditation; GRF, Gaussian Random Field; AAL, Automated Anatomical Labeling; MNI, Montreal Neurological Institute; T, statistical value of peak voxel.\n\nTwo-sample t-test, p < 0.01, GRF-corrected, cluster size > 25 voxels. OM, Orgasmic Meditation; GRF, Gaussian Random Field.\n\nTwo-sample t-test, p < 0.01, GRF-corrected, cluster size > 25 voxels. The regions are based on AAL atlas. Negative peak intensity values reflect decreased metabolism during OM and positive values reflect increases. X, Y, Z coordinates of primary peak locations in the space of MNI. The voxel T threshold for voxel p threshold 0.01 is: 1.75. OM, Orgasmic Meditation; GRF, Gaussian Random Field; AAL, Automated Anatomical Labeling; MNI, Montreal Neurological Institute; T, statistical value of peak voxel.\n\nTwo-sample t-test, p < 0.01, GRF-corrected, cluster size > 25 voxels. OM, Orgasmic Meditation; GRF, Gaussian Random Field.\n\nTwo-sample t-test, p < 0.01, GRF-corrected, cluster size > 25 voxels. The regions are based on AAL atlas. Negative peak intensity values reflect decreased metabolism during OM and positive values reflect increases. X, Y, Z coordinates of primary peak locations in the space of MNI. The voxel T threshold for voxel p threshold 0.01 is: 1.75. OM, Orgasmic Meditation; GRF, Gaussian Random Field; AAL, Automated Anatomical Labeling; MNI, Montreal Neurological Institute; T, statistical value of peak voxel.\n\nIn addition to these significant changes in brain function between the OM and neutral states, we found several significant correlations between changes in these specific brain structures and the intensity of the experience, which were distinct for the male and female participants. There were significant correlations in the female participants between the intensity of the experience and the change in metabolism in the left insula (r = +0.60, p=0.02) and right superior parietal lobe (r = -0.58, p=0.02). No correlations were observed between changes in brain structures and intensity of the experience in the male subjects.\n\nFinally, we did an exploratory analysis to try to determine if there was any relationship between brain function within the pairs of participants. With this in mind, we found a number of significant correlations in the change of brain activity when directly comparing the individuals in each pair. In other words, activity changes in certain brain regions in the male subjects correlated with activity changes in certain brain regions in the concomitant female subjects. We present these findings as hypothesis generating data for potential future studies exploring practices that involve interactions between two or more subjects in which an analysis of the interacting individuals might be of value. The results are provided in Table 5. Notably, the intensity of the experience in the female participants correlated with the activation in several brain structures in the male participants, while the intensity of the experience in the male subjects correlated with the activation in several brain structures in the female subjects (Table 6).\n\nThe regions selected were those that were already found to have differences between the OM and neutral states. OM, Orgasmic Meditation; SUVR, standard uptake value ratio.\n\nThe regions selected were those that were already found to have differences between the OM and neutral states. OM, Orgasmic Meditation; SUVR, standard uptake value ratio.\n\n\nDiscussion\n\nTo the best of our knowledge, this is the first study that has utilized FDG PET to evaluate the neurophysiological changes associated with OM, a practice that uses clitoral stimulation as a paired meditation practice between two individuals. It is important to emphasize that according to the practitioners, the practice is not designed to bring about sexual gratification, but to use clitoral stimulation to facilitate a meditative experience. Thus, the practice does not involve sexual intercourse, and the goal is not sexual climax or orgasm itself, but rather an intense meditative state. This is confirmed by their subjective descriptions of the experience, which do not use words related to eroticism or sexual arousal, but to feelings of awareness, connectedness, oneness, relaxation, energy, and joy. However, it is important to evaluate the neurophysiological mechanism of this practice and evaluate whether the findings resemble meditation, sexual stimulation, or a combination.\n\nThere are a number of aspects of this meditation practice that make it appropriate and interesting for scientific study. Importantly, it is a well-defined meditation practice that has clearly described elements, including enhancement of the meditative effect through the use of clitoral stimulation. The subjects interact in a similar manner each time regardless of the pair involved in the practice as well as how often the practice may be performed. The practice is specifically timed, which also makes it easier to study. Open ended, untimed practices such as mindfulness can sometimes be problematic for study since participants can meditate for several minutes to several hours.\n\nAnother noteworthy aspect of this practice is that it is performed as a pair. Participants have traditionally described that both individuals are engaging in the meditative practice, and while both participants describe the practice as a meditative state, because they are involved in distinct ways, we would hypothesize that male and female subjects would have differences in their subjective response and their physiology during the practice. It should be noted that while a female subject is always the recipient of the stimulation, the other participant can be male or female, although in our study, a male subject performed the stimulation of a female participant.\n\nGiven our team’s background in researching meditative and related spiritual practices, the opportunity to use neuroimaging to evaluate this unique practice can provide important information not only about the practice itself, but can be used for comparison with other practices. We hypothesized that the changes in brain function would be related in part to other meditative practices but could also have some similarities to clitoral or sexual stimulation/arousal. Given the approach and experiences that practitioners of OM report, we expected the pattern of brain activity to more likely represent a meditative experience rather than a sexual one. While we performed a whole brain voxel-based analysis, we hypothesized that specific brain regions, including the frontal lobe, anterior cingulate, temporal lobe, limbic regions, insula, basal ganglia, thalamus, precuneus, and parietal lobe, would be affected in a unique pattern of brain activity. We also hypothesized that there would be some similarities when the entire group is analyzed as a whole, and also patterns of activity distinguishing the male and female partners.\n\nOur results are consistent with our general hypotheses regarding the physiological correlates of the OM practice. When the entire group was compared between the OM and neutral condition, a number of brain regions were found to be significantly different. As a whole group, there were significant decreases in the left insula, left inferior frontal gyrus, left paracentral lobule, left parieto-occipital region, left precuneus, right anterior cingulate, and right postcentral gyrus during the OM practice. There were significant increases in the left cerebellum, right inferior temporal lobe, and right superior temporal lobe.\n\nHowever, as expected, there was a distinct pattern in the metabolic changes observed in the male versus female subjects. In the female participants, we observed multiple regions having significantly reduced metabolism. Specifically, there were significant decreases in the inferior parietal lobe, the precuneus, angular gyrus, and parahippocampus, which are all part of the DMN that has been shown to be decreased in other meditation practices.28 These structures appear to be part of the medial temporal subsystem, which underlies spatial relationships utilizing auditory, visual, and somatosensory input. Furthermore, we have previously argued that decreases in the parietal lobe are associated with the subjective experience of a loss of the sense of self and a sense of connectedness that is common in meditative practices, including the OM practice.15 Changes in parietal lobe activity have frequently been associated with other spiritual experiences such as self-transcendence. In addition, patients with lesions to the parietal lobe are more likely to express feelings of self-transcendence.14 Male subjects also had mostly decreased metabolism in multiple brain regions, but with more frontal involvement, including the middle frontal, superior frontal, and precentral gyrus. There were also decreases in the paracentral and postcentral lobules. Increased metabolism in the male participants was observed in the cerebellum, superior temporal gyrus, postcentral gyrus, and occipital lobe.\n\nThe decreased metabolism observed in most of the brain structures during OM in both male and female participants is in contrast to sexual arousal during which studies have found activations in frontal lobe structures, the thalamus, cingulate cortex, insula, and amygdala.17,18,19 Perhaps the study that most closely resembles the methods of the current study with regard to clitoral stimulation itself was performed by Georgiadis et al.16 In this previous study, 12 female participants underwent clitoral stimulation to induce orgasm while undergoing 15H2O PET imaging to measure changes in cerebral blood flow. Our study is also similar in that, at least for the female participant, the stimulation was performed by a male partner. The results from the previous study observed sexual stimulation of the clitoris (compared to rest), which resulted in a significant increase in rCBF in the left secondary and right dorsal primary somatosensory cortex. In the present study exploring OM practice, we did not observe increased activity in these areas. In a study by Georgiadis et al., compared with the control condition, climax was primarily associated with significantly decreased rCBF in the neocortex, specifically in the left lateral orbitofrontal cortex, inferior temporal gyrus and anterior temporal pole. These findings were not observed in the present OM study, but in the OM practice, climax is not specifically achieved. In male subjects, genital stimulation has been shown to produce activation in the midbrain, cerebellum, and dopaminergic areas, along with various cortical regions.29,30 The current study of OM showed generally decreased metabolism, and it was not in the specific areas involved in sexual stimulation. In particular, we did not see significant increases in metabolism in the limbic areas, basal ganglia, or thalamus.\n\nWith regard to the specific comparison with sexual stimulation, several previous studies have found that climax in men and women is associated with activation of the cerebellum, anterior cingulate gyrus, hippocampus and amygdala, and the dopaminergic pathway structures.20,21 During ejaculation in men, decreased activity has been reported in the temporal lobe and frontal lobe, alongside increased middle temporal gyrus activity.30,31 Furthermore, activation in the orbitofrontal cortex has been reported during ejaculation. Activation of the frontal lobe has been observed in women during orgasm, but decreased activity in the frontal cortical regions has been observed during orgasm in men on PET studies and perfusion fMRI.32 During OM, males in particular do not achieve climax or ejaculation. Furthermore, these patterns associated with sexual experience were not observed in either the male or female subjects performing OM.\n\nAs mentioned, in contrast to the women, men had decreased metabolism primarily in frontal lobe structures such as the inferior frontal gyrus. Such a finding has been observed in a variety of meditative practices and flow states and is consistent with what participants of the OM practice self-described as their typical experience.33,34\n\nNotably, men had increased metabolic activity primarily in the cerebellum. We have not specifically included the cerebellum in our analysis of meditation practices. There are a few studies that have implicated the cerebellum in meditation practices, especially focused based practices.35,36 It is possible that the cerebellum plays a role in the DMN function. Recent studies have also shown the cerebellum is involved in emotional regulation, particularly negative emotions.37 In the context of OM, it may be more related to the hand movements, which are specific and controlled during the practice. While this was supposed to be factored out in the neutral condition during which the male subjects made repetitive hand movements, but during OM, the movements are much more specific and closely monitored to stimulate the female effectively. Thus, future studies of OM and other meditation practices might help determine the role of the cerebellum in such practices.\n\nA number of brain regions are implicated in different elements of meditation practices and are correlated with subjective experiences during meditation practices. For example, studies have shown frontal lobe activity to increase during attention focusing meditation practices.38 Increased activity in the frontal lobe, and particularly the attentional network that includes the lateral prefrontal cortex, premotor cortex, lateral parietal regions, occipital regions, anterior cingulate cortex, and insula, has been observed during concentrative meditation techniques focusing on the breath or a mantra.39 Other studies have linked long-term changes of meditation practice to changes in the precuneus and insula, along with fronto-parietal networks.40 The insula in particular is an important structure with regard to emotional processing and perception. As with other meditation practices that evoke strong emotional changes or affect emotional regulation, the OM practice appears to be associated with altered insula activity supporting the notion that it functions as a meditation practice.41 The precuneus is often linked to self-awareness and self-consciousness as part of its role in the DMN.42 It has also been strongly linked to meditation practices and thus, is similarly affected during OM. In addition, other studies have shown that practices associated with a sense of flow and loss of purposeful control during meditation are associated with reduced frontal lobe activity.11,43 We observed a similar decrease in frontal lobe function in the male subjects performing OM. This appears to be consistent with such flow experiences.\n\nAs mentioned above, several regions in the DMN were reduced during OM, which is consistent with findings from other meditation studies showing that the DMN becomes deactivated during a variety of meditative states. For example, Brewer et al., investigated the impact of several different types of meditation on the DMN.33 The meditation practices studied included focused attention (i.e., concentration), open monitoring (choiceless awareness), and loving-kindness (a member of the constructive family) meditation. The DMN includes brain regions such as the medial prefrontal cortex, posterior cingulate cortex, precuneus, inferior parietal lobule, and inferolateral temporal cortex.44 Brewer et al., showed that the main nodes of the DMN were deactivated in experienced meditators.33 The authors also reported a strong association between activity in the posterior cingulate, dorsal anterior cingulate, and dorsolateral prefrontal cortices. These findings are notable since these regions are involved in self-monitoring and cognitive control during meditation. Although some studies indicate that open monitoring meditation practices diminish DMN activity,45 other studies have observed an increased activation of the precuneus during open monitoring in contrast to focused awareness practices.46 In the current study, we observed a relatively small number of DMN structures affected during OM, suggesting a more specific effect of the OM practice on these structures. Mindfulness practices have also been found to be associated with altered activity in the salience, executive control, and orienting networks.47 Again, in the present OM study, we observed changes in a number of these brain structures consistent with the mindful focus on the clitoral stimulation during the meditation practice.\n\nTo further evaluate some of the findings during the OM practice, we performed correlation analysis between changes in brain activity and the subjective intensity of the meditative experience reported by the participants. The female subjects showed a correlation between the change of activity in the left insula and right superior parietal lobe in comparison to the intensity of the experience. As we have mentioned above, these regions have been implicated primarily during various meditative practices, indicating that the OM practice represents a type of meditation. However, it is noteworthy that there were no correlations observed in the male participants. The reason for this lack of correlation between brain function and intensity is uncertain and future studies will have to try to better evaluate such relationships.\n\nWe also explored correlations between the male and female partners focusing on the structures that were already observed to be significantly affected during OM. While such an analysis is potentially problematic, especially because the men and women are engaged in different elements of the practice, we present these findings as hypothesis-generating data for future studies that may explore practices in which two or more individuals participate with each other. To begin, there were no significant correlations between the intensity of the experience in the male subjects compared to the intensity of the experience in the female subjects. This implies that while two members of the pair are engaged in the same practice, they do not necessarily have to have the same intensity of experience.\n\nIn terms of structures, there were significant correlations particularly between the left precuneus in both partners. Other regions that were also part of these correlations included the left insula, superior temporal gyrus, superior parietal gyrus. These correlations provide at least a potential hypothesis for future studies to explore how this practice, as well as other practices that involve two or more individuals, might result in reciprocal changes among the participants. These results imply that the activation of certain brain areas may have something to do with how the two participants engage in the mutual experience during the OM practice.\n\nA primary limitation of the study centers on determining the best method for evaluating both participants during this practice. We selected FDG PET imaging, but theoretically, we could have considered SPECT imaging, which has tracers with a more rapid uptake into the brain. This might have allowed more precise capturing of the OM state. However, we expected that the majority of FDG was taken up during the practice time and any additional uptake occurred while at rest, which would theoretically diminish our sensitivity for observing significant findings. Thus, we feel that the findings are robust. The ordering of the two conditions (OM and neutral) were randomized so that the findings could not associated with increased comfort of the subjects with the laboratory environment or the imaging procedure. The study paradigm appears to have worked since we did not observe significant increases in the sensory or motor areas, which were accounted for by having similar components in both conditions. However, it is possible that some of the increases observed in the cerebellum were related to more coordinated movements during the practice. We did consider the possibility of having the participants perform clitoral stimulation in both the meditative and neutral conditions. However, the practitioners stated that it would be too difficult not to do the OM practice if they performed clitoral stimulation in the neutral condition. However, future studies might compare brain changes during the OM practice with other sexually stimulating states, including sexual climax, in addition to other meditation practices. Regarding the practitioners, many were highly experienced with the practice, performing it four to five times per day. However, it should be noted that since it is a 15-minute practice, four sessions per day would be one hour, an amount comparable to many other practices. In addition, it was noted that there was a substantial difference between male and female participants in terms of experience level. While it is certainly reasonable that the men and women can have different levels of experience, given that both groups had substantial experience, we achieved the stated goal of working with highly experienced individuals. Whether there are subsequent effects based on the duration or number of times performing the practice is an interesting question that can potentially be addressed in future studies with a larger sample size.\n\nThe findings of this study demonstrate specific patterns of metabolic activity associated with the OM practice that are unique for both the male and female participants. In addition, there are several brain areas that are significantly changed when considering both men and women together. These results are consistent with our initial hypotheses that there would be some similarities when comparing the entire group between the OM practice and the neutral condition. However, we also expected unique patterns of metabolic activity that differentiate the male and female participants. Overall, men tended to show a decrease in anterior structures, while women tended to show a decrease in posterior structures. Structures of the DMN and salience network were also involved.\n\nThe findings from this initial neuroimaging study of OM have potential implications regarding the psychological and neurophysiological processes involved in sexual stimulation and spiritual practices such as meditation. Future research can explore more specific neurophysiological correlates and compare the OM practice to other practices that include both meditative and/or augmentation components. In addition, studies can explore sexual experiences and the OM practice in the context of psychiatric disorders and their treatments, which are frequently associated with sexual problems.\n\nOverall, these results demonstrate that the OM practice has unique characteristics that distinguish it from other meditative practices. Some of the brain changes are similar to those observed in concentrative meditation practices as well as mindfulness when it comes to changes in the frontal lobe and structures of the default mode and salience networks. There were a few brain changes similar to those involved with genital stimulation. However, the unique patterns observed with the OM practice indicates that it is a true hybrid practice.\n\n\nData availability\n\nNeuroVault: OM Meditation Study. https://identifiers.org/neurovault.collection:12567.27\n\nFigshare: Orgasmic Meditation FDG PET Scans. https://doi.org/10.6084/m9.figshare.20113853.22\n\nThis project contains the following underlying data:\n\n- PET_AC.nii files (raw images from PET scans)\n\n- OM Additional Data.2.xlsx (basic demographic information of subjects)\n\n- 11D.412_fMRI PET OM Meditation comp_stamped version 12 10 2019 exp 09.09.2022.pdf (blank consent form and information sheet)\n\n- fMRI PET MEDITATION CRF TC 2017_05_10 revised 2019_07_25.pdf (case report form)\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).", "appendix": "References\n\nNewberg A, Alavi A, Baime M, et al.: The measurement of regional cerebral blood flow during the complex cognitive task of meditation: a preliminary SPECT study. 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PubMed Abstract \| Publisher Full Text" }	[ { "id": "217436", "date": "15 Nov 2023", "name": "Michael Winterdahl", "expertise": [ "Reviewer Expertise PET imaging", "sexology", "behaviour." ], "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 opportunity to review the manuscript entitled 'Alterations in cerebral glucose metabolism measured by FDG PET in subjects performing a meditation practice based on clitoral stimulation'. This manuscript delves into the fascinating intersection of sexuality and spirituality, examining brain activity imaged with FDG PET during a unique practice of Orgasmic Meditation. The study involved 40 participants, comprising 20 males and 20 females, who engaged in a meditative practice enhanced with clitoral stimulation.\nFirstly, I would like to extend my congratulations to the authors. Securing funding and institutional approval for studies of this nature is a significant challenge, one with which I am personally familiar. The ability to conduct a sound and relatively well-powered PET imaging study under these circumstances is indeed impressive and commendable.\nRegarding the manuscript, I have a few concerns:\nThe structure of the manuscript diverges significantly from the conventional format of introduction, methods, results, and discussion. Specifically, the introduction is overly lengthy, while the discussion is notably brief. It would benefit the reader if the introduction were condensed to provide only the necessary background and references to previous work and literature. Furthermore, in the discussion, the results should be contextualized within existing literature, including a thorough examination of the study's limitations. A balanced presentation of the study's strengths and weaknesses is essential (most have been mentioned in the introduction). Finally, the manuscript would be enhanced by suggestions for future research directions.\n\nIn a previous paper, the authors published their findings from the same experiment using fMRI. However, they missed the opportunity to compare the fMRI findings with those from FDG PET, a very different imaging modality. The comparison of results between the two techniques could be a major strength of the present manuscript. It would have been beneficial to explore whether these findings correlate and whether the same regions are \"activated\".\n\nSince the subjects are not being stimulated in the PET scanner, is the argument for using FDG PET imaging really to avoid motion artefacts? Or does the main advantage lie in the biochemical information obtained? Can the authors discuss this further to clarify the details?\n\nIs the dopamine system involved in meditation? What would, e.g. Raclaprice PET have shown? Could other tracers have contributed with important knowledge - Can the authors discuss this further to clarify the details?\n\nIn a few instances, the participants or volunteers were mistakenly referred to as patients.\n\nTest values are typically denoted with a lowercase \"t\" (represented using a colour scale in figures).\n\nAlthough the population has been described previously, a small recap on the demographics could help the reader.\nDespite the difficulty of the subject, the study was well conducted and, with a few necessary adjustments, absolutely publishable.\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": "10782", "date": "16 Jan 2024", "name": "Andrew Newberg", "role": "Author Response", "response": "We greatly appreciate the reviewer's comments which we feel have helped to substantially improve the article. Below is a point-by-point response. Corresponding changes are made in the manuscript in track changes mode. Firstly, I would like to extend my congratulations to the authors. Securing funding and institutional approval for studies of this nature is a significant challenge, one with which I am personally familiar. The ability to conduct a sound and relatively well-powered PET imaging study under these circumstances is indeed impressive and commendable. Thank you for these kind words. It is certainly a challenge performing such studies and we appreciate your comments about this difficulty. Regarding the manuscript, I have a few concerns: The structure of the manuscript diverges significantly from the conventional format of introduction, methods, results, and discussion. Specifically, the introduction is overly lengthy, while the discussion is notably brief. It would benefit the reader if the introduction were condensed to provide only the necessary background and references to previous work and literature. Furthermore, in the discussion, the results should be contextualized within existing literature, including a thorough examination of the study's limitations. A balanced presentation of the study's strengths and weaknesses is essential (most have been mentioned in the introduction). Finally, the manuscript would be enhanced by suggestions for future research directions. Thank you for these suggestions. We have modified the manuscript by shortening the Introduction and adding substantially to the Discussion section. We have also expanded a discussion of limitations and suggested future research directions. In a previous paper, the authors published their findings from the same experiment using fMRI. However, they missed the opportunity to compare the fMRI findings with those from FDG PET, a very different imaging modality. The comparison of results between the two techniques could be a major strength of the present manuscript. It would have been beneficial to explore whether these findings correlate and whether the same regions are \"activated\". We agree and have expanded our discussion regarding the connection of the current reported PET results with those from the MRI analysis and discussed its implications. Since the subjects are not being stimulated in the PET scanner, is the argument for using FDG PET imaging really to avoid motion artefacts? Or does the main advantage lie in the biochemical information obtained? Can the authors discuss this further to clarify the details? Thank you for this question. There were several factors that the PET imaging provided an advantage including the ability to perform the entire practice outside the scanner while still being able to assess metabolic changes in the brain during the practice. This includes accommodating the subjects to be able to be positioned and touching in the prescribed manner of the practice, reduction of motion artifact, and the ability to assess specific metabolic effects in the brain. We have clarified and expanded this in the manuscript. Is the dopamine system involved in meditation? What would, e.g. Raclaprice PET have shown? Could other tracers have contributed with important knowledge - Can the authors discuss this further to clarify the details? This is an important question. There is only one study we are aware of that used raclopride to assess a meditation state, but it would be quite interesting to observe changes in various neurotransmitter systems more specifically. We will include this in the Discussion section and also in future directions. In a few instances, the participants or volunteers were mistakenly referred to as patients. Thank you for pointing this out. They should be referred to as participants or subjects and we will correct this throughout the manuscript. Test values are typically denoted with a lowercase \"t\" (represented using a colour scale in figures). We agree and have modified this in the figure. Although the population has been described previously, a small recap on the demographics could help the reader. We agree and have expanded this discussion in the paper." } ] }, { "id": "188012", "date": "24 Nov 2023", "name": "Helen Lavretsky", "expertise": [ "Reviewer Expertise Integrative medicine", "mind-body practices", "biomarkers", "neuroimaging" ], "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 study reports the findings from the PET study of the OM orgasmic meditation during clitoris stimulation in 20 women and 20 men partnering during this 15 min meditation compared to a neutral control of stroking upper leg.\nThe results include regional reductions in brain glucose metabolism during stimulation compared to neutral state and some correlations between changes in men and women.\nThis is really an interesting study and design, and an relatively unusual meditation with sexual stimulation.\nOne could argue about control conditions- does stroking upper leg cause similar sensations?\nHow about comparing it to meditation without clitoral stimulation? Would the satisfaction and brain results be similar or different.\nit is a nicely done observational study contributing to the literature of neural mechanisms of meditative experiences. Not sure what health benefits it might have other than mutual enjoyment by the partners.\nIt would be nice to comment whether all couples were naïve to this type of meditation or true followers and \"believers\" than also addressing a \"placebo\" response in the the true followers of the practice.\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": "10783", "date": "16 Jan 2024", "name": "Andrew Newberg", "role": "Author Response", "response": "We greatly appreciate the reviewer's comments which we feel have helped to substantially improve the article. Below is a point-by-point response. Corresponding changes are made in the manuscript in track changes mode. This is really an interesting study and design, and an relatively unusual meditation with sexual stimulation. Thank you for these positive comments. One could argue about control conditions- does stroking upper leg cause similar sensations? This is an interesting and important question. In planning for the study, we considered several options and decided that this would be the best as it matches movement by the male and the sensory reception of the female. However, it is not the same type of sensation since it is not a form of sexual stimulation. It might be interesting to compare clitoral stimulation with and without meditation, however, the practitioners were concerned that such a distinction might be difficult as it might overlap with their typical meditation. We have observed such an issue with our studies of other practices. For example, for people who meditate sitting still while focusing on their breath, they might start naturally meditating if placed in a room and asked to sit still and breathe normally. We have expanded on these issues in the manuscript. How about comparing it to meditation without clitoral stimulation? Would the satisfaction and brain results be similar or different. Yes, this would be another interesting comparison. We have expanded this discussion in the manuscript. it is a nicely done observational study contributing to the literature of neural mechanisms of meditative experiences. Not sure what health benefits it might have other than mutual enjoyment by the partners. Thank you for the positive comments. We hope that this data might be useful for informing future clinical studies that might focus on symptoms of depression or anxiety, as examples. We will expand upon possible future directions in the manuscript to address this comment and a similar comment by the other reviewer. It would be nice to comment whether all couples were naïve to this type of meditation or true followers and \"believers\" than also addressing a \"placebo\" response in the true followers of the practice. We agree that this is also an interesting issue. In order to perform this study successfully, we involved experienced practitioners. Future studies might evaluate whether people who are novices have similar effects and whether differences might be able to distinguish potential placebo effects." } ] } ]	1	https://f1000research.com/articles/11-1015
https://f1000research.com/articles/12-756/v1	27 Jun 23	{ "type": "Study Protocol", "title": "Comparative evaluation of clinical performance, child and parental satisfaction of Bioflex, zirconia and stainless steel crowns in pediatric patients", "authors": [ "Ishani Rahate", "Punit Fulzele", "Nilima Thosar", "Punit Fulzele", "Nilima Thosar" ], "abstract": "Background: Pediatric treatment is challenging in patients with early childhood caries. It is difficult due to the adjacency of pulp, miniature tooth size, and thin enamel compared to permanent dentition. Nowadays, aesthetics play an important role in managing decayed teeth, and children need treatment that includes full coverage crowns in either stainless steel or anesthetic crown in zirconia or the recently developed Bioflex crown. The Bioflex crowns are highly flexible and aesthetically preformed pediatric crowns with combined stainless steel and zirconia properties. This study aims to assess the clinical performance and child and parental satisfaction of Bioflex crowns compared to zirconia and stainless steel crowns. Methods: In the current in-vivo comparison of Bioflex crowns with zirconia and stainless steel crowns, children aged three to seven years old will be selected, and 72 primary teeth requiring crowns will be randomly distributed into three groups, n = 24: Group I: Preformed stainless steel crown, control; Group II: Preformed Bioflex crown; Group III: Preformed zirconia crown. Crowns will be evaluated for recurrent caries, plaque accumulation, restoration failure, gingival status opposing tooth wear, and clinicians and parental satisfaction at zero, three, six, and 12 months. Newly introduced aesthetic crowns will serve as a versatile alternative for restoring primary decayed teeth that over-performed aesthetic and conventional crowns. Conclusions: The Bioflex crown will be assessed as a better aesthetic substitute for the future, and the satisfaction level of parents will be evaluated. Trial registration: CTRI registration number: CTRI/2023/05/052256; Date of registration: May 03, 2023. Protocol version: Two; Date: April 22, 2023", "keywords": [ "Bioflex crown", "zirconia crown", "aesthetic", "early childhood caries", "semi-permanent restorations" ], "content": "Introduction\n\nIn most preschoolers, early childhood caries pose a significant problem. If left untreated, they can lead to the degeneration of a child’s oral health.1 Managing deciduous, deformed, decayed, or traumatized teeth with tooth-colored restoration is challenging in children because of their miniature tooth size, larger pulpal chamber, thin enamel, and decreased surface area for restoration, accompanied by specific behavior management problems in young pediatric patients. Aesthetic concern plays a vital role in modern dental practice. Understanding the child’s and parental aesthetic perception is necessary for good clinical practice.2,3\n\nAn optimal anterior restoration should have better durability, ease of handling, be aesthetically acceptable, and be cost-effective. There have been many options for full coverage restoration of deciduous teeth, each with technical, functional, or aesthetic limitations.3,4 The demand for beautiful smiles is increasing among children and adults. A child’s looks can affect their achievement in social acceptance, quality of life, and physical and psychological health. A variety of aesthetic solutions are available, including full-coverage crowns for deciduous anterior teeth, prefabricated primary zirconia crowns, and pre-veneered stainless-steel crowns.\n\nThe primary dentition should be preserved in a non-pathologic and healthy state for the child’s overall well-being. Pediatric dentists have to balance three priorities: the patient’s behavioral management, the conservation of the tooth structure, and the parents’ satisfaction.5 Continually re-evaluating pediatric dental treatment modalities and techniques is necessary because the advancements in dental materials for children over the last few decades have led to constant improvement in dental materials suitable for children. Young patients may not necessarily benefit from a treatment approach that was acceptable in the past. There has been a concerted effort to bring various approaches for full coverage restorations in pediatric dental practice. Every technique and material has its merits and demerits. It is noted that there are numerous possibilities for treating carious teeth in young children, ranging from stainless steel crowns and their modifications to other aesthetic crowns like Bioflex and zirconium crowns, which are becoming more and more popular. Bioflex crowns are flexible, durable, and adaptable. They are available as aesthetic preformed pediatric crowns that offer properties of both stainless steel and zirconia crowns. There is a lack of literary evidence for assessment of the properties of Bioflex crowns and their effect on clinical outcomes and parental satisfaction compared to traditionally available options. Hence, this study plans to assess the clinical performance and child and parental satisfaction for Bioflex, zirconia, and stainless steel crowns in pediatric patients.\n\nThe objectives are as follows:\n\n1. To evaluate the clinical performance of Bioflex, zirconia, and stainless steel crowns in primary dentition based on recurrent caries, gingival health, restoration failure, plaque accumulation, opposing tooth wear, and clinicians’ satisfaction at zero, three, six and 12 months follow up.\n\n2. To compare the clinical performance of Bioflex, zirconia, and stainless steel crowns in primary dentition at zero, three, six and 12 months.\n\n3. To assess the child and parental satisfaction of Bioflex, zirconia, and stainless steel crowns in primary dentition at zero, three, six, and 12 months.\n\n\nMethods\n\nA randomized controlled trial with a parallel group will be the research design for the study. Total 72 primary teeth requiring crowns will be randomly distributed in three groups of 24 each. The allocation will be carried out using computer-generated numbers. After obtaining written informed consent, the subjects will be enrolled, and teeth will be assigned randomly to the groups for receiving the intervention or conventional preformed crowns. The study adheres to the protocol following the Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT) guidelines.6 The allocation of participants and flow diagram for study participants is shown in Figure 1.\n\nThe present study will be conducted in the Department of Pediatric and Preventive Dentistry of Sharad Pawar Dental College and Hospital, Sawangi (Meghe), Wardha, Maharashtra, India.\n\nIn children with more than one tooth requiring a crown, the teeth will be allocated based on random sampling. We will be conducting single blinding in which participants will be blinded. Personal information about potential and enrolled participants will be collected and maintained in order to protect confidentiality before, during, and after the trial. The population of the study is young, healthy children. The research is approved by the institutional ethics committee of Datta Meghe Institute of Higher Education and Research (Deemed to be University) (ref. no: DMIHER (DU)/IEC/2023/565). Date of approval: February 6, 2023.\n\nInclusion criteria5 will be as follows:\n\n• Children aged three to seven years old who are healthy and free of any systemic disease\n\n• Deciduous teeth indicated for crowns\n\n• Deciduous teeth having two-thirds of root structure left radiographically\n\n• Presence of one-third of crown shape\n\nExclusion criteria5\n\n• A pathological discrepancy of root resorption\n\n• Inflammation at the furcation area\n\n• The child having oral parafunctional habits\n\n• Deciduous teeth having not sufficient crown structure\n\n• Teeth with root caries\n\nEvaluation criteria\n\nThe study will be clinically evaluated from the following criteria: crown retention, modified gingival index, plaque index, stain resistance, gingival marginal extension, occlusion, proximal contact, opposing tooth wear, and radiographic assessment.\n\nClinician’s Satisfaction Criteria will be as follows: surface gloss, roughness, stain resistance, aesthetic, anatomical form, crown fracture, recurrent caries. Parental satisfaction ratings of aesthetic characteristics and their impact of treatment on their children will be evaluated on the basis of size, shape, color and stain using five-point Likert’s scale.\n\nA sample size of children aged three- to seven-years-old will be selected and 72 primary teeth requiring crowns will be randomly distributed in three groups of 24, as follows:\n\nRepresents the desired level of statistical significance\n\nZβ=1.28: Represents the desired power = 1.28 for 90%\n\nN = Minimum samples required for each group\n\nWhere,\n\nP1 = Estimated proportion of study outcome (Child satisfaction % Experimental group) = 99.99% (Approximate to 100%)1\n\nP2 = Estimated proportion of study outcome (Child satisfaction % Control group) = 53.33%1\n\nAt a level of significance at 1% and power 90%\n\nThe minimum sample size required:\n\nMathew et al., showed the difference between the two proportions of child satisfaction (%) as the primary variable1\n\nP1(for the experimental group) = 100% (considered as 99.999% approx to 100%) and for the control group (53.333%). We considered a clinically significant margin of difference at 46.666%. Also, we considered the assumption for statistical significance, the highest statistical significance level of 1% alpha value with power (1-beta) at 90%.\n\nWe use the test statistics of two independent proportion sample size calculations with the given formula samples for taking the minimum samples required in each group.\n\nCalculated with 22 samples required in each group, adding 10% of dropout = 2. A total of 22 + 2 = 24 samples are required in each group, with a sample size of 72 children distributed in three groups.\n\nAll the healthy children having more than one deciduous tooth decay requiring a crown will be selected for the study. Parents will be oriented on the implementation of the study.\n\nThe study protocol will be explained to the participating children and their parents. Further, a written informed consent will be obtained from their parents.\n\nThe participants will be allocated based on the inclusion criteria. They will be randomized to preformed Bioflex crown and preformed zirconia crown as the intervention group or preformed stainless steel crown as the control group by computer-generated numbers. The research co-investigator will carry out data collection, data entry, and data analysis and will be blinded to group allocation.\n\nTotal 72 primary teeth requiring crowns will be randomly distributed in three groups of 24 each. The allocation will be carried out using computer-generated numbers. After obtaining written informed consent, the subjects will be enrolled, and teeth will be assigned randomly to the groups for receiving the intervention or conventional preformed crowns.\n\nGroup 1: Preformed stainless steel crown: control group\n\nThe material for coronal build-up for this group is a preformed stainless-steel crown (the control group). An appropriate-sized preformed stainless-steel crown will be selected. Tooth preparation will be carried out with tapered bur to reduce occlusal surface up to 1 to 1.5 mm. The interproximal reduction will be made mesially and distally. The selected crown size will be checked and a trial fit will be done before cementation. It will require crimping pliers and the crown will be cemented using type 1 glass ionomer cement. The excess will be removed and proper occlusion will be checked.7\n\nGroup 2: Preformed Bioflex crown\n\nThe Preformed Bioflex crown (Kids-e-dental) will be used in this group. A similar sized preformed crown will be selected. Tooth preparation will be carried out with a tapered diamond bur for occlusal reduction by 1–1.5 mm, including the central groove. The proximal preparation will be around 0.5 mm to clear the contact area. Placement of the crown will be achieved by a snug fit followed by contouring using a Hover’s plier. Crown cementation will be carried out using a glass ionomer type I and removal of excess cement using floss or explorer.\n\nGroup 3: Preformed zirconia crown\n\nThe material for crown restoration for this group is the preformed zirconia crown. A diamond bur will reduce the occlusal surface by 1.5–2 mm. Interproximally, contacts will be prepared with a tapered fissure bur. About 1–2 mm subgingival preparation will be performed. The selected crown will be placed and checked. The passive fit of the crown will be assessed and will be luted with dual cure resin cement. Consistent firm finger pressure will be applied during cementation. Crown placement will be assessed.7\n\nWe will compare the control group (stainless steel crown) with Bioflex and Zirconia crowns on basis of their clinical performance and parental satisfaction.\n\nPreformed esthetic crowns and preformed stainless steel crown outcomes will be assessed by the research co-investigator at different time intervals of zero, three months, six months, and 12 months follow-up based on clinical performance, and child and parental satisfaction based on three evaluation criteria, which include clinical, clinicians’ and parental satisfaction. The child and parental satisfaction score will be measured using a questionnaire-based five-point rating Likert’s scale.1 Outcome will be evaluated based on durability, flexibility, self adaptability. Bioflex crowns will be a smart option for pediatric tooth-coloured crowns.\n\nThe questionnaire for assessing child and parental satisfaction score consists of four main categories in satisfaction rating of esthetic characteristics.1 These categories are size, shape, color, and stain. The response format will be a five-point Likert scale, ranging from not at all satisfied, with a score of 1, to very much satisfied, with a score of 5.\n\nAnother questionnaire scale based on parental ratings of the impact of treatment on their children8 consists of five categories, including 1) The oral health of the child improved after crowns; 2) Parents concern about appearance before crowns; 3) The child avoided smiling before crowns; 4) Child smiling after crowns; 5) Crowns have improved the appearance of the child’s teeth. The response format will be a five-point Likert scale, ranging from not at all (score of 1) to very much (score of 5).6,8\n\nThe research co-investigator will carry out data entry. The principal investigator will review the data entered for discrepancies such as entry errors, enrolment errors, etc. The data entry errors will be checked by a co-investigator by randomly selecting data sheets.\n\nStatistical analysis will be done using general methodology; continuous variables will be summarized using tables of descriptive statistics: the number of patients with recorded observations, mean, standard deviation, median, minimum, and maximum. Categorical variables will be determined using counts and percentages. Descriptive statistics will be presented by diagnosis and all the results will be calculated using RStudio Version: 2023.03.1+446 (RRID: SCR_000432) will be used. Comparison of continuous parameters between the three groups will be performed using an ANOVA test for quantitative data or Kruskal Wallis test for qualitative data. Categorical variables will be summarized using the frequencies and percentages and compared between the three groups.\n\nEthical approval for the study was obtained from the institutional ethics committee of Datta Meghe Institute of Higher Education and Research (Deemed to be University) (ref. no: DMIHER (DU)/IEC/2023/565); date of approval: February 6, 2023. The trial is registered under the Clinical Trial Registry of India, CTRI registration number: CTRI/2023/05/052256; date of registration: May 03, 2023. A written participant information sheet will be given regarding the details of the study, and it will be explained to participants and their parents before enrolment to the study. Their involvement benefits and harm will be explained to the participants. Written informed consent from the participants will be obtained before involving them in study.\n\nConfidentiality of the research data collected will be maintained strictly as per the ethical standards. Only the research assistants and the researchers will have access to the participants’ data in the study.\n\nOnce complete the study will be published in a PubMed, Scopus and indexed journal. The data and results from this study may be presented at conferences and published in scientific journals without revealing the identity of the participants.\n\nThe study is yet to be started.\n\n\nDiscussion\n\nThe significance of conventional stainless-steel crowns in posterior full coronal restorations in early childhood caries cases are well acknowledged. They have been used for various purposes. To further improvise the longevity and need for better natural-looking restoration in primary teeth, this study plans to compare the Bioflex crown over conventional ones.\n\nStainless steel crowns have been used for decades and fulfill every aspect of a crown except the aesthetic purpose. As a result, tooth-coloured restorations like zirconia were introduced but they require subgingival preparation, which requires more time and is also not cost-effective for parents. The newly emerging Bioflex crown has super flexibility, is more adaptable, is easy to prepare, and is a faster technique for full coronal restorations in early childhood caries cases. Mathew et al. (2020) conducted an in vivo study in which bilateral pulp therapy was performed. Patients were divided into two groups of either zirconia or a stainless-steel crown. Patients were evaluated based on gingival inflammation, plaque accumulation opposing tooth wear, and parental satisfaction. They found no statistical difference between the clinical outcome success rates for zirconia and stainless-steel crowns, but less plaque accumulation was noted with zirconia in comparison to stainless-steel. With both the crown types, it seemed that parental satisfaction rates were high.1\n\nGupta et al. (2020) also conducted an in vivo study to compare three tooth-coloured crowns and evaluate marginal integrity, surface texture, discoloration, anatomical form, and secondary caries in deciduous anterior teeth over a period of three, six, and nine months. Group I included resin strip crowns, Group II had zirconia crowns, followed by Group III, which had Luxa crowns. They found that the results were statistically non-significant for all parameters except the resin strip crowns, which showed secondary caries and irregular marginal integrity. The zirconia crown showed the best results among the three crowns, followed by the Luxa crown.5\n\nOlegário et al. (2021) performed a randomized clinical trial to determine the expectancy of survival rate in one year after endodontic treatment in deciduous molars having restoration with stainless steel and bulk-fill composite crowns. Samples were evaluated and randomized at one, three, six, and 12 months of followup. The survival rate after one year for the stainless-steel crown was 88% and the bulk fill composite was 75%. In intention-to-treat analysis, the success rate of the bulk fill crown was 86.7% and the stainless steel crown was 82.6%. Both the children and their parents were satisfied with the treatments.9\n\nAnother similar study by Murali et al. (2022) compared stainless-steel and zirconia crowns. At follow-up, these crowns were evaluated based on proximal contacts, retention, plaque accumulation, marginal integrity, gingival inflammation, and opposing tooth wear. The author concluded that the success rate of zirconia was 93.5% and for stainless steel full coverage restoration was 96.7%. In their statistical analyses, it was observed that there was no significance between the groups, and the preformed stainless steel and zirconia crowns showed good results but zirconia was preferred aesthetically.7\n\nThe Bioflex crown has been introduced in pediatric practice as a synthetic crown that will provide better adaptation, durability, and ease of handling with improved aesthetic properties compared to conventional crowns. The limitations of this study will be that long-term follow up will be required for more detailed clinical observation and larger sample size will provide more rigorous results.\n\nThe study will help improve the properties of conventional crowns and the Bioflex crown may provide a promising result in terms of the clinician’s and parental satisfaction as aesthetic is a prime concern for parents and children in this era.\n\n\nConclusions\n\nIn this paper, the study design and methodological approach adopted to evaluate the effectiveness of preformed Bioflex crowns to zirconia and stainless steel crowns are described. In this study, we expect to gain a better understanding of the clinical performance, child and parent satisfaction with the tooth-colored Bioflex and zirconia pediatric crowns compared to traditional pediatric crowns.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nZenodo: Extended data for ‘Comparative evaluation of clinical performance, child and parental satisfaction of Bioflex, zirconia and stainless-steel crowns in pediatric patients’, https://doi.org/10.5281/zenodo.7994353. 6\n\nZenodo: SPIRIT checklist for ‘Comparative evaluation of clinical performance, child and parental satisfaction of Bioflex, zirconia and stainless-steel crowns in pediatric patients’, https://doi.org/10.5281/zenodo.7994353. 6\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nMathew M, Roopa K, Soni A, et al.: Evaluation of clinical success, parental and child satisfaction of stainless steel crowns and zirconia crowns in primary molars. J Fam Med Prim Care. 2020; 9(3): 1418–1423. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAshima G, Sarabjot KB, Gauba K, et al.: Zirconia Crowns for Rehabilitation of Decayed Primary Incisors: An Esthetic Alternative. J Clin Pediatr Dent. 2014 Sep 1; 39(1): 18–22. PubMed Abstract \| Publisher Full Text\n\nHamrah MH, Mokhtari S, Hosseini Z, et al.: Evaluation of the Clinical, Child, and Parental Satisfaction with Zirconia Crowns in Maxillary Primary Incisors: A Systematic Review. Pucci CR, editor. Int J Dent. 2021; 2021: 1–6. Publisher Full Text\n\nVignesh K, Kandaswamy E: A Comparative Evaluation of Fracture Toughness of Composite Resin vs Protemp 4 for Use in Strip Crowns: An in vitro Study. Int J Clin Pediatr Dent. 2020 Feb; 13(1): 57–60. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGupta T, Mehra M, Sadana G, et al.: Clinical Comparison of Three Tooth-colored Full-coronal Restorations in Primary Maxillary Incisors. Int J Clin Pediatr Dent. 2021 Mar 31; 13(6): 622–629. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRahate I, Fulzele P, Thosar N: SPIRIT checklist for Comparative evaluation of clinical performance, child and parental satisfaction of Bioflex, Zirconia and Stainless Steel crowns in Pediatric patients. [Dataset]. 2023 Mar 31. Publisher Full Text\n\nMurali G, Mungara J, Vijayakumar P, et al.: Clinical Evaluation of Pediatric Posterior Zirconia and Stainless Steel Crowns: A Comparative Study. Int J Clin Pediatr Dent. 2022 Apr 13; 15(1): 9–14. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHolsinger DM, Wells MH, Scarbecz M, et al.: Clinical Evaluation and Parental Satisfaction with Pediatric Zirconia Anterior Crowns. Pediatr Dent. 2016; 38(3): 192–197. PubMed Abstract\n\nOlegário IC, Bresolin CR, Pássaro AL, et al.: Stainless steel crown vs bulk fill composites for the restoration of primary molars post-pulpectomy: 1-year survival and acceptance results of a randomized clinical trial. Int J Paediatr Dent. 2022 Jan; 32(1): 11–21. PubMed Abstract \| Publisher Full Text" }	[ { "id": "189258", "date": "04 Aug 2023", "name": "Jayakumar Jayaraman", "expertise": [ "Reviewer Expertise Systematic reviews & meta-analysis", "clinical trials", "pediatric 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\nThis study protocol is interesting on a clinically relevant topic. My comments are:\nObjectives 1 & 2 look similar. I suggest deleting Objective 2.\n\nInclude manufacturer details of all the products used. For example, Kids-e-dental, Glass ionomer cements etc.\n\nHow are the examiners trained to place the crowns? What is the education and experience of the providers? Also, who will be conducting the assessment, and how are the examiners calibrated?\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": "189260", "date": "04 Sep 2023", "name": "Giuseppe Minervini", "expertise": [ "Reviewer Expertise TMD" ], "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 has well-designed research methods, appropriate statistical analysis and a relatively good interpretation of the results.\nPlease be sure to use only keywords accordingly to medical subject headings (Mesh word) for a better indexing.\nI suggest you add a table with the list of abbreviations used in the text.\nI suggest you implement the abstract in order to make it more understandable to authors.\nThe introduction should be expanded perhaps by adding a section on temporomandibular disorders.\nThe conclusion is in accordance with the objectives of the research, its results and their interpretation, as well as the relevant literature.\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/12-756
https://f1000research.com/articles/12-1089/v1	01 Sep 23	{ "type": "Research Article", "title": "Predicting gene expression changes upon epigenomic drug treatment", "authors": [ "Piyush Agrawal", "Vishaka Gopalan", "Sridhar Hannenhalli", "Vishaka Gopalan" ], "abstract": "Background: Tumors are characterized by global changes in epigenetic modifications such as DNA methylation and histone modifications that are functionally linked to tumor progression. Accordingly, several drugs targeting the epigenome have been proposed for cancer therapy, notably, histone deacetylase inhibitors (HDACi) such as vorinostat and DNA methyltransferase inhibitors (DNMTi) such as zebularine. However, a fundamental challenge with such approaches is the lack of genomic specificity, i.e., the transcriptional changes at different genomic loci can be highly variable, thus making it difficult to predict the consequences on the global transcriptome and drug response. For instance, treatment with DNMTi may upregulate the expression of not only a tumor suppressor but also an oncogene, leading to unintended adverse effect. Methods: Given the pre-treatment transcriptome and epigenomic profile of a sample, we assessed the extent of predictability of locus-specific changes in gene expression upon treatment with HDACi using machine learning. Results: We found that in two cell lines (HCT116 treated with Largazole at eight doses and RH4 treated with Entinostat at 1µM) where the appropriate data (pre-treatment transcriptome and epigenome as well as post-treatment transcriptome) is available, our model distinguished the post-treatment up versus downregulated genes with high accuracy (up to ROC of 0.89). Furthermore, a model trained on one cell line is applicable to another cell line suggesting generalizability of the model. Conclusions: Here we present a first assessment of the predictability of genome-wide transcriptomic changes upon treatment with HDACi. Lack of appropriate omics data from clinical trials of epigenetic drugs currently hampers the assessment of applicability of our approach in clinical setting.", "keywords": [ "Epigenetics", "HDACi", "DNMTi", "Cancer therapy", "Machine Learning", "Transcriptomics" ], "content": "Introduction\n\nPhenotypic state of a cell or tissue, either in normal homeostasis or in disease such as cancer, is intimately linked to its transcriptional state, which in turn is profoundly determined by its global epigenome.1 Cancer genomes display a substantially altered epigenome relative to their non-malignant counterparts. For instance, global DNA hypomethylation and focal hypermethylation, notably, at tumor suppressor gene promoters, have been noted as a general feature of many cancers.2 Accordingly, drugs that alter the epigenome have emerged as potential candidates for cancer therapy.3 Two of the most common classes of epigenome-altering drugs are DNA methyltransferase inhibitors (DNMTi), such as zebularine, and histone deacetylase inhibitors (HADCi), such as vorinostat. While DNMTi’s are standard of care in some hematological malignancies, across most cancers, the efficacy of epigenomic drugs has been mixed.\n\nOne of the many reasons adversely affecting the success of epigenomic drugs is its lack of locus specificity. Note that the intent of DNMTi, for instance, is partly to reactivate aberrantly silenced genes by demethylating their (aberrantly methylated) promoters.3,4 However, the drug is locus-agnostic and, a priori, can activate many other loci in the genome, some of which may have toxic side effects5 and in the worst case, have pro-tumor effects; indeed, DNMTi’s are known to activate cancer testis antigens, which are known to be pro-tumor. Currently, we lack the sufficient knowledge to predict locus-specific effects of an epigenomic drug on the gene expression, to be able to develop more rational therapies. One of the facts complicating this understanding is incompletely understood interactions between different epigenomic marks. For instance, there is broad antagonism between two key mechanisms of transcriptional suppression, namely, histone modification H3K27me3 and DNA methylation6 which may result in redistribution of one upon perturbation of the other. Because of the complex interactions between epigenomic marks as well as feed-forward and feed-back loops between the epigenome and the transcriptome, the ultimate effect of epigenomic perturbation on the global transcriptome may not be easily predictable, especially based only on the local genomic context.\n\nMotivated by these challenges, our goal here is to assess the scope and extent to which one can predict locus-specific changes in gene expression upon treatment with an epigenomic drug such as HDACi or DNMTi, given the transcriptional and epigenomic state of the tumor sample pre-treatment. This could substantially help assess the clinical efficacy of an epigenomic drug.\n\n\nMethods\n\nFASTQ files were downloaded from Sequence Read Archive (SRA) (HCT116 dataset accession: SRP113250, RH4 accession: SRP151465). We uniformly re-processed both RNA-seq and H3K27ac ChIP-seq data to minimize biases. We ran the fastqc toolkit (v0.11.9) to ensure quality. Trimgalore (v0.6.7) was run with default options to trim any adaptor sequence contamination in reads. For ChIP-seq data, bwa-mem2 (v2.2.1)7 was used to align trimmed reads while salmon (v1.7.0)8 was run to align trimmed reads with the –validateMappings option enabled. For ChIP-seq data, the read counts in each genomic bin (defined below) were normalized to TPM (transcripts per million) scale with genomic bin counts quantified using the Rsubread package.9 Since the RH4 ChIP-seq data contained spike-in reads from the Drosophila melanogaster genome, bwa-mem2 was used to align reads using a joint BWA index of the hg38 and dm6 genome. Thus, for the RH4 data, in addition to the library size normalization that is applied to each sample, we additionally divided the TPM values by the total number of reads that aligned to the dm6 genome assembly following the recommendation in the source publication describing the Drosophila melanogaster spike-in protocol for ChIP-seq data.10 All pseudo-aligned RNA-seq data from salmon was normalized to a TPM scale using the tximport function (v1.28.0).\n\nWe identified 1000 most upregulated and downregulated genes post-drug treatment for HCT116 and RH4 cell line. The genes were selected based on Log10 Fold change i.e., Log10 Treated – Log10 Untreated. For every gene, we created 21 genomic bins to analyze the pattern of histone marks. The genomic bins include promoter region, transcription Start Site (TSS), and Gene Body (GB) region. TSS coordinates were obtained from the ENSEMBL Genes v101 database.11 We defined the promoter as the 2kb region upstream to the TSS which was further divided into 10 equal-sized bins where the TSS was the single nucleotide position. Finally, the gene body was defined as the entire transcribed region and was also divided into 10 equal-sized bins. Overall, this resulted in a total of 21 bins for every gene. H3K27Ac read density was calculated in each of these 21 bins and was used to compare the up and down genes and as features for the prediction of up and down-regulated genes.\n\nWe used the histone mark distribution in 21 genic bins as features to develop machine learning models to distinguish up versus downregulated genes after HDACi-treatment separately for both HCT116 and RH4 cell lines. Using the conventional five-fold cross-validation we computed the area under curve (AUC) as performance measure. We used a python-based library known as Scikit-learn12 and implemented three different machine learning techniques which include Support Vector Machine (SVM), Random Forest (RF), and Gradient Boosting. Models were developed in four different categories (i) using 10 Promoter features; (ii) using single TSS feature; (iii) using 10 GB features, and lastly (iv) using all 21 features. We further performed cross cell line prediction where a model trained on one cell line data was used to predict other cell line data.\n\nWe used clusterProfiler 4.013 to identify biological processes associated with the identified up and downregulated genes. We used the following command to get the enriched significant processes:\n\n“ego <- enrichGO (de$Entrezid, OrgDb = “org. Hs.eg.db”, ont=“BP”, readable = TRUE, minGSSize = 10, maxGSSize = 500, keyType=“SYMBOL”)”\n\nAs there are many redundant processes, we further obtained the parent processes using the following command:\n\n“ego2 <- simplify (ego, cutoff=0.8, by=“p.adjust”, select_fun=min, measure = “Wang”)”\n\nDotplot of the above obtained processes were created using ggplot2 library in R.14\n\n\nResults\n\nFor each of the two cell lines (HCT116 and RH4), for the respective dosage of HDACi drugs (eight doses of Largazole for HCT116, one dose of 1 μM Entinostat for RH4), we first identified the top 1000 up-regulated and 1000 down-regulated genes (Methods). Genes classified as up, down, and unchanged post-treatment for various doses in HCT116 and RH4 cell lines are provided in Tables S1 and S2 respectively of Extended data.15 TPM value of each gene, untreated as well as treated for various concentrations in HCT116 cell line and single concentration for RH4 is also provided in Tables S3 and S4 of Extended data15 respectively.\n\nWe first identified enriched GO terms in each set of up and down-regulated genes (three pairs of gene sets for three representative doses in HCT116 [4.68 nM, 75 nM and 300 nM] and one pair for RH4). In general, the upregulated genes in both the cell lines were broadly enriched for the developmental and signaling processes (Figure 1). The developmental process is in the direction of epithelial to mesenchymal transition (EMT). In the case of HCT116 cell line, we additionally observed response to hypoxia. Likewise, processes associated with downregulated genes are broadly associated with the cell cycle and cell division, whereas for RH4 cell line, additional processes such as histone modification and RNA splicing were also seen (Figure 2). Complete lists of processes associated with the upregulated and downregulated genes in HCT116 [4.68 nM, 75 nM and 300 nM] and RH4 cell lines are provided in Tables S5-S7 and S8 respectively of Extended data.15\n\nTop 20 enriched biological processes associated with upregulated genes in HCT116 cell line after treating with epigenetic drug largazole at 4.68 nM (A); 75 nM (B); 300 nM (C); and Top 20 enriched biological processes associated with upregulated genes in RH4 cell line after treating with epigenetic drug entinostat at 1 μM (D).\n\nTop 20 enriched biological processes associated with downregulated genes in HCT116 cell line after treating with epigenetic drug largazole at 4.68 nM (A); 75 nM (B); 300 nM (C); and Top 20 enriched biological processes associated with upregulated genes in RH4 cell line after treating with epigenetic drug entinostat at 1 μM (D).\n\nNext, we compared the pre-treatment epigenomic profiles of the up- and downregulated genes by plotting the H3K27Ac mark intensity (normalized read counts) in the pre-treatment sample along 21 genic bins (Methods). Distributions for three representative doses for HCT116 (4.68 nM (lowest), 75 nM, and 300 nM (highest)) and 1 μM dose for RH4 are included in Figure 3; all other distributions for the HCT116 cell line are provided in Figures S1-S5 of Extended data.15 Overall, the following general trends emerged: (1) There was substantial variability across the bins around the genic locus in the upregulated versus downregulated H3K27Ac mark density, (2) in the upstream regions downregulated genes had a higher H3K27Ac pre-treatment; (3) this trend was also true in gene body but only at mid and higher dosage, while (4) at low dosage the trend was opposite in gene body where the downregulated genes had lower H3K27Ac; (5) RH4 trends at 1 μm dose of Entinostat most resembled the patterns at 75 nM dose of largazole in HCT116. Overall, while there was a variable pre-treatment epigenomic pattern within the gene body across cell lines, drug, and dosages, there were nevertheless sufficient differences between up- and downregulated genes, motivating us to develop machine learning models to predict transcription effects given the H3K27Ac pattern at a gene locus.\n\nBoxplot distribution of H3K27Ac marks across 21 genomic bins (10 equal sized bins of Promoter, Gene body and 1 bin of TSS) associated with upregulated (blue bars) and downregulated (brown bars) genes when HCT116 cell line is treated with largazole at concentrations 4.68 nM (A); 75 nM (B); 300 nM (C); and when RH4 cell line is treated with entinostat at 1 μM (D).\n\nHere, we assess whether the pre-treatment epigenetic profile at a gene locus can predict whether the gene will be upregulated or downregulated upon treatment with HDACi. The top 1000 upregulated and 1000 downregulated genes were compiled. For every gene, pre-treatment H3K27Ac read count in 21 regions relative to the gene (Methods) were used as features and three machine learning models – Support Vector Machine (SVM), Random Forest (RF), and Gradient Boosting (GB), were benchmarked based on five-fold cross-validation and accuracy was quantified as area under the ROC curve (AUC). A separate model was benchmarked for each of the eight drug dosages in HCT116 data. As shown in Table 1, overall, various machine learning approaches performed comparably and using all features was preferable; specifically, the best performance was achieved by SVM for 75 nM dosage with AUC of 0.89 (Figure 4). Analogous benchmarking for RH4 cell line data available at the single dosage using all features yielded comparable AUC ranging from 0.74-0.76 for the three machine learning methods. Overall, H3K27Ac signal near the gene is informative of the gene expression changes upon treatment with HDACi.\n\nHere the concentration of drugs is in nM and μM. P stands for Promoter; TSS stands for Transcription Start Site; GB stands for Gene Body; and All is the combination of all three features.\n\nPerformance of various SVM based models in terms of Area Under Curve (AUC) at different concentrations when HCT116 cell line was treated with 8 different largazole concentration and RH4 cell line was treated with entinostat.\n\nNext, we assessed whether a model trained on one cell line to predict the transcriptional effect of a certain epigenomic drug can predict the effect in a different cell line treated with a different drug, albeit also HDACi. Toward this, first, a SVM (75 nM) model trained on HCT116 cell line data was able to achieve an AUC value of 0.71 when applied to RH4 cell line data (Figure 5A). Likewise, the model trained on RH4 cell line data when applied to HCT116 data achieved an AUC of 0.81 (Figure 5B), supporting the cross-context generalizability of the model, consistent with similarity of epigenomic profile trends between the two cell lines as shown above (Figure 3B and 3D).\n\n(B) Performance of RH4 data trained SVM model on HCT116 cell line used as testing dataset.\n\nNext, we specifically assessed whether the context-specific differences across the two cell lines in their HDACi-induced gene expression were reflected in their context-specific pre-treatment epigenomic profile in the gene locus. Toward this we compared the data for HCT116 treated with 75 nM largazole with RH4 treated with 1 μM of entinostat. For each cell line we applied stringent criteria to identify genes which were upregulated in one cell line and downregulated in another cell line. We selected those genes whose fold change >3 in one cell line and <1/3 in another. This resulted in two gene sets: (1) 73 genes upregulated in HCT116 and downregulated in RH4, and (2) 184 genes upregulated in RH4 and downregulated in HCT116. To normalize for cell line-specific differences in H3K27Ac, we z-scored the cross-bin H3K27Ac signal for each gene. Then for these two gene sets, we plotted the normalized H3K27Ac intensities along the 21 genic bins, comparing two cell lines features. As shown below, with few exceptions, for the first gene set, HCT116 genes showed higher concentration of H3K27Ac marks and for the second gene set, the opposite was true (Figure 6B), consistent with the patterns in Figure 3.\n\nBoxplot distribution of H3K27Ac marks across 21 genomic bins (10 equal sized bins of Promoter, Gene body and 1 bin of TSS) associated with genes with positive log fold change in HCT116 but negative log fold change in RH4 cell line (A) and Genes with positive log fold change in RH4 but negative log fold change in HCT116 cell line (B).\n\n\nDiscussion\n\nEpigenetic dysregulation is a key characteristic of cancers. A number of mutations have been observed in the genes encoding epigenetic modifiers such as DNA methylation and histone modification enzymes.16 Accordingly, efforts have been made in targeting epigenetic regulators.17 At present, seven epigenetics-targeting drugs have been approved by the FDA.18 However, there are certain challenges associated with this class of drugs, limiting their success. Some of the key challenges include (i) Different epigenetic mutations are associated with different cancer types; (ii) The same gene may have opposite function in tumorigenesis of different cancers. For example, EZH2 deficiency causes myeloid malignancies19 whereas gain-of-function causes B cell lymphomas20; (iii) Another major issue is the selectivity of these drugs. For example, 30 enzymes of the KDM family with similar JMJC domain belong to five subfamilies. These enzymes demethylate different histone residues. Hence, drugs targeting these are broad-spectrum, affecting multiple KDM subfamilies and histone marks with potentially unintended consequences21; (iv) Yet another issue with epigenetics-targeting drugs, focused on in this work, is the selectivity of genomic loci. For instance, a HDACi can both increase as well as decrease histone acetylation in different genomic loci and can thus upregulate certain genes while downregulating others, again with unintended consequences.\n\nHere, we tried to address the selectivity issue by developing a machine learning model based on pretreatment histone mark. In two cell lines, we established that the locus-specific effect of HDACi treatment on gene expression can be predicted to a reasonable accuracy from the pre-treatment histone acetylation pattern at a gene locus, and the model appears to be generalizable across cell lines. While the current study is promising and may potentially be applied to personalized therapy by predicting the transcriptomic consequence of HDACi treatment, there are a few limitations which need to be addressed. Our predictive model is based only on the H3K27ac mark. Several other marks such as H3K9ac, H3K4me3, H3K27me3, among others, should be incorporated in such modeling approaches in the future as and when such data become available. Our model was assessed only in cell lines and its efficacy in bulk tumor data representing the tumor microenvironment remains to be assessed. Last but not the least, pre- and post-treatment tumor epigenetic and transcriptomic data in clinical and pre-clinical models are still lacking, required for assessing the clinical applicability of our approach.\n\n\nAuthor contribution\n\nVG download and processed the data. PA, and SH perform the analysis. PA and SH perform the statistical analysis. PA, VG and SH wrote the manuscript. PA and SH supervised the study. All authors read the article and approved the submitted version.", "appendix": "Data availability\n\nSequence Read Archive: Genome-wide Dose-dependent Inhibition of Histone Deacetylases Reveals Their Roles in Enhancer Remodeling and Suppression of Oncogenic Super-enhancers, https://identifiers.org/insdc.sra:SRP113250. 22\n\nSequence Read Archive: Genome-wide Dose-dependent Inhibition of Histone Deacetylases Reveals Their Roles in Enhancer Remodeling and Suppression of Oncogenic Super-enhancers, https://identifiers.org/insdc.sra:SRP151465. 23\n\nFigshare: Supplementary_Figures, https://doi.org/10.6084/m9.figshare.23736882.v1. 15\n\nThis project contains the following extended data:\n\n- Supplementary.xlsx\n\n- Supplementary_Figures.docx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nAnalysis code available from: https://github.com/hannenhalli-lab/Epigenetic_Project/\n\nArchived analysis code at time of publication: https://zenodo.org/record/8212782. 24\n\nLicense: MIT\n\n\nAcknowledgements\n\nThis work utilized the computational resources of the NIH HPC Biowulf cluster. Authors are also thankful to the other lab members for their valuable suggestions. This work was supported by the Intramural Research Program of the National Cancer Institute, Center for Cancer Research.\n\n\nReferences\n\nHenikoff S, Greally JM: Epigenetics, cellular memory and gene regulation. Curr. Biol. 2016 Jul 25 [cited 2023 Jul 17]; 26(14): R644–R648. Publisher Full Text Reference Source\n\nDawson MA: The cancer epigenome: Concepts, challenges, and therapeutic opportunities. Science. 2017 Mar 17 [cited 2023 Jul 17]; 355(6330): 1147–1152. PubMed Abstract \| Publisher Full Text\n\nJones PA, Issa JPJ, Baylin S: Targeting the cancer epigenome for therapy. Nat. Rev. Genet. 2016 Oct 1 [cited 2023 Jul 17]; 17(10): 630–641. Publisher Full Text Reference Source\n\nAmatori S, Bagaloni I, Donati B, et al.: DNA demethylating antineoplastic strategies: a comparative point of view. Genes Cancer. 2010 [cited 2023 Jul 17]; 1(3): 197–209. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFeehley T, O’Donnell CW, Mendlein J, et al.: Drugging the epigenome in the age of precision medicine. Clin. Epigenetics. 2023 Dec 1 [cited 2023 Jul 17]; 15(1): 6. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nReddington JP, Perricone SM, Nestor CE, et al.: Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb target genes. Genome Biol. 2013 Mar 25 [cited 2023 Jul 17]; 14(3): R25. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMd V, Misra S, Li H, et al.: Efficient architecture-aware acceleration of BWA-MEM for multicore systems. Proceedings - 2019 IEEE 33rd International Parallel and Distributed Processing Symposium, IPDPS 2019. 2019 May 1; pp. 314–324.\n\nPatro R, Duggal G, Love MI, et al.: Salmon provides fast and bias-aware quantification of transcript expression. Nat. Methods. 2017 [cited 2023 Jul 17]; 14(4): 417–419. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLiao Y, Smyth GK, Shi W: The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads. Nucleic Acids Res. 2019 May 1 [cited 2023 Jul 17]; 47(8): e47. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOrlando DA, Chen MW, Brown VE, et al.: Quantitative ChIP-Seq normalization reveals global modulation of the epigenome. Cell Rep. 2014 [cited 2023 Jul 17]; 9(3): 1163–1170. PubMed Abstract \| Publisher Full Text\n\nCunningham F, Allen JE, Allen J, et al.: Ensembl 2022. Nucleic Acids Res. 2022 Jan 7 [cited 2023 Jul 19]; 50(D1): D988–D995. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPedregosa FABIANPEDREGOSAF, Michel V, Grisel OLIVIERGRISELO, et al.: Scikit-learn: Machine Learning in Python Gaël Varoquaux Bertrand Thirion Vincent Dubourg Alexandre Passos PEDREGOSA, VAROQUAUX, GRAMFORT ET AL. Matthieu Perrot. J. Mach. Learn. 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Publisher Full Text Reference Source\n\nNepali K, Liou JP: Recent developments in epigenetic cancer therapeutics: clinical advancement and emerging trends. J. Biomed. Sci. 2021 Dec 1 [cited 2023 Jul 17]; 28(1): 27. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRinke J, Chase A, Cross NCP, et al.: EZH2 in Myeloid Malignancies. Cells. 2020 Jul 8 [cited 2023 Jul 17]; 9(7). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChu L, Tan D, Zhu M, et al.: EZH2 W113C is a gain-of-function mutation in B-cell lymphoma enabling both PRC2 methyltransferase activation and tazemetostat resistance. J. Biol. Chem. 2023 Apr 1 [cited 2023 Jul 17]; 299(4): 103073. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPfister SX, Ashworth A: Marked for death: targeting epigenetic changes in cancer. Nat. Rev. Drug Discov. 2017 Apr 1 [cited 2023 Jul 17]; 16(4): 241–263. PubMed Abstract \| Publisher Full Text\n\nChemistry and Biochemistry, University of Colorado Boulder: Genome-wide Dose-dependent Inhibition of Histone Deacetylases Reveals Their Roles in Enhancer Remodeling and Suppression of Oncogenic Super-enhancers, Sequence Read Archive. [Data set]. 2017. Reference Source\n\nKhan J; Genetics Branch, NCI, NIH: Genome-wide Dose-dependent Inhibition of Histone Deacetylases Reveals Their Roles in Enhancer Remodeling and Suppression of Oncogenic Super-enhancers, Sequence Read Archive. [Data set]. 2019. Reference Source\n\nAgrawal P, et al.: Github. Predicting gene expression changes upon epigenomic drug treatment.2023 [cited 2023 Aug 2]. Reference Source" }	[ { "id": "203232", "date": "20 Sep 2023", "name": "Angelika Merkel", "expertise": [ "Reviewer Expertise transcriptomics", "epigenetics", "bioinformatics" ], "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\nAgrawal et al have presented a comparison of machine learning approaches to predict gene expression from the distribution of histone marks, specifically H3K27 acetylation.\nAlbeit interesting and potentially very useful for cancer specific and personalized treatment with histone deacetylase inhibitors as the authors suggest, the latter has actually not been addressed. The authors present a proof-of-concept study for predicting gene expression from histone marks but not do not address variations in tissues, individual or disease type.\nAs such, this is not a novel approach as there have been numerous studies before addressing the prediction of gene expression (e.g. Karlic et 20101, Singh et al 20162, Chen et al 20223). The authors have failed to cite any of the current literature on the topic.\nMethods and results are presented in a somewhat rough manner and need improvement:\nAbstract and introduction contain poor grammar and sentence structure ('genomic specificity\" is not a new term to be defined, better to to use target specificity)\n\nWhy were the HCT166 and RH4 cell lines chosen and what are these exactly (need description)?\n\nWas peak calling performed to eliminate background noise in the Chip-seq analysis?\n\nWas differential expression analysis performed (normalization, statistical analysis, etc.)? What is the significance of the log10fold change?\n\nThe GO analysis is repeated in the methods and results section\n\nFigure 3: The scale among plots differ; gene bins are of variable size and larger promoter bins. Why have they been plotted them together?\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?\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": "10739", "date": "17 Jan 2024", "name": "Piyush Agrawal", "role": "Author Response", "response": "Agrawal et al have presented a comparison of machine learning approaches to predict gene expression from the distribution of histone marks, specifically H3K27 acetylation. Albeit interesting and potentially very useful for cancer specific and personalized treatment with histone deacetylase inhibitors as the authors suggest, the latter has actually not been addressed. The authors present a proof-of-concept study for predicting gene expression from histone marks but not do not address variations in tissues, individual or disease type. Response: We thank the reviewers for finding our work and interesting and potentially useful. Although we agree with reviewer regarding the importance of addressing variations in tissues, individual or disease type, unfortunately, lack of appropriate data currently prohibits such analysis. Besides the 2 cell lines used in this study, we didn’t come across any dataset (clinical/cell line) where for a given patient, both epigenomic marks and gene expression data is provided for both pre and post drug treatment. We would be happy to do the additional analysis if the reviewer can kindly point us to such data. As such, this is not a novel approach as there have been numerous studies before addressing the prediction of gene expression (e.g. Karlic et 20101, Singh et al 20162, Chen et al 20223). The authors have failed to cite any of the current literature on the topic. Response: We thank the reviewer for pointing out these studies, however, we want to clarify that the above-mentioned studies address a different question than ours, which is “to predict gene expression from the epigenome in a specific context”. Whereas we are interested in predicting the effect on the expression upon drug treatment, given the epigenomic profile in the pre-treatment sample. Our question necessitates availability of pre- and post-treatment gene expression and pre-treatment epigenomic profile, while these previous approaches are not concerned with the changes upon drug treatment. In the revised manuscript, we have highlighted this difference in the Introduction. Methods and results are presented in a somewhat rough manner and need improvement: Abstract and introduction contain poor grammar and sentence structure ('genomic specificity\" is not a new term to be defined, better to to use target specificity) Response: Why were the HCT166 and RH4 cell lines chosen and what are these exactly (need description)? Response: We regret lack of clarity. HCT116 and RH4 cell lines were chosen because the data we required for our study was available only for these 2 cell lines, namely, pre-treatment epigenomic profile and pre- and post-treatment gene expression data. HCT116 is human colorectal carcinoma cell line initiated from an adult male whereas RH4 cell line is for studying alveolar rhabdomyosarcoma and is belongs to soft tissue lineage. In the revised manuscript, we have added the description of these cell lines in the Methods section. Was peak calling performed to eliminate background noise in the Chip-seq analysis? Response: No, peak calling wasn’t performed in the current study. The goal of our analysis was to compare changes in H3K27ac read density upon HDAC treatment. Peak calling represents a 0/1 binarization of a continuous variable (in this case, normalized read counts in promoters and gene bodies). Our model uses the epigenomic signal intensity in specific windows around the gene magnitude, making peak-calling unnecessary. Was differential expression analysis performed (normalization, statistical analysis, etc.)? What is the significance of the log10fold change? Response: The mean Log-TPM values of each gene was computed for both treated and untreated conditions, with the Log-FC computed as the difference between treated and untreated conditions. The top 1000 most up-regulated and 1000 most down-regulated genes were considered to be differentially expressed. We mistakenly mentioned Log10, which is now corrected to Log2. We have corrected this in the revised version. The GO analysis is repeated in the methods and results section Response: We want to clarify that in Methods Section, we mentioned the software and command only used for GO analysis, however, in Result section, we discussed the enriched terms associated with the up and downregulated genes. Figure 3: The scale among plots differ; gene bins are of variable size and larger promoter bins. Why have they been plotted them together? Response: We agree with the reviewer that scale among plots differ and gene bins are of variable size. The only reason for plotting them together was to analyze all the 21 features together in single image i.e. change in distribution of the pre-treatment epigenomic marks in up and down genes post treatment. Is the work clearly and accurately presented and does it cite the current literature? No Is the study design appropriate and is the work technically sound? Partly Are sufficient details of methods and analysis provided to allow replication by others? Partly If applicable, is the statistical analysis and its interpretation appropriate? Partly Are all the source data underlying the results available to ensure full reproducibility? Yes Are the conclusions drawn adequately supported by the results? Partly References 1. Karlić R, Chung HR, Lasserre J, Vlahovicek K, et al.: Histone modification levels are predictive for gene expression.Proc Natl Acad Sci U S A. 2010; 107 (7): 2926-31 PubMed Abstract \| Publisher Full Text 2. Singh R, Lanchantin J, Robins G, Qi Y: DeepChrome: deep-learning for predicting gene expression from histone modifications.Bioinformatics. 2016; 32 (17): i639-i648 PubMed Abstract \| Publisher Full Text 3. Chen Y, Xie M, Wen J: Predicting gene expression from histone modifications with self-attention based neural networks and transfer learning.Front Genet. 2022; 13: 1081842 PubMed Abstract \| Publisher Full Text" } ] } ]	1	https://f1000research.com/articles/12-1089
https://f1000research.com/articles/12-897/v1	28 Jul 23	{ "type": "Research Article", "title": "Effect of lactoferrin in oral nutrition supplement (ONS) towards IL-6 and IL-10 in failure to thrive children with infection", "authors": [ "Nur Aisiyah Widjaja", "Azizah Hamidah", "Marissa Tulus Purnomo", "Eva Ardianah", "Azizah Hamidah", "Marissa Tulus Purnomo", "Eva Ardianah" ], "abstract": "Background: Growth failure due to infection in children is a major health problem throughout the world. It provokes a systemic immune response, with increased interleukin (IL)-6 and reduced IL-10. Lactoferrin (Lf) is a multifunctional iron-binding protein that can be found in whey protein inside formula milk such as oral nutrition supplement (ONS), which can upregulate anti-inflammatory cytokines (IL-10) and modulate pro-inflammatory cytokines. This study investigates the effect of Lf supplementation in ONS on IL-6 and IL-10 levels in children with failure to thrive and infection. Methods: We performed a quasi-experimental pre- and post-study in children aged 12–60 months old with failure to thrive due to infectious illness. The subjects received 400 ml of oral nutritional supplements (ONS, 1 ml equivalent to 1 kcal) each day for 90 days, and their parents received dietary advice and medication based on the underlying illness. Blood was drawn to measure IL-6 and IL-10 before and after the intervention. Results: There were 75 subjects recruited and divided into group-1 and group-2 based on age. The incidence of undernutrition was 37.33%. Lf in ONS intervention improved body weight and body length. Lf also reduced IL-6, although there was not a significant difference before and after the intervention. However, the IL-6 reduction was significantly higher in subjects with undernutrition compared with subjects with weight faltering. Pre-intervention IL-6 levels were higher in children with stunting than in children with normal stature. There was a greater change in IL-6 in children with severe stunting than in children with normal stature or stunting. IL-10 was significantly reduced after the intervention.\nConclusions: In addition to improving body weight and length, Lf supplementation in ONS improved immune response homeostasis by balancing IL-6 and IL-10 levels and by improving the IL-6/IL-10 ratio. ClinicalTrials.gov number ID: NCT05289674, dated May 3rd 2022.", "keywords": [ "IL-6", "IL-10", "lactoferrin", "growth failure" ], "content": "Introduction\n\nGrowth failure is still an important health problem, with weight-for-age (WAZ) and length-for-age (LAZ) declining during the golden period or golden 1,000 days (period during pregnancy until second years of life),1 and insignificant growth thereafter.2 Nutritional intervention during this period will impact a child’s growth, development and ability to thrive.1 Infection in children causes growth failure by provoking a systemic immune response which affects the nutritional status,3 especially as a result of a reduction of insulin-like growth factor 1 (IGF-1).4\n\nUndernutrition refers to children who are underweight, stunted or wasted, or have nutrient deficiency which makes the children vulnerable to infection.5 The induction of the acute phase response and proinflammatory cytokine production caused by infection directly affect bone remodeling which is important for long bone growth,3 and also inhibits chondrogenesis.6 Pro-inflammatory cytokines such as interleukin (IL)-1β, IL-6 and tumor necrosis factor-alpha (TNF-α) were found to have increased in stunted children, which also increases leptin levels leading to a limited appetite.4 These proinflammatory cytokines also cause bone breakdown.6 IL-6 has anti- and pro-inflammatory functions. After it binds with IL-6 receptors in the liver, it stimulates hepatocytes to produce acute-phase proteins and cytokines via multiple signaling pathways.7\n\nOral nutritional supplements (ONS), also known as food for special medical purposes, contain both macro- and micronutrients that are sufficient to meet daily nutritional needs for those at risk of malnutrition.8 ONS is prescribed to increase nutritional intake due to insufficiency in diets to meet daily nutritional requirements,9 particularly protein and calories.10 ONS not only provides some benefits for hospital admission patients such as a reduced length of hospital stay (LOS), reduced inpatient cost, complication rates, readmission rates and improved lean body mass recovery,11 but also improves energy intake and nutritional status such as body weight, length and mid-arm circumference.12 For children, ONS is a dairy milk-based product, which is designed to provide an energy density of 1–1.5 kcal/ml, and it is expected to be effective in improving growth.13\n\nLactoferrin (Lf) concentration within the whey protein that is contained in the modified cow’s milk formula is only 0.1 mg/ml.14 ONS contains 10.8 g of protein per 100 g, which is 46% whey and 54% casein. The effect of Lf supplementation (dose 0.6 g/L and 1.00) compared to standard infant formula on body weight showed no significant difference in children until 12 months old.15 Lf acts as an innate immune regulator and defense due to its antimicrobial properties.16 It can interact with the immune system, such as influencing cytokine activity by upregulating anti-inflammatory cytokines (IL-4 and IL-10) or modulating proinflammatory cytokines.17 An in vitro study showed that Lf (10 mg/mouse i.v.) before thymectomy reduced IL-6 by 70%, and TNF-α by 30% 4 hours after an operation.18 A study in adults showed that Lf reduced systemic inflammatory biomarkers by 61%, improved immune function by 75%, changed immune cell activity by 40% and reduced respiratory tract infection outcomes by 60%. In adults, lactoferrin has been shown to reduce IL-6 by 24.9 pg/mL.19\n\nHere we investigate the effect of lactoferrin in ONS towards IL-6 and IL-10 in failure to thrive children with infection for 90 days of intervention.\n\n\nMethods\n\nThe study passed ethical exemption and was declared to be ethically appropriate by the Health Research Ethics Committee, Airlangga University, Surabaya, Indonesia, number 226/EC/KEPK/FKUA/2021 on October 4th 2021 and registered on ClinicalTrials.gov number ID: NCT05289674, initial released on May 3rd, 2022.\n\nA quasi experimental pre- and post- study design was performed from October 2021 until July 2022 recruiting children aged between 1 years (12-months-old) and 5 years (60-months-old) with failure to thrive due to infectious illness (mainly urinary tract infection and tuberculosis (TB)) diagnosed by a paediatrician (the researcher) based on clinical and laboratory findings at Husada Utama Hospital outpatient unit, Surabaya, Indonesia. The subjects included in the study were excluded if they had fluid retention, organomegaly, a tumor mass, congenital abnormalities, cerebral palsy or hormonal disorders and syndromes. A written informed consent was signed by the parents as approval to participate in the study after the researcher explained the importance, the risks and the benefits of this study.\n\nThe sample size was determined using the formula below:\n\nNote:\n\nN = sample size\n\nZα = standard deviation (α) 5% (1.96)\n\nZβ = power, the researchers determined 90% (0.842)\n\nP1 = clinical judgement 15% = 0.1\n\nP2 = standard effect P2 = 25.5% = 0.25.20\n\nP = ½ (P1+P2) = 0.175\n\nQ = 1-P = 0.825\n\nQ1 = 1-P1 = 0.9\n\nQ2 = 1-P2 = 0.75\n\nThe sample size was 80 subjects; pre- and post-design needed for the study was 160 samples.\n\nThe subjects were given an oral nutritional supplement or ONS with Lf (1 ml ~1 kcal, 400 ml/day), SGM Eksplor Gain Optigrow® prescribed by the researchers for 15 days consumption (equal to 4 boxes of 400 g) for initial intervention to detect any adverse reaction. The authors used this formula due to its relatively cheaper cost compared to other high calorie formula (ONS) available in Indonesia. The parents also had dietary counseling, animal protein was provided and a medication plan was given according to the underlying disease. Parents were asked to report any side effects to the researcher’s team by phone for further medical treatment. The parents were asked to visit the doctor after 14 days of ONS consumption for anthropometric measurements, compliance and side effect monitoring at day 15. While visiting, parents also received ONS for the next 15 days consumption (day 16 to 30), and were asked to visit the doctor again on day30, 60 and 90. At the 30-day visit, parents received ONS for two months’ consumption (day 31 to day 60, and day 61 until day 90) (8 boxes of 400 g) and anthropometric measurements.\n\nBlood was withdrawn via vena cubiti by a laboratory employee at Husada Utama Hospital to measure IL-6 (human IL-6 ELISA kit, code E0090Hu, BT Lab) and IL-10 (human IL-10 ELISA kit, code E0102Hu, BT Lab) before (day 0, when the parents agreed to participate in this study) and after the intervention (day 90). After the blood samples were collected, they were placed in a non-EDTA containing tube for micro-centrifugation to separate blood plasma from blood serum at 3000 rpm for 10 minutes. The supernatant was removed and placed in a PCR tube of 1.5 mL, then kept in a freezer at -4oC.\n\nAn indirect sandwich ELISA was performed to analyse IL-6 and IL-10 levels before- and after nutritional intervention using blood serum. For the sandwich ELISA, all reagents (standard solution, wash buffer, substrate solution A, substrate solution B and stop solution) were brought to room temperature before use (27oC).21\n\nPreparation of standard solution\n\nA total of 120 μL standard solution (640 ng/ml) was diluted with 12 μL standard diluent to produce a 320 ng/L standard stock solution, and it was then allowed to rest for 15 minutes. Standard duplication points were made using a serial dilution of standard stock solution to produce 160 ng/L, 80 ng/L, 40 ng/L and 20 ng/L solutions.\n\nPreparation for wash buffer solution\n\nThen 20 ml of wash buffer concentrate 25 × was added to distilled water to yield 500 mL of 1 × wash buffer. The wash buffer was mixed gently if crystals formed in the concentrate until the crystals had completely dissolved.\n\nAssay procedure\n\nThe assay procedure was performed at room temperature after we determined the number of strips required for the assay, and then we inserted the strips in the frames for use.\n\n1. 50 μL of the standard solution was added into all the sample wells.\n\n2. Then 50 μL standard solution was added into the standard wells.\n\n3. 40 μL of sample was added to the sample wells and then 10 μL of human IL-6 or IL-10 antibody was added. Then 50 μl streptavidin-HRP was added to sample wells and standard wells, but not the blank control well. Each of them were mixed before the wells were placed on the plate and then sealed for incubation at 37oC for 60 minutes.\n\n4. After 60 minutes of incubation, the seals were removed, and the plates were washed 5 times with wash buffer; the wells were soaked in 300 μl of wash buffer for 30 seconds to 1 minute for each wash.\n\n5. 50 μl of substrate solution A and 50 μl of substrate solution B were added to each well and the plate was covered and incubated for 10 minutes at 37oC in the dark.\n\n6. 50 μl of stop solution was added to each well, so that the blue colour changed to yellow immediately.\n\nWe then determined the optical density (OD value) of each well immediately using a microplate reader set at 450 nm of wavelength within 30 minutes after the stop solution was added, and then the standard curve was made.21\n\nBody weight was measured using a Seca 354 digital baby scale or a Seca 813 electronic flat scale) and body length/height was measured using a Seca 415 infantometer or Seca 213 stadiometer). Both measurements were taken twice by a trained nurse in the outpatient department of Husada Utama Hospital. The weight and length/height were the average value of the two measurements. When the subjects were weighed and measured, they wore light clothes without footwear or hair accessories. Anthropometry measurement for weight-for-age z-score (WAZ), length-for-age or height-for-age z-score or height-for-age z-score (LAZ/HAZ) and weight-for-length or weight-for-height z-score or weight-for-height z-score (WLZ/WHZ) were determined using WHO Anthro offline version 3.2.2. All the data are summarized in the underlying data22 and extended data.23\n\nStatistical analysis conducted in this study was a test of normality and homogeneity, independent sample T-test or Mann-Whitney U test, Fischer exact test, Pearson chi-square, paired sample T-test or Wilcoxon, two-way ANOVA and one-way ANOVA using IBM SPSS Statistics version 21.\n\n\nResults\n\nSeventy-five subjects were involved in the study and divided into two groups based on the age of the participant: group-1 (age 1–2 years, n = 39) and group-2 (age 2–5 years old, n = 36), as summarized in Figure 1.\n\nTable 1 summarizes the characteristics of the subjects who participated in the study. The ratio of male/female was 12/13 and there was no significant difference in gender distribution in both groups (p = 0.108). There was no significant difference in the main complaint (p = 0.229), duration of complaints (p = 0.580), WAZ (p = 0.482) and WLZ/WHZ (p = 0.499). Age, ideal body weight and height age were lower in group-1 compared to group-2 (p < 0.05). LAZ was lower in group-1 compared to group-2 (-1.95 ± 1.17 vs. -1.19 ± 0.86, p = 0.002).\n\n1 Mann-Whitney U Test.\n\n2 Fischer’s Exact Test.\n\n3 Pearson Chi Square.\n\n4 Independent Sample T-Test.\n\nThe incidence of underweight and severely underweight children in group-1 and group-2 were 33.33% and 5.33% respectively, and there was no significant difference in WAZ categories in both groups (p = 0.874). While stunted and severely stunted children in group-1 and group-2 were 25.33% and 13.33% respectively, with a higher incidence of stunted/severely stunted children in group-1 compared to group-2 (56.41% vs. 19.45%, p = 0.004). However, the incidence of stunted/severely stunted children in group-1 was predominantly boys (6 boys vs. 1 girl). The incidence of wasted and severely wasted children in group-1 and group-2 were 12% and 2.67% (p = 0.486).\n\nThe effect of ONS on body weight and body length/height change is summarized in Table 2. Initial body weight before treatment was lower in group-1 compared to group-2 (p = 0.000). post intervention body weight was lower in group-1 than in those of group-2 (p = 0.000) but the weight change (Δ body weight) in both groups showed no significant difference (922.56 ± 671.28 vs. 855.55 ± 577.16 g, p > 0.05). The initial body length/height was shorter in group-1 compared to group-2 (p = 0.000), so the late body length/height was shorter in group-1 compared to group-2 (p = 0.000). Body length/height change was greater in group-1 compared to group-2 (3.49 ± 1.43 vs. 2.08 ± 1.04 cm, p = 0.000).\n\n1 Independent sample T-test.\n\nIL-6 and IL-10 levels during the intervention are summarized in Table 3. The levels of IL-6 post-intervention (day 90) were not significantly different from pre-intervention (128.45 ± 109.92 vs. 111.76 ± 78.10 pg/mL, p = 0.554), although there was a decline (-16.68 ± 91.09 pg/mL) in both groups (-13.42 ± 97.80 vs. -20.23 ± 84.46 pg/mL, p = 0.749). There was no significant difference in IL-6 levels before the treatment in both groups (p < 0.232) and after treatment (p < 0.191). IL-10 level was significantly reduced after the intervention (461.20 ± 392.12 became 261.28 ± 163.97 pg/mL, Δ = 199.92 ± 339.01 pg/mL, p = 0.000). The reduction in IL-10 showed no significant difference in either group (-183.24 ± 378.50 vs. -217.99 ± 294.61 pg/mL, p = 0.518).\n\n1 Independent sample T-test.\n\n2 Two-way ANOVA.\n\nThere was significantly improvement in the IL-6/IL-10 ratio after the intervention (0.33 ± 0.22 vs. 0.44 ± 0.12, Δ = 0.11 ± 0.23, p = 0.000). The reduction in the IL-6/IL-10 ratio showed no significant difference in either group (0.11 ± 0.29 vs. 0.12 ± 0.17, p = 0.991).\n\nThe levels of IL-6 based on anthropometric categories are summarized in Table 4. Based on the LAZ categories, there was a significant difference in IL-6 levels pre-intervention (p = 0.045), in which the stunted group had higher levels of IL-6 compared to those with a normal stature (212.06 ± 146.05 vs. 115.81 ± 93.84 pg/mL, p = 0.037). Although there was no significant difference, IL-6 was higher in the stunted group compared to those who were severely stunted (212.06 ± 146.05 vs. 85.45 ± 89.06 cm, p = 0.057). There was no significant difference in post-intervention levels of IL-6 (p = 0.083); however, IL-6 was lower in normal stature children compared to stunted and severely stunted children. Although IL-6 levels were higher in the stunted group compared to the severely stunted group, there was no significant difference between both groups (212.06 ± 146.05 vs. 85.45 ± 89.06 pg/mL, p = 0.057). Changes in IL-6 (ΔIL-6) based on the LAZ/HAZ categories showed no significant difference (p = 0.055), but the changes in severely stunted children were higher compared to the stunted group (47.33 ± 93.48 vs. -41.66 ± 108.69 pg/mL, p = 0.036) and the normal stature group (47.33 ± 93.48 vs. -20.28 ± 77.36 pg/mL, p = 0.031). This was due to increased IL-6 in severely stunted children, but reduced IL-6 in stunted children and those of normal stature.\n\n1 One-way ANOVA.\n\n2 Kruskal-Wallis.\n\nThe levels of IL-6 based on the WAZ categories showed no significant difference pre-intervention (p = 0.903) or post-intervention (p = 0.173), but the change in IL-6 (ΔIL-6) showed a significant difference (p = 0.014), where the WAZ in severely underweight children increased, while the underweight and weight faltering decreased. Therefore, severely underweight children had higher changes of IL-6 compared to stunted children (78.14 ± 32.06 vs. -44.19 ± 137.03 pg/mL, p = 0.012) and weight faltering/normal weight children (78.14 ± 32.06 vs. -16.09 ± 73.95 pg/mL, p = 0.001).\n\nThe initial and late changes of IL-6 (ΔIL-6) based on WLZ/WHZ categories showed no significant difference (p > 0.05). The initial level of IL-6 was higher in good nutritional status subjects compared to wasted and severely wasted. But after the intervention, IL-6 levels in good nutritional status subjects were reduced (-22.05 ± 92.83 pg/ml), while the wasted and severely wasted group increased (9.73 ± 84.73 and 36.22 ± 3.46 pg/ml respectively).\n\nInitial and late levels of IL-10, and changes of IL-10 based on the anthropometric categories are summarized in Table 5. There was no significant difference in IL-10 before and after the intervention, or in changes of IL-10 (p < 0.05) based on the LAZ/HAZ categories. A similar phenomenon was also seen in the WAZ and WLZ/WHZ categories (p < 0.05).\n\n1 One-way ANOVA.\n\n2 Kruskal-Wallis.\n\nThe IL-6/IL-10 ratio based on anthropometric measurements is summarized in Table 6. The IL-6/IL-10 ratio based on the LAZ/HAZ categories showed no significant difference pre- and post-intervention. However, ONS supplementation increased the IL-6/IL-10 ratio in all LAZ/HAZ categories. In the WAZ categories, severely underweight children had a lower IL-6/IL-10 ratio compared to underweight children, even though there was no significant difference. The IL-6/IL-10 ratio increased after ONS therapy in all WAZ categories. A higher increment was seen in the severely underweight, but there was no significant difference. The WLZ/WHZ categories also showed no significant difference in the initial and late changes of the IL-6/IL-10 ratio.\n\n1 One-way ANOVA.\n\n2 Kruskal-Wallis.\n\n\nDiscussion\n\nThe prevalence of stunted and severely stunted children under two-years-old was 33.7%24 and 45.4% in Nigerian children,25 which was higher compared to this study. While the prevalence in two- to five-year-old children in Gaza was 19.6%,26 The prevalence of stunted/severely stunted children was higher in group-1 compared to group-2 in our study, which was similar to the study conducted in Nigeria, accounting for 45.5% vs. 12.2%.25 However, a study in West Sulawesi, Indonesia found that children aged two to five years had a higher incidence of stunted/severely stunted growth compared to children aged one- to two-years-old, 33.64 vs. 23.12%.27\n\nStunted growth was found to be associated with age, and it was more prevalent in children aged less than 24-months-old.28 Due to the incidence of stunted growth, which was higher in group-1, the LAZ value was significantly lower in group-1 compared to group-2. It was also found that children with stunted growth were significantly shorter in length/height than the control group in another study.29 It was reported that children aged 12–23 months old had an increased risk of stunting by 1.8 times.24,30\n\nIn group-2, the incidence of stunted/severely stunted growth was predominant in males, which is in line with Akombi et al. (2017), in which male (sex) was one of the stunting risk factors in 0–5-year-olds.25 This is in line with this study, suggesting that males are more vulnerable to health inequalities.31 The biological reason is due to the sex difference in the immune and endocrine systems, and testosterone, luteinizing hormone and follicle stimulating hormone are suspected to play a role.32 Feeding practice preferences between boys and girls such as early weaning in boys, and boys tend to consume greater than one meal of complementary feed during 24-hours may also play a part.33\n\nONS intervention in undernourished or at nutritional risk children aged nine months to 12-years-old improved body weight by 0.423 kg after six months of intervention and height gain was 0.417 cm compared to the control, with greater gains in weight in the first 7–10 days of intervention (0.089 kg).34 ONS improved growth in underweight children aged five- to 12-years-old after six and 12 months,35 which was in line with this study, where both group-1 and group-2 gained weight. Formula feeding supplemented with lactoferrin is safe for infants under one year old with no difference in growth rate (g/day).15\n\nLactoferrin intervention in children with diarrhoea aged 12–36 months old increased the LAZ/HAZ score (p = 0.03) compared to the placebo,36 and the children also showed an increment in length/height. A similar result was also found in Vietnamese children aged 24–48 months old in a 12-month intervention. The intervention of 450 kcal of additional ONS during the first three months resulted in an increase in height of 1.62 cm,37 which was lower than our results in a similar group (group-2). A higher calorie density intervention (2.4 kcal/ml vs. 1.5 kcal/ml) for 28 days increased the children’s height by 0.87 [0.59–1.16] and 0.55 [0.17–0.93] cm, p = 0.007 in children aged greater than one year and less than 12 years old with growth faltering.13\n\nLactoferrin is known to have a bacteriostatic or bactericidal effect and can activate the immune response of an organism, act accordingly and limits tissue damage.38 It can therefore reduce the incidence of acute gastrointestinal symptoms and reduce the duration of respiratory symptoms in children under 12 months old due to viral or bacterial infection.39 Regarding the immunological profile, when comparing an infant who received Lf supplementation vs. non-Lf supplementation vs. standard infant formula, although there was no significant difference between groups, there was an increase in TGF-β1 (6.5 vs. 4.3 vs. 2.8 ng/mL), TGF-β2 (0.26 vs. 0.26 vs. 0.22 ng/mL) and IL-2 (0.21 vs. 0.5 vs. 0.4 pg/mL), but a decrease in TNF-α (-2.4 vs. -1.5 vs. -1.7 pg/mL) during a four month intervention.40 A study that examined piglets with a 2 ml/day supplementation showed a decrease in bacterial colonies compared to those without Lf supplementation (1.109 × 107 vs. 3.6183 × 108 CFU) via an anal swab after a seven-day intervention.41 It was stated that Lf induced the development of T cell helper type 1 (Th1) immunity, so created the balance of monocytic pro- and anti-inflammatory cytokines. In a dose-dependent manner, Lf enhanced pro-inflammatory response in vitro (splenocyte and adherent (F4/80+) splenocyte populations, bone marrow derived monocytes (BMM), and J774A.1 cultured cells) and induced IL-12 and IL-10 production and increased the ratio IL-12:IL-10 in lipopolysaccharide (LPS) stimulated cells.42 A study of Mycobacterium tuberculosis infection treated with Bacillus Calmette–Guérin (BCG) and Lf emulsified with Freund’s adjuvant in mice showed a decreased mycobacterial load in the lungs and spleen. It also increased the protection against M. tuberculosis,16,43,44 via downregulation of proinflammatory mediators (TNF-α, IL-1β) by modulation of macrophages and dendritic cell ability to present antigens and stimulate T-cells. Lf also increased IFNγ, which was the specific response towards Th1.16 A study examining mice with urinary tract infection due to Escherichia coli showed that Lf intervention orally was able to decrease the number of bacteria in the kidneys and bladder after 24 h of Lf consumption, and reduced IL-6 by urinary leucocytes.45 A study conducted on Senegalese children receiving tetanus vaccine in stunted children aged one- to nine-years-old showed that the production of IFNγ was compromised.2 It was stated that undernutrition is related to immunodeficiency even when it is mild, whether the innate or adaptive immune systems.2\n\nIn our study, even though there was no significant difference in IL-6 levels before and after the intervention, Lf reduced IL-6, which is in line with other studies showing a reduction in undernutrition groups. It was found that IL-6 levels were lower in undernutrition compared to good nutrition groups (2.54 pg/mL vs. 6.02 pg/mL, p < 0.0001).46 Genetic investigation showed that the IL-6 164 gene with a GG and GC genotype (mutant phenotype) was more frequent in undernourished children.47\n\nWhen the groups were examined based on the LAZ/HAZ categories, stunted subjects had higher IL-6 levels compared to normal stature and there was a significant difference compared to severely stunted. This is in line with a study in Egyptian children, where IL-6 was higher in stunted compared to normal stature children (1.6 ± 0.2 vs. 1.5 ± 0.3 pg/mL),48 but it was decreased in malnourished compared to normal children.46 This showed that when the children had an LAZ/HAZ score greater than or equal to -2 SD, IL-6 was increased but it decreased when children had an LAZ/HAZ score greater or equal to -3 SD. On malnutrition, the acute-phase response was attenuated, and the production of cytokines decreased. An animal study showed that IL-1β production decreased in malnourished guinea pigs induced with endotoxins.7 Stunting is a form of growth failure due to long term nutritional deficiency or it is caused by chronic malnutrition or recurrent undernutrition.49,50 After a six-month intervention with food supplementation, stunted Bangladeshi children aged 12–18 months old experienced an IL-6 increment (from 0 [0–1.2] to 1.68 [0.83–4.7] pg/mL, p = 0.001),51 which contradicts this study as IL-6 levels were reduced in stunted and normal stature children. However, IL-6 was found to have increased in severely stunted children, so the post-intervention levels of IL-6 were higher in severely stunted even though there was no significant difference. Severely stunted children might undergo these immune alterations which are similar to severely acute malnutrition, so IL-6 levels were lowest at the outset but increased drastically after the intervention to surpass normal stature and stunted children. It was stated that immune function is an activity with high costs on energy demand, and in developing children the allocation of energy in immune functions may lead to a trade-off with physical growth, particularly those with exposure to infection.52\n\nA similar anomaly was also seen in the WAZ categories even though there was no significant difference. Being underweight has been used as an indicator of undernutrition due to a short-term nutritional deficiency.49 However, an in vitro study using peripheral blood mononuclear cells (PBMC) taken from children suffering from protein energy malnutrition (PEM) contradicted this study, which showed an increment in IL-6 expression after stimulation with LPS,53 even though it was expressed earlier, reached its peak earlier, and lasted longer than controls in rats.54 As the immune function is costly in terms of energy, it has negative effects on growth. In children with mildly elevated immune activity, they experience a growth reduction of up to 49%,52 as seen in underweight children who experienced an increase in IL-6 due to the trade-off in body fat between immune function and growth.52\n\nRegarding malnutrition, lymphatic tissue, particularly the thymus, experiences atrophy, leads to a reduction in delayed-type hypersensitivity responses, followed by a reduction in levels of antibodies in severely malnourished children (≥-3 SD of WLZ/WHZ WHO child growth standards), but it remains intact in moderate malnutrition (leucocyte and lymphocyte, high levels of immunoglobulin, particularly IgA, and acute phase response), and cytokine patterns are skewed towards a Th2-response.55 However, our study found that IL-6 started to reduce in wasted patients, with the lowest levels in those that were severely wasted. Nutritional intervention increases IL-6 in both wasted and severely wasted, but it is reduced with good nutrition, which is in line with research that states undernutrition, even in the mildest form causes immunodeficiency.56\n\nWenling C57BL/6 J mice in a wasting model’s study, which underwent 14 days of weight loss, showed increases of IL-10 in the malnourished group at three and at 14 days.57 It was stated that malnutrition modifies the body’s resistance against infection, particularly the immune response. Lipopolysaccharide (LPS) injection (1.25 μg i.v.) in a protein-energy malnutrition (PEM) mouse model, showed that the circulating levels of IL-10 were increased, and high levels were found in bone marrow cells, which showed immunodeficiency.58 This finding was in-line with a study in children with marasmic-PEM, IL-10 was significantly higher compared to controls (19.08 ± 5.93 vs 10.46 ± 3.90 pg/mL; p = 0.000).59 This may be caused by the deficits of NF-kB activation. NF-kB was the major transcription pathway for proinflammatory cytokine production.60 Using BMI as the parameter to determine malnutrition, subjects with severe malnutrition (BMI <16.5) had higher levels of IL-10 (8.0 ± 3.6 pg/mL) compared to those with moderate malnutrition (BMI = 16.5-18.4) (2.6 ± 4.3 pg/mL) and good nutrition (BMI >18.5) (2.8 ± 0.7 pg/mL) in adults,61 which was similar to the WAZ category where IL-10 was slightly increased in those underweight, and increased drastically in those severely underweight.\n\nNutritional intervention increases IL-10 significantly in children aged 12–60 months old with moderate and severe malnutrition receiving curd (milk product) compared to leaf protein concentrate (LPC) (from 30.9 ± 29.5 to 67.4 ± 96.2 pg/mL vs. 29.2 ± 25.8 to 31.5 ± 24.9 pg/mL). Based on Gomez criteria for malnutrition severity, children with mild malnutrition had lower IL-10 compared to children with severe malnutrition. It was higher in subjects aged more than two years old compared to two- to five-year-olds due to a balancing pro-inflammatory response to minimalize tissue damage.62 In malnourished children, IL-10 was found to be reduced, while in line with this study, IL-10 was depressed in severely wasted subjects.63 However, the level of IL-10 was still normal in severely stunted or severely underweight children. The reduction is due to a deficiency in the number and functional Th cells, which may be caused by incomplete differentiation of T lymphocyte precursors and steroid-induced lympholysis.63 Another study of malnourished children due to inadequate food intake (anorexia nervosa) and diarrhoea receiving nutritional intervention in the form of milk and yogurt, showed increased IFNγ production post intervention,64 which is in-line with this study on severely wasted subjects. However, in undernutrition subjects and weight faltering subjects, IL-10 tends to reduce, and a higher reduction was seen in undernutrition subjects, which showed that before intervention undernutrition subjects may experience immune alterations, as seen in the IL-6/IL-10 ratio, which was higher in undernutrition group-1, but lower in group-2. At post intervention, almost all the group had a similar value, ranging from 0.43 to 0.47. Adipose tissue is the main storage for nutrients, which can sense that nutrients are inadequate by releasing adipokines (particularly leptin) to control cellular metabolism and immune function. So, undernutrition has a direct impact on adipose tissue (volume and number), and directly influences the immune system. Leptin not only mediates glucose and lipid metabolism but also immune function, by stimulating activation, proliferation and production of pro-inflammatory cytokine (IL-6, TNF-α, monocytes, macrophages, dendritic cells, and NK cells). Leptin also promotes T-cell activation and development towards Th-1 and Th-17 cell subset which is proinflammatory. Regarding undernutrition, there was leptin depletion and in contrast adiponectin is produced, resulting in the polarization towards M2 or an alternative macrophage which then secrets IL-10 and IL-1Rα. This limits the activation of the NF-kB pathway, and reduces both T-cells or B-cells. Moreover, cortisol hormone restrains the generation of the proinflammatory immune response, so the ability of macrophages and neutrophils to infiltrate the infection site was also restrained. Proinflammatory cytokine production is also reduced, but anti-inflammatory cytokines (IL-10 and IL-33) are increased.5\n\nIL-6 has been used as a potential biomarker to identify patients receiving anti-inflammatory therapies as it is secreted widely as a response to pathological states such as infection, inflammation and cancer. IL-10 acts as an anti-inflammatory response, it is secreted as the response to dampen pro-inflammatory bursts and minimize tissue damage. The balance of IL-6 and IL-10 is an important biomarker reflecting the homeostasis of the immune response. In Covid-19 patients, each point increment of the IL-6/IL-10 ratio was associated with a 5.6 times more severe outcome.5 In children with pneumonia, the IL-6/IL-10 ratio at 9.61 determines those with severe pneumonia to those with mild disease (sensitivity 76.5% and specificity 93%).65\n\n\nConclusions\n\nLactoferrin in ONS intervention improved immune response homeostasis by balancing IL-6 and IL-10 and improved the IL-6/IL-10 ratio, not only body weight but also body length.\n\n\nConsent\n\nWritten informed consent for publication of the patients’ details was obtained from the parents of the patients.", "appendix": "Data availability\n\nFigshare: Underlying data for ‘Effect of Lactoferrin in Oral Nutrition Supplement (ONS) towards IL-6 and IL-10 in Failure to Thrive Children with Infection’, https://www.doi.org/10.6084/m9.figshare.21813975. 22\n\nThis project contains the following underlying data:\n\n• Data file: Table 1: Data for Manuscript Effect of Lactoferrin in Oral Nutrition Supplement (ONS) towards IL-6 and IL-10 in Failure to Thrive Childre.xlsx\n\n• Data archive 1: Elisa IL-6 Pre Intervention.rar\n\n○ The concentration of IL-6 ng per L, pre intervention.pdf\n\n○ Result of OD + Code.pdf\n\n○ Result of OD Excel.xls\n\n○ Result of OD.pdf\n\n○ Standard curve.pdf\n\n○ Sample scheme & Standard.pdf\n\n• Data archive 2: Elisa IL-6 Post Intervention.rar\n\n○ The concentration of IL-6, ng per L.pdf\n\n○ Result of OD + Code.pdf\n\n○ Result of OD Excel.xls\n\n○ Result of OD.pdf\n\n○ Standard curve.pdf\n\n○ Sample scheme & Standard.pdf\n\n• Data archive 3: Elisa_IL-10 Pre Intervention.rar\n\n○ Result of concentration IL-10, pg per ml.pdf\n\n○ Result of OD + Code.pdf\n\n○ Result of OD Excel.xls\n\n○ Result of OD.pdf\n\n○ Standard curve.pdf\n\n○ Sample scheme & Standard.pdf\n\n• Data archive 4: Elisa_IL-10 Post Intervention.rar\n\n○ Result of calculation concentration pg per ml.pdf\n\n○ Result of OD + Code.pdf\n\n○ Result of OD Excel.xls\n\n○ Result of OD.pdf\n\n○ Standard curve.pdf\n\n○ Sample scheme & Standard.pdf\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: Extended data for ‘Effect of Lactoferrin in Oral Nutrition Supplement (ONS) towards IL-6 and IL-10 in Failure to Thrive Children with Infection’, https://www.doi.org/10.6084/m9.figshare.22210798.v2. 23\n\nThis project contains the following extended data:\n\n• Informed consent: Essential information for potential research participants (WHO-CIOMS 2016)\n\n• Airlangga University: Ethical clearance\n\n• ClinicalTrials.gov: Protocol registration\n\n• ClinicalTrials.gov: Completed study\n\n• Study protocol\n\nFigshare: TREND checklist for ‘Effect of Lactoferrin in Oral Nutrition Supplement (ONS) towards IL-6 and IL-10 in Failure to Thrive Children with Infection’, https://www.doi.org/10.6084/m9.figshare.22210798.v2. 23\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 Danone Indonesia for providing the oral nutritional supplement.\n\n\nReferences\n\nBellieni CV: The Golden 1,000 Days. 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Reference Source\n\nSolis B, Nova E, Gómez S, et al.: The effect of fermented milk on interferon production in malnourished children and in anorexia nervosa patients undergoing nutritional care. Eur. J. Clin. Nutr. 2002; 56: S27–S33. PubMed Abstract \| Publisher Full Text\n\nde Brito R d CCM , Lucena-Silva N, Torres LC, et al.: The balance between the serum levels of IL-6 and IL-10 cytokines discriminates mild and severe acute pneumonia. BMC Pulm. Med. 2016; 16(1): 121–170. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "197395", "date": "29 Aug 2023", "name": "Vinutha U. Muktamath", "expertise": [ "Reviewer Expertise Assessment of children", "Differently abled and elderly" ], "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 is novel and addresses the most important issue of poor nutritional status leading to infant mortality and morbidity in infants and toddlers. Appropriate statistical tool and methodology is adopted. However the title can be more specific as effect of lactoferrin on growth and stunting in children. And the sample size will be 80 and 160 as the same sample will be used for pre and post test.\nThe interpretation and discussion part needs to be rewritten as the present study is measuring only IL-6 and IL-10 levels in failure to thrive children. No where the results indicate the effect on immune system like reduction in morbidity status and increase in weight and length by morbidity status. More reviews can be added to support the effect of lactoferrin in oral nutrition on growth of children. By discussing the studies by other researchers on improvement of immune system cannot be used to conclude as\" Lactoferrin in ONS intervention improved immune response homeostasis by balancing IL-6 and IL-10\". Better to restrict to the results of present 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?\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": "10177", "date": "20 Oct 2023", "name": "Nur Aisiyah Widjaja", "role": "Author Response", "response": "The study is novel and addresses the most important issue of poor nutritional status leading to infant mortality and morbidity in infants and toddlers. Appropriate statistical tool and methodology is adopted. However the title can be more specific as effect of lactoferrin on growth and stunting in children. Dear Mr. Vinutha U. Muktamathk, the reviewer of F1000Research thank you for the suggestion for this article. Here the title we think of “Effect of lactoferrin in oral nutrition supplement (ONS) towards IL-6 and IL-10 on growth and stunting in children” And the sample size will be 80 and 160 as the same sample will be used for pre and post-test. Thank you for the correction. We will change the sample size as you suggest The interpretation and discussion part needs to be rewritten as the present study is measuring only IL-6 and IL-10 levels in failure to thrive children. No where the results indicate the effect on immune system like reduction in morbidity status and increase in weight and length by morbidity status. More reviews can be added to support the effect of lactoferrin in oral nutrition on growth of children. By discussing the studies by other researchers on improvement of immune system cannot be used to conclude as\" Lactoferrin in ONS intervention improved immune response homeostasis by balancing IL-6 and IL-10\". Better to restrict to the results of present study For growth parameters, we made other paper entitled “The Effect of High Calorie Formula on Weight, Height Increment, IGF-1 and TLC in Growth Faltering Children”. in this paper we add total lymphocyte count (TLC) as the immunological parameters in these children. We will include the suggestion in the third version." } ] }, { "id": "197396", "date": "30 Aug 2023", "name": "Rachael Anyim", "expertise": [ "Reviewer Expertise Our combined areas of expertise involve human milk", "maternal-infant health", "biomarkers of stress (e.g.", "cortisol) and immunity/immune responses (e.g.", "cytokines", "antibodies)", "anthropometry", "human skeletal growth and plasticity", "and biological specimen collection (including blood draws", "saliva and milk collections)", "as well as enzyme immunoassay estimations." ], "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\nWidjaja et al.’s manuscript highlights growth failure in children (diagnosed with infectious diseases) and whether lactoferrin in oral nutrition supplementation improves their immune responses, captured here via changes in pro-inflammatory and anti-inflammatory cytokines, interleukin-6 and interleukin-10, respectively. Participating children received lactoferrin in oral nutrition supplementation for a period of 90 days, which the authors claim resulted in increased body length and weight, as well as decreased interleukin-10 and interleukin-6 (though the latter was not statistically significant between pre- and post-intervention). Furthermore, children with severe growth stunting experienced a larger decrease in interleukin-6 compared to children of normal stature.\nAs a whole, the authors’ manuscript is very detailed and well written, evidenced by their thorough references to the current literature. The methods for data collection are written clearly for replication and the study is well executed. However, the paper could benefit from some reorganizing. For example, “stunting” is defined on page 12 in the middle of paragraph 3 but should be discussed much earlier in the paper (i.e., in the introduction). The statistics presented also need a significant overhaul. See “Major Comments” and “Minor Comments” for additional details.\n\nMajor Comments:\nThe introduction section should be expanded to include functions/relevance of interleukin-10 (not just IL-6 and lactoferrin), definitions of stunting versus wasting, and outline the growth standards used. It could also benefit from highlighting the study scope and setting. For example, in the first paragraph in the discussion section (page 11), it is unclear why the authors discuss the prevalence of stunting in other countries when these have not been previously addressed. It might be better to move this information to the introduction to improve the background information presented and flesh out the current relevance to Indonesia in particular. It could be useful to state the rationale for conducting this study in Indonesia, what infectious disease burdens are prevalent in the area (e.g., urinary tract infections and tuberculosis are mentioned in the methods but then COVID-19 and pneumonia are in the discussion) and whether these may be confounding variables in analyses. If available within the data they collected, the authors could also address cultural considerations since part of the intervention includes dietary counseling and dietary supplementation of animal protein, as well as whether participants are still breastfeeding and how this might impact the generated results.\n\nWhile the authors have cited the literature, they have not stated what hypotheses may be driving their analyses and what results they expect to yield. These should be foregrounded in the introduction for readers.\n\nMethods for data collection, including anthropometrics and blood draws, seem appropriate. However, it would have been good to see a discussion on the volume of blood drawn and whether it was a fasting draw, as well as information on time of day for collections since some bioactive properties (e.g., IL-6) can exhibit diurnal variation, thereby confounding the results. The authors have only one sentence detailing their statistical analyses and superscripts in corresponding tables, which severely limits the replicability of their quantitative methods. It would be useful to expand on their methods here - including the results of normality and homogeneity tests and clearly describing which tests were performed on which variables, so that there is no confusion as to how analyses were conducted.\n\nClarification on the results presented would be helpful; as currently written, there seem to be mismatches between the statistics and the authors’ reports/concluding statements. We wonder if, perhaps, different tests are reported in the text versus in the tables; if so, the results yielded in those tests should match those in the tables/text. For example, in the abstract the authors suggest that IL-10 was significantly reduced after intervention. However, the closest value to statistical significance is p-value = 0.076 presented in Table 5. Additionally, they state that their intervention improved the IL-6/IL-10 ratio. However, there are no statistically significant differences in pre- and post-intervention ratios, as seen in Table 6. Convention is moving beyond solely using p < 0.05 as a threshold for data interpretation, so if that is the case here, the authors should disclose their cutoff point for determining “significant” results. Furthermore, the authors should remodel their tables to not only include p-values but also to include the comprehensive test results, test statistics, and effect sizes/magnitude of the effect. The p-values, means, and standard deviations presented do not convey a complete picture of the story written in the abstract and in the paper itself. Additionally, presenting SD as a +/- value suggests symmetry of data without actually testing for it. It could be useful if the authors instead did repeated measures ANOVA of pre- and post-intervention within group changes for IL-6 and IL-10, as well as present the tests of normality and homogeneity and the results of those tests. Additionally, clarification on the specific growth curves being used and how it was determined that Oral Nutrition Supplement intervention improved body weight and length/height could also be useful. For example, Table 1/paragraph 1 states that age, body weight, and height age were lower in group 1 versus group 2. However, the groups were broken up by age, so these changes could largely be innate and not necessarily linked to ONS supplementation. Table 2 presents a similar issue. Were the authors comparing these metrics to external growth standards? If so, those standards are not clearly identified here (aside from mentioning WHO Anthro). If not, how were the authors able to confirm whether the growth is an actual improvement of health due to the ONS intervention and not the result of normal growth over the three-month period? Perhaps, it may also be useful to add the rationale in age group cutoffs (i.e., group 1 vs. group 2).\nMinor Comments:\nSentence Structure: In the introduction section’s first paragraph (page 3), the authors can remove “still”, as it presupposes the audience is aware of growth failure as a historic health problem. In paragraph two, the second to last sentence serves no clear purpose and should either be expanded or removed. The first 2 sentences in the third paragraph can be consolidated a bit. The first sentence in the last paragraph on page 11 (“Lactoferrin…act accordingly and limits tissue damage”) doesn’t seem to make sense with the last clause. This may be due to missing words or punctuation.\n\nTypographical Errors and Points of Clarification: In the discussion section, “secrets” should be “secretes” in the twelfth paragraph (page 13). “Main Complains”, in Table 1, should be “Main Complaints”. Furthermore, “Main Complaints” were not addressed in the methods, so it is unclear how these complaints were documented/assessed (e.g., via survey at the beginning of study) and whether these complaints occurred during the course of the trial. “Liquid pups” should also be corrected in the table. Weight faltering (“normo-weight”) is unclearly defined in the table and in the text of the paper. In the far right column of Table 6, the column is labeled as ΔIL-10 but should be ΔIL-6/IL-10. It could also be useful if the authors clarified in the methods how animal protein supplementation was conducted, the rationale behind it, and how its application was measured.\nOverall, the study design and work presented have academic merit, as well as public health implications. If, for example, a relatively inexpensive intervention demonstrates positive health outcomes, this is a valid justification for using it in potentially low-income, nutrient impoverished, or high disease-burden settings. However, for the reasons stated above, it is a little difficult to accurately assess whether there is a reduction in IL-6 and if this is indeed directly related to the intervention.\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?\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": "10154", "date": "20 Oct 2023", "name": "Nur Aisiyah Widjaja", "role": "Author Response", "response": "As a whole, the authors’ manuscript is very detailed and well written, evidenced by their thorough references to the current literature. The methods for data collection are written clearly for replication and the study is well executed. However, the paper could benefit from some reorganizing. For example, “stunting” is defined on page 12 in the middle of paragraph 3 but should be discussed much earlier in the paper (i.e., in the introduction). The statistics presented also need a significant overhaul. See “Major Comments” and “Minor Comments” for additional details. Response: Paragraph 2 sentences 2, and soon Major Comments: The introduction section should be expanded to include functions/relevance of interleukin-10 (not just IL-6 and lactoferrin), definitions of stunting versus wasting, and outline the growth standards used. Response: Noted: Paragraph 2 sentences 2 to 3. It could also benefit from highlighting the study scope and setting. For example, in the first paragraph in the discussion section (page 11), it is unclear why the authors discuss the prevalence of stunting in other countries when these have not been previously addressed. It might be better to move this information to the introduction to improve the background information presented and flesh out the current relevance to Indonesia in particular. Response: Noted: Paragraph 2 sentences 4 until the last paragraph. It could be useful to state the rationale for conducting this study in Indonesia, what infectious disease burdens are prevalent in the area (e.g., urinary tract infections and tuberculosis are mentioned in the methods Response: Noted. Paragraph 5. But then COVID-19 and pneumonia are in the discussion) and whether these may be confounding variables in analyses. Response: We add COVID-19 due to during the intervention, we found that our subjects were infected. As for pneumonia, we found this infection in several subjects. We thought those disease as the confounding factors, but after we analysed statistically, they didn’t (p>0.05). If available within the data they collected, the authors could also address cultural considerations since part of the intervention includes dietary counseling and dietary supplementation of animal protein, as well as whether participants are still breastfeeding and how this might impact the generated results. Response: All of the subjects had breastfed predominantly (those under 2 years old), but the older ones consume growing up formula. While the authors have cited the literature, they have not stated what hypotheses may be driving their analyses and what results they expect to yield. These should be foregrounded in the introduction for readers. Response: Noted: The last sentences in introduction, and hypotheses in the methods. Methods for data collection, including anthropometrics and blood draws, seem appropriate. However, it would have been good to see a discussion on the volume of blood drawn and whether it was a fasting draw, as well as information on time of day for collections since some bioactive properties (e.g., IL-6) can exhibit diurnal variation, thereby confounding the results. Response: Noted: Paragraph 2 sub heading intervention in Method. Due to the researchers working during evening until night, the subjects were taken the blood at that time by the laboratory employee accompanied by the doctor’s nurses without fasting. The authors have only one sentence detailing their statistical analyses and superscripts in corresponding tables, which severely limits the replicability of their quantitative methods. It would be useful to expand on their methods here - including the results of normality and homogeneity tests and clearly describing which tests were performed on which variables, so that there is no confusion as to how analyses were conducted. Response: Noted: Table 7 Clarification on the results presented would be helpful; as currently written, there seem to be mismatches between the statistics and the authors’ reports/concluding statements. We wonder if, perhaps, different tests are reported in the text versus in the tables; if so, the results yielded in those tests should match those in the tables/text. For example, in the abstract the authors suggest that IL-10 was significantly reduced after intervention. However, the closest value to statistical significance is p-value = 0.076 presented in Table 5. Additionally, they state that their intervention improved the IL-6/IL-10 ratio. However, there are no statistically significant differences in pre- and post-intervention ratios, as seen in Table 6. Convention is moving beyond solely using p < 0.05 as a threshold for data interpretation, so if that is the case here, the authors should disclose their cutoff point for determining “significant” results. Furthermore, the authors should remodel their tables to not only include p-values but also to include the comprehensive test results, test statistics, and effect sizes/magnitude of the effect. The p-values, means, and standard deviations presented do not convey a complete picture of the story written in the abstract and in the paper itself. Additionally, presenting SD as a +/- value suggests symmetry of data without actually testing for it. It could be useful if the authors instead did repeated measures ANOVA of pre- and post-intervention within group changes for IL-6 and IL-10, as well as present the tests of normality and homogeneity and the results of those tests. Additionally, clarification on the specific growth curves being used and how it was determined that Oral Nutrition Supplement intervention improved body weight and length/height could also be useful. For example, Table 1/paragraph 1 states that age, body weight, and height age were lower in group 1 versus group 2. However, the groups were broken up by age, so these changes could largely be innate and not necessarily linked to ONS supplementation. Table 2 presents a similar issue. Were the authors comparing these metrics to external growth standards? If so, those standards are not clearly identified here (aside from mentioning WHO Anthro). If not, how were the authors able to confirm whether the growth is an actual improvement of health due to the ONS intervention and not the result of normal growth over the three-month period? Perhaps, it may also be useful to add the rationale in age group cutoffs (i.e., group 1 vs. group 2). Response: : Dear reviewer, the statement of IL-10 was significantly reduced after the intervention refers to a whole subject’s analysis using Wilcoxon sign rank (Komogorv-Smirnorv, p<0.05). We did not mention the value due to the limitations IL-6 before: 128.45 + 109.92 IL-6 after: 111.76 + 78.10 p=0.554 IL-10 before: 461.20 + 392.12 IL-10 after: 261.28 + 163.97 p=0.000 IL-6/IL-10 ratio before: 0.33 + 0.22 IL-6/IL-10 ratio after: 0.44 + 0.11 p=0.000 as for stated in the table, it was the value after we divided them based on the hypotheses we had. Minor Comments: Sentence Structure: In the introduction section’s first paragraph (page 3), the authors can remove “still”, as it presupposes the audience is aware of growth failure as a historic health problem. Response: Noted. We have erased it In paragraph two, the second to last sentence serves no clear purpose and should either be expanded or removed. The first 2 sentences in the third paragraph can be consolidated a bit. The first sentence in the last paragraph on page 11 (“Lactoferrin…act accordingly and limits tissue damage”) doesn’t seem to make sense with the last clause. This may be due to missing words or punctuation. Response: Noted. Typographical Errors and Points of Clarification: In the discussion section, “secrets” should be “secretes” in the twelfth paragraph (page 13). “Main Complains”, in Table 1, should be “Main Complaints”. Response: Noted. Furthermore, “Main Complaints” were not addressed in the methods, so it is unclear how these complaints were documented/assessed (e.g., via survey at the beginning of study) and whether these complaints occurred during the course of the trial. Response: : The complaints why the subjects visited the doctor were asked in the beginning by the nurse, “such as: what’s wrong with the baby, ma’am” “Liquid pups” should also be corrected in the table. Weight faltering (“normo-weight”) is unclearly defined in the table and in the text of the paper. In the far-right column of Table 6, the column is labeled as ΔIL-10 but should be ΔIL-6/IL-10. Response: Noted. We termed it as weight faltering because WAZ categories in normal range based on WHO child growth standard, but the subjects experienced inadequate weight gain It could also be useful if the authors clarified in the methods how animal protein supplementation was conducted, the rationale behind it, and how its application was measured. Response: ONS Oral Nutrition Supplement / High Calorie Formula / Nutrient Densed Formula SGM Optic Grow contains animal protein with the protein energy ratio of 9.5% (according to WHO, to increase weight gain for catch-up growth 8.5% - 11.5% is needed). The measurement was made based on the administration compliance of high-density formula (ONS) Aside from ONS, subject is also given nutritional counseling to give one egg per day as an additional complementary feeding." } ] } ]	1	https://f1000research.com/articles/12-897
https://f1000research.com/articles/12-874/v1	24 Jul 23	{ "type": "Case Study", "title": "The revitalization of endangered heritage buildings in developing countries: A decision-making framework for investment and determining the highest and best use in Egypt", "authors": [ "Mohanned Selim", "Adham Abulnour", "Sally Eldeeb", "Adham Abulnour", "Sally Eldeeb" ], "abstract": "Background: Egypt's major cities have been losing heritage and historical buildings due to neglect and misuse, prompting non-governmental organizations, academic institutions, and researchers to advocate for adaptive reuse strategies to preserve the cities' heritage and identity. Adaptive reuse involves changing, modifying, or reusing a space based on community needs, business model, location, and proximity to facilities and services. Heritage buildings offer many tangible and intangible benefits that enhance financial returns, making them challenging but feasible and attractive for investors who value authenticity, uniqueness, and sustainability. Methods: This study examines how market value, acquisition opportunities, target clients, age groups, and socioeconomic status affect decision-making. A comparative analysis of three buildings in the Egyptian cities of Alexandria and Cairo is utilized to establish development guidelines and decision-making parameters that significantly impact project design and building functions to determine the highest and best use. In order to complete this study, AutoCAD by Autodesk was used for 2D drawings, SketchUp by Trimble for 3D models, Adobe Photoshop for diagram presentation, and Microsoft Office for tables and diagrams. Results: The comparative analysis provided valuable insights into the adaptive reuse of heritage buildings in developing countries. Findings highlighted how cultural heritage preservation could foster socioeconomic development. Key success factors included stakeholder and community engagement, financial viability, and architectural compatibility. The decision-making framework provides a practical tool for evaluating heritage building reuse. Conclusions: The analysis illustrates successful reuse strategies and considerations. Decision-making frameworks and tools offer practical guidance for future investments and decisions. These findings affect heritage conservation and urban development policymakers, planners, and investors. Stakeholders can make informed decisions and implement strategies to preserve cultural and environmental value by realizing challenges and opportunities. This study hopes to inspire more research and help preserve and revitalize heritage buildings in developing countries, preserving their cultural and socioeconomic value.", "keywords": [ "Adaptive Reuse", "Heritage Buildings", "Mixed-Use", "Real-estate Development", "Decision-making parameters", "Stakeholders", "Investment", "Highest and best use" ], "content": "Introduction\n\nAdaptation is a technique for prolonging the usable life of structures through a mix of modification and conversion (Kohler and Hassler, 2002). Adaptive reuse of historic structures or modifying the original use of a heritage building to meet new conditions or demands and so reusing it, is critical to the sustainable growth of communities by avoiding demolition and rebuilding procedures (Aplin, 2002). Reusing properties may provide important community resources, significantly cut land purchase and building costs, rejuvenate existing communities, and restrict sprawl (Godwin, 2011). Preserving the integrity of an existing building, in particular, may reduce material, transportation, and energy use, as well as pollution, and so contribute significantly to reducing carbon dioxide emissions and improving sustainability (Bullen, 2007; Chung, 2009).\n\nThis realization has become part of redevelopment strategies and visions in countries all over the world (Mısırlısoya and Günc, 2016), and this can be witnessed in Egypt nowadays after several non-governmental organizations (NGOs) have highlighted the issue of heritage building demolition (Power, 2008); the government, alongside a limited number of private sector companies, started to implement adaptive reuse strategies in downtown Cairo and Alexandria as the existing governmental facilities and institutions are all being relocated to new settlements and cities such as the New Administrative Capital.\n\nThis research was created with the goal of providing a framework for developing heritage assets and criteria for investment in order to help investors, designers, and stakeholders prepare for projects and measure their performance (Bond, 2011; Steinberg, 1996). Identifying the factors that must be taken into consideration when deciding to invest in heritage properties or related projects and defining the tangible and non-tangible parameters to facilitate the decision-making process for the highest and best use of each space in a property is essential for developers in order to simplify the process and make it clear for all stakeholders that investing in heritage is a sustainable investment that is feasible and profitable (Shankland, 1975; Yung and Chan, 2012).\n\n\nMethods\n\nThis study performs a thorough analysis of different contemporary literature focusing on adaptive reuse, valorization methods of built heritage, and mixed-use development. This literature review forms the basis for a proposed conceptual framework and technical approach that are formed from the researcher’s experience in the field of adaptive reuse as practiced in the cities of Alexandria and Cairo.\n\nIn the development of the decision-making framework and investment criteria, several tools and software were instrumental in the process. AutoCAD by Autodesk (https://www.autodesk.co.uk/) played a crucial role in creating 2D drawings, providing precise representations of the building’s existing conditions and proposed modifications (students and educators can access a free version, while commercial use requires a subscription). SketchUp by Trimble (https://www.sketchup.com/) was used for generating 3D models, enabling a more immersive and realistic visualization of the adaptive reuse designs (free and pro versions are available). Photoshop by Adobe (https://www.adobe.com/uk/) was utilized for creating visually appealing diagrams and presentations that effectively conveyed project concepts (subscription-based, including a free trial). Additionally, Microsoft Office applications such as PowerPoint and Excel were utilized for organizing data, generating tables, and creating informative diagrams (free versions are available for students and educators, while commercial use requires a subscription). These software tools collectively enabled the author to formulate a comprehensive framework, supporting the successful execution of adaptive reuse projects for heritage buildings. Free alternatives for AutoCAD include FreeCAD (https://www.freecad.org/) and LibreCAD (https://librecad.org/), while alternatives for Photoshop include GIMP (https://www.gimp.org/) and Krita (https://krita.org/en/). For 3D modeling, Blender (https://www.blender.org/) serves as a free alternative to SketchUp. LibreOffice (https://www.libreoffice.org/) and Google Docs are free alternatives to Microsoft Office applications like PowerPoint and Excel.\n\nThe first part of this section discusses the development process of the adaptive reuse of heritage buildings based on existing projects and completed adaptive reuse (AR) scenarios in Egypt. The development process encompasses several vital steps that contribute to its overall detailed execution. Firstly, asset evaluation is conducted to thoroughly assess the physical condition, historical significance, and potential of the heritage building for reuse. This step provides a comprehensive understanding of the building’s unique features and challenges, aiding in decision-making for the adaptive reuse project. The next step involves the identification of programs and functions, where the specific uses and activities to be incorporated into the building are determined. This step ensures that the AR aligns with the desired goals and objectives of the project. Subsequently, the development process moves towards the formulation of a business model and stakeholder agreements, addressing the financial aspects, partnerships, and responsibilities associated with the project. Brand and identity creation are then emphasized to establish a distinct image and positioning for the AR development. In the design phase, architectural and engineering plans are formulated, incorporating both the historical elements and modern requirements of the project. Tendering and contractor selection follow, involving the procurement of necessary services and materials. Finally, the operation and evaluation phase ensures the effective management and ongoing assessment of the adaptive reuse project to maintain its success and address any necessary improvements.\n\nThe development of the decision-making parameters process is then supported by identifying stakeholders and key players in the industry and analyzing the nature of those entities as well as their different roles throughout the process (Wang and Zeng, 2010). The previous is supported by multiple case studies where adaptive reuse was implemented and achieved completely or partially in order to finally come up with simple guidelines and a framework that helps developers and other stakeholders in the decision-making process for the components and activities incorporated in a project. Those projects were utilized by the researcher as a reference due to multiple factors such as functional and economic viability, preservation of heritage value, community engagement and stakeholder collaboration, and finally, the recognition of the local community (Merlino, 2018).\n\nThe comparative analysis followed multiple stages in order to develop a thorough evaluation tool which then ultimately led to the decision-making framework that is meant to help stakeholders decide on the highest and best use. The preliminary evaluation of each building was conducted by considering several decision-making parameters. The first parameter, location, was measured based on its proximity to key amenities, transportation networks, and potential target markets. Accessibility, the second parameter, was graded by assessing the ease of reaching the property through various modes of transportation. The surrounding context was evaluated by analyzing neighboring spaces and buildings with similar or complementary functions, determining whether they could contribute to the success of the mixed-use development. The architectural description and features were examined to determine the property’s aesthetic appeal, historical significance, and potential for adaptive reuse. Spatial challenges and restrictions, such as heights and areas, were measured to assess the feasibility of incorporating desired functions within the existing structure. Existing services and facilities were evaluated to determine the extent of infrastructure that could be utilized or upgraded. Available spaces within the property were assessed to understand the potential for accommodating different uses. Lastly, socioeconomic analysis played a crucial role in grading the property based on the demographics and economic conditions of the surrounding area. This comprehensive evaluation of each parameter provided a brief preliminary assessment of the heritage buildings through a brief description and a grading which ranges between High, Average, and Low based on the aforementioned measurement factors.\n\nThe researcher then developed an evaluation system from the data and analyses gathered throughout this study as shown in Table 1. This method follows a simple evaluative approach for each of the aforementioned parameters based on multiple factors (sub-parameters) that have an impact on the main parameter. The researcher then provides a total grade for each main parameter, which will then be used in the following step of the evaluation system and will also be used to assist with the comparison between the three analyzed case studies, ultimately formulating the general guidelines and decision-making criteria regarding the function, type, category, and scale. The grading was intentionally simplified in order to make the process easy for application to other buildings in any AR project by different stakeholders, but mainly by investors and producers. Each sub-parameter is given a value from 0 to 2. The 0 represents a low evaluation of the parameter, the 1 represents an average evaluation, and the 2 represents a high evaluation.\n\nSource: Author, 2023.\n\nThe researcher performs this assessment by analyzing each parameter and how it affects the four mentioned aspects (function, scale, type, and category) and follows this step by adding the values of all the parameters that have an impact on each of the four aspects, as shown in Table 2 below, which demonstrates which aspect each and every parameter has an impact on. This total value is then converted to a percentage in order to make its evaluation more efficient and legible in the decision regarding each aspect or step.\n\nSource: Author, 2023.\n\nAfter defining all the parameters that have an impact on each aspect as shown in Table 2 above, the researcher adds those values and concludes with the final guidelines that would potentially assist stakeholders involved in AR projects in heritage buildings with the decision-making process from start to finish regarding the highest and best use and optimum component mix to be incorporated in the building, as shown in Table 3 below, and applies those steps to the case studies. The aforementioned four steps are demonstrated as follows:\n\nSource: Author, 2023.\n\nThe recommended types previously mentioned as part of the four-step evaluation process are described in detail by the researcher with regards to every function, as shown below in Table 4. The table determines the general framework where each function will be decided considering the target users and based on the evaluation, where the percentages from 10 to 40 will mainly, but not exclusively, target locals of lower income, and percentages from 40 to 70 will mainly, but not exclusively, target medium-income users and younger generations of tourists and locals, and finally, percentages from 70 to 100 will mainly, but not exclusively, target higher-income users and older generations from the same group.\n\nSource: Author, 2023.\n\nThis methodology is proposed by the author in order to reach an ultimate decision regarding investment opportunities and determine the highest and best use of heritage buildings that are intended for adaptive reuse projects in Egypt and developing countries. The proposed system is generalized in order to make it simple to replicate, readapt, or possibly undergo further development, turning it into a digital tool that would facilitate the decision-making process for different stakeholders involved in the adaptive reuse industry.\n\nAsset evaluation\n\nThe first stage in the adaptive reuse process is the acquisition stage, when investors and developers start to search for unique properties and assets that suit their scope and development vision. These properties must have a special location that is easily accessible via diverse transportation methods (Brandt, 2006). Also related to the location are the views of the building, the main landmarks, the surrounding activities, and the socioeconomic status of the community (Browne, 2006).\n\nAfter analyzing the location, the investors start to analyze the building from the inside, considering the available spaces, interior details, areas and heights, and existing services and facilities (Rabun and Kelso, 2009). Furthermore, historical studies and documentation are made to identify the architect, architectural style, ornaments, and features in order to identify the original designs and restore them where applicable, which then creates a unique product and adds value to the asset (NOUH, n.d.). Finally, structural reports are prepared by experts to ensure the building maintains its structural integrity and is worth the investment.\n\nPrograms and functions identification\n\nAfter acquiring the building, the development process starts with its initial step of identifying the spaces within the property that will be developed within the company’s development pipeline.\n\nThere are various cases regarding available spaces in adaptive reuse scenarios: the building could be a standalone building that is completely available and ready to be developed as a whole; the building could have whole floors that are empty and other floors that are rented or owned, as shown in Figure 1; or it could have separate spaces, such as apartments or stores, that are currently available or leased under a contract that is nearing an end. After that, it is required to perform market research to study the feasibility of a project and forecast the expected return on investment (ROI) and return on asset (ROA) to ensure the project’s success. Finally, based on all the aforementioned steps, the suitable component mix is decided, as well as the percentages of all the functions to be added to the asset (Ribera et al., 2020).\n\nSource: This figure has been reproduced with permission from Sigma Properties, 2019.\n\nKey: ● Unavailable Spaces ● leased old law (Unavailable) ● available (acquired) ● leased new law (available).\n\nBusiness model and stakeholder agreements\n\nIn this phase, the developers, along with real estate advisors, property management companies, and business developers, start to search for suitable operators to manage and run the projects (Menassa and Baer, 2014). Also, the project usually has an estimated budget that is defined based on the target users, categories of provided services, and types of functions.\n\nBrand and identity creation\n\nIn this phase, designers and marketing experts start creating a unique brand for the asset, as well as sub-brands for the available functions, to make it a destination where you can have a unique experience like no other. Part of this brand creation involves the procurement of artworks as shown in Figure 2, photos, and other visual materials that represent the building and portray its identity, which could then be used in websites, social media platforms, and investment and marketing presentations.\n\nSource: Author, 2022.\n\nAlso, the building’s story is highlighted; this story includes the architect, architectural features, and interior and exterior details, all of which play a major role in making the building stand out and deserve special recognition (Abdeen and Ahmed, 2009). Furthermore, restoring lost features, removing transgressions, and preserving existing elements also adds value to the asset (Megahed, 2009).\n\nDesign phase\n\nIn this phase, the design studio starts working in coordination with the developer on the project’s design concept, showing the proposed style, design, inspiration, and overall look and feel of the space. Also, mood boards and material boards are then proposed, along with renders that help elaborate the proposed design, allowing the investor to have a clear image of what the space will look like after development as shown in Figure 3.\n\nSource: This figure has been reproduced with permission from Sigma Properties, 2021.\n\nAfter finalizing the designs, the design team starts preparing the drawings package. The drawings include furniture layouts, electromechanical and plumbing (MEP) plans, reflected ceiling plans (RCP), and demolition and addition drawings that illustrate the as-built plans as well as the proposed new design marking the required modifications as shown in Figure 4.\n\nSource: This figure has been reproduced with permission from Sigma Properties, 2022.\n\nTendering and contractor selection\n\nIn this stage, the design team and the project consultant, representing the investor, coordinate the preparation of the bill of quantities (BOQ) and vendor list based on the data prepared in the design phase to be presented to the contractor or various contractors for cost comparison and selection. During site work, the design team along with the consultant supervise the project and follow-up with the delivery of each phase of site work until the project is successfully delivered.\n\nOperation and evaluation\n\nIn the final phase of the development process, following the successful delivery of the project, the operator initiates the pilot phase of the project. In this phase, the operator works on marketing and public outreach; this includes social media campaigns, public events, online advertisement, and other methods that help the project reach its target audience. This phase happens in coordination with the developer, operator, and design team in order to ensure a smooth pilot phase and work on any issues or modifications that might be required. After that, a major evaluation is made to measure the project’s performance in order to perform any optimizations to the project itself and to future projects (Giles, 2005).\n\nSource: Author, 2022.\n\nMost complicated adaptive reuse challenges require the collaboration of diverse stakeholders with divergent interests to realize mutually gratifying results. Eventually, the identification of important stakeholders and the collaborative rationale that exists between them in a decision-making process will be essential to the effective implementation of any strategy for sustainable development. In the majority of adaptive reuse decision-making scenarios, contradictory views, perspectives, interests, and resources exist among important parties (Aigwi et al., 2019). Therefore, it would be advantageous for all participants in an adaptive reuse decision-making process to understand who the other players are, how their interests are interconnected, and how the collaborative strategy operates (Innes and Booher, 2010; Department of Environment and Heritage, 2004).\n\nInvestors\n\nAn adaptive reuse project could have investors from the government, the private sector, owners of historic buildings, financing groups, renters, foreign communities, and other developers.\n\nProducers\n\nThe producer category includes all the players participating in the production of an adaptive reuse project, which includes the designers, structural engineers, heritage restoration experts, consultants, and contractors.\n\nOperators\n\nIncludes local or international brands and chains representing any of the functions in a building; this includes hotels, offices, retail, food and beverage (F&B) chains, or independent entities.\n\nRegulators\n\nThe regulator category includes all governmental institutions concerned with the governance of real estate development, laws, and permits. Also, entities that identify heritage assets, regulate their existing states, and approve their redevelopment.\n\nUsers\n\nMembers of the local community, visitors, original users (current tenants), or prospective tenants comprise this stakeholder category (Bond, 2011).\n\nProperty assessment for mixed-use developments: decision-making parameters\n\n• Location\n\n• Accessibility\n\n• Surrounding context (neighboring spaces and buildings with similar or complementary functions)\n\n• Architectural description and features\n\n• Spaces (spatial challenges and restrictions such as heights and areas)\n\n• Existing services and facilities\n\n• Available spaces within the property\n\n• Socioeconomic analysis\n\n\nCase Studies of properties in Egypt\n\nLocation\n\nThe Avierino building (AVI) is located in downtown Alexandria, Egypt, along Fouad Street, one of the oldest streets and known to be the oldest functioning street in history, previously named the Canopic Way during the Greek era (Serageldin, 2002). The building’s location is very important due to its close proximity to various nodes of the city’s most significant functions and activities, as shown in Figure 6; the building is considered to be located in the business district of the city, where major consulates, banks, museums, educational institutions, logistics companies, and sports facilities such as the Alexandria Stadium are located. Also, it is near the Alexandria port, where the majority of the country’s imports are received (Selim, 2023).\n\nSource: Author, 2022.\n\nAccessibility and legibility\n\nThe building is easily accessible via diverse methods of private and public transportation, such as personal vehicles, bikes, buses, microbuses, taxis, trams, and trains. The building is within close proximity to Alexandria Railway Station, which provides direct access from all over the city and other cities as well; it is also located near several tram stations and main roads such as El Horeya Street and El Geish, both known to be the main veins of the city where most, if not all, traffic passes through daily (Selim, 2023). The building has several parking spaces in the surrounding area; these spaces are sufficient to accommodate the building’s users. It is sometimes a bit challenging to find parking spaces during the day due to high traffic, but after rush hour and by night, the area has very low traffic, making it much easier for pedestrians and visitors to explore downtown.\n\nSurrounding context\n\nThe building is located in the business district in downtown where consulates, banks, companies, museums, educational institutions, cinemas, antique furniture stores, sports facilities, and cultural attractions such as the Alexandria Opera House are all within proximity, this gives the building significant potential as its location attracts high traffic, this traffic includes businessmen and traders because of the logistics companies and the businessmen association headquarters located within the building; other traffic includes tourists and locals visiting surrounding museums such as the Graeco-roman museum and Alexandria National Museum; also students learning languages at the French, Greek, Russian, Spanish, or Italian cultural centers form a significant number of traffic visiting. Finally, bank employees and consulate representatives are also an important sector of the traffic visiting the building (Awad, 2008; Serageldin, 2002).\n\nSpaces\n\nThe building has vast heights and spacious areas all over, whether in the ground floor where the heights are up to 6.2 meters high or on the typical floors, which are 4.2 meters high. Since the building is a reinforced concrete structure, it is flexible for opening spaces with each other to make bigger spaces that could be used for diverse functions such as a restaurant or café in any food and beverage project, a co-working space in office projects, or an open space for events, workshops, educational courses, the arts, and cultural projects.\n\nArchitectural description and features\n\nThe building was built in 1928 by the Greek architect Petros Nicolas Griparis after being commissioned by the Avierino family, which was known to have been of Italo-Greek origins. The building was designed in a neo-renaissance style and is an exquisite example showcasing the cosmopolitan spirit of Alexandria; the building had tenants from many countries and locals as well, who all lived together in a socially cohesive environment during that time and till this day (Awad, 2008).\n\nThe building is comprised of a basement, a ground floor, a mezzanine, and seven typical floors, as well as a roof and a dome at the top, as shown in Figure 7. The building has a mixed structural system combining bearing walls and reinforced concrete. Avierino has a built-up area (BUA) of around 11,000 m2 and a floor footprint of 1,350 m2. Each typical floor was originally divided into four apartments, but most of them have been connected to each other through a common corridor that circles around the building’s plan (Selim, 2023).\n\nSource: Author, 2021.\n\nExisting services and facilities\n\nThe ground floor has retail spaces; an art space is in the basement; offices are on different floors; and residential apartments are on the typical floors. It has two main vertical circulation cores, each housing a staircase and an elevator, each in one of the building’s two sides; each side has two apartments, and both sides are connected with a central service core with an elevator; this core is used for services, cleaning, and maintenance uses.\n\nAvailable spaces within the property\n\nThis parameter defines the available spaces in the building in order to prepare a development program for each building and make the vision clear for investors, designers, and other stakeholders regarding the potential investment opportunities and the types of activities that could be incorporated in the building (Selim, 2023). In Avierino, the basement and ground floor are completely empty, making it a high potential for a commercial, retail, or F&B project. The floors from the first to the fourth all have empty spaces but are not completely empty, so pilot projects such as offices and hospitality could be initiated until more spaces are acquired, as demonstrated in Figure 8.\n\nSource: This figure has been reproduced with permission from Sigma Properties, 2022.\n\nSocial and economic analysis\n\nThe socio-economic level of the area surrounding Avierino is a mixed one, combining communities from different backgrounds and pay grades in the city, from small to medium entities around the neighboring areas and local businesses and shops, to students and educators from surrounding institutions, all the way to business owners and traders from local antique stores, logistics companies, and banks. The target users and visitors of the building include the local community in downtown, government, banks, and consulates employees and representatives, tourists from foreign countries and other cities in Egypt, and finally, businessmen and merchants visiting the city for commercial purposes (Said, 2016).\n\nDevelopment model\n\nAfter the detailed analysis of the Avierino building and understanding its location, accessibility, surrounding context, spatial characteristics, architectural features, existing service, availability of spaces, and analyzing the socio-economic status of the area and the local community, the program developers, along with the investors and other stakeholders, formulate a general vision regarding the highest and best use. The analytical process that precedes the decision regarding the most suitable function and component mix is what leads the involved stakeholders to develop a program in which all future projects are going to follow; this program also suits the existing functions and uses already existing in the property and surrounding properties as well, as shown in Figure 9.\n\nSource: This figure has been reproduced with permission from Sigma Properties, 2022.\n\nThe development model shown in Figure 9, incorporates the following functions: F&B and retail spaces in the ground floor and rooftop; offices and workspaces in the mezzanine floor up to the third floor; hospitality services in the fourth floor up to the seventh floor; and an art space as an arts and culture function in the basement.\n\n‘Mezzanine Offices and Coworking Spaces’ demonstrated in Figures 10-12, is an example of one of the main uses that have been introduced in the Avierino building as a pilot project to incorporate the function of offices and workspaces and is intended to be one of the brands that could potentially be replicated in other buildings as part of the adaptive reuse strategy (Selim, 2023).\n\nElectrical systems were installed in an exposed manner in order to preserve the vast heights of the interior spaces. Source: This figure has been reproduced with permission from Sigma Properties, 2022.\n\nSource: This figure has been reproduced with permission from Sigma Properties, 2022.\n\nTransgressions were removed and a new window replicating the original design was added once again. Source: This figure has been reproduced with permission from Sigma Properties, 2022.\n\nLocation\n\nThe Little Venice (LV) building is located in a prime waterfront location in downtown Alexandria along El Geish Road; it is the most important and most famous road in Alexandria since it covers the majority of the Mediterranean city’s waterfront and is a critical traffic vein where all types of light transportation methods exist and all of the city’s development and urban sprawl are condensed around due to the road’s importance and its sentimental connection with all citizens of Alexandria, as shown in Figure 13. The building is considered to be located in the historical district of the city, where ancient temples of Egypt previously existed, such as Cleopatra’s Temple, and ancient sites of Roman Egypt. Also, it is near the Alexandria port, where the majority of the country’s imports are received (Serageldin, 2002). The building has a direct view of the waterfront, an area famously known as the Eastern Harbor where Portus Magnus, one of the oldest ports in the world, was built and is now an archeological site with ancient underwater remains of Alexander the Great’s royal fleet (Selim, 2023).\n\nSource: Author, 2022.\n\nAccessibility and legibility\n\nThe building is easily accessible via diverse methods of private and public transportation, such as personal vehicles, bikes, buses, microbuses, taxis, trams, and trains. The building is directly located from the front elevation on El Geish Road, and from the opposite side, it is directly facing Raml Station, the first tram station on the main line of Alexandria’s tramway (Selim, 2023). The building has several parking facilities in the surrounding areas within walking distance, with sufficient spaces making it easy to find parking spots at any time of the day except for rush hour, as is the case in downtown in general.\n\nSurrounding context\n\nThe building is located in a district that could be described as a historical, recreational, commercial, and touristic district in downtown where public squares, hotels, cinemas, consulates, banks, and major cultural and touristic attractions such as the Alexandria Library famously known as the Bibliotheca Alexandrina, are all within proximity; this gives the building significant potential as its location attracts high traffic, this traffic includes tourists and locals visiting the Alexandria Library for attending cultural events or for educational purposes, or staying for touristic purposes in general looking to stay in a prime waterfront location; also, employees or businessmen visiting the city for business meetings and commerce, or locals visiting for convenient shopping, dining, or going to cinemas and theaters in the area (Serageldin, 2002).\n\nSpaces\n\nThe building has considerably high ceilings but limited areas due to structural limitations caused by the building’s design, except for the ground floor, which has open areas and ceilings up to 5.2 meters high. The typical floors are 4.2 meters high, and since the building is a reinforced concrete structure, it is flexible for opening spaces with each other but with certain limitations in order to maintain the building’s structural and architectural integrity.\n\nArchitectural description and features\n\nThe building was built in 1929 with a unique architectural style combining Neo-Gothic and Venetian elements influenced by the local architecture of Alexandria. It was built by Giacomo Alessandro Loria, an architect born in El Mansourah to a Jewish family from Livorno that settled in Egypt during the time of Mohammed Ali. The building had an exquisite exterior design, making it the best façade of the year in 1929. The building had beautiful mosaic medallions and tiles on its corner towers, each with a unique design (Selim, 2023); it also had Moorish arches with Gothic detailing resembling those of the Palazzo Ducale in Venice, Italy (Awad, 2008).\n\nThe building is comprised of a ground floor that is divided on two levels due to the ground’s slope, a mezzanine, and four typical floors, as well as a roof, as shown in Figure 14. The building has a mixed structural system combining bearing walls and reinforced concrete. It has a BUA of around 5,800 m2, and each typical floor was originally divided into four apartments.\n\nSource: This figure has been reproduced with permission from Sigma Properties, 2022.\n\nExisting services and facilities\n\nThe building has empty retail spaces on the ground floor, various offices and clinics on different floors, and a hotel on the first and second floors. It has one main vertical circulation core housing a staircase and an elevator and two courts; each court has a service core supplied with a staircase; this core is used for services, cleaning, and maintenance uses.\n\nAvailable spaces within the property\n\nThe ground floor and mezzanine are currently unavailable due to ‘old law’ lease contracts, and from the typical floors, only the second floor is fully available, which could be developed as a hotel due to the building’s prime location and previously existing functions and permits (Selim, 2023); also, a few apartments are available on the third and fourth floors, which could also be developed as part of a hotel project or other hospitality services, as demonstrated in Figure 15.\n\nSource: This figure has been reproduced with permission from Sigma Properties, 2022.\n\nSocial and economic analysis\n\nThe area surrounding the Little Venice building is similar to Avierino since they are within proximity of each other, meaning that it combines communities from different backgrounds and levels as well. The only difference is that Little Venice’s prime waterfront location gives it a significantly higher potential to attract visitors with a higher economic level and purchasing power in general, so a bigger percentage of hospitality services is required, preferably a boutique hotel, and a higher category of finishes, furniture, materials, and equipment will be required (Said, 2016).\n\nDevelopment model\n\nAfter the detailed analysis of the Little Venice Building and understanding its location, accessibility, surrounding context, spatial characteristics, architectural features, existing service, availability of spaces, and analyzing the socio-economic status of the area and the local community, the program developers, along with the investors and other stakeholders, formulate a general vision regarding the highest and best use, as shown in Figure 16.\n\nSource: This figure has been reproduced with permission from Sigma Properties, 2022.\n\nThe development model incorporates the following functions: F&B on the ground floor and rooftop, and premium hospitality services on the mezzanine floor up to the fourth floor, due to the prime waterfront location of the building.\n\nThe ‘Venetian Suites’ project demonstrated in Figure 17, is an example of one of the main uses that have been introduced in the Little Venice building as a pilot project to incorporate the function of hospitality services and, following its substantial success considering the financial aspects as well as the users’ feedback, it is now part of a larger scale hospitality project that could potentially be replicated in other buildings as part of the adaptive reuse strategy (Selim, 2023).\n\nSource: This figure has been reproduced with permission from Sigma Properties, 2022.\n\nLocation\n\nLocated in downtown Cairo, along Talaat Harb Street, which was previously named Suleiman Pasha Street during the time of Mohammed Ali and renamed in 1954. It is one of the most important streets in downtown Cairo and is considered the main vein connecting Tahrir Square and Talaat Harb Square, as shown in Figure 18. The street was a hub for activities and social interaction among Cairo’s upper class and foreign European communities. The influence of European culture and architecture is still evident and embodied in French neoclassical architecture (Selim, 2023).\n\nSource: Author, 2022.\n\nAccessibility and legibility\n\nThe building is in a prime location considering accessibility, knowing that it is connected directly to the Qasr El Nile Bridge, the 6th of October Bridge, and the Azhar Tunnel and Bridge, connecting downtown to major areas in Cairo. The building’s location is easily accessible via different methods of transportation and through various alternative routes. The building is located within close proximity to metro stations and Ramsis railway station, the most important station to visitors from all around Egypt as the connecting railway trains all stop at Ramsis station and visitors then use other methods of transportation to reach their destinations around Cairo (Selim, 2023). Parking facilities are available directly next to the building, as well as in the surrounding areas such as the Opera garage and the Tahrir garage.\n\nSurrounding context\n\nThe building is considered to be in a commercial area, as locals and the majority of traffic visiting the street visit to shop for conveniently priced clothing and other accessories. Other visitors are employees working with governmental institutions, banks, tourism companies, etc. Also due to the building’s close proximity to Tahrir Square, where visitors from all over Egypt and tourists meet, either as a station to commute to and from their cities or visit the Egyptian Museum and other touristic locations. The building is situated next to consulates and multiple governmental institutions; also surrounding the building are hotels, banks, retail stores, restaurants, cinemas, bookstores, offices, educational institutions such as the Greek campus and the American University in Cairo campus, sporting clubs, and cultural magnets such as the Cairo Opera House. Furthermore, the Nile Corniche and tourist attractions such as the Egyptian Museum, Abdeen Palace, Cairo Tower, and many other locations are close to the building (Mubarak, 1989).\n\nSpaces\n\nThe Ouzonnian building has a relatively small floor footprint, meaning that its areas will be limited considering functions that require open or large spaces; also, the floors have limited heights due to its modern construction system, unlike Avierino and Little Venice. The ground floor height is up to 4.5 meters, and the typical floors are 3.2 meters high. The building has lower heights, smaller courts, and minimal features; this has an impact on technical and design-related decisions.\n\nArchitectural description and features\n\nThis building was built by the Egyptian architect Sayed Karim, born in 1911 in Quesna, Egypt. He was a professor of architecture at Cairo University, and he registered the first consulting office in Egypt for architecture and planning in 1939; he also issued the first architecture and arts magazine in Egypt in the same year (Selim, 2023).\n\nThe building was recognized as one of the first modern buildings in Egypt and the tallest building in Cairo at that time. It has a reinforced concrete structure system and it is comprised of a ground floor that is connected to a spacious backyard, a mezzanine, seven typical floors, four upper floors with different areas that become smaller every floor, and two final floors with even smaller areas as shown in the building’s images. It has a BUA of around 8,200 m2, each typical floor was originally divided to four apartments but some of them have been connected to each other, as demonstrated in Figure 19.\n\nSource: This figure has been reproduced with permission from Sigma Properties, 2022.\n\nExisting services and facilities\n\nThe building was designed to host various functions, with the ground floor containing commercial spaces. The first floor had a restaurant, a dancing hall, and a rotunda that featured an open-air garden. The seven typical floors functioned as apartments and offices, the four upper floors featured a hotel with a private garden, and the top floors housed residential units. Nowadays, the building has retail stores on the ground floor, offices on the mezzanine and first floors, and residential and studio apartments on the typical floors. The building has a central vertical circulation core in its center with three elevators and a staircase, and it has two courts, both of which have a staircase, but only one of them has a service elevator; these service courts were used for services, cleaning, and maintenance (Selim, 2023).\n\nAvailable spaces within the property\n\nThe ground floor has retail stores with old contract rentals; the backyard, on the other hand, is acquired and could be developed as a F&B project; the floors from the first till the fourth are all office spaces; the majority of the spaces are acquired and could be developed as a part of a project. The fifth, seventh, and eighth floors are also not fully acquired, but each floor has available spaces; all are residential spaces (Selim, 2023). The sixth floor is fully available and has been utilized as a pilot for an AirBnB (https://www.airbnb.co.uk) hospitality project that is currently undergoing the extension phase on the tenth through the thirteenth floors, as demonstrated in Figure 20.\n\nSource: This figure has been reproduced with permission from Sigma Properties, 2022.\n\nSocial and economic analysis\n\nThe area surrounding Ouzonnian is similar to those of Avierino and Little Venice considering their locations in downtown areas, but the fact that Ouzonnian is in Cairo significantly changes the equation, knowing that the traffic in Cairo is much higher, especially tourists, backpackers, artists, and entrepreneurs working on the go. This gives Ouzonnian a higher success rate when considering mixed-use developments in general due to the feasibility of the projects in this area. The expected target users are mostly younger generations of entrepreneurs and travelers looking for a local experience and a conveniently priced stay such as AirBnB and studio apartments. Also, such users would require places to work from, such as private offices and co-working spaces that would be complimented with F&B services to complete the component mix in the building, making it an independent, self-sufficient destination.\n\nDevelopment model\n\nAfter the detailed analysis of the Ouzonnian Building and understanding the parameters of the property assessment, the program developers, along with the investors and other stakeholders, formulate a general vision regarding the highest and best use, as shown in Figure 21.\n\nSource: This figure has been reproduced with permission from Sigma Properties, 2022.\n\nThe development model incorporates the following functions: F&B and retail spaces on the ground floor, fourteenth floor, and rooftop; offices and workspaces on the first floor up to the third floor; and hospitality services on the fourth floor up to the thirteenth floor.\n\n‘Grey Studio Apartments’ demonstrated in Figures 22-24, is an example of one of the main uses that have been introduced in the Ouzonnian building as a pilot project to incorporate the function of hospitality services that resemble AirBnB stays and, following its substantial success considering the financial aspects as well as the users’ feedback, it is now part of a larger scale hospitality concept that could potentially be replicated in other buildings as part of the adaptive reuse strategy (Selim, 2023).\n\nSource: This figure has been reproduced with permission from Sigma Properties, 2022.\n\nSource: This figure has been reproduced with permission from Sigma Properties, 2022.\n\nSource: This figure has been reproduced with permission from Sigma Properties, 2022.\n\n\nResults\n\nThe following table summarizes the results derived from the previous analyses, as the author selected three buildings in downtown areas of Alexandria and Cairo to be part of the comparative analysis approach, which was performed with the aim of producing and assessing decision-making parameters that assist developers and other stakeholders involved in the adaptive reuse of heritage buildings by acting as guidelines that those stakeholders could potentially utilize for evaluating heritage properties and reaching an expert decision regarding the highest and best use of the spaces provided in those assets. The table also provides a brief description of the evaluation of those parameters in order to complete the comparative analysis.\n\nSource: Author, 2022.\n\n\nDiscussion\n\nThe following Figure 25 shows the proposed business model for each of the case studies analyzed throughout this research, considering the available spaces and the spaces to be available within a five-year development pipeline. It is evident that the optimum component mix and percentage distribution differ in each property, and in each case, there is a recommended percentage for the main functions as well as secondary ones.\n\nNotes: F&B – food and beverage. Source: Author, 2022.\n\nWhen it comes to the functions forming the component mix in the adaptive reuse of heritage buildings, it is evident that there are a number of common functions that are constant and are replicated throughout other developments. These functions are: retail and commercial, F&B, hospitality, offices and co-working space, educational facilities, and arts and culture. Some of those functions have become of critical significance following the pandemic and international conflicts, while others have always been a permanent component of any property (NSW Department of Planning and RAIA, 2008).\n\nThe outcome of this research shows how these functions are supposed to coexist and be coherent with each other to make a successful adaptive reuse development program, but what is clear is that those functions are not the same in the percentage of their incorporation in the development, but they are variable in scale and category depending on the decision-making parameters (Elsorady, 2020); in one of the cases, the building is a waterfront property in a prime touristic location, so the focus on hospitality is higher and it gets a bigger scale in the building and a higher category considering the level of finishing, furniture, equipment, and overall technology utilized in that project (Willson and Mcintosh, 2007). In other cases, the building could be in a Commercial Business District where existing traffic require F&B services as well as offices and Co-working spaces, in that building the scale of those functions are bigger and more significant, however, this doesn’t mean that hospitality services won’t be provided.\n\nAlso, another adaptive reuse (AR) scenario is when a building is fully available or the majority of its spaces are acquired, and within legible, connected spaces, it has a lot of potential to be developed as a whole and operated as well; this is a common scenario where projects are usually limited to parts of a building, not the building as a whole, since most buildings in downtown have residents, and also because that is a relatively smaller investment considering the acquisition of whole buildings with 100% empty spaces.\n\nFurthermore, for projects located in prime areas with prime views, it is recommended to develop a program with higher percentages of hospitality functions. For hospitality functions in an area where most traffic and locals are of a lower socio-economic level, AirBnB, hostels, and studio apartments are recommended to suit the needs and capabilities of the area. On the other hand, in areas with target users with a higher level of income and economic capabilities and a highly touristic presence, it is recommended to provide the users with premium hospitality services such as hotels, boutique hotels, serviced apartments, or studio apartments as well, but with a higher grade of design considering finishes, materials, and furniture (Freund de Klumbis and Munsters, 2005).\n\nTable 6 demonstrates the implementation of the evaluation system which was developed by the researcher in order to perform an overall grading for the three buildings based on the sub-parameters to achieve a detailed evaluation.\n\nSource: Author, 2023.\n\nThis evaluation is performed on the three buildings of Avierino, Little Venice, and Ouzonnian and shows the differences between them considering each parameter. The total evaluation of each building represents its potential in the AR industry, considering the development model, the building’s historical value and significance, its architectural and structural state, the availability of spaces to be utilized, as well as the building’s degree of ability and flexibility in housing different functions and therefore becoming a hub that serves the needs of the users and local community.\n\nIn the case of the Avierino building, it has the highest overall grade since the building has an overall high grade considering all of the parameters; on the other hand, the Little Venice building has the lowest grade of the three buildings, not because it has less historical significance or poor architectural features, but because it has considerably less available spaces since the roof and ground floor are not available for development in the present state, also because it has limited spaces and deteriorated facilities, and finally because the area’s socioeconomic status is on the lower side compared to the other buildings and in general. Lastly, the Ouzonnian building is in a place between the two buildings based on the evaluation, but it is closer in overall value to Little Venice due to its deteriorated facilities and infrastructure, as well as its poor architectural features, and finally due to its high environmental impact considering the building’s location being along a noisy street with high traffic and overall pollution. Ouzonnian still has a higher grade since it has much more available spaces with large areas, which provide higher flexibility to incorporate diverse functions or activities, and it also has open spaces and bigger openings, unlike Little Venice (Selim, 2023). These factors gave it a higher overall grade regardless of whether Little Venice is a rich building considering its history, architectural features, and overall aesthetic, which make it one of the most iconic buildings in the city of Alexandria. The Little Venice building is in a prime location along the waterfront, but the potential for development is limited due to the lower number of available spaces, while the Ouzonnian building is in an arguably compromised location due to noise and pollution, but it has high traffic and more available spaces considering the BUA and the surrounding amenities, services, and high tourist presence in downtown Cairo compared to Alexandria.\n\nThe radial diagram in Figure 26 shown above demonstrates the evaluation of the three buildings stacked on top of each other, showing the strengths and weaknesses of each parameter and how it compares to the remaining buildings. This diagram represents a tool that has a high potential for being utilized by investors and producers aiming to identify the most efficient investment, as it shows which building is most suitable considering the requirements of the developers or target users. This diagram helps investors formulate a brief idea about each building and decide which one would be worth the investment or which ones have a higher priority for acquisition. Finally, this diagram shows the common area where the three buildings all intersect, which defines the minimum or average values a heritage building must have in order to be considered for AR projects. For example, all of the buildings have a medium to high value considering the location, accessibility, architectural description, and surrounding context, while other values vary considerably between the buildings.\n\nSource: Author, 2023.\n\nAs the final step for this evaluative approach, the researcher applies the developed method to the designated case studies in order to apply the four-step decision-making framework as shown in Table 7 to identify the potential functions that could be introduced in each building, as well as the scale, type, and category of each function.\n\nSource: Author, 2023.\n\nTable 7 demonstrates the outcome of the final step of the evaluation process as an example that could potentially be applied to different buildings and cases in any adaptive reuse project, whether in Egypt or anywhere else. Depending on the building and its context, and the previously described parameters, those parameters form the main framework that any developer or stakeholder could utilize as a guideline for evaluating different buildings and deciding on whether the investment is feasible, in deciding what to invest in considering the building in general and the acquisitions within the building itself, also decide on the possible functions that could be introduced and the scale, type, and category of each of those functions. This evaluation also provides a detailed analysis of any building, as this analysis was the basis on which the researcher performed the final decision-making steps and provides a brief assessment of a building that could be presented to potential investors and other producers.\n\nThroughout this research, the author determines that not all developments are required to incorporate all of the aforementioned components to form a balanced mixed-use development, but some minor functions can always be special and designated to certain destinations and hubs in order to form a healthy fabric on the urban scale and to give each property a certain edge over other properties and developments and also to maintain this cohesive network formed between buildings and each other in an area where functions complete and complement each other, the users could feel that the experience is timeless, doesn’t grow old or obsolete after a short time, and is self-sufficient, and developers always see adaptive reuse as a sustainable investment.\n\nFurthermore, the researcher concludes that in the adaptive reuse industry, the role of different stakeholders such as the designer’s, has grown and evolved into a more holistic, multidisciplinary role that requires major knowledge in various fields; understanding the financial aspects of every project, such as the required budget and feasibility, is of critical importance to ensure a higher success rate for the project (Drivers, 2013). Also, having a basic understanding of the legal aspects of development and acquisition of assets and spaces is important, as it has an impact on decision-making and the selection of functions, which then has an impact on the design approach (Bottero et al., 2019). Finally, property management teachings are fundamental in order to create successful programs, considering each function that was decided to be part of the component mix. All of the aforementioned disciplines have direct implications and influence most, if not all, of the design decisions in the adaptive reuse of heritage buildings and mixed-use developments.\n\n\nConclusions\n\nThe researcher provides those findings as an extension to previous research and literature produced by other studies and aims that this study could assist other researchers and stakeholders involved in the industry with developing a brief understanding and knowledge based on practical experience in the adaptive reuse field, especially in developing countries. This research could potentially be a stepping-stone for the creation of a more developed and advanced method of evaluating heritage buildings and an innovative tool for decision-making parameters that could be resourcefully utilized by regulators and other stakeholders, ultimately for the goal of saving the remaining heritage that has been deteriorated, and in many cases lost, due to the negligence and ignorance of its value to the community and the cities they live in.", "appendix": "Data availability\n\nThe data from this study was provided from Sigma properties and all information about the buildings presented in the case studies including historical and present day photos of the buildings’ exterior and interior, floor plans, and drawings are included in the underlying and extended data alongside the results of this study with permission from Sigma. However, financial data underlying this study including financial figures and budgets is restricted as it is considered confidential information by the supplying entity.\n\nThe author explains the restrictions on the data obtained from a third party as follows:\n\n• Detailed historical data for buildings, such as drawings and ownership documents\n\n• Detailed project packages, such as tendering and design packages\n\n• Financial data and statistics for completed projects or budgets for upcoming projects.\n\nIn order to access any of the aforementioned restricted data from the third party (Sigma Properties), a company representative shall be contacted via email at m.fathy@sigmaproperties.net with the required information along with the institution or organization details, and the reason for the request for access and information shall be provided accordingly. Alternatively, the author shall be contacted via correspondence email at ar.mohanned.selim@gmail.com for assistance with the supply of any information and coordination. The company withholds the right to refuse to disclose detailed financial information if deemed to cause a conflict of interest.\n\nIn order to access the data obtained from the third party (Sigma Properties), the company’s website, http://sigmaproperties.net/, or the website, https://www.coterie-eg.com/, which represents the company’s development arm, should provide any publicly available data and general information regarding the properties, such as photos, historical background, architect information, and building features and spaces. Any reuse of the figures and photos used in this study must receive permission from Sigma Properties. Another means to access necessary information and intermediary data is by contacting the aforementioned company representative through email at m.fathy@sigmaproperties.net or through the author via the correspondence address ar.mohanned.selim@gmail.com.\n\nMendeley data: The revitalization of endangered heritage buildings in developing countries: A Decision-making framework for investment and determining highest and best use in Egypt. https://doi.org/10.17632/998c7bf8jh.1. (Selim, 2023).\n\nThis dataset contains the following underlying data:\n\n• Avierino building (case study 1). (Data for case study 1 used in this study including layout, developments, figures, and photos).\n\n• Little Venice building (case study 2). (Data for case study 2 used in this study including layout, developments, figures, and photos).\n\n• Ouzonnian building (case study 3). (Data for case study 3 used in this study including layout, developments, figures, and photos).\n\n• Axonometric diagrams for 3 case studies (source). (Axonometric diagrams for the 3 case studies and their sources).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nMendeley data: The revitalization of endangered heritage buildings in developing countries: A Decision-making framework for investment and determining highest and best use in Egypt. https://doi.org/10.17632/998c7bf8jh.1. (Selim, 2023).\n\nThis dataset contains the following extended data:\n\n• MAPS (photoshop source). (Maps of all locations in this study including source data).\n\n• Research figures & tables. (All figures and tables included in this manuscript).\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 author wishes to thank all the individuals who assisted in bringing this manuscript to life. Those persons have helped provide the author with the required data as well as motivation and encouragement to complete this study, from family members to work colleagues and friends. Also, special thanks to the professors and co-authors for their unconditional support and guidance throughout the process.\n\n\nReferences\n\nAbdeen N, Ahmed S: Reusing historical buildings as a reference to conservation. MSc thesis, Faculty of Engineering, Cairo University, 2009.2009.\n\nAigwi IE, Egbelakin T, Ingham J, et al.: A performance-based framework to prioritise underutilised historical buildings for adaptive reuse interventions in New Zealand. Sustain. Cities Soc. 2019; 48: 101547. Publisher Full Text\n\nAplin G: Heritage: Identification, Conservation, and Management. Melbourne: Oxford University Press; 2002.\n\nAwad MF: Italy in Alexandria: Influences on the Built Environment. Alexandria, Egypt: Alexandria Preservation Trust; 2008.\n\nBond C: Adaptive reuse: Explaining collaborations within a complex process (Master’s thesis, University of Oregon).2011. Reference SourceReference Source\n\nBottero M, D’Alpaos C, Oppio A: Ranking of Adaptive Reuse Strategies for Abandoned Industrial Heritage in Vulnerable Contexts: A Multiple Criteria Decision Aiding Approach. Sustainability. 2019; 11(3): 785. Publisher Full Text\n\nBrandt M: How to adaptively reuse a community asset? Heritage: the Magazine of the Heritage Canada Foundation. 2006; 9(2): 21–22.\n\nBrowne LA: Regenerate: reusing a landmark building to economically bolster urban revitalization, Master’s Thesis, University of Cincinnati, OH.2006.\n\nBullen P: Adaptive reuse and sustainability of commercial buildings. Facilities. 2007; 25: 20–31. Publisher Full Text\n\nChung T: Valuing Heritage in Macau: On Contexts and Processes of Urban Conservation. J. Curr. Chin. Aff. 2009; 38(1): 129–160. Publisher Full Text\n\nDepartment of Environment and Heritage: Adaptive Reuse, Commonwealth of Australia.2004.\n\nDrivers J: Heritage Works. The use of historic buildings in regeneration. A toolkit of good practice. London: British Property Foundation; 2013.\n\nElsorady D: Adaptive Reuse Decision Making of a Heritage Building Antoniadis Palace, Egypt. Int. J. Archit. Heritage. 2020; 14(5): 658–677. Publisher Full Text\n\nFreund de Klumbis DF, Munsters W: Developments in the hotel industry: Design meets historic properties.Sigala M, Leslie D, editors. International cultural tourism. Oxford: Butterworth-Heinemann; 2005; pp. 26–39.\n\nGiles G: Adaptive reuse in an urban setting: evaluating the benefits of reusing an existing building site in Florida for maximum profit potential and eco-effectiveness. Environ. Des. Constr. 2005; 8(3): 72.\n\nGodwin P: Building Conservation and Sustainability in the United Kingdom. Procedia Eng. 2011; 20: 12–21. Publisher Full Text\n\nInnes JE, Booher DE: Planning with complexity: an introduction to collaborative rationality for public policy. Routledge; 2010.\n\nKohler N, Hassler U: The building stock as a research object. Build. Res. Inf. 2002; 30: 226–236. Publisher Full Text\n\nMegahed MTM: Scientific documentation for the historical palaces before the conservation. MSc Thesis, Minya University, Egypt.2009.\n\nMenassa CC, Baer B: A framework to assess the role of stakeholders in sustainable building retrofit decisions. Sustain. Cities Soc. 2014; 10: 207–221. Publisher Full Text\n\nMerlino KR: Building Reuse: Sustainability, Preservation, and the Value of Design. University of Washington Press; 2018. Reference Source\n\nMısırlısoya D, Günc K: Adaptive reuse strategies for heritage buildings: A holistic approach. Sustain. Cities Soc. 2016; 26: 91–98. Publisher Full Text\n\nMubarak A: El Khitat el Tewfikieh el Guidida. Vol. 7. . Cairo, Egypt: Great Amiria Press of Boulaq; 1989.\n\nNOUH (National Organization for Urban Harmony): Listed Touristic Buildings in Alexandria East District. (Accessed December 11, 2022). Reference Source\n\nNSW Department of Planning and RAIA: New uses for heritage places: guidelines for the adaptation of historic buildings and sites. Parramatta: Heritage Council of New South Wales; 2008.\n\nPower A: Does demolition or refurbishment of old and inefficient homes help to increase our environmental, social and economic viability? Energy Policy. 2008; 36: 4487–4501. Publisher Full Text\n\nRabun S, Kelso R: Building evaluation for adaptive reuse and preservation. Hoboken, NJ: John Wiley and Sons; 2009.\n\nRibera F, Nesticò A, Cucco P, et al.: A Multicriteria Approach to Identify the Highest and Best Use for Historical Buildings. J. Cult. Herit. 2020; 41: 166–177. Publisher Full Text\n\nSaid L: Heritage and Nationalism in Nasser’s Egypt, the Case of Belle Epoque Alexandria. Edinburgh, UK: Scottish Centre for Conservation Studies, The University of Edinburgh; 2016.\n\nSelim M: The revitalization of endangered heritage buildings in developing countries: A Decision-making framework for investment and determining highest and best use in Egypt. Dataset. Mendeley Data. 2023; V1. Publisher Full Text\n\nSerageldin I: Very special places: The architecture and economics of intervening in historic cities, Bibliotheca Alexandria with the World Bank.2002.\n\nShankland G: Why trouble with historic towns? The conservation of cities, UNESCO. Paris: UNESCO Press; 1975; pp. 24–42.\n\nSteinberg F: Conservation and Rehabilitation of Urban Heritage in Developing Countries. Habitat Int. 1996 September; 20(3): 463–475. Publisher Full Text\n\nWang H-J, Zeng Z-T: A multi-objective decision making process for reuse selection of historic buildings. Expert Syst. Appl. 2010; 37(2): 1241–1249. Publisher Full Text\n\nWillson GB, Mcintosh AJ: Heritage Buildings and Tourism: An Experiential View. J. Herit. Tour. 2007; 2: 75–93. Publisher Full Text\n\nYung E, Chan E: Implementation challenges to the adaptive reuse of heritage buildings: Towards the goals of sustainable, low carbon cities. Habitat Int. 2012; 36: 352–361. Publisher Full Text" }	[ { "id": "198498", "date": "04 Sep 2023", "name": "Waled Shehata", "expertise": [ "Reviewer Expertise Heritage Adaptive Reuse-Uncomfortable heritage-Historic Cairo-Heritage Conservation and Management in NSW", "Australia" ], "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 reviewer would like to thank the authors of this paper. The selected topic is much needed in Egypt where, indeed, heritage gets delisted and demolished, or undergo destructive conservation works under the miserable State-branded ‘development’.\nThe research objective which is to develop a framework for heritage adaptive reuse project to increase chances of achieving economically viable developments and best use is a noble objective. However, the intent is lost due to many strategic issues as listed below.\nStrategic issues:\nThe targeted heritage buildings’ category(ies) for this study is not specified. For instance, does it target those listed as monument of Ministry of Tourism and Antiquities, National Organisation for Urban Harmony (NOUH), and/or other identified to have heritage significance by heritage specialists…etc. Different grade of listings of heritage buildings in Egypt have different acceptable levels of intervention for their adaptive reuse, conservation and management. The three selected case studies are also in different regions in Egypt and are of different construction periods and styles. Heritage buildings’ size, level of significance, age and construction system would most likely limit the effectiveness of this framework. It is of high importance for this framework to be sound is to specifically target a group of heritage buildings of homogeneous characteristics. Otherwise if the authors intend to exclusively target heritage buildings such as those already examined, their common characteristics needs to be clearly spelled out (i.e. multi-storey, concrete structural system, listed in NOUH…etc) while providing a short background on the statutory requirements/challenges for their reuse in the Egyptian heritage planning laws according to their listing(s). Once this is done, the research intent would be clearer and the framework would be better targeted and usable.\nThe references are relatively old. With only a couple of references published in 2019–which is still not very recent, most references range between 2005-2016. Referring to recent literature is imperative and I am certain would greatly assist refine the article and the proposed framework.\nThe research aim is not well formulated. Using references in the objective is not justified. The objective should be in your own words unless these references recommend such objective, something that need to be spelled out to be clear. Additionally, please use shorter sentences to be understandable. Once this is done, the objective would sound more focused and achievable.\nSome terms suddenly pop-up in the article without proper explanation or if they were used in literature. Terms and assessable factors which suddenly appear in the article include ‘highest and best use’, ‘function, type, category and scale’, ‘success of mixed-use developments’ and others. The research readily perceive some of these factors as a virtue/advantage but without supporting this argument with one sentence or a credible reference.\nIn P4, the authors wrote: ‘completed adaptive reuse (AR) scenarios’. ‘Completed’ here is very vague. Do the authors mean the work is completed, or the buildings are operational, …etc. Also this instance is the first use of the word ‘scenarios’, which confuses the readers. You may need to carefully choose the terms you use in the article to be connected to the flow of ideas and consistent throughout the article.\n\nThe second paragraph in page 4 explains a usual process of architectural project planning and redevelopment with only a few minor mention to heritage AR peculiarities here and there. I believe it would be more space saver if the authors bluntly say that heritage AR projects are similar to any other architecture refurbishment project with the differences of x,y and z. Multiple refurbishment project processes are also noted in page 11 being Tender and contractor selection and Operation and evaluation, which are irrelevant to the article’s objective and can be eliminated without the slightest effect the quality of the framework.\nThe amount of surveyed literature does not match the intended purpose. To generate a working and valid framework, one usually need to examine a considerable number of literature. Such survey would lead to deducing and\\or inducing a number of factors that are relevant to the research objective. These are referred to here as ‘parameters’. To help the authors in their literature review, they may consider these questions: Are these parameters dependant or independent variables? What primary sources support them being important enough to be considered in this research? What do the authors mean by ‘different’ contemporary literature? How different these literature are classified?…etc.\nI strongly recommend undertaking a targeted literature review (LR) on the success factors of similar projects of heritage adaptive reuse in Egypt while revising this research. The volume of research already existing on this topic in Egypt is enormous and I am certain it will better inform this research. I am aware most of them are not free on the web, but please consider reaching out for assistance if the AASTMT does not provide access to researchers. A LR in the first section of this article would better inform gaps in adaptive reuse process which would enable your research outcome to be more sound.\nThe reason three case studies were selected is not mentioned except in page 33 where the article is closing up. The intent need to be mentioned much earlier, nonetheless, it needs to be well articulated. If these case studies are used to evaluate the framework, you need to explain if these case studies are representative of the heritage buildings in Egypt, why were they are used to test the framework, and other reasons for their selection. Each reason may then require different handling of the case studies and the way their data is analysed and presented. Clearly defining the reason these case studies were selected and formulating the discussion accordingly is crucial to achieve the validity and applicability of the proposed framework.\nAlso related to the previous point, the research mentioned: “projects were utilised by the researcher as a reference due to multiple factors such as functional and economic viability, preservation of heritage value, community engagement and stakeholder collaboration, and finally, the recognition of the local community.” How did they achieve this to be selected at the first place? What literature including media and news shared this point of view? More clarification is required.\nAdditionally, I would argue that selection of three case studies by the same developer (Sigma properties) highly reduces confidence in the generalisability of the proposed framework. Selecting all projects that are realised by the same developer fails to put the framework in test in adaptive reuse projects done by other types of project-driving stakeholders such as government entities-which, by virtue, should target economic viability, international and national cultural institutions—such as Bibliotheca Alexandria… and others.\nThe generalisability of the research is highly questionable. Cairo and Alexandria neither represent Egypt nor the case studies represent developing countries. More careful consideration while referring to the locality of study would be useful, such as simply focusing on Cairo, Alexandria or both, and removing ‘developing countries’ and ‘Egypt’ from the article including the title. Of course, every choice would require changes in the body of the article to best respond to the research focus.\nIn the conclusion, the authors used a bit harsh statements such as “ignorance … to the community”. Kindly revise.\nLong sentences in the conclusion are unclear and ambiguous. Kindly rewrite.\nIn page 4, ‘unique features’ is not a common term in heritage conservation field. Perhaps you need to refer to Assessing heritage significance: Guidelines for assessing places and objects against the Heritage Council of NSW criteria to familiarise yourself with the terms used in the context of heritage AR. Reference link: https://www.environment.nsw.gov.au/-/media/OEH/Corporate-Site/Documents/Heritage/assessing-heritage-significance-guidelines-assessing-places-objects-against-criteria-230167.pdf\nIn page 29, rewrite the 4th paragraph to be understandable and clearer.\nLast but not least, the academic English used is not consistent and some of the terms are not clear, i.e. Target market and the use of past tenses in many occurrences. Nonetheless, long sentences lose their objective and turn to vague statements. The writing style is literal translation from Arabic, something that requires experienced rewriting of many sections of the article.\n\nMinor issues:\nI was hoping that the authors would consider clarifying what would be the impact of an architectural competition for the design of the AR would make on the framework, if any.\nThe article is considerably lengthy. Consider removing unnecessary sections such as: Students and educators versions of programs, free alternative software suggestions, list of abbreviations (you can just use abbreviation following first mention of the full term), Tendering and Contractor Selection Operation and Evaluation as well as other conventional project phases.\nIn Table 1, consider adding Public transport to the Diverse modes of transport.\nAlso consider combining Architectural description and Spatial characteristics.\nConsider using Space Syntax for analysing the spatial layouts and functional programs for the AR of the heritage buildings. Space Syntax may contribute to the quality of the functional usability of the buildings.\nIn the Maps prepared for the case studies, it is imperative to provide a scale. Alternatively, you may use walkability distances via annotated rings/circles. This is important to assist readers understand the sites’ proximity to elements of the urban surroundings. You may also consider distinguishing the location of the case study building with a different colour and providing a map key.\nIn Table 2, kindly elaborate on the impact of whether the building being heritage listed.\nIn page 4, how does Merlino 2018 explain your own preferences of the selected case studies. Kindly revise this section.\nIn the first sentence in the conclusion, kindly explain ‘those’ findings.\n\nIs the background of the case’s history and progression described in sufficient detail? No\n\nIs the work clearly and accurately presented and does it cite the current literature? 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? Yes\n\nAre the conclusions drawn adequately supported by the results? No\n\nIs the case presented with sufficient detail to be useful for teaching or other practitioners? Partly", "responses": [ { "c_id": "10554", "date": "19 Dec 2023", "name": "Mohanned Selim", "role": "Author Response", "response": "The authors would like to thank you for your valuable input and careful inspection of this research, your effort is much appreciated. Strategic issues: The targeted heritage buildings’ category(ies) for this study is not specified. For instance, does it target those listed as monument of Ministry of Tourism and Antiquities, National Organisation for Urban Harmony (NOUH), and/or other identified to have heritage significance by heritage specialists…etc. Different grade of listings of heritage buildings in Egypt have different acceptable levels of intervention for their adaptive reuse, conservation and management. The three selected case studies are also in different regions in Egypt and are of different construction periods and styles. Heritage buildings’ size, level of significance, age and construction system would most likely limit the effectiveness of this framework. It is of high importance for this framework to be sound is to specifically target a group of heritage buildings of homogeneous characteristics. Otherwise if the authors intend to exclusively target heritage buildings such as those already examined, their common characteristics needs to be clearly spelled out (i.e. multi-storey, concrete structural system, listed in NOUH…etc) while providing a short background on the statutory requirements/challenges for their reuse in the Egyptian heritage planning laws according to their listing(s). Once this is done, the research intent would be clearer and the framework would be better targeted and usable. Regarding the listing of the buildings, the indication of this has been added to the introduction section of the comparative analysis and a justification of this has been explained as follows: the first two cases of Avierino and Little Venice are listed as heritage type B which means that those assets are protected by law and indicates that interior modifications are permissible while maintaining the exterior facades, as for Ouzonnian building, it is not listed as heritage but this is justified by its historical/cultural significance which is evident through its architecture, architect, and context. This building was once argued to be the tallest building in downtown Cairo due its modern construction techniques which were considerably new during the time of construction, also Sayed Karim, the architect, was one of the leading figures in the field of Architecture in Egypt, the building has many stories and plays part in the narrative that represents the spirit of downtown Cairo. The justification in this is that the importance and significance of such buildings does not always have to be justified by their listing as heritage which has been evident through the years were heritage buildings with outstanding importance and significance were deteriorated and demolished due to their removal from the heritage listing or due to their nonexistence in the first place. Finally, regarding the justification for selecting the aforementioned buildings, this was based on the fact that the author has worked on the development of those buildings personally alongside a team of experts in the field, which perhaps needed to be clarified in the paper, also the selection of buildings with variable architectural styles, design, components, context, and location, was argued by the authors to add more validation to the framework being applicable to different buildings and producing successful results which were evident in those 3 cases considering revenues (indicated in the last section of each case), asset value, historical and cultural significance. The references are relatively old. With only a couple of references published in 2019–which is still not very recent, most references range between 2005-2016. Referring to recent literature is imperative and I am certain would greatly assist refine the article and the proposed framework. The authors agree that this is of great importance to this study and more recent literature has been referenced in the article, many of which were related to framework development as advised. The references are as follows: Albu, S. 2021. The Economic Value and Valuation of Architectural Heritage. Journal of Building Construction and Planning Research, 9, 1-11. DOI: 10.4236/jbcpr.2021.91001. Available from: https://doi.org/10.4236/jbcpr.2021.91001. Armstrong, G., Wilkinson, S., & Cilliers, E. 2023. A framework for sustainable adaptive reuse: understanding vacancy and underuse in existing urban buildings. Frontiers in Sustainable Cities, 5. DOI: 10.3389/frsc.2023.985656. Fitri, I., Siregar, F., Silvana, S., Ariffin, N., Ginting, R., & Indira, S. 2023. An Adaptive Reuse Development Through Highest and Best Use Assessment: Case Study the Ex-Warenhuis, Medan, Indonesia. IOP Conference Series: Earth and Environmental Science, 1188, 012045. DOI: 10.1088/1755-1315/1188/1/012045. Hamida, M. 2020. Development of a Framework for the Effective Implementation of Building Adaptive Reuse throughout the Project Life-Cycle in Saudi Arabia. DOI: 10.13140/RG.2.2.15488.35840. Haroun, H., Bakr, A., & Hasan, A. 2019. Multi-criteria decision making for adaptive reuse of heritage buildings: Aziza Fahmy Palace. Alexandria University Alexandria Engineering Journal. NSW Environment. 2022. Investigating Heritage Significance [online]. NSW Environment. Available from: https://www.environment.nsw.gov.au/research-and-publications/publications-search/investigating-heritage-significance [Accessed 06 Oct 2023]. NSW Government. 2021. Investigating Heritage Significance: A guide to identifying and examining heritage items in NSW. NSW Government through the Heritage Council of NSW. Pasha, C., Dewi, C., & Djamaludin, M. 2021. Adaptive reuse of old houses as coffee shop: Environmental and spatial aspects. IOP Conference Series: Earth and Environmental Science, 881, 012046. DOI: 10.1088/1755-1315/881/1/012046. Vehbi, B.O., Günçe, K., & Iranmanesh, A. 2021. Multi-Criteria Assessment for Defining Compatible New Use: Old Administrative Hospital, Kyrenia, Cyprus. Sustainability, 13, 1922. DOI: 10.3390/su13041922. The research aim is not well formulated. Using references in the objective is not justified. The objective should be in your own words unless these references recommend such objective, something that need to be spelled out to be clear. Additionally, please use shorter sentences to be understandable. Once this is done, the objective would sound more focused and achievable. References were removed from the objective as advised and the sentences were made shorter for legibility. Some terms suddenly pop-up in the article without proper explanation or if they were used in literature. Terms and assessable factors which suddenly appear in the article include ‘highest and best use’, ‘function, type, category and scale’, ‘success of mixed-use developments’ and others. The research readily perceive some of these factors as a virtue/advantage but without supporting this argument with one sentence or a credible reference. Explanation for those terms has been added to the Methods section when first mentioned as advised, and their virtue/advantage has been supported as well. In P4, the authors wrote: ‘completed adaptive reuse (AR) scenarios’. ‘Completed’ here is very vague. Do the authors mean the work is completed, or the buildings are operational, …etc. Also this instance is the first use of the word ‘scenarios’, which confuses the readers. You may need to carefully choose the terms you use in the article to be connected to the flow of ideas and consistent throughout the article. Yes, the authors mean that the proposed adaptive reuse models developed through the framework are evidently successful based on the fact that they have applied the AR model and provided significant revenues and returns, on Investment and on Asset, and they repositioned the buildings’ significance to the community. This has been explained in the article as advised and the word scenarios was changed to models to avoid confusion. The second paragraph in page 4 explains a usual process of architectural project planning and redevelopment with only a few minor mention to heritage AR peculiarities here and there. I believe it would be more space saver if the authors bluntly say that heritage AR projects are similar to any other architecture refurbishment project with the differences of x,y and z. Multiple refurbishment project processes are also noted in page 11 being Tender and contractor selection and Operation and evaluation, which are irrelevant to the article’s objective and can be eliminated without the slightest effect the quality of the framework. The aforementioned processes were explained in the article as phases of the Adaptive Reuse project from start to finish, or delivering the project and evaluating its operation, and while the tendering and contractor selection phase might indeed be irrelevant but the operation phase was justified by the authors as this is when the projects’ performance undergoes evaluation and assessment which provides feedback and proof of the framework’s success, or failure. Please advise if this is not valid. The amount of surveyed literature does not match the intended purpose. To generate a working and valid framework, one usually need to examine a considerable number of literature. Such survey would lead to deducing and\\or inducing a number of factors that are relevant to the research objective. These are referred to here as ‘parameters’. To help the authors in their literature review, they may consider these questions: Are these parameters dependant or independent variables? What primary sources support them being important enough to be considered in this research? What do the authors mean by ‘different’ contemporary literature? How different these literature are classified?…etc. These parameters are evaluated independently based on the sub-parameters as seen in Table 1, however they are dependent since they are treated as a collective of variables forming an overall general evaluation grade as seen in Table 6. The term ‘different’ indicates different types of sources (Primary, secondary, and tertiary sources) but this term was removed due to being unnecessary. I strongly recommend undertaking a targeted literature review (LR) on the success factors of similar projects of heritage adaptive reuse in Egypt while revising this research. The volume of research already existing on this topic in Egypt is enormous and I am certain it will better inform this research. I am aware most of them are not free on the web, but please consider reaching out for assistance if the AASTMT does not provide access to researchers. A LR in the first section of this article would better inform gaps in adaptive reuse process which would enable your research outcome to be more sound. Your assistance in this matter, if convenient, would be much appreciated as several literature was indeed reviewed however many of the examined open-source data was irrelevant, if it would be possible to recommend some of the sources you mentioned or help with access it would be of immense support. The reason three case studies were selected is not mentioned except in page 33 where the article is closing up. The intent need to be mentioned much earlier, nonetheless, it needs to be well articulated. If these case studies are used to evaluate the framework, you need to explain if these case studies are representative of the heritage buildings in Egypt, why were they are used to test the framework, and other reasons for their selection. Each reason may then require different handling of the case studies and the way their data is analysed and presented. Clearly defining the reason these case studies were selected and formulating the discussion accordingly is crucial to achieve the validity and applicability of the proposed framework. The authors agree that this is necessary for the validity of the proposed framework, and this has been applied and explained in the first question in this document. The authors tried their best to achieve this as advised, nevertheless, the argument of making this study/framework as simplified as possible, which was one of the main goals of this article, to facilitate and simplify the redevelopment of heritage assets in Egypt and present a legible guide for different stakeholders who have the potential of making change. Please advise if you require any further clarification or changes. Also related to the previous point, the research mentioned: “projects were utilised by the researcher as a reference due to multiple factors such as functional and economic viability, preservation of heritage value, community engagement and stakeholder collaboration, and finally, the recognition of the local community.” How did they achieve this to be selected at the first place? What literature including media and news shared this point of view? More clarification is required. As for functional and economic viability, the successful operation and revenues provided by those projects was one of the main reasons for selection, however, the financial data was not permissible for disclosure in this research and are confidential to the developer but were shared with the author. Preservation of heritage value was achieved through the restoration and preservation of original designs and features, and through how those projects highlighted the history of the building, its tenants, and the architect. Community engagement and Recognition of the community was achieved through the traffic visiting those buildings and engagement in various events, exhibitions, and tours. Also, research and documentation performed by various researchers and experts in the field. Stakeholder collaboration was achieved through working along experts such as consultants, operators, investors, and designers in the preparation, execution, and operation phases of those projects. This wasn’t clarified in detail throughout the article to avoid making it longer than it is but was indicated by the authors for possible inquiry by interested persons or researchers through contacting the corresponding author or the owner / developer (Sigma Properties, Coterie). Additionally, I would argue that selection of three case studies by the same developer (Sigma properties) highly reduces confidence in the generalisability of the proposed framework. Selecting all projects that are realised by the same developer fails to put the framework in test in adaptive reuse projects done by other types of project-driving stakeholders such as government entities-which, by virtue, should target economic viability, international and national cultural institutions—such as Bibliotheca Alexandria… and others. The reason behind this is that the author was part of the team that worked on the redevelopment of those 3 buildings, the authors believe that this hands-on experience and professional involvement actually adds more credibility and an accurate view and assessment of the performance of those AR projects. I completely agree that this creates some kind of conflict and that was a point of discussion when preparing this article, but the authors came to an agreement that the aforementioned role of the author adds to the validity and practicality in which this study was based on. The generalisability of the research is highly questionable. Cairo and Alexandria neither represent Egypt nor the case studies represent developing countries. More careful consideration while referring to the locality of study would be useful, such as simply focusing on Cairo, Alexandria or both, and removing ‘developing countries’ and ‘Egypt’ from the article including the title. Of course, every choice would require changes in the body of the article to best respond to the research focus. The authors agree that this is indeed questionable; the author added to the conclusion as part of the recommendations that the proposed framework has the potential of application in developing countries or other contexts where AR is required or studied, however this has not been tested or proven successful in different contexts so this would need to be tested first, and future research could modify or add to the proposed framework in order to suit said different contexts. Regarding the title, I’m not sure if I have the ability to change as per F1000 guidelines but I will attempt to make this change. In the conclusion, the authors used a bit harsh statements such as “ignorance … to the community”. Kindly revise. This has been revised and the term was changed to “unawareness”. Long sentences in the conclusion are unclear and ambiguous. Kindly rewrite. This has been rewritten as advised. In page 4, ‘unique features’ is not a common term in heritage conservation field. Perhaps you need to refer to Assessing heritage significance: Guidelines for assessing places and objects against the Heritage Council of NSW criteria to familiarise yourself with the terms used in the context of heritage AR. Reference link: https://www.environment.nsw.gov.au/-/media/OEH/Corporate-Site/Documents/Heritage/assessing-heritage-significance-guidelines-assessing-places-objects-against-criteria-230167.pdf This has been revised and the term was changed to ‘fabric’ as advised based on the provided reference. In page 29, rewrite the 4th paragraph to be understandable and clearer. This paragraph has been rewritten as advised. Last but not least, the academic English used is not consistent and some of the terms are not clear, i.e. Target market and the use of past tenses in many occurrences. Nonetheless, long sentences lose their objective and turn to vague statements. The writing style is literal translation from Arabic, something that requires experienced rewriting of many sections of the article. The aforementioned unclear terms have been clarified or modified wherever possible but please advise if this still needs revision. Please note that the author’s background must definitely have some kind of influence on the writing style, knowing that the use of translating services (such as Google Translate) of paragraphs or parts of this study was never done, translations of some Arabic terms or words has, but never to full sentences or paragraphs. Please let us know if there are any other critical issues to any specific paragraph which requires rewriting, aside from the ones you requested in the reviewer report as those were rewritten, unless they require further modifications. Minor issues: I was hoping that the authors would consider clarifying what would be the impact of an architectural competition for the design of the AR would make on the framework, if any. This will be analyzed in depth in future studies. However, a competition as such would definitely have an impact on the developed framework as it would provide valuable feedback concerning design aspects and it would provide valuable insight on the developed parameters and potential modifications or additions when assessing the produced projects. The article is considerably lengthy. Consider removing unnecessary sections such as: Students and educators versions of programs, free alternative software suggestions, list of abbreviations (you can just use abbreviation following first mention of the full term), Tendering and Contractor Selection Operation and Evaluation as well as other conventional project phases. The sections you mentioned are required by F1000 so I believe it won’t be possible to remove them as the editors specifically requested their addition. As for project phases, this was explained previously but please advise if invalid. In Table 1, consider adding Public transport to the Diverse modes of transport. Public transport is indeed the most important factor in this sub-parameter, which was indicated through the case studies analysis, but this will be indicated in the table as advised. Also consider combining Architectural description and Spatial characteristics. Both of those parameters were differentiated by the authors as follows: The Architectural Description represents all that is related to the architectural aspects of the building such as the style influenced by the design features and ornaments, the listing of the building and the condition of said features, the architect and the story of the property or narrative derived from the history of the surrounding context in relation to the aforementioned elements. On the other hand, the Spatial Characteristics parameter indicates items related to the structural system and its condition, the availability of spaces within the building, whether this building is fully empty or if it has specific floors or units that are available, and this availability differs as demonstrated in the axonometric diagrams in the case studies analysis, and finally the spatial limitations such as the heights, sizes of openings, and court areas. Consider using Space Syntax for analysing the spatial layouts and functional programs for the AR of the heritage buildings. Space Syntax may contribute to the quality of the functional usability of the buildings. This will be studied and any information with regards to the mentioned technique would be valuable. In the Maps prepared for the case studies, it is imperative to provide a scale. Alternatively, you may use walkability distances via annotated rings/circles. This is important to assist readers understand the sites’ proximity to elements of the urban surroundings. You may also consider distinguishing the location of the case study building with a different colour and providing a map key. The building is currently indicated with a different color to easily distinguish it. Adding walkability distances was not feasible due to technical difficulties. In Table 2, kindly elaborate on the impact of whether the building being heritage listed. This elaboration has been added to the architectural description parameter as advised. In page 4, how does Merlino 2018 explain your own preferences of the selected case studies. Kindly revise this section. The intention here is referring to Merlino’s approach in selecting the case studies, Merlino selected the case studies in his study based on various factors and the authors followed a similar approach. In the first sentence in the conclusion, kindly explain ‘those’ findings. ‘Those’ refers to the developed framework and the parameters forming the evaluation model." } ] }, { "id": "202843", "date": "19 Sep 2023", "name": "Tianchen Dai", "expertise": [ "Reviewer Expertise Architecture", "urban studies", "cultural heritage", "city branding" ], "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 very interesting article that provides a framework for developing legacy assets and investment criteria to help investors, designers and stakeholders prepare projects and measure their performance. It is always difficult to combine architectural practice with research, and this study demonstrates a nice attempt.\nI have a couple of minor suggestions to help improve the quality of this paper before it is ready for indexing:\nThe introduction is rather brief. The authors should extend this section substantially with a thorough literature review and background on this study. The aims and objectives of the study can be incorporated into the Introduction.\n\nSome very long sentences should be cut into shorter ones or rewritten. For example, the last sentence in Section 'Research aims and objectives.\n\nIn Table 1, the developed parameters and sub-parameters are listed by the authors. It would be more convincing to explain more about how these parameters were developed, based on rigorous literature reviews or preliminary studies.\n\nConsidering Table 3, where is the data to support the results in this table? The authors should clearly show the analysis procedure, if not in the main section, at least in the appendix.\n\nIs the background of the case’s history and progression described in sufficient detail? No\n\nIs the work clearly and accurately presented and does it cite the current literature? 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? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes\n\nIs the case presented with sufficient detail to be useful for teaching or other practitioners? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-874
https://f1000research.com/articles/12-154/v1	10 Feb 23	{ "type": "Brief Report", "title": "Comparison of oral iron chelators in the management of transfusion-dependent β-thalassemia major based on serum ferritin and liver enzymes", "authors": [ "Sulaiman Yusuf", "Heru Noviat Herdata", "Eka Destianti Edward", "Khairunnisa Khairunnisa", "Heru Noviat Herdata", "Eka Destianti Edward", "Khairunnisa Khairunnisa" ], "abstract": "Background: Excess iron deriving from a chronic transfusion and dietary intake increases the risk for cardiac complications in β-thalassemia major patients. Deferiprone and deferasirox are commonly prescribed to thalassemic patients who are at risk of iron overload. This study aimed to compare the performance and toxicity of deferiprone and deferasirox in β-thalassemia major patients. Methods: A cross-sectional observation was performed on 102 patients with β-thalassemia major. Serum ferritin along with total, indirect, and direct bilirubin levels were measured. Levels of liver enzymes, transaminase (ALT), and aspartate transaminase (AST), were also determined. Ferritin correlations with serum ALT, AST, and total bilirubin were constructed based on Spearman’s rank correlation. Statistical differences based on the serum parameters were analyzed between deferiprone and deferasirox groups. The differences of iron chelators’ effects between those receiving short-term (≤7 years) and long-term (>7 years) blood transfusion were also analyzed. Results: The averaged levels of bilirubin, ALT, AST, and ferritin were found to be high. Ferritin was positively correlated with ALT (r=0.508 and p<0.001) and AST ((r=0.569; p<0.001). There was no statistical difference in ferritin levels between the deferiprone and deferasirox groups (p=0.776). However, higher total bilirubin and ALT were observed in the deferasirox group than in the deferiprone group (p=0.001 and 0.022, respectively). Total (p<0.001), indirect (p<0.001), and direct bilirubin levels (p=0.015) were significantly higher in patients with long-term transfusions than those receiving short-term transfusions. Higher ferritin was found with a statistical significance of p=0.008 in the long-term transfusions group. Conclusions: Ferritin is high in people with transfusion-dependent β-thalassemia major and positively correlated with ALT and AST. Deferasirox might pose a higher risk of developing hepatic injury as compared with deferiprone. Yet, no significant change of deferasirox efficacy (based on ferritin level) was found between those receiving short-term and long-term transfusions.", "keywords": [ "Alanine transaminase", "aspartate transaminase", "iron overload", "deferiprone", "deferasirox" ], "content": "Introduction\n\nThough the disease was known to be centered around the Southeast Asian and Middle Eastern regions, a recent review has highlighted the increasing prevalence of β-thalassemia in North America and Western Europe.1 Approximately 1.5% of the world’s population are carriers of β-thalassemia, where the number varied across regions, including in specific countries.2 For example, among Southeast Asian countries the number of β-thalassemia carriers ranged between 0.5% and 12.8% as reported in Myanmar and Malaysia, respectively.3\n\nPeople with β-thalassemia require a lifelong blood transfusion due to their inability to produce sufficient normal hemoglobin A. Ineffective erythropoiesis in β-thalassemia patients occurs because of the inherited genetic mutations causing impaired β-globin protein and consequently the imbalance in α- and β-globin chains production.4 The condition leads to the inevitable hyperabsorption of irons deriving from either dietary irons or those from blood transfusion.5 Excessive iron and its deposition could cause cardiac complications, which currently affects 25% of total 26,893 β-thalassemia major patients according to a meta-analysis.6 To prevent the toxicity of iron overload, the patients should receive iron chelating therapy. The life expectancy of people with β-thalassemia major could be improved, even to be similar to those with β-thalassemia intermedia if managed with an iron chelating agent.7\n\nBased on a systematic literature review, a person with transfusion-dependent thalassemia should pay $128,062 for blood transfusion and iron chelating therapy.8 In Indonesia itself, the access to iron chelation therapy is still a challenge, especially in rural areas.9 It is worth mentioning that Indonesia lies in a thalassemia belt area owing to the high prevalence and carrier rate.10 Therefore, it is of importance to focus the research on the Indonesian population to improve the clinical management and monitoring of iron overload among patients with β-thalassemia major. Herein, we compared two oral iron chelating drugs, deferiprone and deferasirox, prescribed to patients with β-thalassemia major and chronic transfusion. Deferiprone has two ligands which could coordinate with Fe forming a complex with three chelator molecules.11 Meanwhile, deferasirox has three ligands that could coordinately bind one Fe atom to form a complex with two chelator molecules.11 Understanding the performance of these two drugs in reducing the iron level could provide an insight into more effective and cost-efficient management.\n\nIn addition, we performed a correlation test between serum ferritin with serum alanine transaminase (ALT), aspartate transaminase (AST), and total bilirubin. The iron storage protein, ferritin, has been suggested as an indicator of iron overload and has been used to monitor iron chelation therapy efficacy.12,13 Its correlation with liver enzymes could be an indicator for liver damage monitoring.14,15\n\n\nMethods\n\nThis research was conducted prospectively on children (1 to 18 years old) with β-thalassemia major who were hospitalized at the Children’s Thalassemia Center at Dr. Zainoel Abidin Hospital in Banda Aceh within the February–March 2022 period. The research aimed to seek the correlation between the administration of the iron chelating agent deferiprone with aspartate aminotransferase (AST), alanine aminotransferase (ALT), ferritin, and albumin. Ethical clearance was provided by the Ethical Committee of Dr. Zainoel Abidin Hospital, Banda Aceh (013/EA/FK-RSUDZA/2022, KEPPKN No 1171012P). Written informed consent for all the patients’ participation was obtained from the patients’ guardians.\n\nDiagnosis of β-thalassemia major was established based on hemoglobin (Hb) electrophoresis. The patient was included if having serum ferritin >1500 ng/mL, being treated with oral Ferriprox® or Exjade® (iron chelation therapies containing deferiprone and deferasirox, respectively), and they were not prescribed with other iron chelation therapy (i.e., injectable deferoxamine) within the last three months. Patients having histories of hepatitis virus (HPV) B and HPV C were excluded. Consecutive sampling was employed to select the study subjects with sampling size calculated based on Equation 1.\n\nα: Type I error at 5%\n\nZα: Standard alpha (1.64)\n\nΒ: Type II error at 10%\n\nZβ: Standard beta (1.28)\n\nr: minimally significant correlation coefficient at 0.5.\n\nDemographic characteristics data included in this study were sex, gender, and educational level, obtained by interviewing patients or their guardians. Nutritional status was calculated through anthropometric measurement from the patient’s body weight (kg) and height (m). The values obtained therein were categorized into obesity (>120%), overweight (>110–120%), healthy weight (90–110%), underweight (70–90%), and short stature (<70%).\n\nVenous blood (10 mL) was drawn from each subject and analyzed for serum bilirubin, ferritin, AST, and ALT. Serum ferritin level was obtained from an analysis using the immunoassay technique. Serum AST and ALT determinations were based on non-pyridoxal phosphate Inverse Fast Fourier Transform (IFFT).\n\nContinuous data were presented as mean±standard deviation (SD). Normality of the data distribution was judged based on a Kolmogorov-Smirnov test. Depending on the normality test, the significant difference was statistically analyzed using independent t-test or Mann-Whitney U test. All statistical analyses were performed on SPSS version 22 (SPSS Inc., Chicago, IL, USA) (SPSS, RRID: SCR_019096).\n\n\nResults\n\nThe patients included in this study were a balanced number of males (50%) and females (50%) with <10 years old as the most predominant age, followed by 10–15 years old and >15 years old, respectively (Table 1). The average body weight and height of the patients were 25.56±9.75 kg and 125.96±18.06 m. As many as 45.1% of the total patients were in the healthy weight category, while another 45% were categorized as underweight. Almost all patients required 1 bag of blood each month. The average ferritin level of 3531.80±2322.44 ng/mL exceeded the normal range (7–140 ng/mL). The averaged total, indirect, and direct bilirubin levels were 1.86±1.00, 1.25±0.88, and 0.62±0.42 mg/dL, respectively. The averaged ALT and AST levels were also found to be higher than the upper limit for children (51.57±32.77 and 49.19±48.32, respectively). High SDs in ALT and AST indicate that there were some patients having these values in the normal range (10–40 UI/mL) but some were abnormal.\n\nCorrelation tests were performed to see if the ferritin level was correlated with ALT, AST, or total bilirubin, where the results have been presented in Table 2. Based on Spearman’s rank correlation analysis, serum ferritin was found to be positively correlated with serum ATL based on r=0.508 and p<0.001. Similarly, serum ferritin was also positively correlated with serum AST with a statistical significance (r=0.569; p<0.001). These correlations suggest the increase in serum ferritin level contributes to the increase in serum ALT and AST levels. No correlation was found between serum ferritin and total bilirubin.\n\n* Statistically significant at p<0.01 based on Spearman’s rank correlation.\n\nComparisons of serum ferritin, bilirubin, ALT, and AST among patients receiving either deferiprone or deferasirox have been presented in Table 3. In this analysis, only 90 patients were included while 12 others were excluded because information about blood types was missing for some patients, or they had been treated with drug combinations. Levels of serum total, indirect, and direct bilirubin were found to be significantly different between the two groups (p<0.05). Higher levels of serum ALT and AST were found in the deferasirox group as compared with the deferiprone group, yet statistical significance was only achieved in terms of serum ALT level.\n\n* Statistically significant at p<0.05 using Mann-Whitney U test.\n\nWe further analyzed the differences in serum ferritin, bilirubin, ALT, and AST levels between patients receiving long-term and short-term transfusions. The data of this analysis have been presented in Table 4. Significantly higher serum ferritin level was observed in the group that had undergone long-term transfusion (p<0.05) among the deferiprone recipients. As in patients receiving deferasirox, long-term blood transfusion did not give a significant effect on ferritin levels. However, among those receiving deferasirox, long-term blood transfusion yielded significantly higher serum total, indirect, and direct bilirubin levels. Neither deferiprone nor deferasirox prescription yielded statistically different effects on serum ALT and AST levels between those undergoing long-term and short-term transfusions.\n\na Otherwise stated, p-value was obtained from independent t-test.\n\nb Obtained from Mann-Whitney U test.\n\n* Statistically significant at p<0.05.\n\n\nDiscussion\n\nIncreased ferritin levels in the sera of thalassemic patients are expected since they have ineffective erythropoiesis conditions, allowing hyperabsorption of dietary irons in the intestines. Multiple reports have suggested the effect of iron overload-associated liver abnormalities, indicated by the raised level of liver enzymes. Egyptian patients with β-thalassemia, aged 1.1 to 17 years old, had a mean serum ferritin level of 1367.52 ± 856.22 ng/mL, which exceeded the normal range in children (7–140 ng/mL).16 Following the blood transfusion, irons are retained in the macrophages due to the increased hepcidin, hence elevation in serum ferritin.17 Elevated ferritin as an iron storage marker was reported to have a strong correlation with iron overload condition.18 Among 291 thalassemic children in Cipto Mangunkusumo Hospital, Indonesia, there was a predominance of mild, moderate, and severe degrees of iron overload (28.2%, 34.7%, and 27.8%, respectively).19\n\nOveraccumulation of iron in the liver could damage the organ following reactive oxygen species (ROS) formation through Haber-Weiss and Fenton reactions.20 Ferric iron could be reduced to ferrous iron resulting in the formation of hydroxyl radicals which promotes DNA and protein damages, oxidation of amino acid side chains, and peroxidation of phospholipid.21 In this present study, we found the abnormally high averaged values of serum AST and ALT (51.57±32.77 and 49.19±48.32, respectively), suggesting the presence of hepatic injury. The correlation tests revealed that serum AST and ALT levels are strongly influenced by ferritin, hence hepatoxicity of iron overload. Similarly, a study on 100 patients with β-thalassemia major reported the strong positive correlation between serum ferritin and AST or ALT.16 Based on the study with a slightly higher number of transfusion-dependent thalassemic patients (n=138), ferritin was also found to be positively correlated with liver enzymes (AST and ALT).14 Among patients with acute dengue fever, similar relationships among serum ferritin, AST, and ALT were also reported, where serum ferritin was proposed as an indicator for liver damage.15 In the light of this iron toxicity, it is of importance for thalassemic patients undergoing blood transfusion to receive iron chelating therapies.\n\nHerein, we observed differences of total, indirect, and direct bilirubin and ALT levels between deferiprone and deferasirox groups. All the aforementioned biomarkers were statistically higher in the latter group. In the correlation test, we did not find a correlation between ferritin and bilirubin, indicating that increased bilirubin was not associated with the efficacy of the iron chelator. In previous studies, hepatoxicity of deferasirox has been reported.22–24 In drug-induced hepatic injury, the drugs induce the detrimental immune modulations after attaching to the enzyme molecules.25 The neo-antigens eventually initiate the immune response cascade which could result in cytotoxicity and apoptosis.25 Nonetheless, the reactions are delayed and required multiple exposures. Another proposed mechanism of the deferasirox-induced hepatic injury is the blockage of salt transport proteins (cholestatic injury),22,23 which is supported by the findings of higher bilirubin levels in this present study. However, a case report suggested mitochondrial injury as the most explaining mechanism of deferasirox-induced liver injury which is consistent with elevations of transaminases.24\n\nThe hepatoxicity effect of deferasirox was found to be more potent in patients with long-term transfusion as compared to those with short-term transfusion. However, interestingly, deferasirox could maintain its iron chelating efficacy even though the patients have undergone blood transfusion for more than 7 years. In the case of deferiprone, serum ferritin was produced at a higher level in patients with long-term blood transfusion. This is an indication that deferiprone lost its efficacy as an iron chelating agent as the patient received more blood transfusion. Our findings are in agreement with a study that continually monitored the long-term efficacy of deferasirox, which appeared to be sustained for 3.5 years.26 Deferasirox uniquely has a longer half-life and bioavailability in the plasma (lasting for 24 hours) than other iron chelating therapies.27 It is worth noting that, among patients receiving short-term blood transfusion herein, lower ferritin was observed in the deferiprone group than in the deferasirox group. In previous studies, deferasirox had a lower rate of effectiveness.12,28\n\nOur study had some limitations. For example, we did not simultaneously assess the effects of deferasirox or deferiprone in the thalassemic patients. The number of patients recruited in the study was too few, limiting the results in terms of being clinically meaningful. Moreover, we did not measure iron overload in specific organs, which could give an important insight since the drugs’ efficacies are dependent on the targeted organ. Diagnosis using magnetic resonance imaging (MRI) or other definitive tools should be carried out to conclude the hepatic injury in the patients.\n\n\nConclusions\n\nPatients with β-thalassemia major have a higher level of serum ferritin, which is strongly correlated with the elevations of serum ALT and AST levels, respectively. Deferasirox poses a higher risk of developing liver dysfunction than deferiprone, as suggested by increased levels of bilirubin and ALT. While deferiprone has reduced efficacy among patients managed with long-term blood transfusion, deferasirox could yield a similar efficacy regardless of the length of the chronic transfusion. These findings could be used as guidance for medical practitioners in determining the oral chelating therapies for iron-overload conditions among β-thalassemia major patients, by considering the net clinical benefits of each drug. Although a higher number of participants is required to obtain meaningful clinical conclusions, medical practitioners should be aware of the net clinical benefit of prescribing the oral chelators to transfusion-dependent β-thalassemia major patients.", "appendix": "Data availability\n\nFigshare: ‘Comparison of oral iron chelators in the management of transfusion-dependent β-thalassemia major based on serum ferritin and liver enzymes’. DOI: https://doi.org/10.6084/m9.figshare.21564114. 29\n\nThis project contains the following underlying data:\n\n‐ Master Data.xlsx. [Table containing the raw data of the study.]\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 all the healthcare workers at the Dr. Zainoel Abidin Hospital who assisted in this study.\n\n\nReferences\n\nKattamis A, Forni GL, Aydinok Y, et al.: Changing patterns in the epidemiology of β-thalassemia. Eur. J. Haematol. 2020; 105(6): 692–703. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nColah R, Gorakshakar A, Nadkarni A: Global burden, distribution and prevention of β-thalassemias and hemoglobin E disorders. Expert. Rev. Hematol. 2010; 3(1): 103–117. PubMed Abstract \| Publisher Full Text\n\nSavongsy O, Fucharoen S, Fucharoen G, et al.: Thalassemia and hemoglobinopathies in pregnant Lao women: carrier screening, prevalence and molecular basis. Ann. Hematol. 2008; 87(8): 647–654. PubMed Abstract \| Publisher Full Text\n\nLee J-S, Im Cho S, Park SS, et al.: Molecular basis and diagnosis of thalassemia. Blood Res. 2021; 56(S1): S39–S43. Publisher Full Text\n\nTaher AT, Saliba AN: Iron overload in thalassemia: different organs at different rates. Hematology 2014, the American Society of Hematology Education Program Book. 2017; 2017(1): 265–271.\n\nKoohi F, Kazemi T, Miri-Moghaddam E: Cardiac complications and iron overload in beta thalassemia major patients – a systematic review and meta-analysis. Ann. Hematol. 2019; 98(6): 1323–1331. PubMed Abstract \| Publisher Full Text\n\nBallas SK, Zeidan AM, Duong VH, et al.: The effect of iron chelation therapy on overall survival in sickle cell disease and β-thalassemia: A systematic review. Am. J. Hematol. 2018; 93(7): 943–952. PubMed Abstract \| Publisher Full Text\n\nTurner M, Deshpande S, Chitnis M, et al.: A Global Systematic Literature Review on the Burden of Illness in Transfusion-Dependent β-Thalassemia. Blood. 2019; 134: 5786. Publisher Full Text\n\nWahidiyat PA, Sari TT, Rahmartani LD, et al.: Thalassemia in Indonesia. Hemoglobin. 2022; 46(1): 39–44. PubMed Abstract \| Publisher Full Text\n\nHusna N, Sanka I, Arif AA, et al.: Prevalence and distribution of thalassemia trait screening. J. Med. Sci. 2017; 49(3): 106–113.\n\nKontoghiorghes GJ, Eracleous E, Economides C, et al.: Advances in iron overload therapies. Prospects for effective use of deferiprone (L1), deferoxamine, the new experimental chelators ICL670, GT56-252, L1NAll and their combinations. Curr. Med. Chem. 2005; 12(23): 2663–2681. PubMed Abstract \| Publisher Full Text\n\nKontoghiorghe CN, Kontoghiorghes GJ: Efficacy and safety of iron-chelation therapy with deferoxamine, deferiprone, and deferasirox for the treatment of iron-loaded patients with non-transfusion-dependent thalassemia syndromes. Drug Des. Devel. Ther. 2016; 10: 465.\n\nKolnagou A, Kleanthous M, Kontoghiorghes GJ: Reduction of body iron stores to normal range levels in thalassaemia by using a deferiprone/deferoxamine combination and their maintenance thereafter by deferiprone monotherapy. Eur. J. 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PubMed Abstract \| Publisher Full Text\n\nPorter JB, Cappellini MD, Kattamis A, et al.: Iron overload across the spectrum of non-transfusion-dependent thalassaemias: role of erythropoiesis, splenectomy and transfusions. Br. J. Haematol. 2017; 176(2): 288–299. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWahidiyat PA, Iskandar SD, Rahmartani LD, et al.: Liver iron overload and hepatic function in children with thalassemia major. Paediatr. Indones. 2018; 58(5): 233–237. Publisher Full Text\n\nThompson JW, Bruick RK: Protein degradation and iron homeostasis. Biochimica et Biophysica Acta (BBA)-Molecular. Cell Res. 2012; 1823(9): 1484–1490. Publisher Full Text\n\nAnderson ER, Shah YM: Iron homeostasis in the liver. Compr. Physiol. 2013; 3(1): 315–330. PubMed Abstract \| Publisher Full Text\n\nCermanova J, Kadova Z, Dolezelova E, et al.: Deferoxamine but not dexrazoxane alleviates liver injury induced by endotoxemia in rats. Shock. 2014; 42(4): 372–379. Publisher Full Text\n\nMenaker N, Halligan K, Shur N, et al.: Acute liver failure during deferasirox chelation: a toxicity worth considering. J. Pediatr. Hematol. Oncol. 2017; 39(3): 217–222. PubMed Abstract \| Publisher Full Text\n\nAslam N, Mettu P, Marsano-Obando LS, et al.: Deferasirox induced liver injury in haemochromatosis. J. Coll. Physicians Surg. Pak. 2010; 20(8): 551–553. PubMed Abstract\n\nChen M, Suzuki A, Borlak J, et al.: Drug-induced liver injury: Interactions between drug properties and host factors. J. Hepatol. 2015; 63(2): 503–514. PubMed Abstract \| Publisher Full Text\n\nCappellini MD: Long-term efficacy and safety of deferasirox. Blood Rev. 2008; 22: S35–S41. Publisher Full Text\n\nCappellini MD: Exjade (R) (deferasirox, ICL670) in the treatment of chronic iron overload associated with blood transfusion. Ther. Clin. Risk Manag. 2007; 3(2): 291–299. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNeufeld EJ: Oral chelators deferasirox and deferiprone for transfusional iron overload in thalassemia major: new data, new questions. Blood. 2006; 107(9): 3436–3441. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYusuf S, Herdata HN, Edward ED, et al.: Underlying data for ‘Comparison of oral iron chelators in the management of transfusion-dependent β-thalassemia major based on serum ferritin and liver enzymes’.Publisher Full Text" }	[ { "id": "164926", "date": "06 Mar 2023", "name": "Pustika Amalia Wahidiyat", "expertise": [ "Reviewer Expertise Thalassemia" ], "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 is a prospective study comparing two oral iron chelating drugs, deferiprone and deferasirox, in reducing iron overload and its effects on serum transaminase and bilirubin levels. This study also evaluated the correlation between serum ferritin with ALT, AST, and bilirubin.\n\nThere are some improvements needed for the manuscript:\nIntroduction\nSince similar studies with greater number of subjects have been established. Please provide the novelty of this study.\n\nPlease provide data from Indonesia\nMethods\nPlease provide data about the dosage of iron chelation used in this study.\n\nConsidering most of the patients with transfusion dependent thalassemia had organomegaly, please re-assessed the nutritional status based on the mid-upper arm circumference.\n\nSince ferritin is easily affected by inflammatory status, please provide the technique to exclude the possibility of inflammatory state\nResults\nPlease provide the analysis data between dosage used and the dependent variables\n\nPlease revised the height data in “metre” unit\nDiscussion\nPlease provide more discussion about the results findings, especially the difference between the two types of drugs.\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? 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": "10769", "date": "16 Jan 2024", "name": "Sulaiman Yusuf", "role": "Author Response", "response": "Dear Reviewer, Thank you for your important suggestions. Here are our responses for each comments. Introduction 1. Since similar studies with greater number of subjects have been established. Please provide the novelty of this study. Response: Thank you. We have added the novelty of the study. Mainly since most of the studies in Indonesia are from Java; studies outside of the Java is important to see of any differences. 2. Please provide data from Indonesia Response: The data of Thalassemia from Indonesia has been added in the text. The references have been adeed: Wahidiyat PA, Sari TT, Rahmartani LD, et al.: Thalassemia in Indonesia. Hemoglobin. 2022;46(1):39-44. doi: 10.1080/03630269.2021.2023565. Wahidiyat PA, Liauw F, Sekarsari D, et al.: Evaluation of cardiac and hepatic iron overload in thalassemia major patients with T2* magnetic resonance imaging. Hematology. 2017;22(8):501-507. doi: 10.1080/10245332.2017.1292614 Wahidiyat PA, Wijaya E, Soedjatmiko S, et al.: Urinary iron excretion for evaluating iron chelation efficacy in children with thalassemia major. Blood Cells Mol Dis 2019;77:67-71. doi: 10.1016/j.bcmd.2019.03.007. Methods 3. Please provide data about the dosage of iron chelation used in this study. Response: The dosage of the iron chelation used in the study has been added in the article. 4. Considering most of the patients with transfusion dependent thalassemia had organomegaly, please re-assessed the nutritional status based on the mid-upper arm circumference. Response: Thank you for your suggestion; however, not all patients have the mid-upper arm circumference data in our database. 5. Since ferritin is easily affected by inflammatory status, please provide the technique to exclude the possibility of inflammatory state. Response: Thank you for your question. In all patients, the level of ferritin was measured only the patients had no infection (assessed through physically and laboratory tests including routine lab, C-reactive protein level and procalcitonin) and had no autoimmune diseases. Results 6. Please provide the analysis data between dosage used and the dependent variables. Response: Thank you for your suggestion. Unfortunately, all the patients in our study were treated with the same dose of iron chelation drugs (deferiprone with dose 75 mg/kg body weight each day and deferasirox with dose of 20 mg/kg body weight each day for single dose). 7. Please revised the height data in “metre” unit Response: The unit of the height has been changed to unit metre. Discussion 8. Please provide more discussion about the results findings, especially the difference between the two types of drugs. Response: More discussion has been added in particular the difference between the two types of oral chelating drugs (deferiprone and deferasirox) used in this study." } ] }, { "id": "208966", "date": "24 Nov 2023", "name": "Ahmed Yahya Dallal Bashi", "expertise": [ "Reviewer Expertise Clinical Biochemistry with Special interest in Thalassemia" ], "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\nConcerning the article titled \"Comparison of oral iron chelators in the management of transfusion-dependent β-thalassemia major based on serum ferritin and liver enzymes\", the work is a reasonable study to compare between 2 oral chelating drugs (Ferriprox (deferiprone) and Exjade (Deferasirox)) and their action in decreasing the level of serum ferritin and their effects on serum transaminases and serum bilirubin and the correlation between serum ferritin and the mentioned parameters. In my opinion the work was well done, and only few notes are required to be revised as follows:\nMethod: The doses of the 2 drugs were not mentioned which are very important as different protocols of treatment use different daily drugs doses.\n\nUnder the title \"serum parameters analysis\" methods for the estimation of serum; ferritin, AST, and ALT were mentioned while method of estimation of serum bilirubin was not mentioned.\n\nResults: The mean length of the patients that was measured in meters was written as \"125.96±18.06\". This is in cm and if a meter unit is required then it is 1.2596±0.1806. The same fault was repeated in table 1.\n\nDiscussion: \"Following the blood transfusion, irons are retained in the macrophages due to the increased hepcidin, hence elevation in serum ferritin.17\". Hepcidin production is suppressed due to erythropoietic activity which allows increased absorption of dietary iron in addition to the iron obtained from blood transfusion.\n\nThe authors used the scientific names of the drugs which are general names of the main constituent of the drug. I think they have to use the trade names of the drugs and in 2 brackets the constituents of the drugs as follows: Ferriprox (deferiprone) and Exjade (deferasirox).\n\nAim of the study was mentioned in the \"background\" only and have to be repeated in more details at the end of the \"Introduction\".\nIn addition, in aim of the study mentioned in the \"Background\" I suggest adding (on the liver) and substituting the word (toxicity) by (adverse effects) so it become (This study aimed to compare the performance and adverse effects of deferiprone and Deferasirox on the liver in β-thalassemia major patients).\nIn my opinion the authors went many times out of the scope of the aim of the study which leads to a relatively long article and can be summarized to fulfill the aim 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? 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": "10770", "date": "16 Jan 2024", "name": "Sulaiman Yusuf", "role": "Author Response", "response": "Dear Reviewer, Thank you for your important suggestions. Here are our responses for each comments. 1. Method: The doses of the 2 drugs were not mentioned which are very important as different protocols of treatment use different daily drugs doses. Response: The dosage of the iron chelation used in the study has been added in the article. 2. Under the title \"serum parameters analysis\" methods for the estimation of serum; ferritin, AST, and ALT were mentioned while method of estimation of serum bilirubin was not mentioned. Response: The method used to measure the serum bilirubin has been added under the heading of \"Serum parameters analysis\". Thank you. 3. Results: The mean length of the patients that was measured in meters was written as \"125.96±18.06\". This is in cm and if a meter unit is required then it is 1.2596±0.1806. The same fault was repeated in table 1. Response: Thank you for pointing this issue. The values are now have been changed to metre: 1.25±0.18. 4. Discussion: \"Following the blood transfusion, irons are retained in the macrophages due to the increased hepcidin, hence elevation in serum ferritin.17\". Hepcidin production is suppressed due to erythropoietic activity which allows increased absorption of dietary iron in addition to the iron obtained from blood transfusion. Response: The text have been revised. Thank you. 5. The authors used the scientific names of the drugs which are general names of the main constituent of the drug. I think they have to use the trade names of the drugs and in 2 brackets the constituents of the drugs as follows: Ferriprox (deferiprone) and Exjade (deferasirox). Response: Thank you for your suggestion. We have used the style “Ferriprox ® (iron chelation containing deferiprone) or Exjade ® (iron chelation containing deferasirox)” in Introduction (aim) and at the beginning of the Methods section. This is help authors to have detailed information of the drugs used. We avoid to write the name of trading names in all texts of the article since it might less appropriate. This might have perception that the study funded by the companies of the drug. In addition, we used one brand only for each of the drug in this study with is Ferriprox ® for deferiprone and Exjade ® for deferasirox. 6. Aim of the study was mentioned in the \"background\" only and have to be repeated in more details at the end of the \"Introduction\". In addition, in aim of the study mentioned in the \"Background\" I suggest adding (on the liver) and substituting the word (toxicity) by (adverse effects) so it become (This study aimed to compare the performance and adverse effects of deferiprone and Deferasirox on the liver in β-thalassemia major patients). Response: Thank you for raising this issue. The aim has been revised in the introduction and located at the end of the Introduction. It is now: “The objective of the study was to compare the performance and adverse effects of two oral iron chelating drugs (i.e., deferiprone (Ferriprox) and deferasirox (Exjade)) on the liver in β-thalassemia major patients with chronic transfusion. The effect on the liver were assessed by measuring the levels of serum ferritin, transaminase (ALT), aspartate transaminase (AST), total bilirubin, indirect bilirubin and direct bilirubin among patients with β-thalassemia major and chronic transfusion. In addition, we performed a correlation test between serum ferritin with ALT, AST, and total bilirubin. 7. In my opinion the authors went many times out of the scope of the aim of the study which leads to a relatively long article and can be summarized to fulfill the aim of the study. Response: Thank you for your suggestion. Since we have two main objectives: To compare the performance and adverse effects as well as to determine the correlation test between serum ferritin with ALT, AST, and total bilirubin; therefore, the article a quite long since we have to prepare the manuscript based on the aims of the study. Now the aims have been articulated clearly in the end of the Introduction." } ] } ]	1	https://f1000research.com/articles/12-154
https://f1000research.com/articles/11-246/v1	28 Feb 22	{ "type": "Research Article", "title": "Modified recurrent equation-based cubic spline interpolation for missing data recovery in phasor measurement unit (PMU)", "authors": [ "Shruthi Thangaraj", "Vik Tor Goh", "Timothy Tzen Vun Yap", "Shruthi Thangaraj", "Timothy Tzen Vun Yap" ], "abstract": "Background: Smart grid systems require high-quality phasor measurement unit (PMU) data for proper operation, control, and decision-making. Missing PMU data may lead to improper actions or even blackouts. While the conventional cubic interpolation methods based on the solution of a set of linear equations to solve for the cubic spline coefficients have been applied by many researchers for interpolation of missing data, the computational complexity increases non-linearly with increasing data size. Methods: In this work, a modified recurrent equation-based cubic spline interpolation procedure for recovering missing PMU data is proposed. The recurrent equation-based method makes the computations of spline constants simpler. Using PMU data from the State Load Despatch Center (SLDC) in Madhya Pradesh, India, a comparison of the root mean square error (RMSE) values and time of calculation (ToC) is calculated for both methods. Results: The modified recurrent relation method could retrieve missing values 10 times faster when compared to the conventional cubic interpolation method based on the solution of a set of linear equations. The RMSE values have shown the proposed method is effective even for special cases of missing values (edges, continuous missing values). Conclusions: The proposed method can retrieve any number of missing values at any location using observed data with a minimal number of calculations.", "keywords": [ "phasor measurement unit", "missing data", "data recovery", "smart grid", "interpolation", "cubic spline", "data quality", "data pre-processing" ], "content": "Introduction\n\nThe worldwide growing power systems highlight the need for better monitoring and control mechanisms to avoid major blackouts. Smart grids are intelligent systems that facilitate the development of communication, network, and computing technologies, protocols, and standards to integrate power system elements for two-way communication. This time-synchronized high-precision measurement device that is also known as a synchrophasor or Phasor Measurement Unit (PMU), gives clear information on the working of the entire grid. The PMU is used to monitor and control the power grid. It can help in providing real-time measurements by eliminating adverse conditions like blackouts. These combined characteristics of data availability, timeliness, and communication network contribute to the better performance of the PMU system. Although the role, impact,1 architecture, technology,2 applications, functionality, standards, and evolution of PMU (timing, measurement, communication, and data storage) have been released since 1995, the North American Synchro Phasor Initiative (NASPI) has highlighted the importance of data quality.3 Data quality issues, their potential causes, and consequences are elaborated.4–6 Generally, incomplete or missing data might affect the functionality of the entire system.7 Hence, a way to handle missing values in PMU is mandatory for the effective functioning of the entire grid system.\n\nIn this paper, a modified recurrent equation-based method termed the Alpha Method (AM) for PMU missing data problem is proposed. The results are compared with the tri-diagonal matrix-based conventional cubic spline interpolation for the spline coefficients which is also termed the Linear Equations Method (LEM).\n\n\nLiterature review\n\nThe need to fill in the missing values in PMU and potential causes have been reviewed.5–7 These works imply the need for missing data recovery techniques for PMU data to enhance the accuracy of the decision-making process and show the data quality and security risks associated with the missing data in PMU. One of the popular approaches is the matrix completion (MC) based on missing data recovery.8–12 The MC is the most exploited technique, however, a few of these were only theoretical approaches and a few approaches were only tested with simulated data.\n\nInterpolation-based missing data recovery techniques13–15 propose a reconstruction of missing values by a spatial interpolation or spatio-temporal interpolation of the values. Yet they require historical data of the same channel’s or time’s data for the interpolation. A few of the advanced/hybrid approaches16,17 like k-nearest-neighbor and recurrent relation-based interpolations are not yet applied over the PMU data.\n\nMissing data is a common problem in all fields of study; hence a variety of solutions are found to be effective based on the data pattern, data processing model, and data quality needs. However, adopting any conventional techniques available for treating missing values can get complex especially when solving the high precision and volume of PMU data.15 Therefore, there is a need for a missing data recovery method for PMU data. NASPI presents a variety of data requirements, attributes, and data quality problems for both static data and real-time data. There is a need for designing an effective data recovery method to work without the need for historical data processing and training.3 So, a data-driven recovery technique capable of recovering missing entries with available or observed data is much needed. Moreover, the technique should not get complex and time-consuming when the size of the data grows.\n\n\nMethods\n\nCubic spline interpolation is a widely used polynomial interpolation method for functions of one variable. Let fbe a function from RtoR. It is assumed that the value of fis known only at x1≤x2.≤xi…≤xnand let fxi=ai. Piecewise cubic spline interpolation is the problem of finding the bi, ciand di coefficients of the cubic polynomials SFifor0≤i≤n−1 written in the form:\n\nWhere x can take any value between xi and xi+1. That is,\n\nLet the first-order derivative of equation (1) be:\n\nThe first-order derivative at xi for values of 1≤i≤n−1 will be\n\nAnd the second-order derivative be:\n\nThe second-order derivative at xi for values of 1≤i≤n−1 will be:\n\nFor a smooth fit between the adjacent pieces, the cubic spline interpolation requires that the following conditions hold:\n\n1. The cubic functions should intersect at the points left and right, for i=0ton−1\n\n2. For each cubic function to join smoothly with its neighbors, the splines should have continuous first and second derivatives at the data points i=1,…,n−1:\n\nIf hi= xi+1−xi and if hi is equal for all ivalues, following Revesz,17 the relation between coefficients ai and ci can be resolved:\n\nEquation (6) represents a system of linear equations for the unknowns ci for 0≤i≤n. As the values of aiare known, the value of ci can be found by solving the tri-diagonal matrix-vector equationAx=B. While there are n+1 numbers of ci constants, equation (6) yields only (n-2) equations. Based on the nature or type of spline assumed two more equations representing the boundary conditions of the spline. In general, two types of splines may be considered: natural cubic spline and clamped cubic spline.\n\nFor natural cubic spline interpolation, the following boundary conditions are assumed: c0=cn=0.0. That is, the second derivatives of the splines at the endpoints are assumed to be zero. Based on equation (4), a system of (N+1) linear equations of (N+1) variables can be formulated as:\n\nFor clamped cubic spline interpolation the following boundary conditions are assumed: b0=f′(x0) and bn=f′(xn), where the derivatives f′(x0) and f′(xn), are known constants. Thus, based on the boundary conditions assumed both natural and cubic splines result in n+1 system of linear equations. The resulting system of n+1 linear equations can be used to get unique solutions by any of the standard methods for solving a system of linear equations.\n\nOnce the values of ci are obtained, using equations (5) and (6) respectively, the values of coefficients bi and di can also be found. Similarly, under clamped spline interpolation,\n\nRevesz,17 chose boundary conditions that need to solve the tri-diagonal system given in equation (6) where xirational variables ei rational constants, r is a non-zero rational constant and A is:\n\nThe first row of the new matrix in (6) is shown to be equivalent to the first row of the clamped b matrix e1 is\n\nThe chosen boundary conditions are such that the first row of the new matrix was the same as that of clamped cubic spline and while that of the last row was that of the natural cubic spline fixing the value of cn as 0.\n\nLet ∝0,∝ifor1<i≤n−1and∝n, respectively be:\n\nBased on the above, the closed form of solution for xi can be given as:\n\nThe above equation solves xi no matter exactly what the initial values for ei. This leads to a faster evaluation of the cubic spline than solving a tri-diagonal system. The major advantage of the method is when new measurements are added to the system. While conventional tri-diagonal matrix-based algorithm requires a complete redo of the entire computation, equation (14) leads to a faster update for each i ≤ n only with the addition of the term:\n\nThe system of linear equations given in equation (7), in general, is solved by the standard solution of linear equations in the matrix form Ax=b. Alternatively, it could be solved for n variables by the recurrence relations given equations (16) and (17). The two methods, the first using the tri-diagonal matrix-based solution for the spline coefficients is termed the Linear Equations Method (LEM) and the second one using recurrence relations is termed the Alpha Method (AM). The algorithmic procedure for LEM and AM are given below.\n\nStep 1: Given the initial vector with missing values, separate them into two sets of vectors, the observed values vector Robs and the missing values vector RMiss, having sizes of NO and NM, respectively, such that NO+NM=N.\n\nStep 2: Robs vector at xi values of the (NO-1) splines shall be theai coefficient vector.\n\nStep 3: Usingai, generate the RHS vector E given in equation (11).\n\nStep 4: Generate a square coefficient matrix A as given in equation (11)\n\nStep 5: Solve for the civector is given in (11), using the relation Ac=E\n\nStep 6: Applyingci in equations compute the bianddi coefficient vectors for n-2 points of the Robs,\n\nStep 7: Using the values ofai,bi, cianddi, missing values can be found by the equation (1) re-written as:\n\nWhere x represents the missing positions, between xi and xi+1 of spline i.\n\nStep 1: Given the initial vector with missing values, separate them into two sets of vectors, the observed values vector Robs and the missing values vector RMiss, having sizes of NO and NM, respectively, such that NO+NM=N.\n\nStep 2: The Robs vector at xi values of the (NO-1) splines are theai coefficient vector.\n\nStep 3: Usingai, generate the RHS vector E given in equation (11).\n\nStep 4: Set ∝0=0and∝n=en,given in equation (11) calculate the alpha vector using the relation.\n\n∝i=ei−∝i−1r=∑0≤k≤i−1−1kei−krk+1 for i values ranging from 1 to NO-1\n\nStep 5: Set xn=∝n and solve for ci values using the relation.\n\nStep 6: Applyingci in equations compute the bi and di coefficient vectors for n-2 points of the Robs,\n\nStep 7: Using the values ofai,bi, cianddi, missing values can also be found using equation (18), re-written here again for convenience:\n\nWhere x represents the missing positions, between xi and xi+1 of spline i.\n\nThe modifications are as follows: In the AM method rather than computing E, alpha vectors andci coefficients for the full range of NO-1 data points only the RHS, E vector, was calculated for the full range of NO-1 data points, while alpha vector and ci were calculated only for iandi+1 data elements, wherei is the missing data element. For the imputation ofi the element, only the Ei vector for all NO-1 data points, ∝i vector and ci vectors for iandi+1 and bi and di coefficients were essential for the calculation ith missing element and its imputation.\n\nIn addition, using the AM, an effective procedure was demonstrated for the computation of the following cases: (i) missing first and the last element of the data vector, (ii) missing multiple data points at the beginning and the end, and (iii) missing multiple elements anywhere in the data vector. That is in equation (18), when the current values of A [i] are replaced either with A [N-1] or A [i-1] based on the position of missing edge values or continuous values the ToC and RMSE values have improved significantly.\n\n\nResults and discussion\n\nA comparison between LEM and AM methods is shown here for the imputation of one-min real PMU system data having a size of 1490 data points for each of the 25 heterogeneous variables obtained from five different PMUs. Since our data does not have any missing values we artificially introduced the missing values of 10%, 20%, 30% in random.\n\nA sample of one minute PMU data for five PMUs’ was used in the study.18 One minute of PMU data with 10%, 20%, 30% missing data respectively for five PMUs were evaluated.\n\nWhen the AM method was employed, the average root mean squared error (RMSE) values were 0.5968, 0.9448, and 1.2445 for 10%, 20%, and 30% of missing PMU data respectively. This can be seen in Figure 1. Moreover, for the same performance, the AM method showed significant improvements in its time of calculation (ToC) as shown in Figure 2. The average ToCs for the proposed AM method were 2.132, 1.9634, and 1.738s when recovering 10%, 20%, and 30% of its missing data. By comparison, LEM had ToC values of 32.7679, 33.4482, and 36.7988s for 10%, 20%, and 30% of its missing data, respectively. The proposed method reduced the ToC by a factor of approximately 10 times.\n\n\nConclusions\n\nIn this study, the proposed AM method was compared with the LEM technique. However, because of the proliferation of the data, there is a need for customization of this technique to handle a high volume of data to reduce computational time and power. In the proposed method, the approaches demonstrated a reduced computational effort and time of calculation for solving the coefficient vectors. This study has made the following contributions: (i) the recurrent relation-based alpha method has been effectively employed in the imputation of PMU data and its advantages are demonstrated as an effective and efficient alternative to the conventional technique, and (ii) an effective procedure for handling special cases (edge, continuous values) is shown, which has not been addressed clearly in other methods. The proposed method has proven effective, and it only requires 10% effort in comparison to the LEM. Future research will focus on the application of the modified recurrent method in the analysis of real-time or stream PMU data.\n\n\nData availability\n\nHarvard Dataverse: Underlying data for ‘Modified recurrent equation-based cubic spline interpolation for missing data recovery in phasor measurement unit (PMU)’, ‘PMU data’, https://doi.org/10.7910/DVN/Y2LLJJ.18\n\nThis project contains the following underlying data:\n\n- Data file: pmu1-1m-10.tab – One minute of data from PMU1 with 10% missing data\n\n- Data file: pmu1-1m-20.tab – One minute of data from PMU1 with 20% missing data\n\n- Data file: pmu1-1m-30.tab – One minute of data from PMU1 with 30% missing data\n\n- Data file: pmu2-1m-10.tab – One minute of data from PMU2 with 10% missing data\n\n- Data file: pmu2-1m-20.tab – One minute of data from PMU2 with 20% missing data\n\n- Data file: pmu2-1m-30.tab – One minute of data from PMU2 with 30% missing data\n\n- Data file: pmu3-1m-10.tab – One minute of data from PMU3 with 10% missing data\n\n- Data file: pmu3-1m-20.tab – One minute of data from PMU3 with 20% missing data\n\n- Data file: pmu3-1m-30.tab – One minute of data from PMU3 with 30% missing data\n\n- Data file: pmu4-1m-10.tab – One minute of data from PMU4 with 10% missing data\n\n- Data file: pmu4-1m-20.tab – One minute of data from PMU4 with 20% missing data\n\n- Data file: pmu4-1m-30.tab – One minute of data from PMU4 with 30% missing data\n\n- Data file: pmu5-1m-10.tab – One minute of data from PMU5 with 10% missing data\n\n- Data file: pmu5-1m-20.tab – One minute of data from PMU5 with 20% missing data\n\n- Data file: pmu5-1m-30.tab – One minute of data from PMU5 with 30% missing data\n\n- README.txt\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).", "appendix": "References\n\nPhadke AG, Bi T: Phasor measurement units, WAMS, and their applications in protection and control of power systems. J. Mod. Power Syst. Clean Energy. 2018; 6(4): 619–629. Publisher Full Text\n\nUsman MU, Faruque MO: Applications of synchrophasor technologies in power systems. J. Mod. Power Syst. Clean Energy. 2019; 7(2): 211–226. Publisher Full Text\n\nAmidan B, et al.: Data Mining Techniques and Tools for Synchrophasor Data. North American SynchroPhasor Initiative (NASPI); 2019, January; 45.\n\nMiller LE, et al.: PMU Data Quality: A Framework for the Attributes of PMU Data Quality and a Methodology for Examining Data Quality Impacts to Synchrophasor Applications.2017; no. March: pp. 1–77.\n\nHuang C, et al.: Data quality issues for synchrophasor applications Part I: a review. J. Mod. Power Syst. Clean Energy. 2016; 4(3): 342–352. Publisher Full Text\n\nHuang C, et al.: Data quality issues for synchrophasor applications Part II: problem formulation and potential solutions. J. Mod. Power Syst. Clean Energy. 2016; 4(3): 353–361. Publisher Full Text\n\nFang X, et al.: PMU Data Quality: A Framework for the Attributes of PMU Data Quality and a Methodology for Examining Data Quality Impacts to Synchrophasor Applications. IEEE Trans. Power Syst. 2017; 7(1): 1–6.\n\nGenes C, Esnaola I, Perlaza SM, et al.: Recovering missing Data via matrix completion in electricity distribution systems. IEEE Workshop on Signal Processing Advances in Wireless Communications, SPAWC, 2016-Augus (July 2016).2016.\n\nGao P, Wang M, Ghiocel SG, et al.: Missing Data Recovery by Exploiting Low-Dimensionality in Power System Synchrophasor Measurements. IEEE Trans. Power Syst. 2016; 31(2): 1006–1013. Publisher Full Text\n\nCai JF, Candès EJ, Shen Z: A singular value thresholding algorithm for matrix completion. SIAM J. Optim. 2010; 20(4): 1956–1982. Publisher Full Text\n\nGenes C, Esnaola II, Perlaza SM, et al.: Recovering missing data via matrix completion in electricity distribution systems. IEEE Workshop on Signal Processing Advances in Wireless Communications, SPAWC, 2016-August, 1–6.2016.\n\nHastie T, Mazu Missing Dataer R, Lee JD, et al.: Matrix completion and low-rank SVD via fast alternating least squares. J. Mach. Learn. Res. 2015; 16: 3367–3402. PubMed Abstract\n\nGräler B, Pebesma E, Heuvelink G: Spatio-temporal interpolation using gstat. R Journal. 2016; 8(1): 204–218. Publisher Full Text\n\nCheng S, Lu F: A two-step method for missing spatio-temporal Data reconstruction. ISPRS Int. J. Geo Inf. 2017; 6(7). Publisher Full Text\n\nDeng M, Fan Z, Liu Q, et al.: A Hybrid Method for Interpolating Missing Data in Heterogeneous Spatio-Temporal Datasets. ISPRS Int. J. Geo Inf. 2016; 5(2). Publisher Full Text\n\nYang Z, Liu H, Bi T, et al.: A PMU data recovering method based on preferred selection strategy. Glob. Energy Interconnect. 2018; 1(1): 63–69.\n\nRevesz PZ: A recurrence equation-based solution for the cubic spline interpolation problem. International Journal of Mathematical Models and Methods in Applied Sciences. 2015; 9(16): 446–452.\n\nThangaraj S, Goh VT, Yap TTV: PMU Data.2021. Harvard Dataverse. Publisher Full Text" }	[ { "id": "125681", "date": "10 Mar 2022", "name": "Mathias Foo", "expertise": [ "Reviewer Expertise Dynamical system modelling" ], "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 general, there is promising aspect of the proposed method but it has to be conveyed in a clearer manner. Here are my comments.\nIn Introduction section, the authors state that the comparison will be made with LEM. Can the author explain why specifically LEM is compared? Is that the current state-of-the-art method?\n\nIn Literature Review section, NASPI is mentioned but without proper definition of the acronym.\n\nIf my understanding is right, Equation (10) is a systems of linear equation of (7). Then, why does the h value in the B matrix have an exponent of 1 instead of 2 as of Equation (7)?\n\nStatement above Equation (11): Unless I'm mistaken, there is no d coefficient to be solved from either equations (5) or (6).\n\nEquation (11): Like Equation (10), can the authors clarify why the exponent of 1 is used for h?\n\nEquation (13): Why is r taking this value? A bit more explanation would be helpful.\n\nEquation (16): Why is there a 'for' in the equation?\n\nStep 3 of LE method: There is no vector E in Equation (11).\n\nStep 3 of AM method: There is no vector E in Equation (11).\n\nStep 4 of AM method: There is no alpha term in Equation (11).\n\nResults and Discussions section: Can the author explicitly write down the equation for RMSE?\nAlso, I am quite surprised with the huge difference in terms of RMSE between the two methods even for the case of 10% missing data considering the same equation (18) is used for both algorithms. The difference in ToC is understandable, but the vast difference in RMSE is a bit out of my expectation. Could the author briefly comment on the plausible reason for this huge difference in the RMSE value despite both algorithm using equation (18).\n\nOverall comment: The mathematical derivation is not easy to follow and there are potential mistakes in citing the equations, which makes it even harder to follow. Thus, it is difficult to ascertain whether the results can be reproduced.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "9134", "date": "27 Dec 2023", "name": "Vik Tor Goh", "role": "Author Response", "response": "The idea of cubic spline is the development of a series of unique cubic polynomials that are fitted between the data points. Based on four continuity relations between points in the spline, the relationships between the spline coefficients shall result in a system of unique n x n linear equations in the matrix form Ax = B. The solution of this unique system of linear equations results in the values of constants at each spline point. Whenever some changes occur in any one of the splines, the system of linear equations must be solved for every specific change to fit the spline. The tri-diagonal method of solving a system of linear equations was employed in this study for comparison. Hence and from the reference, we made such a comparison to linear equation method. The word is already introduced in the introduction section as North American Synchro Phasor Initiative (NASPI). The exponent for h in Equation (10) and (11) should be 2 instead of 1. We have made the corrections accordingly. Thank you. As the reviewer correctly noted, the d coefficient is not solved in Equations (5) or (6). It is instead solved using Equation (9). We have made the amendments accordingly. The r-value in Equation (13) is a non-zero rational constant; the value is adapted from our reference work [17]. We have added this citation in the text. The ‘for’ should not be in Equation (16). It has been corrected. Step 3 and Step 5 of the LE method has been corrected as vector B instead of E. Reference to Equation (11) in Step 4 of the AM method has been removed. The equation for RMSE has been added in the text. Upon inspection, we found that the variables b, c, and d of the cubic spline is found to be similar in both methods as the reviewer correctly predicted. We re-examined our results and have determined that due to an oversight, an error occurred in the final calculations of imputation values in the LE method. Instead of the coordinate numbers, the spline values at the coordinates were used for the calculation of missing values. As such, we have made the corrections to the results and discussions, as well as the plots in Figure 1 and Figure 2. All corrections and suggestions given were incorporated and the revised version of the paper is written. We really appreciate the time spent by the reviewer for the useful suggestions and corrections made." } ] }, { "id": "139819", "date": "12 Jul 2022", "name": "Shaik Mullapathi Farooq", "expertise": [ "Reviewer Expertise Cyber security in smart grid communication network and VANET." ], "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 proposes recurrent relation based alpha method to interpolate missing PMU data. Further, the authors try to prove that the proposed method reduces computational complexity.\n\nHowever, the comments are as follows,\n\nThe Implementation of the proposed method is clearly missing (Hardware or software details used) in the manuscript which does not assist reproducing the results.\n\nMost of the manuscript is dedicated for theoretical discussion about the proposed method. But a comparison between the existing methods with the proposed method is missing.\n\nAdd nomenclature that improves the readability of the manuscript.\n\nOnly data set of PMU values are presented (PMU Data Harvard Data verse) instead need to add discussion about the details of PMU Data.\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?\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? Yes", "responses": [ { "c_id": "9135", "date": "22 Dec 2022", "name": "Vik Tor Goh", "role": "Author Response", "response": "The purpose of this preliminary paper is to introduce our work in missing data recovery using cubic spline interpolation, namely the mathematical foundation and algorithmic logic. These details have been presented and explained accordingly in the paper. Additionally, the data used is also available for download by interested parties. We aim to publish a more detailed paper soon which will contain more information such as those suggested by the reviewer. Thank you for the suggestion. As stated earlier, the purpose of this preliminary paper is to introduce our proposed method, hence the emphasis on theoretical discussion. However, we have made an initial comparison with an existing method, namely the Linear Equation Method. This can be seen in the Results and discussion section. The nomenclature is improved wherever possible to improve the readability of the manuscript. The dataset presented in the work was obtained from a regional Electricity Authority in India. It was obtained for use as realistic data and brief details of the PMU data is now included. However, additional information such as the data source, the acquisition process, and the physical significance of the systemic variables are not detailed at this stage of algorithmic development as the main idea is only to demonstrate the efficacy of the missing data imputation algorithm. Nonetheless, we take note of this suggestion for our next submission. Thank you." } ] } ]	1	https://f1000research.com/articles/11-246
https://f1000research.com/articles/12-627/v1	07 Jun 23	{ "type": "Data Note", "title": "Sociodemographic and clinical characteristics of hospital admissions for COVID-19: A retrospective cohort of patients in two hospitals in the south of Brazil", "authors": [ "Edna Ribeiro de Jesus", "Julia Estela Willrich Boell", "Juliana Cristina Lessmann Reckziegel", "Rafael Sittoni Vaz", "Marco Aurélio Goulart", "Flávia Marin Peluso", "Tiago da Cruz Nogueira", "Márcio Costa Silveira de Ávila", "Michelle Mariah Malkiewiez", "Catiele Raquel Schmidt", "Vanessa Cruz Corrêa Weissenberg", "Millena Maria Piccolin", "Walmiro Martins Charão Junior", "Elisiane Lorenzini", "Julia Estela Willrich Boell", "Juliana Cristina Lessmann Reckziegel", "Rafael Sittoni Vaz", "Marco Aurélio Goulart", "Flávia Marin Peluso", "Tiago da Cruz Nogueira", "Márcio Costa Silveira de Ávila", "Michelle Mariah Malkiewiez", "Catiele Raquel Schmidt", "Vanessa Cruz Corrêa Weissenberg", "Millena Maria Piccolin", "Walmiro Martins Charão Junior", "Elisiane Lorenzini" ], "abstract": "Background: This database aims to present the sociodemographic and clinical profile of a cohort of 799 patients hospitalized with coronavirus disease 2019 (COVID-19) in two hospitals in southern Brazil. Methods: Data were collected, retrospectively, from November 2020 to January 2021, from the medical records of all hospital admissions that occurred from 1 April 2020 to 31 December 2020. The analysis of these data can contribute to the definition of the clinical and sociodemographic profile of patients with COVID-19. Data description: This dataset covers 799 patients hospitalized for COVID-19, characterized by the following sociodemographic variables: sex, age group, race, marital status and paid work. The sex variable was collected as sex assigned at birth from medical records data. Clinical variables included: admission to clinical ward, hospitalization in the Intensive Care Unit, COVID-19 diagnosis, number of times hospitalized due to COVID, hospitalization time in days and risk classification protocol. Other clinical variables include: pulmonary impairment; patients ventilation pattern; high-flow oxygen mask; pulmonary thromboembolism; cardiovascular disease; pulmonary sepsis; influenza exam results. Other health problems: diabetes, systemic arterial hypertension, chronic obstructive pulmonary disease, obesity, tabaco smoking, asthma, chronic kidney disease, overweight, vascular accident, sedentary lifestyle, HIV/AIDS, cancer, Alzheimer's disease, Parkinson's disease. Conclusions: The analysis of these data can contribute to the definition of the clinical and sociodemographic profile of patients with COVID-19. Thus, a great social impact is demonstrated when databases are published. Open data accelerates the research process, facilitates reuse and enriches datasets, in addition to optimizing the application of public resources, that is, enabling more use of the same investment.", "keywords": [ "Coronaviruse", "COVID-19", "COVID-19 pandemic", "COVID-19 Virus Infection", "Epidemic by New Coronavirus 2019" ], "content": "Introduction\n\nThe coronavirus disease 2019 (COVID-19) pandemic has been considered the greatest challenge of the present time, associated with the unprecedented crisis in the health area, due to the expressive demand for hospital beds by patients with severe coronavirus conditions, which resulted in the collapse of health systems worldwide.1–3 Patients affected by COVID-19 have shown clinical and sociodemographic variations, with a mortality rate around 2% in cases where there is massive alveolar damage and progressive respiratory failure.4–7 Sex and gender variables also influenced COVID-19 epidemiology.8 Its lethality varies, above all, according to age group, clinical conditions and pre-existing comorbidities, such as arterial hypertension, diabetes, previous pulmonary disease, cardiovascular disease, cerebrovascular disease, immunosuppression and cancer.9–11 Although there are disparities with regard to clinical variables and comorbidities associated with increased risk of hospitalization and mortality from COVID-19, growing evidence shows that patients with pre-existing diseases, and advanced age, are especially at risk of death due to viral infection.12–15 Therefore, future analyses of this database can contribute to the analysis of characteristics of hospital admissions of patients affected by COVID-19. This database contains relevant information on the sociodemographic and clinical characteristics of patients hospitalized by COVID-19. The publication of the database promotes open science, the integrity and quality of scientific production and the reuse of data.\n\n\nMethods\n\nThis research was approved by the Research Ethics Committee of the Federal University of Santa Catarina (UFSC), (opinion No. 4.323.917/2020) Santa Catarina, Brazil. Patients provided written informed consent for data collection and publication.\n\nThis database comes from a cohort of patients who were admitted with a diagnosis of COVID-19 in two hospitals in southern Brazil. Retrospectively, from November 2020 to January 2021, data were collected from medical records of all hospital admissions that occurred from 1 April 2020 to 31 December 2020. Data related to the sex of the patients refer to the biological characteristics at birth from the patients’ medical records. All patients aged 18 years or older were included. This dataset covers 799 hospitalized patients.\n\nQuestionnaires hosted in the Survey Monkey platform were used, which contained questions about sociodemographic data, health conditions, and clinical, therapeutic, and outcome data. The variables considered for this study were: sex, age, age group, race, marital status, years of education, number of hospitalizations, hospitalization units, length of hospitalizations, risk classification, whether a COVID-19 test was taken, test used to detect COVID-19, respiratory compromise, ventilatory pattern, evolution, and previous diseases.\n\nThe inclusion criteria were: hospital admissions with a medical diagnosis of COVID-19; and being 18 years old or older. Individuals under 18 years of age and those who were not hospitalized due to COVID-19 were excluded.\n\nData were characterized by the following variables: sex, age group, race, marital status and paid work. The following clinical variables are included: admission to clinical ward, hospitalization in the Intensive Care Unit (ICU), COVID-19 diagnosis, number of times hospitalized by COVID, hospitalization time in days and risk classification protocol (green, yellow, red and not informed). Other clinical variables included: pulmonary impairment: <50%, between 50 and 75% or >75%; patients ventilation pattern (presented dyspnea with respiratory effort, dyspnea without effort or without dyspnea); high-flow oxygen mask; pulmonary thromboembolism (PE); cardiovascular disease; pulmonary sepsis; influenza exam results. Other health problems (if yes or no): diabetes, systemic arterial hypertension, chronic obstructive pulmonary disease (COPD), obesity, tabaco smoking, asthma, chronic kidney disease, overweight, vascular accident (Stroke), sedentary lifestyle, human immunodeficiency virus (HIV/AIDS), cancer, Alzheimer's disease, Parkinson's disease. The description of these characteristics is provided in Table 1. The analysis and reuse of sociodemographic and clinical profile data can be performed using descriptive statistics and measures of central tendency (mean and median) and variability (standard deviation and interquartile range), as well as absolute and relative distributions (n-%). The symmetry of the continuous distribution can be assessed using the Kolmogorov-Smirnov test. The predictive power of the variables can be analyzed using logistic regression. The opening of data from research projects is one of the most important elements of the research lifecycle for the success of Open Science. This is a sine qua non for reproducibility and scientific progress. Open Data speeds up the research process, facilitates reuse and enriches data sets, in addition to optimizing the application of public resources, in other words, enabling more use of the same investment. Opening data also allows detecting false, biased and inaccurate conclusions, as they are subject to replicability tests. Thus, great social impact is demonstrated when databases are published.16\n\nLimitations\n\nThis dataset is limited to a retrospective cohort of patients from two hospitals in southern Brazil. This can be considered a limitation. However, the data are very relevant, as there are few published studies and databases available on COVID-19 in Brazil. Researchers interested in the sociodemographic and clinical profile of patients hospitalized for COVID-19 can extensively explore the variables described here.\n\nEthical considerations\n\nThe present study was approved by the Research Ethics Committee of the Federal University of Santa Catarina (UFSC), (opinion No. 4.323.917/2020) Santa Catarina, Brazil. The basis and necessary information about the study objectives and method were given to all participants before the commencement of the study, and written informed consent was obtained from them. Participants consented to data publication. Participants were assured of the confidentiality of data and that only general statistics would be presented.\n\n\nAuthors’ contributions\n\nERJ, EL and JEWB made substantial contributions to the conception and design of the work, or the acquisition, analysis or interpretation of data, and to the writing of the work or critically reviewing important intellectual content. They have given final approval to the version and have agreed to be responsible for all aspects of the work, ensuring that issues relating to the accuracy or completeness of any part of the work are properly investigated and resolved. JCRL, FMP, RSV, MAG, TCN, MCSA, MMP, MMM, CRS, WMCJ, VCCW, made substantial contributions to the acquisition of the data and the writing of the paper. They have approved the final version and agree to be responsible for all aspects of the work, ensuring that issues relating to the accuracy or completeness of any part of the work are properly investigated and resolved. All authors read and approved the final manuscript.", "appendix": "Data availability\n\nFigshare: Covid-19 Hospital Admissions Database.xlsx. https://doi.org/10.6084/m9.figshare.16746073.v4. 17\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nThis is an open access database distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution and reproduction, provided the original work is properly cited.\n\n\nAcknowledgments\n\nThe authors gratefully acknowledge the Foundation for Research Support of Santa Catarina (FAPESC).\n\n\nReferences\n\nPan American Health Organization: Coronavirus Disease (COVID-19) pandemic.2020. Reference Source\n\nNeto J, Viana RAPP, Franco AS, et al.: Nursing diagnosis/outcomes and interventions for critically ill patients affected by covid-19 and sepsis. Texto Contexto Enferm. 2020 [cited 2021 Oct 10]; 29(e20200160): 1–17. Publisher Full Text\n\nBitencourt JVOV, Meschial WC, Frizon G, et al.: Nurse’s protagonism in structuring and managing a specific unit for COVID-19. Texto Contexto Enferm. 2020 [cited 2021 Jun 8]; 29: e20200213. Publisher Full Text\n\nXu Z, Shi L, Wang Y, et al.: Pathological findings of COVID-19 associated with acute respiratory distress syndrome. Lancet Respir Med. Lancet. Respir. Med. 2020 [cited 2021 Oct 12]; 8(4): 420–422. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWu F, Zhao S, Yu B, et al.: A new coronavirus associated with human respiratory disease in China. Nature. 2020 [cited 2021 Oct 12]; 579: 265–269. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHuang C, Wang Y, Li X, et al.: Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet. 2020; [cited 2021 Oct 8]; 395(10223): 497–506. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMenezes H, Lima FR, Camacho ACLF, et al.: Specialized nursing terminology for the clinical practice directed at covid-19. Texto Contexto Enferm. 2020; [cited 2021 Oct 8]; 29: e20200171. Publisher Full Text\n\nKharroubi SA, Diab-El-Harake M: Sex-differences in COVID-19 diagnosis, risk factors and disease comorbidities: A large US-based cohort study. Front. Public Health. 2022; [cited 2022 Feb 17]; 10. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHolshue ML, DeBolt C, Lindquist S, et al.: Washington State 2019-nCoV case investigation Team. First case of 2019 novel coronavirus in the United States. N. Engl. J. Med. 2020; [cited 2021 Jun 30]; 382(10): 929–936. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPellegrine FLPC: Covid-19, a pandemia de 2020: Origem, agente etiológico, transmissão, manifestações clínicas. Acta Sci. Tech. 2020; [Cited 2020 No 20]; 8(1). Publisher Full Text\n\nBrazil: Ministry of Health (BR). Coronavírus: o que você precisa saber e como prevenir o contágio. Brasília (DF): 2020 [cited 2021 Jun 30]. Reference Source\n\nNascimento JCP, Rocha RRA, Dantas JKS, et al.: Management of patients diagnosed or suspected with covid-19 in cardiorespiratory arrest: a scoping review. Texto Contexto Enferm. 2020; [cited 2021 Oct 11]; 29: e20200262. Publisher Full Text\n\nYan L, Zhang HT, Goncalves J, et al.: An interpretable mortality prediction model for COVID-19 patients. Nat. Mach. Intell. 2020; [cited 2021 Oct 8]; 2(5): 283–288. Publisher Full Text\n\nCao Z, Li T, Liang L, et al.: Clinical characteristics of Coronavirus Disease 2019 patients in Beijing, China. PLoS One. 2020; [cited 2021 Mar 30; 15(6): 1–7. Publisher Full Text\n\nHammerschmidt KSA, Bonatelli LCS, Carvalho AA: The path of hope in relationships involving older adults: the perspective from the complexity of the covid-19 pandemic. Texto Contexto Enferm. 2020; [cited 2021 Jun 30]; 29: e20200132. Publisher Full Text\n\nUNESCO: Recommendation on Open Science.November. 2021. Reference Source\n\nJesus ER, Boell JEW, Reckziegel JCL, et al.: Covid-19 Hospital Admissions Database.xlsx. Dataset. figshare. 2021. Publisher Full Text" }	[ { "id": "178045", "date": "14 Jun 2023", "name": "Lirane Elize Defante Ferreto", "expertise": [ "Reviewer Expertise Research area in infectious and contagious diseases with a project similar to the one presented with the collection of information from patients hospitalized with COVID-19." ], "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 information available can be accessed by researchers who are interested in better understanding health policies, planning health actions, and estimating costs and demands in emergency situations. Database studies of this nature are important as they contribute to improving the effectiveness of health promotion and prevention actions. The results of data analysis provide information to managers who can assess the situation and identify critical points and propose strategies in situations that require immediate solutions.\nReview the inclusion and exclusion criteria. The author informs, “The inclusion criteria were: hospital admissions with a medical diagnosis of COVID-19; and be 18 years or older. Individuals under 18 years of age and those who were not hospitalized due to COVID-19 were excluded”, so if being 18 years of age or older is an inclusion criterion and hospital admissions with a medical diagnosis of COVID-19, the exclusion criteria must be those within this population who were included, not being 18 years old and being hospitalized for COVID-19 was already a characteristic or circumstance that prevented the inclusion of the subject in the study.\nIn the variables, the inclusion criterion is having a diagnosis of COVID-19 and being hospitalized, the diagnostic variable for COVID-19 is not justified since everyone in the study has this outcome. Inform how the risk classification (green, yellow, red and not informed) was defined in the protocol in the study patients. Is it relevant that the author informs the distinction between obesity and overweight, would it not be possible to present this information in a single variable? It is not clear in the text how the authors defined a sedentary lifestyle. It is suggested that age in the bank be presented as a continuous variable, which allows the application of numerous statistical methods with better power for inference and modeling. As the authors inform that they collected data regarding income, the information in the database would be interesting.\nAs argued by the authors, “open data streamline the research process, facilitate reuse and enrich datasets, in addition to optimizing the application of public resources, that is, enabling greater use of the same investment”, it would be recommended that the authors inform the geographical location of the two hospitals in southern Brazil, as well as better describing the population from which the sample originated.\nI understand that this information described by the author “Researchers interested in the sociodemographic and clinical profile of patients hospitalized for COVID-19 can widely explore the variables described here”, is not a limitation.\n\nIs the rationale for creating the dataset(s) clearly described? Yes\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? Yes", "responses": [ { "c_id": "9868", "date": "18 Dec 2023", "name": "Edna Ribeiro de Jesus", "role": "Author Response", "response": "Response to reviewer We gratefully thank the reviewer for their interest in our paper and for the invitation to revise this manuscript. Thank you very much for your carefully revision and for spending your time collaborating to improve our manuscript. Below, we will elaborate on how we have responded to each comment and suggestion by the reviewer. We hope you will find that we have dealt satisfactorily with all comments and suggestions made by the reviewer. Yours sincerely, Authors The information available can be accessed by researchers who are interested in better understanding health policies, planning health actions, and estimating costs and demands in emergency situations. Database studies of this nature are important as they contribute to improving the effectiveness of health promotion and prevention actions. The results of data analysis provide information to managers who can assess the situation and identify critical points and propose strategies in situations that require immediate solutions. R: Thank you for your comment. Review the inclusion and exclusion criteria. The author informs, “The inclusion criteria were: hospital admissions with a medical diagnosis of COVID-19; and be 18 years or older. Individuals under 18 years of age and those who were not hospitalized due to COVID-19 were excluded”, so if being 18 years of age or older is an inclusion criterion and hospital admissions with a medical diagnosis of COVID-19, the exclusion criteria must be those within this population who were included, not being 18 years old and being hospitalized for COVID-19 was already a characteristic or circumstance that prevented the inclusion of the subject in the study. R: Thank you for your comment. Yes, there is no exclusion criteria to inform for this study. We have collected data from medical records of all hospital admissions due to COVID-19 of patients 18 years or older, that occurred from 1 April 2020 to 31 December 2020. In the variables, the inclusion criterion is having a diagnosis of COVID-19 and being hospitalized, the diagnostic variable for COVID-19 is not justified since everyone in the study has this outcome. Inform how the risk classification (green, yellow, red and not informed) was defined in the protocol in the study patients. Is it relevant that the author informs the distinction between obesity and overweight, would it not be possible to present this information in a single variable? It is not clear in the text how the authors defined a sedentary lifestyle. It is suggested that age in the bank be presented as a continuous variable, which allows the application of numerous statistical methods with better power for inference and modeling. As the authors inform that they collected data regarding income, the information in the database would be interesting. R: The risk classification (green, yellow, red and not informed) was defined in the protocol according to The Manchester Triage System (MTS). It enables nurses to assign a clinical priority to patients, based on presenting signs and symptoms, without making any assumption about the underlying diagnosis. Sedentary lifestyle was defined as, in addition to not exercising, patient mentioned that usually in their life there is no basic day-to-day activities that increase the body's caloric expenditure. Data related to obesity, overweight and sedentary lifestyle were retrieved from hospitals multidisciplinary team notes registered in medical records, which rely on individual professional evaluation of patients during usual care. The accuracy of this data can not be verified. Data related to patients age was categorized to avoid patient identification. We are open to present this data as well data regarding income, under demand, to editors/researchers. As argued by the authors, “open data streamline the research process, facilitate reuse and enrich datasets, in addition to optimizing the application of public resources, that is, enabling greater use of the same investment”, it would be recommended that the authors inform the geographical location of the two hospitals in southern Brazil, as well as better describing the population from which the sample originated. R: Our study was carried out in two public hospitals in the state of Santa Catarina, Brazil. One from Lages city and on from the capital, Florianópolis. It is a cohort of all patients who were hospitalized with a diagnosis of COVID-19. I understand that this information described by the author “Researchers interested in the sociodemographic and clinical profile of patients hospitalized for COVID-19 can widely explore the variables described here”, is not a limitation. R: Thank you for your comment. We agree that this is not a limitation. A limitation we can now identify is that data about obesity, overweight and sedentary lifestyle were retrieved from hospitals multidisciplinary team notes registered in medical records, which rely on individual professional evaluation of patients during usual care. The accuracy of this data can not be verified." } ] }, { "id": "221267", "date": "23 Nov 2023", "name": "Raúl López-Izquierdo", "expertise": [ "Reviewer Expertise Research area in emergency and infectious. I participated in various studies about COVID-19 prognosis." ], "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 an open database to advance knowledge of the COVID-19 disease. It presents relative data from the beginning of the pandemic until the end of 2020, that is, in the first phase of this. It has been shown, as the authors indicate, that the lethality of this infection is marked by the age of the patients and their comorbidity.\nResearch design and data collection method\nInclusion criteria are appropriate\nData description\nThe description of the variables is partially adequate. I think the age variable should be shown as a continuous and uncategorized variable.\n\nThe authors should better describe some of the qualitative variables they present, and explain the categories that make them up. Among these variables that would have to be explained would be: risk classification protocol, pulmonary impairment and pulmonary sepsis.\n\nIs the rationale for creating the dataset(s) clearly described? Yes\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? Yes", "responses": [ { "c_id": "10747", "date": "13 Apr 2024", "name": "Edna Ribeiro de Jesus", "role": "Author Response", "response": "Response to reviewer We gratefully thank the reviewer for their interest in our paper and for the invitation to revise this manuscript. Thank you very much for your carefully revision and for spending your time collaborating to improve our manuscript. Below, we will elaborate on how we have responded to each comment and suggestion by the reviewer. We hope you will find that we have dealt satisfactorily with all comments and suggestions made by the reviewer. Yours sincerely, Authors This article presents an open database to advance knowledge of the COVID-19 disease. It presents relative data from the beginning of the pandemic until the end of 2020, that is, in the first phase of this. It has been shown, as the authors indicate, that the lethality of this infection is marked by the age of the patients and their comorbidity. R: Thank you for your comment. Research design and data collection method Inclusion criteria are appropriate R: Thank you for your comment. Data description The description of the variables is partially adequate. I think the age variable should be shown as a continuous and uncategorized variable. R: We sincerely appreciate your valuable feedback and thorough review of our work. We have taken into consideration your suggestion regarding the presentation of the age variable. In the specific case of the age variable, we recognize its relevance for understanding the nuances of our study. However, by disclosing specific details about the age of participants, we run the risk of compromising the identity of some subjects. From then on, this variable was kept in groups to maintain anonymity, as is available in the published database. However, we have this variable in its continuous presentation to make it available to researchers who are interested. The authors should better describe some of the qualitative variables they present, and explain the categories that make them up. Among these variables that would have to be explained would be: risk classification protocol, pulmonary impairment and pulmonary sepsis. We are committed to addressing your recommendations and thank you for pointing out ways to improve the description of the variables Risk classification protocol R: The risk classification protocol was defined according to The Manchester Triage System (MTS)1-3. The risk classification protocol is an essential qualitative variable that describes the system used to assess and categorize the severity of patients' clinical condition. This protocol may include criteria such as heart rate, blood pressure, oxygen saturation, among others. Each category within the protocol represents different levels of severity, aiding in identifying patients who require immediate attention, intensive monitoring, or regular care. We will detail the specific categories within the protocol, highlighting the criteria used for risk classification1-3. Reference: 1 Mackway-Jones K, Marsden J, Windle J. Sistema Manchester de Classificação de Risco. 2nd ed. Belo Horizonte: Folium; 2017. 2Farrohknia N, Castrén M, Ehrenberg A, Lind L, Oredsson S, Jonsson H, et al. Emergency Department Triage Scales and their components: a systematic review of the scientific evidence. Scand J Trauma Resusc Emerg Med [Internet]. 2011 [cited 2023 Dec 8]; 19:42. Available from: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3150303/ Pulmonary impairment R: The Pulmonary impairment variable was collected through the medical report of the lung tomography considering the following impairment values: less than 50%, between 50% and 75% and greater than 75%. Pulmonary sepsis R: The pulmonary sepsis variable was collected from electronic medical records based on medical diagnosis." } ] } ]	1	https://f1000research.com/articles/12-627
https://f1000research.com/articles/12-816/v1	11 Jul 23	{ "type": "Research Article", "title": "Postural fall in systolic blood pressure is a useful warning sign in dengue fever", "authors": [ "Chakrapani Mahabala", "Archith Boloor", "Sushmita Upadhya", "Satya Sudish Nimmagadda", "Tejaswini Lakshmikeshava", "Raghav Anand", "Chakrapani Mahabala", "Sushmita Upadhya", "Satya Sudish Nimmagadda", "Tejaswini Lakshmikeshava", "Raghav Anand" ], "abstract": "Background: Capillary leak is the hallmark of development of severe dengue. A rise in haematocrit has been a major warning sign in WHO guidelines. Postural hypotension, which could reflect the intravascular volume reduction in capillary leak has been noted as warning sign in CDC and Pan American Health Organisation guidelines. We evaluated the diagnostic accuracy of postural hypotension as a marker of development of severe dengue. Methods: 150 patients admitted with dengue fever were recruited in this prospective observational study. Diagnostic accuracy of conventional warning signs (abdominal pain, persistent vomiting, fluid accumulation, mucosal bleeding, lethargy, liver enlargement, increasing hematocrit with decreasing platelets) and postural hypotension was evaluated. Results: 23 (15.3%) subjects developed severe dengue. Multiple logistic regression analysis showed that ascites/pleural effusion and postural fall in systolic blood pressure of >10.33% had odds ratio of 5.024(95%CI:1.11 – 22.75) and 11.369 (95% CI:2.27 – 56.87), respectively. Other parameters did not reach statistical significance. Sensitivity and specificity of ascites/pleural effusion were 82.6% and 88.2% for development of severe dengue whereas postural fall in systolic blood pressure had sensitivity and specificity of 87% and 82.7%. Conclusions: These findings present a strong case for including postural hypotension as a warning sign in patients with dengue fever, especially in resource limited settings.", "keywords": [ "Severe Dengue", "hematocrit", "Warning signs", "Postural Hypotension", "Hemoconcentration", "Thrombocytopenia" ], "content": "Introduction\n\nMosquito-borne dengue viral fever is endemic to India. Every year thousands of cases are detected throughout India despite mosquito control measures.1 In 2020, India recorded 44585 cases of dengue and in 2021, it increased to 123106 cases.1 Dengue progresses from a stage of fever without warning signs to dengue with warning signs and then to severe dengue. About 5-15% of patients with dengue fever progress to severe dengue.2 This febrile illness has the potential to transform into severe dengue and result in mortality, even in young healthy population.3\n\nIt’s clinically difficult to identify those patients with dengue fever who later on progress to severe dengue.3,4 World Health Organisation has identified a set of seven clinical and laboratory parameters as warning signs (abdominal pain, persistent vomiting, fluid accumulation, mucosal bleeding, lethargy, liver enlargement, increasing hematocrit with decreasing platelets) which are extensively used in clinical practice for early identification of progression to severe dengue.2 There have been many studies evaluating the diagnostic accuracy of these parameters in dengue fever with mixed results.2,5–7 In general these parameters have high specificity and high negative predictive value but a lower sensitivity and lower positive predictive value.2,7\n\nCapillary leak is the hallmark of onset of severe dengue. In clinical practice, capillary leak is identified by hemoconcentration, a significant rise in hematocrit, and evidence of fluid collection in cavities. Rise in hematocrit and concurrent significant drop in platelet count is an important warning sign. To identify this parameter, patients are subjected to repeated blood investigations. Availability of good laboratories, manpower, and money for repeating these tests frequently would be a challenge in rural areas. Moreover, interpretation of rising hematocrit requires a baseline hematocrit value which is unavailable in most of the patients when they get admitted in resource-limited settings.8,9 Assuming baseline hematocrit with population data is advised when baseline values are not available.4 This is not reliable, because of the wide variability of hemoglobin and hematocrit in third-world countries. It also was noted earlier that many patients did not have a significant rise in hematocrit even when they develop shock in dengue fever.10\n\nCapillary leak leads to hypovolemia and varying degree of hypotension.11 Most of the clinical manifestations of dengue complications can be attributed to capillary leak syndrome.11 Orthostatic blood pressure changes are commonly used to assess intravascular volume.12 Hence, postural fall in blood pressure could be an indicator of significant capillary leak in early part of dengue fever. CDC guidelines and Pan American Health Organisation (PAHO) guidelines include Postural hypotension as one of the warning signs.13,14 Clinical criteria used in dengue management at the Queen Sirikit National Institute of Child Health, Bangkok also include postural hypotension as one of the parameters for admission to the hospital.15 Postural hypotension is not included as warning sign in WHO guidelines. Conventional warning signs (defined by WHO) have been studied extensively as predictors of severe dengue. However, data regarding postural hypotension in this condition is very limited. Hence this study was planned to evaluate the accuracy of postural hypotension in identifying patients with severe dengue and develop a simple model for identifying the subsequent development of severe dengue.\n\n\nMethods\n\nPatients admitted to hospital with dengue fever as per WHO criteria between 2011-2015 were included in this prospective observational study. Patients of 18 years and above with NS1 antigen positive results or positive dengue IgM ELISA report were included. Patients with severe dengue on admission were excluded. In our study, to avoid bias, inclusions, measurements and outcomes were all objective. Descriptive clinical data regarding atypical manifestations of dengue among these patients was published earlier.16 Analytical data regarding diagnostic performance of warning clinical signs and postural hypotension are presented in this paper.\n\nWe calculated the sample size by assuming the expected prevalence to be 15%, with a sensitivity of 70% and specificity of 85%, precision of 20% and 95% confidence interval and a drop out percentage of 5%. The sample size was estimated as 143.\n\nComplete blood count (by pulse detection/fluorescence flow cytometry using Sysmex XN 9000), erythrocyte sedimentation rate (by automated using Sysmex XN9000), liver function test (by 3,5-dichlorophenyldiazonium tetrafluoroborate (DPD) for bilirubin, biuret test for proteins/UV Kinetic colorimetric method for Alanine transaminase and Aspartate transaminase using Cobas Pro.), creatinine (by Jaffe colorimetric using Cobas Pro; the Cobas Pro analyzer series is automated system using a combination of photometric and ion-selective electrode (ISE) determinations, and electrochemiluminescence (ECL) signal in the immunoassay analysis module (e601 module), chest X ray, abdominal ultrasound were done on admission. Hemoglobin, hematocrit and platelet count was done daily for the next 48 hrs.\n\nThe sample was drawn by the nurse in the respective wards (2cc of EDTA and 2 cc of serum sample). The samples were analysed in the central laboratory by automated machines as described. The results were ratified by the laboratory incharge faculty.\n\nRise in hematocrit was calculated by comparing the hematocrit after admission with population mean values.4 Hematocrit was measured by pulse detection method using the Sysmex XN analyser 9000. Mean baseline hematocrit for South Indian males was 44.3% and for females 36.4%.17 Rise of 20% compared to the baseline hematocrit was considered significant (53.2% for males and 43.7% for females).\n\nPatients were treated as per the WHO 2009 Protocol for the management of Dengue. Patients were followed up until they recovered or succumbed to the illness. Patients who developed severe dengue were identified as per the WHO criteria.18\n\nEthical committee clearance was obtained from the institutional ethics committee at Kasturba Medical College, Mangalore, India (approval number – IEC KMC MLR 03/2022/82). Written informed consent was obtained from the participants for collection of data, analysis of data and publication of findings.\n\nData was analysed using the software SPSS version 25 (RRID:SCR_002865). Sensitivity, specificity, negative predictive value, and positive predictive value were calculated for all 7 warning signs and postural fall in systolic blood pressure (SBP). Multiple logistic regression test was performed to find out the adjusted odds ratio of parameters between non-severe and severe dengue patients. Receiver operator characteristic curve analysis was done to find the optimal cut-off value of the continuous variables which would yield the best specificity and sensitivity for severe dengue fever. Based on the logistic regression analysis, parameters that had significant odds ratio were identified and decision tree analysis was performed using those parameters as independent variables and severe dengue as the dependent variable.\n\nCHAID method of model development was used to develop the decision tree model with 70% of the sample for development of the model (training sample) and 30% of the data (test sample) for split sample validation of the model. Accuracy of the model for training and test sample was expressed as accuracy with a 95% confidence interval. Specificity, sensitivity, negative likelihood ratio, positive likelihood ratio, and diagnostic odds ratio were calculated for the entire dataset using the model developed by the decision tree.\n\n\nResults\n\nClinical and laboratory data of 150 dengue patients admitted to the hospital were analysed.22 All 150 subjects who were included were available for evaluation till the end of study except for one patient who succumbed to the illness. 74% were men and 26% were women. The mean age of the subjects was 37.9±15.3 years. 23 patients with dengue developed severe dengue as per the World Health Organisation classification. The median duration of fever before admission was four days (IQ range 3–6). There was a statistically significant difference in hemoglobin, haematocrit, and postural fall in the systolic blood pressure (SBP) on admission between the groups which developed severe dengue subsequently and the group which remained in the non-severe category (Table 1).\n\nWarning signs showed good specificity and positive predictive value for severe dengue, but in general, sensitivity and negative predictive values were low, except for pleural effusion/ascites which had good sensitivity and specificity. Postural fall in SBP also showed higher sensitivity and specificity (Table 2).\n\nReceiver operator curve (ROC) analysis showed an area under the curve of ROC 0.86; p<0.001 (95% CI: 0.77-0.95) and analysis of the coordinates showed that postural fall of more than 10.33% in systolic BP was the ideal cut-off. Multiple logistic regression analysis revealed that except for postural fall in the SBP on admission and the presence of pleural effusion/ascites, none of the other parameters had a statistically significant adjusted odds ratio (Table 3).\n\nHence pleural effusion/ascites and postural fall in the systolic BP were taken as independent parameters for the decision tree analysis. Results of decision tree analysis showed that the model had a very high accuracy of 93.7% (95% CI: 88.9-98.5) for the training data set and 86.7% (95% CI: 76.5-96.9) for the test data set (validation data set). The cross-tabulation of observed and predicted values is mentioned in Table 4.\n\nPatients with less than 10.33% fall on standing SBP were very unlikely to develop severe dengue than those with more than 10.33% fall in the systolic BP. Patients who did not have pleural effusion/ascites were also unlikely to develop severe dengue (Figure 1).\n\nSpecificity, sensitivity, negative likelihood ratio, positive likelihood ratio, negative predictive value, positive predictive value, and diagnostic odds ratio of the model for the entire data set is shown in Table 5.\n\nThree subjects succumbed to the illness and all of them had postural SBP fall of more than 10.33% and had pleural effusion/ascites in the initial screening and were found to have postural SBP fall of more than 18%.\n\n\nDiscussion\n\nWe have studied 150 inpatients with dengue and evaluated the diagnostic performance of warning signs and postural hypotension. Fluid accumulation in cavities and postural fall in SBP of >10.33% were found to have good sensitivity and specificity. Multiple logistic regression showed that other warning signs did not have significant adjusted odds ratio for the development of severe dengue compared to ascites/pleural effusion and postural fall in SBP. Based on decision tree analysis, we developed a model to identify patients with high risk of progression to severe dengue utilizing simple clinical tools (postural hypotension and pleural effusion/ascites). Diagnostic odds ratio of the model is 53.9, making the decision tree a very good diagnostic tool for ruling out the risk of progression to severe dengue. This model performed well both in the development and validation cohort confirming good internal validity.\n\nSevere dengue develops in about 5-15% of patients with dengue fever.2 Capillary leak is a unique and major pathogenetic mechanism in the development of severe dengue. Hence, markers of capillary leak like rising hematocrit and fluid accumulation in cavities have been part of dengue management protocols. WHO has identified seven warning signs for severe dengue: abdominal pain, persistent vomiting, fluid accumulation, mucosal bleeding, lethargy, liver enlargement, increasing hematocrit with decreasing platelets. These markers have been used extensively to triage patients with dengue fever to identify those at higher risk of developing severe dengue. Severe dengue has high mortality of nearly 20% which can be brought down to nearly 1% of patients if identified early and managed appropriately.6 Recently, many studies have been published evaluating the performance of these parameters in predicting severe dengue. In a study published from Malaysia, 700 patients were studied to evaluate the diagnostic performance of warning signs for association with severe dengue. Though specificity was good, sensitivity was suboptimal. Sensitivity of rise in hematocrit was 0.29 which was similar to our study (0.13) and specificity was above 90%.2\n\nCapillary leak occurs secondary to damage of endothelial cell-to-cell junction. It can occur as a primary event (Clarkson’s disease) or secondary to a variety of infections like dengue or other inflammatory conditions.11 Capillary leak can lead to intravascular changes (hemoconcentration, hypovolemia- postural hypotension), extravascular changes (fluid accumulation in cavities) and organ involvement (abdominal pain, vomiting, lethargy, liver involvement). Intravascular changes have been typically assessed with hemoconcentration-rise in hematocrit. Importance of this phenomenon was identified around 1970 in Thailand and management protocols were developed by WHO subsequently based on this concept.15 However, requirement of basal level to calculate rise in hematocrit is a major challenge in third world countries. Other parameters like postural hypotension would be an appropriate alternative to hematocrit in these situations since sensitivity and specificity for postural hypotension were very high for diagnosing severe dengue.\n\nEvaluation of the rise in hematocrit as a predictor of severe dengue has yielded mixed results. In a meta-analysis of 87 studies consisting of 35,184 dengue fever and 8,173 severe dengue, 34 clinical/biochemical factors were associated with severe dengue out of which 9(including plasma leakage) were relevant within the 7 days window.6 The odds ratio for pleural effusion for association with severe dengue was 15.83, p<001. Hematocrit was strongly associated with severe dengue (standardized mean difference=0.327, 95% CI: 0.019-0.546, p=0.003).6 However, these observations were not confirmed in a meta-analysis involving a larger number of studies.5 Sangkaew et al. performed a systematic review and meta-analysis of studies that focussed on predicting severe dengue using clinical and biochemical parameters during the febrile phase of the illness.5 150 research papers were included. Hemoconcentration was not found to be significantly different between the group which developed severe dengue compared to the group which remained non-severe. The standardised mean difference was 0.07 (95% CI: -0.11 to 0.26) which was statistically not significant (p= 0.59).5 Moreover, 53.8% of patients with severe dengue did not have hemoconcentration during an epidemic of dengue in Brazil in 2008.7 Difficulties in identifying plasma leakage by clinicians and the need for clinical parameters instead of laboratory parameters, especially in resource-limited settings, were also highlighted by Horstick et al.9\n\nThere have also been a few studies in the past attempting to create a decision tree to help identify patients with a risk of progression to severe dengue, earlier on in the illness.19–21 These studies either used biochemical parameters, had a lower diagnostic accuracy compared to the decision tree in the current study, or did not have an internal validation. A study by Tamibmaniam et al. tried to find the factors associated with severe dengue infection and to create a decision tree similar to our study.20 Simple logistic regression analysis found many factors to have the ability to predict severity, but multiple logistic regression narrowed it down to pleural effusion, vomiting, and low systolic blood pressure. Using these variables, they created a decision tree with a sensitivity of 0.81, specificity of 0.54, PPV of 0.16, and NPV of 0.96. Our decision tree has a comparable sensitivity and NPV while having a much higher specificity and PPV. Also, the study by Tamibmaniam et al. did not include an internal validation of their decision tree, unlike in the current study where the internal validation provided by the training sample further validates the results of the test sample.\n\nDengue patients can be easily and effectively triaged by checking for postural hypotension on admission and daily thereafter. If SBP fall is more than 10.33%, evaluation for pleural effusion/ascites can be done. Patients with pleural effusion/ascites and postural hypotension are the ones who need close monitoring and complete evaluation with a full battery of investigations as per WHO protocol to confirm the high risk of progression to severe dengue. Other patients may not require this aggressive approach since the model has a negative predictive value of about 94%. Postural hypotension represents intravascular changes and ascites/pleural effusion represents extravascular changes.\n\nIdentifying patients likely to develop severe dengue is a complex clinical decision-making process. Warning signs defined by WHO help the clinician in this process. No single parameter of these signs is definitive. Findings of this study confirm that postural hypotension is an important and useful warning sign in dengue fever. CDC and PAHO have included postural hypotension as one of the warning signs in their guidelines.13,14 WHO guidelines do not include postural hypotension as warning sign. There is a strong case for inclusion of postural hypotension in other guidelines also. Our clinical decision tool could help clinicians in remote places make effective and appropriate clinical judgments when baseline hematocrit is unavailable.\n\nThe sample size is small. The results of our study need to be confirmed in bigger and multicentric settings to establish external validity.", "appendix": "Data availability\n\nDryad: Postural fall in Systolic Blood Pressure is an useful warning sign in Dengue Fever. https://doi.org/10.5061/dryad.jwstqjqfc. 22\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\nWe thank Kasturba Medical College, Mangalore (Constituent unit of Manipal Academy of Higher Education, Manipal, India) for providing the logistic support in conducting the study.\n\n\nReferences\n\nDirectorate General of Health Services MoHaFW G of I 2022. Dengue cases and deaths in the country since 2015.[cited 2023 Feb 12]. Reference Source\n\nAhmad MH, Ibrahim MI, Mohamed Z, et al.: The sensitivity, specificity and accuracy of warning signs in predicting severe dengue, the severe dengue prevalence and its associated factors. Int. J. Environ. Res. Public Health. 2018 Sep 15; 15(9). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKumar A, Mayers S, Welch J, et al.: The spectrum of disease severity, the burden of hospitalizations and associated risk factors in confirmed dengue among persons of all ages: findings from a population based longitudinal study from Barbados. Infect. Dis. 2020; 52(6): 396–404. PubMed Abstract \| Publisher Full Text\n\nWilder-Smith A, Ooi EE, Horstick O, et al.: Dengue. Lancet. 2019 Jan 26; 393(10169): 350–363. Publisher Full Text\n\nSangkaew S, Ming D, Boonyasiri A, et al.: Risk predictors of progression to severe disease during the febrile phase of dengue: a systematic review and meta-analysis. Lancet Infect. Dis. 2021 Jul 1; 21(7): 1014–1026. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYuan K, Chen Y, Zhong M, et al.: Risk and predictive factors for severe dengue infection: A systematic review and metaanalysis. PLoS One. 2022 Apr 1; 17(4 April): e0267186. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nde Cavalcanti LPG , Martins Mota LA, Lustosa GP, et al.: Evaluation of the WHO classification of dengue disease severity during an epidemic in 2011 in the state of Ceará, Brazil. Mem. Inst. Oswaldo Cruz. 2014 Feb; 109(1): 93–98. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRodrigo C, Sigera C, Fernando D, et al.: Plasma leakage in dengue: a systematic review of prospective observational studies. BMC Infect. Dis. 2021 Dec 1; 21(1): 1082. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHorstick O, Farrar J, Lum L, et al.: Reviewing the development, evidence base, and application of the revised dengue case classification. Pathog. Glob. Health. 2012 May; 106(2): 94–101. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGupta P, Khare V, Tripathi S, et al.: Assessment of World Health Organization definition of dengue hemorrhagic fever in North India.2010.\n\nSiddall E, Khatri M, Radhakrishnan J: Capillary leak syndrome: etiologies, pathophysiology, and management. Vol. 92, Kidney International. Elsevier B.V.; 2017; pp. 37–46.\n\nKalantari K, Chang JN, Ronco C, et al.: Assessment of intravascular volume status and volume responsiveness in critically ill patients. Vol. 83, Kidney International. Nature Publishing Group; 2013; pp. 1017–1028.\n\nClinical Presentation\|Dengue\|CDC: [cited 2023 Feb 12]. Reference Source\n\nPAHO, WHO: Regional Arboviral Disease Program Algorithms for the Clinical Management of Dengue Patients.2020.\n\nKalayanarooj S, Rothman AL, Srikiatkhachorn A: Case management of dengue: Lessons learned. J. Infect. Dis. 2017; 215: S79–S88. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSudhish Nimmagadda S, Mahabala C, Boloor A, et al.: Atypical Manifestations of Dengue Fever (DF) - Where Do We Stand Today? J. Clin. Diagn. Res. 2014 Jan 12 [cited 2023 Feb 12]; 8(1): 71–73. Reference Source\n\nPasupula DK, Reddy PS: When is a south Indian really anemic? Indian J. Clin. Biochem. 2014 Oct 1; 29(4): 479–484. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWorld Health Organization: Dengue: Guidelines for Diagnosis, Treatment, Prevention and Control. New Edition.Geneva: 2009. [cited 2023 Feb 7]. Reference Source\n\nLee VJ, Lye DC, Sun Y, et al.: Decision tree algorithm in deciding hospitalization for adult patients with dengue haemorrhagic fever in Singapore. Trop. Med. Int. Health. 2009 Sep; 14(9): 1154–1159. PubMed Abstract \| Publisher Full Text\n\nTamibmaniam J, Hussin N, Cheah WK, et al.: Proposal of a Clinical Decision Tree Algorithm Using Factors Associated with Severe Dengue Infection. PLoS One. 2016 Aug 1 [cited 2023 Feb 12]; 11(8): e0161696. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPhakhounthong K, Chaovalit P, Jittamala P, et al.: Predicting the severity of dengue fever in children on admission based on clinical features and laboratory indicators: application of classification tree analysis. BMC Pediatr. 2018 Mar 13 [cited 2023 Feb 12]; 18(1): 109. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMahabala C, Boloor A, Upadhya S, et al.: Postural fall in Systolic Blood Pressure is an useful warning sign in Dengue Fever. Dryad. Publisher Full Text" }	[ { "id": "204024", "date": "19 Sep 2023", "name": "Soumya Pahari", "expertise": [ "Reviewer Expertise Neurosurgery", "Primary 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\nFirst, I would like to congratulate the authors for their work in helping to improve and simplify the prediction of severe dengue.\nIntroduction/ Methods: Mention the working definition of “severe dengue”.\n\nInclusion/ exclusion criteria: Please state and justify if patients with pre-existing postural hypotension were excluded from the study or not.\n\nSample size: Provide appropriate references for the expected prevalence of dengue being 15%.\n\nThe presence of postural hypotension is assessed only at admission. Since the duration of fever at admission is approximately 4 days in the sample, the majority of them are likely to be at the febrile stage of illness and not entered the critical phase, where more frequent occurrences of plasma leaks and postural hypotension might have occurred. Was postural hypotension assessed for in the subsequent days of admission?\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? Partly", "responses": [ { "c_id": "10313", "date": "06 Oct 2023", "name": "Archith Boloor", "role": "Author Response", "response": "1. WHO definition of severe dengue: Severe plasma leakage, leading to fluid accumulation with respiratory distress or shock Severe organ impairment (including cardiac, liver: ALT>1000 and CNS: altered consciousness) Severe bleeding. 2, Patients with pre-existing postural hypotension were excluded. 3. In a previous study published by Alok kumar et al. 15.3% of hospitalised patients developed severe dengue (190/1234). Ref is given below:Alok Kumar, Shemica Mayers, Janelle Welch, Janine Taitt, Gemma Ann Benskin, Anders L. & Nielsen (2020) The spectrum of disease severity, the burden of hospitalizations and associated risk factors in confirmed dengue among persons of all ages: findings from a population based longitudinal study from Barbados, Infectious Diseases, 52:6, 396-404, DOI: 10.1080/23744235.2020.1749723 4.Patients developing postural hypotension during the stay in the hospital were also included in the group with postural hypotension if they did not have clinical and laboratory features of severe dengue." } ] }, { "id": "220352", "date": "14 Nov 2023", "name": "Rivaldo Steven Heriyanto", "expertise": [ "Reviewer Expertise Pediatric", "Opthalmology", "COVID-19", "General" ], "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\nAn overall well written article. However, a further grammar check is advised.\nThe introduction is concise and explain the importance of analyzing the role of postural hypotension as dengue warning signs well, it is also a novel variable that should be researched further.\nThe methods is also explained well, starting from type of studies, inclusion and exclusion criteria, sample size, to the explanation of the statistical analysis. The usage of CHAID method to make a decision tree model is an excellent decision that differentiate this study from other dengue warning sign research.\nThe results answered the question of the research, starting from the adjusted odds ratio, the optimal cut-off of fall in SBP, up until the diagnostic accuracy of the decision tree. However, there is one comment, why do the author think that the result of the multiple logistic regression analysis resulted in only ascites/pleural effusion and fall in postural SBP that reached significant value? Is it possible that there is some biases that played some role?\nThe discussion discusses the results well, explaining the importance of the results, as well as how this study compare to other. One comment is related to the result, the author should explain why the other warning signs doesn't have a significant value other than ascites/pleural effusion and fall in postural SBP\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": [ { "c_id": "10603", "date": "22 Nov 2023", "name": "Archith Boloor", "role": "Author Response", "response": "WHO has developed a set of clinical warning Symptoms for triaging patients to decide inpatient management. These 7 parameters have been studied in various studies to identify the relative importance of each one of them in predicting severe dengue. Tamibmaniam et al(1) have studied 657 patients with dengue of whom 59 had severe dengue. Even though many parameters were associated with severe dengue in simple logistic regression, adjusted odds ratios were significant for 3 parameters only after multiple logistic regression analysis (Fluid accumulation, vomiting and hypotension). Other parameters did not reach statistical significance in this multiple logistic regression. Our findings are also in line with these observations. It appears that some of the parameters seem to be having stronger independent association compared to other parameters. Our findings suggest that Postural fall in Systolic Blood Pressure and Pleural effusion/Ascites have much stronger independent associations with severe dengue, compared to other warning signs, resulting in relatively lower significance for other warning symptoms. Hence, these findings are unlikely to be due to bias. 1. Tamibmaniam J, Hussin N, Cheah WK, Ng KS, Muninathan P. Proposal of a Clinical Decision Tree Algorithm Using Factors Associated with Severe Dengue Infection. PLoS One [Internet]. 2016 Aug 1 [cited 2023 Feb 12];11(8). Available from: https://pubmed.ncbi.nlm.nih.gov/27551776/" } ] } ]	1	https://f1000research.com/articles/12-816
https://f1000research.com/articles/12-1102/v1	04 Sep 23	{ "type": "Research Article", "title": "Building student loyalty in higher education: the role of corporate reputation", "authors": [ "Estacio Dinazarte Omar Raja" ], "abstract": "Background: Reputation is a vital asset for Higher Education Institutions (HEIs) as it constitutes a source of competitive advantage because it works as a quality sign for the stakeholders. Because of globalisation, decreasing funding and the changing environment in the Mozambican higher education market, HEIs need to build a favourable reputation to stay relevant. This research aims to study how a university's reputation can influence student loyalty. Methods: Utilizing a descriptive and analytical methodology, a quantitative investigation was carried out by surveying 402 students enrolled in higher education institution (HEI) courses in Mozambique. The research employed a survey questionnaire to directly collect information from the study participants. Results: The study concluded that university reputation affects student loyalty, as the relationship between both variables is statistically significant. All dimensions of HEIs reputation, namely, academic competence, social attractiveness, and responsible management, positively impact student loyalty. Although, the latter variable did not have a statistically significant impact, contradicting the current theoretical framework. Conclusions: The study's findings suggest that corporate reputation has a favorable impact on student loyalty, demonstrating a significant relationship between the two factors. Therefore, improve student retention, HEIs should seek to enhance their academic competence and social attractiveness.", "keywords": [ "Africa", "corporate reputation", "higher education institutions", "student loyalty", "Mozambique" ], "content": "Introduction\n\nIn a globalised and increasingly competitive market characterised by increased student mobility and reduced government funding, higher education institutions (HEIs) must compete to attract the best students (Musselin, 2018). Therefore, universities increasingly need an excellent reputation to be distinctive and relevant in the market and consequently competitive (Valtere, 2012).\n\nAn institution’s reputation has to do with the reliability and credibility that an organisation projects to its stakeholders (Morrissey, 2012), and reputation can be measured through the ability that this organisation has to consistently meet the expectations of its target groups over time (Morrissey, 2012). Therefore, reputation is built over time and links to the organisation’s history (Bickerton, 2000; Morrissey, 2012; Nguyen & LeBlanc, 2001). An HEI builds its reputation with the quality of its human resources, the provision of quality education, innovation through relevant scientific research, the quality of its infrastructure and the high degree of employability of its graduates (Sontaite & Bakanauskas, 2011; Valtere, 2012).\n\nReputation is essential for organisations, in general, as it constitutes a strategic resource with the potential to create value (Powell, 2016) and to obtain sustainable competitive advantage (Grant, 2013) because it holds all properties of a strategic resource (Grant, 2013; Hitt et al., 2009; Jekins et al., 2016). In the case of an HEI, reputation benefits can be the ability to attract more and better students, attract and retain the best professionals, obtain alumni support, attract funders and establish strategic partnerships with other institutions (Suomi et al., 2014). HEIs face many challenges that force them to find new sources of competitive advantage. Therefore, reputation and accreditation systems are helping universities to face new threats (Boscor, 2015). A good reputation and image of the HEI increase student loyalty, positively affecting their intentions to collaborate with the institution in the future (Eryilmaz, 2016). Thus, HEIs invest resources to create a favourable perception among their stakeholders (Lafuente-Ruiz-de-Sabando et al., 2017).\n\nThe research agenda in this area of knowledge recommends that further studies be carried out in different contexts (Abbas, 2014, 2019; Keller & Lehman, 2006; Powell, 2016), as most of the research is focused mainly on the western and Asian contexts. There are few empirical studies on this subject in the African continent. Hence, studying the Mozambican context is interesting primarily because, besides the replication of the empirical model, there is ground and opportunity to extend our knowledge about this issue by investigating what factors are set apart from the conventional theoretical models when applied to different contexts.\n\nBesides the fulfilment of the contextual gap, this paper will contribute to the academic debate by yielding a deeper understanding of which factors are more determinant when managing the university’s reputation to improve student loyalty. Furthermore, the study aims to compare perceptions of students between private and public universities, as suggested in s previous study by Rasoolimanesh et al. (2021), to generalise, more confidently, the results among different types of institutions. The insights from the research can give us valuable inputs to improve and refine the model, which explains the relationship between both variables, as suggested by other authors (Rojas-Médez et al., 2009).\n\nSimilar to other countries, the landscape of the HEIs market in Mozambique has changed dramatically in the late years, with the decrease in public funding and a rapid expansion of the number of institutions and student population, resulting in an overcrowded market in the private and public sectors. This rapid transformation was seen by the public opinion with significant concerns about neglecting the educational quality, consequently hindering the image and reputation of the whole country’s tertiary education system. Additionally, in 2012, the approval of the new financing strategy for HEIs in Mozambique, which provides for the financing of higher education institutions based on performance indicators (Ministério da Educação, 2013), comes with new challenges, especially for public institutions.\n\nThus, this study wishes to answer the following questions:\n\n• Which dimensions of university reputation are determinants of student loyalty?\n\n• Do university reputation and student loyalty differ between public and privately owned institutions?\n\nKnowing how university reputation affects student loyalty and what factors are more critical is relevant because HEIs can focus on improving the dimensions essential for their success, depending on the context. The research will highlight that some dimensions may not be as relevant as expected.\n\n\nLiterature review\n\nCorporate reputation has been systematically and more frequently the subject of debates and discussions (Babić-Hodović et al., 2011; Eberl & Schwaiger, 2005; Petrokaite & Stravinskiene, 2013), hence the collection of scientific publications on the subject (Maden et al., 2012; Shamma, 2012). The new dynamics in the relationship between the organisation and its interest groups have increasingly highlighted reputational management as the relevant and determining element (Petrokaite & Stravinskiene, 2013). Proper corporate reputation management can be critical for the success of HEIs in a highly competitive environment (Del-Castillo-Feito et al., 2019; Munisamy et al., 2014).\n\nReputation is a multidisciplinary concept, so there are several definitions with different perspectives in the literature (Eberl & Schwaiger, 2005; Maden et al., 2012). Several branches of knowledge, such as economics, marketing, management, psychology and sociology, have studied the concept (Ponzi et al., 2011). Schwaiger (2004) argues that there are different angles to view corporate reputation: corporate brand, representation of the firm’s goodwill, corporate identity, the barrier to market entry for potential competitors, and a signal of the organisation’s actions and future behaviour. Therefore, the concept is multifaceted and incorporates interrelated characteristics such as credibility, reliability and responsibility (Carmeli & Cohen, 2001; Morrissey, 2012; Puncheva-Michelotti & Michelotti, 2010).\n\nNguyen and LeBlanc (2001) consider credibility as part of corporate reputation, which may result from the contrast between its promises and actions. Corporate reputation is built over time, resulting from accumulated judgements and opinions from different stakeholders (Nguyen & LeBlanc, 2001).\n\nReputation in an HEI can be defined simply as ‘the collective representation maintained over time by the multiple constituents (internal and external) of a university’ (Alessandri et al., 2006). Sontaite and Bakanauskas (2011) argue that corporate reputation results from a subjective and collective assessment of the institution by the stakeholders based on its performance, potential, brand value, communication and past behaviour. Also, in line with the same authors, they claim that managing a university’s reputation is challenging when its constituent units, such as faculties and schools, have a distinct reputation among stakeholders. On the other hand, the institution may have a reputation locally, while internationally, it does not have the same recognition (Suomi et al., 2014).\n\nA definition that summarises the various perspectives presented on the concept describes corporate reputation as ‘the collective representation of the past and present actions and results of the organisation, which describes its ability to obtain different results from different stakeholders’ (Martin de Castro et al., 2006).\n\nSources of corporate reputation\n\nShamma (2012) presents a list of possible sources of corporate reputation: the communication and behaviour of workers, people’s experiences with the organisation, the organisation’s communications, the media’s interpretation of the organisation, word-of-mouth, competition and rumours.\n\nThis concept is formed based on interactions and transactions of stakeholders with the organisation (Eberl & Schwaiger, 2005). Reputation also results from the organisation’s activity in the past, but with an impact on the present behaviour of stakeholders concerning the organisation (Petrokaite & Stravinskiene, 2013). For this reason, reputation takes years to build, which is why it is one of the most challenging resources to accumulate for any organisation (Martin de Castro et al., 2006). However, it is fragile because any action that harms a specific group can jeopardise the accumulated organisation’s prestige or credibility over time (Nguyen & LeBlanc, 2001).\n\nCorporate reputation links to stakeholder theory (Feldman et al., 2014) so the perception of corporate reputation varies depending on the stakeholder group (Petrokaite & Stravinskiene, 2013). According to Helm (2007), the different groups of stakeholders are customers, investors, workers, suppliers and society. The student is an essential stakeholder of an HEI, and his family has an important role, as it influences his choices and preferences (Suomi, 2014).\n\nCorporate reputation measurement\n\nCorporate reputation is a difficult concept to measure, and there is no consensus between academics and practitioners on the subject (Sontaite & Bakanauskas, 2011). Possession of characteristics such as causal ambiguity, social complexity, and slow accumulation associated with the organisational history makes this concept have a high level of intangibility which is why it is a complex construct to measure (Martin de Castro et al., 2006). However, Sontaite and Bakanauskas (2011) sustain that the indicators related to the creation of good or bad attitudes of stakeholders concerning the organisation are the basis for reputation measurement, and such indicators must be weighted differently depending on the importance of each stakeholder.\n\nCaruana and Chircop (2000) present four components that constitute the reputation construct: affection or emotional appeal, image, level of awareness about the organisation, the result of its behaviour and past performance, and the experiences and interactions of stakeholders with the organisation. For Helm (2007), quality of products and services, emotional appeal, vision and leadership, results of financial activity, social responsibility and working conditions constitute the dimensions of corporate reputation.\n\nTelci and Kantur (2014) developed and validated a scale to measure the reputation of universities. The scale consists of 20 indicators divided into three dimensions: academic competence, social attractiveness and responsible management. The academic competence construct reflects the general educational capacity or quality of the university and also the quality of services provided by the institution. In comparison, social attractiveness refers to items such as the innovative capacity of the university among side its physical conditions. Finally, the dimension of responsible management regards the responsibilities of the university management to its stakeholders (Telci & Kantur, 2014). The present study adopted this scale to measure the reputation of HEIs because of the context similarity. The methodological procedure suggested to measure the reputation of HEIs is the use of questionnaires applied to stakeholders.\n\nStudent loyalty is the student’s intention to recommend some type of relationship with the institution to third parties, as well as their satisfaction with the choice of the institution or course they attend and the predisposition to relate to the institution in the future (Østergaard & Kristensen, 2005). The student’s tendency to choose the same institution over another to satisfy a particular need is also related to this concept (Temizer & Turkyilmaz, 2012).\n\nStudent loyalty is affected by a good university image and student satisfaction (Temizer & Turkyilmaz, 2012). Student retention also depends on other factors such as student’s academic abilities (Pantages & Creedon, 1978 in Kara & Deshields, 2004), their adjustment and social integration into the educational institution (Gerdes & Mallinckrodt, 1994; Mallinckrodt, 1988 in Kara & Deshields, 2004) and the expectations formed before enrolling at the institution (Baker, McNeil and Sirky, 1985 in Kara & Deshields, 2004). It is important to note that the student’s motivation to obtain an academic degree and commitment to the institution are also important factors for student retention (Kara & Deshields, 2004).\n\nStudent loyalty plays a crucial role in the success of HEIs, as loyalty not only perpetuates the institutions’ potential revenues but also causes positive synergies through a positive recommendation about the institution (Shahsavar & Sudzina, 2017). The increase in the student retention rate positively affects the life cycle of tuition fees, and it generates synergies in the low-cost recruitment of new students through word-of-mouth recommendations (Kara & Deshields, 2004). Additionally, the probability of retaining a student at a university increases if he/she stays for an extended period in that institution because of the high transaction costs for the eventual move to a competing institution (Kara & Deshields, 2004).\n\nStudent loyalty measurement\n\nStudent loyalty has attached to its measurement the following indicators: the intention to choose the same university, the recommendation to others and the intention to leave the university when possible (Temizer & Turkyilmaz, 2012). Blackmore et al. (2006) in Douglas, Mcclelland, & Davies (2008) present the following indicators of student loyalty: the student’s predisposition to continue their studies at the institution, the level and frequency of use of the university’s services and the intention of recommending the institution or course to friends, neighbours or family members translate the concept of student loyalty.\n\nTaecharungroj (2014) uses a scale that groups these three categories into five items, namely: saying positive things about the university to other people; intention to recommend the university to anyone seeking advice; encouraging friends and family to consider the university and to have a close relationship with it; consider the institution as the first choice when choosing a university to study, and the intention of relating to the university in the future. The present research adopts this last scale to measure student loyalty.\n\nA favourable corporate image and reputation influence the attitudes of the organisation’s stakeholders (Iwu-Egwuonwu, 2011). Among other antecedents, such as student satisfaction, the reputation of the university is one of the key drivers of student loyalty (Alves & Raposo, 2010; Helgesen & Nesset, 2007; Kaushal & Ali, 2020; Nesset & Helgesen, 2009) Because of these arguments the study proposes to test the following hypothesis:\n\nH1: Corporate reputation has a significant relationship with student loyalty.\n\nUniversity reputation for this research contains three main dimensions: academic competence, social attractiveness and responsible management (Telci & Kantur, 2014). For this reason, theoretically, it is plausible to establish the link between these dimensions and student loyalty.\n\nPrior studies have shown that the quality of education an institution provides (Daud et al., 2020; Ismanova, 2019; Lin & Tsai, 2008; Nesset & Helgesen, 2009; Yang et al., 2008), the trustworthiness of the university (Carvalho & de Oliveira Mota, 2010; Ismanova, 2019; Rojas-Méndez et al., 2009), a commitment to academic excellence (Vianden & Barlow, 2014), and graduates’ success (Quintal & Phau, 2016) are crucial ingredients of student loyalty towards the university. Those factors are all items of academic competence in an HEI (Telci & Kantur, 2014). Thus, the following hypothesis arises:\n\nH2: Academic competence has a significant relationship with student loyalty.\n\nThe quality of the facilities (Nesset & Helgesen, 2009; Thomas, 2011; Vianden & Barlow, 2014) such as having a good campus, quality of libraries, among others, and the overall experience the student (Yu & Kim, 2008) has in an HEI affects student loyalty positively. That’sThat’sThat’s why the more social attractive an institution is, the more loyalty it gets from its students (Telci & Kantur, 2014). This argument suggests the following hypothesis:\n\nH3: Social attractiveness has a significant relationship with student loyalty.\n\nThe reputation of the institution’s top management is one of the critical elements of HEIs reputation management. This factor helps to establish good relationships with both internal and external stakeholders, reinforcing their confidence in the university’s administration (Zyryanova et al., 2020), which in turn has a positive impact on student loyalty (Carvalho & de Oliveira Mota, 2010; Telci & Kantur, 2014). Thus, the author formulates the following hypothesis:\n\nH4: Responsible management has a significant relationship with student loyalty.\n\nStrategically, public HEIs increasingly mirror private sector practices (Buckland, 2009). However, Khan et al. (2018) have compared the management practices of private and public universities and found that, although both use similar managerial practices, there are differences in some aspects, such as leadership style and management experience. This view about the existence of different settings between public and private institutions may create different perceptions about their reputations and, consequently, relationships with their stakeholders. For this reason, it is reasonable using the type of institution, whether public or private, as the control variable on the behaviour of both the dependent and independent variables.\n\nStudent perceptions and assessments about their HEI may vary across public and private institutions (Mahmoud & Grigoriou, 2017) due to switching costs (Maden et al., 2012), cost of education (Goh et al., 2017), perceived value (Goh et al., 2017; Taecharungroj, 2014) and overall student experience (Yu & Kim, 2008). Because this study defines university reputation and student loyalty based on student perceptions and evaluations of their institutions, therefore, it is reasonable to expect that:\n\nH5: There is a significant difference in the level of corporate reputation between public and private HEIs.\n\nH6: There is a significant difference in student loyalty between public and private HEIs.\n\nSee Figure 1 for the conceptual model of the study.\n\n\nMethods\n\nThe purpose of this study is to find out and explain the relationship between university reputations of Mozambican public and private institutions and student loyalty. The research design of the study is descriptive and analytical. The research is based on a quantitative survey and analysis. The main instrument for data collection was a closed-question questionnaire consisting of items from the scales of the primary constructs of the study, namely corporate reputation and student loyalty. The items on the scales are measured by a five-point Likert scale, which has the following description, strongly disagree, tend to disagree, neutral, tend to agree, and strongly agree. Respondents provided written informed consent to fill the questionnaire voluntarily, and anonymity and confidentiality were granted to comply with ethical issues. A scientific board approved the ethical compliance of the study, and the author presented the project for approval before a jury, in 2019, as part of his PhD thesis.\n\nThe Scientific Commission of The Faculty of Economics of UEM approved the ethical compliance of the study (Approval number: 000350/FACECO/2023).\n\nThe unit of analysis of this study is public and private higher education institutions operating in Mozambique. The sample unit is students currently attending a course at a higher education institution in the country. The sampling technique was convenience and snowball, and the study’s sample size was 384 respondents. However, 402 questionnaires were collected with 396 valid responses.\n\nThe data was collected online through an electronic survey platform from August to October 2021, where students attending different HEIs from all the regions of Mozambique filled out the questionnaire.\n\nFor data analysis and testing, SPSS version 20 was used. The collected data were subjected to a series of statistical tests, such as multivariate regression, bivariate analysis, ANOVA test, and exploratory factor analysis.\n\n\nResults\n\nThe sample has a slightly higher male representation (50.5%), with the most expressive age group being 21 years old or less with 41%, slightly above the 22-30 age group, representing 40.8%. Regarding educational establishments, 82% of respondents belong to public institutions. Universities represent 88.4%, followed by Higher Institutes with 10.4%. The first three years concentrate a higher proportion of students (62.8%). See Table 1.\n\nThe original authors tested already the indicators of the scales of the main constructs of the present study and presented a high index of reliability measured through Cronbach’s Alpha. However, to reinforce the validity of the scales in the Mozambican context, the author tested the reliability of the constructs, and the results showed that all constructs have good reliability. See Table 2.\n\nH1: Corporate reputation has a significant relationship with student loyalty.\n\nThe results show that the independent variables (academic ability, social attractiveness and responsible management) explain in 45% (adjusted R2) the variation of the dependent variable (Student Loyalty). Therefore, the model manages to explain almost half of the dependent variable, leaving a significant part of 55% explained by other variables. The hypothesis of R2 being zero being statistically significant (F(3.391)=109,627; p<0.001) is rejected.\n\nThe independent variables (Academic competence, social attractiveness and responsible management) show a statistically significant correlation (p<0.00) with the independent variable (Student loyalty). Correlations range from moderate for Responsible management (0.442) and Social attractiveness (0.588) to high for Academic competence (0.63). The coefficient table shows the equation of the estimated line which is: Student Loyalty=-0.187+0.622 Academic competence+0.388 Social attractiveness+0.032 Responsible management.\n\nH2: Academic competence has a significant relationship with student loyalty.\n\nH3: Social attractiveness has a significant relationship with student loyalty.\n\nAcademic competence (p<0.001) and social attractiveness (p<0.001) have both a high significance in the dependent variable. The results confirmed the hypotheses positively.\n\nH4: Responsible management has a significant relationship with student loyalty\n\nThe variable responsible management, in addition to having a shallow impact on the dependent variable (H4), that is, in the model, not an explanatory determinant of student loyalty, and this relationship is not statistically significant (p=0.629). Thus, H4 was not verified.\n\nH5: There is a significant difference in the level of corporate reputation between public and private educational institutions.\n\nIn public (3.71) and private (3.74) institutions, corporate reputation is higher than the centre of the scale, slightly higher in private institutions. The difference in means is not statistically significant (H5) (t(393) =-0.327; p=0.326). Students from private institutions believe their institutions have a slightly higher reputation. A slightly higher percentage (38.2%) believe that the reputation level of their institutions is high. In comparison, only 37% of students from public higher education institutions say the same. The hypothesis H5 was not validated.\n\nH6: There is a significant difference in the level of student loyalty between public and private educational institutions.\n\nAs for the level of student loyalty, the results show that in both public and private institutions, student loyalty is higher at the centre of the scale, being slightly higher in public institutions. The difference in means is statistically significant (H6) (t(87793)=2,373; p=0.04). Students from public institutions showed more loyalty towards their institutions. A higher percentage (48%) of students from public institutions claimed to be very loyal. In contrast, the percentage of students from private institutions said the same was 36.8%. The hypothesis was confirmed (Table 3).\n\n\nDiscussion\n\nThis study aimed to investigate the influence of university reputation and its dimensions, namely academic competence, social attractiveness and responsible management, on student loyalty. The research targeted student loyalty as a dependent variable as previous studies proved that loyalty plays a crucial role in creating the success of HEIs, which is why it requires special attention and resources. This variable impacts increasing the funding of institutions through high retention rates and lasting relationships and synergies through positive recommendations, by students and other stakeholders, about the institution (Kara & Deshields, 2004; Shahsavar & Sudzina, 2017).\n\nThe study’s empirical evidence showed a positive and significant relationship between university reputation and student loyalty in the context of HEIs in Mozambique, both for public and private institutions. The results of the study confirmed previous thoughts that the reputation of an HEI helps to increase student loyalty, positively affecting their intentions to collaborate with the institution in the future (Eryilmaz, 2016). Thus, reinforcing the belief that corporate reputation is a strategic asset crucial for value creation or the production of tangible results (Powell, 2016), allowing it to create conditions for obtaining sustainable competitive advantage (Grant, 2013). For this reason, HEIs invest a significant part of their resources in having a favourable perception among their stakeholders, emphasising the students (Lafuente-Ruiz-de-Sabando et al., 2017).\n\nThe study also confirmed previous knowledge that academic competence and social attractiveness are crucial in influencing student loyalty, as the regression analysis demonstrated a significant relationship between those dimensions and the dependent variable. When students perceive that the HEIs provide them with quality education and a robust physical and social infrastructure, they tend to be more loyal to the institution (Daud et al., 2020; Ismanova, 2019; Lin & Tsai, 2008; Nesset & Helgesen, 2009; Vianden & Barlow, 2014; Yang et al., 2008).\n\nThe research could not confirm the significant impact of the variable responsible management on student loyalty. At the same time, theory suggests that a favourable top management reputation is critical to building solid relationships with the university stakeholders ((Zyryanova et al., 2020). Strong leadership and good governance are vital components of corporate reputation (Suomi, 2014). Thus, it is wise not to completely rule out the importance of trust in university good administration practices from the model.\n\nThe study also aimed to compare students’ perceptions of reputation and loyalty between public and private HEIs to assess if there are significant differences that would justify different treatment of each group of institutions. The results showed that while the differences in university reputation between the two groups are not significant, there are differences in student loyalty between public and private HEIs. Students from public HEIs showed higher loyalty compared with private institutions. What stands out about the results is that besides recognising the effect of university reputation on student loyalty, other factors influence the behaviour of the dependent variable.\n\n\nConclusions, implications and limitations\n\nThe study concluded that corporate reputation positively affects student loyalty. Corporate reputation can explain 45% (adjusted R2) of the variance of the dependent variable, student loyalty. The relationship between the two variables is significant. The dimensions of corporate reputation with the most impact are academic competence and social attractiveness. The results showed that responsible management has a residual and non-significant impact on student loyalty.\n\nThe results also allow us to conclude that both corporate reputation and student loyalty have a moderate level and above the average of the scale in the respondents’ statements, both for public and private institutions.\n\nThe analyses show no significant differences between public and private institutions regarding institutional reputation. However, as for student loyalty, the results attest to a statistically significant difference between the nature of the institutions, pointing to a greater intensity of loyalty in public educational institutions.\n\nThis study contributes to the literature by providing empirical evidence of a different context in which university reputations play a key role in fostering student loyalty, both from private and public HEIs. The research results showed that strengthening the activities of the HEIs’ core business, which is the improvement of their academic competence, proves to be a logical path to the success of the institutions, as this dimension is the one that reveals the most significant impact on student loyalty.\n\nThe study’s practical implications are that it gives a framework for HEIs administrators, both from public and private institutions, to manage the factors of university reputation that better affect student loyalty. Thus, to retain their students, HEIs must continuously improve their academic competence, thus guaranteeing a quality education that ensures the employability and success of their graduates, recruiting the best students, and making themselves respected and recognised by the various social groups. They must also create attractive social conditions by offering the essential resources for student success, investing in their campus and, among others, diversifying their cultural experiences. These actions will significantly impact student loyalty, which is a fundamental element of the success of higher education institutions in an increasingly competitive environment. Specifically, Mozambican HEIs managers have empirical evidence from scientific research that could back up their decisions to allocate resources to improve their reputation and ultimately, affecting, positively student loyalty.\n\nThe present study has some limitations that are worth considering. First, the sample composition can be improved as, for example, there is a lower representation of respondents from private sector institutions with 17.2%, while the representation in the population is 39.8%. The other underrepresented groups are the post-graduate students (10.7%) and students enrolled in Academies, Colleges and Superior Institutes (11.7%). Thus, for future research, to generalise the results with more confidence, it is recommended to increase the proportion of representatives of those groups, as it might yield richer insights.\n\nSecondly, bearing in mind that the responsible management construct was the one that presented the lowest degree of reliability of Cronbach’s Alpha (0.71), it is recommended that for future research, a deeper exploration of the construct with the inclusion of other indicators that reflect and adapt to the local context. Previous research (Zyryanova et al., 2020) pointed out that trust in managerial capabilities and responsibilities is crucial to engaging relationships with key stakeholders. Thus, a better understanding of the constructs and how they fit into the model is worth considering.\n\nFinally, the model can only explain 45% (adjusted R2) of the variance of the dependent variable. The results showed no significant differences in reputation between public and private universities. While regarding student loyalty, the result presented significant differences between both groups. This finding may suggest that there are other variables intervening in the model. Thus, to better understand the mechanisms of the relationship between university reputation on student loyalty, other variables such as service quality (Teeroovengadum et al., 2019), student satisfaction (Alves & Raposo, 2006), image (Alves & Raposo, 2006; Quintal & Phau, 2016; Teeroovengadum et al., 2019), trust (Bergamo et al., 2012; Bowden, 2011; Goh et al., 2017; Ismanova, 2019; Rasoolimanesh et al., 2021), switching costs (Maden et al., 2012) and student commitment (Ismanova, 2019; Rojas-Médez et al., 2009; Snijders et al., 2020), should be included in the model to explain the variance on the dependent variable. Further studies may include mediators in the model or even change the role of university reputation in the model to explain its relationship with student loyalty.", "appendix": "Data availability\n\nFigshare: Survey_of_Moz_HEis_Students_clean.csv, https://doi.org/10.6084/m9.figshare.20212751.v1 (Raja, 2022).\n\nFigshare: Questionnaire reputation and student loyalty.pdf,\n\nhttps://doi.org/10.6084/m9.figshare.23844462.v1 (Raja, 2023a).\n\nFigshare: Appendix_1.docx (Items of the university reputation scale),\n\nhttps://doi.org/10.6084/m9.figshare.23843316.v1 (Raja, 2023b)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0)\n\n\nReferences\n\nAbbas SA: Brand Management of Higher Education Institutions. Int. J. Innov. Appl. Sci. 2014; 2(6): 151–172.\n\nAbbas SA: Brand Loyalty of Higher Education Institutions. Mark. Manag. Innov. 2019; 1: 46–56. 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Publisher Full Text" }	[ { "id": "214490", "date": "24 Oct 2023", "name": "Sallaudin Hassan", "expertise": [ "Reviewer Expertise Quality Management System", "Operation Management", "Supply Chain Management", "Service Quality", "TVET Education 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\nThis paper is related to the current issue especially in the effort to increase number of student and keep them retain on the same university.\n\nPerhaps, please consider the following input for improvement:\n\nAbstract- please include briefly on future research.\n\nIntroduction - please clearly indicate the impact of poor reputation toward student loyalty.\n\nLiterature review - please consider to more reference for higher TVET institution as well. Prior to the developing of hypothesis, please clearly relate this study with related underpinning theory. In addition, need to ensure that the hypothesis is developed based on past research.\n\nMethod - sampling method needs to clearly defined.\n\nResult- need to clearly explain the current performance.\n\nDiscussion - adequate. However, better to have supporting docs.\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": "10699", "date": "17 Jan 2024", "name": "Estacio Denazarte Omar Raja", "role": "Author Response", "response": "A section for future research was included in the abstract. A statement about the negative impact of poor reputation on student loyalty was included. The study intends to have a broader view of higher education institutions and not pivot toward certain types of institutions. Before each hypothesis statement, there are references to past research. A more detailed explanation of the sampling technique used is provided in this section. I don’t understand what is expected with the comment: \"Result- need to explain the current performance clearly.\". I need more clarification, please. The author discusses the results confronting them with relevant literature." } ] }, { "id": "214479", "date": "24 Oct 2023", "name": "Pilar Zorrilla", "expertise": [ "Reviewer Expertise Marketing" ], "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\nStarting from the consideration the relevance of the topic discussed, namely, the impact of reputation on student loyalty in the framework of Higher Education. This is a topic of interest that is addressed in this specific case in a geographical context, Mozambique, where there does not seem to be any research on the matter. Therefore, one of the essential contributions of the work is just this: covering the research gap in Africa context.\nThe research questions are relevant and well focused.\n\nWhich dimensions of university reputation are determinants of student loyalty?\n\nDo university reputation and student loyalty differ between public and privately owned institutions?\nBesides, the answer to these questions allows us to address the implications for reputation management in universities.\nThe strategic importance of image and reputation of organisations is widely recognized. However, despite the extensive body of knowledge generated around the concept of reputation in organisations, researchers continue to underscore the existence of important conceptual inconsistencies surrounding them. In this paper, the author recognizes that reputation is a multidisciplinary concept but assumes a definition as a valid definition. The lack of conceptual clarity is one of the most significant research gap, so I would like to read a better argumentation about why the author has chosen Alessandri et al as the best definition of reputation.\nThe following quote contains errors in one of names: Lafuente-Ruiz-de-Sabando A, Zorrilla P, Forcada, J: A Review of Higher Education Image and Reputation Literature: Knowledge Gaps and Research Agenda. Eur. Res. Manag. Bus. Econ. 2017; 282: 1043–1064.\nThere are problems in several of the links to the articles cited in the bibliography.\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": [ { "c_id": "10700", "date": "17 Jan 2024", "name": "Estacio Denazarte Omar Raja", "role": "Author Response", "response": "In a new version, the author has provided a statement with the argument for choosing Alessandri et al. to define the reputation of HEIs. The error in the reference was corrected. I’ve corrected the links that seem to have problems." } ] }, { "id": "214486", "date": "06 Nov 2023", "name": "Poh Ling Tan", "expertise": [ "Reviewer Expertise Communication Strategies / Branding / CSR" ], "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 introduction jumps quickly into the topic without establishing the broader relevance of corporate social responsibility (CSR) in the context of HEIs. It could benefit from a sentence or two explaining how CSR specifically ties into the reputation and competitive advantage of HEIs.\nThe introduction could benefit from a clearer explanation of how Corporate Social Responsibility (CSR) specifically influences the reputation of higher education institutions. While the introduction discusses reputation at length, the direct impact of CSR initiatives on reputation and student loyalty is not explicitly stated. The author should consider detailing the mechanisms through which CSR practices contribute to the reputation of HEIs, potentially influencing student perceptions and decisions, and how this might differ in the context of Mozambique compared to other regions.\nWhile the study highlights the significant impact of academic competence and social attractiveness on student loyalty, it would be beneficial to discuss the implications of responsible management's non-significant impact. The author could speculate on why this might be the case and what it could mean for HEIs' CSR strategies.\nThe author notes that both corporate reputation and student loyalty are above average, but does not elaborate on the implications of this finding. It would be insightful to discuss whether this is consistent with expectations and how it compares to other studies in similar contexts.\nAddress the Unique Context of Mozambique: The recommendations are somewhat generic. The author could provide more tailored advice for Mozambican HEIs, considering the country's specific educational, economic, and cultural context.\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? Partly", "responses": [ { "c_id": "10701", "date": "17 Jan 2024", "name": "Estacio Denazarte Omar Raja", "role": "Author Response", "response": "n the new version, the author provides an explanation in the introduction of how Corporate Social Responsibility (CSR) explicitly influences the reputation of higher education institutions and the mechanisms through which CSR practices contribute to the reputation of HEIs, potentially influencing student perceptions and decisions. In the new version, the author discusses more about the implications of the lack of significance of responsible management both in the Managerial implications section and in future research. The new version addresses this issue. The author addresses the issue that corporate reputation and student loyalty are above average by explaining the implications of the findings in the new version. The author made a few adjustments to the text to address this issue about the uniqueness context of Mozambique." } ] } ]	1	https://f1000research.com/articles/12-1102
https://f1000research.com/articles/11-1080/v1	21 Sep 22	{ "type": "Research Article", "title": "Predictors of face mask use during the COVID-19 pandemic in Indonesia: Application of the health belief model, psychological distress and health motivation", "authors": [ "Devi Wulandari", "Fredrick Dermawan Purba", "Alfikalia Alfikalia", "Fatchiah Ekowati Kertamuda", "Tia Rahmania", "Olivia Ayu Sabrina", "Kurnia Nurul Hidayah", "Syarifah Fatimah", "Fredrick Dermawan Purba", "Alfikalia Alfikalia", "Fatchiah Ekowati Kertamuda", "Tia Rahmania", "Olivia Ayu Sabrina", "Kurnia Nurul Hidayah", "Syarifah Fatimah" ], "abstract": "Background: High infection rates of COVID-19 in Indonesia require attention, especially transmission and prevention behaviors. One way to lower infection rates is the use of face masks. However, people's adherence to its usage when in public is still low. This necessitates the exploration of predictors of the use of masks to increase community compliance. This study further aims to investigate the predictors of face mask use by applying the Health Belief Model, anxiety, stress, depression, and health motivation. Methods: A total of 255 respondents from Jakarta, Bandung, Tangerang, and Banten filled out an online questionnaire. Furthermore, hierarchical multiple regression was used to detect predictors associated with face mask use. Results: The results showed that the high perceived benefits and health motivation were higher in individuals who used a face mask when in public, while those who have high perceived barriers likely do not use masks. The respondent's level of psychological distress, including depression, anxiety, and stress were not associated with face mask use. Conclusions: Therefore, these findings highlight the importance of personal appraisal regarding COVID-19 and its prevention behaviors. Comfortable mask design, and emphasizing the benefits of using masks in the community improve compliance.", "keywords": [ "health belief model", "face mask use", "COVID 19", "health motivation", "psychological distress" ], "content": "Introduction\n\nCOVID-19 received worldwide attention due to its rapid spread (Li et al., 2020a). The first confirmed case occurred in Wuhan City, Hubei, China, at the end of 2019, and various countries took efforts as early as possible to suppress its spread (WHO, 2020). This disease began to spread worldwide on January 3, 2020 (Lathifa et al., 2021). In this regard, Indonesia has the highest number of COVID-19 cases in Southeast Asia with a total of 4,026,837 in August 2021 (Satgas COVID-19, 2021).\n\nTo cope with the COVID-19 pandemic, the Indonesian government enacted various programs on national levels. They launched the health protocols campaign that encourages people to wear a mask, wash hands, social distance, stay away from crowds, and maintain mobility (KEMENKES RI, 2021). The government also intensified the national COVID-19 vaccination program. However, various essential obstacles will potentially hamper the process of reducing cases in Indonesia.\n\nOne of the obstacles faced by the implementation of health protocols program originates from the community. People need to be continuously reminded to implement the health protocols in their daily activities, especially in terms of wearing face masks correctly and appropriately (Buana, 2020). The World Health Organization (WHO) (2020) stated that face mask use is a comprehensive effort to prevent the spread of COVID-19. The virus is spread due to droplets originating from a patient’s respiratory tract within one meter. In line with Shereen et al. (2020), face masks are absolute and have become a new habit to be implemented outside the home (when interacting with other people). However, there is still a refusal or neglect to use face masks. In Jakarta, 10,416 people were given sanctions for violating the rules for using face masks during the week the Emergency Community Activity Restriction (PPKM) policy was implemented from 3rd-9th July, 2021 (Paat, 2021). Likewise, an increasing number of violations also happened in Bandung and Tangerang (Naufal, 2021).\n\nIn a study by Firdayanti et al. (2020) on the prevention of COVID-19 through community service activities, the distribution of face masks was carried out door to door. This distribution was usually accompanied by demonstrations of their use by lecturers, students, community leaders, religious leaders, or local government officers. This was in line with Li et al. (2020b) that showed the effective use of masks combined with social distancing was successful in flattening the curve of the pandemic. Additionally, Brooks & Butler (2021) stated that using face masks in the community can substantially reduce the transmission of the acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in two ways. First, face mask use prevents infected people from spreading SARS-CoV-2 by blocking respiratory droplets containing the virus from entering the air, also known as source control. This aspect is essential as it is estimated that 50%+ of COVID-19 transmission comes from people who have never experienced symptoms or individuals in the presymptomatic phase. Second, masks can protect uninfected users.\n\nAlthough face mask use is essential in eradicating COVID-19, people’s compliance is still low. Sinuraya et al. (2018) stated that several factors predict low compliance of health protocols, including knowledge, motivation, perception, and belief in efforts to control and prevent disease and access available resources. Lathifa et al. (2021) also stated that the aforementioned factors determine the level of community compliance with health protocols in the era of globalization.\n\nTo determine how individuals comply with face mask use, a cognitive model might help. The Health Belief Model (HBM) was proposed to understand disease prevention behavior, especially medication adherence, in the 1950s (Champion & Skinner, 2002). HBM has been widely used to understand behavioral change, even more often than social cognitive theory, reasoned action theory, and transtheoretical model (Sulat et al., 2018). Some of the health behaviors that have been studied using HBM include influenza prevention behavior (Karimi et al., 2016).\n\nThe HBM has four constructs: perceived severity, perceived barriers, perceived benefit, and perceived susceptibility (Rosenstock et al., 1988). Perceived severity refers to a person’s perception of the severity of the disease, while perceived barriers refer to factors that prevent a person from adopting a healthy behavior. Furthermore, perceived benefit is the perception one has on the benefits of carrying out healthy behavior, while perceived susceptibility is one’s perception of the level of vulnerability they have (Sulat et al., 2018). A person’s tendency to carry out healthy behaviors depends on the perception that a disease has a high severity and vulnerability, that one has the benefits of health behavior, and does not experience significant obstacles when carrying out these behaviors (Champion & Skinner, 2002).\n\nSeveral studies have applied the HBM in predicting healthy behaviors related to the COVID-19 disease. Erawan et al. (2021) explained that significant positive predictors of interest in COVID-19 vaccination were perceived susceptibility and perceived severity. Meanwhile, the perceived barrier was a significant negative predictor in this study. HBM was also able to predict intentions to receive the COVID-19 vaccine (Wong et al., 2020), COVID-19 prevention behavior in Iran Shahnazi et al. (2020b), and other various healthy behaviors. The HBM may also be used in interventions and models that predict healthy behavior (Sulat et al., 2018).\n\nAlthough HBM has already been applied in determining face mask use (Bressington et al., 2020; Shahnazi et al., 2020b; Zhang et al., 2019), the role of health motivation and psychological distress on face mask use was still unclear. A person’s motivation to stay healthy (health motivation) can be a predictor that influences their compliance with using a mask. Health motivation comes from the Self-Determination Theory (SDT) proposed by Ryan and Deci (2017). Intrinsic motivation will promote a person to act based on interest and enjoyment. Meanwhile, extrinsic motivation will inspire a person to perform a healthy behavior to obtain the approval of others, increasing self-esteem, appreciation from others, and pressure from outside (Ntoumanis et al., 2021).\n\nAlthough health protocols such as social distancing are beneficial in reducing the spread of COVID 19, they may also cause psychological distress to the Indonesian people (Rias et al., 2020). Wolff et al. (2020) explained that pandemic containment requires people to cope with reduced social contact that may create lack of freedom, boredom and negative affects among people. Moreover, Seiter and Curran (2021) stated that the level of depression during the COVID-19 pandemic was negatively related to adherence to COVID-19 prevention measures.\n\nThis present study utilized the HBM as a theoretical framework. It is hypothesized that individuals with high perceived severity, high perceived susceptibility, high perceived benefit, and the low perceived barrier will tend to use face masks. Furthermore, the levels of depression, anxiety, and stress will be associated with low use of masks. With a more thorough understanding of the related factors, the government will be able to develop various intervention programs to increase public compliance with the use of masks. This study aimed to further determine the role of the Health Belief Model (HBM) construct, stress, depression, anxiety, and health motivation on the use of masks after controlling for demographic factors in the cities of Jakarta, Bandung, Tangerang, and Banten in Indonesia.\n\n\nMethods\n\nThis study was conducted using a cross-sectional research design from September 2020 – February 2021 in Indonesia during the outbreak of COVID-19.\n\nThe respondent criteria were as follows: must be at least 18 years old, must have a minimum of a junior high school education, must live in DKI Jakarta, Banten, or Bandung areas.\n\nA non-probability sampling method was used to gather a sample of Indonesian people who lived in Jakarta, Banten, and Bandung.\n\nData collection was done using the SurveyMonkey online platform. We composed an announcement consisting of general information about the study, inclusion criteria, and the study link. We circulated this announcement on discussion forums, college students’ groups and community peer groups via several channels: social media accounts of the research team (e.g., Facebook, Instagram) and instant messenger applications (e.g., WhatsApp, Line, Facebook Messenger). People who were interested in participating then clicked on a link at the bottom of the announcement and were directed to the online questionnaire. The respondents filled in all questions after agreeing to the informed consent form included in the online questionnaire. A total number of 255 respondents were recruited from December 11, 2020 – February 25, 2021.\n\nThe Ethics Committee of Padjadjaran University approved this research (approval number: 430/UN6.KEP/EC/2020). Informed written consent was obtained from participants and they were assured that only researchers would have access to the data and it would only be used for research purposes. Participants could complete the questionnaire anonymously.\n\nThe constructs of the HBM were measured by instruments developed by the researchers. An open-ended questionnaire was distributed to 30 respondents as an initial step in developing the questionnaire and statements that had the most responses were included. The measures were rated on a four-point Likert scale. The scoring was from 1 (strongly disagree) to 4 (strongly agree) with a total number of 24 items. There were five items for the perceived barrier such as “wearing a mask makes it difficult for me to breathe”; five items for perceived benefit including “I feel safer if wearing a mask”; five items for perceived susceptibility, such as “I have low body resistance”; five items perceived severity, such as COVID-19 causes death; and four health motivation items, including “health is the main thing for me”. Three items measured face mask use behavior, for instance, “I never forget to use a face mask every time I go outside”. Furthermore, a validity analysis was carried out using the content validity method with the help of two experts in the fields of health and psychology. These instruments were proven reliable, shown by Cronbach Alpha values of 0.805, 0.894, 0.811, 0.639. and 0.697 for the perceived barrier scale, perceived benefit scale, perceived susceptibility scale, perceived severity scale, and mask use behavior, respectively.\n\nDASS-18 was used to measure depression, stress, and anxiety (Lovibond and Lovibond, 1995). Six items measured depression, such as “I feel my life is meaningless”; six items of anxiety, including “I feel my hands are shaking”; and six items measured stress, involving “I tend to overreact to certain situations”. For samples of this study, DASS-18 was shown as reliable, with Cronbach’s Alpha values of 0.813, 0.790, and 0.703 for depression, anxiety, and stress scale, respectively. A copy of the questionnaire can be found under Extended data (Wulandari et al., 2022).\n\nData was analyzed using SPSS 25. Descriptive statistics were carried out for respondents’ demographic analysis. Afterwards, the relationships between sociodemographic variables, HBM variables and face mask use were evaluated using Pearson Product Moment and T-Test. Hierarchical multiple regression analysis was also carried out to examine the role of predictors based on HBM regarding mask-use behavior.\n\n\nResults\n\nBased on the data in Table 1, the respondents mean age was 33.1 years old (SD=11.9), the majority were females (72.6%), had a university-level education (69.4%), and more than half had a monthly income of IDR 2.5 million and above and were living in urban areas (65.6%). Note that Several respondents did not complete part of their demographic data, therefore the sum of each demographic characteristics were not equal to 255.\n\n* Several respondents did not complete part of their demographic data, therefore the sum were not equals to 255.\n\nTable 2 shows the correlation between the variables. The behavior of face mask use has a significantly positive correlation with the perceived benefits (r=0.547, P<0.001) and perceived severity (r=0.242, P<0.001). A negative correlation was observed in the association between face mask use and the perceived barrier (r=0.376, P<0.001).\n\n* P-value<0.05.\n\n** P-value<0.01.\n\nTable 3 shows the results of multiple regression analysis that examined the role of predictors based on HBM on mask-use behavior. In step 1, the respondents’ sociodemographic variables significantly contributed to the variance of their behavior of using a mask (R2=9.5%; F (4,233)=6.087, P<0.001)). In step 2, after including the HBM variables, this model was proven to significantly predict face mask use, (R2=53.1%; F (9.228)=28.701, P<0.001). Therefore, the addition of variables based on HBM adds to the variance explained by the model by 43.7%. Stress, anxiety, and depression were included in step 3 and showed that all variables were able to explain the variance of mask use behavior of 53.5% (F (12.225)=21.553, P<0.001). Additionally, perceived barriers were a negative predictor of face mask use, while positive predictors were health motivation and perceived benefits.\n\n* P-value<0.05.\n\n P-value<0.01.\n\n* P-value<0.001.\n\n\nDiscussion\n\nThis study aimed to investigate the predictors of compliance of face mask use by applying the Health Belief Model, health motivation, anxiety, stress, and depression. The results showed that of the 12 predictors tested, only four contributed significantly to the behavior of using masks. Predictors that contribute positively to the magnitude of their contribution include health motivation, perceived benefit, and gender. The predictor that contributed negatively was the perceived barrier. Therefore, these results indicate that when combined with the health belief model predictors, health motivation, which is intrinsic from within, possesses the most significant contribution. From the health belief model predictors, only perceived benefits and perceived barriers contributed significantly to the use of masks during the COVID-19 pandemic. Gender was also a significant predictor of mask use, with women being more likely to wear masks than men. Furthermore, depression, anxiety, and stress were not proven to be significant predictors of face mask use.\n\nThe Social Determination Theory (SDT) hypothesized that the psychological condition essential to make a change is having an autonomous motivation and assessing that one is competent to make changes or a behavior (Ryan & Deci, 2017). Regarding SDT, autonomous motivation is required from the individual to make someone bring up behavior related to their health, such as using a mask to prevent the spread of the COVID-19 virus. The SDT argues that behavior based on autonomous motivation comes from within and is a self-expression of the individual. Therefore, individuals were willing and agreed voluntarily to perform the behavior. The autonomous motivation intrinsic to healthy living shows that individuals perceive that they have personal responsibility for their health, which promotes them to live a healthy life, in this case using masks, during the COVID-19 pandemic. Based on the results, the SDT was proven to have the most significant contribution to the behavior of using masks.\n\nIntrinsic health motivation as a predictor of face mask use was in line with Hartmann et al. (2015), which shows that autonomous motivation, compared to introjected and external motivation, is the only predictor of healthy food consumption within a year. Intrinsic health motivation could predict weight management, choosing healthy foods, and having vigorous physical exercise in their spare time in one year.\n\nChan et al. (2014) explored the integration of SDT approaches and the Theory of Planned Behavior (TPB) to explain the behavioral intention of wearing masks to prevent the transmission of the H1N1 virus using quasi-experimental research, analytical methods, and structural equation modelling (SEM) data. The results showed that promoting messages in supporting individual autonomy, including providing reasons why face mask use needs to be carried out, emphasizing individual personal values, initiating own face mask use and showing concern and understanding that wearing masks can be uncomfortable or cause difficulties, is positively correlated with the support of perceived autonomy. The perceived support for autonomy then significantly contributed positively to intrinsic autonomous motivation, autonomous motivation contributed to attitudes, subjective norms, and perceived behavioral control in the behavior of wearing masks. These three TPB determinants were positive predictors that contributed significantly to the intention to use face masks. Furthermore, controlled motivation, which does not support individual autonomy, only contributes to subjective norms and perceived behavior control. Chan et al. (2014) observed that autonomous motivation initiates TPB indicators, which signifies that autonomous motivation plays a role as a driver in explaining not only behavioral intentions but also to the behavior around face mask use.\n\nOf the four HBM predictors, namely perceived benefit, perceived susceptibility, perceived severity, and perceived barrier, only perceived benefit and perceived barrier contributed significantly to face mask use. Perceived severity did not have a significant direct contribution but showed a positive correlation with the use of masks. Perceived susceptibility did not have a direct contribution or significant correlation to the behavior of using masks. Therefore, this study agrees with similar studies in Indonesia conducted by Winarti et al. (2021), who examined the effect of knowledge and determinants of HBM on face mask use. The four determinants of HBM were shown in these studies to be a significant determinant of face mask use.\n\nThe significant positive contribution of the perceived benefit shows that the positive perception that face mask use benefits respondents, helps to prevent the transmission of COVID-19 by promoting them to wear it more often. These results are in line with research conducted in Iran (Shahnazi et al., 2020a), where the perceived benefit was a significant predictor of COVID-19 prevention behavior. Similarly, respondents believe that the benefits of action will be related to their willingness to take action and preventive efforts to deal with the COVID-19 pandemic. As in Iran, research in Hong Kong (Lee et al., 2021) showed similar results that the more respondents perceive the benefits/advantages of using masks, the more willing they are to use masks. Another potential perceived benefit could be avoiding government sanctions. The results of a survey on 90, 967 respondents on the behavior of the Indonesian people during the COVID-19 pandemic (7-14 September 2020) (Central Statistics Agency, 2020) showed that more than half of the respondents stated that the reason for not implementing health protocols was because there were no sanctions. Related to the results of the BPS research (2020) and this research, it could be that apart from the belief that wearing a mask can reduce the threat of contracting the COVID-19 disease, one of the other benefits that are strongly felt from face mask use during the COVID-19 pandemic was not being subject to the threat of sanctions when wearing a mask in certain locations.\n\nThe results of this study indicate that the perceived barrier provides a significant negative contribution to using masks. Therefore, it shows that factors considered obstacles are believed to make respondents more unwilling to use their masks. The results of a survey of the Indonesian people from the BPS (2020) showed that there were several reasons why respondents did not apply health protocols ranging from the highest to the lowest results, namely: the absence of sanctions if they did not apply the health protocols; the absence of COVID-19 cases in the surrounding environment; work becomes difficult if you have to apply health protocols due to difficulties in social interactions and the price of masks, face-shields, hand sanitizers or PPE which tends to be expensive; other people were not using face masks and officials or leaders not setting an example. A person’s tendency to carry out healthy behaviors will be higher if they perceive less significant obstacles when enacting healthy behaviors (Champion & Skinner, 2002). In this case, several factors observed from the BPS survey (2020) made the barrier to not wearing masks appear to be more related to social context, rather than health related factors.\n\nAnother result of this study is that the perceived severity does not have a significant effect but still positively correlates with using masks. Therefore, the more respondents perceive the high severity of COVID-19, the more favorable it will be. In line with Lee et al. (2021), the higher the confidence of research respondents on the seriousness of COVID-19 disease, the more willing they are to display the behavior of wearing masks.\n\nPerceived susceptibility does not have a significant contribution to the behavior of using masks. This variable is not even significantly correlated with the behavior of using masks. As previously stated, perceived susceptibility refers to a person’s assessment of their level of vulnerability to a particular disease (Sulat et al., 2018). Champion & Skinner (2002) also explain that a person’s tendency to carry out healthy behavior depends on their perception of a disease’s severity and vulnerability. The analysis results per statement item showed that the average respondent considered themselves not vulnerable to COVID-19.\n\nFurthermore, an analysis of the survey responses regarding whether family members, neighbors, and co-workers/friends on campus were positive for COVID-19, shows that not many people are affected by COVID-19 in the environment close to the respondent. Therefore, it can be concluded that most respondents do not consider themselves and the people immediate around them vulnerable to the disease. These results may explain the absence of a significant contribution of perceived susceptibility to mask-wearing behavior.\n\nThis study showed that depression, anxiety, and stress were not significant determinants for face mask use. There were also no significant correlations between depression, anxiety, and stress to face mask use. This result was in line with Wang et al. (2020) who studied the association between mental health and face mask use during the COVID-19 pandemic in Poland and China. Some of the results from Wang et al. (2020) showed that depression, anxiety, and stress were not significant determinants of face mask use in both Poland and China. Furthermore, the results of this present study were in contrast with Xu et al. (2022) that showed the association between anxiety symptoms and face mask use in junior and senior high school students in China. Bressington et al.’s (2020) study in Hong Kong also showed that respondents with higher frequency of reusing masks, wearing face masks for self-protection, and the perceived high severity of COVID-19 were more likely to report depressive symptoms. There were 46.5% of respondents in the Bressington et al. study that were reported to have probable depression, which was high compared to the previous study in Hong Kong.\n\nCompared to the study by Bressington et al. (2020), respondents in this research can be categorized as low in depression, anxiety, and stress as the mean scores were 3.33, 2.76, and 2.55 respectively. These scores can be considered low when compared to the maximum score of each DASS Scale which was 21. The low level of depression, anxiety, and stress experienced by our respondents explains why there was no significant contributions of depression, anxiety, and stress to face mask use.\n\nThere were several limitations in this study: first, the sampling strategy being used was non-random, thus the representativeness of the population and generalizability of the study may be compromised. The strategy of using instant messaging and social media apps to reach potential respondents was potentially biased to include mostly middle-to-high socioeconomic statuses and the level of education of respondents. Therefore, any generalization to other populations should be conducted cautiously. Second, the measure of mask behavior is self-reported, thus it is prone to social desirability.\n\n\nConclusions\n\nIn Indonesia, wearing a face mask is a highly important strategy in reducing the spread of COVID-19. This study showed that health motivation and the perceived benefit increased mask use, while perceived barrier decreased it. Therefore, these results shed light on the importance of human motivation regarding the infection and prevention of COVID-19. The behavioral intervention to increase people’s compliance in face mask use should emphasize the benefits to their health and work to design more comfortable face masks.\n\n\nData availability\n\nThe underlying data for this research is available on request for research purposes only. To access the data, please contact the corresponding author Devi Wulandari (devi.wulandari@paramadina.ac.id). Any researcher interested in the data must send their research proposal and proof of affiliation.\n\nFigshare: Questionnaire for Face Mask Use Behavior, DASS and Health Belief Model. https://doi.org/10.6084/m9.figshare.20763226.v1 (Wulandari et al., 2022).\n\nThis project contains the following extended data:\n\n- Questionnaire\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication)", "appendix": "References\n\nBressington DT, Cheung TCC, Lam SC, et al.: Association Between Depression, Health Beliefs, and Face Mask Use During the COVID-19 Pandemic. Front. Psych. 2020; 11(October): 1–12. PubMed Abstract \| Publisher Full Text\n\nBrooks JT, Butler JC: Effectiveness of Mask Wearing to Control Community Spread of SARS-CoV-2. JAMA Insight. 2021; 325(10): 998–999. 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PubMed Abstract \| Publisher Full Text\n\nNaufal M: Sepekan PPKM Darurat, Pelanggaran Terbanyak di Tangerang adalah Tak Pakai Masker. 2021.\n\nNtoumanis N, Ng JYY, Prestwich A, et al.: A meta-analysis of self-determination theory-informed intervention studies in the health domain: effects on motivation, health behavior, physical, and psychological health. Health Psychol. Rev. 2021; 15(2):214–244. PubMed Abstract \| Publisher Full Text\n\nPaat Y: Sepekan PPKM Darurat, 10.416 Orang di Jakarta Langgar Penggunaan Masker. 2021.\n\nRias YA, Rosyad YS, Chipojola R, et al.: Effects of Spirituality, Knowledge, Attitudes, and Practices toward Anxiety Regarding COVID-19 among the General Population in INDONESIA: A Cross-Sectional Study. J. Clin. Med. 2020; 9(12):3798. PubMed Abstract \| Publisher Full Text\n\nRosenstock IM, Strecher VJ, Becker MH: Social Learning Theory and the Health Belief Model. Health Educ. Q. 1988; 15(2):175–183. 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PubMed Abstract \| Publisher Full Text\n\nShereen MA, Khan S, Kazmi A, et al.: COVID-19 infection: Origin, transmission, and characteristics of human coronaviruses. J. Adv. Res. 2020; 24:91–98. PubMed Abstract \| Publisher Full Text\n\nSinuraya RK, Destiani DP, Puspitasari IM, et al.: Pengukuran tingkat kepatuhan pengobatan pasien hipertensi di Fasilitas Kesehatan Tingkat Pertama di Kota Bandung. Jurnal Farmasi Klinik Indonesia. 2018; 7(2): 124–133.\n\nSulat JS, Prabandari YS, Sanusi R, et al.: The validity of health belief model variables in predicting behavioral change: A scoping review. Health Educ. 2018; 118(6): 499–512. Publisher Full Text\n\nWHO: Anjuran mengenai penggunaan masker dalam konteks COVID-19. 2020.\n\nWinarti E, Wahyuni CU, Rias YA, et al.: Citizens’ health practices during the COVID-19 pandemic in Indonesia: Applying the health belief model. Belitung Nurs. J. 2021; 7(4):277–284. Publisher Full Text\n\nWolff W, Martarelli CS, Schüler J, et al.: High boredom proneness and low trait self-control impair adherence to social distancing guidelines during the COVID-19 pandemic. Int. J. Environ. Res. Public Health. 2020; 17(15): 1–10. PubMed Abstract \| Publisher Full Text\n\nWong LP, Alias H, Wong PF, et al.: The use of the health belief model to assess predictors of intent to receive the COVID-19 vaccine and willingness to pay. Hum. Vaccin. Immunothe. 2020; 16(9):2204–2214. PubMed Abstract \| Publisher Full Text\n\nWulandari D, Purba F, Alfikalia A, et al.: Questionnaire for Face Mask Use Behavior, DASS and Health Belief Model. figshare. [Dataset].2022. Publisher Full Text\n\nXu Q, Mao Z, Wei D, et al.: Association between mask wearing and anxiety symptoms during the outbreak of COVID 19: A large survey among 386,432 junior and senior high school students in China. J. Psychosom. Res. 2022; 153(December 2021):110709. 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PubMed Abstract \| Publisher Full Text" }	[ { "id": "151141", "date": "06 Oct 2022", "name": "Jan Passchier", "expertise": [ "Reviewer Expertise Medical Psychology" ], "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\nGeneral Remarks\nThe manuscript (entitiled Predictors of face mask use during the COVID-19 pandemic in Indonesia: Application of the health belief model, psychological distress and health motivation) describes an investigation of psychological predictors of face mask use in Indonesian cities. Perceived benefits and health motivation were found to be relevant predictors.\n\nThe study is interesting and gives insight into the determinants of preventative behavior of COVID-19 during its most dangerous phase in a Low-Middle Income Country. The research is straightforward, with a simple cross-sectional design using a convenient sample. It is clearly written, although the English can be improved. Some discussion parts should be elaborated more than is written here. Details of my review are presented below:\n\nIntroduction\n1st sentence add: 'and its severe consequences'\n\n3rd paragraph: instead of 'is a comprehensive effort', 'should become a comprehensive effort' might be better, I think. In the sentence 'In line with ..' the word 'absolute' is not clear.\n\n4th paragraph: Mention the country of the study of Firdayanti (probably Indonesia) Next sentence: 'that showed': better: 'showing that'.\n\n5th paragraph: please give the figure on compliance in Indonesia if available.\n\n7th paragraph: 'vulnerability' seems more a characteristic of a person than of a disease.\n\n8th paragraph: mention the countries in which the referred studies were carried out.\n\n9th paragraph: mention the outcome of the HBM studies.\n\n10th paragraph: it might be mentioned that psychological distress in Indonesian people is in particular the case since social contact is very important in Eastern cultures like Indonesia.\n\nMethods\nStudy Design\nsee general remarks\nSampling\nplease give a short description of 'non-probability sampling method' for readers with a reference.\n\nData collection\nperform a power analysis to demonstrate that n=255 is a sufficient sample fo analyzing the number of predictors.\nInstruments\nThe HBM version and its development should be described more. It was probably an Indonesian version? Were the items developed by the researchers or translated from existing English versions? Was the development carried out on the current-data set or another one?\n\nAdd \" \" to the item COVID-19 causes death.\n\nThe use of three decimals for the Cronbach alpha's suggests preciseness that is not realistic. Two decimals suffice. If data are available about the validity of this version please report it as well.\n\n2nd paragraph: start with 'The' DASS etc. See further my remarks above on the HBM.\n\nData Analysis\nOverall the statistical analysis used, seem appropriate. Its application on other than psychological variables (i.e. the demographic variables) should be mentioned here as well.\n\nThe use of 3 decimals for the Cronbach alpha's suggests an exactitude that is not realistic. Two decimals suffice.\n\nResults\n\n1st paragraph: the sentence starting with 'Note' about non-response regarding the demographic data is already put under Table 1 and can be deleted in the text. The use of 3 decimals suggests an exactitude that is not realistic. Two decimals are sufficient.\n\n2nd paragraph: In the heading of Table 2 and the text the word 'psychological' should be added to 'variables'. 'The behavior of face mask use..': omit 'behavior of'. It would be interesting when Cohen's d's are presented for the significant correlations (and in Table 3 the regression coefficients) to see the qualification in terms of a small, moderate or large effect.\n\n3rd paragraph: Mention 'gender' as a significant predictor.\n\nDiscussion\n1st Paragraph: the sentences about the predictive value of perceived benefits and barriers can be merged. I would also recommend one or more sentences stating in which respect the outcome of this study is new, respectively, add to what we already know. It is good to mention that depression, anxiety, and stress were no significant predictors when corrected for the demographic and other psychological variables.\n\n4th paragraph: I prefer not to describe the study of Chan in detail, or otherwise to do so in the introductory section. Better to restrict yourself to which of your findings are in line with that and other studies; and which are different with an explanation for the difference. R6: add 'perceived' to 'support'.\n\n5th paragraph: be more clear about the independent and respectively dependent contribution of the predictors. Mention which population was studied by Winarti et al. and if their HBM predictors were analyzed with correction for other variables or not.\n\n10th paragraph: Last sentence: 'The analysis results ...': in the present study or in that of Champion and Skinner?\n\n11th paragraph: 2nd sentence: 'it can be concluded' is my opinion too strong 'it is plausible' might be better.\n\n12th paragraph: It is important to note that stress, anxiety, and depression are measured as general concepts and not focused on contamination by Covid-19. 3rd sentence: 'Some of the results' can be deleted. 'Furthermore': better changed to 'However'.\n\n13th paragraph: 'explains' is too strong: 'may explain' leaves room for other explanations.\n\n15th paragraph: an important limitation that is not mentioned here is the cross-sectional design of this study which does not allow firm conclusions about cause-effect relations between the variables. Further: explanations how the bias due to the sample selection in the present study might have influenced the outcome can be added (in particular the demographic variables, such as gender). A paragraph should be added on future research and possible application of the current results. It should also be noted that currently many measures, also face mask use are now (partly) abolished due to the dominance of a less dangerous COVID-19 variant. (Omicron).\nAbstract\nI could not find the outcome on 'comfortable mask use' in the results section.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "9294", "date": "28 Apr 2023", "name": "Devi Wulandari", "role": "Author Response", "response": "We already add several changes in the manuscript accordingly: Introduction: We made several revisions to the mentioned sentences in paragraphs 1st, 3rd, and 7th the country of the study in the 4th paragraph was mentioned We provide more data on compliance in Indonesia in paragraph 5th We added the name of the country in paragraph 8th We explained more about the outcome of HBM studies in paragraph 9th More rationale in the 10th paragraph was already added Methods We already gave a short description of non probability sampling method We already perform power analysis to show sufficient of the sample Explanation regarding HBM version were already added We already added “ to the item COVID 19 causes of death Tables using two decimal were already updated Further explanation regarding DASS was already added in the manuscript Data Analysis We already mentioned demographic variables in the results section Results 2nd paragraph added the word psychological. Gender as a significant predictor is already mentioned Discussion We already merged some sentences and added significance to the study and reduced the explanation from the study of Chan In 5th paragraph, the discussion regarding independent contribution was revised, and the population from the study of Winarti et al. was already mentioned 10th paragraph: the sentence was revised 11th paragraph: We changed concluded into plausible 12th paragraph: definition of stress, anxiety and depression as a general concept was noted, and suggested revisions were already applied 13th paragraph: explains changed into may explain 15th paragraph: limitation of the study was mentioned in the article Abstract: The suggestion for comfortable face mask use was for perceived barrier results" } ] } ]	1	https://f1000research.com/articles/11-1080
https://f1000research.com/articles/12-1598/v1	18 Dec 23	{ "type": "Systematic Review", "title": "Development, validation and use of artificial-intelligence-related technologies to assess basic motor skills in children: a scoping review", "authors": [ "Joel Figueroa-Quiñones", "Juan Ipanaque-Neyra", "Heber Gómez Hurtado", "Oscar Bazo-Alvarez", "Juan Carlos Bazo-Alvarez", "Juan Ipanaque-Neyra", "Heber Gómez Hurtado", "Oscar Bazo-Alvarez", "Juan Carlos Bazo-Alvarez" ], "abstract": "Background: In basic motor skills evaluation, two observersers can eventually mark the same child’s performance differently. When systematic, this brings serious noise to the assessment. New motion sensing and tracking technologies offer more precise measures of these children’s capabilities. We aimed to review current development, validation and use of artificial intelligence-related technologies that assess basic motor skills in children aged 3 to 6 years old. Methods: We performed a scoping review in Medline, EBSCO, IEEE and Web of Science databases. PRISMA Extension recommendations for scoping reviews were applied for the full review, whereas the COSMIN criteria for diagnostic instruments helped to evaluate the validation of the artificial intelligence (AI)-related measurements. Results: We found 672 studies, from which 12 were finally selected, 7 related to development and validation and 5 related to use. From the 7 studies, we tracked 10 other publications updating and/or using these technologies. Engineering work and technological features have been prioritised in studies about AI-related technologies. The validation of these algorithms was strictly based on engineering criteria; it means, no substantive knowledge of the medical or psychological aspects of motor skills was integrated into the validation process. Technical features typically evaluated in psychometric instruments designed for assessing motor skills in children were also ignored (e.g., COSMIN criteria). The use of these AI-related technologies in scientific research is still limited. Conclusion: Clinical measurement standards have not been integrated into the development of AI-related technologies for measuring basic motor skills in children. This compromises the validity, reliability and practical utility of these tools, so future improvement in this type of research is needed.", "keywords": [ "Basic motor skills", "fundamental movements", "machine learning", "motion detection", "prediction techniques" ], "content": "Introduction\n\nDeveloping basic motor skills (BMS) is a fundamental process for children.1 These skills involve a series of body movements such as walking, jumping and running, throwing and catching objects, and the sense of balance.2 Several studies have shown the social and well-being benefits of healthy BMS development. For example, children with BMS stimulation tend to participate more in physical activities (e.g., scholarly games and sports), suggesting other benefits such as the early prevention of obesity.3 Several intervention programs, as well as early interventions for promoting healthy BMS development, have been designed, applied and recommended.4 To evaluate the efficacy of these interventions and monitor the optimal BMS development in children, valid and reliable measurement tools are needed.\n\nSeveral instruments are frequently used to assess BMS. For example, the Test for Gross Motor Development Second Edition (TGMD-2),5 the Peabody Motor Development Scale-2 (PDMS-2),6 the Bruininks-Oseretsky Test of Motor Proficiency-2 (BOT-2),7 and the Movement Assessment Battery for Children-2 (MABC-2).8 These assessment instruments have been translated and adapted for people in different countries, such as the USA, China and Iran.9 For all these instruments, BMS assessment is expected to be performed by trained professionals who observe, describe and measure children’s responses to physical tasks.10,11 However, differences between observers (e.g., small differences when marking each task, even after being trained) can introduce noise in the BMS measurements, making the evaluation less accurate and leading to wrong conclusions. For example, two children with similar BMS evaluated with the same instrument but by two different observers can be marked with different BMS levels in the same task, which is an undesirable error. When it becomes systematic (i.e., a constant deviation from the correct BMS measurement), this error is known as observer bias and has been largely investigated.12,13 The BMS evaluation based on artificial intelligence (AI) is a good alternative to avoid observer bias.14\n\nAI-related technology for the recognition and classification of human motion patterns involves several components and steps.15 We describe these general steps in Figure 1, providing some details in the next lines. Sensor or video devices are needed for collecting data on human movement. These data are pre-processed by applying filtering techniques such as Fast Fourier Transformation or wavelets or by reducing the high dimensional space with tools such as principal components analysis or linear discrimination analysis.16 Next, feature selection methods come into play, determining a subset of features from the initial set that is highly suitable for subsequent classification while adhering to various optimisation criteria. Among the efficient methods for feature selection are Sequential Forward Selection, which starts with an empty set and iteratively adds the feature that best meets the optimisation criterion, and Backward Selection, which involves removing features from the set in a repetitive manner.16 Finally, AI or machine learning classifiers are required to identify the corresponding class of motion, in our case, a class that reflects the BMS development of a child (e.g., delayed, normal or advanced for its age group). Machine learning tools include binary classification trees, decision engines, Bayes classifiers, k-Nearest Neighbour, rule-based approaches, linear discriminant classifiers and Support Vector Machines.17 More sophisticated deep learning tools, such as neural networks, are also used.18 From here onwards, we indistinctly use the expression ‘AI-related technology’ for referring to the full process described in Figure 1 or just the classification tools.\n\nThere is a growing use of AI-related technology for physical performance assessment.19 For example, machine learning techniques have been applied to assess the intensity of physical activity performed by an adult.20 In a recent review, at least 53 studies on motion detection with deep or machine learning were identified, of which 75% have been performed since 2015.21 AI has also been used to recognise alterations in walking or walking style and identify specific health problems related to walking22,23 or to detect certain difficulties in motor skills associated with initial symptoms of other diseases.24 Other AI algorithms are implemented to identify and evaluate psychomotor learning performance in students.24 However, to date, there is no formal review of the multiple technologies used to assess BMS in children.\n\nWe aimed to perform a scoping review on studies related to the development and use of AI-related technologies to assess BMS in children. Our objectives were to: 1) determine the general characteristics of the studies; 2) describe the engineering of the AI technologies designed to assess BMS in preschoolers; 3) determine the substantive validation performed on the AI technologies identified, and 4) describe the current use of these AI technologies in applied research.\n\n\nMethods\n\nThe protocol for this review is available here.44 The PRISMA Extension recommendations for scoping reviews were applied for the full review, whereas the COSMIN guidelines were applied for objective 2.25,26 The checklists of these guidelines can be found here.47\n\nWe were interested in published studies focused on engineering, substantive validation, or the use of AI-related technologies developed to evaluate BMS in children. A study was focused on engineering when it was strictly dedicated to developing algorithms for motor skills recognition and classification. A study was focused on substantive validation when the validity and reliability of the AI-related technology were evaluated following psychometric international standards.26 A study only used AI-related technology when it did not include engineering or validation; in other words, it just used the technology developed by someone else.\n\nWe searched the target publications in Medline (SCR_002185), Web of Science (SCR_022706), IEEE (SCR_008314), and EBSCO (SCR_022707) that were published before January 30, 2023. The search terms included combinations of the keywords such as “child,” “preschool,” “basic motor skills,” “artificial intelligence,” “motion sensing,” and “calibration,” and others similar. The search strategy and a complete list of search terms available here.45\n\nAfter the application of the search formulas, the articles found were depurated. To perform an objective selection, we loaded all the publications detected by the search strategy into the Rayyan platform. We removed all duplicates and selected the target publications based on a review of titles and abstracts. This review was performed by two independent groups (two persons each) who were previously trained medical students. In case of discordance, the principal investigator decided to choose or not to choose the study. In the second phase, a full-text article review was performed using the same procedure and independent peers.\n\nAdditionally, we mapped those studies that updated or used the AI-related technology identified as engineered and validated in the previous step, by exploring the citations/references reported in the latter.\n\nThe authors developed a form to extract data from the chosen studies.46 The form included data about the general characteristics of the studies, the engineering of the AI-related technologies, the substantive validation of these technologies, and their current use for BMS assessment in children.\n\n1. General information: First author of the study, country of the study, year of publication, number and sex of participants, health condition (e.g., children with a medical condition that could influence their motor skills).\n\n2. Engineering: Motion capture interface type, basic composition of technologies, system used for motion capture, type of programming language used for system development or modelling, and technology accessibility.\n\n3. Substantive validation: Type of technology developed and validated, validation method, data collection methods, data for COSMIN (see next section), feasibility and usability of the technology.\n\n4. Use: Type of technology used, training of the evaluation team, reported technology reliability, limitations during the technology use, advantages of the technology application, complementary tools, reference to a publication on the technology used.\n\nAll data collected were summarised as categorical variables, organised and presented in tables, using descriptive statistics such as simple frequencies and percentages.\n\nThe COSMIN standards were applied to assess the technical quality of the substantive validation of the AI-related technologies for BMS evaluation.27 In practice, these technologies (e.g., algorithms) work like psychometric tests (e.g., producing similar BMS measurements); thus, the former can be ‘substantively validated’ as the latter usually are. COSMIN is an international standard for reviewing the technical quality of validation studies of psychometric tools (e.g., tests for measuring BMS).\n\nTo perform the COSMIN assessment, two investigators independently assessed and scored eight psychometric properties or indicators (content validity, internal consistency, structural validity, reliability, measurement error, criterion validity, construct validity, and responsiveness). Each indicator was evaluated according to the checklist proposed by Mokking et al.28 For this study, we scored as follows: 1 = N. A, 2 = inadequate, 3 = doubtful, 4 = adequate and 5 = very good. A total score was calculated for each indicator, keeping similar levels for interpretations (very good, adequate, doubtful, inadequate, N.A.). All results from COSMIN assessment were presented in a table.\n\n\nResults\n\nWe identified 672 studies in the first search step, from which 12 studies were finally selected. Among these studies, five were focused on AI-related technology use, while seven were focused on AI-related technology engineering and/or validation (Figure 2).\n\nDuring the last decade, most studies were performed in Asian and European countries (n=9/12, 74.9%) (Table 1). Almost all studies were carried out in children of both sexes (n=9/12, 75%), and only one was focused on children with some type of motor problem.\n\nTo capture the child’s movement, researchers mostly used simple devices such as digital video cameras (n=5/7, 71.4%) (Table 2). More sophisticated devices were less common, such as sensors attached to the body (n=2/7, 28.6%) or multimedia devices connected to personal computers (n=2/7, 28.6%). The software used for each device was different for each study. The most common type of AI-related technology was machine learning tools for movement pattern recognition (n=4/7, 57.1%), while deep learning algorithms were rarely used (n=1/7, 14.3%). Only a few of these tools are free-access (n=2/7, 28.6%). Most codes were implemented in Python (SCR_008394) and supported by libraries such as OpenGL (which produces 2D and 3D graphics)29–31 and Numpy (SCR_008633) (which creates vectors and matrices, and mathematical functions) (45) that helps to process images that are captured in real-time and obtain an accurate representation of the movement.\n\nFor the COSMIN evaluation, we considered seven studies that developed a substantive validation of AI technologies (Table 3). More than half of the studies reported the evaluation of content validity (n=4/7, 57.1%), reliability (n=1/7, 14.2%), and construct validity (n=1/7, 14.2%) with an adequate level. However, other measurement properties, such as structural validity, measurement error and responsiveness, were inadequately or not evaluated in all studies, according to COSMIN standards (n=5/8, 62.5%). It was not unusual that a declared formal evaluation of a psychometric property (e.g., reliability) was followed by no reporting of final results.\n\nIn studies using AI-related technology, the children’s movements were captured by trained personnel (n=2/5, 40%) using digital cameras or camcorders (n=4/5, 80%) (Table 4). In addition, some supporting technologies that provide high-quality video motion capture, such as “Quintic Biomechanics software”, was also reported. Users reported some advantages of these technologies; for example, the short-term evaluation needed and precise and consistent measures that allow a detailed analysis of motor skills. However, no formal generalization of the conclusions to larger populations was reported as a technical limitation.\n\nWe identified 10 studies that updated and/or applied the exact AI-related technology reported in Tables 2 and 3 (Table III, supplemental material). Among those studies, 7/10, (70%) were used for the assessment of motor skills; and 3/10, (30%) were updated and used (i.e., a new version of the technology).\n\n\nDiscussion\n\nWe performed a scoping review of AI-related technologies developed and used to assess motor skills in children. Engineering work and technological features have been prioritized in these studies; for example, the use of advanced systems for motion capture or the training of sophisticated machine learning algorithms for movement patterns recognition. More importantly, the validation of these algorithms was strictly based on engineering criteria; it means, no substantive knowledge of the medical or psychological aspects of motor skills was integrated into the validation process. Technical features typically evaluated in psychometric instruments designed for assessing motor skills in children were also ignored (i.g., COSMIN criteria). The use of these AI-related technologies in scientific research is still limited.\n\nMost studies on AI technologies engineering ignored the standard psychometric validation process (i.e., COSMIN standards). Although many of them complied with the good practices in the development of image processing-oriented software, none of them integrated a substantive validation. AI-related technology is good for identifying movement patterns that are rare in children or patterns that children of a certain age should show, and they are not. This capacity has enormous value for clinical and educative purposes. However, for these AI measures to be integrated into a formal clinical evaluation, some technical features must be confirmed. For example, the measurement error estimate is essential for evaluating individuals from the target population, allowing the definition of critical ranges (i.e., minimum and maximum values) to contrast individual measures and conclude an advantaged, normal or sub-normal motor skill development. Another important psychometric characteristic is responsiveness, which reveals whether any change seen between within-individual AI measurements performed before and after an intervention corresponds to true changes in motor skills (smallest detectable changes), which is linked to investigating when these changes are clinically relevant (minimal important changes).\n\nA previous review of AI technologies for evaluating motor skills in paediatric populations warns that the validation of these tools is limited.32 As we do here, they concluded that this limitation has practical implications in the assessment precision and applicability in clinical contexts. Without a standard psychometric validation process, AI developers do not collect the correct and sufficient evidence to ensure the minimal validity and reliability required for this kind of measurement. For example, one of our reviewed studies reported that the AI algorithm was reliable and valid because it was based on a test previously declared reliable by its original author.33 Differences between the population for which the original test was created and the sample used to develop the AI version can seriously compromise the reliability of the measures and their clinical interpretation criterion due to cultural/ethnic, linguistic, social, economic and age differences.12 In practice, clinical interpretation is an essential component of measurement validity and usually requires evidence beyond the standard qualification norm. For example, the recent study reported a new video-based technology that was based on a classical motor skill test (i.e., that needs paper, pencil and evaluator’s criteria), showing concurrent validity against another measure of motor skills.34 Contrasting AI measurements against external independent criteria is essential, not only to confirm that the algorithm is measuring what we intend to but also to connect these measurements with other signs and symptoms clinically relevant.35–37 In this way, AI measurements become more informative and useful for a full evaluation of a children’s healthy development.\n\nThere are some factors explaining the limited production of AI-related technologies for evaluating motor skills in children. There is a priority for using AI to assess other health problems in this and other populations. During the last two decades, most AI for health has been developed for the diagnosis and follow-up of physical problems such as cancer, cardiovascular diseases, or neurodegenerative disorders in adult subjects.19,38 High costs slow the production of these AI-related technologies,39,40 especially in low-and-middle-income countries. Rich countries promote the investment of significant amounts of money for developing new cutting-edge technology,41 although for a wide range of purposes. In low- and middle-income countries, AI development suffers from some extra limitations, such as insufficient economic and human resources, limited data, non-transparent AI algorithm sharing, and scarce collaboration between technological institutions.42\n\nThe use of AI-related technologies in scientific research is also limited, and this is linked to other factors. As expected, developers focused on engineering and not research to facilitate the use of their technologies. For example, only one of our reviewed studies performed a usability and feasibility analysis,43 which is important to make the technology friendlier and more accessible to future users.33 This can be explained, in part, because most of them is still developed within the academia, and not yet in the private sector and for commercial purposes. However, considering how they can improve the speed and precision of BMS evaluation of children for doctors and teachers, these AI-related technologies have great commercial potential in the educative and clinical contexts.\n\nThis is the first scoping review emphasising the substantive validation processes of AI-related technologies produced to assess motor skills in preschool children. The databases consulted during the identification and selection of studies were specialised and extensive; thus, there was a limited loss of relevant information.\n\nTo facilitate use, developers might perform studies that assess the acceptance and ease of use of these technologies. For example, most technologies are based on sensors and monitors that can be difficult to apply in the real world for doctors, teachers, therapists or professionals unfamiliar with these technologies. Alternative technology could be closer to more universal devices such as video cameras, smartphones and tablets that can evaluate and report motor skills in real-time.\n\nNew validation studies for these technologies should include validation standards for BMS tests. To make this possible, the engineering teams could incorporate specialists in psychometrics, psychology, development therapy and medicine to work collaboratively. This will promote synergy in a multidisciplinary team, facilitating the integration of medical knowledge and psychometric standards into future software versions. Developers should consider providing an open code of their AI-related work so that other developers can continue their work, ensuring reproducibility and clinical improvement in future efforts.\n\n\nConclusions\n\nEngineering work and technological features have been prioritized in the studies about AI-related technologies. The validation of these algorithms was strictly based on engineering criteria; it means, no substantive knowledge of the medical or psychological aspects of motor skills was integrated into the validation process. Technical features typically evaluated in psychometric instruments designed for assessing motor skills in children were also ignored (e.g., COSMIN criteria). The use of these AI-related technologies in scientific research is still limited.", "appendix": "Data availability\n\nZenodo: JC. (2023). Protocol for a scoping review. Zenodo. https://doi.org/10.5281/zenodo.8052777 44\n\nThis project contains the following data:\n\n• AI for BMS_Scopig Review Protocol_Zenodo.docx\n\nZenodo: Development, validation and use of artificial-intelligence-related technologies to assess basic motor skills in children: a scoping review, https://doi.org/10.5281/zenodo.8056742 45\n\nThis project contains the following extended data:\n\n• Appendix 1. Supplementary Tables\n\n• Appendix 2. Search formulas\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nZenodo: Figueroa-Quiñones, Joel. (2023). date extension. Zenodo. https://doi.org/10.5281/zenodo.8190823 46\n\nThis project contains the following extended data:\n\n• Information extraction form\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nZenodo: Joel. (2023). data extension https://doi.org/10.5281/zenodo.8253201 47\n\nThis project contains the following extended data:\n\n• 1. COSMIN checklist\n\n• 2. Scoping Reviews (PRISMA-ScR) Checklist\n\n• 3. Flowchart\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 report is independent research supported by the National Institute for Health and Care Research ARC North Thames. The views expressed in this publication are those of the author(s) and not necessarily those of the National Institute for Health and Care Research or the Department of Health and Social Care. We thank Miguel Moscoso for his help in the initial stage of this project.\n\n\nReferences\n\nGallahue DL, Ozmun JC, Goodway J: Understanding motor development: infants, children, adolescents, adults. New York: McGraw-Hill; 2012.\n\nFigueroa R, An R: Motor Skill Competence and Physical Activity in Preschoolers: A Review. Matern. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBredt S: Artificial Intelligence (AI) in the Financial Sector—Potential and Public Strategies. Front. Artif. Intell. 2019; 2: 16. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nUNESCO: Artificial intelligence for sustainable development: challenges and opportunities for UNESCO’s science and engineering programmes.2019. Reference Source\n\nJC: Protocol for a scoping review. Zenodo. 2023. Publisher Full Text\n\nFigueroa-Quiñones J, Ipanaque-Neyra J, Hurtado HG, et al.: Development, validation and use of artificial-intelligence-related technologies to assess basic motor skills in children: a scoping review (Last version). [Data set]. Zenodo. 2023. Publisher Full Text\n\nFigueroa-Quiñones J: data extension. Zenodo. 2023. Publisher Full Text\n\nJoel: data extension. [Data set]. Zenodo. 2023. Publisher Full Text" }	[ { "id": "349533", "date": "30 Jan 2025", "name": "Abraham M. Joshua", "expertise": [ "Reviewer Expertise Neurorehabilitation", "Upper limb functional evaluation", "AI for rehabilitation", "Exercise therapy", "Balance 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\nABSTRACT Background\n\n-\n\nRedundant phrasing: \"two observersers\" is misspelled and repetitive.\n\nResults\n\n-\n\nTracking of \"10 other publications\" is unclear and vague.\n\n-\n\nOveruse of technical language without explanation for general readers (e.g., \"engineering criteria\").\nKeywords\n\n-\n\nMissing potential keywords like \"assessment tools,\" “functional abilities,”\n\nand\n\n\"gross motor” based on the ‘title and the contents of the study\nIntroduction: suggestions 1. Overly Technical Language:\nWhile the introduction is generally informative, it becomes very technical in certain sections, especially when describing the AI process (e.g., \"Fast Fourier Transformation,\" \"principal components analysis,\" \"linear discriminant analysis\"). This might be difficult for readers unfamiliar with these terms or the AI field. Suggestion: Simplify the explanation or provide brief definitions or context for these terms.\n2. Lack of Clear Connection Between BMS and AI:\nWhile the introduction discusses BMS, AI technologies, and their potential to address observer bias, the connection between these topics could be more explicit. The introduction seems to jump between BMS, traditional measurement tools, observer bias, and AI without a smooth flow that ties everything together. Suggestion: Strengthen the connection between the problems with current BMS assessment and how AI could specifically address them. A clearer explanation of how AI can solve observer bias and improve accuracy in BMS assessment would help make the argument more compelling.\n3. Limited Emphasis on the Scope of the Problem:\nThe issue of observer bias and its impact on BMS assessment is raised, but it’s not explored in-depth. The extent of the problem (how often it happens, how significant the impact is) isn’t fully explained. Suggestion: Provide more concrete examples or data to highlight the real-world implications of observer bias in BMS assessments. This would help emphasize the need for better solutions like AI.\n4. Vague Description of \"AI-Related Technologies\":\nThe term “AI-related technologies” is introduced, but it remains somewhat vague. While the steps of motion recognition are detailed, it’s not entirely clear what specific AI tools or algorithms are most effective in this context or how these methods directly translate to motor skill assessment in children. Suggestion: Clarify the specific AI tools used or might be used in BMS assessment. This could make the introduction feel more grounded in practical applications.\n5. Inconsistent Flow and Structure:\nThe flow between sections could be smoother. For example, the transition from talking about BMS instruments (TGMD-2, BOT-2) to observer bias is a bit abrupt. Similarly, after discussing the issue of observer bias, the leap to the technicalities of AI feels disconnected. Suggestion: Reorganize the content so that each section builds more naturally on the previous one. Consider adding a paragraph that ties observer bias to the introduction of AI as a solution before jumping into the technical aspects.\n6. Missing Emphasis on the Target Age Group (3-6 Years):\nThe introduction discusses BMS in general terms but doesn’t emphasize the importance of assessing motor skills in children aged 3 to 6 years. Since this is a specific target group, more focus on why this age range is critical for BMS development would strengthen the relevance of the study. Suggestion: Provide a brief explanation of why this age group is the focus and what makes BMS development particularly crucial at this stage.\n7. Lack of Citations for Claims About AI in Other Fields:\nThere are a few claims about AI applications in other fields (e.g., assessing physical activity in adults, recognizing walking alterations), but not all of these are fully supported by citations. The mention of “a recent review” and other general statements could be more precise. Suggestion: Provide specific references or clarify that the claims about AI in other fields are based on the literature review cited earlier.\n8. No Clear Statement of the Research Gap:\nWhile the introduction implies a gap in the literature (i.e., a lack of formal review of AI in BMS assessment for children), this could be more explicitly stated and emphasized. It could be clearer why this review is necessary and what new insights it might offer. Suggestion: Make the research gap more prominent by rephrasing the last couple of sentences to more forcefully explain why this scoping review is essential.\n9. Repetitive Mention of AI:\nThe introduction repeatedly mentions “AI-related technologies,” which could be streamlined. The term is used several times in close proximity without adding new information each time, which can feel redundant. Suggestion: Try to vary the phrasing (e.g., \"machine learning tools,\" \"AI classifiers\") to keep the introduction engaging and avoid repetition.\n10. Unfinished Sentence in Objective Statement:\nThe final sentence of the introduction (before the objectives) seems cut off. This makes the last thought feel incomplete and leaves the reader hanging. Suggestion: Complete the sentence and ensure that all points are concluded before introducing the research objectives.\nMethods and discussion:\n1. Lack of Detail in Study Selection Criteria\nWhile the article clearly defines the types of studies it targeted (engineering, substantive validation, and use of AI-related technologies), it doesn’t provide much detail on what specific inclusion and exclusion criteria were applied beyond these categories. For example, were studies excluded for reasons like sample size, study design, or methodological rigor? Suggestion: Provide more specific inclusion and exclusion criteria. Were only randomized controlled trials considered? Were there any restrictions based on the publication type (e.g., peer-reviewed articles only)?\n2. Vague Explanation of Search Strategy\nThe search strategy mentions specific databases but does not explain the rationale for selecting these particular sources over others. Are there other databases relevant to the field that might have been excluded? How were the keywords selected, and were any synonyms or related terms considered? Suggestion: Provide a clearer justification for the selection of these particular databases and search terms. Did you consider any grey literature (e.g., theses, dissertations, reports from non-peer-reviewed sources) to broaden the search?\n3. Details on the Rayyan Platform\nThe mention of the Rayyan platform for managing studies is helpful, but the text doesn't clarify whether Rayyan was used for the full review process or just the initial screening. The review process appears to be manual in nature, but it could benefit from some details on how disagreements were handled between reviewers (e.g., was there a consensus meeting or did one reviewer have final say on the study’s inclusion?). Suggestion: Provide more detail on how Rayyan was used throughout the review process. How were disagreements between the two independent groups resolved, and what role did the principal investigator play in the final decisions?\n4. Potential Bias in Study Selection\nThe method states that the initial review of titles and abstracts was done by two independent groups, but there is no mention of any specific strategies to minimize bias during this phase. Given that the authors are likely familiar with the topic, it could be helpful to acknowledge how any biases in study selection (e.g., confirmation bias or publication bias) were minimized. Suggestion: Mention strategies to reduce bias in study selection. For example, were studies randomly assigned to reviewers, and was there a protocol to ensure that preconceived notions didn’t influence the selection process?\n5. Limited Details on Data Extraction Process\nWhile the data extraction form is outlined with categories such as general information, engineering, substantive validation, and use, there is little detail on how the data were extracted from the studies. For example, was any kind of reliability check conducted between reviewers, or were discrepancies resolved through discussion? Suggestion: Provide more details on the data extraction process, such as whether two independent reviewers performed the extraction and how discrepancies were resolved. Additionally, were any statistical methods used to assess inter-rater reliability in the extraction process?\n6. Lack of Clarity on Data Analysis\nThe description of data analysis mentions the use of descriptive statistics (frequencies and percentages) and the COSMIN standards for evaluating psychometric properties. However, there is no clear explanation of how the data were analyzed or how the results were synthesized. Were any meta-analysis or qualitative synthesis methods considered? How were the studies compared and summarized? Suggestion: Provide more clarity on how the data were synthesized. Was any quantitative or qualitative analysis beyond simple descriptive statistics performed, such as meta-analysis or thematic analysis? Did you perform a subgroup analysis for specific types of AI technologies or specific study characteristics?\n7. Lack of Discussion on Potential Confounding Variables\nThere is a brief mention of the use of psychometric standards (COSMIN) to evaluate AI technologies, but the article doesn't discuss how confounding factors (e.g., differences in sample size, age groups, or types of technology used) might impact the validity of the conclusions. Were these factors taken into consideration in the evaluation process? Suggestion: Acknowledge potential confounding variables and how they might affect the validity of the studies reviewed. How did the authors control for these variables, if at all, in the synthesis process?\n8. Unclear Rationale for Data Collection Methods\nIn the section about data extraction, the mention of \"feasibility and usability\" as part of the data form is important but lacks further context. Was there a specific framework used to evaluate these factors? Were the usability and feasibility criteria standardized across the included studies? Suggestion: Provide more information on the frameworks or criteria used to assess usability and feasibility. Were these evaluations subjective or based on standardized measures? Clarifying this would help readers understand how the data extraction process assessed these aspects. Discussion\n\n-\n\nDiscuss usability, cost-effectiveness, and accessibility challenges. -Emphasize the need for interdisciplinary collaboration in future validation studies. -Propose specific psychometric properties (e.g., construct validity) to prioritize future AI validation research. - Add practical recommendations for improving AI tools (e.g., integrating psychometric standards, improving usability for non-specialists).\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.) Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-1598
https://f1000research.com/articles/12-261/v1	10 Mar 23	{ "type": "Research Article", "title": "Thinking process templates for constructing data stories with SCDNEY", "authors": [ "Yue Cao", "Andy Tran", "Hani Kim", "Nick Robertson", "Yingxin Lin", "Marni Torkel", "Pengyi Yang", "Ellis Patrick", "Shila Ghazanfar", "Jean Yang", "Yue Cao", "Andy Tran", "Hani Kim", "Nick Robertson", "Yingxin Lin", "Marni Torkel", "Pengyi Yang", "Ellis Patrick" ], "abstract": "Background: Globally, scientists now have the ability to generate a vast amount of high throughput biomedical data that carry critical information for important clinical and public health applications. This data revolution in biology is now creating a plethora of new single-cell datasets. Concurrently, there have been significant methodological advances in single-cell research. Integrating these two resources, creating tailor-made, efficient, and purpose-specific data analysis approaches can assist in accelerating scientific discovery.\nMethods: We developed a series of living workshops for building data stories, using Single-cell data integrative analysis (scdney). scdney is a wrapper package with a collection of single-cell analysis R packages incorporating data integration, cell type annotation, higher order testing and more.\nResults: Here, we illustrate two specific workshops. The first workshop examines how to characterise the identity and/or state of cells and the relationship between them, known as phenotyping. The second workshop focuses on extracting higher-order features from cells to predict disease progression.\nConclusions: Through these workshops, we not only showcase current solutions, but also highlight critical thinking points. In particular, we highlight the Thinking Process Template that provides a structured framework for the decision-making process behind such single-cell analyses. Furthermore, our workshop will incorporate dynamic contributions from the community in a collaborative learning approach, thus the term ‘living’.", "keywords": [ "single-cell analysis", "data analysis", "data story", "thinking process template", "living workshop" ], "content": "Introduction\n\nRecent advancements in biotechnology have empowered scientists to generate unprecedented amounts of data at the cellular level that carry critical information for important clinical and public health applications (Goodwin, McPherson, and McCombie, 2016; Stark, Grzelak, and Hadfield, 2019). These data provide a unique opportunity for us to inspect individual cells through the lens of genomics, transcriptomics, proteomics and so on, providing insight into different aspects of a cell and representing a data revolution in biomedical data. To extract scientific discoveries from these data, over one thousand analytical methods have been developed (Zappia and Theis, 2021) to exploit diverse kinds of data and answer a broad range of questions. These analytical methods can be used as ‘black box’ tools to analyse data without knowledge of the methodological details. Hence, it can be difficult to determine how ‘robust’ a data analysis should be conducted. To make the most of the single-cell data revolution in omics science, it is important for researchers to first navigate and determine the optimal analytical tools for each question while being aware of their hidden pitfalls and assumptions.\n\nAnalysing omics data often involves complex workflows including data cleaning, processing, and downstream analysis. A critical component in a successful analysis is the thinking process, which involves the analyst considering the steps in the workflows and making informed decisions that are appropriate for the research questions at hand. For example, the workflow for single-cell analysis often involves multiple interdependent steps such as data filtering and normalisation, feature selection, clustering, dimensionality reduction, alongside further downstream analytical steps. Each of these steps can require analysts to make context-specific decisions, such as deciding thresholds (e.g., filtering or feature selection), selecting parameters (e.g., normalisation or clustering) or selecting an algorithm (e.g., dimensionality reduction). As these analytical choices are dependent on earlier steps, they can have cascading impacts on the downstream analysis, and eventually, the conclusions that are drawn (Krzak et al., 2019; Raimundo, Vallot, and Vert, 2020). Thus, it is crucial that users are guided through the thinking process in order to make the most appropriate decisions at each step given their specific context.\n\nThere is a difference between offering a tutorial or workflow and offering a thinking process. Computational methods are often accompanied by a tutorial that demonstrates how to apply the method to perform a specific task on an example dataset. These tutorials can be straightforward to follow and understand, helping users run the method on their own data. Workflows describe a sequence of analytical methods for processing and analysing certain types of data (Breckels et al., 2016; Lun, McCarthy, and Marioni, 2016; Borcherding, Bormann, and Kraus, 2020). Workflows can help users identify a set of seemingly disparate methods into a cohesive whole. However, simply copying an existing tutorial or workflow leaves the risk of treating the methods as a ‘black box’, potentially leading to false discoveries. We believe that it is important to not only instruct analysts on how to apply a method or workflow, but also to guide them to critically assess their results at each stage. Indeed, efforts are underway to make more transparent what happens ‘behind the paper’ such as the Springer Nature protocols and methods community (https://protocolsmethods.springernature.com/channels/behind-the-paper) with discussions surrounding experimental and analytical choices throughout the project. Critical thinking and assessment of results at each stage enables the analysts to identify where problems arise and guides them to customise their analysis for their specific context. Thus, there is a pressing need to build on existing tutorials and workflows in a way that incorporates such critical thinking.\n\nTo this end, we present a Thinking Process Template to formalise the thought process an analyst should undertake to ensure robust analysis that is tailored to their data. Here, we demonstrate this through scdney, a collection of analytical packages and living workshop materials, which can be updated based on feedback and suggestions from users. In this paper, we demonstrate two examples of our Thinking Process Template in inferring and assessing a cell lineage trajectory, and in performing patient disease classification. We envision that our Thinking Process Template and scdney’s living workshops will complement existing resources and will be a model for future tutorials to encourage transparent and robust research practices for the bioinformatics and biomedical data science community.\n\n\nMethods\n\nHere we showcase two data stories to illustrate scdney. These workshops were developed to showcase scdney as part of this study, not from previous studies nor have them been published somewhere else. The first data story describes the use of scdney on cell level analysis through inferring and assessing the developmental trajectory of individual cells. The second data story details the use of scdney on patient level analysis by extracting and summarising information obtained from each cell. The code for both data stories are hosted on Github as reproducible Rmarkdown files, reported in the code availability section. The underlying data are reported in the data availability section.\n\nA summary of the case study is provided below with detailed information including R code hosted on our Github (Lin, Kim and Chen, 2023).\n\nTo predict the gene pairs associated with the developmental course of the differentiation of mouse hippocampal cells, we downloaded the publicly available data (from GEO with accession number GSE104323) profiling eight cell types from neural lineages of the mouse hippocampus harvested from two post-natal timepoints (day 0 and 5) (La Manno et al., 2018). For speed, we removed the Nbl1, Nbl2, Granule and CA cell types from the dataset and reduced the dataset from 18,213 to 12,935 cells. To evaluate the accuracy of the original cell type labels, we applied scReClassify (Kim et al., 2019) from the scdney package. scReClassify generates cell-type-specific probabilities for each cell, where a probability of 1 denotes the highest accuracy in classification and 0 denotes lowest accuracy. Using the maximum probability assigned to each cell, we re-labelled the cell-type annotations of cells that have inconsistent labels and have a maximum probability greater than 0.9. Then, we used the re-labelled cell-type annotations to perform marker gene analysis using Cepo, a method to determine cell-type-specific differentially stable genes (Kim et al., 2021).\n\nTo build the trajectories, we applied two commonly used trajectory inference tools, Slingshot (Street et al., 2018) and destiny (Angerer et al., 2016). Finally, to predict gene-pairs that change over the trajectory course, we used our previously developed package scHOT (Ghazanfar et al., 2020), which is available on Bioconductor. scHOT enables detection of changes in higher-order interactions in single-cell gene expression data.\n\nA summary of the case study is provided below with detailed information including R code hosted on our Github (Cao and Tran, 2023).\n\nWe predict patient disease outcome using COVID-19 datasets and the packages scFeatures (Cao et al., 2022), and ClassifyR (Strbenac et al., 2015). To build the prediction model on distinguishing mild and severe outcomes, we used the publicly available Schulte-Schrepping data (Schulte-Schrepping et al., 2020). We randomly sampled 20 mild and 20 severe patient samples for the purpose of demonstrating the workshop in a reasonable amount of time. Then, we applied scFeatures from the scdney package to generate patient representations from the single-cell data. scFeatures generates interpretable molecular representations from various feature types. By doing so, we were able to represent each patient with more information than a matrix of gene expressions. At the same time, it also transformed the scRNA-seq data into a matrix of samples by features, which is a standard form for machine learning models. We generated a total of 13 matrices, one for each feature type across the feature categories of (i) cell type proportions, (ii) cell type specific gene expressions, (iii) cell type specific pathway expressions, (iv) cell type specific CCI scores and (v) overall aggregated gene expressions. The details of the feature types can be found in the scFeatures publication (Cao et al., 2022).\n\nTo build a patient outcome classification model from the patient representations, we used our previously developed package ClassifyR (Strbenac et al., 2015), which is available on Bioconductor (https://bioconductor.org/packages/ClassifyR/). ClassifyR provides an implementation of cross-validated classifications, including implementation for a range of commonly used classifiers and evaluation metrics. For this case study, we ran SVM on each of the feature types using a repeated five-fold cross-validation framework with 20 repeats. The accuracy was measured using the metric ‘balanced accuracy’ that is implemented in ClassifyR.\n\nTo assess the generalisability of the constructed model, we used the Schulte-Schrepping data as training data and another publicly available COVID-19 scRNA-seq dataset, the Wilk data (Wilk et al., 2020), as an independent testing data. First, we processed the dataset in the same way using scFeatures to generate the patient representations. Given that different datasets generate slightly different sets of features, for example, due to the difference in the genes reocrded, we subset the features derived from the Schulte-Schrepping dataset and the Wilk data by their common features. We then rebuilt the model using the Schulte-Schrepping dataset as the training dataset using the same cross-validation framework as above. The best model from the 100 models (i.e., from the 20 repeated five-fold cross-validation) was identified based on balanced accuracy and evaluated on the Wilk dataset.\n\n\nResults\n\nTypically, in scientific research papers involving cellular data technologies, there are three key components: (1) Data, (2) Narratives, and (3) Visuals (Figure 1). Through narratives, we explain the data; through visuals, we enlighten the data; through narratives and visuals we engage. At the intersection of the three components are the product: the data stories. However, what is hidden behind these components are the critical thinking questions such as evaluation and parameter choices that happen behind the decision-making process.\n\nHere, we present a Thinking Process Template, to uncover the thinking process behind the construction of data stories, guided by analytical decisions. We demonstrate this in two distinct data analytical scenarios, presented as scientific questions. First, we ask, what are the cell types present in our developmental single-cell dataset, and what are the correlated gene pairs in each trajectory? Second, what features are important for disease outcome classification? In both cases we illuminate the underlying thinking strategy taken by analysts/data scientists in extracting biological knowledge from the data and drawing from the vast compendium of prior knowledge to reveal novel scientific knowledge.\n\nScdney - Single cell data integrative analysis\n\nAs a vehicle to demonstrate the Thinking Process Template, we present scdney (Figure 2), a series of foundational methods for single cell data analysis, including\n\n• data integration approach for scRNA-seq data that enables tailored prior knowledge (Lin et al., 2019);\n\n• a novel cell type classification method based on cell hierarchy (Lin et al., 2020);\n\n• a novel method for identifying differential stable genes (Kim et al., 2021);\n\n• a multi-modal workflow for analysing CITE-seq data (Kim et al., 2020);\n\n• an analytical approach to test for higher-order changes in gene behaviour within human tissue (Ghazanfar et al., 2020); and\n\n• A feature extraction method that creates multi-view feature representation on patient level from single-cell data (Cao et al., 2022).\n\n(A) Collection of Data - The data stories start with data. (B) Collection of methods of scdney - The collection of methods are used for the computational analysis of data. (C) Critical Thinking - Through critical thinking, we derive the final data story.\n\nBuilding upon the collection of vignettes, the Thinking Process Template examines various critical thinking questions that analysts need to make, which drives the decision for the next step in the analysis workflow. Next, using the scdney workflow, we will illustrate the process of generating two data stories. The scdney workflow start with data (Figure 2A), the series of methods are used for the analysis of data (Figure 2B), and through the critical thinking (Figure 2C), we derive the final data story.\n\nNarrative for data story 1 - to identify key gene-pairs associated with the developmental course\n\nIn the first data story, the aim was to identify key gene-pairs associated with the developmental course of the differentiation of mouse hippocampal cells, enabling us to find key gene sets that distinguish hippocampal development in mice from scRNA-seq data (La Manno et al., 2018) (Figure 3). Box 1 lists some questions and our thought process during the development of the story.\n\nThe thinking process begins from the processed data with cell type annotations and proceeds to constructing a trajectory and extracting biological insight through identification of correlated gene pairs. The orange diamonds highlight potential questions that help us quality check the data analysis, and the orange hexagonal shapes denote the specific computational tasks that are required to answer the questions above.\n\nQuestion: Which tools should I use and what format does the data need to be in?\n\nThinking process: Several tools have been developed to construct trajectories from single cell data. Different tools may require different types of input data; therefore, it is important to understand the tools and your data before selecting a tool. Another key aspect of working on trajectory reconstruction is to judge which cell populations to include in the trajectory analyses. Some cell types or cell populations not involved in the differentiation system of interest should be excluded in the trajectory inference.\n\nQuestion: Which trajectory method should I use?\n\nThinking process: Depending on the complexity of the trajectory, the choice of tools can have a large impact on the accuracy of the resulting trajectory built. A large body of work has been performed to evaluate current single-cell trajectory inference methods (Saelens et al., 2019). They provide guidelines and a framework to test which trajectory tool and setting are most appropriate for your data. Again, this requires you to have a good understanding of the expected underlying biology in your data, such as the topology and the number of branches of the expected trajectory.\n\nQuestion: Are the cell type labels accurate?\n\nThinking process: Evaluating the quality of the cell type labels is important, as the quality of this may directly impact downstream analyses such as determining cell-type markers. By quantifying the proportion of cells accurately labelled in the dataset, we are not only able to assess the quality of the overall dataset, but also to re-classify any mislabelled cells.\n\nQuestion: Is the trajectory stable?\n\nThinking process: This can be achieved in many ways, such as testing the reproducibility of the trajectory when different tools are used or when permuting the features (gene sets or cells) in the data. A consistent trajectory across various permutations provides stronger support for the final trajectory.\n\nQuestion: Is the trajectory sensible?\n\nThinking process: Inspecting how sensible a trajectory is critical. We should inspect various features of the trajectory such as the direction of the trajectory (which includes evaluating the root of the trajectory), the number of branches, and the number of terminal nodes (e.g., terminal populations) in the data. Whilst these evaluations require an in-depth understanding of your biological system through literature search, there are computational tools that help guide this. For example, CYTOTRACE can be used to predict the root cell (i.e., the most undifferentiated cell) in a cell population.\n\nQuestion: How reliable are the top regulated gene-pairs?\n\nThinking process: This question essentially asks whether the extracted gene-pairs are expected for the current biological system. This often requires prior knowledge of experimentally validated ground truths, which can be employed to evaluate the validity of our results. The presence of one or more biological truths increases the confidence that the current framework is appropriate.\n\nQuestion: How accurate are the identified top gene-pairs?\n\nThinking process: It is important to bear in mind that the presence of known biological truths in our results do not necessarily mean that the other predicted gene pairs are also biological truths. There are many ways we can validate the accuracy of the predicted gene-pairs, and these validation approaches can be done experimentally or computationally. Computationally, one of the ways we can validate the accuracy is to assess the reproducibility of our framework on a new dataset derived from the same biological system. When such independent datasets are not available, a simple train-test split can be performed on the data to test the reproducibility of the findings.\n\nThe dataset we use contains eight cell types from neural lineages of the mouse hippocampus harvested from two post-natal timepoints (day 0 and 5) (La Manno et al., 2018). Whilst the main goal in the original study was to demonstrate the RNA velocity fields that describe the fate decisions governing mouse hippocampal development, our data story aims to uncover novel gene-pairs associated with these neural lineages using scHOT (Ghazanfar et al., 2020).\n\nWe start by asking whether the cell type annotations in the original data are accurate. Here our expectation is that most of the labels are accurate, and by using scReClassify (Kim et al., 2019) we demonstrate that approximately 88.4% of cells show an original classification accuracy over 0.9 (Figure 4A). Among these cells, only 1.5% (177 cells) were re-classified, suggesting that a small proportion of cells may have been mislabelled. These findings were confirmed through marker analysis using Cepo (Figure 4B), and the cells with high confidence scores were re-labelled for subsequent analyses. Once we have confirmed with further quality control questions as shown in the box and ensured the quality of the cell type annotations, we can then use these labels to perform marker gene analysis and to construct the lineage trajectories (Figure 4C).\n\n(A) Shows the proportion of cells in each confidence level, defined by scReClassify, for each cell type group. (B) The distribution of gene expression of top five marker genes in Immature Granule 2 cells as per the original labels (bottom panel) and re-classified labels (top panel). (C) UMAP of mouse brain cells coloured by cell type and faceted by cells that maintain their original labels (left) and those that have been re-classified (right).\n\nAfter performing the quality control of the original annotations, we then can ask questions relating to trajectory reconstruction. In the trajectory building stage, we ask questions (see Box 1) to ensure the stability and robustness of the trajectories by testing the concordance of the pseudo-times between various trajectory reconstruction tools. In our Thinking Process Template, we indicate at various points at which one can use prior knowledge (indicated by the glasses icon) to guide the analysis. For example, we can use prior knowledge to ask whether the reconstructed trajectories show the correct branching expected in the underlying biology of the differentiation and whether key gene-pairs that are known to be co-regulated are identified by scHOT. Together, these analyses demonstrate that the final trajectories are in line with our expectations and provide more confidence in the new biological insights extracted from these trajectories.\n\nNarrative for data story 2 - develop a PBMC biomarker model to predict COVID-19 patient outcomes\n\nIn our second data story, we aim to predict COVID-19 patient outcomes (mild or severe) from scRNA-seq data of peripheral blood mononuclear cells (Schulte-Schrepping et al., 2020) (Figure 5). Below, we list some questions and our thought process during the development of the story. Here, we showcase the story we derived on the COVID-19 patient outcome prediction. The story begins with the question of what models and input format we will use to build a prediction model (see Box 2). Here, we decided to use classical machine learning instead of deep learning, given the small sample size of 20 mild and 20 severe patients. We utilise scFeatures, a package that generates interpretable multiscale features from scRNA-seq data, such as cell-type proportions, pathway expression, ligand-receptor interactions and more. These features can then be used as input to facilitate an interpretable classification model. Once we have asked quality control questions as shown in the box and ensured the quality of generated features, we then used these features to build models to predict mild or severe outcomes.\n\nThe thinking process begins from processed data with cell type annotations and branches into two questions, each with a different focus. The top part focuses on using the disease classification model to extract biological insights into the disease, such as what features are important towards disease classification. The bottom part focuses on examining the model properties, such as whether the model is generalisable.\n\nQuestion: What model should I use and what data structure is required by the model?\n\nThinking process: There exist a number of advanced deep learning tools that can obtain various biological insights from the count matrix (Bao et al., 2022). However, a small sample size, which is often what’s typical in single-cell patient data, may not be ideal to train a deep learning model. We might consider the alternatives such as classification machine learning methods like random forest. These methods requires the input in the format of samples by features. In this case, we can consider manually extracting the features such as cell type proportion.\n\nQuestion: Is the data preprocessed appropriately?\n\nThinking process: The quality of the data itself has a direct impact on the quality of the extracted features, and subsequently the quality of the model. Therefore, it is important to perform “quality control” both on the original count matrix and on any of the extracted features derived from the count matrix.\n\nQuestion: Should I downweight any samples?\n\nThinking process: Class imbalance can have a negative effect on the model, as the model would be biassed towards the over-represented class. One potential strategy to alleviate this is to downweight the over-represented class.\n\nQuestions: Do the generated features make sense? Are the extracted features sensible?\n\nThinking process: This is really asking whether the extracted features are expected. This often requires finding a handful of the top differentially expressed genes through DE analysis and checking if they are mentioned in literature.\n\nQuestion: Does the overall graphical representation of the features look sensible?\n\nThinking process: In this question, we are looking at the overall distribution of the generated features. For example, if we examine the heatmap or volcano plot, are we seeing what we expect to see? Also, see below for examples of quality control checks.\n\nQuestion: Are there any missing values or outliers in the generated features?\n\nThinking process: We should inspect the generated features to ensure they are not saturated with missing values. Features where many values are missing may not be informative for downstream analysis and should be removed prior to model building.\n\nQuestion: Are the generated features heavily correlated?\n\nThinking process: Having many heavily correlated features can negatively affect a model by introducing noise and instability.\n\nQuestion: There are a lot of the generated features, how do I make sense of them?\n\nThinking process: Given the number of features in a single-cell matrix (typically around 20,000 genes for a scRNA-seq data), one may end up with many derived features. One strategy is to perform an association study, where we examine the association of the features with the outcome. We could also conduct a literature search or consult with biologists to determine whether these top features are biologically significant.\n\nQuestions: How good is my prediction? How does it compare to the current state-of-the-art?\n\nThinking process: The expected accuracy of a prediction can vary depending on the specific task at hand. For example, an accuracy of 0.6 may be what the current state-of-the-art is for a difficult disease classification task, whereas for a clear cell type classification task, an accuracy of 0.9 may be the baseline.\n\nQuestions: Is the result different using different metrics? Different models?\n\nThinking process: It may be necessary to try a number of machine learning models and a number of evaluation criteria to assess model performance. For example, when there are imbalanced class sizes, balanced accuracy and F1 score are better measures of model performance compared to precision and recall.\n\nQuestions: Is my model overfitting to the data? Do I need further testing?\n\nThinking process: One needs to be careful with model overfitting. A model may have very high accuracy on the dataset it is built from, but performs poorly on an unseen dataset. To assess model overfitting, we could test the performance of the model on an unseen dataset to assess its generalisability.\n\nQuestion: Are the top features stable across the models?\n\nThinking process: After we obtain the model, we may wish to inspect the top features selected by the model. The repeated cross-validation framework is often used when building machine learning models as it provides a better assessment of model predictability than a simple train-test split. Therefore, we need to check whether the top features are similar across all models from the cross-validation framework.\n\nWhen building machine learning models, it is crucial that we ask questions on the model performance on a variety of models and metrics. Therefore, we choose to use ClassifyR, as it provides a user-friendly implementation on a number of common machine learning models and evaluation metrics. We created models for each feature type and compared the utility of these feature types for patient classification. We found that a support vector machine classifier consistently achieves a cross-validation accuracy over 0.7 (Figure 6A), demonstrating the usefulness of these features to classify disease outcomes. Once we obtain the final models, we include questions that users can ask themselves to ensure the robustness of the constructed models. To assess the generalisability of the model, we tested the performance of these models on a different data set (Wilk et al., 2020). We found that four of the feature types have a balanced accuracy over 0.7 (Figure 6B), with cell-cell interaction achieving a balanced accuracy of 0.78, suggesting that these feature types have good generalisability on the independent data. Finally, to extract biological insights from the fitted models, we guide users to interpret the fitted models to identify important features and reflect on whether the features make sense.\n\n(A) Shows the balanced accuracy of each feature type on classifying the mild and severe patients in the Schulte-Schrepping dataset. Models were run using five fold cross-validation with 20 repeats. For each feature type, the best model from the cross-validation was then selected and used to predict on the mild and severe patients in the Wilk dataset, as shown in (B).\n\n\nDiscussion\n\nHere, we have presented a Thinking Process Template to not only guide users how to perform a single cell data analysis, but also to encourage critical thinking, ensuring that each part of the workflow successfully performs its desired task. We demonstrated this through the use of scdney, a collection of analytical packages that can perform a wide range of single-cell data processing and analyses. In the previous section, we demonstrated the importance of the process with two examples: identification of key gene pairs that distinguish hippocampal development in mouse cells and generation of features from human cells for disease outcome prediction. We envisage use of the Thinking Process Template as a valuable framework for critical thinking in single-cell data analysis.\n\nBioinformatics analysis workflows involve many steps, each often requiring decisions to be made, dependent on the earlier choices. The most appropriate decisions will differ between datasets and analyses. Therefore, performing a robust analysis requires significant training and experience. However, our Thinking Process Template conveys this training as critical thinking questions that less-experienced users can easily follow for their specific context. The template can be adapted to a wide range of analyses, complementing the existing learning resources, to lower the barrier to entry for performing reproducible bioinformatics analysis. Furthermore, the template enables an asynchronous learning approach (Bishop and Verleger, 2013), where the users can learn at their own pace and on their own time without the constraints of traditional workshop schedules. This is particularly useful for bioinformatics analysis, where the decisions and steps can vary depending on the specific datasets and analyses and need to be thoroughly thought about prior to drawing conclusions.\n\nIn the last decade, partly in response to the replicability crisis (Guttinger and Love, 2019), there has been an increased emphasis on open and transparent science and an increased culture among bioinformaticians of sharing data and code so that key findings can be reproduced. However, sharing code alone does not address all aspects of the replicability of scientific conclusions and further, does not explicitly contribute towards the sharing of analytical strategies. In our Thinking Process Template, we believe acknowledging the critical thinking steps ensures a better understanding of the stability and robustness of analytical decisions made in an analysis, making it possible to assess if the same conclusions would be drawn if different decisions were made. Further, sharing the key critical thinking steps of a project, in addition to the code, will improve replicability of results by making it clear where, when, and why analyses can differ when the same code is applied to different data. This will enhance reproducibility of studies performed by different researchers and institutes, and by promoting open examination of the practices, may help to promote replicability in the broader research field.\n\nThe thinking process of data analysis is dynamic, constantly evolving and specific to the dataset and the research questions. In practice, when addressing similar research questions, the data analysis workflow that works well on one dataset may not be universal to all other datasets. The thinking process proposed in this paper could serve as useful tips and tricks to address these problems. The output from the thinking process can potentially stimulate a new thinking process, which may further inspire the scientists to ask different questions about the data. The complex thinking process involved in publication is starting to be acknowledged on collaborative learning platforms, such as the one established by F1000. These platforms enable authors to describe the behind-the-scenes stories leading to their publications, as well as for others to contribute analytical suggestions and ideas in a dynamic way. It is known that groups of people with cognitive diversity are often able to solve problems more effectively than a group of cognitively similar people (Reynolds and Lewis, 2017). Sharing ideas therefore supports the development of effective bioinformatics analysis. By offering an approach for researchers to share and discuss the methods and decisions involved in their analysis, the Thinking Process Template also promotes a deeper level of transparency in bioinformatics analysis. This includes not only the sharing of positive results, but also the sharing of negative or null results. In many cases, null results can be just as important to science, as they provide valuable information about what does not work and can help the broader community to avoid repeating failed experiments or approaches. However, the current scientific field leans more towards the reporting of positive results only. We see the Thinking Process Template to be a tool that can support the sharing of both positive and negative results by providing a structured framework for documenting the decisions and findings in various steps of the analysis. The document can later be shared with the community to increase the transparency of the work.\n\nA distinct and complementary component to the Thinking Process Template is related to the ease for researchers to reproduce open data analyses on their local computer systems. Robustness of computational tools is an enduring issue in various analytically-driven fields and challenges with reproducing data analytics is often due to the difference in software versioning and the large variety of operating systems. To address these issues, in the R programming community tools, such as BiocManager and Renv, have been developed to help with the installation and documentation of R package dependencies. The use of containers such as Docker allows for the creation of fully reproducible software and analytical environments that can be easily shared and run on different operating systems. In the case of SCDNEY, we have taken steps to improve the robustness of the tool. The scdney wrapper package (https://github.com/SydneyBioX/scdney) and its individual packages are incorporated into controlled repositories such as Github and Bioconductor. In addition, scdney is provided as a Docker container which contains all the necessary dependencies for installation, making it easy for researchers to install and use scdney on their local systems.\n\n\nConclusion\n\nIn conclusion, the advancement of computational methodologies for integrative analysis of single-cell omics data is transforming molecular biology at an unprecedented scale and speed. Here we introduce the design thinking process template that structures analytical decision making. Together with scdney, a collection of wrapper packages presented in the context of several data stories. By establishing scdney as a collection of living workshops, we highlight the current solutions in generating novel biological insights. By emphasising the Thinking Process Template and the critical thinking process behind in our workshops, we aim to empower users to more effectively and confidently use scdney to gain insights from their single-cell data. Finally, we discuss various key aspects such as reproducibility, replicability, and usability of the computational tools. We hope scdney serves as a foundation for future development and application of computational methods for integrative analysis of and biological discovery from single-cell omics data.\n\n\nAuthor contribution\n\nJY, SG conceived, designed and funded the study. HK completed the analysis and design of data story 1 with feedback from YL, PY. YC and AT completed the analysis and design of data story 2 with guidance from JY, and SG. The implementation and construction of the R package for the case study were done jointly between YC and AT. NR tested all R packages; MT and YL develop the graphics with feedback from JY, SG and EP. The development of the designed Thinking Process Template was done jointly by all authors and all authors wrote, reviewed and approved the manuscript.", "appendix": "Data availability\n\nNCBI Gene Expression Omnibus (GEO): Transcriptome analysis of single cells from the developing mouse dentate gyrus. Accession number, GSE104323, https://identifiers.org/ncbigene:104323.\n\nEuropean Genome-phenome Archive (EGA): ScRNA-seq of PBMC and whole blood samples reveals a dysregulated myeloid cell compartment in severe COVID-19. Access number EGAS00001004571, https://ega-archive.org/studies/EGAS00001004571.\n\n\nAcknowledgments\n\nThe authors thank all their colleagues, particularly at The University of Sydney, Sydney Precision Data Science and Judith and David Coffey Life Lab in Charles Perkins Centre for their support and intellectual engagement. Special thanks to Daniel Kim, Mohammad Javad Davoudabadi and Lijia Yu for their contribution in our weekly discussion. Dario Strbenac for providing ClassifyR support which enabled the writing of story 2.\n\n\nReferences\n\nAngerer P, Haghverdi L, Büttner M, et al.: destiny: diffusion maps for large-scale single-cell data in R. Bioinformatics. 2016; 32(8): 1241–1243. PubMed Abstract \| Publisher Full Text\n\nBao S, Li K, Yan C, et al.: Deep learning-based advances and applications for single-cell RNA-sequencing data analysis. Brief. Bioinform. 2022; 23(1). PubMed Abstract \| Publisher Full Text\n\nBishop J, Verleger MA: The flipped classroom: A survey of the research. 2013 ASEE Annual Conference & Exposition. 2013. Reference Source\n\nBorcherding N, Bormann NL, Kraus G: scRepertoire: An R-based toolkit for single-cell immune receptor analysis. F1000Res. 2020; 9: 47. Publisher Full Text\n\nBreckels LM, Mulvey CM, Lilley KS, et al.: A Bioconductor workflow for processing and analysing spatial proteomics data. F1000Res. 2016; 5: 2926. 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PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "170725", "date": "23 May 2023", "name": "Jun Li", "expertise": [ "Reviewer Expertise Single-cell data analysis", "data science education", "data processing and 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\nThis article described an important effort to improve the teaching of data science skills through \"thinking process templates\". In the past, static knowledge was taught in didactic lectures, whereas data analysis workflow was taught in step-by-step tutorials. What remains lacking is to treat the analysis of each dataset as a unique journey, containing decision points that require context-specific diagnosis and judgement. This article focused on single-cell data analysis in the scdney system, which is a collection of related R packages performing data integration, cell type annotation, statistical modeling such as differential expression analysis and, importantly, \"constructing data stories\".\nSuch an effort is much needed, as most of the time the tutorials for popular analysis workflows were presented as a single path through the data, without highlighting key forking points, measures of confidence, and reasons to select certain algorithms for normalization, projection, or visualization. The article stated this problem very well, and sought to design the thinking template to uncover \"hidden pitfalls and assumptions\".\nIt also drew attention to the importance of the \"interdependence\" of data analysis steps (such as imputation-then-normalization versus normalization-then-imputation), as the choices \"have cascading impacts on the downstream analysis\".\nThe main part of the article described two use cases, using different datasets for different end goals. They illustrate how thinking process needs to be customized for the situation, even though the basic codes and the statistical principles are similar. The single most important value of such an exercise is to advocate for a new way of combining scholarship with pedagogy, in which the analysts strive to provide \"a structured framework for documenting the decisions and findings in various steps of the analysis\". As such, the emphasis is to go beyond the practice of recording the workflow, by being responsible for sharing the reasons, alternative decisions, and inevitable compromises as one brings a story out of a data object.\n\nIn terms of improvement, my main suggestion is to highlight one or two examples where the standard workflow would proceed unwittingly into the wrong decision (such as using the default choice of normalization method or embedding parameters), but a more circumspect, thinking-along-the-way approach would have produced relevant diagnostics and turned the analysis unto another path. Similarly, it would be useful to provide an example where a decision depends on the earlier choices, or when the same dataset needs different treatments for different goals.\nVery minor issues:\nA typo in page 4 \"reocrded\".\n\nPlease concisely explain \"differential stable genes\" and \"higher-order changes\", in page 5.\n\nIn the paragraph before \"Conclusions\", in the sentence \"To address these issues,…\" there is probably a misplaced comma.\n\nIn Conclusion, the sentence \"Together with scdney,…\" needs fixing.\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": [ { "c_id": "10727", "date": "17 Jan 2024", "name": "Yue Cao", "role": "Author Response", "response": "We thank the reviewer for supporting our teaching philosophy on critical thinking. We have now re-written the section on the second data story to highlight examples where critical thinking is needed for diagnosis. The modified section is copied below: “Once the final models are obtained, we ask questions on the robustness of the models. One approach on this involves assessing the generalisability of the model on an independent dataset. We examined the performance of the 13 models on a different COVID-19 dataset obtained from the Wilk study that also contain mild and severe patients (Wilk et al., 2020). We found while the 13 models have close balanced accuracy between 0.75 and 0.88 on the Schulte-Schrepping dataset, their performance varied greatly in the Wilk dataset and ranged between 0.49 to 0.78 (Figure 6A, B). It is noteworthy that models built from feature types such as “gene proportion cell type” that have high accuracy do not necessarily maintain good performance on the Wilk dataset. On the other hand, the feature type “CCI” achieved an accuracy of over 0.75 in both datasets, indicating potential for further examination. Finally, to extract biological insights from the fitted models, we guide users to interpret the fitted models to identify important features and reflect on whether the features make sense. Here, it is important not to select the top features based on a single model, but to ask about the stability of these top features. To illustrate this idea, we examined all features that appeared at least once as top 10 features in the cross-validated models. Figure 6C highlights that while the majority of the features were consistently ranked as top features across all models, a proportion of features were ranked in the hundreds and thousands position in some models. These two scenarios illustrate the importance of critical thinking to avoid heading down a wrong decision path.” Below we provide point-to-point response on the minor issues. Very minor issues: A typo in page 4 \"reocrded\". Response: This is now fixed. Please concisely explain \"differential stable genes\" and \"higher-order changes\", in page 5. Response: We have added a concise description to each of the terms: “a novel method for identifying differential stable genes, that is, genes that are stably expressed in one cell type relative to other cell types” and “By higher-order changes, we refer to higher order interactions such as variation and coexpression that are beyond changes in mean expression”. In the paragraph before \"Conclusions\", in the sentence \"To address these issues,…\" there is probably a misplaced comma. Response: We have rephrased this sentence into: “To address these issues, the R programming community has developed tools such as BiocManager and Renv to help with the installation and documentation of R package dependencies.” In Conclusion, the sentence \"Together with scdney,…\" needs fixing. Response: We have rephrased the sentence into: “Here we introduce the design thinking process template that structures analytical decision making together with scdney, a wrapper package with a collection of packages presented in the context of several data stories.”" } ] }, { "id": "173874", "date": "15 Jun 2023", "name": "Kelly Street", "expertise": [ "Reviewer Expertise Single-cell transcriptomics", "computational biology software 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\nThe authors present a Thinking Process Template for the analysis of complex datasets. This template encourages researchers to think critically about each step in their analysis and to be more transparent in the reporting of their results through the use of data stories that acknowledge the subjective decisions that had to be made along the way.\nThe thinking process template is demonstrated through two example analyses of single-cell RNAseq data with methods from the scdney package. These examples are highly relevant, as a typical analysis in this field generally involves multiple interconnected steps with the choices made at each step having (potentially major) downstream consequences. These example data stories show what additional questions the researchers asked at each step of the analysis in order to establish confidence in their results to that point. These questions and the associated supplemental analyses are generally not included in the final products of most research projects (papers, software, etc.), but are of critical importance to the validity of the results.\nI strongly agree with the authors' call for greater transparency in method selection and the educational advantages of training analysts to think critically about their pipelines. While I found some of the concepts presented in this manuscript confusing, I think the overall message is both timely and critically important.\nThe biggest source of confusion for me was the notion of the Thinking Process Template. The authors claim that this template will \"formalize the thought process an analyst should undertake to ensure robust analysis that is tailored to their data,\" which is quite a lofty goal. This template is referenced throughout and demonstrated by the two example analyses, but I was never clear on its definition or practical use (Figures 3 and 5 and Boxes 1 and 2 all seem more useful and generalizable than Figures 1 and 2). As such, I failed to see the connection between the different Results subsections. I think the paper could be improved by providing a more concise definition of the Thinking Process Template. Alternatively, I think removing/de-emphasizing these sections and focusing on advocating for the use of data stories (as demonstrated), would make for a more effective message, as I'm not sure what is gained from the additional terminology.\n\nOn a related note, the title mentions \"Thinking process templates\" (plural, not capitalized), whereas the text itself often refers to a Thinking Process Template (singular, capitalized). Given my confusion related to point (1), I found myself wondering if the \"templates\" actually referred to the example analyses, or if it was indeed supposed to be something more general.\n\nIt took me a little while to find the workshop materials mentioned, particularly for the second data story, which is not listed on the scdney website (at least, not the one I found: https://sydneybiox.github.io/scdney/ ). Since these materials are central to the results, it would be helpful to include direct links to them in the text, if possible, or otherwise in the Data/Software Availability sections (I'm referring to https://sydneybiox.github.io/scdneyAdvancedPhenotyping/articles/advanced_phenotyping.html and https://sydneybiox.github.io/scdneyDiseasePrediction/articles/disease_outcome_classification_schulte.html , and apologize if these are not the intended definitive versions of the data stories).\nMinor comments\n\nThe full data stories make use of several methods that are not mentioned or cited, but perhaps could be. I noted Monocle 3, tradeSeq, velocyto, clusterProfiler, CellChat, and CYTOTRACE for the first data story and Seurat for the second.\n\nFigure 4B could use more explanation. The top five marker genes seem to do a much better job of identifying the original set of \"ImmGranule2\" cells than the re-classified set. Why do these markers become less informative in the re-classified data? Wouldn't that indicate that the original labels were more biologically meaningful?\n\nI think the phrase \"through visuals, we enlighten the data\" only works if you use the archaic definition of \"enlighten\". \"Illuminate\" might be a better choice.\n\nThe following sentences/phrases could stand to be re-written for clarity:\nIntroduction: \"...how 'robust' a data analysis should be conducted\"\n\nIntroduction: \"...help users identify a set of seemingly disparate methods into a cohesive whole\"\n\nMethods: \"not from previous studies nor have them been published somewhere else\"\n\nFigure 1: \"Critical thinking questions to what we have to make from the Data, drive our decision with the Narrative and enlighten with the Visuals.\"\n\nResults: \"...creates multi-view feature representation on patient level...\"\n\nResults: \"The scdney workflow start(s) with data...\"\n\nResults: \"...gene sets that distinguish hippocampal development in mice from scRNA-seq data...\" (sounds like you are contrasting \"hippocampal development\" and \"scRNA-seq\")\n\nConclusion: \"...scdney, a collection of wrapper packages...\" (scdney is the wrapper package)\n\nThe bulleted list of methods in the scdney package should be consistently formatted (ie. should all start with a lower case \"a\" or \"an\").\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": "10728", "date": "17 Jan 2024", "name": "Yue Cao", "role": "Author Response", "response": "Response: We thank the reviewer for the support in the transparency of method selection. Below we provide point-to-point response. The biggest source of confusion for me was the notion of the Thinking Process Template. The authors claim that this template will \"formalize the thought process an analyst should undertake to ensure robust analysis that is tailored to their data,\" which is quite a lofty goal. This template is referenced throughout and demonstrated by the two example analyses, but I was never clear on its definition or practical use (Figures 3 and 5 and Boxes 1 and 2 all seem more useful and generalizable than Figures 1 and 2). As such, I failed to see the connection between the different Results subsections. I think the paper could be improved by providing a more concise definition of the Thinking Process Template. Alternatively, I think removing/de-emphasizing these sections and focusing on advocating for the use of data stories (as demonstrated), would make for a more effective message, as I'm not sure what is gained from the additional terminology. Response: We appreciate the reviewer’s perspective and would like to provide some clarification on the Thinking Process Template. Thinking Process Template is a general term that refers to the data analysis procedure from data input to final analysis outcome that involves critical thinking processes and goes beyond directapplication of tools. It is distinct to data stories which are the products of data analysis efforts. We have now clarified the terminology in the introduction section: “We use Thinking Process Template as a general term to refer to the data analysis procedure from data input to final analysis outcome that involves critical thinking processes and goes beyond the simple application of tools or the products of data analysis.” On a related note, the title mentions \"Thinking process templates\" (plural, not capitalized), whereas the text itself often refers to a Thinking Process Template (singular, capitalized). Given my confusion related to point (1), I found myself wondering if the \"templates\" actually referred to the example analyses, or if it was indeed supposed to be something more general. Response: We refer to the “Thinking Process Template” as the general term that encapsulates the critical thinking process rather than specific templates. In single-cell, the analysis that researchers perform are diverse and there is no Thinking Process Template applicable to all tasks. Therefore, we provided two examples in Figures 3 and 5 and Box 1 and 2 to illustrate two examples of Thinking Process Templates in the context of two data stories: 1) the identification of gene pairs and 2) patient prediction. It took me a little while to find the workshop materials mentioned, particularly for the second data story, which is not listed on the scdney website (at least, not the one I found: https://sydneybiox.github.io/scdney/ ). Since these materials are central to the results, it would be helpful to include direct links to them in the text, if possible, or otherwise in the Data/Software Availability sections (I'm referring to https://sydneybiox.github.io/scdneyAdvancedPhenotyping/articles/advanced_phenotyping.html and https://sydneybiox.github.io/scdneyDiseasePrediction/articles/disease_outcome_classification_schulte.html , and apologize if these are not the intended definitive versions of the data stories). Response: We thank the reviewer for this suggestion and have updated the https://sydneybiox.github.io/scdney/workshops.html to include the second data story. Minor comments The full data stories make use of several methods that are not mentioned or cited, but perhaps could be. I noted Monocle 3, tradeSeq, velocyto, clusterProfiler, CellChat, and CYTOTRACE for the first data story and Seurat for the second. Response: We have added the relevant packages and references: “as well as asking which genes are differentially expressed across a pseudotime using tradeSeq (Van den Berge et al. 2020) and performing functional annotation of these gene sets through clusterProfiler (Yu et al. 2012). Together, these analyses demonstrate that the final trajectories are in line with our expectations and provide more confidence in the new biological insights extracted from these trajectories. The story includes other downstream analysis of the data such as cell-cell communication using CellChat (Jin et al. 2021) and RNA velocity analysis using scVelo (Bergen et al. 2020), which the users can perform to further explore their data.” Figure 4B could use more explanation. The top five marker genes seem to do a much better job of identifying the original set of \"ImmGranule2\" cells than the re-classified set. Why do these markers become less informative in the re-classified data? Wouldn't that indicate that the original labels were more biologically meaningful? Response: We apologise for the confusion. We have corrected the mislabel in the legend. The visualisations show that the cell-type specific markers show a better distribution in the newly annotated cell type group (blue, re-classified) than in the original grouping (red, original). A higher expression of the top marker genes suggests that new groupings now better represent the cell-type profile of ImmGranule2. I think the phrase \"through visuals, we enlighten the data\" only works if you use the archaic definition of \"enlighten\". \"Illuminate\" might be a better choice. Response: We have now replaced the word “enlighten” with “illuminate”, including the occurrence in Figure 1. The following sentences/phrases could stand to be re-written for clarity: Introduction: \"...how 'robust' a data analysis should be conducted\" Response: We have rephrased this into: “Hence, this can create challenges when it comes to deciding how rigorous a data analysis is.”. Introduction: \"...help users identify a set of seemingly disparate methods into a cohesive whole\" Response: We have rephrased this into: “Workflows can help users identify a set of seemingly disjoint methods into a unified and coherent process.” Methods: \"not from previous studies nor have them been published somewhere else\" We have rephrased this into: “These two data stories and the accompanying workshops were not derived from previous studies nor have they been published elsewhere.”. Figure 1: \"Critical thinking questions to what we have to make from the Data, drive our decision with the Narrative and enlighten with the Visuals.\" Response: We have rephrased this into “Critical thinking questions from the data drive our decision with the Narrative and illuminate with the Visuals.“ Results: \"...creates multi-view feature representation on patient level...\" Response: This is now corrected. Results: \"The scdney workflow start(s) with data...\" Response: This is now corrected. Results: \"...gene sets that distinguish hippocampal development in mice from scRNA-seq data...\" (sounds like you are contrasting \"hippocampal development\" and \"scRNA-seq\") Response: We have changed the word “from” to “using” to avoid the confusion. Conclusion: \"...scdney, a collection of wrapper packages...\" (scdney is the wrapper package) Response: We have corrected this sentence. The bulleted list of methods in the scdney package should be consistently formatted (ie. should all start with a lower case \"a\" or \"an\"). Response: This is now fixed." } ] } ]	1	https://f1000research.com/articles/12-261
https://f1000research.com/articles/12-805/v1	10 Jul 23	{ "type": "Research Article", "title": "Reimaging study in the management of blunt abdominal trauma in children: a low income country single center experience", "authors": [ "Sabrine Ben Youssef", "Marwa Mesaoud", "Myriam Ben fredj", "Nouha Boukhrissa", "Mabrouk Abdelaaly", "Maha ben Mansour", "Sana Mosbahi", "Sami Sfar", "Sawsen Chakroun", "Amine Ksia", "Lassaad Sahnoun", "Mongi Mekki", "Ahmed Zrig", "Mohsen Belghith", "Marwa Mesaoud", "Myriam Ben fredj", "Nouha Boukhrissa", "Mabrouk Abdelaaly", "Maha ben Mansour", "Sana Mosbahi", "Sami Sfar", "Sawsen Chakroun", "Amine Ksia", "Lassaad Sahnoun", "Mongi Mekki", "Ahmed Zrig", "Mohsen Belghith" ], "abstract": "Introduction: The abdomen is the most prevalent site of primarily unidentified fatal injury after blunt trauma, and represents the third major affected part. However, follow-up strategies of intra-abdominal injuries remain controversial. The aim of this study is to describe the characteristics of children with blunt abdominal trauma (BAT) and who presented radiographic amendments in re-imaging studies and predict factors that could identify patients group requiring control in this population.\n\nMethods: A retrospective study was conducted in the department of pediatric surgery and the intensive care unit of Monastir involving all patients under the age of 14 years old who were admitted for blunt abdominal trauma between January 2010 and December 2021.An analysis of epidemiological, clinical, radiological and therapeutic management characteristics were performed. Results: A total of 151 patients were included in this study with a mean age of six years. The sex ratio (m/f) was 2.7. Most trauma circumstances were related to road accidents (43.7%) and falls (32.4%). The liver, the spleen, and the kidneys were the most frequently affected organs. A combination of intra-abdominal lesions was recorded in 32 cases. 84% of the cases (110/131) of the reimaged patients had no complications, compared to 16% (21/131) who developed intra-abdominal complications. The complicated reimaging findings were significantly associated with high grade hepatic and renal injuries (p=0.019 and 0.002, respectively), and patient symptom persistence or development (p=0.001). Conclusion: It is safe to avoid performing reimaging studies if clinical progression remains uneventful in children with low-grade hepatic, splenic, and renal lesions. However, the clinical assessment is the most crucial consideration during BAT management in children.", "keywords": [ "Abdominal trauma", "Blunt", "Children", "Imaging", "Follow-up" ], "content": "Introduction\n\nThe abdomen is the third major affected part in children’s trauma and intra-abdominal lesions are, in over 80% of cases, closed.1 An early recognition of a severe injury is crucial to guide the subsequent management. Contrast-enhanced computed tomography (CT) is the gold standard for stable or stabilized cases. It provides the ability to identify and assess the severity of intra and/or retroperitoneum lesions, according to the American Association for the Surgery of trauma guidelines (AAST).2 The conservative management is now standard in the solid visceral injuries (SVI) care. In fact, the distinctive physiological and anatomical features of children make this approach more available than in adults with a high successful rate (90–95%).3 After the first radiological assessment, follow-up imaging is controversial and raises several issues. According to the American Pediatric Surgical Association (APSA) guidelines, the routine follow-up imaging for asymptomatic, low-grade solid visceral injuries in children is not indicated since there is no evidence of any lesion progression or complication in the major cases and medical management is seldom adjusted on follow-up imaging results.4 However, limited data are available to support the need for follow-up imaging for high grade injuries.5\n\nTherefore, we conducted a retrospective study aiming to describe the characteristics of children with blunt abdominal trauma (BAT) and presenting complications on reimaging studies, and predict the factors that might identify patients requiring a control in this population.\n\n\nMethods\n\nThis study was a cross-sectional retrospective study. This study received retroactive approved by the Ethical Committee for Research at Faculty of Medicine of Monastir (approval number: IORG 0009738 No125/OMB 0990-0279). Patient consent for the use of data records was waived by the ethical committee due to the retrospective nature of the study.\n\nThis is a single center retrospective study carried out from January 2010 to December 2021 to examine the records of children with BAT admitted to the Pediatric Surgery Department and intensive care unit (ICU) at Fattouma Bourguiba Hospital Tunisia.\n\nWe included all patients younger than 14 years old, hospitalized for BAT associated or not to other concomitant body region injuries and who had undergone successful or unsuccessful non-operative management (NOM). The patients with penetrating traumas (four cases) or useless medical records (nine cases) were excluded.\n\nThe demographic characteristics, injury mechanism, physical examination; vital signs, abdominal and general exam, laboratory tests, imaging modality and findings were analyzed. Liver, spleen, kidney, pancreas, and adrenal glands were regarded as SVI. The bowel (duodenal, jejunoileal) and mesentery were defined as hollow viscera injuries (HVI). The urologic injuries included bladder and ureteral lesions. The scoring scale of these lesions was assessed according to the AAST grade. Grades I, II, and III liver, spleen and kidney injuries and grade I and II pancreas injuries were classified as a low-grade, while grade IV and V liver, spleen, and kidney injuries and grade III, IV, and V pancreatic injuries were classified as a high-grade. The hemoperitoneum extent was characterized by the Federle score as large, moderate, or minimal.\n\nOverall, traumatic children were treated according to the protocol as shown in Flowchart I. During hospitalization, the management ensures adherence to the patient’s needs including bed rest, regular clinical assessment of vital signs and abdominal status, hemoglobin measurements, pain management, null-per-os for at least 24 hours, imaging control, and blood transfusion: if hypotension, tachycardia (age-adjusted) or hemoglobin less than 7g/dl. Throughout the monitoring process, both clinical and imaging evolution thus follow-up were recorded.\n\nA statistical analysis was realized by comparing two groups. Group one (G1) had no complication on reimaging controls and group two (G2) included patients with complications on reimaging studies (increased hemoperitoneum, occurrence of pseudoaneurysms, pseudocysts, perirenal hemato-urinoma expansion or infection, venous thrombosis, devascularized or hypotrophic organ) needing surgical or radiological intervention or additional tests.\n\nA descriptive statistic was used to summarize patients, injuries grading, clinical and imaging characteristics. The data were summarized as counts and rates for categorical variables or mean for ordinal variables. A subset univariate analysis was done to assess complication rates in relation to the lesion grade of each SVI. Chi-Square tests and Fisher’s exact tests were used to compare results. The relationship between various variables and the complications identified in the reimaging studies was assessed using univariate analysis thus binary logistic regression. The calculations were made for the odds ratio (OR) and 95% confidence interval (CI). A p value of 0.05 or lower was regarded as significant.\n\n\nResults\n\nA total of 151 patients were admitted to our department with BAT. The mean age was six years (range one- 13 years) with a high frequency between three and eight years old. Males were 111 (73.5%) and females 40 (26.4%) with sex ratio of 7:2. Trauma circumstances are described in Table 1.\n\nThe first physical examination showed abdominal tenderness in all cases. The hemodynamic status was unstable in only 10 cases requiring resuscitative efforts. Gross hematuria was noted in 16 cases. Extra-abdominal injuries were reported in 75 cases: thoracic trauma in 32 patients, limb injuries in 18 patients, head injuries in six patients, and various injuries in 19 others.\n\nOn laboratory tests, we found hemoglobin level under 8g/dl in six cases, and elevated liver enzymes and lipase in 41 and 13 cases respectively.\n\nThe abdominal US was performed in 44 cases and showed an isolated low-level hemoperitoneum in six cases, and a solid organ injury in 38 cases. CT scan was performed in 144 cases; 99 children (78%) had a single organic lesion. The most frequently damaged organs were the liver, the spleen, and the kidneys (Table 2), with median grade II (29/59), III (25/49), and III (14/26), respectively. Other organs were involved: pancreas (13), adrenal gland (eight), hollow viscera (four), and bladder (two). Additionally, various intra-abdominal lesions combinations were seen in 32 case (22%). The most frequent association was liver and spleen injuries (n=10) then spleen and kidney injuries (n=6). At the trauma event, the abdominal imaging revealed incidentally intra-abdominal pathologies: hydatid cysts in five cases (complicated in three cases), malignant tumor in three cases confirmed later by biopsy (neuroblastoma: one, Burkitt lymphoma: one, pseudopapillary and solid tumor of the pancreas: one) and obstructive uropathy (ureteropelvic junction obstruction) in two cases.\n\n35 (23%) patients were initially admitted to the ICU due to the severity of mechanism or organ injury (25 cases) and/or initial hemodynamic instability (10 cases). The mean length of stay (LOS) in ICU was four days (range 1–22 days). The remaining patients were admitted to the surgical ward with mean LOS of six days (range 1–140 days).\n\nAfter primary resuscitation, two patients underwent initial operative intervention for pneumoperitoneum; jejunal perforation and a duodenal transection and three for complicated hydatid cysts.\n\nNOM was firstly adopted in the other cases. During monitoring, 35 patients persisted or developed symptoms (abdominal pain or tenderness, fever and/or vomiting). A decrease in hemoglobin level more than 2 g was recorded in 35 cases, nineteen of them required blood transfusion.\n\nAmong the 151 included patients, 131 (86.7%) underwent reimaging studies. The first control was performed for a median of 5 days after trauma and had a median number of controls per patient of two (range 1–13 exams). In total, 21/131 (16%) patients had complications, three of them had more than one complicated organ, as described in Table 2. Using univariate analysis, initial unstable status (p=0.000), ICU primary admission (p=0.004), associated intra-abdominal lesions (p=0.007) patient symptom persistence or development (p=0.000), and a decrease in hemoglobin level greater than 2 g/dl (p=0.01) were statistically correlated to high rate of complications. On the multivariate analysis, as showed in Table 3, complicated reimaging findings were only associated with patients’ symptoms (p=0.001, OR=10.12).\n\nFour patients failed NOM and resuscitation. The reimaging study, performed for tachycardia and hemoglobin drop, revealed enlarged hemoperitoneum in three cases, and devascularized left liver with ongoing bleeding from the left portal vein in one case, required thus operative intervention. On the 15th day after surgery, one of them experienced a pseudoaneurysm (PA) dependent on the left hepatic artery branch. This patient underwent conservative treatment with imaging control until the PA was completely removed from the circulation around the 24th day. Angiography/angioembolization (AG/AE) was necessary in a grade III injury case that developed a pseudoaneurysm. Anti-coagulant treatment was prescribed in two cases of portal branch thrombosis, one of them developed cavernoma without portal hypertension. However, complicated reimaging findings were significantly correlated to high grade hepatic injuries (29.4% (5/17) of high-grade vs 5% (2/41) of low-grade, p=0.019).\n\nNOM was effective in all cases, with 100% of low and high-grade reimaged splenic lesions showing no complications on control, thus, no statistics were computed.\n\nThere were two patients with severe reno-vascular lesions due to the dissection of the right renal artery, and the left renal artery and venous thrombosis resulting in a non-enhancement of the right kidney. NOM was decided in both patients given the associated severe liver and spleen injuries. Both patients developed atrophic kidneys, without hypertension during the three years of follow-up. Therefore, the complicated reimaging findings were also significantly correlated to high grade renal injuries 55.5% of high-grade vs no complication in low-grade, p=0.002.\n\nTwo cases of extra-peritoneal bladder rupture were successfully treated by urinary drainage via a urethral catheter. The CT-scan with delayed phase imaging carried out one month later revealed no extra-bladder leakage.\n\nThe patient who initially had a grade IV pancreatic lesion associated with duodenal transection died two days later from severe post-traumatic pancreatitis and multiple organ failure. During the follow-up, 10 children developed pseudocysts. One child with grade IV lesion developed corporeal caudal pancreatic atrophy within one year, but no other long-term complications were observed. There were no significant differences detected among the patients with low and high-grade pancreatic lesions in terms of complication rates 87.5% of high-grade vs 80% of low-grade, p=0.6.\n\nThe patient with intramural hematoma complained of abdominal pain with distended and diffuse abdominal tenderness associated with septicemia four days after admission. The second CT revealed pneumoperitoneum. At exploration, there was a fecal peritonitis owing to two perforations. Reimaging studies conducted eight days following admission revealed the resorption of the mesenteric root hematoma.\n\nSeven patients (7/20) with an isolated hemoperitoneum required a re-imaging for persistent abdominal pain in three cases, for concomitant vomiting in two cases and for tachycardia associated with decreased hemoglobin (2 g/dl) in two cases. No radiological amendments were observed in all cases, and they were discharged after 48 hours.\n\n\nDiscussion\n\nOur study explored the management and imaging follow-up of intra-abdominal injuries in children after BAT in low-resource setting. We are the only center in central Tunisia, managing BAT in children under 14 years. Conventionally, pediatric BAT requires close monitoring, based on physical examination and biological analysis, to assist prioritize the most appropriate treatments, as well as radiological control whenever necessary. In our center, we perform the radiological follow-ups especially in children living far from our center to ensure lesions have healed and no complications have occurred. In order to reduce imaging controls number and healthcare cost while ensuring patients’ safety, we analyzed the intra-abdominal complications rate after BAT based on injured organs and global clinical assessment.\n\nThe liver injury is one of the most common life-threatening injuries in children trauma,6 and the most severely affected organ in our series. The successful rate of NOM is being expanded by endovascular procedures (AG/AE) in case of an active bleeding (contrast blush).3,4 However, in stable status, the presence of a contrast blush on the initial CT scan is not an absolute indication for the AG/AE and serial clinical evaluations through physical exams and laboratory testing must be performed to detect a change in clinical status during NOM.4 While routine follow-up imaging in children is clearly not indicated and the category of patients who might benefit has not been obviously defined, a small number of patients with grade IV or V liver injury have shown significant complications.5,7\n\nWe performed a follow-up imaging in 98.3% (58/59) of hepatic injury cases, for a clinical indication in 27 cases and routine control in 31 cases. It showed a stabilization or healing signs in 88% of cases and complications in 12%.\n\nWe observed that the high rate of complications was statistically correlated with the high-grade hepatic lesion. The rate of post-trauma liver-related complications is greater in our results than that reported in the literature which generally varies from 0% to 7.4%.8,9\n\nIn fact, some authors identify the presence of an active contrast extravasation as an independent predictor for a pseudo aneurysm formation in children, regardless of the injury grade. They suggest a follow-up during NOM of these patients, so as to obtain an early identification and angiographic treatment of pseudoaneurysm.10 In our study, one patient required AE and one resolved spontaneously.\n\nIn addition to the high-grade injury, centrally located liver injuries are significant risk factors for major bile duct injury and complications.11,12\n\nGiven our findings, we suggest that the imaging controls be performed in all symptomatic patients with or without modified laboratory tests, regardless of the severity of the lesion, and systematically in patients with high-grade and central liver lesions on pre-discharge and 2 to 3 weeks post-discharge, and then it will depend on control findings.\n\nThe splenic injury was the second most injured organ in our series, while it is the most frequent in the pediatric trauma according to the literature.13 NOM is based on a close clinical monitoring with the assessments of the hemoglobin and the hematocrit levels every 12–24 h if no complication occurs.13\n\nIn our series, 34.6% of cases had associated lesions and 14% had high-grade injuries; all patients were successfully treated with NOM and no complications were documented in the reimaged patients. Most studies showed a low rate of complications in pediatric patients with post-traumatic splenic injuries, particularly low-grade ones.5 Therefore, follow-up imaging cannot be considered mandatory for low-grade and uncomplicated injuries or asymptomatic patients, but it may be considered in high-grade injuries for the risk of developing life-threatening complications.13 In fact, the risks of delayed splenic rupture and posttraumatic pseudocysts seem to be increased within the first one to three weeks13,14 with an incidence of 0.2 and 5–13%, respectively.15,16 The 2022 WSES consensus preconizes, imaging follow-up with contrast-enhanced ultrasonography (CEUS) before return to major physical activity in children with AAST grades III–V splenic injuries treated observantly although the repeated imaging in children is rarely needed in the acute phase during NOM.14 The patients with low- and high-grade injuries didn’t develop any complications. Thus, we propose reimaging before discharge and return to scholar activity.\n\nThe kidney is affected in 10% of all BAT.17 The isolated urinary extravasation, in itself, is not an absolute contra-indication to NOM, and the presence of non-viable tissue (devascularized kidney) is not an indication to operative management in the acute setting in the absence of other indications for laparotomy.18 In our study, the renal trauma involved 17% of patients. Most cases presented low-grade injuries (17/26), and were observantly managed. In fact, the complication rate after blunt renal injury has been estimated at 3-30%.19 No issues were documented in low-grade cases. A high-grade lesion, observed in 35% of cases, was strongly associated with the high complication rate reported on follow-up imaging in our series. Indeed, low-grade kidney injuries have a very low rate of late complication in pediatric patients; therefore, scheduled imaging follow-up is not indicated.18 Follow-up imaging in pediatric patients should be limited to moderate (AAST III) and severe (AAST IV-V) injuries. In pediatric patients, US and CEUS should be the first choice in the early and delayed follow-up phases, if cross-sectional imaging is required, magnetic resonance should be preferred.18 Some authors preconize periodical monitoring of the injury to rule out complications. They recommended time points range from four-24 hours to 48 to 72 hours following the initial scan.20,21 However, the usefulness of this measure in asymptomatic children has not been satisfactorily proven.22 Some also propose imaging follow-up 3 months following trauma, though there is no unanimous consensus on this.23 Moreover, periodically examine patients with high-grade injuries should be performed in order to rule out the development of hypertension.22\n\nOur results concur with the literature data, therefore we propose US/CEUS follow-up imaging for renal high-grade and urologic tract injuries on the third day if the patient is still asymptomatic and at two, six, and 12 weeks after the injury.\n\nPediatric pancreatic injury is rare, with an incidence of 0.6 to 9.5% of all abdominal injuries,24,25 which is similar to our results and represents 8.6%.\n\nCT-scan is usually the first-line imaging tool in the assessment of late complications of pancreatic trauma and very useful in driving management.26 However, US or CEUS is used as an alternative to CT for follow up of fluid collections, pseudocysts, and pancreatic disruptions after pancreatic trauma mainly in children or in low-resource settings.26 Furthermore, regular followed up at two, four, eight and 12 weeks to monitor serum amylase, lipase and blood glucose, as well as to perform the abdominal US was also mentioned.27 In fact, in low resource settings, amylase and lipase, in combination with US, can be considered cost-effective tool of patient risk stratification.28 Otherwise, WSES recommend that the necessity for follow-up imaging should be driven by clinical symptoms (i.e., onset of abdominal distention, tenderness, fever, vomiting, jaundice). Endoscopic retrograde cholangiopancreatography (ERCP) is also useful for obtaining an exact diagnosis and determining the status of the main pancreatic duct and location of the pancreatic injury and plan management strategies.29\n\nPatients with hollow viscera and mesenteric injuries account for 2–6% of BAT, and more often cause clinical uncertainty,30,31 because even the hemoperitoneum can lead to an abdominal tenderness. Usually, the pneumoperitoneum detected on CT scan requires an operative management. However, due to the diagnostic complexity and the lack of agreed consensus on clinical management of patients with hollow viscera injury, surgical intervention is often delayed.32\n\nOur work has some limitations as it is a retrospective study involving information bias. Additionally, the contemporary, and the worldwide recommendations were not followed while treating our patients. Therefore, it is anticipated that prospective studies with updated and adopted guidelines, including management and imaging follow-up, will really be carried out and assessed.\n\n\nConclusion\n\nFor the pediatric surgeons, the management of blunt abdominal injuries in children remains controversial and challenging. There are various recommendations for monitoring and radiological follow-up strategies, that are firstly dependent on the organ involved, and the severity of the injury (lesion grade). Actually, it is safe to avoid performing reimaging studies if the clinical progression remains uneventful in children with low-grade hepatic, splenic, and renal lesions. Absolutely, the clinical assessment is the most crucial consideration during BAT management in children.", "appendix": "Data availability\n\nFigshare: Data for the article reimaging study for blunt abdominal trauma in children. https://doi.org/10.6084/m9.figshare.23518944.v1. 33\n\nThe project contains the following underlying data:\n\n• spss trauma abd_1 (1) english (2).sav.sav. (Anonymised patient data used in this study).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nRothrock SG, Green SM, Morgan R: Abdominal trauma in infants and children: prompt identification and early management of serious and life-threatening injuries. Part I: injury patterns and initial assessment. Pediatr. Emerg. Care. 2000; 16(2): 106–115. Publisher Full Text\n\nAmerican Association for the Surgery of Trauma: Injury Scoring Scale: a resource for trauma care professionals. 2022.\n\nMedina AE, Uribe CHM, Marín VMV, et al.: Associated factors to non-operative management failure of hepatic and splenic lesions secondary to blunt abdominal trauma in children. Rev. Chil. Pediatr. 2017; 88(4): 470–477.\n\nSivit CJ: Abdominal trauma imaging: imaging choices and appropriateness. Pediatr. Radiol. 2009; 39: 158–160. Publisher Full Text\n\nGates RL, Price M, Cameron DB, et al.: Non-operative management of solid organ injuries in children: An American Pediatric Surgical Association Outcomes and Evidence Based Practice Committee systematic review. J. Pediatr. Surg. 2019; 54(8): 1519–1526. PubMed Abstract \| Publisher Full Text\n\nCoccolini F, Coimbra R, Ordonez C, et al.: Liver trauma: WSES 2020 guidelines. World J. Emerg. Surg. 2020; 15: 1–15.\n\nDuron V, Stylianos S: Strategies in liver Trauma. Elsevier; 2020; 150949.\n\nMalhotra AK, Fabian TC, Croce MA, et al.: Blunt hepatic injury: a paradigm shift from operative to nonoperative management in the 1990s. Ann. Surg. 2000; 231(6): 804–813. Publisher Full Text\n\nTiwari C, Shah H, Waghmare M, et al.: Management of traumatic liver and bile duct laceration. Euroasian J. Hepato-Gastroenterol. 2017; 7(2): 188–190. Publisher Full Text\n\nKatsura M, Fukuma S, Kuriyama A, et al.: Association between contrast extravasation on computed tomography scans and pseudoaneurysm formation in pediatric blunt splenic and hepatic injury: a multi-institutional observational study. J. Pediatr. Surg. 2020; 55(4): 681–687. PubMed Abstract \| Publisher Full Text\n\nYuan KC, Wong YC, Fu CY, et al.: Screening and management of major bile leak after blunt liver trauma: a retrospective single center study. Scand. J. Trauma Resusc. Emerg. Med. 2014; 22: 1–9.\n\nWahl WL, Brandt MM, Hemmila MR, et al.: Diagnosis and management of bile leaks after blunt liver injury. Surgery. 2005; 138(4): 742–748. PubMed Abstract \| Publisher Full Text\n\nPodda M, De Simone B, Ceresoli M, et al.: Follow-up strategies for patients with splenic trauma managed non-operatively: the 2022 World Society of Emergency Surgery consensus document. World J. Emerg. Surg. 2022; 17(1): 1–37.\n\nCoccolini F, Montori G, Catena F, et al.: Splenic trauma: WSES classification and guidelines for adult and pediatric patients. World J. Emerg. Surg. 2017; 12: 1–26.\n\nNotrica DM, Sayrs LW, Bhatia A, et al.: The incidence of delayed splenic bleeding in pediatric blunt trauma. J. Pediatr. Surg. 2018; 53(2): 339–343. PubMed Abstract \| Publisher Full Text\n\nYardeni D, Polley TZ Jr, Coran AG: Splenic artery embolization for post-traumatic splenic artery pseudoaneurysm in children. J. Trauma Acute Care Surg. 2004; 57(2): 404–407. Publisher Full Text\n\nPoyraz N, Batur A, Balasar M: Rupture of Renal Pelvis in Occult Hydronephrosis after a Simple Football Injury: A Case Report. J. Emerg. Med. Case Rep. 2014; 5(1): 21–23. Publisher Full Text\n\nCoccolini F, Moore EE, Kluger Y, et al.: Kidney and uro-trauma: WSES-AAST guidelines. World J. Emerg. Surg. 2019; 14(1): 1–25.\n\nda Costa IA , Amend B, Stenzl A, et al.: Contemporary management of acute kidney trauma. J. Acute Dis. 2016; 5(1): 29–36. Publisher Full Text\n\nFernández-Ibieta M: Renal trauma in pediatrics: a current review. Urology. 2018; 113: 171–178. PubMed Abstract \| Publisher Full Text\n\nGaither TW, Awad MA, Leva NV, et al.: Missed opportunities to decrease radiation exposure in children with renal trauma. J. Urol. 2018; 199(2): 552–557. PubMed Abstract \| Publisher Full Text\n\nSinger G, Arneitz C, Tschauner S, et al.: Trauma in pediatric urology. vol. 30. . Elsevier; 2021; p. 151085. Publisher Full Text\n\nCanon S, Recicar J, Head B, et al.: The utility of initial and follow-up ultrasound reevaluation for blunt renal trauma in children and adolescents. J. Pediatr. Urol. 2014; 10(5): 815–818. PubMed Abstract \| Publisher Full Text\n\nEnglum BR, Gulack BC, Rice HE, et al.: Management of blunt pancreatic trauma in children: review of the National Trauma Data Bank. J. Pediatr. Surg. 2016; 51(9): 1526–1531. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMattix KD, Tataria M, Holmes J, et al.: Pediatric pancreatic trauma: predictors of nonoperative management failure and associated outcomes. J. Pediatr. Surg. 2007; 42(2): 340–344. Publisher Full Text\n\nCoccolini F, Kobayashi L, Kluger Y, et al.: Duodeno-pancreatic and extrahepatic biliary tree trauma: WSES-AAST guidelines. World J. Emerg. Surg. 2019; 14(1): 1–23.\n\nZhang D, Yan J, Siyin ST, et al.: Nonresection management of the pancreas for grade III and IV blunt pancreatic injuries in children: a single center’s experience. BMC Pediatr. 2021; 21(1): 1–9. Publisher Full Text\n\nMahajan A, Kadavigere R, Sripathi S, et al.: Utility of serum pancreatic enzyme levels in diagnosing blunt trauma to the pancreas: a prospective study with systematic review. Injury. 2014; 45(9): 1384–1393. Publisher Full Text\n\nMaeda K, Ono S, Baba K, et al.: Management of blunt pancreatic trauma in children. Pediatr. Surg. Int. 2013; 29: 1019–1022. Publisher Full Text\n\nD’Andrea KJ, Kunac A, Kinler RL, et al.: Diagnosing blunt hollow viscus injury: is computed tomography the answer? Am. J. Surg. 2013; 205(4): 414–418.\n\nWatts DD, Fakhry SM; EAST Multi-Institutional HVI Research Group: Incidence of hollow viscus injury in blunt trauma: an analysis from 275,557 trauma admissions from the East multi-institutional trial. J. Trauma Acute Care Surg. 2003; 54(2): 289–294. PubMed Abstract \| Publisher Full Text\n\nHarmston C, Ward JBM, Patel A: Clinical outcomes and effect of delayed intervention in patients with hollow viscus injury due to blunt abdominal trauma: a systematic review. Eur. J. Trauma Emerg. Surg. 2018; 44: 369–376. PubMed Abstract \| Publisher Full Text\n\nBen Youssef S: Data for the article reimaging study for blunt abdominal trauma in children. Dataset. figshare. 2023. Publisher Full Text" }	[ { "id": "190025", "date": "03 Aug 2023", "name": "Paolo Aseni", "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 authors of the article deserve my congratulation for reporting this interesting experience in treating blunt abdominal trauma in children in low-income countries.\nHere are some suggestions to improve the paper:\nClarify your Research Objective: While the abstract mentions the aim of the study, it might be helpful to provide a more specific research objective as a hypothesis to investigate in the introduction. This can help readers understand the study's main purpose.\n\nMethods Section: The methods section lacks some crucial details. Provide more information on the selection criteria for study participants. Explain the rationale for choosing the specific age group (under 14 years old patients are in the paediatric domain?) and the reasons for the study's time frame (January 2010 to December 2021). Additionally, specify how patients were followed up after discharge. In addition, specify whether there was a standardized protocol for reimaging or if it was left to the discretion of the treating physicians after clinical evaluation.\n\nI note that eFAST was not cited in your protocol study. Ultrasound has revolutionized the care of traumatic injuries. Numerous studies, albeit mostly observational, have demonstrated that the eFAST protocol is a clinically significant adjunct in the evaluation and treatment of trauma patients. The EAST (Eastern Association for the Surgery of Trauma) guidelines, Western Trauma Association, and ATLS recommend the eFAST as the standard of care in trauma resuscitation protocols.\n\nData Analysis: Provide more details on the statistical methods used for data analysis. Describe if you have some missing data and how these were handled and whether any adjustments were made for potential confounding variables.\n\nComparison with Guidelines: While the study provides some conclusions about reimaging strategies, it would be helpful to compare your findings with existing guidelines or recommendations from established medical literature on the subject. This can help clinicians understand how your findings align with current best practices.\n\nLimitations and Future Directions: Discuss the study's limitations. In addition to the retrospective design, discuss potential sources of bias and confounding factors. Suggest possible directions for future research to address these limitations, including prospective studies with updated guidelines.\n\nDiscussion of Clinical Implications: In the discussion section try to emphasize the clinical implications of this study's findings. How can your results influence the management of blunt abdominal trauma in low-income countries? Discuss potential changes in clinical practice based on the study's conclusions.\n\nData Availability: Consider providing information on the availability of the dataset used in the study for other researchers to promote transparency and reproducibility.\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?\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": [ { "c_id": "10381", "date": "15 Dec 2023", "name": "Sabrine Ben Youssef", "role": "Author Response", "response": "Firtst of all, I want to thank you for your interest for our study. I will respond to your comments one by one. 1- We agree with this point. We will change it in the new version 2- Methods Section: In our department, we hospitalize only children under the age of 14 years old. We wanted to assess our protocol during 10 years of exercise and after an epidemiologist consultation who approved our choice. Patients were followed up after discharge at the consultation at 1, 3, 6 and 12 months after the accident. In our practice, reimaging was left to the discretion of the treating physicians after clinical evaluation. 3- We totally agree with the interest of e-fast, however it is not available in our Department. 4-Patients with an unexploitable data were excluded from our study 5-Due to our local conditions (low income country) we avoided to compare to other countries 6- Limitations and Future Directions: We agree with you and we are working on a prospective study. 7- Discussion of Clinical Implications: The implication of our results is to decrease the number of an unnecessary reimaging study especially in low vicera injury and reduce hospitalisation cost. Clinical and biological finding are the most important indicator to radiological reassessment of viscera injury. 8- Data Availability: We have already published our data with DOI : 10.6084/m9.figshare.23250848. On the behalf of all authors, please accept our best regards" } ] } ]	1	https://f1000research.com/articles/12-805
https://f1000research.com/articles/12-1471/v1	15 Nov 23	{ "type": "Software Tool Article", "title": "Towards inventory control excellence: An innovative approach based on a web-based platform", "authors": [ "Miguel Ramos-Miller", "Alex Pacheco", "Miguel Ramos-Miller" ], "abstract": "Background Inventory management in educational institutions presents unique challenges due to the diverse sources of information and the need for improved team collaboration. This research aims to enhance inventory processes in educational institutions by leveraging information technology to optimize efficiency and ensure data integrity and reliability.\n\nMethods The study employed a five-phase methodology to develop a web-based inventory optimization system. The initial phase involved a comprehensive analysis of inventory requirements, considering multiple data sources and team needs. Subsequently, in the planning phase, requirements were prioritized, and tasks with corresponding deadlines were established. The implementation phase adhered to the requirements outlined in the planning phase, utilizing appropriate information technologies to ensure efficient and reliable operation. A thorough system review was conducted to assess the achievement of each requirement’s objectives, with necessary adjustments made as needed. Finally, following the completion of the previous phases, the developed software was deployed, and additional testing was conducted to ensure proper functionality.\n\nResults Following the implementation of the web-based system, significant improvements were observed: an 85.51% increase in efficiency for goods searches, streamlining the process and reducing location times; a 90.31% enhancement in goods registration, ensuring greater accuracy and data reliability; an 83.11% improvement in annual goods report generation, simplifying reporting and offering a clearer view of the inventory. Overall, the inventory process experienced an 86.31% improvement, leading to enhanced efficiency and collaboration among administrative and teaching staff. The utilization of information technology reduced inventory processing times and ensured the uniqueness and reliability of information.\n\nConclusions This research focuses specifically on optimizing inventory management in educational institutions through information technology. The study’s uniqueness lies in its tailored web-based system designed to address the specific needs of educational institutions. The results demonstrate the effectiveness of this approach and its positive impact on inventory management.", "keywords": [ "Inventory", "system", "web system", "inventory control" ], "content": "Introduction\n\nOver the past decade, there has been a significant surge in the popularity of web-based systems worldwide, primarily attributed to their intricate nature and ability to facilitate simultaneous user support (Mora, 2011). A notable example is the study by Qin et al. (2021), which implemented a system for reagent chemicals to facilitate searches and instantly know their location, allowing scientists to focus on developing new drugs. Research by Chila and Susi (2019) in the United States also highlighted the importance of information technology (IT) systems in inventory management, finding that supply management was time consuming in interventional radiology patient care. Using Lean principles, which refer to a set of practices and concepts designed to optimize efficiency and eliminate waste in business processes (Kumar et al., 2022), evaluated and improved an outdated process and implemented an inventory control system that resulted in significant time and cost savings.\n\nOne of the most prominent types of systems are web systems or applications. According to Molina-Ríos and Pedreira-Souto (2020), these systems are similar to traditional software and require development processes that include requirements gathering and programming in different languages, which can lead to heterogeneity during their development. In addition, the widespread adoption of web systems, driven by their rapid growth and numerous advantages, has significantly impacted e-commerce (Castilla et al., 2020). These systems facilitate direct interaction between end-users and the content of web pages. In addition, research in the UK has developed a machine learning-based computer system that can perform quality control by identifying defective parts and stopping the production process (Papananias et al., 2020).\n\nIn the South American country of Peru, many public and private organizations have implemented software to automate their processes (Centrum-PUCP, 2023). This gives them a competitive advantage by allowing them to save resources in terms of money, time and personnel (Wilson & Mergel, 2022). In this regard, Figure 1 shows the sectors of companies that have invested the most in technology, highlighting the following “electricity (42.3%), private education (39.0%), information and communication (37.4%), professional, scientific and technical activities (32.0%), manufacturing (31.4%) and hydrocarbons (30.8%), among the most important” (Instituto Nacional de Estadística e Informática, 2019).\n\nNote: Percentage of investment in science and technology by company according to economic activity. Source: (Instituto Nacional de Estadística e Informática, 2019) – Reproduced with permission under the terms of the Instituto Nacional de Estadística e Informática's open licensing policy.\n\nIn the public education sector, entities are responsible for accounting, controlling and reporting their goods in a responsible manner. These educational institutions are subordinated to the Local Education Management Unit (UGEL), as an example of decentralisation of local government, and depend on the Regional Directorate of Education (DRE) for administrative, normative and technical support (D. S. No 019-2019-VIVIENDA, 2019). Management follows the rules of the National Superintendence of State Goods (SBN), which standardises codes and processes for each public good. Failure or delay in sending this information may result in a call for attention, a memorandum or the withholding of economic resources.\n\nIn Ancash, Peru, a web-based inventory management system was implemented in UGEL Aija, resulting in a 43.15% improvement in the supply rate and a 36.3% increase in the inventory turnover rate (Sena, 2021). On the other hand, in Piura with Chiroque (2018), an inventory system was developed and the average times for registering goods, generating reports, searching for an good and ordering an good were improved. Similarly, Ramos (2016) implemented a system in the Telematics Office of the Police Front of Puno, Peru, using the agile methodology Extreme Programming (XP), which, thanks to its flexibility, allowed iterative acceleration and achieved functionalities such as improving the inventory work by 60% of the total.\n\nCurrently, according to information provided by officials at public educational institutions in San Vicente de Cañete, Lima, Peru, such as the José Buenaventura Sepúlveda Public Educational Institution, good information is recorded on physical documents and then transcribed into Excel spreadsheets. This has reportedly resulted in disorganized and duplicated records throughout the year, as well as the generation of reports with incorrect or outdated data. Therefore, the aim of this research is to implement web-based software that will improve the inventory control process and provide the institution with a technological advance to meet new educational challenges. In addition, it aims to provide accurate information about the goods, which will allow efficient management of the institution’s resources and indirectly promote quality education for both students and society.\n\nWhile it is true that there are several applications with similar purposes in other sectors (Pereira et al., 2022), it is important to note that the application described in this article has been developed specifically for the education sector, taking into account the particular needs and requirements of an institution that lacks both technological tools and knowledge in the implementation of technology in educational processes. In addition, the application complies with the laws and regulations of the education sector regarding information management. (Chiroque, 2018). It is important to highlight that this tool is innovative in the educational context and represents an important solution to improve the inventory control process of educational institutions. In particular, the application demonstrates how technology can be used to improve public services and promote digital transformation (Castilla et al., 2023). This may be relevant for other institutions that wish to implement digital solutions to improve information management (Ramos, 2016). It therefore represents an innovation in the local context and contributes to the advancement of the implementation of digital solutions in the education sector.\n\n\nMethods\n\nIn this section, we provide a detailed account of the methods employed in the development and operation of our software tool tailored for educational institution inventory control.\n\nDevelopment Technologies: Our software tool was meticulously crafted using a combination of cutting-edge technologies. The backend is powered by Laravel 9, an open-source PHP framework known for its robust feature, leveraging the robust features of PHP 8.1, while the frontend is built on Vue3, an open-source Javascript framrwork that ensuresing a dynamic and responsive user interface.\n\nStrategic Plug-in Integration: To augment the functionality of our software tool, we judiciously integrated several essential plug-ins and libraries, including:\n\n• “laravel-dompdf” for PDF report generation.\n\n• “laravel/sanctum” to fortify application programming interface (API) authentication.\n\n• “maatwebsite/excel” for advanced Excel export capabilities.\n\nCustomization for educational institutions: The core framework of our software was customized to align with the unique requirements of educational institutions. This involved tailoring good categorization, user roles, and reporting functionalities to cater specifically to the needs of educational inventory management.\n\nMinimal system requirements: Our web-based inventory control system operates smoothly with minimal system prerequisites. These include:\n\n• Server:\n\n○ A server environment compatible with Laravel 9.\n\n○ PHP 8.1 support.\n\n○ Adequate storage capacity for housing inventory data.\n\n• Client:\n\n○ A modern web browser with JavaScript enabled.\n\n○ Internet connectivity for web-based access.\n\nBy adhering to these minimal system requirements, we ensure that our software tool remains accessible and functional, even in resource-constrained educational settings.\n\nThis software tool boasts distinctive features that set it apart from existing solutions:\n\n• Educational institution-centric: our software is purpose-built for educational institutions, accommodating their specific workflows and requirements for efficient inventory management.\n\n• Tailored customization: users can seamlessly customize workflows, good categorization, and reporting features to suit their institution’s needs, making it a versatile solution.\n\n• Enhanced functionality: intergration of essential plug-ins and libraries enhances the software’s capabilities, ensuring comprehensive inventory management.\n\nBy outlining these methods and unique features, we provide a clear blueprint for the development and implementation of our software tool within educational institutions, enhancing its replicability and utility.\n\n\nUse cases\n\nPreface: Data Initialization\n\nThe system data is loaded automatically following the installation steps detailed in the “Readme.md” file found in the repository (Ramos-Miller (b), 2023).\n\nTo demonstrate the software’s functionality, we present a specific use case involving the search for goods within the educational institution’s inventory. In this scenario, a user initiates a goods search by specifying criteria such as the item’s name, category, location, or status. Upon submission, the software retrieves and displays a list of matching goods based on the provided criteria. This practical example illustrates the software’s effectiveness in helping staff quickly locate specific goods within the institution’s inventory, as show in Figure 2.\n\nInput: Search input query: “Computadora”\n\nOutput: List of coincidences:\n\n• MODULO DE MELAMINA PARA COMPUTADORA\n\n○ Description, Status, Inventory Area, etc …\n\n• COMPUTADORA DE MANO - WORKPAD\n\n○ Description, Status, Inventory Area, etc …\n\n• MODULO DE METAL PARA MICROCOMPUTADORA\n\n○ Description, Status, Inventory Area, etc …\n\nIn this scenario, we demonstrate how the software facilitates the generation of statistical reports related to goods. Users can select the type of report they require, such as inventory levels, asset depreciation, or goods distribution by category. The software processes the data and generates comprehensive statistical reports, which can aid in decision-making processes and provide insights into the institution’s goods management, as show in the Figure 3.\n\n\n\nInput:\n\n• Access the “Dashboard” view\n\nOutput:\n\n• Statistical Report “Goods by acquisition date”\n\nIn this scenario, we demonstrate the software’s capability to generate reports that strictly adhere to the guidelines established by the SBN. Users can access the Report menu, where they have the option to generate reports based on specific areas or encompassing all areas. The software will compile and format the necessary data to produce reports that precisely meet SBN standards. This functionality ensures that the institution can efficiently fulfill its reporting obligations to regulatory authorities, as shown in Figure 4.\n\nInput:\n\n• Access the “Reports” view\n\n• Select the “Inventory Area”\n\n• Click in “Generate Report” button\n\nOutput:\n\n• SBN Good Report (PDF)\n\n• Report Date: Current date\n\nThese use cases demonstrate how the software enhances goods management and reporting processes within an educational institution, offering valuable tools for inventory control and compliance with regulatory requirements.\n\n\nDiscussion\n\nThe implementation of the web-based system resulted in a substantial enhancement of the inventory control process, significantly optimizing goods and inventory management. As a result of our software implementation, staff had the opportunity to redirect their efforts toward other administrative or teaching tasks that could enhance the educational institution’s overall performance. This is in line with (Chancasanampa-Mandujano et al., 2019), where a warehouse management system was used to reduce the stock of raw materials, thus obtaining a more accurate inventory of inputs. In the same way (Ramos, 2016), reported improved telematics office operations with the implementation of the ISO 9126 standard, resulting in centralized and comprehensive information management. On the other hand, (Chila & Susi, 2019), highlighted that the management of supply inventory in radiology is one of the main causes of wasted time, with a potential negative impact on patient care in interventional radiology. Therefore, using Lean principles, we evaluated an outdated process and implemented an inventory control system with good results, saving time and money. In turn, these results agree with (Tejesh & Neeraja, 2018), where a warehouse inventory control system was developed based on IOT (Internet of Things) architecture, which was designed to track products using their corresponding tags and timestamps for further analysis and accurate verification. The developed warehouse inventory management system was efficient, as it was able to perform real-time search operations from the database and update information with the help of web servers.\n\nThe enhancement in goods search and localization further streamlined the identification and localization of educational institution goods. This is in agreement with (López & Pérez, 2016) who obtained an improvement in the search of technical files thanks to the implementation of the computer system, as well as an improvement in the process of patient care. Similarly (Chiroque, 2018), witnessed changes that greatly benefited institution staff, with goods search, filtering, and reporting processes improving. This work introduced an automated solution to goods management issues, ultimately leading to enhanced inventory management in the institution (Nemeshaev & Fatkullina, 2021), who studied the processes of collecting, recording and analysing data on their inventory system, found that the pilot implementation of the inventory system improved equipment monitoring, reduced labour costs and the number of errors in the preparation of inventory lists. Similarly, the findings of Ho et al. (2021) who developed a blockchain-based system operating under a decentralised accounting mechanism, improved the quality of traceability data and the exchange of reliable information within the spare parts supply chain.\n\nThe accuracy and completeness of information regarding educational institution goods significantly improved. The data now remains error-free, unaffected by process distortions, and exhibits consistency between physical and virtual records. Additionally, the software has introduced secure data access mechanisms, granting or restricting personnel access based on their designated roles as administrators or managers. This is in line with (Fajardo & Lorenzo, 2017), who managed to highlight the result of obtaining truthful information to maintain the optimal inventory, thus achieving optimal and accurate customer service, all as a result of the implementation of the web system. Similarly (Bonett et al., 2019), reported a reduction in inventory loss due to stock-outs and increased inventory service levels. Their primary objective was to address stock-out issues in SMEs, which previously lacked such effective tools. Similarly Praveen et al. (2019), show that the development of a model using artificial neural networks to accurately predict demand contributed to sudden customer demand and minimised the mismatch between supply, demand and associated costs, resulting in increased profit margins. In turn, this is in line with (De Giovanni, 2021), where the implementation of an intelligent application allows the supply chain to increase sales and improve the production rate, as more consistent and reliable information was obtained from the managed inventory.\n\nEffective reporting saw significant improvement, facilitating better communication between the educational institution and UGEL 08 Cañete, thereby aiding the objectives of both entities. Moreover, it furnishes UGEL 08 Cañete with precise and high-quality information to make informed organizational decisions with the educational institution’s resources. This is in line with (Rosas & Valecilla, 2019), who pointed out that after the phase following the implementation of a web system in inventory management, operations were optimised in terms of response times for receiving reports and monitoring administrative processes. Similarly (Guevara, 2019), claimed that, after the development of an inventory management system, it was possible to control materials in a more orderly manner, providing timely and reliable reports for correct and appropriate decisions. The results showed a high degree of agreement with the research of (Dennert et al., 2021), where it was demonstrated that the use of a universal inventory system allows the rapid generation of physical inventory reports, which in turn preserves the quality of the sample by reducing redundancy and location time. Inventory information was presented in a more user-friendly manner, allowing it to be easily analysed for statistically significant trends, samples had reliable traceability and data was checked for accuracy.\n\n\nConclusions\n\nThe web system has significantly improved the inventory control process at the José Buenaventura Fernández Public Educational Institution. After its implementation, the software demonstrated notable enhancements in the three dimensions proposed (search for goods, inventory coverage, and inventory reports). These improvements have greatly benefited the school by optimizing the inventory control process.\n\nFinally, it is recommended that this research be applied in other schools, both public and private, in order to improve and have access to accurate and rapid information on the movable and immovable goods of the institution, since the SBN regulations are applied. At the same time, it is recommended to extend the methods with QR code or barcode, in order to optimise the time of the inventory, and at the same time, this functionality should communicate with the web system of the inventory control process and, for a future stage, consider a connection with the National Goods System of the Ministry of Education.", "appendix": "Data availability\n\nThe data supporting this research can be found in the “app/database/seedes/data” folder of this repository under the filename “goods-data.csv.” Additionally, a snapshot of the data is archived and available on Zenodo under the following DOI: https://doi.org/10.5281/zenodo.10041267 (Ramos-Miller (b), 2023).\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 Universidad Nacional de Cañete, great professors, valuable students and collaborators for carrying out this scientific article throughout these years of study.\n\n\nReferences\n\nBonett J, Silva L, Viacava G, et al.: Integrated inventory system for forecasts based on knowledge management for the reduction of stock breaks in a distribution SME. Proceedings of the LACCEI International Multi-Conference for Engineering, Education and Technology, 2019-July. 2019. 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\nCastilla R, Pacheco A, Robles I, et al.: Digital channel for interaction with citizens in public sector entities. World Journal of Engineering. 2020; 18(4): 547–552. Publisher Full Text\n\nCentrum-PUCP: Empresas que aprovechan la tecnología e innovan poniendo al cliente en el centro lideran ranking de experiencia del cliente en el Perú - Centrum.2023. Reference Source\n\nChancasanampa-Mandujano J, Espinoza-Poblete K, Sotelo-Raffo J, et al.: Inventory management model based on a stock control system and a kraljic matrix to reduce raw materials inventory. ACM International Conference Proceeding Series. 2019; 33–38. Publisher Full Text\n\nChila M, Susi LC: Implementing a Web-Based Inventory Tracking System: A Quality Improvement Initiative. Journal of Radiology Nursing. 2019; 38(4): 277–280. Publisher Full Text\n\nChiroque O: Implementar un sistema de inventario para el proceso de control de bienes en la institución educativa Horacio Zevallos Gámez Laynas La Matanza [Tesis de Pregrado, Universidad Nacional de Piura].2018. Reference Source\n\nD. S. No 019-2019-VIVIENDA: Decreto Supremo que aprueba el Texto Único Ordenado de la Ley No 29151, Ley General del Sistema Nacional de Bienes Estatales. El Peruano. 2019; 39. Reference Source\n\nDe Giovanni P: Smart Supply Chains with vendor managed inventory, coordination, and environmental performance. European Journal of Operational Research. 2021; 292(2): 515–531. Publisher Full Text\n\nDennert K, Friedrich L, Kumar R: Creating an Affordable, User-Friendly Electronic Inventory System for Lab Samples. SLAS Technology. 2021; 26(3): 300–310. PubMed Abstract \| Publisher Full Text\n\nFajardo J, Lorenzo K: Implementación de un sistema web para el control de inventario en la ferretería Christopher [Tesis de Pregrado, Universidad de Ciencias y Humanidades].2017. Reference Source\n\nGuevara D: Sistema de gestión de inventario basado en la teoría de inventarios y control de producción utilizando tecnología QR, para mejorar la gestión del inventario en la empresa Ecovive SAC [Tesis de Pregrado, Universidad Católica Santo Toribio de Mogrovejo].2019. Reference Source\n\nHo GTS, Tang YM, Tsang KY, et al.: A blockchain-based system to enhance aircraft parts traceability and trackability for inventory management. Expert Systems with Applications. 2021; 179: 115101. Publisher Full Text\n\nKumar N, Shahzeb Hasan S, Srivastava K, et al.: Lean manufacturing techniques and its implementation: A review. Materials Today: Proceedings. 2022; 64: 1188–1192. Publisher Full Text\n\nInstituto Nacional de Estadística e Informática: Perú: Tecnologías de Información y Comunicación en las Empresas, 2018.2019. Reference Source\n\nLópez C, Pérez G: Sistema informático de administración de pacientes y control de citas e inventario para la clínica del ISTA [Tesis de Pregrado, Universidad de El Salvador].2016. Reference Source\n\nMolina-Ríos J, Pedreira-Souto N: Comparison of development methodologies in web applications. Information and Software Technology. 2020; 119: 106238. Publisher Full Text\n\nMora JT: Arquitectura de software para aplicaciones Web.2011.\n\nNemeshaev S, Fatkullina A: Predictive analytics of the state of computer devices in the inventory system. Procedia Computer Science. 2021; 190: 647–650. Publisher Full Text\n\nPapananias M, Obajemu O, McLeay TE, et al.: Development of a New Machine Learning-based Informatics System for Product Health Monitoring. Procedia CIRP. 2020; 93: 473–478. Publisher Full Text\n\nPereira TF, Matta A, Mayea CM, et al.: A web-based Voice Interaction framework proposal for enhancing Information Systems user experience. Procedia Computer Science. 2022; 196: 235–244. Publisher Full Text\n\nPraveen U, Farnaz G, Hatim G: Inventory management and cost reduction of supply chain processes using AI based time-series forecasting and ANN modeling. Procedia Manufacturing. 2019; 38: 256–263. Publisher Full Text\n\nQin T, Grabski M, Fitzpatrick D, et al.: An efficient and reliable chemical inventory system at a growing drug discovery company. SLAS Technology; 2021. Publisher Full Text\n\nRamos H: Sistema de información para el Inventario y control de equipos de cómputo de la unidad de telemática del Frente Policial de Puno - 2015 [Tesis de Pregrado, Universidad Nacional del Altiplano].2016. Reference Source\n\nRamos-Miller (a), M: mmartinrm97/api-sepulveda-notus-frontend: Add Status Bar for Reports.2023. Publisher Full Text\n\nRamos-Miller (b), M: mmartinrm97/api-sepulveda-backend: Add Good Data.2023. Publisher Full Text\n\nRosas M, Valecilla R: Sistema web de inventario de bienes patrimoniales [Tesis de Pregrado, Universidad Central del Ecuador].2019. Reference Source\n\nSena Y: “Sistema web para el sistema de control de inventario para la UGEL Aija, 2020,” Tesis de Pregrado, Universidad César Vallejo, Lima, 2021. Accessed: Nov. 14, 2022. [Online]. Reference Source\n\nTejesh BSS, Neeraja S: Warehouse inventory management system using IoT and open source framework. Alexandria Engineering Journal. 2018; 57(4): 3817–3823. Publisher Full Text\n\nWilson C, Mergel I: Overcoming barriers to digital government: mapping the strategies of digital champions. Government Information Quarterly. 2022; 39(2): 101681. Publisher Full Text" }	[ { "id": "224015", "date": "28 Nov 2023", "name": "Luis de los Santos Valladares", "expertise": [ "Reviewer Expertise Data processing" ], "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 highlight the importance of inventory management in educational institutions and the challenges associated with it. The work reflects a careful and thoughtful approach to optimising the management of educational facilities through information technology. The decision to use information technology to improve inventory processes demonstrates a dynamic response to current needs.\nHowever, before accepting the manuscript for indexing, the authors should provide more details on the specific information technologies used during implementation, as well as the evaluation criteria used during system review. This could enhance understanding of the effectiveness and applicability of the system developed.\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": "10745", "date": "18 Jan 2024", "name": "Alex Pacheco", "role": "Author Response", "response": "This new version provides more details on the specific information technologies used during implementation, as well as the evaluation criteria used during the system review. Information on development technologies, strategic plug-in integration, technological details for indexation consideration and evaluation criteria during system review has been added." } ] }, { "id": "224020", "date": "27 Feb 2024", "name": "Andy Reyes", "expertise": [ "Reviewer Expertise Red Hat Certified Architect - RHCA", "Linux", "OpenSource", "Software Development", "IaaS", "PaaS", "SaaS", "CaaS", "IT Automation" ], "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 research methodology is very well applied.\nThe scope is delimited to the educational sector and the research objectives are limited to them, maintaining correct traceability of the research elements.\nThe project modules are focused on use cases, although it is a traditional approach, it meets what is necessary to facilitate the design, construction, implementation and maintenance of the proposed system for inventory management in this research.\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": [] } ]	1	https://f1000research.com/articles/12-1471
https://f1000research.com/articles/11-68/v1	20 Jan 22	{ "type": "Research Article", "title": "Aging with long-term physical disability: Cohort analysis of survey sample in the U.S.", "authors": [ "Kerri A. Morgan", "Michelle Putnam", "Sandra M. Espin-Tello", "Marian Keglovits", "Margaret Campbell", "Yan Yan", "Aimee Wehmeier", "Susan Stark", "Michelle Putnam", "Sandra M. Espin-Tello", "Marian Keglovits", "Margaret Campbell", "Yan Yan", "Aimee Wehmeier", "Susan Stark" ], "abstract": "Background: Chronic health conditions, secondary conditions, and decreasing functional ability related to aging and/or changes in underlying impairment may influence participation for persons aging with long-term physical disability (AwD). Objective: To examine sample integrity and baseline findings through exploration of associations of sociodemographic, health, and disability factors with social participation for persons AwD. Methods: This is a longitudinal cohort study following persons AwD over three years, reporting baseline cohort study data. A convenience sample of 474 persons AwD aged 45–65 reporting physical disability of ≥5 years’ duration was recruited through community organizations and social media. The cohort was majority female (66.7%) and single (62.0%), and over one-third (38.6%) was non-White. Pain, fatigue, depression, ability to participate in, and satisfaction with, social roles and activities were measured with the Patient Reported Outcomes Measurement Information System. Results: Participants aged 55–60 and 61–65 had significantly lower rates of employment and marriage and higher rates of living alone than participants aged 45–54. Participants reported higher rates of fatigue, pain, and depression and lower ability to participate in, and satisfaction with, participation in, social roles and activities than the general population. Ability to participate and satisfaction with participation were highest among Black/African American participants. Conclusions: Participants reported higher rates of common AwD symptoms and lower ability to participate and satisfaction with participation than the general population, consistent with prior studies of AwD samples. This cohort reflects the AwD population and can be considered an AwD sample, comparable to those found in existing literature. The focus of future analyses will be to gain a greater understanding of chronic health conditions, incidence of falls, engagement in everyday life activities, and the impact of the environment.", "keywords": [ "aging with disability", "physical disability", "cohort", "health", "participation" ], "content": "Introduction\n\nAging with a disability is the phenomenon of living long-term with impairment and disability that begins in early and/or mid-life and continues over the lifecourse.1,2 Although investigation of aging with long-term physical disability (AwD) dates back over 30 years, to date, most of the research has been small-scale and focused primarily on individuals with lifelong and early-onset disabilities.3–5 In contrast, our research focuses on persons AwD between the ages of 45 and 65 living in the United States, with disability onset from birth to age 60, to understand participation patterns and changes in this mid-life phase. It is fairly well-established that these individuals often experience the aging process earlier, at a faster rate, and report greater difficulty with independent living than their peers without physical disabilities.6,7 The growing body of research related to AwD links disability-related fatigue, pain, and depression to problems participating in general or to reduced social participation.8–10 Existing studies have also shown that increased levels of functional impairment, secondary health conditions (e.g., depression, fatigue, and sleep disturbance), and reduced mood and energy related to secondary health conditions significantly decrease satisfaction with social roles among persons AwD.11 Additionally, there is a substantial body of evidence showing differences in the severity of disability and disability symptoms and trajectories among individuals in mid-life based on race and ethnicity.12,13 However, limited research has investigated participation among persons AwD as a population group.9 Only a few research studies have explored AwD longitudinally.1,14,15 Of those, the Aging and Quality of Life Survey at the University of Washington was the longest running, collecting seven waves of data from 2009–2018.16 That study produced important findings regarding persons AwD and health and wellness but offers limited information about participation. We seek to build on these findings by expanding our understanding into the realm of participation in life activities.\n\nOur three-year cohort survey of persons AwD considers how and why participation changes over time. We aim to inform evidence-based interventions implemented by community organizations and service providers designed to facilitate participation of people with disabilities. Here, we report cohort sociodemographic, health, and disability traits from our first wave of data (collected August 2018 - July 2019) by age group. We also explore sample integrity by considering how our population compares to those existing in the current literature, based on the presence of normative AwD symptoms reported in the literature. The population of persons AwD is not well-represented in national datasets, as very few general population–based surveys in the United States include age of onset of conditions, symptoms, or disability, nor do they typically contain measures of pain, fatigue, and depression, which are often-measured symptoms related to AwD.1,2 We take this first step to help validate our sample given the paucity of research focused on AwD. We want to ensure that we indeed have recruited a sample of individuals that reflects the traits of AwD samples in published research. There is no standard set of parameters for what makes a sample an AwD sample, versus a more generic sample of persons with disabilities.1,2 We believe that the presence of AwD symptoms—given the commonality of their existence in the small body of AwD research—and one’s age at disability onset are the best current markers for identifying this subset of the broader disability population.\n\nAfter we assess demographic and disability characteristics, we then assess ability to participate in, and satisfaction with, participation in social roles and activities to further review our cohort. This will be compared with findings in existing literature, in order to gain a better understanding of baseline social participation prior to the COVID-19 pandemic. Specifically, we identify sociodemographic, health, and disability variables associated with one’s ability to participate in, and satisfaction with, their participation in social roles and activities, and we then quantify the independent effects of the variables on these two aspects of social participation. Our social activity measures are drawn from the PROMIS (Patient Reported Outcomes Measurement Information System) measurement bank and have been evaluated across multiple populations.17–19\n\nAwD research study samples are frequently composed of persons who identify their race as White and who have a specific diagnosis such as spinal cord injury, multiple sclerosis, or polio,20 which represent some of the common conditions found among persons AwD, but often do not include other conditions that cause disability. Guidelines from the United States federal funding agencies including the National Institutes of Health and the National Institute on Disability, Independent Living, and Rehabilitation Research21 have required researchers to improve the racial and ethnic diversity of their study samples, given the substantial differences in health and wellness outcomes for non-White individuals in the United States.22\n\nIn our study, we actively sought to create a broader sample base by increasing the proportion of non-White participants and by recruiting participants based on self-report of physical disability, regardless of diagnosis. We worked closely with our Community-Based Research Network (CBRN),23 a network of aging and disability providers and advocacy groups located in the state of Missouri in the United States, that work together to close the gap in the availability of evidence-based practices for persons AwD. The CBRN supported this cohort by identifying areas of importance for data collection, assisting with recruitment, and strategizing about increasing recruitment of participants of specific groups, including men and non-White individuals. Because of this, our study sample is distinct from other study samples of persons AwD in the literature. This reinforced our interest in evaluating the traits of our sample against those of other samples, before we begin our longitudinal analysis.\n\nOur cohort study is guided by disability models considering person–environment interactions24,25 and the World Health Organization’s International Classification of Function, Disability, and Health26; Active Ageing policy framework27; and Conceptual Framework for Action on the Social Determinants of Health.28 Fundamentally, our study process and choices for measures are anchored in building our understanding of how the knowledge gained from this study can be useful to CBRN members and other community-based organizations, to support the participation of persons AwD. Finally, our study is situated within the COVID-19 pandemic. The pandemic has exacerbated socioeconomic, health, and independent living disparities for persons with disabilities in the United States.29,30 Although this cohort study was not intended to evaluate participation among persons AwD before and during a pandemic, it has. Therefore, we believe it is crucial to understand how findings for baseline sample and social participation measures fit within the extant literature, so that we may have a better ability to tease apart the effects of the pandemic from more expected changes over time.\n\nThe questions we ask of our sample in this initial analysis are as follows. How do the sociodemographic and disability characteristics of our sample compare with those of other samples in AwD research and with the general population? How do social participation and predictors of social participation in our sample compare with findings in related studies of persons AwD? These questions support our dual aim of understanding how our sample compares with AwD samples reported in the published literature and providing a context for our future longitudinal analysis.\n\n\nMethods\n\nEthics approval was granted by the Washington University Institutional Review Board (IRB) (IRB# 201710186). This study presented minimal risk to participants; therefore, the IRB approved a request to waive documentation of informed consent. Participants were provided the consent information either online or over the phone and were asked if they would like to continue with participation in the study. Only participants who indicated yes online or over the phone continued with the survey and were included in the analysis. The consent information sheet explained that, when writing reports about the study, the research team will do so in a way that participants cannot be individually identified and that information the research team shares will be de-identified.\n\nThis is a longitudinal cohort study, collecting survey data once a year for three years at 12-month intervals: study enrollment (T0), 1-year follow-up (T1), and 2-year follow-up (T2). Here, we report findings from T0.\n\nTo enroll, participants had to be aged 45–65 years, have experienced physical disability for a duration of ≥5 years, speak English, and autonomously provide consent. Purposive recruitment occurred through a CBRN,23 local events, and social media. The organizations and agencies in the CBRN shared IRB-approved information about the study to their clients and participants through e-mail, mailed letters, and/or posts on their social media platforms. Local disability and aging events in the St. Louis, Missouri, area were attended by members of the research team. These events included bus pass distribution events and disability fairs. In addition, a Facebook advertisement was purchased, and an IRB-approved social media statement on the research study was posted for a limited amount of time. Statistical power calculations estimated a T0 sample of 470–500 participants, assuming a 25% attrition rate at T1 and T2. Gift cards were provided for completed surveys.\n\nRecruitment for T0 occurred between August 2018 and July 2019. The eligibility screen was completed by 1254 individuals; 977 passed the screening, and 516 were eligible and agreed to consent. We excluded 42 responses primarily due to duplicate survey completions, meaning participants completed the survey twice, and inconsistencies between screener and survey responses. A total of 474 unique participant responses were valid for analysis at T0. Interested participants used the information distributed for recruitment (a phone number and an e-mail address) to contact the research team to express interest and determine eligibility. To broaden the opportunity for completion, a mixed methods approach of either telephone or online administration of the screener and survey was offered. Half of the participants chose to be screened, provide consent, and complete the survey online, the other half over the phone. All surveys were the same for online and telephone administration and were completed using REDCap (Research Electronic Data Capture; Legacy Version 7 Server), a secure, web-based application.31 A secure link was sent with a password login to participants who selected online administration. These individuals directly recorded their responses into the online REDCap survey. For those who selected telephone administration, an appointment with a trained member of the research team was scheduled. During this appointment, the research team member directly read the questions and response options to the individual and recorded the individual’s responses into the REDCap survey. The average time for completion was 45–60 minutes.\n\nThe assessments for all three time points consisted of self-reports of health, disability, and social support characteristics; activity, participation, and environmental factors; and long-term service and support use (for the measures used in the survey, see Extended Data). Measures were selected in consultation with the CBRN. In this paper, we report the sociodemographic, health and disability, and social participation measures at T0.\n\nSociodemographic characteristics included age, race/ethnicity, sex at birth, gender, marital status, education, living arrangement, employment status, food security, sources of income, and health insurance. Race and ethnicity were asked as a combined question with response options of White, Black/African American, Hispanic or Latino, Asian/Asian Indian, Middle Eastern, American Indian/Native American, Native Hawaiian or Pacific Islander, and other. Sex at birth had response categories of female, male, intersex, I do not identify with any of these, and prefer not to say. Gender identity responses included man, woman, transgender, none of these describe me, and prefer not to say. Annual income was measured using the individual income eligibility limit at T0 for Missouri’s Medicaid program of $10,008 annually32 for older adults and persons with disabilities not enrolled in the Home and Community Based Services Waiver.33 The response for primary health condition causing physical disability was open-ended; we coded answers categorically based on the Social Security Administration’s (SSA) Listing of Impairments (Part A) for Adults.34 The duration of this condition was reported in years, ranging from birth to age 60. Self-rated physical and mental health were measured on a five-point scale (5 = excellent, 1 = poor).\n\nWe employed several measures from the PROMIS35 that have been validated with persons with physical disabilities.36 The PROMIS Physical Function with Mobility Aid Short Form35,37 measures one’s self-reported capability of standing and moving with and without support. The short form includes a screening item that asks about one’s ability to walk 25 feet with or without support. Based on the participant’s response, some items are skipped. Raw scores were submitted to the HealthMeasures Scoring Service, which calculated t-scores. The score range is 12–58, with higher scores representing better physical function. Three commonly reported AwD symptoms were measured with PROMIS instruments using the computerized adaptive testing (CAT) versions (REDCap Legacy Version 7 Server). The PROMIS Fatigue Profile evaluates a range of fatigue symptoms, from mild feelings of tiredness to an overwhelming sense of exhaustion.35,36,38 PROMIS Pain Interference measures the consequences of pain on relevant aspects of a person’s life, including the extent to which pain hinders engagement with social, cognitive, emotional, physical, and recreational activities.36,39 PROMIS Depression assesses negative mood, views of self, and social cognition, as well as decreased positive affect and engagement.36 These three measures use a five-point scale, with higher scores representing higher levels of the symptom over seven days. T-scores generated from the PROMIS scales are compared against a mean general population score of 50.\n\nWe measured social participation using: (1) the PROMIS Adult Ability to Participate in Social Roles and Activities40 CAT version, which is not time-bound and assesses the perceived ability to perform one’s usual social roles and activities, and (2) the PROMIS Satisfaction with Participation in Social Roles and Activities19 CAT version, which assesses self-reported contentment with social roles, such as work and family responsibilities, over the past seven days. Items are reverse-coded so that higher scores represent fewer limitations (i.e., better abilities).\n\nWe used SAS/STAT software (version 9.4, SAS Inc., Cary, NC, USA)41 for analysis, setting significance at p ≤ .05. To explore differences by age, we divided participants into three categories (45–54, 55–60, and 61–65) for univariate analysis. We performed bivariate analyses including chi-square tests and analysis of variances (ANOVA) to examine the differences of categorical and continuous variables across age groups. We then explored differences in the two social participation outcome scores by demographics. We examined univariate associations of each participant’s characteristics with the two social participation outcomes. For categorical variables, we examined the means of each outcome in each level of categorical variable, and we used two-sample t tests (two levels of categorical variables) and ANOVA (more than two levels of categorical variables) to test for statistically significant differences.\n\n\nResults\n\nThe sample was two-thirds female, one participant identified as transgender, and four participants preferred not to answer the question. Participants had a mean age of 56.8 years (SD = 5.6) and a mean of 19.0 years living with their disability (SD = 13.7, range = 5–65). Seventy percent of participants resided in the state of Missouri; the state with the second most participants was Illinois, with 6.5%. Twenty-eight additional states across the United States were represented, each with ≤2% of participants The most frequently self-reported primary causes of physical disability were neurological (37%; e.g., cerebral palsy, multiple sclerosis, spinal cord disorders, traumatic brain injury) and musculoskeletal (26%; e.g., degenerative and osteoarthritis, spinal stenosis, amputation). Conditions related to respiratory (e.g., asthma, COPD, lung disease), endocrine (e.g., diabetes and thyroiditis), and immunological (e.g., rheumatoid arthritis, connective tissue disorders) systems each ranged from 5%–6% representation. Categories ranging between 0.5%–3% representation included the cardiovascular system, special senses and speech, digestive system, and hematological disorders. Eighty percent of participants reported reasons for their primary disability that can be categorized as having one cause of primary disability, based on SSA listing.\n\nChi-square tests showed that older participants (aged 55–60 and 61–65) had significantly lower rates of employment and marriage, higher rates of living alone, and had lived with their disability for longer (Table 1). Rates of Medicare,42 Social Security Disability Insurance (SSDI),43 and Social Security retirement44 benefits receipt were also higher among older participants (aged 55–60 and 61–65).\n\n* p ≤ .05\n\n† Chi-square tests for similarity of frequency distribution of each variable in column one.\n\na Cell size ≤ 8 participants.\n\nOver half of participants had at least some difficulty with seeing (53%), self-care (52%), or remembering or concentrating (63%); about one-quarter reported difficulty with hearing (25%) or communicating (22%). Ninety-four percent of participants were unable to walk or climb steps or had difficulty doing so. In the past 12 months, approximately 46% of participants reported that their health status had declined, and 54% of participants reported that their ability to do what they wanted to do in their daily lives had decreased. Table 2 presents health and function information for the total sample and differences by age group. Participants’ mean scores of AwD-related symptoms were all above general population averages of 50, with a fatigue mean of 59.0 (SD = 9.3, range = 24.3–84.7), a pain interference mean of 60.4 (SD = 10.0, range = 38.7–83.8), and a depression mean of 54.9 (SD = 10.1, range = 34.2–84.4). We did not find significant differences by age group for health and function measures.\n\nParticipants reported lower average ability to participate in social roles (M = 44.1, SD = 9.0, range = 21.5–67.5) and satisfaction with their participation in social roles (M = 43.5, SD = 9.8, range = 22.0–68.7) than the general population (t-score = 50). Table 3 presents data on each social participation measure by sociodemographic characteristics. Both ability to participate in, and satisfaction with, participation in social roles and activities were higher among Black/African American participants in comparison to White participants and those of other races.\n\n* p < .05;\n\n p < .01;\n\n* p < .001.\n\n\nDiscussion\n\nFindings from our analyses show that our cohort is distinct yet similar to other AwD study populations. Its racial representation of nearly 39% non-White participants is higher than the only other cohort study of persons AwD we are aware of, which was roughly 90% White participants.36,45 This may be a factor of study location or recruitment strategies. Seventy percent of our participants live in the state of Missouri where our study is based, which has a Black and African American population of approximately 12% overall; this increases to 25%–50% in urban areas.46 Although there are notable exceptions in which studies have actively focused on non-White participants—for example, work by Harrison et al.47 focuses on predominantly Latina participants—broader racial and ethnic diversity is a major limitation in existing AwD research. We believe that the diversity of our sample will help broaden the applicability of cohort findings.\n\nOur cohort has similar percentages of college/advanced education (71%) to the US general population (68%). A higher percentage, 62%, are single, compared to roughly 48% of their age-matched general population peers48; a higher percentage also lives alone (41%) compared to their age-matched general population peers (12%–13%).33 Compared to other samples of persons AwD, our cohort has the same proportion of female participants (66.7%); however, fewer individuals are married (37.8%), a higher percentage is financially poor (35%), and a greater percentage (94%) has difficulty walking or climbing steps.8–10,45 In general, our cohort members seem to have fewer social, financial, and physical resources than those in other studies.13–15,29\n\nThe majority of participants in our cohort (71.9%) receive SSDI. For health insurance, 58% have Medicare,42 and 38% have Medicaid.49 We did not find comparable data for SSDI, Medicare, and Medicaid rates in studies with cross-diagnosis AwD samples to compare our results against. Given the low employment rate of our sample, we reviewed SSDI receipt and determined that 88% are insured by Medicare and 43% by Medicaid. At the time of baseline data collection, the state of Missouri, where most participants reside, had not passed the Affordable Care Act’s Medicaid expansion programs,50 suggesting that some participants may have forgone employment in order to retain public health insurance through traditional Medicaid state guidelines.51\n\nOur participants experience common AwD symptoms found in other studies. For example, using a PROMIS Pain measure in a sample of persons with neurological conditions, Molton et al.45 found scores of 51.9 for persons aged 45–54 and 51.6 for persons aged 55–64. Using a PROMIS Fatigue measure with the same dataset, Cook et al.36 found mean scores ranging from 52.4–58.7, similar to our cohort’s mean score. Amtmann et al.39 used a PROMIS measure, and Jensen et al.52 used the PHQ-9 (Patient Health Questionnaire-9),53 and both found elevated depression levels compared to the US general population; we found this too. Based on these comparisons, we have confidence that our cohort does reflect the AwD population in regard to the presence of common AwD symptoms. We did not find comparable data for self-rated physical and mental health. Although there were some significant differences between age groups in demographics, including employment, this was not the case for health and function, where age group membership was not significant.\n\nOur analysis of social roles and social activities had similar results to those found in the Aging and Quality of Life Survey and other studies of diagnostic-specific populations9,11,54 examining ability to participate and satisfaction with participation. We believe the similarity in findings related to AwD symptoms demonstrates that our cohort is representative of the AwD population. Quite notable, though, is our finding that social participation scores are higher for Black/African American participants compared to White cohort members. We will continue to explore this difference in future analyses.\n\nSeventy percent of our cohort is from one state in the United States, and the sample is predominantly female; thus, the cohort likely is not fully representative of the AwD population. Racial and ethnic diversity in our sample is primarily limited to Black/African American participants; other groups are underrepresented.\n\n\nConclusions\n\nWe believe that our cohort reflects the AwD population and can be considered an AwD sample comparable to those found in existing literature. The findings from this analysis add to the growing body of research that can be used to both better understand AwD in midlife and inform the design of intervention studies and programs aimed at facilitating participation. Our future analyses will further explore social participation, as well as interactions among disability status and chronic health conditions, incidence of falls, influence of environmental factors on participation, engagement in life activities, and associations between use of long-term services and participation for persons AwD. We believe this cohort study will help inform interventions and programs that support persons AwD to engage in their communities as we assess changes in participation over time.\n\n\nData availability\n\nThe underlying data generated and analyzed during the current study cannot be sufficiently de-identified and, therefore, cannot be made publicly available due to ethical considerations. De-identified data could be made available upon reasonable request, for the purpose of further research, via the corresponding author.\n\nThe publicly available measures used in the study survey can be accessed via the links below:\n\n• PROMIS Physical Function with Mobility Aid 11a\n\n• PROMIS Bank v1.0 - Fatigue (CAT version)\n\n• PROMIS Bank v1.1 - Pain Interference (CAT version)\n\n• PROMIS Bank v1.0 - Depression (CAT version)\n\n• PROMIS Bank v2.0 - Ability to Participate in Social Roles and Activities (CAT version)\n\n• PROMIS Bank v2.0 - Satisfaction with Participation in Social Roles and Activities (CAT version)", "appendix": "Acknowledgments\n\nThe authors would like to thank the cohort participants for their time and effort in completing the surveys; the organizations in the Community-Based Research Network for their input, guidance, and recruitment assistance; Szu-Wei Chen, PhD, Washington University, for her assistance with data management of the cohort database; and Megen Devine, MA, Washington University, for her assistance with editing the manuscript.\n\n\nReferences\n\nCoyle CE, Putnam M: Identifying adults aging with disability using existing data: The case of the Health and Retirement Study. 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PubMed Abstract \| Publisher Full Text" }	[ { "id": "173578", "date": "20 Jul 2023", "name": "Kenzie Latham-Mintus", "expertise": [ "Reviewer Expertise Sociologies of health", "aging", "and disability" ], "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 general, there are a limited number of publicly available datasets that enable researchers to examine aging with disability experiences, particularly among those in midlife or late midlife. Likewise, longitudinal data sources are even rarer and typically were not constructed to assess aging with disability experiences. Given these data limitations, this research contributes to the existing literature by creating a prospective longitudinal cohort study of midlife (aged 45–65) individuals who are aging with disability. This article outlines the recruitment and data collection processes and analyzes baseline characteristics. The article is well written, and the analysis is appropriate. The research team clearly describes the data limitations of their convenience sample including the over-representation of one state in the US. Most findings are in line with previous research; however, some novel findings (e.g., social participation differences by race/ethnicity) highlight the contributions of this study and the need for more research.\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": "9954", "date": "16 Nov 2023", "name": "Susan Stark", "role": "Author Response", "response": "We thank the reviewer for the time and effort taken to review the manuscript. We appreciate their summary and comments related to our study." }, { "c_id": "10712", "date": "17 Jan 2024", "name": "Susan Stark", "role": "Author Response", "response": "Thank you for these comments. We greatly appreciate the reviewer's time and feedback." } ] }, { "id": "173572", "date": "21 Nov 2023", "name": "Ellen Melbye Langballe", "expertise": [ "Reviewer Expertise ageing", "epidemiology", "disability", "psychology" ], "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 timely and important study. The included original data and statistical analysis are well-described and sufficiently discussed.\nHowever, a significant weakness of the paper in its present form is that sample integrity, investigated by comparing the results of the original analysis with results reported in existing literature, is not described or discussed in the abstract’s method section, in the methods section of the paper (e.g. how comparable papers were retrieved (systematically search?), number of comparable studies), or in the discussion section (e.g. limitations). Necessary details of the methods used regarding the comparison of results from existing literature should be provided.\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?\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? Partly", "responses": [ { "c_id": "10713", "date": "17 Jan 2024", "name": "Susan Stark", "role": "Author Response", "response": "Reviewer 2 comment: A significant weakness of the paper in its present form is that sample integrity, investigated by comparing the results of the original analysis with results reported in existing literature, is not described or discussed in the abstract’s method section, in the methods section of the paper (e.g. how comparable papers were retrieved (systematically search?), number of comparable studies), or in the discussion section (e.g. limitations). Necessary details of the methods used regarding the comparison of results from existing literature should be provided. Response: Thank you for the opportunity to answer these questions about sample integrity. We now see that our description of our process of considering our sample was too brief and also not specific enough. Given the word limitations, we have attempted to provide a brief, but fuller, description of this with the following edits to the manuscript: 1. We edited the Abstract Methods to add the following sentence: “Results were manually compared against AwD study samples identified through a focused literature review and national census data.” 2. At the end of the Methods section, we added a paragraph titled “Focused literature review and sample comparisons.” This section describes how we reviewed the literature, which articulates the databases we used and the search criteria. We did not complete a search using a systematic review protocol, but rather identified articles through a focused review that involved pursuing citations of discovered articles in an attempt to find further studies. Because this area of literature is quite small, and often differently indexed with inconsistent keywords, for example, it is difficult to find literature. As we mention in this new section, we found only four separately published studies, but all came from the same parent data source. For that reason, we also drew on U.S. Census Bureau data to consider our sample. “Focused literature review and sample comparisons Using PubMed and Google Scholar databases, we conducted a focused literature review of peer-reviewed journal articles in English, seeking U.S.-based cross-disability samples (composed of more than a singular disease or impairment diagnosis group) from 2011–2021 of over 100 individuals who had self-reported long-term physical disability, were between the ages of 18 and 65, and who were asked about pain, fatigue, and/or depression using measures similar to the PROMIS measures we used in our study. We located four articles that met these criteria; however, they all used the same or similar data collected at a single university. We reviewed the demographic traits of our sample against the samples used for those four studies and also 2019 U.S. Census Bureau data to better understand differences in our sample compared to the general U.S. and the state-specific populations in the same age range.” 3. In the first paragraph of the Discussion section, we changed the wording of the first sentence from “Findings from our analyses show that our cohort is distinct yet similar to other AwD study populations” to: “Findings from our analyses show that our cohort is distinct yet similar to the other AwD cohort study samples we identified.” We also updated one reference in the first paragraph of this section, replacing Harrison et al. with Walker et al.: “…for example, work by Walker et al.47 focuses on predominantly Latina participants” In the fourth paragraph of the Discussion, we modified the first sentence, changing it from, “Our participants experience common AwD symptoms found in other studies,” to: “Our participants experience common AwD symptoms found in the four studies we identified.” Later in the same paragraph, we added the phrase “as we understand it at this time” to the end of the fifth sentence. 4. In the Study Limitations section, we added two sentences to further clarify the limitations of our analysis: “The cross-disability AwD literature is quite small. Our sample comparison was narrow and targeted; it may not fully reflect AwD samples found more broadly in the literature or capture information present in study samples of single-disability, -impairment, or -disease groups, for example. As noted in our introduction, however, pain, fatigue, and depression are commonly found among participants in these studies.” 5. In the Conclusions section, to increase clarification and reduce word count (as our edits added words) we rephrased the conclusion of our findings to be more limited in scope, eliminating phrases we believed were not necessary or perhaps redundant, stating: “These findings add to the growing body of knowledge about what common traits AwD study populations may have.”" } ] } ]	1	https://f1000research.com/articles/11-68
https://f1000research.com/articles/12-1373/v2	23 Oct 23	{ "type": "Research Article", "title": "Stenotrophomonas goyi sp. nov., a novel bacterium associated with the alga Chlamydomonas reinhardtii", "authors": [ "María Jesus Torres", "Neda Fakhimi", "Alexandra Dubini", "David González-Ballester", "María Jesus Torres", "Neda Fakhimi", "David González-Ballester" ], "abstract": "Background: A culture of the green algae Chlamydomonas reinhardtii was accidentally contaminated with three different bacteria in our laboratory facilities. This contaminated alga culture showed increased algal biohydrogen production. These three bacteria were independently isolated.\nMethods: The chromosomic DNA of one of the isolated bacteria was extracted and sequenced using PacBio technology. Tentative genome annotation (RAST server) and phylogenetic trees analysis (TYGS server) were conducted. Diverse growth tests were assayed for the bacterium and for the alga-bacterium consortium.\nResults: Phylogenetic analysis indicates that the bacterium is a novel member of the Stenotrophomonas genus that has been termed in this work as S. goyi sp. nov. A fully sequenced genome (4,487,389 base pairs) and its tentative annotation (4,147 genes) are provided. The genome information suggests that S. goyi sp. nov. is unable to use sulfate and nitrate as sulfur and nitrogen sources, respectively. Growth tests have confirmed the dependence on the sulfur-containing amino acids methionine and cysteine. S.\ngoyi sp. nov. and Chlamydomonas reinhardtii can establish a mutualistic relationship when cocultured together.\nConclusions: S. goyi sp. nov. could be of interest for the design of biotechnological approaches based on the use of artificial microalgae-bacteria multispecies consortia that take advantage of the complementary metabolic capacities of their different microorganisms.", "keywords": [ "algae", "bacteria", "consortia", "cocultures", "Chlamydomonas", "Stenotrophomonas", "vitamins", "metabolic complementation" ], "content": "Introduction\n\nThe first described species of the Stenotrophomonas genus was S. maltophilia, which was a Gram-negative bacterium originally named as Pseudomonas maltophilia, and later transferred in 1993 to the new genus Stenotrophomonas, which was solely composed of S. maltophilia. In 2001, this species was moved to the genus Xanthomonas before it was finally moved back again in 2017 to its own genus when Stenotrophomonas pictorum was identified (Ryan et al., 2009; Wei et al., 2021). Currently, Stenotrophomonas is a genus comprising at least 19 validated species (https://lpsn.dsmz.de/genus/stenotrophomonas) (Parte et al., 2020). However, the molecular taxonomy of the genus is still somewhat unclear, and all its members are considered as “orphan species”. All Stenotrophomonas spp. have shown intraspecific heterogeneity with high phenotypic, metabolic, and ecological diversity (Ryan et al., 2009).\n\nThe main reservoirs of Stenotrophomonas spp. are soil and plants, although they are ubiquitously present in different environments, including opportunistic human pathogens such as S. maltophilia (Ryan et al., 2009).\n\nStenotrophomonas spp. show promising potential for different biotechnological applications. Some Stenotrophomonas spp. are of interest to agriculture due to their ability to promote growth in different plant species. Some Stenotrophomonas spp. are even capable of establishing symbiotic relationships with plants. This plant growth promotion is related to the capacity of some Stenotrophomonas spp. to produce the plant growth hormone indole-3-acetic acid (IAA), fix nitrogen, oxidate elemental sulfur (S) to sulfate, or biocontrol plant pathogens (Banerjee and Yesmin, 2008; Park et al., 2005; Ryan et al., 2009; Suckstorff and Berg, 2003).\n\nMoreover, they are also considered good candidates for bioremediation due to their tolerance to heavy metals and capability to metabolize a large variety of organic molecules, including phenolic and aromatic compounds (Liu et al., 2007; Mora-Salguero et al., 2019; Pages et al., 2008; Ryan et al., 2009). Finally, some Stenotrophomonas spp. can synthetize useful bioproducts such as antimicrobial and enzymes of biotechnological interest (Rivas-Garcia et al., 2022; Wolf et al., 2002).\n\nHere we report the genome of Stenotrophomonas goyi. sp. nov. isolated from a contaminated microalgae (Chlamydomonas reinhardtii) culture. This alga culture was simultaneously contaminated with S. goyi, Microbacterium forte (Fakhimi et al., 2023a) and Bacillus cereus. The metabolic interactions established between these four microorganisms are analyzed and discussed in a related publication where the ability of this multispecies consortium to sustain hydrogen production is highlighted (Fakhimi et al., 2023b).\n\n\nMethods\n\nThis study took place at Campus Universitario de Rabanales, Cordoba, Spain. S. goyi sp. nov. where it was isolated from a fortuitously contaminated Chlamydomonas reinhardtii culture in the laboratory. Initially, the Chlamydomonas reinhardtii culture was simultaneously contaminated with three different bacteria (Fakhimi et al., 2023b). Individual members of this bacterial community were isolated by sequential rounds of plate streaking in Yeast Extract Mannitol (YEM) medium (handmade in our lab, described here), until three different types of bacterial colonies were visually identified. Colonies were grown separately, and the subsequent isolated DNA was used for PCR-amplification of their partial RNA 16S sequences. After sequencing, the three independently isolated bacteria were identified as members of the genus Microbacterium, Stenotrophomonas, and Bacillus (Fakhimi et al., 2023b).\n\nDNA extraction and whole genome sequencing using PacBio (Pacific Biosciences) RS II Sequencing System (RRID:SCR_017988) were performed by SNPsaurus LLC (https://www.snpsaurus.com/). Whole genome sequencing generated 102,238 reads yielding 832,209,774 bases for 166 read depth over the genome (Table 1). Genome was assembled with Canu (RRID:SCR_015880) 1.7 (Koren et al., 2017) generating a 4,487,389 pb circular genome. The genome completeness was checked by BUSCO 3.0.2 (RRID:SCR_015008) (Manni et al., 2021) and was 94.6% complete, with 94.6% of the genome single copy and 0.0% duplicated. Any other prokaryotic contamination was discarded using ContEst16S 1.0 (RRID:SCR_000595) (Lee et al., 2017).\n\nPhylogenetic analyses were performed using the Type (Strain) Genome Server (TYGS) at Leibniz Institute DSMZ (German Collection of Microorganisms and Cell Cultures GmbH) (Camacho et al., 2009; Farris, 1972; Kreft et al., 2017; Lagesen et al., 2007; Lefort et al., 2015; Meier-Kolthoff et al., 2022, 2013; Meier-Kolthoff and Göker, 2019; Ondov et al., 2016). Information on nomenclature, synonymy and associated taxonomic literature was provided by TYGS's sister database, the List of Prokaryotic names with Standing in Nomenclature (LPSN). Trees were inferred with FastME 2.1.6.1. Phylogenetic trees were drawn with iTOL (RRID:SCR_018174) (Letunic and Bork, 2021).\n\nTentative annotation of the S. goyi sp. nov. genome was performed using the RAST tool kit, RASTtk (RRID:SCR_014606) at The Genome Annotation Service (Brettin et al., 2015; Overbeek et al., 2014). BlastKOALA service was used to automatically assign K numbers to the predicted proteins, which allowed Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology assignments, the putative characterization of individual gene functions, and the reconstruction of KEGG pathways (Kanehisa et al., 2016). The PHAge Search Tool Enhanced Release (PHASTER) (RRID:SCR_005184) was used to locate potential phage sequences within the S. goyi sp. nov. genome (Arndt et al., 2016)\n\nBacterial precultures were grown on Yeast Extract Mannitol (YEM) or Luria Broth (LB) media (handmade in our lab). Some growth experiments were done in Mineral Medium (MM) (Harris, 2008) supplemented with different nutrient sources (handmade in our lab). Tris-Acetate-Phosphate (TAP) medium (Harris, 2008) (handmade in our lab, described here) was also used occasionally. In some experiments, a vitamin cocktail (riboflavin, 0.5 mg⋅L-1; p-aminobenzoic acid, 0.1 mg⋅L-1; nicotinic acid 0.1 mg⋅L-1; pantothenic acid, 0.1 mg⋅L-1; pyridoxine, 0.1 mg⋅L-1; biotin, 0.001 mg⋅L-1; vitamin B12, 0.001 mg⋅L-1; thiamine, 0.001 mg⋅L-1) was added to bacterial cultures. More specific details for each experiment can be found in the corresponding figure and table legends. All the bacterium cultures were incubated at 24-28°C and under continuous agitation (130 rpm).\n\nChlamydomonas cells were cultured for 3-4 days in TAP medium until mid-logarithmic growth phase, harvested by centrifugation (5.000 rpm for 5 min) and washed twice with fresh MM. Bacterial batch-cultures were incubated in TYM or LB medium until the Optical Density at 600 nm (OD600) reached 0.8-1, then harvested by centrifugation (12.000 rpm for 5 min) and washed twice with fresh MM. Algae and bacteria were cocultured in 250 mL flasks containing 100 mL of the corresponding medium. Alga-bacterium cocultures were set to initial chlorophyll concentration of 10 μg·mL−1 for the alga and an initial OD600 of 0.1 for the bacterium. Algal and bacterial monocultures were used as controls. All cultures were incubated at 24°C with continuous agitation (120-140 rpm) and under continuous illumination (80 PPFD).\n\nThe algal growth was assessed in terms of chlorophyll content. Chlorophyll measurements were done by mixing 200 μL of the cultures with 800 μL of ethanol 100%. The mix was incubated at room temperature for 2-3 min, and afterward centrifuged for 1 min at 12.000 rpm. The supernatant was used to measure chlorophyll (a + b) spectrophotometrically (DU 800, Beckman Coulter) at 665 and 649 nm (Wintermans and de Mots, 1965).\n\nBacterial growth in monocultures was estimated spectrophotometrically in terms of OD600 evolution (DU 800, Beckman Coulter). However, estimation of the bacterial growth in cocultures required bacterium cells separation from the alga cells. To do this, a customized Selective Centrifugal Sedimentation (SCS) approach was used. This approach consisted in finding the centrifugation parameters that led to maximize algal cell sedimentation while minimizing bacterial cell sedimentation (Torres et al., 2022). Thus, measuring the OD of the supernatant after centrifugation can provide an estimation of the bacterial growth in the cocultures. To do this, the percentages of precipitated cells of each monoculture were calculated at different forces (from 100 to 500 x g) and times (1 and 2 min) using the measured OD before (ABC) and after (AAC) the centrifugation. Centrifugation at 200 x g for 1 min led to 87.9% of Chlamydomonas sedimentation, while only 2.1% of the bacterial cells dropped (meaning that 97.9% of the S. goyi cells remained in the supernatant). These parameters were chosen as a good compromise for SCS and used to evaluate the contribution of the bacteria to the OD in cocultures (SCSOD600).\n\n\nResults\n\nA fortuitous contaminated Chlamydomonas reinhardtii culture (strain 704; CC-3597; https://www.chlamycollection.org/) was studied due to its enhanced hydrogen production capability. This alga culture turned out to be contaminated with three different bacterial strains (Fakhimi et al., 2023b), one of them consisting in a white-pigmented bacterium (Figure 1). This bacterium was isolated after several rounds of plate streaking in TYM medium. First, partial PCR amplification and sequencing of the ribosomal 16S gene allowed the identification of this bacterium as a member of the Stenotrophomonas genus. Afterwards, the whole genome sequence was obtained. Genome assembling provided one single circular contig of 4,487,389 pb (Table 1). No plasmids or extrachromosomal elements were identified.\n\nThe RAST server identified 4,147 genes (4,066 CDS + 81 rRNAs and tRNAs) (Table 2). Out of these 4,066 CDS identified by RAST, 1,096 of them were in subsystems. Tentative genome annotation derived from the RAST server is available in Supplemental Table 1 as Extended data (González-Ballester et al., 2023).\n\ntRNA, transfer RNA; rRNA, ribosomal RNA.\n\nPhylogenetic analyses were performed with both, the whole genome (Figure 2) and the inferred 16S rDNAs (Figure 3). Pairwise comparisons with the closest type strains genomes are shown in Table 3. These phylogenetic analyses revealed that the sequenced genome belonged to a new Stenotrophomonas sp.; all dDDH values (d0, d4 and d6) were below 70% (Meier-Kolthoff et al., 2013) (Table 3). This new bacterial species was named as Stenotrophomonas goyi sp. nov. The closest related bacteria in terms of whole genome and 16S rDNA similarities were Stenotrophomonas rhizophila DSM 14405 and Stenotrophomonas nematodicola W5, respectively (Figures 2 and 3). S. goyi sp. nov. genome was deposited in the NCBI as SUB12103906.\n\nTree inferred with FastME 2.1.6.1 using the Genome BLAST Distance Phylogeny (GBDP) distances calculated from genome sequences. The branch lengths are scaled in terms of GBDP distance formula d5. The numbers above the branches are GBDP pseudo-bootstrap support values > 60% from 100 replications, with an average branch support of 91.6%. The tree was rooted at the midpoint. Branch lengths (black) and bootstraps (red) values are indicated. Genome sizes: 3,906,271–5,177,426 pb. Average δ statistics: 0.078 (Holland et al., 2002). Phylogenetic tree drawn with iTOL (Letunic and Bork, 2021).\n\nTree inferred with FastME 2.1.6.1 using the Genome BLAST Distance Phylogeny (GBDP) distances calculated from 16S rDNA gene sequences. The branch lengths are scaled in terms of GBDP distance formula d5. The numbers above branches are GBDP pseudo-bootstrap support values > 60% from 100 replications, with an average branch support of 78.6%. The tree was rooted at the midpoint. Branch lengths (black) and bootstraps (red) values are indicated. RNA16S lengths: 1,385–1,535 pb. Average δ statistics: 0.236 (Holland et al., 2002). Phylogenetic tree drawn with iTOL (Letunic and Bork, 2021).\n\nThe digital DNA-DNA Hybridization (dDDH) values are provided along with their confidence intervals (C.I.) for the three different Genome BLAST Distance Phylogeny (GBDP) formulas: a) formula d0: length of all High-Scoring segment Pairs (HSPs) divided by total genome length; b) formula d4: sum of all identities found in HSPs divided by overall HSP length; formula d6: sum of all identities found in HSPs divided by total genome length (Meier-Kolthoff et al., 2013).\n\nBlastKOALA (Kanehisa et al., 2016) service allowed KEGG orthology assignments to characterize individual gene functions and reconstruct KEGG pathways of S. goyi genome (Supplemental Table 2; Extended data (González-Ballester et al., 2023)). Some important pathways were either absent or incomplete in S. goyi sp. nov. including assimilation of nitrate (the whole assimilatory pathway is missing including nitrate transporters) and sulfate (only sulfite reductase is present). On the other hand, putative complete pathways for the glyoxylate cycle and biosynthesis of biotin, coenzyme A, pantothenate, riboflavin, tetrahydrofolate, glutathione, pyridoxal-P, lipoic acid, dTDP-L-rhamnose, UDP-N-acetyl-D-glucosamine, C5 isoprenoids, bacterial lipopolysaccharides, and antimicrobial proteins, among others, were present. Incomplete pathways for the degradation of aromatic compounds (including phenol, toluene, xylene, methylnaphthalene, 3-hydroxytoluene, and terephthalate) and myo-inositol biosynthesis, were also present.\n\nSearch with PHASTER (Arndt et al., 2016) revealed one intact prophage (PHAGE_Erwini_phiEt88_NC_015295) located at position 753112-799783 of the S. goyi sp. nov. genome.\n\nS. goyi sp. nov. showed no growth on MM, or in MM supplemented with different C sources (sucrose, glucose, lactose, mannitol, or glycerol) (Table 4). The addition of vitamins to the MM supplemented with glucose or lactose did not support the bacterium growth either (Table 4). However, the bacterium showed an excellent growth when cultivated in MM supplemented with yeast extract, tryptone, peptone or even Bovine Serum Albumin (BSA) (Table 4), suggesting that this bacterium has a great capacity to use peptides/amino acids as C source, and probably also as N source. Moreover, the peptides/amino acids could also provide, in addition to C and N sources, other essential nutrients or even palliate potential amino acids auxotrophies. Note that MM medium has sulfate as only S source. As commented before, the genome of S. goyi sp. nov. is lacking a functional sulfate assimilation pathway. Thereby S-containing amino acids, such as cysteine and methionine, could support the growth in medium rich in peptides/amino acids.\n\nMineral Medium (MM) was supplemented with different nutrients at 5 g·L-1 each, but methanol and ethanol (5 ml·L-1). For acetic acid, Tris-Acetate-Phosphate (TAP) medium was employed (1.05 g·L-1 of acetic acid). Vitamins cocktail included riboflavin (0.5 mg⋅L-1), p-aminobenzoic acid (0.1 mg⋅L-1), nicotinic acid (0.1 mg⋅L-1), pantothenic acid (0.1 mg⋅L-1), pyridoxine (0.1 mg⋅L-1), biotin (0.001 mg⋅L-1), vitamin B12 (0.001 mg⋅L-1), thiamine (0.001 mg⋅L-1). ++, significant growth; +, poor growth; -, no growth.\n\nTo confirm this hypothesis, S. goyi sp. nov. was inoculated in plates of MM + glucose supplemented with different combinations of cysteine, methionine, biotin, and thiamine. Only plates containing cysteine and methionine supported the bacterial growth for several culturing rounds (Figure 4). This result confirms the cysteine and methionine growth dependence of S. goyi. sp. nov. Cysteine and methionine could provide either a reduced S source or complement an auxotrophy for these two amino acids. Since S. goyi sp. nov. genome has complete pathways for all the essential amino acids, is more likely that cysteine and methionine are being used as reduced S sources. Similar results were found for M. forte, where cysteine and methionine are required as S sources (Fakhimi et al., 2023a).\n\nS. goyi sp. nov. was inoculated in: A) plates of Mineral Medium (MM) + glucose (5 g·L-1); B) MM + glucose + biotin (0.001 mg·L-1) + thiamine (0.001 mg·L-1); C) MM + glucose + cysteine (4 mM) + methionine (4 mM); and D) MM + glucose + cysteine + methionine + biotin + thiamine.\n\nS. goyi sp. nov. showed optimal growth between 24 and 32°C and pH 5-9 (Table 5). Despite the presence of the complete multidrug resistance efflux pump MexJK-OprM in the genome (Chuanchuen et al., 2005), no resistance to tetracycline, rifampicin, chloramphenicol and polymyxin (50 μg/mL each) was observed.\n\nLysogeny broth (LB) medium was used in all the conditions.\n\nTorres et al., (2022) reported that cocultures of S. goyi sp. nov. (published as Stenotrophomonas sp.) and C. reinhardtii promoted the growth of the microalga (nearly doubled) when incubated in MM supplemented with glucose and mannitol, but not when supplemented with acetic acid (Torres et al., 2022).\n\nHere, it was also checked if the bacterium also benefited when co-cultivated with C. reinhardtii in glucose- and mannitol-containing media. First, we observed that the chlorophyll content in the cocultures was 2.4 times higher than in the C. reinhardtii monocultures after 13 days (Figure 5A), which is in accordance with previous results (Torres et al., 2022). Additionally, the dry biomass resulting from the consortia was 2.2 times higher than the sum of the respective monocultures (Figure 5B). Finally, the growth of the bacterium in cocultures was very efficient, unlike S. goyi sp. nov. monocultures (Figure 5C).\n\nS. goyi-C. reinhardtii consortium, and respective control monocultures, were incubated in Mineral Medium (MM) supplemented with glucose (5 g·L-1) and mannitol (5 g·L-1). A) Chlorophyll content; B) dry weight biomass after 13 days; C) bacterial growth in terms of ODSCS; D) actual picture of the cultures after 13 days.\n\nThese results indicate that S. goyi sp. nov. and C. reinhardtii can establish a mutualistic relationship when incubated in sugars-containing media. On the one hand, S. goyi sp. nov. can greatly support the growth of the C. reinhardtii in media supplemented with glucose or mannitol, which are two carbon sources that the alga cannot utilize. Likely, this growth promotion is due to the release of acetate and/or CO2 from the bacteria after the sugar fermentation. Acetate is the sole organic carbon source that C. reinhardtii can utilize during heterotrophic/mixotrophic growth (Chaiboonchoe et al., 2014). On the other hand, S. goyi, sp. nov. can grow in media without amino acids/peptides supplementation when cocultured with C. reinhardtii, suggesting that the alga must provide some essential nutrients for the bacterium. Reduced S forms excreted by the alga (e.g., cysteine or methionine) could potentially explain the bacterium growth in the consortium.\n\n\nDiscussion and conclusions\n\nStenotrophomonas spp. are common constituents of the rhizosphere, and their potential for agricultural biotechnology is arising. However, their association with algae is poorly explored. Most plant growth-promoting bacteria (PGPB) are firstly identified in the rhizosphere and in association with plants. However, many PGPB are then also often commonly found in association with algae. This is likely reflecting that the kind of relationships established between bacteria and plants are similar to the relationships between bacteria and algae. This could potentially be the case for Stenotrophomonas spp., although the relative poor taxonomic curation and heterogeneity of the genus may prevent the tracking of its association with algae.\n\nSome Stenotrophomonas spp. show a limited nutritional range, while others are capable of metabolic versatility (Ryan et al., 2009). S. goyi sp. nov. is unable to grow in the absence of a source of peptides/amino acids, which imply that in natural ecosystems it may rely on other microorganisms to obtain essential nutrients. As stated before, S. goyi sp. nov. is unable to use sulfate as S source. The peptides/amino acids are likely providing S-reduced forms (such as cysteine and methionine) to S. goyi sp. nov.\n\nStenotrophomonas goyi sp. nov. was isolated from an alga culture (C. reinhardtii) that showed an enhanced capacity to produce hydrogen and biomass when incubated in mannitol and yeast extract containing medium (Fakhimi et al., 2023b). This algal culture was simultaneously contaminated with two other bacteria: Microbacterium forte and Bacillus cereus. Out of the three bacteria, M. forte was the main responsible for the enhanced algal hydrogen production. However, C. reinhardtii-M. forte cocultures were unable to produce hydrogen and biomass concomitantly. In addition to M. forte, the presence of S. goyi sp. nov. and B. cereus in the cocultures was needed to produce joinlty hydrogen and algal biomass (Fakhimi et al., 2023b), which stresses the biotechnological interest of S. goyi sp. nov.\n\nM. forte showed auxotrophy for biotin and thiamine, and like S. goyi sp. nov. was unable to grow on inorganic S sources (Fakhimi et al., 2023a). In this multispecies association, S. goyi sp. nov. and C. reinhardtii could alleviate the auxotrophy of M. forte sp. nov. for biotin and thiamine. S. goyi sp. nov. could also provide ammonium derived from the mineralization of the amino acids to the alga. On the other hand, the alga could provide S-reduced sources such as cysteine and methionine for S. goyi sp. nov. and M. forte. In any case, this multispecies association was mutually beneficial and prevented an excessive bacterial growth in cocultures, which could be one of the main drawbacks when algae-bacteria cocultures are used for biotechnological applications.\n\nNevertheless, the precise metabolic relationships established in this multispecies consortium that led to the extension of the C. reinhardtii cells viability during hydrogen production condition is not yet unraveled and need to be further investigated.\n\n\nEthical considerations\n\nNot applicable.", "appendix": "Data availability\n\nSpanish Type Culture Collection (CECT): Stenotrophomonas goyi sp. nov. bacterium. Accession number CECT30764; https://www.cect.org/vstrn.php?lan=en&cect=30764 (Universidad de Cordoba, 2022).\n\nNCBI Gene: Stenotrophomonas goyi sp. nov. genome sequence. Accession number CP116871; https://identifiers.org/ncbi/insdc:CP124620 (Fakhimi et al., 2023).\n\nZenodo: Supplemental Files, https://doi.org/10.5281/zenodo.8091305 (González-Ballester et al., 2023).\n\nThis project contains the following extended data:\n\n- Supplemental Table 1 [Tentative annotation of the S. goyi sp. nov. genome]\n\n- Supplemental Table 2 [KEGG orthology assignments]\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 acknowledge Dr. Gregorio Gálvez Valdivieso for his invaluable contribution to this research: perfection sometimes kills new discoveries. We thank the Bio knowledge Lab (BK-L) Ltd. for their kind support. An earlier version of this article can be found on bioRxiv (doi: https://doi.org/10.1101/2023.05.04.539380).\n\n\nReferences\n\nArndt D, Grant JR, Marcu A, et al.: PHASTER: a better, faster version of the PHAST phage search tool. 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Publisher Full Text\n\nWolf A, Fritze A, Hagemann M, et al.: Stenotrophomonas rhizophila sp. nov., a novel plant-associated bacterium with antifungal properties. Int. J. Syst. Evol. Microbiol. 2002; 52: 1937–1944. Publisher Full Text" }	[ { "id": "224972", "date": "27 Nov 2023", "name": "Rosa Leon-Bañares", "expertise": [ "Reviewer Expertise Biochemistry and Biotechnology of microalgae" ], "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 is clearly presented and describes an interesting study, which is detailed presented. In this paper, the authors describe the characterization of a new bacterial species of the genus Stenotrophomonas, found as contaminant in a culture of the chlorophyte Chlamydomonas reinhardtii. The bacterial genome has been sequenced and tentatively annotated. Phylogenetic trees based on both whole genome and 16S rDNA sequences were stablished. The growth of the new bacteria, either with or without the microalga, was evaluated.\nFunctional annotation of the genome of the new bacteria reveled that some important pathways are not present in S. goyi genome. This data, beside several growth test carried out with aminoacids and /or peptide hydrolysates make the authors suggest that peptides and amino acids are a good C source, and probably also a good N or S source, for S. goyi, which can not grow in minimal medium not supplemented with aminoacids or peptides. Addition of aminoacid/peptides or co-cultivation with the microalga is necessary for the growth of this bacterial. Moreover, the microalga growth rate is practically doubled when cultured in the presence of the bacteria. The authors propose the establishment of a mutualistic relationship between C. reinhardtii and the bacteria, in which the bacteria would provide a carbon source (acetate or CO2 obtained from bacterial sugar fermentation) to the microalgae and the bacteria would obtain S-aminoacids excreted by the alga.\nThe authors suggest that many microalgal-associated bacteria can promote higher plant growth, being the characterization of this algal-bacterial consortium of interest to identify potent plant growth-promoting bacteria.\nSuggestions:\nThe assessment of the bacterial growth by determination of optical density is adequate for pure cultures, but it is difficult to carry out in mixed algal-bacterial cultures. The authors have optimized and validated a selective centrifugal sedimentation approach to separate bacteria and microalgae. Although the approach seems to work well, I would suggest determination of colony forming units (CFU) to follow bacterial growth in future occasions. In may experience, the sedimentation properties of the microalga can change along the growth cycle\n\nIndicate in the legend of Figure 1, that shows a plate with Chlamydomonas reinhardtii and Stenotrophomonas goyi sp. nov., the culture medium used. Is it bacterial or algal growth médium? Is it MM or has been supplemented with sugars?\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": "224973", "date": "27 Nov 2023", "name": "Gergely Maroti", "expertise": [ "Reviewer Expertise Algal biotechnology" ], "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 describes the characteristics of a novel Stenotrophomonas sp. bacterium isolated from a complex algal-bacterial association. The genome description is clear and concise, the nutrient requirements of the bacterium were also clearly determined.\nThe mutualistic growth promoting effects were proven experimentally. The potential molecular mechanisms behind the observed effects are not shown or hypothesized, however, it is not the goal of this manuscript.\nThe conclusions are correct, the application of multispecies consortia including bacteria and green algae is a promising way for biological hydrogen production in an economically viably manner.\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/12-1373
https://f1000research.com/articles/12-639/v1	12 Jun 23	{ "type": "Case Study", "title": "Well-being as a tool to improve productivity in existing office space: Case study in Alexandria, Egypt", "authors": [ "Miral Hamadah", "Ahmed ElSeragy", "Sally ElDeeb", "Ahmed ElSeragy", "Sally ElDeeb" ], "abstract": "Background: The green building industry has significantly impacted the construction market, providing various sustainable solutions for the community. However, conventional green building standards have yet to adequately address occupant health and well-being, leading to challenges with performance. This has caused many businesses to take note of the latest report from the Bureau of Labour Statistics, which indicated that productivity in the US has dropped by the sharpest level since the 1940s [1]. Addressing these issues, organisations like International WELL Building Institute (IWBI) developed WELL Building Rating System (WELL), prioritising occupant health and well-being as critical components for improving performance and avoiding potential vulnerabilities brought about by sickness or pandemics. For this reason, this study will explore how to improve employee productivity within office buildings by bettering their overall health and well-being. Methods: The methodology is designed to collect data from traditional office design, new trended successful office designs, and the WELL Building Rating System to understand healthy building design. Additionally, using DesignBuilder computer software simulates natural daylight, ventilation, and thermal heat gain in the case study to compare implementation results to the base case result. Results: Showing thermal comfort, ventilation, and natural daylight significantly influence employees’ productivity. Implementing conducted design features from WELL achieved an average of 20.2%-35.6% decrease in thermal gain throughout the year, a 20% increase in airflow, an average 2.4%-6.5% decrease in Air temperature, enhanced temperature distribution by 7%, and direct sunlight minimum reduction by 9% in Winter and maximum 21.9% in Spring. Conclusion: Our research analysed that new design features in famous office buildings positively impact employee productivity. We particularly examined the features outlined by WELL Building Rating System to identify the most influential factors affecting occupant productivity. The results of this study informed recommendations for enhancing productivity in existing office buildings in Alexandria, Egypt.", "keywords": [ "WELL", "Rating System", "well-being framework", "Sick Building Syndrome", "post-pandemic office buildings design standards", "designing for occupants", "Enhancing office productivity", "Productivity design standards", "Healthy Buildings Design" ], "content": "1. Introduction\n\nThe operation and construction of current and new buildings negatively impacted the environment for countless years. In addition to the 1970s energy crisis, builders and building owners were encouraged to turn to green building rating systems to assist them in designing more environmentally conscious buildings and communities.2 However, most of the well-known green building standards that surfaced due to this movement were solemnly focused on achieving sustainability in buildings to provide a better environment while inadequately covering the matter of occupants’ health and wellness, as it can be a dominant factor for poor productivity and health of the society, especially in the business field as employees performance is essential.1,3\n\nThus, another movement started in 2014 that included human health and well-being and how buildings affect occupants as a new factor to the green movement equation.3 That is when International WELL Building Institute (IWBI) created the WELL Building Standard, the first system of its kind that tracks, measures, and certifies how building features affect the people inside.4\n\nStudies indicate that 90% of people’s time is spent in enclosed spaces, which impacts their health. During this time, they can be exposed to multiple pollutants, such as air pollution, inadequate lighting and ventilation, toxic materials indoors, uncomfortable temperatures, and disregarding mental health and the well-being of their social and community environment, all of which can be up to five times higher than average outdoor concentrations,5 leading to negative short-term and long-term well-being and health outcomes that are held responsible for employees’ poor productivity and health vulnerability to pandemics in the workspace,6,7 recently followed by the rise of the pandemic (COVID-19), which urged the need to change how we operate. Meanwhile, architects on a global scale started reconsidering current building design strategies and considering updating existing building standards to alleviate vulnerability to future pandemics and increase productivity and well-being.8,9\n\nWhile recent research has found that Air Quality, Thermal Comfort, and Natural Light are the three highest factors affecting office productivity, this is a significant finding as it shows that these factors directly impact employee performance. The findings suggest that companies should prioritise improving air quality, providing adequate thermal comfort, and increasing natural light in their office spaces to maximise staff productivity. Additionally, this data can help inform businesses about office design and layout decisions to create an environment conducive to employees’ well-being and success.10\n\nThe problem is that most office buildings in Egypt are closed, with inadequate operable windows, natural light, and thermal comfort. This leads to vulnerability to pandemics and a lack of motivation and productivity.11 All caused by the fact that architecture development is unsynchronised with building occupants’ well-being and mental health, which should be considered a significant factor for a healthy community and sustainable environment, especially for the post-pandemic future.11\n\nThis paper aims to direct architects and construction firms in Egypt to include the well-being of occupants as an essential key factor of building design to connect occupants’ well-being to sustainability in design. To achieve this connection and complete the deficiency in the design criteria between architecture and occupant well-being, a thorough study of the WELL Building Rating System is submitted to resolve occupants’ issues within buildings in Egypt, along with analysing standard office design strategies and new trending office designs. To reach the paper’s aim, the following objectives will be achieved: Study and analyse the new WELL Building Standard rating that seeks the health and well-being of people, and understand all new categories developed by IWBI to develop a strategy to solve problems and boost efficiency in office buildings in Egypt.\n\nThe research focuses on the well-being of occupants in existing office buildings in Alexandria, Egypt, and highlights the Cairo Petroleum Complex office building as a case study.\n\nThrough analysing and studying the traditional and new design criteria of office design, we explore two famous successful office buildings, the Googleplex HQ and the Amazon Spheres, to analyse their productivity-derived design criteria in which we conduct their productivity derived design criteria.\n\nThe methodology is designed to conclude a checklist to enhance the productivity and well-being of occupants through studying the WELL building rating system concepts and features to conduct the design derived features that affects occupants’ health and productivity. Thus, we focus on six concepts: air, light, thermal comfort, movement, sound, and mind to conduct the features applicable on office buildings in Egypt. Next, we study three certified offices, which are the Centre of Sustainable Landscapes office building, the American Society of Interior Designers HQ office, and the 425 Park Avenue office building to analyse the impact of WELL certification on the employee’s productivity and understand the application of WELLs concepts in office buildings to conduct a summarised checklist to implement on the case study building “Cairo Petroleum Complex” in Alexandria/Egypt.\n\nThe methodology of this study used DesignBuilder computer software to simulate natural ventilation, lighting, and thermal comfort in the case study building in two stages:\n\nFirst, simulation in the base case:\n\nTo ensure that the results obtained through the DesignBuilder software can be replicated, it is important to follow a systematic and rigorous process:\n\n1. Data collection: Collect detailed and accurate data on the building’s geometry, construction materials, HVAC systems, lighting, occupancy, and other parameters that may affect its energy performance.\n\nApplied through: This data can be obtained through site visits, and other sources involves collecting detailed and accurate data on the building’s geometry, construction materials, HVAC systems, lighting, occupancy, and other parameters that may affect its energy performance; in this paper we obtained the data from a site visit to the case study building.\n\n2. Model creation: Use the DesignBuilder software to create a detailed and accurate model of the building, considering all the relevant parameters and inputs.\n\nApplied through: This involves inputting the data collected in step 1 and configuring the various parameters of the simulation, such as building orientation, window size and placement, in this paper we create a model of the base case five floor building of 3370 m2 total construction area. The building is a rectangle shape of dimensions 60 m × 67 m and a 20 m building height with uninsulated exterior brick walls thickness of 20 cm and 2 cm interior and exterior plaster with the total u-value of 1.5 W/m2K and 4 m single floor height. The building main structure is reinforced concrete with uninsulated fixed curtain wall elevations with no shades externally and uses mechanical ventilation system. The building roof is flat 20 cm reinforced concrete and insulated with four single glazed skylights of 240 m2 total area above the main court.\n\n3. Calibration: Calibrate the model by comparing its predicted energy performance against the actual energy consumption data for the building and adjusting the inputs as necessary to improve the model’s accuracy.\n\nApplied through: This process involves iteratively adjusting the input parameters, running the simulation, and comparing the results against actual data until the model is accurately calibrated that is not available in this case so Appling step 5.\n\n4. Sensitivity analysis: Conduct sensitivity analyses to determine the sensitivity of the model’s results to changes in the input parameters and identify the most important variables that affect the building’s energy performance.\n\nApplied through: This step helps identify the most important variables that affect the building’s energy performance and provides insights into how the model can be improved.\n\n5. Verification: Verify the accuracy of the model by comparing its predicted results against independent data sources, such as published literature or other validated models.\n\nApplied through: This step helps ensure that the model is reliable and can be trusted to provide accurate predictions. In this paper we validate the air temperature of the base case simulation to that of Alexandria weather and use the “correlation coefficient” parameter to validate the results as correlation coefficient (R2) should range between -1 and 1, in this case, the result was 0.993 which is within the acceptable range of the correlation coefficient -1 and 1, thus indicating that the base case results are reliable.\n\n6. Documentation: Document the model creation process, including the input data, assumptions, and any modifications made during the calibration and verification steps.\n\nApplied through: This documentation should include the input data, assumptions, and any modifications made during the calibration and verification steps. Proper documentation also helps to ensure that the model can be updated and maintained over time as necessary.\n\nBy following these steps, it is possible to create an accurate and reliable model of a building’s energy performance using the DesignBuilder software, and to ensure that the results obtained can be replicated and verified.\n\nSecond, simulating daylight, thermal heat gain, and natural ventilation after implementing the conducted criteria on the case study building to compare the impact results with the base case results.\n\nData input: Cairo Petroleum Complex base case, EGYPT region, energy code ASHRAE 90.1-2007, location simulation using weather data “EGY_AL ISKANDARIAH_ ALEXANDRIA_ETMY”, the yearly design temperatures using 0.4% dry-bulb cooling design temperature with maximum value 33.2 OC, minimum value 27.1, and a Coincident wet-bulb temperature value is 22.3 OC, the climate zone used in ASHRAE 2B.\n\nThe building activity template is “office buildings” as the ASHRAE 90.1 Settings for heating source is “fossil fuel”, the occupancy density (people/m2) = 0.05 based on the building survey.\n\nFor the Environmental control the heating set point temperatures for heating is 20.0 °C, and heating set back is 13.0 °C, the cooling set point temperatures cooling is 26.0 °C, and the cooling set back 32.0 °C. the computers and office equipment supplied to each zone according to the building visit.\n\nThe building constructions for the exterior wall the U-value equals 2.094 (W/m2-K), and for the internal partitions equals 1.490 (W/m2-K), and the typical floor equals 2.353 (W/m2-K).\n\nFor the opening the external windows layout using wall façade types for 40% vertical glazing ASHRAE 90.2 Appx with a single layer of generic Clear 6 mm glass panel.\n\nThe lighting system through ASHRAE classification is space-by-space method with HVAC template is fan coil unit (4-Pipe), Air cooled.\n\nAll these parameters also applied for the post implementation scenario expect proposing a shading device (Vertical and horizontal Louvers) for the curtain walls windows as described and switching single glazing to double glazing additionally adding 30% operable windows externally and internal windows to allow cross ventilation.\n\nThis paper will follow four parts:\n\n1.4.1 Literature review: Involves studying the definition of well-being, what are the main points that lead to achieving it and learning the WELL Building Rating System, which focuses on the study of people and how to make them thrive, to reach a design solution to improve the performance, productivity, and health of building occupants.\n\n1.4.2 Qualitative study: Performed to see how different buildings and companies implement different design strategies to improve the overall health performance of their employees and how it all reflects on their productivity. The analytical part will include analysing the WELL framework and studying existing office building examples to understand how to improve the design strategies in Egypt to increase productivity.\n\n1.4.3 Quantitative study: Concluding a checklist to be implemented in Egypt office spaces designed to improve productivity and well-being of employees and implement it in the case study office.\n\n1.4.4 Practical part: Implementing the design strategy on a single office in the chosen case study building, “Cairo Petroleum Complex” office building in Alexandria/Egypt, using the computer software DesignBuilder to compare the simulation results to the same office pre-implementation. DesignBuilder is a paid computer software that has a free 30-day trial period. Alternatively, a free version of TRNSYS is available to use.\n\n\n2. Results\n\nAccording to the “Health, Wellbeing & Productivity in Offices” research article published by the World Green Building Council (WorldGBC), among other research concluded that the critical factors in designing powerful office space to boost productivity and well-being are location, layout, size, appeal, atmosphere, and the dimension of the area.12–15\n\nIn 2012, workspace design studies concluded that the average office space per employee was around 5.4 to 6.5 m2 and approximately 10 m2-16.4 m2 for an office room (see Figure 1 and Figure 2).16\n\nOther studies, like the research done by the British Council for Offices (BCO), concluded that the average density in offices was around 14.8 m2/employee in 2001 and decreased to 9.6 m2/employee in 2018 (see Figure 3).17 From 2000 to 2012, the average space per employee decreased by about 21% due to the growth in flexible workspaces and remote working trends.18\n\nBetween 2010 and 2012, the area per employee decreased from 21 m2 to 16.4 m2 (see Figure 4).16 At the start of the 21st century, this number was as high as 30.2 m2.18 By contrast, with employers concentrating on returning to the office while maintaining physical distance in response to the COVID-19 pandemic, the amount of space per worker began increasing again.16 While there is no single size that fits all types of businesses, US research showed that in 2020 the average area per employee increased from 16.4 m2 to 18.2 m2 (see Figure 4) (considering various needs depending on the kind of work done in that space).16 This considers dedicated desk space and surrounding spaces such as meeting rooms and shared areas.19 Additionally, The British Council for Offices suggests a generous allocation of space based on people rather than desks to satisfy companies’ current requirements for maximising staff performance and comfort by providing a range of settings at work.20 This report points out that with a 10-12 m2 ‘Sweet Spot’ for each person, most common workspace issues like overcrowding and noise pollution can be addressed. On the contrary, higher office densities with less than 8 m2 per person are more likely to cause complications and negatively affect occupant comfort, well-being and performance for most businesses20 (see Figure 5 and Figure 6).\n\nIt was also believed that the way density is measured can vary depending on the degree of enclosure (e.g., open plans and screens/partitions, etc.) and the office design and desk layout all influence the effect of office density on employees’ productivity.17\n\nConsidering the recommendation to increase the size of the average workspace per person by 50% as a precautionary measure against COVID-19.19 Some companies followed the ‘Hybrid work schedule’ method (assigning half the employees to work remotely and switching shifts the following week) while maintaining the same office footprint. In contrast, others chose to apply the distancing in a larger office or reduction of employees.21\n\nAt the start of the 21st century, companies realised the significance of their office setting. Now, when designing a workspace, there are some standard key considerations13,14:\n\n• Location: amenity-rich central location.22–24\n\n• Appeal/Utilization (e.g., relaxed dress codes, a splash of colour, natural light, greenery, soft furnishing, Etc).23–26\n\n• Well-being (biophilic design, the distance between desks, areas for socialising, opportunities for fresh air, self-care amenities, private mothers’ rooms, fitness amenities, things that are meaningful for the users).9,22,23,27\n\n• Flexibility (e.g., open plan with flexible seating areas, Open and private offices, staff rotating schedules for remote and office attendance, ETC).9,21,22,25,27\n\n• Designing the office by noise level (e.g., Public, Semi-Private, Private, adding a space for employees to unwind, ETC).21,25,26\n\n• Good Design (Passive solutions, shading, natural ventilation, and daylight when possible).9,24\n\n• User in control (giving occupants control over their indoor environment).24\n\nWith this in mind, we look at some of the supreme paradigms of successful office buildings that applied unusual design strategies to enhance employee productivity.\n\nGoogleplex\n\nWith around 190 km2 footprint of office space in California, USA (see Figure 7). Clive Wilkenson Architects Firm designed the building to mimic the university campus feel and merge the idea of the workplace with the experience and knowledge found within the educational environment. By applying 13 different office settings, the building components were proven effective in boosting employees’ well-being, ergo productivity. Google aimed to decrease everyday concerns and stress by providing all daily needs in one campus.28 The building registered a 31% increase in revenue in 2013,29 which means their philosophy benefited the company (see Table 1 for building content).\n\nAmazon Spheres\n\nAt 299.6 m2 footprint located in Washington DC, USA (see Figure 8).30 The Amazon Spheres was designed by NBBJ with the idea of mimicking the forest atmosphere while still being in touch with the urban areas’ comfort and luxury. After doing their research, they found that nature decreases stress, reduces cortisol levels and improves focus, and that’s how they came up with the building’s concept (see Table 2 for buildings content).30\n\nBy analysing the past examples and studying Table 1 and Table 2, we conduct a replicated design criteria followed by the two companies to boost employee productivity. Thus, the following table concluded the best design criteria for office buildings to increase the productivity and well-being of their employees (see Table 3).\n\n\n3. Occupants’ well-being ranking systems\n\nThe WELL Building Standard (WELL) created by the International WELL Building Institute (IWBI) is a cutting-edge rating system that considers energy use, water consumption, waste production and other environmental impacts, as well as several socioeconomic measures. This has helped lead to the increasing global importance of green building construction and design that works towards creating a workspace where employees can thrive.39\n\nWELL is a holistic approach that needs the equal effort of four aspects: Design, Operation, Behaviour, and People for it to succeed. WELL is designed to complement other top-tier green building standards while conducting thorough research into how the building environment can be improved for its occupants. As a result, projects are encouraged to seek dual certifications from both WELL and green building standards to achieve higher quality results.\n\nIWBI upgraded WELL V1 (consisting of seven concepts and three point-based scorings) to WELL V2 in 2018 (see Figure 9 for a detailed WELL timeline), which includes ten concepts and four point-based scorings. These include Air, Water, Nourishment, Light, Mind, Movement, Materials, Thermal Comfort, Sound and Community.39\n\nThis paper will discuss solely the concepts that have an architectural value to apply to the design strategies in Egypt (see Figure 10. For selected WELL concepts content categories).\n\nSource: IWBI.\n\nThe recent Global Burden of Disease study put household air pollution as the 10th highest cause of poor health for the world’s population,40 making it one of the most important concepts within WELL. Light has also been shown to profoundly impact occupants’ moods and symptoms of depression.41 For this reason, WELL looks to provide an environment where light can positively affect sleep quality and reduce circadian phase disruption to promote better moods and productivity.\n\nThe WELL Movement concept encourages physical activity, movement, and active living and discourages sedentary behaviour [1] from combating the global trend of physical inactivity. In 2016, more than 23% of adults were reported as physically inactive,42 and a 2011 study suggested that adults worldwide sit for 3-9 hours each day.43 This sedentary behaviour has been linked to obesity, type II diabetes, cardiovascular risks, and premature mortality.44–48 If just 10% of this physical inactivity was reduced globally, it is estimated that at least 500 000 deaths could be prevented annually; reducing physical inactivity by 25% could result in over 1 million fewer deaths per year.48\n\nThe WELL Thermal Comfort concept strives to maximise thermal comfort and accommodate individual preferences, resulting in higher productivity levels using improved HVAC system design and control. Where we live and work can be significantly impacted by thermal comfort; thus, it is one of the most critical factors influencing building satisfaction. This includes individual motivation levels, alertness, focus, and mood.49\n\nMental health is essential for individuals to reach their full potential, cope with everyday challenges, work productively, and give back to the community.50 Unfortunately, mental health issues and substance abuse affect 13% of the global burden of disease, accounting for up to 32% of years lived with disability.51 1 in 6 adults suffer from common mental health conditions such as depression, anxiety, or substance abuse at any given moment, and over 30% will experience a mental health condition throughout their lives.52 These conditions also profoundly impact the workplace - impeding daily productivity and costing the global economy $1 trillion.53 The WELL Mind concept seeks to address this issue by implementing design strategies that support cognitive and emotional health through prevention and treatment efforts - this can significantly improve individuals’ short-term and long-term mental well-being.\n\nFinally, the WELL Sound concept prioritises occupants’ health and comfort by identifying and addressing acoustical parameters in built environments to improve the user experience.\n\nFollowing this general introduction to WELL Building Standards’ six Architectural based concepts is the conducted checklist to implement in office buildings in Egypt.\n\nThe WELL Building Standard centres around ten core concepts, each contributing to creating a healthy living and working environment. Six of these ten concepts are particularly relevant to architecture design: air, light, movement, thermal comfort, sound, and mind. These concepts will be discussed in more detail below:\n\nAir\n\nChoosing four key features from the Air concept, each with its own set of points, ensures these goals are met.\n\nThe first feature is Enhanced Ventilation, where automated air conditioning systems should supply conditioned air through individual diffusers positioned 0.8 m above the occupants’ heads.\n\nThe second feature is Operable Windows, which provides access to natural ventilation when possible. At least 75% of occupied spaces should have operable windows of at least 4% of the floor area, and these should be designed with universal access in mind so they can be operated easily without tight grasping or twisting of the wrist.\n\nPollution Infiltration Management is the third feature, where the entryways of regular entrances (excluding terraces) should use entryway design elements such as grilles, grates, slots, or roll-out mats that have widths of at least 3 m and length in the circulation direction.\n\nFinally, Source Separation examines separating rooms with high-volume printers, copiers, and humidity using automatic operating doors and negative-pressure exhaust fans that redirect outside air into higher-pressure areas.39\n\nLight\n\nThis concept is centred around the idea of light exposure with six selected features. The first feature is Light exposure focusing on the interior layout. 30% of all occupied areas must be within 6 meters of envelope glazing, and common areas must have seating for at least 15% of regular occupants, with a 5-meter distance between seatings and envelope glazing for 70% or more of said seating.\n\nThe second feature is Visual Lighting Design - 90% or more of space types in the project area must meet illuminance thresholds based on their purpose (offices need 320 lux at task surfaces while lobbies, atriums, and transition spaces need a minimum of 110 lux at floor levels). Eateries, lounge, and restroom levels are required to achieve a minimum of 110 lux at the task surface).\n\nCircadian Lighting Design is the third feature - meeting lighting requirements for day-active people such as applying light levels on vertical planes at eye level, achieving 4 hours (min. start by noon) of light over work surfaces at 45 cm height and 140 cm in the centre of all seating areas and kitchens.\n\nElectric Light Glare Control follows this as the fourth feature - buildings needing strategies to manage glare from electric lighting either through luminaire, considerations that limit UGR values to 16 or lower, and luminance do not exceed 6,000 cd/m2 between angles 450-900 from nadir; or through space consideration where UGR values must also be 16 or lower.\n\nDaylight Design Strategies is the fifth feature - two options present themselves: 70% of workstations within 7.5 m from transparent envelope glazing with VLT > 40%, 15% minimum envelope glazing area, or 70% within 5 m with VLT > 40%, 25% minimum envelope glazing area; both facilitated by solar shading in manual mode controllable by occupants (opening throughout the working day), automated shading for glare prevention.\n\nLast up is Occupant Lighting Control - ambient lighting systems should be in place per 60 m2, one per 10 occupants’ zones; differing criteria if rooms are smaller than needed or occupancy is lower than allocated quota; plus supplemental lighting available controlled by occupants.39\n\nMovement\n\nThis concept focuses on creating a healthy and comfortable working environment. There are four selected features in this concept. The first feature is Ergonomic Workstation Design which requires a minimum of 25% of workstations to be adjustable by users to support standing and seated positions. This includes flexible device heights, chairs, anti-fatigue mats or impact-reducing flooring, toe space, and footrests/footrails.\n\nThe second feature is Circulation Network which looks at aesthetically designed staircases with music, artwork, light levels, access to daylight and natural design elements for each floor. Visible stairs should be promoted over elevators and escalators from the entry-level onwards.\n\nThe third feature is Facilities for Active Occupants which provides cycling infrastructure with short-term bike parking located 30 m from the entrance accommodating at least 2.5% of visitors, and long-term bike parking located within building boundaries accommodating at least 5% of occupants. Furthermore, within a 200 m walk distance from the building boundary, there must be showers, lockers and changing facilities available for every 0-100 regular occupants, plus one shower per 150 occupants for every 101-999 regular occupants and 8 showers plus 1 per 500 occupants for every 1000-4999 regular occupant as well as 16 showers plus 1 per 1000 occupant for more than 5000 regular occupants with a minimum of five lockers associated with each shower facility.\n\nThe last feature is Physical Activity Spaces and Equipment, which requires the provision of an indoor activity space with dedicated fitness facilities offering two types of exercise equipment that can be used by at least 5% of building users, as well as outdoor physical activity spaces such as green spaces like parks or trails, blue spaces like swimming areas, recreational fields or courts and fitness zones.39\n\nThermal Comfort\n\nThis concept has six selected features that improve users’ thermal comfort.\n\nThe first feature is Verified Thermal Comfort. The first point under this feature is a Thermal Comfort Questionnaire - occupants must participate in an anonymous questionnaire, and the number of responses required depends on the number of occupants: if there are more than 45, then a minimum of 35% should respond, 20-45 requires 15%, and fewer than 20 requires 80%. The results of responses must also meet target satisfaction thresholds: 80% or 90%.\n\nThe second feature is Thermal Zoning. The first point is to Provide Thermostat Control for at least 90% of occupied spaces; temperature in each room must be controlled via a thermostat or digital interface accessible via a smart device; maximum size per thermal zone should not exceed 60 m2 or 10 occupants. Sensors should be placed at least 1 metre away from exterior walls, doors, windows, direct sunlight, air supply diffusers, mechanical fans, heaters etc.\n\nThe third feature is Individual Thermal Control. It includes two points. The first point provides Personal Cooling Options such as rooms/thermal zones with adjustable thermostats connected to building cooling systems that one person can regularly occupy; desk/ceiling fans; mechanical cooling system chairs; any other solutions capable of affecting a PMV change of -0.5 within 15 minutes without changing PMV for other occupants. The second point lists Personal Heating Options such as rooms/thermal zones with direct user-adjustable thermostats connected to buildings heating systems that can only be regularly occupied by one person; electric parabolic space heaters; electric heated chairs/footwarmers; any other solutions capable of affecting a PMV change of +0.5 within 15 minutes without changing PMV for others.\n\nThe fourth feature is Radiant Thermal Comfort, with Implement Radiant Heating and Cooling being the only point - at least 50% of occupied areas should have radiant ceilings/walls/floors or radiant panels attached, covering half the wall/ceiling area minimum.\n\nFifth is Enhanced Operable Windows, where Provide Windows with Multiple Opening Modes has four points: At least 70% open so no more than 1.8 m above finished floor (1 window per room); 30% open with whole opening 1.8 m above finished floor (1 window per room), Operation controls min 1.7m above the finished floor and low openings used in mild/warm weather, high in cold weather.\n\nThe last feature is Outdoor Thermal Comfort which consists of two points: Manage Outdoor Heat where pedestrian pathways and building entrances must have tree canopies, awnings or other structures providing shade for ≥50%, parking spaces ≥25%, plazas seating areas and other outdoor areas covered between 25%-75%; Avoid Excessive Wind where 5 m/s not expected more than 5% hours yearly in seating areas and 10% on paths and parking lots while 15 m/s no more than 0.05% hours throughout the year across all areas.39\n\nSound\n\nThis concept has three selected features, starting with sound mapping as the first feature, offering an Acoustic Design Plan. Sound barriers are the second feature, with Doors and Walls Sound Isolation Design as its primary point. Lastly, Impact Noise Management is the third feature, with Specify Impact Noise Reducing Flooring being its main point.39\n\nMind\n\nThere are five selected features in this concept. The first feature is devoted to promoting mental health and well-being with a dedicated space for restoration and relaxation, as well as work policies allowing breaks.\n\nNature and Place is the second feature that establishes a connection to nature through materials, patterns, shapes, colours, images, or sounds. It also entails celebrating culture and the integration of art.\n\nThe Restorative Opportunities feature, which is the third feature, provides a nap space and policy with at least one acoustically and visibly separated environment in a designated quiet zone, plus one reclining furniture for every 100 employees.\n\nThe Restorative Spaces is the fourth feature and offers an environment considering specific criteria such as lighting, sound, thermal comfort seating arrangements, calming colours, textures, and forms.\n\nLastly, the Enhanced Access to Nature fifth feature guarantees that 75% of workstations and seating areas have views of indoor plants/water/natural elements, and 70% of outdoor spaces include plants or natural elements within 200 m walk distance from the rooms available to occupants.39\n\nCreating a productive office environment is essential for any business to succeed. After studying WELL concepts, other sources stated that the most critical factors for achieving success in office buildings are natural air, ventilation, and thermal comfort.10,54 Good indoor air quality helps keep employees energised and productive while keeping air-borne diseases at bay. Quality ventilation systems help ensure that fresh air constantly enters the office, aiding in concentration and morale. Additionally, thermal comfort should be considered to prevent uncomfortable working conditions due to too hot or cold temperatures. All these elements combined create the perfect workspace environment where productivity can flourish. Thus, those are the three points that will be focused on in the design implementation.\n\nEmployee productivity significantly impacts profits, yet it isn’t something that can easily be measured, and it’s not a one-size-fits-all rule to follow. Meanwhile, companies use three standard productivity calculation methods to measure productivity. This has nothing to do with what employers think of their employee’s performance because their opinion can be wrong.\n\nOne way to evaluate the impact of physical features on employee productivity is by collecting data such as physical features, outcome metrics (e.g., physical complaints) and HR department data (e.g., worker attitudes, performance data, absenteeism, medical costs, retention rates etc.), as well as financial directors’ data concerning revenue and financial metrics. These can be used to compare and calculate the overall effect on employee productivity.\n\nAnother method used is the direct use of the Labour Productivity Formula, a simple equation derived from the basic definition of productivity. It is output per unit input; you can use it to track productivity per individual, team, or even department.55\n\nFor example, an organisation produced goods or services worth $100,000 in 2000 hours. The output is worth $100,000, while the input is 2000 hours. Then, using these values in the formula, we get:\n\nOf course, in this equation, we calculate the work hours, not the paid hours (as paid hours can mean vacation pay and sick leave salaries, too).56\n\nNext is the Percentage of Goals Met method; companies’ productivity levels are synonymous with the number of goals employees accomplish. By calculating the percentage of goals met, we can determine where the workforce stands regarding efficiency.57\n\nFor example, an architectural firm gave their junior architects the goal of submitting 30 villa concepts within a week. The firm’s team submitted 45 concepts, then the percentage goals met will be:\n\nThis implies that the firm’s junior team met 150% of the goal.\n\nAfter analysing and reviewing the previous examples and various sources, it was determined that the three most influential features for improving building occupant productivity are natural light, natural ventilation, and thermal comfort. With this in mind, we have identified several features that can be easily implemented in existing buildings in Alexandria/Egypt (see Table 4).\n\n\n\n• 75% of occupied areas have operable windows.\n\n• Minimum 4% area of net floor area.\n\n• Weather indicator light.\n\n• Manual shading controllable by occupants.\n\n• Automating shading to prevent glare.\n\n• Operable windows must be opened at least halfway, with the maximum height from the finished floor not exceeding 1.8 m and a minimum dimension of 0.3 m for the smallest opening.\n\n• Window operation control is at least 1.7 m above the finished floor.\n\n• Low opening windows for mild/warm weather.\n\n• High opening windows for wintry weather.\n\n• Easy to operate windows with minimum use of force and operates single handily, with enough space around it to operate.\n\n\n\n• Within a 5 m distance between seatings and envelope glazing, VLT > 40%\n\n\n\n• Minimum 320 lux at task surface.\n\n\n\n• The necessary light levels should be achieved from a height of 45 cm above the work plane.\n\n• Regular users can control their own lighting environment with manual controls found in the same area as each light zone.\n\n• Minimum one portable supplemental light is available.\n\n\n\n• Height adjustable desk.\n\n• Height and depth adjustable chair.\n\n• Height adjustable devices.\n\n• Footrest.\n\n• Recessed toe space (min. 10 cm depth and height).\n\n\n\n• Availability of thermostat in the room.\n\n• Temperature sensors should be positioned at least 1m away from exterior walls, doors and windows, direct sunlight, air supply diffusers, mechanical fans, etc.\n\n• Radiant panels with minimum coverage of half the wall.\n\n\n\n• Design elements that celebrate culture and space, integration of art, and human delight.\n\n• View of indoor plants and/or water and natural elements.\n\n\n\n• Doors and walls sound isolation design.\n\n\n4. Case study building\n\nFor the purpose of this paper, we focused on the “Cairo Petroleum Complex”, a medium-sized office building, as our case study. Access to the building and its blueprints have been granted to measure natural ventilation, daylighting, and thermal gain through simulations in DesignBuilder computer software for both base case and after criteria implementation.\n\nThe “Cairo Petroleum Complex” office building is located in Alexandria/Egypt, on the Alexandria-Cairo desert road, km 17.5. Alexandria’s climate is Mediterranean, with January and February the coolest months, featuring an average daily maximum temperature of 9 to 19 °C. July, August, and September are the hottest months, with an average daily maximum temperature of 30-31 °C (see Figure 11).\n\n“Cairo Petroleum Complex” Office Building was designed in 1995 and finished construction in 2000 (see Figure 12). It is composed of a total of 3370 m2, with a rectangular shape measuring 60 m × 67 m and a height of 20 m, consisting of a ground floor and four typical floors. It is structured using reinforced concrete, with blue double-glazed curtain walls and aluminium frames, and no exterior shading. It accommodates 600 employees arriving at 8 a.m. until 4 p.m. for their eight-hour shifts on weekdays, aside from the control rooms, which operate 24/7. Presently, the building rents offices to eight different companies and a single bank. The offices are mechanically ventilated, with exterior walls constructed out of 20 cm brick, 2 cm exterior and interior plaster combination, and a total U-value of 1.5 W/m2K. Meanwhile, the window-to-wall ratio across all elevations is 80%, except for the 90% that the North and Northwest double-glazed curtain walls have, with a U-value of 2.7 W/m2K. Due to this, high mechanical loads are expected due to heat gain on the south and east-facing elevations. The northeast, northwest, southwest, and southeast elevations have 880 m2, 198 m2, 1072 m2, and 960 m2 of unshaded windows exposed to direct sunlight, totalling an overall exposed window area of 4010 m2. The building contains four single-glazed skylights with a combined area of 240 m2 and a U-value of 3.7 W/m2K located above the primary court, with a flat, insulated roof with 3130 m2 of reinforced concrete, interior paint, and insulation material with a U-value-of-0.5-W/m2K (using the DesignBuilder computer software to identify the U-value within the building).58\n\n“Cairo Petroleum Complex” office building is a perfect example of modern architecture in Egypt, demonstrating an advanced mechanical ventilation system and a façade made mostly of curtain walls (see Figure 13). However, this combination has created various issues within the building due to thermal gain and glare caused by inadequate shading devices causing the West and South offices to be uncomfortable for employees to work in (see Figure 14 for solar path diagram and selected office).58 Additionally, the building has inadequate natural ventilation as some facades have only 25% of the windows operable while others have none. Together these difficulties form a complex challenge requiring detailed consideration to ensure comfortable conditions with minimal energy consumption.\n\nAccording to the employees’ statement, we chose a standard office room on the typical floor located on the South-East façade that was reported to suffer from thermal heat gain from the exterior façade and direct sunlight (see Figure 15). We apply the following modifications to the selected office for comparative simulation:\n\n• Curtain Wall: Designing different height operable windows in the façade to allow natural ventilation, higher operable windows for winter, and lower operable windows for summer. Operable windows must be opened at least halfway, with the maximum height from the finished floor not exceeding 1.8 m and a minimum dimension of 0.3 m for the smallest opening. Window operation control is a minimum of 1.7 m above the finished floor.\n\n• Shading: Application of automatic shading devices of curtain wall facades (louvres) to decrease direct sunlight entering the offices and eliminate glare.\n\n• Cross Ventilation: Applying a high operable window opposite the curtain wall creates cross-ventilation.\n\n• Circadian Lighting Design: The necessary light levels should be achieved from a height of 45 cm above the work plane.\n\n• Location of Furniture: The distance between envelope glazing and seating area is within 5 m, VLT>40%.\n\nThe photos (A), (B), (C), and (D) were acquired from the researcher’s work on the “Cairo Petroleum Complex” office building using Autodesk: AutoCAD software.\n\nA modelling validation method was needed to conduct reliable results for modifying the base case model based on the comparison between observation and simulation. Through various modelling validation parameters, we selected “the Correlation Coefficient” parameter. The Pearson product-moment correlation coefficient, also known as “the correlation coefficient [2],” is a widely used statistical tool that measures the strength of the relationship between two variables. The correlation coefficient ranges from -1.0 to 1.0 and indicates the relative movements of the two variables being measured. A value of 1.0 indicates a perfect positive correlation, while a value of -1.0 shows a perfect negative correlation. A value of 0.0 indicates no relationship between the two variables. Pearson’s correlation coefficient is denoted by R, with R2 representing the squared value of the correlation coefficient. It is commonly used in various scientific fields.59\n\nThe formula states:\n\n“r” stands for “the correlation coefficient”, “n” stands for “number in the given dataset”, “x” stands for “first variable in the context”, and “y” stands for “second variable”.\n\nBy comparing the temperature data from the previous Figure 11 of Alexandria’s 2023 monthly weather data chart and the base case resulting data from DesignBuilder software, we conduct the following table:\n\nBy using the variables from Table 5 in the Correlation n Coefficient formula, we get the following results (see Figure 16):\n\nThe results show R2 = 0.993, which is within the acceptable range of the correlation coefficient -1 and 1, thus indicating that the base case results are valid, reliable, and applicable.\n\nThe following analysis diagrams compare the office base case and post-implementation results. Starting with the direct sunlight simulation results.58\n\nUsing DesignBuilder computer software to simulate the base case of direct sunlight entering the office, we find that January and October are the highest recorded sunlight rate entering the building. January recorded direct sunlight of 7335-9168 lux reaching around 28% office space, while 60% is Indirect daylight of about 5502 lux, and 12% is daylight 0-1836 lux. April records 27.1% direct sunlight of around 12911 lux, 9.1% 10329 lux, 1.6% 5165 lux and the rest 62.1% between 0-2583 lux. July records 21.7% direct sunlight of 11364 lux, 7.9% records 9092 lux and the rest, 70.4%, records between 0-4548 lux. Lastly, October records 30% direct sunlight of 9449-11811 lux, 35% indirect sunlight of around 7087 lux, and the other 35% records 0-2363 lux (see Figure 17).\n\nThe photos (A), (B), (C), and (D) were acquired from the researcher’s work on the “Cairo Petroleum Complex” office building using DesignBuilder software.\n\nWhile direct sunlight simulation post-implementation shows significant improvement and decrease in the area exposed to direct sunlight, the results were simulated after adding an automatic shading device (louvres) on the southeast façade. The results show January recorded 19% of exposed area in the range between 6798 lux to 8497 lux of direct sunlight, 27% records around 5099 lux, and the 54% remaining area are recorded at between 0-3400 lux, April records only 5.2% of the area is direct sunlight of 11623 lux, 5.9% records 6975 lux, and the rest 88.9% records between 2327-4651 lux. July records only 7.4% area of direct sunlight at 10120 lux, and the rest of 92.6% area is recorded between 2024-4048 lux. Lastly, October recorded 20% of direct sunlight area at 8909-11136 lux, 9.34% records 6682 lux, and 70.26% records between 2228-4455 lux (see Figure 18).58\n\nThe photos (A), (B), (C), and (D) were acquired from the researcher’s work on the “Cairo Petroleum Complex” office building using DesignBuilder software.\n\nComparing the base case and post-implementation results, we see that in January, there was a decrease in the total lux by 7.3% and a decrease in the direct sunlight exposure area by 9%. In April, the total lux decreased by around 10%, and the direct sunlight exposed area decreased by 21.9%. In July, total lux decreased by 10.9%, and the direct sunlight exposed area decreased by 14.3%. Lastly October, total lux decreased by 5.7%, and the direct sunlight exposed area decreased by 10%.\n\nIt was conducted through the previous studies that applying around 25% operable windows to the office façade and placing a high window opposite to the curtain wall windows creating cross ventilation, indicated an increase in air flow in the space (see Figure 19).7\n\nThe photos (A), and (B) were acquired from the researcher’s work on the “Cairo Petroleum Complex” office building using DesignBuilder software.\n\nPicture (A) Figure 19 shows the base case 3D simulation for airflow; the simulation indicates that the airflow is minor, and its velocity ranges between 0.01-0.10 m/s closer to the floor, increasing to 0.19 m/s near the curtain wall. While in picture (B), after adding windows to the façade and opposing it to create cross ventilation, the airflow increased to cover all the office area with a slight increase in the velocity ranging between 0.06-0.12 m/s all around the office while not affecting the comfort of users. The air velocity at the building envelope remains the same. Thus, making a 20% improvement in air flow.58\n\nAs for the thermal distribution analysis, providing an automatic shading system to the building’s façade along with windows that increased airflow indicated the wider distribution of cooler temperature, leading to thermal comfort. Figure 20, picture (A) shows the three-dimensional thermal distribution in the base case office to cover less area, with the average temperature for user area ranging between 17.85 °C and 19.67 °C (colour indication: orange, yellow, light green, and green). While after implementation in the picture (B), it shows the 3D temperature distribution after modification increases to cover the whole office area leading to an increase in the temperature affected by thermal gain. As the colour indication shows, the orange zone colour decreased (indicating a temperature zone of 19.67 °C), and the usable zone temperature records range between 16.49 °C and 18.31 °C (colour indication: cyan, green, and light green). Thus, the average temperature decreases by 1.37 °C, which is a 7% improvement.58\n\nThe photos (A) and (B) were acquired from the researcher’s work on the “Cairo Petroleum Complex” office building using DesignBuilder software.\n\nAs shown in Figure 21, Figure 22, and Figure 23, in January and February, air temperature decreased by 5.9%, 6% in March, 4.7% in April, 3.2% in May, 2.4% in June, 2.6% in July, 3.3% in August, 4.5% in September, 5.6% in October, 6.5% in November, and 5.7% in December.58\n\nShowing the increase in natural ventilation and decrease in solar glare and thermal gain. The photos (A) and (B) were acquired from the researcher’s work on the “Cairo Petroleum Complex” office building using the computer software “DesignBuilder” to simulate the changes on the space.\n\nShowing increased natural ventilation and decreased solar glare and thermal gain. The photos (A) and (B) were acquired from the researcher’s work on the “Cairo Petroleum Complex” office building using the computer software “DesignBuilder” to simulate the changes in the space.\n\nFor the thermal gain/solar gains exterior windows comparison simulation results, January records 34.5% decrease in thermal gain, 34.1% in February, 33.9% in March, 30.5% in April, 24.3% in May, 20.2% in June, 22.1% in July, 27.9% in August, 33.4% in September, 35.5% in October, 35.6% in November, and 34.3% in December (see Figure 21, Figure 22, and Figure 24).7,58\n\nMechanical Ventilation, Natural Ventilation, and infiltration decreased by 18% in January, 21.2% in February, 19% in March, 6.7% in April, 2% in May, no effect in June and July, 0.65% in August and September, 1.3% in October, 4.1% in November, and 15.7% in December (see Figure 21, Figure 22, and Figure 25).\n\nIn addition to providing supplemental light 45 cm above the worksurface to influence employees’ circadian rhythm. According to the future workplace wellness study and other research, it was assured that by achieving thermal comfort, natural ventilation and natural light, an increase in productivity is inevitable.10,58\n\n\n5. Conclusion and recommendations\n\nStudying WELL Building standards and other green building rating systems and recognising the success of popular existing office buildings shows great promise for improving occupants’ well-being and productivity. This is especially crucial after the pandemic, as business districts in Egypt must implement these structures to ensure a safe yet productive environment. Regarding present and future circumstances, this kind of research is increasingly vital for establishing better practices in the workplace.\n\nThis paper studies successful design criteria for existing office buildings to reach a conducted design criteria for healthy office design to enhance productivity in the workspace.\n\nBy studying successful office designs like Googleplex building and Amazon spheres, we conducted the first design criteria indicating that natural light, thermal comfort, natural ventilation, nature, and mental health design are key for a successful and productive environment.\n\nNext, by studying and analysing WELL Building Rating system concepts, we conducted the second design criteria, which explains how to achieve adequate levels of natural light, natural ventilation, and thermal comfort in addition to sound and designing for the mind to get employees to thrive in their work area.\n\nLastly, by applying our findings to the selected case study building, we see the building simulation results calculated using DesignBuilder computer software.\n\nThe simulations show that by applying the design implementations on the selected case study, the thermal heat gain was reduced after using automatic shading devices by an average of 20.2%-35.6% throughout the year, Airflow increased by 20% after adding 25% user-friendly designed operable windows to the building’s façade and opposite operable windows for cross ventilation. Lastly, adding double-glazed glass for the curtain wall and the automatic shading device enhanced the illuminance distribution, temperature distribution, and air temperature. Direct sunlight area decreased by 9% in January (Winter), 21.9% in April (Spring), 14.3% in July (Summer), and 10% in October (Autumn). Air temperature decreased by a minimum of 2.4% in June and a maximum of 6.5% in November—temperature distribution enhanced by an average of 7%.58\n\nThis paper concluded the top three effective design features from the literature review, example analysis and applying and testing their effect on a selected case study in a medium sized-office building; there is a possibility that the conducted design features can be used on an entire existing office building in Egypt. This paper proposes some criteria for increasing productivity in existing office buildings scale as well as individual workplaces, including:\n\n• Providing adequate natural ventilation and air quality through windows and cross ventilation while considering easy window operation management.\n\n• Providing adequate natural light while considering circadian rhythm design elements.\n\n• Use automatic shading devices (such as louvres, etc.) to function in all seasons.\n\n• Seeking thermal comfort, proper temperature distribution and furniture placement.\n\n• Connecting to nature boost productivity and health.\n\nIt is recommended that productivity measuring method is used to rate the existing buildings’ employees’ productivity. These productivity rates could be enhanced by using the conducted criteria. We recommend that architects and construction firms consider this design criteria in the designing phase of buildings to enhance the performance of occupants through encouraging healthy building design. Additionally, the legislative authorities and the government should be required to include conditions that support the health and well-being of occupants in the new construction law for those requesting construction permits.", "appendix": "Data availability\n\nMendeley data: Well-being as a tool to improve productivity in existing office space. Doi: https://doi.org/10.17632/d5g9vwt28s.1. 58\n\nThis project contains the following underlying data:\n\n- Adobe Photoshop [Cairo Petroleum Complex architecture plans and cross-sections presentations]\n\n- Autodesk AutoCAD [An architectural detailed plans and cross-section for the Cairo Petroleum Complex office building]\n\n- DesignBuilder [A three-dimensional simulation of the Cairo Petroleum Complex case study building for the base case and the post-implementation of the conducted criteria]\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nTED: The Economics Daily: 2022 [cited 2023 25 March]. Reference Source\n\nDONOFF E: The Energy Crises of the 70s. ARCHITECT: THE JOURNAL OF THE AMERICAN INSTITUTE OF ARCHITECTS; 2016.\n\nArnett A: Why is the WELL Building Standard Worth Striving For? 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Sports Med. 2014; 48(3): 174–177.\n\nYoung DR, et al.: Sedentary behavior and cardiovascular morbidity and mortality: a science advisory from the American Heart Association. AHA Journals: Circulation. 2016; 134(13): e262–e279.\n\nChau JY, et al.: Daily sitting time and all-cause mortality: a meta-analysis. PLoS One. 2013; 8(11): e80000.\n\nPatterson R, et al.: Sedentary behaviour and risk of all-cause, cardiovascular and cancer mortality, and incident type 2 diabetes: a systematic review and dose response meta-analysis. Eur. J. Epidemiol. 2018; 33: 811–829.\n\nBiswas A, et al.: Sedentary time and its association with risk for disease incidence, mortality, and hospitalization in adults: a systematic review and meta-analysis. Ann. Intern. Med. 2015; 162(2): 123–132.\n\nNicol JF, Humphreys MAJE: Adaptive thermal comfort and sustainable thermal standards for buildings. Buildings. 2002; 34(6): 563–572. Publisher Full Text\n\nMental health: strengthening our response. Fact sheets. 2022 [cited 2023 15 Feb]. Reference Source\n\nVigo D, Thornicroft G, Atun R: Estimating the true global burden of mental illness. Lancet Psychiatry. 2016; 3(2): 171–178. PubMed Abstract \| Publisher Full Text\n\nSteel Z, et al.: The global prevalence of common mental disorders: a systematic review and meta-analysis 1980–2013. IEA: Int. J. Epidemiol. 2014; 43(2): 476–493.\n\nMental Health and Substance Use: Mental health at work. [15/2/2023]. Reference Source\n\nMeister JC: The #1 Office Perk? Natural Light. Harvard Business Review. 2018.\n\nSchreyer P, Pilat D: Measuring productivity. J. EconPapers. 2001; 2001(2): 127–170. Publisher Full Text\n\nStatistics, U.S.B.o.L: HOW IS PRODUCTIVITY MEASURED? Labour Input. [cited 2023 9 March]. Reference Source\n\nMiller K: 7 best ways to measure productivity of employees. AboutLeaders. 2023.\n\nHamadah M: Well-being as a tool to improve productivity in existing office space. Mendeley Data. 2023. Publisher Full Text\n\nSoftware, A.a.M: AgriMetSoft. R2 (correlation coefficient).2019 [cited 2023 6 april]. Online Calculators. Reference Source\n\n\nFootnotes\n\n1 Sedentary behavior is distinct from physical inactivity and is characterized as very low-intensity, low-effort activities, such as sitting.\n\n2 The correlation coefficient was developed by Karl Pearson in the 1880s based on an idea from Francis Galton, with the mathematical formula established by Auguste Bravais in 1844." }	[ { "id": "183497", "date": "05 Jul 2023", "name": "Osama Omar", "expertise": [ "Reviewer Expertise Environmental Studies", "Sustainable Design", "Zero Energy Buildings", "Smart Cities", "Intelligent Buildings", "Sick Building Syndrome" ], "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,\nI would like to thank the author/s for their effort.\nA significant effort has been made by the authors to improve the design strategies in Egypt to increase productivity through concluding a checklist to be implemented in Egypt office spaces designed to improve productivity and well-being of employees and implement it in the case study office. But there are some minor comments that need from authors to modify it to enhance the research:\nIn Abstract: I prefer if the author can rewrite the Methods with more summarized and clarification for what he/ she mentioned in page 3 & 4.\n\nIn Keywords, The authors should be more specific and presize when select the keywords. For Example, post-pandemic office buildings design standards its too long to be a keyword. For that, I prefer if the author can change the keywords to be like the following: Well Standard, Sick Building Syndrome, Occupant`s Productivity, well–being framework, Office Building Design.\n\nIn the Introduction: it`s so brief and short. So, I prefer to expand the references in this area especially in Introduction with more updated references related to the topic specially when it come to the references, most of references exceed more than 10 years.\n\nThis paper focuses only on Well Building Rating System and ignores Pyrmid Rating System, so I recommend the author add a comparison part in the introduction and mention the missing parts between them.\n\nDue to the different weather and architecture features in Egypt, the selected examples on page 8 & 9 are not relevant to the case study in Egypt. In that case, I suggest the author remove them from the paper and keep Tables 1, 2 &3 as a summary of design features from international examples.\n\nIt would be better if the author provide the WELL Check list criteria as mention in page 13 (10 core concepts) for Building Certification. Also, Its more important to clarify for the reader why the authors focus on just six concept as mention in first line in page 4.\n\nIn page 27, 28 the word conclusion were repeated twice in section 5.1 and section 5.2.\nBy the end, I want to say that you did a great job and all this comments is to encourage the author to enhance the quality of paper.\nThank you for your efforts.\nBest Wishes\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nIs the work clearly and accurately presented and does it cite the current literature? 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\n\nIs the case presented with sufficient detail to be useful for teaching or other practitioners? Yes", "responses": [ { "c_id": "10415", "date": "14 Dec 2023", "name": "Miral Hamadah", "role": "Author Response", "response": "Dear Dr.Osama, we are grateful for the time and effort you've invested in providing such comprehensive and insightful feedback on our manuscript. Your comments have been instrumental in improving the quality of the paper, and we appreciate your suggestions. In response to your comment about the abstract's Methods section, I have made revisions for more clarity and succinctness. However, I would like to note that the brevity was necessitated by the 300-word limit on the abstract, which compelled a more concise approach. I have accommodated your feedback regarding the specificity of the keywords. The suggested terms 'Well Standard', 'Sick Building Syndrome', 'Occupant`s Productivity', 'well–being framework', and 'Office Building Design' have now been incorporated into the revised manuscript. Following your advice, I have added more recent references related to the subject matter, enhancing the paper's relevance and depth. As for the focus on the WELL Building Rating System, it was chosen due to its emphasis on well-being design features impacting workforce productivity and being a complementary system to other green building rating systems. The Green Pyramid Rating System, while valuable, wasn't included because of its lesser adoption by buildings in Egypt, making it challenging to study, and as other green building rating systems does not necessarily focus on aspects directly impacting productivity. However, I value your suggestion and will contemplate including a comparative analysis in future research. As the aim of this paper was to maintain a clear and focused narrative on the influence of WELL's well-being design features on productivity, which is why additional information on other green building systems was omitted. The examples of Googleplex and Amazon Spheres were chosen for their recognized success in office building design. While these examples may not directly correspond to Egypt's architectural and weather conditions, they offer valuable insights that can be adapted to various contexts. Nevertheless, I have made modifications to Tables 1 and 2 for better clarity. I have elaborated on the WELL Building Standard's 10 core concepts in response to your feedback. A detailed explanation of why only six of these concepts were focused upon has been provided in the revised manuscript. These specific concepts were selected due to their design-oriented nature and direct impact on workforce productivity, making them integral elements in the context of this research. In response to the suggestion about providing a complete WELL Building Standard checklist, it is important to note that due to its extensive nature, incorporating the full list directly into the paper might disrupt the flow and conciseness of the content. However, I acknowledge that this information could be beneficial for the comprehensive understanding of the topic. Thus, I recommend referring to the official WELL Building Standard website which has the complete and most updated checklist and can be easily accessed (https://v2.wellcertified.com/en/wellv2/overview/) for a comprehensive understanding. Lastly, the repetition in subtitles was an oversight and has been corrected in the revised manuscript following your keen observation. Once again, thank you for your perceptive feedback. Your comments have significantly contributed to improving the paper's quality and coherence. Best Regards. Miral H." } ] }, { "id": "183493", "date": "10 Jul 2023", "name": "Mark Mulville", "expertise": [ "Reviewer Expertise Building performance evaluation" ], "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 is clear and concise, the 'methods' section here could include (in brackets) what specific data is collected. There are too many key words - 5-6 is plenty (unless journal requires more).\n\nThere is a clear rationalle for research of this type - it highlights the disjointed approach to building design vs building operation and the reality of occupant satisfaction/comfort/productivity/health.\nSome of the sentences could be revised for better flow, i.e. first sentence in section 1.0. The work could generally do with a review to ensure the flow of writing is easy to follow. Some of the sentences in the work are very long - try to stick to a maximum of 40 words in the sentence.\nParagraph three in section 1.0 the first sentence needs to be supported with a reference, likewise first sentence in paragraph four - the work should be reviewed to ensure all such statements are fully referenced.\n\nSection 1.2 is it just Architects and Construction Firms? I would think the entire design team needs to be involved. Construction firms will build what they are instructed to (as long as it meets relevant requirements). Building Services Engineers will be important in this as will those who set regulations/policy.\nSection 1.3 how many office buildings in Alexandria? 3? On what basis where they chosen? Do you have permission to name the specific buildings (if they are the case studies used) - this is potentially a significant issue - my approach would be to describe the type (i.e. a high end cooperate head quarters, of x size, design etc, built in xxxx.)\nI would like to see section 1.3 revised to add clarity - perhaps a diagram would be of help, I currently find it difficult to follow the methods. Is it three case study buildings or four? on what basis where the specific criteria to be evaluation chosen?\nMethodology and method mean different thinks, but are used interchangeably here\nI would like to see more detail on how the data collection was carried out - it would not be possible to gather all of this information through a walk through, what 'other sources' were used?\n\nSometimes in the work past tense is use then present tense in the next sentence, this could be revised to help the flow of the work.\nIn terms of the model creation, more detail on data collection is needed to ensure the reader understands the level of accuracy. The overall section needs revision as I am not clear why one model was built when there seems to be multiple case studies?\nWas any monitoring of actual environmental conditions in the building(s) carried out?\nSection 1.4 should be earlier in the work\nSection 2.0 is titled 'results' but in reality this is a literature review - consider renaming this section\nI do not understand the statement in section 2.2 that the building increased its revenue in 2013 - this linkage between the design and revenue generation seems tenuous as it is presently presented.\nThere is a good deal of literature highlighting the importance in indoor air quality, light, noise, configuration, privacy etc and the impact on occupant health, wellbeing, productivity (which the WELL standard was developed as a result of). At present there is, in my view, a lack of depth in the literature review in relation to these factors. Some interesting case study buildings are presented, but the link between their design and the wellbeing/health/productivity benefit and reason for this is not fully explored. There is quite a bit of descriptive text in relation to the WELL standard - it would be of greater benefit to utilise the literature to demonstrate why specific factors are of importance.\nProvide the sources and a rationale for the chosen design criteria in table 4.\nIs it a single case study building being used? the methods section seemed to suggest multiple case studies. Is the office building in section 4.2 the one that was modelled in DeisgnBuilder? the description of the building may be better placed in the methods section.\nSection 4.4 may also better fit in the methods section.\nSome of the data described in section 4.6 would work better in a table.\nThe modelling work is interesting, but I believe the data could be better presented to max it easier to follow/compare. In the text then the focus could be on the implications etc.\n\nIs the background of the case’s history and progression described in sufficient detail? Partly\n\nIs the work clearly and accurately presented and does it cite the current literature? 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? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes\n\nIs the case presented with sufficient detail to be useful for teaching or other practitioners? Yes", "responses": [ { "c_id": "10417", "date": "14 Dec 2023", "name": "Miral Hamadah", "role": "Author Response", "response": "Dear Dr. Mark, Thank you for your detailed feedback and constructive criticism. We appreciate your time in helping to improve the manuscript. First, i would like to clarify that the revised manuscript sections has been rearranged for better flow and clarification. In response to your suggestions, the following major revisions have been made: 1. Regarding the clarity and conciseness of the abstract. In response to your suggestion, I have now amended the 'methods' section of the abstract to include specific details about the data collected in this study. 2. Regarding the keywords, I acknowledge your recommendation for a more focused selection. The list has been revised and narrowed down to six keywords that accurately reflect the core themes of the paper. However, I would like to note that the initial extensive list was due to certain journal requirements. 3. Regarding the flow of the manuscript and the length of the sentences. In response to your comments, I have revisited the document and made necessary revisions, particularly focusing on the first sentence of section 1.0 and other similar instances throughout the text. The aim was to improve the overall readability and ensure that the narrative is easier to follow. Moreover, I have tried to adhere to your recommendation of keeping sentences within a maximum limit of 40 words. 4. Regarding referencing in the manuscript. I understand the importance of properly citing all statements that are not common knowledge, and I appreciate your attention to detail in this regard. In response to your feedback, I have thoroughly reviewed the document, particularly focusing on paragraph three in section 1.0 and the first sentence in paragraph four. References have been added wherever necessary to support the statements made. 5. Section 1.2. I concur with your observation that the entire design team, not just architects and construction firms, plays a crucial role in the process. As per your suggestion, the section has been revised to reflect this broader perspective. It now emphasizes the importance of collaboration amongst all stakeholders, including Building Services Engineers and regulators, who indeed have significant contributions to make. 6. In response to your comments, I have revised Section 1.3 to clarify that the case study pertains to a single office building in Egypt, not three or four as may have been previously misinterpreted. This building was chosen as it exemplifies typical modern office buildings in Egypt, especially those with prevalent design issues. To address your concerns about confidentiality, the specific name of the building has been removed from the paper. Instead, it is now referred to in a more general way that preserves anonymity while still providing necessary context. 7. I have expanded and modified section 1.4 Methods to provide more detail about the process. 8. In response to your feedback, I have revised the section on model creation to provide more explicit details about the data collection process. This should enhance the reader's understanding of the level of accuracy involved in our study. To address your query, the case study pertains to a single office building in Egypt, not multiple buildings. The reason for this is that the selected building represents typical modern office buildings in the region, making it an ideal subject for our analysis. Any other examples mentioned in the paper were used to help formulate the scenario, but were not themselves subjects of the case study. Moreover, as part of our data collection process, we did conduct monitoring of actual environmental conditions in the building ( Indoor Air temperature). This was essential in validating our base-case building model results. thus, the paper was modified to clarify this process. 9. As per your request section 1.3 and 1.4 were switched . Along side other arranging in the paper for clarity purpose and better information flow. 10. The title of Section 2 has been modified as per your suggestion. 11. The reference to increased revenue in 2013 for the Googleplex building is an indirect way of indicating enhanced employee productivity, which is a central theme of our study and Revenue calculation is a way of calculating productivity which was explained in the paper as one of productivity measuring methods. Successful design features in buildings, like those in Googleplex and Amazon Spheres, have been shown to boost employee productivity, and by extension, revenue. However, I agree that the link between design and revenue generation needed clearer explanation. Therefore, I have revised this section to better elucidate the relationship between the two. The focus is on understanding how specific design features can impact productivity, and consequently, the economic success of a company. This understanding is pivotal to our study's aim of identifying design-oriented features that can be effectively implemented in office buildings in Egypt to enhance productivity. 12. I agree that the literature review could benefit from a more in-depth exploration of the factors affecting occupant health, wellbeing, and productivity. In light of your comments, I have revised the literature review to delve further into these aspects. 13. as for the rationale for Table 4. A comparative study that resulted in the design criteria has been added to the revised paper as Section 4. 14. A description of the case study office building was placed in the methods section for clarification. 15. Modifications to the case study section was made and additional figures was added for clarifications. We highly value your insightful suggestions, which have contributed significantly to refining the manuscript. Best Regards, Miral H." } ] } ]	1	https://f1000research.com/articles/12-639
https://f1000research.com/articles/12-1593/v1	14 Dec 23	{ "type": "Brief Report", "title": "To swim or not to swim after eating: a randomised controlled crossover feasibility trial", "authors": [ "Sehriban Harmankaya", "Stina Öberg", "Jesper Ryg", "Marianne Vogsen", "Jacob Rosenberg", "Sehriban Harmankaya", "Stina Öberg", "Jesper Ryg", "Marianne Vogsen" ], "abstract": "Background The aim was to investigate and challenge the belief that swimming immediately after eating is dangerous and also to investigate what potentially could happen when swimming immediately after a meal. We wanted to explore feasibility and get background data to perform sample size calculations and choose outcome parameters for a full-scale randomized trial.\n\nMethods The trial was performed during lunch breaks at a medical writing course in Turkey in June 2022. Participants were randomised on the first trial day to swim 14 meters breaststroke immediately after lunch or wait 30 minutes after eating, with crossover on the second trial day. Main outcomes measures were mortality, and mood, discomfort, and adverse events were assessed in participant-reported questionnaires. Participants completed a Profile of Mood States-Adolescents questionnaire, a visual analogue scale for discomfort, and a questionnaire of adverse events after each swim.\n\nResults A total of 26 participants completed the trial. No cases of mortality, drowning, resuscitation, side stitch, or muscle cramps were reported. The participants reported no significant difference in their mood states after each swim and no significant difference was found regarding the participants’ swimming time (P = 0.53). However, more discomfort was reported when swimming immediately instead of 30 minutes after eating (P = 0.05).\n\nConclusions It seems that swimming after eating is safe since no mortality or cramps were registered. However, a significant level of discomfort was found when swimming immediately after eating lunch. This feasibility trial provides background data for a future full-scale randomised trial.\n\nClinicaltrials.gov registration NCT05401396 (25/05/2022).", "keywords": [ "Eating", "swimming", "cramps", "crossover trial" ], "content": "Introduction\n\nThere is a common belief that swimming immediately after having a meal is dangerous and might cause cramps that potentially could lead to drowning.1 Interestingly, the World Health Organization does not mention food intake before swimming as a risk factor for drowning.2 This narrative about the danger of swimming or playing in water immediately after eating is regarded by many as a myth.3 Nevertheless, many still believe it to be true. It is doubtful how long this belief has flourished, however, in a manual for boy scouts from 1908, the author instructed the scouts to avoid bathing in deep water right after a meal as this could cause cramps resulting in drowning.4 According to the narrative, one should usually wait half an hour to two hours after having a meal before swimming.5 After a meal, postprandial hyperemia occurs with increased blood flow to the gut resulting in less peripheral circulation.6 This is probably one explanation to why there is a fear of less peripheral blood circulation resulting in cramps. In contrast, synchronous swimmers with an intense exercise program are encouraged to consume a well-balanced diet both before, during, and after the exercise.7\n\nA review of relevant research in the field found no direct association between food intake before swimming and fatal outcomes such as drowning.1 The review found a few observational studies conducted in the 1960s that assessed the impact of eating and swimming after different time intervals. No effect on swimming performance or any case of discomfort with nausea or cramping were reported.1 Nonetheless, to our knowledge, no randomised study has been conducted to assess the danger of swimming after eating. In order to provide background data for a future full scale randomised trial enabling sample size calculations based on proper choice of outcome parameters, we chose to perform a feasibility study. With the current feasibility study and a future full scale randomised trial, we wanted to challenge the myth that it may be dangerous to swim immediately after eating.\n\n\nMaterials and methods\n\nThe trial was conducted over two days as a randomised controlled trial with a crossover design. We have reported the study according to the Consolidated Standards of Reporting Trials (CONSORT) statement extension to randomised crossover trials,8,12 and the trial was registered at www.clinicaltrials.gov (NCT05401396) before initiation on 25th May 2022.\n\nThe study and collection of data were conducted during lunch-breaks at a research retreat at a hotel in Turkey in June 2022 with participants from Denmark.\n\nParticipants were researchers attending the writing course. They were eligible for inclusion if they were adults, could swim, and complied with local pool regulations.\n\nThe lunch restaurant and the pool area were in close proximity. Participants received written information about the study by e-mail one week before departure and were informed orally on the day of departure at the airport. The water temperature and pH were constant on the study days, being 29 °C and 7.6, respectively, whereas the weather temperature ranged from 29–32 °C. The pool was 1.4 meters deep and 7 meters wide, making the total swimming distance 14 meters.\n\nOn the first trial day, participants were randomised to either swim immediately after lunch or 30 minutes after. On the second day, each participant crossed over and performed the opposite of either swimming immediately or 30 minutes after lunch. The trial course is illustrated in Figure 1. The trial intervention was swimming immediately after eating while the control was waiting 30 minutes, hence every participant served as their own control. The participants were instructed to have lunch as they normally would to reflect their usual behaviors. Participants who swam 30 minutes after lunch jumped in the water 30 minutes after their last bite. Participants who swam immediately after eating were observed when walking from the dining table to the pool to ensure that they ate until they arrived at the pool area.\n\nBaseline vital signs of blood pressure and oxygen saturation were measured during lunch on the first trial day. Blood pressures were measured with a blood pressure monitor (Seagull-Healthcare, model HL888HA, Taipei, Taiwan) and oxygen saturation with a fingertip pulse oximeter (CONTEC LED CMS50M Pulse Oximeter, China). Participants were instructed to walk and slowly enter the pool by the ladder and swim breaststroke briskly with their head over the water. Up to three participants swam simultaneously with the presence of lifeguards and observers in case of any incidents. The time to complete the swimming distance was noted on all participants. Immediately after swimming, the participants filled in three questionnaires: the validated Profile of Mood States – Adolescents (POMS-A) questionnaire,9,10 a visual analogue scale (VAS) about discomfort, and a self-reported questionnaire on adverse advents.\n\nThe trial was designed and conducted in collaboration with a professional lifeguard, an experienced swimmer, and a restaurant chef to reflect user perspectives. Each user reviewed the study protocol and provided valuable insight and feedback to the research team. The lifeguard provided information on the impact of swimming distance and mentioned that during swimming competitions, he regularly experienced parents forcing their children not to swim immediately after eating. The experienced swimmer focused on the importance of swimming style, which had to be identical on both days. He also stressed the importance of swimming at the same timepoint as performance might vary throughout the day. The previous Michelin restaurant chef expressed no concerns about the safety of the trial, but he experienced many restaurant guests being tired and inflated after eating a meal. Therefore, he worried that the participants might lack amusement and attention when swimming immediately after eating.\n\nAs this was a feasibility trial, we arbitrarily chose the primary outcome to be mortality after swimming. Secondary outcomes included differences in POMS-A, discomfort, adverse events, pulse rate, and swimming time. The adjectives in the POMS-A questionnaire were translated to Danish using back- and forward translation by two authors and face-validation was performed on two different laymen. The POMS-A questionnaire evaluates mood by focusing on different categories involving tension, depression, anger, fatigue, confusion, and vigour with adjectives in each category on a five-point scale from one to five. The scores for each category were calculated by adding the raw scores from the adjectives for the specific category. A high vigour score and low scores on the other five categories indicate a person with a more stable and positive mood profile. The VAS was face-validated and measured current level of any discomfort, ranging from no discomfort to the worse imaginable discomfort (0–100 mm). Furthermore, a questionnaire of adverse events was developed within the author group for the participants to self-report (see Extended data12). Face-validation was performed to ensure the correct interpretation of the questions. The questionnaire assessed adverse events such as drowning, resuscitation, experience of any gastrointestinal symptoms, side stitch, or muscle cramps both during and immediately after swimming. Since all participants served as their own control, secondary outcomes were assessed as the difference between outcomes on the two study days, i.e., swimming immediately versus 30 minutes after eating.\n\nRandomisation of each participant was performed by the same investigator by throwing dice at the dining table after each participant had selected their lunch. Participants with an even dice number were randomised to swim immediately after lunch the first day, while participants with an uneven dice number were randomised to wait 30 minutes.\n\nConvenience sampling was used, hence, participants were included based on availability, time, and interest. The statistical analyses were performed in SPSS Statistics 28 (IBM). Continuous data were assessed for normal distribution by visual inspection of histograms and QQ-plots. Since data were not normally distributed, continuous data are presented as median, interquartile range (IQR), and range and were analysed with the Wilcoxon signed-rank test. Categorical data are presented as numbers and percentages and were analyzed with the Fisher’s exact test since expected values were <5 in at least one cell. POMS-A is an ordinal categorical scale, however, it was handled as continuous data in our statistical analyses. We considered statistical significance when P ≤ 0.05.\n\nAccording to Danish legislation, the Regional Ethics Committee in Copenhagen waived ethical approval (journal number 22020290). Written consent was obtained from every participant before participation, and data were stored in a secure database.\n\n\nResults\n\nA total of 31 medical researchers attended the writing course, and 27 participants were eligible for inclusion. A flowchart of the inclusion process, participation, and randomisation is illustrated in Figure 2. Unfortunately, one participant dropped out since she was dropped in the pool by some of her colleagues after being randomised and having lunch on the first day. Consequently, 26 participants were included and completed the trial as intended with 100% complete data. The baseline characteristics of the study participants are illustrated in Table 1.\n\nn: number.\n\nNo cases of mortality were registered. Similarly, no adverse events of drowning, resuscitation, and experience of any side stitch or muscle cramps were found. Two participants reported gastrointestinal symptoms while swimming 30 minutes after lunch: one participant experienced flatulence and the other participant reported a bloated feeling. However, there was no statistically significant difference in gastrointestinal symptoms when comparing the intervention and control (P = 0.41).\n\nParticipants reported their level of discomfort with a median VAS of 2 (scale 0–100) both after swimming immediately (range 0–34, IQR: 0–4) and after 30 minutes (range 0–4, IQR: 0–3) after lunch (Table 2). However, when swimming 30 minutes after lunch, the participants reported significantly less discomfort compared with swimming immediately after lunch (P = 0.05).\n\nSwimming time is reported in seconds, pulse is reported per minute, and level of discomfort is reported in millimeters based on a visual analogue scale. IQR: interquartile range; VAS: visual analogue scale; P: p-value.\n\nThe participants’ mood profile was assessed for the six mood categories of tension, depression, anger, fatigue, confusion, and vigour. After calculating the participants’ mood score when swimming immediately and 30 minutes after lunch for each category, we found no significant difference (Table 2). Overall, the participants’ mood weighted to be more positive than negative with a high vigour score and low scores in the negative mood categories. The reported median vigour score was 6 when swimming immediately and 7 when swimming 30 minutes after lunch (P = 0.23). Similarly, no significant difference was found among the negative mood categories of tension, depression, anger, fatigue, and confusion (Table 2).\n\nWe found no significant difference (P = 0.53) when comparing the participants’ performance in swimming time when they swam immediately or 30 minutes after lunch (Table 2). The observed median swimming time was 17 seconds (IQR: 15–20) and 16 seconds (IQR: 14–20) when swimming immediately and half an hour after eating, respectively (P = 0.53). Furthermore, the participants’ pulse rate was measured after each swim and no significant difference was found (P = 0.99) with a median of 82 beats per minute on both days.\n\n\nDiscussion\n\nThis trial showed that swimming 14 meters in a pool with limited depth immediately or half an hour after lunch did not result in any deaths or other serious adverse events. Furthermore, the overall result of the trial did not find differences in the mood categories after the two swimming regimens. The only disadvantage when swimming immediately after lunch was a higher level of discomfort compared with swimming half an hour after.\n\nThere are some important limitations to this trial. Since the participants were all from Denmark where the population rarely swim in outdoor pools, some level of adaptation might have occurred on the second trial day. Nevertheless, an equal number of participants were randomly distributed to undergo the intervention or comparison swim during day 1 and 2. A further limitation is that it remains unknown whether the participants had lunch as they usually would since they were in a hotel with plenty of food, however, no participants informed the investigators that they overate or were on a diet. A strength of the trial was that we required the participants to follow the local pool regulations. Another strength is that the design of the trial minimised recall bias since the participants filled the questionnaires immediately after each swim. Furthermore, the POMS-A, VAS, and questionnaire of adverse events were face-validated thoroughly, which avoided any potential misinterpretations and thereby optimised the assessment. Another strength is the user involvement in the design phase of the trial, thus reflecting user perspectives of swimming after eating.\n\nA recent study found that the time-of-day (morning or evening) can influence the swimming performance in an adolescent population with swimming experience, however, with variations depending on the swimming distance and sex.11 The importance of varying performance depending on the time-of-day was also stressed by the experienced swimmer involved in the design phase and we minimised this time-of-day variance in our study since the participants swam during the lunch breaks on both days. The same study also demonstrated the importance of sleep quality as a factor influencing participants’ level of anxiety and depression, consequently affecting their performance in swimming.11 Since our study investigated an adult population during a course with an intense scientific program, it is possible that the participants worked from early mornings til late nights, which could have affected their swimming performance because of less sleep.\n\nSince this study found that swimming directly after a meal was not dangerous, we judge it to be safe to perform a full-scale randomised trial with swimming directly after eating as long as routine safety instructions are followed. However, swimmers may expect a higher level of discomfort when swimming directly after a meal, and this parameter seems to be the obvious primary outcome for a future randomised trial. Our data can be used as background data for sample size calculations for such a full-scale trial, which may employ different swimming distances and/or swimming in sea water rather than in a pool.\n\n\nConclusions\n\nIn conclusion, we found that swimming immediately after eating seems to be unhazardous and safe but may in some be associated with discomfort. The present feasibility trial, being the first randomised trial on the subject, will form basis for future large scale conclusive trials.", "appendix": "Data availability\n\nZenodo: To swim or not to swim after eating: a randomized controlled crossover feasibility trial. https://doi.org/10.5281/zenodo.10074765. 12\n\nThis project contains the following underlying data:\n\n- Data overview.csv\n\n- Description of data overview.pdf\n\n- Adverse events questionnaire.pdf\n\nZenodo: CONSORT checklist for ‘To swim or not to swim after eating: a randomized controlled crossover feasibility trial’. https://doi.org/10.5281/zenodo.10074765. 12\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nChambers P, Quan L, Wernicke P, et al.: American red cross scientific advisory committee scientific review: eating before swimming. Int. J. Aquat. Res. Educ. 2011; 5: 483–492. Publisher Full Text\n\nWorld Health Organization: Drowning.[Cited 2022 Sept 18]. Reference Source\n\nBartholdy K, Hoff A: 100 myter om sundhed og sygdom. 1st ed.Denmark: FADL; 2015.\n\nBaden-Powell R: Scouting for boys: the original. 1908th ed.United States of America: Dover Publications; 2007.\n\nBritannica: The editors of encyclopaedia Britannica. Is it really dangerous to swim after eating?[Cited 2022 Sept 18]. Reference Source\n\nJeays AD, Lawford PV, Gillott R, et al.: A framework for the modeling of gut blood flow regulation and postprandial hyperaemia. World J. Gastroenterol. 2007; 13: 1393–1398. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRobertson S, Benardot D, Mountjoy M: Nutritional recommendations for synchronized swimming. Int. J. Sport Nutr. Exerc. Metab. 2014; 24: 404–413. PubMed Abstract \| Publisher Full Text\n\nDwan K, Li T, Altman DG, et al.: CONSORT 2010 statement: extension to randomised crossover trials. BMJ. 2019; 366: l4378. 31. Publisher Full Text\n\nTerry PC, Lane AM, Lane HJ, et al.: Development and validation of a mood measure for adolescents. J. Sports Sci. 1999; 17: 861–872. Publisher Full Text\n\nTerry PC, Lane AM, Fogarty GJ: Construct validity of the profile of mood states – adolescents for use with adults. Psychol. Sport Exerc. 2003; 4: 125–139. Publisher Full Text\n\nNunes RSM, Freitas AFL, Vieira E: The influence of time of day on the performance of adolescent swimmers. Chronobiol. Int. 2021; 38: 1177–1185. PubMed Abstract \| Publisher Full Text\n\nHarmankaya S, Öberg S, Ryg J, et al.: To swim or not to swim after eating: a randomized controlled crossover feasibility trial. [Data set]. Zenodo. 2023. Publisher Full Text" }	[ { "id": "239263", "date": "08 Feb 2024", "name": "Antonio Laguna Camacho", "expertise": [ "Reviewer Expertise Psychology", "Nutrition", "Behaviour change", "Experimental 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 submitted manuscript describes an experiment in which participants reported experiencing more discomfort when swimming immediately after lunch compared to when swimming 30 minutes after lunch.\nThe authors note that this was a feasibility trial and that the data will be used for sample size calculations. However, the sample size of the reported experiment was small, which likely resulted in underpowered results.\nAlthough the authors mention that eligible participants took part in the experiment, the manuscript lacks information on the eligibility criteria. Furthermore, there is no mention in the manuscript regarding the information provided to participants about the experiment.\nPlease address potential limitations arising from participants' reports aligning with researchers' expectations or from participants' beliefs that swimming immediately after eating causes adverse events.\nAdditionally, please clarify whether the analyses were conducted within subjects; for example, were the data from both sequences combined and then intervention and control conditions were compared.\nI am curious why a mood scale for adolescents was applied if the participants were adults.\nFinally, I question whether the median swimming time of only 17 seconds was a limitation and whether longer swimming times would contribute to adverse events.\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? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-1593
https://f1000research.com/articles/12-1592/v1	14 Dec 23	{ "type": "Research Article", "title": "The assessment of educational and supportive care to the infertile females undergoes In Vitro Fertilization procedure by clinical pharmacist: a randomized clinical trial", "authors": [ "Ali Abbas Ibrahim", "Abeer Abdulhadi Rashid", "Abeer Abdulhadi Rashid" ], "abstract": "Background Infertility affects approximately 10-15% of married individuals, and may trigger various emotional reactions. Females undergoing in vitro fertilization (IVF) are more susceptible to experiencing depression. This study aims to assess the influence of pharmacist counseling on quality of life, depression scores, and pregnancy rates among infertile females undergoing IVF treatment.\n\nMethod The research examined women who visited the infertility clinic at Kamal Al-Samaraie Hospital in Baghdad, Iraq to achieve pregnancy. These individuals were separated into a control group and an intervention group. The intervention group received an educational program consisting of five visits, while the control group got a conventional hospital procedure. The present research evaluated the quality of life-related to fertility using the FertiQoL (Fertility Quality of Life) questionnaire. It examined the participants’ depression levels using the CES-D (Center for Epidemiologic Studies Depression) scale. These assessments were conducted at the commencement and conclusion of the in vitro fertilization (IVF) cycle.\n\nResults The present research included 150 women diagnosed with infertility, whose average age was 30.32 ± 5.64 years. The participants had a mean body mass index (BMI) of 27.12 ± 3.57. No statistically significant difference was seen in the FertiQoL evaluation scores between the control and intervention groups at the beginning of the study. The FertiQoL, assessed at the end of the trial, exhibited a statistically significant increase in the interventional group, with a P-value of 0.025. The prevalence of Depression risk patients decreased from 83% to 69%, and the interventional group exhibited a substantially greater proportion of favorable pregnancy outcomes (48%) compared to the control group (29.3%).\n\nConclusion Infertile women who undergo IVF operations have higher rates of depression. Depression may be reduced, and quality of life improved with education and supportive counseling. Pregnancy rates rise as a result of clinical pharmacist counseling.\n\nTrial registration This study was registered on Clinical Trials.gov (NCT06022640).", "keywords": [ "In Vitro Fertilization", "Depression", "FertiQoL", "Supportive care", "Clinical Pharmacist." ], "content": "Introduction\n\nInfertility impacts around 10-15% of married individuals, including males and females, and can result in a range of emotional responses such as anxiety, distress, pain, and disappointment.1 This significant life event has the potential to impact several dimensions of a couple’s existence.2 Preconception counseling is an essential need for the initiation of infertility therapy, as it encompasses a comprehensive assessment of several aspects, including medical, social, genetic, environmental, and occupational factors, which have an impact on both fertility and the overall well-being throughout pregnancy.3 Depression is a prevalent concern among women experiencing infertility, and pharmacists assume a pivotal role in the provision of treatment for those affected by depression.4,5\n\nThe underlying cause of female infertility remains unclear; however, a significant proportion of cases (81%) may be attributed to ovulatory problems, endometriosis, pelvic adhesions, tubal obstruction, other tubal abnormalities, and hyperprolactinemia.6,7 The decline in fertility is influenced by advancing age, and the incidence of infertility due to age increases as the reproductive lifespan diminishes. Infertility treatment aims to address remediable factors and overcome refractory ones.8,9 The fundamental concepts of care for couples experiencing infertility include the identification and assessment of the underlying causes, as well as the subsequent implementation of appropriate treatment strategies.10 Additionally, recommendations may be made about behavioral modifications to enhance fertility, such as smoking cessation and minimizing exposure to potentially detrimental drugs.11\n\nAssisted reproductive technology (ART) is a medical intervention to address infertility, including therapeutic approaches that include ova and sperm. In assisted reproductive technology (ART), in vitro fertilization (IVF) is usually considered the most productive approach.12 in vitro fertilization (IVF) is widely recognized as a very effective treatment for infertility, yet it sometimes requires numerous rounds of egg retrieval and embryo transfer.13 This treatment has shown efficacy in addressing unexplained infertility and conditions such as blocked or damaged fallopian tubes, hereditary abnormalities, uterine fibroids in women, ovulation difficulties, early ovarian failure, and cases where ovaries have been surgically removed.14\n\nThe process of IVF entails ovarian stimulation, which encompasses the administration of fertility medications to induce the development of eggs and control the operation of ovulation.15 Emotional alterations often occur among individuals undergoing in vitro fertilization (IVF), particularly those with a history of mental illness, experienced miscarriage, faced a prolonged period of infertility or received a conclusive medical diagnosis.16 The stress levels of IVF patients tend to rise as the intensity and duration of treatment grow, resulting in higher stress levels compared to women in the early stages of their infertility examination.17\n\nThe experience of infertility and the administration of corresponding drugs may elicit significant psychological distress among patients, particularly those who have undergone several in vitro fertilization rounds without achieving successful outcomes.18 Patients may lack familiarity with self-injecting gonadotropins, using hormone supplements, and adhering to other essential therapies required for ovulation induction cycles.19 Research indicates a negative association between depression and in vitro fertilization (IVF) conception rates. However, the specific influence of depression on emotional discomfort remains unknown.20\n\nGrief reactions are often reported in couples who are facing infertility. However, these usual grief reactions may develop into pathological grieving, characterized by prominent melancholy symptoms.21 Infertility-related depression in women varies between 10% and 25%, with women exhibiting significant depressive symptoms at two to three times greater rates than males.22,23 The presence of depression has been shown to have adverse effects on several aspects of therapy, follow-up, and future perspective, as well as the strength and longevity of the relationship between the afflicted pair.24\n\nPharmacists are crucial in providing education and supportive care for individuals suffering from depression.25 They provide valuable guidance, suggestions, and counseling about drugs while monitoring patients for drug-related issues and evaluating patient adherence to prescribed treatments.26 Pharmacists’ professional role includes pharmaceutical care concepts, transitioning them from their conventional role as mere dispensers of medications to being integral members of the healthcare team.27 The primary objective of patient-centered treatments is to enhance therapeutic results via identifying, preventing, and managing drug-related issues, promoting appropriate medication use, and providing general health education.28 In Iraq, it has been observed that a significant number of chronic illnesses are not effectively addressed via the collaborative efforts of healthcare professionals, including pharmacists, despite their recognized position within the broader healthcare framework.29 It is important to enhance the professional growth of pharmacists to enable them to carry out their duties proficiently. The concept of care centers on cultivating the pharmacist-patient relationship and strengthening the therapeutic result by active engagement in the treatment approach.30\n\nIt has been shown that collaborative counseling may lead to a 3.6-fold decrease in stress levels among infertile women undergoing in vitro fertilization (IVF) compared to a control group. Psychotherapy emerges as a compelling treatment option due to its efficacy in enhancing patients’ likelihood of achieving pregnancy.31 Psychological counseling, interpersonal therapy, and behavioral activation are often used as the first treatment modalities for depression.32 Several studies have shown that infertile women seeking to undergo in vitro fertilization (IVF) may have unsuccessful outcomes and fail to achieve pregnancy due to pre-existing depressive symptoms in the patient.33,34 Consequently, it is essential to implement health education and raise awareness of the need to ensure a satisfying state before undergoing surgery, with a particular emphasis on women due to their heightened vulnerability to this kind of depression in comparison to males.35\n\nThe primary goal of this study was the assessment of clinical pregnancy rates as a measure of the result of in vitro fertilization cycles after the introduction of educational support program by the clinical pharmacist. Secondary outcome measures were the completion of The Centre for Epidemiological Studies Depression Scale (CES-D) and The Fertility Quality of Life Tool (FertiQoL) evaluation by both groups at the beginning and end of the in vitro fertilization process.\n\n\nMethod\n\nThis study was registered on Clinical Trials.gov (NCT06022640).\n\nThe ethics committee of the College of Pharmacy at Mustansiriyah University, Iraq, formally approved the research methodology. Written consent was acquired from every individual enrolled in the study after providing a comprehensive explanation of the study’s objectives and maintaining the confidentiality of patient information.\n\nThis study used a prospective two arms parallel-group in an interventional randomized control trial design to examine the effects of an educational support program led by a clinical pharmacist on the pregnancy rate of infertile females who completed in vitro fertilization cycles and had symptoms of depression. Research including a sample of 206 women experiencing infertility and using in vitro fertilization technology (Figure 1). However, 32 participants were excluded from the study because they failed to match the predetermined inclusion criteria. Out of the total sample size of 174 women experiencing infertility, 24 individuals declined participation, while 150 individuals consented to participate in the research, as seen in CONSORT flow diagram below.36 The trial had a total of 75 participants assigned to the intervention group, whereby they were provided with an instructional and supporting program specifically developed by a clinical pharmacist. The intervention group was assisted via a series of five visits, including an initial visit upon admission, subsequent visits for monitoring medication, ovulation, and any negative effects, and visits dedicated to giving emotional support. A follow-up visit was also conducted after the egg harvesting process and embryo transfer. The control group comprised 75 married women experiencing infertility and seeking treatment at the hospital. These women were handled according to the standard practice used by the hospital system.\n\nThis research recruited infertile females’ participants seeking pregnancy at the Kamal Al-Samaraie hospital, a government-run infertility facility located in Baghdad, Iraq, from January 1st 2022 to July 1st 2022.\n\nTo qualify for inclusion in the research, participants must satisfy certain criteria. These requirements included being a woman experiencing infertility (the inability to conceive after at least one year of marriage). To be within the reproductive age (18-45 years old) and to have the ability to read and understand.\n\nThe exclusion criteria for the patients includes those who had experienced past failure of an in vitro fertilization. Morbid obesity (a body mass index (BMI) over 40).37 Individuals under consideration to have mental conditions that necessitate their admittance to a psychiatric institution, or those grappling with addiction or having progressive neurological disorders. Any individual who has a condition that hinders their ability to engage in effective communication due to challenges related to language and hearing.\n\nThe primary objective of the research was to examine the correlation between the pregnancy rate of infertile females who underwent in vitro fertilization (IVF) cycles and the presence of accompanying depressive symptoms throughout this process. The CES-D scale was used to evaluate the level of depression in each participant. The CES-D questionnaire is a standardized evaluation consisting of 20 items that prompts individuals to evaluate the frequency with which they experienced symptoms associated with depression over the course of the preceding week.38 The CES-D utilizes cutoff values of 16 or above in order to identify individuals who may be at risk of experiencing clinical depression. Elevated scores are indicative of a greater manifestation of depressive symptoms. The assessment has exceptional levels of sensitivity, specificity, and internal consistency and has been successfully used in many age groups.\n\nThe FertiQoL questionnaire is a widely recognized instrument for assessing the quality of life related to fertility. It examines the impact of reproductive challenges on multiple aspects of individuals’ lives, encompassing overall well-being, self-perception, emotional states, interpersonal relationships, familial and social ties, occupational satisfaction, and aspirations for the future. The questionnaire has been translated into a total of 20 languages, which notably includes Arabic.39 The present research evaluated the FertiQoL at two distinct time points: before to the implementation of the management program and subsequent to the completion of embryo transfer.\n\nThe intervention that was given was educational that disseminate knowledge related to the issue of infertility. The education interventions consisted of comprehensive information associated with the pathophysiology of infertility, etiological factors, guidelines for therapy, strategies for managing psychological distress, techniques for stress reduction, and encouraging the development of healthy interpersonal connections. The objective of educational interventions is to enhance the health literacy of women experiencing infertility. The instructional materials used in this study were adopted from evidence-based guidelines involving disseminating educational resources focused on psychological assistance for individuals experiencing infertility.40–42\n\nA computerized randomization method was used to allocate patients into two groups in a randomized manner. Following the first interview, the patients were sequentially assigned numbers and then randomized into two groups via the online program Research Randomizer.\n\nThe recommended minimum sample size is calculated according to the formula:\n\nWhere: z = 1.96 for a confidence level (α) of 95%, p = prevalence of infertility which was reported to be as high as 8.9% among the general population,43 e = margin of error e = 0.05. The minimum sample size was equal to 125.\n\nThe data collected was entered into Microsoft Excel 2021 (RRID: SCR_016137) and then inserted into SPSS statistical software/version 26 (RRID: SCR 016479). The Chi-Square Test was performed to determine the significance of relationships between related categorical variables. The independent-sample T-test was used to assess the significance of numerical variables in the intervention and control groups at the beginning and end of the trial in terms of FertiQoL score and depression score. The 95% confidence interval has been set. The P-value of 0.05 was used as the cutoff for significance.\n\n\nResults\n\nA total of 150 infertile females exposed to IVF procedures were eligible for the study (Table 1).\n\nThe study found no significant association between group of study and age, duration of marriage and BMI (body mass index) (Table 2).\n\n* Independent sample T-test was used compare two distinct samples. NS: No significant differences (P-value > 0.05).\n\nAccording to the data shown in Table 3, the average pre-FertiQoL score for the control group is 53.48 ± 13.98, which is statistically insignificant from the average score of 51.66 ± 14.87 for the interventional group (P-value = 0.443). While the FertiQoL measured at post-time (post-FertiQoL) was found to be significantly higher among the interventional group, P-value = 0.025.\n\n* Independent sample T-test was used compare two distinct samples. NS: No significant differences (P-value > 0.05), S (P-value ≤ 0.05) is considered significant.\n\nThe CES-D provides cutoff scores (16 or greater) that aid in identifying individuals at risk for clinical depression, with good sensitivity and specificity and high internal consistency.44 The cutoff point of 16 was considered to be indicative of mild depression, and the degree of depression was shown to rise as the score increased.45 The percentage of at-risk participants evaluated for depression dropped from 83% at the beginning to 69% at the end of the study, as shown in Figure 2.\n\nThe overall risk of depression in the interventional group was considerably reduced compared to the control group at the end of the study, with a P-value of 0.001 (as presented in Table 4).\n\n* Chi-square is used for statistical analysis of descriptive parameters. NS: No significant differences (P-value > 0.05), S (P-value ≤ 0.05) is considered significant.\n\nThe interventional group exhibited a significantly greater rate of positive pregnancy (48%) compared to the control group (29.3%), as shown by a P-value of 0.019 (Table 5).\n\n* Chi-square is used for statistical analysis of descriptive parameters. S (P-value ≤ 0.05) is considered significant.\n\nThere was no statistically significant difference seen between the pre-FertiQoL and post-FertiQoL scores among the research participants who had a negative pregnancy outcome. The p-values for the two variables were 0.795 and 0.497, respectively. The post-FertiQoL mean score in the interventional group was substantially higher compared to the control group among individuals who had positive pregnancy outcomes P-value = 0.016 (Table 6). A statistically significant difference was seen among participants in terms of their depressive condition after the completion of the IVF cycles, including between those with a positive pregnancy result and those with a negative outcome (Table 7).\n\n* Independent sample T-test was used compare two distinct samples. NS: No significant differences (P-value > 0.05), S (P-value ≤ 0.05) is considered significant.\n\n* Chi-square is used for statistical analysis of descriptive parameters. NS: No significant differences (P-value > 0.05), HS (P-value <0.01) considered highly significant value.\n\n\nDiscussion\n\nIndividuals experiencing difficulties in achieving conception often experience symptoms of despair and anxiety.46 Research has shown that infertile women have emotional issues comparable to those struggling with malignancies.47 Infertility is a widespread public health concern that has many medical, psychological, and social consequences.48 Depression may influence an individual’s cognitive processes, behaviors, emotional experiences, and overall state of health.\n\nWe performed a randomized controlled trial to evaluate the impact of supportive and educational intervention on depression scores and pregnancy outcomes in infertile women. The present research reveals that women who are facing infertility issues and actively seeking medical intervention had been in a marital relationship for an average duration of 3.74 ± 2.17 years, with the longest reported duration being 12 years. According to the findings of an earlier study carried out in the Erbil Kurdistan Region of Iraq, it was observed that a majority of 55.5% of women experiencing infertility and actively seeking infertility treatment had been married for a length ranging from 3 to 7 years.49 Based on available research, the average period of infertility in India is around 8.38 years.50 In Korea, this time is estimated to be around four years.51 In Italy, it has been observed that over fifty percent of couples choose Assisted Reproductive Technology (ART) after being married for less than 3 years.52 The observed variations may be attributed to the distinct sociocultural characteristics of each nation.\n\nThe objective of this research is to enhance awareness of the fertility-related quality of life among women who are facing infertility and to demonstrate the impact of supportive care on their quality of life. The quality of life experienced by women enduring infertility therapy may be substantially decreased. The quality of life experienced by women enduring infertility therapy may be substantially decreased. This phenomenon has the potential to induce treatment discontinuation and possibly generate resistance against seeking assistance from the patient.53\n\nThe present study analyses the quality of life experienced by infertile women in Iraq who receive in vitro fertilization (IVF) treatment. The average FertiQoL score at the beginning of the study (before implementing any interventions) was 53.48 ± 13.98 for the control group and 51.66 ± 14.87 for the intervention group. The baseline mean of all included cases was calculated to be 52.57 ± 14.417. The findings of this study revealed a significant gap in the assessment of quality of life among infertile women compared to a survey conducted in Kazakhstan. In the Kazakh study, 453 infertile women who received IVF treatment reported a FertiQoL score of (59.6 ± 11.5), with a P-value of 0.001.54 The findings presented in research conducted in Germany, Italy, France, Poland, and Taiwan showed substantial and statistically significant variations.55–57 Potential factors contributing to this observed disparity may include elevated living standards and increased accessibility to mental health care within these industrialized nations.\n\nThe findings of the comparative analysis conducted on different study groups about FertiQoL indicate that no statistically significant differences were seen during the first assessment. However, it was observed that the intervention group had markedly elevated levels compared to the control group at the end of the study. The observed effect is hypothesized to be attributable to supportive care’s impact on enhancing the experimental cohort’s overall well-being. This finding aligns with previous research on Iranian women experiencing infertility, whereby the group that received counseling had a notably higher average score in terms of quality of life than the control group.58\n\nThe research findings indicate that the initial prevalence of depression among all participants included in the study at the beginning of the in vitro fertilization cycle was 83%. The results presented in this research are similar to another study in Kazakhstan, whereby a sample of 304 females experiencing infertility were interviewed across three distinct locations. The results indicated that over 80% of respondents exhibited CES-D scores of 16 or above, indicating a greater susceptibility to the onset of clinical depression. The above rate has decreased to 69% following the implementation of educational interventions and supporting measures for females experiencing infertility after the in vitro fertilization cycle is completed. During the examination of the interventional group’s depression state before and after the in vitro fertilization cycle, it was observed that the prevalence of depression decreased from 80% to 48%.\n\nThere was no statistically significant difference in depression scale scores between the control and intervention groups at the beginning of the study (p-value = 0.273). However, at the end of the study, there was a significant difference in depression scale ratings between the two groups (p-value = 0.001). The observed decline may be attributed to the provision of educational and supportive care within the IVF program. This finding is consistent with previous research in which a statistically significant difference in the outcome was observed after the intervention was carried out, providing further support for the present conclusion.59,60 Providing patients with psychological interventions and emotional support is crucial for infertility healthcare professionals.61\n\nThe research findings revealed that the favorable conception rate differed between the control and intervention groups regarding IVF outcome rates, with 29.3% and 48%, respectively. The results of this study suggest that the intervention group exhibited a 1.6-fold increase in the likelihood of achieving pregnancy compared to the control group. The findings above were deemed similar to those of another research done in Brazil, whereby the intervention group exhibited a notably higher pregnancy rate (39.8%) compared to the control group 23.2%.62\n\nThe intervention group exhibits a greater proportion of positive pregnant women than the control group, with 29.3% and 48%, respectively. Additionally, the overall pregnancy success rate for all participants is 39%. Initially, it was seen that both groups exhibited similar levels of FertiQoL about the outcome of a positive or negative pregnancy test. The female individuals in the intervention group showed a notable enhancement in FertiQoL compared to the control group towards the end of the research. Furthermore, significant variations in pregnancy rates were seen across the groups, with the intervention group exhibiting a greater rate than the control group. Consequently, after providing information and comprehensive assistance, the enhancement of FertiQoL shows a positive correlation with the incidence of successful pregnancies. This is similar to a research study conducted among a cohort of Chinese women receiving their first in vitro fertilization procedure at a specialized reproductive clinic.63\n\nThis research has several limitations; the first is related to the measurements used. The present study used self-report measures exhibiting inherent limitations, such as a potential deficiency in self-awareness. Another limitation is the absence of control over individual aspects. Participants may have exaggerated the impact of the intervention due to personal drive, optimism, and related variables. In future research investigations, it is advisable to include pseudo-therapy programs, also called placebo programs, inside control groups to mitigate the influence of anticipation effects. Finally, the participants were recruited from Kamal Al-Samaraie Hospital in Baghdad, Iraq, and had undergone an in vitro fertilization treatment cycle. Researchers should implement programs on additional individuals in other healthcare facilities to broaden the scope of the study’s results.\n\n\nConclusion\n\nInfertile women who undergo IVF operations have higher rates of depression. Depression may be reduced, and quality of life improved with education and supportive counseling. Pregnancy rates rise as a result of clinical pharmacist counseling.", "appendix": "Data availability\n\nZenodo: The assessment of educational and supportive care to the infertile females undergoes in vitro Fertilization procedure by clinical pharmacist: A Randomized Clinical Trial, https://doi.org/10.5281/zenodo.8348310. 64\n\nThis project contains the following underlying data:\n\n• RCT data.xlsx (Demographic details, as well as questionnaire scores)\n\nZenodo: Trial protocol for the assessment of educational and supportive care to the infertile females undergoes in vitro Fertilization procedure by clinical pharmacist: a randomized clinical trial, https://doi.org/10.5281/zenodo.10076029. 65\n\nThis project contains the following extended data:\n\n• Trial protocol.pdf\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY).\n\nZenodo: CONSORT Checklist for ‘The assessment of educational and supportive care to the infertile females undergoes in vitro Fertilization procedure by clinical pharmacist: A Randomized Clinical Trial’, https://doi.org/10.5281/zenodo.8348485. 66\n\nZenodo: CONSORT flow diagram for ‘The assessment of educational and supportive care to the infertile females undergoes in vitro Fertilization procedure by clinical pharmacist: A Randomized Clinical Trial’, https://doi.org/10.5281/zenodo.10075894. 36\n\nTrial registration: This study was registered on Clinical Trials.gov (NCT06022640).\n\n\nAcknowledgment\n\nThe authors express their gratitude to everyone who participated in our recruiting process, demonstrating their keen interest in and endorsement of our study.\n\n\nReferences\n\nRimer L: The effect of family structure and family support on women’s coping with fertility treatments. 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Publisher Full Text\n\nEl-Feshawy NI, Zromba AM, El-Ansary E-S: Effect of Collaborative Infertility Counseling on Coping Strategies and Marital Satisfaction among Women Undergoing in vitro Fertilization a Randomized Control Trial. Assiut Scientific Nurs. J. 2023; 11(37): 1–13.\n\nLee E, Han Y, Cha YJ, et al.: Community-based multi-site randomized controlled trial of behavioral activation for patients with depressive disorders. Community Ment. Health J. 2022; 1–13.\n\nFernandez-Ferrera C, Llaneza-Suarez D, Fernandez-Garcia D, et al.: Resilience, perceived stress, and depressed mood in women under in vitro fertilization treatment. Reprod. Sci. 2022; 29(3): 816–822. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGabnai-Nagy E, Bugán A, Bodnár B, et al.: Association between emotional state changes in infertile couples and outcome of fertility treatment. Geburtshilfe Frauenheilkd. 2020; 80(02): 200–210. Publisher Full Text\n\nGeoffrion R, Koenig NA, Zheng M, et al.: Preoperative depression and anxiety impact on inpatient surgery outcomes: a prospective cohort study. Ann. Surg. Open. 2021; 2(1): e049. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIbrahim AA: CONSORT flow diagram for The assessment of educational and supportive care to the infertile females undergoes in vitro Fertilization procedure by clinical pharmacist: a randomized clinical trial.2023. Publisher Full Text\n\nBooth HP, Charlton J, Gulliford MC: Socioeconomic inequality in morbid obesity with body mass index more than 40 kg/m2 in the United States and England. SSM Popul. Health. 2017; 3: 172–178. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVan Dam NT, Earleywine M: Validation of the Center for Epidemiologic Studies Depression Scale—Revised (CESD-R): Pragmatic depression assessment in the general population. Psychiatry Res. 2011; 186(1): 128–132. PubMed Abstract \| Publisher Full Text\n\nBoivin J, Takefman J, Braverman A: The fertility quality of life (FertiQoL) tool: development and general psychometric properties. Hum. Reprod. 2011; 26(8): 2084–2091. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBach M: Psychosocial interventions for individuals with infertility.2018.\n\nKremer F, Ditzen B, Wischmann T: Effectiveness of psychosocial interventions for infertile women: A systematic review and meta-analysis with a focus on a method-critical evaluation. PLoS One. 2023; 18(2): e0282065. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHa J-Y, Park H-J, Ban S-H: Efficacy of psychosocial interventions for pregnancy rates of infertile women undergoing in vitro fertilization: a systematic review and meta-analysis. J. Psychosom. Obstet. Gynecol. 2023; 44(1): 2142777. PubMed Abstract \| Publisher Full Text\n\nKatole A, Saoji AV: Prevalence of Primary Infertility and its Associated Risk Factors in Urban Population of Central India: A Community-Based Cross-Sectional Study. Indian J. Community Med. 2019; 44(4): 337–341. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLewinsohn PM, Seeley JR, Roberts RE, et al.: Center for Epidemiologic Studies Depression Scale (CES-D) as a screening instrument for depression among community-residing older adults. Psychol. Aging. 1997; 12(2): 277–287. PubMed Abstract \| Publisher Full Text\n\nIrwin M, Artin KH, Oxman MN: Screening for depression in the older adult: criterion validity of the 10-item Center for Epidemiological Studies Depression Scale (CES-D). Arch. Intern. Med. 1999; 159(15): 1701–1704. Publisher Full Text\n\nGreil AL, Slauson-Blevins K, McQuillan J: The experience of infertility: a review of recent literature. Sociol. Health Illn. 2010; 32(1): 140–162. Publisher Full Text\n\nRooney KL, Domar AD: The relationship between stress and infertility. JDicn. 2022.\n\nMoeenizadeh M, Zarif H: The efficacy of well-being therapy for depression in infertile women. Int. J. Fertil. Steril. 2017; 10(4): 363–370. PubMed Abstract\n\nGardi AHH, Mohammed SH: Assessment of Psychological status of Infertile Women in Erbil Kurdistan Region. kufa Journal for Nursing sciences. 2013; 3(1): 149–160. Publisher Full Text\n\nMalhotra N, Bahadur A, Singh N, et al.: Does obesity compromise ovarian reserve markers? A clinician’s perspective. Arch. Gynecol. Obstet. 2013; 287: 161–166. PubMed Abstract \| Publisher Full Text\n\nYoo JH, Cha SH, Park CW, et al.: Comparison of mild ovarian stimulation with conventional ovarian stimulation in poor responders. Clin. Exp. Reprod. Med. 2011; 38(3): 159–163. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChiaffarino F, Baldini MP, Scarduelli C, et al.: Prevalence and incidence of depressive and anxious symptoms in couples undergoing assisted reproductive treatment in an Italian infertility department. Eur. J. Obstet. Gynecol. Reprod. Biol. 2011; 158(2): 235–241. Publisher Full Text\n\nSong D, Li X, Yang M, et al.: Fertility quality of life (FertiQoL) among Chinese women undergoing frozen embryo transfer. BMC Womens Health. 2021; 21(1): 1–7. Publisher Full Text\n\nSuleimenova M, Lokshin V, Glushkova N, et al.: Quality-of-Life Assessment of Women Undergoing in vitro Fertilization in Kazakhstan. Int. J. Environ. Res. Public Health. 2022; 19(20): 13568. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMadero S, Gameiro S, García D, et al.: Quality of life, anxiety and depression of German, Italian and French couples undergoing cross-border oocyte donation in Spain. Hum. Reprod. 2017; 32(9): 1862–1870. PubMed Abstract \| Publisher Full Text\n\nWdowiak A, Anusiewicz A, Bakalczuk G, et al.: Assessment of quality of life in infertility treated women in Poland. Int. J. Environ. Res. Public Health. 2021; 18(8): 4275. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHsu P-Y, Lin M-W, Hwang J-L, et al.: The fertility quality of life (FertiQoL) questionnaire in Taiwanese infertile couples. Taiwan. J. Obstet. Gynecol. 2013; 52(2): 204–209. PubMed Abstract \| Publisher Full Text\n\nGolshani F, Mirghafourvand M, Hasanpour S, et al.: The effect of cognitive behavioral therapy on anxiety and depression in Iranian infertile women: a systematic and meta-analytical review. Iran. J. Psychiatry Behav. Sci. 2020; 14(1). Publisher Full Text\n\nShirin A, Atefeh A, Mahlegha D, et al.: The effect of cognitive behavior therapy on attitude of infertile individuals toward child adoption. J. Prev. Med. Hyg. 2022; 63(1): E97–E103. PubMed Abstract \| Publisher Full Text\n\nFaramarzi M, Alipor A, Esmaelzadeh S, et al.: Treatment of depression and anxiety in infertile women: cognitive behavioral therapy versus fluoxetine. J. Affect. Disord. 2008; 108(1-2): 159–164. Publisher Full Text\n\nRooney KL, Domar AD: The relationship between stress and infertility. Dialogues Clin. Neurosci. 2022.\n\nGorayeb R, Borsari ACT, Rosa-e-Silva ACJS, et al.: Brief cognitive behavioral intervention in groups in a Brazilian assisted reproduction program. Behav. Med. 2012; 38(2): 29–35. PubMed Abstract \| Publisher Full Text\n\nLi J, Long L, Liu Y, et al.: Effects of a mindfulness-based intervention on fertility quality of life and pregnancy rates among women subjected to first in vitro fertilization treatment. Behav. Res. Ther. 2016; 77: 96–104. PubMed Abstract \| Publisher Full Text\n\nIbrahim AA: The assessment of educational and supportive care to the infertile females undergoes in vitro Fertilization procedure by clinical pharmacist: A Randomized Clinical Trial.2023. Publisher Full Text\n\nIbrahim AA: Trial protocol for the assessment of educational and supportive care to the infertile females undergoes in vitro Fertilization procedure by clinical pharmacist: a randomized clinical trial.2023. Publisher Full Text\n\nIbrahim AA: CONSORT Checklist for The assessment of educational and supportive care to the infertile females undergoes in vitro Fertilization procedure by clinical pharmacist: A Randomized Clinical Trial.2023. Publisher Full Text" }	[ { "id": "232012", "date": "22 Jan 2024", "name": "Meng-Hsing Wu", "expertise": [ "Reviewer Expertise IVF" ], "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 tried to examine the correlation between the pregnancy rate of IVF female and the presentation of depression symptoms.\n\nThe authors need to use suitable analysis method to evaluate the correlation between the pregnancy rate of IVF female and the presentation of depression symptoms, not just showed the results of pregnancy. The exclusion criteria include the female who had past history of IVF cycle. Therefore, the authors need to more clearly demonstrate they were first time for IVF treatment due to different depression status after failure of embryo transfer. In addition, this is a prospective study. It seems not possible that these female all can receive fresh embryo transfer. The depression status between fresh and frozen embryo transfer should be different and it also possible that failure of TVOR and embryo transfer. There are rare publications to evaluate clinical pharmacist for counseling infertility patients. In page 4 the educational program includes many psychologic strategies. If these pharmacists receive basic training for psychologic counselling and how many times they took for these procedures. There are too many figures and tables those can write into the manuscript. The total scores of FertiQoL are much lower than average of previous studies. For example, Fertility quality of life tool: update on research and practice considerations (Koert E et al, 2021)[Ref1] . The range of median FertiQoL Core, Treatment and subscale (scaled) scores was between 60 and 75. The authors need to explain the reason and further FertiQoL subscale scores analysis is need.\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? No", "responses": [] }, { "id": "257240", "date": "09 May 2024", "name": "Unyime Israel Eshiet", "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\nGeneral Comment: A brilliant study with important findings of public health importance.\nAbstract:\n\nWell structured. However, does not capture important details.\n\nMethod:\nNot properly presented. What type of study was conducted? Cross-sectional? Randomized control? Case control? Etc. Please explain. \"The intervention group received an educational program consisting of five visits” - what was the interval between each clinic visit? What statistical application was used to run the analysis?\nResults:\n“No statistically significant difference was seen in the FertiQoL evaluation scores between the control and intervention groups at the beginning of the study. The FertiQoL, assessed at the end of the trial, exhibited a statistically significant increase in the interventional group.\" - kindly present the statistical values.\nConclusion:\nDoes not reflect the objectives of the study as no mention is made of the impact of pharmacists’ counselling on the quality of life and depression scores of the study population.\nIntroduction:\nHighlights importance of the study. However, the authors should make it more concise and straight to the point.\nMethods:\nSatisfactory.\nResults:\nWell presented.\nDiscussion:\nAuthors have not satisfactorily discussed their results in comparisons with previous studies. Some important aspects of the results presented is not discussed.\nConclusion:\nDoes not reflect the objectives of the study as no mention is made of the impact of pharmacists’ counselling on the quality of life and depression scores of the study population.\nReferences:\nAuthors should ensure that the references comply with the recommended referencing style of 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? 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? No\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-1592
https://f1000research.com/articles/12-1591/v1	14 Dec 23	{ "type": "Research Article", "title": "Assessing the impact of frequent mammography after breast cancer treatment from a single-institution retrospective analysis", "authors": [ "Kellie Spector", "Alexis LeVee", "Scott Karlan", "Farin Amersi", "Arjan Gower", "Heather McArthur", "Alexis LeVee", "Scott Karlan", "Farin Amersi", "Arjan Gower", "Heather McArthur" ], "abstract": "Background Despite prior attempts to establish guidelines, many radiologists still recommend frequent (every six month) mammography after breast conserving surgery. Ideally this recommendation would be based on the incremental value (recurrences detected earlier) of non-annual screening, compared to the associated harm (from false positive results leading to patient distress, unnecessary biopsies/procedures and costs). The aim of this study was to analyze the outcomes of performing biannual mammograms at our institution in order to determine if this may provide any additional benefit to annual mammograms.\n\nMethods A retrospective analysis of 359 female patients with stage 0-III breast cancer who underwent breast-conservation surgery was performed. Data were obtained on breast cancer characteristics, imaging, pathology, and recurrence rates. Descriptive analyses were subsequently performed.\n\nResults A total of 569 6-month and 18-month mammograms were completed after breast-conservation therapy. This led to 22 biopsies, only one of which detected a recurrence (in a high-risk patient who was unable to complete recommended treatment).\n\nConclusions The data suggest that annual surveillance mammography following breast conserving therapy (BCT) is likely sufficient for detection of recurrences, with increased screening leading to increased harm without benefit. More frequent screening should be limited to select high-risk patients.", "keywords": [ "Breast Neoplasms", "Mammography", "Mastectomy", "Segmental", "Recurrence", "Survivorship" ], "content": "Introduction\n\nBreast cancer screening leads to earlier diagnoses, as evidenced by the more than doubling in early-stage breast cancer incidence within three decades after the incorporation of routine mammography in women over 40 years old. Moreover, the incidence of late-stage breast cancer decreased by 8% with mammography.1 However, mammography is also associated with a false-positive rate that leads to additional imaging and biopsies.2 In one recent study of nearly 450,000 women, half of the women that completed 10 years of annual screening mammography had at least one false-positive result and 11% had one subsequent false-positive biopsy,3 so there is some physical, psychological and financial harm. This risk-benefit tension is best illustrated in women with mammograms reported as BI-RADS 4, for whom biopsy is almost always recommended, although the positive predictive value is only 21.1%.4\n\nIn the United States alone, there are over 3.8 million breast cancer survivors, and that number continues to grow.5 These survivors are at risk for both local and distant recurrence regardless of surgical treatment (lumpectomy or mastectomy). A meta-analysis concluded that earlier detection of recurrence confers a survival advantage.6 Consequently, ‘regular’ mammography is recommended for surveillance after breast conserving therapy (BCT). However, the definition of ‘regular’ is subject to some debate, leading to wide variation in the timing of initiation and in the frequency of surveillance mammography.7 Consequently, the American Society of Clinical Oncology (ASCO) and the National Comprehensive Cancer Network (NCCN) published breast cancer surveillance guidelines recommending that, “Women treated with breast-conserving therapy should have their first post-treatment mammogram no earlier than 6 months after definitive radiation therapy. Subsequent mammograms should be obtained every 6 to 12 months for surveillance of abnormalities. Mammography should be performed yearly if stability of mammographic findings is achieved after completion of locoregional therapy” (National Comprehensive Cancer Network, NCCN clinical practice guidelines in oncology: Breast cancer. V.3.2020, 2020).8 The guidelines attempted, in part, to limit the use of semi-annual mammography after BCT, except when mammographic abnormalities are detected; however, they have not been universally accepted. The American College of Radiology has not taken a position on this policy (although their website posted eight other position statements related to mammography in April 2022). Consequently, numerous institutions continue to recommend and perform semi-annual mammography for two or more years after BCT. In this single institution retrospective study, we investigate the impact of biannual mammography after BCT on breast cancer specific outcomes.\n\n\nMethods\n\nAfter approval from the Cedars-Sinai Institutions Review Board (IRB # Pro00057198; April 10, 2019), a retrospective analysis was performed from May 1, 2019, using an institutional database at Cedars-Sinai Medical Center. Patient consent was deemed not necessary and was waived by the Cedars-Sinai Institutions Review Board. Female patients with stage 0-III breast cancer, diagnosed between January 1, 2015, and December 31, 2017 and treated with BCT were included. Patients had to meet the following inclusion criteria: (i) had a new diagnosis of invasive or in situ breast cancer (excluding classic lobular in situ); (ii) completed breast conserving surgery; (iii) were then advised to get screening mammograms every 6 months for two years following surgery; and (iv) had at least one mammogram within 0-12 months, and at least one mammogram within months 13-24 following surgery. Patients with evidence of distant metastases at diagnosis, incomplete records, or a prior history of invasive breast cancer were excluded. Of the 1,056 identified patients, 359 met inclusion criteria.\n\nClinical data was collected including mammography BI-RADS scores, breast biopsy results, recurrence data, and imaging that led to biopsies. Electronic medical records were independently audited by one of the senior authors (S.K.) to verify that no recurrences were missed.\n\nDescriptive analyses were performed by the authors on the data including frequency distributions and measures of central tendency. No software was used.\n\n\nResults\n\nWe identified 359 eligible women. The median age was 65 years (range 25-88 years). A total of 339 patients (94.4%) had unilateral breast cancer and 20 patients (5.6%) had bilateral breast cancer. Breast cancer stage ranged from 0 to IIIC, and multiple histologic subtypes were included. Neoadjuvant chemotherapy was administered in 28 patients (7.8%), adjuvant chemotherapy was administered in 39 patients (10.9%), adjuvant radiation was administered in 305 patients (85.0%), and adjuvant endocrine therapy was administered in 259 patients (72.1%) (Table 1).\n\nHR, hormone receptor; HER2, human epidermal growth factor receptor 2.\n\nDuring the 24 months of follow-up, 47 biopsies were performed on 46 patients (12.8%). 31 of these were performed on the ipsilateral breast and 16 were performed on the contralateral breast. Pathology was benign in 35 of the biopsies (74.5%) and malignant in 12 of the biopsies (25.5%). The imaging studies leading to these biopsies were a combination of surveillance mammography, magnetic resonance imaging (MRI), or diagnostic imaging based on clinical findings (Table 2).\n\nDCIS, ductal carcinoma in situ; IDCA, invasive ductal carcinoma; ILCA, invasive lobular carcinoma; MRI, magnetic resonance imaging.\n\nMammograms were obtained 6 months after BCT in 289 patients (80.5%), with a median time to completion of 6.7 months. In total, 11 (3.8%) of these mammograms led to biopsies, seven (2.4%) of which were in the ipsilateral breast. One detected recurrent invasive ductal carcinoma; the other 10 were benign.\n\nMammograms were obtained 12 months after BCT in 309 patients (86.1%). Overall, 12 (3.9%) of these mammograms led to biopsies, eight (2.6%) of which were in the ipsilateral breast. This led to the identification of three recurrences (invasive ductal carcinoma in one patient and ductal carcinoma in situ (DCIS) in two) and one new primary (DCIS); seven biopsies were benign.\n\nMammograms were obtained 18 months after BCT in 282 patients (78.6%), with a median time to completion of 18.6 months. A total of nine (3.2%) of these mammograms led to biopsies, four (1.4%) of which were in the ipsilateral breast. One detected a new focus of DCIS in the contralateral breast; the other eight were benign (Table 3). In these nine patients, the prior mammograms (done at 6 and 12 months) showed no significant abnormalities. The only findings were benign-appearing calcifications (in two patients), a simple cyst a (in one patient) and scarring at the prior surgical site (in one patient).\n\nMammograms were obtained 24 months after BCT in 275 patients (76.6%). A total of six (2.2%) of these mammograms led to biopsies, four (1.5%) of which were in the ipsilateral breast. Two showed recurrent DCIS, one found new DCIS, and three were benign.\n\nThus, among the 359 patients included in the study, nine (2.5%) patients had DCIS or cancer identified by screening mammography within 24 months of surgical treatment. This included six loco-regional recurrences in the ipsilateral breast and three new primaries in the contralateral breast. Three additional recurrences were detected by imaging that was ordered because of clinical signs/symptoms. Among the 6-month and 18-month mammograms, only one recurrence was diagnosed (by 6-month mammogram, see below). All recurrences were local without evidence of metastatic disease.\n\nRecurrences identified on 6-month surveillance mammogram\n\nPatient A is a 61-year-old-woman with a severe cardiomyopathy and an external left ventricular assistance device (LVAD). She presented with a large triple-negative left breast cancer and a small ER-positive right breast cancer. Bilateral lumpectomies (and a left sentinel node biopsy) were performed. Left breast pathology revealed a 4 cm, grade 3, ER negative 0%, PR negative 0%, human epidermal growth factor receptor 2 (HER2) negative (FISH ratio 1.3), invasive ductal carcinoma with negative margins, no lymphovascular invasion, and two negative sentinel nodes. Right breast pathology revealed a 1 cm, grade 3, ER positive 97%, PR negative <1%, HER2 negative (FISH ratio 1.2), invasive ductal carcinoma with negative margins and no lymphovascular invasion. Adjuvant treatment was recommended but delayed three months because of a wound dehiscence. She was then given four cycles of adjuvant AC (doxorubicin and cyclophosphamide) and five doses of paclitaxel, with doses reduced substantially. Nonetheless, she became dehydrated and this caused her LVAD to malfunction. Chemotherapy was then discontinued. Before starting radiation therapy, she underwent a 6-month mammogram. This was reported as BI-RADS 4 and showed a new mass at the left breast surgical site. A biopsy demonstrated recurrent “triple negative” invasive ductal carcinoma. Staging studies showed no evidence of metastatic disease.\n\nRecurrences identified on 12-month surveillance mammogram\n\nPatient B is a 59-year-old woman with left breast ER positive (4%), PR positive (4%), and HER2 positive (3+ IHC) DCIS. She underwent lumpectomy with subsequent re-excision to achieve negative margins, followed by adjuvant radiation therapy. She declined an aromatase inhibitor.\n\nPatient C is a 49-year-old woman diagnosed with ER positive (1%), PR positive (1%), and HER2 negative (IHC 1+, FISH ratio 1.0) left breast DCIS on core biopsy. She had extensive DCIS on lumpectomy and underwent re-excision to achieve negative margins. She subsequently received adjuvant radiation therapy and tamoxifen.\n\nPatient D is a 78-year-old woman who had a left breast lumpectomy done for a 3.5 cm poorly differentiated, ER positive (98%), PR Positive (2%), HER-2 negative (IHC 0) infiltrating ductal carcinoma with several satellite foci and negative margins. A sentinel node biopsy was not performed, and radiation was not attempted due to co-morbidities. She declined an aromatase inhibitor.\n\nRecurrences identified on 18-month surveillance mammogram\n\nNo recurrences were detected at 18 months.\n\nRecurrences identified on 24-month surveillance mammogram\n\nPatient E is a 62-year-old woman with right breast ER positive (99%), PR positive (99%), and HER-2 Negative (IHC 1+, FISH ratio 1.5) invasive ductal carcinoma. She had a right breast lumpectomy with negative margins and was then treated with accelerated partial breast radiation. She declined an aromatase inhibitor.\n\nPatient F is a 56-year-old woman diagnosed with ER positive (99%), PR positive (99%), HER-2 negative (IHC 1+) right breast DCIS. She underwent a lumpectomy, followed by re-excision to obtain negative margins. She then significantly delayed her care for more than six months, so adjuvant radiation therapy was not performed. She declined Tamoxifen.\n\nRecurrences identified by methods other than surveillance mammography\n\nThree recurrences were detected clinically due to patients reporting abnormalities (one palpated a breast mass, one palpated an axillary mass, and one noted nipple retraction and pain in her breast and axilla.). Diagnostic imaging studies revealed recurrent invasive carcinomas, all of which were localized.\n\nIn this retrospective study, one recurrence was detected with 6-month surveillance mammography and no recurrences were detected with 18-month surveillance mammography. 289 6-month mammograms were performed and 282 18-month mammograms were performed, for a total of 571 mammograms. The single recurrence was in a high-risk patient with triple negative breast cancer who was unable to complete recommended therapy (chemotherapy and radiation). Delaying systemic therapy in triple negative breast cancer is associated with a higher recurrence risk, so this shouldn’t be all that surprising. Nonetheless, the cumulative detection rate was only 0.18%. Had we excluded patients at particularly high-risk for local early recurrence, we would have concluded that there was no benefit from 6-month and 18-month surveillance mammograms.\n\nThe 289 6-month mammograms led to 11 biopsies, of which 10 were benign. The malignant biopsy was the recurrence discussed above. The 282 18-month mammograms led to nine biopsies, of which eight were benign. The malignant biopsy detected a new contralateral focus of DCIS.\n\n\nDiscussion\n\nIn this study, 571 mammograms were completed at 6- and 18-months after BCT among 359 patients, and lead to 20 biopsies, of which two identified malignancy (10%) and 18 were false positives (90%). The added value of interval mammograms is likely limited by the natural history of breast cancer, which has few early recurrences, and by successful drug development which had reduced recurrence rates further. There are very few recurrences that occur within two years.9,10 By contrast, 15% of local recurrences present more than 20 years after diagnosis.11 Thus, it is difficult to undertake a prospective randomized trial studying the impact of treatment within two years of diagnosis, and this presumably explains why the literature consists of retrospective single institution studies with low recurrence rates.\n\nThe largest study supporting semi-annual mammography compared patients that “complied” with their institutional recommendation for five years of semi-annual surveillance to “noncompliant” patients. They found more early-stage cancers in “compliant” patients.12 As with other studies, this was a single-institution retrospective non-randomized study, and while they enrolled 2,329 patients, it was still limited by small numbers of events (e.g., 4 vs. 6 patients with stage 2 disease at recurrence). In addition, they failed to differentiate new primary breast cancers from recurrent disease, did not delineate whether the recurrences were ipsilateral, and most important, failed to determine whether the recurrences were identified on the standard-of-care annual mammograms or the additional 6-month interim mammograms.\n\nOther studies have concluded that annual surveillance is adequate. In one study of 1,425 patients, two recurrences (both noninvasive) were identified on mammograms done less than one year from BCT, and nine recurrences (three invasive, six noninvasive) were identified during the second year. The yield of mammography was thus similar to the general population, suggesting that annual screening should be adequate after BCT.13 Other studies have reinforced the conclusion that the yield is simply too low to justify additional screening. One study with 408 patients looked at mammography done within one year of completing radiation therapy (after BCT). Only two cases of DCIS (no invasive cancers) were identified.14 A third study concluded, after looking at their institutional experience, that the rate of ipsilateral breast cancer recurrence was extremely low during the first two years after BCT (two recurrences out of 375 patients), and the addition of interval ipsilateral mammograms at 6 months and 18 months provided no additional clinical benefit.15\n\nAs another consideration, mammography is less sensitive in women with a history of breast cancer [65.4% (95% CI, 61.5–69.0%)], compared to those with no such history [76.5% (95% CI, 71.7–80.7%)].16 Sensitivity is also lower within the first five years after primary breast cancer treatment [60.2% (95%CI, 54.7%-65.5%)] compared to after 5 years from treatment [70.8% (95% CI, 65.4%-75.6%)].16 Often in clinical practice, mammograms are obtained 6 months after BCT to serve as a baseline. However, there may be limited value at this time as the patient heals from surgery and radiation therapy. By one year, mammography provides a more reliable baseline.17,18\n\nThe argument for interval mammography hinges on the benefit of catching a recurrence 6 months earlier. If this is unlikely, then the harm becomes more relevant. Although much of the incurred harm is difficult to quantify (anxiety and pain from biopsies), cost is the one aspect that can be quantified. For example, in one study of 128 patients that had mammography within one year of treatment, there was no benefit, but cost-of-care was markedly increased.19 Specifically, among the 87 patients who underwent post-operative mammography within 3 to 15 months, 78% of post-operative imaging costs were incurred by tests performed less than 12 months after completion of treatment (USD 32,506/USD 41,571). An additional USD 13,856 was spent on additional imaging and procedures that were clinically inconsequential. Six patients required further intervention at a cost of over USD 2,300 per patient, and three patients required invasive procedures, without clinical benefit.\n\nTo fill the void left by the absence of a multi-center prospective randomized trial, we have reviewed our institutional experience and reached similar conclusions. The risk of recurrence within two years of BCT is extremely low. There is limited value from adding mammograms at 6-month and 18-month intervals. These additional imaging studies are associated with false positives and unnecessary biopsies. Consequently, we found that our institutional policy, that recommends semi-annual mammography for two years after BCT is not supported by our institutional data. Specifically, we found minimal benefit despite numerous biopsies.\n\nThis does not preclude the possibility that certain sub-groups may benefit from semi-annual surveillance mammography. Perhaps we should be adopting biologically tailored imaging practices as we have for most other aspects of breast cancer care. At a minimum, additional mammography should be limited to patients that have a non-trivial risk of recurrence in two years. This could limit semi-annual screening to selective high-risk populations, such as patients with HER2 positive or triple-negative disease. The 6-month mammograms may also be of value in cases where we are concerned about missing a focus of cancer, e.g., patients with multi-focal disease, extensive DCIS, difficulty obtaining negative margins, or close margins. Failure to complete recommended treatment may be an additional factor.\n\nWe acknowledge that our study suffers from many of the same limitations. It is a retrospective single-institution study with a small sample size (359 patients). In addition, we did not consider compliance. All subjects that had an institutional treatment plan to complete 6-month mammograms were included, although there was variable compliance with some patients only completing 2 or 3 mammograms within the 2-year period.\n\nIn summary, guidelines vary on recommended frequency and duration of mammographic surveillance following primary breast cancer surgery. In our study of 359 patients, only one breast cancer recurrence was detected by 6-month interval surveillance mammography, and no recurrences were detected by 18-month mammograms. The recurrence was in a patient with high-risk features who was unable to complete recommended treatment. In addition, a significant number of false positive mammograms at 6-months and 18-months led to biopsies. Therefore, our patients would have benefited from the ASCO and NCCN endorsed guidelines for annual surveillance mammography following BCT. While we support this guideline for most patients, we acknowledge that select high-risk patients may benefit from more frequent mammography.", "appendix": "Data availability\n\nThe data were provided by a third party therefore restrictions to data include change of institution by authors involved with data management and cessation of access to institutional database. If the reader or referee is interested in gaining access to primary data, they may contact the primary author ( kelliespector@gmail.com ) who can facilitate access via institutional IRB board.\n\n\nReferences\n\nBleyer A, Welch HG: Effect of three decades of screening mammography on breast-cancer incidence. N. Engl. J. Med. 2012; 367(21): 1998–2005. PubMed Abstract \| Publisher Full Text\n\nSeely JM, Alhassan T: Screening for breast cancer in 2018-what should we be doing today? Curr. Oncol. 2018; 25(Suppl 1): S115–S124. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHo TH, Bissell MCS, Kerlikowske K, et al.: Cumulative Probability of False-Positive Results After 10 Years of Screening With Digital Breast Tomosynthesis vs Digital Mammography. JAMA Netw. Open. 2022; 5(3): e222440. Published 2022 Mar 1. Publisher Full Text\n\nElezaby M, Li G, Bhargavan-Chatfield M, et al.: ACR BI-RADS Assessment Category 4 Subdivisions in Diagnostic Mammography: Utilization and Outcomes in the National Mammography Database. Radiology. 2018; 287(2): 416–422. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMiller KD, Nogueira L, Mariotto AB, et al.: Cancer treatment and survivorship statistics, 2019. CA Cancer J. Clin. 2019; 69(5): 363–385. Publisher Full Text\n\nLu WL, Jansen L, Post WJ, et al.: Impact on survival of early detection of isolated breast recurrences after the primary treatment for breast cancer: a meta-analysis. Breast Cancer Res. Treat. 2009; 114(3): 403–412. Publisher Full Text\n\nLam DL, Houssami N, Lee JM: Imaging Surveillance After Primary Breast Cancer Treatment. AJR Am. J. Roentgenol. 2017; 208(3): 676–686. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKhatcheressian JL, Hurley P, Bantug E, et al.: Breast cancer follow-up and management after primary treatment: American Society of Clinical Oncology clinical practice guideline update. J. Clin. Oncol. 2013; 31(7): 961–965. Publisher Full Text\n\nVeronesi U, Cascinelli N, Mariani L, et al.: Twenty-year follow-up of a randomized study comparing breast-conserving surgery with radical mastectomy for early breast cancer. N. Engl. J. Med. 2002 Oct 17; 347(16): 1227–1232. PubMed Abstract\n\nMcBain CA, Young EA, Swindell R, et al.: Local recurrence of breast cancer following surgery and radiotherapy: incidence and outcome. Clin. Oncol. (R. Coll. Radiol.). 2003; 15(1): 25–31. Publisher Full Text\n\nLyngholm CD, Laurberg T, Alsner J, et al.: Failure pattern and survival after breast conserving therapy. Long-term results of the Danish Breast Cancer Group (DBCG) 89 TM cohort. Acta Oncol. 2016; 55(8): 983–992. PubMed Abstract \| Publisher Full Text\n\nArasu VA, Joe BN, Lvoff NM, et al.: Benefit of semiannual ipsilateral mammographic surveillance following breast conservation therapy. Radiology. 2012; 264(2): 371–377. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHymas RV, Gaffney DK, Parkinson BT, et al.: Is short-interval mammography necessary after breast conservation surgery and radiation treatment in breast cancer patients? Int. J. Radiat. Oncol. Biol. Phys. 2012; 83(2): 519–524. Publisher Full Text\n\nLin K, Eradat J, Mehta NH, et al.: Is a short-interval postradiation mammogram necessary after conservative surgery and radiation in breast cancer? Int. J. Radiat. Oncol. Biol. Phys. 2008; 72(4): 1041–1047. PubMed Abstract \| Publisher Full Text\n\nGunia SR, Merrigan TL, Poulton TB, et al.: Evaluation of appropriate short-term mammographic surveillance in patients who undergo breast-conserving Surgery (BCS). Ann. Surg. Oncol. 2012; 19(10): 3139–3143. Publisher Full Text\n\nHoussami N, Abraham LA, Miglioretti DL, et al.: Accuracy and outcomes of screening mammography in women with a personal history of early-stage breast cancer. JAMA. 2011; 305(8): 790–799. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDershaw DD: Mammography in patients with breast cancer treated by breast conservation (lumpectomy with or without radiation). AJR Am. J. Roentgenol. 1995; 164(2): 309–316. Publisher Full Text\n\nBuckley JH, Roebuck EJ: Mammographic changes following radiotherapy. Br. J. Radiol. 1986; 59(700): 337–344. Publisher Full Text\n\nAllen A, Cauthen A, Vaughan J, et al.: The Clinical Utility and Cost of Postoperative Mammography Completed within One Year of Breast Conserving Therapy: Is It Worth It? Am. Surg. 2017; 83(8): 871–874. Publisher Full Text" }	[ { "id": "245781", "date": "21 Mar 2024", "name": "Louiza S Velentzis", "expertise": [ "Reviewer Expertise epidemiology of breast and cervical cancer prevention" ], "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 is a single-institution retrospective review of short-term mammographic surveillance data of women who have undergone breast conserving surgery following a breast cancer diagnosis to determine whether 6-month and 18-month mammography confers additional benefit to annual mammography. Although the study is small (n=359) results provide additional evidence to the existing international literature consisting on similar single-institution studies, towards identifying the optimal interval for mammographic surveillance post breast-conserving surgery. Costing of biopsies, imaging and any other associated expenses as a result of 6- and 18-month mammographic surveillance would have complemented the results, however, the existing findings directly address the aim. Please find below suggested edits: 1. Although patient and tumour characteristics (from breast conserving surgery) as well as treatment details are presented in the results it is not clear in the methods section how these were obtained as this information is not mentioned. 2. The aim of the study at the end of the introduction refers to the impact on breast cancer specific outcomes. In the methods the authors need to specify the outcomes assessed. 3. Results section: the initial number of women within the timeframe of 1st Jan 2015 to 31st Dec 2017 prior to exclusions being applied needs to be mentioned. Additionally, the number of women excluded for each exclusion criterion also needs to be mentioned. 4.Table 1: although the table is comprehensive it would be more informative if characteristics were presented separately for those who had a recurrence vs those who did not. Also, please report numbers for nodal involvement as a separate characteristic. 5. Table 3: for completeness, data from 12 months and 24 months should be added to this table. 6. Table 2: If the data is available the range in months of when the mammograms were performed could be added. For example for the 6 month mammogram the range could be 5-8 months. 7. With the exception of patient A, tumour characteristics (type, grade, HR status) of the recurrent tumours or new primaries have not been provided. 8. Recurrences detected due to clinical signs and symptoms: information on the time of clinical detection or time of imaging (since surgery) for these additional recurrences not detected through mammography, should be provided.\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": [] } ]	1	https://f1000research.com/articles/12-1591
https://f1000research.com/articles/12-1587/v1	14 Dec 23	{ "type": "Systematic Review", "title": "Risk factors of post-operative optic nerve injury after vitrectomy: a systematic review", "authors": [ "Ari Djatikusumo", "Andi Arus Victor", "Anggun Rama Yudantha", "Ananda Kukuh Adishabri", "Kemal Akbar Suryoadji", "Andi Arus Victor", "Anggun Rama Yudantha", "Ananda Kukuh Adishabri", "Kemal Akbar Suryoadji" ], "abstract": "Background Vitrectomy is a common procedure used to treat various disorders in the back of the eye. Although it is generally considered safe and effective, there is a risk of complications, including optic nerve damage, which can lead to vision problems. The aim of this study is to determine risk factors of optic nerve injury after vitrectomy for various indications.\n\nMethods We conducted a systematic review through literature search via Cochrane, PubMed, Scopus, and Embase, as well as a hand search of relevant journals with the keywords: “(postoperative optic nerve injury) AND (vitrectomy) AND (risk factor)”. The inclusion criteria were: (1) patients with postoperative optic nerve injury after vitrectomy, (2) clinical trial, case-control, or cohort study, (3) analyzing risk factors of optic nerve injury after vitrectomy, (4) published in the last 15 years and conducted in English. For risk of bias assessment, we used the risk of bias (RoB) 2.0 for randomized controlled trials and the ROBINS-E tool for observational studies.\n\nResults Thirteen eligible studies were included in this study. We found that damage to the optic nerve can happen either during or after a vitrectomy procedure. This is linked to four main risk factors: removing the internal limiting membrane, having a lower average ocular perfusion pressure, using silicone oil as a tamponade agent, and using ICG as an ILM staining agent.\n\nConclusions Removing the internal limiting membrane, having a lower average ocular perfusion pressure, using silicone oil as a tamponade agent, and using ICG as an ILM staining agent were associated with the occurrence of optic nerve injury following vitrectomy. Our study has limitations, including more retrospective studies than prospective ones and difficulties in combining and analyzing information from individual studies. Additionally, merging data from various studies is challenging due to differences in original research.\n\nPROSPERO registration CRD42023453533 (22/08/2023).", "keywords": [ "postoperative optic nerve injury", "risk factor", "vitrectomy" ], "content": "Introduction\n\nVitrectomy is a standard procedure during surgical repair of many posterior eye segment disorders, such as retinal detachment, epiretinal membrane, macular hole, vitreous hemorrhage, and ocular trauma. The procedure of vitrectomy involves removing vitreous gel from the eye and replacing it with saline solution, silicone oil, or gas bubble.1 Recent progress in instrumentation, technology, and surgical technique has resulted in the increasing use of vitreoretinal surgeries to treat posterior eye segment disorders. These developments have created an increase in expectations from both doctors and patients regarding anatomical and functional outcomes.2\n\nWhile vitrectomy is considered safe and effective, there is a risk of complications, including optic nerve injury, which can result in visual field defects and reduced visual acuity.1 The optic nerve is a component of the visual pathway that is responsible for transmitting visual information from the retina to the brain.3 A review conducted by Taban et al. (2007) reported the outcomes of 1,104 patients who underwent vitrectomy, revealing that 160 cases (14.5%), with a range of less than 1% to 71%, experienced unexplained postoperative visual field defects. Out of these cases, 31 eyes (19.4%) showed indications of optic nerve damage after vitrectomy, such as pallor, relative afferent pupillary defect, and intrapapillary hemorrhage.4\n\nIt is important to note that the consequences of this complication can be significant and may lead to permanent vision loss or blindness.1 In this review, we will discuss any risk factors regarding postoperative optic nerve injury after vitrectomy. By understanding the risk factor of this serious complication, it could minimize the risks and achieve the best possible outcomes.\n\n\nMethods\n\nWe submitted a protocol for registration before drafting this review and meta-analysis. The protocol was successfully registered in the International prospective register of systematic reviews (PROSPERO) under the code CRD42023453533 on 22nd August 2023.\n\nWhat is the risk factor of optic nerve injury following vitrectomy for various indications?\n\nWe conducted a systematic review through a literature search using electronic databases, including Cochrane, PubMed, Scopus, and EMBASE, as well as a hand search of relevant journals with the keywords “(postoperative optic nerve injury) AND (vitrectomy) AND (risk factor)”. Postoperative optic nerve injury was defined as the damage of the optic nerve component which occurs as a complication of ocular surgery. Postoperative optic nerve damage was measured through imaging techniques, clinical examination, or electrophysiological tests. Vitrectomy refers to a surgical procedure in the eye by removing the vitreous gel in the eye and replacing it with saline, silicone oil, or gas. This study used the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) guidelines.53\n\nThe inclusion criteria of this study are: (1) patients with postoperative optic nerve injury after vitrectomy, (2) clinical trial, case-control, or cohort study, (3) analyzing risk factor of optic nerve injury after vitrectomy, (4) published in the last 15 years and is conducted in English. Exclusion criteria of this study are: (1) studies published >15 years ago, (2) case report or review study, (3) studies with diabetic retinopathies or previous optic neuropathy patients, (4) full-text article is not available, (5) non-English article.\n\nFive investigators independently reviewed titles and abstracts, excluding irrelevant studies. Subsequently, authors AD, AAV, ARY, AKA, and KAS individually assessed each entry using ‘Yes,’ ‘No,’ or ‘Maybe’ based on inclusion and exclusion criteria.\n\nFive researchers independently reviewed extracted data from eligible studies using a standardized data extraction form. The data extracted included study design, patient demographics, length of follow-up, indication for vitrectomy, surgical procedure, risk factor assessed, optic nerve injury complication, and primary outcomes of the study. Discrepancies were resolved through discussion, and the remaining studies were checked for duplicates. Systematic evaluation, following the inclusion and exclusion criteria, was conducted on the final retrieved studies.\n\nThe quality of the eligible studies was assessed using the risk of bias (RoB) 2.0 for randomized controlled trials and the ROBINS-E tool for observational studies.\n\nData extracted from eligible studies were synthesized using a narrative approach. Meta-analysis was not performed due to the heterogeneity of study designs and outcomes.\n\n\nResults\n\nA total of 13 studies were included in this systematic review. The flow chart is shown in Figure 1. Study characteristics are shown in Table 1.\n\n\n\n- Coexisting macular lesion\n\n- ILM peeling\n\n- Gas tamponade\n\n- Combined cataract sugery\n\n\n\n- ILM peeling\n\n\n\n- Age\n\n- Gender\n\n- Medical History\n\n- Anesthesia technique\n\n- Scleral Buckle\n\n- Total operative time\n\n- MOPP of ≤30 mmHg\n\n- Time MOPP <30 mmHg\n\n\n\n- Vitrectomy timing\n\n\n\n- Air (group 1) vs. C3F8 (group 2) vs. BSS (group 3) tamponade\n\n\n\n- SO vs. C3F8 gas tamponade\n\n\n\n- SO vs. C3F8 gas tamponade\n\n\n\n- SO vs. C3F8 gas tamponade\n\n\n\n- SO vs. sterilized air tamponade\n\n\n\n- DoubledyneTM vs. TwinTM\n\n\n\n- ICG vs. BBG vs. TA\n\n\n\n- MBB vs. AV 17-M\n\n\n\n- BBG vs. ICG\n\nThis systematic review included 3 randomized clinical trials (RCT) and 10 observational studies. Quality assessment was conducted using the risk of bias (RoB) 2.0 for RCT and ROBINS-E for observational studies. Bias arising from the randomization process was seen in all RCTs, due to none reported a concealment of allocation sequence. Nikolaenko et al.9 and Picirillo et al.14 also had possible bias due to missing outcome data. The risk of bias in RCT is shown in Figure 2 and Figure 3.\n\nBias due to confounding was reported in four studies. Demographic data (e.g., age, gender) were different between groups in study conducted by Speide, et al.,6 Elghawy et al.,8 and Moharram et al.10 The confounding factor that may affect study outcome was type of gas used in the study conducted by Rohrig, et al.16 Selection bias was seen in Spaide et al.6 due to no clear explanation regarding eligibility criteria for patient selection. The risk of bias in observational studies is shown in Figure 4 and Figure 5.\n\nPark et al. (2016) investigated the risk factors for a dissociated optic nerve fiber layer (DONFL) after epiretinal membrane surgery. There was no significant difference between the DONFL group and control group in this study regarding mean age (p = 0.745), sex (p = 0.674), mean follow-up time (p = 0.482), mean preoperative best corrected visual acuity (p = 0.967), mean duration of symptoms (p = 0.562), and mean axial length of the eye (p = 0.284). ILM peeling was performed in 29 of 30 eyes (96.7%) in DONFL group and 126 of 266 eyes (47.4%) in control group peeling (odds ratio, 32.22 [4.33–240.0]; p = 0.001).5 Similar result was shown in Spaide et al. (2012), in which ILM peeling was performed in 13 of 13 eyes (100%) in patients with postoperative inner retinal dimpling and 5 of 12 eyes (42%) in patients without postoperative inner retinal dimpling (p = 0.001). In the areas of the dimples, imaging examination showed a thinning of ganglion cell layer with decreased reflectivity from nerve fiber layer.6\n\nBansal et al. (2012) examined the clinical characteristic and potential risk factors associated with optic neuropathy after vitrectomy for macula-sparing primary RRD. All 7 patients with post-vitrectomy optic neuropathy had visual acuity less than 20/200, RAPD (+), visual field defect, and pallor optic nerve. This study showed that 5 of 7 patients (71%) with post-vitrectomy optic neuropathy experienced a reduced mean ocular perfusion pressure (≤30 mmHg) compared with 7 of 42 patients (17%) in control group (odds ratio, 15.39 [1.56 – 774]; p = 0.01). Furthermore, patients with post-vitrectomy optic neuropathy had longer durations during which the mean ocular perfusion pressure was ≤30 mmHg (70 min) compared with control group (15 min) (p = 0.02).7\n\nAccording to Elghawy et al. (2022), while postoperative visual acuity between early repair group (<48 h) and moderately delayed repair group (3-7 days) showed no difference (p = 0.163), post-operative visual acuity was significantly better in early repair compared to late repair group (> 7 days) (p = 0.010). However, this study reported no significant difference regarding postoperative complications among the groups including the development of glaucoma (p = 0.52).8\n\nNikolaenko et al. (2019) reported the effect of tamponade type used in vitrectomy for vitreomacular traction syndrome on retinal and optic nerve functional activity. Electrophysiological testing was performed to assess the functional activity of retina and optic nerve. The functional activity of neurons in inner retinal layers was assessed by electrical sensitivity (ES) threshold and critical frequency of phosphene disappearance (CFPD) values, while the functional activity of optic nerve was evaluated by flash visual evoked potential (FVEP) latency. This study reported that the functional activity of retinal inner layers and the optic nerve in group 1 (vitrectomy + air tamponade) and group 3 (vitrectomy + BSS tamponade) restored twice as actively as that in group 2 (vitrectomy + C3F8 gas tamponade). Park et al. (2016) also reported that the use of intravitreal gas tamponade was significantly associated with DONFL formation (odds ratio, 2.33 [1.03–5.28]; p = 0.042).9 Another study by Lee et al. (2018) reported a greater reduction of RNFL thickness in eyes with silicone oil (SO) tamponade compared to eyes with C3F8 gas group at 6 months and 9 months after surgery in macula-sparing RD (p = 0.006 and p = 0.005, respectively).11 On the contrary, Inan et al. (2020) reported no significant difference of RNFL thickness between SO and C3F8 gas group, even though a thinning in the layers of the ganglion cell layer, outer plexiform layer, and outer nuclear layer of the central subfield was found significantly greater in the SO group.12 Zhou et al. (2020) compared the effect of SO tamponade and sterilized air tamponade on RNFL thickness in macula-on RRD patients. This study reported a greater reduction of RNFL thickness in eyes with SO tamponade compared to sterilized air tamponade at 6 weeks postoperatively.13 Moharram et al. (2020) reported no significant difference between silicone oil tamponade and gas tamponade groups regarding postoperative glaucoma and ERM formation in retinal detachment associated with giant retinal tears. Both groups in this study also achieved similar favorable anatomical outcomes.10\n\nPicirillo et al. (2021) reported no significant difference regarding average RNFL thickness before and after surgery (6 months follow-up) in the use of DoubledyneTM and TwinTM as a dye to perform peeling of epiretinal membrane or internal membrane peeling (p > 0.05). This study also reported no toxic dye-related complications were observed in either group.14 Similar result was shown in Toba et al. (2014), this study compared the changes of RNFL thickness in macular holes after vitrectomy with indocyanine green- (ICG-), brilliant blue G- (BBG-), and triamcinolone acetonide (TA-) assisted ILM peeling. This study reported no significant difference regarding RNFL thickness between those groups for at least 12 months postoperatively.15 Rohrig et al. (2019) also reported no significant difference between the use of MBB and AV 17-M in terms of inner segment/outer segment defect.16 However, Baba et al. (2012) reported faster restoration of inner segment/outer segment junction in brilliant blue G (BBG) group compared to indocyanine green (ICG) group. Also, the central foveal thickness was significantly thinner in ICG used. Therefore, this study suggested that BBG may be a better agent than ICG.17\n\n\nDiscussion\n\nVitrectomy is a common procedure used in the surgical treatment of various disorders affecting the back of the eye, such as retinal detachment, epiretinal membrane, macular hole, vitreous hemorrhage, and ocular trauma. Although vitrectomy is considered to be a safe and effective treatment, it does come with the risk of complications, such as optic nerve injury. Optic nerve injury can lead to a reduction in visual acuity and visual field defects.1 In this systematic review, fourteen studies revealed four main risk factors of optic nerve injury following vitrectomy for various indications, including removal of the internal limiting membrane, reduced mean ocular perfusion pressure, the use of particular tamponade agent, and the use of ICG as ILM staining agent.\n\nAfter a standard surgical procedure of pars plana vitrectomy (PPV), the ILM peeling can be performed by carefully detaching and removing the posterior hyaloid to prevent the growth of cells and the subsequent traction of the retina.18 In our review, two studies reported that the removal of the internal limiting membrane was significantly associated with dissociated optic nerve fiber layer (DONFL) formation. DONFL was seen postoperatively using fundus photographs and optical coherence tomographic (OCT) scan.5,6 There are various possible explanations for the formation of DONFL after ILM peeling procedure. It may occur as an acute response due to direct surgical damage to the inner layer of the retina during the ILM peeling procedure.19 However, Runkle et al. (2018) reported that the DONFL formation is more likely to be caused by the tractional forces from peeling over a large area, rather than the physical contact between the surgical instruments and the tissue.20 Another potential explanation is that membrane peeling might cause harm to the footplates of Müller cells that are attached to the ILM.6 According to Pan et al. (2014), intraoperative trauma to the retinal nerve fiber layer during membrane peeling led to central scotoma and decreased visual acuity postoperatively.21 More research regarding intraoperative OCT in the development of minimally traumatic ILM peeling procedures is needed to achieve the best possible outcome.\n\nOcular perfusion pressure (OPP) is determined by calculating the difference between the mean arterial pressure (MAP) and the intraocular pressure (IOP). The corresponding mean ocular perfusion pressure (MOPP) in the supine position was calculated as MOPP = 115/130 x (MAP – IOP).22 Thus, a decrease in systemic blood pressure or an increase in IOP can lead to a decrease in OPP. The body’s natural ability to regulate blood flow to the optic nerve and retina occurs within a broad range of perfusion pressures, which helps to minimize the risk of ischemic damage. However, in this review, Bansal et al. (2012) reported a significant association between reduced mean ocular perfusion pressure (≤30 mmHg) and post-vitrectomy optic neuropathy, as manifested by visual acuity less than 20/200, RAPD (+), visual field defect, and pallor optic nerve.7 This result is consistent with Hayreh et al. (2001), which suggested that when the ocular perfusion pressure (OPP) drops below 30 to 35 mmHg, the autoregulation of blood flow is disrupted, and there is a risk of ischemic damage to the optic nerve.23 This scenario is also similar to cases of ischemic optic neuropathy that have been observed following spinal and cardiothoracic procedures, in which hypotension, blood loss, and increased intraocular pressure (IOP) have been associated with decreased ocular perfusion.24 Moreover, Bansal et al. (2012) also reported that patients with post-vitrectomy optic neuropathy had longer durations during which the mean ocular perfusion pressure was <30 mmHg compared with control group, suggesting that the duration of reduced ocular perfusion also has an influence on the occurrence of post-vitrectomy optic neuropathy.7\n\nIn the surgery of retinal detachment, an intraocular tamponade agent is used to create surface tension around retinal breaks, which helps to stop additional fluid from entering the subretinal space until a permanent seal is provided by retinopexy. The two primary types of tamponade agents frequently used are gases and silicone oils.25 Air, SF6, and perfluoropropane (C3F8) are the most frequently used gas tamponade in the USA.26 Air tamponade does not expand, unlike 100% SF6 which expands approximately two times over 1-2 days, and 100% C3F8 which expands around four times over 3-4 days.27 After a complete gas-fluid exchange, gas tamponade agents will be absorbed spontaneously from the vitreous cavity, with air taking about 5-7 days, 20% SF6 approximately 2 weeks, and 14% C3F8 around 8 weeks.28 In contrast with gases, silicone oils are permanent and will stay in the eye until they are removed surgically.29 1.000 and 5.000 centistokes (cSt) silicone oils are the most frequently used silicone oils in the USA.30 Gases possess greater surface tension and buoyancy force compared to silicone oils.31\n\nIn this review, we compared the effect of each type of intraocular tamponade agent on the occurrence of optic nerve injury. Nikolaenko et al. (2019) reported that the functional activity of retinal inner layers and the optic nerve in air tamponade group and BSS group restored twice as fast as that in C3F8 gas tamponade group in vitreomacular traction syndrome.9 It could possibly be caused by a rise in intraocular pressure (IOP), which is a common complication that occurs when gas tamponades are used. Thus, increased IOP following vitrectomy can result in damage to the optic nerve, retinal ischemia, and subsequent vision loss. This can occur through an open-angle mechanism, closed-angle mechanism, or both. In the case of an open-angle mechanism, the rise in IOP is due to the expansion of intraocular gas tamponade agent.32\n\nWhile gas tamponade agent has worse outcome compared to air tamponade regarding retina and optic nerve functional activity, gas tamponade is believed to be the preferred agent if compared with silicone oils in many cases. Lee et al. (2018) showed a significantly greater reduction of RNFL thickness compared with eyes in the C3F8 gas group at 6 months and 9 months postoperatively in macula-sparing RD.11 On the contrary, Inan et al. (2020) reported no significant difference of RNFL thickness between SO and C3F8 gas group in macula-off RRD, even though a thinning in the layers of the ganglion cell layer, outer plexiform layer, and outer nuclear layer of the central subfield was found significantly greater in the SO group.12 Different from Lee and Inan, Zhou et al. (2020) compared the effect of SO tamponade and sterilized air tamponade on RNFL thickness in macula-on RRD patients. However, this study also reported a greater reduction of RNFL thickness in eyes with SO tamponade compared to sterilized air tamponade at 6 weeks postoperatively.13 Thinning of RNFL can indicate a loss of retinal ganglion cells which can lead to decreased vision.33 The number of surviving ganglion cells and the regeneration of axons are crucial for preserving and recovering vision after optic nerve injury. Therefore, the thickness of the RNFL can serve as an indicator of changes in visual function.34 There are several possible explanations regarding the effect of SO on RNFL thickness. First, mechanical stress caused by silicone oil in the fovea may lead to the premature loss of outer nuclear layer (ONL) cell bodies.35 Second, subretinal migration of silicone oil due to its use as a tamponade could result in severe optic neuropathy.36,37 The migration of macrophages that have phagocytosed emulsified oil bubbles could be a potential mechanism for the subretinal migration of silicone oil.38 There have been reports that the small molecules in silicone oil may diffuse from the oil and enter the retinal tissue, which could cause inflammation and toxicity in the retina.39,40 Third, retinal thinning may also occur as a result of SO-related idiopathic reactions or changes in the retinal ionic environment. These changes could be caused by localized alterations in potassium concentration due to the failure of potassium siphoning by Müller cells and apoptosis, leading to neuronal degeneration.41,42 Further research is required to clarify the exact mechanism of the reduction in the thickness of RNFL associated with the use of silicone oil.\n\nILM staining is a technique used in vitreoretinal surgery to visualize and facilitate the removal of the inner limiting membrane (ILM), a thin and transparent layer that separates the retina from the vitreous humor. ILM staining has become an important tool in the treatment of various retinal diseases, including macular holes and epiretinal membranes. This technique involves the use of dyes, which selectively bind to the ILM and make it easier to identify and remove during surgery.14–16 Indocyanine green (ICG) was the initial dye utilized for macular hole (MH) surgery.43 However, it was subsequently discovered that the concentrations of ICG utilized during vitrectomy were toxic to the retina.44 Both in vitro and in vivo studies revealed that exposure of retinal ganglion cells (RGCs) to ICG resulted in damage to the RGCs.45,46 As an alternative to ICG, Brilliant blue G (BBG) has been introduced and can selectively stain the ILM. Studies conducted on rats and monkeys have suggested that BBG is less toxic to the retina than ICG.47,48 However, it has been found that prolonged exposure and high concentrations of BBG can also cause damage to retinal ganglion cells (RGCs).46 In this review, we compared the effect of each type of ILM staining agent on the occurrence of optic nerve injury. Overall, our review revealed that BBG may be a better agent than ICG even though there was no significant difference regarding optic nerve injury complications. Unlike previous studies that used high concentrations of ICG with prolonged exposure during surgery, Toba et al. (2014) used a low concentration of ICG and removed it quickly after application. This may explain why there was no significant decrease in the thickness of the RNFL in the group of patients who received ICG in this study. However, even though ICG did not cause a significant reduction in the thickness of the RNFL compared to BBG or TA, this study found a significant reduction in the photopic negative response (PhNR) of the electroretinogram (ERG) after macular hole (MH) surgery.15 It is in line with Ueno et al., in which also found a reduction in the PhNR of the ERG after ICG-assisted MH surgery.49 These results indicate that reduced function of retinal ganglion cells (RGCs) may occur after MH surgery without loss of RGC axons.\n\nOver the past decade, various new dyes have been developed for the visualization of epiretinal membranes (ERMs) or inner limiting membranes (ILMs).50,51 These dyes are unique in that they possess a high specific weight, which eliminates the need for the potentially unsafe “under air” application that is required for dyes like Trypan Blue (TB) or BBG.52 Picirillo et al. (2021) reported no toxic dye-related complications or long-term ones affecting the retina were observed in DoubledyneTM (soluble lutein 2%, BBG 0.05 and TB 0.15%.) and TwinTM (Trypan blue 0.18% and Blulife 0.03%) group.14 Rohrig et al. (2019) also reported no significant difference between the use of MBB and AV 17-M in terms of inner segment/outer segment defect.16\n\nOur study has a few limitations. First, there are more retrospective studies than prospective studies included, which may hinder data clarification and recoding. Secondly, the patient population was diverse, and the sample sizes varied widely, which could introduce bias. Additionally, there were many risk factors and complications related to optic nerve injury examined in the review. Given these limitations, we need more well-designed prospective studies with lower heterogeneity to further investigate this issue. Limitations in the review process include subjective interpretation, in which how information from individual studies is combined and analyzed can differ between one reviewer and another, potentially affecting the final result. Additionally, limitations in data integration, it can be difficult to merge data from various studies due to differences in original research.\n\n\nConclusion\n\nAlthough vitrectomy is considered to be a safe and effective treatment, it does come with the risk of complications, such as retinal nerve fiber layer damage and optic nerve injury, which can result in visual field defect and reduced visual acuity. After examining the available information, we found that the damage can happen either during or after a vitrectomy procedure. This is linked to four main risk factors: removing the internal limiting membrane, having a lower average ocular perfusion pressure, using silicone oil as a tamponade agent, and using ICG as an ILM staining agent. More research is needed to find out other risk factors that can lead to optic nerve injury. By understanding the risk factor of this serious complication, we can minimize the risks and achieve the best possible outcomes.", "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 ‘Risk factors of post-operative optic nerve injury after vitrectomy: a systematic review’. https://doi.org/10.6084/m9.figshare.24556711.v1. 53\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nOmari A, Mahmoud TH: Vitrectomy. Bethesda: StatPearls Publishing; 2023. [cited on 2023 Apr 3]. Reference Source\n\nFujii GY, de Juan Jr, Humayun MS, et al.: A new 25-gauge instrument system for transconjunctival sutureless vitrectomy surgery. Ophthalmology. 2002 Oct 1; 109(10): 1807–1812. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRunkle AP, Srivastava SK, Yuan A, et al.: Factors associated with development of dissociated optic nerve fiber layer (DONFL) appearance in the PIONEER intraoperative OCT study. Retina (Philadelphia, Pa.). 2018 Sep; 38(Suppl 1): S103–S109. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPan BX, Yee KM, Ross-Cisneros FN, et al.: Inner retinal optic neuropathy: vitreomacular surgery–associated disruption of the inner retina. Invest. Ophthalmol. Vis. Sci. 2014 Oct 1; 55(10): 6756–6764. PubMed Abstract \| Publisher Full Text\n\nLiu JH, Gokhale PA, Loving RT, et al.: Laboratory assessment of diurnal and nocturnal ocular perfusion pressures in humans. J. Ocul. Pharmacol. Ther. 2003 Aug 1; 19(4): 291–297. PubMed Abstract \| Publisher Full Text\n\nHayreh SS: Blood flow in the optic nerve head and factors that may influence it. Prog. Retin. Eye Res. 2001 Sep 1; 20(5): 595–624. 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PubMed Abstract \| Publisher Full Text\n\nDooley I, Treacy M, O’Rourke M, et al.: Serial spectral domain ocular coherence tomography measurement of outer nuclear layer thickness in rhegmatogenous retinal detachment repair. Curr. Eye Res. 2015 Oct 3; 40(10): 1073–1076. PubMed Abstract \| Publisher Full Text\n\nKnecht P, Groscurth P, Ziegler U, et al.: Is silicone oil optic neuropathy caused by high intraocular pressure alone? A semi-biological model. Br. J. Ophthalmol. 2007 Oct 1; 91(10): 1293–1295. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMajid MA, Hussin HM, Biswas S, et al.: Emulsification of densiron-68 used in inferior retinal detachment surgery. Eye. 2008 Jan; 22(1): 152–157. PubMed Abstract \| Publisher Full Text\n\nBudde M, Cursiefen C, Holbach LM, et al.: Silicone oil–associated optic nerve degeneration. Am J. Ophthalmol. 2001 Mar 1; 131(3): 392–394. PubMed Abstract \| Publisher Full Text\n\nGonvers M, Hornung JP, de Courten C : The effect of liquid silicone on the rabbit retina: histologic and ultrastructural study. Arch. Ophthalmol. 1986 Jul 1; 104(7): 1057–1062. PubMed Abstract \| Publisher Full Text\n\nGabel VP, Kampik A, Burkhardt J: Analysis of intraocularly applied silicone oils of various origins. Graefes Arch. Clin. Exp. Ophthalmol. 1987 May; 225: 160–162. PubMed Abstract \| Publisher Full Text\n\nWinter M, Eberhardt W, Scholz C, et al.: Failure of potassium siphoning by Muller cells: a new hypothesis of perfluorocarbon liquid–induced retinopathy. Invest. Ophthalmol. Vis. Sci. 2000 Jan 1; 41(1): 256–261.\n\nNewsom RS, Johnston R, Sullivan PM, et al.: Sudden visual loss after removal of silicone oil. Retina. 2004 Dec 1; 24(6): 871–877. Publisher Full Text\n\nKadonosono K, Itoh N, Uchio E, et al.: Staining of internal limiting membrane in macular hole surgery. Arch. Ophthalmol. 2000 Aug 1; 118(8): 1116–1118. Publisher Full Text\n\nEnaida H, Sakamoto T, Hisatomi T, et al.: Morphological and functional damage of the retina caused by intravitreous indocyanine green in rat eyes. Graefes Arch. Clin. Exp. Ophthalmol. 2002 Mar; 240(3): 209–213. Publisher Full Text\n\nIriyama A, Uchida S, Yanagi Y, et al.: Effects of indocyanine green on retinal ganglion cells. Invest. Ophthalmol. Vis. Sci. 2004 Mar 1; 45(3): 943–947. PubMed Abstract \| Publisher Full Text\n\nBalaiya S, Brar VS, Murthy RK, et al.: Comparative in vitro safety analysis of dyes for chromovitrectomy: indocyanine green, brilliant blue green, bromophenol blue, and infracyanine green. Retina. 2011 Jun 1; 31(6): 1128–1136. PubMed Abstract \| Publisher Full Text\n\nEnaida H, Hisatomi T, Hata Y, et al.: Brilliant blue G selectively stains the internal limiting membrane/brilliant blue G–assisted membrane peeling. Retina. 2006 Jul 1; 26(6): 631–636. 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Reference Source" }	[ { "id": "264900", "date": "03 May 2024", "name": "Angeline L Wang", "expertise": [ "Reviewer Expertise Retina" ], "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 the opportunity to review this paper. Overall, the paper is well-written and easy to understand. However, I have some disagreement about the studies included in the review. Optic nerve injury as I think most people would understand it would include optic neuropathy (ischemic, traumatic, toxic) and glaucoma. But I don't think most people would agree that localized nerve fiber layer defects are the same as optic nerve injury; presumably the optic nerve itself would still be functioning normally. Similarly, various ILM dyes that might impact the nerve fiber layer would also be impacting a localized area of the nerve fiber layer where the dye is applied, not the optic nerve itself. I'm not sure that the ILM dye studies or the DONFL studies should be included in this review. Study #13 in particular seems to mostly be focused on retinal side effects of the ILM dyes, rather than optic nerve side effects.\nIf the authors feel that their data search encompassed all studies involving optic nerve injury and nerve fiber layer injury, then perhaps the title and purpose could be changed to reflect that and the included studies would not need to be changed significantly. (I would still recommend removing study #13, as it is mostly focused on the retina.)\nAdditional comments: - Abstract: results and conclusions sections are repetitive. Please adjust one section or the other to include additional information. - ILM staining type: much more discussion in this section on the retina rather than the optic nerve. The relative focus should be changed to the optic nerve.\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? 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": [] } ]	1	https://f1000research.com/articles/12-1587
https://f1000research.com/articles/12-1586/v1	14 Dec 23	{ "type": "Systematic Review", "title": "Comparative analysis of pharmacologic and mechanical methods for labor induction in patients at full-term pregnancy—A systematic review", "authors": [ "Victor Juncu", "Edvin Vaso", "Olga Cernețchi", "Mihai Emil Căpîlna", "Edvin Vaso", "Olga Cernețchi", "Mihai Emil Căpîlna" ], "abstract": "Background Induction of labor is performed for either maternal or fetal indications to reduce perinatal morbidity and mortality without increasing maternal morbidity. The aim of this study was to review the scientific literature regarding induction of labor in patients with full-term pregnancy and create a systematic review of the literature to answer the question: “In patients with full-term gestation - does combining the Foley balloon with dinoprostone for the artificial induction of labor - offer better perinatal results over time from the application of the labor induction method until birth?”.\n\nMethods A literature search was performed on 23/08/2023 in the PubMed database; only articles published within the past 5 years were considered. We included articles in which labor was triggered with a vaginal device with dinoprostone, oxytocin, and/or a Foley catheter in full-term patients who met the following criteria: monofetal pregnancy, cranial presentation, intact membranes, and no history of uterine scar. We used the keywords “induction,” “labour,” “term,” “Foley,” “dinoproston,” “oxytocin.”\n\nResults The Pubmed database currently has approximately 20,000 scientific papers about labor induction. Only two studies met the proposed criteria. Considering the small volume of eligible data for the proposed research, the main meta-analysis addressing the topic was also considered.\n\nConclusions The use of dinoprostone and oxytocin infusion is effective for triggering labor under conditions of compliance with obstetrical indications and pharmacological characteristics. Studies that compare the success of artificial induction of labor with Foley balloon and Foley+dinoprostone in patients with full term gestation are limited, but nevertheless, the association of Foley balloon with artificial induction with dinoprostone seems to be a cost-effective method. The limited number of scientific studies on this topic determines a risk of bias, inconsistency and imprecision, and for the future, we propose to carry out a randomized prospective study to study the topic.", "keywords": [ "labor induction", "birth", "full-term", "Maternal medicine", "Intrapartum care", "General obstetrics", "Fetal medicine" ], "content": "Introduction\n\nLabor induction methods have been described in academic journals since 1573 when Ambroise Paré implemented amniotomy and detachment of membranes to trigger labor in patients with antepartum hemorrhages, as well as in patients with pelvic dystocia.1 Over time, these techniques have become common practice to decide on the delivery of patients in whom the continuation of pregnancy involves significant maternal or fetal risks. The modern era adds value to labor induction methods by introducing convenience as an indication.\n\nTo date, many methods and combinations have been described for inducing labor. The most reliable methods involve the use of drugs (oxytocin and prostaglandins) and mechanical intracervical devices (Foley balloon, Cook balloon). For these reasons, we aimed to describe and compare features of the different methodologies for triggering labor in patients at full-term pregnancy.\n\n\nMethods\n\nIn this review we created a protocol following the recommendations of preferred reporting criteria for systematic reviews (PRISMA 2020) for the systematic review protocol checklist.15 Furthermore, we tried to guide our study rationale and create a systematic review of the literature to answer the question: “In patients with full-term gestation - does combining the Foley balloon with dinoprostone for the artificial induction of labor - offer better perinatal results over time from the application of the labor induction method until birth?”\n\nThe studies will be included after searching in MEDLINE database (using PubMed). A search of the PubMed database was conducted on 23/08/2023 to identify articles showing the use of dinoprostone + Foley catheter and/or a Foley catheter in full-term patients to induce labor. We used the “AND” and “OR” tools and the search method: “(dinoprostone OR Foley+dinoprostone) AND (artificial induction of labor at full term gestation)” and we limited the search to articles published within the past five years, only in English, excluding reviews, abstracts and others shorts communication.\n\nTwo reviewers screened independently articles for relevance, according to the flow chart in Figure 1. A third reviewer was assigned to mediate any issues that might arise in the selection process. Articles were included in which labor was induced through these techniques in full-term patients who met the following criteria: monofetal pregnancy, cranial presentation, intact membranes, and no history of uterine scar - 2 articles.\n\nA full-text analysis of included articles was performed for comparison between methodologies. The literature search yielded 19 articles that analyzed the aforementioned methods or their association, of which 8 were published in the last 5 years. After applying the proposed criteria, four studies involving patients with spontaneous ruptured membranes before the application of labor induction methods, and another study that included patients with misoprostol-induced labor were excluded. Thus, only three studies met the proposed criteria, all of which were randomized clinical trials.\n\nThe outcomes for which data was searched were time from placement of the transcervical Foley catheter to vaginal delivery, caesarean section rate, infectious complications, Apgar scores and neonatal intensive care unit admission. All results that were compatible with each outcome domain from each study were searched, the data were manually extracted by 2 evaluators who worked independently and later compared.\n\nRegistration: the review was not registered.\n\n\nResults and discussion\n\nFor the median time for delivery in Foley and Foley+dinoprostone induced labor, two studies were identified. The studies’ characteristics (study type, condition of the cervix, method of labor induction, including population and its repartition (primiparous and multiparous), time to delivery, p-value) are shown in Table 1. The limits of this study are represented by the small number of studies that address the proposed theme, the relatively small number of patients included, the different population characteristics (body mass index, age).\n\nThe randomized clinical trial published by Edwards et al. (2021) involved 100 patients with full-term pregnancy (>37 weeks) who were randomly divided into four categories: 26 primiparous women in whom labor was induced with a Foley catheter and dinoprostone, 24 primiparous women in whom labor was induced with a Foley catheter, and two other groups with 25 multiparous patients each as control groups.2 The results revealed that the median time for vaginal delivery in Foley and dinoprostone-induced labor was 21.2 hours, compared with 31.3 hours in the patients where labor was induced with a Foley catheter (Wilcoxon p<0.05).2 The median time of delivery for multiparous patients triggered with the Foley catheter and dinoprostone was 17.1 hours, while in multiparous patients triggered with the Foley catheter alone, it was 14.8 hours (Wilcoxon p=0.21).2 Analyzing the cesarean delivery rate, labor in nulliparous patients induced with the Foley catheter and dinoprostone appears to have lower cesarean delivery rates than those induced only with Foley catheter, but the difference is not statistically significant (Gray test, p=0.34).2 In multiparous patients, combining the Foley catheter and dinoprostone produced higher rates of cesarean delivery, compared with those triggered only with the Foley catheter.2 However, this difference is not statistically significant (Gray test, p=0.20).2\n\nAnother randomized clinical trial by Vallikkannu et al. (2022) compared the time required until delivery, rate of cesarean section, and satisfaction from induction of labor among term, nulliparous patients, with a Bishop score <5, using a Foley catheter alone and Foley catheter + dinoprostone administered vaginally.3 Consistent with the previous trial, the time from the application of the labor induction method to delivery was shorter in patients who received the combined Foley catheter and dinoprostone method (22.5 hours), compared with the Foley-catheter-only method (35.1 h, p<0.001); no differences were detected in terms of patient satisfaction and the rate of cesarean section in patients receiving the combined method (34%) compared with those where labor was triggered using the Foley catheter alone (49.5 hours, p=0.02, RR: 0.7 (95% CI 0.5–0.9)).3\n\nThe third randomized clinical trial that met the search criteria was conducted by Barda et al. (2018). It consisted in a randomization of 300 patients with an unfavorable Bishop score at term to compare the efficacy of triggering labor using a Foley catheter and dinoprostone administered vaginally.4 The results showed that the time from the application of the labor induction method was shorter in patients induced with the Foley catheter alone, but this group required the administration of a higher dose of oxytocin.4 In addition, inducing labor using a Foley catheter resulted in a lower cesarean section rate, and neonatal indicators were similar in both study groups.4\n\nAnalysis of papers describing labor induction methods revealed several meta-analyses. A recent study (Dong et al. 2022) of 8796 full-term pregnancies examined the indications and main outcomes of induced labor in patients at 39/40 weeks of gestation.5 The findings demonstrated that there was no increase in cesarean section rate or perinatal morbidity when labor was triggered at 39/40 weeks of amenorrhea for non-medical indications.5 At the same time, inducing labor at the above-mentioned gestational age is associated with a lower incidence of maternal hypertensive complications during pregnancy, shorter duration of the first period of labor, fewer cases of meconium amniotic fluid during birth, lower mean birth weight, longer maternal hospitalization, and a higher rate of epidural usage.5\n\nTo assess the effectiveness of labor induction methods, Quach et al. (2022) conducted a meta-analysis of 2990 patients based on the PROBAAT trials, in which they determined the maternal and fetal characteristics that influenced the cesarean section rate following induction of labor in patients with full-term, single-fetal pregnancy, intact membranes, cephalic presentation, and unfavorable cervix.6 The authors developed mathematical models to determine the failure rate of induction of labor and conversion of birth to cesarean section.6 Of the 2990 patients who underwent labor induction, 10.5% had a cesarean section because of lack of dilation progress, and 7.6% had a cesarean section owing to fetal distress.6\n\nThe risk of cesarean section was higher in women aged 31–35 years (aOR: 1.15 (95% CI: 1.15–1.99)), nulliparous (aOR: 8.07 (95% CI: 5.34–12.18)), and of sub-Saharan African descent (aOR: 2.09 (95% CI: 1.33–3.28)).6 The main indications for cesarean section due to lack of dilation progress were increased BMI (aOR, 1.06 (95% CI: 1.04–1.08)) and fetal growth greater than the 80th percentile (aOR, 4.08 (95% CI: 2.75–6.05)).6 The main indications for cesarean delivery due to fetal distress were increased maternal age (aOR: 1.09 (95% CI: 1.05–1.12)), increased BMI (aOR: 1.05 (95% CI: 1.03–1.08)), and fetal growth below the 10th percentile (aOR: 1.93 (95% CI: 1.22–3.05)).6 The Bishop score did not demonstrate a statistically significant association with the risk of cesarean delivery, for both lack of progression of labor and fetal distress.6 Thus, maternal age, BMI, parity, ethnicity, and fetal growth percentile are predictive of the risk of cesarean section in patients who had a triggered labor; however, the direction and magnitude of the association differ in the weight of determining the decision to perform cesarean section.6\n\nRegarding maternal age, another meta-analysis (Fonseca et al. 2020) involving 81,151 patients revealed that induction of labor in patients aged 35 years or older was not associated with a higher risk of cesarean delivery (OR: 0.97 (95% CI: 0.86–1.1)), instrumental delivery (OR: 1.12 (95% CI: 0.96–1.32)), or postpartum hemorrhage (OR: 1.11 (95% CI: 0.88–1.41)).7 If the indications for triggering labor are not clear based on maternal health status, the primary consideration in inducing labor from the fetal point of view is fetal distress and the risk of deterioration of fetal well-being in utero.7\n\nA Cochrane meta-analysis was conducted by Middleton et al. (2020) on approximately 21,000 patients based on 34 randomized clinical trials to investigate the impact of triggering labor at or after 37 weeks of gestation in terms of antenatal fetal death.8 According to published results, triggering labor at or after 37 weeks of gestation significantly reduces the risk of antenatal fetal death (0.4 deaths versus 3 deaths reported per 1000 pregnancies (induced births versus expectant management, respectively)).8 It is also important to note that the cesarean section rate was even lower in patients in whom labor was induced compared with those who received expectant management (RR: 0.90 (95% CI: 0.85–0.95)) and probably a lower rate or no difference in the instrumented birth rate (RR: 1.03 (95% CI: 0.96–1.10)).8 On the other hand, triggering labor may increase the risk of perineal trauma (severe perineal trauma RR: 1.04 (95% CI: 0.85–1.26); 5 trials, 11,589 patients) and postpartum hemorrhage (RR: 1.02 (95% CI: 0.91–1.15)).8 Neonatal admission rates to intensive care units were lower in patients who received induction of labor compared with patients who received expectant management (RR: 0.88 (95% CI: 0.80–0.96)), based on a study of 17 trials and 17,826 neonates.8 Additionally, there were fewer newborns with an APGAR score <7 in patients who received labor induction compared with those who received expectant management (RR 0.73 (95% CI: 0.56–0.96)), according to a review of 20 trials accounting for 18,345 neonates.8 No statistically significant differences were observed in the length of hospital stay, rate of outpatient newborn breastfeeding, neonatal encephalopathy, or neonatal trauma.8 Additionally, no randomized clinical trials have reported neurodevelopmental disorders or childhood depressive disorders during the follow-up.8 Thus, a discussion on induction of labor at or after 37 weeks of gestation should focus on the risk profiles of each patient, complemented by paraclinical results and patient preferences.8\n\nA similar meta-analysis examining elective labor induction at 39 weeks of gestation versus expectant management was conducted by Grobman and Caughey (2019). The authors identified 375 studies with a total of 66,019 patients who underwent elective triggering of labor at 39 weeks and 584,390 patients who received expectant management.9 The study revealed that triggering labor at 39 weeks, compared with expectant management after this gestational age, was associated with a significant decrease in the rate of cesarean delivery (26.4% versus 29.1%, RR 0.83 (95% CI: 0.74–0.93)) and peripartum maternal infections (2.8% versus 5.2%, RR 0.53 (95% CI: 0.39–0.72)), and an improvement in other outcomes including neonatal intensive care unit admission (3.5% versus 5.5%, RR 0.8 (95% CI: 0.72–0.98)), respiratory morbidity (0.7% versus 1.5%, RR 0.71 (95% CI: 0.59–0.85)), and mortality (0.04% versus 0.2%, RR 0.27 (95% CI: 0.09–0.76)).9\n\nThe role of early amniotomy in triggering labor was studied in a systematic review and meta-analysis (Kim et al. 2019) that included seven studies and a total of 1775 patients.10 Two Cochrane meta-analyses that independently investigated the role of early amniotomy alone and early amniotomy associated with oxytocin infusion were included in the review.10 The authors showed that early amniotomy does not produce any benefit in terms of shortening the first period of labor and does not influence the risk of cesarean delivery, and amniotomy associated with oxytocin infusion can shorten the duration of the first period of labor by up to 1.28 hours compared with expectant management.10 It should be noted that the studies were performed in patients who presented with spontaneous labor and were subsequently associated with amniotomy or amniotomy plus oxytocin infusion.10 The role of early amniotomy is less clear. Therefore, several randomized trials have investigated the maternal and neonatal outcomes of early amniotomy in the setting of triggered labor; however, data are inconclusive regarding the time to delivery, rate of cesarean delivery, and rate of infectious complications.\n\nAnother meta-analysis (Orr et al. 2020) summarized 30 randomized clinical trials involving 6465 patients that compared labor induction using a Foley catheter, Foley catheter and oxytocin, Foley catheter and prostaglandins, and single-use prostaglandins (misoprostol and dinoprostone).11 The authors concluded that combining oxytocin with a Foley catheter versus a Foley catheter alone reduced the time to delivery by 4.2 hours (median: -4.2 hours (95% CI: -6.5 to -1.9)), and combining prostaglandins with a Foley catheter versus a Foley catheter alone reduced the time to delivery by 2.9 hours (median: -2.9 hours (95% CI: -5.7 to 0.0, p=0.05)).11\n\nThere were no differences in the rates of cesarean delivery, chorioamnionitis, use of epidural analgesia, tachysystole, postpartum hemorrhage, meconium amniotic fluid, neonatal admissions to ATI units, and 5-min APGAR scores for the Foley catheter-oxytocin and Foley catheter-dinoprostone combinations; instead, the rate of endometritis was higher in patients who received the Foley catheter-prostaglandin combination.11 The Foley catheter-misoprostol, Foley catheter-dinoprostone, and Foley catheter-oxytocin combinations did not demonstrate a statistically significant difference in the duration of delivery; however, the Foley catheter-dinoprostone combination was associated with a longer duration of delivery compared with the Foley catheter-oxytocin and Foley catheter-misoprostol combinations (p=0.05).11 It should be noted that the randomization criteria did not consider parity and term of pregnancy (>24 weeks of gestation), and it was not mentioned whether the volume of fluid used to fill the Foley balloon was taken into account. There were significantly fewer patients who received dinoprostone compared with the other study groups.\n\nThe Foley catheter and Cook balloon are the most commonly used mechanical methods for induction of labor. Liu et al. (2019) conducted a meta-analysis on 1326 articles including 7 randomized clinical trials and 1159 patients.12 The primary result for comparison was the cesarean section rate, and the secondary outcomes were effectiveness, efficiency, safety, and patient satisfaction.12 No statistically significant differences for the primary outcome (RR: 0.88 (95% CI: 0.65–1.2)) or secondary outcomes were noted.12\n\nA meta-analysis by Zhu et al. (2018) compared a Foley catheter and dinoprostone for labor induction.13 The primary outcome was the time from the application of the method to delivery, and the secondary outcomes were maternal (uterine hyperstimulation, postpartum hemorrhage, and infectious complications) and neonatal (1- and 5-min APGAR scores) conditions.13 Eight randomized clinical trials included 1191 patients in labor who were induced with a Foley catheter and 1199 patients who received dinoprostone.13 No statistically significant difference was observed for the duration of labor based on the induction method (mean difference: 0.71 h (95% CI: -2.5 to 3.91, p=0.67)) or for cesarean delivery rate (RR 0.91 (95% CI: 0.78–1.07, p=0.24)).13 Additionally, the rates of maternal infectious complications, postpartum hemorrhage, uterine hyperstimulation, and fetal outcomes did not show statistically significant differences.13\n\nThe Foley catheter has clear advantages over dinoprostone in terms of wide availability, simple storage, and low cost.13 Low-volume Foley balloons (30 mL) and high doses of dinoprostone (≥6 mg) may provide the shortest time from triggering labor to delivery.13\n\nA pilot study conducted by the author in 2017 at Brugmann University Hospital, Brussels, on a cohort of 68 patients with a scarred uterus and 61 patients without a scarred uterus, triggered with a Foley catheter and oxytocin, revealed that 69% of the patients with scarred uterus managed to give birth vaginally while 70.5% of the control group had vaginal births. Thus, the Foley catheter-oxytocin combination also represents an interesting option for inducing labor in patients with a scarred uterus after a cesarean section.\n\n\nConclusions\n\nFull-term pregnancies tend to become high-risk pregnancies, as it is often necessary for the birth to be induced artificially.14 Scientific studies have not yet identified an ideal method of artificial labor induction, a fact that offers an interesting track for scientific research.\n\nPatients with overdue pregnancy have a significant risk of antenatal fetal mortality,14 which is why, according to simple rules in obstetrics, after exceeding the due date for delivery by 7–10 days, pregnant women are more carefully monitored (every 48 hours) to opportunistically induce labor using the appropriate method, if necessary.", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nFighsare: PRISMA checklist for ‘Comparative analysis of pharmacologic and mechanical methods for labor induction in patients at full-term pregnancy—A systematic review’. https://doi.org/10.6084/m9.figshare.24431305.v1. 15\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nPublication of this paper was was possible due to studying at the George Emil Palade University of Medicine, Pharmacy, Science and Technology of Targu Mures and Nicolae Testemițanu State University of Medicine and Pharmacy, Chișinău, Republic of Moldova.\n\n\nReferences\n\nhttp\n\nEdwards RK, et al.: Controlled Release Dinoprostone Insert and Foley Compared to Foley Alone: A Randomized Pilot Trial. Am. J. Perinatol. 2021; 38(S 01): e57–e63. PubMed Abstract \| Publisher Full Text\n\nVallikkannu N, et al.: Foley catheter and controlled release dinoprostone versus foley catheter labor induction in nulliparas: a randomized trial. Arch. Gynecol. Obstet. 2022; 306(4): 1027–1036. PubMed Abstract \| Publisher Full Text\n\nBarda G, et al.: Foley catheter versus intravaginal prostaglandins E2 for cervical ripening in women at term with an unfavorable cervix: a randomized controlled trial. J. Matern. Fetal Neonatal Med. 2018; 31(20): 2777–2781. PubMed Abstract \| Publisher Full Text\n\nDong S, et al.: Induction of labour in low-risk pregnancies before 40 weeks of gestation: A systematic review and meta-analysis of randomized trials. Best Pract. Res. Clin. Obstet. Gynaecol. 2022; 79: 107–125. PubMed Abstract \| Publisher Full Text\n\nQuach D, et al.: Maternal and fetal characteristics for predicting risk of Cesarean section following induction of labor: pooled analysis of PROBAAT trials. Ultrasound Obstet. Gynecol. 2022; 59: 83–92. PubMed Abstract \| Publisher Full Text\n\nFonseca MJ, et al.: Does induction of labor at term increase the risk of cesarean section in advanced maternal age? A systematic review and meta-analysis. Eur. J. Obstet. Gynecol. Reprod. Biol. 2020; 253: 213–219. PubMed Abstract \| Publisher Full Text\n\nMiddleton P, et al.: Induction of labour at or beyond 37 weeks’ gestation. Cochrane Database Syst. Rev. 2022; 7(7). [Accessed 12 January 2023]. Publisher Full Text\n\nGrobman WA, Caughey AB: Elective induction of labor at 39 weeks compared with expectant management: a meta-analysis of cohort studies. Am. J. Obstet. Gynecol. 2019; 221(4): 304–310. PubMed Abstract \| Publisher Full Text\n\nKim SW, et al.: Role of early amniotomy with induced labor: a systematic review of literature and meta-analysis. Am. J. Obstet. Gynecol. MFM. 2019; 1(4): 100052. PubMed Abstract \| Publisher Full Text\n\nOrr L, et al.: Combination of Foley and prostaglandins versus Foley and oxytocin for cervical ripening: a network meta-analysis. Am. J. Obstet. Gynecol. 2020; 223(5): 743.e1–743.e17. PubMed Abstract \| Publisher Full Text\n\nLiu X, et al.: Double- versus single-balloon catheters for labour induction and cervical ripening: a meta-analysis. BMC Pregnancy Childbirth. 2019; 19(1): 358. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhu L, et al.: Intracervical Foley catheter balloon versus dinoprostone insert for induction cervical ripening: A systematic review and meta-analysis of randomized controlled trials. Medicine (Baltimore). 2018; 97(48): e13251. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGregory EC, et al.: Fetal Mortality: United States, 2020. Natl. Vital Stat. Rep. 2022; 71(4): 1–20.\n\nJuncu V: PRISMA_2020_checklist.pdf. Dataset. figshare. 2023. Publisher Full Text" }	[ { "id": "267796", "date": "17 Sep 2024", "name": "Anna Maria Marconi", "expertise": [ "Reviewer Expertise Obstetrics", "induction of labor" ], "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 don't think a systematic review can include only two studies with a total of 303 cases. Furthermore, the title is absolutely not congruent with what is included in the text since the studies analyzed are only two and, specifically, only a comparison between foley + dinoprostone versus foley. In addition, in the discussion an extensive revision is made to articles that use other mechanical methods and other pharmacologic methods.\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? No\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/12-1586
https://f1000research.com/articles/12-1584/v1	14 Dec 23	{ "type": "Case Report", "title": "Case Report: Thanatophoric dysplasia", "authors": [ "Aakriti Poudel", "Manish Upreti", "Asmita Pantha", "Aakriti Poudel", "Asmita Pantha" ], "abstract": "Thanatophoric dysplasia (TD) is a rare and lethal skeletal dysplasia caused by a de novo mutation in the fibroblast growth factor receptor 3 gene (FGFR3), with a frequency range of 1 in 20,000 to 50,000. We report a case of a 19-year-old primigravida from rural Nepal who presented with ultrasonographic findings suggestive of TD at 26 weeks and three days of gestation. The pregnancy was terminated due to the lethal nature of the condition. Accurate prenatal diagnosis and comprehensive counselling are paramount for families affected by this condition. This case has been reported due to its rarity, with the aim of raising awareness among healthcare professionals about this devastating condition.", "keywords": [ "birth defects", "micromelia", "skeletal dysplasia", "thanatophoric dysplasia" ], "content": "Introduction\n\nThanatophoric dysplasia (TD) is rare, sporadic and lethal skeletal dysplasia attributed to a de novo mutation in the fibroblast growth factor receptor 3 gene (FGFR3) located on chromosome 4p 16.3.1 We encountered a 19-year-old primigravida at 26 weeks and three days of gestation presenting with ultrasonographic findings suggestive of thanatophoric dysplasia. She delivered a dead fetus with macrocephaly, a narrow bell-shaped thorax, a protruding abdomen and shortened limbs. Only a few cases of this devastating condition have been reported from Nepal. Here, we report a case of a dead female fetus born with TD at a tertiary hospital in rural Nepal.\n\n\nCase report\n\nThis case report describes a case of a 19-year-old primigravida housewife in a non-consanguineous marriage. She had attended three antenatal visits before presenting for a routine antenatal check-up at our tertiary hospital in rural Nepal at 26 weeks and three days of gestation. She has no known chronic medical conditions or family history of congenital anomalies. She is a non-smoker and non-alcoholic, with no history of fever, skin rashes, spotting per vaginum, any drug intake, or radiation exposure.\n\nUpon arrival, the patient’s vital signs were within the normal range. General physical examination revealed absence of pallor, edema, lymphadenopathy, or thyroid swelling. Systemic examination findings were not significant. Per abdomen examination revealed uterus at 28 weeks of gestation, non-tender with no contractions. However, fetal lie, presentation and heart rate could not be appreciated. Routine blood investigations including complete blood count, blood sugar, blood group and Rh typing and serum thyroid stimulating hormone (TSH) were within normal limits. HIV, HBsAg, HCV, and rapid plasma reagin (RPR) were non-reactive.\n\nUltrasonography revealed a single live fetus with an unstable lie at 26 weeks three days of gestation with all four limbs significantly shorter than expected for the gestational age, suggestive of micromelia (Figure 1). A diagnosis of thanatophoric dysplasia was made and the patient was counseled for termination of pregnancy, which she consented to. Labor was induced with Tab Mifepristone 200mg orally followed by Tab Misoprostol 200mcg vaginally three doses on the next day. Subsequently, she delivered a dead female fetus weighing 800 grams with coarse edematous facies, frontal bossing, long forehead with a saddle nose, low-set ears, short neck, a bell-shaped thorax with protruded abdomen, and shortened upper and lower limbs with stubby fingers and deep skin creases (Figure 2). Additionally, there was flat back with a small dimpling over the sacral region (Figure 3).\n\nBased on the clinical features, the newborn was diagnosed as a case of TD type 1. The couple was counseled regarding the severity and lethal nature of this condition and advised for routine ultrasonography screening in subsequent pregnancies for the timely identification and management of this lethal disorder.\n\n\nDiscussion\n\nThanatophoric dysplasia (TD) is the most common lethal neonatal skeletal dysplasia, with an approximate incidence of one in 20,000 to 50,000. The term “thanatophoric” is derived from the Greek words “thanatos” meaning ‘death’ and “phoros” meaning ‘bearing’. Marotux initially coined this term to describe dwarf newborns who tragically passed away within the first hour of their lives.1 Thanatophoric dysplasia is attributed to a de novo mutation in the FGFR3 gene located on chromosome 4p16.3, which encodes for one of the members of the FGFR3 protein. This protein influences the development and maintenance of bone and brain tissues.2\n\nBased on the shape of skull and morphology of femur, thanatophoric dysplasia is classified into two types: type I and type II. Type I is the more common form and is characterized by the typical short and bowed “telephone receiver” shape of the femur with no clover-leaf skull. Type II is a less common variety characterized by a straight femur and a trilobal clover-leaf skull.1 Both types share a set of features, including short ribs, a narrow bell-shaped thorax, relative macrocephaly, specific facial traits, short fingers and toes, hypotonia, and redundant skin folds on the limbs.3 Most of the fetuses with TD die in utero. Respiratory insufficiency, primarily attributed to the constrained chest cavity and underdeveloped lungs, as well as the brainstem compression resulting from a narrow foramen magnum or a combination thereof, is the primary underlying cause of mortality in both types of this condition.4\n\nThanatophoric dysplasia requires accurate prenatal diagnosis to facilitate counseling and enable parents to make informed decision-making regarding whether to process with or terminate the pregnancy. Antenatal ultrasonography in the second trimester aids in diagnosis and also helps to differentiate it from other non-lethal dysplasias.3 Scans done in the third-trimester help to distinguish between the types based on fetal skeletal morphology. Diagnosis can be further confirmed with autopsy and histopathological examination.5 Unfortunately, these confirmatory examinations were not conducted in our case due to the lack of consent from the parent.\n\nLong-term survival with thanatophoric dysplasia is rare, but it is more common in type 1 than in type 2.6 A case report illustrates a nine-year-old male with TD who survived with the assistance of advanced medical and surgical interventions. The report emphasizes the need for pediatric palliative care providers to approach the labeling of TD as “lethal” cautiously as the prognosis of the condition remains uncertain. This highlights the importance of adopting an individualized approach in providing care and support to individuals and families affected by TD.7\n\n\nConclusion\n\nWe report a rare case of thanatophoric dysplasia leading to termination of pregnancy in a 19-year-old primigravida residing in rural Nepal. Accurate prenatal diagnosis with comprehensive counselling are paramount for families affected by this devastating condition. Furthermore, incorporating routine ultrasonography screening during subsequent pregnancies facilitates prompt identification and effective management of this lethal disorder.\n\nWritten informed consent for publication of their clinical details and clinical images was obtained from the patient on behalf of herself and her child.", "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: CARE checklist for ‘Case Report: Thanatophoric dysplasia’. https://doi.org/10.6084/m9.figshare.24107604.\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 Department of Obstetrics and Gynaecology and Department of Radiology of Lumbini Medical College and Teaching Hospital.\n\n\nReferences\n\nJahan U, Sharma A, Gupta N, et al.: Thanatophoric dysplasia: a case report. Int. J. Reprod. Contracept. Obstet. Gynecol. Jan. 2019; 8(2): 758. Publisher Full Text\n\nWainwright H: Thanatophoric dysplasia: A review. S. Afr. Med. J. May 2016; 106(6): 50. Publisher Full Text\n\nBadal S, Roy S, Singh D: Thanatophoric Dysplasia. J. Nepal Paedtr. Soc. Jun. 2016; 35(3): 304–306. Publisher Full Text\n\nJagun OE, Olusola-Bello MA, Adekanmbi FA, et al.: Thanatophoric dysplasia- a case report. Pan Afr. Med. J. 2020; 37: 220. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAnjum F, Daha SK, Sah G: Thanatophoric Skeletal Dysplasia: A Case Report. J. Nepal Med. Assoc. Mar. 2020; 58(223): 185–187. Art. no. 223. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNikkel SM, Major N, King WJ: Growth and development in thanatophoric dysplasia – an update 25 years later. Clin. Case Rep. Dec. 2013; 1(2): 75–78. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCarroll RS, Duker AL, Schelhaas AJ, et al.: Should We Stop Calling Thanatophoric Dysplasia a Lethal Condition? A Case Report of a Long-Term Survivor. Palliat. Med. Rep. Apr. 2020; 1(1): 32–39. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "253296", "date": "18 Mar 2024", "name": "Ozge Ozdemir", "expertise": [ "Reviewer Expertise maternal fetal medicine", "fetal abnormalities", "fetal autopsy", "fetal skeletal dysplasia", "pregnancy termination", "prenatal ultrasonography." ], "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-There are serious deficiencies in the article about the management of the case. First of all, epidemiological information like those inside 1-4-5-7. articles references get case report. It is recommended that they be collected from species guides or comprehensive articles.\n2- Wasn't amniocentesis recommended for the case? Why weren't genetic tests done? couldn't it be done?\n3-Why has the autosomal dominant character of the disease never been mentioned?\n4-\"According to the clinical features, the newborn was diagnosed with TD type 1.\" According to this sentence, you have made the diagnosis based on clinical findings. There is a serious lack of information regarding excision of skeletal dysplasias.\n5- ''Most fetuses with TD die in the womb. Respiratory failure would be more accurate, that is, perinatal rather than inutero. Also, I think it would not be right to reference this case from another case report.[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? Partly", "responses": [] }, { "id": "253287", "date": "23 Mar 2024", "name": "Lamidi Audu", "expertise": [ "Reviewer Expertise Perinatology" ], "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 case report of a fetus diagnosed as Thanatophoric dysplasia following abdominal ultrasonography. The pregnancy was terminated following parental counseling and pictures of the expelled fetus are presented to illustrate the physical features of the disease.\nObservations: 1. Although this disease is rare, existing literature is replete with comprehensive information on the epidemiology, clinical features and the genetic basis of the disorder. The authors should therefore further justify what their manuscript adds to existing literature. 2. The format of presentation by the authors gives the impression that the 19- year old pregnant woman from Nepal was the case being reported with the abnormality. This is evident in the 'Summary', 'Introduction' and the 'Case report' segments of the manuscript. 3. It is expected that the introduction should briefly define the condition, mention the clinical relevance and indicate why the particular case is being presented. The authors here on the contrary, included a summary of the case report. 4. The Case Report segment provides an elaborate information about the mother and even refers to the mother in the 3rd paragraph as the 'patient'. The patient in this case report is the fetus with Thanatophoric dysplasia and not the pregnant mother. 5. The telephone handle appearance of the Femur on X-R, which characterizes type 1 TD is not displayed in the manuscript. What the authors mentioned is 'shortened upper and lower limbs' which is not specific for TD.\n\n6. The first 2 paragraphs of discussion are not focused on the reported case. Some of the information here are best suited for the introductory part of the manuscript. 7. If most cases of TD die in-utero, does intrauterine death result from respiratory insufficiency and brainstem compression as stated in the manuscript? These pathologies rather contribute to neonatal death. What is the mode of inheritance of TD?\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": [] }, { "id": "245011", "date": "27 Mar 2024", "name": "Charu Sharma", "expertise": [ "Reviewer Expertise Fetal Medicine consultant", "Experience in Genetics (Done the ICMR-approved course on medical Genetics)" ], "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 is nicely written but unfortunately it is only the clinical diagnosis. Ideally the work up would have been completed if 1. Prenatal (Amniocentesis) or postnatal molecular diagnosis should have been confirmed. 2. All cases are not de novo. TD have an autosomal Dominant Inheritance. Hence, without a molecular diagnosis and inheritance pattern, counseling for future pregnancies would be incomplete. 3. Even if the patient refused autopsy, a postnatal skeletal survey should have been done. 4. All genetic cases are assigned an OMIM number. This should be mentioned while talking about TD. For TD it is OMIM #187600 5. The same mutant gene (FGFR2) is involved in Achondrodysplasia. Hence it needs to be differentiated from that, especially homozygous achondroplasia which are lethal. 6. Although prenatal diagnosis of TD had been accomplished by ultrasonography in the second trimester it is not always possible to distinguish between TD and other osteochondrodysplasias in utero\nhttps://www.omim.org/entry/187600?search=%22thanatophoric%20dysplasia%22&highlight=%22thanatophoric%20%28dysplastic%7Cdysplasia%29%22\n\nIs the background of the case’s history and progression described in sufficient detail? No\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/12-1584
https://f1000research.com/articles/12-1582/v1	14 Dec 23	{ "type": "Research Article", "title": "The role of active pedagogies in architectural design studios: post-pandemic adaptation", "authors": [ "Amany Kassem", "Yasser Farghaly", "Nermine Hany", "Yasser Farghaly", "Nermine Hany" ], "abstract": "Background: Architectural design studio courses are the core of architecture education where learners collaborate, brainstorm, and share their ideas to obtain the most beneficial outcome in a shared creative environment. The COVID-19 crisis has brought a variety of amendments in the architecture education world which therefore introduced a vast number of challenges to both architecture students and tutors. Since the beginning of 2020, all architecture universities from all over the world started to depend thoroughly on remote learning and according to previous studies, the majority of the students were highly satisfied with online learning when it came to architectural theoretical courses; however, the most challenging part was the architecture studio courses. Such interference lead to an educational shift from a physical interactive studio environment to a remote learning environment which caused a heated debate among the researchers. Hence, the study aims to test the architecture studio pedagogies in order to obtain an efficient and interactive studio environment leading to more satisfactory outcomes regarding the studio courses. Methods: Two questionnaire surveys were distributed online on google docs to both the studio courses staff members and students at the AAST Campus in Alexandria, Egypt at the end of the 15th week of the course and collected three weeks later. A comparative analysis of the individual and the collaborative phase for both surveys was anonymously achieved through the online forms for an unbiased active learning and pedagogical approaches assessment. Results: The survey results of 73 students and 13 staff participants emphasized the most beneficial active learning criteria and architecture pedagogies to be used for architectural studio courses. Conclusion: According to the results, the study will propose updated active learning guidelines for architectural design studio courses adapting to any emergency.", "keywords": [ "Architecture pedagogies", "Active learning strategies", "post-pandemic adaptation", "collaborative learning", "Hands-on experience", "Potential learning", "Hybrid learning", "and architectural studio courses." ], "content": "Introduction\n\nA vast number of institutions have shifted towards remote learning in order to proceed with the ongoing academic year. Due to the various learning environments in higher education institutions; based on the type of courses, students can be taught in different places, such as; design studios, laboratories, lecture halls, or seminar rooms. During the pandemic phase, practical courses in the architecture and urban design fields were held online, which made an educational dilemma between the tutor and the learner as such educational techniques won’t be suitable for these types of courses. Since Architecture is known as a design-oriented artistic discipline, it’s most inclined to be taught in a studio environment where students are supplied with knowledge, common skills, and a background that permits multiple applications to be applied in a variety of educational courses. Hence, the studio environment is essential for the practical architectural courses which facilitate the student’s ability to design and create, in contrast with the theoretical courses, which mainly depend on the teacher and a narrative curriculum where it can be easily held in lecture halls or online platforms (Elrawy and Abouelmagd, 2021).\n\nIn order to achieve active learning inside a design studio, some specific aspects are needed to be taken into consideration. Interactive discussions lead to an efficient studio pedagogy as nowadays, analysis and work process developments play an important role in active learning, however, their application must be guided properly in order to achieve beneficial outcomes. Therefore, the studio offers an essentially social context where learning is best done in the presence of a master or a guide “Tutor” as well as in the company of peers who aspire to the student to compare, criticize and enhance his abilities (Salama, 2010).\n\nThe studio environment draws attention to two lessons for future notice:\n\nSince design is a problem-solving strategy, critical thinking must be an essential aspect to be taught inside a design studio. Based on previous studies, it has been established that a design studio has great potential for architecture pedagogy and acts as a foundation for diverse methods of studio pedagogies and typologies (Salama, 2010).\n\nIdeological assumptions, the nature of values, or a specific skill are better left discussed inside the design studio whether amongst the teacher and student or the students themselves as well as enabling a collaborative environment; this is where good judgment comes from (Salama, 2010).\n\nThe World Health Organization (WHO) declared COVID-19 a pandemic crisis on March 2020, and ever since, remote learning was obligated in order to minimize the spread of the coronavirus. Consequently, design studio courses’ instructors have been forced to teach remotely (Ibrahim et al., 2021). McKinsey et al., estimated that the overall average percentage of students who received high-quality remote instruction was a minority with a percentage of 32% only (Komarzyńska-Świeściak et al., 2021). When offered a choice between a fully offline design studio versus a fully online method, architecture students prefer studying in a face-to-face environment (Komarzyńska-Świeściak et al., 2021). On an international scale, it was found that the majority of architecture students struggled with distance learning and almost 59 percent of students mentioned that E-learning is worse compared to face-to-face interaction (Bailey, Doty & Pinkerton, 2020).\n\nThe research aims to support active learning strategies concerning the architectural design studio courses adapting to any sudden transitions in the design studio settings. The study aim can be achieved through providing insights into architecture pedagogical approaches with, the significance of active knowledge where it can be actively applied rather than passively received by the learners. Also, the study will shed light on the opportunities and challenges that can be of benefit from the pandemic phase and therefore, exploit them to achieve the most efficient pedagogical approaches in studio courses under any circumstances (Ibrahim et al., 2021).\n\n\nLiterature review\n\nHistorically, architecture studio pedagogy relies on intuitive and cognitive learning. As an example, learning by doing is considered a crucial pedagogical approach that occurs through various trials and errors throughout the interactive process of the design and therefore obtaining a satisfactory solution to the design problem (Olotuah et al., 2016).\n\nA successful pedagogy works on clearly transferring the body of knowledge to students and assessing their performances as well as their interactions. Not to mention that a tutor should play a great role in counseling and guidance in order to achieve proper teaching and integration of teaching methodology, learners’ psychology, skills, and knowledge should be taken into consideration. Moreover, effective learning is achieved by an ideal way of instruction where students are fed with a highly productive and beneficial learning experience which will therefore enhance their skills as learners. The previously mentioned definition is what’s known as “trenchant teaching” (Olotuah et al., 2016).\n\nIn comparison to traditional classrooms, design studios act as active sites where students engage socially and intellectually (Lueth, 2008).\n\nAs shown in Figure 1, there are five pedagogical formats that can be adapted to suit certain studio disciplines and situations (Olotuah et al., 2016; Salama, 2010):\n\ni. Collaborative pedagogical approach\n\nii. Integrative pedagogical approach\n\niii. Problem-solving/Inquiry-based pedagogical approach\n\niv. Reflective pedagogical approach\n\nv. Constructivism pedagogical approach\n\nAfter conducting a literature review analysis, the active learning criteria regarding architecture education have been accurately tested and updated into topics and sub-topics shown in Figure 2. The percentages shown beside each sub-criterion resemble its impact and effectiveness on architecture education according to the previous literature reviews’, researches’, and examples analysis.\n\nLearning by doing approach has been classified into sub-topics such as a design-build approach which can occur in a physical or virtual medium. Moreover, experiential learning involves site visits and observations, collaborative learning and finally project-based learning.\n\nAs for the second active learning aspect, providing a collaborative context has proven to be a crucial aspect, however, establishing proper communication channels which can occur through online platforms for discussions whether in a traditional studio setting or in a virtual room through the virtual reality (VR) intervention, encouraging interdisciplinary collaboration with other fields and emphasizing the value of diverse perspectives must be taken into account in order to achieve an effective collaborative context in an architectural design studio (Figure 2).\n\nOne of the most noticeable aspects analyzed was encouraging the potential learning allowing the students to use their academic learning and knowledge gained inside the design studios in their professional careers later on. Potential learning can be achieved by providing access to a network of industry professionals, introducing project management skills into the curriculum, and providing design competition opportunities.\n\nFurthermore, technological interventions should be an essential part of the design process such as creating online communication channels and VR software for the students, introducing a library of digital models, incorporating 3D printing or fabrication tools, and offering workshops on emerging technologies for both the staff members and students.\n\nLast but not least, the process-focused criterion is an essential active learning aspect that occurs through a design process emphasis, fostering the student’s critical thinking and collaboration and encouraging hands-on experiences since it is a student-centered learning approach instead of focusing on the end result. Finally, all four phases of reflective learning focus on students’ self-reflection in specific.\n\n\nMethods\n\nThe study was approved by the Arab Academy for Science and Technology and Maritime Transport University (AASTMT), Architectural Engineering and environmental design department (AEED) Ethics Committee (Reference number 15/22) on September 15th, 2022. A written consent form was furnished to respondents for review and signature before starting interviews/questionnaires and approved by the AASTMT committee.\n\nIn order to enhance the active learning experience in an architectural design studio, the study will implement a qualitative and quantitative data collection technique by conducting two questionnaires inside a specific design studio course. Consequently, more valuable insights will be provided and the areas needed for improvement will be identified (Figure 3).\n\nThe initial questionnaire will be distributed to the interior design (1) staff and the second questionnaire will be taken by interior (1) design students at the end of the spring semester. Both questionnaires will include questions related to the entire studio duration; the individual and the collaborative context.\n\nStudents and instructors will have the opportunity to provide feedback on their active learning experiences. Accordingly, this feedback can be used to improve the overall quality of education received in architectural design studios and to develop new pedagogical approaches into the curriculum.\n\nThe case study took place in the academic year; spring 2022/2023 with a duration of 16 weeks. The researcher selected ‘Interior Design (1) – AR416’ to be the case study for various reasons. Firstly, interior design (1) is a design studio course, thus the design phases will be applicable in this case as well as the researcher has access to the studied course which will lead to more accurate results. Secondly, the course is taught in the 8th semester; 4th year, and is Royal Institute of British Architects (RIBA) accredited within the Arab Academy for Science Technology and Maritime Transport (AAST) university. Finally, this course is divided into an individual phase and a group work phase where students work in a collaborative environment, thus active learning strategies will be assessed in two different contexts through a comparative case study (Figure 4).\n\nAdditionally, all case study participants were found in the same subject, whether the academic staff or the students themselves to obtain accurate results. The course consisted of 4 design studios with a total of 90 students, however, only 73 students agreed to participate in the survey after being given a clear explanation on the research in a verbal form. Additionally, the survey was meant to be totally anonymous for unbiased results. Students were classified into groups by the beginning of the 8th week. Each student was required to answer a questionnaire that focused on the individual and the collaborative project equally.\n\nRegarding the interior design (1) academic staff, they were divided into lecturers and teaching assistants. The total number of academic staff in this case study was almost 13 persons. Each one of the staff members was required to answer a questionnaire anonymously as well, however, this survey was based on interior design (1) staff point of view (Figure 4).\n\nThe study experienced two various phases with different architecture pedagogies in the same interior design (1) studio course. The initial phase was the individual phase where each student encountered the entire design phase on his own with the course staff’s guidance. The individual phase took place in the first seven weeks focusing on the AAST staff’s cafeteria’s renovation. Starting from the 8th week till the 15th week, a collaborative phase was held where students were divided into groups and experienced the design process together (Figure 5).\n\nInitially, interior design (1) students were asked to renovate the AAST staff indoor cafeteria without any changes in the campus’ elevation or the structure system. During the first week, interior design (1) lecturers prepared a brief introduction explaining the basics of design principles, color philosophy, concepts, different design styles, furniture samples, and materials samples regarding cafeteria designs providing a complete introduction to the first individual project. Furthermore, students were assigned to undertake a site visit to the existing cafeteria, take some photos, measure the dimensions, and understand the user’s problems and needs if possible, in order to design a more appealing and practical cafeteria through ‘Experiential Learning’.\n\nMoreover, students were given another lecture expanding their critical thinking and imagination through a variety of relevant cafeteria examples located inside universities and campuses. Afterward, staff members were distributed evenly so that each teaching assistant had an even number of students to correct their work on a weekly basis. Students started to brainstorm with their TAs and lecturers about their preliminary design concept sketches, keywords, and interior design philosophies.\n\nDuring their third week, there was noticeable progress achieved by students. For instance, each student settled on his/her final concept and design style, designed his/her cafeteria’s mood board, and obtained some furniture samples related to his/her interior design styles and philosophy.\n\nFurthermore, the majority of the students’ furniture plans started to be more clear in the fourth week. Based on the student’s progress, the tutors began selecting the most successful furniture plans according to interior design concepts, circulation, zoning, and furniture samples as shown in Figure 6.\n\nInterior design (1) staff member proceeded to guide the students during the fifth week. In particular, the most suitable floor patterns, materials, false ceiling designs, and lighting fixtures were selected in order to reveal the looking up and floor plans in the most ideal approach.\n\nLast but not least, students worked on their cafeteria’s sections, elevations, and 3D virtual shots using 3D programs such as 3D Max, Revit, Time Motion, and Lumion to demonstrate their ideas. Finally, students were able to submit a full individual project in their seventh week.\n\nFinally, the entire staff has agreed to prepare certificate prizes for students who have reached the project goal in the most applicable way by meeting the users’ needs and fixing the project challenges. Those prizes were made as an appreciation for their hard work and effort.\n\nThe individual approach was a beneficial experience when it came to both; integrative and inquiry-based pedagogies as shown in Table 1. The staff cafeteria has a serious issue regarding its interior design and according to this, the project’s main aim was to renovate the old cafeteria into a more pleasing and functional one. Thus, students’ designs were highly needed to intervene in this problem. Furthermore, in order to obtain a realistic design, integrative learning was needed so students can understand all theories and project dimensions thoroughly.\n\n\n\n- Inquiry-based\n\n- Integrative\n\n- Reflective\n\nAdditionally, the individual experience was a highly student-centered approach with instructors working as guides and there was almost no peer interaction. In this project, the majority of the students fully understood the data received from their analysis and instructors’ explanation, offered virtual application, but they did not construct or deal with an actual human scale giving them a fine opportunity for criticizing as there wasn’t a clear and accurate perception.\n\nThe 8th week started with the collaborative project brief given by the lecturers. The project’s aim was to create an exhibition through a ‘learning by doing’ pedagogical approach allowing students to translate the knowledge received into an actual application using their bare hands in the architecture building atrium inside the AAST campus. The exhibition is classified into four main categories; students’ projects, historical timeline, successful student outcomes, and sponsors. Subsequently, interior design (1) staff began to divide the students into groups of five to six maximum. Each group was assigned to bring analyzed relevant examples for exhibitions which they will benefit from in their designs.\n\nAdditionally, all groups started to brainstorm and present their analyzed examples with their peers, staff members, and lecturers during their ninth week. Each example analyzed benefited the students with a certain outcome. For instance, the visual presentations allowed the students to select certain materials and high-tech solutions so they can use them in their 3D models, other examples presented new fixation techniques in a clear manner, creating a more engaging and interactive learning experience. As a result, students were asked to filter their options into 3 models only to simplify their design process.\n\nFurthermore, in the 10th and 11th weeks, students revealed their two or three models’ choices on a small scale to train themselves on handling the choice of the material with the chosen fixation method (Figure 7).\n\nAll students worked on their mistakes throughout the 12th and 13th weeks in order to enhance their work and picked only one display unit to transform into a 1:1 scale model without any obstacles (Figure 8).\n\nLast but not least, students presented their final 3D models that demonstrated their learning by doing and comprehension of the active learning techniques they had studied throughout the semester in the 14th week. The models were submitted in various forms, materials, visual presentations, interactive simulations, structures, and fixation mechanisms. The students were able to showcase their creativity and critical thinking skills in their models, and the projects were a testament to the effectiveness of the active learning approach utilized in the course (Figure 9).\n\nFinally, all groups submitted their final charts at the beginning of the 15th week revealing all their concepts, mood boards, display units, circulation and zoning diagrams, plans, sections, and their virtual 3D shots (Figure 10) (researcher).\n\nThe collaborative experience has achieved almost 90% of the pedagogical approaches inside an architectural design studio as shown in Table 2. As an example, diverse interactions and sharing of different opinions with peers and instructors have ensured the presence of a collaborative context. Regarding constructivism inside an architectural design studio, students were able to translate their knowledge and theories into a 1-1 physical model which made them learn thoroughly about different materials and new fixation techniques.\n\n\n\n- Constructivism\n\n- Collaborative\n\n- Integrative\n\n- Reflective\n\nMoreover, students and staff reached the critical reflection level by improving their teaching and learning experience and coping with nowadays needs by providing new presentations, teaching methods, and hands-on experience. Hence, both parties were able to criticize and negotiate throughout the design process till the final outcome. Furthermore, all studied theories were an accumulative learning process that helped the students to comprehend and connect all materials whether in theory or practice. However, the inquiry-based pedagogy was not highly supported in the collaborative project as the main aim of the project was to experience a hands-on experience through constructing 1-1 scale units to be eventually displayed in an exhibition. Thus, there was no actual problem with the exhibition zone in order to be fixed.\n\nAfter acknowledging the design process in the studio course (interior design 1) which lasted for 15 weeks, two questionnaires were created on an online google documents at the end of both course’s phases; the individual and the collaborative phases. The questionnaires were distributed by the end of week 15 and collected by the end of week 18 anonymously on an online platform (google docs). All 13 staff members have participated in the survey, however 73 out of 90 students have submitted the survey (Kassem, 2023).\n\nAll active learning strategies found in Figure 2 were mentioned in both surveys, in order to test the new active learning strategies, identify areas for improvement and help refine the existing ones.\n\nIn addition to this, the questionnaires focused on two working modes; the individual and the collaborative mode as a comparative study experience to achieve the most efficient pedagogical methods inside a studio course. The surveys also revealed the type of studio setting that each one of the students and staff members experienced during the pandemic and whether the studio setting influenced the pedagogical strategies inside the studio course or not.\n\nThe following criteria were focused on in both surveys;\n\n• ‘Learning by doing’ or ‘hands-on experience’\n\n• ‘Collaborative learning’\n\n• ‘Potential learning’\n\n• ‘Technological intervention’\n\n• ‘Process-focused’\n\n• ‘Reflective learning’\n\nAll previous criteria were anonymously analyzed and collected via the online google documents platform through comparative charts for both parties; staff members and students (Kassem, 2023).\n\n\nResults\n\nThe results of the two completed surveys presented students and staff who experienced different types of studios, therefore, according to their anonymously collected answers during the current post pandemic stage clarified the most effective pedagogical learning strategies based on their individual and their collaborative projects. Both projects occurred in the same physical/conventional architectural design studio, the individual project focused more on fixing the project problem through self-reflection, while on the other hand, the collaborative project through hands-on approach.\n\nThe survey target is to reveal the learning strategies points of weakness which needs to be improved and points of strength which needs to be maintained regardless of any emergency changes by obtaining valuable feedback from instructors’ and students’ points of view. 73 participants joined the student’s questionnaire in Interior Design (1) studio course while 13 staff members answered the staff questionnaire who were classified as lecturers and teaching assistants.\n\nThe staff members were an average of 33% lecturers to 67% teaching assistants distributed among the studios. As shown in Figure 11, a variety of staff members have experienced an online studio during the pandemic, followed by a lower percentage of hybrid studios and the least percentage experienced a traditional design studio.\n\nOn the other hand, when interior design (1) staff were asked which studio type was the most effective in the process of teaching design studio courses, their responses were totally different. 61.5% preferred the traditional design studio (PSD), 30.8% chose hybrid studios and only 7.7% supported online learning in a studio course (Figure 12).\n\n‘Learning by doing’ or ‘hands-on’ experience active learning strategy includes four main sub-criterions; experiential learning (site visits and observations), inquiry-based learning (fixing the design problem through the students’ designs), collaborative learning (allowing peers to brainstorm and interact with each other) and finally design-build programs (where students build a 1:1 scale model either using their bare hands or virtually). According to this, the staff was asked which criteria were mainly achieved in both the individual and collaborative projects based on their personal opinions (Figure 13).\n\nThe ‘collaborative context’ was mainly achieved in the collaborative project only according to the staff’s opinions. Encouraging collaboration with other fields, supporting diverse opinions, and gaining new skills were the main sub-criterions achieved (Figure 14).\n\nMoreover, ‘potential learning’ was 84% achieved in both projects through three main aspects; offering new competition opportunities between all groups in the entire studio course, providing professional guidance through lecturers, teaching assistants, and talks and finally gaining new management, programs, and business skills (Figure 15).\n\n‘Reflective learning’ includes four modes/phases; habitual reflection (where students receive the material taught without comprehension), understanding (where students start to understand the material taught as facts or theories without an actual application), reflection (where students fully understand and apply the material taught) and finally critical reflection (where diverse opinions and criticism are revealed by students). Based on this, the staff was asked about their opinions about the majority of students’ reflection levels in both the individual and collaborative projects (Figure 16).\n\nAs for the staff reflection, all lectures and power points were updated to match the new pedagogical approach; ‘hands-on/learning by doing’ experience, new teaching assistants with new visions, and all four studios shared the same experience which lead to fair outcomes and assessments.\n\nMoreover, 92% of the staff participants agreed that both projects achieved a ‘process-focused’ strategy and the final 8% agreed that it was achieved in the collaborative project only. Based on the staff perspective, hands-on and workshop experiences had the most percentages, followed by collaboration and interaction encouragements followed by supporting critical thinking (Figure 17).\n\nLast but not least, the technological intervention was mostly equal in both projects and it was minor as well. However, the staff offered accessibility to the digital library and incorporated 3D fabrication in the collaborative project (Figure 18).\n\nThe staff members’ level of satisfaction was biased toward the collaborative project than the individual project as the ‘hands-on experience’ or ‘learning by doing’ revealed students’ skills and reflection vividly (Figure 19).\n\n72 participants with different grade point averages (GPAs) completed the students’ survey. The majority of the students’ scores were between 2.4-3.6 and the rest were either more than 3.6 or below 2.0 as shown in Figure 20.\n\nBased on the students’ points of view, the majority preferred the hybrid studio followed by the traditional studio and the online studio respectively, unlike the staff’s opinion (Figure 21).\n\nAdditionally, according to the student’s results, the design-build or hands-on experience and the collaborative context in the collaborative project have overweighed the individual project (Figure 22). However, experiential and inquiry-based learning overweighed the individual project compared to the collaborative project as there was a major issue in the staff cafeteria which made them observe the site clearly, take photos, take accurate dimensions, and therefore fix the project problem through their own designs. On the contrary, the collaborative project (Exhibition) did not have a major problem to be fixed, hence, the students were assigned to make the architecture atrium a more representable space only.\n\nAs for the collaborative context, the students’ results were almost equal to the staff’s results, however, not all students knew how to collaborate with external fields (Figure 23).\n\nRegarding the students’ opinions, potential learning was achieved in both projects with nearly 52%, followed by a 33.3% in the collaborative project only unlike the staff’s results. A vast number have voted for the collaborative project only because group works and brainstorming plays a huge role in professional careers. In addition to this, 4.2% have added a new potential learning sub-criterion which is learning new software and 3D rendering methods (Figure 24).\n\nIn comparison with the staff’s results, methods of reflection were almost similar to students’ results. However, the collaborative project’s materials were received as facts in the beginning and the students’ reflection levels improved gradually (Figure 25).\n\nFurthermore, almost 66% of the participants agreed that both projects achieved a ‘process-focused’ strategy, followed by 17.1% who voted for the individual project only, and the rest were distributed amongst other options. Based on the students’ experience, they highly think that studio interaction and collaborations supported the process-focused strategy more than workshops (Figure 26).\n\nLast but not least, students’ votes between both projects and the collaborative project only were almost the same concerning the technological intervention inside the studio course. Moreover, an up-to-date staff, incorporating 3D fabrication into the studio course, and accessing a digital library benefited all students in their projects (Figure 27).\n\nThe students’ levels of satisfaction were almost absolutely satisfactory, however, the collaborative project was preferable and beneficial based on their statistics (Figure 28).\n\nThe average results of the staff and students survey in the comparative case study have established that the collaborative approach achieved higher percentages of active learning strategies than the individual one (Figure 29).\n\n\nDiscussion\n\nAll in all, previous studies conducted by the researcher have proved that implementing strategies such as hands-on experience in a collaborative environment resulted in a nearly 20% increase in active learning in architectural design courses.\n\n\n\n- Learning by Doing\n\n- Potential Learning\n\n- Process-Focused\n\n- Reflective Learning\n\nThe collaborative context percentage ranged between 50% to 70%, achieving a very good result. However, more improvement was needed as some group members worked as ‘free riders’ neglecting their peer’s work and effort throughout the learning-by-doing journey. One of the most recognizable drawbacks was the integration of technology integration in the architectural design studio courses was almost lacking and needs to be taken into consideration.\n\nAs an example, hands-on experience in the collaborative approach overweighed the individual approach due to two criteria, the collaborative context and the final constructivism phase. Although the percentage of the individual approach was not too low due to the presence of experiential and inquiry-based learning criteria as the individual project had a serious problem that needed to be fixed through new designs and perspectives, unlike the collaborative project.\n\nIn addition to this, the majority of the survey results have proven that the potential learning was biased more towards the collaborative approach due to group work negotiations, dealing with professionals, and allowing a sense of competition amongst peers. Furthermore, the process-focused strategy played a greater role in the collaborative context than the individual based on both surveys’ average results as students were able to detect and improve their models step by step by trying different scales by using the hands-on experience approach.\n\nThe technological intervention was poor in both approaches due to lacking interactive VR environments, online collaborative tools and introduction workshops, and 3D fabrication as a normal studio aspect.\n\nConcerning reflective learning pedagogy, the majority of the respondents reached critical reflection in the collaborative approach, however in the individual one, the reflective phase had the highest percentages.\n\nOverall, the level of satisfaction for both the students and studio staff members was almost satisfactory in both approaches in the studied course, however, the majority of people were biased more towards the collaborative approach as they highly agreed that the collaborative learning experience not only had a great impact throughout their education years, but they will also benefit from it in their upcoming professional years.\n\nThe study highlighted the need for more flexible and adaptable approaches to teaching and learning. It has also brought to the forefront the importance of active learning strategies in architectural design studio education and the light on three main crucial aspects of architecture; the architecture studio setting, the curriculum and the pedagogy.\n\nThe setting: the architectural design studio\n\nThe presence of technology will continue to play a significant role in architecture education even after the pandemic subsides as it facilitates the design process. One of the most recommended technological approaches in studio course education is the ‘Metaverse’.\n\nHence, it is important to recognize that virtual learning should exist in the architecture design setting however, it cannot replace the value of face-to-face interaction and hands-on experience. Therefore, it is crucial for educators to find a balance between virtual and in-person learning experiences to ensure that students receive a well-rounded education which is known as a hybrid or blended design studio as previously mentioned.\n\nThe curriculum: the architectural design studio courses\n\nOne of the noticeable comments was coping with nowadays technology systems such as allowing virtual reality rooms, augmented reality and ‘Metaverse’ integration into the architectural design studio curriculum. The suggested technological interventions will therefore provide students with a more interactive and immersive pedagogical experience, save time and money, and prepare undergraduate architects for their future careers in an up-to-date manner.\n\nThe pedagogies: students and staff\n\nSupport the learning-by-doing approach either physically or virtually by creating more activities and field trips, and providing more resources for students and staff in order to offer a better experience. For instance; offering an interactive environment, providing various resources such as different materials, workshop rooms, connection materials, 3D fabrication or printing, laser cutting, VR goggles and rifts. Moreover, work and time schedules should be essential tools inside an architecture design studio. One of the most effective ideas concerning projects’ efficiency is using heat maps during the project’s correction and evaluation phase in order to rapidly detect areas of improvement and points of strength.\n\nOverall, incorporating active learning strategies such as project-based learning, hands-on experiences, peer-to-peer learning, and problem-based learning can provide students with valuable opportunities to develop critical thinking, problem-solving, and collaboration skills. These strategies can be implemented both in virtual and in-person learning environments. Moreover, it is crucial for educators to continue to adapt and evolve their teaching methods to meet the changing needs of the industry and ensure that students are well-prepared for a future in their professional architecture practice. Figure 30 shows an updated checklist of the active learning strategies after all previous analyses and recommendations in order to obtain the most efficient outcomes inside architectural studio courses regardless of any urgent shifts.\n\n\nConclusion\n\nAll in all, it has been concluded that the architectural design studio setting does not have a significant impact on the process of teaching and learning. However, implementing active learning strategies in any architectural design studio course will play a crucial role in enhancing the efficiency of architecture pedagogies in any studio setting.\n\nFurthermore, it is important to recognize that virtual learning cannot replace the value of a physical or a face-to-face interactive studio with hands-on experience. Hence, supporting a hybrid/blended architectural design studio will provide the students with a more comprehensive education as well as prepare them for their professional careers. Needless to say, incorporating feedback from students and industry professionals from time to time can also improve the curriculum, allow the students to gain more skills for future notice and surely increase their levels of confidence.\n\nIn conclusion, the COVID-19 pandemic has presented an opportunity for educators to reflect on their teaching methodologies and adapt to new forms of pedagogy in architecture education. Moreover, the pandemic has emphasized the importance of technology in education and its potential to bridge geographical and societal barriers to learning. By leveraging technology, educators can create an immersive and interactive learning experience for students, enabling them to engage with architecture on a global scale. The shift towards virtual learning has highlighted the need for greater emphasis on active learning strategies to foster student engagement, critical thinking and participation in studio courses.", "appendix": "Data availability\n\nZenodo: Students and Staff Questionnaires. https://doi.org/10.5281/zenodo.8253348 (Kassem, 2023).\n\nThe project contains the following underlying data:\n\n• Staff.pdf (Anonymised responses from staff in the study).\n\n• Students survey.pdf (Anonymised responses from students in the study).\n\nZenodo: Students and Staff Questionnaires. https://doi.org/10.5281/zenodo.8253348 (Kassem, 2023).\n\nThe project contains the following underlying data:\n\n• Staff survey - Google Forms.pdf (Blank copy of staff survey).\n\n• Students.pdf (Blank copy of student survey).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nBailey J, Doty K, Pinkerton J: Effective Virtual Instruction Using The 4Rs: Strategies to Improve Relationships, Classroom Routines and Procedures, Students Roles and Academic Rigor. Learning Sciences International. 2020. Reference Source\n\nElrawy S, Abouelmagd D: Architectural and Urban Education in Egypt in the Post Covid-19 Pandemic. European Journal of Sustainable Development. 2021; 10(2): 91–112. Publisher Full Text\n\nIbrahim AF, Attia AS, Bataineh AM, et al.: Evaluation of the online teaching of architectural design and basic design courses case study: College of Architecture at JUST, Jordan. Ain Shams Engineering Journal. 2021; 12(2): 2345–2353. Publisher Full Text\n\nKassem A: Students and Staff Questionnaires. F1000 Journal. 2023. Publisher Full Text\n\nKomarzyńska-Świeściak E, Adams B, Thomas L: Transition from Physical Design Studio to Emergency Virtual Design Studio. Available Teaching and Learning Methods and Tools—A Case Study. Buildings. 2021; 11(7): 312. Publisher Full Text\n\nLueth PLO: The architectural design studio as a learning environment: A qualitative exploration of architecture design student learning experiences in design studios from first- through fourth-year (p. 7045025) [Doctor of Philosophy, Iowa State University, Digital Repository].2008. Publisher Full Text\n\nOlotuah AO, Taiwo AA, Ijatuyi OO: Pedagogy in Architectural Design Studio and Sustainable Architecture in Nigeria. Journal of Educational and Social Research. 2016. Publisher Full Text\n\nSalama AM: Delivering Theory Courses in Architecture: Inquiry-Based, Active and Experiential Learning Integrated. International Journal of Architectural Research Archnet-IJAR. 2010; 4(2/3): 278–295. Publisher Full Text" }	[ { "id": "232914", "date": "25 Jan 2024", "name": "Salih Ceylan", "expertise": [ "Reviewer Expertise architectural design", "architectural education", "virtual reality in architecture", "sustainable design", "retail design", "space architecture" ], "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 an interesting study on the role of active pedagogies in architectural design studios in the post pandemic period. One of the setbacks for this study is that it gets quickly outdated after the pandemic times. There have been many studies focusing on this, but after the situation is back to the \"(new) normal\", it is hard to tell that there is an attempt to go back to the online studios. That is the point where this study needs a stronger literature review with more recent references after the pandemic. The case study workflow seems right. However, the results are not clearly presented. It is not clear how the three aspects, student questionnaire, staff questionnare, and the qualitative analysis by the authors correlate with each other. The results indicate that the study is focused on the comparison between individual and collaborative settings, but it comes all of a sudden. Maybe the structure of the study can be redesigned accordingly. The pie charts and other graphics are too simple and do not have critical roles in the study. The analysis on the data could be more professional, going beyond excel charts. We cannot know if the sample sizes for student and staff questionnaires are representative. There are some statistical methods to prove this. Conclusions seem to generic. They must be derived from the results of the 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? No\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "232916", "date": "22 Feb 2024", "name": "Hermie E Delport", "expertise": [ "Reviewer Expertise Architectural education", "studio teaching", "design-build architecture studio" ], "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 addresses the social context of the studio and the move to online studio teaching during COVID with the aim to look at lessons, both opportunities and challenges, that came to light during this online move. In the authors words the “results, (of) the study will propose updated active learning guidelines for architectural design studio courses adapting to any emergency.” The article is very relevant to our current teaching context, and the results are applicable in other studio situations. Especially the collaborative studio ideas/information might find resonance with academics who are trying to develop more inclusive approaches. Articulation of work: The work is well articulated, and it is easy to follow the writing and the intent. Current literature. The literature review is relevant, and it is clear that the authors made an attempt to take existing theoretical/conceptual frameworks and to develop their own from it. It is however not clear what the literature review sets out to achieve in the context of the aim of the article_ later it becomes apparent that the authors’ frameworks will be used to set up the questionnaires and analyse/interpret the data. A few things need adjustment in the literature review. One cannot make a claim such as “accurately tested” if no measure is given against what this was tested, how and who determined that what is presented here is accurate? It might just be a semantic problem, but please review. The summary of five pedagogical formats (Olotuah and Salama) is very well done. But it is presented and then it is not explained what the aim of identifying the five formats is. The authors then moves on to present further “active learning strategies and sub-strategies” for the studio. It is unclear who the authors are that were used to determine these strategies and how the percentages in Table 2 were calculated from the literature is also unclear. (This literature review could be an article on its own if more detail and other relevant authors are included). The literature review is broad and does not explain why it is applicable to the specific aim of the research. Citing other/more relevant work would contribute to strengthening the literature review. Study design The article starts out by referring to the architectural studio and architectural pedagogy. At the study design the article moves without (enough) explanation into an interior design studio. An explanation is given later, but it would be better to include this in the abstract/introduction as well, else it does not look credible. Explain the context of the interior design studio earlier. The study method is good, and the two questionnaires are relevant. However, most of the questions in the surveys are qualitative, not quantitative. Although the data is presented in graphs and with percentages, the data is still qualitative. It is based on the perception and experience of individuals_ staff and students. It is not necessarily replicable but bound to context. The analysed data shows how many staff/students said something, which is subjective, not objective.\n\nConclusions “The collaborative experience has achieved almost 90% of the pedagogical approaches” _ was this achieved or is this how the project was conceived/designed for the students by the authors? By using 4 out of the 5 approaches? The collaboration is incredibly valid, and it would be great if more studios did this work. Maybe it should be framed that the collaborative project were experienced by the majority of participants (emphasis on the experience of the participants) as containing the pedagogical approaches. Not sure that I am correct here, but please consider. “All in all, previous studies conducted by the researcher have proved that implementing strategies such as hands-on experience in a collaborative environment resulted in a nearly 20% increase in active learning in architectural design courses.” Should be “active learning” or “active learning strategies”. It is not clear that active learning was/could be measured? Other comments If possible, do not use acronyms such as TAs (teaching assistants?) which might be specific to the authors context. Rather write this out. When referring later in the article to the framework created by the authors _ the five pedagogical approaches, make sure to use exactly the same wording and order in which it was first presented. For example, in Table 1_ referring to inquiry-based, integrative, reflective _ it is not clear that this aligns with what was done in the lit review. Introducing new concepts such as the ‘metaverse’ in the recommendations? Please review the sentence structure and grammar. Make sure that sentences make sense.\n\nThanks for an informative piece of work.\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? Partly", "responses": [] }, { "id": "263924", "date": "15 Apr 2024", "name": "Hassan Abdel-Salam", "expertise": [ "Reviewer Expertise Architectural Education and Environmental Design" ], "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 review of the submitted manuscript and its contents reveals the following:\nDeveloping novel concepts and adapting approaches for architectural education constitute core concerns in the field of pedagogics geared towards creativity and innovative thinking in Architecture. Addressing the new situations faced during the recent pandemic, and the ensuing limitations, while maintaining the desired output qualities / learning objectives is a broad subject worthy of investigation. The study aim and objectives are evident and well-targeted at fostering a responsive educational environment which promotes interaction in studio spaces, in addition to achieving efficiency and optimization of communication among parties involved. A mixed methodology is adopted with a concise experiment to establish then assess qualitative attributes based on clear/simple comparison between staff and students' views, and inference of results. The paper could benefit from an overall re-arrangement under specific numbered headings or bulleted points in order to better present the research discourse and to follow the build-up of argument leading to findings and recommendations deduced from this study. The paper has an explanatory introduction to clarify the theoretical grounding upon which the authors develop their rationale. The case study is thoroughly described with both text and non-text formats. The results’ section (from page 12 to page 21) presents the outcome of the questionnaire survey (the core Quantitate Analysis within the empirical part of this research). However, this part needs to be condensed in size and extent in favor of more clarification/discussion of how findings support the postulated views / agenda advocated by the authors. The above would also benefit, similarly, the closing sections (such as Final Results on page 20; Recommendations on page 22; and the very short Conclusion on page 24). These could be expanded with more discussion outcome to better validate the research findings and to provide better guidance addressed to designers/decision makers. (Note: it would be useful if the authors can add a concise statement about the possibility of generalizing upon the results across more courses / programs of architectural education). The research propositions and the manuscript contents are valid. The overall quality and clarity of the research would be much improved with the above suggested minor revision and amendments.\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/12-1582
https://f1000research.com/articles/12-1581/v1	14 Dec 23	{ "type": "Brief Report", "title": "Dataset from two pilot studies: the effect of emotional and motivational factors on peer support in context of adolescent smoking cessation program, evidence from Indonesia", "authors": [ "Mohammad Eko Fitrianto", "Basu Swastha Dharmmesta", "Bernardinus Maria Purwanto", "Basu Swastha Dharmmesta", "Bernardinus Maria Purwanto" ], "abstract": "Background: This study examines the effect of emotional and motivational factors on peer support in the context of adolescent smoking using datasets from two pilot studies. Although there are studies available on adolescent smoking cessation, only a few have focused on developing classroom-based prevention programs.\n\nMethods: Two datasets from each pilot study were collected using an online survey technique (n=102). Data were collected using convenience sampling from grade 11 high school students in Palembang, the capital city of South Sumatera province, Indonesia. We used descriptive statistics to explore the phenomenon in classroom settings in study I (n=31), and logistic regression to predict peer support in study II (n=71).\n\nResults: This dataset contains preliminary findings regarding peer support in the context of adolescent smoking. We discovered through descriptive statistics that student opinions and reactions regarding cigarette products and smoking are diverse. In addition, an associative study revealed that emotional and motivational factors have a substantial effect on peer support. Conclusions: There are no publicly available datasets that employ emotional and motivational factors affecting peer support in classroom settings, making the dataset unique. In addition, the dataset included in this brief report can be utilized to develop school-based smoking cessation programs for adolescents.", "keywords": [ "pilot study", "school-based program", "peer support", "empathy", "altruistic motivation" ], "content": "Background and objectives\n\nFew studies1–3 have focused on the development of prevention programs in a classroom setting, which was the impetus behind the creation of the dataset. Although there are studies available on school-based smoking prevention programs,3–5 it is unknown how students felt and reacted to their smoking peers, as well as how emotion and motivation can influence peer support. Adolescent smoking is not only a persistent global threat to adolescents,6–8 but it also leads to significant health issues during childhood and adolescence. These health problems include respiratory illnesses, decreased physical fitness, and potential hindrance in lung growth rate.9 Previous studies have highlighted the importance of students’ understanding and viewpoints regarding cigarette products and smoking behavior in the development of effective school-based prevention programs for adolescents.10,11 The traditional approach to smoking cessation programs typically emphasizes the relationship between the provider and the consumer.12 In contrast, the alternative perspective highlights the importance of a collaborative relationship to drive action.13\n\nOn the contrary, there is an increasing body of literature that incorporates emotional elements and motivation in health campaigns aimed at communicating the risks of smoking.14,15 By incorporating emotional elements, these campaigns aim to foster more effective collaboration among adolescents and promote shared responsibility.16,17 However, due to the limitations identified in previous studies, a pilot study is necessary to explore the phenomenon and assess the feasibility before conducting the main study. Therefore, this study aims to explore: 1) student opinion and reaction regarding cigarette product and smoking behavior; and 2) the effect of emotional element (e.g., empathy) and motivational (e.g., altruistic motivation) factors on peer support in the context of developing adolescent smoking prevention programs in a classroom setting. This dataset is a valuable resource for researchers studying the development of school-based smoking cessation programs for adolescents.\n\n\nMethods\n\nThis pilot study utilized cross-sectional data and adhered to the The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) guidelines for study design and reporting.18 The study protocol and research questionnaire were registered on protocol.io (dx.doi.org/10.17504/protocols.io.36wgq3r45lk5/v1) to ensure transparency and replicability. Additionally, we followed the The Sex and Gender Equity in Research (SAGER) guidelines relevant to this study.19 As a pilot study, a small number of participants or observations were included, and the calculation of sample size was not deemed necessary.20 However, it was important to ensure that the sample in the pilot study was representative of the intended main study.21 Thus, inclusion and exclusion criteria were established for participant recruitment.\n\nThe present study specifically targeted students residing in Palembang, the capital of South Sumatra Province, Indonesia. Statistics Indonesia’s report indicated that young individuals from this province were among the highest consumers of cigarettes in the country.22 Non-probability sampling was employed, specifically convenience sampling, to select the schools and participants for the study. Data collection was carried out through an online self-administered survey conducted during two pilot studies conducted from 2021 to 2022. The data collection process involved the participation of the homeroom teachers, who assisted in distributing the online questionnaire link to the students. Study I aimed to provide insights into specific interactions within the classroom and explore the potential for peer support among students. Meanwhile, Study II focused on understanding how individual factors impact peer support within the classroom environment. For the purpose of this study, the term ‘classroom setting’ was defined to encompass the range of daily interactions between students and their classmates.\n\nParticipants in this study had to meet the following inclusion criteria: 1) registered as grade 11 students, 2) male or female students, and 3) between the ages of 15 and 17. This pilot study is designed and will be implemented as a school-based program for students in Grade 11 who are between the ages of 15 and 17. We did not address the issue of gender differences in this study because we allowed participants of both genders (male and female). The SAGER guidelines are only implicit in the study’s relevance (how sex and gender are accounted for in the study design). Our exclusion criteria were a non-grade 11 high school student or an individual aged 18 and up. Participants were drawn from state and non-state high schools in the area where the study was conducted.\n\nParticipants in this study were provided with a Google Form link by their homeroom teacher and were asked to complete the questionnaire online. The questionnaire survey took approximately 10-15 minutes to complete. Informed consent was obtained from all participants, and the consent process was included at the beginning of the questionnaire. For more information on the study procedures, including the steps, guidelines, and materials used, please refer to the protocol available at protocol.io with the DOI: https://doi.org/10.17504/protocols.io.36wgq3r45lk5/v1.\n\nTwo primary independent variables were used in this study: empathic concern and altruistic motivation. The measurement of empathic concern and altruistic motivation was adapted from Batson’s empathic-altruism hypothesis.23,24 Empathic concern refers to emotions that are focused on others and congruent with their perceived well-being when they are in need. On the other hand, altruistic motivation refers to a state of motivation that aims to enhance the well-being of others.25 This form of motivation can drive individuals to provide peer support or engage in prosocial actions. The criterion variable in this study is peer support, which refers to the provision of emotional, appraisal, and informational assistance by a member of the social network who possesses experiential knowledge of a specific behavior or stressor and shares similar characteristics with the target population26 We measured empathic concern and altruistic motivation using well-validated scales,27–29 using a five-point Likert scale ranging from 1 (strongly disagree) to 5 (strongly agree). On the other hand, we measured peer support using a dichotomous scale (willingness to help). Logistic regression was used to predict the group membership for the question “Are you willing to help your friend stay away from cigarette products?” with two possible answers: “0” for “no, that is not my business” and “1” for “yes, of course.”\n\nThis study was approved by the Institutional Review Board at Universitas Gadjah Mada (Ethical clearance ref. KE/UGM/037/EC/2022).\n\nAll individual participants in this study provided informed consent. All procedures involving human participants were approved by the Universitas Gadjah Mada Institutional Review Board and were in accordance with the 1964 Helsinki Declaration and its subsequent amendments or comparable ethical standards.\n\nBefore using the data for further analysis, we performed dataset validation to ensure its integrity, accuracy, and structure. All of the data collection, recoding, and analysis procedures were meticulously carried out. To maintain the validity of the data source, we enlisted the assistance of homeroom teachers in distributing questionnaires. Furthermore, construct validity was assessed using confirmatory factor analysis (CFA) to ensure the convergence of the construct (e.g., construct of empathic concern, altruistic motivation, and peer support). We determined that there is no potential bias because the study was exploratory and the data collection medium was transparent (see published research protocol and data availability). In addition, the researchers had no control over how the questionnaire was distributed.\n\nThe dataset used in this study consists of two files with the SPSS *.sav extension that describe and define the sample and variables. The first dataset contains demographic information about participants, as well as their knowledge and opinions about cigarettes. The second dataset contains main variables and their measurements (for example, empathy variable and its item measurement). Table 1 contains information about the characteristics and data description of data in datasets.\n\n\n\n1. Number of respondents\n\n\n\n2. Sex\n\n\n\n3. Care1\n\n\n\n4. Care2\n\n\n\n5. Care3\n\n\n\n6. Care4\n\n\n\n7. Care5\n\n\n\n8. TocOpinion1\n\n\n\n9. TocOpinion2\n\n\n\n10. TocOpinion3\n\n\n\n11. TocOpinion4\n\n\n\n12. TocOpinion5\n\n\n\n13. TocOpinion6\n\n\n\n14. SmkActivity1\n\n\n\n15. SmkActivity2\n\n\n\n16. SmkActivity3\n\n\n\n17. SmkActivity4\n\n\n\n18. SmkActivity5\n\n\n\n19. EC01 to EC05\n\n\n\n• EC01: Feeling sympathy\n\n• EC02: Feeling moved\n\n• EC03: Feeling compassionate\n\n• EC04: I know he/she must be uncomfortable\n\n• EC05: I know he/she must be suffering\n\n\n\n20. AM1 to AM2\n\n\n\n• AM01: I am motivated to assist him/her.\n\n• AM02: My ultimate goal is to improve his or her well-being.\n\n\n\n21. PS1 to PS3\n\n\n\n• PS01: Persuading him or her to stay away from cigarette products\n\n• PS02: Willing to discuss the negative effects of smoking\n\n• PS03: Showing a negative attitude toward cigarette products\n\n\n\n22. EC\n\n\n\n23. AM\n\n\n\n24. PS\n\n\n\n25. Reaction\n\n\n\n26. Action\n\nThe data was processed using Microsoft Excel and SPSS version 23. The raw data from a Google Form (.xls extension) was then re-encoded for further processing (e.g., string data is converted to numeric data). Each question (column) in the raw Excel data was then coded (e.g., male=1, female=2, and so on). The data was carefully transferred to the SPSS dataset after it had been recoded. To accommodate the research purpose, two SPSS datasets were created for each study. To accommodate the wide range of student opinions in Study I, we allowed participants to provide more than one answer (multiple answers). Figures 1 and 2 were graphically processed in Microsoft Excel.\n\n\nResult\n\nA total of 102 participants were confirmed as eligible participants in two pilot studies, with no participants dropping out. Thirty-one students from High School A participated in Study I, and seventy-one students from various high schools in Palembang participated in Study II. The overall analysis of this result is divided into two parts: 1) investigating student reactions to their smoking peers (study I), and 2) investigating the effect of emotional and motivational factors on peer support (study II). Study I discovered that student opinions on cigarette products and smoking behavior range from popular to unpopular (see Figures 1 and 2). For example, cigarette product is a dangerous product and related to tobacco product, which has become a popular opinion toward cigarette product (64.52 percent). In other words, 90.32 percent of students believe that smoking is a harmful activity to their health.\n\nThe second section focuses on an associative study to predict a group member based on peer support (n=71). According to Table 2, logistic regression was used to predict group membership. The results showed that the higher their empathic concern (OR=2.494, Wald=4.029, p=.045) and altruistic motivation (OR=2.014, Wald=4.426, p=.035), the more likely they are to perform helping behavior (peer support) than a student with low empathy and altruistic motivation.\n\n\nDiscussion\n\nOverall, the findings from these datasets suggest that we should pay more attention to popular opinion about cigarettes and smoking behavior. According to the findings, popular opinion may describe the majority of adolescent beliefs in the classroom setting. As expected, ‘cigarette as a tobacco product’ and ‘cigarette as a dangerous product’ are the most popular views on the cigarette product. Furthermore, most participants perceived smoking as a harmful activity to their health. Furthermore, our findings suggest that influencing student emotion (e.g., empathy) and motivation (e.g., altruistic motivation) may contribute to increased peer support. Non-responsive peer support, on the other hand, is caused by a lack of empathy and motivation to help. This finding lends support to the idea of using emotional and motivational elements to foster more effective collaboration and shared responsibility among adolescents.15,33\n\nThe dataset has some key limitations, primarily stemming from the small number of participants. It is important to interpret the results of this pilot study with caution due to these limitations. The findings cannot be generalized to a larger population but can still provide valuable insights for the development of school-based programs within the specific context. Descriptive statistics and association tests can be helpful in informing program development within this limited scope. Additionally, it should be noted that this pilot study did not address sex differences, while other studies on emotions have examined this aspect.34–36 Exploring participant reactions based on sex differences could be beneficial for developing specific interventions to promote peer support.26\n\nThe significant findings of this study have important implications for the successful implementation of evidence-based policies and prevention activities, particularly within a classroom setting. The empirical results offer valuable insights for health practitioners, as well as professionals in health marketing or social marketing. The study has shown that students with high levels of empathy and altruistic motivation are more likely to engage in helping behaviors compared to those with lower levels. Based on these findings, it is recommended to develop school-based adolescent smoking cessation programs that incorporate empathy and altruism training for students, aiming to encourage them to provide peer support.\n\n\nConclusion\n\nThe datasets obtained from this pilot study offer valuable preliminary findings regarding the impact of emotional and motivational factors on peer support in classroom settings. The study successfully explored the phenomenon and confirmed the feasibility before commencing the main study. The results suggest that interventions based on emotions hold promise for the development of school-based smoking prevention programs, aligning with the growing use of emotional elements in health campaigns.37,38 In conclusion, future main studies should take into account important considerations based on the insights from this pilot study, such as ensuring the use of consistent inclusion and exclusion criteria, increasing the number of participants to enhance external validity, and incorporating program evaluation measures.", "appendix": "Data availability\n\nMendeley Data: A cross-sectional dataset containing demographic characteristics, student opinions, student knowledge, empathy, altruistic motivation, and peer support, DOI: https://doi.org/10.17632/rggnsww87w.1. 39\n\nThe project contains the following underlying data:\n\n• Study I Dataset - Peer Support (31).sav\n\n• Study II Dataset - Peer Support (71).sav\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 thank all staff and homeroom teachers from High School A (located in Palembang City, Indonesia) for helping the data collection process in Study I.\n\n\nReferences\n\nSchreuders M, Van Den Putte B, Mlinarić M, et al.: The Association between Smoke-Free School Policies and Adolescents’ Perceived Antismoking Norms: Moderation by School Connectedness. Nicotine Tob. Res. 2020; 22(11): 1964–1972. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJayawardhana J, Bolton HE, Gaughan M: The Association Between School Tobacco Control Policies and Youth Smoking Behavior. Int. J. Behav. Med. 2019; 26(6): 658–664. Publisher Full Text\n\nXu Y, Chen X: Protection motivation theory and cigarette smoking among vocational high school students in China: a cusp catastrophe modeling analysis. Glob. Health Res. Policy. 2016; 1(1): 3–9. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSudo A, Kuroda Y: Media exposure, interactive health literacy, and adolescents’ susceptibility to future smoking. Int. J. Adolesc. Med. Health. 2015; 2015.\n\nRobert PO, Grard A, Mélard N, et al.: The effect of school smoke-free policies on smoking stigmatization: A European comparison study among adolescents. PLoS One. 2020; 15(7): 1–15. Publisher Full Text\n\nTobacoatlas: Report: Global Tobacco Users at 1.3 Billion.2022 [cited 2022 Oct 10]. 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The altruism question: Toward a social-psychological answer. Hillsdale, NJ, US: Lawrence Erlbaum Associates, Inc; 1991; vol. ix. : 257–ix. 257.\n\nBatson CD, Lishner DA, Stocks EL: The Empathy–Altruism Hypothesis.Schroeder DA, Graziano WG, editors. The Oxford Handbook of Prosocial Behavior. 2014; pp. 1–43.\n\nSeo HJ, Kim SY, Park D, et al.: Peer support for smoking cessation: a protocol of systematic review and meta-analysis. Syst. Rev. 2021; 10(1): 296–296. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nXiao W, Lin X, Li X, et al.: The Influence of Emotion and Empathy on Decisions to Help Others. SAGE Open. 2021; 11(2): 215824402110145. Publisher Full Text\n\nYan Z, Pei M, Su Y: Children’s empathy and their perception and evaluation of facial pain expression: An eye tracking study. Front. Psychol. 2017; 8(DEC): 1–12. Publisher Full Text\n\nFry BN, Runyan JD: Teaching empathic concern and altruism in the smartphone age. J. Moral Educ. 2018; 47(1): 1–16. 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PubMed Abstract \| Publisher Full Text\n\nSimpson B, Van Vugt M : Sex differences in cooperation and prosocial behavior. Altruism and Prosocial Behavior in Groups. Emerald Group Publishing Limited; 2009; pp. 81–103. Publisher Full Text\n\nMcFayden TC, Albright J, Muskett AE, et al.: Brief Report: Sex Differences in ASD Diagnosis—A Brief Report on Restricted Interests and Repetitive Behaviors. J. Autism Dev. Disord. 2019; 49(4): 1693–1699. PubMed Abstract \| Publisher Full Text\n\nHoffman ML: Sex differences in empathy and related behaviors. Psychol. Bull. 1977; 84(4): 712–722. Publisher Full Text\n\nKim N, Leshner G, Miller C: Native Americans’ Responses to Obesity Attributions and Message Sources in an Obesity Prevention Campaign. J. Health Commun. 2022; 27(11–12): 777–789. PubMed Abstract \| Publisher Full Text\n\nKim J, Cao X, Meczkowski E: Does Stigmatization Motivate People to Quit Smoking? Examining the Effect of Stigmatizing Anti-Smoking Campaigns on Cessation Intention. Health Commun. 2018; 33(6): 681–689. PubMed Abstract \| Publisher Full Text\n\nFitrianto ME, Dharmmesta BS, Purwanto BM: Dataset From Two Pilot Studies: The Using of Emotional and Motivational Factors on Peer Support in Context of Adolescent Smoking Cessation Program. Mendeley Data. 2023; V1. Publisher Full Text" }	[ { "id": "285651", "date": "24 Jun 2024", "name": "Fithria Fithria", "expertise": [ "Reviewer Expertise Family Health Nursing and adolescent 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\nThe objective of study stated in the abstract section (line 1) is different from the aim of study in the background section (line 15), please rewrite that part of manuscript. In the background section, please add the data of smoking prevalence globally and in Indonesia. Then, in the background section, please focus more about the study variable (emotional element and motivational), why this variable is important for smoking prevention, how they relate to adolescent smoking behavior? In the methods section (informed consent), please explained how the researcher obtained the informed consent? (verbal or written consent). Then, the participants still under 18 years old, which need consent from parents or guardian. Please add this information in the manuscript. In the discussion section, please explain more about the study finding base on the study variable. Please also add any study which is support the finding of this 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? 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? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-1581
https://f1000research.com/articles/12-1207/v1	25 Sep 23	{ "type": "Research Article", "title": "Prevalence of pre-operative anxiety and associated risk factors among patients awaiting elective surgery in a tertiary care hospital", "authors": [ "Suman Prasad Adhikari", "Bishnu Deep Pathak", "Bhuwan Ghimire", "Sunil Baniya", "Prabhas Joshi", "Pooja Kafle", "Prawesh Adhikari", "Aakanksha Rana", "Laxmi Regmi", "Bishal Dhakal", "Nabin Simkhada", "Om Prakash Tandon", "Indra Dev Pathak", "Namrata Mahara Rawal", "Suman Prasad Adhikari", "Bhuwan Ghimire", "Sunil Baniya", "Prabhas Joshi", "Pooja Kafle", "Prawesh Adhikari", "Aakanksha Rana", "Laxmi Regmi", "Bishal Dhakal", "Nabin Simkhada", "Om Prakash Tandon", "Indra Dev Pathak", "Namrata Mahara Rawal" ], "abstract": "Background: Patients undergoing surgery have a fear of anesthesia and surgical procedures that results in anxiety. The global incidence of pre-operative anxiety is estimated at 60–92%. Age, gender, education, marital status, type of family, type of anesthesia and surgery, and history of surgery are the contributing factors. High levels of anxiety during the pre-operative period has negative impacts on surgical outcomes. The main objective of this study was to find out the prevalence of pre-operative anxiety and associated risk factors in a hospital setting of a developing country.\nMethods: This was a single center, analytical, cross-sectional study conducted among the admitted patients scheduled for elective surgeries in a tertiary care hospital. Non-probability consecutive sampling was adopted. The researchers themselves collected the data using questionnaires comprised of two parts: semi-structured questionnaires prepared via literature review and Amsterdam Pre-operative Anxiety and Information Scale (APAIS). Data were analyzed in SPSS version 23. Bivariate and multivariate analyses were performed appropriately.\nResults: The prevalence of pre-operative anxiety was 53 (25.85%). The median anaesthesia related, surgery related, and total anxiety scores were 4.00, 5.00 and 9.00 respectively. Likewise, the median score of information desired component scale was 5.00. Different anxiety scores were positively correlated with the information desire component score. The patients living in a nuclear family (adjusted OR, 2.480; 95% CI, 1.272–4.837, p = 0.008) and those without past history of surgery (adjusted OR, 2.451; 95% CI, 1.107–5.424, p = 0.027) had approximately 2.5 times higher risk of having pre-operative anxiety. Those receiving spinal anesthesia had approximately two times lower risk of anxiety (adjusted OR, 0.511; 95% CI, 0.265–0.985, p = 0.045).\nConclusions: One fourth of the patients had pre-operative anxiety. Type of family, type of anesthesia and past history of surgery were found to be the independent predictors of anxiety.", "keywords": [ "anxiety", "surgery", "elective surgical procedures", "anesthesia" ], "content": "Introduction\n\nAnxiety is defined as an uneasy feeling about something which is uncertain.1 It is common in patients awaiting surgical procedures.2 Patients undergoing surgery are afraid of anesthesia and its implications. This fear results in anxiety.3,4 Globally, the incidence of pre-operative anxiety is reported to range from 60% to 92%.2 High levels of anxiety during the pre-operative period have deleterious effects on intra-operative and post-operative care.5\n\nAnxiety causes variable responses in patients scheduled for surgery. These include tachycardia, hypertension, sweating, elevated body temperature, apprehension, increased mental tension and aggression.6,7 Pre-operative anxiety has unfavourable effects on induction and maintenance of anesthesia. Anxious patients require larger doses of anesthetic drugs and may have autonomic fluctuations as well.8–10 Anxiety aggravates perception of pain and increases the need for post-operative analgesia. It delays recovery and lengthens the hospital stay. It has been found that such patients have increased nausea and vomiting, and higher risk of infections during the post-operative period.7–9 There are several factors that contribute to significant levels of pre-operative anxiety. Some of these are age, gender, level of education, marital status, economic status, type and extent of surgery planned, past surgery and anaesthesia exposure, personal susceptibility and tolerance to stress, social security and existing psychiatric disorders.1,2\n\nIt is obvious that pre-operative anxiety adversely affects the overall surgical outcomes and patients’ satisfaction. Hence, it should be addressed in the right way. Assessment of anxiety before surgical procedures is therefore very important. Research of this kind has very rarely been conducted in Nepal. The main objective of this study was to find out the prevalence of pre-operative anxiety in adult patients scheduled for elective surgery, and its associated risk factors in our setting.\n\n\nMethods\n\nThis study was conducted in the surgery ward of Shree Birendra Hospital, a tertiary care hospital of Nepal from the beginning of May 2022 till mid-October 2022. It is a teaching hospital of the Nepalese Army Institute of Health Sciences, College of Medicine, Kathmandu, Nepal. The ward consisted of two units: male and female, with a total of 150 beds. All the cases scheduled for elective surgeries are admitted here after surgical consultation.\n\nThis was a single-center, analytical, cross-sectional study conducted in elective surgery patients admitted to the surgery ward. Adult patients more than 18 years old who were scheduled for elective surgery under spinal or general anesthesia were included. Patients aged less than 18 years, with known psychiatric disorders under medication, and who could not understand Nepali language well were excluded. The included patients were scheduled for different major surgeries like gastrointestinal, hepato-biliary, urological and orthopedic surgeries.\n\nNon-probability consecutive sampling method was adopted. All the pre-operative patients in the surgery ward were taken consecutively according to their admission to the hospital for major elective surgeries.\n\nThe minimum sample size was calculated by using Cochran’s formula as follows:\n\nWhere:\n\nn = sample size\n\nZ = 1.96 at 95% confidence interval\n\np = Prevalence from previous study (prevalence of pre-operative anxiety in reference no. 1 study is 31%)1\n\nq = 1 – p = 0.69\n\ne = standard error (taking 7%)\n\nThe calculated minimum sample size was approximately 167. However, we took 205 cases in our study.\n\nThe researchers approached the patients’ ward one day before surgery. Written informed consent from the pre-operative patients who were willing to participate in the study was obtained after explaining the research objectives and processes in detail. Then, the researchers asked the patients questions while they were comfortably seated or lying down.\n\nThe questionnaires were comprised of two parts. Part-I contained semi-structured questions prepared through extensive literature review. These included socio-demographic variables like age, gender, religion, profession, education, type of family and marital status. Likewise, it also incorporated clinical and surgical characteristics that could possibly affect pre-operative anxiety levels like presence of co-morbidities, duration of hospital stay before surgery, type of surgery and anesthesia, past history of major surgery. Similarly, part-II included the Amsterdam Pre-operative Anxiety and Information Scale (APAIS)11–14 which contained six questions in total. Two questions were related to patients’ anxiety about surgical procedures, the next two questions concerned anxiety of anesthesia, and the remaining two questions evaluated the need for information regarding surgery and anesthesia. Each question was scored subjectively by the patient in a 5-point Likert scale graded from 1 through 5, where ‘1’ denotes ‘minimal’ or ‘not at all’ and ‘5’ denotes ‘extremely.’ A total anxiety score of more than 10 was considered having pre-operative anxiety. Likewise, in the information scale, a score of 2–4 was classified as having no or little information requirement, 5–7 as having an average information requirement and a score of 8–10 as having a high information requirement.\n\nThe reliability of APAIS in our study sample was high with Cronbach’s alpha = 0.852 (acceptable with >0.7). Before starting data collection, pre-testing was done in 10% of the study sample.\n\nEthical approval was obtained from the Institutional Review Committee of the Nepalese Army Institute of Health Sciences (IRC Reg. No. 420, Ref No. 245). Before conducting the study, permission was obtained from the hospital authority and the Head of the Department of Surgery. Written informed consent was taken from the patients themselves. In case of uneducated patients, the investigators themselves explained the entire content of the consent form in their native language, and the consent was approved by taking their finger stamps.15 The privacy and anonymity of patient information were well-maintained.\n\nInitially, the collected data was entered in Microsoft Excel, 2010 after which it was imported and analyzed in IBM SPSS (Statistical Package for the Social Sciences), version 23. The Shapiro-Wilk W test was performed to check the normality of continuous data. The median/interquartile range was calculated for non-normally distributed variables, which included age of patients, duration of hospital stay before surgery, pre-operative anxiety scores, and information desired component scores. The dependent variable was pre-operative anxiety (yes/no), while the rest of the variables influencing anxiety levels were independent variables. The categorical variables were expressed in frequency and percentages. First, Chi-square/Fisher’s exact test was applied to check the association between dependent and independent categorical variables. For continuous variables, a Mann Whitney U test was performed to check association. Thus, statistically significant variables showing no collinearity among themselves were further tested by performing binary logistic regression analysis. The significance level was taken as p <0.07, with a 95% confidence interval considering a 7% standard error throughout the analysis. Likewise, the Spearman’s correlation between different anxiety scores and information desire component scores was also calculated.\n\n\nResults\n\nA total of 205 cases were taken and analyzed. Among them, 105 (51.22%) were males and 100 (48.78%) were females. The overall median age was 47 (34–59) years. Of these, 108 (52.68%) and 97 (47.32%) belonged to age groups less than or equal to 50 years and above 50 years respectively. One hundred and two (49.76%) patients lived in a nuclear family whereas the rest (50.54%) were from a joint family. Most of the patients followed Hinduism (178, 86.83%) followed by Buddhism (24, 11.71%) and Islam (3, 1.46%). Regarding occupation, only nine (4.39%) were health professionals. Most of the participants (179, 87.32%) were educated to different academic levels, i.e., primary or secondary or above secondary. One hundred and seventy (82.93%) were married, 19 (9.27%) were unmarried and 16 (7.81%) were widows/widowers (Table 1). The full dataset can be found under underlying data.16\n\nThe most common co-morbidity was hypertension (58, 28.29%) followed by diabetes mellitus (25, 12.20%) and chronic obstructive pulmonary disease (17, 8.29%). All these co-morbidities were well controlled, and the patients were well optimized in their pre-operative period. Most of the cases (71, 34.63%) were undergoing gastrointestinal surgery followed by hepato-biliary (55, 26.83%), urology (44, 21.46%) and orthopedic surgery (35, 17.07%). Among them, 61 (29.76%) had a past history of surgery performed under spinal or general anesthesia. Among the cases undergoing these surgeries, the majority were planned to receive spinal anesthesia (117, 57.07%), and the remaining 88 (42.93%) would be operated on under general anesthesia. Likewise, the median duration of hospital stay before surgery was three (one to four) days. (Table 1)\n\nOut of the total pre-operative cases, 53 (25.85%) had pre-operative anxiety (i.e. a total anxiety score ≥11). The median anesthesia related, surgery related, and total anxiety scores were 4.00, 5.00 and 9.00 respectively. Likewise, the median score of information desired component scale was 5.00. Seventy-two (35.12%) patients had little or no information requirement regarding the surgical procedure and/or anesthesia, 101 (49.27%) had an average information requirement, and 32 (15.61%) had a high information requirement. There was a statistically significant positive correlation between different anxiety scores and the information desired component score (Table 2).\n\nThe bivariate analyses showed that the patients living in a nuclear family had significantly higher pre-operative anxiety compared to those from a joint family (35[34.31%] vs 18[17.48%], p = 0.006). Likewise, the patients who were to receive general anesthesia for their surgeries reported a significantly higher anxiety level than those receiving spinal anesthesia (29[32.95%] vs 24[20.51%], p = 0.044]. Similarly, the patients who had a past history of surgery were significantly less anxious during the pre-operative period than those with no significant past surgical history (10[16.39%] vs 43[29.86%], p = 0.044). All other parameters did not show any significant difference in pre-operative anxiety in surgical patients.\n\nThe binary logistic regression analysis showed that the patients who were living in a nuclear family had approximately 2.5 times higher risk of having pre-operative anxiety compared to those living in a joint family (adjusted OR, 2.480; 95% CI, 1.272–4.837, p = 0.008). Likewise, the cases who were going to receive spinal anesthesia had approximately two times lower risk of anxiety in the pre-operative period than those undergoing general anesthesia (adjusted OR, 0.511; 95% CI, 0.265–0.985, p = 0.045). Similarly, the patients who did not have a past history of surgery were approximately 2.5 times more likely to have pre-operative anxiety in comparison to those who had some surgery in the past (adjusted OR, 2.451; 95% CI, 1.107–5.424, p = 0.027). In this way, type of family, type of anesthesia and past history of surgery (yes/no) were found to be the independent predictors of pre-operative anxiety (Table 3).\n\n\nDiscussion\n\nIn our study, the prevalence of pre-operative anxiety was 25.85%, with average total anxiety score being 9.00 (7.00–11.00) and information desired component score being 5.00 (4.00–6.00). Almost half of the patients (49.27%) had an average information requirement, and 15.61% had a high information requirement. The anxiety scores and information scale score were significantly positively correlated. The patients living in a nuclear family, not having a past history of surgery, and scheduled to receive general anesthesia had 2 to 2.5 times higher risk of having anxiety during the pre-operative period.\n\nThe prevalence of pre-operative anxiety in our study is comparatively lower than that of worldwide data that estimates its incidence to be around 60 to 92%.2 A study done in Ethiopia showed that significant anxiety was present in 70.3% of the patients scheduled for surgery.8 Likewise, in Saudi Arabia, 60% of the pre-operative patients had high anxiety.5 Prevalence of anxiety was also found to be high (76.7%) amongst Sri Lankan patients admitted for surgery.3 To the contrary, a study conducted in India depicted that overall prevalence of anxiety in elective surgical patients was 31%, which is comparable to our findings.1 On the other hand, a similar study in Nepal showed the presence of severe pre-operative anxiety in the majority (57.3%) of surgical patients.2 These differences could be due to the difference in sample size, sampling techniques, different study population and hospital settings, and different types of anxiety measuring tools being used in these studies worldwide. Moreover, we assessed the anxiety level on the day before surgery. Had we evaluated it on the day of surgery, the anxiety level would have been raised significantly.\n\nSurgery is indeed a psychologically stressful experience. So, some degree of anxiety is natural to this unpredictable and potentially threatening situation. However, high anxiety during pre-operative period has negative impacts on surgical outcomes.5 The patients start to have anxiety as soon as the surgery is planned, and it increases to a maximum on admission to hospital.6 Anxiety causes unnecessary fear, irritability and autonomic fluctuations in admitted patients. These unpleasant symptoms may compel them to refuse the planned surgeries.8 Pre-operative anxiety negatively affects induction of anesthesia. It causes different problems like difficult venous access, delayed jaw relaxation and coughing during induction.8,9 It has been found that such patients have increased nausea and vomiting, and higher risk of infections during post-operative period.7–9\n\nAddressing patients’ anxiety during the pre-operative period is a must.3 There are both pharmacological and non-pharmacological methods of reducing anxiety in the pre-operative period. Patients are routinely administered hypnotic/anxiolytic medications before surgery. Non-pharmacological methods include effective communication strategies, and provision of surgical information in videos or written form.17 Past studies have found that patient education may decrease anxiety and reduce the need for sedation to relieve anxiety and pain.18–20\n\nThere are a few limitations of this study to be mentioned. First, non-probability convenience sampling was adopted with a smaller sample size. Moreover, this is a single center study, so the findings may not be generalizable for a larger population or whole country. Future studies should include multiple study centers in different parts of the country with a relatively larger sample size. Next, anxiety level was measured at a single instance. However, past studies have shown that anxiety in pre-operative patients differs significantly in the perioperative period. Moreover, it would have been relevant if post-operative anxiety had also been studied. Likewise, pediatric patients were excluded from our study. Children also suffer significant anxiety during the pre-operative period, so including this group in the research would have increased the clinical relevance. In addition to this, we did not use the translated tool because none of the patients were educated, and a few of them could not read or write. To avoid this barrier, the researchers asked the participants questions in a standard way and assisted them to complete the questionnaires in an unbiased manner. APAIS has been validated in different countries21–26 including South East Asia, so using this tool in our setting was considered to be appropriate.\n\nDespite many limitations, our study provides some useful clinical information. First, it puts light on the anxiety burden among pre-operative patients in developing countries like ours. Next, it depicts the possible underlying risk factors contributing to significant anxiety during the pre-operative period and makes clinicians aware of the management of these factors beforehand. This adds to the existing medical knowledge, and possibly enhances patient care and satisfaction. Besides, this research encourages further analytical studies with a larger sample size and superior design to be conducted in the future. All these contribute to enhanced perioperative care and management of surgical patients in hospital settings.\n\n\nConclusions\n\nIn our study, one fourth of the patients experienced anxiety during the pre-operative period. The majority of them had an average information requirement regarding the surgical procedure and anesthesia. Type of family, type of anesthesia and past history of surgery were the independent predictors of pre-operative anxiety. These factors should be assessed and addressed well before performing surgery.\n\n\nConsent\n\nWritten informed consent for publication of the participants’ details was obtained from the participants. In the case of uneducated patients, the consent was approved via taking their finger stamps after explaining all the contents of consent form in their native language.", "appendix": "Data availability\n\nFigshare: Underlying data for ‘Prevalence of pre-operative anxiety and associated risk factors among patients awaiting elective surgery in a tertiary care hospital’, https://www.doi.org/10.6084/m9.figshare.23244059. 16\n\nThis project contains the following underlying data:\n\n• Data file 1: Excel data.xlsx\n\n• Data file 2: Preoperative data.sav\n\nFigshare: Extended data for ‘Prevalence of pre-operative anxiety and associated risk factors among patients awaiting elective surgery in a tertiary care hospital’,\n\nhttps://www.doi.org/10.6084/m9.figshare.23541501. 15\n\nThis project contains the following extended data:\n\n• Supplementary file 1: Questionnaire.pdf\n\n• Supplementary file 2: Consent form in English and Nepali.pdf\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0)\n\n\nReferences\n\nVadhanan P, Tripaty DK, Balakrishnan K: Pre-operative anxiety amongst patients in a tertiary care hospital in India- a prevalence study. J. Soc. Anesthesiol. Nepal. 2017 Jun 28 [cited 2023 May 9]; 4(1): 5–10. Publisher Full Text Reference Source\n\nDhungana M, Limbu R, Shrestha M: Assessment of Pre-Operative Anxiety among Patients in Selected Hospitals of Rupandehi, Nepal. J. Psychiatr. Assoc. Nepal. 2019 Nov 14 [cited 2023 May 10]; 8(1): 28–32. Publisher Full Text Reference Source\n\nMatthias AT, Samarasekera DN: Preoperative anxiety in surgical patients - experience of a single unit. Acta Anaesthesiol. Taiwanica. 2012 Mar 1; 50(1): 3–6. PubMed Abstract \| Publisher Full Text\n\nRuhaiyem ME, Alshehri AA, Saade M, et al.: Fear of going under general anesthesia: A cross-sectional study. Saudi J. Anaesth. 2016 Jul 1 [cited 2023 May 10]; 10(3): 317–321. PubMed Abstract \| Publisher Full Text Reference Source\n\nGangadharan P, Assiri RAM, Assiri FAA: Evaluating the level of anxiety among pre-operative patients before elective surgery at selected hospitals in kingdom of saudi arabia. Int. J. Curr. Res. Rev. 2014.\n\nPritchard MJ: Identifying and assessing anxiety in pre-operative patients. Nurs. Stand. 2009 [cited 2023 May 10]; 23(51): 35–40. Publisher Full Text Reference Source\n\nAkinsulore A, Owojuyigbe AM: Assessment of preoperative and postoperative anxiety among elective major surgery patients in a tertiary hospital in nigeria. J. Anesth. 23(2): 2015.\n\nNigussie S, Belachew T, Wolancho W: Predictors of preoperative anxiety among surgical patients in Jimma University Specialized Teaching Hospital, South Western Ethiopia. BMC Surg. 2014 Sep 5 [cited 2023 May 10]; 14(1): 1–10. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlmalki MS, Hakami OAO, Al-Amri AM: Assessment of Preoperative Anxiety among Patients Undergoing Elective Surgery. Egypt J. Hosp. Med. 2017 Oct 1 [cited 2023 May 9]; 69(4): 2329–2333. Publisher Full Text Reference Source\n\nPearson S, Maddern GJ, Fitridge R: The role of pre-operative state-anxiety in the determination of intra-operative neuroendocrine responses and recovery. Br. J. Health Psychol. 2005 May 1 [cited 2023 May 10]; 10(2): 299–310. PubMed Abstract \| Publisher Full Text\n\nMoerman N, Van Dam FSAM, Muller MJ, et al.: The Amsterdam Preoperative Anxiety and Information Scale (APAIS). Anesth. Analg. 1996 [cited 2023 May 9]; 82(3): 445–451. PubMed Abstract \| Publisher Full Text\n\nWattier JM, Barreau O, Devos P, et al.: Measure of preoperative anxiety and need for information with six issues. Ann. Fr. Anesth. Reanim. 2011 Jul [cited 2023 May 10]; 30(7–8): 533–537. Reference Source\n\nZemła A, Nowicka-Sauer K, Jarmoszewicz K, et al.: Measures of preoperative anxiety. Anaesthesiol. Intensive Ther. 2019 [cited 2023 May 10]; 51(1): 64–69. Publisher Full Text Reference Source\n\nBoker A, Brownell L, Donen N: The Amsterdam preoperative anxiety and information scale provides a simple and reliable measure of preoperative anxiety. Can. J. Anesth. 2002 [cited 2023 May 10]; 49(8): 792–798. PubMed Abstract \| Publisher Full Text\n\nPathak BD: Prevalence of Pre-operative Anxiety and associated risk factors among Patients awaiting Elective Surgery in a Tertiary Care Hospital. [Dataset]. figshare. 2023. Publisher Full Text\n\nPathak BD: Prevalence of Pre-operative Anxiety and associated risk factors among Patients awaiting Elective Surgery in a Tertiary Care Hospital. [Dataset]. figshare. 2023. Publisher Full Text\n\nAlanazi AA: Reducing anxiety in preoperative patients: a systematic review.2014 May 6 [cited 2023 May 9]; 23(7): 387–393. Publisher Full Text\n\nBondy LR, Sims N, Schroeder DR, et al.: The Effect of Anesthetic Patient Education on Preoperative Patient Anxiety. Reg. Anesth. Pain Med. 1999 Mar 1 [cited 2023 May 10]; 24(2): 158–164. PubMed Abstract \| Publisher Full Text Reference Source\n\nLin SY, Huang HA, Lin SC, et al.: The effect of an anæsthetic patient information video on perioperative anxiety. Eur. J. Anaesthesiol. 2016 Feb 1 [cited 2023 May 10]; 33(2): 134–139. PubMed Abstract \| Publisher Full Text Reference Source\n\nKiyohara LY, Kayano LK, Oliveira LM, et al.: Surgery information reduces anxiety in the pre-operative period. Rev. Hosp. Clin. Fac. Med. Sao Paulo. 2004 [cited 2023 May 10]; 59(2): 51–56. Publisher Full Text Reference Source\n\nWu H, Zhao X, Chu S, et al.: Validation of the Chinese version of the Amsterdam Preoperative Anxiety and Information Scale (APAIS). Health Qual. Life Outcomes. 2020 Mar 11 [cited 2023 May 10]; 18(1): 66–66. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVergara-Romero M, Morales-Asencio JM, Morales-Fernández A, et al.: Validation of the Spanish version of the Amsterdam Preoperative Anxiety and Information Scale (APAIS). Health Qual. Life Outcomes. 2017 Jun 7 [cited 2023 May 10]; 15(1): 110–120. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMaurice-Szamburski A, Loundou A, Capdevila X, et al.: Validation of the French version of the Amsterdam preoperative anxiety and information scale (APAIS). Health Qual. Life Outcomes. 2013 Oct 7 [cited 2023 May 10]; 11(1): 166–167. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMaurício S, Rebêlo I, Madeira C, et al.: Validation of the Portuguese version of Amsterdam Preoperative Anxiety and Information Scale (APAIS). Health Qual. Life Outcomes. 2021 Dec 1 [cited 2023 May 10]; 19(1): 95–99. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBuonanno P, Laiola A, Palumbo C, et al.: Italian validation of the Amsterdam preoperative anxiety and information scale. Minerva Anestesiol. 2017 Jul 1 [cited 2023 May 10]; 83(7): 705–711. PubMed Abstract \| Publisher Full Text Reference Source\n\nALMesned S, Alsalhi AA, Abdelsalam S, et al.: Arabic Validation of the Amsterdam Preoperative Anxiety and Information Scale. Cureus. 2022 Aug 14 [cited 2023 May 10]; 14(8). Publisher Full Text Reference Source" }	[ { "id": "210143", "date": "17 Oct 2023", "name": "Khagendra Kafle", "expertise": [ "Reviewer Expertise Psychiatry" ], "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 research topic is very relevant in the Nepalese context because there are very few studies done in this field. The methodology is sound. The tools used are fine. I have some comments on this article which I have mentioned below.\n\nAbstract: The background section can be rewritten. It should be shorter. It should normally contain what is known about the research topic and what is to be known about it (or the research objective) in 2-4 sentences.\n\nThere is a discrepancy about the included samples: elective surgeries (mentioned under study setting) or major elective surgeries (mentioned under sampling).\n\nAPAIS being a self-rated instrument, it should be in the native language of the research participants. Less education of the participants may not be the proper justification for not translating/validating it into the Nepali language. This is a major limitation of this study.\n\nThere is a discrepancy in the sampling technique mentioned in the article. It is mentioned as consecutive sampling at one place and convenience sampling in another place. Please correct it.\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": "10737", "date": "17 Jan 2024", "name": "Bishnu Deep Pathak", "role": "Author Response", "response": "Dear Reviewer, Thank you for reviewing our article. We have made the necessary changes in the manuscript as suggested by you and as appropriate. We agree that the lack of translation of the APAIS tool in the native language is a major limitation of our study and hence we think that future studies on this topic need to rectify this aspect. Regarding sampling, we have used the term 'convenience sampling' throughout the text. We have tried to make our abstract as concise as possible. Thank you." } ] }, { "id": "210142", "date": "24 Oct 2023", "name": "Suraj Shakya", "expertise": [ "Reviewer Expertise I am an academic faculty and clinical psychologist", "with research interest in psychometrics and psychological 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\nThe authors have undertaken an important study on pre-operative anxiety in a tertiary-level hospital in Kathmandu. Undoubtedly, this is an important research, and the write up is okay too. However, there are some points for improvement. Most of the points are minor comments, except one major comment:\n\nHeading: Consider removing the word 'prevalence' from the heading, as it appears fine without it. Just a suggestion only.\n\nAbstract: Include the number of participants in the methods section of the abstract.\n\nAbstract: In the first sentence of the results section, present only percentages rather than raw numbers.\n\nAbstract (Result): When stating, \"The patients living in a nuclear family...approximately 2.5 times higher risk of having pre-operative anxiety,\" specify the reference group for comparison (e.g., 2.5 times higher risk than...?).\n\nIntroduction, 3rd paragraph, 4th sentence: Rephrase the word 'rarely' since there are some researches in Nepal as well.\n\nMethod, Study Design, 1st sentence: Reevaluate whether the design can be termed analytical; it seems more like a 'cross-sectional descriptive' design. Just my opinion, but please seek input from colleagues in this field.\n\nSampling and sample size: Please justify why this is consecutive sample (instead of purposive, or convenience method); and this statement is not clear 'all the patients were taken consecutively'.\n\nSampling and sample size (sample size calculation): I was curious, why were data from similar studies in Nepal not used? Not necessary to incorporate this suggestion, if the team think this is justified.\n\nData Collection and Study Variables, 2nd paragraph, 2nd sentence: Provide citations for the literature being referred to, if possible, to enhance authenticity.\n\nData Collection and Study Variables (this is a Major Comment): If translation was performed, particularly for illiterate participants, clearly describe the process. Please mention clearly how many enumerators were involved, and how did they maintain uniformity in instant translation during data collection, in method section (in data collection section). As you have mentioned 'standard way' (2nd last para of discussion section), please elaborate on what this means. This is very important; otherwise, this would seem a major flaw and limitation of this study.\n\nData Analysis: Confirm whether the significance level is set at 0.05 or 0.07.\n\nResults, Socio-Demographic/Surgical Characteristics: Simplify and condense the wording in this section, as detailed information may be found in the tables. For instance, this sentence 'Of these, 108 (52.68%) and 97 (47.32%) belonged to age groups less than or equal to 50 years and above 50 years respectively.' could be deleted.\n\nEnsure uniformity in the presentation of numbers and percentages [3, 5% vs 3(5%)] throughout the entire article, especially in the results section.\n\nTable 1: Remove the '(100.00)' in the entire third column with the heading 'Total.'\n\nTable 2 and its elaboration in the Results Section: Clarify the rationale for correlating the 'information desire' component with other components. If there's a specific reason, this could be explained in the introduction, results, or discussion sections. Otherwise, other components could be correlated with each other too. The second sentence in the discussion section also mentions about 'information requirement'. I was wondering, if this 'information requirement' could be rephrased, rather than just repeating the same jargon from the anxiety tool. It would be meaningful, if it is rephrased.\n\nResults, Preoperative Anxiety Section, last sentence: Mention the strength of the correlation, whether it's strong, moderate, or weak.\n\nDiscussion, 1st Paragraph, 2nd sentence: Eliminate the restatement of 'median/mean score' in this context.\n\nDiscussion, 1st Paragraph, last sentence: Specify the reference (comparison) group when discussing the '2.5 times greater risk than...'.\n\nTime frame when patients were assessed: In the Discussion section, 2nd paragraph, 2nd last sentence, you have mentioned about the time frame when patients were assessed. This is important. If this time duration is also mentioned in the method section of the abstract, it would be more meaningful to readers.\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?\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? Yes", "responses": [ { "c_id": "10736", "date": "17 Jan 2024", "name": "Bishnu Deep Pathak", "role": "Author Response", "response": "Dear Reviewer, Thank you for reviewing our article. We have made necessary changes in the manuscript as appropriate and as suggested by you. We hope you will kindly consider our article for further approval. Below are the replies to your comments: 1. Thank you for this comment. We have edited this in the manuscript. 2. Thank you for this comment. We have added total number of cases in the abstract method section. 3. Thank you for this comment. We have used only percentage in the result of abstract and have omitted the raw numbers. 4. Thank you for this comment. We have edited it as you have suggested (eg. compared to reference groups like joing family, having past surgical history, etc). 5. Thank you for this comment. The word 'rarely' has been replaced and the sentence has been rewritten appropriately. 6. Thank you for this comment. We totally agree with your opinion that this is a cross sectional study. But, since we have used an inferential statistics in this study, this now becomes an analytical cross sectional study rather than just descriptive. 7. Thank you for this comment. We have used the term 'convenience sampling' as suggested by you. The word consecutive sampling has been replaced accordingly 8. Thank you for this comment. The study referenced in sample size calculation looks very similar to our setting and in terms of design and methodology. Due to this reason, we found this study to be more appropriate for our sample size calculation. Please kindly consider it. 9. Thank you for this comment. This sentence is intended to describe the different variables that we used in our questionnaire apart from APAIS tool while collecting data. And, these questions were prepared after extensive literature review by the investigators themselves. Almost all the studies included in the reference section were reviewed meticulously for the questionnaire. So, we think that referencing is not relevant in this part. Please kindly consider it. 10. Thank you for this comment. We totally agree that lack of tranlation of APAIS tool into the native language is a major limitation of our study. But, as stated in the manuscript, the investigators had themselves asked the questions of this tool in a 'standard way.' Before doing this, the investigators had a discussion regarding how to ask each of the question to the patients in their native language. We had discussed about how much information to provide to the patients and also the way of asking each question. A special care was taken regarding the possibility of discrepancies that may arise while interviewing the cases. To avoid this error, all of the investigators involved in data collection had done a rehearsal beforehand as well. So, we had tried our best to minimize differences and possible bias in this scenario. But, still, this is a weak part of this study that needs to be rectified in future studies on this topic. 11.Thank you for this comment. In our study, the margin of error has been taken as 7% and level of significance being 0.07. 12, 13, 14. Thank you for these valuable comments. We have made edits in the manuscript as suggested by you 15. Thank you for this comment. We have added a few sentences in the manuscript to address this. As described in the past literature, the information desired component is related to anxiety scores in the pre-operative period. It has been found that the higher the information score, the higher would be the anxiety level. In other words, those patients who were not properly informed about their surgical procedure, they would remain anxious and fearful regarding their surgery and would be expecting someone to provide them detail information leading to higher information component score in APAIS tool. Therefore, we used this statistical analysis in our study. 16-19. Thank you for these valuable comments. We have made necessary changes in the manuscript as suggested." } ] } ]	1	https://f1000research.com/articles/12-1207
https://f1000research.com/articles/12-1342/v1	16 Oct 23	{ "type": "Research Article", "title": "Cytotoxicity of dental cement on soft tissue associated with dental implants at different time intervals", "authors": [ "Prashanth Bajantri", "Shobha J. Rodrigues", "Shama Prasada Kabekkodu", "Akshar Bajaj", "Puneeth Hegde", "Sandipan Mukherjee", "Sharon Saldanha", "Mahesh Mandatheje", "Thilak Shetty B", "Umesh Y. Pai", "Ann Sales", "Vignesh Kamath", "Prashanth Bajantri", "Shama Prasada Kabekkodu", "Akshar Bajaj", "Puneeth Hegde", "Sandipan Mukherjee", "Sharon Saldanha", "Mahesh Mandatheje", "Thilak Shetty B", "Umesh Y. Pai", "Ann Sales", "Vignesh Kamath" ], "abstract": "Background: To investigate and compare the effect of four commercially used dental cement at 24 hours, 48 hours,72 hours (h) and 6 days on the cellular response of human gingival fibroblast (HGF).\nMethods: 3 cement pellet samples were made for each 4-test cement (n=12). The cement used for this study were zinc phosphate (ZP), zinc oxide non-eugenol (ZOE), RelyX U200 (RU200), and glass ionomer cement (GIC). The cytotoxicity of peri-implant tissues was investigated using one commercial cell line. All processing was done following International Organization for Standardization (ISO) methods 10993-5 and 10993-12 (MTT assay Test). Cell cultures without dental cement were considered as control. Standard laboratory procedures were followed to permit cell growth and confluence over 48 hrs after sub-cultivation. Before being subjected to analysis, the cells were kept in direct contact with the cement samples for the suggested time period. To validate the results the specimens were tested three times each. Cell death and inhibition of cell growth were measured quantitatively. Results were analyzed using 1-way ANOVA (a=0.05) followed by Tukey B post hoc test.\nResults: The study showed the dental cement test material was cytotoxic. ZOE, ZP, GIC, and RU200 were cytotoxic in decreasing order, respectively, significantly reducing cell viability after exposure to HGF (p <0.001).\nConclusions: Within the limitations of this in-vitro cellular study, results indicated that HGF were vulnerable to the test the dental cement. The highest cytotoxicity was observed in ZOE, followed by ZP, GIC, and RU200.", "keywords": [ "Gingival fibroblast", "implants", "MTT assay", "Luting cements", "Resin" ], "content": "Introduction\n\nEndosseous implants to replace lost teeth have become the gold standard in dentistry. The implant-supported prosthetic reconstruction uses both cement- and screw-retained restorations. Regarding cost, aesthetics, ease of fabrication and passivity, cement-retained implant supported prosthesis (CRISP) restorations function better than screw-retained ones.1\n\nDental professionals often choose dental cement for CRISP based on preferences of the product’s characteristics, such as material properties, mixing method, delivery system, or consistency.2–4 There are many kinds of luting dental cement that can be usedto lute bridges, crowns, veneers, and implant crowns, and dental materials that are biocompatible are gaining more attention from dentists and patients.3,4 CRISP have both advantages and disadvantages. One of them is related to the leftover cement in subgingival areas.5–7 In these instances, it is very hard to remove all the dental cement.8 Peri-implant diseases are complex, inflammatory conditions caused by a group of bacteria that are usually anaerobic and Gram-negative and proliferate subgingivally.9–17 One of the most important aspects of implant therapy success is the type of luting cement used to bond prostheses.18 It has been proved that residual cement left in CRISP can be an etiological factor for peri-implantitis in 8.6-14.4% of cases.19–23\n\nZP cement is a dental cement that has been shown to be very effective in dental practice.24–27 However, it has some disadvantages, such as being soluble, low pH, and inability to bond with the tooth chemically. Zinc oxide non eugenol (ZOE) is a temporary cement that uses different substitutes instead of eugenol, because eugenol can interfere with resin bonding. Traditional GICs have some benefits, such as being biocompatible, releasing fluoride, having a thermal expansion and an elasticity similar to dentin.28\n\nTraditional GICs have drawbacks such as dehydration, susceptibility, high solubility, and slow setting rate despite their benefits. Due to further developments in GICs, resin-modified GICs—which have greater physical and mechanical properties than regular GICs—have been introduced.29 Resin cement includes a significant amount of composite resin, which chemically attaches to the tooth.30 Despite their biocompatibility issues, dentists have been increasingly using this cement since they are said to improve restorative retention. However, certain material components can triggers a pulpal or gingival reaction, raising concerns about cytotoxicity.29,31–33 Furthermore, despite GICs' increased mechanical qualities, only a few studies have shown their biocompatibility and harmful consequences.29,30\n\nDental cement can significantly influence the growth or suppression of various bacterial strains associated with peri-implant disease. Furthermore, the effect of dental cements on the proliferation of host cells can provide additional insights for choosing the appropriate cement material.\n\nIn clinical scenarios where cement might be applied during the early healing phase, such as temporary restoration or abutment placement during surgery, or at a later stage in implant restoration where harmful bone alterations might occur if cement comes into contact with host tissues, it's particularly crucial to assess the effects of bacteria and host cells on dental component surfaces.34\n\nBone loss around dental implants typically follows a specific pattern, moving from the crestal bone level towards the apex of the implant. This resorption profile may be primarily due to the interaction between soft tissue and remnants of cement from cement-retained prosthesis.35\n\nRaval et al. conducted a study on the bacterial response of many late-stage Gram-negative colonisers, which are implicated in peri-implant disease.36\n\nDifferent cement formulations (zinc oxide with eugenol, zinc oxide with noneugenol, zinc phosphate, and resin components), according to the authors' hypotheses, would produce various bacterial reactions. Several commercially available dental cements were exposed to Aggregatibacter actinomycetemcomitans, Fusobacterium nucleatum, and Porphyromonas gingivalis, and the bacterial viability was monitored to ascertain how the bacteria responded to the dental cement. The composition of dental cement has a substantial influence on whether certain bacterial strains linked to peri-implant illness proliferate or are inhibited. A previous study by the authors studied the impact of dental cement on cell proliferation at 24 hrs.37 However, the impact of dental cement on host cellular proliferation in different time intervals may throw some light in choosing the right cement material as these cement may remain in contact with host tissues for varied time periods depending on the purpose and duration of the restoration.\n\nSeveral factors may restrict the application of in vitro cell-based experiments to clinical scenarios. Primary cells, which maintain the same natural ploidy, gene expression regulation, stress response, and other biological parameters seen in humans, may provide more relevant data for clinicians compared to immortalised cell lines.38\n\nHuman gingival fibroblasts are commensals of the oral environment and make interesting models for invitro evaluation of dental materials on account of the release of growth factors and cytokines suggesting immunological response. The current study therefore employed human gingival fibroblasts.\n\nThis study investigated and compared the effect of four commercially used dental cement at 24h, 48h, 72h, and six days on human gingival fibroblast (HGF) cellular response. The Null Hypothesis was that commercially used dental cement would have had no effect on the cellular response of HGF.\n\n\nMethods\n\nThe test cement used in the study is presented in Table 1.\n\nThe preparation of the cement samples was done as follows: The powder was stirred into the liquid in modest increments as per the manufacturer's directions. Once the cement acquired the right consistency, it was transferred to three polytetrafluoroethylenes (PTFE) polymer moulds. The cement takes roughly 5-9 minutes to set.\n\nThe GIC powder and liquid were combined as per the manufacturer's instructions. The mixture was immediately transferred to three PTFE moulds to preserve the gel structure. The GIC cement was left to cure for 24 hours.\n\nThe base and catalyst were mixed according to the manufacturer's guidelines on a mixing pad, then transferred to three PTFE moulds. The setting time for this cement was approximately 3 minutes and 30 seconds.\n\nThe required amount of resin was dispensed from the automix syringe's clicker dispenser, mixed, and poured into three PTFE moulds. The RU200 cement set in about 30 seconds.\n\nAll tests used a mould of size 7x3x3mm. The cement was kept at room temperature for two days, then washed with phosphate buffer saline pH7.4, and air-dried in a NUAIR biosafety cabinet hood to clean the surface of the solidified cement and remove any unsolidified items.\n\nThe cytotoxicity of the four test cements on human gingival fibroblast (HGF) cells was assessed using the MTT assay Test [(3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazoliumbromid], as previously described. The HGF cells were cultured in DMEM supplemented with 10% FBS and maintained in a class II biosafety cell culture hood (Nuair, USA) in a CO2 incubator (ThermoFisher Scientific, USA).\n\nIn brief, 1X104 HGF cells were grown in a 96-well plate and immediately exposed to the four test cements for a day at 37°C with 5% CO2. Direct contact testing was used to closely simulate an in vivo setting and assess the cytotoxicity of the dental cements under investigation. HGF cells unexposed to cement served as a control group. After the incubation period (24h, 48h, 72h, and six days), the cement was removed, and the cells were treated with MTT (5 mg/ml, Sigma, USA) for 4 hours at 37°C with 5% CO2. The formazan crystals formed were dissolved in 150 μL of DMSO (Sigma, USA), and the absorbance was measured using a microplate reader (Varioskan, ThermoFisher Scientific, USA) at 570 and 630 nm. All tests were performed in duplicate and repeated three times for validation.\n\nThe experiments were conducted with appropriate replicates and repeated three times. Intergroup comparison was done using the post-hoc Tukey Test. Statistical significance was defined as P > 0.05 using the Tukey post-hoc test.\n\n\nResults\n\nThe present study was undertaken to determine the cytotoxic effect of four different dental cement on HGF. Cell viability was measured 24hrs, 48hrs, 72hrs, and 6 days post-exposure with four dental cements. The intergroup comparison was carried out using post-hoc Tukey Test. P > 0.05 by Tukey post-hoc test was considered statistically significant. (Figure 1)\n\nHGF viability was 99.99% in the control cement at 24 hours, 10.84% in the ZOE cement, 20.82% in the ZP cement, 81.73% in the GIC, and 107.78% in the RU200 cement, respectively (Figure 1). Compared to the other three cement it was tested, RU200 had the highest cell viability, and ZOE cement had the lowest cell viability. There is a statistically significant difference between all of the groups (P <0.0001) except for the control and RU200 cement group (P=0.5635).\n\nHGF viability in control, ZOE, ZP, - GIC and RU200 was 99.99 percent, 11.03 percent, 26.76 percent, 30.79 percent, and 48.29 percent, respectively, after 48 hours. Compared to the other three cements, RU200 has the highest cell viability. Cell viability is lowest in ZOE and ZP cement. There is a statistically significant difference between all groups, P< 0.0012, except for the zinc phosphate and GIC group (P=0.7575).\n\nHGF viability was 99.99 percent, 35.11 percent, 11.86 percent, 56.34 percent, and 51.71 percent at 72 hours in control, ZOE, ZP, GIC, and RU200, respectively. GIC has the most excellent cell viability compared to the other three cement groups, while ZP cement has the lowest. Of the four cement groups, ZOE and ZP cement had the lowest cell vitality. The results were statistically significant between all of the groups. (P< 0.0001) except ZOE and ZP (p=0.7954) and ZOE and GIC(P=0.0669)\n\nOn 6th day the HGF viability in control, ZOE, ZP, GIC cement and RU200 cement was 99.99%,7.14%,4.53%,23.51%, and 45.85%, respectively. RU200 cement shows the highest cell viability, while zinc oxide non-eugenol cement shows the least cell viability among all 4 cement. The results were statistically significant between all of the groups. (P<0.0001) except for ZOE and ZP (P =0.7811)\n\nThis study evaluated the cytotoxic impact of four distinct dental cement on Human Gingival Fibroblasts (HGF). The viability of the cells was assessed at 24 hours, 48 hours, 72 hours, and 6 days after exposure to the cements. The Tukey post-hoc test was used for intergroup comparisons. A p-value greater than 0.05 was deemed statistically significant (Figure 1).\n\nAt the 24-hour mark, the viability of HGF was highest in the RU200 cement and lowest in the ZOE cement, compared to the other three cements tested. The difference between all groups was statistically significant (P <0.0001), except for the control and RU200 cement group (P=0.5635).\n\nAfter 48 hours, RU200 cement continued to show the highest cell viability among the four cements. The lowest cell viability was observed in ZOE and ZP cement. All groups showed a statistically significant difference (P< 0.0012), except for the zinc phosphate and GIC group (P=0.7575).\n\nAt the 72-hour interval, GIC showed the highest cell viability among the four cements, while ZP cement showed the lowest. The results were statistically significant between all groups (P< 0.0001), except between ZOE and ZP (p=0.7954) and ZOE and GIC (P=0.0669).\n\nOn the sixth day, RU200 cement demonstrated the highest cell viability, while zinc oxide non-eugenol cement showed the least among all four cements. The results were statistically significant between all groups (P<0.0001), except for ZOE and ZP (P =0.7811).\n\n\nDiscussion\n\nThe experimental arrangement of this research displayed that human gingival fibroblast displayed susceptibility to alterations in viability when subjected to commercial dental cement. Furthermore, these fibroblasts can trigger biological responses. The Null Hypothesis was invalidated due to significant fluctuations in fibroblast viability, which suggests that the proximity of cement to periimplant tissue during cementation plays a role in causing potential toxic tissue damage. The extent of this damage is proportional to the quantity of cement in proximity with oral tissues and the leaching of components. Variations in individual sensitivity could exist, emphasizing the crucial necessity of removal of excess cement.39\n\nThe evaluation of the cytotoxic potential of dental cement was carried out using a standardized technique in this experimental investigation. Utilizing in-vitro cytotoxic assays offers straightforward control over experimental parameters that are complex to manage in in-vivo studies.40–42\n\nThe impact of ZP, ZOE, GIC, and RU200 cement on HGF cells was investigated using the MTT test. Chemical constituents released from tooth restorative materials target fibroblasts. HGF cells were chosen for this study due to their ease of production and cultivation. These cells offer benefits in terms of in-vitro growth efficiency and result reproducibility. They yield findings comparable to primary human gingival fibroblasts, potentially serving as a model for in-vitro studies on gingival toxicity.43–45\n\nThe MTT test, a widely recognized method for assessing cell vitality, was employed. In the current investigation, when the MTT assay was conducted on cell cultures exposed to the test cement for 24 hours, the highest cell viability, at 107.78%, was observed with resin cement at 24 hours 48 hours, and 66 days. Conversely, the lowest viability was found with ZOE and ZP cement, respectively. Significant differences were found between the control, ZOE, and ZP groups.\n\nAt all the various time intervals, ZOE and ZP cement exhibited the most pronounced cytotoxicity. ZOE cement samples displayed severe cell cytotoxicity, with cell viability measuring below 30%. In the case of ZP cement, cell viability stood at 10.84%, 11.03%, 11.86%, and 4.53% at 24, 48, 72 hours, and the sixth day, respectively. This occurrence can be attributed to the release of leachable substances from the materials, an impact that progressively diminishes and eventually falls below detectable levels after a span of six weeks.46 A preceding investigation conducted by the researchers revealed GIC to exhibit the highest cytotoxicity.37However, it's noteworthy that the time frame analyzed in that study was limited to 24 hours.37 Discrepancies in methodology could play a role in yielding differing outcomes. Potential explanations for the cytotoxic impacts of these cements include the liberation of zinc and fluoride ions, as well as acidity and the discharge of other substances.27\n\nLeirskar and Helgeland conducted an analysis of the culture conditions involving ZP cement and observed the released zinc had detrimental effects on the studied cell line. In addition since cell death was noted from the first to the third day, it indicated that factors apart from acidification were incriminated. These findings aligned with research by Welker and Neupert, as well as Leirskar et al.40,41\n\nDuring cell death, proinflammatory cytokines generally increase, making the suppression of inflammatory responses a key aspect of effective anti-inflammatory ingredients. The extent of cytotoxic effects was linked to the quantity of zinc released from ZP cement, suggesting that other elements, like the acid produced by the cement, might amplify the zinc's impact. Earlier studies revealed that zinc absorption in certain cell types reduced as pH dropped.47\n\nZn2+ acts as an anti-inflammatory ingredient by regulating proinflammatory cytokines, which is why a higher zinc dose is recommended to lower these cytokine levels in the blood plasma of inflammation patients. Another study found that Harvard ZP cement exhibited greater cytotoxicity compared to Fuji PLUS cement (RM-GIC). Fuji PLUS had varying levels of cytotoxic effects, ranging from mild to severe, while Fuji I GIC showed the least cytotoxicity.\n\nLewis et al. suggested that the leachable components of GICs might affect the rate of cell cycle progression rather than causing immediate cell death.47According to Oliva et al., RM-GIC has notable cytotoxic effects attributed to its leaching poly-acidic phase. The higher HEMA content in Fuji PLUS cement which quickly diffuses into dentine might contribute to its greater cytotoxicity compared to Fuji I.22–24\n\nThe levels of HEMA permeating into pulpal tissue are considerably lower than those causing acute toxicity. Thus, RM-GIC's cytotoxicity could be linked to the leaching of a hazardous mix of components, including resin monomers and fluoride ions. Kanjevac et al. established a connection between cytotoxicity and fluoride leakage in current GIC cement, also noting that other components like strontium and aluminum ions had more harmful effects on cell cultures when leached. Due to higher fluoride release, Fuji PLUS (RMGIC) exhibited more cytotoxicity than Fuji I (GIC).33,48,49\n\nThe quantities of HEMA capable of permeating into pulpal tissue are notably lower than those causing acute toxicity. Consequently, the leaching of a hazardous mixture of components, including resin monomers and fluoride ions, could be suspected in the case of RM-GIC.21,22 Kanjevac et al. conducted a study linking cytotoxicity to fluoride leakage in current GIC cement.44 They also highlighted that other elements like strontium (Sr2+) and aluminum ions (Al3+) had more pronounced harmful effects on cell cultures when leached. Due to increased fluoride release, Fuji PLUS (RMGIC) exhibited greater cytotoxicity than Fuji I (GIC).50,51\n\nPrevious in-vitro investigations have shown that when diffusates are extracted from cells using a dentin barrier test device, the apparent cytotoxicity of materials is reduced.52 Dentin can absorb chemicals in the tubules and hinder the diffusion of harmful compounds into the pulp, as explained by Hanks et al.53\n\nSelf-adhesive resin cements, composed of filled polymers, are designed to bond to tooth structure without requiring additional adhesives or etchants. These cements might undergo a slower rate of polymerization and attain a lower final polymerization degree compared to traditional resin cements, whether in dual- or self-cured modes, as noted by Moraes et al.54 Their final polymerization degree often proved higher in the dual-cure mode. Dual-cured specimens of resin-based cement (Duo-Link and BisCem) were demonstrated to be more harmful than chemically set cement. BisCem exhibited more cytotoxicity than Rely-XTM Unicem in the study by Ulker and Sengun.55 This aligns with Schmid-Schwap et al., who found that self-adhesive cement (Rely-XTM Plus) was more cytotoxic than adhesive resin cement.46\n\nHowever, certain monomers in resin composite cement can enter dentin tubules, potentially causing pulpal damage and hindering pulp tissue healing.56–58 These monomers exhibit cytotoxicity in vitro for pulp and gingival cells, and ions could trigger cell changes.35 Bakopoulou et al. demonstrated that the cytogenetic effects were caused by released chemicals like TEGDMA found in the composition of resin cement. The cytotoxicity ranking of commonly used monomers was identified as Bis-GMA > UDMA > TEGDMA > HEMA > MMA.57,59–61 The cytotoxic effects of Duo-Link cement could be attributed to the presence of UDMA and inorganic fluoride. The most severe cytotoxic effects in this study were associated with BisCem composite resin cement, which comprises TEGDMA and HEMA.62,63 Additionally, BisCem lowered the pH to 3-4, potentially explaining the decreased cell viability compared to Duo-Link cement's impact. Reduced drying time increases the cytotoxicity of resin cement, emphasizing the need for adequate curing time.64\n\nThe findings also suggest that the choice of cell system may impact results in advanced biocompatibility assays, such as protein expression or -omics studies, or assessments of cell-cell interactions. This should be explored in future research with larger sample sizes for each experimental group. This is particularly relevant considering the need to prioritize more relevant and mechanistic insights into hazardous pathways over isolated cytotoxicity endpoints. Therefore, while the clinical relevance of in vitro assays needs careful consideration, the results of this study must be approached cautiously. Despite resin cement's strong retention and preferred status as a luting agent in CRISP, clinical reports indicate a high incidence of peri-implantitis and difficulties in prosthesis retrieval in complication cases. Thorough clinical practices are necessary to reduce soft tissue exposure to these cements during attempts to remove excess cement.\n\n\nConclusion\n\nWithin the limitations of this in-vitro study, the following conclusions were drawn:\n\n• All the luting cement is cytotoxic to the gingival fibroblast cells.\n\n• Maximum cytotoxicity was demonstrated in ZOE, followed by ZP, GIC and RU200 cement.", "appendix": "Data availability\n\nFigshare: Cytotoxicity of dental cements associated with dental implants, https://doi.org/10.6084/m9.figshare.23702505.v1. 65\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nHebel KS, Gajjar RC: Cement-retained versus screw-retained implant restorations: achieving optimal occlusion and esthetics in implant dentistry. J. Prosthet. Dent. 1997; 77: 28–35. PubMed Abstract \| Publisher Full Text\n\nChee W, Jivraj S: Screw versus cemented implant supported restorations. Br. Dent. 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Publisher Full Text" }	[ { "id": "218095", "date": "20 Nov 2023", "name": "Roseline Meshramkar", "expertise": [ "Reviewer Expertise Esthetics", "Smile design", "Implants." ], "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 a meticulously crafted introduction, thorough exploration of materials and methods, and a comprehensive presentation of results. However, it is suggested that the discussion section be augmented with additional references, particularly those that present contradictory findings.\nClinical applications of cements are ubiquitous, and their biocompatibility is of paramount importance. Despite the widespread clinical use of cements, the findings of this study warrant careful consideration. Notably, the results strongly advocate against the use of any cement for prosthetic applications. Consequently, it is imperative to address the clinical acceptability of utilizing cements in such contexts. To bolster the discussion and it is recommended to incorporate references that elucidate contrasting perspectives and outcomes.\nIn conclusion, the study underscores the need for a cautious approach to the use of cements in prosthesis, challenging conventional clinical practices.\nAdding references in the discussion makes the study more thorough and helps us understand the bigger picture of cytotoxicity of cements and its clinical relevance.\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": "10624", "date": "24 Nov 2023", "name": "Dr Prashanth Bajantri", "role": "Author Response", "response": "User Comment, Thank you very much Madam for your critical appraisal of our article . As suggested by you indeed Cements are ubiquitously used in prosthodontics and as per our study, they need to be cautiously considered in implant-related prosthesis. This as you suggest warrants additional references and we are happy to work on this. we thank you again for the time and effort you have invested in providing your constructive critical appraisal Our kind regards, Dr Prashant" }, { "c_id": "10731", "date": "18 Jan 2024", "name": "Dr Prashanth Bajantri", "role": "Author Response", "response": "As suggested by the first reviewer we have made modifications to the manuscript to increase the number of references and to augment the discussion. Please find the edited manuscript. We look forward to the early indexing of this article on account of our professional compulsions. Kindly look into this matter. Kind regards, Shobha Rodrigues" } ] } ]	1	https://f1000research.com/articles/12-1342
https://f1000research.com/articles/12-798/v1	10 Jul 23	{ "type": "Study Protocol", "title": "Stereotactic radiotherapy for ventricular tachycardia: A study protocol", "authors": [ "Mariko Kawamura", "Masafumi Shimojo", "Yasuya Inden", "Takeshi Kamomae", "Kuniyasu Okudaira", "Tomohiro Komada", "Sumire Aoki", "Yurika Shindo", "Ryotaro Yasui", "Yusuke Yanagi", "Masayuki Okumura", "Takehiro Yamada", "Yuka Kozai", "Yumi Oie", "Yutaka Kato", "Shunichi Ishihara", "Toyoaki Murohara", "Shinji Naganawa", "Masafumi Shimojo", "Yasuya Inden", "Takeshi Kamomae", "Kuniyasu Okudaira", "Tomohiro Komada", "Sumire Aoki", "Yurika Shindo", "Ryotaro Yasui", "Yusuke Yanagi", "Masayuki Okumura", "Takehiro Yamada", "Yuka Kozai", "Yumi Oie", "Yutaka Kato", "Shunichi Ishihara", "Toyoaki Murohara", "Shinji Naganawa" ], "abstract": "Background: Currently, the standard curative treatment for ventricular tachycardia (VT) and ventricular fibrillation (VF) is radiofrequency catheter ablation. However, when the VT circuit is deep in the myocardium, the catheter may not be delivered, and a new, minimally invasive treatment using different energies is desired. Methods: This is a protocol paper for a feasibility study designed to provide stereotactic radiotherapy for refractory VT not cured by catheter ablation after at least one catheter ablation. The primary end point is to evaluate the short-term safety of this treatment and the secondary endpoint is to evaluate its efficacy as assessed by the reduction in VT episode. Cyberknife M6 radiosurgery system will be used for treatment, and the prescribed dose to the target will be 25Gy in one fraction. The study will be conducted on three patients. Conclusion: Since catheter ablation is the only treatment option for VT that is covered by insurance in Japan, there is currently no other treatment for VT/VF that cannot be cured by catheter ablation. We hope that this feasibility study will provide hope for patients who are currently under the stress of ICD activation. Trial registration: The study has been registered in the Japan Registry of Clinical Trials (jRCTs042230030).", "keywords": [ "Radioablation", "Stereotactic Radiotherapy", "Stereotactic Radioablation", "Ventricular Tachycardia (VT)" ], "content": "Introduction\n\nSustained ventricular tachycardia (VT) and ventricular fibrillation (VF) are arrhythmias that significantly reduce blood circulation and cause sudden cardiac death. According to a statistical analysis by the Fire and Disaster Management Agency, the percentage of cardiogenic cardiac arrests in Japan was 62% or 79,400 of 127,718 patients who had cardiac arrest transported by emergency medical services in 2018. Furthermore, among 25,756 patients (20%) who suffered cardiac arrests that were witnessed by the general public, the one-month survival rate was 36.2%, and the one-month return to society rate was 25.1% when the initial electrocardiogram (ECG) waveforms were VT and VF, which indicates an increase from 10 years ago; however, the prognosis remained poor.1 Furthermore, a study of 132 patients with fatal arrhythmias during Holter ECG recordings revealed that 73% had tachyarrhythmia, and 27% had bradyarrhythmia.2 According to the Japan Ministry of Health, Labor, and Welfare’s Vital Statistics of 2020, the number of deaths due to arrhythmia in Japan is nearly 30,000, suggesting that approximately 20,000 people may have died from VT or VF.\n\nIn the treatment of patients with VT, electrical cardioversion is performed first followed by administration of medication. In patients with recurrent ventricular arrhythmias, an implantable cardioverter defibrillator (ICD) is placed to continuously monitor cardiac activity. If VT or VF is detected, an electrical defibrillator restores the normal pulse. Although ICD therapy is considered the most reliable treatment for preventing sudden death, frequent VT attacks and electroshock therapy with ICDs have been reported to worsen patients’ quality of life and long-term prognosis.3,4\n\nCurrently, the standard curative treatment for VT and VF is radiofrequency catheter ablation with a three-dimensional (3D) mapping system. The conventional ablation therapy involves ablation from the endocardial side; however, in the case of ablation of the VT, ablation from the epicardial side may be performed depending on the thickness and location of the myocardial tissue to be ablated. However, a previous study has reported that more than half of the VT cases after myocardial infarction or other congenital cardiac diseases recur within one year of ablation.5 Furthermore, although catheter ablation therapy clearly reduces the recurrence rate of VT, improvement in life expectancy remains unconfirmed. A key factor is the high recurrence rate, and improvements in treatment techniques are warranted.\n\nThe causes of tachyarrhythmia include arrhythmias due to abnormal automaticity and re-entry through the tachycardia circuit. To interrupt the tachycardia circuit, catheter ablation is performed as a curative treatment for arrhythmias caused by re-entry. Catheter ablation generates Joule heat in the myocardial tissue around the catheter electrode and cauterizes the tissue, thereby interrupting the tachycardia circuit. However, when the VT circuit is deep in the myocardium, under epicardial fatty tissues, or near the coronary arteries, the catheter may not be delivered, and a new, minimally invasive treatment using different energies is desired.\n\nSince 2012, several case reports on stereotactic radiotherapy for VT have been published.6–9 A systematic review published in 2021 revealed the safety and short-term reduction in sustained VT/VF burden.10 To implement this method in Japan, the technique needs to be converted to one that can be implemented in Japan, and the safety of the method should be clarified in Japanese patients.\n\nThis study aimed to convert the results of overseas research into a feasible method in local practice and to verify whether radioablation using stereotactic radiotherapy techniques for patients with VT not cured by catheter ablation can reduce the number of VT occurrences compared to before radioablation treatment and whether the use of antiarrhythmic drugs can be reduced.\n\n\nProtocol\n\nThis prospective, single-arm, single-center study was approved by the Nagoya University ethics committee (CRB4180004) and registered to the Japan Registry of Clinical Trials (jRCTs042230030). Patients who are refractory to at least one catheter ablation and had received more than one antiarrhythmia drug treatment with over three episodes of VT in the last three months are considered eligible to participate in the study. Because data from Asian countries are very limited, we will first design a feasibility study at a single center. The inclusion criteria are as follows: age of ≥18 years; received antiarrhythmic drug treatment after ICD implantation; with recurrent VT after at least one catheter ablation; have experienced ≥3 VT attacks within the past three months while taking at least one antiarrhythmic drug; with VT that cannot be treated with catheter ablation; without history of cardiac irradiation; and provided written informed consent.\n\nMeanwhile, the exclusion criteria are as follows: with heart failure requiring a left ventricular assist device; with a low probability of survival of >6 months because of factors other than VT; with contraindications for irradiation; undergoing maintenance hemodialysis or peritoneal dialysis; with organic heart disease requiring surgery; with acute coronary or heart disease requiring hospitalization; at a high risk of radiation pneumonitis (e.g. idiopathic pulmonary fibrosis); with difficult-to-control pericardial or pleural effusions; having difficulty in resting in supine for 1 h; and with other illnesses or reasons that make it difficult to perform necessary examinations or follow-up investigations, or for which the principal investigator/participating physician determines that the patient is unfit to participate in this study. The discontinuation criteria are as follows: withdraws consent, or no longer meets the eligibility criteria while on the treatment waiting list, or difficult to continue the research due to an adverse event, or Accredited Clinical Research Review Committee instructs to discontinue the research, or the principal investigator/participating physician determines that the patient is unfit to participate in this study.\n\nAny additional standard treatment of VT is acceptable. Changes in medication will be always monitored during the study. Medications will not be restricted if necessary. However, medications will be monitored throughout the study even if they are not considered directly relevant to the study.\n\nThe primary endpoint is the short-term safety of the treatment. Safety evaluations will be performed on days 0, 0.5, 1, 1.5, 2, 3, 4, 5, 6, 9, and 12 months after treatment. Myocardial dysfunction (e.g., contractility, diastolic dysfunction, pericarditis, pericardial effusion, myocardial ischemia, and heart failure), lung injury, and other treatment-related acute and subacute (up to 6 months after irradiation) complications greater than G3 in the Common Terminology Criteria for Adverse Events ver. 5.0 will be monitored. The secondary endpoint is the efficacy of the treatment. Cardiac function assessed by imaging, reduction in arrhythmias by ICD record, presence of dose reduction of antiarrhythmic drugs, overall survival, and patient quality of life will be measured using the 36-Item Short Form Survey and EuroQol-5D. All data are registered to Research Electronic Data Capture (REDCap) at required timing as described previously. As this is the first treatment of VT using CyberKnife in Japan, we will evaluate the safety and efficacy of the treatment in three patients. If a patient enrolled in the study is not treated after enrollment, the patient is not counted, and individual enrollment will be continued until three eligible cases are treated. The enrollment will be terminated upon accumulation of three eligible cases.\n\nTarget delineation and planning\n\nPatients will undergo expiratory and inspiratory breath-holding and respiratory-gated contrast-enhanced computed tomography (CT) to create a stereotactic body radiotherapy (SBRT) plan. A 3D map from the electroanatomic mapping system (CARTO; Biosense-Webster, Israel) and ECG-gated CT scan will be fused to the planning CT to locate the target region and calculate the motion according to the heartbeats. The precision treatment system and CyberKnife M6 radiosurgery system (both from Accuray Inc., USA), which contain Synchrony, a respiratory compensation technology, are used to plan and deliver the planned dose.11 Positron emission tomography/CT and contrast-enhanced magnetic resonance imaging could be used as reference images. ICD leads are used for respiratory tracking. A 3-mm planning target volume (PTV) margin will be added to the target, and a dose of 25 Gy will be delivered to the PTV in a single session. The dose constraints are listed in Table 1. The PTV margin can be varied to account for setup errors and motion uncertainty, and the PTV dose can be reduced to 20 Gy to prioritize dose constraints for organs at risk. The maximum allowable dose is 32.5 Gy.\n\nTreatment\n\nThe treatment as an inpatient procedure for at least 24 h after irradiation will be performed by a cardiologist and a radiation oncologist. During treatment, the ICD will be turned off, while the ECG will be carefully monitored by a cardiologist. The ICD will be turned on after completion of irradiation following an equipment check.\n\nAfter treatment, a planned follow-up will be performed as described in the endpoint section.\n\nQuality control and quality assurance\n\nMonitoring will be conducted in accordance with the monitoring protocol and plan separately prescribed by the monitoring supervisor. (On-site monitoring will be conducted at least three times for each patient.) Documentation monitoring will be conducted twice during on-site monitoring, once at the beginning of the study and once at the end of the study. The audit will be conducted in accordance with the audit protocol and audit plan separately specified by the person in charge of the audit. (One system audit and one case audit will be conducted on-site.)\n\nThe study is registered and is open in the Japan Registry of Clinical Trials (jRCTs042230030). The outcome of the study will be published in jRCTs.\n\nParticipant recruitment has not started\n\n\nDiscussion\n\nCatheter ablation is the only curative treatment for VT and is covered by insurance in Japan. Catheter ablation allows treatment while directly searching for the origin using intracardiac electrocardiography and is undoubtedly a logical treatment method. However, because it uses Joule heating from the tip of the catheter, arrhythmias originating deep in the myocardium cannot be treated. Thus, VT requiring treatment of the deep myocardium, which is a weakness of catheter ablation, requires a different energy source than catheters, and there are great expectations for radioablation using SBRT.\n\nTo provide completely noninvasive treatment, treatment plans have been developed and implemented using epicardial electrocardiography at leading institutions; however, using this device in Japan is difficult because it is not approved in the country. Moreover, catheter ablation may demonstrates better long-term outcomes than SBRT for cases treatable by catheter ablation with a small ablation size. Therefore, catheter ablation should be performed as the first choice, and SBRT should be performed in selected patients who are refractory to treatment until more long-term data are available. Thus, the best way to confirm the feasibility of this treatment is to first select patients who have undergone catheter ablation at least once, have recurrence, and have intracardiac ECG data that prove the electrophysiological origin of VT. The facility where this study will be conducted has experience in treating >50 patients with VT with catheter ablation annually, which is a very high volume in Japan. Therefore, although this will be a single-center study, we believe that the facility is appropriate for evaluating resistance to catheter ablation. As no other treatment options are available for VT and VF, this study may serve as a guide to help clinicians in treating patients who failed to catheter ablation. Furthermore, we hope that this feasibility study will provide hope for patients who are currently under the stress of ICD activation.\n\nEthics approval and consent to participate: The study was approved by the appropriate institutional ethics committee (CRB4180004) and registered to the Japan Registry of Clinical Trials (jRCTs042230030) (registration date 06/02/2023, protocol ver. 1.2).", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nJCS/JHRS: JCS/JHRS 2022 Guideline on Diagnosis and Risk Assessment of Arrhythmia. JCS/JHRS 2022 Guideline on Diagnosis and Risk Assessment of Arrhythmia. Published 2022. Accessed May 08, 2023. Reference Source\n\nWatanabe E, Tanabe T, Osaka M, et al.: Sudden cardiac arrest recorded during Holter monitoring: prevalence, antecedent electrical events, and outcomes. Heart Rhythm. 2014; 11(8): 1418–1425. Publisher Full Text\n\nMcCready MJ, Exner DV: Quality of life and psychological impact of implantable cardioverter defibrillators: focus on randomized controlled trial data. Card. Electrophysiol. Rev. 2003; 7(1): 63–70. PubMed Abstract \| Publisher Full Text\n\nCarroll DL, Hamilton GA: Quality of life in implanted cardioverter defibrillator recipients: the impact of a device shock. Heart Lung. 2005; 34(3): 169–178. Publisher Full Text\n\nCalkins H, Epstein A, Packer D, et al.: Catheter ablation of ventricular tachycardia in patients with structural heart disease using cooled radiofrequency energy: results of a prospective multicenter study. Cooled RF Multi Center Investigators Group. J. Am. Coll. Cardiol. 2000; 35(7): 1905–1914. Publisher Full Text\n\nRobinson CG, Samson PP, Moore KMS, et al.: Phase I/II Trial of Electrophysiology-Guided Noninvasive Cardiac Radioablation for Ventricular Tachycardia. Circulation. 2019; 139(3): 313–321. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCuculich PS, Schill MR, Kashani R, et al.: Noninvasive Cardiac Radiation for Ablation of Ventricular Tachycardia. N. Engl. J. Med. 2017; 377(24): 2325–2336. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBonaparte I, Gregucci F, Surgo A, et al.: Linac-based STereotactic Arrhythmia Radioablation (STAR) for ventricular tachycardia: a treatment planning study. Jpn. J. Radiol. 2021; 39(12): 1223–1228. PubMed Abstract \| Publisher Full Text\n\nAras D, Çetin EHÖ, Ozturk HF, et al.: Stereotactic body radioablation therapy as an immediate and early term antiarrhythmic palliative therapeutic choice in patients with refractory ventricular tachycardia. J. Interv. Card. Electrophysiol. August 30, 2022; 66: 135–143. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKovacs B, Mayinger M, Schindler M, et al.: Stereotactic radioablation of ventricular arrhythmias in patients with structural heart disease - A systematic review. Radiother. Oncol. 2021; 162: 132–139. PubMed Abstract \| Publisher Full Text\n\nOzhasoglu C, Saw CB, Chen H, et al.: Synchrony--cyberknife respiratory compensation technology. Med. Dosim. 2008; 33(2): 117–123. Publisher Full Text" }	[ { "id": "216046", "date": "24 Oct 2023", "name": "Ji Hyun Chang", "expertise": [ "Reviewer Expertise radiotherapy" ], "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 am pleased to review Japan's inaugural clinical trial protocol. I eagerly anticipate a successful progression of this clinical research, with hopes of making a valuable contribution to the field.\nMinor points:\n\nRegarding the exclusion criteria within the protocol, it appears that '<6 months' would be more appropriate to denote a low probability of survival due to factors other than VT, rather than '>6 months.'\nSpecifying a maximum allowable dose may not be deemed necessary. Some of the researchers intentionally increase the dose within the GTV.\n\nIn the second paragraph of the discussion, the transition from epicardial ablation to SBRT appears somewhat incongruous.\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": [ { "c_id": "10547", "date": "29 Nov 2023", "name": "Mariko Kawamura", "role": "Author Response", "response": "Thanks for your very kind and thoughtful comments. I found them very helpful. I will briefly respond to you below. I agree that minimally invasive therapy is preferable for patients who are unlikely to survive long term for reasons other than VT. However, since this is a feasibility study, we considered it difficult to fully evaluate the safety of this treatment in patients for whom long-term survival is unlikely for reasons other than VT, and therefore we included patients who are likely to survive for more than 6 months. As for the upper limit of the dose, it may depend on the target size, but I am sure that your point is true, and I understand the idea that there is no need to set an upper limit. Based on the results of this study, we hope to have an answer in the future as to whether an upper limit is really necessary or rather the target dose should be higher. Since the history of SBRT is a little shallower than that of catheter ablation, we have kept a low profile. As the long-term results of SBRT become clearer, we hope to be able to recommend SBRT a little more strongly." }, { "c_id": "10729", "date": "22 Mar 2024", "name": "Mariko Kawamura", "role": "Author Response", "response": "Dear reviewers Thanks for your very kind and thoughtful comments. I found them very helpful. I will briefly respond to you below. To reviewer 1 Regarding the exclusion criteria within the protocol, it appears that '<6 months' would be more appropriate to denote a low probability of survival due to factors other than VT, rather than '>6 months.' I agree that minimally invasive therapy is preferable for patients who are unlikely to survive long term for reasons other than VT. However, since this is a feasibility study, we considered it difficult to fully evaluate the safety of this treatment in patients for whom long-term survival is unlikely for reasons other than VT, and therefore we included patients who are likely to survive for more than 6 months. Specifying a maximum allowable dose may not be deemed necessary. Some of the researchers intentionally increase the dose within the GTV. I am sure that your point is true, and I understand the idea that there is no need to set an upper limit. Based on the results of this study, we hope to have an answer in the future as to whether an upper limit is really necessary or rather the target dose should be higher. We added some comments on this in discussion part as follows. Since experimental animals have shown that reducing the dose to 32 Gy or less can produce an antiarrhythmic effect in the short term without causing fibrosis, this protocol was designed with an upper limit on the irradiation dose. At this point, however, there is some debate as to whether it is more effective to promote fibrosis with a higher target dose to obtain antiarrhythmic effects in the long term, and we hope that setting a maximum dose in this clinical trial will provide an answer to this part of the question. In the second paragraph of the discussion, the transition from epicardial ablation to SBRT appears somewhat incongruous. We have edited as follows: Because catheter ablation has a smaller ablation area than radioablation, and although this narrower ablation area may be the cause of VT recurrence, there are many uncertainties, such as the long-term effect of irradiating a wider area on cardiac function. In deference to catheter ablation, which has more long-term data than radioablation, we will change the energy to be irradiated from Joule heat to radiation dose based on the findings obtained with catheter ablation. It is highly possible that the mechanism of antiarrhythmic effect of irradiation is different from that of ablation, and furthermore, the mechanism may be different between ischemic and non-ischemic diseases. Therefore, it is essential to continue radioablation trial with prospective manners. To reviewer 2 The introductory part is comprehensive, however, I have a few minor comments. Some sentences from the 1st paragraph seem redundant in relation to cardiac SBRT. We agree so we have deleted most of the part. The 2nd paragraph contains a minor inaccuracy - there are also primo ICD implantations. we have corrected as following Treatment of patients with VT involves electrical cardioversion or implantable cardioverter defibrillator (ICD) implantation followed by administration of medication. specially in patients with recurrent ventricular arrhythmias, it is essential to wear an ICD to continuously monitor cardiac activity and to restore a normal pulse with an electrical defibrillator when VT or VF is detected. 5th paragraph - To the best of our knowledge, the first reports in vivo studies were published in 2014-20151,2. Thank you for your kind information. We added those papers. Study design and patient eligibility - VT attacks should be described more clearly. Anti arrhythmic drugs are meant with or without dose escalation? We have edited as follows. Patients who are refractory to at least one catheter ablation and had received one or more anti-arrhythmia drug treatment with over three episodes of VT episode with therapeutic intervention (anti-tachycardia pacing (ATP) or shock) in the last three months are considered eligible to participate in the study. Endpoints section - How will the safety evaluation be performed? Clinically or imaging methods, etc.? Is the follow-up interval too frequent? How will monitoring be carried out (Clinically, laboratory, imaging methods)? We added table to clarify what we will be monitoring. Study plan section - PET and MR imaging could be used as reference images - We think they will be used as a secondary series, the reference series will be CT. yes, we use them as secondary references. Thank you for pointing out our unclear writing. Dose constraints - related to the report of TG101 you listed the dose limits for smaller airways, not large bronchus. We have edited some dose constraint. Thank you." } ] }, { "id": "197297", "date": "16 Nov 2023", "name": "Lukas Knybel", "expertise": [ "Reviewer Expertise Radiation oncology- SBRT and SRS. Experience with SBRT of VT." ], "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 opportunity to review this paper. SBRT of the heart is still a relatively new method. Valid data from prospective studies are limited and therefore this project is considered to be resonable.\nThe introductory part is comprehensive, however, I have a few minor comments. Some sentences from the 1st paragraph seem redundant in relation to cardiac SBRT.\nThe 2nd paragraph contains a minor inaccuracy - there are also primo ICD implantations.\n\n5th paragraph - To the best of our knowledge, the first reports in vivo studies were published in 2014-20151,2.\nStudy design and patient eligibility - VT attacks should be described more clearly. Anti arrhythmic drugs are meant with or without dose escalation?\nEndpoints section - How will the safety evaluation be performed? Clinically or imaging methods, etc.? Is the follow-up interval too frequent? How will monitoring be carried out (Clinically, laboratory, imaging methods)?\nStudy plan section - PET and MR imaging could be used as reference images - We think they will be used as a secondary series, the reference series will be CT.\nDose constraints - related to the report of TG101 you listed the dose limits for smaller airways, not large bronchus.\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": [ { "c_id": "10729", "date": "22 Mar 2024", "name": "Mariko Kawamura", "role": "Author Response", "response": "Dear reviewers Thanks for your very kind and thoughtful comments. I found them very helpful. I will briefly respond to you below. To reviewer 1 Regarding the exclusion criteria within the protocol, it appears that '<6 months' would be more appropriate to denote a low probability of survival due to factors other than VT, rather than '>6 months.' I agree that minimally invasive therapy is preferable for patients who are unlikely to survive long term for reasons other than VT. However, since this is a feasibility study, we considered it difficult to fully evaluate the safety of this treatment in patients for whom long-term survival is unlikely for reasons other than VT, and therefore we included patients who are likely to survive for more than 6 months. Specifying a maximum allowable dose may not be deemed necessary. Some of the researchers intentionally increase the dose within the GTV. I am sure that your point is true, and I understand the idea that there is no need to set an upper limit. Based on the results of this study, we hope to have an answer in the future as to whether an upper limit is really necessary or rather the target dose should be higher. We added some comments on this in discussion part as follows. Since experimental animals have shown that reducing the dose to 32 Gy or less can produce an antiarrhythmic effect in the short term without causing fibrosis, this protocol was designed with an upper limit on the irradiation dose. At this point, however, there is some debate as to whether it is more effective to promote fibrosis with a higher target dose to obtain antiarrhythmic effects in the long term, and we hope that setting a maximum dose in this clinical trial will provide an answer to this part of the question. In the second paragraph of the discussion, the transition from epicardial ablation to SBRT appears somewhat incongruous. We have edited as follows: Because catheter ablation has a smaller ablation area than radioablation, and although this narrower ablation area may be the cause of VT recurrence, there are many uncertainties, such as the long-term effect of irradiating a wider area on cardiac function. In deference to catheter ablation, which has more long-term data than radioablation, we will change the energy to be irradiated from Joule heat to radiation dose based on the findings obtained with catheter ablation. It is highly possible that the mechanism of antiarrhythmic effect of irradiation is different from that of ablation, and furthermore, the mechanism may be different between ischemic and non-ischemic diseases. Therefore, it is essential to continue radioablation trial with prospective manners. To reviewer 2 The introductory part is comprehensive, however, I have a few minor comments. Some sentences from the 1st paragraph seem redundant in relation to cardiac SBRT. We agree so we have deleted most of the part. The 2nd paragraph contains a minor inaccuracy - there are also primo ICD implantations. we have corrected as following Treatment of patients with VT involves electrical cardioversion or implantable cardioverter defibrillator (ICD) implantation followed by administration of medication. specially in patients with recurrent ventricular arrhythmias, it is essential to wear an ICD to continuously monitor cardiac activity and to restore a normal pulse with an electrical defibrillator when VT or VF is detected. 5th paragraph - To the best of our knowledge, the first reports in vivo studies were published in 2014-20151,2. Thank you for your kind information. We added those papers. Study design and patient eligibility - VT attacks should be described more clearly. Anti arrhythmic drugs are meant with or without dose escalation? We have edited as follows. Patients who are refractory to at least one catheter ablation and had received one or more anti-arrhythmia drug treatment with over three episodes of VT episode with therapeutic intervention (anti-tachycardia pacing (ATP) or shock) in the last three months are considered eligible to participate in the study. Endpoints section - How will the safety evaluation be performed? Clinically or imaging methods, etc.? Is the follow-up interval too frequent? How will monitoring be carried out (Clinically, laboratory, imaging methods)? We added table to clarify what we will be monitoring. Study plan section - PET and MR imaging could be used as reference images - We think they will be used as a secondary series, the reference series will be CT. yes, we use them as secondary references. Thank you for pointing out our unclear writing. Dose constraints - related to the report of TG101 you listed the dose limits for smaller airways, not large bronchus. We have edited some dose constraint. Thank you." } ] } ]	1	https://f1000research.com/articles/12-798
https://f1000research.com/articles/12-890/v1	26 Jul 23	{ "type": "Research Article", "title": "The factors affecting the survivability of malignant cancer patients with deep vein thrombosis among subjects with gynecologic and non-gynecologic cancer: An ambispective cohort study", "authors": [ "Andhika Rachman", "Griskalia Christine", "Rachelle Betsy", "Samuel Juanputra", "Widya Pratiwi", "Griskalia Christine", "Rachelle Betsy", "Samuel Juanputra", "Widya Pratiwi" ], "abstract": "Background: Gynecologic cancer is a significant public health concern worldwide, with three of the top ten most common cancers affecting women. The increasing incidence of deep vein thrombosis (DVT) and the disproportionately poor outcomes in cancer patients necessitates urgent intervention. This study aimed to analyze the factors affecting the survivability of cancer patients with DVT, especially among gynecologic and non-gynecologic cancers. Methods: An ambispective cohort study was conducted among gynecologic and non-gynecologic cancer patients with DVT, from January 2011 until August 2013. Results: Among 223 cancer subjects with DVT, 61.4% of the subjects developed short-term mortality. In the overall group, the survival time was significantly lower in subjects who developed immobilization status (p-value <0.001), advanced cancer stages (p-value <0.045), and infection status (p-value <0.001). In the gynecologic cancer group, the survival time was significantly lower in subjects who developed immobilization (p-value 0.007) and infection status (p-value 0.021). In the non-gynecologic cancer group, the survival time was significantly lower in subjects who developed immobilization (p-value 0.008), infection (p-value 0.002), undergo cancer surgery (p-value 0.024), and received high-risk systemic therapy (p-value 0.048). Additionally, the most common infection was pneumonia (29.6%). Conclusions: Both gynecologic and non-gynecologic cancer patients who experienced DVT developed a high short-term mortality. Our finding of immobility, infection, advanced cancer stages, systemic therapy, and cancer surgery as risk factor that affect the survivability highlights the necessity of administering secondary prophylaxis as a standard procedure in clinical practice.", "keywords": [ "cancer", "gynecologic", "deep vein thrombosis", "survival" ], "content": "Introduction\n\nGynecologic cancer is a major threat to global health and comprises three of the top ten most prevalent cancers affecting women worldwide.1,2 Ovarian cancer is considered to be the deadliest gynecologic malignancy, with the highest mortality rate and the worst prognosis when compared to other types of gynecologic cancers.2–6 Cervical cancer ranks fourth in terms of both incidence and mortality in women worldwide. In countries with a lower Human Development Index (HDI), cervical cancer is the second most prevalent cancer and cause of mortality, following breast cancer. Nonetheless, it is the most frequently diagnosed cancer in 28 countries and the primary cause of cancer-related deaths in 42 countries. The majority of these countries are located in Southeast Asia and Sub-Saharan Africa.7 After cervical cancer, endometrial cancer is the second most frequent malignancy in developing countries.2–4,8,9\n\nGynecologic cancer is a challenging and complex disease that poses significant diagnostic and management difficulties.10 It has been found to be underdiagnosed and undertreated, leading to a remarkable 85% of worldwide deaths in developing countries. Furthermore, low-income and middle-income countries have been significantly impacted, with death rates 18 times higher than those observed in wealthier countries.7,10 For these countries, the massive economic impact posed by lost years of productivity and cancer-related deaths is an extensive challenge.2–4,11,12\n\nOver the past two decades, the association of malignancy with thrombosis events has been established by a significant number of epidemiological studies.13 The incidence of venous thromboembolism (VTE) in patients with active malignancy is four to seven times higher than in the healthy population, ensuring malignancy is one of the most prevalent and significant acquired risk factors for deep vein thrombosis (DVT).14–16 DVT is a generally treatable condition that poses a significant threat to patients with malignancies. In fact, it is the second-greatest cause of death and has been found to be correlated with reduced survival rates in cancer patients.14,17 The rising incidence of cancer-associated thrombosis poses an increasing burden on the healthcare system due to the high mortality rate and treatment costs.18\n\nThe increasing burden of DVT in cancer patients, along with the disproportionately poor outcomes, requires urgent attention.18 The survival rate is a critical factor in determining the effectiveness of cancer prevention and treatment approaches.19 However, factors affecting the survivability of patients with venous thromboembolism, especially malignancies with DVT, remain unclear.20–22 To the best of our knowledge, this was the first study conducted to determine the factors affecting the survival time of cancer patients with DVT, specifically among gynecologic and non-gynecologic cancers. Understanding the impact of these factors is essential for establishing targeted preventive and treatment strategies for this specific patient population.\n\n\nMethods\n\nThis was an ambispective cohort study (combination of prospective and retrospective methods) conducted at Dr. Cipto Mangunkusumo General Hospital (CMGH), Jakarta, Indonesia. Data were collected from January 2011 until August 2013. On the prospective method, we collected samples of cancer patients who had DVT at the Division of Hematology and Medical Oncology of CMGH. Retrospective data were extracted from the medical records of CMGH. All subjects were observed for 3 months. The included subjects were aged ≥ 18 years old; subjects with active cancers; subjects with DVT that were confirmed with Doppler ultrasound. Active cancer was defined as newly diagnosed cancer, up to 3 months before DVT diagnosis, or cancer that is being treated.23,24 Subjects were excluded if they were not available for a 3-month of follow-up (for prospective), or if the medical record data was incomplete (for retrospective).\n\nExtracted data were analyzed with Statistical Package for the Social Sciences (SPSS) version 27 for Macintosh. Any graph or plot was created using GraphPad Prism 9 for Macintosh. The analysis was conducted with Kaplan-Meier survival analysis. The significance was measured using log-rank/Mantel-Cox test.\n\nD-dimer levels were measured by immunometric flowthrough sandwich ELISA (Nycocard Reader II). According to the assay manufacturer, the D-dimer cut-off values for DVT was ≥300 ng/mL.25\n\nEthical approval for this study was granted by The Ethics Committee of The Faculty of Medicine, Universitas Indonesia (ethical approval number: 495/H2.F1/ETIK/2013). This research was performed in accordance with the Declaration of Helsinki. Prior to recruitment, written informed consent was obtained from the subjects.\n\n\nResults\n\nThis cohort study included 223 cancer subjects with deep vein thrombosis (DVT). From the 223 recruited subjects, 76.2% were female. Approximately 48.4% of the subjects were diagnosed with gynecologic cancer, which included ovarian, cervical, and endometrial cancers. Non-gynecologic cancers, including lymphoma, leukemia, hepatoma, and breast cancer were found in 51.6% of the subjects (Table 1).\n\nSubjects who received tamoxifen, aromatase inhibitors, thalidomide, lenalidomide, bevacizumab, cisplatin, nitrogen mustard, or anthracycline were considered as high-risk systemic therapy for developing DVT.1,26–41 Subjects who did not receive high-risk systemic therapy other than those mentioned above were considered low-risk for developing DVT (Table 1).\n\nWells score has been utilized for over a decade and has predictive value in determining DVT risk in patients who are hospitalized.22,42 We divided the Wells score into two categories: subjects with <3 points were considered to have a low probability of developing DVT, whereas subjects with ≥3 points were considered to have a high probability of developing DVT (Table 1).\n\nInfection was found in 126 patients (56.5%). The most common infections were pneumonia (29.6%), urinary tract infections (19.3%), and chronic viral hepatitis (18.8%). Most of the infected patients had one source of infection (30.5%) (Table 2).\n\nIn Figure 1A, the survival time was significantly lower in subjects who developed immobilization status compared to subjects without immobilization status in the overall groups (p-value <0.001), the gynecologic cancer group (p-value 0.007), and the non-gynecologic cancer group (p-value 0.008).\n\nFigure 1B indicates that, across all cancer groups, the survival duration was significantly shorter in late-stage cancer than in early-stage cancer (p-value <0.045).\n\nAs seen in Figure 1C, subjects with infection status had significantly shorter survival times than subjects without infection in all categories (p-value 0.001), those with gynecologic cancer (p-value 0.021), and those without gynecologic cancer (p-value 0.002).\n\nIn the non-gynecologic cancer group shown in Figure 1D, the survival time was significantly longer in subjects who underwent cancer surgery than in those who did not (p-value 0.024).\n\nFigure 1E demonstrates that there was no significant survival time difference between subjects who received radiotherapy (RT) and those without RT in all groups.\n\nFigure 1F shows that in the non-gynecologic cancer group, subjects who received high-risk systemic therapy had significantly greater survival times than those who received low-risk systemic therapy (p = 0.048).\n\nFigure 2 demonstrates that although patients with gynecologic cancer generally had shorter survival times than those with non-gynecologic cancer, there was no significant difference in survival times between the two types of cancer.\n\n\nDiscussion\n\nDeep vein thrombosis (DVT) in cancer patients is a life-threatening condition that may emerge regardless of whether they have a good prognosis. By understanding the factors that affect survivability, the effectiveness of prophylactic and therapeutic measures in preventing mortality can be more fully established.23\n\nOur cohort analysis revealed that the mortality of gynecologic and non-gynecologic cancer patients doubled during the initial 3-month period following the DVT event, emphasizing the high short-term mortality resulting from a DVT event (Table 1).23,24 Our finding was supported by the worldwide Registro Informatizado de la Enfermedad TromboEmbólica (RIETE) registry study, which demonstrated that individuals with cancer with DVT are at a higher risk for short-term mortality.24 The proposed theory suggests that the clinical hypercoagulable state may serve as a proxy for aggressive tumor biology, leading to a poor association with prognosis.24,43 According to the latest available data, thrombosis is estimated to contribute to approximately 10% of cancer-related deaths in patients undergoing chemotherapy. Our study, which focused on gynecologic and non-gynecologic cancer patients with DVT, has confirmed this finding, albeit to a slightly greater degree.24,44\n\nTable 1 demonstrates a greater number of subjects experiencing immobilization (> 3 days) compared to those who did not (76.2% vs. 36.8%). The survival rate was significantly lower in subjects who developed immobilization status when compared to subjects without immobilization status in the overall groups (p-value <0.001), gynecologic cancer group (p-value 0.007), and non-gynecologic cancer group (p-value 0.008) (Figure 1A). The lower survival time among immobilized subjects is a crucial finding that can be assigned to various factors. First, immobilized cancer patients frequently showed more severe clinical signs than non-immobilized patients.45 Second, immobility increases the risk of DVT, due to stasis of blood flow in the venous system and hypercoagulation, which will lead to a higher mortality rate.46,47 On the other hand, the American Physical Therapy Association (APTA) recommends that cancer patients with DVT commence mobilization as an effective way of reducing the risk of mortality and minimizing complications.48,49 Another systematic review by Segal et al. that identified 2 guidelines, 18 systematic reviews, and 29 randomized controlled trials (RCT) demonstrates that exercise is safe and beneficial in improving quality of life, including muscular and aerobic fitness for cancer patients. The current literature provides adequate support for urging exercise among cancer patients.50 Thus, we strongly recommend physical exercise based on the clinical condition of cancer patients, as it could potentially serve an essential function in improving both survival and quality of life.\n\nFigure 1B shows that survival time was significantly lower in the advanced stages of cancer than in the early stages in the overall cancer groups (p-value <0.045). Our finding was consistent with a study that was conducted by Spencer, which found a negative correlation between cancer stage and survival.51 Mark et al. found in their retrospective analysis that a diagnosis of DVT doubled the cancer-related death rate, which had similar effects on mortality as having advanced stage cancer.52 Cancer staging is an anatomic representation of the disease’s progression based on tumor size, lymph node involvement, as well as clinical and imaging examinations.53,54 The impact of metastases in DVT has been substantially highlighted in the medical literature. The process of disseminating metastatic cells could be the explanation for the increased risk of DVT reported in patients with distant or regional lymph node metastases. The presence of metastasis has been found to be significantly correlated with increased hypercoagulability due to the hemostatic system, which may play a significant role in the metastatic capability of malignancies. Substantial metastasis occurs when tumor cells reach the bloodstream or lymphatic system. Thereby, after the distant metastasis, tumor cells interact with the hemostatic system, which emphasizes that hypercoagulability already exists in patients with localized cancer spread.55 Studies have shown that detecting cancer at an early stage can significantly improve the chances of survival. However, over 50% of cancer cases are diagnosed at an advanced stage. When diagnosed in later stages, the available treatment options may be limited, and the overall prognosis tends to be unfavorable. The timely identification of cancer or precancerous alterations enables prompt intervention with the purpose of preventing or minimizing cancer progression and mortality.56\n\nIn this present study, pneumonia was the most prevalent infectious disease (29.6%) (Table 2). In contrast with the study by Gussoni G, et al. that showed non-infectious chronic pulmonary disease contributed to the high prevalence of malignancy associated with DVT (9.8%).24 This is due to the high prevalence of infectious diseases in Indonesia. The vast majority of infected patients have one source of infection (30.5%). This demonstrates that the severity of that illness has the potential to alter mortality, even if the patient is only exposed to a single source of infection. Figure 1C shows that the overall (p-value <0.001), gynecologic (p-value 0.021), and non-gynecologic (p-value 0.002) cancer groups had significantly shorter survival times for subjects who developed infection status compared to subjects without infection. Infection remains a leading killer in all types of cancer. The investigation of infection management in cancer patients is an important strategy for enhancing the patient’s survivability. The nature of certain chemotherapeutic agents is accompanied by their immunosuppressive effects, which can limit their application ranges. These side effects include neutropenia, inhibition of the neutrophils, bone marrow suppression, damage to the anatomical barriers, and irritation of the veins.57 Those who undergo cytotoxic chemotherapy are at risk of developing severe neutropenia, which can lead to life-threatening infections and sepsis.58 The findings indicate that further efforts are required to reduce the frequency of lethal infections. Thus, we strongly recommend several strategies to decrease the mortality of infections in cancer patients, including the use of prophylaxis or preemptive therapy with broad-spectrum antimicrobial agents targeted at the most common infecting pathogens.57\n\nFigure 1D demonstrates that the survival time for patients with non-gynecologic cancer who received cancer surgery is considerably longer than that of patients who do not undergo surgery (p-value 0.024). The present study aligns with prior cohort study of advanced stage non-small cell lung cancer (NSCLC) patients from the National Cancer Database, which indicated patients who had surgery had significantly better overall survival (p<0.001).59 Contrary to the findings of Gussoni G, et al. in the RIETE Study, surgical treatment for malignancy had no influence on mortality in the first three months of malignancy DVT.24 These differences in outcomes may be explained due to the fact that the patients who received surgery tended to be diagnosed at an earlier stage, which enhanced their chances of survival. As the advanced stage of cancer progresses, the clinical condition of the patient deteriorates, rendering them ineligible for cancer surgery and/or systemic therapy for malignancy. In the execution of a surgical procedure, it is imperative to carefully evaluate the potential hazards and advantages. This critical assessment is crucial in ensuring the safety and well-being of the patient. The risk-benefit analysis is the key of clinical decision making, with the ultimate goal of producing the best possible patient outcomes.60\n\nIn Figure 1E, there was no significant difference in survival time between subjects who received RT and without RT across all groups. Based on our findings, we identify that RT-treated cancer patients with DVT do not appear to have substantial alterations that lead to short-term mortality. Our study was in line with Bosco et al. that conducted a large study among 9000 Swedish male patients who had curative radiation for prostate cancer. They concluded that external beam radiation and brachytherapy were not shown to increase the risk of thromboembolic events.61,62 Contradicting the results of a previous sub-analysis of prospective, multicentre, longitudinal Prospective Comparison of Methods for thromboembolic risk assessment with clinical Perceptions and AwareneSS in real life patients-Cancer Associated Thrombosis (COMPASS–CAT study), a significant association was found between RT and VTE (HR 2.47; 95% CI 1.47-4.12; p-value 0.011).61,63 A small series by Guy et al. reported a sufficient association between brachytherapy and the development of VTE in patients with gynecologic malignancies.63,64 These differences among studies might be explained by multiple suggested processes that raised the risk of thrombosis during and after radiation. Radiation has been shown to promote secondary venous hemostasis by increasing inflammatory molecule release, which in turn activates the endothelium and promotes a thrombotic environment. Ionizing radiation has also been shown to affect several anticoagulant molecules (protein C and thrombomodulin) and prothrombotic molecules (activated factor VIII, platelet, tissue factor, D-dimers, NF-kappa B, and von Willebrand activation), altering the balance towards a hypercoagulable state.61,62,65 However, most of the chronic vascular processes leading to clinical outcomes are reported to occur several years after RT, and our follow-up period was 3 months. Thus, additional studies with longer time periods are warranted to fully comprehend the clinical significance of the prospective cellular toxicity related to radiotherapy.61,62\n\nAs can be observed in Figure 1F, the survival time was significantly higher in subjects who received high-risk systemic therapy compared to those who received low-risk systemic therapy (p-value 0.048). According to recent research, the administration of tamoxifen, aromatase inhibitors, thalidomide, lenalidomide, bevacizumab, cisplatin, nitrogen mustard, or anthracycline has been linked to a higher incidence of DVT.1,26–41 These agents have been reported to initiate vascular injury by inducing apoptosis. The administration of cisplatin leads to the release of prothrombotic particles, leading to the production of thrombin through tissue factor-independent pathways and a substantial increase in the activity of von Willebrand factor (vWF). However, other agent such as the vascular endothelial growth factor inhibitor (bevacizumab) do not initiate thrombosis directly. Instead, it ‘primes’ the endothelium by placing it in a depleted condition, thus rendering it more prone to injury. Furthermore, in the context of immunomodulatory agents (thalidomide and lenalidomide), platelet activation via PAR-1 and enhanced Gp IIb/IIIa exertion provide the “primed” condition. The identification of antineoplastic agents that are highly associated with thrombosis can enhance healthcare provider awareness and facilitate prompt diagnosis and treatment.66,67 On the other hand, prior studies have extensively demonstrated the effectiveness of systemic therapy in improving overall survival rates and minimizing the potential of disease recurrence. Although generally well-tolerated, there have been reports of various adverse effects associated with the pharmacological activity of these agents.67 Thus, high-risk systemic therapy for cancer patients should be considered after carefully assessing the risks and benefits of treatments.68\n\nTo the best of our knowledge, no study to date has investigated the comparison of survival time for DVT in the cancer population, especially among gynecologic and non-gynecologic malignancies. Although the difference in survival time between the two groups was not statistically significant (p-value 0.674), the results indicated that patients with gynecologic cancer generally had a lower survival time compared to non-gynecologic cancer (Figure 2). Cancer is a life-threatening disease that warrants serious attention, regardless of its type.69 According to prior research, VTE is a significant cause of mortality in patients with gynecologic cancer. Studies have shown that the risk of DVT in women undergoing gynecologic surgery is estimated to be between 17-40%.55 The relationship between gynecologic cancers and thrombotic events is believed to be linked to lymphadenectomy and venous congestion caused by tumors or enlarged lymph nodes.70 Lymphadenectomy is a frequently utilized procedure in the evaluation of lymph node status and staging of gynecologic malignancies, as well as a therapeutic intervention for patients with gynecologic cancer. Complications, such as hemorrhage, hematoma, and lymphocele, are frequently observed in association with it. Lymphocele is a frequently observed postoperative complication that can result in the development of VTE due to venous compression. A literature review indicates that the incidence of VTE after lymphadenectomy ranges from 0.8% to 25%.55 A large cohort study conducted by Chew et al., revealed that the incidence of DVT in cancer patients is linked to a 3.7-fold rise in mortality risk.71 The identification of DVT as a major risk factor has been established for decreased survival in cancer patients. The mortality rate of cancer patients with DVT could be associated with the existence of DVT and its complications, as well as the advanced stage of malignancies that are frequently correlated with DVT and have the potential to progress progressively.24\n\nThe strength of this study lies in the fact that it is the first study to analyze factors affecting the survivability of malignant patients with DVT, especially in gynecologic and non-gynecologic malignancies. Second, this study utilizes a pragmatic approach by conducting research in authentic settings that reflect routine clinical practice. Third, this research was conducted at CMGH, which is the national referral center hospital in Indonesia, in order to accurately reflect the target population. However, this study has several limitations that should be considered to improve further research. First, this study did not evaluate the development of anticoagulant targets in DVT therapy in patients with malignancy. The examination parameters for each anticoagulant vary, making it challenging to perform this task. Second, this study did not differentiate between varying levels of clinical severity of infection.\n\nHence, despite these limitations, the findings of our cohort study have significant clinical implications, indicating that prompt identification of these factors may enhance the survival rate of cancer patients with DVT.72 Although cancer is a significant risk factor for DVT, the risk is not sufficiently substantial to warrant initiating prophylaxis. On the other hand, if any of these risk factors are present, the doctor should have a low threshold for considering prophylaxis.73 Comprehensive consideration of the risks and benefits of anticoagulant usage is required before deciding to use thromboprophylaxis in cancer patients with DVT.68 Nonetheless, the existing literature provides limited guidance for decision-making and implementation of management strategies. Further studies are warranted to evaluate the extent of the issue and determine the necessity of secondary prophylaxis.24,73\n\n\nConclusion\n\nThis cohort study identified that both gynecologic and non-gynecologic cancer patients who experienced DVT developed a high short-term mortality. Our finding of immobility, infection, advanced cancer stages, systemic therapy, and cancer surgery as risk factors that affect the survival raises the need to give secondary prophylaxis in routine clinical practice. The possibility for increasing survival could be maximized through the alteration of these critical factors. Thus, further study is warranted to establish a comprehensive management guideline that will be crucial for optimizing prevention and treatment strategies.", "appendix": "Data availability\n\nFigshare: Raw Data - The Factors Affecting the Survivability of Malignant Cancer Patients with Deep Vein Thrombosis among Subjects with Gynecologic and Non Gynecologic Cancer An Ambispective Cohort Study.sav, https://doi.org/10.6084/m9.figshare.22838087.v1. 74\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\nThe authors would like to thank all the participants for their involvement.\n\n\nReferences\n\nHuang H, Korn JR, Mallick R, et al.: Incidence of venous thromboembolism among chemotherapy-treated patients with lung cancer and its association with mortality: a retrospective database study. J. Thromb. Thrombolysis. 2012 Nov 13; 34(4): 446–456. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGuy JB, Falk AT, Chargari C, et al.: Thromboembolic events following brachytherapy. J Contemp Brachytherapy. 2015; 1: 76–78. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nByrne M, Reynolds JV, O’Donnell JS, et al.: Long-term activation of the pro-coagulant response after neoadjuvant chemoradiation and major cancer surgery. Br. J. Cancer. 2010 Jan 1; 102(1): 73–79. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOppelt P, Betbadal A, Nayak L: Approach to chemotherapy-associated thrombosis. Vasc. Med. 2015 Apr 1; 20(2): 153–161. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMeier CR, Jick H: Tamoxifen and risk of idiopathic venous thromboembolism. Br. J. Clin. Pharmacol. 1998 Jun 4; 45(6): 608–612.\n\nLyman GH, Eckert L, Wang Y, et al.: Venous Thromboembolism Risk in Patients With Cancer Receiving Chemotherapy: A Real-World Analysis. Oncologist. 2013 Dec 1; 18(12): 1321–1329. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSung H, Ferlay J, Siegel RL, et al.: Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries. CA Cancer J. Clin. 2021 May 4; 71(3): 209–249. PubMed Abstract \| Publisher Full Text\n\nOkushi Y, Kusunose K, Okayama Y, et al.: Acute Hospital Mortality of Venous Thromboembolism in Patients With Cancer From Registry Data. J. Am. Heart Assoc. 2021 Jun; 10(11).\n\nChew HK, Wun T, Harvey D, et al.: Incidence of Venous Thromboembolism and Its Effect on Survival Among Patients With Common Cancers. Arch. Intern. Med. 2006 Feb 27; 166(4): 458. Publisher Full Text\n\nFlinterman LE, van Hylckama VA , Cannegieter SC, et al.: Long-Term Survival in a Large Cohort of Patients with Venous Thrombosis: Incidence and Predictors. PLoS Med. 2012 Jan 10; 9(1): e1001155. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFennerty A: Venous thromboembolic disease and cancer. Postgrad. Med. J. 2006 Oct 1; 82(972): 642–648. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRachman A: Raw Data - The Factors Affecting the Survivability of Malignant Cancer Patients with Deep Vein Thrombosis among Subjects with Gynecologic and Non Gynecologic Cancer An Ambispective Cohort Study.sav. figshare. Journal Contribution. 2023. Publisher Full Text" }	[ { "id": "195071", "date": "01 Sep 2023", "name": "Susanna Hutajulu", "expertise": [ "Reviewer Expertise Clinical oncology", "cancer prognostication", "cancer registry" ], "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 study aimed to analyze the factors influencing the short-term survival (3 months) of cancer patients with DVT, particularly among those with gynecologic and non-gynecologic cancers. Employing an ambispective cohort study design, a total of 223 cancer patients diagnosed with DVT via Doppler ultrasound were included in this study.\nThe findings revealed that, across the entire cohort, survival time was notably reduced among subjects who experienced immobilization, were at advanced cancer stages, or developed infections. Within the gynecologic cancer subgroup, survival time was significantly lower in individuals who experienced immobilization and infection. Conversely, within the non-gynecologic cancer subgroup, survival time exhibited a significant decline in subjects who faced immobilization, infection, cancer-related surgeries, and high-risk systemic therapy for DVT.\nThis study presents novel evidence for the local population, underscoring the significance of both preventing and managing DVT in cancer patients.\nThere are certain concerns that the authors might need to take into consideration:\nThe method section of abstract is not so clear. I’m sure it needs brief details of methods applied in the study.\n\nThe content within the second and third paragraphs of the results section, which elucidates the classification of DVT risk based on the chemotherapy regimen and provides an explanation of the Wells score, would be better placed within the method section. This relocation would contribute to a comprehensive depiction of the operational definition of the variables.\n\nProportion of radiotherapy utilization can be incorporated into Table 1, as this aspect has not yet been delineated within the existing presentation of the table.\n\nTo enhance clarity, it would be better to add the \"number at risk\" and \"number censored\" below each individual point segment of the survival curve.\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": [ { "c_id": "10204", "date": "16 Nov 2023", "name": "Andhika Rachman", "role": "Author Response", "response": "Response To The Reviewer: Dear Dr. Susanna Hutajulu, We would like to thank you for your time and consideration in handling our manuscript. Sincerely, Andhika Rachman, MD, PhD Medical staff, Division of Hematology and Medical Oncology, Department of Internal Medicine, Faculty of Medicine, Universitas Indonesia - Dr. Cipto Mangunkusumo General Hospital This study aimed to analyze the factors influencing the short-term survival (3 months) of cancer patients with DVT, particularly among those with gynecologic and non-gynecologic cancers. Employing an ambispective cohort study design, a total of 223 cancer patients diagnosed with DVT via Doppler ultrasound were included in this study. The findings revealed that, across the entire cohort, survival time was notably reduced among subjects who experienced immobilization, were at advanced cancer stages, or developed infections. Within the gynecologic cancer subgroup, survival time was significantly lower in individuals who experienced immobilization and infection. Conversely, within the non-gynecologic cancer subgroup, survival time exhibited a significant decline in subjects who faced immobilization, infection, cancer-related surgeries, and high-risk systemic therapy for DVT. This study presents novel evidence for the local population, underscoring the significance of both preventing and managing DVT in cancer patients. There are certain concerns that the authors might need to take into consideration: 1. The method section of abstract is not so clear. I’m sure it needs brief details of methods applied in the study.  Response: Thank you for your constructive comment. We have added more details on the method section of the abstract. Methods: An ambispective cohort study was conducted among gynecologic and non-gynecologic cancer patients with DVT, from January 2011 until August 2013. All subjects were observed for three months. The presence of DVT was confirmed using Doppler ultrasound. The analysis was performed using Kaplan-Meier survival analysis. The statistical significance was determined using the log-rank/Mantel-Cox test. 2. The content within the second and third paragraphs of the results section, which elucidates the classification of DVT risk based on the chemotherapy regimen and provides an explanation of the Wells score, would be better placed within the method section. This relocation would contribute to a comprehensive depiction of the operational definition of the variables.  Response: We have relocated the second and third paragraphs of the results section into the method section. Wells score has been utilized for over a decade and has predictive value in determining DVT risk in patients who are hospitalized. 22 , 42 We divided the Wells score into two categories: subjects with <3 points were considered to have a low probability of developing DVT, whereas subjects with ≥3 points were considered to have a high probability of developing DVT. Subjects who received tamoxifen, aromatase inhibitors, thalidomide, lenalidomide, bevacizumab, cisplatin, nitrogen mustard, or anthracycline were considered as high-risk systemic therapy for developing DVT. 1 , 26 – 41Subjects who did not receive high-risk systemic therapy other than those mentioned above were considered low-risk for developing DVT. 3. Proportion of radiotherapy utilization can be incorporated into Table 1, as this aspect has not yet been delineated within the existing presentation of the table.  Response: We have added the proportion of radiotherapy utilization into Table 1. 4. To enhance clarity, it would be better to add the \"number at risk\" and \"number censored\" below each individual point segment of the survival curve. Response: Thank you for your valuable advice. We have added the “number at risk” below each individual point segment of the survival curve. Thank you for your attention. We are eagerly awaiting your response." } ] } ]	1	https://f1000research.com/articles/12-890
https://f1000research.com/articles/12-5/v1	03 Jan 23	{ "type": "Research Article", "title": "Degree of organ damage and inflammatory markers in sepsis mice models inducted by various doses of lipopolysaccharides ", "authors": [ "Arifin -", "Bambang Purwanto", "Dono Indarto", "Brian Wasita", "Tatar Sumanjar", "Eti Poncorini", "Soetrisno -", "Bambang Purwanto", "Dono Indarto", "Brian Wasita", "Tatar Sumanjar", "Eti Poncorini", "Soetrisno -" ], "abstract": "Background: Sepsis is a life-threatening disease, and animal models of sepsis are minimal. This study aims to find the optimal dose to make a sepsis mouse model by examining the presence of target organ damage. Methods: This study used 30 mice divided into four groups. The control group injected 0.5 cc NaCl 0.9% intraperitoneally (i.p.). Group A was injected with lipopolysaccharides (LPS) 0.25 mg/kg B.W. i.p. given on the first and second day, group B was injected with LPS 0.3 mg/kg B.W. i.p. given on the first and second days, and group C was injected by LPS 0.3 mg/kg B.W. single dose i.p. Each group was terminated on the third, fourth, and fifth days. Results: NF-κB, C-reactive protein (CRP), alanine aminotransferase (ALT), NF-κB examinations, and tumor necrosis factor-α (TNF-α) in all treatment groups increased when compared with the control. The highest degree of histopathological features of the kidneys and liver and the results of immunohistochemistry examinations on the liver and kidneys were shown in group C. Conclusions: Inflammatory markers (CRP, TNF-α, NF-κB, and expression of NF-κB in liver and kidneys) and characteristics of organ damage (ALT, liver, and kidneys histopathology scores) increase on day 3. The highest increase was in the group administered with LPS 0.3 mg/kg B.W. single dose.", "keywords": [ "Organ damage", "inflammatory markers", "sepsis mouse models", "lipopolysaccharides" ], "content": "Introduction\n\nThe incidence of sepsis in Indonesia and abroad is increasing, a concern in the medical world today. In Europe and America, the incidence of sepsis ranges from 0.4 ro 1/1,000 of the population. Moreover, sepsis mortality is also high, reaching 30%, whereas sepsis shock gets 80%. Therefore, the early diagnosis of sepsis and rapid management can improve the prognosis of the patients. More than 30 million people are estimated to be exposed to sepsis each year globally, and it potentially causes 6 million deaths each year. As per data from the Surviving Sepsis Campaign in 2012, the mortality rate from sepsis is approximately 41% in Europe, which is higher than in the United States, that is, approximately 28.3%.1–3\n\nSepsis is a set of biological, pathological, and biochemical symptoms of the body in response to infection. In 1991, the criteria for sepsis were divided into sepsis, severe sepsis, and septic shock. The diagnosis of sepsis is established if it meets at least two of the four criteria of Systemic Inflammatory Response Syndromes, namely, body temperature of >38°C or <36°C, heart frequency of >90 x/min, breath rate of >20 x/min or PaCO2 of <32 mmHg, leukocyte count of >12000/mm3, or <4000/mm3. Severe sepsis is considered if the sepsis criteria are met and accompanied by organ malfunction.3\n\nIn 2017, Rhodes et al., in Survival Sepsis Campaign: International Guideline for Management of Sepsis and Septic Shock: 2016, presented the latest definitions for sepsis and septic shock. According to the guidelines, sepsis is the life-threatening functioning of organs caused by the failure of the body’s response to infection. Severe sepsis, as found in the previous guidelines, is eliminated and goes directly to the criteria for septic shock. Septic shock is defined as the continuation of sepsis with circulatory and cellular/metabolic malfunctions and is associated with high mortality risk.3 Furthermore, to establish the diagnosis of sepsis and septic shock, an assessment was carried out using SOFA (Sequential Organ Failure Assessment) scores. As for the criteria for septic shock, if sepsis is obtained, which requires vasopressor therapy to increase MAP ≥ 65 mmHg and increase lactate levels > 2 mmol/L (18 mg/dL), although adequate fluid resuscitation has been carried out.3\n\nThis change in the definition of sepsis has consequences for animal models for sepsis. Thus far, sepsis model animals still use inflammatory criteria to establish a diagnosis of sepsis. In this study, we will make a sepsis model animal seen from the requirements of inflammation and organ damage as evidenced by histopathological features of the kidneys and liver. This study aimed to find the optimal lipopolysaccharides (LPS) dose to make a sepsis model in mice. This study is also to determine when sepsis will occur.\n\n\nMethods\n\nThis experimental study with a posttest-only control group design was conducted on mice with septic AKI. The study’s sample size was calculated using an Institutional Animal Care and Use Committee formula.4\n\nThe study protocol has received ethical approval from the Health Research Ethics Committee of Moewardi Hospital (approved number: 7686/VIII/HREC/2021).\n\nThe study subjects were male mice subspecies of Mus musculus strain Balb/C aged 3–4 months, body weight 20–30 g, obtained from the Faculty of Veterinary Medicine, Gajah Mada University. This experiment used 30 mice, which were randomized and divided into four groups. The sampling method used in this study was purposive sampling. The control group consisted of three mice injected with 0.5 cc NaCl 0.9% i.p. Group A was injected with LPS 0.25 mg/kg B.W. divided dose i.p. administered on the first and second days, group B was injected with LPS 0.3 mg/kg B.W. i.p divided dose administered on the first and second days, and group C was injected with LPS 0.3 mg/kg B.W. single dose i.p. On the third, fourth, and fifth days, the termination of each group of three mice and examination of the NF-κB, tumor necrosis factor-α (TNF-α), C-reactive protein (CRP), alanine aminotransferase (ALT), the expression of NF-κB in the liver and kidneys, and histopathology in the liver and kidneys were conducted.\n\nInduction of sepsis using LPS from Escherichia coli 0111:B4-purified by phenol extraction production Sigma-Aldrich USA, Product Number: L2630. NF-κB examination used the enzyme-linked immunosorbent assay (ELISA) method with mouse NF-κB (Nuclear factor kappa B) ELISA kit reagent (Product Number: NFκB p65 (F-6):sc-8008) from Santa Cruz Biotech. Alanine aminotransferase (ALT) examination using reagents from DiaSys response®920 with optimized UV-test method according to International Federation of Clinical Chemistry and Laboratory Medicine. Assessment of TNF-α via the ELISA method using mouse TNF-α ELISA kit reagent (BZ-087661F-AM) from Bioenzy. CRP examination via the ELISA method using mouse CRP ELISA kit reagent (A19003) from Abclonal.Inc.\n\nMice were kept in four cages made of plastic tubs covered with wire at the top. The conditions during acclimatization and treatment were controlled in a fixed environmental range, with a room temperature ranging from 23-26°C with the aim that the test animals could adapt according to the animal’s biological time and the conditions to be occupied during the experiment. Temperature, water supply, the number of mice in the cage, and the change of husks were all done the same for all groups of mice. Adaptation to mice with care in cages with a size of 28 × 30 × 12 cm so that they can move freely and not be stressed. After all the research processes were completed, the experimental animals were terminated by anesthetizing them with inhalation of chloroform and then decapitation was carried out.\n\nInterventions of BALB/c mice, the examination of NF-κB, TNF-α, ALT, and CRP, histopathological preparations and immunohistochemistry examinations on the liver and kidneys were conducted at the Experimental Animal Care Center (PAU UGM, Yogyakarta), Histology and Cell Biology Laboratory (Faculty of Medicine, UGM, Yogyakarta), and Anatomical Pathology and Histology Laboratory (Faculty of Medicine, UNS Surakarta), respectively. The authors were unaware of the allocation group so that all the mice were handled, monitored and treated in the same way while conducting the experiment.\n\nThe kidneys and livers of all mice were embedded using paraffin and sliced at 0.5 mm thickness. The slides were incubated with 1:1,200 antimouse NF-κB antibodies (from Santa Cruz Biotech) overnight. After washing with buffer solution, the slides were incubated with an IgG Rabbit Probe HRP secondary antibody (from Biocare Medical) for 30–45 min. The slides were washed with buffer solution and stained with DAB solution for 10 min to remove an excessive amount of the secondary antibody. Finally, the slides were counterstained with hematoxylin solution for several minutes. The stained slides were observed under a light microscope (Model: Olympus CX21, manufacturer: Ningbo Huasheng Precision Technology Co.Ltd) 400× magnification, and positive staining of NF-κB was scored 0% = 0, <25% = 1, 26%–50% = 2, 51%–75% = 3, and >75% = 4.5\n\nOnce the mice’s kidneys and liver had been embedded using paraffin, they were cut into 0.5 πm thickness and stained with hematoxylin–eosin. Degeneration, necrosis, inflammation, and bleeding were assessed under a light microscope (Model: Olympus CX21, manufacturer: Ningbo Huasheng Precision Technology Co. Ltd) with 40 and 100 times magnification. Two independent pathologists carried out the histopathological examination. The results of renal histopathology were graded into 0 = none, 1 = mild, 2 = moderate, 3 = strong, and 4 = severe.6 The results of liver histopathological were graded to 0 = histological features of liver cells in the normal centrilobular region, 1 = the histological features of liver cells undergoing necrosis is limited in the centrilobular region (necrosis is limited to zone III of the liver), 2 = the histological features of liver cells undergoing an expansion of necrosis covers the centrilobular region 22 until it reaches zone II in the liver, and 3 = the histological picture of liver cells undergoing an expansion of necrosis covers the centrilobular region to the middle of the trial portal area (necrosis reaches zone I in the liver).7\n\nThe statistical analysis used was IBM®SPSS®Statistics 25 for windows. The data of NF-κB, TNF-α, CRP, and ALT were presented as mean ± S.D., whereas the data of NF-κB and matrix metalloproteinase (MMP)-9 were presented as percentages of positive staining cells. Numerical data were assessed for normality and homogeneity using Shapiro–Wilk and Levene’s tests, respectively. Comparative analysis of TNF-α among groups was analyzed statistically using a one-way analysis of variance, followed by the least significant difference (LSD) post hoc test at a significance level of p < 0.05. Meanwhile, categorical data of NF-κB and numerical data that did not pass the normality and homogeneity test (NF-κB, TNF-α, CRP, and ALT) were analyzed statistically using the Kruskal–Wallis test followed by the Mann–Whitney test.\n\n\nResults\n\nE-coli LPS administration induced the septic AKI, leading to increased NF-κB levels. Figure 1 shows that levels of NF-κB increased in all mice groups treated with LPS. The results of the Kruskal–Wallis NF-κB test showed statistically significant differences (p < 0.001). Statistical analysis continued with the post hoc test with the Mann–Whitney test to determine which groups had statistical differences.\n\nThe results of the Mann–Whitney Test showed significant differences between the control group and all treatment groups (p = 0.05). NF-κB levels increased in the entire treatment group starting on day 3. NF-κB levels increased the most in group B (average day 3 729.57 ng/mL, day 4 735.49 ng/mL, and day 5 742.86 ng/mL). Mann–Whitney test results showed no difference between the treatment groups (p > 0.05). Based on these results, giving a dose of LPS 0.3 mg/kg B.W. in divided doses (group B) can increase the highest NF-κB levels when compared with the other groups.\n\nHigh levels of NF-κB stimulated TNF-α secretion, as shown in Figure 2. TNF-α levels increased statistically significantly (p < 0.01) in comparison with the control group. The results of the LSD test showed that there were significant differences between the control group and all treatment groups (p < 0.05). TNF-α levels increased in the entire treatment group starting on day 3.\n\nTNF-α levels increased the highest on day 5, which can be seen in groups B (50.98 ± 0.29 pg/mL) and group C (50.22 ± 0.43 pg/mL). The statistical analysis results in the two groups showed no statistical difference (p = 0.44). On the third day of comparison between groups A and B, there was a statistically significant difference (p = 0.001), this was also found in the comparison between groups A and C (p = 0.000), but there was no significant difference in groups B and C (p = 0.918). The average value in group B (48.59 ± 0.38 pg/mL) was greater than that in group C (48.44 ± 0.38 pg/mL). Based on these results, giving a dose of LPS 0.3 mg/kg B.W. in a divided dose can provide the highest increase in TNF-α levels in comparison with the other groups.\n\nAn increase in TNF-α levels was followed by an increase in CRP levels, as shown in Figure 3. The results of statistical analysis using the Kruskal–Wallis test showed a significant difference with a p-value of <0.01.\n\nThe results of the Mann–Whitney Test showed significant differences between the control group and all treatment groups (p = 0.05). CRP levels increased in the entire treatment group starting on day 3. CRP levels increased the most in group B4 (18.22 ± 0.17 ng/mL). The results of the Mann–Whitney test showed no difference between the treatment groups (p > 0.05). The average in group B (17.88 ± 0.61 ng/mL) was greater than group C (16.73 ± 0.17 ng/mL). Between groups B3, B4, B5, C3, C4, and C5, there was no significant difference (p > 0.05). Based on these results, giving a dose of LPS 0.3 mg/kg B.W. in divided doses (B) can provide the highest increase in CRP levels in comparison with the other groups.\n\nIncreased levels of NF-κB, TNF-α, and CRP indicate the activation of the inflammatory cascade. In this study, one of the markers of inflammation at the tissue level was marked by increased expression of NF-κB in the liver and kidneys. NF-κB expression in the liver obtained a statistically significant difference (p = 0.004).\n\nFigure 4 shows that NF-κB expression on the liver significantly differed between the control group and all treatment groups with p-values of <0.05. The NF-κB expression on the liver began to increase on day 3 in all groups. The highest increase was in group C. Statistical analysis in group C with group A showed a statistically significant difference (p < 0.05). NF-κB expression in group B did not have significant differences. Based on these results, giving an LPS dose of 0.3 mg/kg B.W. in single doses can provide the highest increase in NF-κB expression in other groups. Figure 5 shows an immunohistochemistry examination of NF-κB expression on the cytoplasm of liver tissue hepatocyte cells (yellow arrows).\n\nThe results of the Kruskal–Wallis test on the renal NF-κB expression obtained a statistically significant difference (p = 0.026). Figure 6 shows the results of the renal NF-κB expression.\n\nIn Figure 7, we can see an immunohistochemistry examination showing NF-κB expression on the cytoplasm of epithelial cells of proximal tubules of the renal tissue (yellow arrows).\n\nThe results of the Mann–Whitney test showed significant differences between the control group and all treatment groups (p < 0.05). In all groups, the renal expression of NF-κB begins to increase on the third day. The highest increase was in group C5. Group C5 had significant differences with group B3 (p = 0.034) and B4 (p = 0.034). However, it has no significant differences between groups A (all day) and B5. These results show that LPS dose administration of 0.3 mg/kg B.W. in single doses (group C) can increase the highest NF-κB expression in comparison with the other groups.\n\nUncontrolled inflammation due to LPS induction can result in tissue and cell damage. The results of the Kruskal–Wallis test on the liver histopathological score found no statistically significant difference (p = 0.061). The results of the renal histopathology score can be seen in Figure 8. Although there was no statistically significant difference, the treatment group had a greater mean rank than the control group. The largest mean rank was found in group C with LPS levels of 0.3 mg/kg B.W. Liver histopathology scores began to increase on day 3 after LPS injection in all treatment groups. Figure 9 shows the histopathological depiction of hepar, showing inflammatory images (yellow arrows) and necrosis (green arrows) in hepar tissue. A. Normal control group score 0. B. Group A3 score 2. C. Treatment group A4 score 2. D. Treatment group A5 score 2. E. Treatment group B3 score 2. F. Treatment group B4 score 2. G. Treatment group B5 score 3. H. Treatment group C3 score 3. I. Treatment group C4 score 3. J. Treatment group C5 score 3.\n\nA. Normal control group score 0. B. Group A3 score 2. C. Treatment group A4 score 2. D. Treatment group A5 score 2. E. Treatment group B3 score 2. F. Treatment group B4 score 2. G. Treatment group B5 score 3. H. Treatment group C3 score 3. I. Treatment group C4 score 3. J. Treatment group C5 score 3. Hematoxylin–eosin with microscope magnification of 200×.\n\nRenal histopathology scores increased in all treatment groups. The increase started on day 3 and peaked on day 5 after the LPS injection. The Kruskal–Wallis test on the renal histopathology score obtained a significant difference statistically (p = 0.001). The results of the renal histopathology score can be seen in Figure 10.\n\nThe test between the control and all treatment groups has a significant difference (p < 0.05). Statistically, group A3 has significant differences when compared with groups B and C (p < 0.05). Group B4 had no significant difference when compared with groups B5, C3, C4, and C5 (p > 0.05). Group C3 had significant differences when compared with group A3 (p = 0.034) but did not differ significantly from groups B3, B4, B5, C4, and C5 (p > 0.05). Based on these results, it can be concluded that starting from day 3, there has been kidney damage, with the most severe damage in group C (LPS dose 0.3 mg/kg B.W.). Figure 11 shows histopathological features of the kidneys showing inflammatory markers (yellow arrows), necrosis (green arrows), hemorrhage (red arrows), and degeneration (blue arrows) in renal tissue. A. Normal control group score 0. B. Group A3 score 1.25. C. Treatment group A4 score 1.25. D. Treatment group A5 score 1.25. E. Treatment group B3 score 1.5. F. Treatment group B4 score 2. G. Treatment group B5 score 2. H. Treatment group C3 score 2. I. Treatment group C4 score 2. J. Treatment group C5 score 2.\n\nA. Normal control group score 0. B. Group A3 score 1.25. C. Treatment group A4 score 1.25. D. Treatment group A5 score 1.25. E. Treatment group B3 score 1.5. F. Treatment group B4 score 2. G. Treatment group B5 score 2. H. Treatment group C3 score 2. I. Treatment group C4 score 2. J. Treatment group C5 score 2. Hematoxylin–eosin with a 200× microscope magnification.\n\nOne of the earliest indicators of liver damage increase, when liver damage occurs, is ALT levels. In this study, ALT levels increased in all treatment groups. This increase significantly differs from the control group (p = 0.002). Figure 12 shows the results of ALT levels.\n\nThe results of the Mann–Whitney test showed a significant difference between the control group and all treatment groups (p = 0.05). ALT levels increased in the entire treatment group starting on day 3. ALT levels increased the most in group B5 (38.84 ± 0. 48 U/L). The results of the Mann–Whitney test showed no difference between the treatment groups (p > 0.05). The average in group C (36.79 ± 0.73 U/L) was greater than that in group B (36.46 ± 1.11 U/L) between groups B3, B4, B5, C3, C4, and C5; there was significant difference (p > 0.05). Based on these results, administering a dose of LPS 0.3 mg/kg B.W. in a single dose (C) can provide the highest increase in ALT levels when compared with the other groups.\n\nNF-κB, CRP, ALT, and TNF-α levels in all groups increased on day 3 after treatment. There were significant differences when compared with the control group. NF-κB and CRP levels increased the most in the LPS injection group at 0.3 mg/kg B.W. divided dose (B). Histopathological features of the kidneys and liver and the results of immunohistochemistry examinations on the liver and kidneys showed the highest increase in the LPS injection group at a dose of 0.3 mg/kg B.W. single dose (C).\n\n\nDiscussion\n\nThe host’s response to the invasion of pathogens can cause excessive inflammation, inhibit the immune system, and disappear the homeostasis of the immune system. In the early phases of sepsis, the innate immune system mediated by pattern recognition receptors (PRRs) will interact with pathogen-associated molecular patterns (PAMPs) that activate NF-κB and translocate into the nucleus. Ultimately, such stimulation increases the secretion of proinflammatory cytokines, including TNFα, interleukin-1β (IL-1β), IL-6, IL-12, and IL-18 involved in the pathogenesis of sepsis.8,9 In this study, at the beginning of sepsis, there was an increase in inflammatory markers of NF-κB in plasma and expression in the liver and kidneys. In this study, an assessment of NF-κB was carried out not only in plasma but also in the target organs, namely, the liver and kidneys. This is because all acute inflammatory conditions anywhere will also increase NF-κB in plasma. Research conducted by Liu et al. showed an increase in NF-κB expression in renal tubular cells in the mice in the LPS-induced sepsis mouse model.10 This is also in line with research by Ren et al., which proves that in mouse kidneys induced with LPS, there is a higher level of phosphorylation of NF-κB and IκB.11 LPS will bind to toll-like receptor 4, which is PRR found in kidney cells, resulting in the activation of several signaling pathways, one of which is NF-κB. Activation of the signaling pathway increases the transcription of proinflammatory cytokines, such as TNF-α, IL-6, and IL-1β, which then bind to several transmembrane receptors and strengthens the inflammatory response that occurs. Excessive inflammation can impact the renal parenchyma directly and cause tubule cell apoptosis.11\n\nIn this study, higher NF-kB expression in the sepsis mouse model follows a study conducted by Li et al., which showed a higher NF-kB expression in the liver of the mice in the sepsis mouse model.12 Another study by Li et al. also showed that in the liver of the mice in a sepsis mouse model, an increase in phosphorylated NF-kB was obtained.13 Kupfer cells will respond to the presence of LPS by secreting proinflammatory cytokines, such as IL-6, IL-8, and TNF-α and other proinflammatory mediators, such as IL-1β, IL-12, reactive oxygen species, and nitric oxide, which together cause damage to endothelial cells and hepatocytes. Additionally, neutrophils were recruited to the liver due to the release of TNF-α and leukotriene B4, which inflicted further damage to hepatocytes. Liver sinusoid endothelial cells also respond to the presence of LPS by releasing endothelin-1, which activates proinflammatory cytokine transcription factors, such as NF-κB.14\n\nThe inflammatory markers assessed in this study were CRP and TNF-α. In this study, CRP and TNF-α in plasma also increased. This is similar to a study by Li et al. in 2018, which showed an increase in CRP and TNF-α levels in a sepsis mouse model.15 Research on patients with sepsis conducted by Patel et al. also showed similar results, namely, higher levels of TNF-α in patients with sepsis than in healthy controls.16 The liver response to LPS is the secretion of a wide variety of proinflammatory cytokines by Kupfer cells, mainly IL-6 and IL-18. The secretion of IL-6 causes the synthesis of acute-phase proteins, one of which is CRP.\n\nMeanwhile, IL-8 plays a role in hepatocyte apoptosis and an increase in TNF-α concentrations.14 Inflammatory markers began to increase on day three after intraperitoneal LPS administration. LPS doses of 0.3 mg/kg B.W. single dose gave the highest results compared with other groups. This study follows the criteria for early sepsis that has been adhered to, which is 3 days.17 In this study, inflammatory markers also experience the highest increase in the group given an LPS dose of 0.3 mg/kg B.W. at a single dose. This is in accordance with research conducted by Hijma et al., which shows that the higher the amount of LPS given, the higher the inflammatory markers.18\n\nThe assessed organs damaged due to sepsis were the brain, lungs, heart, liver, and kidneys; coagulation function was also assessed. In this study, evidence of organ damage due to LPS administration was carried out in the liver and kidneys. The results of the ALT examination in plasma increased significantly starting day 3 with the administration of a single dose of LPS 0.3 mg/kg, which had the highest value when compared with the other groups. Organ damage in the liver and kidneys was also evaluated as histopathological. The most severe liver and kidney damage occurred in administering a single dose of LPS 0.3 mg/kg. Kidney damage experienced by the sepsis mouse model in this study follows research conducted by Huang et al. and Sun et al., which proved that there was an increase in tubule damage scores in the kidneys of sepsis mice.19,20 Sepsis can interfere with the functioning of endothelial cells through inhibition of endothelial regeneration, induce leakage of fluids and cells, cause inadequate perfusion of organs, cause local ischemic and tubular injury, and even pose a risk of organ failure and shock.21 The bond between inflammatory mediators, such as damage-associated molecular patterns and PAMPs, and membrane receptors in renal tubule epithelial cells will increase oxidative stress and mitochondrial damage.\n\nMeanwhile, the coagulation cascade and signaling of the activated autonomic nervous system will also lead to capillary occlusion by leukocytes and platelets and endothelial damage accompanied by vasodilation and endothelial leakage. This will result in peritubular edema and a decrease in oxygen supply to the renal tubules.22 Additionally, the expression of MMPs that degrade extracellular matrix proteins has also increased, such as MMP-9. This protein is involved in the degradation of type IV collagen, a major component of the kidneys’ basal membrane, for remodeling the basal membrane during embryonic growth.23 Endothelial cells in the kidneys also undergo necrosis that will produce neutrophil gelatinase-associated lipocalin (NGAL) as a form of self-defense and biomarker of growth and differentiation of kidney tubular cells so that changes in NGAL levels can be used to predict kidney injury due to bacterial infections and sepsis.24–26\n\nIn this study, an increase in ALT characterized liver damage in the sepsis mouse model. The degree of histopathological damage was supported by research by Zhang et al., which proved that in the LPS-induced mice in the sepsis mouse model, there was an increase in ALT serum and an increase in pathology scores in liver histopathological features.27 Other studies by Dai et al. also showed that in the sepsis mouse model, there was hepatocyte damage characterized by a vague nucleus picture and vacuole degeneration, and an increased ALT serum was obtained.28 In clinical settings, increased ALT describes acute damage to liver cells.15 Besides necrosis in kidney cells, sepsis causes inflammation of hepatocytes through the proinflammatory cytokine IL-6. It will stimulate the synthesis of acute-phase proteins such as CRP, antitrypsin α-1, fibrinogen, prothrombin, and haptoglobin. The increased concentration of such acute phase proteins can lead to inhibition of the protein pathway C. Thus, the disorder is responsible for the increased activity of coagulation factors.14 LPS will also stimulate Kupfer cells to secrete TNF-α, IL-1β, IL-12, and IL-18, where Il-18 plays a significant role in the process of liver damage induced by LPS. Interleukin-18 will cause interferon-γ secretion responsible for hepatocyte apoptosis, increased TNF-α concentrations, and increased CD14 expression. CD14 is a monocyte/macrophage surface receptor that plays a role in the binding of the lipopolysaccharide-binding protein complex.14\n\nThe change of sepsis definition, which was once caused by inflammation due to infection, became organ dysfunction caused by the dysregulated host response to infection, making an impact on making experimental sepsis animal model. This study advantage is to make a sepsis animal model based on both definitions, either inflammation parameter (CRP, NFKB, TNF-α) and organ damage (NGAL, ALT, and Histopathology) caused by LPS induction. In addition, this study previewed the onset of sepsis occurs from time to time.\n\nThe disadvantage of this study is that it is only done in male animals, while sepsis can occur in both males and females. This study also didn't assess the onset when the organ damage caused the death. This study only measured until the fifth day after the induction of LPS. At the end of this study, there were no mice who died after the induction of LPS.\n\n\nConclusion\n\nIn this sepsis mouse model, there has been an increase in inflammatory markers (CRP, TNF-α, NF-κB, and NF-κB expressions of the liver and kidneys) and organ damage markers (ALT, liver, and renal histopathology scores) on day 3. The highest increase was found in the group with a dose of 0.3 mg/kg single dose.", "appendix": "Data availability\n\nFigshare: Arifin (2022): degree of organ damage and inflammatory markers in sepsis mice models data and histopathology.xlsx. figshare. Dataset. https://doi.org/10.6084/m9.figshare.21710438.v1. 29\n\nThis project contains the following underlying data:\n\n- degree of organ damage and inflammatory markers in sepsis mice models 2.xlsx\n\n- degree of organ damage and inflammatory markers in sepsis mice models.xlsx\n\n- histopathology data\n\nFigshare: ARRIVE Guidelines for ‘Degree of organ damage and inflammatory markers in sepsis mice models inducted by various doses of lipopolysaccharides’, https://doi.org/10.6084/m9.figshare.21710618.v1. 30\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\nWe acknowledge research assistants, assistant laboratories in histology, and biomedical laboratories of the Faculty of Medicine of Sebelas Maret University and the Research and Community Service Institute of Sebelas Maret University.\n\n\nReferences\n\nGotts JE, Matthay MA: Cell-based therapy in sepsis: A step closer. Am. J. Respir. Crit. Care Med. 2018; 197(3): 280–281. PubMed Abstract \| Publisher Full Text\n\nGyawali B, Ramakrishna K, Dhamoon AS: Sepsis: The evolution in definition, pathophysiology, and management. SAGE Open Med. 2019; 7: 205031211983504. 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. Crit. Care Med. 2017; 45: 486–552. Publisher Full Text\n\nOffice of Laboratory Animal Welfare: Institutional Animal Care and Use Committee Guidebook.2002.\n\nFedchenko N, Reifenrath J: Different approaches for interpretation and reporting of immunohistochemistry analysis results in the bone tissue - a review. Diagn. Pathol. 2014; 9: 221. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKiyonaga N, Moriyama T, Kanmura Y: Effects of dexmedetomidine on lipopolysaccharide-induced acute kidney injury in rats and mitochondrial function in cell culture. Biomed. Pharmacother. 2020 May 1; 125: 109912. Publisher Full Text\n\nWongnawa M, Thaina P, Bumrungwong N, et al.: The protective potential and possible mechanism of Phyllanthus amarus Schum. & Thonn. aqueous extract on paracetamol-induced hepatotoxicity in rats.2006.\n\nSteinhagen F, Schmidt S v, Schewe JC, et al.: Immunotherapy in sepsis - brake or accelerate? Pharmacol. Ther. 2020; 208(January): 107476. Publisher Full Text\n\nvan der Poll T , van de Veerdonk FL , Scicluna BP, et al.: The immunopathology of sepsis and potential therapeutic targets. Nat. Rev. Immunol. 2017; 17: 407–420. PubMed Abstract \| Publisher Full Text\n\nLiu Z, Tang C, He L, et al.: The negative feedback loop of NF-κB/miR-376b/NFKBIZ in septic acute kidney injury. JCI Insight. 2020 Dec 17; 5(24). PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nRen Q, Guo F, Tao S, et al.: Flavonoid fisetin alleviates kidney inflammation and apoptosis via inhibiting Src-mediated NF-κB p65 and MAPK signaling pathways in septic AKI mice. Biomed. Pharmacother. 2020 Feb 1; 122: 109772. Publisher Full Text\n\nLi Z, Jia Y, Feng Y, et al.: Methane-Rich Saline Protects Against Sepsis-Induced Liver Damage by Regulating the PPAR-γ/NF-κB Signaling Pathway. Shock. 2019 Dec 1; 52(6): e163–e172. PubMed Abstract \| Publisher Full Text\n\nLi Q, Tan Y, Chen S, et al.: Irisin alleviates LPS-induced liver injury and inflammation through inhibition of NLRP3 inflammasome and NF-κB signaling. J. Recept. Signal Transduct. 2021; 41(3): 294–303. PubMed Abstract \| Publisher Full Text\n\nWoźnica E, Inglot M, Woźnica R, et al.: Liver dysfunction in sepsis. Adv. Clin. Exp. Med. 2018 Apr 30; 27(4): 547–552. PubMed Abstract \| Publisher Full Text Reference Source\n\nLi JL, Li G, Jing XZ, et al.: Assessment of clinical sepsis-associated biomarkers in a septic mouse model. J. Int. Med. Res. 2018 Jun 1; 46(6): 2410–2422. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPatel P, Walborn A, Rondina M, et al.: Markers of Inflammation and Infection in Sepsis and Disseminated Intravascular Coagulation. Clin. Appl. Thromb. Hemost. 2019 Apr 15; 25: 107602961984333. Publisher Full Text\n\nOgundare E, Akintayo A, Aladekomo T, et al.: Presentation and outcomes of early and late onset neonatal sepsis in a Nigerian hospital. Afr. Health Sci. 2019 Sep 1; 19(3): 2390–2399. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHijma HJ, Moss LM, Gal P, et al.: Challenging the challenge: A randomized controlled trial evaluating the inflammatory response and pain perception of healthy volunteers after single-dose LPS administration, as a potential model for inflammatory pain in early-phase drug development. Brain Behav. Immun. 2020 Aug 1; 88(88): 515–528. PubMed Abstract \| Publisher Full Text\n\nSun XY, Ding XF, Liang HY, et al.: Efficacy of mesenchymal stem cell therapy for sepsis: a meta-analysis of preclinical studies. Stem Cell Res Ther. 2020 Dec 3; 11(1): 214. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHuang M, Cai S, Su J: The pathogenesis of sepsis and potential therapeutic targets. Int. J. Mol. Sci. MDPI AG. 2019; 20. Publisher Full Text\n\nBermejo-Martin J, Martín-Fernandez M, López-Mestanza C, et al.: Shared Features of Endothelial Dysfunction between Sepsis and Its Preceding Risk Factors (Aging and Chronic Disease). J. Clin. Med. 2018; 7(11): 400. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJarczak D, Kluge S, Nierhaus A: Sepsis—Pathophysiology and Therapeutic Concepts. Front. Med. 2021; 8. Publisher Full Text\n\nZakiyanov O, Kalousová M, Zima T, et al.: Matrix metalloproteinases in renal diseases: A critical appraisal. Kidney Blood Press. Res. 2019; 44(3): 298–330. PubMed Abstract \| Publisher Full Text\n\nDai X, Zeng Z, Fu C, et al.: Diagnostic value of neutrophil gelatinase-associated lipocalin, cystatin C, and soluble triggering receptor expressed on myeloid cells-1 in critically ill patients with sepsis-associated acute kidney injury. Crit. Care. 2015; 19(1): 1–10.\n\nWajda J, Dumnicka P, Maraj M, et al.: Potential prognostic markers of acute kidney injury in the early phase of acute pancreatitis. Int. J. Mol. Sci. 2019; 20(15): 1–20.\n\nWang K, Xie S, Xiao K, et al.: Biomarkers of sepsis-induced acute kidney injury. Biomed. Res. Int. 2018; 2018: 1–7. Publisher Full Text\n\nZhang X, Su C, Zhao S, et al.: Combination therapy of Ulinastatin with Thrombomodulin alleviates endotoxin (LPS) - induced liver and kidney injury via inhibiting apoptosis, oxidative stress and HMGB1/TLR4/NF-κB pathway. Bioengineered. 2022; 13(2): 2951–2970. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDai JM, Guo WN, Tan YZ, et al.: Wogonin alleviates liver injury in sepsis through Nrf2-mediated NF-κB signalling suppression. J. Cell. Mol. Med. 2021 Jun 1; 25(12): 5782–5798. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nArifin:Degree of organ damage and inflammatory markers in sepsis mice models inducted by various doses of lipopolysaccharides data and hystopathology unedited pictures. [Dataset]. figshare. 2022. Publisher Full Text\n\nArifin: ARRIVE Guidelines. figshare. Journal Contribution. 2022. Publisher Full Text" }	[ { "id": "202272", "date": "27 Sep 2023", "name": "David Fernando Colon Morelo", "expertise": [ "Reviewer Expertise Basic and Applied immunology", "Sepsis", "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\nGeneral comments:\nSepsis is a life-threatening multi-organ dysfunction caused by dysregulated host response to infection with unmet clinical needs. This manuscript aims to determine the optimal dose of LPS to induce mice endotoxemia by assessing makers of tissue damage. However, in our opinion, the present study has several concerns that need to be addressed, as listed below:\nMajor:\nThe authors only assessed organ damage markers, despite wanting to determine LPS dosage. Why not perform a survival curve?\n\nAccording to the authors, the serum levels of NF-kB, CRP, and TNF showed the most increase in experimental Group B (LPS 0.3mg/kg, two days treatment). However, the authors also noted that there were no significant differences observed between the groups. Therefore, the conclusions drawn by the authors can be supported.\n\nThe study demonstrated that the histopathological characteristics of the liver and kidneys, as well as the immunohistochemistry analysis, exhibited the most significant increase in Group C. This finding is inconsistent with the results of the previous study conducted on Group B. As a result, the data as a whole is inconclusive. How do the authors explain this discrepancy?\nMinor:\nIn the Background section, the authors said: “This study aims to find the optimal dose to make a sepsis mouse model by examining the presence of target organ damage”. Include the expression “dose of LPS”\n\nIn the Introduction section, second line: change “ro” for “to” in the sentence\n\nImprove all figure legends including details such as experimental repetitions, “n” of mice, etc.\n\nIn histology figures, include the magnification scale.\n\nIn the Result section Fig 2, double-check the statistical analysis since it’s hard to claim they were significant.\n\nIn the Result section, combine Fig 6 and 7, Fig 8 and 9 and Fig 10 and 11, since one is the histology pic and the other is the quantification\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? No", "responses": [] }, { "id": "202118", "date": "12 Oct 2023", "name": "Kenji Hashimoto", "expertise": [ "Reviewer Expertise Neuroscience" ], "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 has several concerns.\nThe dose of LPS is too low for sepsis model.\n\nIn the Figures, we found \" p = 0.05*\". If the data are P<0.05, groups are significantly different.\n\nThe bars of SD in the all figures are the same. The raw data should be calculated well.\n\nFigure legends should be stated clearly. The results (F-values with df and P-values) of statistical analysis should be included.\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?\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": [] } ]	1	https://f1000research.com/articles/12-5
https://f1000research.com/articles/10-1303/v1	22 Dec 21	{ "type": "Case Report", "title": "Case Report: Case report: Administration of anticoagulant therapy after neuro-anesthesia procedure for hemorrhagic stroke patients with COVID-19 complications and its ethical and medicolegal consideration", "authors": [ "Taufik Suryadi", "Kulsum Kulsum", "Kulsum Kulsum" ], "abstract": "Background: Ethical dilemmas can occur in any situation in clinical medicine. In patients undergoing neuro-anesthesia for surgical procedure evacuation of intracerebral hemorrhage with a history of hemorrhagic stroke, anticoagulants should not be given because they can cause recurrent bleeding. Meanwhile, at the same time, the patient could also be infected with coronavirus disease 2019 (COVID-19), one of treatment is the administration of anticoagulants. Methods: A case report. A 46-year-old male patient was admitted to hospital with a loss of consciousness and was diagnosed with intracerebral hemorrhage due to a hemorrhagic stroke and was confirmed positive for COVID-19. Giving anticoagulants to patients is considered counterproductive so, an ethical dilemma arises. For this reason, a joint conference was held to obtain the best ethical and medicolegal solutions for the patient. Results: By using several methods of resolving ethical dilemmas such as basic ethical principles, supporting ethical principles, and medicolegal considerations, it was decided that the patient was not to be given anticoagulants. Conclusions: Giving anticoagulants to hemorrhagic stroke patients is dangerous even though it is beneficial for COVID-19 patients, so here the principle of risk-benefit balance is applied to patients who prioritize risk prevention rather than providing benefits. This is also supported by the prima facie principle by prioritizing the principle of non-maleficence rather than beneficence, the minus malum principle by seeking the lowest risk, and the double effect principle by making the best decision even in a slightly less favorable way as well as the medicolegal aspect by assessing patient safety and risk management.", "keywords": [ "Anticoagulants", "COVID-19", "Ethics and medicolegal", "Hemorrhagic stroke", "Neuro-anesthesia" ], "content": "Introduction\n\nA stroke is a brain disorder caused by blood vessel disorders that occur suddenly, this can be focal or global and can result in death within 24 hours of the onset of symptoms.1 Strokes are the second leading cause of death worldwide, and the fourth in the United States.2 Types of stroke consist of ischemic stroke and hemorrhagic stroke.3 Epidemiological studies show that only about 8-18% of strokes are hemorrhagic strokes. However, a hemorrhagic stroke has a higher risk of death compared to ischemic stroke.1,2 Hemorrhagic stroke can occur due to the rupture of a blood vessel in the brain. Based on the location of the bleeding, hemorrhagic stroke is divided into intracerebral hemorrhage (ICH) and subarachnoid hemorrhage (SAH).4 ICH penetrates the brain parenchyma, while SAH penetrates the subarachnoid space.5 Because the brain is a vital organ, if there is a hemorrhagic stroke, it can cause severe morbidity and high mortality rates.5,6\n\nICH has been traditionally divided into two categories primary (spontaneous) and secondary. The incidence of primary ICH is 10-15%.2 A primary ICH can be due to the rupture of small arteries and arterioles that have been damaged by chronic hypertension (60%),2,7 and then successively caused by cerebral amyloid angiopathy (30%),2 and then 10% is caused by advanced age, anticoagulation intensity, white matter disease, prior stroke, hematologic abnormalities, chronic kidney disease.8 A secondary ICH is due to trauma, aneurysms and vascular malformations, vasculitis, hemorrhage conversion of infarct.2 One of the main causes of ICH is hemorrhagic stroke, is spontaneous hemorrhagic stroke as it is the most severe complication of chronic hypertension.9 Hemorrhagic stroke is a fatal disease and only 30% of patients survive within six months after the event.6,9 Common causes of ICH are due to an aneurysm, bleeding from an arteriovenous malformation.2,5 ICH is generally correlated with hypertension, anticoagulant therapy, coagulopathy, drug and alcohol abuse, neoplasms, or amyloid angiopathy.2,5,9 Mortality within 30 days of the attack is 50%.9 The outcome for hemorrhagic stroke is worse than for ischemic stroke with a mortality of about 10-30%.5,6,9 ICH has a case fatality rate of about 40% per month and 54% per year.4\n\nThere is an ethical dilemma for the administration of anticoagulants in these patients. Administration of oral anticoagulants (OAC) is considered a risk in hemorrhagic stroke because it can cause intracerebral re-bleeding,10 in patients resuming OAC can increase the risk of recurrent bleeding 2.5-8%.11 Enhancement use of OAC will increase the risk of bleeding.12 However, in patients who are confirmed positive for coronavirus disease of 2019 (COVID-19), anticoagulation is recommended as an attempt to prevent blood clots that can worsen the patient's condition.12 For patients suffering from both COVID-19 and a hemorrhagic stroke, the use of anticoagulants could be contradictory to their best interests.2,5,10,12 It is necessary to solve the problem by reviewing the ethical and medicolegal aspects.\n\n\nCase report\n\nA 46-year-old male, driver, Acehnese patient, came with decreased consciousness from two days before admission to the Zainoel Abidin Hospital. The patient claimed to have a headache that got worse then suddenly fell and experienced loss of consciousness. The patient denied any nausea and vomiting before loss of consciousness. When the patient was admitted to the emergency department of the hospital, an antigen swab was performed on the patient and it was declared negative for COVID-19. Examination of vital signs obtained level of consciousness with Glasgow Coma Scale (GCS) Eye-2, Motoric-5, Verbal-3 (E2M5V3), pupils were isochoric with diameter 2 mm/2 mm. Blood pressure (BP) 160/81 mmHg, heart rate (HR) 87 beat/minute, respiratory rate (RR) 20 times/minute, body temperature 36.7oC. The patient had uncontrolled stage II hypertension. He denied history of diabetes mellitus, allergies, and asthma.\n\nLaboratory blood test results showed anemia (hemoglobin levels 8.2 gr/dl, hematocrit 24%, erythrocytes 2.8 × 106/mm3), leukocytosis (leukocytes 12.1 × 103/mm3), increased D-dimer (10570 ng/mL), platelets 299 × 106/mm3, eosinophils 3%. basophils 1%, neutrophil band 0%, segmented neutrophils 71%, lymphocytes 18%, monocytes 7%. In arterial blood gases test, it was found: respiratory alkalosis (pH 7,490 mmHg, pCO2 31 mmHg, pO2 110 mmHg, Bicarbonate (HCO3) 24 mmol/L, total CO2 25 mmol/L, base excess (BE) 1.6, oxygen saturation 94%). X-ray examination of the chest revealed, the heart size was within normal limits and the lungs indicated bronchopneumonia. From the head computed tomography (CT) scan, it was shown that there was intracerebral bleeding in the basal ganglia area. Because the patient could not saturate spontaneous breathing trial, the reverse-transcription polymerase chain reaction (RT-PCR) swab was performed. The RT-PCR results confirmed the patient was positive for COVID-19. The patient was diagnosed with intracerebral hemorrhage due to hemorrhagic stroke and COVID-19 complication. The medical treatment taken was ICH evacuation craniotomy.\n\nNeuro-anesthesia management was performed when preoperative found the patient's status was stage 3 (American Society of Anesthesiologists),13 with loss of consciousness, acute increase in intracranial pressure (ICP), level of consciousness GCS E2M5V3, with history of headache and vomiting, but no history of seizures. Neurological deficit was found in the form of left hemiparesis. The patient had stage II hypertension with BP 160/90 mmHg. Cardiac examination revealed no murmur or gallop rhythm. The electrocardiography showed a sinus rhythm of 90 times/minute. The patient was obese grade II with a body mass index (BMI) of 37.14 The planning that was carried out was a general anesthetic procedure with intubation, and postoperatively the patient was admitted to the intensive care unit (ICU). In the ICU, the patient had respiratory failure and was assisted with a ventilator. The patient was admitted to the ICU for 2 days, there was no improvement in the patient's level of consciousness using GCS. In this case, there was a dilemma as to whether anticoagulants could be given to hemorrhagic stroke patients with COVID-19 complications. An ethical and a medicolegal analysis is needed in making clinical decisions in these patients.\n\nOn the first day of ICU admission, the patient still experienced a decrease in consciousness with GCS of E2M5V3, BP of 159/81 mmHg, HR of 92 beats/minute, RR of 18 times/minute, and oxygen saturation of 99% (intubated). The patient was treated with intravenous fluid drip (IVFD) ringer lactate 500 cc/24 hours, head up position 30°, ceftriaxone IV 2 g/12 hours, omeprazole IV 40 mg/12 hours, phenytoin IV 100 mg/12 hours, propofol drip titration dose, fentanyl drip titration dose, amlodipine per-oral (PO) 10 mg/24 hours, and valsartan PO 160 mg/24 hours. Postoperative evaluation did not show any sign of recurrent bleeding, proven by the absence of tachycardia.\n\nThe condition of patient on the second day was similar with GCS of E2M5V3, BP of 148/61 mmHg, HR of 135 beat per minute, RR 18 times per minute, and oxygen saturation of 98% (intubated). Patient was treated by IVFD ringer lactate 500 cc/ 24 hours, head up 30° position, levofloxacin drip 750 mg/24 hours, omeprazole IV 40 mg/12 hours, phenytoin IV 100 mg/12 hours, propofol drip titration dose, fentanyl drip titration dose, Perdipine drip titration dose and paracetamol drip 1g/8 hours. There was a replacement of oral amlodipine to Perdipine drip since resistant hypertension was observed as also as the prevention of recurrent stroke and re-bleeding risks.\n\nAs the patient had severe symptoms of COVID-19, the patient was transferred to the respiratory intensive care unit (RICU) on the third day of hospital admission. The treatment remained similar from the second to eleventh day. Remdesivir 200 mg/24 hours and Combivent nebule 1 res/6 hours was added on the eight day. Tracheostomy was performed to prevent ventilator-associated pneumonia. Levofloxacin 750 mg/24 hours was replaced by meropenem 1 g/8 hours due to higher sensitivity. On the eleventh day, weaning ventilator and breathing trial was performed through tracheostomy. Clinical improvement was noticed since the twelfth day.\n\n\nDiscussion\n\nIn a hemorrhagic stroke common symptoms including nausea, vomiting, headache, and changes in the level of consciousness can indicate increased ICP and this is more common in hemorrhagic strokes.3 Seizures are more common in hemorrhagic stroke where the incidence is up to 2-20% and is common at the onset of ICH or within the first 24 hours.15 Physical examination of ICH patients in the form of changes in consciousness, shows that 30% of ICH patients are in a coma, while 28% of them have compos mentis.16 There is a focal neurologic deficit with headache and vomiting. Upon physical examination there were also other commonly seen symptoms including moderate and hemi sensory hemiparesis deficit, lateral vision paresis, homonym, hemianopia, aphasia, positive Babinski's sign, unreactive dilated pupils.3,15,16 Imaging examination in the form of a CT scan is mandatory because it is an important step in the evaluation of suspected hemorrhagic stroke, as it is used to distinguish it from ischemic stroke and can identify complications.3 Magnetic resonance imaging (MRI) is also sensitive in determining bleeding but, it is difficult to perform in the acute phase.17 Laboratory tests that need to be considered are prothrombin time (PT), partial thromboplastin time (PTT), international normalized ratio (INR), complete blood count (CBC), intermittent blood sugar, kidney function (ureum and creatinine), and electrolytes.18\n\nAdministration of anticoagulants in patients with ICH is still controversial. Based on one study that showed medication to improve ICH outcomes,2 otherwise, other studies found that the use of anticoagulants for the prevention of coronary stent thrombosis and thromboembolic stroke increased the incidence and severity of ICH.19 The main problem with the use of anticoagulants is the increased risk of bleeding in general and in ICH patients in particular.12 Use of warfarin in ICH can lead to hemorrhage-related death. Warfarin is thought to increase the risk of developing ICH sevenfold with a mortality rate of 60%.2\n\nIn the management of neuro-anesthesia for ICH evacuation craniotomy with COVID-19 complication, it must be ensured that there is no airway obstruction. Giving 100% O2 and targeted O2 saturation 98-100%. The respiratory rate should be around 20 breaths per minute, especially if brain herniation has occurred. Neuro-anesthesia should be ensured deep enough during intubation by endotracheal tube (ETT), so that there is no cough or increase in blood pressure that can increase intracranial pressure. Caution should be performed in patients with cervical fractures, try not to hyperextend the head, only a jaw thrust. During induction, fentanyl 200 μg and propofol 150 mg were given. The benefits of propofol in addition to induction are also useful for lowering blood pressure and intracranial pressure, followed by giving the muscle relaxant rocuronium 50 mg. Neuro-anesthesia must be ensured deep enough so that there is no increase in blood pressure fluctuations during intubation and surgery.2,9,16–18,20\n\nA rapid decrease in intracranial pressure can be achieved with the administration of diuretics. The two most commonly used diuretics are the osmotic diuretic mannitol and the loop diuretic furosemide. Mannitol is given as an intravenous bolus at a dose of 0.25-1 g/kg body weight. It is given slowly as an infusion over 10-20 minutes and is performed in conjunction with maneuvers that decrease the intracranial volume (e.g. hyperventilation). The duration of action of mannitol is 10-15 minutes and is effective for about 2 hours.2,9,20 Anesthesia was maintained using a syringe pump propofol 60 mg/hour, fentanyl 50 μg/hour, rocuronium 10 mg/hour in combination with an inhalation ratio of O2: water: sevoflurane = 2:2: 1. Intraoperatively, it is necessary to control the intracranial pressure and try not to swell the brain further. Brain perfusion and oxygenation should be adequate. Vasopressors or epinephrine boluses should be available if needed. If possible, an invasive monitor may be placed to measure arterial blood pressure, central venous pressure, and intracranial pressure during surgery. Checking blood sugar every hour to avoid hypo or hyperglycemic.2,9,20 Brain resuscitation for at least 6 hours was performed. Target O2 saturation was 98–100%, end-tidal CO2 30 mmHg. Avoiding the occurrence of hypotension or hypertension. Balanced (zero balance), avoiding negative balance. Give oral intake via nasogastric tube (NGT) if the NGT is clear. End-tidal CO2 is maintained at 30-35 mmHg. Avoid hypotension and hypovolemia preoperatively, during and after surgery.20 The presence of loss of consciousness with GCS E2M5V3, intracerebral hemorrhage, increased intracranial pressure, concludes that the prognosis is dubia at malam (doubtful tending to bad).2,9,20\n\nThe incidence of hemorrhagic stroke in COVID-19 patients was 0.3% (216 of 67,155 patients) with a fatality rate of 44.72%.3 COVID-19 is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Infection from this virus can be transmitted by patients who are asymptomatic, pre-symptomatic, or symptomatic. COVID-19 can cause severe pneumonia, acute respiratory distress syndrome (ARDS), respiratory failure, and death.21–23 As of November 18, 2021, Indonesia registered 143,709 deaths from the coronavirus.24 The mortality rate from this disease is 4-5% with most deaths occur in the age group over 65 years.25 The symptom varies depending on the severity of the diseases, ranging from asymptomatic patients to severe pulmonary disease with multi-organ failure.26 The main symptoms are fever, cough, myalgia, shortness of breath or difficulty breathing, nausea or vomiting, and diarrhea.3,21,27,28\n\nSupporting tests consist of thorax radiography, then thorax CT-scan with contrast if needed. Pneumonia on thorax radiography imaging caused by COVID-19 would appear from normal to ground-glass opacity or consolidation. A chest CT scan can be performed to see more details of abnormalities such as ground-glass opacity, consolidation, pleural effusion, and other features of pneumonia.21,27\n\nExamination of procalcitonin will increase when a bacterial infection is suspected. Other tests are essential to see comorbidities and evaluate possible complications of pneumonia, for example, kidney function, liver function, albumin and blood gas analysis, electrolytes, blood sugar, bacterial cultures, and sensitivity tests are all used to see possible causes of bacterial infection or if a double infection with bacteria is suspected.18 RT-PCR examination is a molecular examination that is often used to detect ribose-nucleic acid (RNA) that is specific for pathogenic viruses in the respiratory tract. RT-PCR examination is the gold standard in diagnosing COVID-19 due to its high sensitivity and specificity.21\n\nManagement of COVID-19 patients is divided into four categories: asymptomatic, mild symptoms, moderate symptoms, and severe symptoms. In asymptomatic patients, the management of COVID-19 is self-isolation at home for 10 days after being confirmed positive. Giving non-acidic vitamin C (500 mg per 6-8 hours orally in 14 days), inhaled vitamin C (500 mg per 12 hours orally in 30 days), and multivitamins containing vitamins C, B, E and zinc (1-2 tablets per 24 hours for 30 days) are recommended. Administration of vitamin D 1000 IU or 5000 IU percutaneous and other supportive therapy are given as needed.21,29\n\nMeanwhile, COVID-19 patients with mild symptoms can be managed conservatively by self-isolation at home for 10 days after being confirmed positive and 3 days free of symptoms (fever and respiratory problems). Oral route vitamins are recommended to support the patient, such as non-acidic vitamin C 500 mg per 6-8 hours (for 14 days), inhaled vitamin C 500 mg per 12 hours (for 30 days), or multivitamins containing vitamins C, B, E and zinc 1-2 tablets per 24 hours (for 30 days). Vitamin D 1000 IU or 5000 IU percutaneous can also be given. Favipiravir with a loading dose of 1600 mg per 12 hours orally on the first day followed by a maintenance dose of 600 mg per 12 hours orally for the next 5 days. Besides, symptomatic and co-morbid therapy are given as needed.21,29\n\nCOVID-19 patients with moderate symptoms are managed by hospitalization and bed rest, administration of vitamin C (200-400 mg/8 hours in 100 cc of 0.9% NaCl intravenous drip in 1 hour), and administration of vitamin D (1000 IU or 5000 IU percutaneous). Administration of chloroquine phosphate 500 mg/12 hours orally (for 5 days) or hydroxychloroquine in preparations of 200 mg or 400 mg/24 hours/oral (for 5 days), azithromycin 500 mg/24 hours/oral (for 5 days). When antiviral medicine is required, Favipiravir can be given with a loading dose of 1600 mg per 12 hours orally on the first day followed by a maintenance dose of 600mg/12 hours for the next 5 consecutive days. Remdesivir can also replace Favipiravir with initial dose of 200 mg intravenous drip on the first day followed by a maintenance dose of 100 mg/24 hours intravenous drip on the next 4-9 consecutive days. Anticoagulants such as low molecular weight heparin (LMWH) and unfractionated heparin (UFH) should only be given based on the clinical judgement of doctors whom in charge of the patient. Besides, symptomatic and co-morbid therapy are given as needed.21,29\n\nCOVID-19 patients with severe symptoms are managed by hospitalization and bed rest, administration of vitamin C (200-400 mg/8 hours in 100 cc of 0.9% NaCl intravenous drip in 1 hour), administration of vitamin B (1 ampoule intravenously) and administration of vitamin D (1000 IU or 5000 IU percutaneous). Administration of chloroquine phosphate 500 mg/12 hours orally (for 5 days) or hydroxychloroquine available preparations 200 mg or 400 mg/24 hours/oral (for 5 days), azithromycin 500 mg/24 hours/oral (for 5 days). When antiviral medication is required, Favipiravir can be given with a loading dose of 1600 mg per 12 hours orally on the first day followed by a maintenance dose of 600 mg/12 hours on the next 5 consecutive days. Remdesivir can also replace Favipiravir with initial dose of 200 mg intravenous drip on the first day followed by a maintenance dose of 100 mg/24 hours intravenous drip on the next 2-10 consecutive days. Dexamethasone 6 mg/24 hours can be given intravenously for 10 days. Anticoagulants such as low molecular weight heparin (LMWH) and unfractionated heparin (UFH) should only be given based on the clinical judgement of doctors whom in charge of the patient. In critical phase with severe pulmonary symptoms, combination therapy with intravenous methylprednisolone, high-dose intravenous ascorbic acid, thiamine (vitamin B1), and low molecular weight heparin can be provided, this combination therapy is called MATH.27 Besides, symptomatic and co-morbid therapy are given as needed.21,26,27,29\n\nThere is an ethical dilemma between; (a) can anticoagulation be given to patients post craniotomy for evacuation of bleeding? or (b) is it necessary to give anticoagulants to patients with confirmed COVID-19? Below, the description of solving this problem uses the basic ethical principles, namely beneficence and non-maleficence. The schematic for solving ethical dilemmas can be seen to the Figure 1. Therefore, ethical and medicolegal considerations in hemorrhagic stroke patients with COVID-19 complications should be carried out by reviewing several ethical and medicolegal principles such as prima facie, minus malum, double effect, patient safety, and risks management.\n\nThe decision to administer anticoagulation in hemorrhagic stroke patients with confirmed COVID-19 with moderate to severe symptoms using basic ethical principles is still a dilemma. However, using basic ethical principles and other supporting principles can help resolve this ethical dilemma.30 Ethical decision making should be performed by balancing all ethical principles, whether beneficence with non-maleficence, autonomy with justice, non-maleficence with justice or others. Of course, the best decision is that if all the principles can support each other, but it is possible that one of these ethical principles contradicts another, in this instance the choice is determined by which ethical principle at that time has the strongest moral justification.31,32 In cases as complex as this case study, an ethical dilemma arises, then the doctor can apply prima facie principles among the four basic ethical principles above in Figure 1 to make ethical decisions.30,33,34 In applying the prima facie principle, a valid new context is needed for the patient or family at the time of medical treatment (medical decision making can change if there is a more appropriate context. For example, in this case not giving anticoagulants, is a more appropriate context as preventing harm is more important than providing benefits). In this context, non-maleficence beats beneficence, in other situations it could be in that beneficence changes to non-maleficence.30–32\n\nThe beneficence principle aims to provide maximum benefit for the patient while balancing benefits and risks.30,31 The principle of beneficence is defined as the obligation of doctors to provide actions that are beneficial to patients. This principle will support several moral rules to protect patient rights such as to prevent harm and save patients from harm.30,33,34 According to the previous discussion, patients who are confirmed positive for COVID-19 need to be given anticoagulants because of the high risk of blood coagulation.10,11,12,22 With the provision of anticoagulants, it is expected that the disease burden of COVID-19 patients will be reduced so that the patient's body can resist infection with the SARS-CoV-2 virus.22 Aspects of the principle of beneficence are expected to lead to an improvement in the patient's condition.30,32–34\n\nThe principle of non-maleficence is that any medical service should not harm the patient.30,31 The principle of non-maleficence stems from the doctor's obligation not to harm the patient.30,32–34 In this case, the administration of anticoagulants to patients who have previously suffered intracranial bleeding are at risk for recurrent bleeding.6 This principle focuses on not hurting or reducing the ability of the patient.31,32 Therefore, doctors must always consider the benefits and risks that will be felt by the patient.30,31,33 By using the principle of non-maleficence, it means that the doctor must consider the harm that will be experienced by the patient, either directly or indirectly,30,31 when given anticoagulants.\n\nHowever, it is important to understand that solving ethical dilemmas is not always easy.33,34 There are times when we have to make complicated decisions by choosing which of the two conditions is the most important.30,32,33 For example, in this case where giving anticoagulants is dangerous for hemorrhagic stroke patients but if they are not given, there is a risk for patients with COVID-19, here the doctor must choose between them. In this condition, the minus malum principle can be used, the minus malum principle is making decisions by choosing the least risk or harm.30–32 In this patient it was decided not to be given anticoagulants because the patient had just undergone ICH evacuation surgery. Treating the patient with anti-coagulants could cause re-bleeding endangering the patient. No anticoagulation was planned for a while until there was no longer a potential for recurrent bleeding. Delaying anti-coagulant administration is certainly also a risk for COVID-19 patients because it can cause thrombosis which has the potential to become ARDS. Both of these risks are bad, but the doctor should make what they feel is the right decision, namely choosing the lightest risk.\n\nThe administration of anticoagulants in this case has a double effect, one of which is treatment for COVID-19 patients but is contraindicated in hemorrhagic stroke patients.34,35 Not giving anticoagulants to these patients is certainly not a good deed when viewed from the context of handling COVID-19, but of course the goal is the health and safety of the patient regards to avoiding ICH re-bleeding. In such conditions, the principle of double effects can be used. The principle of double effect is decision making where good goals can only be done in a bad way. The double effect principle supports the principle of non-maleficence.33–35 The use of prima facie, double effect and minus malum principles can be used together in synergy to make it easier for doctors to make medical decisions. In this principle, the action taken is the maximum benefit for the patient and the least risk of harm that may be caused.30–33\n\nDetermination of medical indications in hemorrhagic stroke patients can be done using the principles of beneficence and non-maleficence. The principle of beneficence means that therapy must provide medical benefits, while non-maleficence means that it must not harm the patient medically.30,31,34 Measurement of quality of life is determined using the principles of beneficence, non-maleficence and autonomy.33,34 Quality of life is a form of satisfaction, value statement, experienced in all aspects good or bad. The quality of life of a post neuro-anesthesia patient needs to be considered because the condition of pre-anesthesia patients is already bad. In this condition, ethical considerations can be created with a prima facie approach by prioritizing the interests of the patient or with a minus malum approach by choosing a more minimal loss or with the principle of double effects.30,32,34,35\n\nAccording to the explanation of Article 43 of the Indonesian Health Law number 36 of 2009 what is meant by patient safety is a process in a hospital that provides safer patient services.36 This includes risk assessment, identification and management of patient risks, incident reporting and analysis, the ability to learn and follow up on incidents, and implement solutions to reduce and minimize risks.36–38 Risk management in neuro-anesthesia includes preventive measures and management evaluations that have been carried out to reduce morbidity and mortality.9,37 Risk management is an effort that tends to be proactive and can also be an evaluation of previous experience to be applied in an effort to reduce or prevent similar problems in the future.38 There are four risk management steps in neuro-anesthesia: (1) problem detection (2) problem assessment (3) problem resolution, and (4) verification.37\n\nThe first step in risk management is to detect the problem, in this case, patients with hemorrhagic stroke with intracerebral bleeding have an increased risk of recurrent bleeding when given anticoagulants.10–12 The second step is to assess the problem, the problem experienced by the patient is that when the patient has finished the intracerebral bleeding evacuation operation, the patient has respiratory failure, so an RT-PCR swab examination is found and confirmed positive for COVID-19. This means patients would benefit from anticoagulants to reduce COVID-19 symptoms.26,27 Here there is a dilemma between anticoagulants being given or not given considering the contradictory clinical condition of the patient. The third step, solving the problem, in this case it the solution to the problem was to prevent re-bleeding so no anticoagulants were given for a while. Meanwhile, to reduce the symptoms of COVID-19, airway management is carried out in the form of tracheal intubation.26,39 The fourth step is verification, perioperative neuro-anesthesia management starting from the emergency room, in the operating room and in the ICU also affects the outcome of postoperative patient conditions.40-42\n\nTo reduce postoperative risk, ETT removal was not performed, the patient had a respiratory failure due to COVID-19 symptoms. In this case, as in most neurosurgery patients, the patient was awakened from the effects of anesthesia as soon as possible, so that the neurological status can be evaluated as soon as possible due to surgery.39 This is also in accordance with the procedure that in patients with intracerebral bleeding, complications or potential for recurrent bleeding, ETT removal is not performed immediately which is often referred to as slow weaning or delayed ETT removal. Delayed ETT removal can be performed on the conditions: poor preoperative level of consciousness, risk of edema or increased edema such as prolonged surgery, heavy bleeding, near vital areas, extensive surgery, and preoperative difficult airway management.42,43\n\nRisk management of neuro-anesthesia procedures in hemorrhagic stroke patients focused on early resuscitation, hemodynamic stabilization, and emergency surgery to evacuate bleeding. Surgery is performed by keeping the brain relaxed (by giving adequate relaxants, adequate analgesics, normal body fluid volume, and maintaining hemodynamics), lowering cerebral blood flow (CBF) thus ICP is low, protecting nerve tissue from ischemia and injury, maintaining cerebral perfusion pressure (CPP), reduce cerebral metabolic oxygen level (CMRO2), and optimize brain oxygen delivery (DO2).41–43 Hemorrhagic stroke is a big matter in the medical practice due to the high mortality and morbidity. There are three goals of the anesthesiologist besides facilitating surgery, namely (1) controlling intracranial pressure and brain volume, (2) protecting nerve tissue from ischemia and injury,(3) reducing bleeding.9,42\n\n\nConclusions\n\nBy using the basic ethical principles which are assisted by the medicolegal principles, it is concluded that in hemorrhagic stroke patients with COVID-19 complications are not given anticoagulants considering the ethical principles of beneficence and non-maleficence and are supported by prima facie principles, double effect and minus malum as well as medicolegal aspects by examining patient safety and risks management. Giving anticoagulants is controversial because it can harm the patient (non-maleficence principle), although it is beneficial for patients with COVID-19 (beneficence principle), in this case, preventing harm is of higher than providing benefits. The prima facie principle in this case, is that beneficence turns into non-maleficence. Based on the minus malum principle, in this case the smallest risk was chosen, namely not giving anticoagulants to a patient with COVID-19 to prevent a greater risk of re-bleeding. The principle of double effect is carried out for the same reason, namely doing bad deeds (not giving anticoagulants) with good intentions (preventing harm to the patient if re-bleeding occurs). Risk management in patients similar to this case is to minimize the risks that occur for overall patient safety.\n\n\nData availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nPatient perspective\n\nAfter discussing with the medical team in charge of the patient, the family was conscious of the medical reasoning and agreed to the doctor's clinical consideration of not giving anticoagulants for a certain duration for the sake of patient safety. After several days of admission in ICU and RICU, clinical improvement was noticed, hence the patient was discharged from hospital followed by outpatient management.\n\n\nConsent\n\nWritten informed consent for publication of their clinical details and or clinical images was obtained from the son of the patient because when we discussed this case, the patient was unconscious.\n\n\nAuthor contribution\n\nSuryadi T: Project Administration, Writing-Original Draft Preparation, Writing-Review and Editing; Kulsum K: Supervision, Validation, and Visualization.", "appendix": "References\n\nJohnson W, Onuma O, Owolabi M, et al.: Stroke: A global response is needed. Bull. World Health Organ. 2016; 94(9): 634–634A. PubMed Abstract \| Publisher Full Text\n\nMack PF: Intracranial haemorrhage: therapeutik interventions and anaesthetic management. British J Anaesthesia. 2014; 113(52): ii17–ii25. 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PubMed Abstract \| Publisher Full Text\n\nWolff HN: Total number of deaths from COVID-19 in Indonesia as of November 18, 2021.https://www.statista.com/statistics/1103816/indonesia-covid-19-number-of-deaths/\n\nHandayani D: Coronavirus disease 2019. J Resp Indon. 2020; 40(2): 119–129. Publisher Full Text\n\nCarfora V, Spiniello G, Ricciolino R, et al.: Anticoagulant treatment in COVID-19: a narrative review. J Thromb Thrombolysis. 2021; 51: 642–648. PubMed Abstract \| Publisher Full Text\n\nMarik PE, Kory P, Varon J, et al.: MATH+ protocol for the treatment of SARS-CoV-2 infection: the scientific rationale. Expert Rev Anti-Infect Ther. 2020; 0: 1–8.\n\nYazmin GT, Felipe V, Lopez-Hernandez MN, et al.: Considerations for the emergency and perioperative management of patients with COVID-19. Panam J Trauma, Crit Care Emerg Surg. 2020; 9(2): 133–141. Publisher Full Text\n\nRepublic of Indonesia: Decree of the Minister of Health of the Republic of Indonesia number HK.01.07/Menkes/5671/2021 concerning in clinical management of COVID-19 treatment in health facilities. Indonesia: Jakarta; 2021.\n\nVarkey B: Principles of clinical ethics and their application to practice. Med Princ Pract. 2021; 30(1): 17–28. PubMed Abstract \| Publisher Full Text\n\nMappaware NA, Sima S, Syahril E, et al.: Stage III-B cervical-cancer of young age in medical, bioethics, and clinical ethics perspectives. Indian J Forens Med Toxicol. 2020; 14(2): 2565–2570.\n\nGillon R: Defending the four principles approach as a good basis for good medical practice and therefore for good medical ethics. J Med Ethics. 2015; 41: 111–116. PubMed Abstract \| Publisher Full Text\n\nPage K: The four principles: Can they be measured and do they predict ethical decision making?. BMC Med Ethics. 2012; 13(10): 1–8.\n\nKemparaj VM, Kadalur UG: Understanding the principles of ethics in health care: a systematic analysis of qualitative information. Int J Community Med Public Heal. 2018; 5(3): 822–828. Publisher Full Text\n\nWholihan D, Olson E: The doctrine of double effect, a review for the bedside nurse providing end of life care. J Hosp Palliat Nurs. 2017; 0: 205–211.\n\nRepublik of Indonesia: Indonesian Health Law number. 36 of 2009 concerning in Health. Indonesia: Jakarta; 2009.\n\nCabrini L, Levati A: Risk management in anesthesia. Minerva anesthesiologica. 2009; 75(11): 638–643.\n\nCevik B, Yuce Y: Risk assessment in surgical patients: American Society of Anesthesiologists (ASA) classification vs. intraoperative therapeutic and diagnostic interventions (I-ITS). Am J Clin Med Res. 2018; 6(1): 15–19. Publisher Full Text\n\nOkunlola AI: Awake craniotomy in a COVID-19 positive patient: The challenges and outcome. Interdiscip Neurosurg Adv Tech Case Manag. 2021; 24: 101064.\n\nCurry P, Viernes D, Sharma D: Perioperative management of traumatic brain injury. Int J Crit Illn Inj Sci. 2011; 1(1): 27–35. PubMed Abstract \| Publisher Full Text\n\nBasuki WS, Suryono B, Saleh SC: Perioperative management of severe traumatic head injury with cushing signs. J Neuroanes Indon. 2015; 4(1): 34–42.\n\nWullur C, Bisri DY: Anesthesia management of a patient with large supra-tentorial brain tumor suspected convexity meningioma. J Neuroanes Indon. 2014; 3(2): 96–102. Publisher Full Text\n\nSyah BIA, Suarjaya IPP, Rahardjo S, et al.: Anesthesia management in severe head injury patients from acute epidural hematoma with pregnancy. J Neuroanes Indon. 2017; 6(3): 169–177." }	[ { "id": "118436", "date": "08 Feb 2022", "name": "Aladeen Alloubani", "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 current case report discussed an ethical dilemma which can occur in any situation in clinical medicine. In patients undergoing neuro-anesthesia for the surgical procedure evacuation of intracerebral hemorrhage with a history of hemorrhagic stroke, anticoagulants should not be given because they can cause recurrent bleeding. Meanwhile, at the same time, the patient could also be infected with coronavirus disease 2019 (COVID-19), for which one of treatments is the administration of anticoagulants.\nTitle: The case report was repeated twice in the title. So, please delete one.\nPage 3: I suggest deleting the name of the hospital \"Zainoel Abidin Hospital\" to maintain privacy.\nPage 5 and 6: Need to provide citation support for all statements of fact that are not common knowledge. Would you please review and revise throughout the document?\nPage 8: I advise adding a recommendation section.\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": "8532", "date": "17 Nov 2023", "name": "Taufik Suryadi", "role": "Author Response", "response": "Dear Dr Aladeen Alloubani, Thank you for the excellent comments and suggestions for improving this manuscript Regarding the title that contains the word \"case report\" twice, yes, we agree to delete one of them. We request the editor to remove it from the publication manuscript. Page 3: Yes we agree to remove the name of the hospital \"Zainoel Abidin hospital\" to maintain privacy. We request the editor to remove the hospital's name from the publication manuscript. Page 5 and 6: We have compiled reading sources from the latest references that we found including the COVID-19 management guidelines that apply in our country (Indonesia). Page 8: We add recommendations namely: In making medical decisions, it should be based on ethical decisions, both in dilemma and non-dilemma cases. Medical decision making based on ethical decisions will add value to these decisions both morally, medically and professionally." } ] }, { "id": "220572", "date": "15 Nov 2023", "name": "Aldy Safruddin Rambe", "expertise": [ "Reviewer Expertise Neurovascular", "Neurology" ], "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 report was quite straightforward and clear, except for the last part where the author stated \"Clinical improvement was noticed since the twelfth day.\" It would be more helpful to explain what clinical improvement was shown (ex; did the level of consciousness got better? etc.,).\nThe author also stated that the patient got better without the use of anticoagulant to treat the patient's COVID-19. It would be better to explain the use of the medication in this condition in the discussion section, what could be the effect of the lack of use. On the other hand, there's sufficient reasoning about the lack of use of said medication, that is good.\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": "10725", "date": "18 Jan 2024", "name": "Taufik Suryadi", "role": "Author Response", "response": "Dear Prof.Aldy Safruddin Rambe, Thank you for the excellent comments and suggestions for improving this manuscript. We would like to provide additional information regarding clinical developments after 12 days of treatment: Clinical improvement in patients can be seen from improved consciousness, patients no longer feel nauseous and vomiting, complaints of headaches disappear, patients no longer experience shortness of breath and fever, and coughing is less common. We also provide additional information if anticoagulants are used in small doses: If anticoagulants are given, even in small doses, to hemorrhagic stroke patients, there is a risk that bleeding will occur again, which will increase intracranial pressure which will result in decreased consciousness." } ] } ]	1	https://f1000research.com/articles/10-1303
https://f1000research.com/articles/12-180/v1	15 Feb 23	{ "type": "Research Article", "title": "Impact of multiple different high-fat diets on metabolism, inflammatory markers, dysbiosis, and liver histology: study on NASH rat model induced diet", "authors": [ "Syifa Mustika", "Dewi Santosaningsih", "Dian Handayani", "Achmad Rudijanto", "Dewi Santosaningsih", "Dian Handayani", "Achmad Rudijanto" ], "abstract": "Background: The spectrum of non-alcoholic fatty liver disease (NAFLD), known as non-alcoholic steatohepatitis (NASH), can lead to advanced liver disease. It is known that a variety of diets play a significant role in the development of NAFLD/NASH. The goal of this study was to determine the most appropriate composition of diet to induce NASH in an animal model. Methods: This research used Rattus norvegicus strain Wistar (n=27), which were divided into four groups and given each diet for 12 weeks: normal diet (ND, n=7), high-fat diet (HFD, n=6), western diet (WD, n=7) and high-fat-high-fructose diet (HFHFD, n=7). Subjects were documented for body weight. Blood samples were taken for biochemical analysis: low-density lipoprotein (LDL), triglyceride, alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP), hepatic lipase, tumor necrosis factor-alpha (TNF-α), interleukin-6 (IL-6), and lipopolysaccharide (LPS). Feces were taken for short-chain fatty acid (SCFA) analysis. Liver histology was analyzed using NAS (NAFLD activity score). The comparison test was carried out using the one-way ANOVA or Kruskal–Wallis test. Results: The highest average body weight was in the WD group (346.14 g). Liver enzymes, LDL, triglyceride, propionic acid, and acetic acid in each group were not significantly different. TNF-α, IL-6, and hepatic lipase were significant (p = 0.000; p = 0.000; p = 0.004) and the highest was in the HFD group. Butyrate level was significant (p = 0.021) and the least was in the HFHFD group (4.77 mMol/g). Only WD and HFHFD had an NAS ≥ 5 (14% and 14%). The highest percentage of borderline NAS was found in WD (57%). Conclusions: The HFD group showed significant liver inflammation but did not produce NASH histologically, whereas the WD and HFHFD groups had the potential to develop NASH because the diets affected metabolic and inflammatory parameters as well as liver histology.", "keywords": [ "diet", "non-alcoholic steatohepatitis", "Rattus norvegicus strain Wistar" ], "content": "Introduction\n\nNon-alcoholic fatty liver disease (NAFLD) is becoming a common medical problem because of its high incidence and treatment complexity. According to the most recent epidemiology, NAFLD has become the second most common liver disease after viral hepatitis, with a 20–30% incidence rate, and obesity rates of up to 57.74% in the global population.1\n\nThe NAFLD subtype, non-alcoholic steatohepatitis (NASH), has become a major public health concern.2 NASH is defined via liver biopsy as the presence of ≥5% hepatic steatosis and inflammation with hepatocyte injury (e.g., ballooning), with or without any fibrosis. It is a potentially progressive liver disease that can lead to cirrhosis.3 Risk factors for the development of NASH include excessive calorie-dense food intake, lack of physical activity and exercise, and genetic susceptibility.4\n\nPoor dietary habits may induce NASH, directly by affecting hepatic triglyceride accumulation and antioxidant activity, and indirectly by impairing insulin sensitivity and fat metabolism.5 According to a previous study, there will be a 33.5% increase in the total prevalence of NAFLD by 2030. This condition is associated with a significant increased incidence of NASH complications, such as decompensated cirrhosis (168%), hepatocellular carcinoma (137%), and liver-related mortality (178%).6\n\nThe current problem with NAFLD/NASH is that there is no universally accepted treatment as standard. Furthermore, clinical research on the NASH/NAFLD mechanism is limited by ethical considerations when using humans as research subjects, as it involves obtaining tissue samples from patients.7 Besides that, the development of NASH in humans can take a long time, up to several decades. Therefore, research related to NASH requires an appropriate experimental animal model to represent NASH.\n\nDiet can facilitate the development of NAFLD/NASH. The high-fat diet (HFD), western diet (WD), and high-fat-high-fructose diet (HFHFD) are the types of diet used to induce NASH.8,9 Of the various diets, there is no standard composition to describe the condition of NASH. Based on the problems above, we need to create an animal model of NASH based on diet intervention. This study is aimed to determine the most representative diet for inducing NASH in the Rattus norvegicus Wistar strain.\n\n\nMethods\n\nThe Ethical Committee of the Faculty of Medicine, Universitas Brawijaya reviewed and approved all procedures (No. 66/EC/KEPK/02/2021). A total of 27 male Wistar rats were obtained from Universitas Gadjah Mada. Rat inclusion criteria included: male rat with shiny white fur, healthy, active, and had normal behavior; about 8-12 weeks old; the average body weight was 150-180 grams. Exclusion criteria included: the appearance of dull fur, loss and baldness; less or inactive activity; rats that during the study did not want to eat; weight loss >10% after adaptation period; disabled, sick and/or dead rat. This research used the refinement principle for ensuring the welfare of experimental animals until the end of the study to minimize pain and discomfort. We provided food and drink regularly every day with a certain type of diet according to the type of treatment. Cage maintenance, cage cleaning, and wood husk replacement were carried out every day with attention to light, temperature, and humidity. We monitored and evaluated the rats’ condition every day and placed them individually in each cage. Before being treated, the rats were acclimatized for two weeks, given a standard diet, and placed inside cages at the Pharmacology Laboratory, Faculty of Medicine, Universitas Brawijaya. The Wistar rats were randomly assigned using a table of random numbers, then categorized into four groups: normal diet (ND) (67% carbohydrate, 21% protein, 7% fat, 5% fiber); HFD (67.1% carbohydrate, 16.5% fat, 16.4% protein), WD (52% carbohydrate, 16.1% protein, 31.7% fat), and HFHFD (41.5% carbohydrate, 10.3% fat, 10.2% protein, 38% fructose). All diets were given for 12 weeks. All four groups were euthanized with ketamine–xylazine intravenously to relieve pain on the same day before surgery was performed.10 The entire liver was taken out and weighed. For further analysis, the livers were either collected and stored at −20°C or fixed in 10% paraformaldehyde.\n\nRat serum was used to analyze biochemical parameters in the Clinical Pathology Laboratory, Universitas Brawijaya, Indonesia.11 Serum alanine aminotransferase (ALT), aspartate aminotransferase (AST), and alkaline phosphatase (ALP) were analyzed chemically using colorimetric analysis (ADVIA 2400 Clinical Chemistry System (Siemens, Germany). Serum hepatic lipase, tumor necrosis factor-alpha (TNF-α), interleukin-6 (IL-6), and lipopolysaccharide (LPS) were analyzed with the sandwich enzyme-linked immunosorbent assay (ELISA) method.12\n\nA total of 0.5 gram fecal samples from the colon were collected, labelled, and placed into container tubes. These samples were immediately stored at −40°C until the analysis day. At the time of analysis, 0.2 g of the fecal sample supernatant poured into a 2 mL microtube and then added with sterile aquabidest water for injection. This suspension underwent 20 minutes of sonification, followed by centrifugation (14,000 rpm, 4°C, 10 min). The second centrifugation step (1,000 rpm, 4°C, 10 min) was performed while the natant was discarded. The final supernatant was injected to a gas chromatography (Shimadzu, GC-2010 Plus, Kyoto, Japan). Fecal pH measurement was used using pH meter (pH Spear Eutech, Eutech Instruments, Paisley, United Kingdom).13 This procedure was performed at the Food Technology and Agricultural Products Laboratory, Universitas Gadjah Mada, Indonesia.\n\nThe liver was sliced, fixed with 10% buffered formalin, embedded in paraffin, and stained with hematoxylin–eosin (HE) stain at a thickness of 5 μm.11 The sample preparation was performed at the Anatomical Pathology Laboratory of Universitas Brawijaya, Indonesia. Liver histopathology was used to find the NAFLD Activity Score (NAS). Three parameters (steatosis score 0–3; lobules inflammation score 0–3; ballooning score 0–2) were used to know NAFLD staging. Scores of 0–2 are defined non NASH, scores of 3–4 are defined as borderline, while scores ≥ 5 are considered diagnostic of NASH.14\n\nData were presented as the mean ± standard deviation and were analyzed with SPSS 25.0 (RRID:SCR_002865) for Windows. A one way ANOVA was carried out when the data were normally distributed and then continued with the Tukey Honest Significant Difference (HSD) post hoc test if the data were significant. The Kruskal–Wallis test was used when the data distribution was not normal. If the results were significant then the Mann Whitney test was performed. When p <0.05, data were considered significant.\n\nThe research flow (Figure 1) consisted of: 1). Rattus norvegicus acclimatization for two weeks; 2). Several diets intervention (ND, HFD, WD, HFHFD) for 12 weeks; 3). Dissection and data analysis at the end process. Several samples such as liver, stool, and blood were obtained for further analysis.\n\n\nResults\n\nThis research was done by following the method and research flow that has been explained above. The data of baseline characteristics and biochemical parameters of the rats were gathered and analyzed using the one-way ANOVA test and Kruskal–Wallis test. The need of this analysis was to obtain the data samples of baseline characteristics and biochemical parameters of rats after several diets intervention (ND, HFD, WD, HFHFD) for 12 weeks (Table 1).\n\n* One-way ANOVA test.\n\n# Kruskal–Wallis test.\n\nBased on Table 1, regarding metabolic parameters, the highest average body weight and triglyceride levels were in the WD group, while the HFD group seemed to have the greatest increase in LDL. The HFD group had the highest levels of hepatic lipase, indicating a significant difference (p = 0.004) between the four groups. The post hoc test resulted in significant differences in hepatic lipase levels in the ND vs HFD, HFD vs WD, and HFD vs HFHFD groups (Figure 2). From these results, the provision of fat-based diets affected the metabolic conditions of rats.\n\nNote: Symbols represent significant post hoc result (p < 0.05). p = 0.003 for ND vs HFD; +p = 0.003 for HFD vs WD; ++p = 0.015 for HFD vs HFHFD. ND: normal diet; HFD: high-fat diet; WD: western diet; HFHFD: high-fat-high-fructose diet.\n\nWhen evaluating the inflammatory response and liver damage, TNF-α and IL-6, as well as liver enzymes like ALT, AST, ALP, and total bilirubin, are important parameters. ALT, AST, and total bilirubin did not show any significant differences between the four groups, as shown in Table 1. However, the levels of TNF-α and IL-6 were significantly different, and showed the highest levels in the HFD group, followed by WD, then HFHFD. The post hoc TNF-α test showed significant differences in all comparisons between groups, except for ND compared with HFHFD (p = 0.369) (Figure 3). Meanwhile, in post hoc IL-6, the results were not significant only for HFD compared with WD (p = 0.568) (Figure 4). The four groups also had significantly different levels of ALP, with WD having the highest levels, followed by HFD, then HFHFD (Table 1). Based on the post hoc ALP test, the results were not significant only in the HFD group compared with the WD group (Figure 5).\n\nNote: Symbols represent significant post hoc result (p < 0.05). p = 0.000 for ND vs HFD; *p = 0.001 for ND vs WD; +p = 0.001 for HFD vs WD; ++p = 0.000 for HFD vs HFHFD; #p = 0.037 for WD vs HFHFD. ND: normal diet; HFD: high-fat diet; WD: western diet; HFHFD: high-fat-high-fructose diet.\n\nNote: Symbols represent significant post hoc result (p < 0.05). p = 0.003 for ND vs HFD; p = 0.002 for ND vs WD; p = 0.002 for ND vs HFHFD; ++p = 0.003 for HFD vs HFHFD; #p = 0.002 for WD vs HFHFD. ND: normal diet; HFD: high-fat diet; WD: western diet; HFHFD: high-fat-high-fructose diet.\n\nNote: Symbols represent significant post hoc result (p< 0.05). p = 0.003 for ND vs HFD; p = 0.002 for ND vs WD; p = 0.002 for ND vs HFHFD; +p = 0.046 for HFD vs WD; #p = 0.002 for WD vs HFHFD. ND: normal diet; HFD: high-fat diet; WD: western diet; HFHFD: high-fat-high-fructose diet.\n\nMicrobial dysbiosis is described by the parameters of LPS and SCFA levels. Based on Table 1, the LPS and butyrate levels were significantly different in all groups. The ND group had the highest LPS level, while the HFHFD group had the lowest. Based on LPS post hoc analysis (Figure 6), there was a significant difference between ND vs HFHFD, and HFD vs HFHFD. The highest butyrate was in the ND group and the lowest was in the HFHFD. In post hoc analysis of butyrate (Figure 7), we found p < 0.05 for ND vs HFHFD, and ND vs HFD.\n\nNote: Symbols represent significant post hoc result (p< 0.05). p = 0.001 for ND vs HFHFD; +p = 0.013 for HFD vs HFHFD. ND: normal diet; HFD: high-fat diet; WD: western diet; HFHFD: high-fat-high-fructose diet.\n\nNote: Symbols represent significant post hoc result (p< 0.05). p = 0.046 for ND vs HFD; *p = 0.004 for ND vs HFHFD. ND: normal diet; HFD: high-fat diet; WD: western diet; HFHFD: high-fat-high-fructose diet.\n\nLiver histological analysis can be seen in Figure 10. Based on Table 2, the highest percentage of histological features in the HFD group was lobular inflammation; only 33.33% developed hepatocyte ballooning. Meanwhile, in the WD and HFHFD groups, all rats had lobular inflammation and most developed hepatocyte ballooning. Based on the NAS score, only the WD and HFHFD groups had NAS ≥5 with the same percentage (Figure 8). The WD group had 57% of rats potentially experiencing NASH (borderline NAS), which was higher than the HFHFD group (43%) (Figure 9).\n\nA). ND group; B). Steatosis in HFD group (black arrow); C). Lobular inflammation in HFD group (red arrow); D). Hepatocyte ballooning in HFD group (blue arrow); E). Steatosis in WD group (black arrow); F). Lobular inflammation in WD group (red arrow); G). Hepatocyte ballooning in WD group (blue arrow); H). Lobular inflammation in HFHFD group (red arrow); I). Hepatocyte ballooning in HFHFD group (blue arrow).\n\n\nDiscussion\n\nSeveral factors have a role in the development of NASH, such as genetic variation, abnormal fat metabolism, oxidative stress, mitochondrial dysfunction, inflammatory response, and dysbiosis of gut microbiota.15 Diet contributes to the pathophysiology of NAFLD. Some dietary consumption habits such as a high-fat and high-fructose diet can lead to liver fat accumulation and an increased risk of insulin resistance.16 Boland et al. stated that a diet high in saturated fat and fructose plays a role in increasing oxidative stress and lipogenesis, stimulating an inflammation response, and triggering changes in the gut microbiota composition.17 Different diet compositions can alter the natural course of NAFLD, therefore it is important to discuss the impact of different types of diet on the development of NAFLD.\n\nSystemic low-grade inflammation, which has the potential to increase reactive oxygen species (ROS) and pro-oxidative stressors, is a hallmark of obesity. Obesity is associated with hyperglycemia and increased levels of free fatty acids (FFAs), which then induce lipotoxicity.18 Increased FFAs and insulin resistance trigger hepatic steatosis. This condition has an impact on increasing hepatic lipase activity. Hydrolyzing hepatic triglycerides and lipoprotein phospholipids is the job of hepatic lipase. The degree of hepatic steatosis is positively correlated with hepatic lipase.19 In our study, metabolic changes were found in the HFD, WD, and HFHFD groups. However, only rats on HFD and WD developed an obese phenotype by the end of the study, although the data were not significant. Triglyceride was found in the highest level in the WD group, while LDL was the highest in the HFD group. Hepatic lipase was found in excessive levels in the HFD group. A previous study proved that high-fat animals had significantly higher body weight than high-fructose animals.20 Lee et al. stated that rats induced by high-fat and high-fat-high-fructose had significant higher body weights than high-fructose only.21\n\nThe adiposity index, an increase in body weight, and excessive fat accumulation are all signs of obesity. Fat and sugar composition in the WD may contribute to increase of body weight by increasing abdominal fat mass and adiponectin expression in adipose tissue. Micronutrient composition in the WD could be possible factor that could affect a rat’s body weight gain. These results were in line with Bortolin et al. who concluded that the WD was the most effective diet to promote obesity in rats. Micronutrient content and diet palatability are the factors that contribute to weight gain in rats.22\n\nCirculating inflammatory cytokines are primarily derived from adipose tissue. Through the inflammatory pathway, high levels of circulating inflammatory signals can cause insulin resistance and provide positive feedback that increases liver inflammation. By activating the c-Jun N-terminal kinase (JNK) and nuclear factor-kappa B (NF-κB) signaling pathways, obesity increases the production of pro-inflammatory cytokines like TNF-α and IL-6.23 In our study, obese rats that were in the HFD and WD groups also developed higher levels of TNF-α and IL-6. These results were also consistent with other studies that revealed the effect of HFD rat and obese diabetic patients on TNF-α and IL-6.24,25\n\nCholesterol and saturated fatty acids (SFAs) are examples of WD ingredients that relate to the inflammatory response in the immune system.26 Insulin resistance in the WD model may cause hypertriglyceridemia and hypercholesterolemia, which induce lipotoxicity and hepatic steatosis. SFAs and cholesterol accumulation in the WD could cause hepatic oxidative stress by disruption of the glutathione system and superoxide dismutase (SOD) levels. Furthermore, oxidative stress may trigger the activation of NF-κB, mitogen-activated protein kinase (MAPK), and the JNK cascade, which results in the increase of several cytokines such as TNF-α and IL-6 in the hepatocytes and Kupffer cells.27\n\nMetabolic changes and inflammatory conditions are closely related to the disruption of the intestinal barrier, leading to microbial dysbiosis. Gram-negative bacteria contain LPS, which in large quantities can induce an inflammatory response, leading to endotoxemia. The presence of LPS translocation that enters through the portal circulation can trigger the occurrence of repeated liver exposure, leading to liver injury.28 Consuming high levels of fructose and fat was found to be strongly correlated with increased serum LPS levels, toll-like receptor 4 (TLR4) expression, as well as circulating cytokines.29 A previous study confirmed the activation of the LPS–TLR4 pathway in obese rats induced by the HFHFD.30 However, in our study, the results of LPS were not linear with other inflammatory cytokines (TNF-α and IL-6) and were inconsistent theoretically. This was caused by a short duration of intervention between groups.\n\nDisruption of gut microbiota also contributes to the production of SCFA such as acetic, propionic, and butyric acids. Our study elucidated that the lower levels of butyric acid were found in HFHFD group (p = 0.03). Our findings were supported by those of previous studies. Consumption of HFHFD has previously been proven to affect the homeostasis of gut microbiota and increased cholesterol levels, which is associated with increased risk of intestinal disease such as Crohn’s disease, ulcerative colitis, and colon cancer.31,32 Some supporting evidence also revealed that the levels of butyric acid in patients with ulcerative colitis and Crohn’s disease was lower than a healthy control,33 indicating that butyric acid might have a protective effect against inflammatory bowel disease. In our study, a HFHFD might contribute to the disruption of gut microbiota homeostasis and thereafter cause the impaired production of butyric acid, a type of SCFA produced by gut microbiota in the colon.34 This indicates that a HFHFD might cause a decrease of butyric acid levels.\n\nThe theory on how a HFHFD affects the levels of butyric acid remains to be properly defined. However, some previous studies have proposed a possible mechanism. Briefly, a HFHFD may cause the alteration of gut microbiota composition by reducing the Megasphaera elsdenii bacteria, a bacteria belonging to the Firmicutes group which have an ability to convert lactates into butyrate. In addition, after a HFHFD, it was reported that the beneficial Bifidobacteria and Lactobacilli, which interact with Firmicutes bacteria to produce butyric acid through cross-feeding, decreased in abundance.35,36 This possible theory may explain the proposed mechanism on how a HFHFD affects the impaired production of butyric acid.\n\nThe duration, type of diet, and genetic factors all play a role in the development of NAFLD-associated liver histology.37 In our study, steatosis, lobular inflammation, and hepatocyte ballooning were found in the HFD and WD groups, while only lobular inflammation and hepatocyte ballooning were found in the HFHFD group. NAS scores ≥ 5 were found in the WD and HFHFD groups. Although both the WD and HFHFD fulfill criteria of NASH histologically by the NAS score in the same percentage, we found a higher percentage of borderline NASH in the WD group. This result was in line with a previous study, which evaluated the effect of different diets (WD, cafeteria diet, and HFD) and found that the WD group had the highest steatosis score among others.22\n\nThe development of NAFLD/NASH is influenced by metabolic factors, inflammatory factors, and microbiota dysbiosis factors that cause changes in liver histology. Research on the appropriate diet in inducing NAFLD/NASH needs to be analyzed based on these multifactors. For metabolic factors, administration of the HFD and WD causes obesity, while the WD and HFHFD cause an increase in triglycerides. This condition was related to the high levels of TNF-α and IL-6 in the three groups. Microbiota dysbiosis is characterized by impaired SCFA production, in this case found in the HFHFD group, which has the lowest butyrate levels among others. Based on histopathology, the WD and HFHFD groups met the criteria for the occurrence of NASH, but in percentage terms, borderline NASH was higher in the WD. We found that the WD cause changes in metabolic and inflammatory markers, but has less impact in SCFA production than HFHFD. However, it had more potential in liver histology alteration. We conclude that WD is the most appropriate diet-type model for NASH studies in rats.\n\nThe limitation of this study is that it did not assess how multiple types of high-fat diets affected different rat strains. In addition, further research regarding the different duration of food consumption needs to be compared and evaluated.\n\n\nConclusions\n\nIn summary, different types of diet especially the WD significantly influenced inflammatory markers and dysbiosis for NASH progressivity in rats. The HFD group induced significant liver inflammation but did not produce NASH histologically, whereas the WD and HFHFD groups had the potential to develop NASH. So, among the four different types of diet, the WD is the most appropriate diet to induce NASH.", "appendix": "Data availability\n\nDryad. Data of Multiple Different High-Fat Diets. https://doi.org/10.5061/dryad.np5hqbzxx.38\n\nThis project contains the following underlying data:\n\n• Data file 1: Data of Normal Diet Conditioning\n\nData files contain all measurements conducted during the ND conditioning of rats, including body weight, biochemical analysis using blood samples, SCFA analysis using feces, NAS analysis through liver histology, mean, Q1, Q3, and deviation standard of each measurement.\n\n• Data file 2: Data of High Fat Diet Conditioning\n\nMeasurements conducted during the HFD conditioning of rats, including body weight, biochemical analysis using blood samples, SCFA using feces, NAS analysis through liver histology, mean, Q1, Q3, and deviation standard of each measurement.\n\n• Data file 3: Data of Western Diet Conditioning\n\nMeasurements conducted during the WD conditioning of rats, including body weight, biochemical analysis using blood samples, SCFA analysis using feces, NAS analysis through liver histology, mean, Q1, Q3, and deviation standard of each measurement.\n\n• Data file 4: Data of High Fat High Fructose Diet Conditioning\n\nMeasurements conducted during the HFHFD conditioning of rats, including the body weight, biochemical analysis using blood samples, SCFA analysis using feces, NAS analysis through liver histology, mean, Q1, Q3, and deviation standard of each measurement.\n\n• README.md\n\nREADME.md is a note that contains information and a summary of the dataset, as well as an explanation of the variables under study, the abbreviations, and units of measurement.\n\n• Related Work – Supplemental Information\n\nThis project consists of the 10 supplemental figures, the document of SCFA analysis using shimadzu, and the full ARRIVE author checklist. Data are available under the terms of the Creative Commons Attribution 4.0 International. https://doi.org/10.5281/zenodo.7583400.39\n\nData are available under the terms of the Dryad’s Term of Service and under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nReferences\n\nMitra S, De A, Chowdhury A: Epidemiology of non-alcoholic and alcoholic fatty liver diseases. Transl Gastroenterol Hepatol. 2020; 5(16): 1–17. Publisher Full Text\n\nOmagari K, Suzuta M, Taniguchi A, et al.: A non-obese, diet-induced animal model of nonalcoholic steatohepatitis in Wistar/ST rats compared to Sprague-Dawley rats. Clin Nutr Exp. 2020; 30: 1–14. Publisher Full Text\n\nChalasani N, Younossi Z, Lavine JE, et al.: The diagnosis and management of nonalcoholic fatty liver disease: Practice guidance from the American Association for the Study of Liver Diseases. Hepatology. 2018; 67(1): 328–357. 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Pharm Bio. 2018; 56(1): 567–572. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKamil RZ, Murdiati A, Juffrie M, et al.: Gut microbiota and short-chain fatty acid profile between normal and moderate malnutrition children in Yogyakarta, Indonesia. Microorganisms. 2021; 9(1): 1–15. Publisher Full Text\n\nLee G, You HJ, Bajaj JS, et al.: Distinct signatures of gut microbiome and metabolites associated with significant fibrosis in non-obese NAFLD. Nat Commun. 2020; 11(1): 1–13.\n\nMarchisello S, Di PA, Scicali R, et al.: Pathophysiological, Molecular and Therapeutic Issues of Nonalcoholic Fatty Liver Disease: An Overview. Int J Mol Sci. 2019; (20, 1948): 1–33.\n\nBuzzetti E, Pinzani M, Tsochatzis EA: The multiple-hit pathogenesis of non-alcoholic fatty liver disease (NAFLD). Metabolism. 2016; 65(8): 1038–1048. Publisher Full Text\n\nBoland ML, Oró D, Tølbøl KS, et al.: Towards a standard diet-induced and biopsy-confirmed mouse model of non-alcoholic steatohepatitis: Impact of dietary fat source. World J Gastroenterol. 2019; 25(33): 4904–4920. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDuan Y, Zeng L, Zheng C, et al.: Inflammatory Links Between High Fat Diets and Diseases. Front Immunol. 2018; 9(2649): 1–10.\n\nCedo L, Santos D, Rivas-urbina A, et al.: Human hepatic lipase overexpression in mice induces hepatic steatosis and obesity through promoting hepatic lipogenesis and white adipose tissue lipolysis and fatty acid uptake. PLoS One. 2017; 12(12): 1–14. Publisher Full Text\n\nWoodie L, Blythe S: The differential effects of high-fat and high-fructose diets on physiology and behavior in male rats. Nutr Neurosci. 2017; 21(5): 328–336. PubMed Abstract \| Publisher Full Text\n\nLee JS, Jun DW, Kim EK, et al.: Histologic and metabolic derangement in high-fat, high-fructose, and combination diet animal models. Sci World J. 2015; 2015(306326): 1–9. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBortolin RC, Vargas AR, Gasparotto J, et al.: A new animal diet based on human Western diet is a robust diet-induced obesity model: Comparison to high-fat and cafeteria diets in term of metabolic and gut microbiota disruption. Int J Obes. 2018; 42(3): 525–534. PubMed Abstract \| Publisher Full Text\n\nChen Z, Yu R, Xiong Y, et al.: A vicious circle between insulin resistance and inflammation in nonalcoholic fatty liver disease. Lipids Health Dis. 2017; 16(1): 1–9. Publisher Full Text\n\nGoyal R, Faizy AF, Siddiqui SS, et al.: Evaluation of TNF-α and IL-6 Levels in Obese and Non-obese Diabetics: Pre- and Postinsulin Effects. N Am J Med Sci. 2012; 4(4): 180–184. PubMed Abstract \| Publisher Full Text\n\nAdegbola PI, Fadahunsi OS, Ajilore BS, et al.: Combined ginger and garlic extract improves serum lipid profile, oxidative stress markers and reduced IL-6 in diet induced obese rats. Obes Med. 2021; 23: 100336. Publisher Full Text\n\nChrist A, Lauterbach M, Latz E: Western Diet and the Immune System: An Inflammatory Connection. Immunity. 2019; 51(5): 794–811. Publisher Full Text\n\nSabir U, Muhammad H, Ullah A, et al.: Downregulation of hepatic fat accumulation, inflammation and fibrosis by nerolidol in purpose built western-diet-induced multiple-hit pathogenesis of NASH animal model. Biomed Pharmacother. 2022; 150(112956): 112956. PubMed Abstract \| Publisher Full Text\n\nAn L, Wirth U, Koch D, et al.: The Role of Gut-Derived Lipopolysaccharides and the Intestinal Barrier in Fatty Liver Diseases. J Gastrointest Surg. 2022; 26(3): 671–683. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLambertz J, Weiskirchen S, Landert S, et al.: Fructose: A dietary sugar in crosstalk with microbiota contributing to the development and progression of non-alcoholic liver disease. Front Immunol. 2017; 8(1159). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLi KP, Yuan M, Wu YL, et al.: A High-Fat High-Fructose Diet Dysregulates the Homeostatic Crosstalk Between Gut Microbiome, Metabolome, and Immunity in an Experimental Model of Obesity. Mol Nutr Food Res. 2022; 66(7): 2100950. Publisher Full Text\n\nHold GL, Smith M, Grange C, et al.: Role of the gut microbiota in inflammatory bowel disease pathogenesis: What have we learnt in the past 10 years? World J Gastroenterol. 2014; 20(5): 1192–1210. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSánchez-Alcoholado L, Ramos-Molina B, Otero A, et al.: The role of the gut microbiome in colorectal cancer development and therapy response. Cancers (Basel). 2020; 12(1406): 1–29. Publisher Full Text\n\nTang X, Li X, Wang Y, et al.: Butyric Acid Increases the Therapeutic Effect of EHLJ7 on Ulcerative Colitis by Inhibiting JAK2/ STAT3/SOCS1 Signaling Pathway. Front Pharmacol. 2020; 10(1553): 1–10.\n\nOnyszkiewicz M, Gawrys-kopczynska M, Konopelski P, et al.: Butyric acid, a gut bacteria metabolite, lowers arterial blood pressure via colon-vagus nerve signaling and GPR41/43 receptors. Pflugers Arch. 2019; 471: 1441–1453. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHorne RG, Yu Y, Zhang R, et al.: High Fat-High Fructose Diet-Induced Changes in the Gut Microbiota Associated with Dyslipidemia in. Nutrients. 2020; 12(11): 3557. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMarkowiak-kope P, Śliżewska K: The Effect of Probiotics on the Production of Short-Chain Fatty Acids by Human Intestinal Microbiome. Nutrients. 2020; 12(4): 1107. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKucera O, Cervinkova Z: Experimental models of non-alcoholic fatty liver disease in rats. World J Gastroenterol. 2014; 20(26): 8364–8376. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMustika S, Santosaningsih D, Handayani D, et al.: Data of Multiple Different High-Fat Diets. Dryad. 2023. Publisher Full Text\n\nMustika S, Santosaningsih D, Handayani D, et al.: Data of multiple different high-fat diets. Zenodo. 2023. Publisher Full Text" }	[ { "id": "165523", "date": "24 Mar 2023", "name": "Pabulo Henrique Rampelotto", "expertise": [ "Reviewer Expertise Microbiome", "molecular microbiology", "metagenomics", "omics", "next-generation sequencing", "microbial ecology", "bioinformatics", "biotechnology", "system biology", "grand challenges" ], "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, the manuscript provides a comprehensive overview of the factors involved in the development of non-alcoholic fatty liver disease (NAFLD) and its progression to non-alcoholic steatohepatitis (NASH). The authors cover a wide range of topics, including the role of diet, inflammation, oxidative stress, mitochondrial dysfunction, dysbiosis of gut microbiota, and genetic factors in the pathogenesis of NAFLD/NASH.\nThe manuscript also includes data from an animal study investigating the effects of different diets on metabolic changes and inflammatory conditions. The authors provide a detailed analysis of the results, highlighting the differences in body weight, lipid profiles, and inflammatory cytokine levels between the high-fat diet (HFD), Western diet (WD), and high-fat high-fructose diet (HFHFD) groups. However, there are several areas where the manuscript could be improved.\n\nFirstly, the manuscript lacks a clear research question or hypothesis that the study aims to answer. Without a clear research question, the manuscript can come across as a collection of unrelated findings. A clearly stated research question would provide a framework for the manuscript and help readers understand the significance of the study.\nSecond, the authors could improve the clarity of the writing. Some of the sentences are overly complex and difficult to follow, making it hard for readers to understand the main points. Simplifying the language and breaking down complex ideas into smaller, more manageable pieces would help readers engage with the manuscript.\nThird, the authors should provide more detail on the methods used in the animal study. For example, the authors do not mention the number of animals used in each group, the euthanasia process (did the rats fast before euthanasia?), etc. Providing this information would help readers understand the study design and assess the reliability of the results.\nFourth, several relevant parameters for NASH models were not measured, like cholesterol, insulin, microbiota, as well as other key lipid metabolites. This should be clearly discussed as the limitations of the study.\nFifth, no discussion is provided regarding other well-established nutritional models of NASH (e.g., high-fat + choline-deficient diet). On this aspect, authors should also provide a discussion on the challenges encountered in NAFLD animal models, i.e., how to establish the optimal animal model which could mirror human disease by providing the same pathological triggers, as well as reproducible mechanisms of progression towards NASH and its complications.\n\nFinally, while the manuscript provides a good overview of the current understanding of NAFLD/NASH, there are several recent developments in the field that the authors could incorporate into the discussion. For example, recent studies have identified novel genetic variants associated with NAFLD/NASH, and there is growing interest in the role of the gut-brain axis in the pathogenesis of these conditions. Including these recent findings would help the manuscript stay up-to-date and relevant.\n\nIn conclusion, the manuscript provides a comprehensive overview of the factors involved in the development of NAFLD/NASH and presents data from an animal study investigating the effects of different diets on metabolic changes and inflammatory conditions. However, the authors could improve the manuscript by providing a clear research question, improving the clarity of the writing, providing more detail on the methods used in the animal study, and better discussing the limitations of the study in comparison with other robust experimental models of NAFLD/NASH, as well as incorporating recent developments in the field into the 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?\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": "10717", "date": "17 Jan 2024", "name": "Syifa Mustika", "role": "Author Response", "response": "1. the manuscript lacks a clear research question or hypothesis that the study aims to answer. Without a clear research question, the manuscript can come across as a collection of unrelated findings. - We have made changes in the manuscript: This study aims to compare and determine the most representative diet for inducing NASH in the Rattus norvegicus Wistar strain. In order to ascertain whether the rats have developed NASH, many parameters, including metabolic, inflammatory, and liver damage, microbial dysbiosis, and liver histology, were investigated. 2. the authors could improve the clarity of the writing. Some of the sentences are overly complex and difficult to follow, making it hard for readers to understand the main points. -Thank you for the suggestion, we have made changes on the manuscript. 3. the authors should provide more detail on the methods used in the animal study. For example, the authors do not mention the number of animals used in each group, the euthanasia process (did the rats fast before euthanasia?), etc. Providing this information would help readers understand the study design and assess the reliability of the results. - Thank you for your suggestion. The number of animals used in each group was mentioned in the Figure 1 research flow. But, to clarify this study, we mentioned the number of animals used in each group in the method section, animals, and diet sub-section. - The euthanasia process is mentioned in the animals and diet subsection and revised below: After the last diet intervention administration, the rats fasted for 12 hours but consumed water freely. After that, all groups were euthanized with ketamine–xylazine intravenously to relieve pain on the same day before surgery was performed. The blood serum and liver were taken for further testing. 4. several relevant parameters for NASH models were not measured, like cholesterol, insulin, microbiota, as well as other key lipid metabolites. This should be clearly discussed as the limitations of the study. - Thank you for your suggestion. We have made changes to the manuscript in the limitation section 5. there are several recent developments in the field that the authors could incorporate into the discussion. For example, recent studies have identified novel genetic variants associated with NAFLD/NASH, and there is growing interest in the role of the gut-brain axis in the pathogenesis of these conditions. Including these recent findings would help the manuscript stay up-to-date and relevant. - Thank you for your suggestion. We have made changes to the manuscript in the discussion section 6. the authors could improve the manuscript by providing a clear research question, improving the clarity of the writing, providing more detail on the methods used in the animal study, and better discussing the limitations of the study in comparison with other robust experimental models of NAFLD/NASH, as well as incorporating recent developments in the field into the discussion. - Thank you for your suggestion. We have made changes to the manuscript." } ] }, { "id": "163637", "date": "12 Apr 2023", "name": "Endang Sutriswati Rahayu", "expertise": [ "Reviewer Expertise Gut microbiome", "food microbiology" ], "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 discussed different high-fat diets of animal models with NASH which may affect the metabolism, inflammatory markers, dysbiosis and liver histology. Overall, the study reports interesting results. However, some revisions are needed on how the results are presented.\nThe statistical analysis, as I have filled out as partly appropriate, needs to be revised on how it is presented. In Table 1, the baseline characteristics and biochemical parameters of rats are shown. The term baseline characteristics are used for data before the intervention is done, yet the table seems to show the data after the intervention is conducted. If the data shown is after the intervention, then it is advised to change the title which also mentions the intervention period.\nThe author should mention which data is different after posthoc comparison in Table 1 (e.g., with superscript letters that can be found using the cld function in R).\nPlease refrain from using personal pronouns (i.e., We) in writing scientific papers.\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": [ { "c_id": "10718", "date": "17 Jan 2024", "name": "Syifa Mustika", "role": "Author Response", "response": "1. In Table 1, the baseline characteristics and biochemical parameters of rats are shown. The term baseline characteristics are used for data before the intervention is done, yet the table seems to show the data after the intervention is conducted. If the data shown is after the intervention, then it is advised to change the title which also mentions the intervention period. The author should mention which data is different after posthoc comparison in Table 1 - The title in Table 1 is revised to “Comparison of various diets induction in rats after 12 weeks of intervention”. The posthoc test result was presented in the graph and mentioned in the subsection below: Comparison of metabolic parameters of rats (in Figure 2) Comparison of inflammatory and liver injury of rats (in Figure 3, Figure 4, and Figure 5) Comparison of microbial dysbiosis (in Figure 6 and Figure 7) 2. Please refrain from using personal pronouns (i.e., We) in writing scientific papers. - Thank you for your suggestion. We have made changes to the manuscript" } ] } ]	1	https://f1000research.com/articles/12-180
https://f1000research.com/articles/11-378/v1	31 Mar 22	{ "type": "Research Article", "title": "Problem-based learning in research method courses: development, application and evaluation", "authors": [ "Yani Ramdani", "Nia Kurniati Syam", "Yayat Karyana", "Diar Herawati", "Nia Kurniati Syam", "Yayat Karyana", "Diar Herawati" ], "abstract": "Background: The undergraduate curriculum in Indonesia generally requires students to take a research methods course as a prerequisite course for the preparation of scientific reports. The objective of this course is to teach students how to present research results both orally and in writing using the styles and forms of each university. However, this course is not popular among students because the material is complex and technical. As a result, there is a gap between learning outcomes and their application when students prepare scientific reports. Improving pedagogy and teaching interventions through student-developed research projects is important in complementing lectures. The purpose of this study was to analyze the improvement of students' ability in writing scientific reports through research method courses using problem based learning (PBL). Methods: This study reports the integration of scientific report writing in research methods courses through PBL at the Universitas Islam Bandung in Indonesia. PBL was implemented by involving students in research-related tasks with the following stages: writing research questions, determining the research design, collecting data, analyzing data, and presenting research results. Results: The results showed that there was an increase in scientific writing skills with good categories on indicators of possible plagiarism using Turnitin, use of report preparation formats, suitability of literature, mastery of research report content in-class presentations. Conclusions: This finding implies that assigning students to write scientific reports using PBL in the research method classroom is useful for improving learning outcomes, presentation, reasoning, communication, ambiguous problem-solving, and reducing plagiarism. The findings of this study strengthen the findings of previous researchers, namely increase students' abilities in using formatting to prepare scientific reports, using appropriate literature, mastering research materials as well as reducing the level of plagiarism.", "keywords": [ "problem-based learning", "courses of research methods", "learning outcomes", "scientific reports" ], "content": "Introduction\n\nUniversities have an important role in generating new knowledge through scientific writing to develop science and create innovation in order to improve people’s lives. Scientific writing is an essential competency for a career in science. Many scientific writing techniques are contained in research methods courses. However, this course is usually less attractive to students because the material is complex and technical.1Students often do not understand the purpose of this course, so they follow it with trepidation and skepticism.2,3 As a result, students still find it difficult to apply what they have learned in research methods lectures in the preparation of proposals and thesis reports.4 Some scholars state that conventional lecture-based teaching is not effective in overcoming barriers to understanding and applying research methods.5 Improving pedagogy and teaching interventions in research methods courses is important.6–8 There are suggestions for implementing learning to develop competencies that allow students to make strategies to find new knowledge and the ability to solve problems.9 Some of the suggested learning techniques are problem-based learning (PBL),10 exploratory data analysis,11 and learning focused on research articles.12,13\n\nThe Indonesian government regulation through research and higher education technology (Peraturan Menteri Riset Teknologi dan Pendidikan Tinggi/MENRISTEKDIKTI) number 44, year 2015 states that to be able to realize graduate competency standards, the lecture model developed must be interactive, holistic, integrative, scientific, contextual, thematic, effective, collaborative, and student-centered.14 One of the learning models that meet these characteristics is problem-based learning (PBL). PBL is a learning model to develop competence.15 It is collaborative and student-centered and requires students to play an active role in re-discovering knowledge by applying the principles of constructivism based on their initial knowledge.12 This learning model promotes the exploration of new knowledge and is integrated with different courses.15\n\nThis paper explores the results of research on the application of the PBL method in a research methods course in a mathematics study program at an Universitas Islam Bandung in Indonesia. In general, in the curriculum for the Bachelor Program (S1) in Indonesia, every student must write a scientific paper called a thesis to complete their study period. To equip students in thesis writing, students must take a research methods course. The general objective of this course is to teach students how to present research results both orally and in writing using the style and form of each university. PBL allows students to construct new knowledge by relating their prior knowledge more easily.16 PBL allows students to search for information, solve problems, make decisions, work in groups, write reports, make presentations, be independent and responsible in dealing with complex problems from real life.17\n\nPBL is thought to be the right learning method to create an awareness of the important role of understanding and applying research methods for thesis completion and career development. The objective of this research was to analyze the application of the PBL method in improving the competence of students in preparing scientific reports. The indicators measured were the level of plagiarism using Turnitin, use of scientific report preparation formats, literature suitability and mastery of research report content in in-class presentations.\n\nThe characteristics of the learning process in Permenristekdikti no 44 of 2015 article 11 consist of the following characteristics:\n\n- Interactive – the learning outcomes of graduates are achieved by prioritizing the two-way interaction process between students and lecturers through offline and online teaching and learning processes.\n\n- Holistic – the learning process encourages the formation of a comprehensive mindset by internalizing local and national excellence and wisdom.\n\n- Integrative – the learning outcomes of graduates are achieved through an integrated learning process to meet the overall learning outcomes of graduates in one multidisciplinary process.\n\n- Scientific – graduate learning outcomes are achieved through a learning process that prioritizes a scientific approach to create an academic environment that is based on a system of values, norms, and scientific principles and upholds religious and national values.\n\n- Contextual – graduate learning outcomes are achieved through a learning process that is adapted to the demands of the ability to solve problems in the realm of expertise.\n\n- Thematic – graduate learning outcomes are achieved through a learning process that is adapted to the scientific characteristics of the study program and is linked to real problems through a transdisciplinary approach that is implemented through structured assignments where students are trained to solve problems taken from everyday life.\n\n- Effective – the learning outcomes of graduates are achieved effectively by emphasizing the internalization of the material properly and correctly in an optimum period.\n\n- Collaborative – graduate learning outcomes are achieved through a shared learning process that involves interaction between individual learners to produce the capitalization of attitudes, knowledge, and skills that are implemented on student projects as a group.\n\n- Student-centered – graduate learning outcomes are achieved through a learning process that prioritizes the development of creativity, capacity, personality, and student needs, as well as developing independence in seeking and finding the knowledge by applying student-centered learning methods such as problem-based learning, contextual teaching, and learning.\n\nThe above characteristics are in line with the PBL method. PBL places more emphasis on active, interactive, and collaborative learning, problem resolution, and decision-making providing opportunities for independent study and presentation18,19 to develop critical thinking and analytical skills20,21 The PBL method has advantages over conventional learning.22 This learning model has been widely applied in universities and is used to develop skills needed by the jobs market such as group work and relationships, as well as collaborative, proactive and entrepreneurial skills23,24 in the field of engineering,25–28 medicine,29,30 economics,31 pharmaceuticals,32 psychology33 and others.\n\nThe main objectives of the PBL course are (1) to encourage independent learning in students, which leads to higher motivation, better retention of material, development of reasoning, and problem-solving abilities, and (2) to develop a better understanding in students of the process and the skills necessary for successful work collaboration.1 There are similarities between PBL goals and research methods learning objectives that we have in undergraduate mathematics programs. The field of applied mathematics can be more interesting by using PBL as an alternative methodology to deal with current and future problems.24 The learning process in mathematics generally requires good reasoning skills. The PBL approach has been developed to improve students’ reasoning abilities.30\n\nThe purpose of implementing PBL in the research method classroom was to measure students’ ability to write scientific reports through problems that must be solved so as to encourage students to learn actively, have independent learning, and be able to apply mathematical problems in mathematics, mathematics in other fields, and mathematics in real life.\n\n\nMethods\n\nThis study was approved by Universitas Islam Bandung (Nomor: 500/B.04/Bak-k/XII/2019) after due consultation and all participants provided their written informed consent.\n\nThe participants were third-year students at an Universitas Islam Bandung Indonesia (a total of 40 students including nine males and thirty-one females, thirteen of whom had high abilities, eighteen were moderately capable and nine had low abilities. Information on the grouping based on gender and students’ ability levels was obtained from the Cumulative Achievement Index/GPA) enrolled in the courses of research methods. In general, each student had different abilities in thinking and communicating. One of the differences could be seen from the value of the GPA. GPA was the measure performance of student at the academic field which was obtained by combining all the grades of the courses that had been taken up to a certain semester.34 All students met the requirements agreed to: (1) case presentation, (2) conduct discussions, (3) make a summary, (4) participate in online learning, and (5) compile scientific reports.\n\nStudents and researchers in the field of science are generally trained and motivated to design, conduct experiments, and analyze data.35 PBL was carried out in three stages, namely preparation, implementation, and evaluation. First, a semester lesson plan with learning sub-achievements was developed so students could understand the meaning of research, definitions, and methods, explain research and decision-making processes, make systematic decisions, formulate research problems, present a literature review, develop a theoretical framework and formulate hypotheses, design a study and compile research proposals. Integration of research proposal writing in research methods courses was claimed to play a role in improving student research learning,36 selecting representative research samples, collecting data appropriately, measuring and designing surveys, conducting data analysis and descriptive studies and compiling reports study. Second, the case determination scenario was based on the areas of specialization determined by the mathematics study program, namely: (1) financial and industrial mathematics; (2) mathematics computer science. Research topics were then developed based on research titles proposed by students to encourage class discussion. Arguably, the most popular active learning experience in research methods courses is student-developed research projects.37 The implementation of PBL was carried out in three stages, namely case presentations, discussions, and compiling research reports. Third, evaluation: the preparation of research reports was done individually, the similarity test was determined not to be more than 25%. Students received a very good score (A) if they successfully used the report preparation format correctly, used appropriate literature, there was a maximum plagiarism rate of 25% and they mastered the content of research reports through presentations in class. On the other hand, students received a very poor score (D and E) if they reviewed research reports without showing proper understanding.\n\nThis course was designed for students who would write a final year project in mathematics. The material provided is an introduction to mathematical theory and applied mathematics, research paradigms in mathematics and their applications, and how the ontological and epistemological assumptions used by researchers affect research methods.31 This course teaches an introduction to research design and relevant research methods in the field of mathematics. It includes a discussion of various methods that can be used to solve mathematical problems and their application. Each student conducted small-scale research which was used as a pilot in the final undergraduate project. The course must be taken in the previous semester or in the same semester when students work on their final project. Lectures are held for 100 minutes every week for 16 weeks in one semester. Students were divided into eight groups. The grouping of students was based on research topics proposed by students, namely: pure mathematics (analysis and algebra) and applied mathematics (economics, industry, and computers). Each student was allocated 20 minutes for the presentation. The role of the lecturer was the facilitator during the discussion.\n\nPBL activity\n\nResearch method learning was held in the form of lectures and seminars. Teaching materials were mostly related to their small-scale research assignments. One week before the implementation of PBL, the lecturer assigned students to do homework according to research topics such as (1) searching and reading information on websites, reading the results of scientific research focusing on the goals and objectives of students’ specific research, for example, articles in published journals and books. (2) collecting 14 relevant articles and (3) making a table of other peoples’ research results containing references, abstracts, conclusions, and suggestions. The task table was used to inspire the background, objectives, methodology, findings, significance, follow-up, and references of the research. Such tasks play an important role in developing students’ learning and interest in conducting research.38,39 This research activity applies the five research phases namely: (1) writing research questions, (2) determining the research design, (3) collecting data, (4) analyzing data, and (5) presentation of research results. In general, the five-phase process for this student research project allows for the allocation of time for each phase, on average one week, except for the research methodology.1\n\nPhase 1: Creation of research questions. Students were assigned to review 14 articles that were relevant in terms of theory and method and then make a summary in tabular form. This assignment was expected to generate new ideas so that research topics could be obtained. Lecturers grouped the topics of articles collected by students into groups of specialization fields, namely, pure mathematics (analysis and algebra) and applied mathematics (economics, industry, and computers). Students formed groups based on the area of interest and brainstormed some research questions to be investigated individually. Lecturers acted as facilitators of brainstorming activities through class discussions. Each group wrote each research question proposed by each student on the blackboard. Students reviewed their ideas outside of class. This activity was carried out to avoid overlapping questions.\n\nPhase 2: Research design. The students formulated the problem and research objectives and they were approved by the lecturer. The lecturer then equipped students with materials for developing theoretical frameworks, formulating hypotheses, planning research, and compiling research proposals. Students compiled a literature review as well as a bibliography on their research proposals by examining theories that strengthen the research methods used.\n\nPhase 3: Data collection. Lectures were given on techniques for selecting representative research samples, collecting data correctly, and techniques for measuring and designing surveys. Data could be obtained by students through the Internet, books, articles, or theses. Students used these data by, for example, comparing two methods. This activity aimed to prevent students from plagiarizing other work.\n\nPhase 4: Data processing and analysis. Students prepared data files, processed data according to settlement methods, conducted consultations, discussed the results of data processing and analyses and interpreted the findings. The limited experience of students doing data analysis encouraged lecturers to play an important role providing confidence about the accuracy of student findings.\n\nPhase 5: Presentation of research results. The lecturer provided direction for the entire class to prepare presentation materials including publication style, article format, PowerPoint techniques, speaking style, presentation skills, and optimization of presentation time. Each student was given 20 minutes of presentation time followed by 10 minutes of discussion. Lecturers acted as facilitators who directed and validated findings. Research questions posed by students are presented in Table 1.\n\nIn the implementation of PBL, lecturers presented to the students the research topics they had proposed. Lecturers guide students to form groups based on keywords. The students in each group discussed and exchanged ideas and discussed theoretically the problems that would be selected in the research.\n\nThis study examined whether PBL can improve students’ competence in writing scientific reports with competencies developed including the level of plagiarism, accuracy of the use of research formats, suitability of the literature, and mastery of research material through presentations. The research hypotheses were as follows:\n\nThe research data was taken from the results of the evaluation of student research reports with similarity test indicators using Turnitin, the use of the report preparation format, the suitability of the literature, mastery of the content of research reports in-class presentations. The research was conducted twice, namely in the mid-semester exam (week eight was evaluation of stage 1) and the final exam (week sixteen was evaluation of stage 2). The results of the mid-semester exam and the final exam can be found in the underlying data.40 To increase students’ ability in compiling research reports, the normalized gain is used with the formula:\n\nWith normalized gain categories (g) are: g < 0.3 is low; 0.3 g < 0.7 is moderate; and 0.7 g is high. Hypothesis testing used Independent sample t-test (df = 95) and Wilcoxon Signed Ranks Test, which compared the average score of each stage for each indicator compared with a significance value of α = 0.05. We used IBM SPSS statistics version 22 (RRID:SCR_019096).\n\n\nResults and discussion\n\nThis study involved 40 college students (nine boys and thirty-one girls) with an average age of twenty-one years. The age and gender of students did not have a significant effect on the competence of preparing research reports. The student’s ability level (high, medium, and low) was only associated with the cumulative achievement index and was not examined in this study because every student in the research method class must be able to complete the scientific report. The increase in accuracy using the research report format was g = 0.064 including the low category, suitability using literature and research methods was g = 0.209 including the low category, and plagiarism levels was g = 0.509 including the medium category. An overview of the research data is shown in Figure 1. Table 2 describes students’ abilities in compiling research reports.\n\nThe results for stage one and stage two show that the accuracy of using the research report format, the suitability of using literature and research methods, presentation skills, and the competence of preparing research reports were normally distributed and homogeneous. While the level of similarity (plagiarism) stage one was normally distributed and stage two was not normally distributed. The results show that all hypotheses were rejected, meaning that there was a significant increase in the average score between stage one and stage two on indicators of accuracy using the research report format, suitability of using literature and research methods, presentation skills, and competence in preparing research reports with an average score at stage-1 higher than stage-2 and they fall in the good and very good categories. There is a significant decrease between the likelihood of plagiarism in stage one and stage two.\n\nThe results of the study indicated that the application of PBL in research methods courses could improve learning outcomes related to the preparation of research reports in good categories with indicators of possible plagiarism, use of report preparation formats, suitability of literature, and presentations. PBL resulted in significant improvements in learning outcomes, students’ perceptions of university social responsibility, their capacity to deal with complex and ambiguous structural problems, their ability to put professional knowledge into practice, team building, and communication skills.35 The possibility of plagiarism was reduced because the research process was monitored during the creation of research topics, research proposals and the submission of research reports.3 The PBL approach provides significant benefits for students in presentation skills.41 PBL enables students to develop information seeking, problem-solving, decision making, group work skills. and other skills such as writing reports, making presentations, independent learning, being able to face and solve complex problems in real life.17 PBL could improve learning achievement, problem solving skills, and interaction skills of students.42 PBL experiments make it easy to link previous understanding of the material with new knowledge to increase the ability to construct knowledge for students.\n\nThis article discusses a simple way to overcome one of the difficulties of students in compiling research reports. Assigning the preparation of small-scale research reports through the PBL approach in the research methods class helps students apply the theory of research methods in solving the problems they face. This approach does not require special technology so that it can be used in various conditions without having to add commitment from the lecturer. However, it requires a higher level of student participation to contribute to discussions and other activities. This learning inspires students on research that is relevant for research in the field of mathematics and its applications. Students are trained to develop different research designs and methods in collecting, processing, and analyzing data. The goal is to enable each student to find ideas that lead to the emergence of researchable questions and to determine the appropriate method to answer research questions. Students are also encouraged to develop current research issues that can be linked to other courses to enable students to conduct scientific research for thesis writing. Research methods courses should be in the same semester as the preparation of the thesis so that the material can be directly implemented. In general, before the preparation of the thesis, each student already has a proposal supervisor so that the feasibility level of research assignments in learning research methods gets an assessment from the student proposal supervisor. Of course, empirical research that examines the quality of research products provided by students in the method course will help support this claim. Finally, further research is needed to test the product of their completed research.18 Some criticisms of PBL raise concerns regarding the ability of lecturers to monitor and evaluate each student’s research project at the same time. The support needs in research writing are supervisory support, peer support,43 skills, and research development support.44 Supervision is required in three phases including 1) purification and completion of research proposals; 2) data creation; and 3) analyzing data and ‘writing it down’.45 Peer support can take the form of a peer tutor. In addition, scientific writing support is recognized as an area that all students need.46 Some PBL authors recommend the use of peer tutors to cope with demands on lecturers for larger classes.47\n\nThis study is a single study so the findings may be equivocal. In the absence of a control group, the advantages of implementing PBL cannot be compared. In addition, a standardized evaluation system is needed to review the optimization of PBL implementation. However, the research results can be used as a basis for experimentation for future research with PBL applications because it has significant challenges to develop student competencies such as reasoning, communication, problem solving, learning community, preparation of research reports, and presentations. These skills are needed by future students.\n\n\nConclusions\n\nThe results of this study indicate that the integration of research report writing through the PBL approach in the research method class can develop students’ abilities in compiling research reports. This integration is one of the best ways to engage and apply research methods theory directly in student research. The improvement in overall learning outcomes at the end of the positive PBL process indicates that integrated teaching is an effective way to reduce student barriers in compiling research reports. Students also realize that writing scientific reports is a learning process whose mastery of skills must be done through experience. Finally, some students feel trained and motivated in designing, conducting experiments, processing, and analyzing data. Based on the findings of this study, the PBL approach is recommended to support research at the undergraduate level. To ensure the quality of scientific reports, the support for scientific writing needs to get better attention. Supervision can involve other lecturers to form peer teaching. Peer support is developed to form a mutually supportive learning community.\n\n\nData availability\n\nFigshare: Underlying data for ‘Problem-based learning in-class of research methods: Development, application and evaluation’. https://doi.org/10.6084/m9.figshare.1708774740\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0)\n\n\nConsent\n\nWritten informed consent for publication of the participants’ details was obtained from the participants.\n\n\nAuthor contributions\n\nYR – Investigation, Validation, Data Curation, Visualization, and Writing – Original Draft Preparation\n\nNKS – Supervision, Conceptualization, Methodology, Project Administration – Review & Editing\n\nYK – Supervision, Conceptualization, Project Administration and Writing – Review & Editing\n\nDH – Data Collections, Writing –Review & Editing", "appendix": "Acknowledgements\n\nThank you to all the respondents who made their time available and to Universitas Islam Bandung.\n\n\nReferences\n\nBall CT, Pelco LE: Teaching research methods to undergraduate psychology students using an active cooperative learning approach. 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Publisher Full Text\n\nDuch BJ, Groh SE, Allen DE: The power of problem-based learning: a practical “how to” for teaching undergraduate courses in any discipline. Stylus Publishing, LLC; 2001." }	[ { "id": "190225", "date": "18 Sep 2023", "name": "Dean Iliev", "expertise": [ "Reviewer Expertise Methodology of Research", "Didactics", "Methodology of action research", "Life-long learning of teachers", "Social pedagogy" ], "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 topic of the article was chosen based on the experience of people who know this issue. The problem of studying research methodology exists everywhere in higher education and in the education of future teachers. Anyone who wants to improve their work and is concerned with developing the research competencies of their students will benefit from this research. The research is simple and limited in terms of research sample, but offers a sufficient basis for replication in different settings, for the same purpose. If the methodology in the paper were more complex and the statistics at a higher level, it would reduce its use and application by a greater number of our colleagues who are looking for a way to improve the study of research methodology in their classroom. I encourage other researchers and practitioners to follow this example and to create and conduct research on the impact of other contemporary learning and teaching strategies in advancing research methodology learning processes.\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": "145910", "date": "21 Nov 2023", "name": "Achmad Samsudin", "expertise": [ "Reviewer Expertise Education" ], "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:\nMethods: The research method is not yet clear. This section should include the method, is the research qualitative, quantitative, survey, case study, or what?\n\nResult: How much is it worth? Include the resulting value for the category earned.\nIntroduction:\n\nAdding research schemes, or research concept maps may be useful.\nMethods:\nDesign: The research method is not yet clear. This section should include the method, is the research qualitative, quantitative, survey, case study, or what?\n\nParticipants: It's best to present it in tabular form for (a total of 40 students including nine males and thirty-one females, thirteen of whom had high abilities, eighteen were moderately capable and nine had low abilities. Information on the grouping based on gender and students’ ability levels was obtained from the Cumulative Achievement Index/GPA) and for gain categories.\n\nAdd data analysis from IBM SPSS to the abstract.\nConclusions:\nAdd value for each result you get.\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?\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": "10704", "date": "17 Jan 2024", "name": "Yani Ramdani", "role": "Author Response", "response": "I am Author Abstract: Methods: The research method is not yet clear. This section should include the method, is the research qualitative, quantitative, survey, case study, or what? This research was a case study to report the integration of scientific report writing in research methods courses through PBL at the Bandung Islamic University, Indonesia. PBL is carried out by involving students in research-related tasks with the following stages: writing research questions, determining research design, collecting data, analyzing data, and presenting research results. Result: How much is it worth? Include the resulting value for the category earned. The research results showed that there was an increase in scientific writing skills in the good category. Normalized gain for indicators of increasing accuracy using research report formats, suitability for using literature and research methods is 0.064 and 0.209, including the low category, and the plagiarism level is 0.509, including the medium category. Introduction: Adding research schemes, or research concept maps may be useful. This article examines the results of basic research to apply the PBL method in research methods courses in the mathematics study program at the Islamic University of Bandung Indonesia. In general, in the Undergraduate Program (S1) curriculum in Indonesia, every student is required to write a scientific work called a thesis to complete their study period. To equip students to write a thesis, students must take research methods courses. The general aim of this course is to teach students how to present research results both orally and in writing using the style and form of each university. PBL allows students to construct new knowledge by connecting previous knowledge more easily. 16 PBL allows students to search for information, solve problems, make decisions, work in groups, write reports, make presentations, be independent and responsible in facing complex problems from the start. real life.17 Methods: Design: The research method is not yet clear. This section should include the method, is the research qualitative, quantitative, survey, case study, or what? This research is a case study. The participants were third-year students at an Universitas Islam Bandung Indonesia (a total of 40 students including nine males and thirty-one females, thirteen of whom had high abilities, eighteen were moderately capable and nine had low abilities. Information on the grouping based on gender and students' ability levels was obtained from the Cumulative Achievement Index/GPA) enrolled in the courses of research methods. In general, each student had different abilities in thinking and communicating. One of the differences could be seen from the value of the GPA. GPA was the measure performance of student at the academic field which was obtained by combining all the grades of the courses that had been taken up to a certain semester.34 All students met the requirements agreed to: (1) case presentation, (2) conduct discussions, (3) make a summary, (4) participate in online learning, and (5) compile scientific reports. Participants: It's best to present it in tabular form for (a total of 40 students including nine males and thirty-one females, thirteen of whom had high abilities, eighteen were moderately capable and nine had low abilities. Information on the grouping based on gender and students’ ability levels was obtained from the Cumulative Achievement Index/GPA) and for gain categories. Table 1. Data Description based Gender Gender Frequency Relative Frequency (%) Male 9 22,5 Female 31 77,5 Total 40 100 Tabel 2. Data Description based Ability Ability Frequency Relative Frequency (%) High 13 32,5 Middle 18 45,0 Low 9 22,5 Total 40 100 Add data analysis from IBM SPSS to the abstract. The research results showed that there was an increase in scientific writing skills in the good category. Normalized gain for indicators of increasing accuracy using research report formats, suitability for using literature and research methods is 0.064 and 0.209, including the low category, and the plagiarism level is 0.509, including the medium category. Conclusions: Add value for each result you get. The results of this research indicate that integrating research report writing through the PBL approach in research methods classes can develop students' abilities in compiling research reports with a significance value of 0.00. This integration is one of the best ways to engage and apply research methods theory directly in student research. The improvement in overall learning outcomes at the end of the positive PBL process indicates that integrated teaching is an effective way to reduce student barriers in compiling research reports. Students also realize that writing scientific reports is a learning process whose mastery of skills must be done through experience. Finally, some students feel trained and motivated in designing, conducting experiments, processing, and analyzing data. Based on the findings of this study, the PBL approach is recommended to support research at the undergraduate level. To ensure the quality of scientific reports, the support for scientific writing needs to get better attention. Supervision can involve other lecturers to form peer teaching. Peer support is developed to form a mutually supportive learning community. Is the work clearly and accurately presented and does it cite the current literature? Yes Is the study design appropriate and is the work technically sound? Partly Are sufficient details of methods and analysis provided to allow replication by others? Partly If applicable, is the statistical analysis and its interpretation appropriate? Yes Are all the source data underlying the results available to ensure full reproducibility? Yes Are the conclusions drawn adequately supported by the results? Yes Competing Interests No competing interests were disclosed." } ] } ]	1	https://f1000research.com/articles/11-378
https://f1000research.com/articles/12-107/v1	27 Jan 23	{ "type": "Review", "title": "Mechanisms behind the pharmacological application of biochanin-A: a review", "authors": [ "P.V. Anuranjana", "Fathima Beegum", "Divya K.P", "Krupa Thankam George", "G.L. Viswanatha", "Pawan G. Nayak", "Abhinav Kanwal", "Anoop Kishore", "Rekha R. Shenoy", "K. Nandakumar", "P.V. Anuranjana", "Fathima Beegum", "Divya K.P", "Krupa Thankam George", "G.L. Viswanatha", "Pawan G. Nayak", "Abhinav Kanwal", "Anoop Kishore", "Rekha R. Shenoy" ], "abstract": "This review was aimed at summarizing the cellular and molecular mechanisms behind the various pharmacological actions of biochanin-A. Many studies have been reported claiming its application in cancers, metabolic disorders, airway hyperresponsiveness, cardiac disorders, neurological disorders, etc. With regard to hormone-dependent cancers like breast, prostate, and other malignancies like pancreatic, colon, lung, osteosarcoma, glioma that has limited treatment options, biochanin-A revealed agreeable results in arresting cancer development. Biochanin-A has also shown therapeutic benefits when administered for neurological disorders, diabetes, hyperlipidaemia, and other chronic diseases/disorders. Isoflavones are considered phenomenal due to their high efficiency in modifying the physiological functions of the human body. Biochanin-A is one among the prominent isoflavones found in soy (glycine max), red clover (Trifolium pratense), and alfalfa sprouts, etc., with proven potency in modulating vital cellular mechanisms in various diseases. It has been popular for ages among menopausal women in controlling symptoms. In view of the multi-targeted functions of biochanin-A, it is essential to summarize it's mechanism of action in various disorders. The safety and efficacy of biochanin-A need to be established in clinical trials involving human subjects. Biochanin-A might be able to modify various systems of the human body like the cardiovascular system, CNS, respiratory system, etc. It has shown a remarkable effect on hormonal cancers and other cancers. Many types of research on biochanin-A, particularly in breast, lung, colon, prostate, and pancreatic cancers, have shown a positive impact. Through modulating oxidative stress, SIRT-1 expression, PPAR gamma receptors, and other multiple mechanisms biochanin-A produces anti-diabetic action. The diverse molecular mechanistic pathways involved in the pharmacological ability of biochanin-A indicate that it is a very promising molecule and can play a major impact in modifying several physiological functions.", "keywords": [ "Biochanin-A", "Isoflavones", "Mechanism", "Cancer", "Diabetes", "Neuroprotection", "Cardiovascular", "Anti-oxidant" ], "content": "1. Introduction\n\nBiochanin-A, a phytochemical obtained from soy, alfalfa sprouts, red clover plants, chickpeas, etc., has recently gained attention in research due to its various pharmacological applications (Ferrer and Thurman, 2013). It has the potency to benefit humans in various systems. Biochanin-A has been tested for its effect in various cancers, inflammation, osteoarthritis, metabolic disorders, cardiovascular diseases, anti-oxidant properties, hormone-dependent diseases, etc (Sehdev, Lai and Bhushan, 2009; Kole et al., 2011; Szliszka et al., 2013; Bhardwaj et al., 2014; D. Q. Wu et al., 2014). Biochanin-A has been shown to have a potential neuroprotective impact by modulating multiple critical neurological pathways. Further, biochanin-A is a chief phytoconstituent of the red clover plant, which is well known for alleviating menopause symptoms through its oestrogenic and antioxidant properties (Romm et al., 2010; Raheja et al., 2018). Patients with prostate and breast malignancies have proven to show a defensive effect from an isoflavone-rich diet with evidence to various epidemiological studies and the mechanism behind such an action is by isoflavone and oestrogen receptor binding resulting in osteoprotective actions (Messina and Hilakivi-Clarke, 2009; Shu et al., 2009; Lecomte et al., 2017). Common dietary mixtures have gained consideration because of their synergistic impacts with several anticancer drugs seen in different kinds of malignancy. The pleiotropic effects of isoflavones on tumour cells work through modulation of various cellular signalling pathways. As indicated by various in vitro investigations, genistein is more powerful than biochanin-A as far as both oestrogenic activity and cancer prevention ability are concerned (Ullah et al., 2009). However, biochanin-A is effectively changed over to genistein in first-pass digestion, and genistein can be identified in human plasma after treatment with biochanin-A (Setchell et al., 2001).\n\nAdministration of isoflavones is known to produce a significant pharmacokinetic problem identified with their deprived bioavailability (Passamonti et al., 2009). Isoflavones are non-nutrient plant components and a subclass of flavonoids. They principally exist as β-glucosides (Panche, Diwan and Chandra, 2016). Higher content of biochanin A is found in red clover plants (Lemežienė et al., 2015). The harmful clastogenic effect presented in genistein is less exhibited in biochanin-A, adding to its more clinical acceptance (Snyder and Gillies, 2002; Michael McClain et al., 2006). Mutagenicity related to geinstein use is not presented in biochanin-A associated studies. The low incidence of cancer exhibited in the Asian population has been a widely discussed topic globally (Jin et al., 2016; Tran et al., 2018). It has a close connection to the soy-rich diet of the population (Hawrylewicz, Zapata and Blair, 1995; He and Chen, 2013; Wei et al., 2017; Ziaei and Halaby, 2017). Soy isoflavones have significance over selective oestrogen receptor modulators (SERMs) and hormone replacement in breast cancer treatment as they possess oestrogen-like rings in their structure (Sarkar et al., 2009). Though there are no conclusive reports, isoflavones are preferred by women due to their best safety profile and improved quality of life in comparison with hormone replacement therapy to treat menopausal symptoms (Franco et al., 2016; Ahsan and Mallick, 2017; Chen, Ko and Chen, 2019). Thus, this review was focused on summarizing the pharmacological applications of biochanin-A along with the various cellular and molecular pathways involved in it. The deprived water solubility along with minimal oral bioavailability confined the application of biochanin-A as a drug molecule. Nano-sized biochanin-A phospholipid complex “nBCA-PLCs” have the potential to overcome this limitation and boost its oral bioavailability. When compared to other formulations such as normal biochanin-A phospholipid complex and the suspension of biochanin-A, nBCA-PLCs have relatively higher bioavailability (Singh et al., 2021). There is compelling evidence that biochanin-A is a bioactive compound with a wide range of biological and pharmacological activities. To help understand the beneficial and myriad therapeutic effects of biochanin-A, our review evaluated past and current findings of the literature and proposed molecular mechanisms behind various disorders such as different types of cancers, diabetes, airway and cardiovascular disorders, neurological disorders etc.\n\n\n2. Biochanin-A and its pharmacological benefits\n\nBiochanin-A has shown efficacy against different types of cancers. Figure 1 depicts the types of cancers where biochanin-A has an impact in controlling the disease. Various kinds of cancer are a) breast cancer, b) prostate cancer, c) lung cancer, d) pancreatic cancer, e) colon cancer, f) osteosarcoma, g) glioma, h) leukaemia. The molecular structure of biochanin-A is depicted in the centre of diagram.\n\nBiochanin-A has shown efficacy against different types of cancers. a) breast cancer, b) prostate cancer, c) lung cancer, d) pancreatic cancer, e) colon cancer, f) osteosarcoma, g) glioma, h) leukaemia. The molecular structure of biochanin-A is depicted in the centre of diagram.\n\n2.1.1 Breast cancer\n\nBreast cancer is the most widely reported form of cancer, presented with several subtypes and varying vulnerability to anti-cancer agents. Tumour cells have shown a unique pattern in terms of uncontrolled growth, dedifferentiated morphology, and resistance to apoptosis (Baba and Câtoi, 2007). During breast cancer development the normal signalling pathways are interrupted, stimulating the refractory growth, no cell death, and progressive invasion to neighbouring tissues. Soy-rich diets in controlling hormone-dependent cancers have gained wide attention lately (Shu et al., 2009; Kang et al., 2010; Varinska et al., 2015). Good levels of isoflavones in serum serve as protection from the risk of breast cancer (Kang et al., 2010). Various studies have been tested for the effect of biochanin-A being one of the most beneficial constituents of red clover and soy isoflavones on breast cancer. Unlike chemical agents such as chemotherapeutic agents, isoflavones have shown zero toxicity to humans (Pop et al., 2008).\n\nWith the influence of biochanin-A, HER2 receptor activation is inhibited, resulting in blockade of downstream signalling pathways of cancer cell development, viability, and metastasis. In HER2-positive breast cancer, the transcriptional unit nuclear factor (NF)-κB is suppressed (Sehdev, Lai and Bhushan, 2009). MAPK or ERK 1/2 phosphorylation is inhibited causing the poor mitogenic effect (Sehdev, Lai and Bhushan, 2009; Bhardwaj et al., 2014). The major downstream signalling pathway Akt is dephosphorylated, consequently down-regulates the mTOR signalling pathway which regulates the cell cycle in SK-BR-3 breast cancer cells (Sehdev, Lai and Bhushan, 2009). MMP-9 enzyme which facilitates metastasis of cancer cells using the extracellular matrix is repressed in SK-BR-3 cells treated with biochanin-A (Sehdev, Lai and Bhushan, 2009). Flavonoids, having structural similarity to oestrogens, enable oestrogen receptor binding, and possess anti-oestrogenic and oestrogenic properties. Phytoestrogen inhibits oestrogen alpha receptors hence effective in oestrogen receptor-based treatment for breast cancer (Collins, McLachlan and Arnold, 1997; Le Bail et al., 1998). Reducing endogenous oestrogen levels in the body by inhibition of enzymes such as HSD and Cyp19 would defend against breast cancer. Phytoestrogen intake decreases oestrogen biosynthesis and prolongs menstrual cycle length thereby decreases lifetime exposure to oestrogen (Mense et al., 2008). Biochanin A which is an AhR activator act as a cell cycle apoptotic stimulator, inhibiting DMBA (7,12 Dimethylbenz [a]anthracene) which can implicate in hormone-dependent cancer therapy and prevention (Han, Ji and Hye, 2006; Medjakovic and Jungbauer, 2008). Biochanin-A inhibits CYP19 and negatively affects the synthesis of oestrogen in the body which enhances the anti-oestrogenic property in hormone-influenced cancer such as prostate cancer and breast cancer (Mense et al., 2008). Biochanin-A when combined with genistein and daidzein, significantly reduced Cyp19 enzyme activity and eliminated transcription of Cyp19 mRNA (Rice, Mason and Whitehead, 2006). Biochanin-A blocks the cell proliferation in ER+ve MCF7 breast cancer cells (Collins, McLachlan and Arnold, 1997). Oestradiol inhibition of biochanin-A at half maximal inhibitory concentration (IC50) dose is found with the highest inhibitory effect to 3-galactosidase action. The anti-oestrogenic activity of biochanin A follows a mechanism analogous to tamoxifen (Collins, McLachlan and Arnold, 1997). Topoisomerase II inhibition affects DNA replication. Biochanin-A through Topoisomerase II inhibition prevented the mammary tumor growth in N-nitro-N-methyl urea treated rat, interleukin 2-dependent CTLL-2 cells (Azuma et al., 1995; Gotoh et al., 1998). Biochanin-A has shown synergism with 5-fluorouracil (5FU) in oestrogen receptor (ER) positive breast cancer cell lines such as triple-negative breast cancer cells, MDA-MB231 and MCF7. The combination of 5FU and biochanin-A producing a synergistic anti-tumour effect partly attributed to the inhibitory capability of biochanin-A through ER-α/Akt (Mahmoud et al., 2022). The mechanism of action of biochanin-A in breast cancer by dephosphorylation of HER-2 receptor and MAPK or ERK1/2 causing blockade of cancer cell development, growth, metastasis, and mitogenesis, the inhibition of Akt phosphorylation and downregulation of mTOR signals that disrupt the cell cycle, the inhibition of NF-kB and interrupted transcription and blockade of topoisomerase-II and DNA replication is depicted in Figure 2.\n\nBiochanin-A dephosphorylates HER-2 receptor and MAPK or ERK1/2 causing blockade of cancer cell development, growth, metastasis, and mitogenesis. Biochanin-A inhibits Akt phosphorylation thereby downregulates mTOR signals and disrupts the cell cycle. It inhibits NFkB and interrupts transcription. It inhibits topoisomerase-ll and DNA replication (Azuma et al., 1995; Gotoh et al., 1998; Sehdev, Lai and Bhushan, 2009; Bhardwaj et al., 2014).\n\n2.1.2 Prostate cancer\n\nProstate cancer has been reported as a commonly found cancer in men and the second prominent death reason in western countries (Siegel, Miller and Jemal, 2020). Diet can influence the prostate carcinogenesis process (Bostwick et al., 2004). Isoflavone contained dietary intake had presented with an association of reduced prostate cancer risk in different countries (Jacobsen, Knutsen and Fraser, 1998; Applegate et al., 2018).\n\nBiochanin-A elevates the level of testosterone-UDPGT (Uridine 5′-diphospho-glucuronosyltransferase) enzyme activity and disrupts the androgen metabolism in connection with UDP-glucuronic acid. PLK-1 (Polo-like kinase-1) is responsible for various cell cycles activities such as Cdc2 (Cyclin-dependent kinase) stimulation and mitosis. Biochanin-A induces p21 which is a negative regulator for PLK-1 leading to prostate cancer cell apoptosis (Seo et al., 2011). The EGF (epidermal growth factor)-stimulated growth of cell lines, such as DU-145 and LNCaP prostatic cancer, were inhibited by biochanin-A without affecting its autophosphorylation. Biochanin-A has shown inhibitory behaviour in prostate cancer by antagonizing tyrosine kinase events within the signal transduction pathway (Peterson and Barnes, 1993). The level of testosterone and development of prostate carcinoma in Lobund-Wistar rats were influenced through a soy-rich diet, signifying preventive action of soy isoflavones in prostate cancer (Pollard, Wolter and Sun, 2000). Using the orthotopic prostate tumour animal model, the influence of soy proteins on cancer advancement has been studied. PSA androgen sensitivity, and cancer metastasis was inhibited significantly by different soy-derived compounds (Zhou et al., 2002). ER-β, when activated in prostate cells, inhibits cell proliferation, and exerts anti-cancer effects. Red clover supplemented diet in mice exhibited increased ER-β and E-cadherin levels leading to the disruption of cell morphology and cancer formation (Slater, Brown and Husband, 2002). Biochanin-A in a LNCaP cell line induced apoptosis incorporated by 3H-thymidine with increased DNA fragmentation, low p21, and cyclin B expression. Animal study with LNCaP xenografts, biochanin-A subsided the prostate cancer load and size of the tumour (Rice et al., 2002). The prostatic androgen 5α-dihydrotestosterone synthesized using a 5α-reductase enzyme which is responsible for prostate cell development and function has been influenced by biochanin-A, thus generate a role in the prevention of prostate malignancy (Evans, Griffiths and Morton, 1995).\n\nPhytoestrogens have been predicted as compounds liable for chemoprotective activity on prolonged exposure. Prostatic cell proliferation in PC-3, LNCaP, and DU145 were inhibited by biochanin-A with variable mechanisms (Hempstock, Kavanagh and George, 1998). Aromatase enzyme has an impact on the level of oestrogen. Biochanin-A upon competitive inhibitory action on aromatase minimizes oestrogen level and exhibit anti-cancer activity (Campbell and Kurzer, 1993). TRAIL-induced cell death is an epitome in cancer prevention. Biochanin-A through deactivating NF-kB and death receptor (DR) 4/5 mediated caspases causes TRAIL-associated cell death in prostatic cancer cell lines (Szliszka et al., 2013). Increased activity of UDP-glucuronosyltransferase (UDGPT) is found in biochanin-A-exposed LNCaP cells. It enhanced intracellular glucuronidation of testosterone, steroid UDGPT transcript, and lowered prostate-specific antigen (PSA), hence showed an effect in prostate cancer prevention (Sun et al., 1998). The patients with clinically significant prostate cancer were treated with red clover isoflavones such as biochanin-A before surgical intervention. Markedly, higher apoptosis was found in the treatment group, indicates cessation of prostate cancer progression in low- moderate grade malignancy (Jarred et al., 2002).\n\nIn Figure 3 the inhibition of aromatase enzyme and lowering of oestrogen level by biochanin-A, the activation of p21 and antagonization of PLK-1 action, increased level of testosterone UDGPT enzyme disrupting androgen metabolism with the treatment of biochanin-A, the interrupted level of tyrosine kinase blocking the signal transduction, the prompted ER- β and E-cadherin level leading to the inhibition of cell proliferation, via biochanin-A inhibition of NF-kB inducing the TRAIL associated apoptosis and the increased conversion of testosterone into glucuronide resulting low appearance of prostate-specific antigen (PSA) is illustrated.\n\nBiochanin-A inhibits aromatase enzyme and decreases estrogen levels. It activates p21 and antagonizes PLK-1 action. Increased level of testosterone UDGPT enzyme disrupts androgen metabolism with the treatment of biochanin-A. The level of tyrosine kinase is interrupted and inhibits signal transduction. It induces ER-β and E-cadherin and inhibits cell proliferation. Biochanin-A inhibits NF-kB and induced TRAIL associated apoptosis. It increased conversion of testosterone into glucuronide resulting low appearance of prostate-specific antigen (PSA) (Sun et al., 1998; Seo et al., 2011; Szliszka et al., 2013).\n\n2.1.3 Lung cancer\n\nCancer affecting the most vital body parts elucidate the difficulty of its therapy. Lung cancer has often been reported and is one of the supreme death causes in cancer patients. The fight against cancer with phytochemicals will benefit mankind greatly. Studies have been carried out on soy isoflavones, utilized as an integral system for the treatment and to boost the radiation viability on lung tumors (Hillman and Singh-Gupta, 2011; Singh-Gupta et al., 2011). Soy-rich foods may reduce the likelihood of lung malignant growth in the general population, according to epidemiology researches (Yang et al., 2011). Like genistein which has proven its effectiveness in cancer, biochanin-A displays anti-cancer properties in lung tissue.\n\nThe mechanism with which soy isoflavones boost radiation therapeutic effect is through inhibiting APE1/Ref-1 DNA repair in A549 cells, which leads to cell killing (Singh-Gupta et al., 2011). Soy isoflavones exhibited a synergistic effect and significantly improved the radiation-induced cell killing. in vitro observation on biochanin-A treatment in 95D and A549 lung cancer cells revealed that the level of P21 (cyclin dependent kinase-1), Caspase-3, and Bcl-2 were stimulated causing cell cycle arrest and death. Dose-proportional apoptosis and prevention of DNA replication in the S phase by biochanin-A were observed. A good level of caspase-3 and reduced Bcl-2/Bax proportion facilitates apoptosis and lung cancer prevention (Li et al., 2018). Biochanin-A elicited pro-inflammatory properties beneficial to anti-cancer effect in lung cancer. AML 193 and A427 were tested with exposure of biochanin-A, the release of IL-6 cytokines and TNF-α, low level of E cadherin, and Snail blocking to epithelial–mesenchymal transition (EMT) which is essential in tumour growth and metastasis (Wang, Li and Chen, 2018). In an in vivo study with benzo(a)pyrine-induced lung cancer, the biochanin-A treated group had displayed a marked decrease in the development of tumour at a dose less than dose causing a 10% lethality (LD10) (Lee et al., 1991). When soy and red clover extracts were tested in NSCLC in combination with anti-cancer agents like gefitinib, erlotinib, afatinib, and osimertinib, the results were satisfactory. Particularly, the red clover extract which essentially contains biochanin-A showed a synergic effect with EGFR inhibitors and significant inhibition of tumor growth (Ambrosio et al., 2016).\n\nFigure 4 demonstrates the apoptotic pathway by biochanin-A on lung cancer. p21, caspase-3, and Bcl-2 levels are elevated by biochanin-A, which causes lung cancer to undergo apoptosis. Both metastasis and E-cadherin are reduced. TNF-a, IL-6, and cytokines are only a few examples of the pro-inflammatory mediators that are generated to aid in apoptosis. Soy isoflavones along with radiation therapy shows a synergistic effect in causing cell death by inhibiting APE/Ref-1 as depicted in the figure.\n\nBiochanin-A cause apoptosis in lung cancer by increasing p21, caspase-3, and Bcl-2 levels. It lowers E-cadherin and blocks metastasis. Pro-inflammatory mediators such as TNF-α, IL-6, and cytokines are released to facilitate apoptosis. Soy isoflavones along with radiation therapy shows a synergistic effect in causing cell death by inhibiting APE/Ref-1 (Singh-Gupta et al., 2011; Li et al., 2018; Wang, Li and Chen, 2018).\n\n2.1.4 Pancreatic cancer\n\nThe low survival rate of pancreatic cancer with limited anti-cancer agents makes it difficult to manage the disease. It is also known to be the most aggressive one among other cancers (Baghurst et al., 1991; Moore et al., 2003). Mutations in the tumour-suppressor and tumour-promoting gene are attributed to the aggressiveness of the disease (Saif, 2007). Association with high-calorie diet and increased incidence of pancreatic cancer are reported (Lowenfels and Maisonneuve, 2005; Li, 2009; Arslan et al., 2010; Chang et al., 2017). Consequently, it is important to conduct research on the role of isoflavones in pancreatic cancer (Silverman et al., 1998). Biochanin-A had a negative influence on pancreatic cancer progression with variable mechanisms.\n\nThe cluster formation ability of pancreatic cancer cells Panc1 was hindered by biochanin-A with dose-dependent toxicity. It inhibited mitosis, migration, and invasion of pancreatic cancer progression. EGFR, Akt, and MAPK pathways are deactivated resulting in apoptosis in Panc1 and AsPC-1 cell lines suggesting combination therapy with biochanin-A could be considered for treatment (Bhardwaj et al., 2014). Biochanin-A along with atorvastatin enhanced anti-cancer properties on AsPC1, MIAPaCa-2, and PANC-1 cell lines by lowering cell invasiveness and cell cycle progression. Biochanin-A interferes with cell survival by decreasing MAPK and Akt hence affects mitogenic signalling (Desai et al., 2018). Concentration-dependent cellular invasiveness and migration are found with biochanin-A by reducing the level of matrix metalloproteases (MMP) indicating pancreatic cancer cell migration is inhibited (Bhardwaj et al., 2014).\n\n2.1.5 Colon cancer\n\nIt is the most prevalent type of cancer in existence today. Statistics by the American Cancer Society, 2019, shows that colon cancer is the second leading source of mortality in cancer. As specified by American Institute for Cancer Research and World Cancer Research Fund reports dietary factors may elucidate the risk of having colorectal cancer. Intake of isoflavone-contained food like soy influences gastric cancer occurrence (Yan, Spitznagel and Bosland, 2010; Ko et al., 2013).\n\nThe synergism of biochanin-A with 5-fluorouracil evidenced in Caco-2 and HCT-116 cell lines indicates the modulatory influence of biochanin-A in colon cancer treatment. The biochanin-A on its own shows cytotoxicity in the cell lines. It blocked the “Akt and GSK3β phosphorylation and boosted the degradation of β-catenin” (Mahmoud et al., 2017). Biochanin-A when combined with gamma radiation on HT29 cells, which is resistant to radiation, had revealed a reduction in cell proliferation. Raised levels of ROS, lipid peroxidation, MMP, caspase-3 have been observed more in the treatment group with significant apoptosis (Puthli, Tiwari and Mishra, 2013). Biochanin-A and other isoflavones displayed a growth-retarded effect on HCT-116/SW-480 in a time and dose-reliant manner (ZHANG et al., 2013). Stomach cancer cell lines SH101-P4, HSC-45M2, HSC-41E6, and colon cancer cell lines have been treated with isoflavones including biochanin-A and observed cytostatic effect. DNA fragmentation, chromatin condensation, and nuclear fragmentation of each cell line are seen with the apoptotic result (Yanagihara et al., 1993). Oestrogen sensitive cancer cell lines including colon cancer cell 320DM when treated with biochanin-A and other isoflavones revealed antiproliferative effect which is beneficial as a cancer preventative (Kohen et al., 2007).\n\nThe inhibitory mechanism of biochanin-A on colon cancer is shown in Figure 5 explaining biochanin-A when given in combination enhanced the anti-cancer effect exerted by 5-fluorouracil and gamma radiation in colon cancer cells. Biochanin-A has inhibited Akt and GSK3β phosphorylation.\n\nBiochanin-A boosted the anti-cancer effect exerted by 5-fluorouracil and gamma radiation when given in combination in colon cancer cells. Biochanin-A has inhibited Akt and GSK3β phosphorylation (Puthli, Tiwari and Mishra, 2013; Mahmoud et al., 2017).\n\n2.1.6 Glioma\n\nGlioblastoma multiforme (GBM), the most widely reported and destructive brain malignancy, has a high death rate. GBM tends to reappear since it displays both intra- and inter-tumoral heterogeneity (Shergalis et al., 2018). The therapy becomes especially challenging due to the existence of BBB and rapid penetration to neighbouring tissue (Desai and Bhushan, 2017). The chemo preventive and anti-angiogenic properties of isoflavones along with refining the adequacy of chemotherapy and radiotherapy for the treatment of GBM have received much attention lately (Tedeschi-Blok et al., 2006; Sarkar et al., 2009).\n\nIn a dose-dependent manner, biochanin-A influenced the tumour invasion capacity by lowering matrix-degrading enzymes (MMP 2 and MMP 9) tested in U87MG cells (Puli, Lai and Bhushan, 2006). Biochanin-A inhibited endothelial cell functions in rat brain tumour, brain endothelial cells, and chick chorioallantoic membrane model with its anti-angiogenic properties through ERK/AKT ex vivo/mTOR dephosphorylation (Jain, Lai and Bhushan, 2015). Biochanin-A along with temozolomide disclosed exceptional anti-cancer activities in human glioblastoma cells, U87 MG, and T98-G. Biochanin-A by lowering EGFR, p-ERK (Extracellular signal related kinases), p-AKT (Protein kinase-B), c-myc, and MT-MMP1 (Membrane type matrix metalloproteinase) activation, inhibited cell survival. It influenced the abilities of cancer cells in viability, DNA repair, proliferation, and cell cycle arrest. Biochanin-A synergistically improved temozolomide anti-cancer ability in GBM (Desai et al., 2019). Biochanin-A augments temozolomide by lowering the number of colonies and p-EGFR, p-ERK, uPAR (Urokinase type plasminogen activator receptor), MMP-2 levels in GBM cells (Jain, Lai and Bhushan, 2011). Biochanin-A has proven to be a better candidate in GBM management in comparison with other isoflavones. It is understood that biochanin-A exhibits neuroprotective effect in a multimodal treatment methodology via testing in glioma cells (in vitro), IP injection to tumour-implanted Fisher rats (in vivo), and organotypic brain slices as ex-vivo experiments (Sehm et al., 2014). Cell signalling pathways MAP kinase, PI3 kinase, mTOR, matrix metalloproteases, hypoxia-inducible factor, and VEGF were inhibited by biochanin-A, making it suitable in treating GBM (Bhushan, Jain and Lai, 2015). In glioma C6 cells, the activation of ERK/Akt, the pro-angiogenic proteins were blocked by biochanin-A, and also VEGF and HIF-1α (hypoxia-inducible factor 1 alpha) were inhibited (Jain, Lai and Bhushan, 2015). While testing the effect of rapamycin combined with biochanin A in U87 glioma cells, there was decrease in cancer invasion and matrix-degrading enzymes. The combination dephosphorylated Akt and eIF4E (Eukaryotic translation initiation factor) augmenting rapamycin drug effect (Puli, 2006). In individuals with glioblastoma, tolerance to temozolomide (TMZ) chemotherapy is the most common cause of the relapse of GBM. Biochanin-A was found to be a strong TMZ sensitizer in GBM, by increasing the cell sensitivity through AMPK/ULK-1 pathway (Dong et al., 2022).\n\n2.1.7 Osteosarcoma\n\nOsteosarcoma (OS), a malignant bone tumour, is generally seen in children and adolescents. The low survival rate of OS is associated with drug resistance causing the poor response to chemotherapy. Hence, phytochemicals that can contribute to OS treatment are significant.\n\nBiochanin-A and doxorubicin together suppressed the tumour development by promoting the release of apoptotic factors, damaging mitochondrial membrane potential, eliciting “the intrinsic mitochondrial pathway, caspase-9 and -3 activation” and increasing “Bax: Bcl-2/Bcl-XL ratio” (Hsu et al., 2018). MG63 and U2OS osteosarcoma cells treated with biochanin-A revealed cytotoxicity at the molecular level. It is an apoptosis inducer (caspase-3), cell proliferation and invasion inhibitor, and dephosphorylates PCNA (proliferating cell nuclear antigen) and cyclin D1 gene expression (Zhao et al., 2018b). The expression of caspase-3 controlled by biochanin-A while regulating cell death is one possible mechanism to manage osteosarcoma. With the molecular docking technique it was found that certain proteins were identified as effective targets of biochanin-A for osteosarcoma. Among those “BGLAP, BAX and ATF3” were recognized as the potential target of interest in blocking cancer cell proliferation using biochanin-A (Luo et al., 2019). Biochanin-A tested in MG63 and U2OS cell lines exhibited a time and dose-related inhibitory effect on cancer proliferation, cell death, infiltration, and metastasis (Zhao et al. 2018b).\n\n2.1.8 Leukaemia\n\nLeukaemia or blood cancer affects the most important connective tissue of our body: blood, and the blood-forming tissue. It is considered a deadly and serious form of cancer (Leukaemia Care, 2020). However, isoflavones have revealed their protective role in several investigations (Xu et al., 2008). Soy derivative isoflavones obstruct the cell cycle of leukemic cells (Yamasaki et al., 2007).\n\nBiochanin-A in JCS cells prompted monocytic differentiation to macrophages (markers “Mac-l and F4/80”) showing increased phagocytic activity. The cytokines production (“IL-la, IL-lo, IL-4 and TNF-α”) is regulated in the late stage of monocytic differentiation of JCS cells by biochanin-A (Fung et al., 1997). Biochanin-A affects intracellular antioxidant response system via Nrf2-Anti oxidant response element signalling pathway in tert-butyl hydroperoxide (t-BHP)-induced oxidative damage in HepG2 cell line. Biochanin-A binds to Keap1’s pocket, causing Nrf2 signalling to be activated. These results suggest that dietary isoflavones may protect liver cancer patients from oxidative damage (Liang et al., 2019).\n\nAnti-cancer effects of biochanin-A substantiated through in vivo and in vitro experiments is summarized in Table 1.\n\n(↑increase, ↓decrease or × inhibit, + activation).\n\n2.2.1 Diabetes\n\nDiabetes mellitus, an age-old metabolic disorder, has a high rate of occurrence around the world. It is described as “hyperglycaemia” caused by deformities in insulin secretion, insulin activity, or both (American Diabetes Association, 2009). The long-term presence of diabetes is associated with many other complications. Even though currently, accessible medications might be significant in the control of diabetes, these medications are joined with certain side effects as well. A few varieties of phytochemicals have shown potential for the management of diabetes with minor or no side effects (S.Mohana Lakshmi, Rani and Reddy, 2012; Surya et al., 2014). Bioflavonoids are remarkable for their hypoglycaemic abilities (Vinayagam and Xu, 2015). It has been exhibited that flavonoids can go about as “insulin secretagogue or insulin-mimetic agents” (Patel et al., 2012; Singh and Sahu, 2018).\n\nBiochanin-A action in streptozotocin-induced diabetic rats displayed improved glucose digestion and dropped HbA1C levels. Serum visfatin amount was enhanced (Azizi, Goodarzi and Salemi, 2014). STZ diabetic rats on oral treatment with biochanin-A exposed anti-diabetic properties by lowering FBS and hyperglycaemia-induced free radicals (Sadri et al., 2017). Red clover extract was tested in “db/db diabetic mice” to see the anti-diabetic and anti-hyperlipidemic activities. Increased hepatic PPARα/γ stimulation and reduced hepatic fatty acid synthase levels contributed to achieving glucose and lipid homeostasis by red clover compounds (Qiu, Ye, et al., 2012b). STZ-diabetic C57BL/6 mice were treated with red clover extracts including biochanin-A and formononetin. The lipid profile of the animal was influenced by biochanin-A rather than glucose levels through mechanisms in connection with hepatic PPARa (Qiu, Ye, et al., 2012a). The raised levels of plasma glucose, HbA1C, and gained weight were normalized with biochanin-A treatment (Harini, Ezhumalai and Pugalendi, 2012). At certain doses, biochanin-A reduced glucose tolerance and insulin resistance, developed insulin sensitivity and increased SIRT-1 expression which might explain the anti-diabetic properties of the drug (Oza and Kulkarni, 2018). Biochanin-A acts as a strong PPAR receptor activator (PPARalpha/PPARgamma) even at low doses signifying its anti-diabetic and anti-hyperlipidaemic properties (Shen et al., 2006). Nesfatin-1, a regulatory peptide level, and insulin were increased upon biochanin-A treatment in type-1 diabetic rats, which can hint to its one probable mechanism behind the hypoglycaemic property (Eskandari Mehrabadi and Salemi, 2016). The structural relationship and activity of biochanin-A and other isoflavones were checked. Biochanin-A derivative (7-diethyl phosphite-O-biochanin-A) had shown greater anti-hyperglycaemic activity compared to all other compounds (Wei et al., 2017). The role of serum adiponectin and serum resistin as a glucose metabolism regulator in diabetes is discoursed and it is found that biochanin-A improved adiponectin release and augments insulin activity. The elevated resistin usually observed in the type-1 diabetic condition is decreased after biochanin-A intake. The oxidative stress produced in diabetes was also taken care of by biochanin-A (Salemi et al., 2018).\n\nThe influence of biochanin-A in diabetic neuropathy using an STZ-induced rat model revealed that, mechanical allodynia and hyperalgesia (paw withdrawal threshold) were reversed upon treatment. Hence, biochanin-A could be a drug of choice in diabetic neuropathy (Chundi et al., 2016). The retina of diabetic rats was tested to rule out diabetic retinopathy after biochanin-A treatment. It was uncovered that it significantly prolonged the event of retinal damage with its anti-inflammatory and anti-angiogenic property (Mehrabadi et al., 2018). Diabetic nephropathy caused due to increased oxidative stress and TGF-β, was monitored in type 2 diabetes mellitus-induced rats to know if biochanin-A can play a role. It had significantly improved kidney function through modulating TGF-β expression and minimizing oxidative stress (Ahad, 2013). Hyperlipidaemia is a common comorbidity seen in diabetic patients. Biochanin-A administered to diabetic animals demonstrated low fasting blood sugar (FBS) as well as small dense low density lipoprotein cholesterol (sd-LDLC), favourable in diabetic dyslipidaemia conditions (Ghadimi et al., 2019). A formulation containing biochanin-A with or without its analogues will be beneficial in treating diabetes and diabetic cardiomyopathy, with evidence through increasing IGF1R (insulin-like growth factor 1 receptor), INSR (insulin receptor), and IRS2 (insulin receptor substrate 2) levels, thereby leading to the up-regulation of Lin28 gene and insulin sensitivity (Boominathan L, 2017). Biochanin-A was administered for 16 weeks orally once in a day to HFD-fed rats with single dose streptozotocin and showed that it has the ability to increase SIRT1 expression in heart tissue while also controlling hyperglycaemia and oxidative stress. Biochanin A could be a promising candidate for lowering the advancement of cardiomyopathy in people with type 2 diabetes (Oza and Kulkarni, 2022). A study designed to examine the diabetic and diabetic nephropathy effects on diabetic rats revealed that administering biochanin-A markedly reduced the expression of transforming growth factor-β1 (TGF-β1), protease-activated receptors 2 (PAR-2) genes, and fasting blood glucose (FBG) (Amri et al., 2021).\n\nThe anti-diabetic mechanism of biochanin-A is by decreasing oxidative stress. SIRT-1 influences the progression of insulin sensitivity. Biochanin-A act as a PPAR gamma receptor activator and produces anti-diabetic effect. The increased release of adiponectin and low resistin level to improve the diabetic condition is depicted in Figure 6.\n\nBiochanin-A decreases the oxidative stress and helps in diabetes condition. It increases the expression of SIRT-1 and progresses insulin sensitivity. Biochanin-A is a PPAR-γ receptor activator producing an anti-diabetic effect. It increases the release of adiponectin and decreases the resistin level to improve the diabetic condition (Shen et al., 2006; Oza and Kulkarni, 2018; Salemi et al., 2018).\n\n2.2.2 Dyslipidaemia\n\nDyslipidaemia or hyperlipidaemia is a very common metabolic disorder characterized by a high level of triglycerides and low-density lipoproteins, responsible for cardiovascular diseases (Thompson, 2004). The association between soy diet and hyperlipidaemia is a discussed topic among researchers. Soy can normalize the increased cholesterol level while taken in combination with conventional hyperlipidaemic drugs (Costa and Summa, 2000). A randomized control trial on isoflavones in hypercholesterolaemia showed that there was a minor significant positive impact on triglycerides levels supporting this fact (Qin et al., 2013).\n\nTreatment with a moderate dose of biochanin-A in HFD mice has shown a substantial lowering of LDL and total cholesterol. Lipoprotein lipase and hepatic triglyceride lipase levels are increased. Molecular docking studies on biochanin-A displayed a noteworthy role in reducing cholesterol-ester transport (Xue et al., 2017). Biochanin-A over formononetin reduced LDL cholesterol in men, though the same was not observed in women (Nestel et al., 2004). Biochanin-A lowers blood lipid levels, blood fibrinogen, and blood thickness levels of rats with hyperlipidaemia, increases blood circulation, and alters the blood coagulation system in lipid metabolism disorders (Ling-hui et al., 2012). Plant sterol combined with soy constituent such as biochanin-A was administered to a human to check LDL cholesterol level and the impact on atherosclerosis. It was shown to be efficacious to co-administer plant sterol and isoflavones (Waggle, Potter and Henley, 2003).\n\n2.2.3 Obesity\n\nObesity has been the most serious global health concern that is rapidly turning into an outbreak, currently affecting both developing and developed countries to varying degrees. Despite the fact that obesity and overweight are on the rise in modern society, there are no pharmacological treatments available. As a result, both researchers and health-care systems must prioritise the development of safe and effective treatments for obesity.\n\nIn HFD-induced obesity, oral treatment of biochanin-A significantly reduced the physiological changes that have occurred during trace element metabolism. This could be due to the inhibition of pathological mechanisms that derange trace elements, possibly by reverting hyperglycemia and insulin resistance and changing hepcidin and HO-1 levels. These findings strongly suggest that biochanin-A has therapeutic potential in the treatment of obesity and the prevention of cardiovascular disease (Antony Rathinasamy et al., 2020). Biochanin-A enhanced the expression of PPAR-α and its regulatory proteins in the liver by stimulating the transcriptional activation of PPAR-α in vitro. In the livers of obese mice, biochanin-A treatment increased the recovery of metabolites involved in phosphatidylcholine production, lipogenesis, and beta-oxidation. Biochanin-A also inhibited the expression of glucose 6-phosphatase and pyruvate kinase, two enzymes involved in gluconeogenesis. In diet-induced obesity, biochanin-A modulated lipid and glucose metabolism, improving metabolic abnormalities such as hepatic steatosis and insulin resistance (Park et al., 2016). Furthermore, biochanin-A administration in obese rats had a higher therapeutic effect, returning the altered parameters to near-normal levels. Biochanin-A up-regulated the Nrf-2 pathway while suppressing the NF-κB cascade, increasing the activity and mRNA expressions of enzymatic antioxidants. By activating the Nrf-2 pathway and inhibiting NF-κB activation, biochanin-A may reduce obesity and its related cardiomyopathy by decreasing oxidative stress and inflammation (Rani A, et al., 2021).\n\nBiochanin-A promotes AMPK signalling in C3H10T1/2 MSCs, leading to upregulation of brown fat adipocyte. According to the findings, biochanin-A treatment improves mitochondrial biogenesis and lipolysis, modulating the thermogenic process. Biochanin-A improves energy expenditure by boosting mitochondrial respiration while preserving the functional mitochondria. These data imply that biochanin A might be a new antiobesity drug (Rahman et al., 2021). Leptin is a hormone that regulates energy intake and body weight. Leptin resistance has been identified as a significant component in the development of obesity in recent studies. Endoplasmic reticulum (ER) stress, induced by the development of unfolded protein in the ER, causes leptin resistance. Biochanin-A decreased the ER stress related cell death in neuronal cells, restricted the glucose-regulated protein expression and modified the leptin signalling induced by ER stress. These findings imply that biochanin-A may have pharmacological characteristics that might reduce ER stress and hence alleviate leptin resistance (Horiuchi et al., 2021). A study deals with the evaluation of the cholesterol esterase inhibitory activity of biochanin-A using in silico docking approach. Biochanin-A contributed cholesterol esterase inhibitory activity, these molecular docking analyses could lead to the further development of potent cholesterol esterase inhibitors for the treatment of obesity (Sivashanmugam et al., 2013).\n\nAsian countries usually presented lower cardiovascular disease (CVD) mortality rates as it has very different dietary patterns from that of Western countries. Benefits over cardiovascular disease risk is an appreciated capability of soy protein and isoflavones. Isoflavones restore the disrupted endothelial function (Sacks et al., 2006; A. Gil-Izquierdo et al., 2012; Sathyapalan et al., 2018). By the year 1999, the US Food and Drug Administration (FDA) permitted to give soy protein-enriched foods as a protective agent in coronary heart disease routinely to lower the risk of cardiovascular disease (U.S. FDA, 1999).\n\nBiochanin-A mitigated myocardial injury by inhibiting the anti-inflammatory pathway, TLR4/NF-kB/NLRP3 signalling. It perfected the injury area and stopped the release of aspartate transaminase (AST), creatine kinase (CK-MB) and lactic dehydrogenase (LDH) enzyme. Biochanin-A further decreased inflammatory cytokines and protected rats from myocardial infarction (Bai et al., 2019). Reverse cholesterol transport (RCT) stimulated by biochanin-A and lowered pro-inflammatory cytokines make it a remarkable drug of choice in managing atherosclerotic cardiovascular disorder (Yu et al., 2020). Treatment with biochanin-A in isoproterenol-induced myocardial infarction rats normalized anti-oxidant levels and produced cardio-protective effects by controlling lipid peroxidation and detoxifying enzyme systems (Govindasami et al., 2020).\n\nIn the 19th and 20th centuries, people were drinking red clover tea or tincture (ethanolic extract) as an antispasmodic to give relief in whooping cough, measles, bronchitis, laryngitis, and tuberculosis (Felter and Lloyd, 1999). Biochanin-A being the major constituent of red clover can act as an anti-spasmodic agent in asthma and COPD (chronic obstructive pulmonary disease) (Ko et al., 2011).\n\nIt has been proven that biochanin-A diminishes airway resistance and improves respiratory health in methacholine (MCh) induced mice. Inflammatory mediators released were under control and ovalbumin (OVA)-specific immunoglobulin E (IgE) levels were low, hence, evidencing significant effect in allergic asthma and COPD (Ko et al., 2011). Biochanin-A reduced allergic asthma in mice with histological evidence through inhibitory effects on inflammatory cytokines, cell infiltration, protein leakage into the airways and expression of haem oxygenase-1 in OVA-induced lungs (ovalbumain). The action is mediated through PPAR-γ activation (Derangula, Panati and Narala, 2021). Biochanin-A exposed defensive effect in particulate matter with an aerodynamic diameter of 2.5 μm (PM2.5)-associated pulmonary disease rat model, it decreased cell death, the release of pro-inflammatory mediators, malondialdehyde (MDA), lactate dehydrogenase (LDH), and alkaline phosphatase (AKP) while increasing antioxidant enzymes levels (Xue et al., 2020). The risk of pulmonary and heart injury can be exacerbated by particulate matter with an aerodynamic diameter less than 10 μm (PM10). When examined in an in vitro model of lung injury caused by PM10, biochanin-A showed an anti-inflammatory effect that lessened lung injury and produced low levels of intracellular catalase and LDH. It regulates the phosphatidylinositol 3 kinase/protein kinase B (PI3K/Akt) signalling pathway and activates PI3K protein (Li et al., 2021a).\n\nOsteoarthritis is a condition that affects articular cartilage and synovial joints with structural and functional failure and diminishes the quality of life (Hunter and Felson, 2006). It is a chronic and irreversible disease causing pain and disability. Soybean isoflavones stopped the cartilage damage in animals with an ovarian hormone deficiency, which is indicative of its effect on osteoarthritis (Toda, Sugioka and Koike, 2020).\n\nBiochanin-A controlled the cartilage damage by deactivating the expression of MMP, NF-κB, and activation of TIMP-1, hence effective in OA cases (D. Q. Wu et al., 2014). Biochanin-A blocked the adipocyte differentiation considerably and the level of PPAR-γ, lipoprotein lipase (LPL), and leptin and osteopontin (OPN) mRNA expression were lowered and prompted the osteoprotegerin (OPG) to put forward its ability of osteoblast differentiation stimulation and adipogenesis inhibition (Su et al., 2013). The significance of biochanin-A on the resolution of the neutrophilic inflammatory response in an antigen-induced arthritis model, using wild-type BALB/c mice showed that biochanin-A reduced the number of migrating neutrophils which was linked to decreased levels of myeloperoxidase activity, IL-1 and CXCL1, as well as the histological score in periarticular tissues. Treatment with biochanin-A improved joint dysfunction as indicated by mechanical hyper-nociception (Felix et al., 2021).\n\nInflammation, biological feedback of the human body to damaging stimuli, is also associated with a wide range of diseases such as “obesity, atherosclerosis, rheumatoid arthritis, and even cancer”. Isoflavones are famous for their anti-inflammatory properties. Underlining the evidence for isoflavones is required in managing chronic diseases in which inflammation plays a vital role. Isoflavones that are an assured agent in various inflammatory diseases, show exciting anti-inflammatory effects proven in animal and human studies through better anti-oxidant properties, reduced pro-inflammatory enzymes, and NF-κB regulation (Su et al., 2013).\n\nBiochanin-A repressed LPS induced TNF-α and IL-8 production, NF-κB. Through PPAR-γ activation, biochanin-A displayed an anti-inflammatory effect hence, can be considered as an agent in the therapeutic management of inflammatory cardiovascular disease (Su et al., 2013). Biochanin-A is considered an anti-inflammatory agent with regards to its inhibitory effect in the release of nitric oxide (NO) production by LPS (Lipopolysaccharide), IkB kinase (IKK) activity, and NF-κB activation and lowered IL-6, IL-1β, and TNF-α production in RAW264.7 cells (Kole et al., 2011). It competes with the inflammation by impeding release of pro-inflammatory cytokines and modulating NF-κB and MAPKs pathways.\n\nAntioxidant rich foods may lower the chance of developing a number of ailments including heart disease and certain cancers. Free radicals are removed from cells by antioxidants, which minimizes oxidation related damage in the body. Biochanin-A being a good natural anti-oxidant can produce various health benefit in human biological system.\n\nWater-soluble urban particulate matter is a major lung toxicant shown to induce oxidative damage in human alveolar basal-epithelial cells. Biochanin-A tested in this model produced a protective effect by increasing anti-oxidant markers such as catalase, superoxide dismutase and glutathione. The malondialdehyde (MDA) and nitric oxide (NO) levels were found to be reduced and mitigated the lung injury by regulating MEK5/extracellular signal-related kinase 5 (ERK5) nuclear factor-erythroid factor 2-related factor 2 (Nrf-2) pathway (Xue et al., 2021). Several anti-oxidant assays have shown biochanin-A to be a powerful free radical scavenger molecule with its activity comparable to ascorbic acid. Biochanin-A when assessed in anti-oxidant assays such as nitric oxide scavenging activity assay, 1,1-diphenyl-2-picryl hydrazyl (DPPH), 2,2′-azinobis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS), ferric reducing antioxidant power (FRAP), hydroxy-radical activity assay, superoxide anion scavenging activity, hydrogen peroxide radical assay, metal ion chelating activity and phosphomolybdenum assay, it was observed that biochanin-A is able to produce efficient free radical scavenging ability in a dose reliant manner (Vennila L, Asaikumar L, Sivasangari S, Jayaraj D, 2019).\n\nThe hepatoprotective abilities of biochanin-A were explored in carbon-tetrachloride hepatotoxicity animal model. The anti-oxidant and anti-inflammatory capacity of biochanin-A influence the elevated hepatic enzyme level, such as AST, ALP, ALT, bilirubin, etc., and found to be a promising molecule in hepatotoxicity models (Breikaa et al., 2013).\n\nNatural isoflavones have exposed anti-microbial activity in various studies. The specific inhibitory action of biochanin-A was explored against possible Clostridium spp. bacterial infections of the human digestive system and was found to be beneficial to the human microbiota. “Clostridium tertium and clostridium clostridioforme” had exhibited high sensitivity to biochanin-A with a minimum inhibitory drug concentration of 0.13 mM whereas, Lactobacillus spp. or bifidobacteria showed resistant activity (Flesar et al., 2009; Sklenickova et al., 2010). Out of many isoflavones, biochanin-A exhibited a growth inhibitory effect against a number of Gram-positive and Gram-negative bacteria (Hummelova et al., 2015). Augmenting the immune response of host is a novel strategy to fight against microbial infections. Biochanin-A has proven its effect as intra-cellar and extra-cellular bactericidal on HeLa cells and inhibited the Salmonella spp. infection through mTOR/AMPK/ULK1 pathway (Zhao et al., 2018a). Biochanin A was the most effective Chlamydia spp. growth inhibitor among the various isoflavones tested, with an IC50 of 12 μM on Chlamydia pneumoniae inclusion counts and 6.5 μM on infectious progeny generation (Hanski et al., 2014). Biochanin-A by moderating the alterations associated with starch fermentation ex vivo, may be an efficient alternative to antibiotics for mitigating sub-acute rumen acidosis (SARA), according to a research to investigate the effect of biochanin-A on amylolytic bacteria and rumen pH during a SARA challenge (Harlow et al., 2021).\n\nNeurological disorders hampering the brain and nervous system are associated with a wide group of disorders as well as varying pathophysiology and symptoms. Inflammation is thought to be one important pathogenesis to cause peripheral (neuropathic pain, fibromyalgia) and central nervous systems disorders (e.g., Parkinson's disease, ischaemia, and traumatic brain injury, etc.) (Skaper et al., 2018). Multiple sclerosis (MS) is another chronic inflammatory neurodegenerative disease of the central nervous system. In a study conducted to explore the positive impacts of biochanin-A on cuprizone (CPZ)-induced MS model on mice, found that biochanin-A was able to modify the neurological harm of the condition with five weeks of treatment period. When compared to the CPZ group, biochanin-A boosted up the spatial memory in the Y-maze and recognition memory in the novel arm discrimination task (NADT) and novel object recognition task (NORT) of the animals (Aldhahri et al., 2022).\n\n2.10.1 Cerebral ischaemia\n\nTwo key pathways in the development of cerebral ischaemia/reperfusion damage are oxidative stress and neuroinflammation. Biochanin-A pretreatment on experimental animals induced with stroke, showed that the neurological deficiency is improved and the size of neural infarct and brain oedema was reduced. Biochanin-A reduced oxidative stress in the brain by augmenting SOD (superoxide dismutase) and GSH-Px (glutathione peroxidase) and repressing MDA (malondialdehyde) levels. The neuroprotective effects of biochanin-A might be attributed to the activation of the Nrf2 pathway and suppression of the NF-κB pathway (Guo et al., 2019). An L-glutamate-induced cytotoxic PC12 cell line when treated with biochanin-A exposed a protective effect by reducing cytotoxicity. It aided the release of glutathione while stopping LDH, caspase-3 effects, and act as an anti-apoptotic agent to produce neuroprotective activity (Tan et al., 2013). Middle cerebral artery occlusion (MCAO) subjected animals treated with biochanin-A, aiming to produce a protective effect against cerebral ischaemia/injury, presented with suppression of inflammatory response like TNF-α and IL-1β levels, MPO activity, and downregulation of p38 signalling (W. Wang et al., 2015). The elevated level of glutamate may be the principle cause that leads to cerebral ischaemia. By screening various phytomolecules, biochanin-A was found to be the most effective GOT (glutamate oxaloacetate transaminase) gene expression inducer in neural cells to alleviate ischemic injury. The glutamate induced cell death was lowered by biochanin-A administration, which was also proven when tested in GOT knock-down model as it did not have any protective effect. The ischaemic stroke presented animals were injected with biochanin-A and experienced a high level GOT protein in their brain tissues. Biochanin-A diminishes the stroke volume and amended the sensory motor abilities (Khanna et al., 2017).\n\n2.10.2 Parkinson’s disease\n\nParkinson’s disease (PD) is related to the degeneration of dopaminergic neurons in the SNpc. Oxidative stress in connection with the neurodegenerative symptoms has been found in this condition. Studies on lipopolysaccharide (LPS)-injected animals revealed that treatment with O-methylated biochanin-A amended the behavioural patterns of animals, stopped the dopamine neuronal loss, and prevented the harmful microglia activation. Biochanin-A additionally blocked the activation of NADPH-oxidase, MDA formation, SOD, and GPx actions in the brain preferring its choice as an anti-oxidant in PD management (J. Wang et al., 2015). Neurodegeneration due to inflammatory response through activating microglia is one of the reason in PD pathophysiology. It is found in rat mesencephalic neuron-glia cultures treated with biochanin-A, decreased dopamine uptake, and blocked LPS-related microglia activation. Low levels of TNF release, NO/SO release is associated with a protective effect towards LPS induced neurodegeneration (Chen, Jin and Li, 2007). While proving the anti-inflammatory ability of biochanin-A on LPS-treated mice BV 2 microglial cells observed that the levels of TNF-α, IL-1β, nitric oxide, and ROS were lowered. Biochanin-A influences pro-inflammatory responses induced by LPS and produces a protective effect on glial cells (Wu et al., 2015). Additionally, it up-regulated PPAR-γ levels, limited NF-κB release, and acts as an anti-inflammatory agent (Zhang and Chen, 2015). Increased neonatal iron supplementation (120 μg/g body weight) to the rats may contribute to the pathogenic mechanism of PD, and iron and rotenone co-treatment may worsen neurochemical and behavioural impairments by generating a redox imbalance. Biochanin-A had considerably lowered the malondialdehyde levels and significantly improved the glutathione levels in the substantia nigra amongst iron and rotenone co-treated male and female rats. It reduced the behavioural impairments by reducing striatal dopamine depletion. Furthermore, biochanin-A may protect dopaminergic neurons by preserving redox equilibrium (Yu et al., 2017). In another study where iron co-treated with 1-methyl-4-phenylpyridinium (MPP+), it raised the level of superoxide in microglia via p38 mitogen-activated protein kinase (MAPK) stimulation and resulted in deteriorated neurochemical and behavioral features of animals. Biochanin-A has been shown to repress the activation of p38 MAPK (Li et al., 2021b).\n\n2.10.3 Alzheimer's disease\n\nThe neuroprotective efficacy of various phytoestrogenic isoflavones including biochanin-A was screened against oxidative stress-induced cell death in the HCN 1-A (human cortical cell line) maintained in culture using the Alzheimer's disease-associated hydrogen peroxide (H2O2) model. Due to the anti-oxidant efficacy of isoflavones, the concentration-reliant reduction in neuron viability by H2O2 was prevented (Occhiuto et al., 2009). The neuroprotective benefits of biochanin-A as a possible alternative to oestrogen replacement treatment, against Aβ25–35 (amyloid beta) related toxicity, as well as its putative modes of action in PC12 cells, were investigated. In the presence of biochanin-A, the effects of Aβ25–35 were considerably reversed as it lowered cell death, LDH release, and cellular caspase activity, reducing the cytotoxic impact of the Aβ25–35 protein. Furthermore, it was found that in the presence of biochanin-A, there was decreased cytochrome-c and Puma (p53 up-regulated modulator of apoptosis) expression, along with reduced Bcl-2/Bax and Bcl-xL/Bax ratio (Tan and Kim, 2016).\n\nThe neuroprotective effects of biochanin-A on LPS-induced dopaminergic neuron injury in in vivo and in vitro models, as well as the molecular processes involved were explored. Biochanin-A therapy for 21 days substantially reduced behavioural impairment in PD rats, lowered dopaminergic neuronal loss, and suppressed microglia activation in LPS-induced PD rats. Biochanin-A protects LPS-induced PD rats, and the mechanisms are thought to be related to the suppression of the inflammatory response and the MAPK signalling pathway. Biochanin-A prevented primary microglial activation and protected dopaminergic neurons, reduced the amount of nitric oxide, IL-1, and TNF-α in supernatants, and suppressed the formation of reactive oxygen species (Wang et al., 2016). Rats lesioned with the PD-related neurotoxin 6-OHDA (6-hydroxydopamine) showed less motor impairment after receiving isoflavone-rich soy extract. These results imply that plant-derived isoflavones might be used as a dietary supplement to prevent the onset of Parkinson's disease in at-risk patients and to reduce neurodegeneration in the brains (de Rus Jacquet et al., 2021).\n\nThe behavioural and neurochemical effects of biochanin-A among cognitive-impaired animals in scopolamine-induced amnesia and naturally occurring aged animal amnesia models were assessed. In exteroceptive behavioural paradigms such as the elevated plus maze and the passive shock avoidance paradigm, biochanin-A decreased the transfer latency and increased the step through latency considerably in scopolamine-treated and natural aged mice. Acetylcholinesterase activity was found decreased in a dose-reliant manner amongst biochanin-A treated animals. A high level of GSH suppressed the pyknotic neurons formation, noradrenalin and dopamine expression thereby revealed the protective ability of biochanin-A against Alzheimer's disease (Biradar, Joshi and Chheda, 2014). The enzyme beta-site amyloid precursor protein cleaving enzyme-1 (BACE1) is involved in the aberrant synthesis of the amyloidogenic peptide Aβ, and is one of the primary causes of Alzheimer's disease (AD). BACE1 is found to be a crucial target protein in the identification of novel strategies to minimize and prevent Alzheimer's disease. Biochanin-A non-competitively inhibited BACE1 with an IC50 value of 28 μM. With a binding energy of −8.4 kcal/mol, biochanin-A might strengthen the chemical's strong interaction with the allosteric site of BACE1, leading to more effective BACE1 inhibition (Youn et al., 2016).\n\nIn postmenopausal women, oestrogen insufficiency is a major risk factor for Alzheimer's disease. In the Morris water-maze test, chronic treatment with biochanin-A replicated the capacity of β-estradiol (E2) to restore learning and memory deficits in ovariectomized (OVX) rats. Biochanin-A also lowered MDA levels and increased SOD and GSH-Px enzyme levels eventually produced neuro-protective effect and can be used to treat memory loss in postmenopausal women who are suffering from an oestrogen imbalance (Zhou et al., 2021).\n\nThe several pharmacological models explained in the review are collectively summarized in Table 2 and Table 3 emphasizing the model either in vitro or in vivo along with the dose of biochanin-A used in the study and the molecular mechanism behind the activity.\n\n(↑increase, ↓decrease, × inhibit, + activation).\n\n(↑increase, ↓decrease, × inhibit, + activation).\n\n\n3. Clinical trial on biochanin-A\n\nA clinical trial is underway to check the effect of red clover extract including biochanin-A among post-menopausal women with osteopenia. The results are yet to be concluded (University of Aarhus, 2015). The clinical trial data are summarized in Table 4\n\n\n4. Conclusion\n\nThis review discusses various pharmacological applications of biochanin-A focussing on the molecular pathway that might be responsible for its beneficial action. Biochanin-A might be able to modify various systems of the human body like the cardiovascular system, CNS, respiratory system, etc. It has a remarkable effect on hormonal cancers and other types of cancers. The growing amount of research on biochanin-A in breast, lung, colon, prostate, pancreatic cancers is an illustration of its impact in medicine. Through modulating oxidative stress, SIRT-1 expression, PPAR-γ receptors, and other multiple mechanisms, biochanin-A produces anti-diabetic action. The diverse molecular mechanistic pathways involved in the pharmacological ability of biochanin-A indicate that it is a very promising molecule and can play a major impact in modifying several physiological functions.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nAcknowledgments\n\nThe authors would like to express their gratitude to Manipal Academy of Higher Education and Manipal College of Pharmaceutical Sciences for the support provided in the preparation of this manuscript.\n\n\nReferences\n\nAhad A: Biochanin-A ameliorates experimental diabetic nephropathy by reducing the hyperglycemia induced oxidative stress and renal TGF-β expression. Journal of Diabetes & Metabolism. 2013; s4: 6156. Publisher Full Text\n\nAhsan M, Mallick AK: The effect of soy isoflavones on the menopause rating scale scoring in perimenopausal and postmenopausal women: A pilot study. J. Clin. Diagn. Res. 2017; 11(9): FC13. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWu W-Y, et al.: Biochanin A attenuates LPS-induced pro-inflammatory responses and inhibits the activation of the MAPK pathway in BV2 microglial cells. Int. J. Mol. Med. 2015; 35(2): 391–398. PubMed Abstract \| Publisher Full Text\n\nXu J-W, et al.: Isoflavones regulate secretion of leukemia inhibitory factor and transforming growth factor β and expression of glycodelin in human endometrial epithelial cells. J. Endocrinol. 2008; 196(2): 425–433. PubMed Abstract \| Publisher Full Text\n\nXue Z, et al.: Potential Lipid-Lowering Mechanisms of Biochanin A. J. Agric. Food Chem. 2017; 65(19): 3842–3850. PubMed Abstract \| Publisher Full Text\n\nXue Z, et al.: Amelioration of PM2.5-induced lung toxicity in rats by nutritional supplementation with biochanin A. Ecotoxicol. Environ. Saf. 2020; 202(May): 110878. Elsevier Inc. PubMed Abstract \| Publisher Full Text\n\nXue Z, et al.: Biochanin A alleviates oxidative damage caused by the urban particulate matter. Food Funct. 2021; 12(5): 1958–1972. PubMed Abstract \| Publisher Full Text\n\nYamasaki M, et al.: Soy-derived isoflavones inhibit the growth of adult T-cell leukemia cells in vitro and in vivo. Cancer Sci. 2007; 98(11): 1740–1746. PubMed Abstract \| Publisher Full Text\n\nYan L, Spitznagel EL, Bosland MC: Soy consumption and colorectal cancer risk in humans: a meta-analysis. Cancer Epidemiol. Biomarkers Prev. 2010; 19(1): 148–158. PubMed Abstract \| Publisher Full Text\n\nYanagihara K, et al.: Antiproliferative effects of isoflavones on human cancer cell lines established from the gastrointestinal tract. Cancer Res. 1993; 53(23): 5815–5821. PubMed Abstract\n\nYang W-S, et al.: Soy intake is associated with lower lung cancer risk: results from a meta-analysis of epidemiologic studies. Am. J. Clin. Nutr. 2011; 94(6): 1575–1583. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYoun K, et al.: The Identification of Biochanin A as a Potent and Selective β-Site App-Cleaving Enzyme 1 (Bace1) Inhibitor. Nutrients. 2016; 8(10): 637. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYu L, et al.: Neurochemical and Behavior Deficits in Rats with Iron and Rotenone Co-treatment: Role of Redox Imbalance and Neuroprotection by Biochanin A. Front. Neurosci. 2017; 11. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYu X, et al.: Biochanin A Mitigates Atherosclerosis by Inhibiting Lipid Accumulation and Inflammatory Response. Oxidative Med. Cell. Longev. 2020; 2020: 1–15. Edited by A. Lloret. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhang Y, Chen W: Biochanin A Inhibits Lipopolysaccharide-Induced Inflammatory Cytokines and Mediators Production in BV2 Microglia. Neurochem. Res. 2015; 40(1): 165–171. PubMed Abstract \| Publisher Full Text\n\nZhang Z, et al.: Genistein induces G2/M cell cycle arrest and apoptosis via ATM/p53-dependent pathway in human colon cancer cells. Int. J. Oncol. 2013; 43(1): 289–296. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhao X, et al.: Biochanin a Enhances the Defense Against Salmonella enterica Infection Through AMPK/ULK1/mTOR-Mediated Autophagy and Extracellular Traps and Reversing SPI-1-Dependent Macrophage (MΦ) M2 Polarization. Front. Cell. Infect. Microbiol. 2018a; 8. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhao Y, et al.: The effect of biochanin A on cell growth, apoptosis, and migration in osteosarcoma cells. Pharmazie. 2018b; 73(6): 335–341. PubMed Abstract \| Publisher Full Text\n\nZhou J-R, et al.: Inhibition of orthotopic growth and metastasis of androgen-sensitive human prostate tumors in mice by bioactive soybean components. Prostate. 2002; 53(2): 143–153. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhou Y, et al.: Biochanin A Attenuates Ovariectomy-Induced Cognition Deficit via Antioxidant Effects in Female Rats. Front. Pharmacol. 2021; 12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZiaei S, Halaby R: Dietary Isoflavones and Breast Cancer Risk. Medicines. 2017; 4(4): 18. MDPI AG. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "161697", "date": "14 Jul 2023", "name": "Sai Balaji Andugulapati", "expertise": [ "Reviewer Expertise Cancer Biology", "Pulmonary fibrosis (IPF)", "NASH and hepatic fibrosis" ], "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 gone through the article entitled 'Mechanisms behind the pharmacological application of biochanin-A'. It was written well however, the authors need to address the following comments and need additions in a few places.\nOn page no. 3, biochanin shows therapeutic actions in various cancers, need to mention about multiple myeloma as well, because biochanin-A showed anti-MM activity, and need to describe in the blood cancer section or wherever it is appropriate.\n\nOn page no. 3, the authors wrote: \"During breast cancer development the normal signalling pathways are interrupted, stimulating the refractory growth, no cell death, and progressive invasion to neighbouring tissues. Soy-rich diets in controlling hormone-dependent cancers have gained wide attention lately.\" This can happen in the majority of solid cancers, is there any specific reason to specify only breast cancer?\n\nOn page no. 5, the authors wrote: \"Biochanin-A has shown synergism with 5-fluorouracil (5FU) in oestrogen receptor (ER) positive breast cancer cell lines such as triple-negative breast cancer cells, MDA-MB231 and MCF7.\" But MCF7 cells are not triple-negative cells, authors need to check and re-write these sentences.\n\nOn page no. 6, the authors mentioned: \"The patients with clinically significant prostate cancer were treated with red clover isoflavones such as biochanin-A before surgical intervention. Markedly, higher apoptosis was found in the treatment group, indicates cessation of prostate cancer progression in low- moderate grade malignancy (Jarred et al., 2002).\" I failed to understand if is a clinical study or in vitro study, the first sentence shows as a clinical study, but the second sentence is depicted as an in vitro study. Please clarify, such confusion is there in multiple places...please correct it.\n\nOn page no. 6, the authors wrote: \"Soy-rich foods may reduce the likelihood of lung malignant growth in the general population, according to epidemiology researches...\" Maybe it should be written as: \"Soy-rich foods may reduce the occurrence of getting cancer in the general population, according to epidemiology researches\", please check it.\n\nOn page no. 9, it's written that \"biochanin-A exhibits neuroprotective effect\" and gave references for cancer studies, please give references for neuroprotective not for neuro cancer.\n\nFew of the references are not suitable, please check it.\n\nBiochanin-A is known to show anti-fibrotic activity as well, especially lung (IPF) and liver, authors should explore that as well.\n\nAdding limitations of biochanin-A would improve the manuscript.\nOverall the review is good.\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": [ { "c_id": "9990", "date": "16 Nov 2023", "name": "Krishnadas Nandakumar", "role": "Author Response", "response": "Response for Comment-1: As per the reviewer's suggestion, the following part has been added to the content of the paper 2.1.8 Leukemia & other cancers A study has found that Biochanin-A can be used to treat multiple myeloma, which is a type of cancer that affects plasma B cells in the bone marrow. The application of Biochanin-A has been shown to reduce the level of CD38, which is one of the key therapeutic targets for combating Multiple Myeloma. It has also been found to trigger apoptosis in Multiple Myeloma cells and reduce cytokine expression. The study further explored NOD/SCID mice with U266-induced tumors. Biochanin-A treatment was found to significantly reduce tumor growth. Mechanistic studies have shown that Biochanin-A’s anti-cancer effects are achieved by modulating the NF-κB and MAPK signaling pathways. This study suggests that Biochanin-A could be a novel treatment option for multiple myeloma with superior efficacy and reduced toxicity (Jaina et al., 2022). Response for Comment-2: The reason to specify breast cancer in the sentence was to give a general description of the topic under the subheading (2.1.1. Breast cancer) and elaborate on the pharmacological effects of Biochanin-A on breast cancer. As per the reviewer's suggestion, the text is changed as follows: “In most types of solid cancers like breast cancer, the normal signalling pathways are interrupted, stimulating refractory growth, no cell death, and progressive invasion of neighbouring tissues. Soy-rich diets in controlling hormone-dependent cancers have gained wide attention lately.” Response for Comment-3: The sentence has been re-written as follows: Biochanin-A has shown synergism with 5-fluorouracil (5FU) in oestrogen receptor (ER) positive breast cancer cell lines such as MCF7, and triple-negative breast cancer cells such as MDA-MB231. Response for Comment-4: The study was a nonrandomized, nonblinded clinical study performed in men with clinically significant prostate cancer before radical prostatectomy. The apoptosis markers in prostate tumor cells from radical prostatectomy specimens were compared among the red clover-derived isoflavones including Biochanin-A treated groups. The study is not an in vitro study. The authors would like to modify the sentence as: The patients with clinically significant prostate cancer were treated with red clover isoflavones such as biochanin-A before surgical intervention. The apoptosis markers in prostate tumor cells from radical prostatectomy specimens were analysed. Markedly, higher apoptosis was found in the treatment group with a dietary supplement of isoflavones, indicating cessation of prostate cancer progression in low to moderate-grade malignancy (Jarred et al., 2002). Response for Comment-5: The sentence has been rewritten as suggested. Soy-rich foods may reduce the occurrence of cancer development in the general population, according to epidemiology research”. Response for Comment-6: The sentence has been rewritten as suggested. Soy-rich foods may reduce the occurrence of cancer development in the general population, according to epidemiology research”. Response for Comment-7: The current manuscript is revised and has suitable references quoted at appropriate places. If the reviewer feels still there is scope for improvement in this area, I request the reviewer to specify it so that it can be suitably altered. Response for Comment-8: The authors would like to add a section with subheading 2.11 Anti-fibrotic activity 2.11 Anti-fibrotic activity Studies have been conducted to explore the role of biochanin-A in idiopathic pulmonary fibrosis (IPF), a chronic inflammatory disease characterised by fibrotic cascade events such as epithelial-mesenchymal transition, synthesis of extracellular matrix, and collagen formation in the lungs. The study was conducted on LL29 cells (lung fibroblast from IPF patient), NHLF (normal human lung fibroblast), and DHLF (diseased human lung fibroblast). Furthermore, the research focused on evaluating the effect of biochanin-A in bleomycin-induced pulmonary fibrosis. Biochanin-A treatment produced increased levels of Smad7 expression and decreased Smad2mRNA expression in cell lines, suggesting that biochanin-A contributes to pulmonary fibrosis by inhibiting TGF-/Smad signalling. Invivo results of the research revealed that lung index was increased in the bleomycin-induced pulmonary fibrosis group (BML) and biochanin-A reversed the same. The study proved that via modulating the TGF-β/Smad Pathway, biochanin-A prevented the onset and progression of pulmonary fibrosis (Andugulapati et al., 2020). Biochanin-A was investigated for its antifibrotic effects on a rat liver model wherein hepatotoxicity was induced through intraperitoneal chloroform. Hepatic fibrosis is the consequence of the wound-healing action of the liver which results in the accumulation of high fibrous scar tissue. The fibrotic lesions in the biochanin-A treated group were found to be minimum, and it also decreased α-SMA levels which confirms its anti-fibrotic effect. The study observed that biochanin-A improved blood flow and have good antioxidant properties. Biochanin-A decreased the TNF-α and NO levels. Thus, biochanin-A in the liver has anti-fibrotic properties by reducing oxidative stress while preserving hepatic function (Breikaa et al., 2013). Response for Comment-9: The authors would like to add a separate subheading after the clinical trial section as below: The authors would also like to correct the number of subsections of the conclusion as 5 4. Limitation of Biochanin-A Biochanin-A is a poorly soluble bioflavonoid, which prevents its oral absorption, despite having a rapid clearance and a broad apparent volume of distribution. The bioavailability of biochanin-A is poor. It was reported that biochanin-A undergoes extensive metabolism. The pharmacological value of biochanin-A was limited by its poor water solubility and low bioavailability. Numerous attempts have been made to increase the solubility and bioavailability of biochanin-A, including the use of dispersants, silver nanoparticles, liposomes, different film formulations for buccal delivery, nanostructured lipid carriers with and without polyethylene glycol, and cyclodextrin inclusion complexes. Esters of biochanin-A and carbamate ester derivatives have also been developed, and they have higher metabolic stability than biochanin-A. Thus, several attempts are being made worldwide to enhance biochanin-A’s solubility and bioavailability without compromising its effectiveness (Yu et al., 2019)." } ] } ]	1	https://f1000research.com/articles/12-107
https://f1000research.com/articles/11-914/v1	09 Aug 22	{ "type": "Research Article", "title": "New findings on ligand series used as SARS-CoV-2 virus inhibitors within the frameworks of molecular docking, molecular quantum similarity and chemical reactivity indices", "authors": [ "Alejandro Morales-Bayuelo", "Jesús Sánchez-Márquez", "Jesús Sánchez-Márquez" ], "abstract": "Background: The severe acute respiratory syndrome coronavirus (SARS-CoV)-2 virus causes an infectious illness named coronavirus disease 2019 (COVID-19). SARS-CoV is a positive-sense single-stranded RNA virus from the Betacoronavirus genus. The SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) has an important role in the viral life cycle and its active site is a very accessible region, thus a potential therapeutic approach may be to target this region to study the inhibition of viral replication. Various preexisting drugs have been proposed for the treatment of COVID-19 and the use of existing antiviral agents may reduce the time and cost of new drug discoveries, but the efficacy of these drugs is limited. Therefore, the aim of the present study was to evaluate a number of ligands used as SARS-CoV-2 virus inhibitors to determine the suitability of them for potential COVID-19 treatment. Methods: In this study, we selected a series of ligands used as SARS-CoV-2 virus inhibitors such as: abacavir, acyclovir, amprenavir, ascorbic acid vitamin C, azithromycin, baloxavir, boceprevir, cholecalciferol vitamin D, cidofovir, edoxudine, emtricitabine, hydroxychloroquine and remdesivir. These ligands were analyzed using molecular docking, molecular quantum similarity, and chemical reactivity indices defined within a conceptual density functional theory framework. Results: The analysis of molecular quantum similarity indices on inhibitors showed a high number of differences from a structural point of view. However, they are quite similar in their electronic density, obtaining the highest values in the electronic similarity index. Global and local chemical reactivity indices were analyzed. Conclusions: These studies allowed for the identification of the main stabilizing interactions using the crystal structure of SARS-CoV-2 RdRp. The molecular quantum similarity and chemical reactivity descriptors provide novel insights into these ligands that can be used in the design of new COVID-19 treatments.", "keywords": [ "RNA dependent RNA polymerase", "SARS-CoV-2 virus", "COVID-19 treatments", "molecular docking", "molecular quantum similarity", "chemical reactivity indices", "density functional theory" ], "content": "Introduction\n\nThe severe acute respiratory syndrome coronavirus (SARS-CoV)-2 virus causes an infectious illness named coronavirus disease 2019 (COVID-19). SARS-CoV is a positive-sense single-stranded RNA virus from the Betacoronavirus genus.1 Most RNA viruses require an RNA-dependent RNA polymerase (RdRp) for replication and transcription of the viral genome, thus making it essential for their survival, which is why it is a noteworthy topic to investigate. Its protein ranges from 240 to 450 kD and consists of a catalytic core and is a conserved protein within RNA viruses, and therefore it has been proposed as a potential option for the development of antiviral drugs.2\n\nNumerous drugs are being studied to treat COVID-19. In the USA, the first antiviral drug to treat COVID-19 in adults and children aged 12 years and older was remdesivir (Veklury). For hospitalized COVID-19 patients, remdesivir that is injected intravenously may be prescribed (Mayo Clinic).\n\nMolecular docking, molecular quantum similarity (MQS), and global and local reactivity indices were used in this study to evaluate remdesivir and other related compounds such as abacavir, acyclovir, amprenavir, ascorbic acid vitamin C, azithromycin, baloxavir, boceprevir, cholecalciferol vitamin D, cidofovir, edoxudine, emtricitabine and hydroxychloroquine to obtain novel insights into how the process of stabilization of these ligands at the active site in the receptor structure takes place. Previous studies have demonstrated positive responses with different levels of effectiveness for these aforementioned compounds in the treatment of COVID-19 (Mayo Clinic).\n\nBesalú et al., introduced MQS 30 years ago to study the similarity of molecules.4 The density functional theory (DFT) framework is used to connect quantum mechanics and quantum chemistry utilizing molecular docking and chemical reactivity indices.5 This research is leading to advances in the discovery of new treatment alternatives for COVID-19 and determining whether approved drugs, such as remdesivir, interact with other potential ligands.\n\n\nMethods\n\nSystem preparation\n\nThe receptor structure, for the docking analysis, was extracted from the crystal structure of the SARS-CoV-2 RdRp (Protein Data Bank (PDB accession number, 6M71), which was adjusted using the Schrödinger (RRID:SCR_014879) suite 2017-1 Protein preparation Wizard (RRID:SCR_016749) module. i) The hydrogen bond network (H-bond) was optimized, and the protein structure refined, ii) at physiological pH, protonation states were determined using the PropKa utility, iii) The Impact Refinement (Impref) module was used to run a molecular minimization with heavy atoms constrained to a low root mean square deviation (RMSD) from the initial coordinates.6–8\n\nMoreover, the molecular structures of the compounds were sketched using Maestro Editor (Maestro, version 11.1, RRID:SCR_016748, Schrödinger, LLC). Then, 3D conformations were obtained with the LigPrep (RRID:SCR_016746) module, with ionization/tautomeric states predicted under physiological pH conditions with Epik (RRID:SCR_016745). Subsequently, energy minimization was used to comply with the Macro model using the OPLS2005 force field. The free alternative is AutoDock Vina (RRID:SCR_011958).\n\nMolecular docking\n\nGlide (RRID:SCR_000187)9,10 with default parameters and Standard Precision (SP) model were used for docking investigations. The docking grid was created using default settings, with the co-crystallized ligand in the center. For the van der Waals radii of the nonpolar protein atoms, a scaling factor of 0.8 was applied to facilitate the binding of larger ligands. Extra precision (XP) was also utilized to expand alternate receptor conformations appropriate for binding ligands with unusual orientations via induced fit docking (IFD); this method allows the protein to undergo side-chain and/or backbone movements upon ligand docking. The results were optimized using the best predictions made by the 20 ns molecular dynamics.\n\nMolecular quantum similarity measure\n\nA molecular quantum similarity measure (MQSM) amid two A and B systems, known as ZAB, compares two molecules using their respective density functions (DFs). Both DFs can be multiplied and integrated in terms of their electronic coordinates, which are then weighted using a predetermined positive operator Ω(r1,r2):11–13\n\nThe nature of the operator used in Equation 1 provides the information being compared between the two systems and determines the similarity measure. For instance, if the chosen operator is the Dirac delta function (an efficient approach for functions with high peak values, such as the electronic density), i.e., Ω(r1,r2)= δ(r1- r2). One of the first similarity metrics employed is the overlapping MQSM; another widely used alternative is the Coulomb operator, i.e., Ω(r1,r2)=\|‌1- r2\|‌‌-1, resulting in a Coulombic MQSM. Even if the two molecules are equivalent, a similarity measure can be employed, which is known as a self-similarity measure (ZAA for the case of molecule A).12\n\nGiven a group of N molecules, we can generate a similarity measure for each of them with regard to the other molecules in the group, including themselves. With this, a symmetric matrix can be constructed where the i-th column of the matrix is the collection of all similarity measures between the i-th molecule and each of the components of the group, including itself. Each vector (column of the matrix) is a discrete representation (in N dimensions) of the i-th structure. These sets of vectors are a set of chemical descriptors that do not simply express another set of molecular descriptors as is often done, but rather each descriptor has its own set of unique properties.12,13\n\ni. It is universal in that it can be derived from any collection of molecules and any individual molecule within that group.\n\nii. It is impartial because there are no other possibilities available in the construction process than those given the density functions and similarity measurements involved.\n\nMQSM similarity index manipulation and visualization techniques\n\nThe similarity measure obtained for the group is unique once we have chosen a group of study objects and the operator in Equation 1; however, these measures can be combined or transformed to gain a new class of additional terms, which can be called Quantum Similarity Indices (QSI).\n\nThere are varieties of possible manipulations of the MQSM that result in a variety of QSI definitions. The most common ones are the following and are used in this paper13–16:\n\nCarbó's similarity index\n\nCarbó's similarity index between two molecules I and J is constructed from Equation 2. Because this index is also known as the cosine similarity index, it corresponds to the cosine of the angle formed by the density functions when considered as vectors. For any pair of compared molecules, this Carbo QSI has a value between 0 and 1, depending on the similarity between the two molecules (when I = J, the index approaches 1).13–17\n\nQuantum similarity using Euclidean distance\n\nTaking into account the similarity of Equation 3:\n\nIt can be simplified to the so-called Euclidean distance index when k = x = 2 and can also be defined as follows:\n\nThis Equation 4 forms the distance index of infinite order.18\n\nMQSM definition\n\nQuantum similarity measurements are in accordance with psychological perception and the apparent principle of similarity: “the more similar two molecules, the more similar their properties are.” This statement necessitates the construction of a molecule-to-molecule comparison, and the comparison of their densities is used to derive a quantitative measure of the quantum similarity of two molecules. Generally, the MQSM can be defined as the integral computational measure between two density functions, where the density functions are multiplied and integrated for the electronic coordinates in the relevant domain.19–21\n\n{r1, r2} are sets of electronic coordinates related to the corresponding wave function, and the operator Ω (r1,r2) is positively defined and supported on the electronic coordinates.22–26\n\nTypes of measurements in molecular quantum similarity\n\nThe types of measurements are mainly determined by the information required, the selection of supported operators and the form of MSQM.18–20\n\nMQSM overlap considering Equation 2:\n\nThe distribution of Dirac's delta, Ω (r1, r2) = δ (r1, r2), is the most typical and intuitive choice for such a positively defined operator. These selections transform the broad definition of MQSM to compute the overlap MQSM that obtains measurements of the volume by both electronic density functions when they are superimposed.17–20\n\nThe Dirac delta distribution, Ω (r1, r2) = δ (r1, r2), is the most typical and intuitive choice for a positive definite operator. This choice transforms the broad definition of MQSM to compute the overlap MQSM.17–20 The MQSM calculates the degree of overlap between molecular densities using information about the electron “concentration” in the molecule16–21:\n\nMQS coulomb considering Equation 2:\n\nWhen the operator (Ω) is replaced with the Coulomb operator, Ωr1r2=1\|r1−r2\|, the coulomb MQS is generated, which defines the electrostatic Coulomb repulsion energy between two charge densities20,21:\n\nThe Coulomb operator affects the overlap density functions. When considering molecular density functions as an electron distribution in space, this equation is simply an extension of the Coulomb operator for a distribution of continuous charge, thus can be used as electrostatic potential descriptors in some instances. This operator is correlated to electrostatic interactions and obtains the measurement of electrostatic repulsion between electronic distributions.15–19\n\nEuclidean distance index considering Equation 3:\n\nAnother major transformation that can be expressed in terms of the classical distance is:\n\nHere Δxj=xaj−xbj is the distance between a and b, and k = 2 is the definition of distance. Subsequently, the Euclidean distance between A and B (two quantum objects) is defined by:17–21\n\nOccasionally it is written as: DAB=ZAA+ZBB+ZAB, where DAB has values in the range of [0,∞} but for situations where the compared items are identical, it converges to zero17–21:\n\nThe norm of the differences of the density functions can be used in the definition Equation 9. The distance or dissimilarity index can be used to define the Euclidean distance index, which can also be represented as15–21:\n\nAlignment method: Topo-Geometrical Superposition Algorithm (TGSA)\n\nIn this research, the TGSA23 approach has been used to align the data. Gironés proposed the TGSA, in addition to programming and implementing it. This method assumes that the best way to align molecules is to superimpose them on a typical skeleton, with only the type atoms and the interatomic bonding interactions. The program accomplishes its purpose by examining the pairs of molecules and aligning the common substructure for a group.23 Only topological and geometrical considerations are used in the procedure, including molecular topology and how distant bonds are compared. The superposition of two molecules is unique and is independent of the type of operator used to determine the similarity.23,24\n\nOur research group has used several reactivity indices with Quantum Similarity.26–35 The reactivity indices used in this work are chemical potential (μ),36–38 hardness (ɳ),39 and electrophilicity (ω),38,39 which will be calculated.\n\nThe electrophilicity index (ω) measures the stabilization energy of the system when it is saturated by electrons from the external environment, and is mathematically defined as38,39:\n\nIn this study, the local reactivity descriptors are the Fukui functions. Equations 15 and 16 represent the response of the chemical potential of a system to changes in the external potential. It is defined as the derivative of the electronic density with regard to the number of electrons at the constant external potential:\n\nWhere fk− is for nucleophilic attack and fk− for the electrophilic attack.40–42 In this approach, using the global and local reactivity descriptors makes it possible to compare the molecular reactivity at the sample set. All the structures were developed using M02X/6–31G(d, p)43 methods in Gaussian 09 package.44\n\n\nResults\n\nIn this work, the stabilization process of a set of ligands related with activity against the novel SARS-CoV-2 was studied to understand the main ligand interactions in the active site, starting from the PDB crystal structure of SARS-CoV-2-dependent RNA polymerase code: 6M71.45,46 The crystal structure of SARS-CoV-2 RdRp was selected taking into account the outcomes reported by Elfiky et al.47 Figure 151 shows the docking interactions using remdesivir. In the conformation of Figure 1A and B, the docking interaction for the structure of remdesivir with a higher RMSD shows an -H bond with ARG555, ARG553 with two lengths of 2.28 Å and a length of 2.35 Å, LYS621 with a length of 2.22 Å, CYS622 with a length of 2.42 Å, and ASN691 with a length of 2.38 Å.\n\nA. Docking interactions using remdesivir with the crystal structure of SARS-CoV-2 RdRp (PDB accession number 6M71). B. Docking interactions using Receptor (gray) and ligand (blue) surfaces. C. Docking interactions with the receptor site. D. Surface of the binding pocket with the receptor site. SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; RdRp, RNA-dependent RNA polymerase; PDB, Protein Data Bank.\n\nAnother of the best conformations of remdesivir (Figure 1C and D) involved a -H bond with residue ASN691 with a length of 2.46Å, two ARG553 and ARG555 with lengths of 2.35Å and 2.38Å, CYS622 with a length of 2.41Å, and LYS621 with a length of 2.39Å. The interactions with the residue ARG553 and ARG555 and LYS621 were very similar to Figure 1A and B. These interactions play an important role in the interaction of the active site, generating a good bonding surface (see Figure 1B and D).\n\nFigure 2 shows the docking interactions using ascorbic acid vitamin C structure of SARS-CoV-2 RdRp from SARS-CoV-2. The ligand and receptor surfaces show the active site zone defined by the stabilization interactions. A phosphate group was found to reside well inside a local binding pocket within the grip with residue CYS622.\n\nA. Docking interactions using ascorbic acid vitamin C with the crystal structure of SARS-CoV-2 RdRp (PDB accession number 6M71). B. Receptor (gray) and ligand (blue) surfaces. C. Docking interactions with the receptor site. D. Surface of the binding pocket with the receptor site. SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; RdRp, RNA-dependent RNA polymerase; PDB, Protein Data Bank.\n\nIn Figure 2A and B, the ascorbic acid vitamin C has -H bonds with the residues LYS621 at a distance of 2.20Å, ARG553 at a distance of 1.86Å, and LYS551 at a distance of 1.86Å, respectively. The ligand has the same interaction as remdesivir with residue LYS621. This conformation showed a good stabilization in the pocket, generating a good contour surface (see blue surface). Conformation 2 (Figure 2C and D) shows three -H bonds with the same residue LYS621 at distances 2.18Å, 2.25Å and 2.27Å. This residue LYS621 is also shown in the conformations of remdesivir.\n\nConformation 1 of Figure 3A and B shows the structure of cholecalciferol vitamin D, the largest RMSD corresponding to an -H bond with the residue SER759 at a length of 2.24Å. For conformation 2 in Figure 3C and D the -H bond is with the residue GLU166 with a length of 2.28Å. Finally, the compound has interactions with the residue TRP617 with a length 2.26 Å. Although this compound only interacted with the residue SER759, the ligand surface is well defined near the receptor, even though it is a single -H bond. The interaction is good enough to generate an active conformation with stabilizing capacity (Figure 3C and D), in agreement with previous reported results.48\n\nA. Docking interactions of cholecalciferol vitamin D with the crystal structure of SARS-CoV-2 RdRp (PDB accession number 6M71). B. Receptor (gray) and ligand (blue) surfaces. C. Docking interactions with the receptor site. D. Surface of the binding pocket with the receptor site. SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; RdRp, RNA-dependent RNA polymerase; PDB, Protein Data Bank.\n\nConformation 1 of azithromycin (Figure 4A and B), like those of remdesivir and ascorbic acid vitamin C, has -H bond with LYS621 with a length of 2.28Å. In addition, it has two interactions with the residue ASP760 at lengths of 2.26Å and 2.34Å, with ASP761 at a length of 2.32Å. On the other hand, for conformation 2 of azithromycin of Figure 4C and D, we can see two -H bonds with the residues ASP760 with lengths of 2.41Å and 2.38Å, ASP761 with a length of 2.38Å and TRP617 with a length of 2.28Å. These ASP760, ASP761 and TRP617 interactions agree with the recent work published by Abdrabbo et al.49 In this work, once the stable binding mode was located, free energy perturbation (FEP) calculations were carried out to estimate the binding affinity of RemTP and ATP to COVID-19, and to identify the key residues in the binding process.\n\nA. Docking interactions using azithromycin with the crystal structure of SARS-CoV-2 (PDB accession number 6M71). B. Receptor (gray) and ligand (blue) surfaces with a receptor (gray) and ligand (blue) surfaces. C. Docking interactions with the receptor site. D. Surface of the binding pocket with the receptor site. SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; RdRp, RNA-dependent RNA polymerase; PDB, Protein Data Bank.\n\nThe docking interactions in conformation 1 of Figure 5A and B for hydroxychloroquine with higher RMSD shows a -H bond with the residue ARG553 with a length of 2.38Å, with ASP760 at lengths of 2.36 Å, 2.28 Å and 2.32 Å. For the best conformation 2, Figure 5C and D involved ASP462, ASP623 and ASP760 with lengths of 2.36 Å, 2.31 Å and 2.28 Å, respectively.\n\nA. Docking interactions using hydroxychloroquine with the crystal structure of SARS-CoV-2 RdRp (PDB accession number 6M71). B. Receptor (gray) and ligand (blue) surfaces with a receptor (gray) and ligand (blue) surfaces. C. Docking interactions with the receptor site. D. Surface of the binding pocket with the receptor site. SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; RdRp, RNA-dependent RNA polymerase; PDB, Protein Data Bank.\n\nIn this study, a molecular quantum similarity study was developed to systematically investigate and analyze the structural and electronic considerations involved in active site stabilization. An electronic similarity study has been designed to find the relationship between ligands and the active site of RdRp proteins.\n\nBecause conformations are crucial in docking studies, we have analyzed the impact that molecular alignment has on the generation of interactions (-H bond) at the active site. These molecular alignments, which generated the best poses, were related to potential COVID-19 inhibitors. For this analysis we have used four similarity descriptors (structural, electronic and their Euclidean distances) and molecular quantum similarity indices were calculated using the overlap and coulomb descriptors (Equations 6 and 7).\n\nThe compounds analyzed in the docking results were compared with a series of ligands with SARS-CoV-2 activity such as abacavir, acyclovir, amprenavir, ascorbic acid vitamin C, azithromycin, baloxavir, boceprevir, cholecalciferol vitamin D, cidofovir, edoxudine, emtricitabine, hydroxychloroquine and remdesivir. These compounds have been associated with COVID-19 treatment.\n\nThe molecular quantum similarity indices are defined on the interval (0,1), where 0 means dis-similarity and 1 means self-similarity. Table 1 shows the molecular quantum similarity indices using the overlap descriptor. Based on the distribution of Dirac's delta, Ω (r1, r2) = δ (r1, r2), this operator can be related to the structural characteristics of the compound analyzed. The highest values were for abacavir/acyclovir (0.6286) with an Euclidean distance of 3.5612 (Table 2), emtricitabine/abacavir (0.6011) with an Euclidean distance of 3.7645 and emtricitabine/edoxudine (0.6079) with a Euclidean distance of 3.8020. The lowest values were for boceprevir/azithromycin (0.1374), and remdesivir/cholecalciferol (0.1476) with a Euclidean distance of 7.1944.\n\nThe molecular quantum similarity indices using the Coulomb descriptor were calculated to obtain insights into the electronic similarity (see Table 3). The Coulomb descriptor is related to the electronic similarity in the molecular set. Table 3 shows that the highest values for emtricitabine/edoxudine (0.9390) with an Euclidean distance of 14.4795 (see Table 4), emtricitabine/abacavir (0.9311) with an Euclidean distance of (16.2459) and edoxudine/acyclovir (0.9165) with a Euclidean distance of 22.2556. Unlike the overlap descriptor, the values are near to 1. This means that despite having significant structural differences, these structures have high electronic similarities.\n\nThis work has also explored the global and local chemical reactivity indices within the DFT framework. Table 5 shows that the least reactive molecule was hydroxychloroquine, whose electronic chemical potential μ= -1.7070 eV, chemical hardness Ƞ=1.606 eV, softness S=0.6226 eV and electrophilicity ω=0.4536 eV. The most reactive compound was baloxavir-marboxil hydroxychloroquine, whose electronic chemical potential μ= -3.7335 eV, chemical hardness Ƞ=2.1441 eV, softness S=0.4664 eV and electrophilicity ω=1.6253 eV. These electrophilicity values play an essential role in ligands stabilized by non-covalent interactions and determine the stability of the active site.\n\nThe compounds with the highest chemical potential (negative electronegativity) were hydroxychloroquine with μ= -1.7070 eV, abacavir with μ= -2.6330 eV and cholecalciferol vitamin D with μ= -2.9825 eV. These compounds are commonly used in COVID-19 treatment.48–50 On the other hand, abacavir is used to treat HIV infection and some studies have shown its relationship with COVID-19.50 However, some countries are skeptical about its use for COVID-19 treatment. Other important compounds often used for the treatment of SARS-CoV-2 virus are azithromycin and remdesivir, with a chemical reactivity of μ= -3.5621 eV and -3.6097 eV, chemical hardness Ƞ=2.5532 eV and 2.3253 eV, softness S=1.2136 eV and 0.4300 eV and electrophilicity ω=1.6253 eV and 1.4009 eV, respectively. Both are very reactive and have high electrophilicity values. Figure 6 shows the Fukui functions that have been used to describe the local chemical reactivity of remdesivir and cholecalciferol vitamin D.\n\nA. Fukui function f−r≈HOMO2 and B. Fukui Function f+r≈HOMO2 related with remdesivir. C. Fukui Function f−r≈HOMO2 and D. f+r≈HOMO2 related with cholecalciferol vitamin D.\n\nFigure 6 and Figure 7 show the Fukui functions f−r≈HOMO2 and f+r≈HOMO2 for the compounds selected. The Fukui function f−r≈HOMO2 is associated with the susceptibility of a site to being attacked by electrophilic species, while f+r≈HOMO2 represents the susceptibility of a site to being attacked by nucleophilic species. In these figures, we can see the functions of Fukui (-) and (+) on the identical zones in the molecular structure. These can be related to the stabilization process on the active site, showing the zones associated with global reactivity indices like electrophilicity and softness. These reactivity parameters can help understand the destabilization process and the bond formation (-H bonds) in non-covalent interactions. All these outcomes can be useful for the rapid assessment of the currently available antiviral drugs used for treating COVID-19 patients, which is crucial at this time of crisis, as well as for discovering newer drugs.\n\nA. Fukui function f−r≈HOMO2 and B. f+r≈HOMO2 related with ascorbic acid vitamin C. C. Fukui function f−r≈HOMO2 and D. f+r≈HOMO2 related with azithromycin. E. Fukui function f−r≈HOMO2 and F. f+r≈HOMO2 associated with hydroxychloroquine.\n\n\nConclusions\n\nIn this study, a number of ligands related to the treatment of COVID-19 and used as inhibitors of SARS-CoV-2 virus, such as abacavir, acyclovir, amprenavir, ascorbic acid vitamin C, azithromycin, baloxavir, boceprevir, cholecalciferol vitamin D, cidofovir, edoxudine, emtricitabine, hydroxychloroquine and remdesivir, have been analyzed by molecular docking, molecular quantum similarity and chemical reactivity indices to study their active site stabilization interactions from a structural and electronic point of view.\n\nIn this study, to develop the docking experiments, some compounds were selected as references, these compounds are frequently related with the treatment of COVID-19. Some important anti-polymerase drugs were tested that are currently in clinical trials or on the market to stop viral infection on an emergency basis. The docking interaction for remdesivir, cholecalciferol vitamin D, azithromycin and ascorbic acid have shown good interaction (-H bonds) in the active site. The main idea is to extrapolate these outcomes and find novel insights into inhibitors for COVID-19.\n\nThe analysis of molecular quantum similarity indices on inhibitors showed high differences from a structural point of view. However, they are quite similar in their electronic density, obtaining the highest values in the electronic similarity index. Global and local chemical reactivity indices were calculated. These indices allow for the identification of the zones of chemical reactivity involved in the non-covalent stabilization of these inhibitors on the active site. Moreover, new outcomes about compounds such as abacavir, which is used to treat HIV infection, were shown and some studies have shown their relationship with COVID-19. In addition, it sheds light on the use of novel ligands for the treatment of this challenging disease that has claimed millions of lives worldwide.\n\n\nData availability\n\nProtein Data Bank: SARS-Cov-2 RNA-dependent RNA polymerase in complex with cofactors. Accession number 6M71; https://identifiers.org/pdb:6M71\n\nHarvard Dataverse: New insights in series of ligands used as SARS-CoV-2 virus inhibitors within molecular docking, molecular quantum similarity, and chemical reactivity indices frameworks. https://doi.org/10.7910/DVN/MSIGUS.51\n\nData are available under the terms of the Creative Commons Zero D. “No rights reserved” data waiver (CC0 1.0 Public domain dedication).", "appendix": "Acknowledgments\n\nAMB would like to thank the Universidad del Sinú, Seccional Cartagena.\n\n\nReferences\n\nYang L, Wu Z, Ren X, et al.: Novel SARS-like Betacoronaviruses in Bats, China, 2011. Emerg. Infect. 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Publisher Full Text" }	[ { "id": "185712", "date": "17 Jul 2023", "name": "Truong Tan Trung", "expertise": [ "Reviewer Expertise Computational chemistry", "DFT", "Nanotechnology", "Docking simulation" ], "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 of good importance, however, there are various things that need to be addressed and the amount of work is not sufficient. Without addressing them, I would not recommend the indexing of this manuscript.\nWhat are the novelties of the manuscript? What’s new in this manuscript compared to similar papers?\n\nThe introduction section should be written in a higher quality way, i.e. more up-to-date references. The research gap should be delivered more clearly with the directed necessity for the novelties of the work.\n\nHave the selected compounds been reported as potential ligands in the treatment of SARS-CoV-2?\n\nThe position of reference 3 was not defined in the manuscript.\n\n“Ascorbic acid vitamin C” should be written as ascorbic acid (vitamin C). Same for cholecalciferol vitamin D “cholecalciferol (Vitamin D3)”.\n\nPage 6: I think it should be \"fr+ \" is for nucleophilic attack.\n\nThe sentence “The lowest values...of 7.1944” at the bottom of page 10 is confusing, rephrase it (missing value Euclidean distance of 8.6174 of Boce/Azythr).\n\nPage 11, the value of Euclidean distance of edox/acyc is 22.2556. It is different from the value shown in Table 4 (16.8664). The author should reconsider.\n\nPages 11 and 16, character symbol of unknown, e.g. chemical hardness.\n\nPlease add the HOMO and LUMO energy values in Table 5. Furthermore, the band energy gap of compounds in the binding pocket of the receptor. This will depict the reactivity with the receptor.\n\nPage 16, the value of softness (S=1.2136 eV) and electrophilicity (w=1.6253) of Azithromycin is different from the values shown in Table 5. Carefully check the manuscript for similar errors.\n\nPage 3, need ≥ 100 ns molecular dynamics.\n\nAbout the docking results: The author clearly presents the results obtained from the docking in the form of data in the table, which is used as evidence for 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? 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": [ { "c_id": "9918", "date": "10 Aug 2023", "name": "Alejandro Morales-Bayuelo", "role": "Author Response", "response": "1. What are the novelties of the manuscript? What’s new in this manuscript compared to similar papers? Answer: There is currently no effective treatment for Covid-19. Therefore, there are a series of drugs such as those listed in this article that have been used for the treatment of this disease, however they have not been associated as solutions for covid-19. That is why carrying out studies that show that the drugs used are directly related to the Covid-19 proteins is pertinent. 2. The introduction section should be written in a higher quality way, i.e. more up-to-date references. The research gap should be delivered more clearly with the directed necessity for the novelties of the work. Answer: Done. 3. Have the selected compounds been reported as potential ligands in the treatment of SARS-CoV-2? Answer: The molecular datasets used for the docking study were reported by Sipos et al.4 , Székely et al.5 , Lougheed [6] , Chapman [7] and finally Pato [8] (see Table 1–Table 6). To select this molecular dataset, the structural diversity and uniform distribution of IC50 was taken into account. Logarithmic IC50 (μM) (PIC50=−log IC50) was employed as the dependent variable instead of IC50. All molecular set, has been used as treatment for the Covid-19. 4. The position of reference 3 was not defined in the manuscript. Answer: Pkn A reported by Sipos [3]. 5. “Ascorbic acid vitamin C” should be written as ascorbic acid (vitamin C). Same for cholecalciferol vitamin D “cholecalciferol (Vitamin D3)”. Answer: Done. 6. Page 6: I think it should be \"fr+ \" is for nucleophilic attack. Answer: Done. 7. The sentence “The lowest values...of 7.1944” at the bottom of page 10 is confusing, rephrase it (missing value Euclidean distance of 8.6174 of Boce/Azythr). Answer: Done. 8. Page 11, the value of Euclidean distance of edox/acyc is 22.2556. It is different from the value shown in Table 4 (16.8664). The author should reconsider. Answer: Done. 9. Pages 11 and 16, character symbol of unknown, e.g. chemical hardness. Answer: The Chemical Hardness (Ƞ) has been symbolized using the standard Density Functional Framework. 10. Please add the HOMO and LUMO energy values in Table 5. Furthermore, the band energy gap of compounds in the binding pocket of the receptor. This will depict the reactivity with the receptor. Answer: In the Supporting Information has been added the output files used for the calculations of the reactivity indexes for each compound. 11. Page 16, the value of softness (S=1.2136 eV) and electrophilicity (w=1.6253) of Azithromycin is different from the values shown in Table 5. Carefully check the manuscript for similar errors. Answer: Done. 12. Page 3, need ≥ 100 ns molecular dynamics. Answer: In this study, the best predictions of the poses were predicted by 30ns molecular dynamic calculations. This values by 30ns for molecular dynamic has been used by our research group in several publication taking account the docking values. 13. About the docking results: The author clearly presents the results obtained from the docking in the form of data in the table, which is used as evidence for discussion. Answer: ok." } ] } ]	1	https://f1000research.com/articles/11-914
https://f1000research.com/articles/12-1262/v1	04 Oct 23	{ "type": "Study Protocol", "title": "Onchocerciasis-associated epilepsy: an explorative case-control study with viral metagenomic analyses on Onchocerca volvulus", "authors": [ "Amber Hadermann", "Stephen Raimon Jada", "Wilson J. Sebit", "Thomas Deng", "Yak Y. Bol", "Joseph N. Siewe Fodjo", "Lander De Coninck", "Jelle Matthijnssens", "Inge Mertens", "Katja Polman", "Robert Colebunders", "Amber Hadermann", "Stephen Raimon Jada", "Wilson J. Sebit", "Thomas Deng", "Yak Y. Bol", "Joseph N. Siewe Fodjo", "Lander De Coninck", "Jelle Matthijnssens", "Inge Mertens", "Katja Polman" ], "abstract": "Background: A high prevalence of onchocerciasis-associated epilepsy (OAE) has been observed in onchocerciasis-endemic areas with high ongoing Onchocerca volvulus transmission. However, the pathogenesis of OAE remains to be elucidated. We hypothesise that the O. volvulus virome could be involved in inducing epilepsy. With this study, we aim to describe the O. volvulus virome and identify potential neurotropic viruses linked to OAE.\nMethods: In Maridi County, an onchocerciasis endemic area in South Sudan with a high prevalence of OAE, we will conduct an exploratory case-control study enrolling 40 persons aged 12 years and above with palpable onchocerciasis nodules. Cases will be participants with OAE (n=20), who will be age- and village-matched with controls without epilepsy (n=20). For each study participant, two skin snips at the iliac crest will be obtained to collect O. volvulus microfilariae, and one nodulectomy will be performed to obtain adult worms. A viral metagenomic study will be conducted on microfilariae and adult worms, and the O. volvulus virome of persons with and without OAE will be compared. The number, size, and localisation of onchocerciasis nodules in persons with and without OAE will be described. Moreover, the pre- and post-nodulectomy frequency of seizures in persons with OAE will be compared.\nEthics and dissemination: The protocol has been approved by the Ethics Committee of the University of Antwerp and the Ministry of Health of South Sudan. Findings will be disseminated nationally and internationally via meetings and peer-reviewed publications.\nRegistration: https://clinicaltrials.gov/ registration NCT05868551 (https://clinicaltrials.gov/study/NCT05868551)\nProtocol version: 1.1, dated 09/05/2023", "keywords": [ "Onchocerciasis", "epilepsy", "nodulectomy", "pathogenesis", "metagenomics", "Onchocerca volvulus", "virome" ], "content": "Introduction\n\nOnchocerca volvulus is a filarial nematode parasite transmitted by blackflies (Simulium), which causes onchocerciasis, commonly referred to as “River Blindness.” Recent epidemiological studies strongly suggest that onchocerciasis may directly or indirectly induce epilepsy, known as “Onchocerciasis-associated epilepsy” (OAE).1,2 Onchocerciasis-associated epilepsy appears in previously healthy children between the ages of 3–18 years, with a peak onset at 8–11 years,1 and comprises a broad spectrum of seizures, including generalised tonic-clonic, absence and nodding seizures, the latter as part of nodding syndrome.3,4 Some OAE cases may also have stunting with delayed puberty, as part of Nakalanga syndrome.1 Until now, diagnosing OAE has been difficult. An OAE case definition for epidemiological studies has been proposed,5 but there is currently no test to confirm that epilepsy in a child is caused by onchocerciasis. Moreover, the fact that the pathogenesis of OAE remains unknown has kept this important public health problem from being internationally acknowledged and made it challenging to direct the necessary resources to the affected communities which are often very remotely located.5\n\nMultiple hypotheses concerning the pathogenesis of OAE are currently being explored.6 It has been suggested that Wolbachia, an intracellular symbiotic microorganism critical for the survival of the O. volvulus parasite, could be involved, as Wolbachia has been linked to the disease mechanism of onchocerciasis-related blindness.7 However, recent studies did not detect Wolbachia DNA in cerebrospinal fluid and post-mortem brain tissue of persons with OAE.8\n\nTo our knowledge, the virome of O. volvulus has never been investigated. In other parasites, a wide range of RNA viruses have been identified. For some of these parasite-hosted viruses, such as the rhabdoviruses found in Schistosoma solidus and a series of nematodes, it has been suggested that they may contribute to the infection dynamics.9–12 Rhabdoviruses are negative-sense single-stranded RNA viruses known to infect a range of different hosts, from mammals, including humans, to arthropods, plants, and parasites.13 The fact that these viruses have such a wide range of hosts raises the question of whether these viruses are impacting multiple species by being able to infect multiple hosts naturally and/or through evolution by host jumping. We hypothesise that the O. volvulus virome could be involved in the pathogenesis of OAE.\n\nIn a pilot exploratory viral metagenomic study, we performed virus-like particle (VLP) enrichment according to the NetoVIR protocol,14 followed by Illumina deep sequencing on O. volvulus adult worms obtained from persons without epilepsy in Cameroon (62 worms from nine individuals) and Ghana (46 worms from 11 individuals). Worms from different sites were collected using different protocols. During metagenomic analysis, we found that the storage of worms in RNAlater resulted in high viral read counts. Preliminary results identified a novel rhabdovirus. We are currently designing and validating a polymerase chain reaction (PCR) to be able to test serum samples of OAE patients for the presence of this virus. All other viruses were either from families not known to infect humans or sequenced in extremely low abundance.\n\nIn the current project, we propose to collect adult worms by nodulectomy and microfilariae by obtaining skin snips from persons with OAE and persons without epilepsy residing in an onchocerciasis-endemic area in South Sudan, and store them in RNAlater to optimise the yield. These will then be used for viral metagenomics analysis.\n\nTo describe the O. volvulus virome and to identify viruses linked to onchocerciasis morbidity, specifically OAE.\n\nThis study aims to collect, in an onchocerciasis endemic area in South Sudan, good quality samples of O. volvulus worms (microfilariae and adult forms). Collected samples will be analysed using viral metagenomics and investigated for the presence of the novel rhabdovirus identified in a pilot study in samples from Cameroon and Ghana.\n\nMoreover, we will compare the number, size, and localisation of onchocerciasis nodules in persons with and without epilepsy. In addition, in the persons with epilepsy we will assess the effect of nodulectomy on the frequency of seizures.\n\nThe virome of O. volvulus worms obtained from persons with OAE differs from that obtained from persons without epilepsy. A novel rhabdovirus may also be found in O. volvulus samples from South Sudan.\n\n\nMethods\n\nAn explorative case-control study.\n\nSouth Sudan is known to have multiple endemic hotspots of onchocerciasis, including Maridi County in the Western Equatoria state (Figure 1). Maridi County is home to over 115,000 individuals and is traversed by the Maridi River, upon which a dam was built in the 1950s.15 The dam spillway was identified as the sole blackfly breeding site in Maridi,15 fuelling onchocerciasis transmission in the neighbouring villages. In 2018, a high prevalence of epilepsy (4.4%) was documented in selected villages in Maridi, with a prevalence of 11.9% in Kazana-2, an area close to the Maridi Dam (Figure 2).16 Most (85.2%) of the persons in Maridi with epilepsy met the criteria of OAE in Maridi.17\n\nAnnual community-directed treatment with ivermectin (CDTi) is the main method used for onchocerciasis control internationally and was introduced in Maridi in the early 2000s. However, there have been several years without treatment due to insecurity, which has allowed the disease to remain endemic in the area. The CDTi intervention was reintroduced in Maridi in 2017. Onchocerciasis transmission was assessed in December 2019 via an O. volvulus antibody serosurvey (using the OV16 rapid diagnostic test) in children aged 3 to 6 years and a seroprevalence of 40.0% was found in Kazana-2 village, suggesting very high ongoing onchocerciasis transmission.18 Moreover, blackfly biting rates of 202 flies per man per hour were observed at the Maridi Dam.18 Annual CDTi was interrupted in 2020 because of the COVID-19 pandemic but was continued biannually (six-monthly) in 2021. Additionally, in 2019, a community-based vector control strategy known as “Slash and Clear” was implemented at the Maridi Dam. This method consists of clearing the trailing vegetation at blackfly breeding sites to reduce biting density in the nearby communities.18\n\nThese onchocerciasis elimination measures reduced the transmission of O. volvulus and OAE incidence in Maridi.19 However, overall coverage of ivermectin of 80% is recommended to reach elimination of parasite transmission.20 The CDTi coverage has been increasing but remains low in Maridi (only 56.6% of the population took ivermectin in 2021), and the onchocerciasis elimination goals remain far from being attained.19\n\nThe major milestones for this study will be spread over time as follows:\n\n• Study preparation, including community sensitisation: August 2023\n\n• Recruitment, including nodulectomies: September to December 2023\n\n• Metagenomic analysis: January 2024\n\nBased on limited preliminary data, no sample size can be calculated. The 20 cases and 20 controls represent a convenience-based sample size and are proposed for reasons of feasibility and acceptability. The prevalence of onchocerciasis nodules in persons with and without OAE has so far not been well assessed. In a study concerning the clinical manifestations of epilepsy in Maridi, onchocerciasis nodules were only reported in 5.8% of persons with nodding syndrome and in 0.7% of persons with epilepsy without nodding syndrome.21\n\nTwenty OAE cases (≥12 years old) with at least one onchocerciasis nodule and 20 age- and village-matched non-epileptic controls with at least one onchocerciasis nodule will be recruited into the study. A person will be considered having OAE if he/she matches the criteria of the most recent case definition of OAE.5\n\nSelection and enrolment of the study participants\n\nAfter obtaining informed consent, persons with epilepsy attending the epilepsy clinic at Maridi Hospital, at least 12 years old and living in Kazana-1 or Kazana-2 villages, will be carefully examined for the presence of onchocerciasis nodules by trained personnel. The main parts of the body that will be examined are the head, neck, chest, arms, lumbar region, buttocks, thighs, and legs. Persons with epilepsy will also be interviewed to assess whether they meet the criteria of OAE.5 If they meet these criteria, they will be asked to participate in the study. Recruitment of OAE cases will be consecutive.\n\nAfter all persons with OAE have been selected for the study, controls will be identified during a house-to-house survey in Kazana-1 and Kazana-2. All persons without epilepsy between the ages of 12 and 30 years will be examined for the presence of onchocerciasis nodules. For each case with OAE, a control with at least one onchocerciasis nodule with a similar age (±3 years), sex and ivermectin use will be asked to participate in the study. Both OAE cases and controls will only be enrolled after written informed consent is obtained, as well as assent from the children 12–17 years old.\n\nInterview and examination\n\nFor each study participant, pre-tested questionnaires22 will be completed. This questionnaire will include questions about potential onchocerciasis-related symptoms (epilepsy, cognitive decline, skin, and eye problems) and past ivermectin use. All participants will be examined, and the number, size, and localisation of the nodules will be noted. Moreover, in follow-up questionnaires,23 we will record the status of the wound and the number of seizures since the nodulectomy 10 days and one-month post-nodulectomy.\n\nNodulectomy\n\nExtraction of adult worms by nodulectomy will be performed at Maridi Hospital by the project physician. Transport to the hospital and post-nodulectomy care will be organised by the research team. Nodulectomies will be performed under local anaesthesia and aseptic conditions by a medical doctor (TD) trained in the procedure. The skin above the nodule will be disinfected with 70% alcohol, followed by a povidone-iodine solution. Only superficially located nodules will be selected for nodulectomy. After extraction of the nodule, the skin wound will be sutured and covered by a band aid. Ten days after wound closure the wound will be inspected, and sutures removed.\n\nNodules will be incubated in collagenase (Gibco™; ThermoFisher; CNr° 17101015) to break up the outer layer. All worms will be washed thrice with 20% Percoll® (Sigma-Aldrich; PNr° P1644-25ML). All collected worms from one person will be pooled and submerged in RNAlater for storage.\n\nSkin snip testing\n\nOne skin snip will be taken from either side of the iliac crest using a sclerocorneal biopsy punch. The skin snip will immediately be put into a 96-well microtitre plate with approximately 40 μL physiological saline. Biopsies will be incubated for 12–24h at room temperature. Afterwards, the emerged microfilariae will be counted using an inverted microscope (Leica DM IL LED; VWR CNr° 630-3462) and aspirated from the plate into a labelled tube for storage in RNAlater.\n\nO. volvulus antibody testing\n\nBlood will be obtained by finger prick for Ov16 rapid diagnostic testing. Moreover, four dry blood spots on filter paper and 5 mL of venous blood will be collected per person to allow for the possibility of using these samples for future pathogenesis and O. volvulus diagnostic studies.\n\nEvaluation of seizures\n\nIn persons with epilepsy, the number of seizures will be assessed pre-nodulectomy and 10 days and one-month post-nodulectomy.\n\nStorage and transfer of samples\n\nThe O. volvulus worms in RNAlater will be preserved initially at the Maridi hospital in a -20°C freezer. Later samples will be transferred under cold chain conditions, first to a -80°C freezer at the Public Health Laboratory of the Ministry of Health of South Sudan in Juba and later to a -80°C freezer at the Rega Institute at the KU Leuven in Belgium.\n\nViral metagenomic analysis\n\nAll collected worms will be sent to the Rega Institute under the Nagoya agreement. Worms will be processed following the NetoVIR protocol adapted for adequate homogenization.14 In short, worms will be diluted in 500μl PBS and homogenized in a Precellys® Evolution tissue homogenizer (Bertin Technologies) with 2.8 mm zirconium oxide beads (Precellys) at 4500 rpm for 1 min. For each processed batch of worms, a negative control consisting of only PBS will be taken along. Next, the samples will be centrifuged at 17,000 g for 3 min and 150 μl supernatant of each sample will be subsequently filtered through a 0.8 μm filter (Sartorius). This filtrate will be treated with a mix of Benzonase (50 U, Novagen) and Micrococcal nuclease (2000 U, New England Biolabs) to digest remaining free-floating eukaryotic and bacterial nucleic acids. Viral DNA and RNA will be then extracted using the Kingfisher Flex system (Thermofischer), Applied Biosystems in combination with the MagMAX™ Viral/Pathogen Nucleic Acid Isolation Kit (Thermofischer). DNA and RNA will be amplified using the Complete Whole Transcriptome Amplification kit (WTA2, Merck), and resulting PCR products will be further purified and prepared for sequencing with the Nextera XT kit (Illumina). The final sequencing libraries will be cleaned up with Agencourt AMPure XP beads (Beckman Coulter, Inc.) using a 0.6X ratio of beads to sample. Finally, paired-end sequencing will be performed on the Nextseq 550 platform (Illumina) for 300 cycles (2x150bp) with an estimated 10 million reads per sample. All resulting sequences will be run through the ViPER pipeline (https://github.com/Matthijnssenslab/ViPER) on the infrastructure of the Vlaamse (Flemish) Supercomputer Center® (VSC) to evaluate the read quality, perform de novo assembly, virus identification and classification to produce a first overview of virus species found in the obtained reads. Relevant viruses will be evaluated on their potential to infect humans and compared between cases and controls.\n\nStudy outcomes and data analysis plan\n\nO. volvulus viromes will be examined for the potential presence of viruses related to families/clades able to infect humans, including the rhabdoviruses detected during the pilot study in samples from Cameroon and Ghana. In addition, the O. volvulus viromes of persons with and without OAE will be compared.\n\nData handling and storage\n\nResearch data management will be done according to the FAIR principles (research outputs are findable, accessible, interoperable, and reusable). All personal information will be encoded and treated confidentially with REDCap (Version: 13.7.3). Codified data will be entered into secure, password-protected spreadsheets and stored in a secured central server. All coded individual participant data underlying the results will be made available immediately and indefinitely via the Zenodo repository following publication for anyone who wishes to access the data for any purpose.\n\nThe study was prepared in collaboration with the Neglected Tropical Disease department of the Ministry of Health of the Republic of South Sudan. Prior to the study, communities will be sensitised and mobilised about the importance of preventing OAE by participating in the CDTi programme. The study rationale, objectives and procedures will be explained during interactive community meetings. Study findings will be communicated to the village communities as the project advances.\n\nThe protocol has received ethical approval from the Ethics Committee of the University of Antwerp (Ref: 6 July 2023, B3002023000098) and of the Ministry of Health of South Sudan (Ref: 1 September 2023, MOH/RERB 45/2023). Written informed consent will be obtained from all participants and assent from the 12- to 17-year-old children. All collected data during the study will be treated confidentially. Only coded data relevant to the study will be recorded in a database. Findings will be disseminated nationally and internationally via meetings and peer-reviewed publications.\n\nStudy status\n\nEnrolment of the first participants is planned for September 2023.\n\n\nDiscussion\n\nRecent epidemiological studies have shown that OAE is an important, still insufficiently recognised public health problem in many remote onchocerciasis endemic areas in sub-Saharan Africa with onchocerciasis elimination programmes that have been interrupted or work sub-optimally.1 To address this public health problem, it is important to prove that onchocerciasis can induce epilepsy directly or indirectly. Strong epidemiological evidence for the association between onchocerciasis and epilepsy may not suffice to convince public health decision makers to take appropriate action, as solid proof of a causal relationship between onchocerciasis and epilepsy still needs to be established. Therefore, we proposed a viral metagenomic study of the O. volvulus worm to detect a potential unknown virus in the worm that could play a role in the pathogenesis of OAE. To do so, we will obtain microfilariae by skin snips and adult worms by nodulectomies from persons with and without epilepsy in Maridi County, South Sudan.\n\nSo far, little is known about the prevalence, number, size, and localisation of nodules in persons with and without OAE in onchocerciasis-endemic areas. In 2011, in an onchocerciasis-endemic area in west Uganda, Kaiser et al. observed a trend for both a higher proportion of nodule carriers (P = 0.065, Mantel–Haenszel chi-squared test) and a higher mean number of nodules per individual (P = 0.061, Kruskal–Wallis test) in persons with epilepsy than controls.24 In a study in 2011, in the Mbam Valley, an onchocerciasis-endemic area in Cameroon, it was found that persons with epilepsy were two times more likely to present with a palpable nodule than controls (odds ratio = 2.5, 95% confidence interval = 1.24–5.36).25 More recently published data suggest that the prevalence of onchocerciasis nodules in persons with OAE is low.21,26 In a study in an onchocerciasis endemic region in Ituri in the Democratic Republic of Congo nodules were only reported in 3.7% of the person with epilepsy.26 In Maridi in South Sudan nodules were palpated in 5.8% of persons with nodding syndrome and in 0.7% of persons with other forms of epilepsy.21 However, it is important that the nodule prevalence among persons with OAE is reassessed in a study in which all participants are carefully examined by a person with onchocerciasis nodule palpation experience.\n\nWe do not expect that extraction of the adult worms by nodulectomy will significantly influence the frequency of seizures of persons with OAE during the short follow-up period. Prior to the introduction of ivermectin in the control of onchocerciasis, nodulectomy was used as the principal method of disease control in Mexico, Guatemala, and Ecuador. The widespread use of nodulectomy, particularly for the removal of head nodules, was associated with decreasing rates of blindness in Guatemala27; and in Ecuador it was shown to reduce dermal and ocular microfilarial loads.28,29 However, a study in Nigeria showed that in patients with established O. volvulus infections who remain exposed to reinfection, nodulectomy did not reduce microfilarial density to any significant degree.30 So far, the effect of nodulectomy on the frequency of seizures in persons with OAE has never been evaluated. Monitoring the clinical and parasitological parameters of our study participants for a longer period (at least one year) may provide more insight about the impact of nodulectomy on human onchocerciasis.\n\nTo the best of our knowledge, this will be the first viral metagenomic study of O. volvulus worms from South Sudan. Given our preliminary findings of a novel rhabdovirus in O. volvulus worms from Ghana, this new study may provide new insights in the pathogenesis of OAE. Notwithstanding, a weakness of our study is that we will perform nodulectomies in persons with OAE who are at least 12 years old, meanwhile onset of OAE can be as early as three years of age. Therefore, the microfilariae we will obtain might not be the same that initially induced OAE. As such, we might not be able to detect a virus that might have induced epilepsy, except if the latter has persisted in the adult worms which can live for up to 10 years. Nonetheless, describing the virome of O. volvulus will provide us with invaluable information on the viruses present in this parasite. If we detect viruses that could potentially infect humans, we could design PCR tests to screen young children with and without epilepsy in onchocerciasis-endemic areas.\n\nAnother possibility would be that the virus, potentially playing a role in the pathogenesis of OAE, may be present in most or even all O. volvulus worms. Following this hypothesis, the event to induce epilepsy would be an introduction of the virus into brain facilitated by an increased permeability of the blood-brain barrier, for example, because of an inflammatory reaction during a systemic infection in a young child.6 Considering this hypothesis, there would be no difference between OAE and non-OAE worm viromes.\n\nThis study will be the first to describe the number, size, and localisation of nodules in persons with and without OAE in an onchocerciasis-endemic area in South Sudan. However, given the short follow-up period (one month) it will be difficult to evaluate the effect of nodulectomy on the long-term frequency of seizures.\n\nOur study will increase our knowledge about the biology of O. volvulus and may lead to new insights into the pathogenesis of OAE. Additional studies should compare the O. volvulus viromes from South Sudan with the O. volvulus viromes from other countries. Moreover, viral metagenomic studies should be conducted in Onchocerca ochengi31 and other filarial worms. Our project also has diagnostic and therapeutic potential since a virome specific to OAE could be used as a target for molecular tests or drugs. More knowledge about the pathogenesis of OAE could convince public health decision-makers and funders that the O. volvulus parasite is able to directly or indirectly cause epilepsy, and that onchocerciasis-endemic regions with a high prevalence of epilepsy need to be prioritised for strengthening onchocerciasis elimination programmes.", "appendix": "Data availability\n\nNo data are associated with this study.\n\nZenodo: Questionnaire Onchocerciasis-associated epilepsy, an explorative case-control study with viral metagenomic analysis of Onchocerca volvulus, https://doi.org/10.5281/zenodo.8146410. 22\n\nZenodo: Follow up questionnaire Onchocerciasis-Associated Epilepsy, an explorative case-control study with viral metagenomic analysis of Onchocerca volvulus, https://doi.org/10.5281/zenodo.8334911. 23\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 grateful to the Maridi Health Sciences Institute and Amref Health Africa for offering to use its facilities, equipment, and vehicles; to the Western Equatoria State and the Maridi County governments for their support; to the population of Maridi for their cooperation and to Charles Mackenzie for his advice concerning the nodulectomy procedure.\n\n\nReferences\n\nColebunders R, Njamnshi AK, Menon S, et al.: Onchocerca volvulus and epilepsy: A comprehensive review using the Bradford Hill criteria for causation. 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Dis. 2017; 11(1): e0005240. [published Online First: 20170118]. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWalker PJ, Dietzgen RG, Joubert DA, et al.: Rhabdovirus accessory genes. Virus Res. 2011; 162(1-2): 110–125. [published Online First: 20110914]. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nConceicao-Neto N, Zeller M, Lefrere H, et al.: Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis. Sci. Rep. 2015; 5: 16532. [published Online First: 20151112]. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLakwo T, Oguttu D, Ukety T, et al.: Onchocerciasis Elimination: Progress and Challenges. Res Rep Trop Med. 2020; 11: 81–95. [published Online First: 20201007]. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nColebunders R, Carter JY, Olore PC, et al.: High prevalence of onchocerciasis-associated epilepsy in villages in Maridi County, Republic of South Sudan: A community-based survey. Seizure. 2018; 63: 93–101. [published Online First: 20181113]. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nColebunders R, Carter JY, Olore PC, et al.: High prevalence of onchocerciasis-associated epilepsy in villages in Maridi County, Republic of South Sudan: A community-based survey. Seizure. 2018; 63: 93–101. [published Online First: 20181113]. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLakwo TL, Raimon S, Tionga M, et al.: The Role of the Maridi Dam in Causing an Onchocerciasis-Associated Epilepsy Epidemic in Maridi, South Sudan: An Epidemiological, Sociological, and Entomological Study. Pathogens. 2020; 9(4). [published Online First: 20200424]. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJada SR, Amaral LJ, Lakwo T, et al.: Effect of onchocerciasis elimination measures on the incidence of epilepsy in Maridi, South Sudan: a 3-year longitudinal, prospective, population-based study. Lancet Glob. Health. 2023; 11(8): e1260–e1268. PubMed Abstract \| Publisher Full Text\n\nWorld Health Organization: Guidelines for Stopping Mass Drug Administration and Verifying Elimination of Human Onchocerciasis.2006. Reference Source\n\nAbd-Elfarag G, Carter JY, Raimon S, et al.: Persons with onchocerciasis-associated epilepsy and nodding seizures have a more severe form of epilepsy with more cognitive impairment and higher levels of Onchocerca volvulus infection. Epileptic Disord. 2020; 22(3): 301–308. [published Online First: 2020/06/17]. Publisher Full Text\n\nColebunders R: Initial Questionnaire.2023. Publisher Full Text\n\nColebunders R: Follow-up Questionnaire.2023. Publisher Full Text\n\nKaiser C, Rubaale T, Tukesiga E, et al.: Association between onchocerciasis and epilepsy in the Itwara hyperendemic focus, West Uganda: controlling for time and intensity of exposure. Am. J. Trop. Med. Hyg. 2011; 85(2): 225–228. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPion SDS, Boussinesq M: Significant association between epilepsy and presence of onchocercal nodules: case-control study in Cameroon. Am. J. Trop. Med. Hyg. 2012; 86(3): 557. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLenaerts E, Mandro M, Mukendi D, et al.: High prevalence of epilepsy in onchocerciasis endemic health areas in Democratic Republic of the Congo. Infect. Dis. Poverty. 2018; 7(1): 68. [published Online First: 2018/08/02]. Publisher Full Text\n\nDiaz F: Notes and observations on onchocerciasis in Guatemala. Bull. World Health Organ. 1957; 16(3): 676–681. PubMed Abstract\n\nGuderian RH: Effects of nodulectomy in onchocerciasis in Ecuador. Trop. Med. Parasitol. 1988; 39 Suppl 4: 356–357. PubMed Abstract\n\nGuderian RH, Proano R, Beck B, et al.: The reduction in microfilariae loads in the skin and eye after nodulectomy in Ecuadorian onchocerciasis. Trop. Med. Parasitol. 1987; 38(4): 275–278. PubMed Abstract\n\nKale OO: Controlled studies on the effect of nodulectomy on the concentration of microfilariae in the skin of patients exposed o continuing transmission of Onchocerca volvulus in the rain-forest zone of Western Nigeria. Tropenmed. Parasitol. 1982; 33(1): 40–42. PubMed Abstract\n\nHildebrandt JC, Eisenbarth A, Renz A, et al.: Reproductive biology of Onchocerca ochengi, a nodule forming filarial nematode in zebu cattle. Vet. Parasitol. 2014; 205(1-2): 318–329. [published Online First: 20140614]. PubMed Abstract \| Publisher Full Text" }	[ { "id": "221394", "date": "28 Nov 2023", "name": "Jeffrey Loeb", "expertise": [ "Reviewer Expertise Parasitology" ], "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 present a very interesting plan for what could be a really landmark study - but we think that they need to make some refinements for the study to be robust and have meaningful results.\nThe authors are investigating the virome of oncho-infected individuals to try and identify any viruses that could play a role in oncho-associated epilepsy. Importantly, the authors have identified a novel rhabdovirus present in oncho-infected individuals without epilepsy in two countries. They will also test individuals with epilepsy to see if they are infected with this virus (although the fact that those WITHOUT epilepsy are known to be infected with the virus means that even if it is present in those with epilepsy it will be tough to prove that the virus causes epilepsy). However, the overall goal of studying the virome in those with oncho with and without epilepsy is very important and will make for a very interesting study. The additional information they will collect regarding nodule distribution among these groups will also provide interesting information.\n\nWe're not sure why they have selected a population of individuals >12 years old to study when the peak incidence of oncho-associated epilepsy is 8-11 years. Unless there is a really good reason, they may want to change the study protocol to include kids >8 years old.\n\nFor evaluation of seizures, they say they will assess the number of seizures pre- and post-nodulectomy - it's not discussed, but we think the authors should also gather information about seizure semiology and see if this changes following nodulectomy as well.\n\nAnother weakness we foresee in the study design is that they will only remove one oncho nodule - this may not have a significant impact in the overall immunology or clinical condition of the host - why not remove all of the nodules (at least even in a small subset of patients)? Removing 1 of several nodules wouldn't completely answer the question of what impact removing nodules will have, as it still could be argued that any lack of changes seen could be due to the remaining nodules.\nFinally, we're not sure a one-month follow-up will really be sufficient to detect a difference in seizures. We think the authors should seriously consider extending this follow-up period, and if they do not, they need to justify this fully.\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": [ { "c_id": "10674", "date": "30 Nov 2023", "name": "Robert Colebunders", "role": "Author Response", "response": "We selected individuals >12 years old because nodulectomy is an invasive procedure and we prefer not to perform this procedure in small children without their consent. Children >12 years old will need to provide assent and their parents informed consent. We will document seizure semiology but there is currently no evidence that this will change after nodulectomy. Moreover the samples size is small and the persons with epilepsy are also treated with anti-seizure medication. We do not want to remove more than one nodule because nodulectomy is an invasive procedure. Investigating the clinical impact of the nodulectomy is only a secondary objective of the study. If there could be an effect of the nodulectomy on the frequency of seizures we expect this to be observed shortly after removal. After one month, all persons with epilepsy will continue to be followed at the epilepsy clinic in Maridi, where they receive anti-seizure medication, however not part of a study protocol." }, { "c_id": "10715", "date": "17 Jan 2024", "name": "Robert Colebunders", "role": "Author Response", "response": "Response to reviewer 1 The authors present a very interesting plan for what could be a really landmark study - but we think that they need to make some refinements for the study to be robust and have meaningful results. The authors are investigating the virome of oncho-infected individuals to try and identify any viruses that could play a role in oncho-associated epilepsy. Importantly, the authors have identified a novel rhabdovirus present in oncho-infected individuals without epilepsy in two countries. They will also test individuals with epilepsy to see if they are infected with this virus (although the fact that those WITHOUT epilepsy are known to be infected with the virus means that even if it is present in those with epilepsy it will be tough to prove that the virus causes epilepsy). However, the overall goal of studying the virome in those with oncho with and without epilepsy is very important and will make for a very interesting study. The additional information they will collect regarding nodule distribution among these groups will also provide interesting information. We're not sure why they have selected a population of individuals >12 years old to study when the peak incidence of oncho-associated epilepsy is 8-11 years. Unless there is a really good reason, they may want to change the study protocol to include kids >8 years old. Response We selected individuals >12 years old because nodulectomy is an invasive procedure and we prefer not to perform this procedure in small children without their consent. Children >12 years old will need to provide assent and their parents informed consent. Reviewer For evaluation of seizures, they say they will assess the number of seizures pre- and post-nodulectomy - it's not discussed, but we think the authors should also gather information about seizure semiology and see if this changes following nodulectomy as well. Response We will document seizure semiology but there is currently no evidence that this will change after nodulectomy. Moreover, the samples size is small and the persons with epilepsy are also treated with anti-seizure medication. Text change: In persons with epilepsy, the number and types of seizures will be assessed pre-nodulectomy and 10 days and one-month post-nodulectomy. Reviewer Another weakness we foresee in the study design is that they will only remove one oncho nodule - this may not have a significant impact in the overall immunology or clinical condition of the host - why not remove all of the nodules (at least even in a small subset of patients)? Removing 1 of several nodules wouldn't completely answer the question of what impact removing nodules will have, as it still could be argued that any lack of changes seen could be due to the remaining nodules. Response We do not want to remove more than one nodule because nodulectomy is an invasive procedure. However, we do expect to collect multiple nodules per incision as most ‘mother nodules’ are surrounded by smalles ‘satallite’ nodules. Investigating the clinical impact of the nodulectomy is only a secondary objective of the study. Moreover all participants will receive ivermectin twice a year. Therefore, it is unlikely that removing additional nodules may have an added value. Text change: “Only superficially located nodules will be selected for nodulectomy. All nodules accessible through a single incision will be extracted, as multiple smaller nodules are to be expected surrounding the larger ‘mother’ nodule. After extraction of the nodule(s), the skin wound will be sutured and covered by a band aid. Ten days after wound closure the wound will be inspected, and sutures removed.” Reviewer Finally, we're not sure a one-month follow-up will really be sufficient to detect a difference in seizures. We think the authors should seriously consider extending this follow-up period, and if they do not, they need to justify this fully. Response If there could be an effect of the nodulectomy on the frequency of seizures, we expect this to be observed shortly after removal. After one month, all persons with epilepsy will continue to be followed up at the epilepsy clinic in Maridi, where they receive anti-seizure medication, however not as part of a study protocol." } ] }, { "id": "222520", "date": "30 Nov 2023", "name": "Sébastien Pion", "expertise": [ "Reviewer Expertise Parasitology", "epidemiology" ], "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 exploratory study, the investigators will compare the presence and diversity of viruses contained in Onchocerca volvulus worms.\nWhat is the use of O. volvulus antibody testing if all participants harbor onchocercal nodules? A positive test will confirm the obvious whereas a negative test would be quite confusing.\nThere is at least one step missing in the protocol: from the nodulectomy to the worm processing: nodule digestion. This step usually takes hours and requires collagenase enzyme to act at a temperature of about 40°C. Can this step affect the survival of RNA viruses?\nImpact of nodulectomy on frequency of seizures: one can expect a short term impact if the presence of the nodule is directly involved in triggering the seizures, for example like cysticercosis nodules pressuring some parts of the brain. Here, the relationship between nodules and seizure is certainly indirect, and delayed. In addition, it is unlikely that a person harbor one single nodule. Most nodules are located in deeper tissues/organs. Therefore, for the above reasons, removing a single nodule will probably have no consequence on the frequency of seizures.\nIt is unclear if microfilariae present in the skin snips will be screened for viruses too.\nIf viruses are found after processing the worms, how to be sure that those viruses originate from the worms and not residual human tissues?\nCommunities where OAE is observed are communities where onchocerciasis transmission is intense. If a pool of O. volvulus worms contain neurological impairing viruses is present in the community, they will be randomly transmitted to the whole population and those worms would be in competition to infect humans (or not) with O. volvulus population not containing the neurological viruses. Sampling one nodule per person is therefore subject to very unrepresentative results (and it is a well known limitation of examining one nodule and extrapolating during clinical trials for example).\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? Not applicable", "responses": [ { "c_id": "10714", "date": "17 Jan 2024", "name": "Robert Colebunders", "role": "Author Response", "response": "Response to reviewer 2 Reviewer In this exploratory study, the investigators will compare the presence and diversity of viruses contained in Onchocerca volvulus worms. What is the use of O. volvulus antibody testing if all participants harbour onchocercal nodules? A positive test will confirm the obvious whereas a negative test would be quite confusing. Response The Ov16 test will be used to select persons with O. volvulus nodules, because certain nodules may not be caused by onchocerciasis but could be for example a cysticercosis cyst. Text change: à The following text will be replaced above “Nodulectomy” O. volvulus antibody testing Blood will be obtained by finger prick for Ov16 rapid diagnostic testing as an additional prerequisite to verify the origin of the nodule. Moreover, four dry blood spots on filter paper and 5 mL of venous blood will be collected per person to allow for the possibility of using these samples for future pathogenesis and O. volvulus diagnostic studies. Reviewer There is at least one step missing in the protocol: from the nodulectomy to the worm processing: nodule digestion. This step usually takes hours and requires collagenase enzyme to act at a temperature of about 40°C. Can this step affect the survival of RNA viruses? Response We will perform nodule digestion (“Nodules will be incubated in collagenase (Gibco™; ThermoFisher; CNr° 17101015) to break up the outer layer.”) for a total of 9h in 0.5mg/ml collagenase in RPMI, at 37°C and 90RPM. We will check on the nodules every hour, and eventually tease away the human tissue and wash them trice to reduce contact time of the worm with the collagenase. As the worm has a sturdy cuticle, we expect the viruses inside of the worm to still be intact and the DNA/RNA will remain detectable. Text change: Nodules will be incubated in 0.5mg/ml collagenase (Gibco™; ThermoFisher; CNr° 17101015) for an expected total of 9h at 37°C and 90RPM to break up the outer layer. To reduce worm-collagenase contact time, nodules will be checked every hour until signs of digestion occur, to eventually manually tease away the human tissue. Subsequently, all worms will be washed thrice with 20% Percoll® (Sigma-Aldrich; PNr° P1644-25ML) to remove any remnants of collagenase and most potential human viral contaminants. All collected worms from one person will be pooled and submerged in RNAlater for storage. Reviewer Impact of nodulectomy on frequency of seizures: one can expect a short-term impact if the presence of the nodule is directly involved in triggering the seizures, for example like cysticercosis nodules pressuring some parts of the brain. Here, the relationship between nodules and seizure is certainly indirect, and delayed. In addition, it is unlikely that a person harbor one single nodule. Most nodules are located in deeper tissues/organs. Therefore, for the above reasons, removing a single nodule will probably have no consequence on the frequency of seizures. Response We agree that the likelihood that the nodulectomy will have an effect on the frequency of seizures is small but as we will follow-up the persons with epilepsy anyway at the Maridi clinic data on frequency of seizures will be available. Reviewer It is unclear if microfilariae present in the skin snips will be screened for viruses too. Response Screening for viruses in skin snips is not planned in a first phase but will be considered at a later phase using PCR confirmation of the presence of viruses. Skin-snips are planned to determine the infection status and burden. As CDTI is given bi-annually in Maridi, South Sudan, we expect low positivity or negative skin snip results. This will provide us with additional data on individual ivermectin intake and the state of the worms we collected, as we don’t know the impact of ivermectin on the worm’s virome. Moreover, any additional metadata on clinical outcome of onchocerciasis, might reveal preliminary results on the effects of the virome on the infection dynamics. Text change: “To determine infection status, and the impact of ivermectin intake, one skin snip will be collected from either side of the iliac crest using a sclerocorneal biopsy punch.” “the identified viromes might not be the same that initially induced OAE.” Reviewer If viruses are found after processing the worms, how to be sure that those viruses originate from the worms and not residual human tissues? Response In a second phase, we plan to demonstrate the presence of the virus in the worms by immunofluorescence and electron microscopy. However, seeing that we will wash the worm thrice with 20% percoll, we aim to reduce the amount of human tissue contamination on the worm itself. “Subsequently, all worms will be washed thrice with 20% Percoll® (Sigma-Aldrich; PNr° P1644-25ML) to remove any remnants of collagenase and most potential human viral contaminants.” Reviewer Communities where OAE is observed are communities where onchocerciasis transmission is intense. If a pool of O. volvulus worms contain neurological impairing viruses is present in the community, they will be randomly transmitted to the whole population and those worms would be in competition to infect humans (or not) with O. volvulus population not containing the neurological viruses. Sampling one nodule per person is therefore subject to very unrepresentative results (and it is a well known limitation of examining one nodule and extrapolating during clinical trials for example). Response We acknowledge that collecting one nodule per person might not be enough to represent the total exposure of the person, especially as we are collecting worms years after seizure onset. Though, we expect to collect multiple nodules from a single incision due to the occurrence of smaller ‘satellite’ nodules surrounding the ‘mother’ nodule. Nonetheless, we are in a very early stage of investigating the virome of O. volvulus and therefore any additional information will be valuable. To learn more about the dynamics of the virome in this worm, we will perform metagenomics on single worms to identify intranodular variability. In addition we will investigate internodular variability if multiple nodules are recovered from the same person. It is possible that this virus is present in all O. volvulus worms and is not directly associated with epilepsy. However, this study will provide a valuable amount of data on the virome of O. volvulus in the context of an OAE case-control study. Text changes: “Relevant viruses will be evaluated on their potential to infect humans and compared between cases and controls. Single worm viromes will be compared between and within patient nodules to identify inter- and intranodular virome variability to better understand the virome dynamics among worms.” “Only superficially located nodules will be selected for nodulectomy. All nodules accessable through a single incission will be extracted, as multiple smaller nodules are to be expected surrounding the larger ‘mother’ nodule. After extraction of the nodule(s), the skin wound will be sutured and covered by a band aid. Ten days after wound closure the wound will be inspected, and sutures removed.”" } ] } ]	1	https://f1000research.com/articles/12-1262
https://f1000research.com/articles/11-704/v1	27 Jun 22	{ "type": "Research Article", "title": "Leveraging on digital technology for financial inclusion of women agripreneurs in Southern Nigeria", "authors": [ "Ugwuja Vivian Chinelo", "Ekunwe Peter Ayodeji", "Ekunwe Peter Ayodeji" ], "abstract": "Background Women are key players in agriculture, but they are under-resourced, particularly in terms of finance. Microfinance has long been recognized as the most effective method of financially empowering these women, but using the benefits of digital technology can help scale it up and ensure its long-term viability. Methods The study area was Southern Nigeria. Respondents were women agripreneurs (n=479), from six states. 239 women agripreneurs who accessed digital financial products and 240 women agripreneurs who did not access financial products participated in the survey in 2019. Results The tests for significant difference between income of participants and non-participants in digital finance indicated a T-value of 3.214 (P< 0.001), which implies that there was a significant difference in the income of those that are accessing digital financial products (DFPs) and those that are not accessing DFPs. The tests for significant difference between savings of participants and non-participants indicated a T-value of 2.479 (p<0.05), which also implies that there was a significant difference in the women agripreneurs’ savings for participants and non-participants in DFPs. Only 2.5% of women agripreneurs are participating in micro-insurance in Southern Nigeria. Conclusions Women agripreneurs who are accessing digital financial products earned more income and saved more than those who are not accessing digital financial products. This implies that you are more advantaged in using digital finance in business. Micro-insurance is poorly accessed in Nigeria, and awareness of insurance products is moderately low. This study recommends that Central Bank of Nigeria should engage in more outreach programmes to enable all women in Nigeria access digital financial products because of its convenience and contributions to success in business. Insurance companies should capitalize on business models that incorporate mobile technologies in order to increase insurance penetration in rural areas.", "keywords": [ "Women Agripreneurs", "Digital Finance", "Digital Financial Products and Services", "Micro-insurance" ], "content": "Introduction\n\nInformation and communication technologies (ICTs) are a broad category of technological tools and resources used to create, disseminate, preserve, add value to, and manage data. Telecommunications, television and radio broadcasting, computer hardware, software services, and electronic media are all part of the ICT sector.1 Microfinance relies heavily on information. Microfinance institutions (MFIs) collect and keep a massive amount of vital business data, ranging from basic client information to in-depth analysis of portfolio statistics. ICTs now have a greater impact on the structure and operations of businesses than any previous technology.\n\nWomen are key players in agriculture, but they are under-resourced, particularly in terms of finance. Microfinance has long been recognized as the most effective method of financially empowering these women, but using the benefits of digital technology can help scale it up and ensure its long-term viability.\n\nThis new wave of digital finance presents tremendous opportunity for the financial sector and customers alike, promoting individual well-being and nationwide financial inclusion. Using the same dataset as this research, the authors have previously reported on a variety of digital financial products and services.2 Digital financial products and services made available through digital finance are ATM/debit cards, SMS alert services, USSD banking codes, point of sale (POS), balance inquiry, online fund transfer, email alerts, online bill payments, e-statements, online purchases, remittances, online loans, online deposit accounts, online savings accounts and micro-insurance. According to the authors’ previous research,2 micro-insurance notwithstanding its benefit is the least accessed digital financial product. Micro-insurance protects the agripreneurs against losses caused by crop failure. It acts like a tool that allows farmers to manage their yield and price risks. Farmers are able to repay their loans even during the time of crop failure with the support of the right insurance partner.\n\nDespite improvement in financial technology, women remain underrepresented among the banked and formally served, and women remain significantly excluded compared to men,3 Enhancing Financial Innovation and Access (EFINA)3 also indicated that 35 percent of Nigerian rural women have no bank account compared with 60 percent of urban women. The majority of these rural women are agripreneurs whose main occupation is mostly farming.\n\nSome studies have identified financial availability and accessibility as one of the primary impediments and restrictions to economic progress.4 Women as a group who are usually available and willing to embark on entrepreneurial ventures, are hindered sometimes due to the following factors; absence of start-up capital, lack of awareness of existing credit schemes; high interest rates; long and rigorous processes for loan applications; and lack of collateral security for loans.4\n\nWhen we talk about agripreneurship, we refer to the totality of activities which include making profit through commercializing different types of agricultural produce.5 This will range from earning income from farming activities like crop cultivation to fish farming and animal husbandry.6 An agripreneur is a risk-taker, an imaginative and creative genius who has the ability to design and introduce new products capable of drawing customer’s attention. Agripreneurs are productive and can spot unique business opportunities as they look for better methods to organise their farms, try new crops and cultivars, breed better animals, and use alternative technology to boost productivity, diversify production, minimise risk, and improve profit.\n\nAccording to a study embarked upon by Ref. 7, women entrepreneurs, given their position and educational level, could have fantastic business ideas but would lack the requisite capital to executive those ideas. In their view, if they were provided with the right assistance financially and the right guidance, these women could transform to labour employers in no time. The scholars advanced their study by positing that “before the coming of the colonial administrations, African women had led the way, or at least played important roles, in the social and economic development of their different traditional communities”. Nevertheless, the injection of a Victorian culture or idea where women were sidelined in the public organization of things brought about women’s role marginalization. The result in Nigeria became that women could not have a direct access to credit despite the amount involved. Many of them would have their husband, father or brother guarantee them before they got the loan8 also found similar evidence in Latin American communities, that aspiring women entrepreneurs were less likely to access formal credit than men were.\n\nWomen typically do not have access to assets or family property, which contributes to their poverty. It is necessary to conduct a study that evaluates their bad state in order to formulate appropriate policy. Hence the need for this study.\n\nThe specific objectives of this study were to:\n\ni. identify conditions for accessing digital financial products and services (DFS) among women agriprenuers in Southern Nigeria;\n\nii. compare assets, income and savings of women agriprenuers with and without digital financial products and services in Southern Nigeria;\n\niii. examine the level of awareness, perception and participation of women agripreneurs in micro-insurance schemes in Southern Nigeria.\n\nHo1: There is no significant difference in assets, income and savings of women agripreneurs with and without digital financial products and services (DFS) in Southern Nigeria.\n\n\nMethods\n\nThe study was reviewed and approved by the University of Port Harcourt Research Ethics Committee on 2/2/2018 to make sure the research meets high ethical and scientific standards. Verbal consent was obtained from the women agripreneurs; a consent form was attached to the questionnaire which every participant verbally agrees to before participating in the research, this was approved by ethics committee. The reason for verbal consent is because this is the form of consent we obtain when some of the respondents are not literate. The purposes and importance of this study were explained to all women agripreneurs. The responses of each respondent were kept confidential by coding. The data were collected and analyzed anonymously.\n\nThe area of the study was Southern Nigeria. It has a population of 64,978,376 people and covers a total land area of 193,347 km2 (NPC, 2006). Nigeria is divided into six geopolitical zones, three of which make up Southern Nigeria. It is made up of 17 states out of Nigeria's 36. It is covered by a diverse range of vegetation belts, from Nigeria's largest rain forests to mangrove swamps, savannahs, mountains, and waterfalls, all of which are teeming with rare animals, endangered species, and unusual plant families, making it one of the world's richest biodiversity hotspots, attracting both scientists and tourists. The Niger Delta is a Southern Nigerian. This is where the lion's share of the country's oil is discovered.\n\nA multistage sampling procedure was used to choose the respondents for this study. Southern Nigeria is divided into three geopolitical zones: southeast (five states), southwest (six states), and south-south (six states). In each geopolitical zone, two states were chosen at random using simple randomization method, making a total of six states for the study. Abia, Enugu, Bayelsa, Rivers, Ekiti, and Ondo were the states selected. Two Local Government Areas (LGAs) were purposively picked in each selected state, giving a total of 12 LGAs. The LGAs in Abia were Umuahia North and Umuahia South LGAs, in Bayelsa, Yenagoa and Sagbama LGAs, in Enugu, Orji River and Nkanu West LGAs, in Rivers, Ikwerre and Khana LGAs, in Ekiti, Ikere and Ado-Ekiti LGAs, and in Ondo, Akure North and Ifedore LGAs. The study selected two farming communities purposively from each LGA, totaling 24 farming communities. Purposive selection was made based on the presence of financial institutions in the farming communities. Enumerators, who are professional data collectors, assisted in gathering the participants, using key informants in the selected communities. Respondents were approached in their farms, shops, homes and their meeting venues. In each selected community, there was a purposive selection of ten women agripreneurs who use digital financial products and ten women agripreneurs who don't use digital financial goods. This gave a total of 240 of them who have access to digital financial products, and another 240 who do not have access to financial products. For the entire survey, there were 480 women agripreneurs.\n\nPrimary data were collected starting from 26/10/2018, using structured questionnaires where literate participants filled in the questionnaire themselves, and for illiterate participants an oral interview was conducted with the help of enumerators filling the questionnaire on their behalf. The research instrument was validated by a panel of experts in Agricultural Economics and Cybersecurity to make sure it possessed both face and content validity. The researchers ensured that all the corrections pointed out were incorporated before making the final draft. The study used two sets of questionnaires: one for women agripreneurs who use digital financial products, and another for women agripreneurs who do not. The questionnaires have open ended and Yes/No questions.\n\nThe data were analyzed using two distinct approaches: descriptive statistics and inferential statistics such Z-Test. Objectives i and iii were achieved using descriptive statistics such as mean, frequencies and percentages. The software that was used for analysis is SPSS version 25 (2017).\n\nObjective ii was achieved using Z-test. The analysis was done separately for assets, income and savings comparing these variables for women agripreneurs that are using digital financial products and services and those that are not using digital financial products and services. The Z –statistic is mathematically specified as;\n\nZ = the value by which the statistical significance of the mean difference would be judged\n\nX̂ = Mean amount of assets/income/saving women agripreneurs that are accessing digital financial products and services (DFS)\n\nŶ = Mean amount of assets/income/savings of women agripreneurs that are not accessing DFS\n\nS2x = Variance of mean amount of assets/income/savings of women agripreneurs that are accessing DFS\n\nS2y = Variance of mean amount of assets/income/savings of women agripreneurs that are not accessing DFS\n\nnx = Sample size of women agripreneurs that are accessing DFS\n\nny = Sample size of women agripreneurs that are not accessing DFS\n\n\nResults and discussion\n\nResults from Figure 1 show that all (100%) the female heads agreed that they must meet the following conditions before they could access digital financial products (DFPs) (1) Must provide a completed application form; (2) Must use a device (phone, laptop, point of sale (POS) and ATM machines, etc.); (3) Must have a password and a username; (4) Must have a personal identification number; (5) Must have a bank verification number; (6) Must open an account. Finding 2 conforms with expectations because digital financial products are accessed through electronic devices. The majority (95.4%) of the respondents indicated that you must provide a valid identification card, while 94.6% indicated that you must provide your phone number. About 72.4% of the respondents agreed that you must provide a recent passport photograph, while 70.3% agreed that you must download and install a mobile bank application. This finding corroborates with the report of Ref. 9 who stated that Palestinian bank customers accessed digital financial products and services through ATMs and mobile banking applications.\n\nAdditionally, analysis on the results shows that respondents agreed moderately with the following conditions: 1) You must be online (60.3%); 2) You must provide your email address (62.3%); 3) You must have a token (56.1%). None (0%) indicated that you must provide a referee. Participants agreed that they were subjected to the indicated conditions before accessing digital financial products and services.\n\nIn Table 1, the different means of income, savings and assets of women agripreneurs that are accessing DFPs and those that are not accessing are presented. The tests for significant difference between income of participants and non-participants indicated a T-value of 3.214 (p<0.001), which implies that there was a significant difference in the annual income of those that are accessing DFPs and those that are not accessing DFPs. The tests for significant difference between annual savings of participants and non-participants indicated a T-value of 2.479 (p<0.05), which also implies that there was a significant difference in the women agripreneurs’ savings for participants and non-participants in DFPs. The tests for significant difference for assets between participants and non-participant in DFPs was not significant. The mean annual income was NGN372,938.22 and NGN288,720.06 for participants and non-participants respectively, and mean annual savings were NGN132,534.23 and NGN86,304.17 for participants and non-participants respectively. This implies that women agripreneurs who accessed DFPs had more successful businesses than those who did not access DFPs.\n\nAnalysis from Figure 2 shows that majority (66.5%) of women agripreneurs that are accessing digital financial products agreed that they are aware of micro-insurance schemes in Southern Nigeria. Analysis from Figure 3 also indicated that majority (65.0%) of women agripreneurs who are not accessing digital financial products indicated that they are not aware of micro-insurance schemes, implying that women agripreneurs who access digital financial products know more about micro-insurance than those who are not accessing digital financial products. Pooled response from Figure 4 indicated that 50.5% of the women agripreneurs in Southern Nigeria are aware of micro-insurance schemes in Nigeria, implying that on average half of the respondents are aware of micro-insurance schemes.\n\nResults from Figure 5 shows that majority (95.8%) of female heads who are accessing digital financial products are not participating in micro-insurance schemes. Also, Figure 6 shows that none (0%) of the female heads who are not accessing digital financial products participates in micro-insurance schemes. Figure 7 shows pooled responses from women agripreneurs who are accessing and not accessing digital financial products on participation in micro-insurance schemes. Only 2.5% of the respondents are participating in micro-insurance. The implication of this is that many Nigerians do not access micro-insurance products. This corroborates the findings of Ref. 10 which states that out of 96.4 million adults, only 0.3 million use micro-insurance products. The findings of Ref. 2 also reported poor participation of women in accessing insurance products.\n\nFigure 8 shows the perceptions of women agripreneurs who are accessing digital financial products on insurance. Most of them agreed with the following statements: (1) Insurance is beneficial to farmers because it helps to cushion the effects of risks (70.3%); (2) I perceive that compensation to be paid will not cover losses (64.9%); (3) The premium rate is very high (64%); (4) Insurance is not a priority to me compared to other needs (64%); (5) Insurance reduces farmers’ worries and stress (63.6%);(6) I have the fear that compensation will be delayed for a long time (62.9%); (7) I have fears that claims may not be paid (59.4%) and (8) There is usually long bureaucracy in obtaining an insurance cover (51.5%).\n\nA minority of the respondents agreed to the following statements: (1) Insurance is not needed to cushion the effects of losses or damages (6.7%); (2) Recovering farmers’ losses is government liability (21.8%); (3) Insurance should be mandatory (37.2%).\n\nResults from Figure 9 shows the perception of women agripreneurs who are not accessing digital financial products on insurance. They agreed moderately to the following statements: (1) I have the fear that compensation will be delayed for a long time (49.6%); (2) Insurance is not a priority to me compared to other needs (48.3%); (3) Insurance is beneficial to farmers because it helps to cushion the effects of risks (48.3%) (4) I perceive that compensation to be paid will not cover losses (47.1%); (5) The premium rate is very high (44.6%); (6) Insurance reduces farmers’ worries and stress (43.3%); (7) I have fears that claims may not be paid (41.3%); (8) There is usually long bureaucracy in obtaining an insurance cover (40.4%).\n\nA minority of the respondents agreed with the following statements: (1) Insurance is not needed to cushion the effects of losses or damages (13.3%); (2) Insurance should be mandatory (21.3%); (3) Recovering farmers’ losses is government liability (20.0%).\n\nFrom the findings of this research, the perceptions of these women on micro-insurance could be a major reason why they don’t participate in insurance schemes.\n\n\nConclusion\n\nDigital finance through the use of financial technology may be very convenient but has many conditions required to access it. Findings from this study shows that users must use a device (phone, laptop, POS and ATM machines, etc.), must have a password and a username, must have a personal identification number, must have a bank verification number and you must open an account. Women agripreneurs who are accessing digital financial products earned more income and saved more than those who are not accessing digital financial products. This implies that you are more advantaged in using digital finance in business. Micro-insurance is poorly accessed in Nigeria, and awareness of insurance products is moderately low. Most of the women agripreneurs perceive that insurance is beneficial to farmers because it helps to cushion the effects of risk, and also perceive that compensation to be paid will not cover losses and that the premium rate is very high. This study recommends that Central Bank of Nigeria should engage in more outreach programmes to enable all women in Nigeria access digital financial products because of its convenience and contributions to success in business. Insurance companies should capitalize on business models that incorporate mobile technologies in order to increase insurance penetration in rural areas. This is the first research that has studied digital finance and perception on insurance of women agripreneurs in Southern Nigeria. A limitation is that it was not able to study men agripreneurs, and therefore it is recommended that future research should be carried out on the digital finance and perception on insurance of men agripreneurs.\n\n\nData availability\n\nUnderlying data figshare: Leveraging on Digital Technology for Financial Inclusion of Women Agripreneurs in Southern Nigeria. https://doi.org/10.6084/m9.figshare.19657671.v111\n\nThis project contains the following files\n\n- Non participants.sav (raw data file)\n\n- Participants.sav (raw data file)\n\nfigshare: Leveraging on Digital Technology for Financial Inclusion of Women Agripreneurs in Southern Nigeria. https://doi.org/10.6084/m9.figshare.19657671.v111\n\nThis project contains the following files\n\n- Questionnaire for participants.sav\n\n- Questionnaire for non-participants.sav\n\n- Data key for participants\n\n- Data key for non-participants\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).", "appendix": "Acknowledgements\n\nWe would like to thank the women agripreneurs who willingly participated in the study, extension agents and field enumerators who conducted the survey. The project recognizes the support of the host University, University of Port Harcourt, and most importantly, the AXA Research Fund Community for funding this research.\n\n\nReferences\n\nPardhasaradhi Y, Nagender RV: Women empowerment: Information Technology as a critical input. Indian Journal of Public Administration. 2014; LX(3): 126–516.\n\nUgwuja VC, Adesope OM: Cyber risks in Microfinance Digitization: Exposures and Preventions among Female Headed Farm Households in Southern Nigeria. European Journal of Agriculture and Food Sciences. 2021; 3(3): 62–68. Publisher Full Text\n\nEnhancing Financial Innovation and Access (EFInA): Access to Financial Services in Nigeria 2020 Survey.2021.Reference Source\n\nIfelunini IA, Wosowei EC: Does microfinance reduce poverty among women entrepreneurs in South-South Nigeria? Evidence from propensity score matching technique. European Journal of Business and Management. 2013; 21: 76–87.\n\nIrobi NC: Microfinance and poverty alleviation: A case study of Obazu progressive Women association Mbieri, Imo State, Nigeria. (An Unpublished Master Thesis) Sverigesantbruks University, Uppsala, Sweden.2008.\n\nYusuf A, Ahmad NH, Abdulhalim H: Entrepreneurial orientation and Agropreneurial intention among Malaysia Agricultural student: Impact of Agropreneurship.2017.Reference Source\n\nOdejimi DO: Agabada: “Industrialization: key to socio-economic development in Nigeria”. International Journal of Economic and Development Studies. 2014; 5(2): 69–78.\n\nSabarwal S, Terrell K: Access to credit and performance of female entrepreneurs in Latin America. Frontiers of Entrepreneurship Research. 2009; 29(18): 6–14.\n\nSuliman AE, Mazen JAS, Samy SA: Electronic Banking Services from the Point of View of Bank Customers in Palestine. International Journal of Academic Accounting, Finance & Management Research (IJAAFMR). 2019; 3(10): 45–60.\n\nEnhancing Financial Innovation and Access (EFInA): Access to Financial Services in Nigeria 2016 Survey. http\n\nVivian Chinelo U, Peter Ayodeji E: Leveraging on Digital Technology for Financial Inclusion of Women Agripreneurs in Southern Nigeria. figshare. [Dataset].2022. Publisher Full Text" }	[ { "id": "151576", "date": "04 Oct 2022", "name": "Lee-Ying Tay", "expertise": [ "Reviewer Expertise Area of research: Digital finance", "Stock price", "Digital financial products and services" ], "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, the manuscript is satisfactory with improvement needed. The comments are as below:\nIs the work clearly and accurately presented and does it cite the current literature?\nAnswer: Partly. The manuscript should add a section of literature review discussing the latest issues on (1) digital technology for financial inclusion; (2) evidence of financial inclusion of women agripreneurs; (3) variables of interest including income, savings, and others. The authors should also cite sufficient and updated references in recent five years.\nIs the study design appropriate and is the work technically sound?\nAnswer: Partly. The authors should add in research questions that are consistently mapped with research objectives. The authors should also add a short write-up on how the research questions and objectives are mapped since the research objective (1) and (3) are achieved through descriptive analysis.\nAre sufficient details of methods and analysis provided to allow replication by others?\nAnswer: The total sample size is not consistent in ‘’Abstract” and ‘’Methodology”. Please further describe the formation of the sample size. It would be great if the authors can attach the survey instruments in this manuscript.\nAre the conclusions drawn adequately supported by the results?\nAnswer: Reasoning should be given why men agripreneurs were not included in the study and provide suggestions for future research on how men agripreneurs can be studied.\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?\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? Partly", "responses": [ { "c_id": "10720", "date": "17 Jan 2024", "name": "ugwuja vivian", "role": "Author Response", "response": "Sorry for responding late, I will make all the necessary corrections as pointed out by the reviewer" }, { "c_id": "10749", "date": "13 Apr 2024", "name": "ugwuja vivian", "role": "Author Response", "response": "I have made all the necessary corrections." } ] }, { "id": "170322", "date": "02 May 2023", "name": "Jean-Claude KOULADOUM", "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\nThank you for giving me this opportunity to review this paper. This paper is entitled as: Leveraging on digital technology for financial inclusion of women agripreneurs in Southern Nigeria The objective conducts by the authors are very interesting and the method used to achieve this is appropriate. Reading this article raises some questions:\nWhy is the case of Southern Nigeria important to study in the relationship between digital technologies and financial inclusion? Your general introduction does not provide this information.\n\nYour general introduction contains almost no authors. This is surprising.\n\nThe literature review appears incomplete, is not critical, nor is there sufficient academic support for the arguments in the article. You can provide at the beginning of this section the theoretical and empirical foundation of digital technology for financial inclusion.\n\nThe policy recommendation part needs to be revised.\n\nReferences to previous research: Either compare your results with the findings from other studies or use the studies to support a claim. This can include re-visiting key sources already cited in your literature review section or saving them from citing later in the discussion section if they are more important to compare with your results instead of being a part of the general literature review of prior research used to provide context and background information.\nConsideration of the above comments will improve the quality of this article.\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?\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": "9651", "date": "29 Nov 2023", "name": "ugwuja vivian", "role": "Author Response", "response": "Why is the case of Southern Nigeria important to study in the relationship between digital technologies and financial inclusion? Your general introduction does not provide this information. Reply: I will attend to that Your general introduction contains almost no authors. This is surprising. I am surprised to see this comment, because I have more than 5 authors in the introduction The literature review appears incomplete, is not critical, nor is there sufficient academic support for the arguments in the article. You can provide at the beginning of this section the theoretical and empirical foundation of digital technology for financial inclusion. Reply: I will do that The policy recommendation part needs to be revised. \\ Reply: I will attend to that References to previous research: Either compare your results with the findings from other studies or use the studies to support a claim. This can include re-visiting key sources already cited in your literature review section or saving them from citing later in the discussion section if they are more important to compare with your results instead of being a part of the general literature review of prior research used to provide context and background information. Reply: The previous study was cited twice, in the literature review and discussion section" } ] } ]	1	https://f1000research.com/articles/11-704
https://f1000research.com/articles/12-381/v1	11 Apr 23	{ "type": "Research Article", "title": "The dosage of thiopental as pharmacological cerebral protection during non-shunt carotid endarterectomy: A retrospective study", "authors": [ "Pimwan Sookplung", "Pathomporn Suchartwatnachai", "Phuping Akavipat", "Pathomporn Suchartwatnachai", "Phuping Akavipat" ], "abstract": "Background: Thiopental has been used as a pharmacological cerebral protection strategy during carotid endarterectomy surgeries. However, the optimal dosage required to induce burst suppression on the electroencephalogram (EEG) remains unknown. This retrospective study aimed to determine the optimal dosage of thiopental required to induce burst suppression during non-shunt carotid endarterectomy. Methods: The Neurological Institute of Thailand Review Board approved the study. Data were collected from 2009 to 2019 for all non-shunt carotid endarterectomy patients who received thiopental for pharmacological cerebral protection and had intraoperative EEG monitoring. Demographic information, carotid stenosis severity, intraoperative EEG parameters, thiopental dosage, carotid clamp time, intraoperative events, and patient outcomes were abstracted. Results: The study included 57 patients. Among them, 24 patients (42%) achieved EEG burst suppression pattern with a thiopental dosage of 26.3+10.1 mg/kg/hr. There were no significant differences in perioperative events between patients who achieved burst suppression and those who did not. After surgery, 33.3% of patients who achieved burst suppression were extubated and awakened. One patient in the non-burst suppression group experienced mild neurological deficits. No deaths occurred within one month postoperative. Conclusions: The optimal dosage of thiopental required to achieve burst suppression on intraoperative EEG during non-shunt carotid endarterectomy was 26.3+10.1 mg/kg/hr.", "keywords": [ "Carotid endarterectomy", "barbiturate", "thiopental", "burst suppression", "electroencephalogram" ], "content": "Introduction\n\nStroke is one of the leading causes of death and disability in Thailand,1 and carotid stenosis is one of the leading causes of stroke.2 The surgical treatment to prevent stroke is carotid endarterectomy (CEA). It is associated with periprocedural risks, including stroke (embolic or hemodynamic), myocardial infarction, and death. Therefore, strict selection criteria are applied for patients undergoing CEA. Current selection criteria support CEA for symptomatic low-risk surgical patients with 50% to 99% stenosis and asymptomatic patients with stenosis of 70% to 99%.3 However, the ability of the patient to tolerate the cross-clamp depends on the sufficiency of collateral flow through the circle of Willis. Inadequate collateral cerebral perfusion during the cross-clamp period increases the risk of perioperative stroke.4 Despite routine intraluminal shunt during the temporary occlusion of the ipsilateral internal carotid artery being controversial, intraoperative electrophysiological monitoring, such as electroencephalogram (EEG), is a valuable tool to detect cerebral hypoperfusion and determine selective shunting.5,6 When the neurosurgeon performed the non-shunt technique, adequate cerebral perfusion during carotid cross-clamping could be achieved using several methods to protect the brain.7 Spetzler et al.8 reported excellent non-shunt surgical outcomes using intra-operative barbiturate and microsurgical techniques. The clinical use of barbiturates is known for cerebral protection against the prevention of focal cerebral ischemia,9 especially when barbiturate was administered before the ischemic insult with doses large enough to produce burst-suppression activity on the EEG.10 However, no definite predetermined amount of barbiturate-induced burst-suppression activity on EEG; to reach the burst-suppression pattern, the optimal dosage, timing, and administration mode vary among studies.\n\nThe Neurological Institute of Thailand is one of the few medical centers with EEG for intraoperative surveillance. Thus the authors aimed to study the optimal dose of barbiturates as thiopental for inducing EEG burst-suppression patterns in anesthetized patients undergoing carotid endarterectomy with a non-shunt technique.\n\n\nMethods\n\nThe study was approved by The Research Ethics Committee of the Neurological Institute of Thailand (approval number IRB53068). Written informed consent was waived, as this study was a retrospective observational without patient interventions. Data were collected from all consecutive patients with carotid artery stenosis who underwent CEA at the Neurological Institute of Thailand, Bangkok, from January 2009 to December 2019. Patients scheduled for CEA with intraoperative EEG were included, while Patients undergoing CEA without thiopental as pharmacological cerebral protection were excluded.\n\nIn our institution, neurosurgeons perform carotid endarterectomy under general anesthesia using a non-shunt technique with pharmacological cerebral protection strategies.11\n\nIn addition to standard anesthetic monitoring with an arterial line, all patients were monitored with the two-channel cortical EEG using the EEG pod of Infinity Delta Series (Drager Medical AG & Co. Lubeck, Germany). The EEG signal was obtained using silver-silver chloride electrodes located according to the international 10-20 systems. The differential montage was recorded: left and right frontal (FP1-C3, FP2-C4; channels 1 and 2), with a neutral electrode placed at the ear lobe. The impedance was recommended at < 5,000 ohms. Power Spectra analysis (Fast Fourier transform: FFT) was used to simplify the complex EEG to computer-processed EEG (CEEG) for an 8-second epoch. Trained anesthesiologists visually assessed the raw EEG and compressed spectral EEG parameters [Spectral Edge Frequency 95% (SEF95%), Median (MED), and Burst Suppression Ratio (BSR)]. Burst Suppression Ratio (BSR) was defined as the percentage of time the EEG waveform is flatlined over the last 60 seconds (when flatline EEG alternates with “bursts” of activity).\n\nAnesthesia was induced with thiopental (Pentothal Sodium®) (3-5 mg/kg) or propofol (1-2 mg/kg), followed by fentanyl (1-2 mcg/kg), atracurium (0.5-0.6 mg/kg), or cis-atracurium (0.15 mg/kg) to facilitate tracheal intubation. The anesthesia was maintained with sevoflurane or desflurane (<1 MAC) and continuous infusion of a neuromuscular blocking agent (atracurium 0.3-0.5 mg/kg/hr or cis-atracurium 0.06-0.1 mg/kg/hr). An additional dose of fentanyl 25-50 mcg was titrated during the operation. Antihypertensive medications were administered for hypertension, and fluids or vasopressors were used to treat hypotension.\n\nBefore the temporary occlusion of the carotid artery, a single dose of heparin 5,000 units and thiopental (5 mg/kg) was given intravenously (IV) followed by continuous infusion of 10 mg/kg/hr with an additional 50 mg titrated intravenously to achieve burst suppression on EEG throughout the ischemic period. During the carotid clamp time, the blood pressure was raised 10% above the pre-operative level to induce collateral circulation. The inhalation agent was suspended during the thiopental infusion. At the end of the operation, the neuromuscular blockade was reversed with glycopyrrolate 0.2 mg for each 1.0 mg of neostigmine or atropine 0.02 mg/kg and neostigmine 0.02 to 0.07 mg/kg. The patient was extubated if the patient had adequate ventilation, eye-opening, and purposeful responses. All patients were transferred to the neurosurgical intensive care unit for postoperative care.\n\nElectronic database searches and manual data were abstracted, including demographic data, clinical courses, and outcomes. Patient characteristics were age, gender, American Society of Anesthesiologists Physical Status classification (ASA), Glasgow Coma Scale (GCS), and history of any comorbidities: cerebrovascular accident or transient ischemic attack (TIA), coronary artery disease (CAD), hypertension (HT), diabetes mellitus (DM), and dyslipidemia. Pre-operative investigation data such as the site and degree of stenosis measured by carotid duplex ultrasonography and magnetic resonance angiography (MRA) or conventional angiography were abstracted.\n\nIntraoperative data including EEG parameters [Burst suppression ratio (BSR), Spectral edge frequency 95% (SEF95%), Median (MED)], thiopental dosage, carotid clamp time, intraoperative events (hypertension, hypotension, cardiac arrhythmias), duration of surgery, fluid administration, estimated blood loss, perioperative blood product transfusions (units), and successful extubation after surgery. Extubation time in the neurosurgical intensive care unit, Glasgow outcome scale (GOS) at discharge, and one-month postoperative were studied.\n\nThe study's primary outcome was the amount of thiopental required to achieve burst suppression on EEG during cerebral protection. In addition, the study investigated several secondary outcomes related to the patient's recovery, including the percentage of successful extubations after surgery, the time to extubation in the neurosurgical intensive care unit, and the Glasgow Outcome Scale (GOS) at discharge and one month postoperatively. These measures were analyzed to assess the patient's recovery following the procedure.\n\nStatistical analysis was performed using SPSS Statistical software, version 22 (IBM SPSS Inc., Chicago, IL). Descriptive statistics were presented as means±standard deviations, percentages, and numbers. The Chi-square test was used to compare categorical variables, while unpaired t-tests were employed for analyzing continuous variables. Paired t-tests were utilized to compare EEG data before and the average of EEG data during the carotid cross-clamp. A significance level of P-value≤0.05 was considered statistical significance.\n\n\nResults\n\nThere were 69 carotid endarterectomies performed during the study period, with 12 cases excluded. Of the remaining 57 patients analyzed (Figure 1), only 24 achieved burst suppression on intraoperative EEG despite receiving continuous thiopental infusion with additional titration. These 24 patients were classified as the burst suppression group (BS) for the analysis. The demographic data and related details of both the BS and non-BS group are presented in Table 1. The group had a significantly higher average age of 72.8±9.1 years than the non-BS group, with an average age of 66.7±7.2 years (p-value=0.007). However, there were no significant differences in gender, body weight, ASA physical status, comorbidities, or pre-operative investigation data between the two groups. Hypertension was a common condition in both groups. The percentage of patients who received thiopental or propofol as induction agents and the dosages were not significantly different between the two groups (Table 2). Perioperative doses of fentanyl and end-tidal concentrations of sevoflurane or desflurane also showed no significant differences. The amount of thiopental required to achieve burst suppression on intraoperative EEG was significantly higher in the BS group compared to the non-BS group (26.3±10.1 mg/kg/hr vs. 18.7±8.8, p-value=0.004). Although the carotid clamp time was slightly shorter in the BS group, it did not reach statistical significance (73.2±23.7 min vs. 83.3±34.8, p-value=0.225).\n\nThe spectral edge frequency 95% (SEF95%) of both the BS and non-BS groups tended to decrease after carotid clamping, as indicated in Table 3. However, the two groups had no significant difference regarding MED or SEF95% before and after the clamping. Similarly, neither group significantly differed between the left and right MED or SEF95%. After carotid clamping, the BS group had an average BSR of 36.0±20.4 (right) and 36.3±20.6 (left), but this difference was not statistically significant. In contrast, the non-BS group did not exhibit any burst suppression pattern.\n\nThe incidence of hypertension, hypotension, and arrhythmias did not show a statistically significant difference between the two groups. Following the operation, eight patients (33.3%) in the BS group and sixteen (48.5%) in the non-BS group were awake and extubated. Most patients in both groups were intubated and transferred to the neurosurgical intensive care unit. There was no significant difference in extubation time for patients who were initially unable to extubate between the two groups (BS group 872.4±593.3 min. vs. non-BS group 601.6±473.9 min). One patient experienced a mild neurological deficit. No deaths were reported one month after the operation (Table 4).\n\n\nDiscussion\n\nThis study aimed to determine the amount of thiopental required to induce burst suppression patterns on intraoperative EEG monitoring in patients undergoing carotid endarterectomy without a shunt and to evaluate patient outcomes. The main findings indicated that not all patients achieved burst suppression despite the intention to maximize cerebral protection through a continuous thiopental infusion and titrated intravenous administration. Patients who received significantly higher doses of thiopental (26.3±10.1 mg/kg/hr) were likelier to achieve burst suppression on EEG. However, no significant difference was observed in postoperative outcomes between the burst suppression (BS) and non-burst suppression (non-BS) groups. Currently, limited data is available on the efficacy and optimal dosage of thiopental for inducing pharmacological burst suppression to prevent perioperative stroke during selective shunting in CEA.\n\nBarbiturates, such as thiopental, are commonly used to prevent cerebral ischemia during cerebrovascular surgery. Thiopental is a fast-acting, short-duration barbiturate anesthetic that may exert its neuroprotective effects through various mechanisms, including antioxidant activity, GABA-ergic activity, stimulation of protein synthesis, removal of free radicals, and modulation of excitatory synaptic neurotransmission via adenosine.12 Animal studies have shown that barbiturates can decrease brain oxygen demand and the size of cerebral infarction.13–15 In cerebrovascular procedures that require temporary clips, such as extracranial-intracranial bypasses, carotid endarterectomies, and aneurysm clipping, barbiturates have been demonstrated to reduce the cerebral metabolic rate of oxygen and increase blood flow to ischemic regions.16–18\n\nThe thiopental dose required for EEG burst suppression patterns during cerebrovascular surgery can vary depending on several factors, including variability in monitoring and assessing burst suppression levels among healthcare providers. Sreedhar and Gadhinglajkar19 have reviewed several dosing regimens of thiopental for cerebrovascular surgery, including a bolus dose (4 mg/kg), a low dose followed by IV infusion (1 to 3 mg/kg IV followed by 0.06 to 0.2 mg/kg/min), and a high dose followed by infusion (loading 25 to 50 mg/kg followed by 2 to 10 mg/kg/hr).\n\nThe initial bolus doses of thiopental used in our study did not result in EEG burst suppression for most patients, which differs from the findings of Ramesh VJ.20 According to Ramesh VJ, almost all patients who received a bolus dose of 3 to 5 mg/kg experienced EEG burst suppression with a BSR greater than 25%. The initial bolus doses of thiopental only resulted in temporary suppression durations, consistent with previous studies by Moffat et al.21 and Gelb et al.,22 which provided limited cerebral protection during the intraoperative period.\n\nOur study used a continuous thiopental infusion to maintain EEG burst suppression during the carotid cross-clamp procedure. We administered a high dose of thiopental, similar to previous studies by McConkey PP et al.23 and Frawley JE et al.24 However, not all patients in our study achieved EEG burst suppression, unlike the abovementioned studies where incremental bolus doses of thiopental were titrated. Nonetheless, none of our patients experienced a significant period of ischemia, as defined by a decrease in SEF95% to 50% of the baseline.25\n\nEEG-confirmed burst suppression is commonly accepted as the optimal endpoint for cerebral protection following barbiturate therapy during cerebrovascular surgery. Intraoperative monitoring of burst suppression is typically conducted using electroencephalography (EEG) or Bispectral Index (BIS).26,27 However, BIS-derived BSR may underestimate the duration of EEG suppression, potentially reducing sensitivity for detecting burst suppression.28 Our study opted for direct visualization of the EEG trace to achieve a more accurate and real-time comparison of raw EEG changes and BSR values between both sides of the brain. This EEG trace allowed us to detect potential cerebral ischemia and determine the level of cerebral protection.\n\nThe study found that older patients were more likely to achieve burst suppression on EEG with thiopental therapy, potentially due to age-related factors.29 Although not all patients achieved burst suppression, the BS and non-BS groups had favorable clinical outcomes without significant perioperative complications. The BS group did have a more extended postoperative intubation period. However, their Glasgow Outcome Scale was not significantly different from the non-BS group at discharge or one month after surgery. These outcomes could be attributed to barbiturate therapy, as research on rats suggests that EEG burst suppression may not be necessary for maximum cerebral protection.30,31 Barbiturates can offer sufficient brain protection at lower doses that do not require EEG burst suppression. Further research is needed to verify this concept in humans.\n\nThe dosage of thiopental that does not lead to EEG burst suppression may impact cerebral protection during carotid endarterectomy. However, thiopental-induced cerebral protection is only one of several strategies for cerebral protection. Other factors, such as the degree of stenosis, pre-existing medical conditions, and perioperative risks associated with carotid endarterectomy, influence patient outcomes.32\n\nLimitations of this study include the fact that it only focused on the dosage of thiopental and its effects on intraoperative EEG monitoring as a direct tool for evaluating brain electrical activity during carotid endarterectomy. It is important to note that EEG only provides information on brain electrical activity and does not directly measure cerebral blood flow or cerebral oxygen saturation (SjVO2). Therefore, relying solely on EEG may not accurately reflect the actual level of cerebral protection. Multimodal intraoperative monitoring techniques, such as transcranial Doppler (TCD) ultrasound, somatosensory evoked potentials, and cerebral oxygen saturation monitoring, are recommended for a more comprehensive patient status assessment. Additionally, this study did not assess the thiopental serum levels for barbiturate coma treatment. The retrospective cohort design also limited the quality of data collection. Therefore, a prospective randomized study is recommended to investigate further the role of intraoperative monitoring and barbiturate therapy in optimizing cerebral protection during carotid endarterectomy.\n\nIn conclusion, thiopental at a dosage of 26.3+10.1 mg/kg/hr can induce burst suppression on intraoperative EEG during carotid endarterectomy, potentially providing cerebral protection. Further research is needed to understand thiopental's neuroprotective mechanisms and explore alternative monitoring techniques.", "appendix": "Data availability\n\nFigshare: DATA of ThioBS_CEA, https://doi.org/10.6084/m9.figshare.22132898.v1. 33\n\nThis project contains the following underlying data:\n\n- f1000-ThioBSR_2_21_23.xlsx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nHanchaiphiboolkul S, Poungvarin N, Nidhinandana S, et al.: Prevalence of stroke and stroke risk factors in Thailand: Thai Epidemiologic Stroke (TES) Study. J. Med. Assoc. Thail. 2011; 94(4): 427–436. PubMed Abstract\n\nBellosta R, Luzzani L, Carugati C, et al.: Routine shunting is a safe and reliable method of cerebral protection during carotid endarterectomy. Ann. Vasc. Surg. 2006; 20(4): 482–487. PubMed Abstract \| Publisher Full Text\n\nAbuRahma AF, Avgerinos ED, Chang RW, et al.: Society for Vascular Surgery clinical practice guidelines for management of extracranial cerebrovascular disease. J. Vasc. Surg. 2022; 75(1S): 4S–22S. PubMed Abstract \| Publisher Full Text\n\nde Borst GJ , Moll FL, van de Pavoordt HD , et al.: Stroke from carotid endarterectomy: when and how to reduce perioperative stroke rate?. Eur. J. Vasc. Endovasc. Surg. 2001; 21(6): 484–489. Publisher Full Text\n\nWiner JW, Rosenwasser RH, Jimenez F: Electroencephalographic activity and serum and cerebrospinal fluid pentobarbital levels in determining the therapeutic end point during barbiturate coma. Neurosurgery. 1991; 29(5): 739–742. Publisher Full Text\n\nReuter NP, Charette SD, Sticca RP: Cerebral protection during carotid endarterectomy. Am. J. Surg. 2004; 188(6): 772–777. Publisher Full Text\n\nSultan S, Acharya Y, Barrett N, et al.: A pilot protocol and review of triple neuroprotection with targeted hypothermia, controlled induced hypertension, and barbiturate infusion during emergency carotid endarterectomy for acute stroke after failed tPA or beyond 24-hour window of opportunity. Ann. Transl. Med. 2020; 8(19): 1275. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSpetzler RF, Martin N, Hadley MN, et al.: Microsurgical endarterectomy under barbiturate protection: a prospective study. J. Neurosurg. 1986; 65: 63–73. PubMed Abstract \| Publisher Full Text\n\nNussmeier NA, Arlund C, Slogoff S: Neuropsychiatric complications after cardiopulmonary bypass: cerebral protection by a barbiturate. Anesthesiology. 1986; 64(2): 165–170. PubMed Abstract \| Publisher Full Text\n\nKim TK, Park IS: Comparative Study of Brain Protection Effect between Thiopental and Etomidate Using Bispectral Index during Temporary Arterial Occlusion. J. Korean Neurosurg. Soc. 2011; 50(6): 497–502. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLiengudom A, Tirakotai W, Vuttiopas C: Surgical outcome of the non-shunt carotid endarterectomy. J. Med. Assoc. Thail. 2012; 95(6): 782–789. PubMed Abstract\n\nSchifilliti D, Grasso G, Conti A, et al.: Anaesthetic-related neuroprotection: intravenous or inhalational agents? CNS Drugs. 2010; 24(11): 893–907. PubMed Abstract \| Publisher Full Text\n\nMcDermott MW, Durity FA, Borozny M, et al.: Temporary vessel occlusion and barbiturate protection in cerebral aneurysm surgery. Neurosurgery. 1989; 25(1): 54–62. Publisher Full Text\n\nHayashi S, Nehls DG, Kieck CF, et al.: Beneficial effects of induced hypertension on experimental stroke in awake monkeys. J. Neurosurg. 1984; 60(1): 151–157. PubMed Abstract \| Publisher Full Text\n\nSelman WR, Spetzler RF, Roessmann UR, et al.: Barbiturate-induced coma therapy for focal cerebral ischemia. Effect after temporary and permanent MCA occlusion. J. Neurosurg. 1981; 55(2): 220–226. PubMed Abstract \| Publisher Full Text\n\nAstrup J: Energy-requiring cell functions in the ischemic brain. Their critical supply and possible inhibition in protective therapy. J. Neurosurg. 1982; 56(4): 482–497. PubMed Abstract \| Publisher Full Text\n\nAstrup J, Rosenørn J, Cold GE, et al.: Minimum cerebral blood flow and metabolism during craniotomy. Effect of thiopental loading. Acta Anaesthesiol. Scand. 1984; 28(5): 478–481. PubMed Abstract \| Publisher Full Text\n\nBranston NM, Hope DT, Symon L: Barbiturates in focal ischemia of primate cortex: effects on blood flow distribution, evoked potential and extracellular potassium. Stroke. 1979; 10(6): 647–653. PubMed Abstract \| Publisher Full Text\n\nSreedhar R, Gadhinglajkar S: Pharmacological neuroprotection. Indian J. Anaesth. 2003; 47: 8–22.\n\nRamesh VJ, Umamaheswara Rao GS: Quantification of burst suppression and bispectral index with 2 different bolus doses of thiopentone sodium. J. Neurosurg. Anesthesiol. 2007; 19(3): 179–182. PubMed Abstract \| Publisher Full Text\n\nMoffat JA, McDougall MJ, Brunet D, et al.: Thiopental bolus during carotid endarterectomy-rational drug therapy? Can. Anaesth. Soc. J. 1983; 30(6): 615–622. PubMed Abstract \| Publisher Full Text\n\nGelb AW, Floyd P, Lok P, et al.: A prophylactic bolus of thiopentone does not protect against prolonged focal cerebral ischaemia. Can. Anaesth. Soc. J. 1986; 33(2): 173–177. Publisher Full Text\n\nMcConkey PP, Kien ND: Cerebral protection with thiopentone during combined carotid endarterectomy and clipping of intracranial aneurysm. Anaesth. Intensive Care. 2002; 30(2): 219–222. PubMed Abstract \| Publisher Full Text\n\nFrawley JE, Hicks RG, Beaudoin M, et al.: Hemodynamic ischemic stroke during carotid endarterectomy: an appraisal of risk and cerebral protection. J. Vasc. Surg. 1997; 25(4): 611–619. PubMed Abstract \| Publisher Full Text\n\nIsley MR, Edmonds HL Jr, Stecker M: American Society of Neurophysiological Monitoring. Guidelines for intraoperative neuromonitoring using raw (analog or digital waveforms) and quantitative electroencephalography: a position statement by the American Society of Neurophysiological Monitoring. J. Clin. Monit. Comput. 2009; 23(6): 369–390. PubMed Abstract \| Publisher Full Text\n\nKim TK, Park IS: Comparative Study of Brain Protection Effect between Thiopental and Etomidate Using Bispectral Index during Temporary Arterial Occlusion. J. Korean Neurosurg. Soc. 2011; 50(6): 497–502. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPawar N, Barreto Chang OL: Burst Suppression During General Anesthesia and Postoperative Outcomes: Mini Review. Front. Syst. Neurosci. 2022; 15: 767489. Published 2022 Jan 7. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMuhlhofer WG, Zak R, Kamal T, et al.: Burst-suppression ratio underestimates absolute duration of electroencephalogram suppression compared with visual analysis of intraoperative electroencephalogram. Br. J. Anaesth. 2017; 118(5): 755–761. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPurdon PL, Pavone KJ, Akeju O, et al.: The Ageing Brain: Age-dependent changes in the electroencephalogram during propofol and sevoflurane general anaesthesia. Br. J. Anaesth. 2015; 115 Suppl 1(Suppl 1): i46–i57. PubMed Abstract \| Publisher Full Text\n\nWarner DS, Takaoka S, Wu B, et al.: Electroencephalographic burst suppression is not required to elicit maximal neuroprotection from pentobarbital in a rat model of focal cerebral ischemia. Anesthesiology. 1996; 84(6): 1475–1484. PubMed Abstract \| Publisher Full Text\n\nWestermaier T, Zausinger S, Baethmann A, et al.: No additional neuroprotection provided by barbiturate-induced burst suppression under mild hypothermic conditions in rats subjected to reversible focal ischemia. J. Neurosurg. 2000; 93(5): 835–844. PubMed Abstract \| Publisher Full Text\n\nBozzani A, Arici V, Ticozzelli G, et al.: Intraoperative Cerebral Monitoring During Carotid Surgery: A Narrative Review. Ann. Vasc. Surg. 2022; 78: 36–44. PubMed Abstract \| Publisher Full Text\n\nSookplung P: DATA of ThioBS_CEA. [Dataset]. Figshare. 2023. Publisher Full Text" }	[ { "id": "169287", "date": "19 May 2023", "name": "Masahiko Kawaguchi", "expertise": [ "Reviewer Expertise Neuroanaesthesia", "neuromonitoring" ], "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 retrospectively evaluated the optimal dosage of thiopental required to induce burst suppression during non-shunt carotid endarterectomy. As an analysis of 57 patients, the authors concluded the optimal dosage of thiopental required to achieve burst suppression on intraoperative EEG was 26.3+10.1 mg/kg/hr. This is interesting clinical data. However, there are several concerns which should be clarified.\nIn all patients, non-shunt technique was used. How did the authors evaluate that these patients would not require shunt during carotid clamping? Were there patients in which poor collateral flow was expected during the carotid clamping? Please mention the method of preoperative assessment.\nBased on the results of this study, the outcome of the patients was similar. In addition, previous animal study indicated that burst suppression is not necessary to achieve neuroprotective effect of thiopental (Schmid-Elsaesser et al. (1999)1). So, this reviewer doubts that burst suppression is really required during the clamping of carotid artery. The authors should mention the rationale to get burst suppression on EEG. Please add the data that burst suppression would be required to have neuroprotective effects. This can be a limitation of this study.\n\nWas any monitoring of cerebral hemodynamics and function performed, including near-infrared spectroscopy (NIRS), motor evoked potential or sensory evoked potential? Strategy to identify the function during carotid clamp is also important to prevent postoperative neurological dysfunction. Under the burst suppression on EEG, assessment of function can be disturbed.\n\nFinally, based on the data of this study, what did the authors recommend as a strategy to use thiopental during carotid clamping? Considering the necessity of burst suppression for neuroprotection, the conclusion should be carefully drawn.\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? 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": "9821", "date": "03 Jul 2023", "name": "pimwan sookplung", "role": "Author Response", "response": "Dear Dr. Masahiko Kawaguchi. Thank you very much for taking the time to contribute to the opportunity to improve the research article. I hope our revised paper will be appreciated by you. Regards, Pimwan Sookplung, MD. Department of Anesthesiology, Neurological Institute of Thailand, Bangkok, Thailand Comments: 1.In all patients, non-shunt technique was used. How did the authors evaluate that these patients would not require shunt during carotid clamping? Were there patients in which poor collateral flow was expected during the carotid clamping? Please mention the method of preoperative assessment. Response: To determine whether patients would require a shunt during carotid clamping, the neurosurgeon likely employed preoperative investigation by Carotid Duplex Ultrasound and Magnetic resonance angiography (MRA) to assess the carotid bifurcation disease, the degree of stenosis, and evaluate the adequacy of collateral circulation. Conventional angiography was performed only in some cases to delineate the actual stenosis segment or to evaluate the carotid disease and status of the collateral circulation. Patients with poor collateral flow will undergo a specific intraoperative assessment using the \"Backflow technique.\" If the assessment reveals insufficient blood flow, an intraluminal shunt will ensure adequate blood supply during carotid clamping. 2. Based on the results of this study, the outcome of the patients was similar. In addition, previous animal study indicated that burst suppression is not necessary to achieve neuroprotective effect of thiopental (Schmid-Elsaesser et al. (1999)1). So, this reviewer doubts that burst suppression is really required during the clamping of carotid artery. The authors should mention the rationale to get burst suppression on EEG. Please add the data that burst suppression would be required to have neuroprotective effects. This can be a limitation of this study. Response: The rationale for inducing burst suppression is based on its theorized potential neuroprotective effects. Burst suppression reduces metabolic demand by decreasing neuronal activity and electrical signaling, reduction in cerebral blood flow (CBF), and preserving limited energy resources during critical situations. Reducing metabolic requirements helps conserve oxygen supply, mitigating the risk of oxygen deprivation and preventing additional brain damage. Although Robert Schmid-Elsaesser (1999) indicates that EEG burst suppression is not necessary for maximum cerebral protection. However, animal studies may not be conclusive in humans due to inter-species differences in burst suppression effects and differences in physiology and the human clinical context. Doyle PW (1999) suggests that if the flow-metabolism coupling is intact, complete EEG burst suppression (100% burst suppression) may provide more cerebral protection than 50% burst suppression. However, the study did not evaluate the cerebral protection effects. Thus, human studies regarding burst suppression and cerebral protection effect are still needed. 3. Was any monitoring of cerebral hemodynamics and function performed, including near-infrared spectroscopy (NIRS), motor evoked potential or sensory evoked potential? Strategy to identify the function during carotid clamp is also important to prevent postoperative neurological dysfunction. Under the burst suppression on EEG, assessment of function can be disturbed. Response: During the study period from January 2009 to December 2019, our institute primarily relied on electroencephalography (EEG) for assessing burst suppression. However, we recognize the significance of monitoring cerebral hemodynamics and function, including sensory-evoked potential (SEP), motor-evoked potential (MEP), and near-infrared spectroscopy (NIRS). In 2014, the institute began implementing sensory-evoked potential monitoring (SEP) and motor-evoked potential (MEP) for spinal surgery. However, these methods are not routinely employed for carotid endarterectomy, partly due to the impact of burst suppression on EEG functional assessment. Additionally, cerebral oximetry was first introduced in 2022. 4. Finally, based on the data of this study, what did the authors recommend as a strategy to use thiopental during carotid clamping? Considering the necessity of burst suppression for neuroprotection, the conclusion should be carefully drawn. Response: Based on our study's data, a cautious approach is recommended when using thiopental to induce EEG burst suppression during carotid clamping. While barbiturate-induced cerebral protection is still considered to have a role, the necessity of EEG burst suppression for cerebral protection requires further investigation. Considering the limitations of our retrospective study, the recommended strategy should be individualized for each patient, considering available resources based on institutional protocols. Further evidence from medical studies, neurophysiology studies, and mathematical modeling is needed to gain a comprehensive understanding of burst suppression and its potential therapeutic applications. Therefore, it is crucial to carefully evaluate the potential benefits and risks of using burst suppression in clinical practice and identify the optimal perioperative settings where it may be beneficial." } ] } ]	1	https://f1000research.com/articles/12-381
https://f1000research.com/articles/12-688/v1	16 Jun 23	{ "type": "Research Article", "title": "Challenges in the application of the Tshivenda scientific register for physical sciences classrooms", "authors": [ "Ndivhuwo P Netshivhumbe", "Awelani V. Mudau", "Ndivhuwo P Netshivhumbe" ], "abstract": "Background: This paper investigated some of the challenges in the application of Tshivenda scientific register (TSR) during classroom practices of some physical sciences teachers in some of the public secondary schools in the Vhembe West District, South Africa. Methods: It was an interpretative qualitative case study wherein three physical sciences teachers and 40 learners took part in the study. The study conducted at schools of Vhuronga 2 circuit in Vhembe West District between January 2022 to November 2022. Interviews and classroom observations were used for data collections. Researchers analyzed their data through Data Analysis Scheme (DAS) which comprised of themes, categories, and characteristics in this qualitative study. Texts that belong to a particular theme were highlighted using same colour and track changes was also used to codify categories and characteristics of a theme. Results: The research findings had shown numerous challenges in the teaching and learning of physical sciences including teachers and learners not used to physical sciences being taught and learnt through TSR, not familiar with some scientific words in TSR, difficulties in understanding scientific term in TSR as well as absence of Tshivenda physical sciences resources beside TSR. Consequently, this has impacts on teacher and learner’s ability to implement TSR in the teaching and learning of Physical Sciences. Moreover, the findings also show that teachers and learners participated in the study sometimes switch from Tshivenda Scientific words to English Scientific words during Physical Sciences lessons. Conclusions: Therefore, it is suggested that the above-mentioned challenges in the development and application of TSR for Physical Sciences teaching need to be addressed so that teachers can teach learners Physical Sciences through language they know best. Hence, physical sciences teachers must be developed, trained, and furnished with essential language skills for them to develop Tshivenda scientific language registers on other sciences topics.", "keywords": [ "Classroom practice", "Tshivenda Scientific register", "Physical Sciences", "Challenges", "Teachers", "Learners" ], "content": "Introduction\n\nBefore the birth of democracy in South Africa in 1994, only English and Afrikaans language were used as medium of instruction in the teaching and learning at schools. This means that African languages such as Tshivenda was not recognised within the education system. However, the beginning of democracy has brought many changes within the government organisations in South Africa. There are 11 languages which are granted official status in South Africa; two were official languages during the apartheid era (English and Afrikaans) and nine were African indigenous languages (Tshivenda, isiNdebele, Xitsonga, Sesotho, isiZulu, siSwati, Setswana, Sepedi, and isiXhosa). The constitution of the Republic of South Africa (1996) and the current language in education policy (LiEP) support what is stipulated in the South African School Act that public schools are given the opportunity to elect any of the official languages as a medium of instruction.\n\nSome of the learners in South Africa are currently receiving their primary education through their mother tongue as a medium of instruction in the foundation phase, i.e., until Grade 3. However, starting from Grade 4 to grade 12, only English or Afrikaans is used as the language of instruction to teach and learn all of the curriculum subjects excluding the home language subject. Therefore, it is a reality in South Africa that a majority of learners are receiving their primary, secondary, and tertiary education with a language which is different to their mother tongue. A study conducted by Netshivhumbe (2018) reported that some learners who are taught through an English medium of instruction have difficulties in learning the subject’s concepts. Consequently, this is an indication that the medium of instruction which is different to the learner’s language has an impact on learners’educational achievements in a subject like Physical Sciences.\n\nIt is a reality that learners are presently receiving their school education after foundation phase through English medium of instruction regardless they are not proficient in it. Consequently, such concern gave researchers some interests of developing the Tshivenda Scientific Register (TSR) and requested that some secondary school physical sciences teachers within the Vhembe West District use it during their Physical sciences classroom practices. For this point of view the researchers investigated challenges in the teaching and learning of grade 10 physical sciences classes with the use of the Tshivenda Scientific Register (TSR).\n\nYule (2020) defines register as a conventional way of using language that is suitable in specific context, which can be identified as situational, occupational, or topical. Kabellow, Omulando, and Barasa (2019) reported that learners might employ certain registers within their learning environment which are unique to them to exclude their teachers from hearing and understanding what they are saying. Kabellow et al. (2019) maintain that some teachers mostly use formal English that can be understood by all the learners in the class and only sometimes employ informal English as an alternative when explaining certain concepts to the learners for them to understand what is being taught. In this study, the researchers refer to a language register as a language that is developed by academics for it to be employed in the teaching and learning of a specific subject. Furthermore, the researchers developed the Tshivenda scientific register (TSR) which needed to be employed by both teachers and learners during the entire physical sciences lessons in their classroom setting. The researchers developed the TSR to in order to examine its impact on learners’ participation and performance.\n\nTaylor and Prinsloo (2005) reported that an English medium of instruction is a key factor delaying the progress of learners at school because these learners are required to learn and write in the medium of instruction, which is not the language they use at their households. It is important to understand that learners whose language of learning and teaching (English) differs from their home language are under extreme stress, and this has the potential to cause an underdeveloped home language (Murphy and Evangelou, 2016). Marsh (2006) state that in other countries, attempting to learn through English has led to confusion, despair, and high drop-outs rates. Even though for the majority of learners in the Vhembe West District English is not their home language, it is still preferred as a medium of instruction which has an impact in the learning environment. In addition, Netshivhumbe and Mudau (2021) reported that leaners whose parents can’t speak English have nothing to offer to their children’s education at their household. This means that some learners only come across English at their schools and really struggle to acquire the proficiency required in the language of teaching and learning (Madima and Makananise, 2020). Mogashoa (2017) report that it is difficult for learners to understand and conceptualise content taught when they still struggle with the language used in teaching the subject. Furthermore, Ngema (2016) observed that the problem is worsened if the science teachers are not proficient in English.\n\nAccording to Botha (2022) learners who uses their mother tongue in educational settings enjoy positive learning experiences, especially if they use the language as a language of teaching and learning. Furthermore, from anecdotal evidence, learners who learn in their mother tongue have no problems with connecting newly acquired curriculum content to their existing knowledge because the processing of this new knowledge happens naturally in their mother tongue. Botha (2022) indicated that it would be a great opportunity if learners were to be educated in their mother tongue since the processing of knowledge would be easier in the mother tongue. Additionally, the use of African indigenous languages, for example, Tshivenda, as medium of instruction can increase parental support in learner’s education.\n\nResearch conducted by Awopetu (2016) reported that learners who were communicated to and instructed in their mother tongue achieved better results than their fellow participants who were communicated to and instructed in English. Botha (2022) reported that in order for children to reach their optimal potential, they need to be educated in a language that they can communicate in; a language that is comprehendible, so that they can vocally assert and express themselves. This is supported by scholar Sanchez (2013) and Chavez (2016) which indicates that learners who are taught in their mother tongue can express themselves more freely and improve their self-confidence and thinking skills. However, there are still an unavailability of physical sciences teaching and learning materials written in African indigenous languages (e.g., Tshivenda), which can be used at schools to promote mother tongue education. A study by Netshivhumbe (2018) indicated that there are teachers who do not improvise other teaching materials to assist their learners to learn the subject content as they rely on the resources provided by their schools e.g., textbook. Netshivhumbe (2018) further indicated that teachers should try to improvise teaching and learning materials where possible instead of omitting some of the activities that could possibly assist learners to develop real understanding of the subject matter.\n\nNetshivhumbe (2018) indicated that it is a reality that some of the teachers within the Vhembe district codeswitch from English to Tshivenda to support their learners who experiences difficulties in understanding subjects’ concepts through English medium of instruction. In support of what Netshivhumbe reported, Maluleke (2019) and Sethusha (2015) indicates that some teachers during their classroom practices draw on code switching as a method of teaching to support their learners in learning and understanding the ideas of the lesson taught without difficulties. Consequently, it is a reality that some teachers use learners’ home language to facilitate the teaching and learning of physical sciences and English simultaneously. Consequently, learners are being taught bilingually.\n\nThis research sought to contribute to knowledge about the use of TSR in the teaching and learning of physical sciences and its impacts towards learners’ academic performance. The challenges regarding the change from mother tongue (Tshivenda) instruction to English instruction in South Africa has an impact on learners’ education.\n\nThe study adopted the Classroom Language Investigative Framework (CLIF) which consists of school settings. Figure 1 illustrates the school setting as the main component that describes the school defrayals, school size, and population groups. This is where the scholars can recognise and comprehend what is truly happening in physical sciences classrooms.\n\nCLIF assisted the researchers to diagnosed participants perceptions on developed TSR for physical sciences. Therefore, it is essential for learners to understand the language of science besides learning language of teaching and learning (LoTL). However, this can result in either subtractive or additive bilingualism. Subtractive bilingualism as defined as limitation form of bilingualism which is often connected with negative results and it applies to English second language (ESL) learners (e.g., Venda learners) as they are anticipated to become experts in English as a medium of instruction (Lambert, 1975).\n\nAdditive bilingualism connected with a well-advanced expertise in dual languages, together with optimistic cognitive outcomes is functional in a context in which learners of any language are introduced to L2 in addition to the sustained educational use of the home language of the learner as the LoTL (Lambert, 1975). Moreover, CLIF also assisted the researchers to know how well learners perceive scientific language on developed the TSR in the learning and teaching of physical sciences. Therefore, the researchers prepared interview tools for the purpose of being able to give responses to research questions and accomplish the objectives of this study.\n\nAccording to Wellington and Ireson (2008), the goal of language in science learning and teaching attracted many scholars’ interests with the principle that language is the most vital medium and a main barricade in learning science. The problem of this study is related to English as LoTL for physical sciences, basically in Vhembe West District, Limpopo Province. Vhembe West District is a mutilingual region that uses English as LoTL for curriculum subjects like physical sciences at schools. Though learners are expected to be taught and learn through English, some teachers’ and learners not proficient to teach and learn in English (Nel and Muller, 2010). This means that there are teachers and learners are facing difficulties in their teaching and learning through the English language.\n\nTshotsho (2013) reports that the South African government has not delivered the human resources and physical resources required to encourage mother tongue education and English still has hegemony when compared to other indigenous languages in South Africa. This means that teachers are expected to educate physical sciences with LoTL. As a result, this paper explored some of the challenges in the application of TSR in grade 10 physical sciences. The following research questions guided the study, what are the challenges in the application of Tshivenda scientific register in the teaching and learning of physical sciences? What are the views and perceptions of physical sciences teachers and learners towards the use of the Tshivenda scientific register for physical sciences?\n\n\nMethods\n\nThis study received ethical approval from the Unisa college of education ethics review committee (2021/06/09/55131433/14/AM). Written informed consent was obtained from all participants prior to the study taking place.\n\nThe main purpose of this paper was to explore the impact of TSR for physical sciences teaching and learning at secondary schools. To this study, a qualitative research design was employed to provide rich descriptions of phenomena under exploration. The study targeted Physical Science teachers and learners from the Vhembe West District, Limpopo province. Furthermore, learners who were under the age of 18 years were given a consent form to ask permission from their parents for them to take part in the study. This research used an interpretative qualitative case study to develop a full understanding on the challenges in the use of developed TSR for grade 10 physical sciences. The research sites for this study were rural schools under the Makhado Local Municipality in the Vhembe West District in Limpopo province. These sites were chosen for the study as they were public schools that offer FET Phase physical sciences. The locality of Vhembe West District can be seen on Figure 2.\n\nThe sample of the study consisted of three physical sciences teachers and 40 learners from Vhembe West District, Limpopo province. In this study, purposeful sampling was used because it enables the researchers not to spend more time gathering data from participants. In short, the researchers were favoured in terms of time. In this qualitative study, purposive sampling was employed when making selections of participants for this study. This type of sampling was suitable for this study as McMillan and Schumacher (2001) reported purposive sample as the superlative selection of evidence-rich cases for an in-depth study using participants who are well-informed about the phenomenon under exploration. It was not possible for the researchers to get the entire Vhembe West District physical sciences teachers and learners to participate in the study owing to population size. Hence, purposive sampling was the most suitable sampling which ensured the researchers that only appropriate participants take part in the study.\n\nBy using a purposeful sampling, the researchers managed to include total of 43 participants according to relevant criteria, i.e., Venda teachers, and learners in FET phase physical sciences at Vhembe West District schools. This means that this study targeted participants who were currently teaching physical Sciences and competent in Tshivenda, as well as physical sciences learners in the FET phase, as they were thought by the researchers to be information-rich sources that offered valuable understandings in answering the research questions of this study. For the possibility of the study, a purposive sampling of three Physical Sciences teachers in each of the three selected secondary schools and one class of physical sciences learners from each selected school participated in the study. The researchers elected this number of participants to assure that the data collected was controllable. Purposive sampling in qualitative research includes identifying and selecting participants that have experiences and knowledge about phenomena of interest (Annan et al., 2019).\n\nThe participants selection done based on the following criteria namely, participants (teachers) must be teaching physical Sciences in FET phase schools, particularly in the Vhuronga 2 circuit; participants (both teachers and learners) must be competent in Tshivenda and participants eager to participate in the entire study. The researchers visited sampled schools and presented approval letter obtained from UNISA, LDE and circuit manager to school principals. The researchers explained the study purpose and gave school principals a letter asking permission to conduct research in their schools as well as explaining the details of the research. After obtaining permission from the schools’ principals, the letters requesting permission to conduct the study and outlining the purpose of the study were given to teachers. Learners who were under 18 were given consent form to ask permission from their parents. Thereafter, the researcher worked with the participants throughout the research process. The names of participants and schools appeared in the paper are pseudonyms and that was done to protect the identity of the participants. Hence, the selected participants assisted the researchers in answering research questions and achieving the study aim. Therefore, it was not necessary to collect data from all people in Vhembe west District to acquire valid findings.\n\nClassroom observations and interview tools were used to gather data from physical sciences teachers and learners (Netshivhumbe, 2023b, 2023c). Each one of us (researchers) design data gathering instruments i.e., an interview and observation tool, thereafter we had a formal meeting wherein each of us presented our data collection tools. Thereafter we had a discussion on what we should include on the proposed data collection tools. Therefore, the tools were refined and tested with one teacher and 10 learners of one school which cannot be mentioned for confidentiality purpose. The pilot study was done between 17 January to 19 January 2022 and piloting was conducted after school since it was the only time available. Additionally, the school used for piloting did not participate in this study.\n\nFebruary 2022 the researchers commence with the collection of data of the main study which lasted until November 2022. The researchers observed physical sciences classroom practices of teachers elected to take part in this study and all classroom observations were video- recorded by the researchers. The same applies to interviews with the participants, the researchers’ audio-taped all interviews and the language used during interviews were Tshivenda (Netshivhumbe, 2023b). Data captured by means of recording devices were transcribed to word documents by the researchers and all translation made was done by the researchers. Physical sciences teachers and learners from three schools were interviewed in their school’s settings. Classroom observation was used in order to examine the use of TSR by both teachers and learners in class whereas the interview tools were used to gather data from participants on their views and perceptions toward TSR for physical sciences teaching and learning. Furthermore, interviews and classroom observations with the participants were recorded and transcribed and by so doing the researchers find it easier when analysing data for the study.\n\nInternal validity is explained as the extent at which the results of the research provide a true reflection of the situation (Charamba, 2017). This definition emphasises the need for the researchers to employ content and sources that are accurate and consistent throughout. Researchers developed a data analysis scheme (DAS) and implemented it during the pilot study. The pilot study was conducted in one school with one physical sciences teacher and 10 learners who were not part of the study where proposed instruments, i.e. interview and observation tools were tested to ensure validity of this paper. On the day of piloting, teacher and learners were observed in their classroom setting where TSR was implemented in the teaching and learning of physical sciences and the observation tool was used by the researchers to evaluate what was actual happening during the lesson. Teacher and learners were also interviewed in their school setting, the teacher was interviewed before and after the lesson whereas the 10 learners were interviewed after the lesson. During piloting, it was revealed that some interviews questions were not well organised and there was a necessity to revise such questions.\n\nThe questions which were revised and modified are written in italics as follows, with the revised interview questions in bold:\n\n- What is your view towards the used of mother tongue instruction in the teaching and learning of physical sciences?\n\n- What is your perception towards the used of TSR in the teaching and learning of physical sciences? (Teacher interview question)\n\n- How do you rate your learners’ participation in the learning of physical sciences using Tshivenda instruction?\n\n- How do you rate your learners’ participation in the learning of physical sciences using TSR? (Teacher interview question)\n\n- How comfortable are you in learning physical sciences through Tshivenda instruction?\n\n- How did you feel about learning physical sciences through TSR? (Learner interview question).\n\nIt was, therefore, important for the researchers as the recorder and interpreter of the data to pay attention during observations and interviews with participants. Additionally, the researchers increased the study validity by focusing only on the data obtained from the participants of the study.\n\nIn this study, the three schools (cases) were analysed and interpreted. The researchers transcribed video recorded observations and audio-recorded interviews of each case verbatim to a word document. Thereafter, researchers replayed video recorded observation and audio-recorded semi-structured interviews of each case to verify if the words transcribed corresponded with what was on the recording device. However, any grammatical errors displayed by participants were not corrected to ensure that the data gathered was presented accordingly and does not lose its meaning. The findings of the study were analysed using themes developed from reviewed literature and research questions. The researchers proposed the themes for the study after constructing the research questions and reviewed literature related to this study. Therefore, the themes confirmed during piloting were employed in the study includes, participants view and perceptions towards the developed TSR for physical sciences teaching and learning and experiences of participants in the teaching and learning of physical sciences through TSR. The themes recommended for the study connect for the researchers to be able to answer research questions and achieve the objectives of the study.\n\nThe researchers showed the participants their transcribed data for additions, remarks, or corrections before being considered as a final product. Thereafter, the researchers read the transcribed interviews data of each case with one theme in mind while coding until they are all finished. The data analysis scheme (DAS) that was used in the study was the one implemented during piloting. This means that the DAS suggested confirmed during pilot study before being implemented on this study. The texts that belong to a particular theme were highlighted using same colour and track changes was also used to codify categories and characteristics of a theme. The researchers went through the coded data to confirm the transcripts. The data coded were presented using narratives.\n\n\nResults\n\nThe results of this study obtained from interviews and classroom practices of three schools participated in the study. The study focuses were to divulge challenges in the use of Tshivenda Scientific Register (TSR) during physical sciences lessons. The researchers used codes to present data, for example: school 1/Teacher T1 = S1/T1/, school 2/Teacher T2 = S2/T2, school 3/Teacher T3 = S3/T3, Group 1/Learners 1/school 1 = G1/L/S1, Group 2/Learners/ school 2= G2/L/S2, Group 2/Learners/school 3= G3/L/S3 (Netshivhumbe, 2023d, 2023e).\n\nAfter the researchers developed TSR for teaching and learning physical sciences they requested the views and perception of teachers and learners toward the developed TSR. For this study purpose, the researchers only focus on the views and perceptions of teachers and learners that divulge challenges of TSR were considered. Hence, teachers were given TSR to use during their physical sciences lesson preparation and their physical sciences classroom practices. Due to the fact that implementation of TSR for physical sciences lessons, the teachers indicated the challenges they experienced during their lessons’ preparations. This is evident with the statements reported next:\n\n“During my lesson preparation with TSR I had challenges of not knowing how to draw my lesson plan as I was used to do my physical sciences lesson through English register. Hence, my physical sciences lessons with the use of TSR take a lot of time compared to lesson I do in English. Some of the words presented in the register required me to do some consultation with tshivenda expect, i.e tshivenda educator. I had a discussion with tshivenda educator I work with where I was classified with some of the words, I was not familiar with” S1/T1\n\n“My physical sciences lessons preparations with TSR was not easy even though tshivenda was my mother tongue. Teaching physical sciences with the register the researcher gave me will be my first time using the language used in the register on the entire physical sciences lessons. The language presented was pure unlike the language we use these present days of mixing tshivenda with other languages. The way the science words developed in TSR was awesome and it was not easy for me to prepare my lessons without consulting tshivenda dictionary and ask my colleagues who teaches tshivenda in my workstation” S2/T2\n\n“The biggest challenge I had come across during my Physical Sciences lessons preparations is of the language that was used in the register. In our day to day lives, even though there are Physical Sciences words available in tshivenda, we normally use them in English and forget what they mean in tshivenda. Therefore, the problem is that the language we use every day is no longer a pure tshivenda and that resulted in me having difficulties in the preparation of those lessons using TSR. However, I reach out for help with some clarity in other words appeared in the TSR” S3/T3\n\nDuring physical sciences lessons where TSR was used to teach and learn, there were some learners that teachers had identified to be experiencing difficulties to know and understand science concepts. This is reported by the statements that follows:\n\n“During the physical sciences lesson that I offered through TSR, I had noted that learners were mixing languages (Tshivenda and English). I sometimes reminded them that only the language (Tshivenda) used in the register should be used in the classroom. Some of the words presented in TSR learners were not familiar with even though they were written in their mother tongue” S1/T1\n\n“During my physical science classroom practices where I was implementing TSR, I have seen my learners struggling to read and write some of the words appeared in the register. I think the cause could be that they were not use to physical sciences being taught by TSR” S2/T2\n\n“The biggest challenge that learners’ experiences is the same challenge I as a teacher experience when I was doing lessons preparations which is of not knowing and understanding some of science words used in TSR. Many tshivenda words has disappeared to People including learners. Tshivenḓa language has disappeared or lost in learners as they no longer know many words in tshivenda. Ndi ngazwo nangwe maipfi a santsi kha register o nwaliwa nga Tshivenḓa, vhana vhovha vha si khou divha uri elo ipfi ndi lifhio That is why even though science words in the TSR were written in tshivenda, children were no longer knowing which word is it. You will find that a child knows that word in English but not knowing the word in tshivenda. In English it is his or her everyday language but in Tshivenḓa it seem to be new words, for example there is no child that doesn’t know fridge, each and every learner knew fridge and he or she know that if he or she put water inside the fridge, the water will change and become ice but when you talk about tshixwatudzi (fridge) a child no longer know what tshixwatudzi (fridge) is, but he or she sees tshixwatudzi (fridge) every day. When you talk about muxwatu (ice) a child doesn’t know what muxwatu (ice) is even though ice he or she sees it every day. That the challenge I saw learners experiencing when I was teaching them. Tshivenḓa language has disappear to children, some of the words they no longer know them” S3/T3\n\nThe implementation of TSR in the teaching and learning of physical sciences was new to the learners. Hence, learners had challenges since they were used to physical sciences being taught and learned through the English language register. Learners expressed themselves as follows:\n\n“We had a problem of failing to understand other words used in TSR such as mutsidi (steam), muxwatu (ice) and tshixwatudzi (fridge)” G1/L/S1\n\n“Some of the words used by teachers found in TSR we did not understand words like Tshiomate, muxwatu na tshixwatudzi”G2/L/S1\n\n“There are some words in the TSR which our teacher used to teach us such as tshiomate (solid), this is one of the words that we found to be difficult” G3/L/S1\n\n“Some of the words used in the TSR we are not used to them in tshivenda, words like steam, ice and fridge” G1/L/S1\n\n“There were words that were used in the TSR that were new to us and we failed to understand them, words like fridge, i mutsidi (steam), muxwatu (ice) and tshixwatudzi (fridge) Tshiomate (solid)” G2/L/S2\n\n“Some of the words in TSR were not easy to understand because we never heard about them before, for example fridge” G3/L/S1\n\n“Some of the words in TSR the teacher was talking about I was not knowing them, like the word steam” G3/L/S2\n\nThe use of TSR in physical teaching has resulted in teachers and learners experiencing some difficulties in the learning and teaching of physical sciences since they were used to English language register in the learning and teaching of physical science. Additionally, they were not familiar with some of the Tshivenḓa scientific words.\n\n\nDiscussion\n\nThe study conducted by Botha (2022) reported that for children to reach their optimal potential, they need to be educated in a language that they can communicate in; a language that is comprehendible, so that they can vocally assert and express themselves. The above statement is supported by the study findings which revealed that teachers and learners participated in the study make use of African indigenous language i.e., Tshivenda which was the language used on the developed scientific register for physical sciences teaching and learning. Teachers (i.e., S1/T1, S2/T2, and S1/T3) used TSR during their lessons’ preparations and in their classroom practices of physical sciences. Even though TSR was implemented for teaching and learning of physical sciences, there were some challenges teachers experience in their lessons preparations as it was their first-time doing lessons preparations using TSR instead of English language register (ELR). This is an indication that teaching, and learning happened with only English instruction at school. There were few words that were presented in the developed TSR that were new to them and they used the English-Venda dictionary as well as other translation documents to understand some of the words used in TSR. Additionally, they reached out to their colleagues (Tshivenda educators) in their school setting. During classroom practices, the researchers noted that some learners did experience some difficulties in understanding some of science concepts as they were used to physical sciences concepts being written in ELR. Hence, teachers assisted those learners as they were able to explain those words that seem to be difficult for learners to understand them.\n\nNetshivhumbe (2018) indicated that teachers should try to improvise teaching and learning materials where possible instead of omitting some of the activities that could possibly assist learners to develop real understanding of the subject matter. In support of the above statement, the study findings revealed that beside S1/T1 and S3/T3 being provided with TSR guide they make use of other teaching aids to support their learners. S3/T3 brought some resources that assisted in the teaching and learning of physical sciences, which includes stones, water, jug, beaker, containers of different shapes and other materials that were available in the classroom that relate to the lessons taught for learners to be able to understand what he was teaching using TSR. However, S1/T1 make use of objects available in the classroom which relate to the lesson taught for illustration purposes. S2/T2 physical sciences lessons were taught with the TSR as he did not improvise other teaching materials to support his learners to learn visualisation, however he gave some examples during the lessons. This is an indication that there is availability of teachers who do not improvise other teaching materials to support their teaching. This is evident in a study conducted by Netshivhumbe (2018) where it was reported that there are some teachers who do not improvise other teaching materials to assist their learners to learn the subject content as they rely only on the resources provided by their schools e.g., textbooks. Moreover, the way that physical sciences teachers (S1/T1, S2/T2, and S3/T3) taught phases of matter topic did enable the learners to take notes during the lessons since they wrote notes for learners on the chalkboard.\n\nDuring physical sciences lessons, the researchers noticed that teachers assisted their learners to learn the ideas of the lesson by means of doing many explanations, using examples, doing some demonstrations, and questioning in the classroom. All the activities that S1/T1 and S3/T3 gave their learners were marked with the learners in the classroom. However, S2/T2 marked group activity by himself and no corrections was done with learners. It was also noted that there were few challenges that learners’ experiences during the application of TSR in physical sciences lessons. Mogashoa (2017) report that it is difficult for learners to understand and conceptualise content taught when they still struggle with the language used in teaching the subject. Another finding highlighted by the study is that there were words that some learners found them difficult to understand their meaning through African indigenous language used in the developed register e.g., Tshiomate (solid), muxwatu (ice), tshixwatudzi (fridge), mutsidi (steam), etc. However, the teacher was able to identify the words learners experiences some difficulties and they assisted them by explaining the words e.g., learners did not know what fridge and ice is in their mother tongue. Hence, after some clarity the teacher made on the word’s learners find them difficult in TSR, learners realised that they knew those words in English as they are used to them in the English language.\n\nThis study was limited to three selected secondary schools of Vhuronga 2 circuit in the Vhembe West District of Limpopo Province, South Africa. Only physical sciences teachers and learners of selected schools participated. For the fact that the research only focused on only three secondary schools of Vhuronga 2 Circuit in Vhembe West District may be regarded as limitation of the research. Nevertheless, through explanation offered in data analysis, the outcomes may be applicable to other districts with alike contexts.\n\n\nConclusion\n\nThe purpose of this study was to examine some challenges teachers and learners’ experiences in the developed of TSR for physical science teaching and learning in the FET phase. The application of TSR during teacher classroom practices was not easy as Tshivenda is an African indigenous language which is still in the process of developing. Hence, Tshivenda has limited scientific terms. Most of the scientific terms presented in the TSR were translated and borrowed from English and Afrikaans. The teacher had difficulties in understanding some words which appeared in the TSR, but the teachers understood the words after reaching out to their colleagues and using other translation documents for explanations. Some of the learners indicated that they experienced challenges of failing to understand physical sciences through TSR because English is not their home language. However, few learners specified that language used in TSR is problematic because during teacher classroom practices they experienced difficulties in understanding some of the words such as tshiomate. Consequently, the teachers assisted their learners with understanding the words which were difficult to them.\n\nThe findings of this study provide evidence that there is a multiplicity of challenges in the use of TSR for physical sciences. Therefore, researchers suggested that teamwork is required and it should comprise the following people, senior citizens, physical sciences teachers, physical sciences learners, physical sciences curriculum advisors and PanSALB to develop sufficient terms for this language (Tshivenda) to be developed and not only be recognised as an official language but also as a language of teaching and learning at schools and in institutions offering higher education. Additionally, availability of literature books and multilingual natural sciences and technology term list does promise that eventually Tshivenda will be well developed like Afrikaans and English. Moreover, this study has some recommendations which need to be considered to improve the use of African languages like Tshivenda in any of the education sectors, namely, the expansion of Tshivenda scientific terminology and Tshivenda science learning and teaching materials must be prioritised; physical sciences teachers must be developed, trained and furnished with essential language skills for them to develop Tshivenda scientific language registers on other science topics; and lastly, effort should be made in developing Tshivenda as indigenous language in such a way that not only will it be recognised as official language but language of teaching and learning curriculum subjects such as physical sciences.", "appendix": "Data availability\n\nFigshare: Teachers and learners interviews responses in Tshivenda and English, https://doi.org/10.6084/m9.figshare.22828424.v1 (Netshivhumbe, 2023d).\n\nThe project contains the following underlying data:\n\n• S1 T1 interview responses.pdf. (Anonymised interview responses for teacher 1 in school 1 in Tshivenda with English translation).\n\n• S2 T2 interview responses.pdf. (Anonymised interview responses for teacher 2 in school 1 in Tshivenda with English translation).\n\n• School 1 group 1 learners.pdf. (Anonymised interview responses for group 1 learners in school 1 in Tshivenda with English translation).\n\n• School 1 group 2 learners.pdf. (Anonymised interview responses for group 2 learners in school 1 in Tshivenda with English translation).\n\n• School 1 group 3 learners.pdf. (Anonymised interview responses for group 3 learners in school 1 in Tshivenda with English translation).\n\n• School 2 group 1 learners.pdf. (Anonymised interview responses for group 1 learners in school 2 in Tshivenda with English translation).\n\n• School 2 group 2 learners.pdf. (Anonymised interview responses for group 2 learners in school 2 in Tshivenda with English translation).\n\n• School 2 group 3 learners.pdf. (Anonymised interview responses for group 3 learners in school 2 in Tshivenda with English translation).\n\n• School 3 group 1 learners.pdf. (Anonymised interview responses for group 1 learners in school 3 in Tshivenda with English translation).\n\n• School 3 group 2 learners.pdf. (Anonymised interview responses for group 2 learners in school 3 in Tshivenda with English translation).\n\n• School 3 group 3 learners.pdf. (Anonymised interview responses for group 3 learners in school 3 in Tshivenda with English translation).\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: Transcriptions of classroom observations in English and Tshivenda, https://doi.org/10.6084/m9.figshare.22828205.v1 (Netshivhumbe, 2023e).\n\nThe project contains the following underlying data:\n\n• English lessons S3 T3.pdf (Anonymised classroom observation results for school 3 teacher in English).\n\n• English lessons S1 T1.pdf (Anonymised classroom observation results for school 1 teacher in Tshivenda and English).\n\n• English lessons S2 T2.pdf (Anonymised classroom observation results for school 2 teacher in Tshivenda and English).\n\n• Tshivenda lessons S1 T1.pdf (Anonymised classroom observation results for school 1 teacher in Tshivenda).\n\n• Tshivenda lessons S2 T2.pdf (Anonymised classroom observation results for school 2 teacher in Tshivenda).\n\n• Tshivenda lessons S3 T3.pdf (Anonymised classroom observation results for school 2 teacher in Tshivenda).\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: Interview tools.pdf. https://doi.org/10.6084/m9.figshare.22580209.v1. (Netshivhumbe, 2023a).\n\nThis project contains the following extended data:\n\n• Teacher interview tool.pdf. (Blank Tshivenda questions with English translation for interviews with teachers).\n\n• Learner interview tool.pdf. (Blank Tshivenda questions with English translation for interviews with learners).\n\nFigshare: Classroom observation tool.pdf. https://doi.org/10.6084/m9.figshare.22580215.v1 (Netshivhumbe, 2023b).\n\nThis project contains the following extended data:\n\n• Classroom observation tool.pdf (Blank copy of the interview tool used in the study to focus on teacher-learners classroom interaction and discourse).\n\nFigshare. Completed SRQR checklist for ‘Challenges in the application of the Tshivenda scientific register for Physical Sciences Classroom’. https://doi.org/10.6084/m9.figshare.22580254.v1 (Netshivhumbe, 2023c).\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\nWe would like to acknowledge the teachers and learners from the Vhembe West District who participated in the study.\n\n\nReferences\n\nAnnan ST, Adarkwah F, Abaka-Yawson A, et al.: Assessment of the inquiry teaching method on academic achievements of students in Biology education at Mawuko Girls School, Ho, Ghana. Am. Educ. Res. J. 2019; 7(3): 219–223.\n\nAwopetu AV: Impact of Mother Tongue on Children’s Learning Abilities in Early Childhood Classroom. Soc. Behav. Sci. 2016; 1(233): 58–63.\n\nBotha M: Home Language and Language of Learning and Teaching Dichotomy: Language Support for Foundation Phase Learners. 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Publisher Full Text\n\nNetshivhumbe NP: Teachers and learners interviews responses in Tshivenda and English. Dataset. figshare. 2023d. Publisher Full Text\n\nNetshivhumbe NP: Transcriptions of classroom observations in English and Tshivenda. Dataset. figshare. 2023e. Publisher Full Text\n\nNgema MH: Factors that cause poor performance in science subjects at Ingwavuma Circuit. University of South Africa; 2016.\n\nSanchez ASQ: Literacy Instruction in the Mother Tongue: The Case of Pupils Using Mixed Vocabularies. Journal of International Education Research – Third Quarter. 2013; 9(3): 235–240.\n\nSethusha MJ: An exploration of the challenges facing underperforming Schools in the Vhembe District, Limpopo Province, South Africa. University of South Africa. J. Educ. Sci. 2015. 1680-7456. University of Venda.\n\nTaylor N, Prinsloo C: The Quality Learning Project Lessons for High School Improvement in South Africa. Presentation to the consortium for research on school quality seminar. 2005.\n\nTshotsho BP: Mother Tongue Debate and Language Policy in South Africa. Int. J. Humanit. Soc. Sci. University of Fort Hare; July 2013; Vol. 3(13).\n\nWellington J, Ireson G: Science learning, science teaching. New York: Routledge; 2008.\n\nYule G: The Study of Language. Seventh ed.Cambridge University Press; 2020." }	[ { "id": "221967", "date": "24 Nov 2023", "name": "Sam Ramaila", "expertise": [ "Reviewer Expertise Nature of science" ], "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 investigated the difficulties linked to implementing the Tshivenda Scientific Register (TSR) in the classroom activities of physical sciences teachers in public secondary schools within the Vhembe West District, South Africa. Tshivenda is a language spoken in South Africa. The article discusses challenges related to incorporating the Tshivenda scientific register into physical sciences classrooms, and sheds light on the importance of considering local languages and cultural nuances in education. This is particularly relevant for promoting inclusivity and effective communication in diverse classrooms. The challenges discussed in the article touch upon issues related to teaching methodologies, instructional materials, or the adaptation of scientific concepts to the local language. Understanding these challenges can be crucial for teachers, curriculum developers, and policymakers seeking to improve science education in linguistically diverse settings. The article contribute to the broader field of research on the intersection of language and science education. Insights into challenges faced in specific linguistic and cultural contexts can inform future research and practices aimed at enhancing science education globally.\nThe study provides valuable insights into the challenges faced by teachers and learners in the adoption of TSR for teaching physical sciences in Tshivenda. The challenges identified highlight the importance of considering language dynamics and familiarity in educational materials to ensure effective learning outcomes. The findings suggest a need for additional support, training, and resources to facilitate the transition to using TSR in physical sciences instruction. The study reveals significant challenges in the implementation of TSR, both in terms of teacher preparation and learner comprehension. Addressing these challenges may require targeted interventions, professional development for teachers, and modifications to the TSR to align with the language proficiency and understanding of the learners.\n1. Clarity of Purpose:\nThe paper clearly outlines its objective: to investigate challenges in the application of the Tshivenda Scientific Register (TSR) during classroom practices among physical sciences teachers in public secondary schools in the Vhembe West District, South Africa. The research question is well-defined, focusing on both teachers and learners' experiences with TSR in physical sciences instruction.\n2. Research Design and Methods:The use of an interpretative qualitative case study is appropriate for exploring the challenges in-depth, involving three physical sciences teachers and 40 learners. The study duration, location, and methods (interviews and classroom observations) are clearly described, providing a comprehensive understanding of the research context.\n3. Data Analysis:The Data Analysis Scheme (DAS) is explained, incorporating themes, categories, and characteristics. The approach aligns with qualitative research standards, allowing for a nuanced exploration of challenges in the teaching and learning of physical sciences with TSR.\n4. Results:The presentation of results is clear and directly addresses the identified challenges, including teachers and learners not accustomed to TSR, unfamiliarity with scientific words, difficulties in understanding terms, and the absence of Tshivenda physical sciences resources. The mention of participants switching between Tshivenda and English scientific words adds depth to the findings.\n5. Conclusion:The paper draws meaningful conclusions from the findings, emphasizing the need to address challenges in TSR development and application. The suggestion to provide training for teachers and enhance language skills to develop Tshivenda scientific language registers is a practical recommendation based on the identified challenges.\n6. Recommended minor changes to be effectedIt is crucial to interpret the significant findings within the context of the employed theoretical and conceptual frameworks. Additionally, emphasizing the study's implications for science teaching and learning is essential. Moreover, it is advantageous to offer a thoughtful assessment of the reliability of the qualitative data gathered.\n7. Overall Evaluation:The paper is well-structured, presenting a clear background, robust research design, and insightful results. The study provides valuable insights into the challenges of implementing TSR in the teaching and learning of physical sciences, emphasizing the importance of language proficiency and training for teachers. The recommendations are practical and have the potential to contribute positively to the improvement of physical sciences education in the given context. In conclusion, the paper effectively contributes to the understanding of challenges in using TSR in the context of physical sciences education and provides actionable recommendations for addressing these challenges.\nDecision: Approved\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": "221983", "date": "30 Nov 2023", "name": "Tebogo Nkanyani", "expertise": [ "Reviewer Expertise I am a focusing on teachind science through technological/e-learning methods. I am currently working on blended learning for teaching science", "use of open education resources", "use of Learning management systems for teaching science among others." ], "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\nReview for: Challenges in the application of the Tshivenda scientific register for physical sciences classrooms\nThis study makes a valuable contribution to the field of teaching with indigenous languages. The literature outlined elaborated well how the issue of being taught with the language apart from the mother has an impact on the learning process. However, I recommend that you address the following:\nTitle: Since the Tshivenda scientific register was designed specifically for a certain topic of Physical Sciences in Grade 10, I would recommend that you add the grade together with the topic on your title to eliminate confusion that the register covers all the Physical Sciences topics.\n\nAbstract: Since you specified the type of observation used, you should also specify the type(s) of interviews used.\n\nTheoretical framework: what does L2 stand for? Also indicate who authored the CLIF. Where was it adapted from? Check previous articles on how that is done.\n\nProblem of research: I recommend that you put a double colon (:) before the research questions.\n\nSample and participants: You used purposeful statement, but your ideas in justifying that are not flowing, rather going back and forth. For example, the idea in line 5 of the first paragraph is the same as that of the last sentence of the second paragraph. I recommend a revision of the whole section.\n\nInternal validity: I recommend that you use a table to indicate old questions and piloted (revised) questions from the pilot study outcomes.\n\nData analysis: in the first line of the second paragraph, you indicated “The researchers showed the participants their transcribed data for additions, remarks, or corrections before being considered as a final product.” Please add the rationale for doing that.\n\nDiscussions: line 11 – Can you be specific to the reader if you are referring to the Tshivenda speaking educators or Tshivenda language educators.\nYour manuscript has several language errors. I recommend that it be language edited by a professional language editor. Also write acronyms in full, with the acronym in brackets for the first time before you repeat them as acronyms, the same way you did with the TSR acronym throughout 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? 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": "10705", "date": "17 Jan 2024", "name": "Awelani Mudau", "role": "Author Response", "response": "Title Add the grade together with the topic on your title to eliminate confusion that the register covers all the Physical Sciences topics. The grade and the topic on our title added. Abstract You should also specify the type(s) of interviews used. The type(s) of interviews used indicated and corrected as ‘Semi-structured interviews’ Theoretical framework Write acronyms in full, with the acronym in brackets for the first time. what does L2 stand for? Indicate who authored the CLIF Acronyms written in full, with the acronym in brackets for the first time, e.g., Second Language (L2) L2 stand for Second Language The author of CLIF indicated Problem of research Put a double colon (:) before the research questions. Double colon (:) was used before the research questions. Sample and participants I recommend a revision of the whole section. Revision done on sample and participants’ section. Internal validity use a table to indicate old questions and piloted (revised) questions from the pilot study outcomes. Table used to present old questions and piloted (revised) questions from the pilot study outcomes. Data analysis In the first line of the second paragraph, you indicated “The researchers showed the participants their transcribed data for additions, remarks, or corrections before being considered as a final product.” Please add the rationale for doing that. Rationale for researchers to present participants their transcribed data for additions, remarks, or corrections before being considered as a final product included in the second paragraph in the second line to third line. Discussions Can you be specific to the reader if you are referring to the Tshivenda speaking educators or Tshivenda language educators. Corrected as Tshivenda speaking educators and Tshivenda language educators." } ] } ]	1	https://f1000research.com/articles/12-688
https://f1000research.com/articles/11-513/v1	12 May 22	{ "type": "Research Article", "title": "Current practices of physiotherapists in Switzerland regarding fall risk-assessment for community-dwelling older adults: A national cross-sectional survey", "authors": [ "Morgane Duc", "Anne-Gabrielle Mittaz Hager", "Damiano Zemp", "Guillaume Roulet", "Alice Bridel", "Roger Hilfiker", "Anne-Gabrielle Mittaz Hager", "Damiano Zemp", "Guillaume Roulet", "Alice Bridel", "Roger Hilfiker" ], "abstract": "Background: Falls can strongly impact older people’s quality of life, health, and lifestyle. Multifactorial assessment can determine an individual’s risk of falling as the first step for fall prevention intervention. Physiotherapists have an essential role to play in assessing fall risk by older adults living in the community. In the absence of published data on this topic in Switzerland, this study investigated the current practices of physiotherapists to determine whether those are in line with recommendations. Methods: An anonymous cross-sectional survey was undertaken among physiotherapists practising in Switzerland between the 21st of November and the 31st of December 2020. A priori and exploratory hypotheses were tested. Responses to open-ended questions were grouped into themes for analysis. Results: A total of 938 questionnaires from all three language regions of Switzerland was analysed. Participants worked in different settings, with a higher representation of private practice self-employees (56%). Standardised fall risk assessments or instruments were used by 580 (62%) participants, while 235 (25%) preferred subjective assessment of fall risk only. Differences in fall risk assessment were observed according to the workplace setting (adjusted OR 1.93, 95% CI 1.37 to 2.7) and education level (trend test, p<0.001). The standardised assessments most frequently employed were the Berg Balance Scale (57.5%), the Timed-Up-and-Go (56.5%) and the Tinetti Balance Assessment tool (46.7%). Risk factors for falls were frequently queried, particularly history of falls (88.3%), home hazards (84.1%), and functional ability (81%). Technical resources (39.8%), knowledge (30.3%), and time (22.2%) were common barriers to implement a systematic fall risk assessment. Conclusions: This study provides an overview of the current practices of physiotherapists in Switzerland in fall risk assessment. There is still room to optimise the standardisation and systematisation of this assessment to implement a best practice strategy and prevent avoidable falls.", "keywords": [ "Elderly", "Accidental falls", "Prevention", "Risk assessment" ], "content": "Introduction\n\nThe World Health Organization (WHO) estimates that the proportion of people over 60 years old will have doubled by 2050. This age group will account for more than two billion people by 2050, compared to 900 million in 2015 (World Health Organization, 2018). By general comparison, the Swiss elderly population has a good general health status (Merçay, 2017). However, age-related biological changes including but not limited to sarcopenia, reduced abilities in walking, balance and coordination, sight disorders, cognitive decline and comorbidities are risk factors associated with a sharp increase in falls prevalence. Polypharmacy and home hazards may also enhance this risk (American Geriatrics Society & British Geriatrics Society, 2011; Moreland et al., 2003; Pfortmueller et al., 2014). Worldwide, 28% to 35% of people over 64 years and 32% to 42% of those over 70 suffer of a fall each year. This phenomenon raises with age and level of frailty (Yoshida, 2007).\n\nFatal but also non-fatal injuries amongst the elderly over 65 years old are mainly attributable to falls (Houry et al., 2016). Those can strongly impact people’s quality of life, health and lifestyle (Deandrea et al., 2010). Indeed, 21% to 85% of victims of a fall will experience physical, functional, psychological and social changes (Scheffer et al., 2008). Therefore, a fear of falling can arise, with negative consequences on physical and functional well-being (Legters, 2002), and a heightened risk of future falls (Lavedán et al., 2018; Whipple et al., 2018). The falls consequences remain various and can be far-reaching: chronic pain, loss of mobility and autonomy, anxiety, long-term hospitalisations or placements in healthcare centres (FSO, 2019b; World Health Organization, 2008). This can lead to significant direct financial costs. For example, in Switzerland, hospitalisation for a hip fracture costs CHF 15,000 (Promotion Santé Suisse, 2016), and a year spent in an institution around CHF 100,000 per person (AVALEMS, 2019; Promotion Santé Suisse, 2016). In addition, indirect costs, including losses due to premature death, morbidity or disability, unpaid activities, care services, but also intangible costs related to pain and loss of quality of life, are also attributable to falls (Gannon et al., 2007). Globally, the socio-economic costs (material and immaterial) related to falls amounted to CHF 14.7 billion in 2017 in Switzerland (BFU et al., 2019).\n\nGuidelines (American Geriatrics Society & British Geriatrics Society, 2011; Beauchet et al., 2011; Feder et al., 2000; Moreland et al., 2003; National Institute for Health and Care Excellence, 2013), clinical guidance statements (Avin et al., 2015), and systematic reviews (Deandrea et al., 2010; Gillespie et al., 2012; Hopewell et al., 2018; Lusardi et al., 2017), have emphasised the effectiveness of multifactorial assessments for determining the risk of falling and for informing the implementation of personalised fall prevention strategies (Hill, 2009). It is recommended that older adults over 65 years old should regularly (at least once per year) be assessed for fall risk, e.g. by asking about their fall histories, frequencies, contexts and characteristics (American Geriatrics Society & British Geriatrics Society, 2011).\n\nAs movement specialists, physiotherapists constitute a primary point of intervention in preventing falls (Sherrington & Tiedemann, 2015). They can, for example, inform physicians and home care agencies regarding fall risk factors (BFU, 2017). Effective fall prevention interventions involve three main steps. First, the screening enables detection of increased fall risk. For example, inquiring regularly about falls history can help to identify individuals at higher risk of future falls. Second, intrinsic and extrinsic factors are investigated through additional assessments such as medication review, mobility level, posture, blood pressure, vision, gait and balance, lower extremity joint function, neurologic and cognitive function, muscular strength, proprioception, reflexes, and/or environmental assessment. Finally, appropriate interventions aim to reduce the rate of falls and the severity of injury. Multidimensional individualised exercise programs are considered a reliable method of preventing falls in older persons (Hill, 2009; Rubenstein et al., 2001).\n\nHowever, little is known about the current practices of physiotherapists concerning fall prevention. To our knowledge, there are no published data on the implementation of fall risk assessment guidelines by physiotherapists in Switzerland. To ensure our profession provides guideline-recommended care for older adults, it is necessary to review current clinical practices in screening fall risk in patients over 65 years old.\n\nTherefore, this online survey sought to evaluate to what extent physiotherapists carry out fall risk assessments as the first step towards a fall prevention intervention in the population of community-dwelling older adults in Switzerland. The aim was to determine whether current practices are in line with current recommendations. After identifying barriers and facilitators to fall risk assessment, recommendations on appropriate clinical resources and targeted training will be proposed.\n\n\nMethods\n\nA cross-sectional survey of physiotherapists currently practising in Switzerland was undertaken between the 21st of November and the 31st of December 2020.\n\nRegistered physiotherapists working in Switzerland and providing care to patients over the age of 65 in their daily practice were eligible to participate. Two mandatory screening questions were used to confirm eligibility: i) Are you currently (or in the last 12 months) working as a physiotherapist in Switzerland? ii) Are you managing patients over 65, regardless of their initial pathology?\n\nRecruitment strategy\n\nIn the absence of a federal register comprising all currently practising physiotherapists in Switzerland, a comprehensive recruitment strategy was developed by the research team. It was designed to optimise the results generalisability and sample representativeness. Therefore, a range of organisations was asked to assist with study recruitment by sending the questionnaire to their members, which maintained confidentiality. First, all Swiss cantonal physiotherapy associations were invited to participate. Sending confirmations were received from Bern, Valais, Basel, Neuchâtel, and Aargau organisations. Additionally, the Swiss Association of Independent Physiotherapists (ASPI-SVFP) and the Swiss Association of Sports Physiotherapy (Sportfisio) also agreed to send the study questionnaire to their members. To broaden the sampling frame, Master’s students in physiotherapy at the Bern University of Applied Sciences (BFH) and the Zürich University of Applied Sciences (ZHAW), as well as ALUMNI physiotherapists from the HES-SO Valais-Wallis, were invited to participate. Moreover, lists of physiotherapy practices (n=2000) for each of the 26 Swiss cantons were created manually with online research on local.ch. Finally, the questionnaire was sent to all physiotherapists working on the Swiss CHEF Trial project. This ongoing national randomized controlled trial compares three home-based exercises programs aiming at preventing falls in older people of Switzerland (Mittaz Hager et al., 2019).\n\nNon-monetary incentives\n\nTo maximise responses, all the participants who took part in the survey had the opportunity to participate in a prize draw (Andrews et al., 2003; Edwards et al., 2009; Tuten et al., 2000). Three prizes were offered, consisting of an overnight hotel stay. To ensure the anonymity of the survey responses, a separate webpage was used to collect and store the email addresses. There was no link between survey responses and email addresses stored for the prize draw.\n\nA draft questionnaire was developed using an iterative process with the research team, which included six physiotherapists with several years of experience in fall prevention and geriatrics. Permission to use clinical practice questionnaires developed for similar studies was obtained from two authors (Ackerman et al., 2019; Gaboreau et al., 2016). Ackerman et al. targeted fall prevention by older people with osteoarthritis and Gaboreau et al. focussed their study on general practitioners’ (GPs) routines linked to this topic. Their questionnaires were partially adapted to align with the research question and Swiss healthcare context. To maximise study quality and research rigour, the Checklist for Reporting Results of Internet E-Surveys (CHERRIES, see extended data “CHERRIES Checklist” (Duc et al., 2022)) (Eysenbach, 2004), results of different guidelines, systematic reviews and studies (Andrews et al., 2003; Artino et al., 2018; Edwards et al., 2009; Kelley et al., 2003; Lumsden & Morgan, 2005) as well as websites (Creative Research Systems, 2016; Deckers, 2017; Parrott, 2020) were followed. See extended data “Designing Tools” for brief descriptions of each of the tools mentioned above (Duc et al., 2022).\n\nThe semi-structured online questionnaire consisted of 52 short questions with several branching logics (adaptive questioning). This process allowed some questions to be displayed conditionally based on the answers to prior items, intentionally reducing the responder burden. The survey included a mix of open-ended questions and multiple response options covering first participants characteristics. As no identifying information was collected, the anonymity of the participants was preserved. Workplace, assessed only with the first two postal code numbers, was used to observe the presence of falls prevention programmes by geographical area. Perceived ability to assess and manage older patients was evaluated on two purposed-designed Likert scales ranging from 0 “none” to 100 “excellent”. The responsibility of nine health care professions in fall risk assessment was also questioned on Likert scales ranging from 0 “not at all concerned” to 10 “very concerned”. The way physiotherapists screen for fall risk included questions about the situations leading to testing the patient, the tests used, and the interventions undertaken. Risk factors and the way they are measured were also evaluated. One question specifically targeted the reasons why some therapists never assess fall risk to understand barriers to fall risk assessment. How physiotherapists quantified the risk of falling, reassessed patients and the elements needed to facilitate a more systematic risk assessment were asked at the end of the questionnaire. Three hypothetical patient cases (vignettes) from the musculoskeletal, respiratory, and neurological fields were also presented to respondents and their management related to fall risk assessment evaluated.\n\nThe questionnaire was first developed in French and English. It was translated entirely into three of the four country's main languages, French, German and Italian, to send it throughout Switzerland. As Romansh speakers represent only 0.5% of the total population (FSO, 2019a) and are primarily fluent in German or Italian (FSO, 2020), it was estimated that they could use one of those versions. The forwards translation was completed by the authors with the help of two specialised companies. The survey is also supplied in English in the extended data (see “Survey”) (Duc et al., 2022).\n\nFor ease of reading, no more than three questions were presented per page. At any time, respondents could review and change their answers using the “previous” button functionality. In most cases, the “other” option allowed participants to indicate a missing response option if necessary. Physiotherapists were free to terminate their participation definitively or momentarily at any time. They could proceed to the next page or skip questions. Except for the two screening questions, only one question was mandatory: “Do you usually use fall risk screening tools when assessing your patients over 65 years of age?”. By submitting their email address, the server automatically generated a link allowing participants to receive a partially completed questionnaire as is so that they could complete it later. See extended data “Survey Development” for a short description of the development stages of this questionnaire (Duc et al., 2022).\n\nAce Validity Testing and Preliminary Pilot Testing\n\nWe searched the literature and contacted experts to define and conceptualise relevant topics for the survey item generation. The different steps of survey validation were conducted with the help of 21 physiotherapists who were experienced in the treatment of older adults and measurement properties.\n\nQuestionnaire feasibility was assessed, as well as content and face validity and comprehensibility. Dillman developed a four-step methodological pre-testing process adapted and applied for this study to assess validity according to Artino et al. recommendations (Artino et al., 2018; Dillman, 2000). Refinements were made at each stage as required. In extended data “Survey Pre-testing and Validation” summary tables of Dillman’s pre-testing steps and their application in this study are presented. Questions used for survey comprehensibility assessment are provided in extended data “Comprehensibility Assessment” (Duc et al., 2022). The answers collected during the pre-testing and validation process were deleted before the questionnaire went online.\n\nAssessment of reliability\n\nReliability and validity are essential scores to consider when elaborating a questionnaire (Artino et al., 2018). Validity assessment was undertaken following the pre-test process of Dillman (Dillman, 2000), and modifications were undertaken if necessary. To meet the 31st of December 2020 deadline for completion of data collection, this step was first not evaluated. However, test-retest reliability could be assessed between November 2021 and January 2022 for the publication of this work. The assessment of reliability was the final step in the survey validation. The questionnaire was sent to seventeen French and German speaking physiotherapists who took part twice to assess the test-retest reliability. Intraclass Correlation Coefficient (ICC) was measured for non-dichotomous data using ICC2,1 and Cohen's unweighted kappa was calculated to estimate test-retest reliability of dichotomous items (Streiner et al., 2015). The lower limit values indicating moderate reliability were 0.41 for the kappa (Bland, 1991) and 0.7 for the ICC (Streiner et al., 2015).\n\nA set of 18 a priori hypotheses was established before the start of the data collection. These are presented in extended data “A-priori Hypotheses” (Duc et al., 2022). Hypotheses that emerged after the end of data collection were specified as explorative.\n\nConsistent with the study’s main objectives, a website was specially designed. The survey was available in the three translation languages (French, German and Italian) and contained the key elements of the study organised by subthemes. An anonymous chat provided by Crisp allowed participants to ask questions and obtain almost instantaneous help. No IP tracking or cookies have either been used to ensure the anonymity of individuals visiting this website. The final report of this work will be published on this website for interested participants to access.\n\nOn the 21st of November 2020, physiotherapists received an email with a link to the online survey hosted on the REDCap server of the HES-SO. Physiotherapists could contact the research team at any time for further information, either by email or anonymously via a chat on the project website. To avoid transcription errors, responses were immediately sent to the project’s password-protected REDCap database (Andrews et al., 2003). One reminder was sent to all participants three weeks after the initial mailing (i.e. 08.12.2020) to increase response rates (Andrews et al., 2003; Edwards et al., 2009; Lau, 2017). Data collection was completed by the 31st of December 2020. All details regarding survey distribution and follow-up are described in extended data “Survey Send Out” (Duc et al., 2022).\n\nThe cover letter gave an overview of the study's main objectives and efforts to preserve participant confidentiality and anonymity (see extended data “Cover Letter” (Duc et al., 2022)). It was specified that by submitting the two eligibility assessment questions, informed consent was implied. Eligible participants were led to the survey, and those considered ineligible were informed that they could not take part. Participation could involve any electronic device, and the estimated duration did not exceed 25 minutes. At no time were an IP tracking or cookies used. No other techniques to analyse the log file for the identification of multiple entries were used. The link to the online survey was posted on the project website but no other advertisement was done.\n\nAn approval of Swiss Ethics was obtained via the “Clarification of responsibility” form on the portal of the Business Administration System for Ethics Committees (BASEC) in May 2020. As the survey was anonymous and no health-related data were asked, this study did not fall under the Swiss Human Research Act (CER-VD Req-2020-00515).\n\nData were analysed with R, version 4.0.5 (R: The R Project for Statistical Computing, 2020), RStudio, version 1.4.1106 (RStudio\|Open Source & Professional Software for Data Science Teams, 2020) and Stata (Version 17, StataCorp, College Station, Texas) (Stata: Software for Statistics and Data Science, 2020).\n\nHandling of variable’s grouping\n\nWhen evaluating how physiotherapists assess the fall risk of their patients, of the 938 participants, only 8 (0,1%) reported that they never assess the fall risk. Therefore, it was decided not to use this item to test the hypotheses. Instead, a binary variable “use standardised assessment” was created from the four response options: i) By a subjective evaluation (observation of the patient, discussion…), ii) By a standardised evaluation (scale, functional tests, questionnaires, timed tests…) iii) By instrumental assessment (inertial sensors, force platforms, EMG…) iv) I do not perform an assessment. We dichotomised them as follows: “use standardised assessment”: yes = ii) & iii), no = i) & iv).\n\nWe categorised the year of completion of the highest education level as follows: i) “Before 1990”: < 1990, ii) “1990 to 1999”: > 1990 & < 2000, iii) “2000 to 2009”: > 2000 & < 2010, iii) “2010 or later”: > 2010.\n\nA binary variable “Clinic or Private Practice” was created from the different work settings: i) Hospital, ii) Rehabilitation clinic, iii) Private practice as employee, iv) Private practice as self-employed person, v) Retirement home, vi) Home-based physiotherapist, vi) Other(s). We dichotomised them as follows: “Institution” = i) & ii) & v), “Private practice” = iii) & iv) & v) & vi).\n\nVignettes of patients with musculoskeletal, neurological, or respiratory problems were presented: i) A 65-year-old man consults for rheumatological problems (e.g., Osteoarthritis). His physiotherapy referral mentions \"anti-inflammatory analgesia, improvement of joint and muscle function\". What do you do?\n\nii) A 72-year-old woman consults because of neurological problems (e.g., Parkinson's disease). Her physiotherapy referral mentions \"improvement of joint and muscle function, proprioception/coordination\". What do you do?\n\niii) A 68-year-old man consults because of respiratory disease (e.g., Chronic Obstructive Pulmonary Disease). His physiotherapy referral mentions \"improvement of cardiopulmonary function\". What do you do?\n\nThe response options for the three vignettes were: i) I complete my assessment by using a specific fall risk assessment tool, ii) I do not complete my assessment by using a specific fall risk assessment tool, but I assess the main factors such as muscle strength, static and dynamic balance…, iii) As the patient does not consult for a fall risk problem, I do not assess either his risk or his risk factors for falling, iv) I do not treat this type of pathology in my daily practice. For some analyses, we dichotomised them as follows: “does fall risk assessment”= i) & ii), “does no fall risk assessment” = iii). The last answer option (iv) was excluded from this analysis.\n\nStatistics\n\nThe distributions of the continuous variables were analysed visually, and median, interquartile range, minimal and maximal values were reported. Categorical variables were summarised with absolute and relative frequencies. 95% confidence intervals were reported to document the statistical precision of the estimates. The significance level was set at p<0.05 for all tests.\n\nDifferences between participants with more than 10% missing values and those with fewer missing values were compared with non-parametric tests for continuous variables and with Chi-squared tests for frequency tables. Cohen’s d effect size was calculated for continuous variables. An effect size of 0.2 was considered a slight difference, 0.5 a moderate difference and 0.8 a significant difference. Cramer’s V effect sizes were calculated for categorical variables, where 0.1 was considered small, 0.3 moderate and 0.5 large.\n\nThe hypotheses were tested using multivariable logistic regression for binary dependent variables and Chi-squared tests for categorical dependent variables. The logistical and linear regressions were adjusted for a set of potential confounders. Variables for the multivariable models were selected using Directed Acyclic Graphs (DAGs) according to theoretical considerations (VanderWeele, 2019). Nonparametric Cochran-Armitage statistics was used to test trend (i.e., hypothesis 2, increasing proportion of physiotherapists assessing with increasing education level). Contrast after an ANOVA was used to test whether the responsibility for screening was higher for physiotherapists as for other professions (hypothesis 5).\n\nAn additional exploratory analysis was performed. i.e., it has been clearly stated that no a priori hypothesis was formulated and that this result needed to be interpreted with caution.\n\nThe textual content of the semi-open questions (n=13) was analysed through a content analysis using an inductive approach (Elo & Kyngäs, 2008; Graneheim & Lundman, 2004). This analysis approach was the most feasible due to the extensive data and the human resources available. Each free text response (meaning unit) was closely reviewed and summarised into main concepts (condensed meaning units). Those were then grouped into emerging themes making clinical or theoretical sense. To illustrate them, some participants' responses are provided verbatim in their original language.\n\nFinally, because there was some evidence of differences regarding fall risk activities and admission patterns to nursing home according to Swiss cantons (Merçay, 2017), it was decided to present the descriptive results stratified per language.\n\nAccording to the Swiss Federal Statistical Office (FSO), it was impossible to know the official number of physiotherapists currently practising in Switzerland. Because third parties sent invitation emails, we do not know the number of emails delivered. Therefore, the response ratio could not be calculated.\n\nThe members of the national physiotherapy association, Physioswiss (n=10’652 in December 2019), and the Swiss Association of Independent Physiotherapists, ASPI-SVFP (n=500 in December 2019) were added to estimate the Swiss population of working physiotherapists, acknowledging that not all physiotherapists are members of one of these associations or that a potential overlap might occur. With an estimated precision of 5% (i.e. 95% confidence interval span of 10%) and an estimated population of 11'155 individuals, complete answers of 371 therapists were required (The Survey System). This calculation required the assumption of random sampling, i.e., that our sample is representative of all physiotherapists working in Switzerland. However, we were not able to test this assumption.\n\nThe timestamps associated with questionnaire completion was analysed for each complete questionnaire (submitted or the last question answered) and partially complete questionnaires (not submitted or the last question not answered), all having a completeness ratio ≥ 90%. Data from participants who responded too quickly (i.e., < 5 minutes) were excluded from the analyses. Indeed, as the average time to take part in the questionnaire was estimated at 25 minutes, 5 minutes was not considered a serious attempt (Huang et al., 2012).\n\nThe survey completion ratio was calculated by dividing the number of respondents who submitted the survey or completed the last question per the number of those who completed the informed consent.\n\nParticipant could skip questions if they did not want to respond. Only the inclusion criteria and the screening frequency were set as mandatory. The proportion of missing values per question, and the proportion of missing responses per participant, were calculated considering the branching logics (adaptive questioning). For sensitivity analyses, we analysed the participants with more than 10% missing responses and with less than five minutes completion time separately and compared the results to the other participants with statistical tests and effect sizes (Cohen’s d for continuous variables and Cramer’s V for categorical variables).\n\nIt was intended that study participants should remain anonymous. Therefore, no IP tracking or cookies were used. Hence, it was impossible to know who clicked on the survey invitation link. In addition, due to data protection reasons and the anonymous survey, it was impossible to identify a unique visitor or to test whether a person responded twice. Consequently, the participation ratio (unique participants responding to the survey divided by those clicking on the invitation link) cannot be calculated.\n\n\nResults\n\nThe median ICC (for the ordinal and continuous variables) was 0.86, with only one item below 0.7. The median Kappa value for the dichotomous items was 0.65, with 15% of items with Kappa values below 0.41. The items with lower than moderate Kappa values (i.e. <0.41) were items with many multiple choice response options (e.g. the type of falls screening tool used, the advice given regarding falls risk the type of balance assessments used). Furthermore, the responses for the question about which professionals are responsible for the screening of falls risk, the results for the nurses and occupational therapist had too low Kappa values.\n\nA total of 981 individuals completed the two screening questions to assess their eligibility. Among them, 938 (95.6%) were eligible to participate. 715 (76.22%) physiotherapists (PTs) responded to at least 90% of the questions, 714 (76.12%) to the last question and 224 (23.88%) excited the survey prematurely, only providing partial data. All questionnaire data, even partially completed, were imported, analysed, and the attrition ratio (number of missing values per item) taken into consideration. The participants flow chart is presented in Figure 1.\n\nPTs = physiotherapists, n = number. ? = Number unknown because i) associations did not reveal the number of emails sent, ii) overlap of emails sent (physiotherapists may be in different mailing lists). For the percentages: 100% corresponds to the 938 eligible physiotherapists, except for the percentages in the box of the eligible participants, where 100% corresponds to the 981 participants who submitted the responses on the inclusion and exclusion criteria.\n\nThe median participation time was 17 minutes (IQR 11 to 27), and no participant data were excluded because of atypical time required to complete the questionnaire.\n\nThe completion ratio for this study was 76.1%. The percentage of missing responses per items ranged from 0 to 24% (see extended data “Missing Values” (Duc et al., 2022)).\n\nThe sensitivity analyses with the comparison of those with more than 10% missing responses to those with fewer missing responses showed several differences between both groups. Participants with more missing responses were three years older (Cohen’s d of 0.24, p<0.05) and less frequently had an education with a bachelor’s degree or higher (Cramer’s V effect size 0.13, p<0.05). Moreover, they also had 10% more participants who received their diploma before 1990 (p<0.05), 12% more who worked in private practice as employees (Cramer’s V effect size 0.13, p<0.05), and 7% less who worked in hospitals (Cramer’s V effect size 0.09, p<0.05). Furthermore, those with more missing values reported less confidence in the assessment of the fall risk (Cohen’s d 0.25, p<0.05) and less confidence in the management of people with an increased fall risk (Cohen’s d 0.19, p<0.05), compared to those with less missing values. Because of these systematic differences, it was decided not to exclude those with more than 10% missing as it would induce a sampling bias.\n\nThe characteristics of the respondents are shown in Table 1.\n\nMost PTs were women (n=635, 69.2%), and the median age was 44 years (IQR 33 to 56). Participants came from all three language regions of Switzerland (see Figure 2). Most of the respondents were either graduates of a specialised school (n=321, 35.9%) or had a bachelor’s degree (n=310, 34.7%). Moreover, the most frequent formal training was a Master of Sciences in Physiotherapy (n=110, 12.3%). Several participants also had specific training in geriatrics (n=274, 30.6%). Certificates attesting to the highest education level were obtained after 2010 for 396 PTs (45.3%).\n\nThe numbers correspond to the number of participants in each two-digits zip-code zone.\n\nPercentage of physiotherapists using a specific category of assessments.\n\nThe participants worked in different settings with a high representation of those in private practice as self-employee (n=525, 56%). Of the 349 (39.1%) respondents working in a team, 198 (57.4%) were in a multidisciplinary team, including other health professionals. Most participants (n=536, 61%) worked part-time with a median of 60% (IQR 50 to 80).\n\nThe median number of patients over 65 years of age treated per week by the respondents was 14 (IQR 8 to 20). Within 12 months, about 53 % (n=348) of PTs received less than 5 referrals to reduce the fall risk, 21% (n=137) got between 6 and 10 referrals and 19.2% (n=126) more than 16. Finally, on a Likert scale ranging from 0 “none” and 100 “excellent”, the participant’s median confidence level in assessing the risk of falls in the elderly was 75 (IQR 60 to 83) and 79 (IQR 65 to 87) in managing a patient at risk.\n\nOf the 18 a priori hypotheses formulated before the questionnaire was sent to the participants, two were merged during the analyses because of their similarity (17 and 18). The set of hypotheses as initially drafted is presented in extended data “A-priori Hypotheses” (Duc et al., 2022). The summarised results of each hypothesis are provided in Table 3. Details of the descriptive statistics of the variables related to these hypotheses can be found in Tables 4 to 11.\n\n‡ Due to a cell with 0, the calculation of odds ratio was not feasible, therefore the risk ratio is reported here.\n\n‡ Multiple responses possible, hence percentage do not add to 100%.\n\n‡ Multiple responses possible, hence percentage do not add to 100%.\n\nMultiple responses were possible, therefore percentages to not add up to 100%.\n\n‡ Multiple responses possible, hence percentage do not add to 100%. P value calculated by a χ2.\n\n‡ Multiple responses possible, hence percentage do not add to 100%. P value calculated by a χ2.\n\nMultiple responses were possible, therefore percentages to not add up to 100%.\n\n‡ Multiple responses possible, hence percentage do not add to 100%.\n\n‡ Multiple responses possible, hence percentage do not add to 100%.\n\nThe numbers in the legend correspond to the percentage of physiotherapists knowing at least one fall prevention programme (per two-digit zip region).\n\nCharacteristics of physiotherapists assessing their patients\n\nFirst, the main characteristics related to the practice of fall risk assessment were investigated. Hypothesis 1a (H1a): Standardised tests or instruments are reported to be used by 580 (62%) PTs to evaluate fall risk and subjective assessment was used by 729 (77.7%) PTs (see Table 4). When participants were split into mutually exclusive categories regarding their risk assessment approach, it was observed that 49% performed a combination of subjective and standardised fall risk evaluation while 25% evaluated the risk only with a subjective assessment. Less than 5% used an instrumented evaluation (see Figure 3).\n\nThe odds of using a standardised assessment were 1.93 times higher for participants working in a clinic or hospital setting (institutional context) compared to those working in private practice (adjusted OR 1.93, 95% CI 1.37 to 2.7). H1b: 96 (36%) PTs working in an institutional setting and 129 (21%) of those working in private practice used a standardised instrument for 50% to 94% of their elderly patients. Furthermore, only 38 (14%) of those working in a clinic or hospital setting and 25 (4%) in private practice used it systematically, i.e., in at least 95% of their patients (χ2 70.8662, df 3, p <0.001). Results are presented in Table 2.\n\nH1c: Among the 700 PTs treating older patients with musculoskeletal problems, 640 (91.43%) reported usually assessing them for fall risk or fall risk factors, even if they were not referred for a fall-related problem. The odds of assessing musculoskeletal patients for fall risk was 2.02 time higher for PTs engaged in an institutional setting (adjusted OR 2.02, 95% CI 1.01 to 4.04). H1d: Among the 666 PTs treating older patients with musculoskeletal problems, 660 (99%) reported usually assessing them for fall risk or fall risk factors, even if they were not referred for a fall-related problem. The odds of assessing neurological patients for fall risk was 1.02 time higher in PTs engaged in a clinic or hospital setting (adjusted OR 1.02, 95% CI 0.86 to 1.20). However, the 95% confidence interval range [0.86; 1.20], which was consistent with the null hypothesis that there is no difference in the fall risk assessment between PTs in institutional or private practice. H1e: Finally, among the 580 PTs treating older patients for respiratory diseases, 428 (74%) would usually assess the fall risk or fall risk factors in those patients even without a referral to reduce their risk of falls. PTs working in an institution did not assess these patients more often than those working in private practice (OR 1.51, 95% CI 0.98 to 2.33).\n\nH2: There was a statistically significant increase in the proportion of PTs using a standardised fall risk assessment with a higher education level (test for trend, p<0.001). H3: Part-time PTs did not assess less than full-time PTs (OR 1.18, 95% CI 0.48 to 1.65). H4: PTs working alone used a standardised assessment less frequently than PTs working in a team (adjusted OR 0.52, 95% CI 0.37 to 0.72). H5: Finally, participants were asked to rate on a scale of 0 (not at all concerned) to 10 (very concerned) the responsibility for screening of nine health care professions. PTs practising fall risk assessment considered that this role was mainly incumbent on their profession rather than other professions (p<0.001, see Figure 4).\n\nCurrent practices in fall risk assessment\n\nIn addition, the current practices related to the assessment of the risk of falling were considered. H7: The two most frequently factors leading PTs to assess their patients were the history of falls (n=469, 87.7%) and the evocation of a fear of falling (n=469, 87.7%). Receiving a specific referral to reduce the risk of falls was next (n=430, 80.4%), which only partially confirms the a priori hypothesis (see Figure 5 and Table 6).\n\nH9: PTs who regularly performed fall risk assessment used a specific tool more often than those who evaluated it less often. Significant between-group differences were not always observed, but for those with p<0.05, the physiotherapist reporting evaluating fall risk “always” chose these tests more often compared to the physiotherapist assessing less often. There was one exception, the Timed-Up and Go (TUG), where therapists reporting assessing fall risk \"often\" (n=158, 70.2%) chose it more frequently than those who assess \"always\" (n=44, 69.8%). The standardised assessments most frequently employed by respondents were the Berg Balance Scale (BBS, 57.5%), the Timed-Up and Go (TUG, 56.5%), and the Tinetti Balance Assessment tool (Tinetti/POMA, 46.7%). Only a few PTs mentioned tools directly targeting fall risk such as the Stopping Elderly Accident, Death, and Injuries Algorithm (STEADI, 0.2%), the Fall Risk for Older People in the Community Assessment Tool (FROP-Com, 0%), or the AGS-BGS algorithm (0%) (see Table 8). H10: When assessing the risk factors of falls, PTs focused mainly on fall history (n=655, 88.3%), home hazards (n=617, 84.1%), perceived functional capacity (n=595, 81%) and joint mobility (n=576, 77.9%). All individual risk factors were assessed by at least 57% of the PTs except for blood pressure, which was assessed by 37.7% of PTs (see Table 9). H14: Among PTs using a standardised tool, the odds of quantifying risk was 4.24 higher than those not using it (adjusted OR 4.24, 95% CI 2.70 to 6.65). H15: The most common way participants did this was by classifying patient’s risk as “No risk /low risk /moderate risk/high risk” (n=430, 59.1%) or by dichotomisation “At-risk/not at risk” (n=134, 18.4%) (see Table 4). This does not support our a priori hypothesis. H11: Regarding the reassessment of the risk of falling, PTs who regularly assessed their patients over 65 years old also conducted re-evaluations more often than others (X2 8.9432, df 2, p = 0.0114). H12: In addition, PTs who systematically assessed their patients' risk of falling did 4.5 more reassessments per year than their colleagues who only “sometimes” assessed the risk (95% CI 0.33 to 8.65, adjusted regression).\n\nBarriers affecting systematic fall risk assessment\n\nH6: The main barriers to systematic fall risk assessment were the lack of technical resources (n=88, 39.8%), lack of theoretical knowledge (n=67, 30.3%), lack of time (n=49, 22.2%) and lack of financial recognition, i.e., reimbursement (n=35, 15.8%) (see Figure 6 and Table 5). Other barriers identified by PTs against fall risk assessment are presented in section 3.8 Content analysis (see Barriers against fall risk assessment and Barriers against systematic fall risk assessment).\n\nInterventions to reduce risk of falling\n\nPTs may undertake interventions linked with fall risk assessment. H8: PTs who assessed more often also provided more advice on risk factors. Indeed, whatever the risk factor for which advice was given, a higher value was observed among participants who \"always\" assessed their patients. However, statistically significant differences were not always observed (see Table 7). H13: Additionally, if a patient was found to be at risk, PTs informed them about the situation (n=500, 83.6%) and gave them exercises to do at home (n=486, 81.3%) or during physiotherapy sessions (n=486, 81.3%). In a similar situation, only a small percentage of PTs treated the patient just for the initial reason for consultation (n=4, 0.7%) (see Table 10).\n\nAssumptions on the implementation of guidelines recommendations\n\nH16: The opinion of the PTs regarding the implementation of a systematic assessment, i.e., of every new patient over 65 years of age, was questioned. Only 35% of the PTs agreed with this proposition (see Table 4). H17: A non-mandatory open-ended question was used to test this final hypothesis. The frequency and percentage of each extracted themes were calculated. Among the respondents, 181 (19.3%) desired a quick and easy-to-use tool, 49 (5.22%) more time for their initial assessments and 38 (4.05%) a checklist listing all the risk factors for falls to guide them in their assessment of patients over 65 years old. Moreover, 36 PTs (3.84%) would like to see the establishment of uniform and standardised procedures across the different health care providers in Switzerland (see Table 11).\n\nFigure 7 shows the percentages of PTs aware of at least one programme per two-digit zip-code region. The list of known programmes mentioned, and their respective websites is presented in extended data “Fall-risk Prevention Programmes” (Duc et al., 2022).\n\nA post-hoc hypothesis concerning the influence of the initial pathology on the assessment of the risk of falls was made during the statistical analysis. This result should be treated with caution.\n\nTo address the hypothesis that the assessment rate could be different in patients with musculoskeletal, neurological or respiratory pathologies, three hypothetical patient vignettes were used. In patients with musculoskeletal problems, 91% of the PTs assessed fall risk factors (99% of PTs in patients with neurological, and 74% in patients with respiratory pathologies). For the use of a standardised fall risk tool, only 11.3% of the PTs would have assessed patients with musculoskeletal problems, 48.35% of the PTs patients with neurological and 10% PTs patients with a respiratory disease). Thus, our post-hoc hypothesis that patients with neurological conditions are more frequently assessed for fall risk than those with other pathologies was confirmed.\n\nOpen-ended questions (n=13) allowed participants to express themselves freely on different aspects related to fall risk assessment. The ideas underlying some of the themes are developed below, supported by verbatim quotes in their original language. All themes extracted from the analysis of these open-ended questions are presented in extended data “Extracted Themes” (Duc et al., 2022).\n\nOther situations leading to fall risk assessment\n\nOther situations than those mentioned in the questionnaire may lead PTs to assess their patients' risk of falling. If this is not done during the initial assessment, the therapist might observe that the patient has balance problems when moving, exercising, or using walking aids. This may lead to a more detailed risk assessment. Return home after hospitalisation may also prompt PTs to assess the risk of falls of their patients.\n\nOther standardised assessments used\n\nOther assessments closely or remotely related to the risk of falls used by the PTs interviewed were: i) Functional Independence Measure (FIM), ii) Hierarchical Assessment of Balance and Mobility (HABAM), iii) Limit of stability test (LOS), iv) Modified Romberg Test (mRomberg), v) Multiple Sclerosis Questionnaire for Physiotherapists (MSQPT), vi) Romberg Test, and vii) The de Morton Mobility Index (DEMMI).\n\nStatic balance assessment\n\nStatic balance was assessed through various tests such as the One-Legged stance Test (OLST) or Single Leg Stance (SLS), or the 4-Stage Balance Scale Test. Some tests used such as the Berg Balance Scale (BBS) or the Balance Evaluation Systems Test (BESTest) examine both static and dynamic balance. PTs also mentioned testing balance on an unstable surface or with eyes closed without specifying whether this was done in a standardised way or not. Finally, the use of devices that also assess dynamic balance, such as the Huber 360 Evolution® or the Galileo®, was also stated. Participants who did not assess static balance gave reasons such as lack of knowledge, of specific tests, or of time during the initial assessment. For others, testing did not contribute to diagnosis and management and was therefore not considered necessary. A focus was placed on the reason for the initial consultation, thus favouring treatment over assessment.\n\nDynamic balance assessment\n\nDynamic balance was assessed using walking tests (6 Minutes or 10 Meter Walk Tests), mixed assessments such as the Tinetti Balance Assessment Tool (Tinetti/POMA) or the Short Physical Performance Battery (SPPB), and assessments whose standardisation remains uncertain such as walking on a line, backwards, or sideways for example. Devices such as the GaitUp System® or the Dividat Senso® were also mentioned. The reasons for not assessing dynamic balance were similar to those reported for static balance. However, the lack of space to carry out the assessment was also reported.\n\nMuscle strength assessment\n\nMuscle strength was assessed by Manual Muscle Testing (according to the Medical Research Council, Kendall, Janda, Daniels), using devices such as Legpress or dynamometers or by testing some muscle groups individually such as quadriceps, triceps surae, abdominal muscles, abductors, or gluteus. Some limiting factors to muscle strength assessment were the lack of suitable assessments or devices to quantify this. Some respondents said they did not trust the 0-5 manual muscle testing accuracy, which does not assess, for example, intra-muscular coordination.\n\nOther risk quantification\n\nAnother way of quantifying the risk of falls was to follow the classification proposed by the test used. However, some participants pointed out that a fixed quantification of risk was impossible. Indeed, this one could depend on the use or not of walking aids, the fluctuation of the cognitive state, of the time of day, or of the environment.\n\nOther advice provided in relation to the risk of falls\n\nAdvice regarding concentration during activities of daily living (ADL), foot sensitivity in diabetes, moving around at night, sedentary lifestyle and vestibular pathologies was also provided by PTs regarding fall risk.\n\nOther measures undertaken if the patient is at risk\n\nIf a patient consulted for a reason other than rehabilitation to reduce the risk of falling and the assessment revealed that they were at risk, an additional measure undertaken was to encourage the patient to discuss this directly with their general practitioner. This helps to empower the patient while allowing them freedom to determine what measures they want to take (or not take) regarding this risk.\n\nBarriers against fall risk assessment\n\nSome barriers hindered some PTs from assess fall risk of their patients aged 65 and over for the risk of falling. One of these was the lack of sense in this approach. Indeed, a well-taken anamnesis, observation of the patient during exercises, during movements in the practice (waiting room - treatment room), when undressing or dressing, during functional exercises for example, or simply experience was according to them sufficient to assess the risk of falls.\n\n«Through history and functional tests and inspection in the assessment, the risk is identifiable. » (Translated from German to English by the authors.)\n\n«I believe that my experience is sufficient for an evaluation.” (Translated from French to English by the authors.)\n\nIn addition, many patients were deemed not to be at risk because their gait seemed safe (observation), or they practiced a sport in their leisure time and might therefore find it questionable to assess their risk of falling. This led some therapists to focus on the initial reason for consultation mainly.\n\nBarriers against systematic fall risk assessment\n\nBarriers given against systematic assessment of patients over 65 are various. First, the age criterion alone was not sufficient to justify a systematic risk assessment according to some participants. 75-80 years old would be more appropriate for a so-called \"systematic\" assessment. In addition, this supplementary evaluation was perceived to be too time-consuming.\n\n\"As I find the age limit for a systematic assessment of every patient of 65 years old too low, and we do not have the time and resources to clarify the risk of falls in all these patients regardless of the diagnoses and the A-Z. A large part of the patients I experience as still very fit and active at the age of 65.\" (Translated from German to English by the authors.)\n\nFor some, a case-by-case approach would therefore be preferred in the first instance to a systematic procedure. The patient should be assessed according to his level of activity, his pathologies, his anamnesis, his antecedents, the subjective and objective assessment elements, of the general impression for example. However, other participants considered that everyone should be assessed because \"prevention is better than cure\". Patients are often referred to PTs too late when the situation is already complex (generalised deconditioning, significant and/or disabling joint damage and cognitive disorders…).\n\n\nDiscussion\n\nThis online cross-sectional survey conducted in three language regions of Switzerland and including 938 participants aimed to investigate the current practices of physiotherapists in fall prevention. There were the main findings: i) 62% of physiotherapists perform a standardised fall risk assessment and most of them evaluate the different fall risk factors (e.g., balance or muscular strength). However, only 14% of physiotherapists working in an institutional context and 4% of those in a private practice carry it out in a systematic way. ii) The proportion of physiotherapists using a standardised risk assessment was higher in those with higher education compared to those with lower education, those working full time compared to those working part-time, in those working in teams compared to those working alone, and in those working in clinics or hospitals compared to those working in private practices. iii) Barriers to conducting a fall risk assessment were commonly a lack of technical resources, lack of theoretical knowledge, lack of time and lack of reimbursement. iv) Only 35% of the physiotherapists think that a systematic fall risk assessment of every new patient over 65 years of age should be implemented. v) The most frequent elements that would facilitate a more systematic fall risk assessment are the use of a quick and easy-to-use assessment tool, more time for the assessments and a checklist listing all the risk factors for falls to guide physiotherapists. Moreover, physiotherapists would like to see the establishment of uniform standardised procedures between the different health care providers in Switzerland.\n\nCurrent practices in assessing the risk of falls in patients over 65 years old\n\nOnly 14% of physiotherapists working in an institutional context and 4% of those in a private practice used a standardised test or instrument to assess their patients' risk of falling in a systematic way (i.e., in at least 95% of their patients). Moreover, a disparity in the rate of assessment was also observable according to the initial pathologies (musculoskeletal, neurologic, respiratory). Annual assessment for the risk of falls among every patient 65 years of age or older is recommended (American Geriatrics Society & British Geriatrics Society, 2011). In the light of our results, efforts are still needed to ensure that all patients over 65 are assessed by physiotherapists or other health care providers at least once a year. The implementation of a standardised risk assessment in physiotherapists with lower education, working in private practice, either alone or part-time, should notably be supported considering potential barriers.\n\nThe Berg Balance Scale (BBS) and the Timed-Up and Go test (TUG) were the two most frequently assessments of fall risk used. Many physiotherapists also used the One-Legged Stance Test (OLST) or Single Leg Stance (SLS). These results were similarly observed in two other studies conducted in Australia and Canada with physiotherapists working in the geriatrics field (Ackerman et al., 2019; Sibley et al., 2011) suggesting that these tools are well known and implemented among physiotherapists. In their meta-analysis, Lusardi et al., (2017) concluded that the BBS, the TUG and the Five Time Sit-To-Stand (FTSS) were the most evidence-supported functional measures to determine individual risk of future falls. However, a multifactorial assessment is required to evaluate the risk factors for falls (National Institute for Health and Care Excellence, 2013). It should be underlined that we did not analyse whether participants used these tools in isolation or combination.\n\nGenerally, our results demonstrated a high level of involvement in assessing and advising on risk factors for falls. According literature, history of falls frequently showed a strong association with the risk of falls (odds ratios between 2.4 and 2.6) (National Institute for Health and Care Excellence, 2013). In line with these recommendations, 88.3% (n=655) of physiotherapists in Switzerland assess the history of falls. Another self-reported risk factor for falls is the perceived functional capacity. Indeed, Porto et al., (2020) showed that a poor consideration of self-general health increases the risk of falling (adjusted OR 2.24, 95% CI 1.14 to 4.42, p-value 0.019). This evaluation seems to be also well established among participants as 81% of them (n=595) asked their patients about their perceived functional capacity.\n\nHowever, it should not be forgotten that the use of screening tools can also carry certain risks. For example, if a screening test has moderate or low sensitivity and is applied in a population with a high incidence of falls. If the test is negative, there is a high risk that health care providers will mistakenly believe that the older person is not at increased risk of falls (Oliver, 2008).\n\nBarriers related to fall risk assessment\n\nAccording to our results, fall risk is often not assessed with a standardised approach. Indeed, one-quarter of physiotherapists (n=235, 25%) exclusively performed a subjective fall risk assessment mainly based on observation, anamnesis, or experience. Test-retest reliability may be lower in non-standardised tests than in standardised ones, making it less easy to reassess risk. Furthermore, this may result in the omission of some risk factors, which would be contrary to the recommendations of the guidelines in this area on multifactorial risk assessment (American Geriatrics Society & British Geriatrics Society, 2011; National Institute for Health and Care Excellence, 2013). Among the range of tools designed to standardise this procedure, the Centers for Disease Control and Prevention (CDC) developed the Stopping Elderly Accidents, Death and Injuries algorithm (STEADI). To screen for risk of falling, this valid instrument proposes the Stay Independent Brochure, a fall risk self-assessment tool, or the Three Key Questions, i) \"Have you fallen in the last year?” ii) “Do you feel unsteady when standing or walking?” iii) “Do you worry about falling?”. If the patient is at risk, further assessments are provided to evaluate potential risk factors and define appropriate interventions (Nithman & Vincenzo, 2019; Stevens & Phelan, 2013).\n\nThe survey also highlighted other barriers like the lack of technical resources, theoretical knowledge, time, and financial recognition. Similar findings were made in studies evaluating the practices of fall risk assessment of patients by physiotherapists working with osteoarthritis patients (lack of time: 74%) (Ackerman et al., 2019) or GPs (lack of time: 13.3%, of knowledge: 13.3%, of financial compensation: 11.1%) (Gaboreau et al., 2016). To address those issues, assessment of potential risk could be easily implemented using the Three Key Questions for example. Their application allowed 95% of patients at high risk to be identified while potentially decreasing the screening duration (Eckstrom et al., 2017).\n\nFinally, only 35% of physiotherapists stated that systematic fall risk assessment should be performed. The notion of systematic implies “every new patient over 65 years of age”. Several participants stated that the age of 65 was not appropriate due to the heterogeneity of patients in this age group, stating that 75-80 years would be more appropriate for a systematic procedure. However, if we look at the Swiss statistics on falls during the year 2017, we can see that the proportion of fallers increases by 10% between people aged 65-79 and those over 80 (BFS, 2019). This demonstrates the importance of fall risk assessment at an early stage.\n\nInterventions to reduce risk of falling\n\nIdentifying individual fall risk factors allows planning a specific fall prevention strategy even if the risk is mild (Hill, 2009). In case of proven risk, 81.3% (n=486) of the respondents gave their patients exercises at home or included them during therapy. According to the literature, those should be individualised and based on the identified risks to prevent future falls (Hill, 2009; Cheryl & Butcher, 2017), but our survey did not consider this aspect.\n\nRegarding interventions, it is also interesting to highlight the results of a randomised controlled trial. Greenberg et al. (2020) found that the adoption of a decision tool, in this case the STEADI algorithm, generally encouraged subjects to take part in individualised interventions more than controls. This suggests that using a standardised tool effectively encourages patients to act on their risk of falling.\n\nDespite the multitude of tests available, many participants would like a quick and easy-to-use assessment tool or a checklist listing all the risk factors for falls to guide them in assessing patients over 65 years old. The implementation in Switzerland of a tool directly targeting fall risk assessment such as the STEADI algorithm, could be relevant. Indeed, it was specially created to help caregivers to perform fall risk assessments and treat patients appropriately (Stevens & Phelan, 2013). Physiotherapists working in private practice, either alone or part-time, should particularly be supported to use standardised assessments. Improvements in basic education, continuing education courses, online materials, financial incentives (i.e., remuneration for assessments), and interprofessional prevention campaigns could also potentially increase the implementation of established best practices in fall prevention.\n\nIn addition, many therapists called for the standardisation of current practices between different health care providers. This would enable the adoption of a \"common language\" in terms of testing, risk quantification and interventions. According to Gaboreau et al. 65.3% of French GPs considered the implementation of an annual falls risk assessment useful. Unfortunately, only 28.8% of them performed it each year (Gaboreau et al., 2016). To optimise practices related to falls prevention, it is therefore essential to increase the awareness and involvement of each health professional. More generally, there is still room for improvement in the quality of care, coordination between the treating physician and the specialist, and follow-up care after discharge from hospital in Switzerland (Merçay, 2017).\n\nFuture studies are needed to develop a fall risk assessment adapted to the needs and constraints of physiotherapist’s practice in Switzerland. This tool could be based on the STEADI, which was proven to reduce falls-related hospital admissions in older people and associated health care costs (Johnston et al., 2019). Then, local implementation studies including in-depth qualitative interviews with sub-groups of physiotherapists to identify potential barriers and facilitators could be planned. This tool could thus serve as a basis for discussion and joint decision-making among health professionals.\n\nParticipant’s recruitment\n\nOne limitation was, that we could no address all, or a random sampling of all physiotherapists working in Switzerland. In the absence of a federal register comprising all currently practising physiotherapists in Switzerland, a recruitment strategy was developed to maximise the results generalisability and sample representativeness. The research team sent more than 3600 emails and the partner associations and schools to set up our sample. However, this strategy did not avoid the phenomenon of overlapping; obviously, some physiotherapists have been contacted in several ways while others were omitted. Moreover, physiotherapists who took part may have been more sensitive to this topic than non-respondents, potentially influencing the results. The generalisation of cross-sectional survey findings is often discussed in the literature. For some authors, sources of disparity within the population studied do not allow the results to be generalised between the individuals contacted and the others (Andrews et al., 2003). For others, due to the large number of individuals contacted, this design is more likely than others to acquire data from a representative sample and thus allow extrapolation (Kelley et al., 2003). We assumed that our sample is representative of all physiotherapists working in Switzerland but are not able to test this and therefore these findings should be interpreted with caution. Nonetheless, this study provides a snapshot of the current global situation in Switzerland regarding fall risk assessment, considering that the physiotherapist's practices and knowledge are in constant evolution.\n\nA further limitation was, that few questions showed low reliability. However, these were multiple choice items with many response options. For example, the question that targeted different fall risk assessment tools had 81 different response options.\n\nOpen-ended questions analysis\n\nA quantitative design was chosen to answer questions based on the current practices of physiotherapists in Switzerland in fall prevention. Without pretending to fulfil the criteria of a mixed design, but to allow participants to specify or clarify their answers, twelve open-ended questions were also asked. The analysis of the participants' answers was limited to a content analysis based on the inductive approach proposed by Elo and Kyngäs and Graneheim and Lundman (Elo & Kyngäs, 2008; Graneheim & Lundman, 2004). The lead author (MD) was responsible for summarising each response and then classifying them according to general recurring themes. These were then counted to determine their frequency. This work, although long and tedious, was fascinating. It raised relevant aspects concerning the needs of physiotherapists and the future reflections to be carried out to prevent falls in our country. However, it would have been relevant to carry out this work with the help of a third person to ensure that the answers were well understood and that the classification by themes was adequate and unanimous.\n\nFirst, to our knowledge, it is the first study to explore this topic in Switzerland. Fall prevention is of high importance to improve the care of our elderly. Guidelines have underlined the effectiveness of multifactorial assessment to determine an individual’s risk of falling and implement suitable prevention strategies (American Geriatrics Society & British Geriatrics Society, 2011; Beauchet et al., 2011; Feder et al., 2000; Moreland et al., 2003; National Institute for Health and Care Excellence, 2013). It was, therefore, necessary to review current practices and to propose measures according to physiotherapists needs. Furthermore, our recruitment strategy and the development of a questionnaire in three languages (French, German, Italian) enabled nationwide participation, with the final sample size exceeding our initial expectations. In addition, this study led some participants to reflect on their current practices.\n\n\nConclusions\n\nIn conclusion, this study showed that most physiotherapists working in Switzerland perform some form of fall risk assessment. Moreover, many of them are aware of the problem as they frequently assess and advise on risk factors for falls to their patients over 65 years old. However, despite current recommendations, risk assessment itself is still too often unsystematic and based on subjective criteria. Measures are required to foster the use of standardised assessments by mitigating existing barriers and increasing incentives. To overcome this challenge, education plays an important role and should emphasise the importance of objective fall risk assessments with the use of appropriate screening tools. In addition, the development of an assessment to facilitate the implementation of a fall prevention strategy based on best practice should be considered. This would improve adequate care for our elderly while relieving the health system of the costs associated with this issue.\n\n\nData availability\n\nOpen Science Framework: Current Practices of Physiotherapists in Switzerland Regarding Fall Risk-Assessment for Community-Dwelling Older Adults: A National Cross-Sectional Survey., https://doi.org/10.17605/OSF.IO/MP9U4. (Duc et al., 2022)\n\nThis project contains the following underlying data:\n\n- df_csv.csv\n\nOpen Science Framework: Current Practices of Physiotherapists in Switzerland Regarding Fall Risk-Assessment for Community-Dwelling Older Adults: A National Cross-Sectional Survey., https://doi.org/10.17605/OSF.IO/MP9U4. (Duc et al., 2022)\n\nThis project contains the following extended data:\n\n− CHERRIES Checklist.pdf\n\n− Designing Tools.pdf\n\n− Survey.pdf\n\n− Survey Development.pdf\n\n− Survey Pre-testing and Validation.pdf\n\n− Comprehensibility Assessment.pdf\n\n− A-priori Hypotheses.pdf\n\n− Survey Send Out.pdf\n\n− Cover Letter.pdf\n\n− Missing Values.pdf\n\n− Fall-risk Prevention Programmes.pdf\n\n− Extracted Themes.pdf\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).", "appendix": "Acknowledgement\n\nWe would like to thank all the people who contributed to the proofreading and validation of this questionnaire and all the physiotherapists who took part in it.\n\n\nReferences\n\nAckerman IN, Soh S-E, Barker AL: Physiotherapists’ falls prevention knowledge, beliefs and practices in osteoarthritis care: A national cross-sectional study. Arthritis Care & Research. 2019; n/a(n/a). 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Reference Source" }	[ { "id": "150913", "date": "21 Sep 2022", "name": "Arthur de Sá Ferreira", "expertise": [ "Reviewer Expertise Rehabilitation", "Physical Therapy", "Biomedical Engineering", "Biostatistics" ], "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\nManuscript title: Current practices of physiotherapists in Switzerland regarding fall risk-assessment for community-dwelling older adults: A national cross-sectional survey\nComments:\nThis manuscript reports an online survey study designed to evaluate to what extent physiotherapists carry out fall risk assessments as the first step toward a fall prevention intervention in the population of community-dwelling older adults in Switzerland. The manuscript is written following related guidelines and checklists (e.g., CHERRIES). The background and rationale of the study are clearly posed, with objective aims. The study design seems adequate to the study aims. Given the sampling scheme, the researchers implemented strategies to increase nationwide coverage of the survey and responses. The procedures for development, validity/reliability assessment, and implementation of the questionnaires are fully described and seem sufficient to allow replication. Data analysis follows current best practices labeling the a priori and exploratory hypotheses. Results are very well organized and clearly linked both to the methods and hypotheses. I commend the authors for the well-conducted and reported study. I have only a few comments I would like the authors to consider.\nMinor comments:\nResults, reliability. Consider double-checking whether the observed kappa values were paradoxically low. Other reliability coefficients can be used in such cases1.\n\nIt is curious that polypharmacy, mentioned in the Introduction section, is not presented in Results nor further discussed. The large variability for rating how much the pharmacy assistant/pharmacist should be involved (Figure 4) is intriguing. It may suggest that most PTs do not regard polypharmacy as a criterion for a high risk of falling. Conversely, it may also suggest that PTs who acknowledge the whole of polypharmacy in risk stratification score higher for enrolling pharmacy assistances/pharmacists. I would like to know the authors’ opinion on this matter.\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": "10584", "date": "11 Dec 2023", "name": "Morgane Duc", "role": "Author Response", "response": "Hello, thank you for your very pertinent feedback. Regarding the first point, we now calculated Prevalence and Bias Adjusted kappa (PABAK, also called Brenner-Prediger Kappa) and the values were not substantially higher, therefore we prefer to leave the original kappa calculations. Suggestions regarding your second point will be made in the final document. Best regards Morgane Duc Roger Hilfiker" } ] }, { "id": "180009", "date": "24 Aug 2023", "name": "Tobias Braun", "expertise": [ "Reviewer Expertise physiotherapy", "rehabilitation", "older adults", "neurorehabilitation", "fall risk", "evidence-based 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\nThank you for the opportunity to review this manuscript. I have read it with great interest.\nThe authors performed a Swiss-wide national cross-sectional survey on the current practices of physiotherapists regarding fall risk-assessment for community-dwelling older adults.\nI have reviewed the manuscript and would like to make some minor suggestions on how to improve the quality of reporting. This manuscript is well-written and completely reported, well-structured and easy to read/follow. I gratulate the authors for their great work, which will inform the health care of older people at a high risk of falling.\nTitle & Abstract:\nWell reported. Minor comment: decimal places for relative figures should be reported consistently (either one or no decimal place, please).\n\nIntroduction/Background:\nI recommend avoiding the term “elderly” and use “older adults” etc. instead.\n\nI terms/words such as “mainly” are used, please provide exact figures (e.g., “… are mainly attributable to falls” – how many?).\n\nI recommend referring also to the currently published world guidelines for falls prevention and management for older adults1.\n\nMethods:\nThe methods are reported very transparently, completely and structured logically. Reporting according to CHERRIES has been performed very thoroughly.\n\nResults:\nThe flow chart (fig 1) is a bit confusing at the lower part. It seems that the bloc “eligible physiotherapists (n=938)” separate into 3 blocs (participants “flow” into the three blocs) and that the numbers of the three blocs add up to 938. However, it actually separates into 2 blocs (714 + 224; left and right), and the “middle bloc” seems to be the “sum” of the other 2 blocs, and might be placed at the “bottom”. Otherwise, the “flow” of participants seems not correct according to the numbers.\n\nI recommend reporting relative numbers in relation to the total sample size consistently, with one decimal place, e.g. “224 (23.88%)” -- > 224/938 (23.9%).\n\nI was a bit confused by some headings of the tables, e.g., “Table 4. Hypotheses 1, 2, 3, 4, 5, 11, 12, 14, 15, 16.” or “Table 5. Hypothesis 6.”. The authors might please consider to use more explicit titles, if possible, e.g., “Table 5. Reasons for not performing a systematic fall risk assessment reported by the participants”, and so on.\n\nDiscussion:\nWell reported, no comments.\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/11-513
https://f1000research.com/articles/12-1576/v1	11 Dec 23	{ "type": "Systematic Review", "title": "Defining and conceptualizing patient-centered family planning counseling: A scoping review", "authors": [ "Dominique Meekers", "Aaron Elkins", "Vivian Obozekhai", "Aaron Elkins", "Vivian Obozekhai" ], "abstract": "Background Family planning counseling has long been dominated by the tiered-effectiveness model, which discusses contraceptive methods in order of effectiveness. However, there is growing recognition that patients may prioritize factors other than method effectiveness. This scoping review identifies how patient-centered family planning care has been defined and conceptualized, and discusses the implications for measurement.\n\nMethods We systematically searched PubMed and SCOPUS for documents on “patient-centered family planning counseling or support” published between 2013 and 2022. Eligibility criteria included discussion of 1) strategies for providing patient-centered care, 2) interventions using a patient-centered approach, or 3) the impact of patient-centered approaches. We describe the definitions and domains of patient-centered family planning counseling addressed in the literature.\n\nResults Our scoping review is based on 33 documents. Only 18 documents clearly defined patient-centered family planning counseling or discussed what it entails. We identified important differences in how patient-centered family planning care was defined. However, most studies emphasized patients’ needs and preferences, respect for the patient, and informed decision-making and can be mapped against the McCormack’s framework for patient-centered communication.\n\nConclusions It is important for studies to more clearly state how they define or conceptualize patient-centered family planning. Inconsistent use of indicators makes it difficult, if not impossible, to make generalized conclusions about the effectiveness of the patient-centered approach relative to the tiered-effectiveness approach. Consistent use of comparable indicators of key domains of patient-centered care is needed to address the gap in evidence about the effectiveness of patient-centered family planning counseling on various family planning outcomes, and to support future interventions. Wider use of existing scales to measure patient-centered family planning care may help standardize the definition of patient-centered care and strengthen the evidence base.", "keywords": [ "Family planning", "patient-centered care", "quality of care", "contraceptive decision-making" ], "content": "Introduction\n\nThis scoping review aims to identify how patient-centered family planning care has been defined and conceptualized, and discusses the implications for measurement (for preliminary analyses, see Meekers et al. 2023a). The importance of family planning counseling to facilitate the adoption of modern contraceptive methods is well recognized. The World Health Organization has recommended using the tiered-effectiveness model, which first counsels patients about the most effective contraceptive methods (Brandi and Fuentes 2020). As a result, counseling has a strong focus on long-acting reversible contraceptive (LARC) methods. This focus on the most effective methods may cause providers to unconsciously pressure patients to use a LARC method (Gomez and Wapman 2017, Holt, Caglia et al. 2017, Hazel, Mohan et al. 2021) and to overlook that other method attributes may be more important to the client. For example, patients may prefer a method that is consistent with their personal or religious values, suits their relationship status, or has specific attributes (e.g., limited side effects). They may also want to avoid methods that they previously tried and disliked. Ignoring these preferences can cause clients to adopt a method that they are not fully satisfied with, which may lead to contraceptive discontinuation (Downey, Arteaga et al. 2017, Gomez and Wapman 2017, Morse, Ramesh et al. 2017, Soin, Yeh et al. 2022).\n\nTo address these concerns, there is a growing interest in so-called patient-centered family planning counseling. Broadly speaking, the term patient-centered care, or client-centered care, refers to care that is tailored to the client’s personal circumstances. This involves recognizing the client’s needs, preferences, and values, facilitating informed decision-making, being transparent, and having respect for the client (Holt, Caglia et al. 2017, Ti, Burns et al. 2019, Gawron, Simonsen et al. 2022). Regarding family planning, it is generally agreed that patient-centered counseling implies that providers should consider patients’ fertility goals, contraceptive needs and preferences, offer contraceptive counseling, and encourage open dialogue (Ti, Burns et al. 2019, Dehlendorf, Fox et al. 2021). However, to date, patient-centered family planning counseling has been defined inconsistently. Several authors have highlighted the importance of having standardized definitions (Hui, Mori et al. 2012, Labbok and Starling 2012, Xiao, Brenneis et al. 2021). Lack of consensus about what the term “patient-centered family planning counseling” means and ambiguity concerning its various domains can have implications for program design, research, and knowledge translation through cross-study evaluations. Hence, there is a need for clarification of the term. Scoping reviews are a recommended methodology for clarifying definitions and concepts in the literature (Austad, Chary et al. 2016, Peters, Godfrey et al. 2021, Munn, Pollock et al. 2022, Graham, Haintz et al. 2023). This scoping review addresses the following questions:\n\n• How has patient-centered family planning counseling been defined?\n\n• Which elements or domains of patient-centered family planning counseling does the literature address?\n\nAn enhanced understanding of how patient-centered family planning counseling has been defined and conceptualized in the literature can facilitate the design of comprehensive counseling programs and increase awareness of the range of domains family planning practitioners should aim to address. Assessing how the concept has been measured in the literature is an important first step toward measurement standardization, which is needed to compare intervention impact across study sites and to generalize findings.\n\n\nMethods\n\nOur scoping review is informed by the framework developed by Arksey and O’Malley (2005) and subsequently refined by others (Levac, Colquhoun et al. 2010, Peters, Marnie et al. 2020, Peters, Godfrey et al. 2021). We followed the reporting guidelines described in the PRISMA Extension for Scoping Reviews (PRISMA-ScR) (Tricco, Lillie et al. 2018, McGowan, Straus et al. 2020). Although there is no published protocol, the two lead authors discussed and reached a priori agreement about the study objectives, inclusion criteria, and analytical approach. As recommended (Peters, Marnie et al. 2020, Peters, Godfrey et al. 2021, Peters, Godfrey et al. 2022, Pollock, Peters et al. 2023), we used an iterative process to develop both the search strategy and data extraction process. An initial list of keywords for the search strategy was piloted and adjusted to ensure the search results aligned with the study objectives. We drafted a preliminary charting/extraction table, tested it with a small number of retrieved documents, and revised it before starting the full data extraction. We used basic qualitative data coding to analyze the extracted data (Munn, Peters et al. 2018, Peters, Marnie et al. 2020). Specifically, we identify different definitions of patient-centered family planning counseling used in the field and clarify the different domains addressed by these definitions.\n\nWe limited our search to the PubMed and SCOPUS databases. To ensure that we focused on the most recent thinking, we restricted the search to documents published between January 1, 2013, and December 31, 2022. Although we did not impose formal restrictions on the type of document, publication status, or language of the document, the databases we searched resulted in a de facto restriction to peer-reviewed English-language documents. Our search strategy is shown in Table 1. Using Boolean operators, we conducted a title and abstract search to identify documents that contained the keywords “family planning” or “contraception” as well as “user-centered” or “client-centered” or “patient-centered”. The search was completed on April 1, 2023.\n\nWe used Covidence web-based software (www.covidence.org) to automate removing duplicate documents and to facilitate screening of the search results. The titles and abstracts of the remaining documents were independently screened for relevance by the two lead authors. Documents were considered eligible for full-text review if they discussed a patient-centered family planning approach, strategy, or intervention or presented evidence about the effectiveness of such approaches or interventions on quality of care or various family planning outcomes. If the two reviewers disagreed, the document was discussed to reach a consensus. If consensus could not be reached based on the title and abstract, the document was retained for the full document review. During the full document review, we identified documents irrelevant to our review objectives or did not provide sufficient detail (including documents that only recommended using patient-centered family planning counseling in the future, without further elaboration). We also identified de facto duplicate documents that presented findings on the same study. All these documents were omitted from the data extraction.\n\nThe data were extracted (charted) using an a priori developed Excel data template. Data from each report were extracted by one reviewer and subsequently checked by the second reviewer. Extracted data for each document comprise: the author, title, year of publication, region, and document type (e.g., theoretical/conceptual paper, systematic review, methodological paper, etc.). When applicable, we extracted the type of study population (e.g., family planning clients or providers). To address our key objective, we charted how patient-centered family planning care was defined or described, including the domains of patient-centered care that were addressed. The extracted/charted data for this scoping review are available under Underlying data (Meekers et al., 2023b).\n\n\nResults\n\nAs shown in Figure 1, our initial search produced 76 references from PubMed and 58 from SCOPUS. After the removal of 48 duplicate records, 86 unique documents remained. After we screened the titles and abstracts of the remaining 86 unique documents for relevance, 45 documents were retained for full-text review. Twelve documents were excluded during the full-text review. The most common exclusion reason (6 documents) was that the document did not include a detailed discussion of a patient-centered approach and only recommended their future use. Other reasons included that the document was not relevant (one document), duplicate descriptions of the same studies (2 cases), and lack of detail (3 cases). After these exclusions, 33 full-text documents were included in our scoping review.\n\nThe reviewed documents included five studies that discussed measurement of patient-centered family planning care (Dehlendorf, Henderson et al. 2016, 2018, Carvajal, Mudafort et al. 2020, Dehlendorf, Fox et al. 2021, Welti, Manlove et al. 2022), ten that addressed tools for reproductive goal screening or contraceptive decision-making (Donnelly, Foster et al. 2014, Koo, Wilson et al. 2017, Baldwin, Overcarsh et al. 2018, Dehlendorf, Fitzpatrick et al. 2019, Dehlendorf, Reed et al. 2019, Dev, Woods et al. 2019, Madrigal, Stempinski-Metoyer et al. 2019, Stulberg, Dahlquist et al. 2019, Callegari, Nelson et al. 2021, Gawron, Simonsen et al. 2022), and three that described counseling programs or curricula (Kamhawi, Underwood et al. 2013, Loyola Briceno, Kawatu et al. 2017, Worthington, Oyler et al. 2020). Nine studies described women’s experiences with family planning counseling, counseling preferences, contraceptive decision-making process, and perceived quality of care (Assaf, Wang et al. 2017, Downey, Arteaga et al. 2017, Gomez and Wapman 2017, Holt, Zavala et al. 2018, Callegari, Tartaglione et al. 2019, Ti, Burns et al. 2019, Hazel, Mohan et al. 2021, Singal, Sikdar et al. 2021, Hamon, Hoyt et al. 2022). The full-text review also included three systematic reviews (Fox, Reyna et al. 2018, Gagliardi, Nyhof et al. 2019, Soin, Yeh et al. 2022) and three theoretical and/or conceptual articles (Holt, Caglia et al. 2017, Morse, Ramesh et al. 2017, Brandi and Fuentes 2020). Documents that discussed the implementation of patient-centered family planning interventions focused mostly on the U.S. (n=20). Only four documents described Africa-based interventions (Assaf, Wang et al. 2017, Dev, Woods et al. 2019, Hazel, Mohan et al. 2021, Hamon, Hoyt et al. 2022), and one each the Middle East, Asia, and Latin America (Kamhawi, Underwood et al. 2013, Holt, Zavala et al. 2018, Singal, Sikdar et al. 2021).\n\nIn the literature, the terms “patient-centered” and “client-centered” are used interchangeably (the term “person-centered” generally focuses on more holistic, longer-term goals). Our literature review indicates that there is no universally agreed upon general definition of patient-centered care, and consequently, there are differences in what is considered patient-centered care in family planning counseling and support. That said, only 18 of the 33 documents clearly defined client- or patient-centered family planning counseling or described key features or domains of patient-centered family planning counseling or care. However, studies that identified problems with the quality of family planning care, such as negative experiences with providers, tend to address similar topics without referring to them as domains of patient-centered care (Downey, Arteaga et al. 2017, Gomez and Wapman 2017, Callegari, Tartaglione et al. 2019).\n\nThree studies in our review referred to the 1990 Judith Bruce Quality of Family Planning Care (Assaf, Wang et al. 2017, Holt, Caglia et al. 2017, Hazel, Mohan et al. 2021). That original Bruce framework identified six distinct elements of the quality of family planning care “that clients experience as critical,” including 1) the choice of methods that are offered on a reliable basis, 2) the information provided to the client, 3) the technical competence of the provider, 4) the interpersonal relations between the providers and clients, 5) the mechanism to promote continuity of care (e.g., follow-up visits), and 6) the availability of an appropriate constellation of acceptable and convenient family planning services (Bruce 1990). The Bruce framework emphasizes the importance of the client’s perspective on the quality of care, including the provider-patient relationship. Consequently, the framework forms the basis for much of the contemporary discussions about patient-centeredness family planning care, and women’s autonomy in family planning decision-making.\n\nAlthough the reviewed studies varied in how they defined patient-centered care, several either referred to the 2001 Institute of Medicine definition of patient-centered healthcare or built on that definition (Dehlendorf, Henderson et al. 2018, Ti, Burns et al. 2019, Carvajal, Mudafort et al. 2020). The Institute of Medicine (renamed to National Academy of Medicine in 2015) described patient-centered care as “care that is respectful of and responsive to individual patient preferences, needs, and values and ensures that patient values guide all clinical decisions” (Institute of Medicine 2001: 40). A number of other studies used definitions or descriptions of patient-centered care or counseling that referred to these same elements. For example, Brandi and Fuentes (2020: s876) stated that patient-centered counseling “aims to provide education to patients that integrates evidence-based recommendations based on patient preferences, recognizing that patients’ values and preferences should be an integral factor in decisions made about their health care [and ensures that] patients function as experts on their preferences and needs and providers function as experts on the medical evidence.”\n\nAlthough studies used different terminology, definitions, and approaches for patient-centered care, Holt, Caglia et al. (2017: 1) note that they all acknowledge “the essential role of individuals’ preferences, needs, and values, and the importance of informed decision-making, respect, privacy and confidentiality, and non-discrimination.” Despite these commonalities, Gagliardi, Nyhof et al. (2019) noted that a better understanding of the different domains of patient-centered care can facilitate more accurate – and more consistent – measurement, which can inform the design of strategies to strengthen patient-centered care. In their theoretical rapid review of the evidence on the patient-centeredness of women’s health care, they mapped studies against the dimensions of patient-centered healthcare previously identified by McCormack, Treiman et al. (2011). McCormack argued that there are six main domains of patient-centered care:\n\n1) Fostering the relationship between the provider and client. This domain includes building rapport with the patient, trust in the provider’s technical competency, his/her honesty and openness, demonstrating that the provider cares about what is best for the patient, and discussing the provider and patient’s respective roles and responsibilities.\n\n2) Reciprocal exchange of information between provider and client. Sub-domains include obtaining information about the patient’s information needs, beliefs, and preferences and sharing information and resources with the patient.\n\n3) Recognizing the patient’s emotions and responding to them. By asking the patient questions about their emotions, the provider signals an understanding of the patient’s situation and shows empathy.\n\n4) Managing uncertainty. This domain includes assessing sources of the patient’s uncertainty (e.g., about side-effects or life changes) and using emotion- and problem-focused strategies to address them.\n\n5) Making decisions. Subdomains include communicating what decisional support the patient needs, providing support for decision-making, and offering opportunities to participate in decision-making.\n\n6) Enabling patient self-management, including advising the patient, helping the patient plan, and arranging for follow-up.\n\nThe authors noted that each study in their review defined and measured patient-centered care differently, and none addressed all six domains (Gagliardi, Nyhof et al. 2019). The most addressed domains were exchanging information, making decisions, and fostering the relationship. The authors noted that none of the studies in their review measured patient-centered care as comprehensively as the McCormack framework.\n\nMany of the studies included in our review attempted to measure the extent to which family planning clients perceived the interaction with the provider as patient-centered. However, without a universally agreed-upon definition of patient-centered counseling, we found wide differences in how it has been measured. Illustrative examples of questions asked to assess provider performance concerning each of the domains of patient-centered counseling are shown in Table 2.\n\n\n\n• Did the provider greet you respectfully? (Hazel, Mohan et al. 2021)\n\n• Did the provider make critical or judgmental comments about a) the number of children you have, b) your fertility plans, c) your partner or marital status, d) the involvement of your partner in family planning, e) your sexual activity, f) involvement of your parents, g) your age in reference to family planning, h) your preferred contraceptive method (Hazel, Mohan et al. 2021)\n\n• To what extent do you agree that the provider did not judge you? (Koo, Wilson et al. 2017)\n\n• Did the provider interrupt you while you were speaking? (Hazel, Mohan et al. 2021)\n\n• When it comes to making decisions about birth control, how important is it to young women like you to have privacy and confidentiality (from your parents) with your doctor (Carvajal, Mudafort et al. 2020)\n\n\n\n• Did the provider discuss how many children you would like to have? (Kamhawi, Underwood et al. 2013)\n\n• Did the provider ask what birth control method sounded like a good choice to you? (Brandi and Fuentes 2020)\n\n• Did the provider ask you about your preference in contraceptive methods? (Hazel, Mohan et al. 2021)\n\n• Did the provider ask if you had a method in mind before coming to the clinic? (Kamhawi, Underwood et al. 2013)\n\n• Did the provider make clear the advantages and disadvantages of different methods (Kamhawi, Underwood et al. 2013)\n\n• Did the provider discuss possible side-effects of methods? (Kamhawi, Underwood et al. 2013)\n\n• Did the provider ask what questions you had about any of the methods? (Brandi and Fuentes 2020).\n\n\n\n• To what extent do you agree that the provider showed care and concern about you as a person? (Koo, Wilson et al. 2017)\n\n• How would you rate the health care provider with respect to considering your personal situation when advising you about birth control (Dehlendorf, Henderson et al. 2016, 2018, Dehlendorf, Fox et al. 2021)\n\n\n\n• Did the provider ask what questions you had about any of the methods? (Brandi and Fuentes 2020).\n\n• How confident are you that you will be able to use your chosen method correctly? (Koo, Wilson et al. 2017)\n\n• Did the provider explain how to manage side effects of the chosen method? (Kamhawi, Underwood et al. 2013)\n\n\n\n• How satisfied are you with the decision-making process about which birth control method you will use? (Dehlendorf, Henderson et al. 2018)\n\n• Who do you feel made the decision about the chosen method? (Dehlendorf, Fitzpatrick et al. 2019)\n\n• Do you feel the provider advocated a specific method for you during the consultation? (Hazel, Mohan et al. 2021)\n\n• To what extent was the choice of your contraceptive method a shared decision between you and your provider? (Koo, Wilson et al. 2017)\n\n\n\n• To what extent are you satisfied with the plan to use your chosen method? (Koo, Wilson et al. 2017)\n\n• Did the provider explain where to obtain the method? (Kamhawi, Underwood et al. 2013)\n\n• How would you rate the health care provider with respect to working out a plan for your birth control with you (Dehlendorf, Henderson et al. 2016, 2018, Dehlendorf, Fox et al. 2021)\n\nTo standardize the measurement of the patient-centeredness of family planning counseling, some authors have developed and validated scales to measure the level of patient-centeredness of the family planning counseling visit. One of the most comprehensive tools for measuring patient-centeredness of family planning counseling and services visits we identified was the Interpersonal Quality in Family Planning Care (IQFP) scale (Dehlendorf, Henderson et al. 2016, 2018). The IQFP is a validated 11-item scale that measures distinct aspects of interpersonal communication between provider and patient. Specifically, the scale is based on eleven questions that ask family planning patients to rate the provider on the following issues:\n\n1) Respecting me as a person\n\n2) Showing care and compassion\n\n3) Letting me say what mattered to me about my birth control method\n\n4) Given me an opportunity to ask questions\n\n5) Taking my preferences about my birth control seriously\n\n6) Considering my personal situation when advising me about birth control\n\n7) Working out a plan for my birth control with me\n\n8) Giving me enough information to make the best decision about my birth control method\n\n9) Telling me how to take or use my birth control most efficiently\n\n10) Telling me the risks and benefits of the birth control method I chose\n\n11) Answering all my questions.\n\nPatients rated each of these 11 included items on a 5-point Likert scale, ranging from “poor” to “excellent.” Because most users rated the items as excellent, the authors dichotomized the item responses into the highest possible rating (excellent) versus all lower scores. Validity tests showed that the IQFP scale was associated with clients’ level of satisfaction with the family planning counseling they received and satisfaction with their chosen contraceptive method. Furthermore, higher IQFP scores were associated with positive provider communication practices, including eliciting the patients’ perspectives and demonstrating empathy. Multivariate analyses show that high scores on the IQFP scale were associated with positive family planning outcomes, including continuation of the chosen method at six months (OR=1.81 [1.09-3.00]) and use of an effective method at six months (OR 2.03 [1.16-3.54]). Examination of the different scale items suggested that continuation of the chosen method at six months was higher when the provider invested in the early part of the counseling session (OR=2.32 [1.24-4.32]) and elicited the patient perspective (OR=1.79 [1.01-3.16]). However, showing empathy or investing in the end of the session (e.g., by discussing follow-up, etc.) did not affect contraceptive continuation (Dehlendorf, Henderson et al. 2016).\n\nRecognizing that the large number of items in the IQFP may limit its usefulness for assessing provider performance, a reduced version of the scale has been produced (Dehlendorf, Fox et al. 2021). The Person-Centered Contraceptive Counseling (PCCC) scale asks family planning clients to think about their last provider visit and asks them how they would rate the provider on the following items from the original IQFP scale:\n\n1) Respecting me as a person\n\n2) Letting me say what mattered to me about my birth control method\n\n3) Taking my preferences about my birth control seriously\n\n4) Giving me enough information to make the best decision about my birth control method\n\nBecause the 4-item PCCC scale reduces the burden of data collection compared to the more comprehensive IQFP scale, it is more feasible to use it to measure the quality of the provider-patient interaction. The PCCC scale has since been incorporated into the National Survey of Family Growth (NSFG) questionnaire. Analyses of the NSFG show that while most respondents gave their provider an excellent rating on each of the four scale items, clients’ experiences related to person-centered care varied across sociodemographic groups, with low-income women, sexual minorities, and women with limited English proficiency giving their provider lower ratings for patient-centeredness (Welti, Manlove et al. 2022). The authors hypothesized that these lower ratings may reflect discrimination and/or a lack of cultural competency. The authors also noted that the association between low English proficiency and lower PCCC rating highlights that providing patient-centered care may require language concordance between providers and patients.\n\nThe fact that the 4-item PCCC was incorporated in the NSFG survey suggests it is likely to be more widely adopted. If so, it will further enhance consistency in measuring the level of patient-centeredness of family planning counseling and increase comparability across different studies.\n\n\nDiscussion\n\nOur scoping review aimed to assess how patient-centered family planning counseling has been conceptualized in the literature. Our findings show that there is no universally agreed upon definition of patient-centered family planning counseling. Only 18 of the 33 reviewed documents included a clear definition or described key domains of patient-centered family planning counseling. Consistent with Holt, Caglia et al. (2017), we found that although the definitions and terminology used tend to vary, the role of individual clients’ preferences, needs, and values is widely recognized. Furthermore, it is accepted that respect for the patient and informed decision-making are essential.\n\nPossibly because of the lack of a universally accepted definition, the level of patient-centeredness of the provider-patient interaction has been measured using a wide range of approaches. However, we found numerous commonly used measurement questions that roughly correspond with key domains of patient-centered care (McCormack, Treiman et al. 2011). Dehlendorf, Fox et al. (2021) have developed a Person-Centered Contraceptive Counseling (PCCC) scale that further condensed these topics to 1) respecting the patient as a person, 2) letting the patient say what matters to them about their birth control method, 3) taking the client’s preferences about birth control seriously, and 4) giving enough information to enable the patient to make the best contraceptive decision. Wider adoption of the PCCC scale in family planning surveys would generate consistency in measurement of patient-centered family planning counseling, which would help strengthen the evidence base. It may also help move the field toward a common definition of the concept.\n\nWe restricted our search to two well-established information sources, PubMed and Scopus, which focus heavily on peer-reviewed documents. Hence, our review may have omitted other relevant articles, particularly from the grey literature. While this de facto omission of gray literature is likely to have yielded higher quality publications, it may have resulted in the exclusion of alternative, less widely accepted conceptualizations of patient-centered family planning counseling and support. We also acknowledge that the documents retained for the review are skewed toward US-based studies and authors. Authors from other regions may conceptualize patient-centered family planning counseling differently. A larger evidence base would be needed to assess whether regional or cultural differences exist in how patient-centered family planning counseling is conceptualized.\n\n\nConclusions\n\nThe fact that “patient-centered family planning counseling” has not been defined consistently has resulted in wide discrepancies in how studies have measured different aspects of it. Inconsistent use of indicators makes it difficult, if not impossible, to make generalized conclusions about the effectiveness of the approach relative to the tiered-effectiveness approach. Consistent use of comparable indicators of key domains of patient-centered care is needed to address the gap in evidence about the effectiveness of patient-centered family planning counseling on various family planning outcomes, and to support future interventions. Since patient-centered family planning counseling encompasses several distinct domains, we concur with Street (2019)’s recommendation to map existing measures against the domains of patient-centered care. Wider use of recently developed scales that capture these domains would help increase the evidence base, while collecting essential information about each of the domains.\n\n\nAuthor contributions\n\nDM – funding acquisition, conceptualization, formal analysis, writing – original draft preparation; writing review and editing; AA – Formal analysis, writing – original draft preparation; writing – review and editing; VO – writing – review and editing.", "appendix": "Data availability\n\nHarvard Dataverse. “Replication Data for: Defining and conceptualizing patient-centered family planning counseling: A scoping review.”, https://doi.org/10.7910/DVN/CBHT7P (Meekers et al. 2023b).\n\nThis project contains the following underlying data:\n\n• Data file 1: Meekers et al. Patient-centered FP counseling definitions - extracted data 20230621.xlsx.\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nHarvard Dataverse: PRISMA (ScR) checklist for ‘Defining and conceptualizing patient-centered family planning counseling: A scoping review’, https://doi.org/10.7910/DVN/CBHT7P (Meekers et al. 2023b).\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\nAcknowledgments\n\nThis scoping research was conducted to support the implementation of the “Rapidly test innovations to support contraceptive continuation” project, which is implemented in collaboration with DKT Nigeria and Data Scientists Network (DSN) in Nigeria.\n\n\nReferences\n\nArksey H, O’Malley L: Scoping studies: Towards a methodological framework. Int. J. Soc. Res. Methodol. 2005; 8(1): 19–32. 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Publisher Full Text\n\nLabbok MH, Starling A: Definitions of breastfeeding: call for the development and use of consistent definitions in research and peer-reviewed literature. Breastfeed. Med. 2012; 7(6): 397–402. PubMed Abstract \| Publisher Full Text\n\nLevac D, Colquhoun H, O’Brien KK: Scoping studies: advancing the methodology. Implement. Sci. 2010; 5: 69. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLoyola Briceno AC, Kawatu J, Saul K, et al.: From theory to application: using performance measures for contraceptive care in the Title X family planning program. Contraception. 2017; 96(3): 166–174. PubMed Abstract \| Publisher Full Text\n\nMadrigal JM, Stempinski-Metoyer K, McManus AE, et al.: The family planning quotient and reproductive life index (FPQ/RepLI) tool: a solution for family planning, reproductive life planning and contraception counseling. Reprod. Health. 2019; 16(1): 125. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMcCormack LA, Treiman K, Rupert D, et al.: Measuring patient-centered communication in cancer care: a literature review and the development of a systematic approach. Soc. Sci. Med. 2011; 72(7): 1085–1095. PubMed Abstract \| Publisher Full Text\n\nMcGowan J, Straus S, Moher D, et al.: Reporting scoping reviews-PRISMA ScR extension. J. Clin. Epidemiol. 2020; 123: 177–179. PubMed Abstract \| Publisher Full Text\n\nMeekers D, Elkins A, Obozekhai V: Patient-centered approaches for family planning cousnseling and support: A systematic review. medRxiv. 2023a. Publisher Full Text\n\nMeekers D, Elkins A, Obozekhai V: Replication Data for: Defining and conceptualizing patient-centered family planning counseling: A scoping review. Harvard Dataverse. 2023b; V2. Publisher Full Text\n\nMorse JE, Ramesh S, Jackson A: Reassessing Unintended Pregnancy: Toward a Patient-centered Approach to Family Planning. Obstet. Gynecol. Clin. N. Am. 2017; 44(1): 27–40. PubMed Abstract \| Publisher Full Text\n\nMunn Z, Peters MDJ, Stern C, et al.: Systematic review or scoping review? Guidance for authors when choosing between a systematic or scoping review approach. BMC Med. Res. Methodol. 2018; 18(1): 143. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMunn Z, Pollock D, Khalil H, et al.: What are scoping reviews? Providing a formal definition of scoping reviews as a type of evidence synthesis. JBI Evid. Synth. 2022; 20(4): 950–952. Publisher Full Text\n\nPeters M, Godfrey C, McInerney P, 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\n\nPeters M, Godfrey C, McInerney P, et al.: Chapter 11: Scoping Reviews. JBI Manual for Evidence Synthesis (April 2021). E. Aromataris and Z. Munn, jbi.global.2021.\n\nPeters M, Marnie C, Tricco AC, et al.: Updated methodological guidance for the conduct of scoping reviews. JBI Evid. Synth. 2020; 18(10): 2119–2126. PubMed Abstract \| Publisher Full Text\n\nPollock D, Peters MDJ, Khalil H, et al.: Recommendations for the extraction, analysis, and presentation of results in scoping reviews. JBI Evid. Synth. 2023; 21(3): 520–532. Publisher Full Text\n\nSingal S, Sikdar SK, Kaushik S, et al.: Understanding factors associated with continuation of intrauterine device use in Gujarat and Rajasthan, India: a cross-sectional household study. Sex Reprod. Health Matters. 2021; 29(2): 1–16. PubMed Abstract \| Publisher Full Text\n\nSoin KS, Yeh PT, Gaffield ME, et al.: Health workers’ values and preferences regarding contraceptive methods globally: A systematic review. Contraception. 2022; 111: 61–70. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStreet RL Jr: Mapping diverse measures of patient-centered communication onto the conceptual domains of patient-centered care. Patient Educ. Couns. 2019; 102(7): 1225–1227. PubMed Abstract \| Publisher Full Text\n\nStulberg DB, Dahlquist IH, Disterhoft J, et al.: Increase in Contraceptive Counseling by Primary Care Clinicians After Implementation of One Key Question(R) at an Urban Community Health Center. Matern. Child Health J. 2019; 23(8): 996–1002. PubMed Abstract \| Publisher Full Text\n\nTi A, Burns R, Barnert ES, et al.: Perspectives on Patient-Centered Family Planning Care from Incarcerated Girls: A Qualitative Study. J. Pediatr. Adolesc. Gynecol. 2019; 32(5): 491–498. PubMed Abstract \| Publisher Full Text \| Free Full Text\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\nWelti K, Manlove J, Finocharo J, et al.: Women’s experiences with person-centered family planning care: Differences by sociodemographic characteristics. Contracept X. 2022; 4: 100081. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWorthington RO, Oyler J, Pincavage A, et al.: A Novel Contraception Counseling and Shared Decision-Making Curriculum for Internal Medicine Residents. MedEdPORTAL. 2020; 16: 11046.\n\nXiao J, Brenneis C, Ibrahim N, et al.: Definitions of Palliative Care Terms: A Consensus-Oriented Decision-Making Process. J. Palliat. Med. 2021; 24(9): 1342–1350. Publisher Full Text" }	[ { "id": "229797", "date": "06 Mar 2024", "name": "Kelsey Holt", "expertise": [ "Reviewer Expertise person-centered contraception" ], "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 opportunity to review this article. This scoping review provides a useful reflection on the current state of definitions related to patient-centered family planning counseling. With a few clarifications, the article will certainly be a useful reference. My recommendations are:\nThe piece could benefit from more precision when defining the scope of the review. First, while the review focuses on counseling, in a few places the authors describe patient-centered contraception care more broadly. Second, in at least one place the authors refer to a systematic search, while this was a scoping review. It would be important to acknowledge that the tiered effectiveness counseling model has not, in fact, long dominated –rather, in the last 15 years, there has been increasing use of the WHO tiered effectiveness chart to justify directive emphasis on the most effective methods. Prior to this, an informed choice counseling model predominated. A reflection on human rights-based frameworks for how counseling should be approached is missing, and this is notable both 1) in the lack of acknowledgement of the updated Bruce framework to include a rights-based approach in the section discussing the Bruce framework (see Red[1]) and 2) the authors’ framing of the importance of patient-centered counseling as a means to encourage contraceptive continuation, which is antithetical to a rights-based approach that values individual autonomy in contraceptive decision-making and recognizes that contraceptive use is not a universal good (see for example Ref [2,3]). I recommend they clarify how rights-based frameworks are relevant for conceptualizing and defining patient-centered counseling. The focus on measures towards the end of the piece feels out of place given how the search strategy was defined. It does not appear that the review included a review of person-centered counseling measures, or a review of the impact of person-centered/high quality counseling on outcomes, judging by the search terms? I recommend the authors clarify whether a review of measures was in scope and whether a review of the impact of patient-centeredness on other outcomes was in scope. The lengthy discussion of the IQFP/PCCC measure towards the end of the piece makes important points but it is not clear why this one particular measure and study on its impact is emphasized when other person-centered counseling measures and studies of the impact of patient-centeredness exist in the literature. The Holt, Caglia, et al 2017 citation is the wrong one; should be Holt, Dehlendorf, Langer 2017\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? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes", "responses": [] }, { "id": "242208", "date": "29 May 2024", "name": "Rose Goueth", "expertise": [ "Reviewer Expertise contraceptive care research", "shared decision making", "user-centered design", "systematic reviews" ], "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 scoping review aimed to identify definitions of patient-centered counseling and the implications for lack of an agreed definition. The background was well written. My one question is whether client-centered and patient-centered are interchangeably used within the contraceptive care context. I would provide evidence to support this conclusion and count how many articles within the review have either term within the Results section. The search strategy used was minimal but causes me to wonder why the search was not expanded. An expanded search would have resulted in many more hits to include within the review as is implied within the limitations. Results drawn from the articles look to be sound. The discussion and conclusion do not have the same ideas. The conclusion states, \"Inconsistent use of indicators makes it difficult, if not impossible, to make generalized conclusions about the effectiveness of the approach relative to the tiered-effectiveness approach.\" This is not proven within the discussion section of from your results.\nChanges to make: - Show proof of client-centered and patient-centered being used interchangeably within contraceptive care. - Subsequently provide counts for both terms within the results section of the manuscript. - Provide a clearer explanation of the choice of indices for searching articles. Maybe the smaller search is attributed to a rapid review style? - Make sure the discussion and conclusion have a consensus on the conclusions drawn (see quote listed above).\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.) Partly", "responses": [] } ]	1	https://f1000research.com/articles/12-1576
https://f1000research.com/articles/12-1575/v1	11 Dec 23	{ "type": "Research Article", "title": "A cross-sectional survey measuring social norms, personal norms and altruistic values across responsible computer consumption life cycles", "authors": [ "Yuen Yee Yen", "Paul H.P. Yeow", "WH Loo", "Paul H.P. Yeow", "WH Loo" ], "abstract": "Purpose This study makes a unique contribution to the knowledge by investigating the mediating role of the social and personal norms across the acquisition, use and disposal stages of the responsible computer consumption lifecycle.\n\nOriginality As the pioneer study conducted in Asian countries that provides integrative and holistic comparison on the mediating effect of personal and social norms with regards to responsible computer acquisition, use and disposal. Additionally, this study makes a theoretical contribution to the responsible computer value-behaviour relationships in an emerging market context.\n\nMethodology A large sample of 1000 questionnaires collected from 8 developed cities in Malaysia with the highest level of computer literacy, making this study capable of being generalized to the Malaysian population.\n\nFindings Social norms mediate the relationship between altruistic values and social norms at the acquisition and disposal stages. Personal norms mediate the relationship between altruistic and social norms at the acquisition and disposal stages.", "keywords": [ "Personal norms", "social norm", "altruistic values", "pro-environmental behaviour", "emerging market." ], "content": "1. Introduction\n\nAlmost half of households worldwide owned and used a computer at home (Thomas, 2021). In developing countries, the computer penetration rate is a third of households owned and used a computer (Thomas, 2021). High computer ownership poses serious threats to the environment, accelerating climate change (Ganivet, 2020; Ritchie, Reay & Higgins, 2018). It is crucial for policy makers and marketers to steer individuals towards responsible computer acquisition, use and disposal to mitigate the adverse effects of climate change. According to The Global E-Waste Monitor (2020)’s report, 65% of the consumers worldwide perceive that it is important to minimize computer waste to save energy, choose environmentally friendly computers, and reject computer brands that destroy the environment.\n\nDespite this high awareness, consumer’s commitment for greenness is far lower from expectation (Han, Hwang & Lee, 2017). As a developing country, environmental-friendly computers in Malaysia only account for 1% to 3% of the total market share (Azami, Bathmanathan, & Rajadurai, 2018). According to The Global E-Waste Monitor (2020)’s report, Malaysians generated 364 kilotons of e-waste, mostly discarded computer products with a battery or plug. Majority of the consumers worldwide do not practice responsible computer acquisition, use and disposal as regularly as they promised (Han, Hwang & Lee, 2017). Consumers who showed high awareness and positive attitude towards the environment did not reflect full commitment in responsible computer acquisition, use and disposal (Tan, Johnstone, & Yang, 2016). This great discrepancy between consumer value and actual behaviour indicates a need for mediating variables to convert more perceived value implication to actual behaviours (Lin, Lobo, & Leckie, 2017).\n\nTo the best knowledge of the researchers, there is a scarcity of research in Asia that provides a holistic and integrative examination on responsible computer acquisition, use and disposal. The importance of personal and social norms in influencing consumer value and actual responsible computer acquisition, use and disposal is an important research area which is currently overlooked by researchers (Yeow & Loo, 2022; Yeow, Lee and Yuen, 2022). The Value-belief-norm (VBN) Theory, which has been widely adopted by researchers to examine consumer efficacy and behaviour (Denley et al., 2020; Ghazali et al., 2021; Han, Hwang & Lee, 2017; Hong et al., 2019; Inoue et al., 2017; Liao et al., 2020; Liu et al., 2020; Ogiem wonyi et al., 2020; Sparkman et al., 2021), is yet to be used in comparing the mediating effect of the personal norms and social norms on the responsible computer acquisition, use and disposal (Megeirhi et al., 2020). This is a significant research gap in the responsible computer value-behaviour relationships.\n\nThis study is conducted to provide integrative and holistic comparison of the mediating effect of personal and social norms on the responsible computer acquisition, use and disposal. This study enriches the literature about responsible computer acquisition, use and disposal in the context of emerging economy (i.e. Malaysia), which has fast-growing computer penetration (Thomas, 2021).\n\n\nLiterature review\n\nThis study operationalizes responsible acquisition, use and disposal behaviours as the consumer’s effort and willingness to purchase, adopt and abandon green computers responsibly that offer take-back, upgrading and recycling options after careful deliberation (Denley et al., 2020). The green computers include desktops, laptops, and tablets (Mutum, Ghazali, & Wei-Pin, 2021). Responsible acquisition, use and disposal behaviours seek to minimize the negative impact of human actions on the environment (Roos & Hahn, 2019). It requires individuals to control egoistic tendencies for the benefit of the community (Kiatkawsin & Han, 2017). Individuals have to sacrifice short-term profits for the benefit of their community and the environment.\n\nAs a developing country, in spite of the growing interest in environmentally friendly products, the acquisition of environmental-friendly computers, computers which emits less carbon and consume less energy, only accounts for 1% to 3% of the total market share in Malaysia (Azami, Bathmanathan, & Rajadurai, 2018). With regards to responsible computer use, the majority of the computers used in office Malaysia are standard non-environmentally friendly monitors (Ali et al., 2021). Workers in Malaysia love to turn computers into standby mode after office hours (Ali et al., 2021). During the standby operation mode, the computer continues to consume from 1.5 W to 3 W energy due to timing and sensing functions (Ali et al., 2021). Malaysians are unlikely to practice responsible computer disposal in daily life (Global E-Waste Monitor, 2020). According to The Global E-Waste Monitor (2020)’s report, Malaysians generated 364 kilotons of e-waste in 2019, mostly discarded computer products with a battery or plug. Recycling activities are not keeping up with the amount of computer e-waste that people are generating each day (Global E-Waste Monitor, 2020).\n\nAltruistic values refer to performing activities that prioritize human welfare even though they have to pay high prices, interest, effort, or opportunity costs (Denley et al., 2020). This study operationalizes altruism as the consumer’s willingness to help people in the society to protect the environment through responsible computer acquisition, use and disposal. Çakır and Karaarslan (2019) discovered that altruistic values encourage consumers towards choosing sustainable products that will benefit humans in the long run (Kiatkawsin & Han, 2017). Liu, Zou and Wu (2018) concluded that altruistic values lead to greater willingness to accept high prices for responsible consumption and disposal that will benefit the society.\n\nAltruistic values work best in stimulating responsible computer acquisition, use and disposal (Karimi, 2019). Research conducted by Rezaei-Moghaddam, Vatankhah, and Ajili (2020) found that altruistic values improve the welfare of people in the society, incur personal costs but reduce personal gains. Altruistic values are the strongest among people who engage in pro-environmental activities (Çakır & Karaarslan, 2019) with strong environmental awareness (Denley et al., 2020). Kim and Kim (2018) ascertain the influence of altruistic values on the acceptability of environmentally friendly products among consumers. Megeirhi et al. (2020) further showed that altruistic positively affects participation in recycling activities.\n\nSocial norms refer to the social pressures an individual perceives, as to whether or not he or she should perform a certain behaviour (Fornara et al., 2016). This study operationalizes social norms as consumers’ willingness to comply with their social groups’ opinions when making responsible computer acquisition, use and disposal decisions. This construct measures an individual’s perceptions of what the people who are important to him or her would think, with regard to whether he or she should or should not perform a behaviour. Social norms can be seen as an important reference for an individual to know what rules are commonly accepted or desirable by social circles and vice versa (Hiratsuka, Perlaviciute & Steg, 2018). Social norms work because people have the tendency to behave in conformity with the group (Golob et al., 2019), as people tend to follow the behaviour that other individuals obey (Mortensen et al., 2019) when performing responsible computer acquisition, use and disposal.\n\nSocial norms influence pro-environmental behavioural changes (Loschelder et al., 2019; Mortensen et al., 2019; De Groot, Bondy & Schuitema 2021). Consumers with higher levels of social norms tend to have higher levels of responsible acquisitions (Yeow & Loo, 2022; Pristl, Kilian & Mann, 2021). Social norms play key roles in influencing its citizens’ responsible consumption since most emerging countries practice collectivist cultures that highly value social norms and societal value (Amiot, & Skerlj, 2021). Consumers in emerging countries are easily influenced by the people who are significant to him or her, or those who could judge his or her specific behaviour (Cho et al., 2021).\n\nPersonal norms are defined as individuals’ responsibility to control themselves to behave according to their moral values in a coherent manner (Koklic et al., 2019). Personal norms play important roles in consumer’s willingness to pay for environmental protection (Guagnano, 2001) and to recycle used items (Kim & Seock, 2019). Kim and Seock (2019) asserted that personal norms affect responsible recycling while Koklic et al. (2019) showed that personal norms influence responsible acquisition of environmentally friendly products. Roos and Hahn (2020) showed that personal norms influence the individual’s product acquisition and use. Koklic et al. (2019) said that altruistic shapes the consumer view toward environmental behaviour before personal norms determine responsible acquisition through the awareness of adverse consequences. Ünal, Steg and Gorsira (2018) found that altruism has a positive impact on the sense of obligation to take responsible acquisition and use actions. Kim and Kim (2018) showed that personal norms played important roles on responsible acquisition and use intentions. Furthermore, Landon, Woosnam and Boley (2018) identified positive relations between personal norms and responsible acquisition. Kiatkawsin and Han (2017) uncovered the significant influence of personal norms on intention to behave in an environmentally friendly manner.\n\nThis study operationalizes personal norms as consumers’ moral sense of duty to perform responsible computer acquisition, use and disposal. When consumers have high levels of the personal norm, they are more likely to use, pay more for and recommend responsible acquisition (Kim and Kim, 2018).\n\nThe proposed research framework, as presented in Figure 1, examines the mediating effect of personal norms on the altruistic values and the responsible computer acquisition, use and disposal.\n\nThe proposed research framework, as presented in Figure 2, examines the mediating effect of personal norms on the altruistic and the social norms of responsible computer acquisition, use and disposal.\n\nThe proposed research framework, as presented in Figure 3, examines the mediating effect of social norms on altruistic values and the personal norms of responsible computer acquisition, use and disposal.\n\nAccording to Sargisson, De Groot and Steg (2021), social norms play significant roles in influencing responsible behaviours which are environmentally friendly. Past researchers discovered a positive influence of the society or community on the acquisition of environmentally friendly products (Çakır & Karaarslan, 2019; Mutum, Ghazali & Wei-Pin, 2021; Rezaei-Moghaddam, Vatankhah, and Ajili, 2020; Sargisson, De Groot & Steg, 2021). People with high altruistic values who care about the welfare of human beings conforms to social pressures to perform green behavior to preserve the environment (Ünal, Steg & Gorsira, 2018). Given these facts, this study posits that the people will be more morally obligated to buy, use, and dispose of green computers if they are concerned about the long-term welfare of humans.\n\nThe hypotheses are as follows:\n\nH1a: Personal norms mediate the relationship between altruistic values and responsible computer acquisition.\n\nH1b: Personal norms mediate the relationship between altruistic values and responsible computer use.\n\nH1c: Personal norms mediate the relationship between altruistic values and responsible computer disposal.\n\nConsumers with high altruistic values are more likely to show concern over the needs of other people to receive social recognition from their friends and family (Bernhard, Martin, & Warneken, 2020). When a consumer feels that it is important to preserve the environment in order to gain more social recognition, they will feel more morally obliged to perform collective responsible computer consumption, use and disposal (Bernhard, Martin, & Warneken, 2020).\n\nAltruistic values trigger personal obligation and social recognition (Kim & Seock. 2019). The willingness to resolve environmental problems enhance moral obligation to perform pro-environmental behaviours (e.g. responsible computer acquisition, use and disposal) to improve belongingness to a social group (Levula, Harré, & Wilson, 2018). Therefore, this study hypothesizes that personal norms mediate the relationship between altruistic values and social norms with regards to responsible computer acquisition, use and disposal.\n\nThe hypotheses are as follows:\n\nH2a: Personal norms mediate the relationship between altruistic and social norms of responsible computer acquisition.\n\nH2b: Personal norms mediate the relationship between altruistic and social norms of responsible computer use.\n\nH2c: Personal norms mediate the relationship between altruistic and social norms of responsible computer disposal\n\nOn top of that, Vesely and Klöckner (2020) and Faletar, Kovačić and Cerjak (2021) discovered that personal norms can be triggered through a social norm intervention, where consumers are more easily accepted the society when performing pro-environmental behaviour to help the society to curb global warming (Kim & Seock, 2019). In line with this reasoning, social norms are hypothesized to mediate the relationship between altruistic values and personal norms associated with the responsible computer acquisition, use and disposal. Therefore, this study proposes the following hypothesis:\n\nH3a: Social norms mediate the relationship between altruistic values and personal norms of responsible computer acquisition.\n\nH3b: Social norms mediate the relationship between altruistic values and personal norms of responsible computer use.\n\nH3c: Social norms mediate the relationship between altruistic values and personal norms of responsible computer disposal.\n\n\nMethod\n\nTo comply with the regulations of Monash University, ethical clearance had been obtained from the Monash University Human Research Ethics Committee (MUHREC) prior to the distribution of the questionnaire (Ethical approval number: CF123196). Written informed consent was obtained from all respondents prior to the data collection by assuring the anonymity and confidentiality of the data collected.\n\nThis study used questionnaires for data collection with written consent prior to the data collection. The questionnaire had four items measuring altruistic values, three items measuring personal norms and 3 items measuring social norms. In addition, the questionnaire also had three items measuring responsible computer acquisition, four items measuring responsible computer use and six items measuring responsible computer disposal.\n\nThe questionnaire was pretested by 10 experts to validate its contents (Chan et al., 2020). Based on their feedback, amendments were made to the format, contents and instructions to improve the questionnaire. Thereafter, a pilot study was conducted with a sample size of 100 questionnaires distributed in public places. The collected data was tested for reliability and Cronbach Alpha values of all factors were above the threshold value of .70 (Park et al., 2021). The questionnaire was then finalized with minor amendments to the question arrangement.\n\nPurposive sampling methods were used in selecting the respondents because the complete list of green computer owners in Malaysia was not available since it violates the Personal Data Protection Act. For purposive sampling, respondents must have bought, used and disposed of at least one computer, have basic knowledge of green marketing and 17 years old and above. The authors set the age limit because those below 17 mainly do not have sufficient knowledge and capability to purchase, use and dispose of green computers. Filtering questions such as “Do you know what green marketing is?” and “Are you 17 years old and above?” were asked when approaching respondents face-to-face before inviting qualified respondents to answer the questionnaire.\n\nOne thousand respondents from 8 states in Malaysia that have the highest level of computer literacy, namely the Federal Territory of Kuala Lumpur, Selangor, Malacca, Kedah, Johor, Negeri Sembilan, Perak and Penang were approached. These states were specifically suitable to conduct this research because they are the most developed states in Malaysia. The questionnaire was personally administered to respondents at public places. Each respondent was approached face-to-face so that accurate pre-screening could be conducted to fulfil all purposive criteria. The purpose of the research and meaning of the questions were clearly explained to the respondents before the start of the data collection. Over a three-month period, 1000 questionnaire responses were collected. Three invalid responses with straight-line answers were excluded, 997 valid responses were used for the analysis.\n\nThis study used the covariance-based structural equation modelling (CB-SEM) to examine relations among independent variables, mediating variables and dependent variables in this study (Hair et al., 2016). To conduct the mediation analysis, a Maximum Likelihood Bootstrapping procedure was used with a bootstrap sample of 2000 and confidence interval of 95% (Ullman & Bentler, 2003).\n\nForty-six percent of respondents were female and 54% male. Most respondents (76.6%) were aged 17 to 32 years. Majority of the respondents (81.9%) had low-to-medium monthly incomes of below RM4,000. Additionally, the majority of the respondents (74.1%) had degree- or diploma-level education.\n\n\nResults\n\nConstruct validity was confirmed by assessing reliability, convergent validity and discriminant validity. The reliability test using Cronbach’s Alpha showed values ranging from .71 to .95, which were acceptable as they were above .70 (Hair et al., 2016). Convergent validity was confirmed as the factor loading of each item was >.50, the composite reliability of each construct >.70 and the average variance extracted of each construct >.50 (Hair et al., 2016). The discriminant validity analysis was performed to determine the extent a construct differs from other constructs. Table 1 shows all factors met the discriminant validity criterion, i.e. the square root of average variance extracted (√AVE) exceeds all correlations involving that construct (Hair et al., 2016). The measurement model’s goodness of fit indices was well above the recommended cut-off points: RMSEA = .07 (<.08), GFI = .95 (≥.90), CFI = .97 (≥.90), TLI = .96 (≥.90) and AGFI = .91 (≥.90) (Hair et al., 2016).\n\nThe research tested the mediating effects of mediators using multi-model analysis to verify the condition of mediating effects (Hair et al., 2016).\n\nTable 1 shows that altruistic values significantly affect social norms (β = .480, p < .001) and social norms significantly affect responsible computer acquisition (β = .177, p < .001). Altruistic values significantly affect responsible computer acquisition (β = 0.303, p < .01). The 95% confidence interval ranges from.047 to.126, in which the value of zero is not within the range. H1a is supported that personal norms partially mediate the relationship between altruistic values and responsible computer acquisition.\n\nAs indicated by Table 2, altruistic values significantly affect social norms (β = .098, p = .005) and social norms significantly affect responsible computer use (β = .418, p < .001). Altruistic values do not significantly affect responsible computer use (β = .046, p = .166). The 95% confidence interval ranges from .017 to .063, in which the value of zero is not within the range. H1b supports that social norms fully mediate the relationship between altruistic values and responsible computer use.\n\nAccording to Table 3, altruistic values significantly affect social norms (β = .121, p < .001) and social norms significantly affect responsible computer disposal (β = .431 p < .001). Altruistic does not significantly affect responsible computer disposal (β = .030, p = .414). The 95% confidence interval ranges from .035 to .199, in which the value of zero is not within the range. h1c is supported that social norms fully mediate the relationship between altruistic values and responsible computer disposal.\n\nTable 4 shows that altruistic values significantly affect personal norms (β = .480, p < .001) and personal norms significantly affect social norms (β = .086 p = .001). Altruistic values significantly affect social norms (β = .342, p ≤ .001). The 95% confidence interval ranges from .001 to .076, in which the value of zero is not within the range. H2a is supported that personal norms partially mediate the relationship between altruistic values and social norms of responsible computer acquisition.\n\nIn Table 5, altruistic values significantly affect personal norms (β = .070, p = .023) and social norms significantly affect personal norms (β = .459, p < .001). However, altruistic values do not support social norms (β = .060, p = .066). The 95% confidence interval ranges from.000 to .005, in which the value of zero is within the range. H2b does not support that personal norms do not mediate the relationship between altruistic values and social norms of responsible computer use.\n\nAccording to Table 6 altruistic values significantly affect personal norms (β = .121, p < .001) and personal norms significantly affect social norms (β = .490, p < .001). Altruistic values do not significantly affect social norms (β = .076, p = .414). The 95% confidence interval ranges from .043 to .161, in which the value of zero is not within the range. H5a is supported that personal norms partially mediate the relationship between altruistic values and social norms of responsible computer disposal.\n\nTable 7 reveals that altruistic values significantly affect social norms (β = .383, p <.001) and social norms significantly affect personal norms (β = .078, p = .001). Altruistic values significantly affect personal norms (β = .451, p < .001). The 95% confidence interval ranges from .005 to .069, in which the value of zero is not within the range. H3a is supported that social norms partially mediate the relationship between altruistic and personal norms of responsible computer acquisition.\n\nTable 8 indicates that altruistic values do not significantly affect social norms (β = .015, p = .621). The 95% confidence interval ranges from .000 to .000, in which the value of zero was within the range. H3b does not support that social norms do not mediate the relationship between altruistic values and personal norms of responsible computer use.\n\nAs shown in Table 9, altruistic values significantly affect social norms (β = .129, p < .001) and social norms significantly affect personal norms (β = .492, p < .001). Altruistic values do not significantly affect personal norms (β = .046, p = .159). The 95% confidence interval ranges from .035 to .095, in which the value of zero is not within the range. H3c is supported that social norms fully mediated the relationship between altruistic and personal norms of responsible computer disposal.\n\n\nDiscussion\n\nThis study discovers three important and unique findings which enriches the enrich the current knowledge about responsible computer acquisition, use and disposal in the context of emerging economy (i.e. Malaysia). First important finding, personal norms significantly mediate the relationship between altruistic values and responsible computer acquisition, use and disposal. Malaysian practices collectivism in daily life. This finding is important for marketing practitioners to promote environmentally friendly products to the collectivist country. People in collectivist countries such as Malaysia are found to pay more attention to how their responsible acquisition, use and disposal behaviours affect other people in the society before making decisions to acquire, use and dispose of a computer. Social opinions affect a consumer’s decision to perform pro-environmental computer purchase and disposal to minimize the hazardous impact to the environment. Collectivist people tend to have higher social norms in performing responsible computer acquisition and disposal because they prioritize collective benefits (altruistic) over individual benefits.\n\nAnother important finding of this study is that personal norms mediate the relationship between altruistic and social norms of responsible computer acquisition and disposal. Living in a collectivist society, Malaysians have high altruistic values to place more attention to the benefits of people in the society. Before making any decision to purchase a new computer or dispose of an old computer, they tend to consult important people in their social group to seek approval. Malaysians will act according to the moral obligations set by people in their social groups. When people in the social groups think that it is morally obliged to benefit the society by acquiring and disposing of computers in an environmentally friendly manner, consumers in Malaysia will be more willing to act pro-environmentally according to the moral standards. This finding is important for marketing practitioners to promote environmentally friendly computers to the consumers in a collectivist society. Moral obligations to preserve the environment needs to be highlighted to encourage more environmentally friendly purchase and disposal of computers.\n\nThe third unique finding of this study is that social norms mediate the altruistic values and personal norms of responsible computer acquisition and responsible computer disposal. As members of a collectivist society, Malaysians have a strong moral obligation to contribute for the betterment of the people in the society. Social pressure on whether consumers should carry out responsible behavior to buy a new green computer or dispose of an old in a responsible manner influences their decision-making and moral obligation to preserve the environment. Collectivist individuals are often influenced by the people around them in shaping their moral obligation for green computer purchase and disposal activities, that is, if they participate in green computer purchase and disposal behaviours, their reference group will perceive them as morally correct. This finding is important for the government in setting rules and regulations to preserve the environment by inviting prestigious members in the society to share responsible computer acquisition and disposal practices via mass and social media.\n\n\nConclusion\n\nThis study bridges the research gaps of the Value-belief-norm (VBN) Theory by confirming the mediating role of social norms between altruistic values and responsible computer acquisition, use and disposal. This study also makes a unique contribution to the existing knowledge by confirming the mediating role of personal norms between altruistic values and social norms of the responsible computer acquisition and disposal as well as the mediating role of social the mediating role of personal norms between altruistic values and social norms of the responsible computer acquisition and disposal. This finding is important for marketers and government practitioners to promote responsible computer consumption through shared moral values and social pressures.\n\nThis study is the pioneer studies in Asia countries that provides an integrative and holistic comparison on responsible computer acquisition, use and disposal. A large sample of 1000 questionnaires collected from eight developed cities in Malaysia with the highest level of computer literacy, making this study capable of reflecting the viewpoint of the majority of the Malaysian population.", "appendix": "Data availability\n\nFigshare: Yee Yen, Yuen (2023). Social Norms, Personal Norms and Altruistic Values Across Responsible Computer Consumption Life Cycles. figshare. Dataset. https://doi.org/10.6084/m9.figshare.23591715.v1 (Yuen, 2023).\n\nThis project contains the following underlying data:\n\n• dataset2.xlsx (Survey data)\n\nFigshare: Yee Yen, Yuen (2023). Social Norms, Personal Norms and Altruistic Values Across Responsible Computer Consumption Life Cycles. figshare. Dataset. https://doi.org/10.6084/m9.figshare.23591715.v1 (Yuen, 2023).\n\nThis project contains the following extended data:\n\n• - Questionnaire.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\nAli SBM, Hasanuzzaman M, Rahim NA, et al.: Analysis of energy consumption and potential energy savings of an institutional building in Malaysia. Alex. Eng. J. 2021; 60(1): 805–820. Publisher Full Text\n\nAmiot CE, Skerlj F: The role of dynamic social norms in promoting the internalization of sportspersonship behaviors and values and psychological well-being in ice hockey. Front. Psychol. 2021; 12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAzami N, Bathmanathan V, Rajadurai J: Understanding generation y’s green purchasing decision in Malaysia. Glob. Bus. Manag. Res. 2018; 10(3): 1010.\n\nBernhard RM, Martin JW, Warneken F: Why do children punish? 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Ethics.2020; 158(3): 679–697. Publisher Full Text\n\nSparkman G, Howe L, Walton G: How social norms are often a barrier to addressing climate change but can be part of the solution. Behavioural Public Policy. 2021; 5(4): 528–555. Publisher Full Text\n\nThomas A: Computer Penetration Rate among Households Worldwide 2005-2019.2021. Retrieved January 12, 2021. Reference Source\n\nUllman JB, Bentler PM: Structural equation modeling.Handbook of Psychology, First ed.2. 2003. Publisher Full Text\n\nÜnal AB, Steg L, Gorsira M: Values versus environmental knowledge as triggers of a process of activation of personal norms for eco-driving. Environ. Behav. 2018; 50(10): 1092–1118. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVesely S, Klöckner CA: Social desirability in environmental psychology research: Three meta-analyses. Front. Psychol. 2020; 11(1): 1395. 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Publisher Full Text" }	[ { "id": "233879", "date": "27 Jan 2024", "name": "Kai Wah Cheng", "expertise": [ "Reviewer Expertise Sustainability", "consumer behaviour", "consumer psychology", "recycling & solid waste management", "environmental education" ], "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(1) Is the work clearly and accurately presented and does it cite the current literature? >>> The authors need to present a brief research background, followed by a problem statement or research gap for each of the variables in the framework.\n(2) Is the study design appropriate and is the work technically sound? >>> The explanation of the theoretical contributions is not enough. The authors should explain the application of VBN theory in the previous research works. >>> What about the other types of contributions? >>> The authors need to explain the significant relationships between each IV and DV clearly in the literature review. >>> I would like to suggest the authors combine Figure 1, Figure 2, and Figure 3 in order to construct a unified research framework.\n(3) Are sufficient details of methods and analysis provided to allow replication by others? >>> The authors need to explain the research instrumentation clearly, whether it is formed via adoption or adaptation. >>> Please explain the sampling technique and data collection procedures clearly in the article.\n(4) If applicable, is the statistical analysis and its interpretation appropriate? >>> I would like to suggest the authors combine Table 1, Table 2, Table 3, Table 4, Table 5, Table 6, Table 7, Table 8, and Table 9 into a unified results table. >>> The authors should be able to compare and construct the direction of the current research results with the previous research results. >>> All the explanation under Discussion should be prepared in an academic way and supported by relevant articles.\n(5) Are the conclusions drawn adequately supported by the results? >>> The write-up of Conclusion is too brief. >>> The authors need to explain their research implications in the 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? 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? Partly", "responses": [] }, { "id": "242143", "date": "20 Feb 2024", "name": "Xiaobin Lou", "expertise": [ "Reviewer Expertise environmental psychology" ], "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 am grateful for the opportunity to review this paper. This is a great attempt to apply VBN theory (in its part form) to study environmental behavior in an Asia context. This study has a strength in using a large sample size and in studying a relatively under-studied environmental behavior in a relatively under-studied sample. I also liked the authors grounding their findings in the Malaysian context in their discussions.\nWith these strengths, I still hold some concerns about the work. I hope my feedback can be helpful for the authors to improve their work.\n1. My biggest concern is that the authors framed a very complex conceptual model using a). social norm as a mediator of the link between altruistic value and pro-environmental behavior (PEB). b). Personal norm as a mediator of the link between altruistic value and social norm c). Social norm as a mediator of the link between altruistic value and personal norm\nTo my knowledge, the bi-directional mediation effect between social norms and personal norms is awkward, I have not seen former studies do that; I also doubt the theoretical soundness of this conceptualization; plus, VBN theory did not make such a bi-directional mediation argument. The authors may consider simplifying their model by sticking to the VBN theory.\n2. Perhaps it will be easier for readers to get takeaways by presenting statistical findings in one figure, not in 8 tables.\n3. More justification is needed regarding why the authors focus on a small portion of the VBN theory for statistical tests. For instance, the B (belief) component of the theory is totally ignored. For another instance, only altruistic value is studied.\nI am not saying the authors should stick to the whole model, but it will be good to offer some justifications for their selections.\n4. The methodological section lacks some important details, for instance, the detailed information of measurement tools and their psychometric performances.\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/12-1575
https://f1000research.com/articles/12-679/v1	15 Jun 23	{ "type": "Research Article", "title": "What is the visual behaviour and attentional effort of football players in different positions during a real 11v11 game? A pilot study", "authors": [ "Charles Ballet", "Joana Barreto", "Edward Hope", "Filipe Casanova", "Joana Barreto", "Edward Hope", "Filipe Casanova" ], "abstract": "Background: Visual perception has been defined as the first step to a football player’s decision-making process and it plays an important role in performance in sport. The skill of focussing to prioritize relevant cues has been also considered crucial in sport. This pilot study aims to explore the visual behaviour and attentional effort of three football players (mean age 19 ± 0 years old) in specific-role positions; Right-winger (RW), Centre-Midfielder (CM) and Left-Back (LB), in the five seconds before receiving the ball from their teammate. Methods: Twenty-two male football players performed an 11v11 game, where 24 game sequences (trials) from which 166 fixations were recorded and analysed via the Tobii Pro eye-movement registration glasses and software. The gaze behaviour dependent variables were the mean of fixation duration (FD), time to first fixation (TTF), both measured in milliseconds (ms), and the number of fixations (NF) on eight areas of interest (AOIs). AOIs include teammate with and without the ball, opponent without the ball, space around teammate with and without the ball, space around opponent without the ball, ball and undefined. The mean pupil diameter (PD) correlates to the attentional effort and was measured in millimetres (mm). Results: Descriptive statistics showed nonregular search rate data between the participants in FD, TTF, NF on the AOIs. Mean FD on the ball: (CM, 270 ms), (RW, 570 ms), (CM, 380 ms). They also presented differences in the mean PD during play; (CM: 2.90 mm ± 0.26), (RW: 2.74 mm ± 0.30), (LB 2.77mm ± 0.27). Conclusions: Albeit the sample size was small, the findings demonstrated a promising way to measure the on-field perceptual-cognitive abilities of football players according to their specific positions, since different playing roles revealed to present distinctive visual and attentional patterns.", "keywords": [ "Football", "player-role", "perceptual-cognitive skills", "eye-tracking", "decision making" ], "content": "Introduction\n\nOver the last twenty years, perceptual-cognitive skills of athletes in sports have been studied extensively to understand the mechanisms behind anticipation, decision-making, and expertise in sport.1 Perceptual-cognitive skill of an athlete in team sports refers to their ability to use human perception; seeing, hearing and awareness to pick up cues during play.1 Those would be then integrated and processed with existing (tactical) knowledge so that the right sporting decision could be actioned.2 It has been clearly demonstrated that athletes with higher perceptual-cognitive skills have better anticipation and decision-making abilities.3\n\nResearch has shown that attention in sport is as important as perception for performance.4 Indeed, visual attention (focus) and visual perception are distinct, yet closely linked.4 From a coaching and professional perspective, visual perception is defined as the first step of football players’ decision-making process.5 A player scans the field during a specific style of play to decide their next action accordingly.6 Visual attention is what enables this player to pick-up all important cues and ignore the less relevant before making their decision.4\n\nWhen discussing attention, it is important to distinguish between covert and overt attention.7 The covert is characterised by the attention following the movements of the eyes (linked to central vision).7,8 Overt attention are directed elsewhere than where the eyes are fixating (linked to peripheral vision).7,8\n\nA football game is characterised by 22 athletes whose movements, speed, body, and positioning, vary continuously.9 As a result, football players would use their visual perception and attention differently to pick-up cues such as spaces, teammates, opponents to intend to make the right decision at the right time.8 As a result, we believe it is important for coaches to be aware of individual players’ visual patterns and attention.\n\nResearch on visual perception evidenced that 80% of the information taken from the environment is done through the eyes.10 This allows a player to analyse the game situation and recognised patterns of play.10 Therefore, visual perception is crucial when talking about spatial awareness.10 Visual perception has been previously studied via “scanning”, which is the amount of time a player moves their head towards and away from a ball, teammate, or opponent; not considering their gaze behaviour.9,11 Although, visual exploration can also be done through body movements, it is ultimately through the eyes that the information is mainly picked and processed.9\n\nWhen it occurs the eyes move and fixate to a specific cue, this process is characterised by the steadiness of the gaze on a point of interest.12 It is commonly associated to central vision since it enables individuals to see details clearly and sharply.12 For example, fixation happens when a player keeps their eyes (and therefore gaze) on the ball to get a clearer vision of it.10 Fixation has been previously linked to football performance since its duration can vary depending on the skill level of an athlete.13 An increase in fixation duration can suggest that the player may have more interest in what is fixating on, and/or processing the information.10 Although there has been a general assumption that the players attention is where we fixate, it has also been evidenced otherwise.14 As an example, a player can look at the most obvious free teammate but pass the ball to another teammate they spotted using their peripheral vision.1\n\nMost visual perception studies explored gaze behaviour following Gibson’s theory of perception-action coupling, which explains the mechanism behind the coordination between what we see and what we do.15 During a football game, players are confronted with ever-changing dynamic situations and constraints which they need to consider constantly before their next actions. For example, a player who is in possession of the ball would have to decide to either shoot at goal, pass to a teammate, or dribble the ball depending on how far the goal is and how his/her teammates and opponents are positioning and moving themselves on the pitch.16\n\nAksum et al.9 conducted an on-field observational study investigating eye movements of midfield players during a 11v11 match play. They analysed visual fixation when the ball was at play, during both defence and attack phases. Moreover, the forementioned authors measured fixation duration and the total time spent (as a percentage) of viewing each fixation’s location, categorising the locations as ball, teammate, opponent, space and other.9 They provided valuable insight from their experiment showing that elite midfield players use longer fixation duration (242.49 ms) when facing several cues such as space, teammates, and opponents.9 Furthermore, midfield players fixate more on the player in possession of the ball during a defensive phase of play than during an attacking phase.9\n\nAlthough their experiment provided an understanding into the gaze behaviour of midfield players, more research is needed, as it could be argued that football players, including backs and forwards, have different roles on the pitch and therefore might use different gaze strategies.17 Another limitation of their research lays on the fact that they did not explore visual attention.\n\nAs previously stated, visual perception and attention are closely linked and integrated within the decision-making process of a football player.4 Therefore, our intention was to investigate visual perception by studying our participants gaze behaviour but also their attention by measuring their pupil size during play.\n\nA laboratory study investigated attentional effort of expert and novice horse riding athletes by measuring pupil diameters using video simulations.18 The results found evidenced that the expert group displayed a higher increase of their pupil size diameter than the novice group.18 Conversely, another study highlighted that a player owning a higher amount of tactical knowledge requires less cognitive effort during a laboratory video test.19 This difference could be pointed because football is a team sports with complex situations compared to horse riding.9,18\n\nThe aims of this pilot experiment were to study the differences of the gaze behaviour and attention of three male footballers playing as a left-back (LB), right-winger (RW) and a centre-midfielder (CM), during the five seconds before receiving the ball from a teammate on 11v11 game. Which means that visual data including search rate and order will only be analysed during when the team of the player investigated had possession of the ball. Since different football player positions come with different tactical demands, we hypothesised that there would be different gaze behaviour used between the players.17 Secondly, we predicted that there would be dissimilar values in the attentional effort between the players by showing different pupil size diameters.17\n\n\nMethods\n\nTwenty-two male football players (mean age 19 ± 0 years old; and 6.67 ± 3.79 years of football practice) who play as amateurs in the Portugal National University Championships were recruited We contacted football coaches of the Lusófona University via email who forwarded our invitation letter to the players to voluntary take part to the experiment. They all took part in a 15-minute pre-competitive football game, which were separately recorded the visual behaviour of three of those participants who played as a LB, CM and RW were each analysed and recorded at different moments of an 11 v 11 football game. Participants reported normal or corrected-to-normal levels of visual function. The study complied with the safety guidelines of the Tobi eye tracking devices and was approved by the Ethics Committee of Lusófona University (protocol number M25A21), and the UCL Research Ethics Committee (project identification number 7067/001) which are in accordance with the Declaration of Helsinki. All participants provided voluntary written informed consent, where all procedures were explained in detail, from the data collection to the publication stage.\n\nThe Tobii Pro Glasses 2® (Tobii Pro AB, Stockholm, Sweden) eye-movement registration system was worn by each participant during an 11 v11 football pre-competitive match on a full-size pitch. The Tobii Pro Glasses 2® is a binocular eye tracker that records the point-of-gaze onto a video image of the scene, measuring the relative position of the pupil and corneal reflection. The image recorded was then analysed via the Tobii Pro Lab software (Version X, Tobii Pro AB, Stockholm, Sweden). The Tobi Pro Lab Software was utilized on a Dell Venue 11 Pro 7130, Windows 8/8.1 Pro tablet at a rate of 50 Hz. It is important to highlight that players were not recorded simultaneously. The visual behaviour and attentional effort of three football players were investigated in the five seconds before receiving the ball from their teammate. Jordet et al.11 previously investigated the scanning frequency (players looking over their shoulders) per seconds in the last ten seconds of a team possessing the ball. We chose to analyse our data in the five seconds before the player receive the ball since it might help the coaches and players to interpret another understanding of visual strategies used during a short period of time.\n\nThe procedures were carefully explained to the participants before the beginning of the experiment. The eye-tracking glasses were well fitted onto the participant’s face who also worn a vest holding the recording unit in a small pocket between the shoulder blades. To ensure high gaze data quality, calibration procedures were carried out by asking the participants to focus on the center of the calibration card held in front of them for five seconds. Each investigated participant practiced for five minutes playing football while wearing the eye tracker to ensure familiarity with the testing protocols. In the experiment, our three investigated participants took part in a 20-min 11v11 pre-competitive football game. Each of them worn the Tobii eye tracker for about 5 minutes.\n\nTo control for possible learning biases, no feedback was provided during performance.\n\nSearch rate\n\nThe measurement of visual search rate comprised those of the number of fixations (NF); characterising how often each player looks at each of the eight areas of interest (AOI), as per Casanova et al.10: the ball (B), an opponent without the ball (ONB), the space around opponent without the ball (Space around ONB), any space around a teammate without the ball (space around TNB), space around a teammate with ball (space around TB), teammate with ball (TB), teammate without the ball (TNB) and undefined (U). The “undefined” category is characterised by any gaze data which would not fall into any of the other areas.\n\nThe search rate was measured via the fixation duration (FD) (in milliseconds; ms) which reveals how long each player looks at each of the eight AOIs.\n\nThe gaze data were measured via the Tobii Pro lab software via metrics analysis and tracking pursuit analysing data frame-by-frame using a sampling rate of 50 Hz. The velocity-threshold identification (IV-T) algorithm was used to classify the different eye movements depending on their velocity, measured in visual degrees per second (°/s). This threshold enables the categorization of the raw gaze data into different eye movements as saccades and fixations.20 For instance, if the velocity is above the threshold, it would be categorised as a saccade. On the contrary, if the velocity turns out to be below the threshold for a minimum duration of 120 ms, the eye movement data would be classified as a fixation. In this experiment the IV-T filter was set up so that a fixation presents with a minimum threshold of 120 ms, with velocity below the threshold of 100 visual degrees per second (°/s). The filter was set up with those values because the subjects, targets and objects would be constantly moving under dynamic situations.21\n\nThe analysis of the eye tracking data via the Tobi Pro lab software was done via assisted mapping of the gaze data point (gaze circle) on to a fixation location and into new coordinate system. In the study conducted by Aksum et al.9 the gaze circle was set at 100% so that it could comprise more than one object of interest. For instance, one fixation could include three different areas such as the ball, teammate, and opponent.9 In the present study, we choose to set the gaze circle at 1% to contain only one object of interest, so to make the results more precise.\n\nSearch order\n\nSearch order also defined as fixation order is characterised by the search sequence or order used by the players.22 The search order was measured by analysing the mean time to first fixation (TFF), indicating when each player looks at each AOI.23 A smaller mean time to first fixation value on a specific AOI would indicate that the player looks at this specific AOI earlier in comparison to other AOIs.23\n\nMeasure of pupil dilatation\n\nWe measured the size of the pupil of each of three players which is meant to reflect their attentional effort.24 Pupil data often carries “noises” which are data that cannot be interpreted.25 As a result, the moving average noise reduction filter of the Tobii Pro software was used to filter our data. It produces an output data by creating an arithmetic mean of several data points from the input data.26 The moving average filter also makes an average of the right and left eye data, even in the event of only one eye being recorded.20\n\nTo demonstrate changes in attentional effort, previous studies measured a baseline (at rest) and a “post-stimulus” mean value of a participant‘s pupil diameter.18 Subsequently, the baseline of the pupil data of each player investigated was obtained by measuring the mean of the pupil diameter during the calibration of the eye tracker. The “post-stimulus” value of the pupil dilation of each player was also measured during the five seconds before receiving the ball, as per the gaze behaviour measurements.\n\nReliability\n\nTest-retest reliability comprised a 20-day interval for re-analysis to avoid any familiarity effects with the task performed using the Cohen’s Kappa test.27 Moreover, reliability was verified through the reassessment of more than 25% of trials, as suggested in the literature.3\n\nThe distribution of data sets28 was analysed using Shapiro-Wilk tests. Only descriptive statistics for the results analysis was used since this pilot study had a small sample size and, therefore, is statistically underpowered.29 Descriptive analyses were performed using the Statistical Package for Social Sciences software V24.0 (IBM SPSS Statistics for Mac, Armonk, NY: IBM Corp.) (RRID:SCR_002865).\n\n\nResults\n\nDescriptive analysis revealed that the mean FD of the CM was the highest and accounted for 530 ± 509.42 ms, with minimum and maximum values being 140 ms and 1420 ms, respectively (see Table 1 and Figure 1). The mean FD of the RW was the second highest at 332.50 ± 143.10 ms, with a minimum value of 130 ms and a maximum value of 570 ms. Finally, the mean FD of the LB was the lowest and accounted for 306.25 ± 149 ms, with a minimum value of 130 ms and a maximum value of 480 ms.\n\nThe highest TNF was for LB which accounted for 64, associated with a mean value of 8 ± 4.41, a minimum value of 1 and a maximum of 16.\n\nThe second highest TNF was for the RW which was 59, with a mean value of 7.37± 5.04 and minimum and maximum values of 3 and 19, respectively.\n\nWe found that the TNF for the CM was 43 and the mean value of 5.36 ± 8.07. The minimum and maximum of NF were 1 and 25, respectively.\n\nDescriptive statistics showed that across the explored plays the mean TFF of the LB was the highest and accounted for 22770 ± 18441.24 ms, with a minimum value of 620 ms and a maximum value of 53900 ms.\n\nThe mean of TFF of CM was the second highest and accounted for 10211.25 ± 7000.32 ms, with a minimum value of 0 ms and a maximum value of 20960 ms (see Table 2 and Figure 2).\n\nThe mean TFF of the RW was the lowest (5078.75 ± 6289.68 ms) with a minimum value of 0 ms and a maximum value of 19360 ms.\n\nThe mean pupil size of the CM at baseline was 2.50 ± 0.20 millimetres (mm), with a minimum value of 2.21 mm and a maximum value of 3.34 mm. During play, the CM’s mean pupil size increased by 0.40 mm to 2.90 ± 0.26 mm, with a minimum value of 2.34 mm and a maximum value of 3.63 mm (see Table 3 and Figure 3).\n\n* During the five seconds before receiving the ball from a teammate.\n\nThe mean pupil size of the RW at baseline was 2.64 ± 0.18 mm, with a minimum value of 2.22 mm and a maximum value of 3.04 mm. During play, the RW’s mean pupil size increased by 0.10 mm to 2.74 ± 0.30 mm, with a minimum value of 2.22 mm and a maximum value of 4.59 mm.\n\nThe mean pupil size of the LB at baseline was 2.59 ± 0.35 mm, with a minimum value of 2.38 mm and a maximum value of 5.70 mm. During play, the RW’s mean pupil size increased by 0.18 mm to 2.77 ± 0.27 mm, with a minimum value of 2.35 mm and a maximum value of 3.89 mm.\n\n\nDiscussion\n\nThis pilot experiment was carried out to explore gaze behaviour and attentional effort of football players from LB, RW and CM during the five seconds before receiving the ball from a teammate on 11v11 game. As expected, in the present study we observed dissimilar gaze behaviour and attentional effort from each football player (i.e., CM, RW and LB).\n\nThe mean FD of the CM was the highest of all the specific positions analysed (530 ± 509.42 ms). It can be argued that the CM tends to fixate longer periods of time than the other players, in which is associated with previous studies which explained that the CM players display higher value of mean FD since they usually act as a link between attack and defence.17 Hence, CM players must process more information because they consistently need to scan their surroundings. The RWs, who can be considered as attacking midfielders, displayed the second highest mean value of FD (332.50 ± 143.10 ms). This contradicts previous research which suggested that attacking players display a lower scanning rate because they usually operate against temporal and spatial in critical areas.17 Likewise, players located at the peripheries have also restricted use of their vision field since they do not need to gather information from outside the side line.11 Lastly, the mean FD of the LB accounted for 306.25 ± 149 ms which could be caused by the fact that players having proximity to the goals would have the lowest scanning frequencies.\n\nAnalysis of the mean FD on AOIs showed that CM spent more time looking at spaces, particularly at STB (1420 ms) than ONB (150 ms). This reveals that the CM player had more spatial awareness before receiving the ball, which has been evidenced to enable a player to analyse different options and increase the chance of success of their next tactical action. During the five seconds before receiving a pass, it seemed that the RW was more fixating the ball (570 ms) than the spaces taking individually (STB- 320 ms; STNB- 130 ms; and SONB- 430 ms), which might indicate that the RW player tended to do more “ball watching”. Ball watching has been commonly associated with lower league and amateur players’ lack of spatial awareness and technical experience which led them to focus solely on the ball.3,8 Interestingly, the LB spent most of time fixating on STB (480 ms) and least time on SONB (130 ms). This could be interpreted that the LB somewhat fixates also on spaces. Nevertheless, it is important to highlight that LB longest mean FD on AOIs, including 480 ms on STB, still remains lower than that of CM and RW‘s. This could also be explained by his position on the field, as previously mentioned.\n\nIt can be observed that despite CM looking 25 times at the ball, the player did not spend as much time fixating on it (270 ms) but rather fixated longer on STB (1420 ms). FD and its relation to cognitive process has been deemed as intuitive.18 Nevertheless, it has been conjectured that FD appears to be longer with more a complex task and situation.2 As a result, it can be argued that CM tends to fixate longer on STB because he needed to process more complex information. Moreover, it is important to mention that STB could entail the space surrounding two different teammates who might have possessed the ball during the five seconds before CM received a pass. Contrary to the CM, the RW had the tendency to fixate more often on the ball (19 times) and longer on the ball (570 ms), while less fixating at STNB (9 times) for 130 ms. Indeed, RW used 49 times fixations during five seconds and the highest number of them were used solely on the ball.19 The same pattern could be observed for LB, who used 64 fixations with a high number of them used on ball (16 times). Those findings could be explained by the fact that our participants are all university level, who are known to do more “ball watching” than their elite counterparts.3,8\n\nThe benefits of using TTF as an outcome measure include communicating the visual pattern order of each player.23 Interpretation of TTF on (U) category was not included because it would provide no relevant information in that specific analysis. Subsequently, it can be put forward that during the five seconds before receiving the ball, the CM tends to look first at the ball, then STB followed by SONB, TNB, TB, STNB, and ONB. RW would look at the TB, STB, ONB, STNB, B, SONB and TNB, in order. The LB presented with a different visual search order characterised by firstly fixating at TNB then B followed by ONB, TB, STB, SONB, and STNB.\n\nAs far as we are aware, only a few research studies18 in sport have used pupil diameter measurements to provide information on player’s focus. As a result, it may be difficult to debate our findings to other research studies. Nevertheless, the CM showed a higher increase in pupil size diameter by (0.40 mm) compared to RW (0.10 mm) and LB (0.18 mm), which could be seen regarded as a trait of expertise. Conversely, another study presented that their players with the lowest attentional effort had the highest tactical knowledge.19 For instance, lower and higher tactical knowledge players displayed mean pupil diameter 3.13 mm ± 1.24 and 3.09 mm ± 1.39, respectively during verbalization of their gameplay decision.19 This contradicts our previous statement since CM presented with the highest cognitive effort during play (2.90 mm ± 0.26). Those differences between theirs and our results could be explained by the fact that their study was done with academy players from a higher league (Brazilian first division soccer club) watching a video on a screen.19 Aksum et al.9 also highlighted discrepancies when comparing their findings to those found in laboratory studies, showing that players investigated in those studies presented on average with longer fixation duration (467 ms to 1,002 ms) while had shorter duration (249.29 ms).\n\nOur findings revealed that players acting in different specific positions (roles) presented distinctive visual behaviours and attentional effort during the Football game. From a practical perspective, coaches and practitioners should consider how best to use and adapt their interventions to improve visual search behaviours and attentional efforts according to their role in the field.\n\nThe biggest limitation of this pilot study is the small sample size and the amount of data collected, which do not enable us to demonstrate strongly evidences between the participants.29,30 Likewise, because we only had three participants, the results could not generalize to the players role but rather to individual variations. It would also be interesting to gather more data in different sporting settings (indoors vs outdoors football training sites) since pupil size diameters could vary depending the brightness of an environment.31\n\nIt is proven that conducting pilot studies can assist in assessing whether research is possible on a bigger scale.30 Despite its limitations, the present pilot study gives a new oncoming on-field data that coaches could use to assess and improve their player’s visual behaviour and attentional effort.\n\nThe studies involving human participants were reviewed and approved by the Ethical Committee of Lusófona University (protocol number M25A21) and University College London (protocol number 7067/001). The participants provided their written informed consent to participate in this study, including the data collection and publication.\n\n\nAuthor contributions\n\nFC and CB contributed to the conceptualisation, data collection, data analysis, and writing of the paper. JB contributed to the data analysis and writing of the paper. EH contributed to revising and writing the paper. All authors contributed to the article and approved the submitted version.", "appendix": "Data availability\n\nOpen Science Framework (OSF): Visual Behaviour and Attentional Effort of Football Players, https://doi.org/10.17605/OSF.IO/WAEYJ. 28\n\n- (1) gaze behaviour of football players (Data).csv\n\n- (2) Attentional effort of football players (Data).csv\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAshford M, Abraham A, Poolton J: Understanding a Player's Decision-Making Process in Team Sports: A Systematic Review of Empirical Evidence. Sports (Basel). 2021; 9(5). Publisher Full Text\n\nWilliams MA, Jackson RC: Anticipation and Decision Making In Sport. New York, London: Routledge Taylor & Francis Group; 2019.\n\nRoca A, Ford PR, McRobert AP, et al.: Perceptual-cognitive skills and their interaction as a function of task constraints in soccer. J. Sport Exerc. Psychol. 2013; 35(2): 144–155. PubMed Abstract \| Publisher Full Text\n\nMemmert D: Pay attention! A review of visual attentional expertise in sport. Int. Rev. Sport Exerc. Psychol. 2008; 2(2): 119–138. Publisher Full Text\n\nWorld FN: Coaching Football Intelligence: Scanning vs Situational Awareness. Youtube; 2020. Reference Source\n\nWorld FN: Michael Bunel - Process of Learning From The Game to Design Scanning Training Drills. Youtube; 2021.\n\nBlair CD, Ristic J: Attention Combines Similarly in Covert and Overt Conditions. Vision (Basel). 2019; 3(2). Publisher Full Text\n\nWilliams MA, Williams JG, Davids K: Visual Perception and Action in Sport. USA and Canada: Routledge; 1999.\n\nAksum KM, Magnaguagno L, Bjorndal CT, et al.: What Do Football Players Look at? An Eye-Tracking Analysis of the Visual Fixations of Players in 11 v 11 Elite Football Match Play. Front. Psychol. 2020; 11: 562995. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVitor de Assis J, Costa V, Casanova F, et al.: Visual search strategy and anticipation in tactical behavior of young soccer players. Sci. Med. Footb. 2021; 5(2): 158–164. PubMed Abstract \| Publisher Full Text\n\nAksum KM, Pokolm M, Bjorndal CT, et al.: Scanning activity in elite youth football players. J. Sports Sci. 2021; 39(21): 2401–2410. PubMed Abstract \| Publisher Full Text\n\nPurves D, Augustine GJ, Fitzpatrick DKL, et al.: Types of Eye Movements and Their Functions. Sinauer Associates; 2001. Edition Nn, editor\n\nWilliams AM, Davids K: Visual search strategy, selective attention, and expertise in soccer. Res. Q. Exerc. Sport. 1998; 69(2): 111–128. PubMed Abstract \| Publisher Full Text\n\nVater C, Williams MA, Hossner E-J: What do we see out of the corner of our eye? The role of visual pivots and gaze anchors in sport. Int. Rev. Sport Exerc. Psychol. 2019; 14(1): 81–103. Taylor & Francis Online.\n\nLobo L, Heras-Escribano M, Travieso D: The History and Philosophy of Ecological Psychology. Front. Psychol. 2018; 9: 2228. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPaterson G: Perception – action coupling and decision-making in sport. Amsterdam: Vrije Universiteit; 2020.\n\nLaakso T, Davids K, Luhtanen P, et al.: How football team composition constrains emergent individual and collective tactical behaviours: Effects of player roles in creating different landscapes for shared affordances in small-sided and conditioned games. Int. J. Sports Sci. Coach. 2022; 17(2): 346–354. Publisher Full Text\n\nMoran A, Quinn A, Campbell M, et al.: Using pupillometry to evaluate attentional effort in quiet eye: A preliminary investigation. Sport Exerc. Perform. Psychol. 2016; 5(4): 365–376. Publisher Full Text\n\nCardoso F, Gonzalez-Villora S, Guilherme J, et al.: Young Soccer Players With Higher Tactical Knowledge Display Lower Cognitive Effort. Percept. Mot. Skills. 2019; 126(3): 499–514. PubMed Abstract \| Publisher Full Text\n\nOlsen A: The Tobii I-VT Fixation Filter, Algorithm description.2012.\n\nTobii: When do I use the I-VT Attention filter?2018. Reference Source\n\nWilliams AM, Davids K, Burwitz L, et al.: Visual search strategies in experienced and inexperienced soccer players. Res. Q. Exerc. Sport. 1994; 65(2): 127–135. PubMed Abstract \| Publisher Full Text\n\nTobii: 2022. Reference Source\n\nCampbell MJ, Moran AP, Bargary N, et al.: Pupillometry During Golf Putting: A New Window on the Cognitive Mechanisms Underlying Quiet Eye. Sport Exerc. Perform. Psychol. 2018; 8: 53–62. Publisher Full Text\n\nKret ME, Sjak-Shie EE: Preprocessing pupil size data: Guidelines and code. Behav. Res. Methods. 2019; 51(3): 1336–1342. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTobii: Tobii Pro Lab Gaze Filter 2023.Reference Source\n\nRobinson G, O’Donoghue P: A weighted kappa statistic for reliability testing in performance analysis of sport. Int. J. Perform. Anal. Sport. 2017; 7(1): 12–19. Taylors Francis Online. Publisher Full Text\n\nBallet C, Barreto J, Casanova F, et al.: (Data set) What is the visual behaviour and attentional effort of football players in different positions during a real 11v11 game? A Pilot Study. [Data]. 2023. Publisher Full Text\n\nField A: Discovering Statistics using IBM SPSS Statistics. 5th Eedition.SAGE; 2018.\n\nVan Teijlingen ER, Rennie AM, Hundley V, et al.: The importance of conducting and reporting pilot studies: the example of the Scottish Births Survey. J. Adv. Nurs. 2001; 34(3): 289–295. PubMed Abstract \| Publisher Full Text\n\nKlatt S, Noel B, Brocher A: Pupil size in the evaluation of static and dynamic stimuli in peripheral vision. PLoS One. 2021; 16(5): e0250027. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "178912", "date": "17 Jul 2023", "name": "Vicente Luis-del Campo", "expertise": [ "Reviewer Expertise Visual perception and action in sport" ], "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\nComments to the Authors:\nThe submitted manuscript entitled “What is the visual behaviour and attentional effort of football players in different positions during a real 11v11 game?” describes an interesting study about the visual and attentional demands that young athletes in football have when played some specific game sequences in the playing field.\nFirstly, I appreciate your submission on various accounts. To exemplify, it is an innovative study because there are few studies in the literature about visual perception in sport collecting visual fixations of athletes with portable eye trackers in the playing field. Therefore, this study allowed to evaluate the visual behaviours and attention of football players with an in situ approach during real 11 vs 11 sequences of the play. As a result, the ecological validity of this study was guaranteed because authors used representative tasks for the study of visual behaviours in a naturalistic environment. Additionally, I argue that the rationale of the study is well-focused towards the relevance of the perceptual-cognitive skills and visual attention on the athletes´ performance (e.g, anticipation and decision-making). I also agree with the decision of authors of starting the exploration of footballers´ visual and attention activity with a pilot study because this type of studies would: i) provide an initial tendency of the data, ii) enhance a better replication of the same study in further attempts (e.g., improving reliability of research tools and/or designs, etc.), and iii) achieve a higher external validity of the data if a large sample of participants may be recruited.\nNevertheless, I have two main concerns that require contemplation and appropriate attention in revising the document if it is to contribute appropriately to the extant literature. These two concerns are related to the selected time to analyse fixations and the lack of integration between visual fixations and other behavioural measures of movement:\nWhy did the authors decide to collect and analyze the five seconds before receiving the ball from a teammate on 11v11 games? What is the rationale for this decision? The authors claim that Jordet et al. used a temporal window of 10 seconds for the team possessing the ball, then, why did the authors consider that five seconds would be enough to scan correctly and sufficiently the visual activity of the football players?\n\nThe existing studies about visual perception in sport have usually used not only visual variables but also other motor outcomes due to the strong relation between perception-action loops. However, there is an absence of measures related to the motor behaviour of athletes in this study. Why did the authors not include this type of behavioural variables when players performed their specific actions on-field? (e.g., decision-making, number of correct passes performed, etc.). The combined analysis of visual information and movement would offer a better understanding of the underlying cognitive processes supporting performance of the players for this tactical sport.\n\nThese reservations should be clarified and justified throughout the manuscript before a decision can be made on publication.\n\nIntroduction\nIn my opinion, the background of the paper offers a general viewing of the state-of-the art about visual perception and attention in sport. However, it would be interesting to add more existing studies in football that used variables related to visual performance to address sport performance in controlled laboratory settings. This point would strengthen the need of accumulating more evidence using on-field studies with representative procedures and designs to test visual and motor behaviours of footballers.\nAfter reading this section, it seems clear that there is a lack of studies assessing visual behaviours in the playing field. For an exception, the authors highlight the observational study conducted by Aksum et al. (2021) with midfield footballers while playing a real 11v11 match. This is a similar study compared to Ballet and colleagues, but these last authors have now included the gaze behaviours of footballers with different roles and visual attention. I would also encourage authors to introduce another recent published paper driven by Luis-del Campo and colleagues (2023)1 because they used ocular metrics and saccadic features as biomarkers of the mental load suffered by football players when performed a training session with manipulation of the available time to complete the goals of the tasks. This study would provide authors some interesting results to compare with your data, for instance, of pupil size.\nLuis-Del Campo, V., Morenas Martín, J., León Llamas, J. L., Ortega Morán, J. F., Díaz-García, J., & García-Calvo, T. (2023). Influence of the time-task constraint on ocular metrics of semi-elite soccer players. Science & medicine in football, 1–8. Advance online publication. https://doi.org/10.1080/24733938.2023.2172203\nAdditionally, the authors should include other studies that used ocular metrics in footballers. For example, lower pupil diameter was associated with higher values of tactical knowledge (Cardoso et al. 2019)2 and better tactical behaviour efficiency (Cardoso et al. 2021)3.\nI am not sure if it would be appropriate for a pilot study to drive hypotheses with specific predictions about the impact of role position on visual behaviours when the authors show no previous studies for a different visual exploration of the playing field regarding the specific role in the team. Thus, the number of total fixations collected (n=166) seems scarce to conclude these initial assumptions. Indeed, the authors state at the statistical analysis that only descriptive statistics were used. What is the authors´ opinion about this issue?\n\nMethod\nIt would be fine to add more specific information about the visual and motor experiences of footballers (e.g., the average of hours training by week, or the average of hours watching football matches on TV or in the field).\nAgain, I find lost a scientific approach to decide that the five seconds before receiving the ball from their teammate were sufficient to fully understand the visual behaviours of the three footballers during 11 vs 11 sequences of play. What do the authors mean when refer to “…interpret another understanding of visual strategies used during a short period of time”? Please, clarify this point.\nAgain, the authors did not include any variable related to decisional and/or motor behaviours. The authors should clarify those reasons that prevented them the use of these variables while participants wearing the eye tracking glasses during five minutes of the 11v11 pre-competitive football game. In my opinion, this should be stated as another limitation of the study.\n\nI guess that the number of calibration points was 1 when the authors stated “…participants to focus on the center of the calibration card held in front of them for five seconds”, didn't they? If true, they should specify this technical detail.\nThe specifications showed by the authors were robust for the identification of fixations and search rate. For the search order of fixations, I would recommend authors to use the Graphos software for a better understanding of this type of analysis of fixations. This software would also help readers to better interpret the relevance of certain AOIs and the order in which the footballers moved their gaze from one AOI to another one.\nThe pupil size has showed sensitiveness to different light conditions (Wyatt 1995)4 but also to cognitive states of participants (Beatty, 1982; Mahanama et al., 2022; Mathôt et al., 2015)5,6,7. Taking into consideration that the pupil dilation showed responsiveness to different external and/or internal variables, I wonder if the three participants had the same conditions to measure the attentional effort, at the baseline and at a “post-stimulus”, because their visual fixations were collected at different moments of the 20-min 11v11 pre-competitive football game. I would like to know the opinion of the authors about this issue, and I ask them if they consider that the impossibility of measuring simultaneously would be a limitation of the study.\n\nStatistical analysis and results\nDuring the writing of the results, I would add the information about what participant achieved the highest or lowest values for fixation durations, number of fixations and time to first fixation at the different AOIs.\nTo exemplify, for the fixation durations, the RW participant displayed longer fixations on B, ONB and U, compared to the CM and LB participants. The CM participant showed fixations of longer duration on SONB, STB and TB, compared to RW and LB ones. The LB participant made longer fixations only on the TNB, compared to RW and CM ones. For the time to first fixation, the LB participant showed the highest values for the most AOIs, compared to RW and CM ones (e.g., SONB, STNB, STB, TB, U). The RW participant displayed the highest values for B and TNB, compared to CM and LB. Contrary, the CM participant achieved the highest values only for the ONB, compared to RW and LB ones. Finally, to highlight that the CM participant was the footballer who more increased the values for pupil diameter variables from “baseline” to “duringplay”, compared to the RW and LB participants.\nThis information would help to understand that each participant explored differently the playing field, and what AOIs where more or less relevant for the participants regarding their role in the team. Contrary, I would not specify the values found in the tables during the wording because the authors may duplicate information for readers or be redundant during the presentation of their results.\n\nDiscussion\nThe authors have provided different explanations for their results found, also comparing them to other previous specific studies. I congratulate them because they found well-focused accounts in this attempt.\nAgain, the authors should use the results of Luis-del Campo et al. (2023)1 to compare them with those found for their attentional effort variable. This comparison would enrich the discussion section and may show how the pupil diameter shows a similar or different responsiveness regarding the skill level of footballers.\nI would recommend authors more specification when talked about the practical perspective. In this vein, it would be fine that the authors could show some examples of modifications during 11 vs 11 play games to improve visual behaviours of footballers regarding their player role.\n\nSpecific comments to the Authors:\nIntroduction\nThe authors refer to decision-making as an “ability”. Are they suggesting that decision-making could not be learned (i.e., natural or innate), or aimed at achieving a goal, as opposed to a “skill”?\nI would recommend authors to delete the last “,” at the next phrase: “….body, and positioning, vary continuously”.\nI would recommend authors to change “when talking about” by “for” at the next phrase: “Therefore, visual perception is crucial when talking about spatial awareness”.\nI would recommend authors to add “up” after the verb “picked”, at the next phrase: “…is mainly picked and processed”.\nI would recommend authors that in this phrase “….can vary depending on the skill level of an athlete”, they would add this: “…..can vary depending on the skill level of an athlete and task constraints existing in the sport environments”.\nI would recommend authors to change “fixate on” by “fixate at”. For example: “Furthermore, midfield players fixate more on the player in possession of the ball during a defensive phase of play than during an attacking phase”. Please, change throughout the document if necessary again.\nDiscussion\nI would not introduce the specific vales for the variables at this discussion section.\nI hope that these comments will serve you well in your efforts to improve your 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? 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": [ { "c_id": "10034", "date": "12 Oct 2023", "name": "Charles Ballet", "role": "Author Response", "response": "Reviewer: The submitted manuscript entitled “What is the visual behaviour and attentional effort of football players in different positions during a real 11v11 game?” describes an interesting study about the visual and attentional demands that young athletes in football have when played some specific game sequences in the playing field. Firstly, I appreciate your submission on various accounts. To exemplify, it is an innovative study because there are few studies in the literature about visual perception in sport collecting visual fixations of athletes with portable eye trackers in the playing field. Therefore, this study allowed to evaluate the visual behaviours and attention of football players with an in-situ approach during real 11 vs 11 sequences of the play. As a result, the ecological validity of this study was guaranteed because authors used representative tasks for the study of visual behaviours in a naturalistic environment. Additionally, I argue that the rationale of the study is well-focused towards the relevance of the perceptual-cognitive skills and visual attention on the athletes´ performance (e.g, anticipation and decision-making). I also agree with the decision of authors of starting the exploration of footballers´ visual and attention activity with a pilot study because this type of studies would: i) provide an initial tendency of the data, ii) enhance a better replication of the same study in further attempts (e.g., improving reliability of research tools and/or designs, etc.), and iii) achieve a higher external validity of the data if a large sample of participants may be recruited. Authors: We appreciate your general comments. Reviewer: Why did the authors decide to collect and analyze the five seconds before receiving the ball from a teammate on 11v11 games? What is the rationale for this decision? The authors claim that Jordet et al. used a temporal window of 10 seconds for the team possessing the ball, then, why did the authors consider that five seconds would be enough to scan correctly and sufficiently the visual activity of the football players? Authors: Thank you for your query regarding our decision to collect and analyse data for a 5-second duration before players receive the ball from a teammate in 11v11 games. We understand that the present study is dissimilar to others, especially considering Jordet et al.'s used of a 10-second temporal window for teams possessing the ball in their study. It's also worth pointing out that while they focused on scanning frequency (head movement counts) to explore perceptual outcome measures over a 10-second window, our emphasis was on gaze behaviour (eye movements) which are measured in milliseconds. While a 10-second window could potentially offer more comprehensive data, we carefully considered the balance between data richness and practical application. Longer timeframes could lead to more information, but they might also overwhelm coaching staff with a surplus of data to interpret and apply effectively. Moreover, to mimic the actual game, we intended to reduce the available time of the players actions. As this was a pilot study, our goal was to lay the groundwork for future investigations, and we believe that the insights gained from a 5-second window still provide valuable preliminary findings. In future studies, we can explore longer temporal windows to delve deeper into players' visual behaviours and decision-making processes. It could be interesting to investigate whether analysing visual activity within 5 or 10 seconds would be more useful for coaches and stakeholders. Understanding the optimal duration for capturing essential moments during anticipation and decision-making could have practical implications for player development and coaching strategies in tactical sports like football. We will keep this in mind as we continue to expand our research in this area. Reviewer: Why did the authors not include this type of behavioural variables when players performed their specific actions on-field? (e.g., decision-making, number of correct passes performed, etc.). The combined analysis of visual information and movement would offer a better understanding of the underlying cognitive processes supporting performance of the players for this tactical sport. Authors: We acknowledge the importance of incorporating movement-related measures to gain a deeper understanding of the cognitive processes underlying player performance in football, especially considering the potential differences in visual behaviour and attentional effort based on the various football players' roles and positions. As we move forward with our research, we will certainly include motor behaviour measures in subsequent experiments, allowing us to provide a more comprehensive analysis of the interplay between visual perception and on-field actions. This integration could potentially reveal how visual information processing influences players' actions on the field. Introduction Reviewer: I would also encourage authors to introduce another recent published paper driven by Luis-del Campo and colleagues (2023)1 because they used ocular metrics and saccadic features as biomarkers of the mental load suffered by football players when performed a training session with manipulation of the available time to complete the goals of the tasks. This study would provide authors some interesting results to compare with your data, for instance, of pupil size. Authors: Added. Reviewer: Additionally, the authors should include other studies that used ocular metrics in footballers. For example, lower pupil diameter was associated with higher values of tactical knowledge (Cardoso et al. 2019)2 and better tactical behaviour efficiency (Cardoso et al. 2021)3. Authors: We have aware of both researches, however the instrument and the software used are quite different from our study. We believe that we need to collect and discuss the data using similar procedures and instruments, since it is our intention to establish a research guide in this scientific domain (improving the reliability of the data). Reviewer: I am not sure if it would be appropriate for a pilot study to drive hypotheses with specific predictions about the impact of role position on visual behaviours when the authors show no previous studies for a different visual exploration of the playing field regarding the specific role in the team. Thus, the number of total fixations collected (n=166) seems scarce to conclude these initial assumptions. Indeed, the authors state at the statistical analysis that only descriptive statistics were used. What is the authors´ opinion about this issue? Authors: We appreciate your expert opinion, and our future research will confirm or not the differences between specific position (and roles) of football players (different competitive levels). Method Reviewer: It would be fine to add more specific information about the visual and motor experiences of footballers (e.g., the average of hours training by week, or the average of hours watching football matches on TV or in the field). Authors: Added. Reviewer: Again, I find lost a scientific approach to decide that the five seconds before receiving the ball from their teammate were sufficient to fully understand the visual behaviours of the three footballers during 11 vs 11 sequences of play. What do the authors mean when refer to “…interpret another understanding of visual strategies used during a short period of time”? Please, clarify this point. Authors: It is about the representativeness of the actual game. Since the players had less and less time to see and to act, our intention was to provide other visual possibilities. Reviewer: Again, the authors did not include any variable related to decisional and/or motor behaviours. The authors should clarify those reasons that prevented them the use of these variables while participants wearing the eye tracking glasses during five minutes of the 11v11 pre-competitive football game. In my opinion, this should be stated as another limitation of the study. Authors: Added. Reviewer: I guess that the number of calibration points was 1 when the authors stated “…participants to focus on the center of the calibration card held in front of them for five seconds”, didn't they? If true, they should specify this technical detail. Authors: We included more information, namely: “To ensure high gaze data quality, calibration procedures were carried out by asking the participants to focus on the center-point of the calibration card held in front of them for five seconds.” Reviewer: The pupil size has showed sensitiveness to different light conditions (Wyatt 1995)4 but also to cognitive states of participants (Beatty, 1982; Mahanama et al., 2022; Mathôt et al., 2015)5,6,7. Taking into consideration that the pupil dilation showed responsiveness to different external and/or internal variables, I wonder if the three participants had the same conditions to measure the attentional effort, at the baseline and at a “post-stimulus”, because their visual fixations were collected at different moments of the 20-min 11v11 pre-competitive football game. I would like to know the opinion of the authors about this issue, and I ask them if they consider that the impossibility of measuring simultaneously would be a limitation of the study. Authors: We appreciate your suggestion, however we used the Tobi out-field lenses. Statistical analysis and results Reviewer: During the writing of the results, I would add the information about what participant achieved the highest or lowest values for fixation durations, number of fixations and time to first fixation at the different AOIs. To exemplify, for the fixation durations, the RW participant displayed longer fixations on B, ONB and U, compared to the CM and LB participants. The CM participant showed fixations of longer duration on SONB, STB and TB, compared to RW and LB ones. The LB participant made longer fixations only on the TNB, compared to RW and CM ones. For the time to first fixation, the LB participant showed the highest values for the most AOIs, compared to RW and CM ones (e.g., SONB, STNB, STB, TB, U). The RW participant displayed the highest values for B and TNB, compared to CM and LB. Contrary, the CM participant achieved the highest values only for the ONB, compared to RW and LB ones. Finally, to highlight that the CM participant was the footballer who more increased the values for pupil diameter variables from “baseline” to “during play”, compared to the RW and LB participants. This information would help to understand that each participant explored differently the playing field, and what AOIs where more or less relevant for the participants regarding their role in the team. Contrary, I would not specify the values found in the tables during the wording because the authors may duplicate information for readers or be redundant during the presentation of their results. Authors: In future research we want to increase the sample size and use comparative methods. Discussion Reviewer: The authors have provided different explanations for their results found, also comparing them to other previous specific studies. I congratulate them because they found well-focused accounts in this attempt. Again, the authors should use the results of Luis-del Campo et al. (2023)1 to compare them with those found for their attentional effort variable. This comparison would enrich the discussion section and may show how the pupil diameter shows a similar or different responsiveness regarding the skill level of footballers. Authors: Added. “Interestingly, a recent study which looked at evaluating mental load (attentional effort) in training sessions, showed that the pupil diameter of soccer players changes depending on the time spent training 5. Although this study had different objectives and methodologies, it presented that exploring attentional effort via pupil diameter could be a tool to monitor cognitive load during training sessions and possibly reduce the risk of mental fatigue.” *Specific comments to the Authors: Introduction Reviewer: I would recommend authors to delete the last “,” at the next phrase: “….body, and positioning, vary continuously”. Authors: Done. Reviewer: I would recommend authors to change “when talking about” by “for” at the next phrase: “Therefore, visual perception is crucial when talking about spatial awareness”. Authors: Done. Reviewer: I would recommend authors to add “up” after the verb “picked”, at the next phrase: “…is mainly picked and processed”. Authors: Done. Reviewer: I would recommend authors that in this phrase “….can vary depending on the skill level of an athlete”, they would add this: “…..can vary depending on the skill level of an athlete and task constraints existing in the sport environments”. Authors: Done. Reviewer: I would recommend authors to change “fixate on” by “fixate at”. For example: “Furthermore, midfield players fixate more on the player in possession of the ball during a defensive phase of play than during an attacking phase”. Please, change throughout the document if necessary again. Authors: Done. Authors: We deeply appreciate your valuable feedback on our manuscript, and we will certainly take your suggestions on board with our future experiments." } ] } ]	1	https://f1000research.com/articles/12-679
https://f1000research.com/articles/12-1017/v1	21 Aug 23	{ "type": "Review", "title": "Demographic change and urban health: Towards a novel agenda for delivering sustainable and healthy cities for all", "authors": [ "James Duminy", "Alex Ezeh", "Sandro Galea", "Trudy Harpham", "Mark R. Montgomery", "J. M. Ian Salas", "Daniela Weber", "Amy Weimann", "Danzhen You", "Alex Ezeh", "Sandro Galea", "Trudy Harpham", "Mark R. Montgomery", "J. M. Ian Salas", "Daniela Weber", "Amy Weimann", "Danzhen You" ], "abstract": "The focus is on the demographic drivers and demographic implications of urban health and wellbeing in towns and cities across the globe. The aim is to identify key linkages between demographic change and urban health – subjects of two largely disparate fields of research and practice – with a view to informing arguments and advocacy for urban health while identifying research gaps and priorities. The core arguments are threefold. First, urban health advocates should express a globalized perspective on demographic processes, encompassing age-structural shifts in addition to population growth and decrease, and acknowledging their uneven spatial distributions within and between urban settings in different contexts. Second, advocates should recognize the dynamic and transformational effects that demographic forces will exert on economic and political systems in all urban settings. While demographic forces underpin the production of (intra)urban inequities in health, they also present opportunities to address those inequities. Third, a demographic perspective may help to extend urban health thinking and intervention beyond a biomedical model of disease, highlighting the need for a multi-generational view of the changing societal bases for urban health, and enjoining significant advances in how interested parties collect, manage, analyse, and use demographic data. Accordingly, opportunities are identified to increase the availability of granular and accurate data to enable evidence-informed action on the demographic/health nexus.", "keywords": [ "emography", "urban health", "wellbeing", "population", "urbanization", "cities" ], "content": "Key messages\n\n\n\n• Demographic changes exert powerful forces on health and wellbeing within and between urban areas, and create new needs and challenges for health programming in all cities and regions.\n\n• A nuanced, globalized demographic perspective can generate useful insights that will benefit theory and practice surrounding urban health and wellbeing.\n\n• Improved urban health and wellbeing can help to enhance the positive effects (and alleviate the potentially negative effects) of demographic changes.\n\n• The relationship between demographic and urban changes is dynamic and transformational.\n\n• Political and policy debates around demographic change are remarkably diverse across country contexts.\n\n• A narrow focus on population change, especially when framed in terms of ‘population control’, can be counterproductive when advocating for a renewed focus on demographic issues.\n\n• The relationship between demographic changes, urban health, and economic development is a potential entry point for advocates of urban health and wellbeing.\n\n• Demographic processes will shift the terms of the politics of urban health in ways that can be anticipated and planned for.\n\n\nIntroduction: Demographic change and urban health\n\nIn this article we discuss the key mechanisms that connect demographic change to urban health and wellbeing, with a view to informing arguments and advocacy for urban health. We also identify key research gaps and priorities for an emerging demographic/health agenda centred on urban areas. We argue for a transformed approach to understanding and addressing the interface between demographic change and health in towns and cities. This approach should be based on a globalized recognition of the diverse, dynamic, and transformational demographic processes underway in different parts of the world. Within this perspective, we emphasize that one simply cannot think about demographic change and urban health with a view of urban populations as homogenous. Health in towns and cities is characterized by enormous heterogeneity within and between urban areas of different type and status (Galea, Ettman and Vlahov, 2019). Consequently, we should understand how demographic processes are linked to the production of intra-city social and spatial inequities, alongside urban health outcomes at wider scales, and how demographic change can create opportunities for addressing such inequities and producing positive outcomes for urban health.\n\nUnderstanding and addressing this interface requires bringing together or ‘linking’ two relatively discrete fields of inquiry and practice – demography and urban health – to forge a novel agenda for the delivery of sustainable and healthy cities. In doing so, we would underscore three points. First, an agenda to promote a productive relationship between urban health and demographic change may demand interventions that are not directly related to the health sector itself. Second, this agenda calls for detailed attention to the quality and availability of suitably disaggregated data, and the need for reform of existing data-gathering instruments. And third, the question of linking these two fields should also include a concern with the ‘means of implementation’ – the governance preconditions necessary to give effect to this agenda – if the potential of demographic change to improve the health and wellbeing of urban populations is to be realized.\n\nThe series of papers to which this article contributes addresses a range of themes. A general challenge here is to describe cross-thematic linkages (indicating systemic linkages and key leverage points within current debates) without diluting our central focus on demographic change. We have chosen to discuss the links between demographic change and migration, where migratory processes exert significant effects on how populations are changing (with direct consequences for urban health). We have also identified the links between demographic change and climate change, specifically where urban population change will exert a significant effect on emissions and on the vulnerability of city and town populations to extreme events and the effects of climatic change. These issues are covered in their own right in papers by Sa Machado et al. and Vardoulakis et al. in this collection (both forthcoming).\n\nA principal theme in what follows has to do with the intersection of three spaces: the jurisdictions in which governmental units operate, the space where health and demographic forces are at play, and the spatial bins into which demographic and health data are collected. The lack of coherence in these spaces has given rise to the distinct terms ‘urban’ and ‘city’, which are often mistakenly viewed as synonymous. The differences between the two must be understood to appreciate the governance challenges that lie ahead.\n\nAcross national statistical offices, there is an unmistakable trend underway in the direction of what are often termed ‘statistical definitions of the urban’, by which urbanized areas are defined in terms of population density thresholds, contiguity criteria, and criteria on the total population size of candidate urban areas. The Degree of Urbanization estimates, developed by the European Commission and endorsed by the United Nations Statistical Commission, extend this general approach on a nearly global basis, thereby offering a new, globally-comparable synthetic approach to defining and measuring urbanized areas (Dijkstra et al., 2021). Statistical urbanization methods combine population census data for subnational administrative units with remote-sensing estimates of land covered by structures, with fine spatial detail needed in both of these dimensions. Hence this and other ‘statistical’ approaches depend crucially on the regular production of population censuses and the release of census detail at the level of small spatial units.\n\nOne of the many meanings of the word ‘city’, by contrast, is that of a unit of local governance, and specifically, municipal government. One of the merits of the Degree-of-Urbanization approach is that it highlights geographic spaces in which population is clustered in urban-like conditions. These dense clusters may, and generally do, span the jurisdictions of multiple local governments. The overlay of spatial population estimates, on the one hand, against the legal boundaries within which such governments are allowed to act, on the other, illustrates a central urban governance challenge with direct relevance to urban health promotion (Montgomery, Pinchoff and Chuang, 2022).\n\nWhere health programmes and policies are concerned, further complications arise from the presence of multiple layers and units of government (which are especially evident in larger cities and towns) and the diversity of the private health sector in cities and towns irrespective of size. Sustained discussion of the demographic/health nexus, focused on cities and towns, is thus long overdue.\n\n\nFindings\n\nDemographic change does not refer only to changes in total population size. Rather, it encompasses a range of complex transformations including total population growth and decline, shifts in spatial distribution (across geographies and between urban and rural settings within countries), age-structural shifts (including ageing and youth ‘bulging’) and the evolution of family sizes and structures. These transformations have complex implications for formal healthcare provision and caregiving more generally, as well as for economic development, urban spatial transformation, and other factors, all of which will exert strong forces on urban health and wellbeing in future years.\n\nSome demographic trends can be understood as global in scope. For example, nearly every country across the world is currently experiencing growth in both the size and proportion of its population of older people. Other trends are more specific to context. For instance, rates of population growth differ markedly across countries, regions, cities, income groups, and even by city neighbourhoods. Given this, how do (and will) demographic factors affect urban health and wellbeing? Here we briefly discuss these effects in relation to three key domains: population change, age-compositional change, and migration.\n\nFuture increases in the world’s population will take place almost exclusively in the cities and towns of low- and middle-income countries (LMICs) (United Nations, 2019). This growth will be concentrated in sub-Saharan Africa and South Asia. In these regions, the urban proportion of the population will rise as urban population growth rates overtake rates of population growth overall. The resulting processes of urbanization, especially in poorer settings, often outpace the capacity of governments to make infrastructural investments that promote health and wellbeing in urban settings – including housing, water and sanitation, healthcare and education services. Consequently, increasing numbers of the urban population will be found in informal settlements and slums where health and wellbeing indicators are compromised (Ezeh et al., 2017; United Nations, 2019).\n\nIn some low- and middle-income countries (LMICs), high urban fertility rates linked to an unmet need for family planning1, and which in some African settings will be sustained by stalls in urban fertility declines (Sánchez-Páez and Schoumaker, 2022), are associated with health risks for individual women and children. These are expressed through, for example, resorts to unsafe abortion, perinatal health complications, and knock-on effects for reduced female employment as well as early childhood health and nutrition. In many LMICs, unmet need for family planning and resulting health risks often show significant intra-urban inequalities (Duminy et al., 2021). Meeting unmet need for family planning in urban areas would improve maternal and child health outcomes, facilitate urban fertility declines, and reduce gaps in the provision of urban services and housing in the longer term (Ezeh, Kodzi and Emina, 2010).\n\nAside from the direct health and service implications of high urban fertility rates, population changes will affect health and wellbeing by aggravating or creating new vulnerabilities to climatic change. It is now increasingly critical for researchers and practitioners to understand the spatial distribution of urban population growth and its relationship to the impacts of climate change. Coastal zones, vulnerable to climate change effects including sea-level rise and flooding, already host very large urban populations. These areas tend to be more densely populated than inland areas and see higher rates of population growth (MacManus et al., 2021). The next decades will see significant growth of the global population living in coastal areas at risk from sea-level rise and flooding, with the largest absolute growth in exposure to take place in Asia and the largest relative growth in Africa (Merkens et al., 2018). The urban health implications of these trends include sea-level rise that increases the salinity of groundwater, thereby threatening sources of drinking water and irrigation; the generation of epidemiological risks through the destruction of critical urban infrastructures and the spread of pathogens through flooding; and health-related issues arising from increased internal or international migration into urban areas driven by coastal disasters.\n\nCities are believed to be expanding spatially at rates faster than those at which their populations are growing. In some cases, this is linked to trends towards smaller household sizes. Aside from the well-documented links between urban sprawl, emissions and biodiversity loss, urban sprawl has implications for equity: low-density lifestyles and environments tend to exhibit stronger social inequalities (Wei and Ewing, 2018). Sprawl also generates risks for public health and wellbeing through increased air pollution and traffic incidents, reduced physical activity, and threats to sources of drinking water and the availability of green spaces. Moreover, when coupled with inadequate land-use planning and agriculture and livestock intensification, urban sprawl increases the risk of zoonotic diseases emerging due to increased human exposure to biodiversity at the peri-urban interface. Urban population and spatial growth also exert strong effects (mostly indirectly, through consumption) on biodiversity loss and ecological destruction. Urban population growth driven by high fertility rates will therefore play a significant role in eroding the ecological basis for good human health and improved wellbeing in many urban settings.\n\nFinally, there is now a resurgent debate on the role of demographic change within the generation of climatic risks (primarily through increased emissions) and within potential responses to the global climate emergency. This debate has taken on a far more nuanced form than previous neo-Malthusian arguments, emphasizing the dynamic relationship between changes in population size, structure, and consumption in place of a narrow focus on population growth and resource decline (O’Neill et al., 2010). This work highlights that implementing appropriate policies to satisfy unmet global demand for family planning and reproductive health services could create significant environmental co-benefits by lowering fertility rates. However, we currently lack a detailed understanding of precisely how or to what extent such policies, by reducing emissions, could exert positive effects on urban health and wellbeing. More generally, within this debate it should be recalled that the scale of overconsumption among high-income populations (and the danger that high consumption rates per capita will be replicated as other contexts develop economically) is substantially more significant, in terms of overall impacts, than resource use by low-income urban populations.\n\nThe growth of many urban populations, and the emergence of new health risks in expanding towns and cities, will place additional net demands on formal systems of healthcare provision in those settings. In contexts where this growth is driven by natural population increase, there will be increasing needs for healthcare services and infrastructures catering for growing populations of children and young adults. Where growth is driven by urban in-migration, the health needs of migrants, refugees and internally displaced persons will need to be accommodated and met (see Migration section below).\n\nWhile population growth has historically preoccupied policy discussions, another important dimension of global demographic change is the trend towards population decline or decrease seen in many regions of the world, especially in the countries and cities of Europe, East Asia, and Latin America. Given that many of these countries are already highly urbanized, the implications of population decline and the age-structural changes it brings could have serious consequences for health and wellbeing, especially in the care economy and with respect to old-age support. These trends will raise new urban infrastructural needs and will have to be met in the context of declining per capita tax bases. The full range of implications of population decline and ageing for urban health and wellbeing are not yet fully understood.\n\nDisease burdens vary across age groups, and often between urban and rural areas (Montgomery et al., 2003). Understanding age structural changes of urban populations within and across countries will be key to effective planning and programming to improve health and wellbeing of urban populations. For example, children are most susceptible to vaccine-preventable infectious diseases, young people experience injuries and violence as leading causes of death, while non-communicable diseases tend to drive health and mortality among older populations. Policy and care responses to these disease burdens also vary. Immunization and nutrition programmes can improve health at young ages, policies on violence and injury prevention programmes can reduce the burden of injury-related morbidity and mortality, while non-communicable diseases (NCDs) require improvements in healthcare service delivery, long-term care, and health promotion and prevention programmes. Non-health sector interventions (including infrastructural interventions targeting green/public space, transport, water and sanitation, housing, and so on) can also help address these burdens but may require different thinking and approaches for various groups and contexts. Ultimately, understanding the current age structure of a city, town, or urbanized area and how it is changing is key to formulating responsive approaches for health and wellbeing. When it comes to urban health, one size does not fit all.\n\nAs life expectancy and urbanization increase, many countries and regions can expect to see a growing proportion of their older populations (aged 65 years or more) living in urban rather than rural areas. Where these populations live, and the specific kinds of physical and social infrastructures accessible to them, will decisively shape their health outcomes (Cagney, 2019). To pick just one increasingly important example, a specific urban health concern linked to these trends is the higher vulnerability of older people to the risk of heat stress in urban environments.\n\nIn some settings, the health needs of older people may be relatively well understood and represented. However, in some Asian and African contexts, where many people maintain dual residences in both urban and rural areas, we may not have a sufficient understanding of how older populations experience and manage health risks in urban settings (and for what outcomes), mediated as they are by the dynamics of kinship, culture, village networks and intergenerational mobility and care (McQuaid et al., 2021). Meanwhile, in higher-income settings, we arguably require a better understanding of how ‘healthy ageing’ in urban areas will be mediated by the wider economic and social forces shaping urban transformation. These include fiscal austerity, changing housing markets, and the privatization of urban space (Buffel and Phillipson, 2016).\n\nHaving increasing shares of older populations living in urban areas will increase demand for the provision of long-term care from formal healthcare systems, placing additional stress on available public finances and capacity. While intergenerational care provision is currently a major resource for the long-term care of older people in many settings, lower fertility rates and changing family structures in urban areas may lead people to resort increasingly to formal systems of long-term care. How demographic change will affect the demand for and provision of care – both formal and intergenerational – in diverse urban settings remains a key knowledge agenda item, particularly in under-researched LMIC contexts.\n\nWhile the majority of urban growth in LMICs is contributed by natural increase, urban in-migration remains a key trend and driver of that growth (Duminy et al., 2021). However, the connections between migration, demographic change and urban health are currently not adequately understood. Migration may contribute to the production of intra-urban inequities as new arrivals are excluded from, or cannot afford, adequate educational and healthcare services in their city and town destinations (Galea, Ettman and Zaman, 2022). Whether migration can create opportunities to address those inequalities is less clear.\n\nThe peak ages of internal migration range from the late teens (especially for girls) to the mid-twenties in most populations, thus spanning ages at which formal education is being completed to ages well into the years of marriage and reproduction. As a result, urban moves often situate these young people in environments in which potentially supportive educational and health resources are more plentiful than they tend to be in rural areas; yet there is certainly no guarantee that recent urban in-migrants will have access to such resources (Montgomery et al., 2016). Moreover, and contrary to common belief, urban-to-urban migration now (apparently, and no doubt with much variation across countries) rivals rural-to-urban migration in scope. Little is known about the implications of this shift, but the implication is that recent migrants may not be as uninformed about city life and urban resources as many have commonly thought.\n\nMigration can also influence the processes underlying demographic changes. Most research confirms that rural-urban migration has a downward effect on fertility rates overall, alongside positive effects on contraceptive use. It seems that migrants adapt to their new urban conditions and assume behaviours that are prevalent among permanent or more established populations (Montgomery et al., 2003). Despite a considerable literature on migration and health, we still lack an adequate understanding of how various migration patterns, including the movement of people within and between urban areas – some of which will be driven, accelerated, and reshaped by climate change and natural disasters – impact both demographic and urban change in LMICs, including factors related to urban health and wellbeing (Galea, Ettman and Zaman, 2022).\n\nDiscussions of the demographic/health nexus within urban studies (that is, research from urban subdisciplines of geography, planning, sociology, political science, and so on) tend to focus on processes of rapid urban population growth or urbanization driving the historically unprecedented emergence of ‘megacities’, urban sprawl, the formation of slum-like or informal settlements, and growing risks of infectious disease (Duminy, 2023). By contrast, in the field of ‘urban health’ population ageing is occasionally presented as the most important demographic shift of this century, even if this trend has yet to manifest itself across sub-Saharan Africa and South Asia (Galea, Ettman and Vlahov, 2019). Both emphases are valid, and should form part of a broader perspective on the demographic/health nexus.\n\nWe aspire to a globalized perspective on demographic changes. Demographic changes should be seen as including complex processes related to population change (growth and decrease), age-structural shifts, and family and household structures. These transformations are and will be unevenly distributed geographically, between regions, between types/categories of urban areas, and between different areas within towns and cities. Health programming and research should take greater account of this diversity of demographic characteristics and trends (You et al., 2021).\n\nIn line with a view of urban areas as dynamic and emergent entities, we emphasize that demographic changes will help to drive fundamental changes to the structure of towns and cities, as well as how they grow and function. Cities and towns will not simply be larger or smaller (whether in terms of population size or spatial extent) as a result of demographic changes. Rather, these changes will exert strong transformational effects on how and where people live, on how they organize politically, on how they see themselves subjectively and behave culturally, and on how cities function economically. A holistic approach to urban health and wellbeing could assist in harnessing these transformative demographic forces to promote positive social, economic, and political outcomes.\n\n\nDiscussion: Policy and political debates and implications\n\nDemographic change will have implications for the political basis for addressing urban health and wellbeing in future decades. However, political and policy debates surrounding ‘demographic change’ signal different things in different contexts. In the United States, the question of demographic change may be equated with shifts in the racial and cultural composition of the national population (in part linked to international in-migration). In some LMICs, it may be equated with rapid urban population growth and urbanization (often assumed to be driven primarily by rural-urban migration), associated with the extension of urban poverty and production of slum-like and/or informal settlements. In some upper middle-income countries (UMICs) and high-income countries (HICs), the core issues may be population ageing and (urban) population decrease. In certain settings, addressing a demographic agenda will attract controversy, in others not. Given this variability, here we consider the following questions:\n\n• What are the political challenges or risks of promoting a focus on the relationship between demographic change and urban health?\n\n• How is demographic change altering global, national, and urban policy landscapes?\n\n• What are key policy debates that bear upon the relationship between demographic change and urban health?\n\n• What implications will these factors have for urban health policy and practice over the coming decade?\n\nUntil the last decade of the twentieth century, policy discussions of demographic change often were dominated by the question of whether population growth is a problem for economic development and/or environmental sustainability. The debate remains controversial, especially among non-demographic experts, and advocating a demographic agenda that draws attention to negative effects of high fertility rates in LMICs or pro-natalist policies in higher-income contexts risks attracting accusations of neo-Malthusianism, racism, and/or sexism. In population policy and research circles, these concerns took expression in the 1994 Cairo Programme of Action. This was a landmark event that decisively shifted emphasis from macro-level rationales to justifications based on individual rights, including the right to be free from coercion, bringing welcome attention to women’s reproductive health. Today, many political economists and environmentalists would add that a focus on ‘population control’ distracts from the systems of production, consumption, and inequality that underpin climatic and environmental problems. Nevertheless, there remains considerable resistance to demography-facing interventions such as family planning programmes as routes to sustainable and productive futures.\n\nDemographic changes unfold over a complicated political terrain, but some of the reluctance to engage seen outside the population field could be addressed by:\n\n• Emphasizing the potential impacts on urban health of high unwanted fertility rates (and unmet need for family planning) in some settings alongside the health implications of urban population ageing and decline in others. Here it should be recognized that high fertility rates may co-exist with a growth in the absolute number of older people within the same population.\n\n• Noting that urban levels of unmet need for contraception are often significant, even in seemingly well-resourced cities and towns. The implications of unmet need and unwanted fertility, rather than high fertility as such, should be the entry point and principal theme for a discussion of demographic change and urban health. While we cannot ignore the discomfort that some policymakers experience in addressing contraception, pointing to (scattered) estimates of the incidence of induced abortion in LMIC cities and towns may help.\n\n• Highlighting the systemic links between demographic changes (with respect to fertility rates and age structures), diverse migration patterns, and implications for conflict/security and economic change at a range of geographic and temporal scales.\n\n• Refocusing the energy of current priorities towards ensuring that past mistakes do not reoccur. For instance, it is conceivable that the current push to incentivize childbearing in low-fertility countries may be seen as coercive in future decades as they generally involve financial incentives that work most effectively among the poor.\n\nThere is little debate that population growth, decline, and age-structure changes exert strong effects on economic development from the local to the global scales, with potentially significant implications for health and wellbeing. But less consensus exists on the direction and strength of any one specific effect. Much depends on the trade-offs and potential complementarities among fertility, investments in human capital per child and per student, and investments in physical capital, all of which influence the course of economic growth.\n\nCountries with growing populations of children and/or older persons living in towns and cities are likely to see additional demands placed on state and family budgets. This will likely strain the public finances and services that can be directed to education, systems of healthcare and social security, critical urban infrastructures, and other wealth-generating interventions. High levels of state spending on young-age and older-age dependants have the potential to ‘squeeze’ the living standards of working-age populations (Mason and Lee, 2022).\n\nHowever, demographic changes can also generate policy opportunities to improve healthcare and the health of urban populations. To some, ‘population age structure and health status [are] key demographic determinants of economic progress’ (Bloom and Canning, 2007). The concept of ‘demographic dividends’ and ‘windows of opportunity’ has proven influential in policy circles, often inspired by the astonishing growth (linked to rapid demographic transitions) achieved in East Asian economies such as South Korea and Thailand since the 1970s. Currently, these discussions concentrate on the potential for economic growth in contexts of Latin America, South and South-East Asia, and sub-Saharan Africa.\n\nThe windows of opportunity can take several forms (following Fried, 2016; World Bank, 2016):\n\n• First, mortality decline in its initial stages improves young-age survivorship, leading to larger-than-expected cohorts of surviving children. In time this results in a larger-than-expected cohort of labour market entrants, which may find expression either in a boost in productivity due to the bump in the aggregate labour force, or in a logjam in sorting the new labour market entrants into productive employment.\n\n• Second, as fertility rates drop in response to the initial mortality decline, and young-age dependency ratios decrease, this potentially frees resources to improve human capital investments per child, whether made by the family or the state or both. Economists are increasingly interested in the long-term productive payoffs that result from parental-time-intensive, interactive modes of early childcare and education, which are modes of parental and school-system care that are facilitated by low-fertility environments. Such life-course perspectives apply to the promotion of urban health.2\n\n• Third, as age structure shifts lead to an expansion of production and resources, a second window of opportunity can open as financial instruments and markets mature and stocks of savings grow, making possible increased investments in human and physical capital.\n\n• Fourth, when the benefits for society borne of the social and economic capital of older people are realized, for which health-promoting investments over the life-course of individuals are a critical precondition, another window of opportunity may emerge. This window, associated with improved old-age survivorship, is highly conditional but would likely involve systemic changes that facilitate financial savings specifically to support a lengthening and active period of older age.\n\nMeanwhile, the economic implications of ageing populations and population decrease have also attracted public and policy attention in diverse contexts including Singapore, Lebanon, South Korea, Australia, Vietnam, Italy, Russia, and some countries in Eastern European (for example, Bulgaria) and Latin America (for example, Chile and Costa Rica). Population ageing is often portrayed as being detrimental for economies owing to the reduced size of productive workforces, limited tax revenues, and increased (health)care and pension costs. Yet whether low fertility rates and population ageing are a problem for countries depends on a complex interplay of factors including age-related patterns of income from labour, consumption levels, and the nature and extent of intergenerational transfers of wealth and care (Lee, Mason and members of the NTA Network, 2014). Moreover, recent research indicates that declines in economic growth associated with population ageing can be moderated if older populations are in relatively good health (Cylus and al Tayara, 2021).\n\nThe extension of years of good-quality life is in itself a profoundly beneficial advance. There is a risk of being too narrow in framing economic development in conventionally economic, ‘monetized’ terms. That being said, the conditions under which old-age groups are adequately supported and enjoying good-quality lives is due to prior investments made in the human capital of all population groups, increases in the physical capital with which the labour force works, and rates of innovation and technological progress.\n\nA key ongoing debate centres on the fundamental drivers of declining fertility rates, and hence on the best mechanisms to reduce fertility rates and deliver associated benefits. Recently researchers have argued that investments in human capital such as education are more significant in delivering the demographic dividend than changing age structures (Lutz et al., 2019). There is also some debate concerning the causes of stalls in the fertility declines of African countries and urban areas (Schoumaker, 2019). At minimum, these debates imply that an advocacy agenda centred on the urban health/demographic nexus should be careful to encompass and demonstrate the links between demographic shifts, wider political and economic transformations, and necessary investments in human capital to ensure that the positive effects of these shifts are enhanced, or their negative effects are alleviated.\n\nMuch of the work assessing the economic dynamics and impacts of population change focuses on the national or regional level and has yet to be downscaled to urban and intra-urban areas. How such factors could or will affect urban health and wellbeing in different contexts has not yet emerged as a specific topic of research interest. We could reasonably hypothesize that investments in urban health and wellbeing could play an important role in promoting the positive effects and alleviating the negative effects of demographic changes in towns and cities. No studies have assessed the specific extent to which urban health investments might do so, or how such investments should be optimally targeted in space and time.\n\nChanging age profiles in societies will shift the political influence of various demographic groups; some groups will be better positioned than others to make claims on public and private institutions for the provision of social security, healthcare and other health-promoting services or infrastructures. Alternatively, this political influence may be used to resist changes that would promote the health of other urban groups or urban populations more generally.\n\nDemographic processes will ultimately shift the terms of electoral and patronage politics, and by implication the politics of urban health, in all settings. For example, the political implications of large (often unemployed and deprived) youthful urban populations in African settings is well documented. In India, the politics of the youth attracts public attention, while the significance of youth-led political mobilization has been noted further afield in relation to the Occupy movements of North America, the ‘Arab Spring’ uprisings, the 15-M Spanish anti-austerity movement, and the 2019–20 Hong Kong protests, among other events. As political attention shifts towards the demands and aspirations of urban groups in many contexts, particularly less-urbanized LMICs, we can expect renewed accusations of ‘urban bias’ to emerge and strengthen alongside reactionary political coalitions.\n\nThe growing political influence of older populations in North American and European contexts is also much discussed (Greer et al., 2021). Countries like Singapore, South Korea, Japan, and Russia have adopted pro-natalist policies to compensate for low fertility rates and population ageing. The implications of pro-natalist policies for future consumption, emissions, and climatic/environmental change have not attracted much critical debate. Many countries resorting to pro-immigration policies have experienced ‘nativist’ political backlashes.\n\nMoreover, demographic changes will colour the nature, extent and characteristics of social movements related to urban health. How this happens should be considered both in terms of the participants of social movements – how they shape the goals, ideologies, and tactics of their movements – and in terms of how the demographic characteristics of society more broadly influence such factors (Goldstone, 2015). A paper by Thomas et al. in this collection (forthcoming) examines social justice and equity movements in the context of urban health.\n\nThe emergence of an influential and widespread ‘age-friendly cities and communities’ movement over the past several decades has served as a helpful extension of earlier ‘healthy city’ concerns and programmes (De Leeuw, 2017). In particular, the age-friendly movement has:\n\n• Drawn attention to the specific health and wellbeing needs of certain cohorts, the diversity of settlement and community settings in which age-structural changes take place (including small towns, suburbs, and secondary cities) and the extent to which these settings promote and enhance health throughout one’s life;\n\n• Mobilized concepts and frameworks such as the ‘life course approach’ and ‘person-environment fit’ (WHO, 2015). The notion of the ‘life course’ draws attention to the wide range of protective and risk factors that interplay in health and wellbeing over the lifespan. The notion of ‘person-environment fit’ emphasizes the health risks/outcomes that arise from the dynamic interactions of particular demographic groups and the specific environments they inhabit during the life course; and\n\n• Targeted particular social groups as the ‘entry point’ for thinking about analysis and intervention (rather than using the health sector as the entry point), recognizing the social determinants of health, and potentially extending urban health programmes to a wider range of problem definitions and solutions beyond a biomedical or health sciences model of health promotion.\n\nMore generally, a demographic perspective is useful in highlighting issues of temporality and the necessity of having available and accurate data. That is, a demographic perspective reveals the medium- and long-term structural transformations that will influence how cities and urban health change (including age-structural shifts and related disease burdens), how much money is available to states and societies to invest, how local and national governments plan, and when and where money should be invested. Consequently, promoting urban health and wellbeing should involve anticipating both short-term and multi-decadal demographic changes and their geographic distributions, while planning and investing in health-promoting initiatives through spatial and temporal targeting, including through investments and practices that are not necessarily directly related to the health sector (e.g. urban planning or urban infrastructure finance and management). A demographic perspective therefore highlights the importance of having data that are accurate, recent, and representative of the population, and of collecting longitudinal data that enable the separation of correlation from causality, which is important when attempting to influence policymakers and decision-makers.\n\nThe Global Monitoring Report 2015/2016 (World Bank, 2016) produced a new global typology of countries that ties demographic change to development potential. The typology recognized the various pathways through which demographic change affects the prosperity of nations, enabling the disaggregation of policy priorities and recommendations according to the position occupied by countries within this typology. Countries were grouped into pre-demographic-dividend, early dividend, late dividend, and post-dividend categories.\n\nA holistic approach to urban health and wellbeing could make use of a similar typology that is specifically tailored towards urban areas. Urban health programmes in different contexts could be framed as helping cities to progress positively through the stages of the demographic-developmental transition. Such programmes would take a long-term view and recognize that initial policy priorities (such as increasing access to family planning in pre-dividend cities) may need to give way to other priorities and interventions as cities ‘mature’ (for example, health policies that promote and protect female labour force participation in an early-dividend city). In the same way that a life-course approach draws attention to the ways in which different health risks and needs arise over the course of a lifespan, so a ‘city life-course approach’ would highlight that:\n\n• Urban areas and populations will experience emergent health risks and disease burdens over time that are associated with demographic changes, with implications for where, how and on what money should be spent;\n\n• Certain kinds of health interventions in the short-term and in the lives of children may be necessary to guarantee better health and wellbeing for urban populations in the longer-term as they develop and age; and\n\n• Promoting better health and wellbeing of urban populations is a necessary condition for realizing the potential of cities as drivers of economic development (the ‘urban dividend’).\n\nOur discussion has indicated a range of research areas and topics that demand further attention if we are to better understand and harness the relationship between demographic change and urban health. These should be seen as a complement to the set of global research priorities for urban health recently identified by the World Health Organization, which do not encompass demographic issues or processes (WHO, 2022). Our priorities for data and research include investigation of:\n\n• How different demographic trends may unfold simultaneously with varying implications for urban health – for instance, high rates of (urban) population growth in sub-Saharan Africa and South Asia alongside population decreases in Europe and East Asia;\n\n• The health implications, linked to climate change, of having urban growth increasingly concentrated in coastal areas;\n\n• The ways in which different densities of urban growth (realized as patterns of sprawl or compaction) will affect health through changing patterns of land use, biodiversity loss, the emergence of zoonotic diseases, and so on;\n\n• How changing age structures occasioned by fertility and mortality patterns will create differentiated disease burdens in urban areas – indicating the need to develop a typology of urbanization, population, and health dynamics and how these relate to urban health and wellbeing;\n\n• The health of older people living in urban areas, not only in high-income urbanized contexts with ageing populations, but also in lower-income settings where social systems are shaped by patterns of migration and dual residence; and\n\n• How demographic change will affect the demand for and provision of care in diverse urban settings, particularly in LMICs.\n\nAddressing these research priorities will require considerable advances in the availability and quality of suitably disaggregated data. It is now clear that simple national disaggregation by urban and rural categories will not be sufficient for an accurate understanding of the interface between demographic change and urban health (Duminy et al., 2021). At minimum, researchers and policymakers require data revealing how demographic factors are distributed among different settlements and types/categories of urban areas, including intra-urban differences. Urban demographic data could also be linked to climate projection data to enable a better understanding of how different demographic cohorts living in towns and cities will experience emergent climatic risks such as increased heat stress.\n\nThere are new developments in the domain of spatial data and measurement that present opportunities to make the need to address the demographic/health interface in towns and cities to policymakers and decision-makers more compelling than it may have been in the past. For instance, the ‘Degree of Urbanization’3 measure, which is derived from satellite data and scheduled to be updated every two years, offers a way of approximating, with high specificity, where urban spatial growth is taking place and at least provides a proxy of where urban population growth is concentrated.\n\nIn terms of reforming related programmes and datasets, we have identified the following priority actions:\n\n• The National Transfer Accounts (NTA) programme: This programme and conceptual framework has provided important insights into how population growth and changing age structures influence economic growth, gender and generational equity, public finance, and other important features of the macro-economy. However, it remains to be seen whether the NTA framework can accommodate the effects of demographic change on urban health investments and policies. We urge an extension of the NTA Network to incorporate urban/rural dynamics within each country it analyses.\n\n• The United Nations Population Division: Data released in the World Urbanization Prospects series have not been disaggregated by age or sex, which makes it difficult to analyze urban demographic trends even at the national level. The UN’s companion series, World Population Prospects, addresses a range of demographic indicators, including sex and age, but the tabulations are not spatialized even into broad urban and rural categories. We recommend that the United Nations incorporate disaggregation by urban/rural, age, and sex in its reports and datasets.\n\n• The two major household survey programmes – the Demographic and Health Surveys (DHS) and the Multiple Indicator Cluster Surveys (MICS) – have each placed over 300 surveys into the public domain, focusing principally on high-quality estimation of health and socioeconomic indicators for national and urban/rural strata as well as first-order administrative levels. In an urbanizing era, these programmes face a daunting new challenge: how to expand and reconfigure their sampling frames to enable detection of inequalities in health within cities and towns, ideally at the neighbourhood level. The DHS has taken the essential first step in this direction, by distributing the spatial coordinates of its survey clusters and thus enabling links to be made to other data sources for neighbourhoods, health service locations, schools, transport routes, nearby sites of environmental or health risk, and so on. Although these coordinates are currently released only in displaced form (shifted by as much as two kilometres of random error) to preserve respondent confidentiality, consideration is being given to shrinking the radius of displacement while minimizing disclosure risk, given the high population densities of cities and towns. We hope that the MICS will follow suit, and strongly recommend reforms to both programmes that enable within-city analyses and comparisons.\n\n• National statistical offices: Support is required for national statistical offices to provide spatially-specific subnational disaggregated data from their population censuses, which is an essential and irreplaceable ingredient for the Degree of Urbanization method.\n\nWe have argued that an effective response to the demographic-health agenda in urban areas demands data that are available for most contexts, accurate, recent, and sufficiently spatially and demographically disaggregated. However, discussions of data reform often assume that policymakers and decision-makers will somehow have the appropriate professional and technical capacity to use these data to analyse and act on complex urban relationships. There may be a need for a specific research agenda that considers, for example, the kinds of intellectual, professional, and technical capacities that are required to adequately document, understand, and act on the relationships between demographic change and urban health and wellbeing. This kind of research agenda, which is concerned more with the ‘means of implementation’ than the substantive nature of the demographic-health interface, is all the more pressing given that the agenda addressed by this article calls for the ‘joining up’ of two relatively discrete fields of inquiry and practice: demography and urban health (Harpham et al., 2021). In some cases, that process of ‘linking’ may require:\n\n• The education and training of professionals who are legible across intellectual and technical domains, or at least able to converse with professionals drawn from fields different to their own;\n\n• Leadership development programmes to build the capacity of local leaders to harness spatial-demographic data to solve problems related to urban health; or\n\n• The creation of appropriate partnerships for data collection and management between levels or sectors of government that include but extend beyond health departments or health-focused research centres.\n\nConsequently, there is a need to gather case studies of institutions or initiatives that have attempted to link the demographic and urban health (or perhaps other) fields through data practices, to build capacity to analyse complex urban problems, and to use the resulting information to shift the basis of policy- and decision-making. Examples include the work of the African Population and Health Research Centre, which has used longitudinal data on urban demographic and health change to influence policymaking in Nairobi and Kenya, or the Bloomberg Centre for Government Excellence at Johns Hopkins University, which supports and coaches local leaders to build data-driven approaches to urban governance.\n\n\nConclusion\n\nDiverse demographic changes will have significant and transformative impacts on urban health and wellbeing in all regions of the world, but the demographic/health nexus remains an under-appreciated interface of urban research and governance intervention. A view of this interface should recognize that, globally speaking, demographic changes take diverse forms and are unevenly spatially distributed within and between towns and cities. Demographic forces underpin the production of (intra) urban inequities in health, yet in their transformational nature also present opportunities to address those inequities. A demographic perspective highlights the need for a long-term multi-generational view of the changing societal basis for urban health, calling for significant advances in how interested parties collect, manage, analyse, and use data. Doing so will provide the intellectual and practical basis for an effective response to the urban health and wellbeing challenges of the twenty-first century.", "appendix": "Data and software availability\n\nNo data are associated with this article.\n\n\nAcknowledgements\n\nWe acknowledge the guidance on structure and approach, as well as substantive inputs and feedback, received from José Siri. Nathalie Roebbel (WHO) provided feedback on an earlier draft of this article. 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Publisher Full Text\n\nMerkens JL, et al.: Regionalisation of population growth projections in coastal exposure analysis. Clim. Chang. 2018; 151(3–4): 413–426. Publisher Full Text\n\nMontgomery MR, et al., editors: Cities Transformed: Demographic Change and Its Implications in the Developing World. Washington, D.C.: National Academies Press; 2003.\n\nMontgomery MR, et al.: Urban migration of adolescent girls: Quantitative results from developing countries.White MJ, editor. International Handbook of Migration and Population Distribution. Dordrecht: Springer; 2016; pp. 573–604. Publisher Full Text\n\nMontgomery MR, Pinchoff J, Chuang EK: Cities and their environments.Hunter LM, Gray C, Véron J, editors. International Handbook of Population and Environment. Cham: Springer Nature; 2022; pp. 349–374. Publisher Full Text\n\nO’Neill BC, et al.: Global demographic trends and future carbon emissions. Proc. Natl. Acad. Sci. U. S. A. 2010; 107(41): 17521–17526. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSánchez-Páez DA, Schoumaker B: Fertility transition in Africa: What do we know and what have we learned about fertility stalls?Odimegwu CO, Adewoyin Y, editors. The Routledge Handbook of African Demography. Abingdon and New York: Routledge; 2022; pp. 216–251.\n\nSchoumaker B: Stalls in fertility transitions in sub-Saharan Africa: Revisiting the evidence. Stud. Fam. Plan. 2019; 50(3): 257–278. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSuglia SF: Children and adolescents in cities.Galea S, Ettman CK, Vlahov D, editors. Urban Health. Oxford: Oxford University Press; 2019; pp. 70–75. Publisher Full Text\n\nUnited Nations: World Urbanization Prospects: The 2018 Revision (ST/ESA/SER.A/420). New York: United Nations; 2019.\n\nWei YD, Ewing R: Urban expansion, sprawl and inequality. Landsc. Urban Plan. 2018; 177: 259–265. Publisher Full Text\n\nWHO: World Report on Ageing and Health. Geneva: World Health Organization; 2015.\n\nWHO: Setting Global Research Priorities for Urban Health. Geneva: World Health Organization; 2022.\n\nWorld Bank: Global Monitoring Report 2015/2016: Development Goals in an Era of Demographic Change. Washington, D.C.: World Bank; 2016.\n\nYou D, et al.: Demographic challenges and opportunities for child health programming in Africa and Asia. BMJ. 2021; 372: 19. Publisher Full Text\n\n\nFootnotes\n\n1 The proportion of women who want to avoid or delay another birth but who are not using any method of contraception.\n\n2 ‘A life course approach posits that early experiences are deeply influential on our later behaviours and characteristics, including our health. This puts a particular premium on thinking about early life as a determinant of the health of populations’ (Suglia, 2019). An increasingly influential body of academic research on the long-term economic benefits from early child development, led by James Heckman, is summarized in https://heckmanequation.org/.\n\n3 https://ec.europa.eu/eurostat/web/degree-of-urbanisation/background" }	[ { "id": "212320", "date": "26 Oct 2023", "name": "Lorenzo Paglione", "expertise": [ "Reviewer Expertise Environmental hygiene", "social epidemiology" ], "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 believe that the text is an excellent contribution to the general discussion on the central issue of demography in urban contexts. However, some clarifications are probably necessary.\nIntroduction: regarding the concepts of \"urban\" and \"city\", the distinction is perhaps made in a simplistic way, using fundamentally statistical tools. In this sense, the literature in the urban planning field and the so-called \"critical urban studies\" refers in particular to a more complex vision, which questions forms of dualism between material (through the Latin word urbs) and immaterial (through the Latin word civitas) . This adds, together with the very concept of irreducible dualism between the physical city and the city of social (and political) relations, a further level of complexity, which in the case of the discussion of this article on the deomographic theme, I believe is necessary.\nFindings - population change: regarding this paragraph, I think it is useful to specify, at the end, how there is not only the need for formal health systems, but also for informal support networks, in particular for that segment of the population, which is expanding, with socio-health fragility ( for example chronically ill single elderly people, or single-parent families with disabilities). In this sense, under penalty of collapse - or in any case the need for unlimited resources - the health service cannot also make up for the shortcomings of a widespread \"care society\", which also involves a strengthening of informal care processes.\nDemographic change, economic development, and health: regarding this paragraph I believe it is useful to further underline the link between the working active population, general taxation and sustainability of health services and welfare systems, and not only through the productivist vision of World Bank. This relationship is central and cannot be addressed with just a few general phrases.\nPriority data and research: I believe that in this sense the link between climate change, loss of biodiversity and human health must be made explicit from a one health perspective (zoonoses are also dependent on climate change, which does not only concern the rising sea levels, but also extreme climatic phenomena, such as heat islands, which require careful evaluation in terms of available data and the ability to read contexts at a very high level of detail).\nIn general: I believe we need to improve the connections between the parties. A common thread could be that of the intersectional approach and linked to the concept of vulnerability: the elderly person is vulnerable if alone or of a low socioeconomic class, as is the migrant, but above all the level of vulnerability (and also the vulnerability factor) changes during the life trajectory. Perhaps the possibility of examining these aspects in greater depth should be considered.\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? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Partly", "responses": [ { "c_id": "10690", "date": "13 Apr 2024", "name": "James Duminy", "role": "Author Response", "response": "Response to reviewer 1 Thank you for the helpful and insightful comments and suggestions. 1. Recognize the dialectic between material and immaterial senses of ‘the urban’. We have included reference to this line of thinking in the Introduction as an additional conceptual informant for the discussion. 2. Specify the importance of, and need to support, informal care and support networks. We have highlighted this point in the section addressing ‘Age-structure change’. 3. Underline the economic links between the working population, taxation and sustainability of health services and welfare systems. We have elaborated on this relationship via the concepts of the fiscal support ratio and the support ratio. 4. Make the link between climate change, biodiversity loss, and human health explicit from a ‘one health’ perspective. We have added a reference to climate change in our consideration of zoonotic emergence. We also note that there is a companion paper in this Special Issue dealing specifically with climate change (Vardoulakis et al.); we will liaise with that author team to ensure that they deal with the climate-zoonosis relationship in sufficient detail. 5. Improve the connections between themes through an intersectional approach. We have added an intersectional life-course perspective as an additional priority for data and research." } ] }, { "id": "206395", "date": "08 Nov 2023", "name": "Siddharth Agarwal", "expertise": [ "Reviewer Expertise Urban demography", "urban health", "intra-urban disparities in health", "housing characteristics", "wellbeing" ], "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\nWe recommend adding a few factual statements which will enrich the manuscript:\nExamining differences in health investments within the Global South: In the section “Discussion: Policy and political debates and implications” it will be worth highlighting the health investments made in different LMICs. In Southeast Asia and Africa, countries have invested in reasonably sound policies in the view of changing demographics and urbanisation though the implementation of these policies has been weak.\nThese include:\nCountry urban health policies/strategies: (i) In 2013, India launched the National Urban Health Mission aiming to provide comprehensive last-mile health delivery to the poorest in urban areas. (MoHFW, Government of India, 2013). (ii) Bangladesh launched its National Urban Health Strategy in 2014 (MoHFW, Government of Bangladesh, 2020). Countries in Sub-Saharan Africa are steadily making progress towards policy investments in healthcare with a focus on nutrition and urban agriculture in urban areas. (Kimani-Murage & Wanjohi, 2020). (iii) Ethiopia’s Urban Health Extension Program which is being implemented in major urban areas will be vital to include in the policy section. (USAID, undated)\n\nCiting context relevant primary research will enhance the arguments in the manuscript: The authors are urged to consider providing context appropriate examples from relevant primary research studies to strengthen the arguments. The section on “Population change” where authors have laid emphasis on climate induced migration can benefit from providing examples such as those of cities in Bangladesh which are witnessing increased population not only owing to climate induced migration but also due to opportunities that cities present to migrants. (Adri & Simon, 2018)\nExamples of climate induced migration from rural areas of India to cities will be valuable to mention in this section. Erratic rainfall, droughts are climatic factors that are adversely affecting agriculture and agriculture related wage-earning labour jobs in rural areas in many parts of India, forcing families to migrate to cities for livelihood. (Debnath & Nayak, 2022)\n\nKey examples of disaggregated urban data: Similarly, in the section Priority data and research, the authors have highlighted the crucial importance of disaggregated demographic data particularly examining intra-urban differences. An example which can support this argument is the analysis of India’s National Family Health Survey (NFHS) by wealth-index that unmasks the disparities in Indian cities with respect to child and maternal health, provision for health care and housing conditions. (Agarwal, 2011). Intra-urban differences in health conditions have been studied in Bangladesh in the form of Bangladesh Urban Health Survey 2013. (UHS, 2013).\n\nRecommendations for strengthening the conclusion:\n\nImportance of community-level enumerations in informing data: In identifying priority actions related to reforming datasets, the authors may consider laying emphasis on the challenges of gathering data in urban informal settlements in LMICs and significance of the initiatives that many community-based organizations and researchers are undertaking in pursuing community-driven enumerations to gather data. (Vlahov et al., 2011). These include enumerations by National Slum Dwellers Federation (NSDF) in Mumbai, India (Patel S et al., 2012) and Slum and Shack Dwellers International (SDI) in many African countries. (Kuffer et al., 2019; Lines & Makau, 2018).\n\nSuggestion with a key example of a low-cost method to utilize DHS for analyzing intra-urban differentials at city-level: DHS can do a booster sample of select cities in a country to then enable use of city data for analysing intra-city disaggregation. An example of such a DHS exercise is available from NFHS 3 (India) where the health and wellbeing conditions of populations of eight cities was described in a dedicated report entitled “Health and Living Conditions in Eight Indian Cities” released in 2009. Being part of the country’s DHS, an approach of having an additional sample of select cities is a cost-efficient method of research in urban areas of a country. Cost efficient ways of obtaining urban data with disaggregation are even more crucial in contemporary times where international financial assistance is challenging to get than it was a couple of decades ago. (Gupta et al., 2009)\n\nSummary of the article: The research topic is timely and crucial in the evolving spectrum of global urbanization. The authors have meticulously laid arguments using relevant literature on the importance of a) interplay of urban health with demographic processes; b) impacts of demographic changes on economic and political systems in cities; c) significance of a demographic perspective in understanding urban inequities and using data to enable evidence-informed action.\nCitations/References\nAdri, N., & Simon, D. (2018). A tale of two groups: focusing on the differential vulnerability of “climate-induced” and “non-climate-induced” migrants in Dhaka City. Climate and Development, 10(4), 321-336. DOI 10.1080/17565529.2017.1291402\nAgarwal, S. (2011). The state of urban health in India; comparing the poorest quartile to the rest of the urban population in selected states and cities. Environment and Urbanization, 23(1), 13-28. DOI: 10.1177/0956247811398589\nBangladesh Urban Health Survey (2013). https://www.measureevaluation.org/publications/tr-15-117\nDebnath, M and Nayak, DK (2022) Assessing drought induced temporary migration as an adaptation strategy: evidence from rural India. Migration and Development 11(3): 521–542 DOI 10.1080/21632324.2020.1797458\nGupta, K., Arnold, F., & Lhungdim, H. (2009). Health and living conditions in eight Indian cities. National Family Health Survey (NFHS-3), India, 2005–06. Mumbai: International Institute for Population Sciences. https://rchiips.org/nfhs/urban_health_report_for_website_18sep09.pdf\nKimani-Murage, E., & Wanjohi, M. N. (2020). Urban Health Assessment: Nutrition and Water, Sanitation and Hygiene (WASH) Challenges Facing Children and Adolescents in Urban Slums in Nairobi. African Population and Health Research Center. http://www.jstor.org/stable/resrep26381\nKuffer, M., Persello, C., Pfeffer, K., Sliuzas, R., & Rao, V. (2019, May). Do we underestimate the global slum population?. In 2019 Joint Urban Remote Sensing Event (JURSE) (pp. 1-4). IEEE. DOI 10.1109/JURSE.2019.8809066\nLines, K., & Makau, J. (2018). Taking the long view: 20 years of Muungano wa Wanavijiji, the Kenyan federation of slum dwellers. Environment and Urbanization, 30(2), 407-424. https://doi.org/10.1177/0956247818785327\nMinistry of Health and Family Welfare, Government of India. National Urban Health Mission (2013) https://nhm.gov.in/index1.php?lang=1&level=1&sublinkid=970&lid=137\nMinistry of Health and Family Welfare, Government of the People’s Republic of Bangladesh. National Urban Health Strategy 2020. https://www.nnsop.gov.bd/storage/files/file-2023-08-29-64ed92c16323d.pdf\nPatel, S., Baptist, C., & D’Cruz, C. (2012). Knowledge is power – informal communities assert their right to the city through SDI and community-led enumerations. Environment and Urbanization, 24(1), 13-26. https://doi.org/10.1177/0956247812438366\nVlahov, D., Agarwal, S.R., Buckley, R.M. et al. Roundtable on Urban Living Environment Research (RULER). J Urban Health 88, 793–857 (2011). https://doi.org/10.1007/s11524-011-9613-2\nUSAID (undated). Ethiopia’s Urban Health Extension Program. https://publications.jsi.com/JSIInternet/Inc/Common/_download_pub.cfm?id=22119&lid=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? 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": "10691", "date": "13 Apr 2024", "name": "James Duminy", "role": "Author Response", "response": "Response to reviewer 2 Thank you for the helpful and insightful comments and suggestions. 1. Highlight health investments made in different LMICs. We have added a reference to the Indian, Bangladeshi and Ethiopian urban health programmes, in the context of what they can teach us about the policy and political debates surrounding the links between urban health and demographic changes, which is the focus of this section. 2. Cite context-relevant primary research to enhance the arguments. We note that this paper forms part of a wider suite of papers, two of which will focus on the links between urban health and migration (Sa Machado et al.) and climate change (Vardoulakis et al.). Our focus in the present paper is specifically on how population or demographic change intersects with those themes, which means it only tangentially addresses topics such as climate-induced migration. In terms of adding further citations, we have followed the guidance of the editor of the Special Issue, which is to limit the number of citations (we are already well over the guidance of 25 citations) and instead focus on ‘concisely summarizing knowledge’ on demographic change for ‘use in urban health advocacy’. Our author team plans to produce and publish a companion piece (more akin to a comprehensive scoping review) that gives greater empirical detail on the points addressed, with specific examples and further citations to substantiate key points. 3. Provide examples of climate-induced migration As noted above, there are companion papers in this Special Issue dealing specifically with migration and climate change in greater detail. We will forward the suggested reference to those author teams. Our particular concern in this section was to sketch how population changes will affect health and wellbeing by aggravating or creating new vulnerabilities to climatic change. 4. Give examples of initiatives to secure disaggregated urban health data We have added references to these programmes to the ‘Priority data and research’ section. 5. Highlight the importance of community-level enumerations as a source of data We have added reference to the value and challenges of engaging with a citizen science movement and community self-enumerations within the ‘Priority data and research’ section. 6. Give examples of low-cost methods to utilize DHS programmes to gather intra-urban differences We have added a reference to the potential for DHS ‘urban booster’ samples in the ‘Priority data and research’ section." } ] } ]	1	https://f1000research.com/articles/12-1017
https://f1000research.com/articles/12-1290/v1	09 Oct 23	{ "type": "Research Article", "title": "Factors Associated with Improving Appropriate Medical Sharps Disposal Practice Among Diabetic Patients Using Insulin Therapy", "authors": [ "Ryan Herardi", "Hafidz Naeriansyah Djajawiguna", "Sri Wahyuningsih", "Ida Ayu Kshanti", "Shahnaz Medina", "Lingga Etantyo Praditya", "Hafidz Naeriansyah Djajawiguna", "Sri Wahyuningsih", "Ida Ayu Kshanti", "Shahnaz Medina", "Lingga Etantyo Praditya" ], "abstract": "Background: Diabetic patients are always in contact with medical sharps, such as pen needles, lancets, and syringes. Sometimes, patients improperly dispose of these items and cause needle stick injuries. This study aimed to identify factors that improve appropriate manner in which individuals with diabetes who require insulin therapy dispose of medical sharps. Methods: In December 2019, a cross-sectional investigation was undertaken amongst insulin therapy-dependent diabetic patients visiting Jakarta's Fatmawati General Hospital. A questionnaire was formulated to appraise medical sharps' disposal methodology. The data gathered from the said patients, including their age, gender, educational level, employment status, length of time as a diabetic, duration of insulin treatment, and receipt of formal medical training, were also recorded. Results: Of 103 diabetic patients, 77.3% were over 50 years old, 58.3% were female, 68% were a low level of education, 74.8% were not working, 84.5% were diagnosed with diabetes for more than 5 years, 53.4% were using insulin therapy, and only 65% had got formal training on medical sharp products disposal. Nearby 83.5% still recap the pen needle insulin with the inner needle cap after injecting insulin, and 92.2% still threw medical sharps on the street when traveling outside. Approximately 81.6% of respondents stored their unused needles and lancets in a secured manner that was inaccessible to children. The practice score for proper medical sharps disposal increased from 4.5 to 6.0 as a result of formal training provided by healthcare professionals, as determined by the Mann Whitney Test (p=0.001). Conclusions: Formal training by healthcare workers was the only factor that improved medical sharp products disposal practice among diabetic patients using insulin therapy", "keywords": [ "Keywords: Diabetes", "Insulin", "Medical sharp product", "Disposal Practice", "Formal Training" ], "content": "Introduction\n\nThe medical condition known as “Diabetes Mellitus (DM)” is categorized as a metabolic disease that presents with hyperglycemia. The manifestation of this chronic condition results from malfunctions in either insulin secretion, insulin action, or a combination of both.1 In the years between 2007 and 2010, a significant proportion of individuals - 88.2% of those aged 20 years and above - diagnosed with this condition in the United States sought to manage their symptoms by administering insulin and/or oral medications. Further analysis revealed that within this group, 58.4% relied solely on oral medications, 15.3% only utilized insulin, while 14.5% adopted a combination therapy involving both insulin and oral medications.2\n\nPatients with diabetes who utilize insulin therapy are constantly in contact with medical sharps, including lancets, pen needles, and syringes. Regrettably, patient disposal of these sharps is not always adequate. The presence of medical sharps poses a considerable risk to workers in the waste management sector, as well as janitors, refuse collectors, and members of adjacent communities who are exposed to these materials. This issue is especially concerning, as the individuals are at risk of needle stick injury and contracting infectious diseases such as hepatitis B, hepatitis C, and Human Immunodeficiency Virus (HIV).3–5\n\nA study in Gondar Town, Ethiopia displayed a correlation between proper disposal of insulin injection medical waste and urban residency, high educational attainment, a diagnosis of type 1 diabetes, insulin use duration of less than 5 years, and physician visits within the last six months.4 Conversely, another study performed in New Delhi, India did not identify any connection between knowledge, socio-demographic factors, and attitude regarding household sharp waste disposal and adherence to proper disposal of sharp waste.5 A study conducted in a tertiary hospital in New York, United States, demonstrated that individuals with diabetes for more than 30 years and who received formal training in sharps disposal exhibited a greater likelihood of exercising correct practices.6 Similarly, a report from North-East Peninsula Malaysia describes a correlation between previous guidance on sharp disposal from healthcare providers, patients’ knowledge of safe disposal, and the duration of diabetes being less than five years with proper sharp waste disposal.7 In Sri Lanka, a research study highlighted that level of education, duration of insulin usage, and prior education on safe disposal were all independently associated with proper disposal of sharps.8\n\n\nMethods\n\nA cross-sectional study of convenience sample was conducted to identify factors that improve appropriate medical sharps disposal practices among diabetic patients. The “sharp” related Diabetes Mellitus includes needles, lancets, and syringes. Data was collected from a questionnaire asking type 2 DM patients who visited Fatmawati General Hospital, Jakarta, Indonesia, on December 2019.\n\nIn order to evaluate the disposal of sharp medical products, we constructed a questionnaire following Singh,5 and modified it based on recent literature on proper medical sharps disposal recommended by the Centers for Disease Control and Prevention (CDC), American Diabetes Association (ADA) and National Health Service (NHS) United Kingdom (UK).9–12 Twelve questions were translated into Bahasa Indonesia and conducted with 30 subjects to validate and assess the reliability of the questions. For each question, dichotomous scoring was applied, where one mark was awarded for a correct response and zero for an incorrect response. A score of zero indicated the poorest practice, while a score of 12 demonstrated the best practice.\n\nThe study collected data on various factors associated with the disposal of medical sharps, including age, gender, level of education, employment status, duration of diabetes, duration of insulin use, and formal training from healthcare workers. Age was categorized using a threshold of 50 years, while gender was classified as male or female. Level of education was grouped into low (patients with no schooling, elementary, junior high, and high school education) and high (patients with a diploma, undergraduate, postgraduate, or doctorate) categories. Employment status was classified as actively employed or not working (including retired individuals). The duration of diabetes and insulin use were used as cut-off points of five years each. Additionally, patients were asked about any training they received from doctors, nurses, or other healthcare workers prior to disposing of sharp medical products.\n\nBefore being analyzed by IBM® SPSS® (Statistical Package for the Social Sciences) software version 26.0 for Mac, the last data collection tool was thoroughly checked for completeness. Univariate analysis employed frequencies and percentages to represent different variables, while bivariate analysis utilized the Mann-Whitney test to compare groups. The statistical tests were carried out at a significance level of 0.05.\n\nPrior to conducting this study, each participant was given the opportunity to provide written informed consent. Additionally, this study received approval from “The Health Research Ethics Committee of Universitas Pembangunan Nasional Veteran Jakarta” (UPNVJ), Jakarta, Indonesia (Registration Number: B/2228/XII/2019/KEPK). We used the STROBE cross sectional checklist when writing our report.13\n\n\nResults\n\nThe result in Table 1 pertains to diabetic patients currently undergoing insulin therapy. Most of these patients were over 50 years old (77.3%), female (58.3%), and had a low level of education (68.0%). Additionally, most of the patients were not working (74.8%) and were diagnosed with diabetes for more than five years (84.5%). Among those who had undergone insulin therapy for more than 5 years, 55 individuals were identified. Regarding formal training received from healthcare workers, most patients (65.0%) reported having received any training regarding proper medical sharp disposal.\n\nTable 2 shows the percentage of right answers from each question for evaluating medical sharps disposal. The majority of diabetic patients still recap the pen needle insulin with an inner needle cap after injecting insulin (83.5%), even though it was no longer recommended due to the potential for needle stick injury. In addition, although many patients collected medical sharps into a special container, they still threw sharp medical products on the street when traveling outside (92.2%). Most patients kept their unused needles and lancets in a safe place and were unreachable to children (81.6%).\n\n* Negative statement (answering “No” scored 1).\n\nTable 3 describes the results of the association between influencing factors and disposal practice scores. Training from health workers was associated with improving medical sharps disposal patients among diabetic patients (p=0.001; Mann Whitney Test). Other factors were not significantly associated.\n\n* Mann Whitney Test.\n\n\nDiscussion\n\nThe diabetic patients who use insulin exhibited significant diversity regarding their age, gender, level of education, employment status, duration of diabetes, duration of insulin use, and formal training from healthcare workers. Only two-thirds of diabetic patients admitted to having training related to disposing of proper medical sharps by healthcare workers. It showed that we still have a lot of opportunities to educate diabetic patients more creatively.\n\nAlmost all diabetic patients still recap the pen needle insulin with an inner needle cap after injecting insulin. ADA, CDC, and NHS UK no longer recommend it due to the potential for needle stick injury. Similar studies were reported by Mecuria, Singh, Atukorala, and Montoya.4,5,8,14 Diabetic patients should be advised to cover the insulin pen only with the pen cap or to throw it away without closing the container when no longer used.9–12 Only half of the diabetic patients threw medical sharps into separate containers. The rest threw them directly into household plastic bags. Singh reported almost all patients threw them directly into household garbage bags.5 This can endanger the dustman to getting a needle stick injury. When traveling out of the house, most diabetic patients would bring used needles and lancets back home, but if traveling far away, almost all patients threw them out of hand. Singh found that almost patients did not throw sharps on the street, but they did not bring them back home either, so that finding was unclear.5 Patients’ awareness of bringing used medical sharps back home needs to be increased by reminding them to carry a specific container when they are traveling. Most patients still reuse insulin pen needles for more than one day. American Diabetes Association recommended changing the needle after each injection or at least once daily.9 This may occur because of the limited free pen needles covered by National Insurance. They need extra money to buy pen needles and lancets. Singh reported a similar study in India.5\n\nMost of the patients no longer bent the needle after using it. This is a positive behavior recommended by ADA, CDC, and NHS UK.9–12 In contrast, Singh and Mecuria found that more than half of patients still bent the needle and lancet.4,5 Concern about keeping sharp medical products out of reach of children at home was quite good, similar to that reported in another study by Singh.5 Half of the diabetic patients had regularly disposed of containers containing medical sharps on one particular day, but the majority of patients had never informed the dustman about the existence of sharp medical products in their waste. Different from our study, Singh found almost all patients did not dispose of them on one particular day and also did not inform the dustman. This may be related to the absence of national regulation regarding medical waste disposal in household waste.5 Only half of the diabetic patients actively asked doctors or pharmacy staff about the appropriate way to dispose of pen needles and lancets. Singh and Mecuria found less than a quarter of patients had asked about the appropriate way to dispose of medical sharps.4,5 This makes us need to be more active in providing information about how to properly dispose of medical sharps, especially diabetic-related sharp waste.\n\nThis study showed that the only factor associated with improving medical sharps disposal practice was formal training from healthcare workers (p=0.01; Mann-Whitney Test), while other factors were not. This is similar to the study conducted by Singh,5 education by Health Care Providers was associated with good practice on disposal of sharp waste, while knowledge and attitude levels were not. Singh also found an association between good practice on the disposal waste with the education given by pharmacists and friends, not only from health care providers. Huang found the same results that “formal training on proper sharps disposal was more likely to dispose of sharps correctly, and other factors were not associated.”6 Hasan and Atukorala found similar results that “previous advice on sharp disposal from health care providers was significant contributing factor for sharp waste disposal.”7,8 They also found that “the duration of diabetes (less than five years) was a significant contributing factor due to chronic disease burnout.”7,8 Montoya found similar results that “patients who disposed of needles in an unsafe manner had DM for a longer duration than those who used safe disposal patterns.”14 Similar to our study, Instead of using numerical values, we categorized the length of time someone has had diabetes into less than five years or more than five years. Practicing diabetes management for a shorter time frame of less than five years was found to be more advantageous than practicing for a longer duration of more than five years, although this difference was not statistically significant and may be due to the smaller sample size. Huang, Hasan, Atukorala, and Montoya discovered that “formal training on proper sharps disposal was strongly associated with correct disposal, while other factors showed no significant association.”6–8 Moreover, they found that previous advice on sharp disposal from healthcare providers was a significant contributing factor to proper waste disposal.6–8 Hasan and Atukorala also identified “the duration of diabetes (less than five years) as a significant contributing factor due to chronic disease burnout.”7,8 Montoya observed similar findings, indicating that “patients who disposed of needles unsafely had been diagnosed with DM for a longer duration than those who used proper disposal practices.”14 Our study revealed similar results, suggesting that patients with diabetes for less than five years tend to exhibit better disposal practices than those with a longer duration of diabetes, but the difference was not statistically significant. This might be attributed to the smaller sample size and the categorization of the duration of diabetes as less than or more than five years rather than using a numerical value.\n\nAccording to Mecuria’s study, the factors that significantly affect the proper disposal of insulin injection devices were living in urban areas, educational status, type 1 DM, duration of insulin use, and frequency of physician visits. However, they did not find a direct association between healthcare worker training and good disposal practices. Our study agreed with Mecuria, but they were different considering that we did not divide our patients’ residence (they live in a homogenous area), type of diabetes (almost all of them were type 2 DM patients), and frequency of physician visit (chronic patients were required to visit once a month due to National Insurance regulation). Mecuria also divided education level and duration of insulin use in more detail.4\n\nThe role of repeated formal training from healthcare workers regarding appropriate medical sharps disposal properly is very crucial. A study conducted by Hasan showed “there was a significant increase in the mean knowledge score” after providing health education interventions, as observed at one-month and three-month follow-up assessments.15 The government should formulate a specific regulation regarding the management of medical waste in households. Before the existence of an official regulation, health facilities could persuade patients to collect their medical waste and bring it back to their health facilities that have incinerators to destroy them properly.\n\n\nConclusion\n\nAlmost all diabetic patients still recap the pen needle insulin with a small cap after injecting insulin and throw sharp medical products on the street when traveling outside. Most diabetic patients who used insulin therapy stored their unused needles and lancets in a secure location that was inaccessible to children. Notably, the only factor that was found to have a positive impact on medical sharps disposal practices among these patients was formal training provided by healthcare workers.", "appendix": "Data availability\n\nFigshare: Questionnaire based on collection of socioeconomic, knowledge, attitude and presence of influencing factors, DOI: https://doi.org/10.6084/m9.figshare.22735724.\n\nThis project contains the following underlying data:\n\n• Questionnaire based on collection of socio-economic, knowledge, attitude and presence of influencing factors modified based on recent literature on proper medical sharps disposal recommended by the Centers for Disease Control and Prevention (CDC), American Diabetes Association (ADA) and National Health Service (NHS) United Kingdom (UK).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nSoelistijo SA, Lindarto D, Decroli E, et al.: Guidelines for the management and prevention of diabetes mellitus in Indonesia. Jakarta: Indonesian Society of Endocrinology; 2019.\n\nSaydah SH, Cowie CC, Casagrande SS, et al.: Medication use and self-care practices in persons with diabetes. Diabetes in America. 3rd edition.Bethesda (MD): National Institute of Diabetes and Digestive and Kidney Diseases (US); 2018; (39. ): pp. 1–14.\n\nMarkkanen P, Galligan C, Laramie A: Understanding Sharps Injuries in Home: The Safe Home Care Qualitative Methods Study to Identify Pathways for Injury Prevention. BMC Public Health. 2015 Apr 11; 15: 359. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMekuria AB, Gebresillassie BM, Erku DA: Knowledge and Self-Reported Practice of Insulin Injection Device Disposal among Diabetes Patients in Gondar Town, Ethiopia: A Cross-Sectional Study. J. Diabetes Res. 2016; 2016: 1–7. Article ID 1897517. Publisher Full Text\n\nSingh AP, Chapman RS: Knowledge, attitude and practices (kap) on disposal of sharp waste, used for home management of type-2 diabetes mellitus, in New Delhi. J. Health Res. 2011; 25(3): 135–140.\n\nHuang L, Katsnelson S, Yang J: Factors contributing to appropriate sharps disposal in the community among patients with diabetes. Diabetes Spectr. 2018; 31(2): 155–158. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHasan UA, Hairon SM, Yaacob NM, et al.: Factors Contributing to Sharp Waste Disposal at Health Care Facility Among Diabetic Patients in North-East Peninsular Malaysia. Int. J. Environ. Res. Public Health. 2019; 16(2251): 1–12. Publisher Full Text\n\nAtukorala KR, Wickramasinghe SI, Sumanasekera RDN, et al.: Practices related to sharps disposal among diabetic patients in Sri Lanka. Asia Pac. Fam. Med. 2018; 17(12): 1–7. Publisher Full Text\n\nAmerican Diabetes Association: Insulin pens.2023. Reference Source\n\nGoad K: Discarding sharps.2017. Reference Source\n\nThe National Institue for Occupational Safety and Health (NIOSH): Bloodborne infectious diseases: safe community needle disposal. How to protect yourself from needlestick injuries. Centers for Disease Control and Prevention (CDC); 2014. Reference Source\n\nNational Health Service (NHS) United Kingdom: How should I dispose of used needles or sharps?2019. Reference Source\n\nVon Elm E, Altman DG, Egger M, et al.: The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) Statement: guidelines for reporting observational studies.\n\nMontoya JM, Thompson BM, Boyle ME, et al.: Patterns of sharps handling and disposal among insulin-using patients with diabetes mellitus. J. Diabetes Sci. Technol. 2021; 15(1): 60–66. Publisher Full Text\n\nHasan UA, Hairon SM, Yaacob NM, et al.: Effectiveness of Diabetes Community Sharp Disposal Education Module in Primary Care: An Experimental Study in North-East Peninsular Malaysia. J. Environ. Res. Public Health. 2019; 16(18): 3356. Publisher Full Text" }	[ { "id": "213222", "date": "16 Oct 2023", "name": "Velma Herwanto", "expertise": [ "Reviewer Expertise Internal medicine", "sepsis", "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\nAbstract:\n\n\"53.4% were using insulin therapy\" --> what does this refer to? All of the participant used insulin therapy.\nMethods:\nThis article has not clearly said the inclusion and exclusion criteria of their participant. I suppose the inclusion criterion was diabetes patient on insulin therapy.\n\nAuthors have not explained the procedure to fill out the questionnaire in detail. If, for example, the participant faced difficulty to fill it out (might be due to visual problem or low education), what did he researcher do to make it work?\nDiscussion:\n\"Singh found that almost patients did not throw sharps on the street, but ...\" --> I would guess there is an \"all\" after the word almost.\n\nAuthor could elaborate more on how the formal training was done by the health workers. For example, if the training was conducted routinely in Fatmawati Hospital, it might be useful to explain the training a bit more (the frequency, in group or in private, etc).\nReferences:\nBibliography needs to be fixed, including the punctuation, title sentences. References need to be completely written (eg, reference 9 and 10 need to be corrected).\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": "10563", "date": "20 Nov 2023", "name": "Ryan Herardi", "role": "Author Response", "response": "Dear dr. Velma Herwanto, Thank you for your constructive feedback on our manuscript titled “Factors Associated with Improving Appropriate Medical Sharps Disposal Practice Among Diabetic Patients Using Insulin Therapy” We appreciate the thoroughness of your review, and we have addressed each of your concerns below: Comment 1: In the revised manuscript, we will clarify this point by specifying the inclusion and exclusion criteria in the Methods section. The inclusion criteria now explicitly state that participants are Type 2 diabetes mellitus patients currently using insulin therapy, and the exclusion criteria outline conditions such as unwillingness to participate or incomplete questionnaire submission. Comment 2: We appreciate your observation, and to address this concern, we are going to include detailed inclusion and exclusion criteria in the Methods section, specifying the eligibility of Type 2 diabetes mellitus patients currently using insulin therapy as participants. Comment 3: In response to your comment, we are going to add information in the Discussion section explaining the steps taken during the questionnaire administration. We identified patients using insulin needles from hospital records, provided direct instructions, obtained informed consent, and assisted respondents in completing the questionnaire to minimize errors. Comment 4: Your observation is correct. We are going to amend the sentence to read, \"Singh found that almost all patients did not throw sharps on the street.\" Comment 5: To address this suggestion, we are going to include additional details in the Discussion section, recommending regular individual training sessions, monthly frequency aligned with patients' check-ups, and the possibility of group training through health seminars at Fatmawati Hospital. Comment 6: We have thoroughly reviewed and revised the bibliography, ensuring correct punctuation and complete references, including the correction of references 9 and 10. We believe these revisions strengthen the clarity and completeness of our manuscript. We sincerely appreciate your valuable input, which has contributed to enhancing the overall quality of our work. Thank you for your time and diligence in reviewing our manuscript. Best Regards, Author" } ] } ]	1	https://f1000research.com/articles/12-1290
https://f1000research.com/articles/12-57/v1	13 Jan 23	{ "type": "Study Protocol", "title": "Review of health research and data on racialised groups: Implications for addressing racism and racial disparities in public health practice and policies in Europe: a study protocol", "authors": [ "Marie Meudec", "Clara Affun-Adegbulu", "Theo Cosaert" ], "abstract": "Historically, across Europe, data and research on racialised minority groups have not been collected or carried out in a sufficient, adequate, or appropriate manner. Yet, to understand emerging and existing health disparities among such groups, researchers and policymakers must obtain and use data to build evidence that informs decision-making and action on key structural and social determinants of health. This systematic search and review aims to contribute to closing this gap and promote a race-conscious approach to health research, strengthening the utilisation and deployment of data and research on racialised minority groups in Europe. Its ultimate goal is to improve equality and equity in health. Concretely, the study will do so by reviewing and critically analysing the usage of the concepts of race, ethnicity, and their related euphemisms and proxies in health-related research. It will examine the collection, use, and deployment of data and research on racialised minority groups in this area. The study will focus on Belgium, France, and the Netherlands, three countries with graphical proximity and several similarities, one of which is the limited attention that is given to racism and racial inequalities in health in research and policy. This choice is also justified by practical knowledge of the context and languages. The results of the review will be used to develop guidance on how to use and deploy data and research on and with racialised groups. The review is part of a larger project which aims to promote race-conscious research and data. The project does this by a three-pronged approach which: 1) highlights the need for a race-conscious approach when collecting and using data, carrying out research on racialised minority groups; 2) builds expertise for their effective use and deployment, and; 3) creates a knowledge network and community of practice for public health researchers working in Europe.", "keywords": [ "racism", "racial health disparities", "racialised minority groups", "health data", "health research" ], "content": "Introduction and rationale\n\nWhile health disparities,1 linked to the socio-politically constructed concepts of race,2 and ethnicity* have long been established, the COVID-19 pandemic has brought renewed attention to the issue. Although miost people have been affected by the pandemic, an increasing body of international research3 shows that racialised minority groups* have been disproportionately affected in terms of disease exposure, susceptibility to the disease, the severity of the disease and mortality rates. In addition to this, the measures taken to contain or mitigate the pandemic have had a particularly negative impact on the determinants of health and access to care for people within such groups. This has, in many cases, had negative consequences for their health statuses and health outcomes, which has ultimately further increased already existing health disparities among racialised minority groups (Katikireddi et al., 2021). Addressing this will require evidence-based decision-making and action on key structural and social determinants of health such as racism* and racial discrimination, which are mediated by race, ethnicity, and related concepts.\n\nYet, in many countries across Europe, there is often inappropriate, inadequate, or insufficient use and deployment of data and research* on racialised minority groups. The reasons for this can be grouped into two main categories. One is the continuous emergence of biologically or genetically based race research which is often linked to scientific racism (Roberts, 2011a, 2011b; Saini, 2019). Cerdeña, Plaisime, and Tsai (2020), recognising this, introduced the race-conscious approach* which, in contrast to the race-based approach, focuses on racism and racial health disparities. This race-conscious approach forms the basis and the goal of this project, conducted by a racially diverse team (see below Review team/Positionality). The other category, which this project focuses on, includes issues related to the poor use and deployment of data and research on racialised minority groups, in the monitoring and tackling of health disparities, and public health policymaking and social change (Farkas, 2017; Holtzman, Khoshkhoo, and Nsoesie, 2022).\n\nData and research on racialised minority groups are often underutilised and under-deployed for three broad reasons. The first reason is related to data collection. In many countries, there is a lack of national data systems using race/ethnicity data, which means that there is limited statistical evidence on health disparities among racialised minority groups. This is partly due to national political models and philosophies around immigration and ethnic diversity management. Examples of this can be seen in the recent removal (law proposed in 2013 and accepted in 2018) of the word ‘race’ from the French Constitution (Gay, 2015), and more broadly, in the republican model which is practised in France. According to this model, a recognition of ethnic and/or racial diversity is seen as subversive, and consequently, the collection of ethnic statistics for official purposes is deemed to be unnecessary or even contrary to the ideals of the model (Rivenbark and Ichou, 2020). This can also be seen in Belgium where the Belgian Census does not include any questions on ethnicity, let alone racial identification (Lorant and Bhopal, 2011), or in the Netherlands, where the new population classification is based on the country of birth of the person, which implies a classification by origin and not by identification or experience of discrimination (Statistics Netherlands, 2022). According to advocacy groups like the European Network Against Racism (ENAR)4, this lack of data on ethnic/racialised groups makes it difficult to combat racism and racial inequalities, and it also means that clear guidelines with workable definitions on the subject matter are limited. This lack of (collection of) data at the individual/population level is often exacerbated by the lack of recognition and undervaluing of data such as lived experiences, testimonies, and other similar forms of knowing5. Some of these problems could also be related to the lack of representation of racialised minority groups at high levels of society. In addition to this, even in cases where data exists, and it is valued and recognised as such, it might still not be used for research to address racial health inequities, as many researchers do not have the opportunity and/or expertise to categorise, analyse data on racialised minority groups, or to interpret and communicate the results in such a way as to promote racial health justice.\n\nThe second reason is linked to the research itself. There is disinclination among certain researchers to carry out any research linked to race and/or ethnicity, as the use of such variables in research continues to be seen as contentious, to some degree. Some researchers see these variables as valuable tools for analysing health inequalities* and addressing health inequities as well as the impact of various forms of racism (institutionalised, systemic/structural, interpersonal, internalised racism) on racialised minority groups. Others, on the contrary, disagree, on the grounds that the data and results of research that use these variables can be misused and instrumentalised against racialised minority groups. They also contend that such data and research can be used in ways that are sometimes difficult to anticipate, for instance to fuel stigmatisation and racial stereotyping, quoted as a “problematic use” of data by Nancy Krieger (2021). Additionally, research on racialised minority groups is often seen as too difficult to implement in practice, due to challenges of finding appropriate approaches and solutions to conceptualisation, operationalisation, data collection, data management, data analysis, interpretation, representativeness, transferability and generalisability. For instance, in cases where data is collected on racialised minority groups, it might be done in a “non-standardised” way which, certain researchers may find difficult or impossible to use in research (Simon, 2005).\n\nThe third reason focuses on the results of research on racialised minority groups. In many cases where data on racialised groups is available and it is being used for research, it does not necessarily lead to anti-racist interventions. Moreover, the results are frequently not used for advocacy, and/or the results and recommendations are not implemented or used to effect policy change and achieve real-life impact. This is amongst others because the results are deemed to be too specific, subjective, or politicised. Many researchers also consider transformative research, advocacy and activism to be beyond their mandate. Furthermore, similarly to broader society, within the field of health, there are strong tendencies to erase contributions from marginalised/racialised researchers or to erase race when analysing inequalities, as was for example the case with the concept of intersectionality* in feminist studies (Bilge, 2013). In contrast, when the results are used in research or policymaking, this is generally done either through (un)conscious racial biases in the framing of social problems, or without sufficient attention to unintended consequences which means that in some cases, results, instead of supporting efforts to address racial health disparities, actually (inadvertently) reinforce stereotypes about ethnic/racial groups (Kaplan and Bennet, 2003; Zuberi, 2003; Laveist, 1996).\n\nThe consequence of all this for public health is the adoption and implementation of policies that are intended to be race-neutral but which in fact produce a colourblind paradigm that reproduces ‘methodological whiteness’6 and creates or exacerbates health inequities* and inequalities amongst racialised minority groups. This criticism is reflected in the widespread calls to decolonise health research, improve equality and equity in health in an intersectional way, and ultimately, achieve social and racial justice. Decolonial approaches to global and public health* have been a growing field in recent years and offering many opportunities for collaboration with anti-racist public health and critical race theories (Meghji and Niang, 2022). These calls are being responded to at all levels of society. In 2018, for instance, there was a 65% increase in the number of English articles that were published on racism in healthcare at the global level (Hamed et al., 2022). In the same year, the European Union (EU) High Level Group on Non-discrimination, Equality, and Diversity7 adopted a set of non-binding guidelines on how to improve the collection and use of equality data, compiled practices implemented at national level related to the set of guidelines and developed a diagnostic tool/checklist with which to assess the availability and quality of equality data collected at national level8.\n\nThis project likewise aims to contribute to improving equality and equity in health, by promoting a race-conscious approach to health research and strengthening the utilisation and deployment of data and research on racialised minority groups. We do so by taking a three-pronged approach which highlights the need for a race-conscious approach while using data and research on racialised minority groups; builds expertise for their effective utilisation and deployment; and creates a knowledge network and community of practice for public health researchers working in Europe.\n\n\nResearch steps\n\nThe project begins with a literature review which critically analyses the way race, ethnicity, and related terminology euphemisms and proxies* are conceptualised, operationalised, and used in public health research in three countries in continental Europe. It then goes on to critically examine, using literature from other countries or other research fields on this issue, how research on racialised minority groups is conducted. The results will then be used to develop guidance on how to utilise and deploy data and research on racialised minority groups. Finally, as a follow-up to the review, our findings will be stored in a knowledge repository that is accessible to health researchers (see the project’s research steps in Table 1 below). The overarching goal is to contribute to addressing health disparities among racialised minority groups, across Europe.\n\n* See key definitions section.\n\n\n\n1. Race: Refers to socially and politically constructed differences among people based on characteristics such as skin colour, physical characteristics, accent or manner of speech, name, clothing, diet, beliefs and practices, leisure preferences, places of origin and so forth. Although the sciences have been (and still are) heavily involved in the production of race and racial categorisations, there is no scientifically supported biological basis for racial categorisation, however, societies construct races as real, and this has different and unequal implications for economic, political, social, and cultural life (CIHI, 2022).\n\n2. Ethnicity: A multi-dimensional social construct based on cultural distinctiveness and shared group cultural identity and characteristics. Examples of ethnic characteristics are, amongst others, language, and cultural norms, which are sometimes linked to religion and nationality. Different from, but often used as a euphemism/proxy for race (Song, 2018; CIHI, 2022).\n\n3. Racial and ethnic euphemisms and proxies: A word or an expression which is used to denote and describe racialised minority groups, in cases when ‘race’ and ‘ethnicity’9 are considered inappropriate or inadequate, or in order to depoliticise and deracialise these concepts. This includes the use of terms which are related to concepts like migration, religion, language, origin, postcode (= place-based discrimination), citizenship, nationality, and culture.\n\n4. Racialisation: A complex, contradictory and arbitrary process through which groups and individuals are assigned a particular ‘race’ and on that basis subjected to differential and/or unequal treatment. Put simply, racialisation is “the process of manufacturing and utilising the notion of race in any capacity” (Dalal, 2002, p. 27). While white people are also racialised, this process is often rendered invisible or normative to those designated as white. As a result, white people may not see themselves as part of a race but still maintain the authority to name and racialise ‘others’. The individual and group identities of members of racialised groups shape both their relationships and interactions between each other, as well as with members of the out-group, and it influences social practice, and engagements with time, space, social structures and institutional systems. Racialisation thus has impacts on every aspect of life10.\n\n5. Racialised (minority) groups: Refers to groups that are subject to racialisation and are also minoritised/marginalised/underrepresented based on various characteristics such as skin colour, migration status, citizenship, religion, culture, language or geographic location11. To emphasise the process of racialisation, some authors use the term “racially minoritised people” (Milner and Jumbe, 2020) or “marginalised racial groups” (Barber, 2020).\n\n6. Racism: Organised systems within societies that cause avoidable and unfair inequalities in power, resources, capacities, and opportunities for racialised minority groups (Paradies, Ben, Denson et al., 2015). Racism can manifest through beliefs, stereotypes, prejudices, or discrimination. This encompasses everything from open threats and insults to phenomena deeply embedded in social systems and structures. Racism can occur at multiple levels, including internalised (the incorporation of racist attitudes, beliefs or ideologies into one’s worldview), interpersonal (interactions between individuals) and systemic (for example, the racist control of and access to labour, material and symbolic resources within a society) (Paradies, Ben, Denson et al., 2015: 2).\n\n7. Inequality: Refers to the unequal and/or unjust distribution of resources and opportunities among members of a given society.\n\n8. Inequity: Refers to the avoidable or remediable systemic disparities which occur in groups that are defined socially, economically, demographically, or geographically within a given society, regardless of whether there is equitable and/or just distribution of resources and opportunities among members of the society.\n\n9. Health disparities: Refers to a condition in which disadvantaged social groups such as the poor, racial/ethnic minority groups, women and other groups who have persistently experienced social disadvantage or discrimination systematically experience worse health or greater health risks than more advantaged social groups (Braveman et al., 2004; Braveman, 2007). When systemic barriers to good health are avoidable yet still remain, they are often referred to as ‘health inequities’.12\n\n10. Racial health disparities: Refers to health disparities that occur amongst racialised minority groups, as compared to the racial majority. It describes the increased presence and severity of certain diseases, poorer health outcomes, and greater difficulty in obtaining healthcare services.\n\n11. Intersectionality: The complex, cumulative way in which the effects of multiple forms of discrimination (such as racism, sexism, classism, xenophobia, and religious discrimination) combine, overlap, or intersect especially in the experiences of marginalized individuals or groups (Crenshaw, 1989).\n\n12. Race-based approach: Based on a biologically essentialist conception of race according to which all members of a racial category are believed to have defined shared physical or genetic characteristics, or a specific biological essence. This assumption allows the members of the group to be seen, both by themselves and by others, not as individuals with personal traits, but rather as prototypes of the collective with identical traits and characteristics, which leads to stereotyping, essentialization, fixity, homogenisation.\n\n13. Race-conscious approach: Focuses on racial discrimination and racism as central issues, in contrast to the race-based approach. As a reference point, Cerdeña, Plaisime and Tsai (2020) introduce “race-conscious medicine as an alternative approach that emphasises racism, rather than race, as a key determinant of illness and health, encouraging providers to focus only on the most relevant data to mitigate health inequities”.\n\n14. Race-conscious research and data: Following the previous definition, we would like to define ‘race-conscious research and data’ as an area of research that aims to address racial inequities in health, combat racism in healthcare and promote racial justice in health.\n\n15. Racial justice in health: Using the race-conscious approach to tackle racial health disparities and injustices and improve health among racialised minority groups in an intersectional way, with the aim of advancing equality and equity in health and ultimately, achieving social and racial justice13.\n\n16. Decolonial approaches to Global and Public Health: This field is not homogeneous but decolonising global and public health implies re-politicising and re-historicising health at all levels: epistemic and theoretical (production and distribution of knowledge), ontological, educational, organisational, healthcare-related, etc. (Bhakuni and Abimbola, 2021; Affun-Adegbulu and Adegbulu, 2020; Büyüm et al., 2020; Naidu, 2021).\n\n17. Data: Any type of information that is collected to be examined, considered, and used for research as well as to support decision-making. This includes quantitative information, such as measurements and calculations, and qualitative information, such as lived experiences and blog posts14.\n\n18. Research: “A detailed study of a subject, especially in order to discover (new) information or reach a (new) understanding15”, which involves “weaving together different strands of information, thought, and data16”, amongst others, to contextualise both the research and its findings. As social scientists and public health researchers, we see research as an activity that leads directly to practical applications and engagement/advocacy in the field of health.\n\n19. Othering: Processes of distancing and differentiation in which certain individuals, groups or practices are defined and labelled as ‘Others’, thus not corresponding to the norms of a social group. It refers to a binary conception of ‘us/them’, usually involving stereotypes of ‘them’ and hierarchical power relations, including practices of inclusion and exclusion. See for instance Udah (2019).\n\n20. Xenophobia: In a restricted sense, xenophobia refers to an “an attitudinal orientation of hostility against non-natives in a given population.” An expanded definition describes “attitudes, prejudices and behaviour that reject, exclude and often vilify persons, based on the perception that they are outsiders or foreigners to the community, society or national identity.” “The International Labour Organization (ILO) distinguishes racism from xenophobia, defining racism as a construct that “assigns a certain race and/or ethnic group to a position of power over others on the basis of physical and cultural attributes, as well as economic wealth, involving hierarchical relations where the “superior” race exercises domination and control over others”. Thus, xenophobia leads to civic exclusion of others based on their cultural or national identity as foreign from that of the host country, whereas racism concerns phenotypic differences in appearance and skin colour, related to power and privilege.” (Suleman et al., 2018: 2).\n\nThe objectives of the literature review are to:\n\n1. Examine how data on racialised minority groups is used (= conceived, collected, analysed, interpreted, reported) in health research\n\n2. Examine the ways in which this data is used to address racial health inequities\n\n3. Critically analyse the way race, ethnicity and related euphemisms and proxies are conceptualised, operationalised, and used in health research\n\n4. Develop guidance on how to appropriately utilise and deploy data on racialised minority groups, how to undertake race-conscious research and how to effectively use the results to address racial health disparities\n\nThematic scope: The review will take race and ethnicity in health research as a focus of analysis. It will expand to include related euphemisms and proxies such as migration, citizenship, nationality, religion, culture, language, postcodes, etc. In the analysis, we will consider other characteristics which influence and shape health inequities, such as gender, sexuality, disability, age, socio-economic condition, and geographic location. This will ensure that we integrate relevant intersecting determinants of health inequalities and inequities in our analysis of health disparities among racialised groups (Smedley et al., 2003). It will also allow us to draw attention to the complexities of vulnerabilisation, its different forms and its various causes as well as the interplay between them.\n\nGeographical context: The review will focus on research on Belgium, France and the Netherlands (and their overseas territories), three countries in continental Europe which have been selected for their geographical proximity, as well as their linguistic and cultural similarities and differences. In addition to this, given the personal and professional background of the review team members, the team has an in-depth knowledge of these three countries. Three countries were chosen for the study, for practical reasons, as resources constraints mean that we do not currently have the ability to conduct a Europe-wide study. We however hope to be able to both deepen this work and extend it to other European countries in a second phase.\n\nTimespan: The review will cover the period between 2018 and 2022 which will allow us to take into account data and research on racialised minority groups from before and during the COVID-19 pandemic (two years before, two years during). This is because, as argued above, the COVID-19 pandemic has led to an increased focus and attention on the issue of health disparities among racialised groups.\n\n\nMethods\n\nA systematic search and review approach will be taken to this review, as this combines strengths of a critical review with those of an exhaustive search process. This approach is especially suited for our review because by facilitating the comprehensive exploration of what is known about the topic, it supports the synthesis of best evidence and the generation of recommendations for practice (Grant and Booth, 2009).\n\nThe questions which will guide the review are as follows:\n\n1. What terminology is used for health research on racialised minority groups, and how are they operationalised?\n\n2. What type of data on race, ethnicity and related euphemisms and proxies is used, and why?\n\n3. How is research on racialised minority groups carried out?\n\n4. What evidence is available on the use of racialised minority groups data to promote racial equity in health?\n\n5. What are best practices on research and the use of data on racialised groups, and why?\n\nDatabases\n\nThe databases listed below will be used in this review. They were chosen for their large collections of both peer-reviewed and grey literature, which will ensure that we can capture the variety of published information on the subject matter.\n\n• PubMed: https://pubmed.ncbi.nlm.nih.gov/\n\n• Scopus: https://www.scopus.com/home.uri\n\n• Web of Science: www.webofscience.com\n\n• Cochrane Library: https://www.cochranelibrary.com/central/about-central\n\nSearch strategy\n\nThe search strategy was developed by creating a list of search terms that are relevant to the research questions and combining them as follows:\n\n(race OR racial* OR ethnic* OR cultur* OR language OR linguistic OR religio* OR migra* OR immigrant OR foreign* OR “third country national” OR allochthonous OR residen* OR undocumented OR illegal OR irregular OR refugee OR asylum OR nationality OR citizen OR “non-citizen” OR minorit* OR gyps* OR roma OR traveller OR ancestry OR “family background” OR heritage OR origin OR neighborhood OR neigbourhood OR “postal code” OR postcode OR marginalised OR marginalized OR vulnerable OR precarious OR communit* OR “population group”)\n\nAND\n\n(“health”)\n\nAND\n\n(Belgium OR “Netherlands” OR France)\n\nSearch strings will be created from these terms and adapted to the requirements of each database. Given that the search strategy and this protocol was developed in the very early stages of the review process, we see the above as a non-exhaustive list. In addition to conducting explorative searches to refine the strategy, therefore, we will also take an inductive approach, in which we allow concepts that emerge from the review to further inform the search strategy.\n\nThe results of the search strategy will be refined by language and date to include only publications that were written in English, French, and Dutch and which were published from January 1st, 2018 until July 8th, 2022.\n\nThe database searches will be supplemented by reference mining of the selected publications to ensure that relevant documents or articles that might have been missed, are identified and included. In addition, purposive manual searching of websites of key actors and organisations will be carried out to identify relevant grey literature we might have missed in the database searches.\n\nThe details of the search process, as well as the results of the searches conducted will be documented as meticulously as possible, in order to maximise recall and ensure that the process can be reported and reproduced accurately.\n\nSelection process\n\nThe citations produced by the search strategy will be screened for relevance and for inclusion in the study. To be eligible, the article or report must have both health AND race, ethnicity, or related concepts as its subject matter.\n\nThe research will be done by a core team of three researchers, who will be supported periodically by three master students with relevant experience and knowledge.\n\nIn the first instance, two researchers, in consultation with the third researcher, will search the selected databases for relevant citations, using the developed search string. The results of this search procedure will then be uploaded into Covidence, a systematic review management software which automates some of the steps of the review process.\n\nNext, Covidence will be used to identify and automatically remove duplicates, and this process will be verified by one researcher. Given that Covidence is limited in its ability to recognise duplicates, the selected references will be exported to Zotero by one researcher, who will then do an additional duplicate check.\n\nAfter this, the title and abstract screening of the documents in Covidence will be done by three students, who are supported and supervised by one researcher. From this stage onwards, weekly discussions will be held to streamline and systematise the selection process as much as possible. Following this initial selection, the full texts of the selected documents will be obtained and checked meticulously against the review’s inclusion and exclusion criteria. This full text screening will be done in Covidence by the three researchers and three students, with every document being checked at least twice to minimise bias and error. The process will be set and carried out in such a way as to ensure that each full text is screened by at least one of the three researchers from the core team. Conflicts will be discussed and resolved as a group, during the weekly meetings, and potential deviations from the review protocol will be documented and reported.\n\nThe types of documents to be included are peer-reviewed primary studies and reviews; preprints; commentaries; editorials, published in a scientific journal and of which a full-text version is available. In addition to this, we will also include published grey literature where the full text is available online.\n\nData extraction\n\nOnce the screening process is finished, the data on the study characteristics and other relevant variables will be extracted by the three researchers and one student from the final collection of retained documents, in a systematic way. This will be done in Covidence and the extracted data will be stored in Excel. In order to minimise error, the team will use a standardised extraction sheet that has been designed collaboratively by the three researchers and the three students, with some input from the extended project group (Meudec et al., 2022c).\n\nApproximately 30 variables will be extracted from the publications that are included in the review. This will include information on the:\n\n1. Study characteristics\n\na. Publication (title, year of publication, author(s) and their affiliation, journal, type of document)\n\n2. Variables of interest\n\na. Concepts that are used for health research on racialised minority groups and how they are operationalised\n\nb. Research methodology and methods used\n\nc. The data used, and how this is collected, and applied\n\nA full overview of the variables to be extracted can be found in the Data Extraction sheet (see Data availability).\n\nCitations generated from the search strategy will be reviewed using the Covidence software which will be used to identify publications for inclusion in the review. These will then be uploaded and stored in a Zotero library. The data extraction of selected publications will be done using Covidence.\n\nFirst, a descriptive analysis will be done to provide an overview of the data that is extracted from the included publications, using quantitative and qualitative methods.\n\nFollowing this, a critical analysis will be undertaken to identify the:\n\n1. Concepts that are used for health research on racialised minority groups\n\n2. Types of data on race, ethnicity and related euphemisms and proxies that are used, and arguments put forward to justify their use\n\n3. Methodology and methods that are used for research on/with racialised minority groups, with a particular focus on recommendations, research gaps, innovative approaches, and methods\n\nThe results of the critical analysis will then be used to inform the development of proposed guidelines for best practices in the use and deployment of data and research in racialised minority groups, with the aim of addressing health disparities.\n\nThe first and final drafts of the review protocol are stored on a community platform on Zenodo (Meudec et al., 2022a, 2022b). This protocol has been completed in line with the PRISMA-P reporting guidelines (Meudec et al., 2022d).\n\nThe finalised review protocol will be registered and peer-reviewed on the Open Research Platform F1000Research.\n\nCore team: Marie Meudec, Clara Affun-Adegbulu, Theo Cosaert\n\nReview team: Marie Meudec, Clara Affun-Adegbulu, Theo Cosaert, Eskedar Getie Mekonnen, Lidvine Ngonseu Harpi, Enata Mushimiyimana\n\nExtended project group: Soledad Colombe, Charles Ddungu, Sarah Demart, Cleo Maerivoet, Lazare Manirankunda, Joris Michielsen, Claudia Nieto, Christiana Nöstlinger, Jef Vanhamel, Ella Van Landeghem, Tine Verdonck\n\nFollowing ITM guidelines on authorship (Institute of Tropical Medicine, 2017), the core team has carried out the following tasks: 1) conception of the work; 2) design of the study; 3) execution of the study; 4) data analysis; 5) data interpretation; 6) writing of the review. The review team will participate in tasks 2, 3, 4, 5, 6. The extended group has been, and will be involved in steps 2, 5, and 6.\n\nMarie Meudec is a white researcher who has no personal experience of racism. From personal and professional experience - a) research on health inequalities and discrimination based on gender, sexuality, migratory status, different forms of spatial marginalisation, police racism, etc, b) providing expert court testimony on police racial profiling in Canada and asylum cases in the UK; and c) organising and facilitating anti-racism workshops on whiteness and white supremacy in Canada, Marie has developed a sensitivity to issues of racism and racial justice in the countries where she has lived and worked (France, Canada, UK, Haiti, Belgium).\n\nClara Affun-Adegbulu is a Black woman with a lived and personal experience of anti-Black racism and misogynoir, amongst others. During her nursing studies and throughout her career as a district and psychiatric nurse in Belgium, France and the UK, Clara also gained direct professional experience of anti-Black racism, race- and ethnicity-based discrimination more generally, as well as the intersections of the two with other forms of discrimination. Her understanding of, and sensitivity to these issues has further developed, as a result of her work as a public health researcher studying health equity, including among migrants and displaced populations from fragile and conflict-affected settings.\n\nTheo Cosaert is a white male junior researcher with no personal experiences of racism. He grew up and was trained in a West-European context (Belgium and the UK) and his academic practice is shaped by these schools of thought. He was trained in sociology and in medical anthropology, and all of his previous work focused on experiences of and barriers to the healthcare system. He tries to centralise perspectives of minoritised groups in his research by listening and by creating space where and when he can do so.\n\nThe list of references used in the review will be stored on Zotero, while the project documents will be stored on Zenodo, as well as the Data Science Hub/ITM website. Both the review references and project documents will be open access and freely accessible to the public (Meudec et al., 2022a, 2022b, 2022c, 2022d).\n\nThe finalised review protocol will be shared online on F1000research website. The different links related to the RECoRD project can be seen here https://linktr.ee/record_itm. The review results have been and will be shared and discussed during conferences (AfroEuropeans Conference Sept 2022; European Public Health Conference Nov 2022) and seminars at the Institute of Tropical Medicine (Belgium). The review results will also be submitted to an open access scientific journal after finalisation.\n\nThe primary outcome will be a list of concepts (related to race, ethnicity and their related euphemisms and proxies) that are used in health research on racialised minority groups. This list will also include – if provided – the definitions and justifications for such a use, and the ways these concepts are operationalised in research.\n\nA secondary outcome will focus on the use of such concepts (context, research questions, research methodologies, results).\n\nA third outcome will examine the recommendations, research gaps, and innovative approaches.\n\nA fourth outcome will consist in the development of proposed guidelines for best practices in the use and deployment of data and research in racialised minority groups, with the aim of addressing health disparities.\n\nThe results of this review will be developed in a manuscript submitted to a scientific journal for publication.\n\nAs this is a critical qualitative review which does not focus on the outcomes of the individual studies, we do not perform an assessment of the risk of bias.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nZenodo: Review protocol - First draft - Review of health research and data on racialised minorities: Implications for addressing racism and and racial disparities in public health practice and policies in Europe. https://doi.org/10.5281/zenodo.7155891. (Meudec et al., 2022a).\n\nThis project contains the following extended data:\n\n• First draft of the review protocol, October 7, 2022.\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nZenodo: Review protocol - Final version - Review of health research and data on racialised minorities: Implications for addressing racism and and racial disparities in public health practice and policies in Europe. https://doi.org/10.5281/zenodo.7298547. (Meudec et al., 2022b).\n\nThis project contains the following extended data:\n\n• RECoRD Review protocol_final version.pdf. (Final version of the review protocol, November 7, 2022).\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nZenodo: Data Extraction Sheet for the Review - 2. https://doi.org/10.5281/zenodo.7473314. (Meudec et al., 2022c).\n\nThis project contains the following extended data:\n\n• Data extraction sheet.pdf (Data extraction sheet using approximately 30 variables - study characteristics and various variables of interest).\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nZenodo: PRISMA-P checklist for ‘Review of health research and data on racialised groups: Implications for addressing racism and racial disparities in public health practice and policies in Europe - Study protocol’. https://doi.org/10.5281/zenodo.7458371. (Meudecet al., 2022d).\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\nAffun-Adegbulu C, Adegbulu O: Decolonising Global (Public) Health: from Western universalism to Global pluriversalities. BMJ Glob. Health. 2020; 5(8): e002947. 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Dis. 1996; 6(1–2): 21–29.\n\nLinos N, Bassett MT, Salemi A, et al.: Opportunities to tackle structural racism and ethnicity-based discrimination in recovering and rebuilding from the COVID-19 pandemic. Nat. Commun. 2022; 13: 3277. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMeghji A, Niang SM: Between Post-Racial Ideology and Provincial Universalisms: Critical Race Theory, Decolonial Thought and COVID-19 in Britain. Sociology. 2022; 56(1): 131–147. Publisher Full Text\n\nMeudec M, Affun-Adegbulu C, Cosaert T: Review protocol - First draft - Review of health research and data on racialised minorities: Implications for addressing racism and and racial disparities in public health practice and policies in Europe (first draft). Dataset. Zenodo. 2022a. Publisher Full Text\n\nMeudec M, Affun-Adegbulu C, Cosaert T, et al.: Review protocol - Final version - Review of health research and data on racialised minorities: Implications for addressing racism and and racial disparities in public health practice and policies in Europe. Dataset. Zenodo. 2022b. Publisher Full Text\n\nMeudec M, Affun-Adegbulu C, Cosaert T, et al.: Data Extraction Sheet for the Review - 2. [Data set]. Zenodo. 2022c. Publisher Full Text\n\nMeudec M, Affun-Adegbulu C, Cosaert T: PRISMA-P-checklist for RECoRD_final version (final). Dataset. Zenodo. 2022d. Publisher Full Text\n\nMiconi D, Li Z, Frounfelker R, et al.: Ethno-cultural disparities in mental health during the COVID-19 pandemic: A cross-sectional study on the impact of exposure to the virus and COVID-19-related discrimination and stigma on mental health across ethno-cultural groups in Quebec (Canada). BJPsych Open. 2021; 7(1): E14. 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Office for National Statistics. 2020.Reference Source\n\nWilliamson EJ, Walker AJ, Bhaskaran K, et al.: Factors associated with COVID-19-related death using OpenSAFELY. Nature. 2020; 584(7821): 430–436. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYaya S, Yeboah H, Charles CH, et al.: Ethnic and racial disparities in COVID-19-related deaths: counting the trees, hiding the forest. BMJ Glob. Health. 2020; 5: e002913. Publisher Full Text\n\nZuberi T: Thicker than Blood, How Racial Statistics Lie. University of Minnesota Press;2003.\n\n\nFootnotes\n\n1 All terms followed by an asterisk (*) are defined in the ‘Key definitions’ section of this protocol.\n\n2 The authors follow the widely accepted notion that race has no biological basis. Regardless, race exists as a social reality and thus has real consequences. See also: key definitions.\n\n3 For international literature, see for instance Aldridge et al. (2020), Baqui et al. (2020), Linos et al. (2022), Miconi et al. (2021), Mukumbang et al. (2020), OECD (2020), Poteat et al. (2020), Van Dorn et al. (2020), Wadhera et al. (2020), Williamson et al. (2020), Yaya et al. (2020). For Belgium, see Vanthomme et al. (2021), for France, see Carillon et al. (2020); and for the Netherlands, see Coyer et al. (2021).\n\n4 See https://www.euractiv.com/section/non-discrimination/news/unbalanced-hate-lack-of-data-abets-geography-of-discrimination-in-europe/ (accessed August 26th, 2022).\n\n5 For an illustration, see this scoping review on empirical studies published in Scandinavian Journal of Public Health (Elstad et al., 2022) or see the epistemological discussion made by Lisa Bowleg on the uses of qualitative methodologies in Critical Health Equity Research (Bowleg, 2017).\n\n6 See Bhambra (2017a, 2017b). “‘Methodological whiteness’, I suggest, is a way of reflecting on the world that fails to acknowledge the role played by race in the very structuring of that world, and of the ways in which knowledge is constructed and legitimated within it. It fails to recognise the dominance of ‘whiteness’ as anything other than the standard state of affairs and treats a limited perspective – that deriving from white experience – as a universal perspective. At the same time, it treats other perspectives as forms of identity politics explicable within its own universal (but parochial and lesser than its own supposedly universal) understandings.” (2017b).\n\n7 See https://ec.europa.eu/transparency/regexpert/index.cfm?do=groupDetail.groupDetail&groupID=3328\n\n8 See the Guidance note on the collection and use of equality data based on racial or ethnic origin, accessed online Aug. 26, 2022: https://ec.europa.eu/info/sites/default/files/guidance_note_on_the_collection_and_use_of_equality_data_based_on_racial_or_ethnic_origin.pdf\n\n9 It has to be noted here that the concept of ethnicity is itself sometimes used as a proxy to not talk about race (Song, 2017).\n\n10 Inspired by SOURCE: Alberta Civil Liberties Research Centre, “Racialization” (2018)/Calgary Anti-Racism Education, “CARED Glossary” (2020).\n\n11 See for instance a definition proposed by Souissi (2022) on the Canadian Encyclopedia. Access online, September 1st, 2022: https://www.thecanadianencyclopedia.ca/en/article/racialized-minorities\n\n12 What Is Health Inequity?, see https://www.vdh.virginia.gov/health-equity/unnatural-causes-is-inequality-making-us-sick/what-is-health-inequity/#:~:text=%E2%80%9CDifferences%20in%20health%20status%20among,living%20in%20various%20geographic%20localities.%E2%80%9D (site visited June 22, 2022).\n\n13 Inspired by Reference to the Praxis Project,: see health law as social justice, 2014.\n\n14 Inspired by https://dictionary.cambridge.org/dictionary/english/data\n\n15 See https://dictionary.cambridge.org/dictionary/english/research\n\n16 See https://blog.scienceopen.com/2016/05/why-context-is-important-for-research/" }	[ { "id": "164519", "date": "10 May 2023", "name": "Elie Azria", "expertise": [ "Reviewer Expertise Obstetrics & gynecology", "epidemiology", "health inequalities" ], "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 thank the editorial team for allowing me to review this very interesting project which I found very instructive. Research on racialized groups is a major issue in informing policies to reduce health inequalities.\nThe authors present the protocol for a systematic review of research on the health of racialized groups. The aim of this systematic review is not to assess the health of these groups through health indicators or to measure health inequalities that might exist with a reference group, but to produce a critical analysis of this research and the concepts it mobilises, particularly in the categorisation of social groups. Based on this critical analysis, the authors aim to promote a race-conscious approach to health research and to strengthen the use of health research data in Europe.\nThe authors start from the assumption, which is unfortunately poorly supported by arguments and references, that research on racialized groups in Europe is mostly insufficient and inadequate. This assertion should be further documented.\n\nWhile this is an extremely interesting approach, the authors argue that exposure variables other than those that can identify racialized groups are proxies or euphemisms. I find this problematic in that these variables can be used to good effect for specific purposes. For example, using ethno-racial variables to characterise a group when the research question concerns the study of health inequalities between migrants and native-born patients would be misguided. Place of birth is much more interesting here and is in no way a proxy. Without denying the use of proxies in many research studies, thinking that this is systematically the case when the exposure variables do not allow for the identification of a racialized group risks putting this analysis on the wrong track.\nFurthermore, the choice not to assess the risk of bias seems to me unfortunate in that reporting on the quality of research on this issue could add to the project, even if the study of outcomes is not the objective of this review.\nFinally, this protocol should be registered on the Prospero platform, which leads to the discussion of the relevance of another publication.\nI wish the authors of this interesting project great success.\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? Not applicable", "responses": [ { "c_id": "10680", "date": "07 Dec 2023", "name": "Marie Meudec", "role": "Author Response", "response": "APPROVED WITH RESERVATIONS I would like to thank the editorial team for allowing me to review this very interesting project which I found very instructive. Research on racialized groups is a major issue in informing policies to reduce health inequalities. The authors present the protocol for a systematic review of research on the health of racialized groups. The aim of this systematic review is not to assess the health of these groups through health indicators or to measure health inequalities that might exist with a reference group, but to produce a critical analysis of this research and the concepts it mobilises, particularly in the categorisation of social groups. Based on this critical analysis, the authors aim to promote a race-conscious approach to health research and to strengthen the use of health research data in Europe. Response: We thank the reviewer for their interest. The authors start from the assumption, which is unfortunately poorly supported by arguments and references, that research on racialized groups in Europe is mostly insufficient and inadequate. This assertion should be further documented. Response: These are indeed our hypotheses, but the scale of the problem needs to be demonstrated in our study. We wanted to highlight certain trends in the field of health research, and in particular the fact that the categories and variables used in a certain number of publications (out of a total of 700 articles) are not necessarily in line with the research objectives or with the interpretations made of the results. Although our research has some limitations (we study mostly published articles in scientific journals, and we know that some research is not published (yet)), our objective is indeed to prove our hypotheses. Based on the results of our review, we will be able to give a better idea of the research landscape on/with racially minoritised groups in these 3 countries. For better clarification, we have added this in a revised version of our review protocol: (Page numbers are those of the version with track changes) p.2: Yet, we start from the assumption that, in many countries across Europe, there is often inappropriate, inadequate, or insufficient use and deployment of data and research* on racially minoritised groups. The reasons for this assumption can be grouped into two main categories. One is the continuous emergence of biologically or genetically based race research which is often linked to scientific racism (Roberts, 2011a, 2011b; Saini, 2019). While this is an extremely interesting approach, the authors argue that exposure variables other than those that can identify racialized groups are proxies or euphemisms. I find this problematic in that these variables can be used to good effect for specific purposes. For example, using ethno-racial variables to characterise a group when the research question concerns the study of health inequalities between migrants and native-born patients would be misguided. Place of birth is much more interesting here and is in no way a proxy. Without denying the use of proxies in many research studies, thinking that this is systematically the case when the exposure variables do not allow for the identification of a racialized group risks putting this analysis on the wrong track. Response: We thank the reviewer for their comment and fully agree with their remarks. We agree that concepts are not inherently a proxy or a euphemism, that this is relative to the research question and that different variables can be useful for different purposes. We take this comment as an encouragement to explain our understanding of proxies and euphemisms in a more clear and nuanced way. We do this by rewriting Key definition 3: p5: Racial and ethnic euphemisms and proxies: A word or expression used inappropriately or inadequately to designate and describe racially minoritised groups. We understand concepts as racial and ethnic euphemisms and proxies when there is a clear mismatch between 1) the used concepts or variables and 2) the aim of the research or the interpretation of the results. This includes the use of terms which are related to concepts like migration, religion, language, origin, postcode (= place-based discrimination), citizenship, nationality, and culture. Note however that the concepts mentioned above are not inherently proxies or euphemisms for race and ethnicity , and can be of adequate use depending on the topic of research. Furthermore, the choice not to assess the risk of bias seems to me unfortunate in that reporting on the quality of research on this issue could add to the project, even if the study of outcomes is not the objective of this review. Response: We thank the reviewer for their comment. Because we do not plan to study the outcomes of the studies, we have decided not to make assessments for the risk of bias by study. We understand that this could have benefited the project. However, although we do not use a tool to systematically assess risk of bias, we believe that we largely account for the quality of the research in our critical analysis by examining the concepts and terms used, the types of data, and the methodologies employed in each study. We also added some information in the Risk of bias section. Finally, this protocol should be registered on the Prospero platform, which leads to the discussion of the relevance of another publication. Response: We thank the reviewer for their suggestion. On the website of the Prospero platform the following is stated: “from 1st October 2019, we will only accept reviews provided that data extraction has not yet started.” We have already taken significant steps in the data extraction, thus we are not eligible anymore to register on the Prospero platform at this stage of the research. I wish the authors of this interesting project great success. Response: Thank you very much! We will share our results with you when they are ready." } ] }, { "id": "172212", "date": "06 Jun 2023", "name": "Chinelo L. Njaka", "expertise": [ "Reviewer Expertise race", "racialisation", "racism(s)", "public health", "health inequalities/inequities", "human rights", "cross-national comparison" ], "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 Researchers, advocacy groups, and institutions have long advocated for the collection of disaggregated race data, emphasising its crucial role in promoting equality, combating discrimination, and informing evidence-based decision-making (UN OHCHR 2018). Within the European context, some nations, influenced by various socio-historical factors, have been reluctant to gather demographic data that would highlight such disparities and provide insights into the experiences of different racialised and ethnic groups. This hesitance has led to ‘race-neutral’ policies, which have limited the availability of comprehensive and nuanced data on racialised inequalities, hindering efforts to understand fully the multiple factors that contribute to disparities and design targeted policies and interventions to move toward parity.\n“Review of Health Research and Data on Racialised Groups: Implications for Addressing Racism and Racial Disparities in Public Health Practice and Policies in Europe” offers a timely and exciting study protocol that focuses on assessing the available health data and research in France, the Netherlands, and Belgium, where limited attention has been given to racism and racialised inequalities in research and policy in comparable ways. The aim of the protocol is to highlight the importance of recognising racialisation and racism in public health practice and policies, and to emphasise the challenges in fully capturing and understanding racialised health disparities without consistent and explicit ways of identifying racialised groups within Europe. By systematically examining existing research, this protocol aims to uncover key insights that can inform efforts to address racism and mitigate racialised disparities in healthcare.\nStudy Protocol Assessment The significance and strength of this study protocol, as part of a larger project, lies in its potential to inform and shape future public health interventions and policies that aim to address racialised inequalities and inequities through advocating for a ‘race-conscious’ approach to European public health research. By critically examining the usage of race, ethnicity, and related terms in health-related research and analysing the collection and utilisation of data on racialised minority groups, the protocol provides valuable insights that can contribute to the future development of evidence-based guidance on the effective use of data and research with racialised groups, and promoting health equity across all racialised groups in Europe.\nThe rationale for the protocol is adequately described, highlighting the need to address racism and racial disparities explicitly in public health practice and policies in Europe. The protocol acknowledges the significant health inequities experienced by racialised groups and aims to review existing health research and data to gain a comprehensive understanding of these disparities. The protocol also allows for the examination of the ways that researchers are conceptualising and operationalising racialised terminologies in order to identify disparities along racialised divisions in the first instance. The objectives of the study protocol are well-defined and aligned with the research rationale, focusing on conducting a systematic review of existing research and assessing the quality and accessibility of data on racialised groups. These objectives are relevant and essential for addressing the research scope and informing evidence-based interventions and policies.\nThe study design appears appropriate for addressing the research objectives of reviewing health research and data on racialised groups in Europe. As outlined in the study protocol, a systematic review approach will be used to synthesise and analyse the available research and data using specific search parameters. This design allows for a comprehensive assessment of the determinants and consequences of racial disparities in public health outcomes. A particular strength of note is that, though this article is written in English, the scope of the protocol will analyse research additionally in Dutch and French, which reflects the languages used in the nations studied.\nThe study protocol provides sufficient details of the methods employed in conducting the systematic review. The inclusion and exclusion criteria for selecting relevant studies are clearly described, which helps ensure the broad reproducibility of the review process. Additionally, the study protocol outlines the steps for data extraction, synthesis, and analysis, contributing to the replicability of the study. Due to the nature of the methods used, however, exact reproducibility to achieve the precise research and data identified is essentially impossible, due to the continuous addition of published research, search algorithms, and other factors outside of researchers’ control. This in no way reflects a deficit in the methods of the protocol.\nAreas for Improvement and Recommendations Whilst the study protocol displays the commendable strengths outlined above, several areas could be enhanced to improve its effectiveness and impact.\nThe main critique for the study protocol is the omission of bias consideration for the purposes of this research. It is imperative to acknowledge and address the biases that may arise during the research process. Providing statements of positionality seems to acknowledge this point, which is why it is surprising that there is no further elaboration on potential biases within the study protocol. Although the study is a critical review, the process still generates data and is critically assessed, so bias must be explicitly considered.\nFurther to this point, there are some issues of potential bias present in the protocol that should be addressed. The protocol and broader research need to address the implicit use of Whiteness as the default and move away from binary categorisations of racial(ised) 'majority' and 'minority'. An intersectional lens should be applied to acknowledge the complexities of race and other intersecting social identities that affect the specific disparities seen among particular racialised groups, rather than amalgamating all racialised minorities implicitly into one disparate group. This approach will help highlight the diverse experiences and perspectives among racialised groups and avoid essentialisation or oversimplification. Additionally, ‘disparity’ is often used in the protocol to imply 'worse', which is not always the case. Disparity only refers to the difference or inequality between groups, which means that groups racialised as White are also part of the 'disparity equation'.\nThe phrasing of data and research ‘on’ racialised groups can imply objectification, detachment, or othering of the communities of focus. Consider revising this language used throughout the protocol when discussing racialised and other minoritised or marginalised groups. The use of ‘with’ - also used in the protocol - better conveys the inclusivity advocated for throughout the protocol and wider research, and acknowledges the collaboration and partnership between researchers and the communities of focus.\nWith acknowledgement that only the positionalities of the authors are explicitly described, the claim of a ‘racially diverse’ team may need to be re-evaluated to ensure that it accurately reflects meaningful diversity and avoids tokenism. If the positionality of the authors is reflective of the entire team, then what has been demonstrated is not racialised 'diversity'. Perhaps expand on what is meant by ‘racially diverse’ to acknowledge the range of racialised and ethnic backgrounds represented in the research team, which would also strengthen the robustness of the methods that are informed by the positionalities of all of the team members involved.\nThe research would benefit from a clearer distinction between the definitions of ‘race’ and ‘ethnicity’. As written, it is unclear how some of the characteristics used to define race are meaningfully distinct from the ‘cultural’ aspects used in the definition for ethnicity. The authors may also need to evaluate critically whether the non-phenotypic characteristics offered, such as clothing and speech, should be considered as aspects of race, as this can perpetuate reification and stereotypes of racialised groups (as warned against in CIHI 2022, cited in the protocol). If they do wish to retain these non-phenotypic characteristics as components of race their operational definition, the authors need to strengthen their argument by providing explicit rationale for the purposes of this protocol.\nThe definitions offered for ‘inequality’ and ‘inequity’ in the protocol should be clearly referenced to establish the basis for these particular conceptualisations in this research and context. Depending on the field, area, or sector, these words have varying operational definitions, so the definitions offered are not necessarily universally accepted. Moreover, the definition of ‘inequity’ reads confusingly, and uses ‘equitable’ - a term not defined in the protocol - to explain it. The definitions could be revised to offer more straightforward explanations of the concepts; possibly by alternatively providing definitions in positive terms (i.e., ‘equality’ and ‘equity’) rather than (only) in negation.\nThe protocol would also benefit from clarification and/or additional citations when referencing the definition for ‘xenophobia’. The protocol is mindful against conflation, however the definition given for xenophobia appears to conflate race and ethnicity. The use of terms such as ‘native’ and ‘host-country’ have been used uncritically, as though those who are racialised as minorities are necessarily ‘non-native’ and those who are not are necessarily ‘native’ and ‘hosts’. These terms can be problematised as reinforcing stereotypes or assumptions about individuals based on their racialised or ethnic backgrounds - as not all Europeans are part of a racialised majority, not all who are racialised as minorities are migrants, and especially with free movement within the European Union, not all who are racialised as part of a majority are from the location where they are living.\nApproval Status Based on the above assessment of the “Review of Health Research and Data on Racialised Groups: Implications for Addressing Racism and Racial Disparities in Public Health Practice and Policies in Europe” study protocol, the approval status given is: 'approved with reservations'.\nWhilst the study protocol demonstrates several strengths and merits, there are areas that require improvement or clarification to enhance its effectiveness and impact. The strengths of the study protocol, including the clear rationale and objectives and appropriate study design, contribute to its overall value and support the 'approval with reservations' status. However, certain areas need attention to address reservations and ensure the quality and relevance of the protocol for this part of the research, as well as the wider research project. Recommendations have been provided regarding the need to consider and address potential biases and refine some of the language and key definitions used in the protocol. By implementing these recommendations, the study protocol can strengthen its potential for making a meaningful contribution to addressing racism and racialised disparities in public health practice and policies across Europe.\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": [ { "c_id": "10681", "date": "07 Dec 2023", "name": "Marie Meudec", "role": "Author Response", "response": "APPROVED WITH RESERVATIONS Introduction Researchers, advocacy groups, and institutions have long advocated for the collection of disaggregated race data, emphasising its crucial role in promoting equality, combating discrimination, and informing evidence-based decision-making (UN OHCHR 2018). Within the European context, some nations, influenced by various socio-historical factors, have been reluctant to gather demographic data that would highlight such disparities and provide insights into the experiences of different racialised and ethnic groups. This hesitance has led to ‘race-neutral’ policies, which have limited the availability of comprehensive and nuanced data on racialised inequalities, hindering efforts to understand fully the multiple factors that contribute to disparities and design targeted policies and interventions to move toward parity. “Review of Health Research and Data on Racialised Groups: Implications for Addressing Racism and Racial Disparities in Public Health Practice and Policies in Europe” offers a timely and exciting study protocol that focuses on assessing the available health data and research in France, the Netherlands, and Belgium, where limited attention has been given to racism and racialised inequalities in research and policy in comparable ways. The aim of the protocol is to highlight the importance of recognising racialisation and racism in public health practice and policies, and to emphasise the challenges in fully capturing and understanding racialised health disparities without consistent and explicit ways of identifying racialised groups within Europe. By systematically examining existing research, this protocol aims to uncover key insights that can inform efforts to address racism and mitigate racialised disparities in healthcare. Response: Summary by reviewer -- Study Protocol Assessment The significance and strength of this study protocol, as part of a larger project, lies in its potential to inform and shape future public health interventions and policies that aim to address racialised inequalities and inequities through advocating for a ‘race-conscious’ approach to European public health research. By critically examining the usage of race, ethnicity, and related terms in health-related research and analysing the collection and utilisation of data on racialised minority groups, the protocol provides valuable insights that can contribute to the future development of evidence-based guidance on the effective use of data and research with racialised groups, and promoting health equity across all racialised groups in Europe. The rationale for the protocol is adequately described, highlighting the need to address racism and racial disparities explicitly in public health practice and policies in Europe. The protocol acknowledges the significant health inequities experienced by racialised groups and aims to review existing health research and data to gain a comprehensive understanding of these disparities. The protocol also allows for the examination of the ways that researchers are conceptualising and operationalising racialised terminologies in order to identify disparities along racialised divisions in the first instance. The objectives of the study protocol are well-defined and aligned with the research rationale, focusing on conducting a systematic review of existing research and assessing the quality and accessibility of data on racialised groups. These objectives are relevant and essential for addressing the research scope and informing evidence-based interventions and policies. The study design appears appropriate for addressing the research objectives of reviewing health research and data on racialised groups in Europe. As outlined in the study protocol, a systematic review approach will be used to synthesise and analyse the available research and data using specific search parameters. This design allows for a comprehensive assessment of the determinants and consequences of racial disparities in public health outcomes. A particular strength of note is that, though this article is written in English, the scope of the protocol will analyse research additionally in Dutch and French, which reflects the languages used in the nations studied. The study protocol provides sufficient details of the methods employed in conducting the systematic review. The inclusion and exclusion criteria for selecting relevant studies are clearly described, which helps ensure the broad reproducibility of the review process. Additionally, the study protocol outlines the steps for data extraction, synthesis, and analysis, contributing to the replicability of the study. Due to the nature of the methods used, however, exact reproducibility to achieve the precise research and data identified is essentially impossible, due to the continuous addition of published research, search algorithms, and other factors outside of researchers’ control. This in no way reflects a deficit in the methods of the protocol. Response: We thank the reviewer for their interest and positive remarks. -- Areas for Improvement and Recommendations Whilst the study protocol displays the commendable strengths outlined above, several areas could be enhanced to improve its effectiveness and impact. The main critique for the study protocol is the omission of bias consideration for the purposes of this research. It is imperative to acknowledge and address the biases that may arise during the research process. Providing statements of positionality seems to acknowledge this point, which is why it is surprising that there is no further elaboration on potential biases within the study protocol. Although the study is a critical review, the process still generates data and is critically assessed, so bias must be explicitly considered. Response: We thank the reviewer for their comment. We acknowledge the importance of a thorough reflection on potential biases that may arise during the research. We added the following paragraph in the ‘Risk of Bias’-section : p.15: In addition to asserting our respective positionalities, we also identify several biases and limitations in our work. Firstly, our core team is small and represents only a margin of the diverse intersections of social identities that are present in society. Specifically, the core team is mostly trained in North American and European higher education, which implies that our own frames of reference are primarily Western. The categories and concepts we employ are therefore partial and limited, and inevitably bias our questions, methods and the interpretation and analysis of data both consciously and unconsciously. We are trying to mitigate this bias continually, for example by drawing from the field of Critical Race Theory, by gathering feedback from a larger and more diverse team of researchers, and by holding meetings with a range of stakeholders during future stages of the research (analysis, writing, and guideline development). Second, this research project focuses on ethnic and racial disparities in health, and thus centralises/emphasises race and racism. This may be a bias in that, by focusing on racial disparities, we temporarily sideline other criteria present within intersecting systems of oppression. We see this research as a first step in demonstrating the lack of a racial lens in health research, and we know that future research will need to take an intersectional lens as its starting point. A further bias may arise from the fact that we only have access to published results, and we do not have access to all the internal discussions or specific issues related to the use of specific terms or concepts over other options. As this analysis is something of a retrospective study, our analysis is based solely on the information that the authors decided to incorporate in their published manuscripts. This constitutes a bias in the sense that we may risk attributing certain intentions to the authors even though we cannot confirm this in this review. We regret the fact that, in general, authors of scientific articles in this field are not more explicit in justifying their use of a particular terminology. Another bias could stem from our personal and professional involvement with systemic racism in health. Given our respective positionalities and lived experiences, and given that we do not ultimately aim to achieve objectivity or neutrality in this research, we would like to acknowledge that our judgment in analysing research papers can sometimes be harsh, especially after analysing several documents containing racial/ethnic proxies and euphemisms in the course of a single day. We try to mitigate this by holding weekly meetings with the core team, during which we share our emotions and feelings and discuss elements that emerge in the course of the research. Finally, this research project focuses on systemic racism in a European context. As such, health disparities are conceptualised in such a way that the white racial majority is seen as the benchmark of good health from which racially minoritised groups diverge. While we recognise that this is a simplified and binary way of analysing disparities, we also want to acknowledge that in doing so we are using whiteness as the default. We are aware of the need to decenter whiteness in research, and we urge the reader to be aware of this bias. Here are a few suggestions of intellectual traditions centering the voices of racialised groups that you can get inspiration from: Black Feminist Thought, Black Intellectual Tradition, Critical Race Theory, Indigenous methodologies, etc. -- Further to this point, there are some issues of potential bias present in the protocol that should be addressed. The protocol and broader research need to address the implicit use of Whiteness as the default and move away from binary categorisations of racial(ised) 'majority' and 'minority'. An intersectional lens should be applied to acknowledge the complexities of race and other intersecting social identities that affect the specific disparities seen among particular racialised groups, rather than amalgamating all racialised minorities implicitly into one disparate group. This approach will help highlight the diverse experiences and perspectives among racialised groups and avoid essentialisation or oversimplification. Response: We have fallen into the trap of binary categorisations and the centering of Whiteness, and we thank the reviewer for pointing out this pertinent issue. Based on your comments, we have changed the term ‘racial minority groups’ for ‘racially minoritised groups’, and ‘minorities’ for ‘minoritised’ as suggested in the literature by Gunaratman (2013), Selvarajah et al. (2020), and Rai et al. (2022). We have added these references in the review protocol as well. We have changed Key definition 5 as follow: p6-7: 5. Racially minoritised groups : Refers to groups that are subject to racialisation and are also minoritised, marginalised or underrepresented based on various characteristics such as skin colour, migration status, citizenship, religion, culture, language or geographic location . To emphasise the process of racialisation, some authors use either this wording (Milner and Jumbe, 2020 ; Rai et al., 2022) or “marginalised racial groups” (Barber, 2020). This quote from Selvarajah et al. (2020: 2-3) is particularly interesting for a reflection on the term ‘minoritised’ : “We recommend the term minoritised, which emphasises active processes, shifting beyond binary discussion of minority versus majority. We build on existing explanations to define minoritised, as ‘individuals and populations, including numerical majorities, whose collective cultural, economic, political and social power has been eroded through the targeting of identity in active processes that sustain structures of hegemony.’ Power is emphasised as central to racism and intersecting forms of discrimination. It highlights maintenance of structures which diminish minoritised people’s capability to lead healthy lives. It neither singles out nor creates groups, and adds more nuance than words like marginalised by connecting back to terms such as ethnic minority, thus acknowledging existing literature while resisting its coupling with dubious assumptions about ethnicity. And we have added Footnote 12: p.6: We would like to thank one of the reviewers of the first version of this protocol for their criticism, which helped us to refine our thinking on the risks of falling into binary categorisations and the centering of Whiteness. And this: p7: It is important to acknowledge the fact that racially minoritised groups are not homogenous groups, given the intersecting forms of oppression within minoritised groups. Although we clearly want to avoid any form of oversimplification, and we acknowledge the fact that health inequities cannot be reduced to race alone, we see a stark omission of research analysing racism in health in Europe ; therefore, we see this one-dimensional study as a first essential step to enable the development of more complex research using intersectional lens in the future. -- Additionally, ‘disparity’ is often used in the protocol to imply 'worse', which is not always the case. Disparity only refers to the difference or inequality between groups, which means that groups racialised as White are also part of the 'disparity equation'. Response: We would like to thank the reviewer for pointing out this pertinent issue and by this helping us in communicating more clearly. We have revised our use of the word ‘disparity’ throughout the review and changed it where this was deemed necessary. For example: p2: In many countries, there is a lack of national data systems using race/ethnicity data, which means that there is limited statistical evidence on health disparities between racially minoritised and majoritised groups. Identical corrections have been made throughout the text. Furthermore, definition 8 (health disparities) and 9 (racial health disparities) have been adapted accordingly: p7: Health disparities: Refers to a condition in which different social groups have different health outcomes. Generally, disadvantaged social groups such as the poor, racial/ethnic minoritised groups, women and other groups who have persistently experienced social disadvantage or discrimination systematically, experience worse health or greater health risks than more advantaged social groups (Braveman, 2004, 2007). When systemic barriers to good health are avoidable yet still remain, they are often referred to as 'health inequities'. p7-8: Racial health disparities: Refers to health disparities that occur between racially minoritised groups and the racially majoritised group. It describes the increased presence and severity of certain diseases, poorer health outcomes, and greater difficulty in obtaining healthcare services. Usually, it is the racially minoritised groups who are at a disadvantage compared to the racially majoritised one. -- The phrasing of data and research ‘on’ racialised groups can imply objectification, detachment, or othering of the communities of focus. Consider revising this language used throughout the protocol when discussing racialised and other minoritised or marginalised groups. The use of ‘with’ - also used in the protocol - better conveys the inclusivity advocated for throughout the protocol and wider research, and acknowledges the collaboration and partnership between researchers and the communities of focus. Response: We thank the reviewer for their important observation and valuable suggestions. -- Throughout the text, we have changed ‘research on racially minoritised groups’ into ‘research on/with racially minoritised groups’. In instances where the phrasing ‘data and research on racially minoritised groups’ is used, we have changed this into ‘data on and research on/with racially minoritised groups’. To be consistent, we have also modified this in the title of our review. We have also added the following footnote n.4: p2: The term ‘on/with’ is used deliberately. On the one hand, we want to acknowledge that in reality, much research is not done ‘with’ the communities it focuses on. On the other hand, however, we do not wish to reify and normalise the formulation ‘doing research on’ and the associated academic culture throughout our text. In addition, we only have access to the data that researchers have chosen to publish, so we do not always know whether the research is actually done ‘on’ or done ‘with’ the community in question. For all these reasons, using the formulation ‘on/with’ seems to be the most nuanced and correct way. -- With acknowledgement that only the positionalities of the authors are explicitly described, the claim of a ‘racially diverse’ team may need to be re-evaluated to ensure that it accurately reflects meaningful diversity and avoids tokenism. If the positionality of the authors is reflective of the entire team, then what has been demonstrated is not racialised 'diversity'. Perhaps expand on what is meant by ‘racially diverse’ to acknowledge the range of racialised and ethnic backgrounds represented in the research team, which would also strengthen the robustness of the methods that are informed by the positionalities of all of the team members involved. Response: We thank the reviewer for their valuable comment. Indeed, the team expanded after the review protocol was drafted. In light of your comment and for clarity, we are removing the claim of \"racial diversity\" in the review protocol, and will further elaborate on the positionality of all team members, and their respective contributions to the project, when we publish the article presenting the results of the study. Therefore, we removed the claim as follow: p.2: This race-conscious approach forms the basis and the goal of this project, conducted by a racially diverse team (see below Review team / Positionality). For better clarity, we also added this section in the Description of the review team: p.14: Following ITM guidelines on authorship (2017), the core team has carried out the following tasks: 1) conception of the work; 2) design of the study and drafting of the review protocol. -- The research would benefit from a clearer distinction between the definitions of ‘race’ and ‘ethnicity’. As written, it is unclear how some of the characteristics used to define race are meaningfully distinct from the ‘cultural’ aspects used in the definition for ethnicity. The authors may also need to evaluate critically whether the non-phenotypic characteristics offered, such as clothing and speech, should be considered as aspects of race, as this can perpetuate reification and stereotypes of racialised groups (as warned against in CIHI 2022, cited in the protocol). If they do wish to retain these non-phenotypic characteristics as components of race their operational definition, the authors need to strengthen their argument by providing explicit rationale for the purposes of this protocol. Response: We thank the reviewer for pointing out the confounding nature of these two definitions. We take this as an opportunity to further sharpen our definitions and our writing. The definition of ‘Race’ has been rewritten as such: p5: Race: Refers to socially and politically constructed perceptions of differences among people based on phenotypic characteristics such as skin colour. Although the sciences have been (and still are) heavily involved in the production of race and racial categorisations, there is no scientifically supported biological basis for racial categorisation. However, various societal actors construct races as real, which has a variety of detrimental implications for economic, political, social, and cultural life (CIHI, 2022). -- The definitions offered for ‘inequality’ and ‘inequity’ in the protocol should be clearly referenced to establish the basis for these particular conceptualisations in this research and context. Depending on the field, area, or sector, these words have varying operational definitions, so the definitions offered are not necessarily universally accepted. Moreover, the definition of ‘inequity’ reads confusingly, and uses ‘equitable’ - a term not defined in the protocol - to explain it. The definitions could be revised to offer more straightforward explanations of the concepts; possibly by alternatively providing definitions in positive terms (i.e., ‘equality’ and ‘equity’) rather than (only) in negation. Response: We thank the reviewer for pointing this out and have revised the definitions. We have brought in a more specific focus on health inequality and health inequity, rather than attempting to define the concepts in general (separately from health). This will help us make the definitions less abstract and more relevant and to the point. Therefore, we have removed the definitions of Inequality and Inequity. In addition, we have merged the definition of health inequality with the definition of health disparities: p7: Health disparities or health inequalities: Refers to a condition in which different social groups have different health outcomes. Generally, disadvantaged social groups such as the poor, racially/ethnic minoritised groups, women and other groups who have persistently experienced social disadvantage or discrimination systematically, experience worse health or greater health risks than more advantaged social groups (Braveman, 2004, 2007). When systemic barriers to good health are avoidable yet still remain, they are often referred to as 'health inequities'. p7: Health equity: Refers to the absence of differences in health associated with social disadvantages that are modifiable, and considered unfair. This means everyone has a fair chance to reach their full health potential without being disadvantaged by social, economic and environmental conditions (CIHI, 2022 ; NCCDH, 2014). -- The protocol would also benefit from clarification and/or additional citations when referencing the definition for ‘xenophobia’. The protocol is mindful against conflation, however the definition given for xenophobia appears to conflate race and ethnicity. The use of terms such as ‘native’ and ‘host-country’ have been used uncritically, as though those who are racialised as minorities are necessarily ‘non-native’ and those who are not are necessarily ‘native’ and ‘hosts’. These terms can be problematised as reinforcing stereotypes or assumptions about individuals based on their racialised or ethnic backgrounds - as not all Europeans are part of a racialised majority, not all who are racialised as minorities are migrants, and especially with free movement within the European Union, not all who are racialised as part of a majority are from the location where they are living. Response: Once again, we thank the reviewer for their comment. In fact, their remark is the point we are trying to make in this paragraph discussing the definition of xenophobia and especially discussing how it is distinct from racism. As this is not understood as such, we have rewritten the definition to make it more to the point and the message clearer. p9: Xenophobia: “Attitudes, prejudices and behaviour that reject, exclude and often vilify persons, based on the perception that they are outsiders or foreigners to the community, society or national identity.” (European Commission, Migration and Home Affairs) As such, xenophobia needs to be distinguished from racism, which concerns (systemic) acts of discrimination towards someone based on their perceived affiliation to a racially minoritised group, regardless whether this person is seen as a foreigner or not (Suleman et al., 2018: 2). This distinction is important, as the mechanisms and outcomes of both forms of discrimination are different and can affect different groups. -- Approval Status Based on the above assessment of the “Review of Health Research and Data on Racialised Groups: Implications for Addressing Racism and Racial Disparities in Public Health Practice and Policies in Europe” study protocol, the approval status given is: 'approved with reservations'. Whilst the study protocol demonstrates several strengths and merits, there are areas that require improvement or clarification to enhance its effectiveness and impact. The strengths of the study protocol, including the clear rationale and objectives and appropriate study design, contribute to its overall value and support the 'approval with reservations' status. However, certain areas need attention to address reservations and ensure the quality and relevance of the protocol for this part of the research, as well as the wider research project. Recommendations have been provided regarding the need to consider and address potential biases and refine some of the language and key definitions used in the protocol. By implementing these recommendations, the study protocol can strengthen its potential for making a meaningful contribution to addressing racism and racialised disparities in public health practice and policies across Europe. Response: We thank the reviewer for their thorough feedback and helpful suggestions. We will share our results with you when they are ready." } ] } ]	1	https://f1000research.com/articles/12-57
https://f1000research.com/articles/11-997/v1	06 Sep 22	{ "type": "Opinion Article", "title": "The patent landscape in the field of stem cell therapy: closing the gap between research and clinic", "authors": [ "Dinorah Hernández-Melchor", "Esther López-Bayghen", "América Padilla-Viveros", "Dinorah Hernández-Melchor", "Esther López-Bayghen" ], "abstract": "Stem cell technology is a powerful tool ready to respond to the needs of modern medicine that is experiencing rapid technological development. Given its potential in therapeutic applications, intellectual property rights (IPR) as a protection resource of knowledge are a relevant topic. Patent eligibility of stem cells has been controversial as restrictions to access the fundamental technologies open a gap between research and clinic. Therefore, we depicted the current patent landscape in the field to discuss if this approach moves forward in closing this breach by examining patent activity over the last decade from a transdisciplinary perspective. Stem cell therapeutic applications is an area of continuous growth where patent filing through the PCT is the preferred strategy. Patenting activity is concentrated in the USA, European Union, and Australia; this accumulation in a few key players leads to governance, regulation, and inequality concerns. To boost wealthiness and welfare in society - stem cell therapies' ultimate goal - while at post-pandemic recovery, critical elements in the field of IPR rise to overcome current limitations: to promote bridge builders able to connect the research and business worlds, regulatory updates, novel financing models, new vehicles (startups, spinouts, and spin-offs), and alternative figures of intellectual property.", "keywords": [ "Intellectual property rights", "Patent landscape", "Stem-cell therapy" ], "content": "Introduction\n\nInnovative scientific discoveries, such as cell therapies, are routinely used among clinicians in their medical practice.1 Thus, cell therapies are powerful tools ready to respond to the needs of modern medicine. Furthermore, stem cell therapies face the challenge of improving the quality of life in rapidly aging societies.2 Due to the rapid technological development cell therapies are experiencing and their high potential in therapeutic applications, intellectual property rights (IPR) as a protection resource of knowledge is a relevant topic.\n\nStem cells are traditionally defined as undifferentiated cells with unlimited potential to regenerate cells or tissues lost due to disease and thus restore normal function.2 However, more recent studies have shown stem cells to have reparative properties, homing to injury sites and stimulating tissue repair.3 Those remarkable discoveries beg the question of how they can be protected and to what extent by IPR.4\n\nThe patent eligibility of stem cells – particularly those derived from human embryos and human embryonic stem cells (hESC) – has long been debated in scientific and legal communities. However, precedents established in USA courts significantly narrow the scope of patent eligibility within biotechnology. The implications of recent legal changes on stem cell patent eligibility have already been compared in the European Union (EU) against those applicable to the USA.5\n\nCurrent research has analyzed the challenges for patents based on human stem cells with therapeutic uses and patentability limits.6,7 In addition, the comprehension of state of the art has been analyzed from the legal perspective of applicable regulations in different regions and jurisdictions (Europe, the USA, China, and Japan), considering ethical issues and relevant regulatory restrictions.8\n\nInternational courts have widely treated cases and controversies around patent activities in stem cell technology. An emblematic case is the controversies and legal disputes derived from a family of three patents held by the Wisconsin Alumni Research Foundation (WARF) that covered the first isolation of nonhuman primate stem cells and hESC. The court considered the claims “overly broad and restrictive inhibiting researchers' access to stem cell lines due to high licensing costs”,9 falling within the “Alienation Phenomena of Biotechnology Patents,” where excessive patenting restricts researcher access to the essential technologies to go further.10\n\nWhile surfing the intellectual property outlook, researchers face legal uncertainties, high costs, and limitations on data sharing.11 Even a diligent stem cells researcher or entity that wishes to respect IPR will face uncertainty and enormous expenses in dealing with the IPR landscape.11,12 Furthermore, it is antithetic for one institution or company to hold a “universal patent” that, when licensed, provides total freedom to operate,13 limiting the forthcoming of the promising industry of stem cells.\n\nWARF's patents show how despite limitations, the patent system works in conjunction with robust, nonprofit, and primarily publicly funded scientific research institutions.14 However, the field of stem cell therapies is not a bidirectional relationship between academia and private companies. Instead, it is a complex ecosystem influenced by government policies and court rulings in their respective jurisdictions,9 assembled over a translational model where researchers from the benchside, health professionals from the bedside, communities of healthy populations, and patient groups work together15 to boost wealthiness and welfare in society.\n\nControversy aside, from looking at this outlook, one question arises: is the current arrangement of the patent system a pathway for closing the gap between research and clinic? Therefore, we reviewed the patent landscape of stem cells, the primary tool of various cell therapies, over the last decade (2011-2020) to understand how the patenting activity behaved by analyzing trends in patent records and the stakeholders' contributions. On these grounds, we integrate a transdisciplinary perspective that allows researchers, decision-makers, and investors, to have a broad panorama to effectively address essential factors to enable equal access to technology, tackle the governance challenges, and provide IPR alternative strategies.\n\n\nA sight of the patent landscape in the field of stem cell therapy in the last decade\n\nAs patent data represents inventive activity, in this work, we explore innovations in stem cell therapy over the last decade by analyzing the patenting activity reported at PatentScope, the WIPO's repository.16 PatentScope is an official source of information that encompasses several patent authorities with sufficient technical resources to explore state-of-the-art technology in a particular field.17\n\nWe may say that WARF's patent controversy is the clearest example of how the scope of IPR and policy contexts affect stem cell technology. WARF is a nonprofit foundation that manages intellectual property generated by researchers at the University of Wisconsin at Madison. In the mid-1990s, James Thomson and coworkers developed an approach to maintain long-lasting ESC lines from two species of primates. Afterward, in 1998, the group created an analogous hESC; due to governmental prohibits for using federal funds in research with human embryos, Geron Corporation funded the research in exchange for exclusive and nonexclusive rights under patents that might result. The first application for the IPR patent family was filed by WARF in the US in 1996 and awarded in 2006. However, in 2004 the European Patent Office (EPO) refused the application on moral grounds. While in the US, the controversy around WARF's patent family was centered on technical issues alleging obviousness and lack of novelty, in Europe, WARF's efforts to protect their inventions through the European Patent Office (EPO) failed due to morality concerns as the only means to obtain hESC with the claimed method involved destroying human embryos, making the method unpatentable under the Rule 28 of the European Patent Convention.14\n\nWARF's protection strategy unleashed aggressive critics and accusations of asserting control over a primary science platform needed for health-related research. WARF was challenged by Consumer Watchdog, a California-based consumer rights organization, on the grounds of obviousness at the USPTO in 2006 before the patent was granted. However, it was dismissed. In 2007 WARF liberalized its patents' licensing by eliminating the prohibition against academic researchers from sharing WARF's hESC and extending exemption on licensing fees; by 2009, they had completed 35 licensing agreements for hESC with 27 companies.14 In 2014, after the Leahy–Smith America Invents Act (AIA) was declared and one year before WARF´s patent expiration, Consumer Watchdog challenged USPTO's 2006 decision on the US Court of Appeals for the Federal Circuit appealing to the US Supreme Court's decision on Association for Molecular Pathology vs. Myriad Genetics Inc. on gene patenting. The US Court dismissed the petition again as there was no legal injury related to the patent, considering that Consumer Watchdog was never sued or threatened to be sued by WARF.18\n\nDespite the challenges, inventive activity around clinical applications of stem cells has been growing during the last three decades, reflected in the steady growth of patent filing activity in stem cells since the 1990s.19 A peak and drop in the first decade of the 21st century were observed, being at a stable pace until 2010.11 However, by 2010, the hype of stem cell technology had dropped: added to the ethical and sociopolitical controversy, the timespan for these technologies to reach the clinic, the slow entrance of industry into the field, and the lack of business models specifically engineered for stem cell-based therapies, and regulatory uncertainties created a hard shell for investment.11,13\n\nThe evolution in the number of patent documents (applications and grants) from 2011 to 2020 is presented in Figure 1. From 2013 to 2015, the number of patent documents produced annually remained relatively constant. However, as of 2015, a gradual increase in annual applications began, presenting a maximum peak in 2019. For 2020, the number of submitted patent applications decreased discreetly since the search results were inconclusive, considering that we did not carry out the query at the end of the year.\n\nOwn elaboration with data of PatentScope.16\n\nAgainst the odds, the increasing number of patent filings in the last decade mapped in our research demonstrates that the stem cell field has been an arena of continuous growth and innovation since 2015. This switch resulted logically as discourses and policies changed during the first years of the decade. For example, in 2012, the Nobel Prize in Physiology or Medicine was granted to John B. Gurdon and Shinya Yamanaka for the discovery of reprogramming: mature cells can be reprogrammed to become pluripotent,20 enforcing this new avenue in stem cell therapy; also, in the US, during Obama's administration the AIA was enacted, changing the game in stem cell patent activity, making it a more attractive and competitive environment as it makes more accessible and cheaper to challenge stem cell patents as they become issued.18 After that, in 2014, the EU overturned laws that banned stem cell patents, allowing patent granting if the biological materials are accurately described and have an industrial application.4\n\nWe integrated a core collection of published patent documents constructed to encompass all stem cell applications from the USPTO, the EPO, WIPO's Patent Cooperation Treaty (PCT) filing system, and seven countries, including Australia, Canada, New Zealand, South Africa, United Kingdom, Israel, and South Korea (Figure 2). PCT filings represent the majority of global patent documents, followed by the USA domination as the most prominent target market. The fact that patent documents are being filed through the PCT suggests the intention to protect the invention simultaneously in different countries.\n\nOwn elaboration with data of PatentScope.16\n\nThe United Kingdom National Stem Cell Network (UK NSC) patent watch landscape is a dataset of published patent applications and granted patents to provide a bigger picture regarding the patenting of stem cell technology. However, the UK NSC patent watches dataset is limited to published applications with WO, US, EP, and GB designations, and the granted patents on the USA, EP, and GB. Hence, to place the results of the UK patent watching a more global context and to give a fuller picture of the worldwide activity concerning stem cells, an overview of the complete global dataset would be beneficial given the recent rise in worldwide patent filings from countries such as China and India.21\n\nJapan has been a substantial actor in the stem cell patent during the last decades.19,21,22 Even if not listed in our research among the most active countries - maybe because patents are filed through the PCT pathway– Japan's policies have fostered stem cell innovation. Liberal Democratic Party, elected in 2012, strongly supported research in the field with over 220 million US dollars as part of a stimulus package to lift the Japanese economy from recession.23 Through time, these storylines change the relevance of policy designs, reinforcing the notion that patent law, and national policies (Economic, Educational, and Science-Technology-and-Innovation) affect how novel technologies are fostered to attain societal wellbeing.\n\nTable 1 presents the institutions and private corporations with more patent productivity on stem cell therapies. Almost one-quarter of the patents related to stem cell therapeutic applications are concentrated in ten organizations, with more than 59 contributions each. It is essential to mention that this search considers only the principal patent applicant. In this top ten, six applicants belong to academia, and four can be classified as private corporations. Five institutions are highly prestigious USA universities within academia, and only one is a research center (Memorial Sloan-Kettering Cancer Center). In addition, three organizations are large pharmaceutical companies (Janssen Biotech, Inc., Novartis Ag., and Celgene Corporation) and a research-focused hospital (The General Hospital Corporation DBA Massachusetts General Hospital).\n\nFigure 3 illustrates how patent documents are distributed among holders of different institution types. 73% of the patent documents are held by Academia-related institutions, while private companies presented less than one quarter (24%) of those. The dominant presence of universities in the field suggests that, as stated above, long incubation periods within academia are required for this technology to be ready. Therefore, technology transfer offices and licensing agreements could be fundamental in bringing stem cell technology to society.\n\nOwn elaboration with data of PatentScope.16\n\nA recent patent analytics report of the Centre for Stem Cell Systems of the University of Melbourne investigated technology development related to mammalian pluripotent stem cells.22 Patent families in this technology are predominately directed at differentiation (28%) and stem cell production (26 %). The high number of patent families granted or with protection being sought (98%) for stimulation and tissue engineering indicates the importance of patent protection in this technology. This analysis showed that innovation in mammalian pluripotent stem cells is dominated by universities and research institutes and has a healthy level of collaboration, which indicates that the technology is in the early stages of development. Nevertheless, it is a growing field with enormous opportunities for translating research into applications as technology matures.\n\n\nHow to dilute access to stem cell technologies to achieve social welfare?\n\nPatent systems' primary purpose is to encourage innovation to achieve social welfare by granting exclusive rights over an invention if this fulfills three criteria: novelty, utility, and non-obviousness. Hence, the nature of a patent is to generate profits and gain control over the market, risking its original justification: social benefit.10\n\nOur research shows that innovation in stem cell technology is concentrated within a few hands of the wealthiest sectors: (1) the eight nations with more patent filing activity are listed as high-level income countries by The World Bank,8 (2) nine of the most active organizations in the patenting filed are located at the USA, and (3) four of this top ten are private companies, whose logical-financial-interest for protecting its inventions is to make to most of it. So, how to balance access to stem cell technologies? As the global innovation landscape changes rapidly, a noticeable reshaping of the consumption and use of patent information happens. Brand new technologies, changing business needs, and evolving talent markets continuously affect the patent data's nature, shape, and transformative value. Here we discuss some keystones to consider for bridging the gap.\n\nStem cell and genomic research share controversies around IPR and policy contexts. However, they also have in common the complex and lengthy translational pathways of a complex innovation ecosystem based on working with human materials.11 After that, an essential lesson from genomics can be learned: the progress and use of technology improve its speed and quality while reducing associated costs.\n\nIn 2002, after an international 13-year effort, the Human Genome Project satisfactorily concluded, making publicly available 99% of 3000 million bases comprising the whole sequence of human DNA.24 After this breakthrough event, genome sequencing costs decreased by 10,000 times, from 1000 to 0.1 US dollars per megabase from 2007 to 2015.25\n\nLike genomics before the Human Genome Project, stem cell research for therapeutical applications may be unattainable, so reducing the price of this technology becomes essential to impact the health and life of people around the world. However, clear paths around IPR and a congruent business model are required to make this possible.13\n\nA decade ago, the field of Regenerative Medicine – stem cell therapies included - was dominated by small biotechnology companies focused only on tools and nontherapeutic products or their services and manufacturing.11 However, our findings suggest a shift in this behavior, not only because the two medical facilities focused on clinical research rank among the leaders in the field, but, more patents have been filed under more than one category, and selected IPC codes relate to medical preparations and therapeutical activities of compounds or preparations, implying that on-the-edge technologies tend to incorporate different innovations to achieve a therapeutical alternative.\n\nAdvanced therapies involve a variety of inventions in many technical fields to manufacture a product, such as tissue selection, cell isolation, purification, culture, and specific therapeutical modifications – lineage differentiation, genetic changes, co-culture, and scaffold assembling-, GMP and quality assurance, transportations strategies, and strategies to transplant into the patient. These are just some of the scientific breakthroughs needed to be assembled through diverse technological developments – potentially patentable - to manufacture a stem cell therapy product. Thus, patent strategies used to protect small-molecule compounds are not likely to work well in the stem cell field; a technology portfolio is essential to cover and protect a commercial product.26\n\nA possible strategy to integrate these patent portfolios and seize opportunities to expand new business areas is to take advantage of the existing technological strengths of different institutions. However, under the current patent systems, these results are unthinkable.\n\nTechnology transfer is the span to close the gaps between academic research, industrial applications that allow commercialization of the result, and research's ultimate purpose: social welfare.\n\nTypical licensing agreements had proved wrong for biotechnologies - as stem cells - to be transferred. The enormous fees involved hinder innovation instead of promoting novel developments – as WARF patent licensing fees slowed the advance of stem cells for a timespan.27 Hence, new ventures for technology transfer promise to close the gaps: academic spin-offs to transfer research to industry, corporate spinouts to share technology between private companies, and internal company start-ups to overcome innovation barriers within corporations.28 Nevertheless, endless jigsaws can be arranged based on those approaches.\n\nIn the early 2000s, financing stem cell research with strategies based on classic pharmaceutical models resulted in a \"disappointing commercial history of cell therapy and contributed to the cool reception stem cell companies receive from venture capitalists\".13 However, the scenery changed after these new models matured: \"some of the largest rounds of venture capital ever seen went into 2019 biotech startups\".29\n\nNew stem cell arose start-up companies, whose individual funding accounts for no less than 2 million US dollars, are scattered around the world, with 18 in North America (16 in the USA and two in Canada), seven in the European Union (three in the UK, one in Belgium, Netherlands, Germany, and Switzerland), three at Israel and only one in India.30 By analyzing the behavior in patenting activity of these stem cell-based start-ups, we can give a closer picture of the landscape in this emerging field. The scatter plot in Figure 4 presents patent portfolio size compared to funding amount for the top ten start-ups; funding data was retrieved from Medical Startups30 at the same time, patent information was collected from the Lens patent database31 by searching the number of patent records and families for each patent stakeholder listed (start-ups and associates). The trend shows more funding for start-ups with more solid patent portfolios – more patents with broader cover-, such as Celularity, Century Therapeutics, and Via Cyte; opposite to Rubius Therapeutics, a startup with limited patent families receiving more funding, and Cellular Dynamics, a less funded company with more patent families. Other start-ups listed within the top ten show emerging patent portfolios with more recent patent applications and families, ranging from 1 to 35 patent documents. However, optimistic as this may sound, future challenges will arise when these recently created enterprises consolidate as freedom-to-operate entities with existing patent grants.\n\nFunding and size of the patent portfolio.\n\nThe diameter of the bubble represents the number of simple patent families. Own elaboration with data from Lens31 and Medical Startups.30\n\nCelularity, a $290 million funded Celgene Corporation spinout with a mature patent portfolio, aims to use placenta-derived stem cells as an alternative approach against blood cancer by developing therapies across autoimmune, degenerative disease, immuno-oncology, and functional regeneration. Noteworthy, Celgene Corporation performed as the seventh most productive institution in the stem cell patent filling landscape.30\n\n\nConclusion\n\nUndoubtedly, patents have been a stairway for stem cell research and development to access commercialization; however, the stairs for these products to evolve into therapies that enable social wellbeing are missing in this blueprint.\n\nIn certain jurisdictions, due to the lack of congruent regulatory frameworks to use IPR as a protection resource of knowledge, nondisclosure mechanisms of confidentiality and trade secrets are the only, but not preferred, options available to protect innovations in the stem cell field9; relegating patents as outdated mechanisms to bring stem cell technologies into the market. Thence, from this ground, we hypothesize: what if alternative figures of intellectual property for stem cell technology can overcome the current challenges?\n\nNovel business models use stem cells as the cornerstone for cutting-edge technologies – 3D printing, bioprinting, organs on a chip, and genomic edition – that need a whole IPR-protected toolset to tackle real problems of rapid aging societies. As presented before, advanced therapies require a variety of inventions in many technical fields to manufacture a product, and patent portfolios are essential to cover and protect a commercialized product. Unfortunately, these systems may hamper innovation and development of stem cell technologies; thus, to overcome these limitations, the surge of protection strategies through trademarks, utility models, copyright, or creative commons are alternatives that close the gap.\n\nTranslating research outputs to economic and social benefits is highly challenging and requires a combination of expertise and bridge builders to connect the research and business worlds. Moreover, the challenge of commercializing or translating research into meaningful therapeutic applications has become even more critical as the global community needs to build momentum toward post-pandemic recovery. Therefore, those with expertise in the field must be proactive and work cohesively to improve their knowledge base. These challenges include constructing a more robust conceptual framework and improved metrics around knowledge transfer. A combination of qualitative research, vehicles that can bring that research to the market, startups, spin-offs, spinouts, SMEs, large enterprises, or other entities, and bridge-builders able to connect the worlds of research and business.32\n\nBy analyzing patent activity over the last decade (2011-2020), it becomes evident that limitations notwithstanding stem cells are an area of continuous growth and innovation, evolving in the assembly of technological portfolios to design therapeutic applications patented under diverse IPC codes. The USA, European Union, and Australia are attractive regions for inventive activity protection in the field considering the maturity of their patent systems, leading to patent concentration within a few critical stakeholders with broad coverage through the PCT pathway and concerns about governance regulation, future risks, and inequality. Critical elements are required to build bridges from research to market in a post-pandemic recovery where the global community needs to create momentum. Regulatory updates, novel financing models, new vehicles (start-ups, spinouts, and spin-offs), and alternative figures of intellectual property (nondisclosure mechanisms, trademarks, utility models, copyright, or creative commons) shape plausible avenues in the field of IPR achieve stem cell therapies' ultimate goal, boost wealthiness and welfare in society.\n\n\nData availability\n\nPatent data was obtained from WIPO’s patent database Patentscope (https://patentscope.wipo.int/search/es/search.jsf) on March 2021 through the Advanced Search tool with the query: “CL: ((stem cell* NEAR10 (treat* OR transplant*)) ANDNOT ALL: (“plant” OR “vegetal”))”.", "appendix": "References\n\nPAHO: Regulation of Advanced Therapy Medicinal Products: Concept Note and Recommendations. 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Publisher Full Text\n\nFestel G: Academic spin-offs, corporate spinouts and company internal start-ups as technology transfer approach. J. Technol. Transf. 2013; 38(4): 454–470. Publisher Full Text\n\nEisenstein M, Garber K, Seydel C, et al.: Nature Biotechnology's academic spinouts of 2019. Nat. Biotechnol. 2020; 38(5): 546–554. Publisher Full Text\n\nStrartups M: Top 29 Stem cells startups.2021.\n\nLens: Lens Patent Search and Analysis.2021.\n\nWIPO L, AUTM, & ICC: Harnessing Public Research for Innovation in the 21st Century 2021." }	[ { "id": "149831", "date": "03 Oct 2022", "name": "Verónica A. Palma", "expertise": [ "Reviewer Expertise Stem cells", "regenerative medicine", "cancer", "developmental biology" ], "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 review by Hernandez-Melchor et al. is an interesting opinion article and includes novel approaches. The authors present the total number of patent documents in the last decade (2011-2020) and aim to elucidate which actors can be drivers in the research and clinical field in eight countries. As stem cell therapies are increasingly heading to the clinic, there is a substantial need for the issues discussed within the manuscript i.e. intellectual property rights and their implications for stem cell technology transfer to society. Hence, the subject of the review is interesting and could be significant and of potential interest to researchers in the area.\nTherefore, the study addresses a highly relevant topic and the reviewer thinks there is merit in this paper. But the review is insufficient in its current presentation, it is not offering an optimal advance in the field and, as such, the review is not suitable for indexing unless edited.\nAs a general comment, the reviewer believes that some of the data presented do not adequately convey the ideas discussed. Also, despite including most of the available bibliography on the topic, some important ones are missing (see for instance one suggested reference, such as Takashima et al., 20211) and the authors fail to make a good discussion considering their main goal which is intended to promote the clinical development of stem cell-based interventions and technological transfer to achieve welfare in society.\nThe following are some suggestions that may be of use to the authors to improve the quality of the manuscript.\nComments:\nPoint 1: Figure 1 shows patent documents in stem cell therapies from 2011 to 2020, revealing an increase in the number of patents since 2015 with its peak in 2019. However, to establish a better understanding of the main trends in stem cell patenting activity, it is necessary and favorable to include a detailed approach to the annual stem cell patent applications and grants.\n\nPoint 2: Figure 2 shows the core collection of US, EPO, and PCT documents and eight countries (2011 to 2020). However, to study the evolution of stem cell patent documents, it is necessary to compare this distribution with the data between 2001 to 2010 to check the atomization or concentration of these data over time.\n\nPoint 3: Figure 3 displays the distribution of ownership between the private sector and public sector entities in patents on stem cell therapies. Nevertheless, it would be interesting to compare with data from 2001 to 2010 even though stem cells are still an early-stage technology due to the high percentage involving public sector organizations.\n\nPoint 4: Page 7 paragraphs a relationship with technology transfer and commercialization of the results to achieve welfare in society. The reviewer suggests exemplifying the technology transfer of the stem cell to the community, describing in particular: How are the public biobanks of stem cells funded in developed and developing countries? How does the existence of public banks in these countries improve patients' quality of life? This would be a clear example of what the authors try to convey.\n\nPoint 5: It is recommended to indicate whether the companies listed in table 1 have undergone M&A by larger companies. Surprisingly the larger pharmaceutical companies are not prominent players in stem cell research. Please refer to this point in more detail.\n\nPoint 6: On page 7 paragraph 5, under the newest version of International Patent Classification (IPC), it would be interesting to report the distribution of patent documents under the IPC code.\n\nPoint 7: Another worthy and necessary addition to this issue could come from the elaboration on how the regulatory framework in regenerative medicine affects the total number of patent documents in the eight countries.\nIn conclusion, the review is not suitable for indexing unless edited. It requires minor revisions to be 'Approved'.\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? Yes", "responses": [ { "c_id": "9118", "date": "11 Jan 2023", "name": "Dinorah Hernandez-Melchor", "role": "Author Response", "response": "Dear Dr. Palma Reviewer for F1000Research We are pleased to read that the reviewer considers the subject of this article interesting and of potential interest for researchers. We thank the reviewer for the insightful comments to improve the quality of the manuscript and have considered the valuable points raised by the referee. A point-by-point account of our answers to the points raised by the reviewer follows: Point 1: Figure 1 shows patent documents in stem cell therapies from 2011 to 2020, revealing an increase in the number of patents since 2015 with its peak in 2019. However, to establish a better understanding of the main trends in stem cell patenting activity, it is necessary and favorable to include a detailed approach to the annual stem cell patent applications and grants. We included patent applications and grants data in Figure 1 to encourage better understanding of the activity in the field. Point 2: Figure 2 shows the core collection of US, EPO, and PCT documents and eight countries (2011 to 2020). However, to study the evolution of stem cell patent documents, it is necessary to compare this distribution with the data between 2001 to 2010 to check the atomization or concentration of these data over time. We referred to the distribution reported for the 2000s decade. Furthermore, we include the annual data for each filing route (Figure 2) and national offices (Figure 3) to establish a better understanding of the trends. Point 3: Figure 3 displays the distribution of ownership between the private sector and public sector entities in patents on stem cell therapies. Nevertheless, it would be interesting to compare with data from 2001 to 2010 even though stem cells are still an early-stage technology due to the high percentage involving public sector organizations. As in Point 2, the distribution for the 2000s decade is referred to and the data for annual distribution of patent applicants’ sector is presented to clarify the dynamics’ change in the field. Point 4: Page 7 paragraphs a relationship with technology transfer and commercialization of the results to achieve welfare in society. The reviewer suggests exemplifying the technology transfer of the stem cell to the community, describing in particular: How are the public biobanks of stem cells funded in developed and developing countries? How does the existence of public banks in these countries improve patients' quality of life? This would be a clear example of what the authors try to convey. We discussed the model of stem cell biobanks as a model to distribute and commercialize stem cell products to achieve social welfare. Point 5: It is recommended to indicate whether the companies listed in table 1 have undergone M&A by larger companies. Surprisingly the larger pharmaceutical companies are not prominent players in stem cell research. Please refer to this point in more detail. As recommended by reviewer, the applicable M&A for the companies listed in Table 1 is mentioned. The fact that larger biopharmaceutical companies are not listed within top 10 applicants is stated and the role of these institutions as patent owners or within is referred to, however, further discussion of this is beyond the scope of this review and may be addressed in future research. Point 6: On page 7 paragraph 5, under the newest version of International Patent Classification (IPC), it would be interesting to report the distribution of patent documents under the IPC code. We include the distribution of IPC codes in Figure 6. Point 7: Another worthy and necessary addition to this issue could come from the elaboration on how the regulatory framework in regenerative medicine affects the total number of patent documents in the eight countries. A description of the regulatory framework for advanced therapies was included and its relevance is discussed within sections 2.3. Territoriality of patent documents' filling: leading countries in the field and 3.1. Commercialization of innovations is essential to make them affordable. We hope that you find our answers adequate and that the revised version is now suitable for indexing. Best regards." } ] } ]	1	https://f1000research.com/articles/11-997
https://f1000research.com/articles/11-100/v1	26 Jan 22	{ "type": "Research Article", "title": "The effect of betel habits on blood glucose levels in the Karo ethnic community, Karo district", "authors": [ "Yunita Sari Pane", "Yetty Machrina", "Nurfida Khairina Arrasyid", "Mutiara Indah Sari", "Yetty Machrina", "Nurfida Khairina Arrasyid", "Mutiara Indah Sari" ], "abstract": "Background: Betel is a hereditary tradition from the ancestors of the Batak-Karo tribe, Indonesia. Karo people believe that betel is their unifier. The betel process begins with concocting a mixture of ingredients such as betel leaf, lime, gambier, areca nut, and with/without tobacco addition, then chewed slowly. Our previous study showed that gambier extracts (Uncaria gambier Roxb), can reduce blood glucose levels (BGL) in type 2 diabetes mellitus (T2DM) patients. This study aimed to analyze whether the habit of chewing betel can affect BGL in the Karo ethnic community in the Karo district. Methods: In total, 48 participants from the Karo community were divided into 4 groups (n=12 per group), namely: I. non-T2DM participants without betel habits; II. non-T2DM participants with betel habit; III. T2DM participants without betel habit and IV. T2DM participants with betel habit. The sampling technique was consecutive sampling. Data were collected by interviews and blood sampling (fasted and 2 hours postprandial (2hPP)). The collected data were analyzed by ANOVA then post hoc Bonferroni with a significance level of p-value <0.05. Results: This study showed that fasting BGL had no difference in non-T2DM participants without betel habit (group-I) compared to non-T2DM participants with betel habit (group-II) (84.33±12.32 vs 81.00± 4,84), and T2DM participants without betel habit (group-III) compared to T2DM participants with betel habit (group-IV) (196.25± 104.81 vs 150.00 ± 42.45), p>0.05. On the other hand, there was a significant difference in BGL 2hPP in group T2DM participants with betel habit compared to all groups (p<0.05). T2DM participants without betel habit group had the highest BGL levels compared to other groups. Conclusions: This study concluded that the habit of chewing betel containing gambier is effective in restraining the rate of increase in blood glucose levels. Further research is needed to see the mechanism.", "keywords": [ "betel", "gambir", "T2DM", "blood glucose levels", "Batak-Karo ethnics" ], "content": "Introduction\n\nBetel is a cultural tradition of Indonesian society with one of its compositions being gambier. Gambier (Uncaria gambier Roxb) is mixed with several other ingredients then wrapped in betel leaf which is then chewed slowly. People who chew betel regularly have their own reasons why they have the habit, other than taste. Chewing is a hereditary tradition from ancestors in the Karo tribe. The Karo people believe that betel is a unifying activity for them (Perangin-angin, 2017).\n\nThe habit of betel is usually done 3 times a day, namely in the morning, after lunch and at night (Kanapathy, 2014). The habit of betel is mostly seen in women of the Karo tribe, but there are also men who do it, because chewing betel is always done when meeting with relatives, colleagues or in other social settings (Sinuhaji, 2010). According to data derived from interviews, chewing betel provides benefits, namely to enjoy pleasures such as smoking, for leisure, and to eliminate bad breath. Chewing betel has been done for generations and because of the belief that this activity can strengthen teeth (Flora et al., 2012) as well as maintain health.\n\nChewing betel has been a habit in society for a long time, but nowadays we rarely encounter it, because there has been a shift in values, even though in rural areas there are still many habits that must be participated in because they uphold the traditions of generations (Perangin-angin, 2017). Chewing betel is done in different ways from one country to another and from one region to another in the same country (Gupta & Ray, 2004). However, the composition of betel is relatively consistent, consisting of betel leaf, betel nut (Areca Catechu), lime (calcium hydroxide) and gambier (Uncaria gambier Roxb) (Lombu, 2014).\n\nThe content of catechin polyphenols in gambier is efficacious as an anti-oxidant that may prevent various diseases, such as diabetes mellitus (Umeno et al., 2016). This is evidenced in the research of Pane et al. (2018) which states that gambier extract is efficacious in the treatment of diabetes by increasing levels of superoxide dismutase and lowering blood glucose levels (BGL).\n\nFrom the description above, the researchers wanted to assess whether the habit of chewing betel can affect BGL in subjects with T2DM compared to participants without T2DM, studied in the Batak-Karo tribe in Karo District.\n\n\nMethods\n\nThis research obtained ethical approval from the Health Research Ethics Committee of the University of North Sumatra (No. 468/KEP/USU/2021). Participants gave written informed consent after receiving an explanation from the researcher regarding the research procedure they would undergo (Pane et al., 2022).\n\nThe sample size was estimated following data from Kawamori et al. (2014) for BGL fasting and BGL 2hPP, using the following formula:\n\n* Calculation for sample size of BGL fasting\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n* Calculation for sample size of BGL 2hPP\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nThe calculation of the number of samples in the fasting BGL group is minimal 9 participants, while in the 2hPP BGL group minimal 11 participants.\n\nThe number of samples used in this study was taken from the largest number which calculated based on sample size formula from the two groups (BGL fasting or BGL 2hPP). The largest number of samples was taken from the BGL 2hPP group i.e: 11 participants. However, to anticipate the possibility of dropped out, the number of participants is added by 10% from a total of 11 participants = 12 people.\n\nSo from the 4 groups studied each consisted of 12 participants.\n\nσ2=population variance; σ=population standard deviation (SD); n=total number of samples each group (n1=88; n2=33); Z(1−α2) = value in the standard normal distribution equal to the level of significance α = 1.64; Z(1-β)= value in the standard normal distribution equal to the desired, β= 0.842; µ1=mean outcome exposed/treatment group (-134 mg/dl) for BGL fasting and (-50.2 mg/dl) for BGL 2 hPP); µ2=mean outcome unexposed/placebo group (-14 mg/dl) for fasting BGL and (-4.2 mg/dl) for 2hPP BGL; S1=SD changes from baseline treatment group (107 mg/dl) for fasting BGL and (43.6 mg/dl) for 2hPP BGL; S2=SD changes from baseline placebo group (77 mg/dl) for fasting BGL and (39.8 mg/dl) for 2hPP BGL. (see data from Table 2 in Kawamori et al., 2014).\n\nParticipants were divided into four groups based on feedback from the questionnaire regarding their betel habits: Group-I. Non T2DM participants without betel habit; II. Non T2DMparticipants with betel habit; III. T2DMparticipants without betel habit and IV. T2DMparticipants with betel habit. Inclusion criteria were participants with 2 generations of the native Karo Batak tribe, aged between 20–70 years. Exclusion criteria were subjects who have a chronic disease (complication), such as liver disease, kidney disease, cardiovascular disease, lung disease, etc, and T2DM participants on insulin therapy.\n\nThe sampling technique used was consecutive sampling. The prospective participants were approached to join the study by conducting a survey previously to the research location to see the betel habits of the Karo people. After that, the research team visited the local health service center (Puskesmas Dolat Rayat) to find out about health data and the betel habits of the local community. Then assisted by Puskesmas staff in collecting participants. Then a time was determined at which the research team met directly and gave an explanation of the aims and objectives of the researcher to research the local community. The research team explained the benefits of betel habits for health, especially to reduce blood glucose levels in T2DM patients because of the presence of gambier (Uncaria gambier Roxb) as one of the components in betel which has an antioxidant effect that can reduce BGL.\n\nThis research was conducted from July 2021 to October 2021 at the Puskesmas Dolat Rayat Karo District. Data collection of the betel habits of the subjects in this study was done via questionnaire and blood sampling to measure data BGL. These were done on the same day. The questionnaire asked for the following information: name, age, education, occupation, history of illness, history of medicine, family history of illness, betel habit.\n\nBefore taking blood, subjects were asked to fast (at home) from 10.00 pm to 08.00 am (around 10 hours) the next day. Blood samples were taken at 08.00 am straight after fasting (fasting BGL). Following this, the subjects consumed 100 grams of white bread, and 2 hours later the blood was taken again (BGL 2h postprandial [PP]).\n\nBlood was drawn from the participant’s fingertip and BGL level checked using a glucometer (Family Dr® Blood Glucose Monitoring System, AGM-513S, All Medicus Co., Ltd.). The following steps were taken:\n\n1. Wash the participant’s hands, use an alcohol swab. Make sure the finger are dry before testing.\n\n2. Insert a test strip into the glucometer.\n\n3. Set up the lancing device, unscrew the cap on the lancing device. Insert the lancet into the lancing device, then twist off the cap on the lancet, recap the lancing device by screwing the top back on next set the depth of the lancing device\n\n4. Slide the cocking handle back\n\n5. Hold the finger and place the lancing device firmly on the side of the finger and push the button\n\n6. Squeeze from the palm of the hand down to the tip of the finger to obtain a drop of blood\n\n7. Place the blood sample on the test strip\n\n8. The glucometer does the assessment and gives the result\n\nThe data collected were analyzed using SPSS version 20 by ANOVA and post hoc Bonferroni test with a significance value of p <0.05.\n\n\nResults\n\nThe participants in this study were the Karo tribe from 2 generations of pure Karo natives. Of 49 potential participants, 48 were eligible to take part (Pane et al., 2022). The characteristics of the distribution of participants based on betel habits, as follows:\n\nTable 1 shows there were 12 participants in each of the 4 groups studied. It was found that 14 participants (29,17%) in the betel habit groups had a frequency of betel >10 times a day, and the duration of betel habit as more than 10 years compared to less than 10 years was equal (12 participants, 25% in each group). Most participants (16 people; 33,33 %) reported benefits of betel to maintain health, especially mind relaxation (mood) and extra benefit for healthy and strong teeth, while others had no special reason for using betel, only to follow their customs (8 people; 16,67%). In the T2DM group, there were 21 participants (43,75%) who had chewed betel suffering from diabetes for <10 years. The participants included 11 men (22, 92 %) and 37 women (77,08 %). The most populous age group was 51–60 years (19 participants; 33,3 %) and least was 20–30 years (5 participants; 10,42 %). The most populous BMI category was the normal-weight group (19 participants; 39,58%). The BMI group below normal weight included 1 person (2,08%). The other participants were above normal weight. BMI classification was based on WHO (2021). Most participants had at least Senior High School level education (26 participant; 54,17%). Some worked as farmers (14 participants; 29,17%) but the largest number of participants were housewives (15 participants; 31,25%).\n\nT2DM=type 2 diabetes mellitus.\n\nTable 2 shows the BGL of participants based on with/without betel habits in the non- T2DM and T2DM groups.\n\nT2DM=type 2 diabetes mellitus.\n\nThis study showed that for fasting BGL there was no significant difference between group I vs -II (84.33 ± 12.32 vs 81.00 ± 4.84; p = 1,000), and group-III compared to group-IV (196.25 ± 104.81 vs 150.00 ± 42.45; p=0.317). There was no significant difference in BGL between the comparison of the betel and the no-betel groups. However, there was a difference between group -I compared to group III (84.33 ± 12.32 vs 196.25 ± 104.81; p=0.000) and groups I-IV (84.33 ± 12.32 vs 150.00 ± 42.45; p=0.042) which shows the significant difference of BGL. Similarly, group-II was compared with group-III (81.00 ± 4.84 vs 196.25 ± 104.81; p=0.000) and group-II was compared to group-IV (81.00 ± 4.84 vs 150.00 ± 42.45; p=0.029) showing statistically significant differences in fasting BGL (see Table 2).\n\nIn BGL 2hPP, there was no significantly difference between group-I vs -II (112.25 ± 22.62 vs 108.33 ± 18.99; p = 1,000). On the other hand, comparisons of all other groups showed significant differences in BGL, such as: group-I compared group-III (112.25 ± 22.62 vs 314.92 ± 128.97 mg/dl) (p=0.000); group-I compared group-IV (112.25 ± 22.62 vs 229.25 ± 58.26 mg/dl) (p=0.001); group-II compared group-III (108.33 ± 18.99 vs 314.92 ± 128.97 mg/dl) (p=0.000), group-II compared group-IV (108.33 ± 18.99 vs 229.25 ± 58.26 mg/dl) (p=0.001) and group-III compared group-IV (314.92 ± 128.97 vs 229.25 ± 58.26 mg/dl) (p=0.035) (Table 2).\n\nTable 2 shows the differences in a gap of BGL in each group and the magnitude of the increase in BGL fasting compared to BGL 2 hours postprandial. The difference in the increase in BGL groups I and II was almost the same, namely 26.92 and 27.33 mg/dl, not exceeding normal glucose levels in both fasting and 2 hours postprandial conditions with/without habit betel. But the highest BGL difference was found in group III-T2DM without betel habits, which was 118.67 mg/dl. Meanwhile, in the T2DM with betel habits (group-IV), the gap between BGL fasting and BGL2hPP was only 79.25 mg/dl. This indicates that the betel habit can restrain the increase in BGL as seen in groups IV compared to group III.\n\n\nDiscussion\n\nThe frequency of betel habit among participants in this study varied. In two groups (-II and -IV), 14 participants from a total of 24 participants in those groups had betel habits > 10 times a day (29.17%). The results of this study are the same as Kanapathy's study (2014), in which 14 samples of a total of 25 had betel habit frequency > 10 times a day.\n\nIn the present study, the highest percentage of participants suffering from Diabetes Mellitus (DM) for less than 10 years was 21 participants (43.75%), in contrast to the findings of Budiharto (2018), who found that 15 out of 25 people (60%) who had suffered from DM long-term and had a l betel habit for more than 10 years. The main purpose of betel habits found in this study (16 participants, 33.33%) was to get a sense of comfort and dental health. This is supported by Budiharto's research (2018) which reported that out of a total of 25 participants (13 participants, 52%) the habit of chewing betel had the same effect. In contrast, the results of other researchers showed that as many as 68% of participants experienced porous teeth and poor oral hygiene due to betel. This could be because the subjects studied did not maintain oral hygiene, or lacked the knowledge about how to maintain oral health by chewing betel (Andriyani, 2005).\n\nThe habit of chewing betel is often found in rural areas in Karo Regency. Chewing betel is a hereditary culture that has become a tradition of the Karo tribe to this day. This is supported by research conducted by Perangin-Angin (2017) which states that the Karo people have a tradition that involves betel activities in a series of Karo customs. However, unlike the Karo people in the countryside, the Karo people in urban areas are rarely found to have the habit of chewing betel. This may be due to hygiene factors (when they chew betel, their teeth change to turn blackish red, and also differences in busy urban lifestyles whereas Karo people who live in urban areas do not have much time to gather while chewing betel together).\n\nBetel habit generally uses a mixture of betel leaf, lime (calcium hydroxide), gambier, areca nut, sometimes with or without the addition of tobacco. Gambier is known to prevent various diseases because besides being efficacious as an anti-inflammatory, it is also a strong anti-oxidant. Pane et al. (2018) reported that gambier can reduce blood glucose levels in T2DM patients by increasing levels of superoxide dismutase resulting in a decrease in malondialdehyde formation and an increase in pancreatic function in producing insulin. In the present study, we suggested that the habit of chewing betel can control BGL because of the efficacy of gambier which is one of the components in betel. It was proved in the results that there were differences in BGL in each group with an increase in the rate of fasting BGL and 2 hours postprandial BGL which can be compared as follows: The T2DM group with betel habits (-IV) had a lower difference in the increase in BGL (79.25) mg/dl compared to the T2DM group without betel (-III; 118.67) mg/dl. In the group that has the habit of consuming betel, glucose levels are lower than the group that does not have the habit of consuming betel. We assumed that gambier consumed as part of their betel habit has the ability to bind oxidants produced by metabolism when blood glucose levels are high, thus affecting the function of the pancreas to produce insulin. This therefore causes a suppressed rate of increase in BGL in participants who are suffering from T2DM with betel habit. However, in the non-T2DM group (-I and -II), both groups with or without betel habits had BGL within normal limits. Gambier (Uncaria gambier Roxb) which is rich in catechins plays a role in the normalization of BGL (Sugiyama, 2005). Most importantly, the anti-oxidant catechin molecules in gambier are safe, which were identified as the main bioactive compounds in gambier (Anggraini et al., 2011). Catechins can improve diabetes and its complications by modifying oxidative stress (p<0.05) (Pane et al., 2018; Samarghandian et al., 2017).\n\nComparing the fasting BGL between groups, there was no statistically significant difference between group non T2DM participants without betel habit (-I) and non T2DM participants with betel habit (-II); and also group T2DM participants without betel habit(-III) compared T2DM participants with betel habit (-IV), p>0.05. However, there were statistically significant differences between BGL in group-III and group-I and group-III and group-II; group-IV and group-I; group-IV and group-III, p<0.05.\n\nWhile the comparison of BGL 2 hours postprandial showed a significant difference between each group (p<0.05), except for the comparison of BGL group I and group II there was no significant difference (p=1,000).\n\nThe difference between fasting BGL and 2hPP was found in the non-betel (-III) T2DM group which had the highest BGL compared to the other groups. Similarly, the comparison of the largest differences in the increase in BGL rates was shown in group III. We assume that in group III there is no gambier to suppress BGL levels, in contrast to the group that has the habit of chewing betel, it seems that BGL levels are restrained. The comparison of fasting BGL and 2hPP in group with betel habit (-II and -IV) was lower than the group without betel habit (-I and -III). Another interesting thing in this study showed that there was no suppression of BLG below the normal threshold in BGL fasting and BGL 2hPP condition in the group of non T2DMparticipants with betel habit (group-II). The limit of normal BGL = 72 -108 mh/dL (Mathew & Tadi, 2021).\n\nThe limitations of this study were that it is not easy to collect samples that have betel habits such as groups-II and -IV, due to the small number of samples in the population. In addition, in a pandemic situation, people do not want to be at in the Public Health Center for long, especially for T2DM with/without betel habit groups. However, every step in this study was carried out under strict health protocol procedures.\n\n\nConclusion\n\nThis study concluded that betel habits can restrain the increase in BGL as seen in a comparison of T2DM participants with betel habit (group-IV) compared to T2DM participants without betel habit (group-III). But this wasn’t the case when comparing participants without T2DM.\n\n\nData availability\n\nFigshare: The Effect of Betel Habits on Blood Glucose Levels in Karo ethnic community in Karo District. https://doi.org/10.6084/m9.figshare.17871911 (Pane et al., 2022).\n\nThis project contains the following underlying data:\n\n- 2021-data.xlsx (raw data in Indonesian)\n\n- Output.xlsx (statistical analysis)\n\nFigshare: The Effect of Betel Habits on Blood Glucose Levels in Karo ethnic community in Karo District. https://doi.org/10.6084/m9.figshare.17871911 (Pane et al., 2022).\n\nThis project contains the following extended data:\n\n- Informed Consent.pdf\n\n- Certificate Clinical Trial Yunita Sari Pane.pdf\n\n- ethical clearance.pdf\n\n- QUESIONER PENELITIAN-20122021.docx (questionnaire in Indonesian)\n\n- Lampiran-sign.docx (information sheet in Indonesian)\n\nData are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication).", "appendix": "Acknowledgments\n\nThe authors would like to thank Laboratorium Terpadu, Faculty of Medicine, Universitas Sumatera Utara, for providing the place and facilities to conduct the research.\n\n\nReferences\n\nAndriyani: Efek Menyirih terhadap Gigi dan Jaringan Lunak Mulut. Skripsi: Fakultas Kedokteran Gigi Universitas Sumatera Utara, 2005. Reference Source\n\nAnggraini T, Tai A, Yoshino T, et al.: Antioxidative activity and catechin content of four kinds of Uncaria gambir extracts from West Sumatra, Indonesia. Faculty of Agricultural Technology, Andalas University. West Sumatera. African Journal of Biochemistry Research. 2011; 5(1): 33–38. Reference Source\n\nBudiharto MD: Status Kesehatan Perempuan dengan Kebiasaan Menyirih di Kabanjahe Kabupaten Karo. Skrpsi: Fakultas Keperawatan Universitas Sumatera Utara, 2018. Reference Source\n\nFlora S, Christopher T, Mahmudur R: Betel Quid Chewing and its Risk Factors in Bangladeshi Adult. WHO South East-Asian Journal of Public Health. 2012; 1(2): 162–181. Reference Source\n\nGupta P, Ray C: Epidemiology of Betel quid usage. Ann Acad Med Singap. 2004; 33(4 Suppl): 31–6. PubMed Abstract\n\nKanapathy AP: Hubungan Kebiasaan Menyirih dengan Kanker Mulut pada penduduk Komunitas India di lingkungan Klang, Selangor, Malaysia. Skripsi: Fakultas Kedokteran Gigi Universitas Sumatera Utara, 2014. Reference Source\n\nKawamori R, Kaku K, Hanafusa T, et al.: Effect of combination therapy with repaglinide and metformin hydrochloride on glycemic control in Japanese patients with type 2 diabetes mellitus. J Diabetes Investig. 2014; 5(1): 72–79. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLombu ES: Kebiasaan Menyirih dan Kesehatan Rongga Mulut Lansia di Desa Hilibadalu Kabupaten Nias. Skripsi: Fakultas Kperawatan Universitas Sumatera Utara, 2014. Reference Source\n\nMathew TK, Tadi P: Blood Glucose Monitoring. In: StatPearls. Treasure Island (FL): StatPearls Publishing; 2021; [Updated 2021 Aug 11]. Reference Source\n\nPane YS, Ganie RA, Lindarto D, et al.: The effect of gambier extract on the levels of malondialdehyde, superoxide dismutase, and blood glucose type 2 diabetes mellitus patients. Asian Journal of Pharmaceutical and Clinical Research. 2018; 11(10): 121–124. Publisher Full Text\n\nPane YS, Machrina Y, Arrasyid NK, et al.: The Effect of Betel Habits on Blood Glucose Levels in Karo ethnic community in Karo District. figshare. Dataset, 2022. http://www.doi.org/10.6084/m9.figshare.17871911.v1\n\nPerangin-angin SA: Tokoh Adat Dari Marga Perangin-angin. 2017.\n\nSamarghandian S, Azimi-Nezhad M, Farkhondeh T: Catechin treatment ameliorates diabetes and its complications in streptozotocin-induced diabetic rats. Dose Response. 2017; 15(1): 1559325817691158. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSinuhaji LN: Perilaku menyirih dan dampaknya terhadap kesehatan yang dirasakan wanita karo di Desa Sempajaya Kecamatan Berastagi Kabupaten Karo. Skripsi: Fakultas Kesehatan Masyarakat Universitas Sumatera Utara, 2010. Reference Source\n\nSugiyama S: [Pharmacological action of gambir]. Yakushigaku Zasshi. 2005; 40(1): 29–33. PubMed Abstract\n\nUmeno A, Horie M, Murotomi K, et al.: Antioxidative and antidiabetic effects of natural polyphenols and isoflavones. Molecules. 2016; 21(6): pii:E708. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWHO: Body mass index (BMI). 2021. Reference Source" }	[ { "id": "121181", "date": "12 Apr 2022", "name": "Mustofa Mustofa", "expertise": [ "Reviewer Expertise Pharmacology and Ethnopharmacology." ], "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 manuscript needs extensive revision for language and grammar. Some editing is required.\n2. The inclusion criteria used are not presented specifically.\n3. The methods sections normally presented in narration not in instruction.\n4. The statistical analysis especially between group III and IV needs to be checked again:\nThe main objective of the study was to evaluate the effect of betel habits on BGL. Therefore, analysis and discussion should be focused by comparing the results of groups III and IV. The sample size is too small in this study and the standard deviation (SD) is too wide, especially groups III and IV. Normally, in this case, a nonparametric statistic is recommended. In this study, the Anova was applied. Therefore, I recommend using nonparametric statistics with data presented in median +/- range.\n5. The conclusion needs revision:\nIt was too early to conclude that betel habits can restrain the increase of BGL. The authors did not compare the fasting BGL between group III and group IV. The conclusion just based on the BGL 2 h PP. Moreover, the conclusion should be revised based on the new statistical analysis results.\nOther:\nThe quality of the manuscript should be improved. For example, it is needed to present the calculation of the sample size in this manuscript. The English also should be improved.\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?\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": "8605", "date": "03 Aug 2022", "name": "Yunita Sari Pane", "role": "Author Response", "response": "Thank you for reviewing and suggesting some constructive amendments to the article. Answering the question number: We’ve revised the article for language, grammar, and editing. Inclusion and exclusion criteria have been presented (see page 4). The method section has been presented in narration (see page 4). Statistical analysis of the articles has been adjusted and the discussion has focused more on groups 3 and 4 as suggested. The conclusion of the article has also been fixed The conclusion of the article has been revised based on improved statistical analysis The conclusion of the sample size calculations has been presented since the inception of the publication Thank you for your suggestion, we had been trying to improve our ability in scientific language." } ] } ]	1	https://f1000research.com/articles/11-100
https://f1000research.com/articles/12-1567/v1	06 Dec 23	{ "type": "Research Article", "title": "Clinical parameters as predictors for sperm retrieval success in azoospermia: experience from Indonesia", "authors": [ "Rinaldo Indra Rachman", "Ghifari Nurullah", "Widi Atmoko", "Nur Rasyid", "Sung Yong Cho", "Ponco Birowo", "Rinaldo Indra Rachman", "Ghifari Nurullah", "Widi Atmoko", "Nur Rasyid", "Sung Yong Cho" ], "abstract": "Background Azoospermia is the most severe type of male infertility. This study aimed to identify useful clinical parameters to predict sperm retrieval success. This could assist clinicians in accurately diagnosing and treating patients based on the individual clinical parameters of patients.\n\nMethods A retrospective cohort study was performed involving 517 patients with azoospermia who underwent sperm retrieval in Jakarta, Indonesia, between January 2010 and April 2023. Clinical evaluation and scrotal ultrasound, serum follicle stimulating hormone (FSH), luteinizing hormone (LH), and testosterone levels were evaluated before surgery. Multivariate analyses were conducted to determine clinical parameters that could predict overall sperm retrieval success. Further subgroup analysis was performed to determine the factors that the diagnosis of non-obstructive azoospermia (NOA) diagnosis and sperm retrieval success among patients with NOA.\n\nResults A total of 2,987 infertile men attended our clinic. Men with azoospermia (n=517) who met the inclusion criteria and did not fulfil any exclusion criteria were included in the study. The overall sperm retrieval success was 47.58%. Logistic regression revealed that FSH 7.76 mIU/mL (sensitivity: 60.1%, specificity: 63.3%, p<0.001); longest testicular axis length 3.89 cm (sensitivity: 33.6%, specificity: 41.6%); and varicocele (p<0.001) were independent factors for overall sperm retrieval. The FSH cutoff of 7.45 mIU/mL (sensitivity: 31.3%, specificity: 37.7%, p<0,001); longest testicular axis length 3.85 cm (sensitivity: 76.7%, specificity: 65.4%, p<0.001); and varicocele (p<0.001) were independent factors for NOA diagnosis. Varicocele was the only clinical parameter that significantly predicted the success of sperm retrieval in patients with NOA.\n\nConclusions FSH, LH, longest testicular axis, and varicocele are among the clinical parameters that are useful for predicting overall sperm retrieval success and NOA diagnosis. However, varicocele is the only clinical parameter that significantly predicts sperm retrieval success in patients with NOA. High-quality studies are required to assess the other predictors of sperm retrieval success.", "keywords": [ "Sperm Retrieval", "Azoospermia", "FSH", "LH", "Testosterone", "Varicocele", "Longest Testicular Axis" ], "content": "Introduction\n\nInfertility is defined as the inability of a sexually active couple to achieve a spontaneous pregnancy within one year without the use of contraception.1 Furthermore, the incidence of infertility is increasing annually. A meta-analysis of infertility data from 1990 to 2017 showed an increase in the prevalence of infertility by age in 195 countries: 0.370% per year for women and 0.291% per year for men. In addition, age-adjusted infertility (DALYs) also increased by 0.396%. per year for women and 0.293% for men. This was observed in all countries.2\n\nInfertility in couples can be caused by the man, woman or both. Of all infertility cases, men play a role in 40–50% of cases. In the Middle East, men exhibited the highest infertility prevalence (60–70%), whereas the lowest prevalence was observed in Asia (37%).3 Azoospermia is the lack of sperm in the ejaculate. Among all male infertility cases, azoospermia is the most complex diagnosis. A comprehensive clinical examination including history taking, physical examination, hormonal evaluation, scrotal ultrasonography, and Y-chromosome microdeletion testing are among the clinical parameters that are important for azoospermia diagnosis.1,4,5\n\nThe European Association of Urology guidelines recommend two sperm analyses to diagnose azoospermia.1 Subsequently, crucial decisions are required to guide couples along the path to parenting. The couple should be informed that sperm retrieval and assisted reproduction, including traditional adoption, embryo adoption, and donor or partner sperm use are options that may be explored.6,7\n\nThe success rate of sperm retrieval varies among studies. The success rate of conventional testicular sperm extraction (TESE) is 16.7–49%, whereas the success rate of microdissection testicular sperm extraction (mTESE), the gold standard for sperm retrieval in non-obstructive azoospermia (NOA) is 41–63%.6 The success rates of sperm retrieval have been predicted in many studies.8–10 High levels of follicle stimulating hormone (FSH) have been linked to unsuccessful sperm retrieval, according to studies by Ghalayini et al., and Colpi et al., Further, Colpi et al., reported that there was no real relationship between testicular volume and sperm retrieval, whereas, Ghalayini et al., demonstrated an association between testicular volume and the successful sperm retrieval.8,9 According to a large cohort study by Ramasamy et al.,10 FSH levels are not related to the success of sperm retrieval when sperm are collected using mTESE. Another study reported that testicular biopsy results are the most reliable predictor of sperm retrieval success. However, testicular biopsies are not always available before sperm retrieval. Patients with the most severe testicular histology have a sperm retrieval rate of 5–24%, whereas patients with the least severe form, hypospermatogenesis, achieve a sperm retrieval rate of 80–98%.11 However, to our knowledge, no study has examined the clinical parameters predicting sperm retrieval success in Indonesia.\n\n\nMethods\n\nThis retrospective cohort study aimed to determine the clinical parameters that predict the success of sperm retrieval. All patients who underwent sperm retrieval procedures performed by the author in Jakarta, Indonesia, between January 2010 and April 2023 were included in this study. Before sperm retrieval, the clinical parameters of patients were assessed. Data were collected retrospectively from medical records containing information that is routinely collected by the authors. Data collection began on 1 May 2023 in two hospitals, including Cipto Mangunkusumo Hospital and Bunda General Hospital Jakarta. The study protocol was approved by the Ethics Committee of the Faculty of Medicine, Universitas Indonesia (Approval no: 23-02-0168 6 March 2023), which is the only ethics committee covering the province of Jakarta and both Cipto Mangunkusumo Hospital and Bunda General Hospital Jakarta hospitals are teaching hospitals of Faculty of Medicine Universitas Indonesia. Data were collected from academic teaching hospitals. Informed consent was provided in the Initial patient registration form, stating that every patient data collected at the hospital are eligible to be published in an academic publication anonymously. Therefore, consent was obtained from each subject and this study was conducted in accordance with the Declaration of Helsinki.\n\nThe clinical parameters of the 517 patients were collected and retrospectively analyzed. Clinical evaluation, scrotal ultrasound to evaluate varicocele presence and the longest testicular axis, serum follicle stimulating hormone (FSH), luteinizing hormone (LH), and testosterone levels were considered before surgery. Varicocele was diagnosed based on Sarteschi Classification system for Varicocele. The longest testicular axis was measured in centimeters (cm). All surgeries were performed by the author (PB).\n\nThe inclusion criteria for this study were male infertility presenting with azoospermia, meeting the American Society of Anesthesiologists (ASA) grade I-III criteria, and the availability of complete data. The exclusion criteria were severe cardiac or pulmonary insufficiency, severe coagulation disorders, no history of sperm retrieval procedure, incomplete data, and refusal to provide consent for surgery.\n\nEvery patient was counselled at the urology clinic about the risks and benefits of sperm retrieval. The patients who decided to undergo sperm retrieval were informed about the following procedures: percutaneous epididymal sperm aspiration (PESA), followed by testicular sperm extraction (TESE) only if sperm were not present after PESA.\n\nThe patient was placed in a supine position and fentanyl 1–2 mcg/kg, propofol 1 mg/kg, rocuronium 0.1 mg/kg were administered for general anesthesia. Asepsis and antisepsis of the operative field and surrounding areas were performed using povidone-iodine. The first step involved localization of the epididymis with the operator’s non-dominant hand using a three-finger maneuver, followed by aspiration of the epididymis using a 10 cc syringe. The aspirate was then analyzed under a microscope to identify sperm. If sperm were found, the surgery was complete. However, if sperm were not found, TESE was performed.\n\nThe first step of TESE involves incision of the scrotal median raphe, followed by dissection of the tunica dartos and vaginalis of the testis. Bleeding was controlled using electrocoagulation. When the testis was fully exposed, a longitudinal incision (1–2 cm) was created. A small portion of testicular tissue was extracted for microscopic analysis. The testicular incision was sutured using a monofilament nonabsorbable 5.0 cutting needle, while the tunica dartos and vaginalis of the testis were sutured using a multifilament absorbable 4.0 tapered needle. The scrotum was continuously sutured. Intravenous (IV) dexketoprofen (50 mg) and IV granisetron (1 mg) were administered postoperatively.\n\nIBM SPSS Statistics (RRID:SCR_016479) 25.0 Software (IBM Corp., Armonk, NY, USA) was used for the statistical analyses. Categorical data are presented using n (%). Continuous data are presented as the mean ± SD if the distribution is normal and median (min–max) for non-normal distribution. The Kolmogorov Smirnoff single sample test was used to determine normal distribution of continuous variables. Chi-square tests were performed for bivariate analyses. However, if the chi-square criteria were not met, Fisher’s exact test was performed. Statistical significance was set at p<0.05. Further, multivariate analysis using linear regression was performed for eligible variables to analyze the statistical significance of the indicators.\n\nWe performed two subgroup analyses. The first subgroup analysis was used to confirm obstructive azoospermia (OA) or NOA diagnosis and the associated predictive factors. OA was confirmed by a successful PESA procedure; otherwise, NOA was diagnosed. The second subgroup analysis aimed to determine the predictive factors for successful sperm retrieval in patients with NOA. Similar statistical analyses were performed for both subgroups.\n\nReceiver operating curve (ROC) analysis was done for clinical parameters significant in each subgroup. Area under the curve (AUC) is a measure of predictive power. A p value of <0.05 was considered statistically significant.\n\n\nResults\n\nA total of 517 men with azoospermia (OA: 164, NOA: 353) were included in this study. Patient characteristics are presented in Table 1.22 The mean age of the patients in the successful retrieval group was 37 years old. Overall sperm retrieval success was 47.58% and sperm retrieval success among patients with NOA was 30.62%. The Kolmogorov–Smirnov normality test showed that none of the numeric variables were normally distributed. Bivariate analysis revealed significant differences in varicocele, serum FSH, serum LH, and the longest testicular axis affecting sperm retrieval success. Age and duration of marriage were similar between the groups. Diabetes and history of undescended testes (UDT) were not associated with sperm retrieval success.\n\na Mann–Whitney test.\n\nb Chi-square test.\n\nFurther, logistic regression analysis was performed. FSH level, varicocele, and longest testicular axis were independent predictors of sperm retrieval success (Table 2). The R2 score for this linear regression was 0.410 indicating that this analysis comprises 41.0% of all the factors affecting sperm retrieval success.\n\nReceiver operating characteristic (ROC) curve analysis was performed. The cut- off for FSH 7.76 mIU/mL (sensitivity: 60.1%, specificity: 63.3%), p<0.001); longest testicular axis length 3.89 cm (sensitivity: 33.6%, specificity: 41.6%, p<0.001) (Figure 1). Area under the curve for FSH and longest testicular axis was 0.293 (0.248-0.337, p<0.001) and 0.655 (0.607-0.702, p<0.001), respectively (Figure 2).\n\nFSH, follicle stimulating hormone.\n\nA subgroup analysis was performed to determine the clinical parameters that predicted the diagnosis of OA or NOA in men with azoospermia. The results are presented in Table 3. Higher serum levels of FSH and LH, varicocele, and a shorter testicular axis were significantly associated with the diagnosis of NOA. There were no significant differences in age, marriage duration, and previous illnesses, such as diabetes and UDT, regarding the diagnosis of OA or NOA. Logistic regression analysis revealed that FSH, varicocele, and longest testicular axis were independent risk factors for NOA (Table 4). This logistic regression model comprised 42.0% of all possible factors for determining OA or NOA diagnosis, as indicated by an R2 value of 0.420.\n\na Mann–Whitney test.\n\nb Fisher exact test.\n\nc Chi-square test.\n\nROC curve analysis was performed. For the diagnosis of NOA, the FSH cut-off value was 7.45 mIU/mL (sensitivity: 31.3%, specificity: 37.7%, p<0.001); longest testicular axis length 3.85 cm (sensitivity: 76.7%; specificity: 65.4%, p<0.001). Area under the curve for FSH and longest testicular axis were 0.707 (0.660-0.753, p<0.001) and 0.265 (0.222-0.307, p<0.001), respectively (Figure 3).\n\nFSH, follicle stimulating hormone; OA, azoospermia; NOA, non-obstructive azoospermia.\n\nA subgroup analysis was performed to determine the clinical parameters for predicting sperm retrieval success in patients with NOA. A total of 354 patients with NOA were included in the analysis. The results are presented in Table 5. Among men with NOA, a varicocele is a significant determinant of sperm retrieval success.\n\na Mann–Whitney test.\n\nb Fisher exact test.\n\nc Chi-square test.\n\nTable 6 displays a summary of FSH and longest testicular axis cut-offs for all subgroups. The cut-off value for FSH and longest testicular axis to determine overall sperm retrieval success and predicting NOA diagnosis is not very different. FSH has better sensitivity and specificity in predicting overall sperm retrieval success compared to longest testicular axis, on the other hand, the longest testicular axis has better sensitivity and specificity in predicting NOA diagnosis.\n\n\nDiscussion\n\nThe management of male infertility is challenging because of multifactorial causes. The leading cause of male infertility is idiopathic, comprising 30–40% of all azoospermia.1 Azoospermia is one of the most challenging andrological conditions, and is the most severe form of male infertility. According to the European Association of Urology guidelines, only 10% of all infertile male patients present with azoospermia.1 However, in Indonesia, 53% of infertile patients presented with azoospermia, 46% had at least one normal semen parameter, and 4.9% had normal semen parameters.12\n\nUp to 15% of infertile men have azoospermia, which affects approximately 1% of all men. Azoospermia is roughly divided into NOA and OA, depending on the capacity of the testes to generate and distribute spermatozoa.13 The diagnosis of OA varies among studies. From clinical parameters (normal testicular volume and FSH level),14 performing PESA or testicular biopsy may be indicated.14–16 In this study the diagnosis of OA is established by successful PESA procedure.\n\nNumerous factors of testicular or pre-testicular origin may cause NOA. Genetic conditions such as Klinefelter syndrome and Y chromosome microdeletions, congenital conditions such as cryptorchidism, exposure to radiotherapy and chemotherapy, genital trauma, and complex infections such as mumps orchitis are among the testicular causes of NOA. The primary endocrine factors that lead to pretesticular hypogonadism are abnormalities of the hypothalamic-pituitary-gonadal axis. Additionally, up to 15% of NOA cases may be idiopathic.17\n\nMultivariate analysis revealed that FSH, varicocele, and longest testicular axis were the three independent variables predicting sperm retrieval success and NOA diagnosis. Varicocele was the only independent variable that determined sperm retrieval success in patients with NOA. Another study by Yang et al., also reported that FSH is an independent risk factor in predicting the sperm retrieval rate (SRR) in NOA with a sensitivity of 0.70 (0.66-0.73) and specificity of 0.62 (0.58-0.66).18 The result of a study by Salehi et al., are in line with those of the present study, stating that high levels of FSH and small testicular volume were associated with a lower chance of successful sperm retrieval.19 A systematic review by Major et al., also showed that FSH levels exhibit an inverse relationship with the SRR in conventional TESE. Another study confirmed that varicocele repair is beneficial for increasing the SRR and improving the testicular histopathological pattern (p<0.001) regardless of the patient’s FSH level.20\n\nWhile the surgeon’s experience and laboratory expertise in dissecting and processing the testicular parenchyma can undoubtedly influence the success of sperm retrieval, many other predictors have also been investigated, such as clinical profiles, Klinefelter syndrome status, cryptorchidism, paternal age, testicular volume, and laboratory panels (FSH, inhibin B, Y-chromosome microdeletion, and surgery).21\n\nTo our knowledge, this is the first study to develop a predictive model for successful sperm retrieval in Indonesia. A limitation of this study is that the R2 value of multivariate of the linear regression for sperm retrieval success and NOA diagnosis were only 0.410 and 0.420, respectively, indicating that the factors investigated in this study only comprise 41.0% and 42.0% of all possible factors to predict sperm retrieval success. The authors recommend that further high-quality studies be undertaken to assess other factors that predict sperm retrieval success.\n\n\nConclusions\n\nFSH, LH, longest testicular axis, and varicocele are among the clinical parameters that are useful for predicting overall sperm retrieval success and NOA diagnosis. However, varicocele is the only clinical parameter that significantly predicts sperm retrieval success in patients with NOA. High-quality studies are required to assess the other predictors of sperm retrieval success.", "appendix": "Data availability\n\nOpen Science Framework: Clinical Parameters as Predictors For Sperm Retrieval Success In Azoospermia: Experience From Indonesia. https://doi.org/10.17605/OSF.IO/2EAU4. 22\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\nThe preliminary result of this research was presented at the Société Internationale d’Urologie (SIU) Around the World Dubai 2021 conference as an unmoderated ePoster.\n\n\nReferences\n\nTürk C, Neisius A, Petrik A, et al.: EAU Guidelines on Urolithiasis. Eur. Assoc. Urol. 2018; 2018: 1–87. Reference Source\n\nSun H, Gong TT, Jiang YT, et al.: Global, regional, and national prevalence and disability-adjusted life-years for infertility in 195 countries and territories, 1990-2017: results from a global burden of disease study, 2017. Aging (Albany NY). 2019 Dec; 11(23): 10952–10991. Publisher Full Text\n\nKumar N, Singh AK: Trends of male factor infertility, an important cause of infertility: A review of literature. J. Hum. Reprod. Sci. 2015; 8(4): 191–196. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBirowo P, Putra DE, Dewi M, et al.: Y-Chromosomal Microdeletion in Idiopathic Azoospermic and Severe Oligozoospermic Indonesian Men. Acta Med. Indones. 2017; 49(1): 17–23. PubMed Abstract\n\nKim H, Kim S, Lee B, et al.: Y Chromosome Microdeletions in Infertile Men with Non-obstructive Azoospermia and Severe Oligozoospermia.2017; 18(3): 307–315.\n\nKapadia AA, Walsh TJ: Testicular Mapping: A Roadmap to Sperm Retrieval in Nonobstructive Azoospermia? Vol. 47. . Urologic Clinics of North America. W.B. Saunders; 2020; pp. 157–164.\n\nTurek PJ, Givens CR, Schriock ED, et al.: Testis sperm extraction and intracytoplasmic sperm injection guided by prior fine-needle aspiration mapping in patients with nonobstructive azoospermia. Vol. 71. . FERTILITY AND STERILITY; 1999.\n\nColpi GM, Colpi EM, Piediferro G, et al.: Microsurgical TESE versus conventional TESE for ICSI in non-obstructive azoospermia: a randomized controlled study. Reprod. Biomed. Online. 2009; 18(3): 315–319. PubMed Abstract \| Publisher Full Text Reference Source\n\nGhalayini: Clinical Comparison of Conventional Testicular Sperm Extraction and Microdissection Techniques for Non-Obstructive Azoospermia. J. Clin. Med. Res. 2011; 3(3): 124–131. Publisher Full Text\n\nRamasamy R, Lin K, Gosden LV, et al.: High serum FSH levels in men with nonobstructive azoospermia does not affect success of microdissection testicular sperm extraction. Fertil. Steril. 2009; 92(2): 590–593. Publisher Full Text Reference Source\n\nSousa M, Cremades N, Silva J, et al.: Predictive value of testicular histology in secretory azoospermic subgroups and clinical outcome after microinjection of fresh and frozen-thawed sperm and spermatids. Hum. Reprod. 2002 Jul; 17(7): 1800–1810. PubMed Abstract \| Publisher Full Text\n\nBirowo P: Semen Parameter Profile of Infertile Men Visiting Andro-Urology Clinic. eJournal Kedokt. Indones. 2020; 8(2): 88–92. Publisher Full Text\n\nCocuzza M, Alvarenga C, Pagani R: The epidemiology and etiology of azoospermia. Clinics (Sao Paulo). 2013; 68 Suppl 1(Suppl 1): 15–26. PubMed Abstract \| Publisher Full Text\n\nEnatsu N, Miyake H, Chiba K, et al.: Predictive factors of successful sperm retrieval on microdissection testicular sperm extraction in Japanese men. Reprod. Med. Biol. 2016; 15(1): 29–33. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHao L, Li Z, He H, et al.: Application of percutaneous epididymal sperm aspiration in azoospermia.2017; pp. 1032–1035.\n\nWosnitzer MS, Goldstein M: Obstructive Azoospermia. Urol Clin NA. 2013. Publisher Full Text\n\nEsteves SC: Clinical management of infertile men with nonobstructive azoospermia. Asian J. Androl. 2015; 17(3): 459–470. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYang Q, Huang YP, Wang HX, et al.: Follicle-stimulating hormone as a predictor for sperm retrieval rate in patients with nonobstructive azoospermia: A systematic review and meta-analysis. Asian J. Androl. 2015; 17(2): 281–284. PubMed Abstract \| Publisher Full Text\n\nSalehi P, Derakhshan-Horeh M, Nadeali Z, et al.: Factors influencing sperm retrieval following testicular sperm extraction in nonobstructive azoospermia patients. Clin. Exp. Reprod. Med. 2017 Mar; 44(1): 22–27. Publisher Full Text\n\nBirowo P, Prasetyo D, Pujianto D, et al.: Effect of varicocele repair on sperm retrieval rate and testicular histopathological patterns in men with nonobstructive azoospermia. Asian J. Androl. 2021; 24(July): 84–85. Publisher Full Text Reference Source\n\nArshad MA, Majzoub A, Esteves SC: Predictors of surgical sperm retrieval in non-obstructive azoospermia: summary of current literature. Int. Urol. Nephrol. 2020 Nov; 52(11): 2015–2038. PubMed Abstract \| Publisher Full Text\n\nRachman RI: Clinical Parameters as Predictors For Sperm Retrieval Success In Azoospermia: Experience From Indonesia. [Dataset]. OSF. 2023. Publisher Full Text" }	[ { "id": "229809", "date": "06 Feb 2024", "name": "Doddy Moesbadianto Soebadi", "expertise": [ "Reviewer Expertise Reproductive Urology." ], "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 simple but important study, that gives us, especially in this region, that we have data how many percent we could predict the result of this procedure for azoospermic couple. A very simple (only physical examination and some laboratory examination) and practical, that every physician treating aziospermic patient has evidence to inform the couple the prediction of the procedure. More details and may be if possible a random and more scientific research are needed to support this findings.\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? Yes", "responses": [] }, { "id": "235153", "date": "07 Feb 2024", "name": "Dragos Puia", "expertise": [ "Reviewer Expertise Urology", "male infertility" ], "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\nAfter reading this interesting manuscript, I have some questions and suggestions. 1. Paragraph 2 in the Methods subchapter represents Results 2. Why patients with severe systemic diseases (ASA III) underwent an elective surgery? 3. How many sperm analysis had the patients performed before receiving the diagnosis of azoospermia (current guideline recommends at least 2 tests) 4. In Table 1, please give SD and I would suggest replacing \"marriage duration: with \"infertility duration\" 5. How was obstructive azoospermia differentiated from non-obstructive? Please give details 6. I think this study has severe limitations resulting from the fact that many important predictive factors like genetic test or Inhibin B levels have not been evaluated.\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/12-1567
https://f1000research.com/articles/12-288/v1	15 Mar 23	{ "type": "Research Article", "title": "Maternal anaemia care in Kano state, Nigeria: an exploratory qualitative study of experiences of uptake and provision", "authors": [ "Aisha Kuliya-Gwarzo", "Tara Tancred", "Daniel Gordon", "Imelda Bates", "Joanna Raven", "Tara Tancred", "Daniel Gordon", "Imelda Bates", "Joanna Raven" ], "abstract": "Background: Maternal anaemia (anaemia in pregnancy, childbirth, and the postpartum period) remains a persistent challenge, particularly in Kano State, Nigeria, which has the highest prevalence of maternal anaemia globally, at 72%. Methods: We conducted a qualitative study in Murtala Muhammad Specialist Hospital in Kano State, Nigeria. We aimed to identify factors constraining uptake and provision of maternal anaemia care, exploring perspectives across different stakeholders. We carried out 10 key informant interviews with policymakers and hospital managers, 28 in-depth interviews with healthcare providers and pregnant women using antenatal services and four focus group discussions with pregnant women’s husbands and mothers-in-law. Data were analysed thematically. Results: Issues with provision include a lack of provider training and guidelines specific to maternal anaemia and blood transfusion, insufficient staff to meet increasing demand, and inadequate resources. Issues with uptake include the inability to afford informal user fees, distrust in health services and the blood transfusion process, and a lack of understanding of the causes, consequences, and treatment for anaemia, resulting in poor uptake of care and adherence to treatment. Conclusions: This study recommends the implementation of standardized guidelines and training sessions to better support healthcare providers in offering quality services and increasing funding allocated to supporting maternal anaemia care. Education initiatives for service users and the public are also recommended to build public trust in health services and to improve understanding of maternal anaemia.", "keywords": [ "Maternal anaemia", "experiences of care", "care provision", "qualitative research", "Nigeria" ], "content": "Introduction\n\nIn Sub-Saharan Africa, approximately 57% of pregnant women experience anaemia.1 This is problematic, as even mild anaemia increases perinatal mortality and early neonatal mortality, largely associated with preterm birth and intrauterine growth restriction. The odds of maternal mortality are also more than two times greater for severely anaemic women (haemoglobin < 7.0 g/dL), due to an increase in fatal postpartum haemorrhage.2,3\n\nThe rate of prevalence of pregnancy-related anaemia in Nigeria is among the highest in the world, with prevalence ranging from 35% (Lagos) to 72% (Kano State).4,5 Common causes of anaemia in pregnancy are iron and folate deficiency.2 In Nigeria, parasitic infections such as malaria, hookworm and schistosomiasis, viral infections like human immunodeficiency virus (HIV), hepatitis B and C and inherited conditions affecting red blood cells such as sickle cell disease and thalassemia also contribute to anaemia.6\n\nAlthough physiological factors associated with anaemia have been well described, the health system and sociological factors are important. For example, the diagnosis and management of anaemia during antenatal care. Uptake of antenatal care in Nigeria is lacking, with only 67% of pregnant women attending antenatal care at least once, and only 56% attending four or more times.7 Antenatal care quality may not be consistent, and in similar settings, the use of reliable approaches to measure anaemia occurs infrequently, and is often constrained by the availability of haemoglobin tests and reliance on symptom-based and clinical diagnosis.8,9 Furthermore, though use of supplements or specific guidance around nutrition are key ways that anaemia can be managed in pregnancy,10 adherence may be poor due to the gastrointestinal side effects of iron supplementation, lack of contact with local health services and misconceptions about anaemia.11,12 An understanding of these factors is important to inform effective interventions for anaemia in pregnancy, which are culturally appropriate and address key deficiencies in healthcare provision for anaemia.13 With the highest maternal anaemia prevalence in Nigeria,4,5 Kano State is ideally situated to explore these issues.\n\nThis study aims to identify the factors that influence how maternal anaemia services are provided and used in Murtala Muhammad Specialist Hospital (MMSH) in Kano State. The findings are used to make practical and widely applicable recommendations to reduce anaemia in pregnant women within and beyond Nigeria.\n\n\nMethods\n\nA qualitative study was carried out to explore experiences around the provision and uptake of maternal anaemia care at MMSH.\n\nMMSH is a secondary hospital in the Kano metropolis of Kano State in north-western Nigeria, with a population 13.4 million, most of whom belong to the Hausa or Fulani ethnic groups.14 It is the largest government-owned hospital in Northern Nigeria. No fees are charged for consultation and admission, inclusive of antenatal services. There are 275 beds for obstetrics and gynaecology and a dedicated blood bank to collect from family members, which it screens for HIV and Hepatitis B and C using rapid testing.\n\nKey informant interviews\n\nFour key informant interviews were carried out with two policy makers and two hospital managers. Participants were sampled purposively due to their knowledge of policy-making that impacts care, interventions during pregnancy and childbirth, training of providers and oversight at hospitals. Prospective participants were contacted in-person or by phone by AKG and were given information about the study. They were given more than 24 hours to decide whether they wanted to participate or not. Interviews were conducted by AKG in a private room within the hospital or the participant’s workplace, wherever participants felt comfortable, and lasted for 30–100 minutes.\n\nIn-depth interviews\n\nIn-depth interviews were carried out with ten healthcare providers (doctors, nurses, laboratory staff, or community health extension workers who screen women and refer them to midwives) and 18 pregnant women. Providers were sampled purposively based on their knowledge and experience in pregnancy anaemia management. Pregnant participants were sampled purposively to maximize diversity around the following characteristics: parity; duration of pregnancy; and prior experience of blood transfusion. Sampling was carried out until theoretical saturation had been reached.\n\nAKG identified prospective healthcare providers through working with department heads, and approached them directly to provide information about the study. They were informed that this would be to gain their perspectives about providing anaemia care and would in no way be used to evaluate their performance. They had a week to consider their participation. Pregnant women were recruited in the waiting hall of the MMSH antenatal clinic. They were approached by AKG—who is in no way involved in their care—and were given information about the study, namely that they would be asked questions about their experiences of anaemia care and what might influence their uptake of this care. They had a full day to consider their participation.\n\nInterview guides for providers focused on existing policies and services offered across the spectrum of care during pregnancy, childbirth and into the post-partum period, inclusive of the diagnosis and management of maternal anaemia. Interview guides for pregnant women focused on understanding of anaemia and experiences of care during pregnancy and childbirth. These guides were developed following an extensive reading of the literature and author AKG’s intimate knowledge of the context.\n\nInterviews with providers and pregnant women were scheduled at their convenience, and for providers, took place in private spaces in the hospital. Some women needed permission from husbands or relatives and were given a contact number to confirm participation. Most interviews with pregnant women were held in the matron’s office at the antenatal clinic. However, those who confirmed participation after obtaining permission had their interviews conducted at AKG’s office in Aminu Kano Teaching hospital. Interviews took 30–40 minutes.\n\nFocus group discussions\n\nFour focus group discussions (FGDs) were held with women’s relatives, each with six participants: two groups of six husbands and two groups of six mothers-in-law. Snowball sampling was used to identify participants, as women who participated in interviews were asked to inform their husbands and their mothers-in-law about the research and to invite them to participate in FGDs. Those who agreed were contacted by telephone and FGDs were organized.\n\nDiscussion guides focused on participants’ understanding of anaemia and perceptions of care received by their partners or daughters-in-law during pregnancy and childbirth.\n\nAll interviews and FGDs were carried out in Hausa or English. All interviews and FGDs were audio-recorded, transcribed verbatim, and later translated into English if necessary. Handwritten notes to capture non-verbal communication were made during interviews and FGDs by a research assistant. FGDs took 45–70 minutes.\n\nAll steps of the data analysis were carried out by AKG, TT, and DG. Data were read and re-read for familiarity. Line-by-line inductive coding was carried out and a coding framework was established in Excel. Codes were grouped into higher-order codes and themes. Applying and refining the coding framework was repeated until no new codes were generated and thematic saturation was reached, at which point, participant recruitment ceased.\n\nThe following four themes emerged: guidelines and policies for managing anaemia; quality of care; resources and financing; and knowledge, attitudes and practices of women and family members. These are described in the results that follow.\n\n\nResults\n\nAll participants are described in Table 1.\n\nKey informants and providers summarized the guidelines and policies for managing anaemia. Pregnant women are seen first between 20 and 28 weeks. Before consultation, they receive anaemia education on topics including: issues in pregnancy, childbirth and when breastfeeding; risk factors; signs and symptoms; prevention using diet; treatment; and the importance of child spacing. During antenatal care consultations, pregnancy is confirmed using last menstrual period, the estimated due date is calculated, and the women are tested for blood group, packed cell volume and infections.\n\n‘We offer free laboratory tests at the first antenatal visit which include [packed cell volume] check, blood group and HIV screening and urinalysis. They are all free.’ (Hospital manager)\n\nHealthcare professionals are expected to treat anaemia based on an individual assessment using their clinical judgement, the client’s estimated packed cell volume, severity of anaemia and likely cause. Most pregnant women are administered precautionary oral iron supplements because iron deficiency anaemia is very common. Women with severe anaemia are thought to be from rural areas and may not have attended antenatal care. Blood transfusion is indicated in those with associated dizziness and weakness.\n\nProviders reported there was no concerted effort to ensure that staff were trained on guidelines for anaemia diagnosis and management, or that guidance was fully implemented or monitored.\n\n‘A deliberate policy or methodology to distribute most of these guidelines is usually not in place.’ (Policymaker)\n\nHealthcare professionals reported that, as per Kano state policy, care to women during pregnancy, childbirth, and in the postpartum period is free, including a packed cell volume screen, supplements, and medication to prevent/treat anaemia and dietary advice. Participants clarified that blood transfusions were also included for free, provided patients’ relatives donated blood to replace units used.\n\n‘We offer blood transfusion which is also free […] even the donors that will come and donate the blood they will all be screened free.’ (Hospital manager)\n\n‘The patient has to bring a donor […] we give the transfusion free but the only thing is that she needs to bring the donor.’ (Policymaker)\n\nAs subsequent results suggest, there is a mismatch between the policies and guidelines that exist and the practices that take place.\n\nHealthcare providers were knowledgeable about maternal anaemia and its often-complex origins. There was recognition that there is not always the ability to address all possible causes, which would necessitate nutrition counselling, iron, and folic acid supplementation—and adherence, malaria prophylaxis, deworming, and child spacing, among other interventions. The nutritional and child-spacing aspects were understood as being culturally mediated and difficult to change.\n\n‘Anaemia associated with pregnancy has a lot of issues—it is more like multifactorial. If you look at the way our women are, repeated pregnancies and deliveries actually leads to loss of blood at every delivery, or rather, at every labour, and so many of them, before even the labour, they may have a miscarriage and this also causes a lot of bleeding … The other issue is that if you look at it, our cultural habit of eating … our eating habits do not contain many of the green vegetables that may have the haemoglobin, or rather, the iron component that should be consumed daily. The other issue is … malaria … another key role in developing anaemia [is] haemorrhage, so there are so many things and eh, I must say, anaemia is playing a very bad role in the issue of pregnancy, in pre-term delivery and other issues like that.’ (Healthcare provider)\n\nHealthcare professionals and women reported several issues that affected access to and the quality of care: high staff turnover and inadequate staffing, particularly of specialist physicians; high demand for care; insufficient remuneration for staff; and unsatisfactory supervisory support.\n\n‘The gap is wide because we have a lot of patients here and the staff are few … let’s take the eclamptic patients. We have almost 20-something beds in the eclamptic ward, but you will see only one or two staff running the shift. At times we have a patient that is coming to theatre, and for God’s sake, if it is only one staff, who will take care of the ward and who will come to the theatre, do you understand?’ (Healthcare provider)\n\n‘We have a kind of brain drain if so to say or people are leaving the service of the state for a greener pasture, because if you compare the package of state and federal institutions, definitely there is a sharp difference. So, really, there is difference from the state to the federal institution, so most of our staff leave for the federal institutions and this may account for why staff are not enough in this facility or in the state generally.’ (Healthcare manager)\n\nHospital managers, women and relatives reported that free provision was responsible for a drastic increase in women attending the service, which placed a strain on service delivery. This is because the service was attracting users from nearby states such as Jigawa, as well as an influx of clients previously unable to afford care.\n\n‘So, like Kano, everybody is trooping into Kano [to access maternal care]. So, if you plan for like 10 million people, then you end up having 15 million for example.’ (Policymaker)\n\nHealthcare professionals reported that staff often did not take time to properly consult with patients, in addition to huge workload, because of other commitments outside the hospital.\n\n‘Some are usually in a hurry to finish and go for other issues of theirs. Either some of them may want to go for private practice, or somewhere they have a personal issue.’ (Healthcare provider)\n\nConsequently, time for one-on-one counselling regarding medication compliance was limited, and there was reduced ability to diagnose women with anaemia in the early stages. Many women and relatives felt unable to discuss problems with staff because there was a lack of privacy during consultations due to crowded waiting areas. Staff also appeared rushed and disengaged, which women regularly noted prevented them from raising potential concerns.\n\n‘The time you get is very short and it takes long before you see them because there are too many people to be seen and there is no privacy.’ (Pregnant woman)\n\n‘[After describing a complication and being asked why the nurse was not informed:] I couldn’t talk to her, she seemed to be in a hurry and there were many people in the room waiting.’ (Pregnant woman)\n\nAppropriate maternal anaemia care may be constrained by a lack of training and, as above, lack of specific guidelines. For example, providers understood that maternal anaemia is defined as a low packed cell volume in pregnancy or the postnatal period and relied on estimates of this to diagnose anaemia. However, providers’ perceptions of the cut-off values at which anaemia would be indicated—some stated 20%, others 25% and others 30%—were inconsistent.\n\n‘Investigations and diagnosis is by [packed cell volume] only … honestly, we consider cost most of the time. We think if we ask for a full blood count it may be too expensive, so the only thing we used to ask for is [packed cell volume].’ (Healthcare provider)\n\nFor blood transfusions, staff relied on knowledge from books and the experience of senior colleagues as opposed to local standards of practice, which were not used. Hospital managers and healthcare providers reported no formally scheduled staff training on maternal anaemia, with staff required to use their experience to provide on-the-job training.\n\n‘We train [new staff] here [in maternal anaemia care] as they come, on the job. But no formal training.’ (Hospital manager)\n\nHealthcare providers reported that they were often unable to diagnose causes of maternal anaemia because specific tests were unavailable or too costly. As a result, reliance was on clinical and symptom-based diagnosis, which can often only identify anaemia when it is very severe.\n\n‘We think if we ask for full blood count it may be too expensive so the only thing we use to ask for is [packed cell volume].’ (Healthcare provider)\n\n‘Diagnosis of anaemia, usually the patient will be complaining of dizziness or palpitation. When they come, we have to interview them, we will do physical examination from head to toe, then their conjunctiva.’ (Healthcare provider)\n\nFurthermore, causes of anaemia were rarely investigated, due to too much perceived demand, which may constrain appropriate care.\n\n‘I don’t know of my colleagues but I know I don’t always … investigate the cause [of anaemia]. I know not many people used to be very keen on diagnosing the cause, we just assess if she needs transfusion, then we transfuse, if she doesn’t need transfusion, because maybe we considered the population is too much or something. We are not used to really investigating the cause.’ (Healthcare provider)\n\nHealthcare providers reported stocks of medication were often inadequate because demand out-weighed supply.\n\n‘This program has not been effective and efficient and they will only give drugs that will last for 2 weeks for the whole quarter.’ (Hospital manager)\n\nHospital managers also acknowledged that reporting stockouts was not always well-received at higher levels. These participants therefore reported attempts to generate resources and support free care by diverting funds away from the drug revolving fund—a fund generated by drug sales, laboratory tests and other hospital services intended to maintain services.\n\n‘You don’t ever say that the drug is out of stock because […] if the government or any official that is close to the government gets to know of this […] they will remove you.’ (Hospital manager)\n\n‘We take some funds from the [drug revolving fund] and give it to this free maternity but […] in a way we are decapitalizing the [drug revolving fund].’ (Hospital manager)\n\nDespite existing policies, women and relatives reported often purchasing medications from pharmacies—or from staff—along with making other out-of-pocket expenses, like paying for packed cell volume testing. Women and their husbands corroborated this finding, widely reporting the expenses associated with seeking care. These expenses were seen as making uptake of care, or use of appropriate medications, inaccessible for some due to widespread poverty.\n\n‘If we are out of stock, we ask them to buy. If they can afford to buy, fine, if they cannot afford to buy then may God save them.’ (Hospital manager)\n\n‘There is no free service, it is just politics […] Everything needed for delivery ranging from hand gloves, razor blades and others, have to be provided by the family.’ (Husband)\n\nBlood availability remains a major constraining factor in treating anaemia. In emergencies, medical staff collecting blood for transfusion from the blood bank are responsible for ensuring that, prior to patient discharge, the patient’s family provide replacement blood.\n\n‘They said they will never agree to do that [give blood without a replacement donation] because some of the doctors do not insist that the patient replaces the blood.’ (Healthcare provider)\n\nBecause blood type may be rare and consumables such as blood bags must be bought, significant delays can occur. Relatives are often not available when there is an urgent need, so it can take hours to obtain a donation, screen for infections and crossmatch. The most common reason for rejection of donated blood is the presence of Hepatitis B virus markers. Despite need for transfusion, if blood, or a specialist able to administer the transfusion, is not available, it will not take place. Multiple participants spoke of instances where they or their partner were awaiting a transfusion that never took place.\n\n‘Well the person to donate came after a few hours and donated but in the end she was not even transfused.’ (Husband)\n\nParticipants reported that obtaining donor blood is slow and difficult due to: negative cultural connotations of having another person’s blood in one’s system; low level of awareness of maternal anaemia in the public; fear of being diagnosed with an unknown disease; belief that they do not have enough blood to donate; belief that a financial burden will be incurred; and public distrust of transfusion services. The difficulty in sourcing donors leads some to abscond from the ward after transfusion without replacing blood. Consequently, blood bank staff often refuse to accept emergency requests for blood, exacerbating the issue.\n\n‘It means I have a different blood of someone I don’t know of his character and he may not be a good person.’ (Pregnant woman)\n\n‘We were told to provide the donors and it was quite distressing since she had [need for] transfusion and not many people were willing [to donate blood]. They are usually scared of giving blood … maybe they think you can contact disease from that and they sometimes say they do not have enough to give. Some are also scared of testing [for infections]. You know people know the blood will be tested.’ (Husband)\n\nMost women and relatives described anaemia in terms of its symptoms, some mistakenly equating anaemia to blood pressure. Most reported poor diet and blood loss as causes, but inconsistently related repeated pregnancies at short intervals to anaemia. Relatives mostly related maternal anaemia to low blood levels from inadequate diet or early pregnancy. Healthcare professionals reported that often, even after education, women still become anaemic. There are several reasons for this. Some women reported that many did not engage fully with education and were distracted, while others reported that the time would have been better used for one-on-one consultations.\n\n‘To those that listen it is very useful but many do not listen […] some of the women would rather listen to their phone radios.’ (Pregnant woman)\n\nHealthcare professionals reported that medication and dietary advice are sometimes not followed, in part due to lack of understanding, inconsistent antenatal care attendance, illiteracy and lack of anaemia education as well as poor perception of hospital care. Prescriptions are often lost and not re-administered until the following visit.\n\n‘Honestly, some don’t take their prescriptions, some are negligent. When the drugs are prescribed, they don’t take it. Like during antenatal, there are 4 visits, some will come for 3 visits, but they will not even know what drugs they have been prescribed. And we issue health talks every day, [pregnant women] are being told the importance of taking their drugs, medical tests, but some will tell you they don’t know what they have been asked to do.’ (Healthcare provider)\n\n‘[Pregnant women in the community] will say they are being harassed … some will not agree, you see, this hospital, rumours have been circulating saying people insult each other, the doctor insults this and that. Some they prefer to see male doctors than female doctors … because the male doctors don’t harass you. If you are sick in this hospital, male doctors will look after you better, they follow standard procedures bit by bit, they ask you this and that, but female doctors will not mind … some will not even listen to you; they will harass and embarrass you.’ (Pregnant woman)\n\nSome women dislike taking the medications like iron and folic acid supplementation, which are prescribed routinely, while others were not aware that drugs were prescribed and were unclear on medication guidance.\n\n‘Yes, there are some that tell you when they take the drugs they will vomit [because] they don’t like it.’ (Healthcare provider)\n\nMany women continued to believe that there was no cure for maternal anaemia, but that a range of traditional herbal treatments alleviate symptoms. Traditional healers are cheap, known to the family, live locally, can provide care to women at home, and women do not require permission to seek their assistance.\n\n‘They will start taking the traditional concoction to give the woman [in the village]. Those are the women that will come in with severe anaemia and cardiac failure, but this is rare.’ (Hospital manager)\n\n‘Traditional health care is good because is at home you can help yourself with what you can afford.’ (Pregnant woman)\n\nHowever, women and relatives explained that if traditional treatments fail, the condition may become severe, and women will eventually have to seek hospital care.\n\n‘They believe in the [traditional birth attendants] so much. They only come to hospital when it is late and the woman would have suffered enough.’ (Husband)\n\nHowever, attending hospital care was sometimes seen as burdensome, taking women away from domestic responsibilities, which must be completed upon their return.\n\n‘It is like everybody is in a hurry and sometimes the women would rather listen to their phone radios … some want to go back home early—maybe they have not finished their chores. Some will be chatting and maybe some would like to visit the market.’ (Pregnant woman)\n\nWomen, husbands, and relatives saw anaemia as a source of familial friction, especially because women ordinarily needed to gain the permission of husbands and/or mothers-in-law to attend hospital appointments. Though most husbands reported supporting their wives for healthcare costs, healthcare professionals reported that women were often financially dependent on husbands who could not, or would not, provide enough money for women to treat their anaemia and effectively feed the family. Poor economic status of women often disempowers them and further constrains their decision-making.\n\n‘If you prescribe the drugs the husband will try to get the cheaper alternative which may not be good.’ (Pregnant woman)\n\n‘If you look at cultural issues, our family setting where you have repeated pregnancies on and on, you see a woman having 8, 10 deliveries and her economic status is very poor … there is no empowerment, women are totally under-powered and they are fully dependent, 100% dependent on … what is being dumped on them. If [her husband] has only N200, then he will say, ‘ok take this N200, know how to manage it’, that will be the morning fee for breakfast for her and probably with about 5 children, so who will eat? She’d rather give it to the children and starve herself up to the time when food is available, and if the food is available, is not nutritious in the sense that probably, carbohydrate is more than the protein you can get and then usually they lack the elements that can be used by the body to produce the blood, like the iron.’ (Healthcare provider)\n\nRelatives reported that women did not always accurately relay information to their husbands from the clinic because they may have forgotten or misunderstood. They reported that women were sometimes too shy to raise problems with staff. Some women added that being attended to by male staff would aggravate some husbands.\n\n‘They don’t like a man to attend to their wife because of jealousy.’ (Pregnant woman)\n\nOne woman explained that blood transfusions could also cause arguments between husbands and relatives, because they feel that the need for a transfusion means that the husband does not take proper care of his wife.\n\n‘[Blood transfusion] results in conflicts […]. The general feeling is that the husband has failed.’ (Husband)\n\nMost women reported that they would be happy to have their husbands in attendance at antenatal appointments, because they felt their husbands could communicate concerns directly to caregivers and were more likely to believe advice directly from hospital staff. Women reported that most husbands did not attend because of cultural norms, particularly the fear of embarrassment if seen accompanying a woman to the antenatal care or for childbirth. Some husbands responded that they would be glad to attend the antenatal care with their wives, but that this would mean taking time off work, being in a crowded space in the clinic and interacting with other women. Consequently, only a few reported attending and instead supported their wives financially.\n\n‘The problem with this [information given in antenatal care] is that we are all women. Most of us do not earn and we depend on our husbands, and since the husband is not there with you, even if you tell him, he may think you are just saying it because you want to eat this and that, but if he is there and hears what is being said from the nurses, he will believe it more.’ (Pregnant woman)\n\n‘Financial is the most important support we can give, and outside that, it is to wish them safe delivery.’ (Husband)\n\n\nDiscussion\n\nKey findings from our study highlight that, in Kano, key issues with provision of care for maternal anaemia centred on the service being under-staffed and under-resourced to deal with demand. Tests to determine the causes of maternal anaemia were sometimes unavailable. Providing blood for transfusions in the event of severe maternal anaemia was also problematic, due to difficulties ensuring the replacement of blood. Healthcare providers have limited time and space to provide comprehensive education about maternal anaemia and how it is treated, leaving some misconceptions around treatment unchecked. Uptake of maternal anaemia care was constrained by the understanding that maternity services are not free in practice. Women’s reliance on their husbands for financial resources and permission to seek care was a barrier. Husbands were rarely involved in antenatal care due to social norms, embarrassment, and practical constraints around availability of space in the hospital.\n\nThese issues in provision and uptake suggest that anaemia is not being fully addressed in this vulnerable population, contributing to unacceptably high levels of anaemia and peripartum mortality seen in Kano state.7 Findings around poor quality of maternal anaemia care are consistent across other Nigerian settings and low- and middle-income countries (LMICs).15–17 In Nigeria—and LMICs with “free” maternal care policies—the expectation of both indirect or direct payments for maternity services limits uptake of care and pushes women to receive informal care from traditional healers.18–22 Anaemia is complex, and while our results highlight a generally good understanding of anaemia as a consequence of inadequate nutrition or blood loss among participants who knew what anaemia was, the role of child spacing to prevent anaemia was not well-understood. There is likely to be misunderstanding of how anaemia can be prevented at a household level, which is illustrated through the very high prevalence of maternal anaemia (72%) in Kano.5,6 These findings are consistent with other settings, in which prevention of anaemia at the community level, particularly through nutrition, was poorly understood.23–26 As has been found in other LMIC settings, community-level education around maternal anaemia or initiatives to support community-level distribution of iron and folic acid supplements—possibly mediated through community health extension workers—may increase adherence to medical guidance, improve buy-in from husbands and other family members and equip families to make more informed healthcare decisions.27–30 Targeted, culturally sensitive community education, especially involving young adults, about the purpose and value of blood donation may also reduce stigma and misconceptions around blood donation and increase the number of repeat, voluntary blood donors.31–33 Further research is needed to identify the most effective ways of providing such education, and how this can be done to promote preventative measures for those who are not yet involved with the service.\n\nMany of the issues with care provision are a consequence of inadequate funding, an issue that resonates across maternal health services more broadly.34 Interventions to improve supply chain management for resources like haemoglobin tests have been successful elsewhere in improving diagnosis of maternal anaemia.35 Further research is required to identify other sources of funding for maternal anaemia services, or ways in which the system can be restructured to more efficiently use funds.\n\nFor blood transfusion,36 standards of care for maternal anaemia are present, but inadequately implemented. The enforcement among maternity staff of standardized guidelines and practice for anaemia diagnosis and treatment would be important. Quality improvement approaches such as standards-based audit may be helpful in this respect.37 Furthermore, the introduction of regular training on issues such as patient communication, maternal nutrition and anaemia-related healthcare may lead to a higher standard of service.38–40\n\nA strength of this research is that it draws on multiple perspectives from a range of health systems actors, which allowed both supply- and demand-side factors to be highlighted. Further, there are limited studies around experiences of maternal care services specific to anaemia, which is a significant problem globally, but especially in Sub-Saharan Africa.\n\nA key limitation is that interviews were conducted with women who were already accessing services. These participants had overcome many barriers to accessing these services, and there was an increased likelihood that those interviewed were more sympathetic to institutional healthcare. It is possible that those who were unable to access these services experience other barriers that are not discussed here, requiring further research.\n\n\nConclusions\n\nThough anaemia in pregnancy is well understood from a physiological standpoint, with a significant evidence-base around its prevention, management, and treatment, it remains highly prevalent.41,42 There is a gap around perspectives regarding provision or receipt of care for maternal anaemia, which is needed to understand where improvements in service delivery or community sensitization could be made to drive improved evidence-based practice, adherence to treatments, and uptake of care.43,44 This study explored maternal anaemia services use and provision at MMSH, by drawing from diverse perspectives across a variety of health systems stakeholders. Issues with care provision included a lack of support for healthcare professionals and an under-resourced service attempting to meet increasing demand and difficulties in sourcing donor blood. Issues with care uptake were hidden costs, women’s dependence on husbands for finances and permission to seek care and a lack of anaemia literacy. It is hoped that understanding these barriers will inform future interventions for anaemia in Kano and help to improve services. Many of these findings may be generalizable to other parts of Nigeria when providing care for maternal anaemia. The importance of better resourced facilities and standardized training and guidelines is likely to be cross-cutting, applying to other maternity services as well. Supporting the uptake of maternal anaemia services is critical, and community education is a low-resource way of improving such uptake.\n\n\nEthics and consent\n\nEthical clearance was obtained from the research ethics committees of the Liverpool School of Tropical Medicine (20th July 2016, Reference: 16-015) and Aminu Kano Teaching Hospital (19th June 2016). We confirm that this research was conducted fully in accordance with the ethical principles for carrying out medical research with human participants as stipulated in the Declaration of Helsinki.\n\nAll participants provided written informed consent after receiving detailed information about the study. For illiterate participants, information was read to them, checked for understanding and a literate witness signed on their behalf. All data were collected in private spaces to ensure privacy and confidentiality, were anonymized, and identifying details were removed. Data were stored digitally, and password protected to ensure confidentiality.", "appendix": "Data availability\n\nData are not deposited in an open access repository as participants were not asked to consent to this. Though all data are anonymized, key informants occupy specific roles, and there may be privacy concerns around their data if reviewed by someone very familiar with the context. However, anonymized data sets intended to support secondary data analysis, for example, within a systematic review or qualitative meta-synthesis, may be made available upon reasonable request to the corresponding author, AKG (at akgwarzo.hae@buk.edu.ng or aisha.kuliya@gmail.com).\n\n\nAcknowledgements\n\nWe thank the research assistants who helped support data collection for this work. We also thank the many participants, whose voices are the foundation of this study.\n\n\nReferences\n\nStevens GA, Finucane MM, De-Regil LM, et al.: Global, regional, and national trends in haemoglobin concentration and prevalence of total and severe anaemia in children and pregnant and non-pregnant women for 1995–2011: a systematic analysis of population-representative data. Lancet Glob. Health. 2013; 1(1): e16–e25. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChaparro CM, Suchdev PS: Anemia epidemiology, pathophysiology, and etiology in low-and middle-income countries. Ann. N. Y. Acad. Sci. 2019; 1450(1): 15–31. PubMed Abstract \| Publisher Full Text\n\nRahmati S, Delpisheh A, Parizad N, et al.: Maternal anemia and pregnancy outcomes: A systematic review and meta-analysis. Int. J. Pediatr. 2016; 4(8): 3323–3342.\n\nBukar M, Audu B, Yahaya U, et al.: Anaemia in pregnancy at booking in Gombe, North-eastern Nigeria. J. Obstet. Gynaecol. 2008; 28(8): 775–778. 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Prim. Care Community Health. 2019; 10: 2150132719896447.\n\nTama E, Molyneux S, Waweru E, et al.: Examining the implementation of the free maternity services policy in Kenya: a mixed methods process evaluation. Int. J. Health Policy Manag. 2018; 7(7): 603–613. PubMed Abstract \| Publisher Full Text\n\nDwumfour-Asare B: Anaemia awareness, beliefs and practices among pregnant women: a baseline assessment at Brosankro community in Ghana. J. Nat. Sci. Res. 2013; 3(15): 1–9.\n\nEkwere TA, Ekanem AM, Ekwere T: Maternal knowledge, food restriction and prevention strategies related to anaemia in pregnancy: a cross-sectional study. Int. J. Community Med. Public Health. 2015; 2(3): 331–338. Publisher Full Text\n\nMargwe JA, Lupindu AM: Knowledge and attitude of pregnant women in rural Tanzania on prevention of Anaemia. Afr. J. Reprod. Health. 2018; 22(3): 71–79. PubMed Abstract \| Publisher Full Text\n\nOnyeneho NG, Igweonu OU: Anaemia is typical of pregnancies: capturing community perception and management of anaemia in pregnancy in Anambra State, Nigeria. J. Health Popul. Nutr. 2016; 35(1): 1–8.\n\nBhutta ZA, Das JK, Bahl R, et al.: Can available interventions end preventable deaths in mothers, newborn babies, and stillbirths, and at what cost? Lancet. 2014; 384(9940): 347–370. PubMed Abstract \| Publisher Full Text\n\nKamau MW, Kimani ST, Mirie W, et al.: Effect of a community-based approach of iron and folic acid supplementation on compliance by pregnant women in Kiambu County, Kenya: A quasi-experimental study. PLoS One. 2020; 15(1): e0227351. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPokharel PK, Maharjan M, Mathema P, et al.: Success in delivering interventions to reduce maternal anemia in Nepal: a case study of the intensification of maternal and neonatal micronutrient program. Washington DC, USA: The USAID Micronutrient and Child Blindness Project; 2011.\n\nPrinja S, Bahuguna P, Gupta A, et al.: Cost effectiveness of mHealth intervention by community health workers for reducing maternal and newborn mortality in rural Uttar Pradesh, India. Cost Eff. Resour. Alloc. 2018; 16(1): 25. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAsamoah-Akuoko L, Hassall OW, Bates I, et al.: Blood donors' perceptions, motivators and deterrents in Sub-Saharan Africa–a scoping review of evidence. Br. J. Haematol. 2017; 177(6): 864–877. PubMed Abstract \| Publisher Full Text\n\nSalaudeen A, Durowade K, Durotoye A, et al.: Knowledge of blood donation among adults in north-central Nigeria. J. Community Med. Prim. Health Care. 2019; 31(1): 57–66.\n\nSalaudeen A, Durowade K, Durotoye I, et al.: Determinants of voluntary blood donation among adults in communities of north central region of Nigeria. Res. J. Health Sci. 2019; 7(2): 144–154. Publisher Full Text\n\nRitchie LMP, Khan S, Moore JE, et al.: Low-and middle-income countries face many common barriers to implementation of maternal health evidence products. J. Clin. Epidemiol. 2016; 76: 229–237. PubMed Abstract \| Publisher Full Text\n\nBetrán AP, Bergel E, Griffin S, et al.: Provision of medical supply kits to improve quality of antenatal care in Mozambique: a stepped-wedge cluster randomised trial. Lancet Glob. Health. 2018; 6(1): e57–e65. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWorld Health Organization: The 2016 global status report on blood safety and availability. Geneva: World Health Organization; 2017. Report No.: 9241565438.\n\nWeeks A, Lightly K, Ononge S: Let's Do Audit!: A Practical Guide to Improving the Quality of Medical Care Through Criterion-based Audit. Cambridge University Press; 2010.\n\nRenfrew MJ, McFadden A, Bastos MH, et al.: Midwifery and quality care: findings from a new evidence-informed framework for maternal and newborn care. Lancet. 2014; 384(9948): 1129–1145. PubMed Abstract \| Publisher Full Text\n\nFilby A, McConville F, Portela A: What prevents quality midwifery care? A systematic mapping of barriers in low and middle income countries from the provider perspective. PLoS One. 2016; 11(5): e0153391. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFostering Knowledge-Implementation Links Project: Programmatic strategies for tackling maternal anaemia: lessons from research and experience. Bangalore: IIMB; 2012.\n\nDaru J, Zamora J, Fernández-Félix BM, et al.: Risk of maternal mortality in women with severe anaemia during pregnancy and post partum: a multilevel analysis. Lancet Glob. Health. 2018; 6(5): e548–e554. PubMed Abstract \| Publisher Full Text\n\nRamachandran P: Prevention & management of anaemia in pregnancy: Multi-pronged integrated interventions may pay rich dividends. Indian J. Med. Res. 2021; 154(1): 12–15. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFite MB, Roba KT, Oljira L, et al.: Compliance with Iron and Folic Acid Supplementation (IFAS) and associated factors among pregnant women in Sub-Saharan Africa: A systematic review and meta-analysis. PLoS One. 2021; 16(4): e0249789. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWorld Health Organization: Global anaemia reduction efforts among women of reproductive age: impact, achievement of targets and the way forward for optimizing efforts.2020." }	[ { "id": "201662", "date": "26 Sep 2023", "name": "Apurva Kumar Pandya", "expertise": [ "Reviewer Expertise Public health", "qualitative research", "maternal health", "health technology assessment" ], "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 chosen important topic. However, there are some areas that require authors' attention to improve scientific rigour. Suggestions for improvements are as follow:\nIntroduction\nAs majority participants are from Hausa or Fulani ethnic group, there should be brief paragraph on ethic groups in Nigeria.\nMethodology:\n\nAuthors should re-organize this section as follows:\nResearch design: Specify which qualitative research design was used.\n\nStudy setting: provide justification why this setting was selected.\n\nExplain some characteristics of this ethic group. Hausa or Fulani ethnic groups\n\nSampling technique should be explicitly mentioned.\n\nResearch tools: Explain how each research tools were developed.\n\nData collection procedure: Explain who and how data was collected? In which language data was collected? Was data collector trained in qualitative interviews/qualitative research? What was the duration of data collection?\n\nEthical considerations: Explain how authors ensured human rights protection of participants. Explain how authors dealt with ethical dilemma if they had encountered.\nHow qualitative data managed need to be explained (deidentification, storage of data, protection of privacy, etc.)\nData analysis: Analytic framework used by authors should be explained with appropriate reference (citation) and steps followed in analyzing qualitative data.\nResults: This section is poor. It looks superficial. Authors claim inductive coding was used; however, results do not reflect that. It lacks triangulation of data from different sources and analytic rigour. Authors should follow thematic analytic framework (as mentioned in abstract) and revise results section.\nDiscussion: This sections can be built on key findings. At present, it looks too generic.\nConclusions need to re-write. It should be authors' learning based on results.\nConclusion section doesn't require citation. Remove the sentence, \"It is hoped that understanding these barriers will inform future interventions for anaemia in Kano and help to improve services.\"\n\"Many of these findings may be generalizable to other parts of Nigeria when providing care for maternal anaemia. \" On what basis authors claim the generalization of findings? Such statements should be avoided\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? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "10475", "date": "16 Nov 2023", "name": "Tara Tancred", "role": "Author Response", "response": "Many thanks to the reviewer for their thoughtful reading of our manuscript. We have indicated our responses inline below in bold: As majority participants are from Hausa or Fulani ethnic group, there should be brief paragraph on ethic groups in Nigeria. We have added slightly more on this. Methodology: Authors should re-organize this section as follows: Research design: Specify which qualitative research design was used. We note that this was a qualitative study but have added “phenomenological”. Study setting: provide justification why this setting was selected. This is evident from the introduction and indication that Kano state has the highest levels of maternal anaemia in Nigeria. We have further noted that the hospital in particular draws a wide population, making it a useful site to study from a diverse range of participants. Explain some characteristics of this ethic group. Hausa or Fulani ethnic groups We have noted that they are Muslim. But feel that most of the cultural implications of collecting data from this population are expressed in the qualitative findings. Sampling technique should be explicitly mentioned. This is explicit under “Sampling and data collection”. All participants were sampled purposively. Research tools: Explain how each research tools were developed. This is also explicit under “Sampling and data collection”. We describe the contents of the instruments and how we arrived at those. Data collection procedure: Explain who and how data was collected? In which language data was collected? Was data collector trained in qualitative interviews/qualitative research? What was the duration of data collection? This is also explicitly stated: “All interviews and FGDs were carried out in Hausa or English. All interviews and FGDs were audio-recorded, transcribed verbatim, and later translated into English if necessary. Handwritten notes to capture non-verbal communication were made during interviews and FGDs by a research assistant. FGDs took 45–70 minutes.” We added in a point about the length of data collection for interviews and noted that AKG carried out the data collection and that she has extensive training in social science methodology. Ethical considerations: Explain how authors ensured human rights protection of participants. Explain how authors dealt with ethical dilemma if they had encountered. No ethical dilemmas were encountered. We otherwise are explicit in our upholding of informed consent, privacy, and confidentiality. This is detailed already under “Ethics and consent”. How qualitative data managed need to be explained (deidentification, storage of data, protection of privacy, etc.) It is clear from our preceding text how data were de-identified (we note that all data were anonymised). We have added in slightly more detail around providing a unique identifier and encrypting digital files. Data analysis: Analytic framework used by authors should be explained with appropriate reference (citation) and steps followed in analyzing qualitative data. We have explicitly noted that “thematic analysis” was used, though the steps were already clear. There is no analytic framework. Results: This section is poor. It looks superficial. Authors claim inductive coding was used; however, results do not reflect that. It lacks triangulation of data from different sources and analytic rigour. Authors should follow thematic analytic framework (as mentioned in abstract) and revise results section. Thank you for the feedback, but we respectfully disagree. It is very clear from participants that the overarching themes were reiterated. There is obvious triangulation in that you can clearly see supporting content from different types of participants. These perhaps come across as superficial because they are very “top line” as they encompass many things. We synthesised data into the most top line themes, and this is what emerged. We have made this more of a narrative statement that better encompasses the contents within each theme. Discussion: This sections can be built on key findings. At present, it looks too generic. We built our discussion on key findings—we reflect on these against broader literature, as would be expected within a discussion. Conclusions need to re-write. It should be authors' learning based on results. Conclusion section doesn't require citation. Remove the sentence, \"It is hoped that understanding these barriers will inform future interventions for anaemia in Kano and help to improve services.\" We have slightly reorganised the conclusion, moving the cited text to earlier in the discussion and rephrasing the identified sentence. \"Many of these findings may be generalizable to other parts of Nigeria when providing care for maternal anaemia. \" On what basis authors claim the generalization of findings? Such statements should be avoided We have reflected throughout our discussion about the persistent constraints in anaemia care in other parts of Nigeria and how resonant our findings were, hence this statement." } ] }, { "id": "205949", "date": "17 Oct 2023", "name": "Amy Brenner", "expertise": [ "Reviewer Expertise Maternal health", "postpartum haemorrhage", "traumatic haemorrhage", "randomised trials", "anaemia" ], "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 opportunity to review this article about the provision and uptake of services for maternal anaemia diagnosis/treatment in Kano state, Nigeria. Firstly I would like to thank the authors for highlighting this important public health issue, which is a major risk factor for postpartum haemorrhage (PPH).\nYou may be interested in a recent analysis that explored the association between haemoglobin level, PPH and death or near miss in over 10,000 moderately and severely anaemic women, including women in Nigeria recruited into the WOMAN-2 trial (https://www.sciencedirect.com/science/article/pii/S2214109X23002450).\n\nAn important cause of anaemia in women of reproductive age that is often overlooked (and has been overlooked by the author) in the prevention and treatment of anaemia is menstrual bleeding, particularly heavy menstrual bleeding. The authors may wish to comment on this. e.g. https://doi.org/10.1016/S0140-6736(20)32718-5.\nThe article reports some very interesting insights from FGDs and interviews with HCPs, pregnant women and relatives. It highlights gaps in health services/resources/guidelines/policies/awareness/education, which may be targeted to improve the diagnosis and treatment of anaemia in pregnant women before they give birth. The discussion highlights well some possible actions to overcome the complex barriers to care for maternal anaemia.\nThe author says that healthcare providers were knowledgable about maternal anaemia but this is to be expected as the sample was purposively selected 'based on their knowledge and experience in pregnancy anaemia management'. This statement should be removed from the results to avoid the reader misconstruing this as evidence that HCP training on maternal anaemia is sufficient.\nIt is interesting that intravenous iron infusion is not mentioned as a treatment for maternal anaemia. The authors should comment on this in the discussion. I believe there is an ongoing study of IV iron being conducted in Lagos...\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "10476", "date": "16 Nov 2023", "name": "Tara Tancred", "role": "Author Response", "response": "Many thanks to the reviewer for their review of our manuscript. We have responded inline in bold to the queries raised. An important cause of anaemia in women of reproductive age that is often overlooked (and has been overlooked by the author) in the prevention and treatment of anaemia is menstrual bleeding, particularly heavy menstrual bleeding. The authors may wish to comment on this. e.g. https://doi.org/10.1016/S0140-6736(20)32718-5. We absolutely agree this is an important contributor to anaemia, though not necessarily maternal anaemia, as our participants are pregnant (and therefore not menstruating). The author says that healthcare providers were knowledgeable about maternal anaemia but this is to be expected as the sample was purposively selected 'based on their knowledge and experience in pregnancy anaemia management'. This statement should be removed from the results to avoid the reader misconstruing this as evidence that HCP training on maternal anaemia is sufficient. Thank you for this comment—to be clear, we did not intentionally select those healthcare providers who demonstrated high levels of knowledge—simply those with the responsibility and experience of providing anaemia care (through which knowledge would be expected). We have clarified this in the text. It is interesting that intravenous iron infusion is not mentioned as a treatment for maternal anaemia. The authors should comment on this in the discussion. I believe there is an ongoing study of IV iron being conducted in Lagos... Thank you for the recommendation. This is not used in the study site, but we have briefly commented on this in the discussion." } ] } ]	1	https://f1000research.com/articles/12-288
https://f1000research.com/articles/12-1130/v1	11 Sep 23	{ "type": "Research Article", "title": "Does the merger improve the operating performance of the company? Evidence from the beverage industry in India", "authors": [ "Pravin Narayan Mahamuni", "Shilpa Parkhi", "Raju Ganesh Sunder", "Kiran Karande", "Samuel Gameli Gadzo", "Premendra Kumar Singh", "Pravin Narayan Mahamuni", "Shilpa Parkhi", "Kiran Karande", "Samuel Gameli Gadzo", "Premendra Kumar Singh" ], "abstract": "Background: There is fierce market competition both locally and globally. Every organisation seeks to maintain itself and, more crucially, to develop quickly through inorganic means. The expansion of a company through mergers and acquisitions is an inorganic process. Organic growth takes a very long period and is time-bound, but inorganic growth through mergers may be achieved quickly. This research aimed to determine whether the operating results of Indian beverage firms have improved after the merger or not. Methods: In order to assess merger-related advantages to the acquiring firms, this study used the operating performance technique, which contrasts the pre-merger and post-merger performance of corporations using accounting data. Secondary data were used to carry out this study. The operating performance was assessed on six operating parameters (ratios) i.e. Operating Profit Margin, Gross and Net Profit Margin, Debt-Equity, Return on Net Worth and Capital Employed. The comparison was done for three years pre and post-merger period of these operating ratios. Results: The findings demonstrate that mergers do not seek to increase owner wealth. This finding shows that rather than just becoming larger and achieving covert goals, managers should pay more attention to post-merger integration challenges in order to produce merger-induced synergies. Conclusion: This study shows that the M&As have not had a good effect on a company's operating performance, especially for the chosen beverage companies in India. Since financial measures cannot fully account for the influence of mergers on business performance, future research may create other metrics for merger-related gains. Research that provides profound insights into the causes and trends of post-merger business performance through the different types of mergers and industries would also be beneficial.", "keywords": [ "Merger", "Acquisition", "Financial Performance", "Operating Performance", "Beverage Industry" ], "content": "Introduction\n\nMergers and acquisitions (M&As) in India peaked its activity levels in 2021. Many first-time buyers and an increase in industry disruptors, or insurgents, that too across multiple sectors and business activities, is what led M&As to reach such high levels (Dezan Shira & Associates, 2022). This illustrates how the global economy is undergoing strong upheaval. In reality, this serves as a response to the changes brought about by rapid technological advancements, lower communication and transportation costs that led to the emergence of a global market, elevated competition, the emanation of new industries, a supportive financial and economic environment, and the liberalisation of the majority of economies, which too serve as motivators for mergers (Tambi, 2005). Now a day, corporations across the globe are frequently using M&As as a business restructuring tactic. There are many studies investigating the merger phenomena, in line with the growing M&A trends (Boateng et al., 2011).\n\nThe fact that it is challenging to determine how a merger impacts the financial results of a company is a significant obstacle in completing this assignment. An alteration in profitability might have a number of causes. Mergers may produce an all-around effective reaction to a supply or demand shock in the market. They may also provide a chance to obtain cutting-edge technology or to realise economies of scale.\n\nEven if they are significant, mergers’ impacts are still up for debate. The “market for corporate control,” which sees M&As as ways to transfer underperforming assets to companies that can use them more effectively and therefore realise the value gain, is referred to by proponents. Sceptics point out that while many mergers can be benign or advantageous, others may be driven by market dominance, arrogance, or unintentional errors, all of which have a negative impact on society. Each viewpoint is supported by evidence. The efficient-merger hypothesis appears to be supported by the regular discovery of shareholder advantages from mergers, at least in the short term, in stock market event studies. On the other hand, studies of the actual operational consequences more frequently seem to reveal that merger advantages are the exception as opposed to the rule.\n\nGlobally, Indian economy is lauded as one of the quickest in terms of growth parameters. India survived the aftermath of sub-prime crisis in 2008. With a growing young and educated middle classes, which is the Indian economy’s development engine, India is predicted to surpass industrialised nations like Germany and Japan and achieve third position in the world economic rankings by the year 2030. The Indian economy underwent a dramatic structural revolution during the previous ten years as it switched from being driven by agriculture to being driven by services. Agriculture still employs 60% of the people and generates 14% of the country’s GDP. Despite the fact that the agricultural industry has advanced significantly, there are still many areas that may be improved and, if done so, would promote growth in both agribusiness and its connected industries. In order to satisfy India’s predicted significant rise in consumption over the next 10 years, agriculture and consequently the food and beverage industry would be better equipped if these challenges were addressed. With its growing economy, India’s total yearly household consumption is anticipated to quadruple, which will take India to the fifth rank by 2030 amongst the countries with the largest goods market. F&B occupy the largest space in the basket of goods consumed. This can be considered a significant accomplishment of the F&B sector in India (Grant Thornton, 2014).\n\nBusinesses are increasingly employing M&A (mergers and acquisitions) strategies for their regional and worldwide development in order to expand their company scope or seize new possibilities (Ferreira et al., 2016). Given the context, this research effort has been made to investigate, observe, and evaluate the operational results of the Indian beverages sector with regard to United Spirits Limited and United Breweries Limited, which have participated in M&A activities following the post liberalization, privatization, globalisation (LPG) era in India, and to ascertain whether M&As significantly affected the financial operating performance of merging entities. The purpose of this study is to investigate M&A in the beverage sector in India to analyze whether there were differences in outcomes for various companies operating within the same sector.\n\n\nLiterature review\n\nOur study assesses the consequences of mergers on competition. Various studies have found varying effects from mergers in various industries, which is not surprising. A variety of research has been conducted about the association between M&As and business performances (Bi Z., 2016). Using several types of financial (such as profits and stock prices) and non-financial (such as the reputations of the firms) indicators and of course, the time periods (such as initial market reaction to the M&As, pre and post-measurement, etc.). According to these studies, M&A deals often benefit the target’s shareholders more than the acquirer’s shareholders. In reality, the performance of the buying firm generated a variety of outcomes (Schweiger and Very, 2003).\n\nThe 50 biggest mergers in the US between 1979 and 1984 were quantified and their cash flow performance was assessed by Healy, Palepu, and Ruback in 1992. They found that, compared to their respective industries, the operating performance of merging companies substantially enhanced in post-merger period (Healy et al., 1992).\n\nIn 1983, Katsuhiko Ikeda et al. examined the financial results of forty-three (43) combining enterprises from the manufacturing sector in Japan. In more than half of the cases, they noticed an increased Return on Equity (RoE), whereas only approximately half the cases saw an improvement in the rate of return on total assets. However, “both profit rates improved in more than half of the cases in the five-year test, indicating that improvements in firm performance after mergers began in line with internal adjustments made by the merging firms. This suggests that there was a necessary gestation period during which merging firms learned how to manage their new businesses” (Ikeda and Doi, 1983).\n\nThe impact of M&As on the financial health of 40 United Kingdom corporations were researched by Jallow, Masazing, and Basit (2017) between the years of 2006 and 2010. According to the analysis, M&As had “a large influence on ROA, ROE, and EPS but a negligible impact on NPM”. The study concluded that a lack of managerial effectiveness, an inefficient utilisation of shareholders’ funds, and escalated financial costs are responsible for companies’ insignificant decreases in Return on Assets (RoAs) and RoEs after the mergers took place (Jallow et al., 2017).\n\nBetween 1995 and 2000, Beena (2000) used a set of financial ratios 4 and a t-test to compare the performances of a sample of 115 acquirers, from Indian industrial sector, before and after the merger. “The investigation was unable to identify any proof that the financial ratios for the acquiring corporations had improved in the post-merger era compared to the pre-merger period” (Beena, 2000).\n\nThe financial holding companies’ post-merger banks generated merger synergies. The top 10 banks in financial holding companies and top 10 banks in non-financial holding companies revealed that 3 out of the top 10 financial holding company banks were founded in the banking industry and are connected to financial holding companies that place a strong emphasis on banking. This finding indicates that financial holding companies perform better overall, post-merger, if banking is their primary operating entity (Liu, 2010).\n\nThe study examines a few financial parameters (ratios) before and after a merger of Indian F&B industry acquiring firms to determine the effects of M&As on their operating financial results. The outcome refers to a minor, but not statistically significant, improvement in profitability ratios in the food industry. While the return on invested capital and net worth have decreased. In the post-merger period, both the food and beverage industries have seen a negligible hike in leverage. Post-merger, the combined performance of the food and beverage companies improved significantly, but statistical analysis cannot determine whether the mean of the two variables differed significantly (Mahamuni and Jumle, 2012).\n\nMahamuni and Jumle, in 2018, carried out a study of manufacturing machinery and metal products firms to verify if M&A activity helps the firms in improving their performances after the merger in terms of parameters like improvements in liquidity position, better solvency scenarios, expansion of their businesses, overall improvement in profitability. The result revealed that manufacturing companies which merged “did not achieve liquidity, solvency, profitability after merger”. Also, it is seen that after the merger, the operating results of the combined manufacturing firms has not improved. But the merged companies, post-merger, expanded their business activities (Mahamuni and Jumle, 2018).\n\nAccording to research carried out by Pramod Mantravadi and A Vidyadhar Reddy (2008), mergers appear to have experienced “a marginally positive impact on the profitability of businesses in the banking and finance sector, while they had a marginally negative impact on operating performance (in terms of profitability and returns on investment) for businesses in the pharmaceutical, textile, and electrical equipment sectors”. In terms of profitability margins, ROI, and asset values, the Chemicals and Agri-products industries had experienced a significant decrease due to mergers (Mantravadi and Reddy, 2008).\n\nThe study by Ahmad Ismail, Ian Davidson, and Regina Frank (2009), is focused on European banks. It examined operating performance following the merger event, and found that the industry-adjusted average cash flow return was not substantially changed after the merger but remained positive. Additionally, it was observed, low profitability, conservative credit policies, and robust cost-efficiency status in pre-merger period, which provided the source for increasing these returns post-merger are the major predictors of industry-adjusted cash flow returns (Ismail et al., 2009).\n\nMahesh Kumar Tambi (2005) took forty companies’ database from CMIE’s PROWESS and applied a paired t-test for mean differences for 4 parameters viz. total performance improvement, economies of scale, operating synergy and financial synergy. He investigated the impact of mergers on Indian enterprises. The investigation indicates that Indian companies are comparable to those in various places of the globe and that mergers did not significantly increase performance (Tambi, 2005).\n\nUsing measures 5 of profitability, growth, leverage, and liquidity, Pawaskar V. (2001) focused on the before and after the merger operating performance of 36 acquiring firms between 1992–1995 and revealed that these firms surpassed the profitability average for the sector. Regression analysis, though, discovered that growth in the profitability did not shown growth following the merger period when compared to the acquiring firms’ top rivals (Pawaskar, 2001).\n\nSinha, Kaushik and Timcy (2010) conducted the study to measure Post Merger and Acquisition Performance. Through this research, they investigated selected organizations from Financial Sector in India. With an aim to understand how M&As sway the financial performance of the select Indian ‘Financial Institutions’. The researchers discovered that M&As incidents in India showed “a significant correlation between financial performance and the M&A deal”, in the long-run, along with the fact that the acquiring firms could generate value (Sinha et al., 2010).\n\nAccording to a 2009 study by Murugesan, Manivannan, Gunasekaran, and Bennet titled “Impact of Mergers on the Corporate Performance of Acquirer and Target Companies in India,” the acquirer businesses’ shareholders improved their liquidity performance following the merger event (Selvam et al., 2009).\n\nMarina Martynova, Sjoerd Oosting and Luc Renneboog (2006) looked at the long-term profitability of business takeovers in Europe and observed that “both acquiring and target companies significantly outperformed the median peers in their industry prior to the takeovers, but the profitability of the combined firm decreased significantly following the takeover” (Marina et al., 2006).\n\nFrom 1993 to 2010, Sinha and Gupta (2011) examined the effects of M&As on the Indian financial sector. 80 companies that went through M&A over the past 18 years were examined in the study. The reveals that M&As had ‘a favorable impact on profitability’ represented by the net profit and the ratio of profit before interest, tax, depreciation and amortization (PBITDA), ‘a negative effect on liquidity’, also decreased total and systematic risk (Sinha and Gupta, 2011).\n\nAbdullah Mamun, George Tannous, Sicong Zhang (2021) studied how bank mergers (regulatory mergers) performed (operating) post-merger during and after the 2008-2009 financial crisis. Up to two years after the acquisition, regulated mergers are seen to significantly increase profitability and cost effectiveness. In comparison with rivals who were not involved in the merger, these improvements are significantly higher. However, the operating result of non-regulatory mergers following the merger does not differ substantially from that of their non-merger peers (Mamun et al., 2021).\n\nThe impact of mergers when businesses compete on pricing and cost-cutting efforts was examined by Motta and Tarantino (2021). They discover that following the merger, overall investments and consumer surpluses are lower when efficiency benefits are missing. Only when efficiency improvements are substantial enough are the impacts of a merger competitively advantageous. The effect of horizontal mergers that lead to monopolies on businesses’ incentives to engage in demand-enhancing innovation is examined to discover that a merger’s overall effect on innovation might be either favourable or unfavourable (Motta and Tarantino, 2021).\n\nNumerous research papers have been examined, and it has been determined that the impacts on financial results are inconsistent, mixed, and different depending on the industry. The fact that the researchers’ methodologies varied made it difficult to summarise their findings, as in some of their results, they used a variety of variables, parameters, and financial information. Financial performance metrics were employed in several studies. The majority of studies that employed financial performance measures found no appreciable differences (on either side) between the financial performance prior to and following the M&A.\n\nThese preceding works of research might be used to draw the conclusion that mergers generally do not appear to enhance the post-merger efficiency of acquirers. Gains are either negligible or non-existent by various measurements. Event studies and accounting both fail to provide any proof of value generation. This study’s goal is to investigate these theories in the context of India. There are few studies on the performance following a merger of Indian corporations and consequently a large knowledge gap in this field. The operating efficiency technique is utilised in this study to determine how a merger will affect the efficiency of acquiring organisations.\n\n\nResearch objectives\n\nBased on the literature review, the researcher frames the objective and the hypothesis to carry-out the study as below;\n\nObjective: To measure, compare and study the merger’s impact on the operating performance.\n\nHypothesis: Merged firms have improved their operating performances.\n\n\nMethods\n\nAccording to several merger studies, evaluating and comparing the merged firms to a similar industry group that is based on the performance before and after the merger is an effective way to find operating performance improvements (Behr & Heid, 2011; Fee & Thomas, 2004; Ghosh, 2001; Powell & Stark, 2005). The operating performance is assessed on six operating parameter (ratios) i.e. Operating Profit Margin, Gross and Net Profit Margin, Debt-Equity, Return on Net Worth and Capital Employed. The required financial data are extracted through the Centre for Monitoring Indian Economy (CMIE) Prowess Database. The comparison of three years pre and post-merger period of these operating ratios (Aggarwal and Garg, 2022).\n\nThe researcher used an analytical and quantitative research design to measure and compare the operating result before and after the merger period.\n\nAll data used in this paper can be found at the Centre for Monitoring Indian Economy (CMIE) Prowess Database (Version Prowess IQ v3.0). The relevant data of three years period pre-merger and post-merger, considering the merger year as the baseline year i.e. 0 (zero) were used.\n\nResearch papers, reports of research organization and books used for the study are mentioned in references with URLs.\n\nThe researcher followed the non-probability convenient sampling method to select firms from the Indian beverage industries. United Spirits Limited (USL) and United Breweries Limited (UBL) were selected for the study for the reason that they are two of the most renowned and prestigious companies in India’s beverage industry.\n\nFor all the sample firms that underwent mergers, operating performance ratios both before and after the merger were estimated, and averages (mean) were computed and compared in order to assess the merger’s impact and using a “paired two sample t-test” with a confidence level of 0.05, it was determined whether there had been any statistically significant change in operating performance as a result of mergers. Mean, paired ‘t’-test, and Ratio Analysis, are a few of the methods applied for analyzing and assessing the data that was collected. SPSS (Statistical Package for the Social Sciences), also known as IBM SPSS Statistics. IBM SPSS Statistics Base 29.0 was used for data processing and paired ‘t’ test analysis.\n\n\nResults and discussions\n\nStudy of historical cases of Mergers and Acquisitions have established the changes in financial performance of the restructured firms. However, the previous studies and the current paper confirm that the firm’s performance in terms of profitability, liquidity, and solvency does not show any significant improvement in the short run in the post-merger period. The present study of post-merger activity’s long-term effects may add interesting results which can yield a future research dimension.\n\nTable 1 shows that the Operating Profit Margin (the mean) of both beverage companies is much lower after the merger than it was before the merger. However, in the instance of United Breweries Limited, the operating profit margin post-merger is statistically worse (-14.88 in the pre period and -24.55 in the post period, t-value = 4.964, ‘p’= 0.05). This means both companies are unable to control their costs, and as a result, operational profit after the merger is lower. After covering all operational expenses, operating profit will typically decline throughout the post-merger period.\n\nGross Profit Margin from Table 2 indicates that United Breweries Limited’s mean (pre-merger: 8.38; post-merger: 6.48) is down, while United Spirits Limited’s mean (pre-merger: 1.61; post-merger: 0.69) is up, indicating that both companies can recover their costs from sales (COGS). However, since the ‘p’ value is more than 0.05, changes in the gross profit margins of the two companies are statistically insignificant.\n\nIn Table 3, the Net Profit Margin of acquired businesses during the pre-merger and post-merger periods is shown. The average Net Profit Margin ratio for United Breweries Limited (1.55 in the pre and 2.93 in the post-period) is improving, indicating that the company is better at converting sales to actual profit, but at the required probability level, the gain is not statistically significant. The Net Profit Margin (the mean) of United Spirits Limited, on the other hand, has dropped in after the merger; at the required probability level, the decline is not significant, indicating that the net profit margin has reduced, rather than increased, post-merger. It indicates that not all of the activities are carried out efficiently.\n\nTable 4 provides the sample merged firms’ average Return on Net worth over the pre and post-merger periods. It should be noticed that the variation in average returns on net worth for both of the chosen merged corporations, i.e. United Breweries Limited (pre-merger =19.47 and post-merger = 13.34), and United Breweries Limited (pre-merger = 20.38 and post-merger = 9.67), is lower after following merger as compared to before the merger event Therefore, it may be concluded that although net value has increased substantially as a result of M&As, the merged companies were incapable of delivering the necessary returns on their net worth post-merger.\n\nThe average value of return on capital employed by United Spirits Limited has gone down from 8.36 (before merger) to 5.80 (after merger), based on the analysis of Table 5 of both the Sample Merged Firms during the before and after Merger Periods. Nevertheless, in the case of United Breweries Limited, return on capital employed has improved from 2.26 (before merger) to 5.21 (after merger). It suggests this company, following the merger, proved efficient in utilising its funds. Additionally, it indicates that management exhibited efficiency in employing investments and the creditors. Furthermore, the derived ‘t’ values for the above two firms, at the required degree of probability, are not statistically significant, nor is an increase or decrease in the ratio.\n\nThe findings from the analysis of Table 6 of the sample merged firms’ debt-equity ratios for the pre- and post-merger periods show that United Breweries Limited’s debt-equity ratio was substantially reduced from 1.61 (before merger) to 0.69 (after merger), t-value = 3.267 and p > 0.05). It clarifies that a large portion of assets after the merger are financed by debt rather than equity. It indicates that these companies are embarking on more debt as a result of merger activity.\n\n\nHypotheses testing\n\nThe hypothesis that the Operating performance of the merged firms has improved has been rejected after examining the results mentioned above. As Table 7 clearly indicates, the sample companies’ operating performance has declined as a result of the merger activity they undertook. It reveals a negative impact on the sample companies’ overall profitability over the post-merger period.\n\nThe representative sample firms from the beverage industry’s post-merger operating performance is declining. Profitability ratios are declining along with general falloffs in returns on net worth and capital invested. The earnings ratios for United Breweries Limited have somewhat improved, albeit not statistically significantly. For United Spirits Limited, the return on net worth and investment made has declined. A negligible increase can be observed in leverages of both of the firms that belong to the Indian beverage sector that were picked during the period following the merger. On the reverse hand, this ratio of debt to equity has decreased dramatically since the merger compared to prior. It suggests that debt rather than equity is used to fund a large part of assets in the post-merger era. It demonstrates that these businesses are increasing their debt loads as a result of merger activity. Overall, it can be said that there was a negative on operating performance by the merger activity done by these two representative sample businesses in India’s beverage industry.\n\nOne may draw the conclusion that the three financial variables included in this study do not statistically significantly vary the operating results after merging. The null hypothesis is true because all estimated t-values are lower than (or more on the negative side of) the table value. This outcome indicates that merger activities do not affect the acquired businesses’ operational performance.\n\nAnother reason why profitability did not increase after a merger is because acquisition of a company could have led to “managerial control loss problems.” One may argue that the acquirers encounter unforeseen difficulties while handling and integrating their purchases. The acquiring leadership loses control and is unable to manage the merged firm effectively as it grows more complex. After a merger, profitability levels fall as a result of this loss of control.\n\n\nConclusion\n\nThis research work was conducted to better understand the impact of M&As activity on operating financial results. This study shows that the M&As have not had a good effect on a company’s operating performance, especially for the chosen beverage companies in India. Despite the limited favourable effects, they are statistically negligible.\n\nAlthough there are many motivations for a firm to participate in merger activity, our aim in this search was to understand one crucial feature of M&A activity. It might be difficult to interpret the conclusion or get insights from the quantitative information when these motives or reasons are qualitative. Additionally, it has been noted from several studies that merger and acquisition efforts for numerous organisations in their post-merger phase did not result in beneficial short-term effects. However, if the companies do not conduct thorough research before deciding on M&As, it will not meet their expectations or the objectives for the activity.\n\nBy calculating it and comparing it to the average for an industry or sector, subsequent studies in this area may expand on the present study. Any variations, if any, may then be further investigated to get a better understanding. The results of research demonstrating inferior performance in the post-merger era might be compared and connected to post-merger return to investors of acquiring corporations who are part of mergers taking place in India.\n\nPrevious studies have shown that there was no significant improvement in business performance. It was discovered that merger-induced changes in a company’s industry-adjusted profitability, asset efficiency, and solvency status were statistically negligible. This finding suggests that mergers do not increase the acquirers’ operating performance. These empirical findings allow us to draw the conclusion that merger decisions are not made with the intention of maximising shareholder value through increased profitability. The pursuit of larger scale, market consolidation, and empire building may have served as inspirations for merger choices.\n\nThere may occasionally be unstated goals, such as the post-merger asset stripping of the target firm that provides the promoters with a significant cash premium over and above the net worth.\n\nIn order to accomplish the true goals of the merger, management must continue to concentrate on the company’s operations, especially the post-merger integration phase.\n\nIndustry mergers and acquisitions do not appear to be slowing down. Why do businesses choose mergers and acquisitions (M&A) when, on average, data shows that doing so would hurt them more than help the target? It appears to point to some issues with the conceptual framework, the technique, or the accuracy of the data. This topic may be explored in more detail.\n\nFinancial metrics may not fully reflect the impact of mergers on business performance or reveal the driving forces behind M&A decisions. Therefore, in future research, the post-merger performance gains might be examined in terms of some additional criteria including social value provided, improvements in gains to other stakeholders of the firms engaging in M&A, and advantages at the industry and economy level at both the national and worldwide levels.\n\nDue to several limitations, the research only offers a few explanations for why there was no merger-induced increase in corporate performance. Furthermore, the article does not examine the results to see if any trends in post-merger performance across merger types and industries exist. Future research might address concerns in these areas.", "appendix": "Data availability\n\nData used in this study are from the CMIE (Centre for Monitoring Indian Economy Pvt. Ltd. India). The datasets of the Indian Companies are available from the Centre for Monitoring Indian Economy (CMIE) Prowess Database (Version Prowess IQ v3.0). https://prowessiq.cmie.com/. Anybody who wishes to use the data can register and use the data for academic purposes.\n\nAll data were collated through annual reports of Companies. A guide for how to apply for dataset access is available at: https://register.cmie.com//kommon/bin/sr.php?kall=wcontactus&tab=2060&rrurl=prowessiq.cmie.com.\n\nThe data we extracted for the study are as follows:\n\n\nReferences\n\nAggarwal P, Garg S: Impact of mergers and acquisitions on accounting-based performance of acquiring firms in India. Glob. Bus. Rev. 2022; 23(1): 218–236. Publisher Full Text\n\nBeena PL: An analysis of mergers in the private corporate sector in India. Centre for Development Studies. Trivandrum, Working Paper.2000; 301: 3–56.\n\nBehr A, Heid F: The success of bank mergers revisited. An assessment based on a matching strategy. J. Empir. Financ. 2011; 18(1): 117–135. Publisher Full Text\n\nBi Z: Comparative analysis of pre and post-merger financial performance with reference to it sector in India. 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Publisher Full Text\n\nSinha P, Gupta S: Mergers and Acquisitions: A pre-post analysis for the Indian financial services sector.2011.\n\nTambi MK: Impact of Mergers and Amalgamation on the performance of Indian Companies. Econ WPA Finance. 2005; 0506007." }	[ { "id": "208033", "date": "04 Oct 2023", "name": "Priyanka Tandon", "expertise": [ "Reviewer Expertise Finance" ], "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\nBrief description of an article\nThis study employed the operating performance technique, which compares the pre-merger and post-merger performance of organizations using accounting data, to determine the benefits of mergers to the acquiring company. Using secondary data six operating metrics (ratios), namely Operating Profit Margin, Gross and Net Profit Margin, Debt-Equity, Return on Net Worth, and Capital Employed, were used to evaluate the operating performance. These operating ratios were compared for three years before and after the merger.\nRelevance of an article\nMajor concerns\nIn section-1, author(s) failed to address the research objectives and questions pertaining to the research study. The research objectives which is actually mentioned after LR should be the sub-part of section-1.\n\nIdeally, the introduction section must clarify the gaps, the objectives, the guiding research questions, and the philosophical stance. In the current form, the introduction section fails to meet any one of these criteria. Moreover, the authors’ research questions do not conform to the study.\n\nAuthor(s) must discuss at least three contributions of study (theoretical and practical) which must be convincing towards the novelty of the study.\n\nAuthor(s) must mention the structure/organization of study.\n\nThe literature review is quite descriptive. It lacks critical debates that help shape the theoretical debates which are essential for scientific arguments. I am sorry but the literature review is prepared like a thesis chapter. Moreover, research gaps, research questions, and the research objectives should be presented in the introduction section.\n\nDiscussion should be separate section after results and must specifically discuss the results (linkage to similar and contrary studies) and also implications of study in detail.\nMinor concerns\nI found typos and inconsistencies in citations which should be carefully sorted out.\nOverall, the manuscript is good and it can be indexed after incorporating the above suggestions.\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": "10579", "date": "06 Dec 2023", "name": "Raju Ganesh Sunder", "role": "Author Response", "response": "In section-1, author(s) failed to address the research objectives and questions pertaining to the research study - Thank you for the point, we have added in Significance section of Introduction Ideally, the introduction section must clarify the gaps, the objectives, the guiding research questions, and the philosophical stance - Thank you for the suggestion we have added in Research Question section Author(s) must discuss at least three contributions of study (theoretical and practical) - Thank you for the point we have added in contribution section after the limitation of the study Author(s) must mention the structure/organization of study - Thank you now, added at end of Introduction section The literature review is quite descriptive. Moreover, research gaps, research questions, and the research objectives should be presented in the introduction section - We thank you for the suggestion, both Literature Review and Introduction section revised and updated Discussion should be separate section after results and must specifically discuss the results and also implications of study in detail - This is done I found typos and inconsistencies in citations - Thank you for this now it is corrected" } ] }, { "id": "208032", "date": "13 Oct 2023", "name": "Anurag Bhadur Singh", "expertise": [ "Reviewer Expertise Corporate Finance", "Accounting", "Economic developments" ], "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\nFollowings are the observation, authors may incorporate to improve the quality of papers:\nResearch objectives: Objectives can be separated for comparison and measure purpose.\nHypothesis: can also develop separate as objectives describes.\nResearch Methodology:\nMore details may be given in this section such as no. of firms, no of years of study i.e. from 2005-2015.\n\nShould justify why only two firms has selected for the study, justify the same with citations.\nData Analysis:\nAuthors should justify, why only paired two sample t-test opted for analysis purpose, with some citations.\n\nTable 1, 2, 3, 4, 5, should contains S.D., N, also because to apply t test we need all these information.\n\nA separate table can be develop for t test containing degree of freedom and t stat. value. why it test only at 5% level of significance only with some citations.\n\nDebt equity table not required in the study because of role are different of this ratio.\n\nTrend analysis can also be useful for measure purpose, authors may use this in this section.\n\nFrom page no. 11 seems that authors has selected only three years for comparison of performance of the firms which seems unjustified, must be cite some study who did the same.\n\nMy suggestions that authors may use at least five years each pre and post M&A data to set the comparison in performance, because in short periods of time comparison can not be done specially M&A has taken place or corporate restructuring has done by the entity.\nConclusion:\nAuthors should cite some study who has concluded the same results. or may justify why this study results are different from them.\nIf all above suggestions will incorporate in the study, i am sure the quality of paper will improve.\nWith Best wishes.\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?\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? Partly", "responses": [ { "c_id": "10580", "date": "06 Dec 2023", "name": "Raju Ganesh Sunder", "role": "Author Response", "response": "Objectives can be separated for comparison and measure purpose - Thank you for this point, now it is done More details may be given in this section such as no. of firms, no of years of study i.e. from 2005- 2015 - Thank you for suggestions, we have added in data section Should justify why only two firms has selected for the study, justify the same with citations - Thank you for the point mentioned, we have added in Sampling section Authors should justify, why only paired two sample t-test opted for analysis purpose, with some citations - Thank you now we have added in Data Analysis section Table 1, 2, 3, 4, 5, should contains S.D., N, also because to apply t test we need all these information - Thank you we have added SD in the respective table From page no. 11 seems that authors has selected only three years for comparison of performance of the firms which seems unjustified, must be cite some study who did the same - Thank you, we have added in Limitations section My suggestions that authors may use at least five years each pre and post M&A data to set the comparison in performance, because in short periods of time comparison cannot be done specially M&A has taken place or corporate restructuring has done by the entity - Thank you we have added in Limitations section Authors should cite some study who has concluded the same results. or may justify why this study results are different from them - Thank you we have added in Results and Discussion section" } ] }, { "id": "208030", "date": "06 Nov 2023", "name": "H M Belal", "expertise": [ "Reviewer Expertise Operations 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\nThe application of a Merger and Acquisition (M&A) strategy serves as a substantial and consequential method for maintaining business resilience in highly competitive market environments. Nonetheless, the challenge of assessing a company's performance through the lens of M&A strategies is a complex and multifaceted task. This research endeavor has been undertaken to substantiate the rationale behind the utilization of M&A strategies in the Indian beverage industry. Nevertheless, it is important to acknowledge the forthcoming constructive observations and recommendations designed to elevate the overall quality of the research paper.\nIntroduction:\nThe rationale behind the research issues is presently insufficiently established. To enhance this aspect, it is recommended to augment the reference base with a more extensive array of scholarly sources. Simultaneously, it is advisable to place increased emphasis on both elaborating upon these concerns and providing a comprehensive contextual backdrop for the study.\n\nI did not find any research objectives in the Introduction part. Please develop the Research objectives based on the Research problem and Research questions.\n\nSo, the introduction section requires a redesign, and there is a need for improvement in the academic writing style.\nLiterature Review:\nIn the literature review, the authors are encouraged to construct compelling discussions on the research objectives, drawing upon the insights of esteemed scholars. It is vital to ensure this practice is consistently followed.\n\nThere are lack of using range of relevant literature. Critical evaluation of key concepts and theories is also required.\n\nResearch Objectives should be included in the Introduction part and the Research questions.\nResearch Methodology:\nThe research design lacks adequate information, and it is essential that a more comprehensive explanation is provided.\n\nThe description of the sampling method is deficient in detail, necessitating a thorough exposition of the rationale for opting to utilize CMIE. Clarification in this regard is indispensable.\nDiscussion:\nKindly proceed with the formulation of the Discussion section, utilising the results and findings as the basis.\n\nIn Discussion, authors need to justify the research results through scholars' references.\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?\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? Partly", "responses": [ { "c_id": "10581", "date": "06 Dec 2023", "name": "Raju Ganesh Sunder", "role": "Author Response", "response": "I did not find any research objectives in the Introduction part. Please develop the Research objectives based on the Research problem and Research questions. – Purpose is mentioned in the Significance in the sub-section of the Introduction. In the literature review, the authors are encouraged to construct compelling discussions on the research objectives, drawing upon the insights of esteemed scholars. It is vital to ensure this practice is consistently followed – Discussion and summary of the literature review is mentioned in the last 3 paragraphs of the Literature. Research Objectives should be included in the Introduction part and the Research questions. – Mentioned after the Literature Review A thorough exposition of the rationale for opting to utilize CMIE – Updated in data source In Discussion, authors need to justify the research results through scholars' references - Added in Results and Discussion section" } ] } ]	1	https://f1000research.com/articles/12-1130
https://f1000research.com/articles/12-1566/v1	06 Dec 23	{ "type": "Research Article", "title": "Intention to whistleblow: Perception of reporting skill mediates the predicting role of class consciousness and perceived probability of revenge", "authors": [ "Juneman Abraham", "Christian Jeremia Mangapul", "Destasya Nurcahyani Amaniputri", "Rudi Hartono Manurung", "Wing Ispurwanto", "Christian Jeremia Mangapul", "Destasya Nurcahyani Amaniputri", "Rudi Hartono Manurung", "Wing Ispurwanto" ], "abstract": "Background A number of corruption cases would never have been revealed without the role of the whistleblower. Whistleblowers - as people who know about corruption incidents in their environment - are social capital in preventing and eradicating corruption. For this reason, it is urgent to know the configuration of psychological predictors of a person’s intention to carry out whistleblowing.\n\nMethods Predictive correlational design with a mediation analysis was used in this study. The participants of this study were 374 Indonesians (187 males, 187 females; M age = 25.61 years old; SD age = 6.78 years).\n\nResults The results showed that perception of reporting skill can mediate the predicting relationship between class consciousness, perceived probability of revenge, and intention to blow the whistle.\n\nConclusions Class consciousness and perceived probability of retaliation might encourage someone to feel competent to blow the whistle - or improve their reporting skill - to carry out whistleblowing.", "keywords": [ "corruption", "whistleblowing intention", "reporting skill", "retaliation", "class consciousness" ], "content": "Introduction\n\nThe prevalence of corruption in business is a serious issue that may harm both the company’s finances and society at large. According to Castro and Phillips (2020), corporate corruption is the abuse of official power for personal gain. They also stress that it hinders national growth and undermines effective governance. Bribery, nepotism, and misuse of insider knowledge are just a few of the various ways that corruption in businesses can manifest itself (Argandoña, 2001).\n\nWhistleblowing is considered a potential instrument in the fight against corruption. Salihu (2019) emphasized the benefits of Nigeria’s whistleblowing policy, which led to the identification and recovery of stolen public assets as well as the conviction of offenders. Aruzzi (2019) discussed the implementation of whistleblower systems as a means to discourage and uncover corruption within governmental organizations in Indonesia. Carr and Lewis (2010) examined the potential of employment law to fight corruption by imposing obligations on those within the workplace to report corrupt activities and protecting whistleblowers.\n\nWhen disclosures are made with an accurate intention and adhere to certain communication requirements when addressing matters of public interest, whistleblowing can be justified (Kumar and Santoro, 2017). Lewis et al. (2014) claimed that scholars and policymakers need to better understand the intricacies and effects of whistleblowing since it is an essential procedure for holding institutions accountable.\n\nThe goal of this study is to develop a model that, using a combination of social psychological characteristics, predicts whistleblower intention. Based on the idea of planned behavior, this study draws the assumption that whistleblowing intention is an immediate antecedent of whistleblowing activity (Ajzen, 2020). The degree to which a person has made deliberate arrangements to engage in or refrain from engaging in a certain future activity is known as intention, or behavioral intention (Davis and Warshaw, 1992; Warshaw and Davis, 1985).\n\nNevertheless, the formation of the intention is not simple. Particularly in cases where there is no legal protection, whistleblowers frequently experience personal risk and harsh reprisal. When whistleblowers feel that they have more power and support, they are more likely to be successful in exposing wrongdoing (Miceli and Near 2002). Strong proof and successful whistleblowing go hand in hand (Apaza and Chang, 2011). Whistleblowers must possess specialized knowledge, access, and skill, according to UNODC (n.d.), that enables them to identify corruption or other serious issues that could otherwise go unnoticed. According to MacNab and Worthley (2008), in this situation, the perception of one’s competence to perform a task was a reliable predictor of their inclination to come forward, i.e. to blow the whistle.\n\nFear of reprisal is negatively connected to whistleblowing intents, particularly when it comes to vengeance or retaliation (Dhamija and Rai, 2018; Khan et al., 2022). If they perceive a larger fear of reprisal, whistleblowers are more likely to choose to keep quiet. Positive impressions such as professional identity, ethical orientation, and supervisor trust were dependent on employees’ fear of reprisals in a company (Yang and Xu, 2020).\n\nParadoxically, then, a person could be motivated to become more competent or skilled at making whistleblower reports if they believe that retaliation is likely to happen. Several study findings form the basis for this idea. One may also want to counterblow if they believe that others would retaliate unfairly as a result of their whistleblowing (Kim and Smith, 1993). In this instance, seeking retribution may be a way for a whistleblower to attain (self-)justice in situations when institutionalized advocacies from authorities are scarce (Jäggi and Kliewer, 2016). Whistleblowers need to have more than just bare-bones competence in order to exact “moral, sweet revenge” (Gert, 2020). A whistleblower’s drive to succeed in a later activity that supports their competence can be increased by prior competence dissatisfaction (Fang et al., 2018). People who exaggerate their performance do so in response to a threat to their performance (Wakeman et al., 2019). According to the cognitive dissonance and self-affirmation theories, a person can resolve the discrepancy between their true and false selves by developing their capacities (Aronson et al., 1999). In conclusion, people may be motivated to become more skilled or competent whistleblowers in order to anticipate or manage reprisal if they perceive retaliation or revenge to be likely.\n\nBy affecting the trade-off between justice and loyalty, class consciousness may also be a motivator for whistleblowing (Dungan et al., 2015). According to Crossley (2013), class consciousness—the recognition of oneself (“the proletariat”) as a class and of one’s collective strength—can inspire a revolution against “the bourgeoisie” and maybe thwart corruption. The relative comparisons a person draws between their socioeconomic circumstances and those of other groups are connected to this awareness (Gartrell, 1987; Stacks, 1984).\n\nAnvari (2019) offers a comprehensive theory of whistleblowing that incorporates social identity theorizing. This theory explains when and how social identities and types of power influence group members to report ingroup misconduct by using whistleblowing. The whistleblowing process may be motivated by collective identities and power dynamics, and it may also play a significant role in the control of moral and legal behavior, according to the model. Marxist classics have long underlined the significance of this issue, and Feng-wei’s (2006) conclusions that a systematic cultural mechanism is required to resist corruption and promote incorruptibility support the entire logic that emphasizes the relevance of class consciousness.\n\nWhistleblowing, according to Couto et al. (2020), can be justified as an ethical duty to assist the group, motivated by solidarity and responsibility for the other. In other words, class consciousness can motivate political activity (Portes, 1971); in the case of the current study, this political action is to expose corruption. Because of this, a company employee who is aware of their class must not become mired in a false consciousness that would hinder them from comprehending their shared interest in standing up to their exploiters (Ishfaq et al., 2021).\n\nAccording to the preceding explanation, perceived reporting competence (1) is predicted by class consciousness and the likelihood of retaliation, and (2) predicts the desire to report wrongdoing. Perceived reporting competency may act as a mediator between the two variables’ impacts on whistleblowing intention in an integrative theoretical framework. The aim of this study is to investigate the mediation hypothesis, which claims that perceived reporting abilities can mediate the link between class consciousness and intention to report corruption as well as between perceived likelihood of retaliation and the intention.\n\n\nMethods\n\nThe design of this study was quantitative, predictive correlational. The research was conducted in an online setting and was a cross-sectional study, so no follow-up procedure was applied. Recruitment of participants for this research was carried out from June 2020. At that time, there was a quite prominent case in Indonesia which was the trigger for this research, namely that a whistleblower in a corruption case was made a tax suspect and blackmailed by prosecutors (Tempo, 2020), after various similar cases since 2014 which was recorded in the book entitled Counterattacks against Scandal Whistleblowers: Case Studies Regarding the Challenges, Practices and Effectiveness of Whistleblowers in Indonesia (as cited in Wahidin, 2021).\n\nHowever, due to the COVID-19 pandemic, data collection occurred over several periods, and ended with comprehensive data processing in June 2023. The research for the field of corruption prevention was approved by Bina Nusantara University in 2020, which was then – because it designates a more extensive pool of data to be collected – followed by a grant proposal to the Indonesian Ministry of Research and Technology/National Research and Innovation Agency. However, the Indonesian Government, through the Ministry, realized the 2020 Budget Rationalization by deferring research funding due to the COVID-19 pandemic crisis. Thus, the funding attainment for this research on whistleblowing has been delayed and eventually been resubmitted to the Indonesian Ministry of Education, Culture, Research and Technology in the first quarter of 2023.\n\nThe participants of this study were 374 people (187 women, 187 men; Mage=25.61 years old; SDage=6.78 years) who came from a non-Western country, Indonesia, and were recruited using a convenience sampling technique.\n\nThe eligibility criteria of the samples were workers who worked in an organization or company with a minimum age of 15 years in accordance with Indonesian labor law. Based on data from the Indonesian Central Bureau of Statistics (BPS, 2023), the number of workers referred to is 50,383,238. The number of samples, i.e. 374, slightly exceeding the minimum sample limit coming from a calculation using the Sample Size Calculator (Calculator.net, 2022), with the following parameters: Confidence level of 95%, population size of 50,383,238 and population proportion of 36.34% (i.e. 50,383,238 divided by 138,632,511), i.e. 356.\n\nPotential participants were approached via social media, such as Twitter, Instagram, and WhatsApp. After finding out that someone meets the eligibility criteria - either by asking directly via online messenger or by observing their social media account profile – the researchers conveyed that their voluntary participation is needed to fill out a questionnaire regarding the world of work. Participants were informed that the duration of time required to fill out this research questionnaire is a maximum of 20 minutes, and that the data obtained will be anonymized, not assessed as true or false, and only be used for research purposes. In addition, participants were also informed that the researchers would randomly give prizes to 10 participants in the form of IDR 50,000 (or USD 3.22) which would be transferred to the participant’s mobile phone number, but if they wanted to take part in this “lucky draw”, participants needed to write down their mobile phone number.\n\nWritten informed consent was obtained, with participants giving a check mark in the small box contained in a Google Form stating that they agreed that the data obtained from them is used and published as long as they were anonymized.\n\nTo measure whistleblowing intention, the author combines two concepts, namely intention and whistleblowing. Based on the definition of intention (Davis and Warshaw, 1992; Warshaw and Davis, 1985), the dimensions of intention are (1) Conscious formulation of plan, (2) Specific behavior performance, and (3) Future behavior performance. Meanwhile, because one aspect of intention is specified behavior, vignettes are used (e.g. Ahmad et al., 2013) to illustrate specific cases of corruption contextualized in the world of work. In order to determine the strength of whistleblowing intention, this study asks the question, for example, \"If you were in this concrete situation as an employee, how willing would you be to report this action to the leadership within one week? (INTEND TO means committing, planning with full awareness, deliberate or solid intention to act)” (20 items) with response options ranging from Strongly Not Intend (scored 1) to Strongly Intend (scored 6). This study also combines types of whistleblowing (internal, external, formal, informal, anonymous, identified) (Park et al., 2008).\n\nTo measure the perception of reporting skill or competence, 13 items were used for 13 vignettes/scenarios, “Currently, the reporting competencies or skills that I have regarding this reporting is …”, with response options ranging from Very Low (scored 1) to Very High (scored 6). To measure class consciousness, this study uses a scale developed by Keefer et al. (2015), which consists of the following five dimensions: (1) awareness of social class, (2) beliefs about the permeability of class groups, (3) perceptions of class conflict, (4) personal experience of being treated as a member of one’s class, and (5) identification with a class group (32 items). Examples of items are: “Social class is still an important issue in today’s society”, “People in my social class are often treated unfairly by others”. The response options ranges are from Strongly Disagree (score 1) to Strongly Agree (score 6). To measure the perceived probability of revenge or retaliation, 7 items were used for 7 vignettes/scenarios, “In your opinion, your chance of experiencing revenge if you report this action is …”, with response options ranging from Very Low (scored 1) to Very High (scored 6).\n\nA copy of the questionnaire can be found under Extended data (Abraham et al., 2023).\n\nAll psychological scales in the questionnaire were tested for validity and reliability with the criteria of item validity (corrected item-total correlation) of at least 0.250 and internal consistency (Cronbach’s a) of at least 0.600. The reliability and validity items of the research instrument are shown in Table 1. The JASP 0.16.4.0 for Windows was used to analyze the research data with correlation, regression, and mediation analysis. In the mediation analysis, the predicted variable was whistleblowing intention; the predictors were class consciousness and perceived probability of revenge; and the mediator was perception of reporting skill or competence.\n\nThe underlying data, complete questionnaire, and analysis script are openly available at https://zenodo.org/record/8327360 (Abraham et al., 2023).\n\n\nResults\n\nDemographically, some participants were residents of DKI Jakarta province (N=119) which is the capital of Indonesia. In addition, other participants were residents of the Java Island (non-DKI Jakarta; N=235); Sulawesi Island (N=10); Sumatera Island (N=6); Kalimantan Island (N=2); and Bali Island (N=2). The educational composition of the participants is: Bachelor (N=197), High School (N=133), Master (N=21), Diploma (N=20), dan Doctor (N=3). The management/leadership level composition of the participants is: Non Management (Staff, Officer) (N=216), Lower Level Management (Supervisor) (N=59), Middle Level Management (Manager) (N=58), and Top Level Management (Chief Executive Officer, General Manager, Directors) (N=41).\n\nThe psychometric properties and descriptive statistics of the variables are shown in Table 1.\n\nThe results of this study indicated that:\n\n• All predictors, i.e. perceived reporting skills or competence (r=0.755, p<0.001), class consciousness (r=0.239, p<0.001), and perceived probability of revenge (r=0.248, p<0.001), have positive correlations with whistleblowing intentions (see Table 2).\n\n• However, regression analysis showed that while class consciousness can predict the intention (B=0.151, SE B=0.045, p<0.001), perceived probability of revenge cannot directly predict it (B=0.050, SE B=0.029, p>0.05 (Table 3).\n\n• Mediation analysis showed that class consciousness (B=0.121, SE B=0.049, p<0.05) as well as perceived probability of revenge (B=0.133, SE B=0.032, p<0.001) can indirectly predict the intention through perceived reporting skill or competence (Table 4, Figure 1). Or in other words, perceived reporting skill or competence is functional as a mediator of the relationship between predictors and criterion variable.\n\n* p<0.05.\n\n p<0.01.\n\n* p<0.001.\n\nNotes. INT = Whistleblowing Intention; SK = Perception of Reporting Skill or Competence; CC = Class Consciousness; RV = Perceived Probability of Revenge.\n\n\nDiscussion\n\nThe current study discovered that empirical evidence supports the hypothetical model that claims perceived reporting skill or competence as a mediator that connects the predictive effects of class consciousness and perceived chance of retaliation on whistleblower intention.\n\nNumerous studies have discovered that the perception of possible retaliation does not necessarily reduce the intention to report wrongdoing. For instance, Mesmer-Magnus and Viswesvaran (2005) claimed that the possibility of revenge (such as job loss or promotion) interacts with contextual factors (such as support from supervisors and coworkers, the size of the company, and organizational environment) to produce the choice to report wrongdoing. According to Kanojia et al. (2020), locus of control and perceived status/power were able to reduce the impact of retaliation on the intention of whistleblowers.\n\nIn contrast to earlier studies, the current study is looking for variables that are predicted by perceived retaliation and are also capable of increasing whistleblowing intention, such as perceived reporting competence, rather than variables that moderate the predictive effect of perceived vengeance. The indirect effect that the perception of retaliation probability has on whistleblowing intention is described below.\n\nAccording to Near and Miceli (1985), a potential whistleblower faces a fundamental conundrum. If he/she reports corruption in his company and it turns out that there is a lot of it, its prevalence will be linked to poorer organizational performance. Additionally, he/she has the chance to face backlash or treachery from the business or from disgruntled employees. The company will, however, likewise drift toward anarchy and mayhem if he does not report—or forgive—so that no one takes remedial action.\n\nBased on the research findings, perceived revenge probability does not prevent whistleblowing intents from developing; rather, it can boost efforts by enhancing reporting abilities, allowing these intentions to be carried out successfully. Borrowing insights from the world of consumer behavior, perceived betrayal is the means to understand customer retaliation (Grégoire and Fisher, 2008). When applied in the context of a whistleblower, employees who become whistleblowers are serving the company by exposing the corruption that exists within them.\n\nThe premise of the current study is that a possible whistleblower will be willing to become a “martyr” in order to fulfill his/her noble mission to save the organization from being destroyed by perceived threats of reprisal or revenge (Pegg, 1991; Vinten, 1997). The individual will get ready by improving his or her competence or reporting abilities so that his report does not backfire but is accepted by the organization (for follow-up) and is successful in eradicating corruption. This will ensure that this martyrdom is not in vain.\n\nIndividuals with a class consciousness, on the other hand, are aware of injustice and inequality in their surroundings and are even prepared to fight for systemic change (Solt et al., 2017). Given that critical thinking is a part of the awareness (Kaplan, 1994), this is not shocking. Class consciousness is an effect of colonialism, according to Adenekan (2021). As a result of having been colonized by other nations (the Netherlands, England, and Japan) for several centuries, the Indonesian people are not unfamiliar with the experience of class awareness.\n\nThe awareness has an effect that significantly promotes taking corrective action to lessen inequality, particularly with those that are thought to “have a greater unfair advantage” (Crean, 2018) — in the context of this research, those who engage in corruption — through whistleblowing. The dynamics of class consciousness, which battle against corruption by enhancing reporting abilities to safeguard working-class solidarity and sustainability, are what lead to whistleblowing intention (Mayer, 1993).\n\nThis study’s limitation is the cross-sectional nature of the data collection, which leaves room for the possibility of common method bias to creep in. Future research should employ the longitudinal approach to lessen the inflated correlations that might result from this bias. The research’s conclusion is that additional psychological theoretical models must be developed that (1) help people feel brave or capable of overcoming the possibility of vengeance, and (2) incorporate more psycho-sociological factors like class awareness. Finding models that examine the function of factors that act as a bridge between psychological and sociological ideas is crucial since whistleblowing is neither only an individual or an organizational problem.\n\nThis present study was approved by the Bina Nusantara University Research Committee, vide Letter Number: 149/VR.RTT/VII/2023. The ethical decree is stated in Article 1 Paragraph 2 of the Letter. Written informed consent was obtained from all participants of this study, which included consent for the research procedure to be carried out and for the publication of this article containing anonymized, analyzed, and interpreted data.\n\n\nAuthor roles\n\nJuneman Abraham: Conceptualization, Data Curation, Formal Analysis, Funding Acquisition, Investigation, Methodology, Resources, Supervision, Validation, Visualization, Writing – Original Draft Preparation, Writing –Review and Editing; Christian Jeremia Mangapul: Data Curation, Formal Analysis, Investigation, Methodology, Project Administration, Resources, Software, Validation, Visualization, Writing – Original Draft Preparation; Destasya Nurcahyani Amaniputri: Data Curation, Formal Analysis, Investigation, Project Administration, Resources, Validation, Visualization, Writing – Original Draft Preparation; Rudi Hartono Manurung: Formal Analysis, Funding Acquisition, Resources, Validation, Visualization, Writing – Original Draft Preparation; Wing Ispurwanto: Conceptualization, Formal Analysis, Funding Acquisition, Project Administration, Resources, Validation, Visualization, Writing – Original Draft Preparation.", "appendix": "Data availability\n\nZenodo: ‘Dataset of Intention to Whistleblow: Perception of Reporting Skill Mediates the Predicting Role of Class Consciousness and Perceived Probability of Revenge’. https://zenodo.org/record/8327360 (Abraham et al., 2023).\n\nThis project contains the following underlying data:\n\n- Whistleblowing Intention - Suppl Material - Data.xlsx\n\nThis project contains the following extended data:\n\n- Whistleblowing Intention - Suppl Material - Questionnaire.docx\n\n- Whistleblowing Intention - Suppl Material - Analysis Script (JASP).jasp\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAbraham J, Mangapul CJ, Amaniputri DN, et al.: Dataset of Intention to Whistleblow: Perception of Reporting Skill Mediates the Predicting Role of Class Consciousness and Perceived Probability of Revenge (Version 1). [Data set]. Zenodo. 2023. Publisher Full Text\n\nAdenekan S: African literature in the digital age: Class and sexual politics in new writing from Nigeria and Kenya. James Currey; 2021.\n\nAhmad SA, Smith M, Ismail Z: Internal whistleblowing intentions by internal auditors: A prosocial behaviour perspective. Management and Accounting Review (MAR). 2013; 12(1): 145–181.\n\nAjzen I: The theory of planned behavior: Frequently asked questions. Human Behavior and Emerging Technologies. 2020; 2(4): 314–324. Publisher Full Text\n\nAnvari F, Wenzel M, Woodyatt L, et al.: The social psychology of whistleblowing: An integrated model. Organizational Psychology Review. 2019; 9(1): 41–67. Publisher Full Text\n\nApaza CR, Chang Y: What makes whistleblowing effective: Whistleblowing in Peru and South Korea. Public Integrity. 2011; 13(2): 113–130. Publisher Full Text\n\nArgandoña A: Corruption: The corporate perspective. Business Ethics: A European Review. 2001; 10(2): 163–175. Publisher Full Text\n\nAronson J, Cohen G, Nail PR: Self-affirmation theory: An update and appraisal.Harmon-Jones E, Mills J, editors. Cognitive dissonance: Progress on a pivotal theory in social psychology. American Psychological Association; 1999; pp. 127–147. Publisher Full Text\n\nAruzzi MI: The use of whistleblowing systems to deter and detect corruption in Indonesian government institutions. (Doctoral dissertation, Loughborough University) 2019. Publisher Full Text\n\nBPS: Penduduk Berumur 15 Tahun ke Atas yang Bekerja menurut Provinsi dan Status Pekerjaan Utama, 2023 [Working Population Aged 15 Years and Over by Province and Main Job Status, 2023].2023. Reference Source\n\nCalculator.net: Sample size calculator.2022. Reference Source\n\nCarr I, Lewis D: Combating corruption through employment law and whistleblower protection. Industrial Law Journal.2010; 39(1): 52–81. Publisher Full Text\n\nCastro A, Phillips N: What is corporate corruption? Defining and understanding corruption in management. Academy of Management Proceedings. Academy of Management; 2020; (Vol. 2020(1): p. 12006).\n\nCouto FF, Palhares JV, de Pádua Carrieri A : Corrupção organizacional e uma justificação decolonial para as práticas de whistleblowing. Revista Eletrônica de Ciência Administrativa. 2020; 19(3): 337–358. Publisher Full Text\n\nCrean M: Affective formations of class consciousness: care consciousness. Sociol. Rev. 2018; 66(6): 1177–1193. Publisher Full Text\n\nCrossley N: Class consciousness: The Marxist conception. The Wiley-Blackwell Encyclopedia of Social and Political Movements. 2013. Publisher Full Text\n\nDavis FD, Warshaw PR: What do intention scales measure? The Journal of General Psychology. 1992; 119(4): 391–407. Publisher Full Text\n\nDhamija S, Rai S: Role of retaliation and value orientation in whistleblowing intentions. Asian Journal of Business Ethics. 2018; 7: 37–52. Publisher Full Text\n\nDungan J, Waytz A, Young L: The psychology of whistleblowing. Current Opinion in Psychology. 2015; 6: 129–133. Publisher Full Text\n\nFang H, He B, Fu H, et al.: A surprising source of self-motivation: prior competence frustration strengthens one’s motivation to win in another competence-supportive activity. Frontiers in Human Neuroscience. 2018; 12: 314. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFeng-wei G: Marxism and Culture Against Corruption and for Incorruptibility.2006. Reference Source\n\nGartrell CD: Network approaches to social evaluation. Annual Review of Sociology. 1987; 13(1): 49–66. Publisher Full Text\n\nGert J: Revenge is sweet. Philosophical Studies. 2020; 177(4): 971–986. Publisher Full Text\n\nGrégoire Y, Fisher RJ: Customer betrayal and retaliation: When your best customers become your worst enemies. Journal of the Academy of Marketing Science. 2008; 36: 247–261. Publisher Full Text\n\nIshfaq F, Khan L, Haider MW: Class inequalities: A Marxist study of Uzma Aslam Khan’s The Story of Noble Rot. International Research Journal of Education and Innovation. 2021; 2(3): 249–259. Publisher Full Text\n\nJäggi L, Kliewer W: “Cause That’s the Only Skills in School You Need” A Qualitative Analysis of Revenge Goals in Poor Urban Youth. Journal of Adolescent Research. 2016; 31(1): 32–58. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKanojia S, Sachdeva S, Sharma JP: Retaliatory effect on whistle blowing intentions: A study of Indian employees. Journal of Financial Crime. 2020; 27(4): 1221–1237. Publisher Full Text\n\nKaplan LD: Teaching intellectual autonomy: The failure of the critical thinking movement.Walters KS, editor. Re-thinking reason: New perspectives in critical thinking. SUNY Press; 1994; pp. 205–220.\n\nKeefer LA, Goode C, Van Berkel L: Toward a psychological study of class consciousness: Development and validation of a social psychological model. Journal of Social and Political Psychology. 2015; 3(2): 253–290. Publisher Full Text\n\nKhan J, Saeed I, Zada M, et al.: Examining whistleblowing intention: The influence of rationalization on wrongdoing and threat of retaliation. International Journal of Environmental Research and Public Health. 2022; 19(3): 1752. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKim SH, Smith RH: Revenge and conflict escalation. Negotiation Journal. 1993; 9: 37–43. Publisher Full Text\n\nKumar M, Santoro D: A justification of whistleblowing. Philosophy and Social Criticism. 2017; 43(7): 669–684. Publisher Full Text\n\nLewis DB, Brown AJ, Moberly R: Whistleblowing, its importance and the state of the research. International Handbook on Whistleblowing Research. 2014; 1–34. Publisher Full Text\n\nMacNab BR, Worthley R: Self-efficacy as an intrapersonal predictor for internal whistleblowing: A US and Canada examination. Journal of Business Ethics. 2008; 79: 407–421. Publisher Full Text\n\nMayer R: Marx, Lenin and the corruption of the working class. Political Studies. 1993; 41(4): 636–649. Publisher Full Text\n\nMesmer-Magnus JR, Viswesvaran C: Whistleblowing in organizations: An examination of correlates of whistleblowing intentions, actions, and retaliation. Journal of Business Ethics. 2005; 62: 277–297. Publisher Full Text\n\nMiceli MP, Near JP: What makes whistle-blowers effective? Three field studies. Human Relations. 2002; 20(4): 679–708. Publisher Full Text\n\nNear JP, Miceli MP: Organizational dissidence: The case of whistle-blowing. Journal of Business Ethics. 1985; 4: 1–16. Publisher Full Text\n\nPark H, Blenkinsopp J, Oktem MK, et al.: Cultural orientation and attitudes toward different forms of whistleblowing: A comparison of South Korea, Turkey, and the UK. Journal of Business Ethics. 2008; 82: 929–939. Publisher Full Text\n\nPegg OC: Corporate Whistleblower: Knave or Martyr? Proceedings of the International Association for Business and Society. 1991, July; 2: 763–787. Publisher Full Text\n\nPortes A: On the interpretation of class consciousness. American Journal of Sociology. 1971; 77(2): 228–244. Publisher Full Text\n\nSalihu HA: Whistleblowing policy and anti-corruption struggle in Nigeria: an overview. African Journal of Criminology and Justice Studies: AJCJS. 2019; 12(1): 55–69.\n\nSolt F, Hu Y, Hudson K, et al.: Economic inequality and class consciousness. Journal of Politics. 2017; 79(3): 1079–1083. Publisher Full Text\n\nStack S: Income inequality and property crime: A cross-national analysis of relative deprivation theory. Criminology. 1984; 22(2): 229–256. Publisher Full Text\n\nTempo: Perkara Janggal Peniup Peluit [The Strange Case of the Whistleblower].2020. Reference Source\n\nUNODC: Whistle-blowing systems and protections.n.d.. Reference Source\n\nVinten G: Towards a theology of whistleblowing. Theology. 1997; 100(794): 90–100. Publisher Full Text\n\nWahidin KP: Apes Para Peniup Peluit [The Misfortune of the Whistleblowers].2021, April 22. Reference Source\n\nWakeman SW, Moore C, Gino F: A counterfeit competence: After threat, cheating boosts one’s self-image. The Journal of Experimental Social Psychology. 2019; 82: 253–265. Publisher Full Text\n\nWarshaw PR, Davis FD: Disentangling behavioral intention and behavioral expectation. The Journal of Experimental Social Psychology. 1985; 21(3): 213–228. Publisher Full Text\n\nYang L, Xu R: The effects of retaliation on whistleblowing intentions in China banking industry. Journal of Accounting & Organizational Change. 2020; 16(2): 215–235. Publisher Full Text" }	[ { "id": "237505", "date": "15 Feb 2024", "name": "Karen Paul", "expertise": [ "Reviewer Expertise Business ethics", "social responsibility", "international business" ], "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 article about an important topic (whistleblowing) in an understudied area of the world, so it does contribute to knowledge. The sample is not extremely rigorous but adequate. The model and discussion of meanings is adequate. I think we should have more discussion of the possible significance of Indonesian culture and behavioral norms, and I think Indonesia should be shown in the title or at least the keywords. But overall, a good job!\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": "246255", "date": "21 Feb 2024", "name": "Branislav Hock", "expertise": [ "Reviewer Expertise anti-corruption", "economic crime" ], "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 very much for the opportunity to review this paper. The explores whistleblowing intentions as an immediate antecedent of whistleblowing activity. In doing so it attempts to develop a model, which predicts whistleblower’s intention. It is always great to see empirical work in this area.\nI am not able to comment on statistical/data part of the study.\nI suggest some improvements that will make the paper stronger.\nWhile the paper introduces the research problem well, it is somehow weaker in its theoretical embedding and should attempt to acknowledge the limitation of the model. Most importantly, it should further reflect more deeply on some key incentives in known whistleblowing regimes. Consider reflecting upon the following:\ntransnational character of corruption, including the role of private sector firms, their compliance programmes, and “alternative” justice – [Hock B, 2022 et. al. (Ref 1)] Rewards – provided nationally, but also the fact that whistle-blowers are often foreign citizens being motivated by financial rewards in US and other jurisdictions. [Karpacheva E. 2024, et. al.(Ref 2)]\nConsider introducing this broader set of incentives (beyond retaliation) early in the paper and revisit them later in the final discussion. Use this reflection to consider limitations of the paper and its 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? 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": [] }, { "id": "246260", "date": "29 Feb 2024", "name": "Theresia Dwi Hastuti", "expertise": [ "Reviewer Expertise auditing", "corporate governance", "family business", "SMEs", "Sustainability" ], "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 has been presented clearly and accurately. Most of the citations use recent literature, but there are several reference articles that are used from a long time ago, such as: Argandoña, 2001, Davis and Warshaw, 1992; Warshaw and Davis, 1985). Miceli and Near 2002), Kim and Smith, 1993, Aronson et al., 1999). In general, the design of this research is appropriate, as well as the technical processing and analysis of research data which has been carried out well. The detailed methods and analysis provided are very likely to enable replication by other parties. However, there is statistical analysis and interpretation that needs to be added, such as the interpretation of table 1 regarding validity and reliability results. it is necessary to add the results of model testing and the ability to explain the model and its interpretation.\n\nAll data sources underlying the results are available to ensure full reproducibility, but need to be updated according to local conditions. The conclusions drawn are sufficiently supported by the results obtained. This is the consistency of this research.\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/12-1566
https://f1000research.com/articles/12-1565/v1	06 Dec 23	{ "type": "Study Protocol", "title": "A cross-sectional study for assessment of activity of daily living and health-related quality of life among adults with physical disabilities in the Wardha district", "authors": [ "Aditi Nath", "Dr. Sonali Choudhari", "Dr. Sonali Choudhari" ], "abstract": "Introduction Physical disabilities can affect a person’s ability to operate, move about, and endure physical strain. Physically challenged individuals have fewer social opportunities than physically healthy individuals, which is linked to a lower degree of well-being and a worse standard of living (QoL).\n\nObjectives This study set out to evaluate how physically disabled people’s everyday activities and their physical impairments have an impact on their quality of life in terms of health.\n\nMethods The study will concentrate on physically handicapped persons and how their everyday activities and quality of life are affected by their impairment. To evaluate and obtain insight into their knowledge about the laws and facilities available to them. In order to gather the research on the subject, search terms like “disability,” “quality of life,” and “activities of daily living” were employed in PubMed and Google Scholar.\n\nStudy implications The goal of the study is to address any knowledge gaps regarding how physical disability disrupts a normal lifestyle and how challenging it is to carry out essential daily tasks (activities of daily living).", "keywords": [ "Activities of daily living (ADL)", "Quality of life (QOL)", "Physical disability" ], "content": "Introduction\n\nAccording to the World Health Organization (WHO), “health” refers to a state of complete physical, psychological, and social wellness as opposed to just the absence of disease or incapacity. Disability is not just a physical ailment or a personality attribute; it also includes challenges that people may encounter in social and physical contexts. The term “disability” refers to limitations on function, activities, and participation. Even though health is defined in terms of a person’s ability to function in a range of health categories, such as vision, hearing ability, and agility, the global burden of disease (GBD) uses the term “disability” to refer to a person’s worsening health.1 There are numerous definitions of “disability” that coexist.2 The quality of life, on the other hand, is a person’s perception of where they are in life in respect to their goals, standards, and concerns, alongside the social and cultural context in which they live. It is a broad concept that is profoundly affected by an individual’s mental and physical fitness, degree of independence, social ties, and personal beliefs.3 According to estimates, 10% of people worldwide have a handicap or impairment.2 Due to population increase, aging, the advent of long-term diseases, and preventive advancements that protect and lengthen life, there are an increasing number of persons with impairments.4 Negative outcomes like reliance and institutionalization result from physical disability and functional limits.\n\nUnder the provisions of Article 25 of the United Nations,\n\n1. Without encountering any prejudice, disabled people have the liberty to a higher standard of health care in order to enhance their health.\n\n2. The state will ensure accessibility for persons with disabilities to various services of health that can be gender-sensitive.\n\n3. Inclusion of health care and programs in the area of sexual and reproductive health.\n\n4. Arranging health services as close to their own communities as possible.\n\n5. Provision of services for the identification and early intervention to prevent further worsening of their condition.\n\nThe experience and degree of a handicap are significantly influenced by the person’s environment. Challenges that limit persons with disabilities from actively and completely engaging within the society on a level playing field with others are typically present in unreachable settings. Taking these barriers out of the way and aiding those with disabilities in performing everyday tasks, social engagement can be increased. Compared to auditory perception and physical mobility, people with disabilities place higher value on broader dimensions of state of life, such as safety, taking care of oneself, and attaining independence.5 Assessing the standard of life of patients should be the top priority of every doctor and researcher. Since it is useful for determining needs and monitoring results, it is essential for health promotion activities.6 A person with a disability’s opinion of their health, happiness, and well-being frequently differs from their actual health state and disability, however, as their state of life is a complicated phenomenon.7 Disability (specially challenged condition) leads to deprivation and dependency in underdeveloped countries. Due to physical, social, and psychological hurdles, people with special needs continue to be marginalised in society.8 Aspects of one’s self-perceived well-being that are connected to or impacted by the existence of disease, treatment, and health policies are referred to as health-related quality of life (HRQOL).9 People with and without disabilities must participate in society and the workforce since it is widely known that doing so has a positive impact on one’s health, happiness, and overall state of life.10 Every human must participate in or be involved in daily activities. WHO asserts that participation improves health and wellbeing. It has been found that involvement suffers when there is a disability because there is less variety, more time spent at home, less social ties, and less active recreation.11 The multiple dimensions of quality of life (QOL) can be assessed both subjectively and quantitatively.12 Because they can help understand how patients’ experiences, expectations, beliefs, and perceptions are impacted by their health problems, assessments of health-related quality of life (HRQoL) have become a crucial part of health care.3 A physical impairment has an impact on a person’s mental health as well as their physical health. A few research have shown strategies for improving quality of life.4\n\nSeveral studies have been conducted on the number of cases of disability in India, most of which concentrate on the elderly population. Young adults are rarely the subject of studies. Additionally, there is not a lot of study on the state of life (QOL) of those with physical impairments. Understanding QOL and other related concerns that affect both the younger and older population is the main objective of this study. There are some holes that must be filled in order to support the study’s central claim, which is\n\n1. To gain awareness of the majority of laws and regulations available for the disabled.\n\n2. How physical disability disrupts a normal lifestyle and how difficult it is to perform basic activities of daily living (ADLs).\n\nThus, strengthening the previous knowledge and making it a fundamental basis of what all the lacunas are will help in establishing a mindset for everybody, i.e., the general population, the disabled, the government, and the authorities to fully comprehend the knowledge and bring out necessary changes. It would be helpful to look into the social, contextual, and environmental elements that affect a person’s capacity to manage their condition.13\n\n\nMethods\n\nThe study will be conducted at Acharya Vinoba Bhave Rural Hospital and the participants will be selected from the outpatient department and in patient department of the orthopaedic and physiotherapy department of the hospital. Interaction with patients will be done and prepared questions will be asked for the data. The patients will be selected on the basis of their diagnosis and observing their physical conditions.\n\nA cross sectional study will be conducted among the patients visiting the hospital.\n\nAim\n\nTo evaluate how a physical handicap affects a person’s capacity to perform daily tasks and their ability to live a healthy life.\n\nPrimary objective\n\n1) To study the type and grade of physical disability.\n\n2) To assess the activities of daily living among adults with physical disabilities.\n\n3) To evaluate the health-related state of life for people with physical impairments.\n\n4) To study the association of type and grade of disability with their daily routine task and health-related state of life among adults with physical disabilities.\n\nSecondary objective\n\nTo assess their knowledge regarding the laws/facilities specifically available for them.\n\nPeople who are physically impaired will participate in this study. Simple random sampling will be used to conduct the study. The physiotherapy and orthopedic departments at Acharya Vinoba Bhave Rural Hospital will participate in the investigation. Outpatient department and in patient department patients between the ages of 18 and 60 will be chosen for data collection.\n\nThis study will be conducted on the adult population aged 18–60 years, suffering from a physical disability.\n\nInclusion criteria\n\nIndividuals between the ages of 18 and 60, males and females, who have locomotor disabilities, absence of a hand, a leg, or both due to amputation, inactivity of a body part, paralysis of a limb, deformity or dysfunction of joints impairing their “normal ability to move oneself or move different objects,” as well as other physical deformities like a hunched back, a deformed spine, etc.\n\nExclusion criteria\n\nThere will be an exclusion of those who are severely mentally ill.\n\nTable 1 elucidates the variables involved.\n\n\n\n1) Type of disability\n\nMotor disability\n\nSensory disability\n\nCongenital disability\n\nAcquired disability\n\n2) Grade of disability\n\n\n\n1) Quality of life\n\n2) Activity of daily living\n\n\n\n1) Assessment of ADL – The Barthel Index will be used to assess ADL.14 It comprises of going from a seat to a couch and back, moving around on a level surface and climbing stairs. It also involves eating, washing, dressing, grooming and using the toilet facilities available at home.\n\n2) Assessment of QOL – The WHOQOL-BREF scale will be used for the assessment of QOL. The 26 questions on the WHOQOL-BREF scale were grouped into four primary categories: physical, psychological, social, and environmental.\n\nData collection will be divided into three sections. Table 2 describes the data sources.\n\n\n\n1. Age\n\n2. Caste\n\n3. Type of family\n\n4. Marital status\n\n5. Educational attainment\n\n6. Sociodemographic status\n\n\n\n1. their meals,\n\n2. taking a bath;\n\n3. dressing\n\n4. bowels\n\n5. bladder\n\n6. toilet-use\n\n7. transfers (from couch to seat and return)\n\n8. stairs with mobility (on a level surface).\n\n\n\n1. Physical\n\n2. Pshychological\n\n3. Social\n\n4. Environmental\n\nSection A: Barthel index assessment for\n\na) Activity of daily living (ADL).\n\nSection B: structured questionnaire on\n\na) Socio-demographic status.\n\nb) Disability status.\n\nSection C: WHOQOL BREF Questionnaire for\n\na) Quality of life (QOL)\n\nPopulation size for (the fpc, or fixed population correction factor): N: 1000000\n\nThe population’s estimated percentage frequency of the outcome factor is: 2.21%±5\n\nConfidence levels as a percentage of 100 (absolute ±/%)(d): 5%\n\nCluster survey design effect (DEFF):\n\nThe sample size (n) for different levels of confidence. Table 3 further estimates the confidence interval and the relative sample size.\n\nn: minimum sample size required\n\nDEFF: design effect, which accounts for the effect of clustering or stratification in the sample design (usually set to 1 if not applicable)\n\nNp: an estimate of the number of people in the population who exhibit the desired feature (p is the percentage of the population that exhibits the desired characteristic)\n\n(1-p): an estimate of the number of individuals in the population without the desired characteristic\n\nd: The intended error margin, expressed as a percentage\n\nZ: the standard normal distribution’s critical value that corresponds to the desired level of confidence\n\nAlpha: the level of significance (usually set to 0.005 for a 95% confidence level\n\nN: the size of the population (or an estimate of the population size if it is not known)\n\nSimple random sampling will be used in the study’s administration. Both the inpatient and outpatient orthopaedics and physiotherapy departments will be taken into consideration for the study’s inclusion of individuals with disabilities. Patients between the ages of 18 and 60 will be enrolled. The data will be coded in an Microsoft Excel version 2305 file, and SPSS version 22 (RRID:SCR_002865) software will be used to analyse the data. Calculated descriptive data will take the form of percentages and frequencies.\n\nEthical approval for this study DMIHER (DU)/IEC/2023/644 was provided by Datta Meghe Institute of Higher Education & Research (DMIHER) Sawangi (deemed to be university). Respect shall be shown for the participants. The research will use a written informed consent strategy, in which all participants will be informed of the study’s purpose prior to being interviewed.\n\n\nDiscussion\n\nOne of the key issues for patients with chronic diseases, which can vary depending on the patients’ age, is the environment in which they reside and the individuals who provide care for them. For instance, it has been claimed that partners, women, and younger relatives take on the care of elderly patients.15 A “Clinico-Social Model” for the best care of patients with vision loss is available for those who experience visual impairment. This model’s main objective is to give people with visual disorders access to clinical and vision rehabilitation management components. Such a strategy could potentially enhance the quality of life for those who are blind and offer useful advice to eye care administrators all throughout India. These kinds of approaches can be applied to assist those in need and create an environment that is welcoming to those who have disabilities.16 In elderly people, disability may be brought on by physiopathology or biological changes. As a person gets older, it becomes a significant health issue. From a broad standpoint, older people’s inability to do basic tasks of daily living lowers their state of life, increases sanitary expenditures and hastens their death.17\n\nOne thing which the authors found after reading several articles is that it is planned to create rehabilitation units at Community Health Centres under the National Programme for Health Care of the Elderly.18 However, in order to address geriatric disability at the community level, complete health care services must be made available. Creating possibilities for young people to learn and work, particularly for women, could lower the prevalence of handicap as people age.19 In order to identify individuals at risk for functional impairment, like senior citizens with a history of recurrent falls or hospitalizations, multimorbidity, cognitive decline, and polypharmacy, and complete geriatric assessments are required in both primary care settings and hospital settings.20\n\nThere are many disabled people in India who require education, jobs, and rehabilitation programs. Rural areas demand special attention.21 In order to provide PWDs with a good existence, India must quickly catch up to the worldwide standards that are necessary. This can be done by providing appropriate health care.22\n\nIn addition to a high prevalence of functional disability or restricted functional capacity, ageing is linked to an increased risk of functional reliance. The physiological changes brought on by ageing pose a threat to elderly people’s ability to function independently. Functional limitations decrease an older person’s quality of life, increase their risk of hospitalization, and make them more dependent on their family members.23 All these things should be the focal area around which models, strategies, and assessments must be done to provide people who become vulnerable once tragedy strikes the reprieve to think carefully of their life choices and for them to have multiple options to choose from and continue to live their lives. Lower HRQoL has been associated with a higher prevalence of poor oral hygiene and neglected dental care needs. Therefore, it is essential to raise the social standing and dental health of the elderly.24\n\nParticipant bias or response bias may be present in the study, which may be a significant influence.\n\n\n\n1. To know the nature and severity of physical disability\n\n2. To evaluate daily living activities among the adult population of people with physical imparities.\n\n3. To evaluate the physically impaired population’s health-related state of life.\n\n4. To examine the relationship between the kind and severity of a person’s impairments, everyday activities, and health-related quality of life.\n\nIEC approval has been received and data collection tool for the study has been prepared.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nChaudhary S, Srivastava AK, Vyas S, et al.: Quality of Life among Disabled Persons- A Cross-Sectional Study in Rural Area of Dehradun District. Indian J Community Health. 2019 Sep 30; 31(3): 390–395. Publisher Full Text\n\nBize R, Johnson JA, Plotnikoff RC: Physical activity level and health-related quality of life in the general adult population: A systematic review. Prev Med. 2007 Dec 1; 45(6): 401–415. Publisher Full Text\n\nKosik KB, Johnson NF, Terada M, et al.: Health-Related Quality of Life Among Middle-Aged Adults With Chronic Ankle Instability, Copers, and Uninjured Controls. J Athl Train. 2020 Jul; 55(7): 733–738. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMunce SEP, Perrier L, Shin S, et al.: Strategies to improve the quality of life of persons post-stroke: protocol of a systematic review. Syst Rev. 2017 Sep 7; 6: 184. Publisher Full Text\n\nCrocker M, Hutchinson C, Mpundu-Kaambwa C, et al.: Assessing the relative importance of key quality of life dimensions for people with and without a disability: an empirical ranking comparison study. Health Qual Life Outcomes. 2021 Dec 14; 19(1): 264. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAndrew-Essien NE, Ojule IN: Health-Related Quality of Life of People with Physical Disability in South-South, Nigeria. Int J Innov Res Med Sci. 2020 Nov 21; 5(11): 542–549. Publisher Full Text\n\nGnanaselvam NA, Vinoth Kumar SP, Abraham VJ: Quality of Life of People with Physical Disabilities in a Rural Block of Tamil Nadu, India. J Psychosoc Rehabil Ment Health. 2017 Dec 1; 4(2): 171–177. Publisher Full Text\n\nShivakumar: Assessment of dentition status and treatment needs among children with disabilities attending special schools in Karad City, India.[cited 2023 May 12]. Reference Source\n\nThomas: Health-related quality of life among medical students.[cited 2023 May 12]. Reference Source\n\nGolos A, Zyger C, Lavie-Pitaro Y, et al.: Improving Participation among Youth with Disabilities within Their Unique Socio-Cultural Context during COVID-19 Pandemic: Initial Evaluation. Int J Environ Res Public Health. 2023 Feb 22; 20(5): 3913. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLaw M: Participation in the Occupations of Everyday Life. Am J Occup Ther. 2002 Nov 1; 56(6): 640–649. Publisher Full Text\n\nAnu: Disparities in the quality of life among smokers, nonsmokers, and ex-smokers.[cited 2023 May 16]. Reference Source\n\nLindsay S, Kingsnorth S, Mcdougall C, et al.: A systematic review of self-management interventions for children and youth with physical disabilities. Disabil Rehabil. 2014 Feb; 36(4): 276–288. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIstas A: THE BARTHEL INDEX.\n\nDuzgun Celik H, Cagliyan Turk A, Sahin F, et al.: Comparison of disability and quality of life between patients with pediatric and adult onset paraplegia. J Spinal Cord Med. 2018 Nov; 41(6): 645–652. Publisher Full Text\n\nSenjam SS: Developing a disability inclusive model for low vision service. Indian J Ophthalmol. 2021 Feb; 69(2): 417–422. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCarmona-Torres JM, Rodríguez-Borrego MA, Laredo-Aguilera JA, et al.: Disability for basic and instrumental activities of daily living in older individuals. PLoS One. 2019 Jul 26; 14(7): e0220157. Publisher Full Text\n\nGoswami AK, Ramadass S, Kalaivani M, et al.: Disability and its association with sociodemographic factors among elderly persons residing in an urban resettlement colony, New Delhi, India. PLoS One. 2019 Sep 24; 14(9): e0222992. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGoswami AK, Ramadass S, Kalaivani M, et al.: Disability and its association with sociodemographic factors among elderly persons residing in an urban resettlement colony, New Delhi, India. PLoS One. 2019 Sep 24; 14(9): e0222992. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYau PN, Foo CJE, Cheah NLJ, et al.: The prevalence of functional disability and its impact on older adults in the ASEAN region: a systematic review and meta-analysis. Epidemiol Health. 2022 Jul 12; 44: e2022058. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAgarwal AK, Singh JV, Agarwal M: Prevalence Of Disability In India-An Update. Indian J Community Health. 2009 Jun 30; 21(1): 56–63.\n\nKannabirān K, Hans A: Council for Social Development (India), editors. India: social development report 2016: disability rights perspectives. First ed.New Delhi, India: Oxford University Press; 2017; 336.\n\nKeshari P, Shankar H: Prevalence and spectrum of functional disability of urban elderly subjects: A community-based study from Central India. J Fam Community Med. 2017; 24(2): 86–90. Publisher Full Text\n\nShivakumar: Oral health-related quality of life of institutionalized elderly in Satara District, India.[cited 2023 May 16]. Reference Source" }	[ { "id": "256896", "date": "05 Apr 2024", "name": "Olufemi O Oyewole", "expertise": [ "Reviewer Expertise Musculoskeletal and rehabilitation." ], "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 protocol assesses the activity of daily living and health-related quality of life among adults with physical disabilities in the Wardha district. I will suggest the title to reflect this. Title Assessment of activity of daily living and health-related quality of life among adults with physical disabilities in the Wardha district: A study protocol. Abstract Please don't tag people with their disease/disability. Change throughout the manuscript \"disabled/ physically disabled/disabled people\" to \"people with a physical disability\" or \" people who were physically disabled or people with disability\". Aims and Objectives: Let these come before the methods section. You failed to describe how you will achieve the secondary objective. Methods i. You state that interaction with patients will be done and prepared questions will be asked for the data. This looks like a qualitative study. Can you clarify? ii. Setting: Most of the information in this section has been provided under the methods sections (paragraph 1) above. Please merge the information under the methods section (paragraph 1) with the information under the setting section. You can create another sub-heading 'participants' selection' (after exclusion criteria) to describe how the participants will be selected. iii. Sample size: Let the sample size determination follow the exclusion criteria. Please be specific, how many samples will power your study? Statistical methods i. The first three sentences are repeated. Not relevant here. ii. Please explain in detail how primary objective 4 and secondary objective will be analyzed. Scope and Implications How do these scopes and implications differ from the primary objectives stated above? I will suggest state clinical relevance and implication of the study here.\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/12-1565
https://f1000research.com/articles/12-1564/v1	06 Dec 23	{ "type": "Case Report", "title": "Case Report: Role of comprehensive rehabilitation In gaining recovery in a rare case of Polymyositis", "authors": [ "Nikita H. Seth", "Nishigandha Deodhe", "Irshad Qureshi", "Nishigandha Deodhe", "Irshad Qureshi" ], "abstract": "Polymyositis (PM) is an inflammatory myopathy, a group of illnesses characterized by the presence of inflammatory infiltrates in striated muscle. Proximal muscular weakness is the most common clinical symptom of polymyositis. The exact cause of polymyositis is uncertain, however current research points to an autoimmune condition. We report a rare case of 27-year-old female that presented with the complaints of weakness in upper and lower limbs bilaterally for 2 years which was gradually progressive in nature along with difficulty in swallowing. So after physiotherapy assessment the patient was advised to undergo blood investigations which suggested an increased creatinine phosphokinase enzyme level along with reduced vitamin B12. To make a confirmatory diagnosis the patient underwent electromyography which suggested the presence of myopathy. Although polymyositis is more common in people aged 50 to 70 years this case suggests that it can have an earlier presentation. So along with medical management, a structured physiotherapy protocol was planned. Early diagnosis and management is key to recovery and better quality of life.", "keywords": [ "Polymyositis", "Case report", "Inflammatory Myopathy", "Physiotherapy" ], "content": "Introduction\n\nIdiopathic inflammatory myopathies include dermatomyositis (DM) and polymyositis (PM). Proximal muscular weakness, elevations in serum muscle enzymes, and, in the case of dermatomyositis, skin abnormalities identify them clinically. Immune pathways play an important role in the physiopathogenesis of polymyositis and dermatomyositis to varying degrees. Both diseases, as clinically diagnosed, have a general population prevalence rate of about 1 in 100,000.1 The female to male ratio is roughly 2:1. Adults between the ages of 40 and 50 are most afflicted; however any age group could be affected. Polymyositis is significantly more prevalent in black people than in white people. Inflammatory infiltrates, particularly T-lymphocytes and macrophages, are prominent histology-based findings in muscle and cutaneous abnormalities distinguish dermatomyositis from polymyositis.2\n\nPolymyositis affects the striated skeletal muscles but not the smooth muscles. Although the exact origin of PM is unknown, it has been postulated that some form of microvascular injury may trigger the synthesis of muscle auto antigens, which are then presented to T-lymphocytes by muscle macrophages. T-lymphocytes that have been activated proliferate and release cytokines such as interferon gamma and interleukin.3 Interferon gamma stimulates macrophages and causes the production of pro-inflammatory mediators such as IL-1 and tumour necrosis factor-alpha.4\n\nThe earliest signs are typically an asymptomatic deterioration of the pelvic and proximal lower leg muscles, making being able to walk, climb stairs, or getting from a chair difficult. Neck and shoulder girdle muscles are typically the first to be injured. The severity of the weakening might range from modest to near-paralysis. Weakness normally develops progressively over weeks to a period of time, although in rare circumstances, it may appear suddenly. Muscle weakness is the most typical indication of PM. The weakening is symmetric and affects both proximal limb muscles and neck flexors.5 Distal muscular weakness is unusual, but when it occurs, it should highlight the potential of another type of myopathy, such as inclusion body myositis. On occasion, PM patients may have muscle discomfort and tenderness, which may mimic the symptoms of polymyalgia rheumatica. Involvement of the oropharyngeal and upper esophageal striated muscles occurs in 10–15% of patients, has a poor prognosis, and can result in dysphagia, regurgitation, and aspiration pneumonia. Interstitial lung disease affects 5–10% of the population. Furthermore, because the diaphragm and intercostal muscles are involved, ventilatory failure may occur. Cardiac involvement is frequently asymptomatic.6\n\nWhile there is no treatment for the condition, there has been research showing that medical treatment can reduce symptoms and give patients more control over their illness. Symptom management can help people perform better and live healthier lives. Polymyositis being idiopathic inflammatory myopathies cause a variety of systemic clinical symptoms. Among the most pertinent to the practice of physical therapy are muscle weakness, fatigue, and shortness of breath.7 The proximal musculature suffers the most, with considerable weakening throughout the neck, back, shoulders, forearms, thighs, and hips. Although distal weakness is possible, it is uncommon; however, the trunk is typically strong. Because the respiratory musculature is usually involved, the best evidence suggests combining resistance and aerobic exercise.8\n\nPhysical therapy helps PM patients maintain function and lower their risk of falling. It is critical that patients be active in order to retain function, and it is recommended that they exercise 5–6 times each week. Strengthening exercises should not be performed on consecutive days; instead, patients should take “active rest days,” during which they focus on Range of motion (ROM) posture, and relaxation rather than strengthening.9\n\nA 27-year-old female patient who was a student by occupation visited the outpatient Neuro physiotherapy department with complaints of weakness in upper and lower limbs along with difficulty in swallowing for 2 years. The patient also complained of difficulty in getting up from the floor. The weakness was gradually progressive in nature which started in the shoulder girdle followed by pelvic girdle. There was no medical history of chronic illness. After physiotherapy assessment the patient was advised to undergo blood investigations and electromyography. The electromyography suggested polymyopathy. The patient was then referred for physiotherapy treatment.\n\nA physical examination was conducted after taking informed consent from the patient. The examination was divided into sensory and motor assessment. The sensations were intact. The motor assessment includes tone, reflex and strength assessment. The tone was normal. The reflexes were diminished (+) bilaterally as mentioned in Table 1.\n\nThe strength assessment was done using Manual Muscle Testing Grading which revealed involvement of the proximal girdle (Table 2). The strength of the elbow and wrist, knee and ankle were 5/5.\n\nThere was tightness in the calf, hamstring and a positive Ober’s Test suggestive of iliotibial band tightness. There was hypermobility noted in ankle plantar flexors (Figure 1). There was difficulty in getting up from the floor (Figure 2).\n\nThe investigations included the blood test and electromyography. The blood test revealed increased creatinine phosphokinase level suggestive of myopathy and a reduced vitamin B12 level as mentioned in (Table 3).\n\nElectromyography was done with needle electrodes left gastrocnemius, right tibialis anterior, left bicep muscle, right tibialis anterior shows spontaneous activity is absent with normal motor unit potential, incomplete interference pattern and normal recruitment pattern. The left bicep showed spontaneous activity was absent with normal motor unit potential, a completed interference pattern and a normal recruitment pattern. The electromyography was suggestive of myopathy.\n\nThe interdisciplinary approach was used in managing this patient which was helpful in gaining early recovery. Physical therapy was focused to maintain function and lower their risk of falling. It is critical that the patient should be active in order to retain function, and she was recommended to exercise 5–6 times each week.\n\nStrengthening exercises should not be performed on consecutive days; instead, patients should take “active rest days,” during which they focus on range of motion, posture, and relaxation rather than strengthening.\n\nMuscle function preservation was done to prevent the disuse atrophy so mild resistance exercises were given. Strengthening of the distal muscles was initiated since it has the maximum chance for strength improvements, can significantly aid in a general improvement in activity of daily living function (Figure 3). Open chain exercises use less energy than closed chain workouts, but closed chain activities produce the best results in terms of functional mobility. Energy conservation techniques are essential (avoid high resistance open chain exercises and vigorous closed chain exercises). So adequate pacing was kept between the exercises. To prevent contracture, passive and active range of motion exercises (Figure 4) and stretching for calf, hamstrings and iliotibial band for three sets with 30 second hold each (Figure 5).\n\n\nDiscussion\n\nPhysical activity has been shown to improve health-related quality of life and well-being. Nonetheless, for a long time, it was widely assumed that physical activity could be hazardous to patients with myopathies, particularly inflammatory miopathies. The main concern for healthcare practitioners was that exercise could increase muscular inflammation in people with PM/DM, exacerbating muscle weakness.10\n\nSymptoms vary considerably from patient to patient, and each drug has its own set of side effects. Because of the differences in symptom presentation and individual sensitivities to drugs, each patient’s medical therapy is unique. A combination of pharmacological treatment, physiotherapy, and alternative/holistic medicine may be used in treatment. Corticosteroids and immunosuppressant are often used in pharmacological management. Corticosteroids are used to decrease inflammation, ease pain, and increase strength, whereas immunosuppressant’s aid to minimize the body’s negative immunological response to the patient’s muscles.11\n\nAerobic conditioning and vigorous resistance training are commonly used in the therapy of polymyositis and dermatomyositis patients. Aerobic exercise enhanced the performance of patients with PM/DM in the trials for which they were chosen, both by increasing maximal aerobic capacity and by boosting mitochondrial activity and oxygen uptake in skeletal muscles. After 6 months, an aerobic training programme resulted in a 28% rise in VO2 max and a 12 week increase in CS (citrate synthase) and -HAD (β-hydroxyacyl-CoA dehydrogenase) activities. The analysed research concluded that concentric contractions were preferable for patients with PM/DM during aerobic performance. In reality, muscle fibres are stretched under eccentric contractions.12\n\n\nConclusion\n\nPolymyositis is a potentially lethal condition that can exacerbate the symptoms of swallowing and breathing difficulties if left untreated. PM is more common in women, and the muscles that are most affected are the hips and thighs, upper arms, shoulder and neck. PM can also have an effect on the heart muscles, causing inflammatory myopathy, which is as well as the breathing muscles. Proximal muscular weakness is the most common clinical symptom. Extra muscular involvement may occur, including inflammatory arthritis, Reynaud’s phenomenon, myocarditis, and interstitial lung disease. During active illness, serum muscle enzymes (CK) are frequently increased. Auto antibodies of various types are frequently identified in the serum of PM patients. Electromyography and muscle MRI frequently reveal characteristic anomalies. Muscle biopsy is used to confirm the diagnosis. A steroid is typically used as the first-line treatment for PM. Prednisolone, in particular, is particularly successful at controlling inflammation and restoring swallowing, breathing, and hearing capabilities. To enhance movement and reduce pain, lifestyle changes such as drinking thicker fluids, eating softer or mashed foods, and engaging in light physiotherapy exercises should be implemented.\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\nSasaki H, Kohsaka H: Current diagnosis and treatment of polymyositis and dermatomyositis. Mod. Rheumatol. 2018; 28: 913–921. Publisher Full Text\n\nFindlay AR, Goyal NA, Mozaffar T: An overview of polymyositis and dermatomyositis. Muscle Nerve. 2015; 51: 638–656. Publisher Full Text\n\nHunter K, Lyon MG: Evaluation and Management of Polymyositis. Indian J. Dermatol. 2012; 57: 371–374. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDalakas MC, Hohlfeld R: Polymyositis and dermatomyositis. Lancet Lond. Engl. 2003; 362: 971–982. Publisher Full Text\n\nMcDonald CM: CLINICAL APPROACH TO THE DIAGNOSTIC EVALUATION OF HERDITARY AND ACQUIRED NEUROMUSCULAR DISEASES. Phys. Med. Rehabil. Clin. N. Am. 2012; 23: 495–563. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSchmidt J: Current Classification and Management of Inflammatory Myopathies. J. Neuromuscul. Dis. 2018; 5: 109–129. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHunter K, Lyon MG: Evaluation and Management of Polymyositis. Indian J. Dermatol. 2012; 57: 371–374. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZampieri S, Ghirardello A, Iaccarino L, et al.: Polymyositis-dermatomyositis and infections. Autoimmunity. 2006; 39: 191–196. Publisher Full Text\n\nVoet NB, van der Kooi EL , van Engelen BG , et al.: Strength training and aerobic exercise training for muscle disease. Cochrane Database Syst. Rev. 2019; 2019: CD003907. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVan Thillo A, Vulsteke J-B, Van Assche D, et al.: Physical therapy in adult inflammatory myopathy patients: a systematic review. Clin. Rheumatol. 2019; 38: 2039–2051. PubMed Abstract \| Publisher Full Text\n\nTjärnlund A, Tang Q, Wick C, et al.: Abatacept in the treatment of adult dermatomyositis and polymyositis: a randomised, phase IIb treatment delayed-start trial. Ann. Rheum. Dis. 2018; 77: 55–62. PubMed Abstract \| Publisher Full Text\n\nCorrado B, Ciardi G, Lucignano L: Supervised Physical Therapy and Polymyositis/Dermatomyositis—A Systematic Review of the Literature. Neurol. Int. 2020; 12: 77–88. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "229816", "date": "11 Jan 2024", "name": "Francisco M. Barajas-Olmos", "expertise": [ "Reviewer Expertise Genomics and rare 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\nElias and collaborators presented the report of a case of Polymyositis and its treatment focusing mainly on physical rehabilitation. The topic seems to help progress in the field but the presentation of the results and discussion needs to be improved before publication. I suggest that you review each of the sections of the article carefully, they must include solid data that supports the patient's improvement, photographs that agree with what is discussed as well as improve the photographs (more academic). In general, the authors have to review the article much more carefully, avoiding contradictions such as: \"Adults between the ages of 40 and 50 are most afflicted\" (Introduction), \"Although polymyositis is more common in people aged 50 to 70 years \" (summary). In the conclusion section, you have to focus on your findings and not on a review of the literature.\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? 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": "241186", "date": "16 May 2024", "name": "Vivek Bhat", "expertise": [ "Reviewer Expertise Internal Medicine", "Neurology", "Cardiology", "Medical Education" ], "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 present a case of polymyositis (PM) in a young female, which they managed with physical therapy.\nThere are significant issues with the paper that make it unsuitable in any reputable journal until they are addressed in a satisfactory manner.\nThe diagnosis of PM itself is in doubt. With a CK of 52, how did the authors diagnose PM? What about myositis specific antibodies and muscle biopsy? The EMG does not mention a nerve conduction study to rule out peripheral neuropathy. With normal motor unit potential, how was myopathy suggested? Further, PM affects proximal muscles, so why were peripheral muscles tested? The authors have not included a neurologist or rheumatologist on the paper. While I understand that they intend to highlight the therapy of the condition, the fact that there are factual errors make it necessary to include a clinician.\nThe manuscript is too long with unnecessary detail. There are multiple grammatical errors throughout the manuscript that must be corrected – a simple grammar tool (Grammarly, for example) or proofreading thoroughly will help. However, this is minor in comparison to the multiple concerns about whether the diagnosis of the case itself is correct.\nMy minor comments are structured below in order of the manuscript. Abstract:\nGiven the emphasis of the abstract and text on diagnosis and management of PM (in both abstract and main text), the lack of a neurologist/ rheumatologist as an author is glaring. While I understand that the primary focus is the use of physiotherapy to ameliorate symptoms, a primary physician has to be included. The abstract remains very unclear regarding what the main message of the article is. Are the authors attempting to point out that the patient is young (which is not strictly case-report worthy) or are they attempting to highlight the effect of a physiotherapy regime for PM? Abstracts need to be to the point, and readers must understand an overview of the case. The first 3 sentences are more suited to an introduction and do little to help us understand the significance of the case. A 27-year-old, while on the younger end of the expected spectrum, is not exactly rare. Rare would be a pediatric patient with the same diagnosis. The emphasis on this aspect must be removed.\nIntroduction:\nThis is structured more like a review than a case report. There is no need to go into so much detail. A typical introduction would be a short paragraph giving an overview of PM, then different treatment options, and then what the authors are reviewing. The authors say ‘While there is no treatment for the condition,….’ – this is grossly inaccurate. While PM is not strictly ‘curable’, there are multiple immunosuppressants that control the disease well. Symptom management may be given but immunosuppression is key. Statements like these highlight the need for a clinician on board.\nCase Report:\nTable 1 can be replaced by one sentence, given that all reflexes were the same. ‘Strengthening exercises should not be performed on consecutive days; instead, patients should take “active rest days,” during which they focus on range of motion, posture, and relaxation rather than strengthening.’ – statements like this do not belong in the case report section. The authors should merely describe what was done. These recommendations can be placed in the discussion if necessary.\nDiscussion:\n‘Physical activity has been shown to improve health-related quality of life and well-being’ – non-specific sentence that can be removed. It is unscientific and against current medical guidelines to recommend alternative/ holistic therapy. The authors must avoid overreaching beyond the case. The discussion has to discuss the key messages of the authors’ case, and compare with prior literature. Here, they have merely mentioned facts about PM using nonspecific sentences. ‘Aerobic conditioning and vigorous resistance training are commonly used in the therapy of polymyositis and dermatomyositis patients.’ – this contradicts the first paragraph of the discussion. What is the current evidence and recommendations regarding this for PM treatment?\n\nIs the background of the case’s history and progression described in sufficient detail? No\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? No\n\nIs the case presented with sufficient detail to be useful for other practitioners? No", "responses": [] }, { "id": "271519", "date": "22 May 2024", "name": "Himanshu Jindal", "expertise": [ "Reviewer Expertise Internal Medicine", "Rheumatology", "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\nDear authors,\nThank you for submitting your case report. While the report is detailed and well-written, it lacks a significant contribution to the current understanding of polymyositis. Polymyositis is a recognized condition in rheumatology, and although not frequently seen, it is not so rare. The case report describes a typical instance of polymyositis in a young woman and discusses the role of physical rehabilitation, including strength training exercises and physiotherapy, in improving the quality of life for patients with this condition.\nI have a few queries and suggestions for improvement:\n1. The report does not discuss Antisynthetase Syndrome, which can coexist with polymyositis in a significant proportion of patients. Were anti-Jo-1 antibodies and other antibodies against aminoacyl-tRNA synthetase enzymes tested for in this patient?\n2. The case report lacks a comprehensive presentation of the patient's blood and autoimmune panel results. Providing this information is crucial for a thorough understanding of the case.\n3. The report does not introduce new insights or novel aspects regarding polymyositis. If the focus is on the benefits of physical rehabilitation for patients with polymyositis, the introduction and discussion should emphasize this angle more prominently.\n4. The report is lengthy and challenging to read. Case reports are generally concise and straightforward, presenting a chronological account of the patient's case. The introduction is too long, while the discussion is relatively brief. The discussion should be expanded to include comparisons with other similar case reports or studies on physical rehabilitation in polymyositis patients.\nI hope these suggestions are helpful in revising your manuscript.\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? No\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-1564
https://f1000research.com/articles/12-1562/v1	06 Dec 23	{ "type": "Research Article", "title": "Zinc chloride may regulate hematopoietic stem cell aging and pro-inflammatory cytokines in systemic lupus erythematosus", "authors": [ "Hani Susianti", "Achmad Arrizal", "Bakhtiar Yusuf Habibi", "Friska Supriyanto", "Matthew Brian Khrisna", "Kusworini Handono", "Cesarius Singgih Wahono", "Perdana Aditya Rahman", "Mirza Zaka Pratama", "Syahrul Chilmi", "Hani Susianti", "Achmad Arrizal", "Bakhtiar Yusuf Habibi", "Friska Supriyanto", "Matthew Brian Khrisna", "Kusworini Handono", "Cesarius Singgih Wahono", "Perdana Aditya Rahman", "Mirza Zaka Pratama" ], "abstract": "Background: The immune cells of patients with systemic lupus erythematosus (SLE) age earlier than those of normal subjects. However, the senescence of circulating hematopoietic stem cells (HSCs) in patients with SLE is not well understood, and it is unclear whether zinc treatment can regulate the senescence and proinflammatory cytokine production of HSCs in these patients. Methods: Clinical data were collected on 38 patients with SLE and 35 healthy controls (HCs), and the complete blood count, circulating HSC number, and p16 (a senescence marker) expression in the peripheral blood of these participants were analyzed via flow cytometry. Pooled circulating HSCs were isolated using leukapheresis. The effects of zinc chloride exposure on the pooled HSCs of each group were determined in vitro. Levels of the proinflammatory cytokines IL-6 and IL17, regulatory cytokine TGF-β, p16, and regulator T-cells (Tregs) were evaluated 72 h after incubation with 50 or 100 µM zinc chloride. Results: The number of circulating HSCs did not differ between the two groups (p=0.1685). The expression of p16 in HSCs was higher in the SLE group than in the HC group (p = 0.0043), and patients with SLE exhibited higher levels of IL-6, IL-17, and p16 in pooled HSCs (p =0.0025, p<0.0001, and p = 0.0003, respectively), although TGF-β levels did not differ between the groups (p=0.9816). Zinc chloride reduced IL-6, TGF-β, IL-17, and p16 expression in patients with SLE toward HC levels. Treg frequency in pooled HSCs was comparable between the groups (p=0.3997), although a 100 µM zinc chloride treatment significantly depleted the Treg population of patients with SLE (p=0.0001). Conclusions: Circulating HSCs in SLE are more aged and produce more proinflammatory cytokines. Zinc chloride treatment might prevent immunoaging and inhibit proinflammatory cytokine–producing cells in patients with SLE.", "keywords": [ "systemic lupus erythematosus", "zinc chloride", "aging", "pro-inflammatory cytokines", "hematopoietic stem cells" ], "content": "Introduction\n\nAging is a biological process that not only affects functional homeostasis but also drives pathological conditions in many diseases. Aging involves the senescence of many tissues and cells, including both innate and specific immune cells.1 Cellular senescence not only disrupts the homeostasis of biological processes but also affects disease progression through inflammaging, resulting in increased rates of morbidity and mortality.2 A previous study found that immune aging is associated with an increased risk of autoimmune disease in older individuals due to excessive autoantibody production and increased levels of autoreactive T-cells.3 Interestingly, low-grade chronic inflammation in the absence of infection is also common in older individuals, possibly owing to cellular senescence and dysregulation of innate immunity.4\n\nSystemic lupus erythematosus (SLE) is an autoimmune disease of unclear etiology characterized by immune system dysregulation in which the body’s own tissues are attacked and chronic inflammation persists. SLE has various clinical manifestations, mimicking other diseases in some cases; thus, it is difficult to diagnose and treat.5 Aging is associated with autoimmune diseases such as SLE, reflected by similar immunosenescence characteristics observed in elderly individuals. From a clinicopathological perspective, patients with SLE share common clinical features with elderly individuals, e.g., they are prone to infection and exhibit an increased incidence of tumors and cardiovascular disease.6 Previous studies have found evidence of immunoaging and inflammaging in patients with SLE, particularly in respect of innate and adaptive immunity, e.g., dysfunctional phagocytic capacity, NETosis granulocytes, abnormal T-cell IL-2 production, and T-cell aging.6,7 However, information on higher level immune cells, e.g., hematopoietic stem cells (HSCs), in relation to aging and SLE is currently limited. HSCs have been mainly discussed in the context of lupus as an autologous HSC transplantation treatment in patients with active SLE,8,9 even though the clinical utility of this treatment remains unclear.10\n\nVarious cell aging–related biomarkers have been identified. The American Federation of Aging Research (AFAR) defines a true biomarker of aging as a biomarker that can predict a person’s physical and cognitive function in an age-related manner, is testable and not harmful to the test subjects, and is applicable to laboratory animals as well as humans. The expression of p16, a cyclin-dependent kinase inhibitor that acts on CDK4/6 kinases to prevent the phosphorylation of Rb family proteins and promotes G1 cell cycle arrest, fits the AFAR definition of an effective aging biomarker. The expression of p16 increases with age, and expression levels can be measured quantitatively to detect senescence, a central mechanism encompassing environmental, genetic, and lifestyle damage.11 Patients with SLE are more susceptible to immunosenescence than those without SLE, and immunosenescence increases the susceptibility of patients with SLE to infection, malignancies, and organ damage related to immune system impairment. Immunosenescence also decreases the tumor surveillance ability of the human body, which might explain why the probability of developing malignancies increases with age.12\n\nInterestingly, immune dysregulation in SLE is also associated with nutritional deficiency, particularly elemental zinc deficiency.13 Zinc is an essential trace element involved in many biological processes in almost all living organisms. The key functions of zinc in these processes include enzyme modulation and cell communication, proliferation, differentiation, and survival. Furthermore, zinc plays a role in immunoregulation underlying many pathological conditions and inflammation, in the conditions where zinc deficiency is present, such as in autoimmune diseases.13 Previous studies have found that dietary zinc, along with other macronutrient and micronutrient supplements, has potential benefits as an immunomodulatory agent that can improve the physical and mental well-being of patients with SLE.14,15 Although some evidence suggests that dietary zinc can benefit the health of elderly individuals,16 evidence that zinc supplementation can prevent age-related degeneration is limited.\n\nIn the present study, we investigated the expression of the senescence marker p16 in circulating HSCs as well as proinflammatory cytokine production following zinc chloride treatment in vitro. We hypothesized that HSCs in patients with SLE are more aged than those of healthy individuals and that zinc can prevent age-related degeneration in patients with SLE.\n\n\nMethods\n\nThis study was ethically reviewed based on World Medical Association Declaration of Helsinki, and approval was granted under approval number 400/117/K.3/102.7/2022 granted June 1st, 2022 from the Medical Research Ethics Committee, Saiful Anwar General Hospital, Malang, Indonesia.\n\nThe study was fully explained to all participants before they were enrolled, and written informed consent for publication of the participants’ details was obtained from the participants.\n\nThis was an experimental study with a cross-sectional setting in which a consecutive sampling method was employed. In total, 73 participants were enrolled in the study, including 38 patients with SLE who attended the rheumatology outpatient ward at Internal Medicine Department, Saiful Anwar General Hospital, Malang, Indonesia in 11/07/2022 to 31/08/2022.36 SLE was diagnosed using SLICC criteria for SLE. Eligible participants included patients diagnosed with SLE that frequently attended regular medical visits. The exclusion criteria for SLE participants included patients who had been prescribed medication for nonlupus-related diseases. We also excluded patients with leukopenia (<4000 white blood cells/mm3) and patients with a positive direct agglutination (Coombs) test.17 In total, 35 healthy volunteers were recruited among health workers who met the criteria for participant enrollment, i.e., not being diagnosed with SLE or other autoimmune diseases and having normal results in complete blood count (CBC) tests as well as a negative antinuclear antibody test.\n\nThe participants enrolled from the rheumatology outpatient ward were grouped into the SLE group, whereas the healthy volunteers were grouped in the healthy control (HC) group.\n\nCBC tests were conducted on the blood samples of each participant using a Sysmex XN-1000 hematology analyzer (Sysmex-Japan) to determine the hemoglobin level, white blood cell count, and platelet count.\n\nTo determine the levels of HSCs and p16 expression, 2 mL of EDTA-anticoagulated blood sample was added to red blood cell lysis buffer (1:5 ratio) and incubated at room temperature for 15 min in a dark room, after which the sample was centrifuged at 1500 rpm for 5 min and washed twice using cell staining buffer (BioLegend, USA; Cat# 420201). Subsequently, the pellet was resuspended with 100 μL of cell staining buffer and stained with PE/Cyanine7 anti-human CD45 antibody (BioLegend Cat# 304016, RRID:AB_314404), APC anti-human CD34 antibody (BioLegend Cat# 343510, RRID:AB_1877153), and p16INK4a antibody (F-12) Alexa Fluor® 488–conjugated (Santa Cruz Biotechnology Cat# sc-1661, RRID:AB_628067) according to manufacturers’ protocols.\n\nFollowing 72 h of incubation, suspension cells were analyzed using flow cytometry to determine the intracytoplasmic expression of interleukin 6 (Alexa Fluor® 488–conjugated IL-6, Santa Cruz Biotechnology Cat# sc-28343, RRID:AB_627805), transforming growth factor beta (Alexa Fluor® 488–conjugated TGFβ1, Santa Cruz Biotechnology Cat# sc-130348, RRID:AB_1567351), interleukin 17 (Alexa Fluor® 488–conjugated IL-7, Santa Cruz Biotechnology Cat# sc-374218, RRID:AB_10988239), and senescence marker p16 (Alexa Fluor® 488–conjugated p16INK4a antibody, Santa Cruz Biotechnology Cat# sc-1661, RRID:AB_628067). Regulator T-cells were detected using FOXP3 Alexa Fluor® 488/CD4 PE-Cy5/CD25 PE (BioLegend Cat# 320027, RRID:AB_10120925). A Beckman Coulter Navios Flow Cytometer (Beckman Coulter, USA, RRID:SCR_014421) and BD FACSMelody Cell Sorter, (RRID:SCR_023209) were used in this study.\n\nThe pooled peripheral HSCs of selected participants from the SLE and HC groups were analyzed in vitro. CBC tests and coagulation tests were conducted before and after the procedure to ensure each participant’s safety. Participant data such as height, weight, and hematocrit were inputted into the leukapheresis unit (Haemonetics MCS+ System, USA), and afterwards, we selected the PBSC protocol to run.37 The procedure was performed with the following settings: 16–17 cycles, a 1:6 recirculation ratio, and a target plasma volume of 50 mL. For the initial experimental setup, the frequency of HSCs before and after leukapheresis was analyzed using flow cytometry and CD45 and CD34 markers to verify the leukapheresis efficiency in collecting HSCs (Figure 1).\n\nA flow cytometry analysis determines the frequency of HSCs (CD45+CD34+) in peripheral blood before the leukapheresis procedure and in the blood product of leukapheresis. A different quadrant gating setting was done due to a different flow cytometer that was being used (Beckman Coulter Navios for before leukapheresis-blood and BD FACS Melody for leukapheresis-blood product). The leukapheresis increased the frequency of HSCs approximately by 16 times (from 0.74% to 16.1%).\n\nLeukapheresis blood products underwent further mononuclear cell (MNC) separation using a Ficoll gradient (Lymphoprep, Serumwerk Bernburg AG; Cat#04-03-9391/03) for separation from red blood cells and platelet contaminants. Pooled peripheral HSCs were incubated using Stemline® II Hematopoietic Stem Cell Expansion Medium (Sigma-Aldrich; Cat #S0192) with 10% fetal bovine serum (Sigma-Aldrich; Cat #F7524) and 1% penicillin–streptomycin (Sigma-Aldrich; Cat#P4333) and a cell density of 106 cells/mL in 5% CO2 at 37°C for 72 h. The cultures were then divided into three groups: untreated, treated with 50 μM ZnCl2, and treated with 100 μM ZnCl2 (Sigma-Aldrich; Cat#Z0152). All experiments were conducted in triplicate.\n\nDescriptive data of the HC and SLE groups are shown.36 Independent t-tests were used to compare the variables between participants in the HC and SLE groups when appropriate according to a data normality test. Nonparametric tests (e.g., Mann–Whitney test) were used if data transformation failed. All flow cytometry data were analyzed using FlowJo (Beckton-Dickinson, USA RRID:SCR_008520), whereas statistical analysis and graph production were performed using GraphPad Prism version 9 (RRID:SCR_002798); an open-access alternative that can perform an equivalent function is R (RRID:SCR_001905). Differences in data between the HC and SLE groups were considered statistically significant at p<0.05. This manuscript has been checked against the STROBE checklist.38\n\n\nResults\n\nOf the 38 and 35 participants in the SLE and HC groups, no participants dropped out, and all participant data were analyzed. The mean age (and age range) of the participants was 31.18 (18–53) and 32.82 (20–58) years in the SLE and HC groups, respectively. Patients with SLE exhibited the characteristics shown in Table 1 for disease duration, SLEDAI scores, and treatments. In total, 27 patients (71.05%) had the disease for >2 years, whereas 7 (18.42%) and 4 (10.53%) patients had the disease for 1–2 years and <1 year, respectively. Low SLEDAI scores were observed in 21 (55.26%) patients, whereas 9 (23.68%) and 8 (21.05%) patients had mid and high SLEDAI scores, respectively.18 The patients had received six types of treatment for their diseases, including hydroxychloroquine (37 patients; 97.37%), methylprednisolone (8 patients; 21.05%), methotrexate (1 patient; 2.63%), mycophenolic acid (14 patients; 36.84%), azathioprine (10 patients; 26.32%), and cyclophosphamide (1 patient; 2.63%) (Table 1).\n\nAmong 38 systemic lupus erythematosus (SLE) patients, most of them (71%) are having the disease for between 1–2 years, have non-active disease (45%) as shown by low Systemic Lupus Erythematosus Disease Activity Index (SLEDAI) score, and are routinely treated with drug regimens for SLE.\n\nThe CBC test results and HSC profiles of both treatment groups are shown in Table 2. The CBC parameters were hemoglobin, white blood cells, absolute neutrophil count, absolute lymphocyte count, and platelet count. Hemoglobin parameters differed significantly between the SLE and HC groups [11.50 (5.60–14.30) versus 12.92 (9.00–14.50) g/dL, respectively; p=0.0005] as did platelet count [250.5 (71.0–388.0) vs. 307.5 (191.0–412.0) × 103 cells per microliter of blood, respectively; p=0.0007)]. However, the white blood cells per microliter did not differ significantly between the two groups [SLE: 6,727 (2.72–18.20); HC: 7,234 (3.97–11.59); p=0.0596].\n\nPatients with SLE tend to have lower hemoglobin (11.5 vs 13.0 g/dL, p<0.0001), lower platelet count (250.5 vs 306.1 × 103 cells per microliter, p=0.0006), lower absolute lymphocyte count number (1.438 vs 2.151 × 103 cells per microliter, p<0.0001), and a higher percentage of mononuclear cells (45.85% vs 32.43%, p=0.0068).\n\n* Using Kolmogorov-Smirnov test.\n\nNeither the percentages nor cell numbers of HSCs differed significantly between the SLE and HC groups (p=0.3210 and p=0.1685 for the percentage and absolute number of HSCs, respectively). Although the absolute number of MNCs did not differ between the two groups (p=0.9930), the percentage of MNCs was higher in patients with SLE (p=0.0150) (Table 2).\n\nWe developed a gating strategy for flow cytometry analysis to determine the mean fluorescence intensity of p16 expression in selected HSCs (Figure 2). Intracytoplasmic p16 expression was significantly higher in the circulating HSCs of the SLE group than in those of the HC group (p=0.0043) (Figure 3), suggesting that the level of senescence in circulating HSCs is higher in patients with SLE than in healthy individuals, although the number of circulating HSCs did not differ significantly between the two groups (p=0.1685).\n\nThe population of HSCs in peripheral blood is detected as CD45+CD34+. Further analysis of p16 expression is done by measuring the mean fluorescence intensity of p16 on CD45+CD34+ cells.\n\nRepresentative scattergram data showed the lower frequency of circulating HSCs (CD45+CD34+) in a systemic lupus erythematosus (SLE) patient in comparison with a healthy subject (2.26% vs 3.75%) (A). Further analysis showed no significant difference in HSCs number between SLE patients and healthy subjects (p=0.1653) (B). Representative histogram analysis of p16 expression showed that an SLE patient has a higher expression of p16 in comparison with a healthy subject, the red dashed line showed p16 expression in a healthy patient while the blue line is from an SLE patient (C). Further analysis showed a moderately higher level of p16 on HSCs from SLE patients than in healthy subjects (p=0.0140) (D).\n\nExpression levels of the proinflammatory cytokines IL-6 and IL-17 and the senescence marker p16 were significantly higher in the SLE group than in the HC group (p=0.0025, p<0.0001, and p=0.0003, respectively). However, TGF-β expression levels did not differ significantly between the two groups (p=0.9816). Furthermore, IL-6, IL-17, TGF-β, and p16 expression levels in patients with SLE decreased significantly after they were treated with zinc chloride, reaching expression levels similar to those of their healthy counterparts. Interestingly, IL-17 and p16 expression levels were significantly reduced only in the SLE group after zinc chloride treatment, whereas IL-6 expression levels exhibited a similar tendency in the two groups, although patients with SLE were more sensitive to zinc chloride treatment, as indicated by the gradual reduction in expression levels in line with higher zinc chloride concentrations (Figure 4). In summary, compared with the HSCs of healthy volunteers, HSCs collected from patients with SLE exhibited higher levels of proinflammatory cytokine and p16 expression and were more sensitive to cytokine reduction after long-term zinc chloride exposure.\n\nHistogram analysis of IL-6, TGF-β, IL-17, and p16 expression showed that SLE patient has a higher level of IL-6, IL-17, p16, and a slightly higher level of TGF-β than the healthy subject (p=0.0025, p<0.0001, p=0.0003, and p=0.9816 respectively); treatment of 50 μM and 100 μM of zinc chloride effectively reduced the expression of IL-6, TGF-β, IL-17, and p16 in SLE patient into becoming similar to its healthy subject’s counterpart (A). Mean fluorescence intensity (MFI) of each cytokine was analyzed using two-way ANOVA to determine the difference among the treatment groups (B).\n\nThe frequency of regulatory T-cell (Treg) populations in pooled HSCs was comparable between the treatment groups (p=0.3997); however, long-term zinc chloride treatment induced a decrease in the Treg populations of both groups. Interestingly, following a 100 μM zinc chloride treatment, the Treg population of patients with SLE was significantly depleted relative to that of healthy volunteers (p=0.0001). Therefore, patients with SLE were more sensitive to Treg population reduction after long-term zinc chloride treatment (Figure 5).\n\nAnalysis of Treg frequency as detected as CD4+CD25+Fox-P3+ by flow cytometry in both groups given selected treatment (untreated, 50 μM and 100 μM of zinc chloride) for 72 hours. The frequency of Treg population in pooled hematopoietic stem cells (HSCs) in both groups was comparable (p=0.3997). And at a concentration of 100 μM, Treg population from systemic lupus erythematosus (SLE) patients has been further depleted significantly in comparison with healthy volunteers’ Treg (p=0.0001).\n\n\nDiscussion\n\nImmunoaging occurs naturally in elderly people, characterized by their inability to overcome infections and respond to vaccines in typical manner. Thymic involution–driven loss of naïve T-cell production further reduces cellular responses to foreign antigens, altering self-tolerance and hampering naïve T-cell populations.19 Importantly, aged CD4+ T-cells cannot produce a sufficient level of IL-2, which is required for responding to antigen stimulation through T-cell receptors. These features of immunoaging lead to poor Th1/Th2 polarization, disrupted Th17 differentiation, and a state that favors an inflammatory and autoimmune phenotype.19 Furthermore, the number and functionality of Treg populations decrease during aging, particularly in respect of low IL-10 production and the contribution to Th17 bias (i.e., production of IL-17, IL-21, and IL-22 at higher levels).19 Another unique phenotype in immunoaging associated with autoimmune disease is the shortening of telomere length, which indicates excessive cell replication in response to the autoimmune-related inflammation process.19 Studies on immunoaging at the level of precursor cells rather than mature immune cells are limited; nevertheless, autologous HSCs are increasingly being used to treat active SLE.\n\nThe present study revealed that precursor cells, i.e., circulating HSCs, in patients with SLE also suffer from aging, as indicated by the higher expression level of the senescence marker p16 in these cells. Although the number of HSCs did not differ between the SLE and HC groups, p16 expression levels were significantly higher in the HSCs of patients with SLE. These data support the findings of a previous study, i.e., that the upregulation of p16INK4a promotes the cellular senescence of bone marrow–derived mesenchymal stem cells collected from patients with SLE.20\n\nProinflammatory cytokines associated with immunoaging also play roles in SLE; two such cytokines, IL-6 and IL-17, are commonly found at higher levels in patients with active SLE.21–24 We determined the expression of IL-6 and IL-17 in pooled circulating HSCs collected using a leukapheresis procedure, finding that both cytokines were expressed at significantly higher levels in the pooled HSCs of SLE patients than in those of healthy participants. A previous study revealed that Th17 cells produce significant levels of IL-17 in the kidneys of lupus-prone mice and patients with SLE, and targeting IL-17–producing cells, such as anti-IL-12/23 p40 monoclonal antibodies, was highlighted as a promising treatment strategy for SLE.25 In the present study, the administration of zinc chloride effectively reduced the expression levels of not only IL-17 but also IL-6 in the pooled HSCs of patients with SLE.\n\nWe found no significant difference in TGF-β expression between the SLE and HC groups, and zinc chloride treatment had no significant effect on TGF-β expression. TGF-β is a regulatory cytokine that plays pleiotropic roles in regulating immune responses; thus, several studies have found lower serum levels of TGF-β in patients with SLE.26–28 Our study indicates the potential benefit of administering zinc chloride for reducing proinflammatory cytokine (IL-6 and IL-17) levels without hampering TGF-β production.\n\nZinc chloride also effectively reduced the expression of the senescence marker p16 in the pooled HSCs of patients with SLE. Zinc is involved in regulating immunoaging as well as controlling systemic cellular stress.29 The concept that zinc deficiency leads to an accumulation of senescent cells was proposed by Malavolta et al.30 Excessive zinc may also lead to increased ROS production and induce senescence in vascular smooth muscle cells.31 Consistent with these studies, we found that the high expression of p16 in the HSCs of patients with SLE was significantly reduced after the cells were treated with zinc chloride.32\n\nIn recent years, Tregs have been well-studied in autoimmune disease, particularly in SLE. Although some results are contradictory, most studies have indicated that the loss of Tregs plays a role in the pathogenesis of SLE.33–35 In this study, we found that Treg populations in patients with SLE were slightly decreased compared with those of healthy participants.\n\nWe acknowledge that this study has some limitations. First, we collected patient samples mostly from the outpatient rheumatology clinic, which has a considerably low rate of active SLE cases. Second, we were unable to control the influence of the drug regimens given to enrolled patients, which possibly altered the levels of biomarkers measured in this study. Therefore, our results may not reflect the actual conditions in active SLE.\n\nIn summary, we found that the circulating HSCs of patients with SLE exhibit more signs of aging than those of healthy individuals, as indicated by increased expression levels of intracytoplasmic p16. In addition, the production of proinflammatory cytokines, such as IL-6 and IL-17, was higher in the cells of patients with SLE, although levels of the regulatory cytokine TGF-β were similar in the two treatment groups. Zinc chloride treatment could be a promising therapy for not only preventing immunoaging in the HSCs of patients with SLE but also inhibiting proinflammatory cytokine–producing cells. However, a study with a larger cohort must be conducted to determine the appropriate dose of zinc chloride required to treat SLE.", "appendix": "Data availability\n\nFigshare: Dataset (Data Submit F1000.xlsx (Raw data in Excel format)) https://doi.org/10.6084/m9.figshare.21966263. 36\n\nFigshare: Stem Cell Protocol (Stem Cell Protocol.pdf ) https://doi.org/10.6084/m9.figshare.21980618. 37\n\nFigshare: STROBE checklist for ‘Zinc chloride may regulate hematopoietic stem cell aging and pro-inflammatory cytokines in systemic lupus erythematosus’ https://doi.org/10.6084/m9.figshare.22014911. 38\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 Saiful Anwar General Hospital and Medical Faculty of Brawijaya University for the use of their facilities and for providing the patients.\n\n\nReferences\n\nPerdaens O, van Pesch V : Molecular Mechanisms of Immunosenescene and Inflammaging: Relevance to the Immunopathogenesis and Treatment of Multiple Sclerosis. 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PubMed Abstract \| Publisher Full Text\n\nRekik R, Smiti Khanfir M, Larbi T, et al.: Impaired TGF-beta signaling in patients with active systemic lupus erythematosus is associated with an overexpression of IL-22. Cytokine. 2018; 108: 182–189. PubMed Abstract \| Publisher Full Text\n\nDiwan B, Sharma R: Nutritional components as mitigators of cellular senescence in organismal aging: a comprehensive review. Food Sci. Biotechnol. 2022; 31(9): 1089–1109. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMalavolta M, Costarelli L, Giacconi R, et al.: Changes in Zn homeostasis during long term culture of primary endothelial cells and effects of Zn on endothelial cell senescence. Exp. Gerontol. 2017; 99: 35–45. PubMed Abstract \| Publisher Full Text\n\nSalazar G, Huang J, Feresin RG, et al.: Zinc regulates Nox1 expression through a NF-kappaB and mitochondrial ROS dependent mechanism to induce senescence of vascular smooth muscle cells. Free Radic. Biol. Med. 2017; 108: 225–235. PubMed Abstract \| Publisher Full Text\n\nSalesa B, Sabater ISR, Serrano-Aroca A: Zinc Chloride: Time-Dependent Cytotoxicity, Proliferation and Promotion of Glycoprotein Synthesis and Antioxidant Gene Expression in Human Keratinocytes. Biology. 2021; 10(11). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLi W, Deng C, Yang H, et al.: The Regulatory T Cell in Active Systemic Lupus Erythematosus Patients: A Systemic Review and Meta-Analysis. Front. Immunol. 2019; 10: 159. Publisher Full Text\n\nZhang SX, Ma XW, Li YF, et al.: The Proportion of Regulatory T Cells in Patients with Systemic Lupus Erythematosus: A Meta-Analysis. J. Immunol. Res. 2018; 2018: 1–11. Publisher Full Text\n\nTselios K, Sarantopoulos A, Gkougkourelas I, et al.: CD4+CD25highFOXP3+ T regulatory cells as a biomarker of disease activity in systemic lupus erythematosus: a prospective study. Clin. Exp. Rheumatol. 2014; 32(5): 630–639. PubMed Abstract\n\nKlinik P: Dataset. [Dataset]. Figshare. Publisher Full Text\n\nKlinik P: Stem Cell Protocol. Figshare. Publisher Full Text\n\nKlinik P: STROBE Checklist. Figshare. Publisher Full Text" }	[ { "id": "246165", "date": "10 Apr 2024", "name": "Michelle L Ratliff", "expertise": [ "Reviewer Expertise Human hematopoietic progenitor cells between young and aged individuals. Inflammation effects on hematopoieitic progenitor populations and mature immune cell populations in human aging. Previous projects on hematopoietic progenitor cells and mature immune cell populations between healthy donors and SLE patients. Immune development changes in mouse aging." ], "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\nWhile this study is intriguing, I have several concerns as it is presented. The first issue that should be addressed is the use of the terminology for the cells studied. Hematopoietic stem cells (HSCs) are different than hematopoietic stem and progenitor cells (CD34+, HSPCs) in that while HSCs are included in the CD34+ pool, CD34+ defines the progenitor populations, so the cells investigated here are a mixed population. As such, it remains unknown if the changes reflected in this study are due to changes to the actual long-lived self-renewing HSCs or a later progenitor population in the HSPC CD34+ pool. Many papers define the various HSPC populations, both in healthy individuals and in SLE. I would like to see a justification/reasoning for using the HSPC pool in the introduction. While it is true that there are no changes in the HPSC pool between HC and SLE patients, published data does show that there are increased HSCs in the peripheral blood HSPC pool in SLE patients compared to HC donors, a characteristic that is shared with older individuals, which would have strengthened the argument regarding aging phenotypes in SLE patients. Overall, the concept is interesting, but I am underwhelmed with the data presented in this study. Specific critiques of the methods:\nParticipant Criteria and Table 1 should be part of the Participant Recruitment in this section, as those data are not part of the data collected through the study, but data collected as part of patient care.\n\nThe Flow cytometry part of the methods is disjointed and incomplete. What is incubated for 72 hr? What media are the cells incubated in for those 72 hours? Are the incubations at 37°C, room temperature, on ice? Was the sorter indicated used to sort cells or was it used for analyses? If used for sorting, which cells were sorted? Where are the Tregs coming from? What media conditions were they incubated in for the zinc treatments? Why is there not a section regarding the Treg cultures? Also, there is a typo in this section for the IL17 antibody. These should be fixed. The section post-stim needs to be in the culture part, as these are the cells included. There also needs to be a lot more details about exactly what cells were used where and what cell types are being measured for each data section being presented. In the HSC cultures section, where did the pooled HSCs come from? What is meant by pooled? Were multiple patient HSCs combined into a single pool? Stemline II Hematopoietic Stem Cell Expansion Media is a serum free media that needs the addition of specific cytokines at specific concentrations. Were those cytokines used? Why was FBS added to an animal serum-free expansion media that is already supplemented with human serum albumin? Some cell culture medias already contain zinc. Is this media supplemented with zinc already?\nSpecific critiques of the Results:\nWhile I think the participant data should be part of the methods, some of the information that is missing is: Sex of the participants, as well as ethnicity, should be included. While SLE patients are predominately female, that is not exclusively true. Were males mixed in with females in the healthy controls? Is there any correlations in the data collected between patients that were on methylprednisolone? Zinc supplementation is reported to be contraindicated for the use of methylprednisolone, but this is not mentioned. Further, several of the medications prescribed, including hydroxychloroquine, result in increased serum levels of micronutrients, including zinc, indicating the filtering out of nutrients through urine. Were the actual values for these patients measured to show that they do, in fact, have nutritional deficiencies? I have some major issues with the data presentation as is. The flow data gates in figures 1, 2, and 3 are not consistent with each other. In fact, each has a completely different gating pattern. Further, two of the CD45 gates do not include all of the CD45 cells. Most of the cell populations in peripheral blood express CD45, so the CD45 used in Figure 2 is the closest to acceptable. Further, figure 1 shows the unstained staining pattern, why not use it? Because of the variability in the gating patterns, I don’t even know what to believe about the data, but the data for figures 2, 3 and 4 may change.\n\nThese need to be corrected and the data reevaluated accordingly. In Figure 3B, what exactly is being demonstrated here? Is it MFI? Area under the curve? Percentage of CD45+CD34+ cells in the MNC gate? The figure legend says representative histogram of p16, but this is not a histogram, p16 isn’t in part A at all and Log2(HSC) doesn’t tell me what I am looking at. Labels and the legend need to be corrected. I have some concerns with the presentation in Figure 4. There is clearly a difference in the cell numbers at the conclusion of the cultures between conditions, as the data is presented in mode, which effectively “normalizes” the data. Are there cell counts following the cultures to indicate where the differences are coming from? Did the addition of Zn increase proliferation? Impair proliferation? Could there have been apoptosis involved in some of these cultures? Are there any pre-culture measures that can be used to assess the total numbers of HSPCs that were seeded into the cultures, which can be used to analyze fold increases or decreases? Were there any methods included that could indicate if there were increased cell death in some of the wells? What cells were used in these analyses? Were they HSPCs? Total cells? PBMCs? I suspect these data are for the total PBMC pool, but there is not enough information to be sure. There are 2 possible causes of the loss of the SLE peaks: either the zn addition is preventing the upregulation of IL-4, IL-6, and p16, OR zn addition induces apoptosis in the cells expressing each. While it is, unfortunately, not possible to assess the co-expression of IL-4 and p16 with IL-6 expression (this should have been ideal for IL-6 and p16, as co-expression would make a case for senescence stronger), it would be nice to see if each backgates to the same cells in the CD34+ pool, at least making a case for them actually being the same cells.\n\nFigure 5 seems slightly unconnected to the rest of the data. I understand the connection with TGFb, BUT Tregs also produce their own TGFb. Further, the text indicated long-term treatment, but long-term T cell culture publications I have read indicate more than 2 weeks. So were these kept longer than the rest of the cultures? Were they in specialized media? I am a little concerned about these measurements mostly because I don’t know the culture conditions. If using PBMCs, but not providing IL-2 and the cells weren’t activated, 3 days is on the dangerous side where a lot of death is happening in the T cell pool. Too much Zn can induce cell death, but if these cells are already stressed from IL-2 withdrawal, there is the potential that the Zn addition pushed them over the edge and, therefore, is not indicative of what would happen in vivo. These data, which do not include any dot plots to show the gating strategy, are a bit incomplete. As there is no way provided to determine if treatment is inducing apoptosis or loss of FoxP3, there is no way to determine what exactly is happening. Why was TGFb expression in these cells not measured? Is there a difference in the total CD4+ cells? While there does seem to be a trend to reduced Tregs in SLE with Zn treatment, is that also seen in total CD4+ cells? Is there a difference in the Treg/CD4+ T cell ratios? Is the loss of Treg reflected in an increase in total CD4+ cells? Are there any experiments indicating the starting numbers before the initiation of the cultures? These would provide further insights without needing to perform further experiments and should be reanalyzed.\nDiscussion: Including discussions of some of the points that I made in the results section, I have a few other areas that should be discussed. While I did suggest discussion regarding the specific drugs prescribed to the patients included, I would like to see a section regarding the most commonly prescribed medications (including new use of metformin) and what that could mean for further studies, i.e. shouldn’t be included for patients on certain medications, possible dosage testing for future studies, etc. Further, discussion regarding Zn concentrations should be included. A few published studies have indicated that too much zn can induce apoptosis of cells, both cell lines and primary cells. This is an important caveat that should be acknowledged and discussed. This is also the reason for my question regarding the Zn concentration of the media used for the cultures. Further, the section regarding TGFb is insufficient. There needs to be further discussion regarding TGFb, particularly in Tregs in SLE AND aging. What could be the consequences for reducing Tregs in patients? Could loss of Tregs be more harmful than the reduction of senescence parameters or is the loss of TGFb an acceptable loss in the face of reducing pro-inflammatory profiles and senescence-associated proinflammation patterns?\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?\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": [] }, { "id": "301849", "date": "15 Jul 2024", "name": "Torsten Lowin", "expertise": [], "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 by Susianti et. al analyzes the influence of Zinc chloride on senescence markers of hematopoietic stem cells (HSCs) in blood of SLE and healthy individuals. Although of interest I have several points that need to be addressed.\nMethods\nPatients: Here, pretty much all necessary information is lacking, age, gender, medication, duration of disease, kidney involvement etc. This needs to be added from the results section. Was the control group age and gender matched? Flow cytometry: p16 is intracellular, how were samples prepared for intracellular staining? Were cells fixed after surface staining? In general, the staining protocol needs to be more precise. So, flow cytometry was conducted on whole blood and not after leukapheresis. Why, if only 0,74% of blood cells express CD34? Makes no sense to include all cells in the flow analysis as most of them will be granulocytes.\nResults\n\n4. Participant characteristics: This needs to be moved to the methods section\n\n5. CBC tests and circulating HSC profiles: This needs to be moved to the methods section, along with tables 1 and 2\n\n6. Fig. 2 would also be better suited for the methods section\n\n7. Fig. 3 (B, D): number of patients analyzed should be added\n\n8. Fig. 3C: Here the healthy control shows only one peak, but SLE shows multiple peaks which suggests that there are several subpopulations of CD34+ cells. Did the staining look like this in all SLE patients?\n\n9. Fig.4: Intracellular flow cytometry. Was brefeldin added? When? Concentration? Was TGF beta determined at the plasma membrane from where it can be cleaved off? The statement that SLE has higher cytokine levels is not entirely correct. There is always a second peak in SLE suggesting that only a subpopulation show increased expression of theses cytokines. Flow cytometry is obviously unsuitable to determine differences in cytokine levels. Why didn’t the authors employ an easy technique like ELISA to determine cytokine production?\nWhat was treated here? Isolated PBMCs from patients or CD34+? How many patient samples were analyzed? Have cells been treated? If so, what was the stimulus? I suggest a TLR or T-dependent stimulus, as without anything cells will only produce minute amounts of cytokines. What does “normalized to mode” mean?\n\n10. The histograms should be overlayed differently. In B) the authors show a decrease of IL-6 with Zn100. However, when looking at the histograms this doesn’t stand out. It would help to overlay control, Zn50 and Zn100 for healthy and SLE.\n\n11. Fig. 5: The label on the y axis is Tregs/µl. That information is useless. You should display this as Tregs/T cells in total. Here it shows a decrease of Tregs, but this might be accompanied by a reduction of total cell number leaving the ratio of Tregs/T cells total untouched. Why are there Tregs in pooled hematopoietic stem cells? Why would HSCs produce IL-17?\nDiscussion\n\n12. In discussion the authors state that IL-2 and IL-10 are reduced during ageing. Why then haven’t these cytokines been investigated? Also, telomers are discussed but since no data is shown in this respect, I would maybe mention it later on in a different context. Focus on the findings you have.\n\n13.The authors write that excessive Zinc leads to ROS and senescence. What concentrations are considered excessive? Zinc already induces maximal TRPA1 (sensor for ROS) responses at 100µM, so I would already consider this concentration excessive.\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? 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": [] } ]	1	https://f1000research.com/articles/12-1562
https://f1000research.com/articles/12-1561/v1	06 Dec 23	{ "type": "Research Article", "title": "Evaluation of selected serum biomarkers levels in response to the infliximab reference product (Remicade®) versus its biosimilar (Remsima®) in a sample of ulcerative colitis patients: a cross-sectional study", "authors": [ "Yahya G. Kawri", "Inam Sameh Arif", "Shaymaa Abdalwahed Abdulameer", "Inam Sameh Arif", "Shaymaa Abdalwahed Abdulameer" ], "abstract": "Background: Biologic therapies like Remicade® (infliximab originator) and Remsima® (infliximab biosimilar) have emerged as valuable options for the management of ulcerative colitis (UC) over the years. The purpose of the present study was to provide comprehensive comparison of the efficacy of Remicade® and Remsima® in the treatment of UC by performing a comprehensive analysis of key biomarkers. Methods: The study utilized a cross-sectional observational design. It was conducted at Baghdad Teaching Hospital in Baghdad, Iraq, spanning from July 2022 to February 2023. The study population consisted of individuals aged 21 to 57 years who had previously received a diagnosis of ulcerative colitis (UC). Results: A total of 43 patients were included in the analysis. The mean infliximab trough levels in the Remicade group were 3.264 ng/mL, while in the Remsima group were 3.248 ng/mL. eight Remicade patients developed anti-infliximab antibodies, while 9 Remsima patients tested positive. The mean serum calprotectin level was 5596 μg/ml in the Remicade group and 5795μg/ml in the Remsima group. The mean ESR value was 18.33mm/hr in the Remicade group and 16.43mm/hr in the Remsima group. The mean CRP value was 17.65mg/dl in the Remicade group and 16.19mg/dl in the Remsima group. The mean serum TNFa level measured was 159.5pg/ml in the Remicade group and 158.5pg/ml in the Remsima group. The mean serum Oncostatin M level measured was 107.3ng/ml in the Remicade group and 107.5ng/ml in the Remsima group Conclusion: These findings study suggest that Remsima, as a biosimilar to Remicade, holds promise as a cost-effective alternative in UC management", "keywords": [ "Biomarkers", "Ulcerative colitis", "Disease activity", "Remicade", "Remsima" ], "content": "Introduction\n\nUlcerative colitis (UC) is a chronic inflammatory bowel disease that necessitates effective treatment strategies to alleviate symptoms and improve patients’ quality of life.1 Over the years, biological therapies such as Remicade® (infliximab originator) and Remsima® (infliximab biosimilar) have emerged as valuable options in managing UC.2 One contributing factor to the elevated cost of biologics is the implementation of patent protection, which serves to restrict market competition. However, with the expiration of certain patents in recent years, alternative manufacturers have entered the market, offering biosimilar molecules at more competitive prices. These biosimilars are typically priced at a discount of approximately 45% compared to the original biologic product. In light of the increasing demands placed on healthcare systems to achieve cost effectiveness, biosimilars have emerged as a pivotal asset.3 Biosimilars are medicinal products that possess an amino acid chain that is comparable and exhibit a biochemical activity that is extremely analogous when compared to the original drug. Nevertheless, due to the intricate molecular composition of biologics and biosimilars, slight variations in their molecular structure may result from changes in base materials and manufacturing circumstances, these differences have the potential to impact the effectiveness and safety of the drug theoretically.4\n\nBiosimilar infliximab, referred to as CT-P13 (Remsima® and Inflectra®) and SB2 (Flixabi®), is a monoclonal antibody of significant size that has been granted permission to be marketed in various countries for the treatment of multiple conditions such as rheumatoid arthritis, ankylosing spondylitis, psoriatic arthritis, inflammatory bowel diseases.5 The evidence submitted to regulatory authorities consisted of in vitro assay activity data, comparative pharmacokinetic data from individuals with ankylosing spondylitis, and comparable pharmacodynamic data from individuals with active rheumatoid arthritis treated with the original product. The Canadian regulatory authority, Health Canada, initially differed from its American and European counterparts in its reluctance to accept evidence from patients with rheumatoid arthritis and ankylosing spondylitis as endorsed for the indication of Crohn’s disease and ulcerative colitis. This decision was based on concerns regarding the reliability of in vitro testing activity data and the absence of safety data.6 Despite the forthcoming provision of additional evidence to support the utilization of biosimilars in the treatment of inflammatory bowel disease indications such as Crohn’s disease (CD), fistulizing CD, and ulcerative colitis (UC), there remains a significant gap in knowledge regarding the safety profile and the potential development of neutralizing antibodies when patients are switched between the originator product and the biosimilar, particularly in cases that involve multiple changing.6\n\nThe measurement of infliximab trough levels provides valuable insights into the drug’s concentration in a patient’s bloodstream, serving as an indicator of the therapeutic drug monitoring.7,8 By comparing the trough levels between the two treatment groups, and assess the drug’s pharmacokinetics and determine if there are differences in the drug exposure.8\n\nAnti-infliximab antibodies, known as immunogenicity, play a pivotal role in response to biological therapies.9 The presence of these antibodies can impact drug efficacy by neutralizing the therapeutic effects of infliximab.10 Comparing the development of anti-infliximab antibodies between patients receiving Remicade® and Remsima® allows to evaluate the immunogenic potential of these treatments and their impact on treatment outcomes.11\n\nSerum calprotectin is a non-invasive biomarker used to assess intestinal inflammation.12 It reflects the activity of UC and can indicate response to treatment.13 Comparing the changes in serum calprotectin levels between Remicade® and Remsima®-treated groups provides valuable insights into the drugs’ abilities to reduce inflammation and achieve disease remission.14\n\nErythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) are commonly used markers of inflammation and are indicative of disease activity in UC patients.15–19 By comparing the changes in ESR and CRP levels in patients treated with Remicade® and Remsima®, to evaluate the drugs’ effectiveness in reducing systemic inflammation.20\n\nTumor necrosis factor alpha (TNFa) and oncostatin M are pro-inflammatory cytokines involved in the pathogenesis of UC.21–24 Monitoring their serum levels allows to assess the drugs’ ability to modulate the inflammatory response. Comparing the changes in TNFa and oncostatin M levels between the treatment groups provides valuable information on the drugs’ mechanisms of action and their impact on disease activity.25\n\nBy thoroughly analysing these key parameters, we aimed to provide a comprehensive comparison between the efficacy of Remicade® and Remsima® in the treatment of UC.\n\n\nMethods\n\nThe study adhered to the protocols outlined by the Ethics Committee of the College of Pharmacy at Mustansiriyah University, as indicated by the assigned research number 31, approval number 19, and reference number 72, on 3 July 2022. Written informed consent has been obtained from each participant. No incentives were provided, and the participation was entirely voluntary.\n\nThe research employed a cross-sectional observational design to examine the treatment outcomes of Remicade and Remsima in patients diagnosed with ulcerative colitis. The present investigation adhered to the STROBE guidelines for reporting cross-sectional observational studies.26\n\nThe present study was conducted at Baghdad Teaching Hospital, located in Baghdad, Iraq, lasting from July 2022 to February 2023.\n\nThe G*Power software version 3.1.9.7, with the Research Resource Identifier (RRID) SCR_013726, was utilized to estimate the necessary sample size for the study. The study employed a one-tailed alpha level of 0.05, a confidence interval of 95%, a power of 95%, and an effect size of 0.50. Hence, the minimum sample size required was determined to be 34 (f). The study involved the enrolment of 43 individuals.\n\nThe study included individuals between the ages of 21 and 57 years who had been previously diagnosed with inflammatory bowel disease (IBD), specifically ulcerative colitis (UC). These patients received treatment protocols prescribed by physicians at the Gastrointestinal Tract (GIT) Centre in Baghdad Teaching Hospital, located in Baghdad, Iraq. The patients received biological treatment with infliximab at a dosage of 5mg/kg for a duration exceeding one year. The infliximab administered could either be the originator brand (Remicade®) or the biosimilar brand (Remsima®).\n\nThe study excluded individuals who had the following coexisting conditions: rheumatoid arthritis, systemic lupus erythematosus, diabetes mellitus; cardiovascular, hepatic, or renal diseases; organ transplant recipients; individuals who smoke tobacco; and those taking medications that could potentially affect infliximab levels or accurate measurements. Patients who were previously subjected to any anti-TNF agent before initiating infliximab were excluded from the study.\n\nThis study utilizes random selection, a rigorous and systematic approach, to ensure that each participant from the population of infliximab users (both originator and biosimilar) has an equal opportunity to be included in the sample. The aforementioned concept forms the foundation of probability sampling and holds significant importance in probability methodologies and the ability to generalize findings. The utilization of random selection effectively mitigates the presence of sampling selection bias.\n\nDemographic data such as age, gender, weight, height, working status, disease duration, smoking status, income, marital status, family history, and presence of extra-intestinal manifestations were collected via direct patient interviews using a patient data chart specially designed for this study. The body mass index (BMI) was computed by dividing the weight in kilograms by the square of the height in meters.\n\nFrom each patient, a 10 ml venous blood sample was obtained and divided into 2 samples, first one was used for erythrocyte sedimentation rate (ESR), and C-reactive protein (CRP) and the second one was allowed to clot. Later the clot was removed by centrifuging at 2,000-3,000 rpm for 20 minutes. The resultant supernatant was kept in deep freeze (-80°C) till the time of analysis of biomarkers.\n\nQuantitative analysis of free infliximab in serum samples\n\nThe measurement of infliximab trough levels was conducted using Shikari® (Q-INFLIXI) ELISA kits manufactured by Matriks Biotek® Turkey, as indicated in Table 1. The analysis employed a solid phase enzyme-linked immunosorbent assay (ELISA) based on the sandwich principle. The standards and samples, particularly serum or plasma, were incubated in a microtiter plate that had been infused with the suited reacting agent intended for infliximab. After the incubation process the wells are subjected to a washing procedure. Following this, the horse radish peroxidase (HRP) conjugated probe is added. It establishes a binding association with the immobile infliximab facilitated by the reactant present on the outer layer of the wells. Following the incubation period, the wells undergo a washing procedure to eliminate anything that has not bonded to the surface. The detection of the enzymatic activity immobilized in the wells is accomplished by introducing a chromogenic substrate known as tetramethylbenzidine (TMB). In conclusion, the process is terminated by utilizing an acidic stop solution. The degree of color observed is positively associated with the quantity of infliximab detected in the sample or standard. The determination of sample results can be accomplished by utilizing the standard curve.\n\nQuantitative measurement of total Antibodies to Infliximab\n\nThe method utilizes the enzyme-linked immunosorbent assay (ELISA) technique to quantitatively determine the levels of both total and liberated antibodies specific to infliximab in blood samples. The production of anti-infliximab antibodies was achieved through the utilization of the SHIKARI® (Q-ATIDUO) enzyme-linked immunosorbent assay (ELISA) kit manufactured by Matriks Biotek® in Turkey. In the initial phase of incubation, dissociating buffering was introduced to aid in the disassociation of the antibody-immune complex specific to infliximab, as depicted in Table 1. After transferring the dissociating blend onto the plate, the antibodies present in the blood samples of individuals were isolated from infliximab and bound to the drug infliximab that was immobilized on the walls of the microtiter wells. This binding was facilitated by the use of a horse radish peroxidase (HRP) conjugated probe. The detection of a reaction between tetramethylbenzidine (TMB) chromogen substrate to samples that underwent a washing process to eliminate any unbound components. Subsequently, a stop solution with corrosive properties is employed to terminate the reaction process. A positive correlation exists between the intensity of the reaction color and the number of infliximab antibodies present in the specimen.\n\nTNFa values obtained using (Tumor Necrosis Factor Alpha) ELISA Kit (MyBioscore Inc., USA) Table 1, Sandwich enzyme immunoassay is the testing method utilized by this kit. This preparation includes a microtiter plate pre-coated with a TNFa-specific antibody. Next, the microtiter plate wells are coated with a biotin-conjugated anti-TNFa antibody, which is the suitable choice. Subsequently, the addition of Avidin-Horseradish Peroxidase (HRP) conjugate is carried out, followed by an incubation period within each well of the microplate. The change in color following the addition of the TMB substrate solution will only occur in wells that contain TNFa, a biotin-conjugated antibody, and enzyme-conjugated Avidin. The enzymatic activity of the enzyme-substrate complex is inhibited by the addition of a solution containing sulphuric acid. Subsequently, the resulting change in color is quantitatively assessed using spectrophotometry at a wavelength of 450 nm with a bandwidth of 10nm. Subsequently, the concentration of TNFa in the samples is evaluated through a comparison of the optical density of the specimens with the standard curve.\n\nAll samples and standards have been inserted into the Microelisa Stripplate in duplicate. Establish standard wells and sample wells for the purpose of testing. Dispense 50 microliters of the standard solution into each well designated for the standard. The testing sample should be supplemented with 10 μl. The testing sample well should be supplemented with 40 μl of sample diluent. In every hole, introduce 100 microliters of HRP-coupled reagent. Proceed to seal the wells with a sealing film and subject them to incubation at a temperature of 37 degrees Celsius for a duration of sixty minutes. Perform aspiration and subsequent cleansing of each well in the experimental setup on four occasions, resulting in a cumulative total of five washes. The wells should be filled with 400 μl of Wash Solution using either a spray bottle, manifold dispenser, or automatic washer. The complete removal of all liquid during each phase is imperative for achieving optimal performance. Ensure the complete removal of any residual cleanse solution by employing the method of aspiration or decantation subsequent to the ultimate cleansing process. To achieve the desired outcome, it is necessary to invert the dish and subsequently remove any excess moisture by gently pressing clean paper towels against its surface. It is recommended that each well be allocated a volume of 50l for both chromogen solution A and chromogen solution B. Gently combine the components and subject the mixture to incubation at a temperature of 37°C for a duration of 15 minutes. Protect from exposure to light. The recommended procedure involves the addition of 50 microliters of Stop Solution to each well. Alter the coloration of the wells, shifting them from a blue hue to a yellow hue. In the event that the wells exhibit a green color or if the color change is not uniformly distributed, it is advisable to gently tap the plate to promote comprehensive blending. The Optical Density (OD) at 450 nm should be measured using a microtiter plate reader within a time frame of 15 minutes.\n\nThe calprotectin evaluations were conducted utilizing the Human calprotectin (CAL) ELISA Kit manufactured by MyBioscore.Inc. which is based in the United States. The process can be simply outlined as follows: The ELISA Kit should be taken out of the fridge approximately 20 minutes prior to commencing the test, allowing it to equilibrate at ambient temperature. To achieve a less concentrated washing buffer, it is recommended to dilute it by a factor of 1:25 using double-distilled water. The lyophilized standard vial should be supplemented with 1.0 ml of Standard Diluent, followed by a 30-minute incubation period. Once the standard solution has completely dissolved, combine it and appropriately label the tube gently. To perform the experiment, it is necessary to extract a quantity of Enzyme Conjugate solution that is directly proportional to the number of wells to be tested. This extracted solution should then be diluted with Enzyme Diluent in a ratio of 1:100. It is recommended to allocate a period of 30 minutes prior to the intended usage for adequate preparation. Furthermore, it is advised against reutilizing the prepared material for subsequent testing purposes. The OD values of each sample and standard should have the values of the blank well subtracted from them.\n\nThe statistical analysis in the present research was performed employing GraphPad Prism version 8, which has the Research Resource Identifier (RRID) SCR_002798. The Shapiro-Wilk test was chosen as the statistical test to assess the normality of the data. The data is provided in the format of mean plus or minus standard deviation. The standard error of the mean (SEM) is a statistical metric used to assess the level of variability or uncertainty linked to the estimation of the population mean derived from a sample. The data underwent statistical analysis utilizing an unpaired Student’s t-test and a two-way analysis of variance (ANOVA). Following the identification of significant differences among the datasets through the analysis of variance (ANOVA), a posthoc test called Tukey’s multiple-comparisons test was utilized to compare the datasets. A P-value that falls below the predetermined threshold of 0.05 is deemed to be statistically significant.\n\n\nResults\n\nA total of 43 patients diagnosed with ulcerative colitis were included in the analysis. Of these, 22 patients received Remicade, and 21 patients received Remsima, as presented in Figure 1. The demographic and disease characteristics of the two treatment groups are summarized in Table 2. There were no significant differences in age, gender distribution, disease duration, or extent of colonic involvement between the Remicade and Remsima groups (P > 0.05).\n\nThe mean infliximab trough levels in the Remicade group were 3.264 ± 1.776 μg/mL, while in the Remsima group, the mean trough levels were [3.248 ± 1.889] (microgram) ng/mL. Statistical analysis revealed no significant difference in infliximab trough levels between the two groups (P = 0.977). This suggests comparable drug exposure and pharmacokinetics in patients receiving Remicade and Remsima Figure 2.\n\nAmong patients receiving Remicade, 8 patients, 36% developed anti-infliximab antibodies, while [9 patients, 42%] of patients in the Remsima group tested positive for these antibodies. The difference in the development of anti-infliximab antibodies between the two groups was not statistically significant (P = 0.7799). These findings indicate a similar immunogenic potential between Remicade and Remsima in ulcerative colitis patients Figure 3.\n\nThe mean serum calprotectin level measured just before the second dose of treatment was 596 ± 2982 μg/ml in the Remicade group and [5795 ± 3174] μg/ml in the Remsima group. There was no statistically significant difference in serum calprotectin levels between the two treatment groups (P = 0.8334) Figure 4.\n\nThe mean ESR value measured just before the second dose of treatment was [18.33 ± 18.02] mm/hr in the Remicade group and [16.43 ± 15.13] mm/hr in the Remsima group. There was no statistically significant difference in serum calprotectin levels between the two treatment groups (P = 0.7052) Figure 5.\n\nThe mean CRP value measured just before the second dose of treatment was [17.65±15.61] mg/dl in the Remicade group and [16.19 ± 15.15] mg/dl in the Remsima group. There was no statistically significant difference in serum calprotectin levels between the two treatment groups (p = 0.7546) Figure 6.\n\nThe mean serum TNFa level measured was [159.5 ± 98.34] pg/ml in the Remicade group and [158.5 ± 99.75] pg/ml in the Remsima group. There was no statistically significant difference in serum calprotectin levels between the two treatment groups (p = 0.9179) Figure 7.\n\nThe mean serum Oncostatin M level measured was [107.3 ± 81.5] ng/ml in the Remicade group and [107.5 ± 80.07] ng/ml in the Remsima group. There was no statistically significant difference in serum calprotectin levels between the two treatment groups (P = 0.9919) Figure 8.\n\nOverall, the results of this study suggest comparable treatment outcomes between Remicade and Remsima in ulcerative colitis patients. There were no significant differences in infliximab trough levels, development of anti-infliximab antibodies, and inflammatory markers (serum calprotectin, ESR, CRP, TNFa, and oncostatin M) between the two treatment groups.\n\n\nDiscussion\n\nIn recent years, the treatment of inflammatory bowel disease has been significantly improved because of the introduction of monoclonal antibodies (MAbs).27 Infliximab (IFX) revolutionized the pharmaceutical approach to treating Crohn’s disease and ulcerative colitis.28 MAbs, on the other hand, have hurdles in terms of their immunogenicity, efficacy, and safety because of the intricate interaction that exists between pharmacology and immunology. Inflammatory bowel disease (IBD) and other serious disorders have led to the development of biosimilars, a substitute for the original medicine that is more affordable.29\n\nAccording to the most recent findings, it has been shown that biosimilar versions of IFX in patients with IBD are just as safe and effective as the original versions of these medications.30 However, the use of these products is accompanied by several misunderstandings about their efficacy and safety, in addition to disputes surrounding the interchangeability of these products. As a result, there is a need for empirical evidence on the efficacy and safety of biosimilars when used over extended periods of time, at least until a scientific consensus can be reached.31\n\nThis study aimed to compare the treatment outcomes between Remicade and Remsima, focusing on key parameters, including infliximab trough levels, anti-infliximab antibodies, serum calprotectin, ESR, CRP, TNFa, and serum oncostatin M.\n\nOur results demonstrate comparable infliximab trough levels between the Remicade and Remsima treatment groups, indicating similar drug exposure and pharmacokinetics. This finding suggests that Remsima, as a biosimilar of Remicade, effectively delivers an equivalent concentration of infliximab to patients, supporting its role as a cost-effective alternative in UC treatment. These findings demonstrate similarities to those published in an earlier Norwegian study that aimed to evaluate the trough serum levels of CT-P13 in patients with ulcerative colitis. The study utilized an automated immunofluorometric assay on the automated dissociation-enhanced lanthanide fluorescent immunoassay platform, and the results indicated comparable serum drug levels.32\n\nThe development of anti-infliximab antibodies can impact treatment efficacy by neutralizing the drugs therapeutic effect. In our study, the incidence of anti-infliximab antibodies was comparable between the Remicade and Remsima groups. This suggests that both medications have similar immunogenic potentials, further supporting the bio-similarity of Remsima to Remicade. The findings align with a prior study by Ben-Horin et al., which indicated roughly comparable immunogenicity and the presence of shared immunodominant epitopes on both infliximab agents.33\n\nSerum calprotectin is a non-invasive biomarker used to assess intestinal inflammation in UC patients. Our study revealed no significant difference in serum calprotectin levels between the Remicade and Remsima groups. This finding suggests that both treatments effectively reduced inflammatory activity at the time of the second dose, as indicated by similar levels of this inflammatory marker. However, the lack of multiple serum calprotectin measurements throughout the treatment course limits our ability to assess the dynamic changes in inflammatory activity over time. Future studies incorporating serial measurements of serum calprotectin would provide a more comprehensive understanding of the long-term efficacy of Remicade and Remsima in managing UC. Nikkonen et al. have reported a similar outcome when examining the calprotectin levels, no significant disparity was observed between the original drugs and biosimilar drugs during the initial treatment phase or after one year in the management of patients diagnosed with inflammatory bowel disease.34\n\nESR and CRP are commonly used markers of systemic inflammation and disease activity in UC patients. Our study showed no significant differences between the two treatments. This suggests that both medications effectively mitigated systemic inflammation, as evidenced by improvements in these markers. The levels of C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR) did not exhibit any significant differences between the groups in the EXTENDED REPORT, which investigated the efficacy and safety of transitioning from reference infliximab to CT-P13 in patients with rheumatoid arthritis; these results endorse our findings.35\n\nFurthermore, the reduction in serum TNFa and oncostatin M levels following treatment initiation in both groups suggests that Remicade and Remsima effectively modulate the inflammatory response in UC patients. However, no significant differences were observed between the treatments, indicating comparable mechanisms of action in targeting these pro-inflammatory cytokines.25\n\nIt is important to acknowledge several limitations of our study. Firstly, the relatively small sample size and a single measurement of serum calprotectin restrict the generalizability and ability to assess longitudinal changes in inflammatory activity. Further prospective studies with larger cohorts and multiple measurements of inflammatory markers are warranted to validate our findings.\n\n\nConclusion\n\nIn conclusion, our study provides valuable insights into the comparison of Remicade and Remsima in UC patients. The comparable infliximab trough levels, the incidence of anti-infliximab antibodies, and reductions in serum calprotectin, ESR, CRP, TNFa, and oncostatin M levels suggest that Remsima, as a biosimilar to Remicade, holds promise as a cost-effective alternative in UC management. However, future studies with longer follow-up periods and comprehensive assessments of treatment outcomes are needed to establish the long-term efficacy, safety, and cost-effectiveness of Remsima in the management of UC.", "appendix": "Data availability\n\nZenodo: Evaluation of selected serum biomarkers levels in response to infliximab reference product (Remicade®) versus it’s biosimilar (Remsima®) in a sample of ulcerative colitis patients: a cross-sectional study. DOI: https://doi.org/10.5281/zenodo.8164655. 36\n\nThis project contained the following underlying data:\n\n- Article data.xlsx (Evaluation of selected serum biomarkers levels in response to infliximab reference product (Remicade®) versus it’s biosimilar (Remsima®) in a sample of ulcerative colitis patients: a cross-sectional study).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY ).\n\n\nReferences\n\nGajendran M, Loganathan P, Jimenez G, et al.: A comprehensive review and update on ulcerative colitis. Dis. Mon. 2019; 65(12): 100851. Publisher Full Text\n\nParigi TL, D’Amico F, Peyrin-Biroulet L, et al.: Evolution of infliximab biosimilar in inflammatory bowel disease: from intravenous to subcutaneous CT-P13. Expert. Opin. Biol. Ther. 2021; 21(1): 37–46. Publisher Full Text\n\nKim H, Alten R, Avedano L, et al.: The Future of Biosimilars: Maximizing Benefits Across Immune-Mediated Inflammatory Diseases. Drugs. 2020; 80(2): 99–113. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBen-Horin S, Casteele NV, Schreiber S, et al.: Biosimilars in inflammatory bowel disease: facts and fears of extrapolation. Clin. Gastroenterol. Hepatol. 2016; 14(12): 1685–1696. PubMed Abstract \| Publisher Full Text\n\nGabbani T, Deiana S, Annese V: CT-P13: design, development, and place in therapy. Drug Des. Devel. Ther. 2017; 11: 1653–1661. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFeagan BG, Choquette D, Ghosh S, et al.: The challenge of indication extrapolation for infliximab biosimilars. Biologicals. 2014; 42(4): 177–183. PubMed Abstract \| Publisher Full Text\n\nMoore H, Dolce P, Devas N, et al.: Post-induction infliximab trough levels and disease activity in the clinical evolution of pediatric ulcerative colitis. United European Gastroenterol. J. 2020; 8(4): 425–435. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKampa KC, Loures MR, Ivantes CAP, et al.: The Evaluation of Infliximab Trough Level Favors Maintenance Therapy of Patients with Inflammatory Bowel Disease. Arq. Gastroenterol. 2023; 60(1): 48–56. Publisher Full Text\n\nHa C, Mathur J, Kornbluth A: Anti-TNF levels and anti-drug antibodies, immunosuppressants and clinical outcomes in inflammatory bowel disease. Expert Rev. Gastroenterol. Hepatol. 2015; 9(4): 497–505. Publisher Full Text\n\nRomero-Cara P, Torres-Moreno D, Pedregosa J, et al.: A FCGR3A Polymorphism Predicts Anti-drug Antibodies in Chronic Inflammatory Bowel Disease Patients Treated With Anti-TNF. Int. J. Med. Sci. 2018; 15(1): 10–15. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBen-Horin S, Yavzori M, Benhar I, et al.: Cross-immunogenicity: antibodies to infliximab in Remicade-treated patients with IBD similarly recognise the biosimilar Remsima. Gut. 2016; 65(7): 1132–1138. Publisher Full Text\n\nAzramezani Kopi T, Shahrokh S, Mirzaei S, et al.: The role of serum calprotectin as a novel biomarker in inflammatory bowel diseases: a review study. Gastroenterol. Hepatol. Bed. Bench. 2019; 12(3): 183–189. PubMed Abstract\n\nMori A, Mitsuyama K, Sakemi R, et al.: Evaluation of serum calprotectin levels in patients with inflammatory bowel disease. Kurume Med. J. 2019; 66(4): 209–215.\n\nTurina MC, Yeremenko N, Paramarta JE, et al.: Calprotectin (S100A8/9) as serum biomarker for clinical response in proof-of-concept trials in axial and peripheral spondyloarthritis. Arthritis Res. Ther. 2014; 16: 1–9.\n\nFagan E, Dyck R, Maton P, et al.: Serum levels of C-reactive protein in Crohn’s disease and ulcerative colitis. Eur. J. Clin. Investig. 1982; 12(4): 351–359. Publisher Full Text\n\nAlper A, Zhang L, Pashankar DS: Correlation of erythrocyte sedimentation rate and C-reactive protein with pediatric inflammatory bowel disease activity. J. Pediatr. Gastroenterol. Nutr. 2017; 65(2): e25–e27. Publisher Full Text\n\nTurner D, Mack DR, Hyams J, et al.: C-reactive protein (CRP), erythrocyte sedimentation rate (ESR) or both? A systematic evaluation in pediatric ulcerative colitis. J. Crohns Colitis. 2011; 5(5): 423–429. Publisher Full Text\n\nArif IS, Kamal YM, Raoof IB: Nrf2 as a modulator of oxidative stress. Al Mustansiriyah Journal of Pharmaceutical Sciences. 2021; 21(4): 17–23. Publisher Full Text\n\nKasim AAH, Mohammed MM: Biochemical Evaluation of Some Liver Enzymes in Type 2 Diabetes Mellitus Iraqi Patients. Al Mustansiriyah Journal of Pharmaceutical Sciences. 2012; 12(2): 107–114. Publisher Full Text\n\nvan Hoeve K , Dreesen E, Hoffman I, et al.: Efficacy, pharmacokinetics, and immunogenicity is not affected by switching from infliximab originator to a biosimilar in pediatric patients with inflammatory bowel disease. Ther. Drug Monit. 2019; 41(3): 317–324. PubMed Abstract \| Publisher Full Text\n\nBertani L, Fornai M, Fornili M, et al.: Serum oncostatin M at baseline predicts mucosal healing in Crohn’s disease patients treated with infliximab. Aliment. Pharmacol. Ther. 2020; 52(2): 284–291. Publisher Full Text\n\nVerstockt S, Verstockt B, Machiels K, et al.: Oncostatin M is a biomarker of diagnosis, worse disease prognosis, and therapeutic nonresponse in inflammatory bowel disease. Inflamm. Bowel Dis. 2021; 27(10): 1564–1575. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKomatsu M, Kobayashi D, Saito K, et al.: Tumor necrosis factor-alpha in serum of patients with inflammatory bowel disease as measured by a highly sensitive immuno-PCR. Clin. Chem. 2001; 47(7): 1297–1301. Publisher Full Text\n\nWatanabe N: Clinical significance of measurement of circulating tumor necrosis factor alpha. Rinsho Byori. 2001; 49(9): 829–833. PubMed Abstract\n\nWest NR, Hegazy AN, Owens BMJ, et al.: Oncostatin M drives intestinal inflammation and predicts response to tumor necrosis factor–neutralizing therapy in patients with inflammatory bowel disease. Nat. Med. 2017; 23(5): 579–589. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nvon Elm E , Altman DG, Egger M, et al.: The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement: guidelines for reporting observational studies. Lancet (London, England). 2007; 370(9596): 1453–1457. Publisher Full Text\n\nChen Y, Zhang G, Yang Y, et al.: The treatment of inflammatory bowel disease with monoclonal antibodies in Asia. Biomed. Pharmacother. 2023; 157: 114081. PubMed Abstract \| Publisher Full Text\n\nO’Toole A, Moss AC: Optimizing Biologic Agents in Ulcerative Colitis and Crohn’s Disease. Curr. Gastroenterol. Rep. 2015; 17(8): 32. Publisher Full Text\n\nMehr SR, Brook RA: Factors influencing the economics of biosimilars in the US. J. Med. Econ. 2017; 20(12): 1268–1271. PubMed Abstract \| Publisher Full Text\n\nMazza S, Piazza OSN, Conforti FS, et al.: Safety and clinical efficacy of the double switch from originator infliximab to biosimilars CT-P13 and SB2 in patients with inflammatory bowel diseases (SCESICS): A multicenter cohort study. Clin. Transl. Sci. 2022; 15(1): 172–181. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nScavone C, Rafaniello C, Berrino L, et al.: Strengths, weaknesses and future challenges of biosimilars’ development. An opinion on how to improve the knowledge and use of biosimilars in clinical practice. Pharmacol. Res. 2017; 126: 138–142. PubMed Abstract \| Publisher Full Text\n\nJahnsen J, Detlie TE, Vatn S, et al.: Biosimilar infliximab (CT-P13) in the treatment of inflammatory bowel disease: a Norwegian observational study. Expert Rev. Gastroenterol. Hepatol. 2015; 9(sup1): 45–52. PubMed Abstract \| Publisher Full Text\n\nBen-Horin S, Yavzori M, Benhar I, et al.: Cross-immunogenicity: antibodies to infliximab in Remicade-treated patients with IBD similarly recognise the biosimilar Remsima.2016; 65(7): 1132–1138.\n\nNikkonen A, Kolho KL: Infliximab and its biosimilar produced similar first-year therapy outcomes in patients with inflammatory bowel disease. Acta Paediatr. 2020; 109(4): 836–841. Publisher Full Text\n\nYoo DH, Prodanovic N, Jaworski J, et al.: Efficacy and safety of CT-P13 (biosimilar infliximab) in patients with rheumatoid arthritis: comparison between switching from reference infliximab to CT-P13 and continuing CT-P13 in the PLANETRA extension study. Ann. Rheum. Dis. 2017; 76(2): 355–363. Publisher Full Text\n\nAl-Qaisy Y: Evaluation of selected serum biomarkers levels in response to infliximab reference product (Remicade®) versus it’s biosimilar (Remsima®) in a sample of ulcerative colitis patients: a cross-sectional study. In: Al-Qaisy Y, editor.2023. Publisher Full Text" }	[ { "id": "256080", "date": "27 Mar 2024", "name": "Jun Kato", "expertise": [ "Reviewer Expertise inflammatory bowel diseases" ], "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 examined several serum markers of patients with UC who were administered infliximab originator or biosimilar. The overall results of the measured markers were comparable and the authors concluded that biosimilar infliximab were equivalent to its originator. There are several issues to be addressed.\nThe timing of the measurements of serum markers were not indicated except for serum calprotectin, ESR, and CRP. The trough levels of infliximab and development of anti-infliximab antibody depend on the duration of time since the drug was started. For all the measurements, it should be noted how long after the drug administration was started the sample was measured. It is impossible to estimate the effect of a drug by measuring inflammatory markers including ESR and CRP only at one point, because baseline inflammation varies between individuals. So, authors should measure inflammatory markers with the samples before infliximab administration, and the efficacy of the drugs should be evaluated by comparing between the values before and after drug administration. The method of randomization should be indicated. The unit of CRP may be incorrect. It is not mg/dL but mg/L. The abstract lacks necessary information including the numbers of patients of originator versus biosimilar groups, and the timings of the measurement of the markers.\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? Yes\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [] } ]	1	https://f1000research.com/articles/12-1561
https://f1000research.com/articles/12-389/v1	13 Apr 23	{ "type": "Research Article", "title": "Perceptions of professional nurses towards the inclusion of spiritual activities in oncology practice in the uMgungundlovu and eThekwini Health Districts, KwaZulu-Natal, South Africa: A quantitative descriptive study.", "authors": [ "Vashni Sewkarran", "Emelda Zandile Gumede", "Emelda Zandile Gumede" ], "abstract": "Background: Internationally the inclusion of spiritual activities has been well adopted into nursing care. Spiritual activities could be used as one of the coping strategies for cancer patients in times of emotional distress. The South African perspective highlights a huge gap regarding incorporating spiritual activities into oncology practice. Due to popularity and frequent use, the need for identifying the perceptions of professional nurse’s regarding the inclusion of spiritual activities in oncology nursing practice was vital. Methods: The study followed a quantitative descriptive survey. Four health care institutions were purposively selected in the eThekwini and uMgungundlovu health district. Simple random selection of 89 participants that met the eligibility criteria was conducted. Self-administered questionnaires were used to collect data over a period of four weeks from 3rd January 2022 to 9th February 2022, followed by analysis using the SPSS, version 27. Results: The findings revealed that professional nurses agree that spiritual care can be provided by including various spiritual activities into oncology nursing practice. More than 80% of professional nurses believed in God. Activities like arranging visits by chaplains, showing kindness, cheerfulness, and reassurance were highly rated, exceeding 80%; however, activities like art and creativity were poorly rated, 32.6%. These findings are in line with the hypothesis of the researcher. Conclusion: This study produced empirical evidence that spiritual care can be provided by including various spiritual activities in oncology practice to promote comprehensive nursing care. A module on spirituality should be included in the new oncology program to boost the nurse’s levels of confidence in spiritual care. The study will enhance the nurses’ awareness and expertise in providing a range of activities.", "keywords": [ "Perceptions", "oncology", "spiritual activities", "spiritual care", "professional nurse" ], "content": "Introduction\n\nDuring the 1860s, Florence Nightingale, a pioneer in nursing, emphasized the importance of using complementary and alternative therapies in nursing.1 Nurses constitute more than 80% of the healthcare team. They are the chief providers of holistic nursing.2 Current literature highlights that spiritual interventions are very beneficial to help manage symptoms and improve quality of life among the general population, including cancer patients.3,4\n\nCurrently, studies have identified a link between spirituality, spiritual care, and the oncology patient.3,4 To date, there is a paucity of literature on the inclusion of spiritual activities in oncology practice in South Africa5,6 whilst, internationally, there is growing evidence on the use of spiritual activities in current nursing practice. Researchers have noted this notion with some concerns, that if the inclusion of spiritual activities is not integrated into nursing practice, then nurses will not be mindful of the patient’s spiritual needs, and thus fail to integrate this into their daily practice.6\n\nAlthough studies internationally concur that spiritual activities can be included in nursing practice, but barriers like workload impedes incorporating such. Infrastructure upgrades and adequate distribution of human resources will promote a comprehensive nursing approach.7 The South African health care systems place emphasis on the advancement of science and technology but oncology nursing continues with traditional nursing care due to a paucity of knowledge on spiritual activities.7\n\nThe current health care system should be in a position to provide universally acceptable spiritual care in their daily current practices. Hence, the researcher aims to analyse professional nurse’s perception towards the inclusion of spiritual activities in oncology practice. An earlier preprint version of this article can be found on Research Square.8\n\n\nMethods\n\nThe study was approved by the KwaZulu-Natal Department of Health (KZN-DoH), National Health Research Ethics Committee on 3rd December 2021 (NHRD Ref: KZ _ 202111_ 020). An application for full ethical approval was made to the Biomedical Research Ethics Committee (BREC) at the University of KwaZulu-Natal, and approval was received on 08th December 2021 (BREC/00003395/2021). Information regarding the research study was fully explained in an information letter, which was given to the respondents and was explained by the researcher. Written informed consent was obtained and anonymity was maintained as respondents did not have to reveal their names. During data capturing no personal details of respondents were captured instead each questionnaire was coded. This study was conducted in conformance with the Helsinki Declaration.\n\nA quantitative descriptive survey was used to analyse the perceptions of professional nurses towards the inclusion of spiritual activities in oncology practice.\n\nThe study was conducted in four sites offering oncology care in the uMgungundlovu and eThekwini Health Districts, KwaZulu-Natal. The sites were purposively selected based on their levels of care: a private hospital, offering specialized oncology care; a public-private partnership hospital, offering central and tertiary care; a public hospital, offering tertiary care, and a non-government organisation (NGOs) offering oncology and palliative care.\n\nSimple random sampling was best suited, as the researcher went to the oncology units and sampled all participants from the abovementioned hospitals and NGOs. This ensured that every professional nurse had an equal opportunity of being selected. Professional nurses who had a minimum of six months working experience, were directly involved in oncology nursing care, and who agreed to participate were eligible to take part in this study. Professional nurses included in the pilot study; those working in other departments and in the oncology units for less than six months and were unwilling to participate in this study were excluded. A total of 89 professional nurses were part of the study.\n\nThe researcher requested and received permission from the author, Professor Mc Sherry to use original ‘The Spirituality and Spiritual Care Rating Scale’ (SSCRS) hence allowing the researcher to modify and adapt the scale to the current study. The scale is easily available and can be copied. The SSCRS was developed by Mc Sherry (2002) to assess nurse’s perception of spiritual care9\n\nThis five-point Likert scale includes 17 items and three subdivisions viz. (i) spirituality and spiritual healing. (ii) Religiosity and (iii) personal care. According to Mc Sherry et al10 the SSCRS tool consists of four domains that assess the beliefs and values of nurses viz, beliefs about spirituality; beliefs about the way nurses can provide spiritual care; beliefs about religiosity and the expression of religiosity and values around personalised care.\n\nFor the current study, how professional nurses, conceptualized spirituality personally and in a nursing, context was measured by the SSCRS and were in line with the research objective. The questionnaire was designed along the subsection headings and part of the original questions used by McSherry; and together with the researchers own questions gave rise to a new survey questionnaire (see Extended data).28\n\nThe questionnaire was pre-tested for validity and reliability among four professional nurses, one from each institution. The questionnaire was in English and only the content was adapted to ensure that relevant questions were included in order to determine professional nurse’s perceptions towards the inclusion of spiritual activities in oncology practice. The scale demonstrated consistent levels of reliability and validity having a Cronbach’s coefficient of 0.74.\n\nThe final questionnaire (see Extended data28) consisted of two sections as follows:\n\nSection A is related to the demographic characteristics of the participants: gender, ethnic group, working experience in nursing, and religious affiliation.\n\nSection B is related to the SSCRS; focusing on the professional nurse’s perceptions about spirituality and spiritual activities in oncology nursing practice.\n\nThe Likert scale required the participants to answer the questions with a response (Agree) or (Disagree). The researcher submitted the questionnaire to her supervisor to check if all the questions reflected all the concepts being studied.\n\nGatekeeper permission was obtained from the relevant heads of institutions and units to conduct the study. The researcher arranged with the manager of each unit regarding a convenient day and time to meet with the professional nurses. The researcher met with the participants and explained the process to be followed, and time was given to ask questions. A package including an information letter, questionnaire, and consent form was handed to the participants and collected after three weeks for the two hospitals in the eThekwini Health District due to the distance, nature of the participants’ work, and their availability. Data collection was done over a period of five days at the hospital and NGO in the uMgungundlovu Health District with the same package delivered. Data collection was done over a period of four weeks from 3rd January 2022 to 9th February 2022. The researcher arranged a date and time at their convenience to pick up the completed questionnaires and consent forms from both districts. The completed questionnaires and consent forms were placed into a sealed envelope that was kept in a locked cupboard only accessible to the researcher.\n\nAll questionnaires collected were checked for completeness; were numbered and each question was given a code and then entered onto an excel spreadsheet (see Underlying data).27 Out of the 89 questionnaires distributed, all 89 were completed correctly and included in the final analysis.\n\nThe data collected was analysed using the Statistical Package for Social Science (SPSS) version 27, with the assistance of a statistician. The descriptive statistics results were reported as frequencies and percentages to summarize the categorical variables.\n\nThe questionnaire was tested for validity and reliability. Construct validity ensures that the questionnaire measures accurately what it is supposed to measure.11 The questionnaire was adapted to ensure that relevant questions were included to determine the perceptions of professional nurses towards inclusion of spiritual activities in oncology practice.\n\n\nResults\n\nThe demographic data of the participants was analysed according to their gender, ethnic group, years in nursing experience, and their spiritual orientation as presented in Table 1 below.\n\nOut of the 89 participants included in the study, 94.4% were female and 5.6% were males. The sample was predominantly African 74.2%; Indian forming the next highest grouping 16.9%; followed by an almost equal proportion of Coloured and Whites 5.6% and 3.4% respectively. About 33.7% had between 10-20 years of nursing experience while only 6.7% had under 10 years of experience. The majority, 91% belonged to the Christian faith.\n\nAn average of 68.5% of participants agreed that spirituality is to do with the way one conducts life here and now. Of many professional nurses, 78.7% revealed that spirituality is concerned with a belief and faith in God. However, 21.3 % of participants disagree. In addition, 95.5% of participants recognized that spirituality is a unifying force that enables one to be at peace with oneself and find hope during drastic oncology care. Only 32.6% believed that spirituality does not include art and creativity. A total of 92.1% agreed that spirituality is concerned with counselling, and a need to forgive and be forgiven.\n\nAs indicated in Table 2, the data reflected that professional nurses can provide spiritual care by executing various spiritual activities in their daily nursing practices. Of the sample, 98.9% of participants agreed that they can arrange a religious leader for their patients when the need arises. More than 80% of participants believed that as nurses they can provide spiritual care by showing kindness, listening to and allowing patients to explore their fears, and providing patients with radios, magazines, and extended visiting hours. Overall, all participants (100%) are in agreement that spiritual care can be provided by spending time with patients and respecting their privacy and cultural beliefs.\n\n\| Group % shown \| Mode1-smallest mode \| Nmodes-# of modes \|\n\n\nDiscussion\n\nThe findings revealed that most professional nurses in the uMgungundlovu and eThekwini Health districts do believe in a God or Supreme Being and agree that spiritual care can be provided through a variety of spiritual activities.\n\nWhile the nursing profession has always had male nurses, it remains a female-dominated profession. The findings of this study confirm this notion as the majority of the participants were females. This is in line with Mao et al.,12 who concurs that both caring and nurturing are perceived as primarily female traits needed for the nursing profession.\n\nThe prevalence of the majority of the participants being African, concurs with the racial distribution of people in South Africa.13 The fact that most professional nurses reported having between 10-20 years of nursing experience, as compared to only a small percentage having less than 10 years of experience reflects a sample characterized by extensive years of nursing knowledge and clinical exposure. This confirms that the participants are not novice but instead they are skilled nurses as they have had an opportunity to put what they have learned in the classroom into practice for over three years.14 Hence, they are capable of providing holistic nursing care and strengthening nursing practice by considering the use of spiritual activities to better the well-being of patients.\n\nConcerning spiritual orientation almost all the participants were identified as being Christian. This dimension suggests that the participants could share common spiritual beliefs and practices which can influence their spiritual well-being and how they provide spiritual care.\n\nA large portion of participants agreed that spirituality is to do with the way one conducts one’s life here and now, which signifies that spirituality is relevant at the time of a patient’s illness in terms of how they manage their illness. These results corroborate with Ebenau et al., and Rego et al.,15,16 who noted that spirituality is a dynamic dimension of human life as it encourages one to find meaning and purpose in life during suffering and death.\n\nHaving faith and a relationship with God is universal. Believing that it is God’s power, love, and existence that allows us to find peace and contentment in daily living cannot be over-emphasized. This was evident by the statistics which revealed that only a few professional nurses agreed that spirituality is not concerned with a belief and faith in a God, however, the majority disagreed on this point. This discrepancy is in line with Hu, Jiao, and Li and Siqueria et al.,17,18 who argues that in diseases like cancer, spirituality allows patients to form interrelationships with God, nature, and oneself and this is seen as their coping strategy during their journey.\n\nThe findings of the study highlight that there is a high acceptance of spirituality among professional nurses. This is supported by the fact that almost all the participants agreed that spirituality is a unifying force that enables one to be at peace with oneself and the world thereafter. This signifies that when facing an illness or a life crisis, spirituality allows individuals to find peace within themselves, and with family and not blame others for the situation that they are in.\n\nForming relationships with a higher being during times of ill health allows individuals to gain strength and create hope so that they can cope better.19 Hope is a part of everyone’s life that arises in both good and bad situations. It is associated with resilience and can change the perception of a stressful experience into a comforting and manageable experience.20 This was evident in the statistics revealed, that the majority of the participants reported that spirituality is about having a sense of hope in life during drastic oncology care.\n\nIt was interesting to note that only a small percentage of participants were in agreement that spirituality does not include areas such as art and creativity, but Corry, Tracey, and Lewis20 emphasizes that creativity is an aspect of spirituality that alleviates anxiety, creates joy, and provides self-esteem. The reason for this may be related to the fact that some professional nurses experience heavy workloads and do not have the time to explore these creative avenues or they may be unaware that this could take the patient’s mind off their negative emotions and allow them to express their feelings healthily.\n\nIt was encouraging to note that the majority of professional nurses were in agreement that spirituality is concerned with counselling, and a need to forgive and be forgiven. This issue is very close to the researcher’s ideology because nurses as human beings need to forgive each other to work harmoniously together. This is in line with Siler et al.,21 who concurs that patients who are suffering from a terminal illness, like cancer, begin to question their lives and feel like they have not been forgiven and are now punished by God for all the wrongdoings in their lives. But then again when someone feels that they have been forgiven for their wrongdoings in life, suffering and death become more acceptable.22\n\nIt is recommended that if spiritual practices are integrated into nursing practice, then nurses will become mindful of the patient’s spiritual needs and implement spiritual activities like meditation, prayer, art therapy, and other rituals into nursing practice.6 Nursing literature reveals that these activities are common in nursing care and contribute to the realm of holistic nursing care.7,15 This is in line with the findings of this study as almost all professional nurses agreed that spiritual care can be provided by implementing various spiritual activities into nursing care.\n\nHospitals always aim to provide the best care for their patients, but the care provided by nurses might not always meet the emotional and spiritual needs of their patients. This is in line with Siler et al.,21 who emphasizes that spiritual care is not the sole responsibility of one health care discipline, but it should be a team approach including an oncology nurse, oncologist, psychologist, social worker, and religious leaders who are trained in spiritual care,23 This can be accomplished as majority of the professional nurses stated that spiritual care can be provided by arranging a religious leader to meet the spiritual needs of the patient. Our clients come from different social and spiritual backgrounds, so the availability of a chaplain could not be over-emphasized.\n\nCancer patients might feel lonely, isolated, hopeless, and abandoned by God as reported by Siler et al.,21 whereas almost all the professional nurses stated that oncology nurses can provide spiritual care by showing kindness, concern, and cheerfulness when giving care. During the nurse’s daily routine, an act of kindness such as helping patients take a bath, administering their medication, instilling hope, and creating a positive outlook on life can reduce their stress, anxiety, and depression, which can make their situation and experience more pleasant.\n\nIt was encouraging to note that all professional nurses agreed that spiritual care can be provided by spending time with their patients, providing support and reassurance. Similar findings were made by Starc, Karnjus, and Babnik and Forshaw et al.,2,24 who concur that when patients are reassured and informed about their condition and their treatment modalities, they may feel more prepared to deal with their illness. Nurses can offer support to the patient, visitors, and family during visiting hours by explaining the patient’s condition just to allay any fears and anxieties.\n\nA large percentage of participants agreed that spirituality can be provided by listening to patients and providing them with radio, magazines, and extended visiting hours. The hospitalized patient can benefit from listening to the radio and having an in-house saloon or beauty therapist to improve their physical image. In the case of children, the importance of play cannot be over- emphasized; therefore, a playroom is ideal where children can participate in a variety of activities simultaneously. This notion is supported by Herlianita et al.,25 who stated that Islamic patients cope better with their illness when reading or listening to their Holy Quran. Although, providing such spiritual activities is ideal, financial or structural barriers could prevent such provisions.\n\nAnother interesting finding was that all professional nurses stated that oncology nurses can provide spiritual care by having respect for the privacy, dignity, and religious and cultural beliefs of a patient. For nurses, the important thing is to respect the patient’s rights and beliefs even if you disagree with them. Siler et al.,21 supports this idea that a patient’s belief and view of God or higher power must be respected. Nurses need to accommodate those spiritual needs that do not interfere with the safety of the patients or health care. To handle the situation, nurses need to apply nursing activities that secure the patient’s dignity by addressing them properly and respecting their personal space and possessions. In fact, Bagherian et al.,26 confirms that cancer patients are more vulnerable to the loss of their dignity, hence they need to be handled with care.\n\nThese activities fall in the realm of caring and nurses should be equipped with how to integrate these activities into nursing care to ensure the well-being and recovery of oncology patients. The current study has some limits that should be addressed in future research. The study exclusively addressed the perceptions of professional nurses towards inclusion of spiritual activities in oncology practice. Future research should include other categories of nursing personnel and patients in different hospitals and settings\n\n\nConclusion\n\nThis study reveals a high level of spirituality among professional nurses, with the majority agreeing that various spiritual activities can be provided to oncology patients to help them cope better with their illnesses. It is recommended that a module on effective spiritual care protocols be included in the new post-basic oncology program, in-service training, and workshops to boost the nurse’s levels of confidence in spiritual care. One hospital delayed the gate-keeper approval for three months, thus delaying the data collection process. Furthermore, this study was restricted to professional nurses only, therefore future research would benefit from expanding this research to other health professionals.", "appendix": "Data availability\n\nFigshare: Full anonymised answers of all questionnaires (1).xlsx.\n\nhttps://doi.org/10.6084/m9.figshare.22215139. 27\n\nThis project contains the following underlying data:\n\n• Full anonymised answers of all questionnaires (1).xlsx\n\nFigshare: Coding example for the anonymised response file.pdf. https://doi.org/10.6084/m9.figshare.22256992.v1. 30\n\nFigshare: Questionnaire: Professional nurse’s perceptions towards spirituality and spiritual activities in oncology nursing practice. https://doi.org/10.6084/m9.figshare.21899454. 28\n\nThis project contains the following extended data:\n\n• Quantative tool Questionaire.docx (English language blank copy of the questionnaire used in this study).\n\nFigshare: SRQR checklist for ‘Perceptions of professional nurses towards the inclusion of spiritual activities in oncology practice in the uMgungundlovu and eThekwini Health Districts, KwaZulu-Natal, South Africa’. https://doi.org/10.6084/m9.figshare.22147163. 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\nAcknowledgments\n\nThe authors acknowledge the university which granted ethical clearance, the relevant authorities which granted gatekeeper permission and all respondents who participated in this study.\n\n\nReferences\n\nDossey B: Florence Nightingales message for today. Nebraska Nurses Association. 2004; 13–14.\n\nStarc TM, Karnjus I, Babnik K: Attitudes towards spirituality and spiritual care among nursing employees in hospitals. Obzornik zdravstvene nege. 2019; 53: 31–48. Publisher Full Text\n\nSatija A, Bhatnagar S: Complementary Therapies for Symptom Management in Cancer Patients. Indian J. Palliat. Care. 2017; 23: 468–479. PubMed Abstract \| Publisher Full Text\n\nO’ Callaghan CC, McDermott F, Reid P, et al.: Music relevance for people affected by cancer: A Meta-Ethnography and implications for music therapists. J. Music. Ther. 2016; 53: 398–429. PubMed Abstract \| Publisher Full Text\n\nSibiya MN, Maharaj L, Bhagwan R: Perceptions of professional nurses towards complementary and alternative modalities (CAM) in the uMgungundlovu District, KwaZulu-Natal. International Journal of Africa Nursing Sciences. 2017; 7: 18–23. Publisher Full Text\n\nChandramohan S: Spirituality and spiritual care amongst professional nurses at public hospitals in KwaZulu-Natal.2013; 1–134.\n\nMoosavi S, Rohan C, Borhani F, et al.: Factors affecting spiritual care practices of oncology nurses: a qualitative study. Support. Care Cancer. 2019; 27: 901–909. PubMed Abstract \| Publisher Full Text\n\nSewkarran V, Gumede EM: Perceptions of professional nurses towards the inclusion of spiritual activities in oncology practice in the uMgungundlovu and eThekwini Health Districts, KwaZulu-Natal, South Africa. Research Square, Preprint. 2022.\n\nKaddourah B, Abu-Saheen A, Al-Tannir M: Nurse’s Perception of Spirituality and Spiritual Care at Five Tertiary Care Hospitals in Riyadh, Saudi Arabia: A Cross Sectional Study. Oman Med. J. 2018; 33: 154–158. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMc Sherry W, Draper P, Kendrick D: The construct validity of a rating scale designed to assess spirituality and spiritual care. Int. J. Nurs. Stud. 2002; 39: 723–734. PubMed Abstract \| Publisher Full Text\n\nPolit DF, Beck CT: Nursing Research Generating and assessing evidence for nursing practice. 10th ed. Philadelphia, P.A.: Wolters Kluwer/Lippincott Williams & Wilkins; 2017.\n\nMao A, Cheong PL, Van LK, et al.: “I am called a girl, but that doesn’t matter” – perspectives of male nurses regarding gender - related advantages and disadvantages in professional development. BMC Nurs. 2021; 20(24): 1–9. Publisher Full Text\n\nStatistics South Africa, Improving lives through data. Republic of South Africa: Department: Statistics South Africa; Reference Source\n\nOzdemir NG, Ecevit ZB: The development of nurses individualized care perceptions and practices: Benner’s Novice to Expert Model Perceptive. Int. J. Caring Sci. 2019; 12: 1279–1285.\n\nEbenau A, Groot M, Visser A, et al.: Spiritual care by nurses in curative oncology: a mixed method study on patient’s perspectives and experiences. Scand. J. Caring Sci. 2019; 10: 1–12.\n\nRego F, Goncalves F, Moutinho S, et al.: The influence of spirituality on decision making in palliative care outpatients: a cross-sectional study. BMC Palliat. Care. 2020; 19: 1–14.\n\nHu Y, Jiao M, Li F: Effectiveness of spiritual care training to enhance spiritual health and spiritual care competency among oncology nurses. BMC Pallitative care. 2019; 18: 1–8. Publisher Full Text\n\nSiqueria HCH, de Cecagno D , Medeiros AC, et al.: Spirituality in the health-illness-care of the oncological user process: nurse’s outlook. Journal of Nursing UFPE ON line. 2017; 11: 2996–3004.\n\nNiu Y, McSherry W, Partridge M: Exploring the meaning of spirituality and Spiritual Care in Chinese contexts: A Scoping Review. J. Relig. Health. 2021; 61: 2643–2662. Publisher Full Text\n\nCorry DAS, Tracey AP, Lewis CA: Spirituality and Creativity in coping, Their Association and Transformative Effect: A Qualitative Enquiry. Research Gate. 2015; 6: 499–526. Publisher Full Text\n\nSiler S, Mamier I, Winslow BW, et al.: Interprofessional perspectives of providing spiritual care for patients with lung cancer in outpatient’s settings. Oncol. Nurs. Forum. 2019; 46: 49–58. PubMed Abstract \| Publisher Full Text\n\nKrause N, Hill PC: Assessing the relationships among forgiveness by God, God Images and death images. Journal of death and dying. 2020; 81: 356–369. PubMed Abstract \| Publisher Full Text\n\nTaylor EJ, Li AH: Healthcare Chaplains Perspective on Nurse-Chaplain collaboration: An online survey. J. Relig. Health. 2020; 59: 625–638. PubMed Abstract \| Publisher Full Text\n\nForshaw K, Hall AE, Boyes AW, et al.: Patients experiences of preparation for radiation therapy: A qualitative study. Oncol. Nurs. Forum. 2017; 44: E1–E9. Publisher Full Text\n\nHerlianita R, Yen M, Chen CH, et al.: Perceptions of spirituality and spiritual care among Muslim nurses in Indonesia. J. Relig. Health. 2018; 57: 762–773. PubMed Abstract \| Publisher Full Text\n\nBagherian S, Sharif F, Zarshenas L, et al.: Cancer patient’s perspectives on dignity in care. Nurs. Ethics. 2020; 27: 127–140. Publisher Full Text\n\nSewkarran V, Gumede EZ: Full anonymised answers of all questionnaires. [Dataset]. 2023. Publisher Full Text\n\nSewkarran V, Gumede EZ: Questionnaire. Professional nurse’s perceptions towards spirituality and spiritual activities in oncology nursing practice. [Dataset]. Figshare. 2023. Publisher Full Text\n\nSewkarran V, Gumede EZ: SRQR checklist. Perceptions of professional nurses towards the inclusion of spiritual activities in oncology practice in the uMgungundlovu and eThekwini Health Districts, KwaZulu-Natal, South Africa’. [Dataset]. Figshare. 2023. Publisher Full Text\n\nSewkarran V, Gumede EZ: Coding example for the anonymised response file.pdf. Dataset. figshare. 2023. Publisher Full Text" }	[ { "id": "183471", "date": "17 Aug 2023", "name": "Bert Garssen", "expertise": [ "Reviewer Expertise Psycho-oncology" ], "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 deals with a clinically relevant topic, namely spiritual care by nurses in South Africa. However, I see some serious problems with this study.\nThe study does not build on what is already known in this area. There are some 390 publications about spiritual care by nurses, of which at least 32 focuses on oncological care. The present authors mention only a few in the Introduction (2 a 4).\n\nIf the authors had wanted to compare the situation in South Africa with what is known from the rest of the world, they should have used a questionnaire that has been used frequently elsewhere. However, they used their own questionnaire.\n\nThe questionnaire used in the present study included some of the topics from the SSCRS of McSherry. However, this questionnaire has been criticized (Garssen, B., et al., 2017. A critical analysis of scales to measure the attitude of nurses toward spiritual care and the frequency of spiritual nursing activities. Nursing Inquiry, 24, 1-9. https://doi.org/10.1111/nin.12178). Moreover, the questionnaire of the present study used only two response options, whereas McSherry’s list had a five point Likert scale. The new scale was not psychometrically tested. Only half of the items concerns opinions of nurses about spiritual care, whereas the other half asks about the nurses’ opinions about spirituality. Why ask about opinions about spirituality, if one is interested in opinions about spiritual care?\n\nThere are some questionable items in the new questionnaire: “Oncology nurses can provide spiritual care by providing a radio, magazines and arranging for extended visiting hours” and “Spirituality does not include areas such as art, creativity and self-expression”. What has this to do with spiritual care? The following items concern social care, not necessarily spiritual care: 8-10.\n\nThe heading of Table 2 suggests that the SSCRS is used, whereas in fact the table presents the outcome of the new questionnaire. I doubt whether McSherry is pleased with this heading.\n\nIt would have been useful to know how often nurses actually provide spiritual care. Opinions about spiritual care do not predict the provision of such care.\n\nThe study provides only a summary of the answers to each of the thirteen questions separately, all of which are in detail discussed in the Discussion section. No further analysis is provided. The authors could at least have analyzed relationships between psychometric data and opinions about spirituality and spiritual care.\n\nIntroduction, end of first paragraph, “Current literature highlights that spiritual interventions are very beneficial to help manage symptoms and improve quality of life among the general population, including cancer patients 3,4”: The authors refer to two publications, of which one is about complementary therapy and the other about music therapy. Both are not spiritual interventions. Both are interventions for cancer patients, and not for “the general population”.\n\nNext sentence: “Currently, studies have identified a link between spirituality, spiritual care, and the oncology patient 3,4”: What was the link? A positive or negative relationship? How can you link two abstract concepts with a concrete person? Perhaps the authors mean “the well-being of oncology patients”? The authors refer to the same two publications, which are not about spiritual interventions.\n\nMethods: The authors said to have applied “random sampling”. Random sampling means to have included every Xth nurse, which was not applied in the present study.\n\nDiscussion section, “The findings of the study highlight that there is a high acceptance of spirituality among professional nurses. This is supported by the fact that almost all the participants agreed that spirituality is a unifying force that enables one to be at peace with oneself and the world thereafter. This signifies that when facing an illness or a life crisis, spirituality allows individuals to find peace within themselves, and with family and not blame others for the situation that they are in”: One can accept that the concept of spirituality implies that “spirituality is a unifying force ..”, and disagree with the statement that spirituality is important for oneself, and disagree with the statement that spiritual care is important for nursing care. If nurses agree with the statement that “spirituality is a unifying force ..”, this does not imply that “.. when facing an illness or a life crisis, spirituality allows individuals to find peace within themselves ..”. Please, be more critical.\n\nDiscussion section, “Nursing literature reveals that these activities are common in nursing care and contribute to the realm of holistic nursing care 7,15. One of the referred studies (Ebenau et al.) concluded that “Most patients rarely received spiritual care by nurses”. This is in sharp contrast with what the present authors claim.\n\nNext sentence, “This is in line with the findings of this study as almost all professional nurses agreed that spiritual care can be provided by implementing various spiritual activities into nursing care”: When nurses say that “spiritual care can be provided”, this does not imply that spiritual care is in fact often provided.\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? 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? No", "responses": [] }, { "id": "169409", "date": "17 Aug 2023", "name": "Camelia Rohani", "expertise": [ "Reviewer Expertise Sense of coherence", "Spirituality", "Quality of Life" ], "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 review of the article with the title of 'Perceptions of professional nurses towards the inclusion of spiritual activities in oncology practice in the uMgungundlovu and eThekwini Health Districts, KwaZulu-Natal, South Africa: A quantitative descriptive study.' This is a descriptive study and authors registered 89 oncology nurses to explore their perceptions about integration of spirituality care in the caring of cancer patients. They analysed the data only by mean and standard deviations.\n\nThank you for this opportunity to read this descriptive article. There are several important issues:\nTitle is very long. I suggest removing the names of the places and just writing 'two health districts in South Africa'. Furthermore, the word “quantitative” should be removed, only mention: 'a descriptive study'.\n\nAbstract: Authors wrote that: “Four health care institutions were purposively selected in the eThekwini and uMgungundlovu health district”. Please remove the word \"purposively\" and then in the Methods section explain the reason for choosing two places for the current study.\n\nAbstract: The name of the questionnaires should be written here.\n\nAbstract - Methods section: Authors should write what the hypothesis of the study was (not hypothesis of the researcher) and then write whether it is accepted or not.\n\nMethods: In the Methods section, it is better to have a short explanation about the healthcare system of South Africa and then explain why the authors chose four different places for data collection.\n\nMethods: It seems that this is a descriptive study with cross-sectional design.\n\nMethod: How did the authors do their sampling? How did they know 89 participants were enough for this study? Which formula did they use? This number is not enough for a descriptive study. How many subjects did they recruit from each place? Inclusion and exclusion criteria should be written in detail. How did the authors approach participants?\n\nStudy instrument: The original language of the Spiritual Care Rating Scale was English. Was it translated for this study or used in the original language?\n\nStudy instrument: \"This five-point Likert scale includes 17 items and three subdivisions viz. (i) spirituality and spiritual healing. (ii) Religiosity and (iii) personal care. According to Mc Sherry et al10 the SSCRS tool consists of four domains….” What does it mean? Questionnaire has four domains and three subdivisions? It is not clear, please explain.\n\nStudy instrument: The number of four nurses is not enough for confirmation of the validity and reliability of the study. You need minimum 30 subjects, at least such as a pilot study.\n\nStudy instrument: “The questionnaire was tested for validity and reliability. Construct validity ensures that the questionnaire measures accurately what it is supposed to measure.11” Reference number 11 is a book (Nursing research, 2017), but how is it about the questionnaire that the authors used in this study? Did they measure construct validity of the questionnaire?\n\nHow was the scoring of the questionnaire?\n\nI read the questionnaire in the supplementary file. This is not compatible with the original one? It has only 13 questions and not in five Likert-scales! I think the word \"oncology\" has been added to the \"nurse\" in the questionnaire, and also the phrase \"I believe\" has been removed from the original version. Demographic questionnaire is not complete, some variables such as age and education level are missing. How is it about other related variables which could help the study results? Also, how can professional nurses work for more than 40 years? Is it right?\n\nThe study has only descriptive analysis (mean and standard deviation). It is not enough for a descriptive study and can not answer the study hypothesis.\n\nAuthors used SRQR as a guide for writing. This is a checklist for qualitative study not quantitative.\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?\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? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-389

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