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https://f1000research.com/articles/12-1282/v1	06 Oct 23	{ "type": "Research Article", "title": "Corticosteroids and invasive fungal infections in hospitalized COVID-19 patients – A single-center cross-sectional study", "authors": [ "Venkateswaran Ramanathan", "Hariswar Pari Thenmozhi", "Rakesh Singh", "Srinivasan Bheemanathi Hanuman", "Subathra Adithan", "Venkateswaran Ramanathan", "Rakesh Singh", "Srinivasan Bheemanathi Hanuman", "Subathra Adithan" ], "abstract": "Background: During the coronavirus disease 2019 (COVID-19) epidemic, an increase in the incidence of fungal infections was observed. However, the real magnitude of these fungal infections and their risk factors among COVID-19 patients in the Indian population is unknown. Aim: To study the frequency, and spectrum of invasive fungal infections (IFI) among hospitalized COVID-19 patients, and the risk factors associated with invasive fungal infections. Methods: We performed a retrospective, cross-sectional study; including all adult patients, admitted to Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), a tertiary care hospital in Southern India between April 2020 and August 2021, with COVID-19. Based on clinical-radiological features, patients with fungal infections were grouped into three diagnostic categories. Demographics, clinical, and laboratory features of patients with fungal infections were analyzed to identify the risk factors. Results: About 10% (449 out of 4650) of the admitted patients with recent COVID-19, had some form of IFI. Among the patients with IFI, 80% (366 out of 449) were hospitalized for active COVID-19, whereas almost all the patients admitted with post-COVID complications had IFI. Of the 449 patients with IFI, 377 had mold infections and 88 had invasive candidiasis. Mucormycosis was the most common mold infection. Diabetes and diabetic ketoacidosis were strong independent predictors of IFI. We also found an association between end-stage renal disease, central venous catheterization, antibiotic usage, prior stroke, and corticosteroid therapy with IFI. Conclusions: The frequency of fungal infections among hospitalized COVID-19 patients was high. Special precautions in COVID-19 patients with diabetes mellitus, corticosteroid therapy, and prior antibiotic usage may help to reduce invasive fungal infections.", "keywords": [ "COVID-19", "Invasive fungal infections", "Mucormycosis", "Corticosteroids" ], "content": "Introduction\n\nWhen the epidemic of coronavirus disease 2019 (COVID-19) started, therapeutic options were few and were purported with no evidence. With platform trials, several agents were tried, and corticosteroid therapy was found to be beneficial in a subset of COVID-19 patients who had severe illness-causing hypoxia and not across the entire spectrum of severity.1 It helped us to buttress the hypothesis that corticosteroids mitigate the detrimental effect of exuberant inflammatory response-related morbidity and mortality. However, the patient population included in these platform trials was predominantly from the Western world.\n\nHaving established the role of corticosteroids in severe COVID-19 infection, dexamethasone therapy became the standard of care for all hypoxic COVID-19 patients across the world. In India, while the use of corticosteroids was not routine in the first wave of COVID-19, corticosteroid therapy became a standard of care for the management of hospitalized COVID-19 patients during the second wave as evidence from RECOVERY trial was available by then.1 Being familiar, cheap, and the first drug to show evidence of survival benefit, corticosteroid therapy was welcomed with a lot of enthusiasm. Soon after, in India, several case reports of invasive fungal infections in COVID-19 patients emerged during the second wave. Though corticosteroid therapy was quite beneficial in the Western world, in the Indian population, the real extent of benefit which is probably offset by the increased risk of fungal infections, is not known. Unless the real extent of the benefit of corticosteroid therapy is ascertained in Indian patients, clinicians may tend to use corticosteroids in off-label indications like non-COVID ARDS also.\n\nThere are several reasons for the possible increase in the incidence of fungal infections among Indian patients with COVID-19. Indian people are more susceptible than the Western population to diabetes as indicated by the Y-Y paradox.2,3 Hence, it is possible that corticosteroid therapy, by producing hyperglycemia in non-diabetics, may increase the incidence of fungal infections. Though debatable, other causes like the unscrupulous use of high-dose corticosteroids, climatic conditions favoring fungal spore dissemination, genetic susceptibility, and poor blood sugar control may be leading to an increased incidence of fungal infections in India, especially mucormycosis.\n\nThough at the outset it appeared as if the corticosteroid therapy increased the incidence of fungal infections in India,4,5 we are uncertain about the actual frequency of fungal infections and their risk factors in these Indian patients with COVID-19. There are very few studies from India showing the type of fungal infections. Hence, we undertook the study to determine the frequency of invasive fungal infections in hospitalized COVID-19 patients from India. We also studied the spectrum of fungal infections, the risk factors of fungal infections, and their clinical outcomes in hospitalized COVID-19 patients.\n\n\nMethods\n\nStudy design: We performed a single center, retrospective, cross-sectional analytical study, among patients admitted at a tertiary care hospital at Pondicherry (JIPMER) between April 1st, 2020, to August 31st, 2021.\n\nStudy participants: We defined a patient to have recent COVID-19 if they had tested positive for COVID-19 by RT-PCR/Antigen detection test either at admission or within 90 days of hospital admission. From our hospital electronic health records (EHR), all patients aged 13 and above hospitalized at JIPMER during the study period were identified using a structured query language (SQL) based query. These patients were screened for recent COVID-19 reports, and patients who had recent COVID-19 were included in the study. Patients with either unavailable clinical data or COVID-19 reports were excluded.\n\nEthical statement: The study protocol was reviewed and approved by the Institute Ethics Committee (Human Studies) of Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry (DHR REG.NO.EC/NEW/INST/2020/331). A waiver of Informed consent was approved by the Institute Ethics Committee (Human Studies).\n\nSample size estimation: Based on prior studies,6 the frequency of IFI among hospitalized COVID-19 patients was assumed to be 15%, with an error margin of 5%, with a level of significance at 0.05, the sample size estimated was 196 patients. Our study is a retrospective case record-based study and included all patients who met the selection criteria.\n\nStudy procedure: We had complete access to our hospital EHR, from which, all patients admitted during the study period were identified, and screened for COVID-19 reports. The data from EHR was exported in CSV format and cleaned using the software OpenRefine (version 3.6.2, for Microsoft Windows 11). For patients who had recent COVID-19, baseline characteristics including comorbidities and severity of COVID-19 illness, requirement for ICU admission, treatment details, duration of hospital stay, and clinical outcome at discharge were collected. Fungal culture, and histopathological biopsy reports were noted. In patients who underwent computed tomography based on clinical suspicion, image findings suggestive of fungal etiology were analyzed. Based on the European Organization for Research and Treatment of Cancer (EORTC) guidelines,7,8 which were modified accordingly for COVID-19 patients (see Extended data34), these patients were then categorized to have Possible, Probable or Proven Invasive fungal infection. For the study purpose, patients who had more than one group of IFI were classified as belonging to the IFI group with the highest category of likelihood. Clinical and laboratory data of patients with fungal infection were analyzed to identify the predictors of fungal infection among hospitalized COVID-19 patients.\n\nStatistical analysis: The data were compiled using Microsoft Excel and analyzed using SPSS version 19.0 (SPSS for Windows, version 19.0, Chicago, SPSS Inc.) and R software (version 3.3.1, R Foundation for Statistical Computing). Categorical variables were expressed as percentages and frequencies, and continuous variables were reported as mean and standard deviation or median with the interquartile range. Categorical variables were compared by Chi-square test. The strength of association was expressed as odds ratios. Normality was assessed by the Kolmogorov-Smirnov test. To compare continuous normally distributed data, the two-tailed unpaired t-test was used. All tests were two-sided, and P<0.05 was considered statistically significant. Before performing multivariable analysis, we reduced the dimensions of the variables by multiple correspondence analysis. We found collinearity between the predictors 'corticosteroid and heparin' as well as 'diabetes mellitus and hypertension'. Considering biological plausibility, we chose corticosteroids and diabetes mellitus as predictors from each of the clusters for further analysis. We observed a similar clustering between 'end-stage renal disease (ESRD) and central venous catheter (CVC) usage'. We included both ESRD and CVC for the invasive fungal infection group and removed CVC for the subgroup analysis involving invasive mold infection. Multivariable logistic regression using Enter method was performed to identify the predictors.\n\n\nResults\n\nDuring the study period, there were 69792 admissions, and 4650 patients had a history of recent COVID-19 (including patients admitted for COVID-19 and post-COVID-19 patients), among them, 4565 patients were hospitalized for active COVID-19 and 85 patients were admitted with post-COVID-19 complications.33 These post-COVID patients had received treatment for COVID-19 elsewhere and were hospitalized at JIPMER for post-COVID sequelae (Figure 1).\n\nAmong the hospitalized patients, who had recent COVID-19 (n=4650), the median age was 50 years (interquartile range [IQR], 35 to 62), with 27% of patients aged above 60 years; 59% were male. The most common comorbid illness in these patients was diabetes mellitus (31%) followed by systemic hypertension (25%), chronic cardiac disease (8%), and chronic kidney disease (6.7%). Recent immunosuppressive therapy (corticosteroid or other immunosuppressants) was present in 113 patients (2.4%) (Table 1).\n\na Patients with possible, probable, or proven IFI.\n\nb Includes patients with diabetic ketoacidosis and steroid-induced hyperglycemia.\n\nc Includes ESRD patients who have received renal transplant.\n\nd Includes patients with congenital heart disease, coronary artery disease, and rheumatic heart disease.\n\ne Patients with a history of cerebrovascular patient in the past.\n\nf Both active and recently treated malignancy.\n\nAmong the patients admitted with active COVID-19 (n=4565), 1283 patients (28%) had severe illness at admission, with 85 patients (1.9%) requiring mechanical ventilation at admission and 870 patients (19%) requiring admission to intensive care during their hospital stay. Corticosteroids were used in 2014 patients (44%), remdesivir was given to 448 patients (9.8%), and 26 patients received tocilizumab (0.6%). Many of the patients with COVID-19, also received antibiotics (42%), and 10% of the patients received more than three antibiotics during their hospital stay (Table 2).\n\na Before the development of Invasive Fungal infection.\n\nb Severe COVID-19 according to WHO 10-point ordinal scale (Score of 6 or more).\n\nc Includes hemodialysis catheter.\n\nd Includes low molecular weight heparin and unfractionated heparin.\n\ne Multiple antibiotic therapy was defined as usage of ≥ 3 antibiotics of different class either concurrently or sequentially.\n\nOf the 4650 hospitalized patients with recent COVID-19 infection, 449 (9.7%) had an invasive fungal infection (Figure 1). Among those admitted for active COVID-19, 366 (8%) developed an invasive fungal infection during their hospital stay, whereas 83 out of 85 post-COVID-19 patients had an invasive fungal infection. The number of patients with proven or probable invasive fungal infections was 48.2 per 1000 COVID-19 patients.\n\nThe most common invasive fungal infections were due to mold infections (Mucorales & Aspergillus) occurring in 377 patients, followed by candidiasis (n=88). Out of 4650 patients, proven or probable mold infection occurred in 139 (3.0%) patients, among them 127 (91%) patients had mucormycosis and 36 (26%) had aspergillosis. Radiological evidence of pulmonary mold infection was present in 173 patients. In patients with mucormycosis, rhino-nasal or rhino-orbital-cerebral presentation (96.1%) was the most common presentation, followed by disseminated infection (3.9%), whereas among patients with isolated aspergillosis, pulmonary aspergillosis (67%) was common than rhino-nasal presentation (33%). Invasive candidiasis occurred in 88 patients, with positive fungal blood culture in 64 (73%) patients. Non-Albicans spp. (n=59) were more common than Candida albicans (n=7) (Table 3).\n\na Includes patients with proven, probable, and patients with radiological evidence of IFI.\n\nb Includes patients with coinfection with both molds and candidiasis isolated by fungal culture or by histopathological examination of infected tissue.\n\nc Patients with candidemia.\n\nd Including Candida auris.\n\nAfter adjusting for confounding by multivariable logistic regression, diabetes, diabetic ketoacidosis, prior stroke, steroid usage, and central venous catheter usage were found to be independent predictors of IFI in patients with active COVID-19 (i.e., after excluding patients admitted for post-COVID sequelae). Diabetic ketoacidosis was the most important predictor (odds ratio, 3.31; 95%CI, 1.93 to 5.58). As compared to the risk of IFI among patients who received dexamethasone, the risk of IFI in patients who received methylprednisolone was 2.82 (95%CI, 2.07 to 3.85). In the subgroup of invasive mold infections diabetes, diabetic ketoacidosis, steroid usage, antibiotic usage, and chronic kidney disease were identified as independent predictors and prior stroke did not show an association (Table 4, 5).\n\n* P < 0.001.\n\n† P =0.057.\n\n‡ P =0.003.\n\n§ P =0.013.\n\n* P < 0.001.\n\n† P =0.001.\n\n‡ P =0.037.\n\n§ P =0.008.\n\nCompared to patients without IFI, patients with IFI had a longer duration of hospital stay (8 days vs 14 days, P <0.001), and the in-hospital mortality was more in the IFI group (21.2 vs 41.0%, P<0.001) (Table 6).\n\n* Mann–Whitney U test.\n\n\nDiscussion\n\nAt a global scale, both the absolute incidence of IFI as well as its geographical extent are increasing probably secondary to changing climatic conditions, ease of international travel, increased antifungal use, and frequent immunosuppression.9 Recently, the World Health Organization has enlisted several fungal infections as a major threat to public health.10 In the Indian context, even though IFI is associated with significant morbidity and mortality in hospitalized and immunocompromised patients, the real magnitude of IFI remains largely unknown. In India, during the second wave of COVID-19, there was a sudden increase in the number of IFI cases among COVID-19 patients. Numerous risk factors, such as corticosteroid therapy, diabetes mellitus, climatic conditions favoring fungal spread, genetic predisposition for developing IFI, and COVID-19 per se were implicated in such occurrences.11,12 A recent systematic review found that around 4.1% of Indians have some form of fungal infection and the occurrence of mucormycosis was 70 to 80-fold higher in India compared to Western countries.13–16 In our study, we found about 8% of the hospitalized COVID patients to have IFI and 60 out of 4565 patients (13 per 1000) hospitalized for COVID-19 to have mucormycosis, which are higher than that of previous estimates and the Western population.9,16\n\nInvasive mold infections were present in around 8% of our patients hospitalized with recent COVID-19. While it has been established that pulmonary mold infections are associated with immunosuppression, the rhino-orbital form has previously shown an association with both corticosteroids and hyperglycemia.17 In our patients hospitalized for COVID-19, both rhino-orbital and pulmonary invasive mold infections were common, whereas, among patients hospitalized with post-COVID-19 complications, the rhino-orbital form was more common. The difference could be due to two possible explanations. Firstly, all of our post-COVID-19 patients were previously treated for active COVID-19 in outside hospitals, wherein the possible use of unwarranted and higher than the recommended dose of corticosteroids cannot be ruled out. Both high-dose corticosteroids and related hyperglycemia might have contributed to predominant rhino-orbital mucormycosis in this post-COVID-19 group. Secondly, in this subset of post-COVID-19 patients, early mortality compounded by the difficulty in the detection of pulmonary mold infections might have led to a lesser number of patients with pulmonary presentations among this group. Among patients hospitalized with recent COVID-19, 1.9% had invasive candidiasis. Non-albicans spp. of candida were the predominant species causing candidemia and alarmingly, Candida auris constituted one-third of the entire isolates causing candidemia.\n\nWe found that both diabetes mellitus (adjusted OR, 2.06; 95%CI, 1.62 to 2.62) and diabetic ketoacidosis (adjusted OR, 3.31; 95%CI, 1.93 to 5.58) were associated with invasive fungal infections. Hyperglycaemia causes defective chemotaxis, phagocyte dysfunction, and impaired intracellular killing of fungi.18,19 In addition, the acidosis seen in ketoacidosis and CKD has been shown to predispose to mucormycosis.20–22 We also found corticosteroids to be associated with invasive fungal infections (adjusted OR, 1.39; 95%CI, 1.07 to 1.81). Steroids predispose fungal infections by causing phagocyte dysfunction and hyperglycemia. We found no association between the occurrence of invasive fungal infections and other immunosuppressive states, however, the numbers were small. About 40% of patients admitted for COVID-19 received antibiotics during their hospital stay before the development of IFI and it was associated with IFI (adjusted OR, 1.65; 95%CI, 1.27 to 2.14). Exposure to antibiotics can disrupt the commensal flora and can predispose to IFI.23\n\nPrior stroke, which has not been shown to be associated with fungal infections, emerged as an independent predictor of IFI (adjusted OR, 2.23; 95%CI, 1.28 to 3.72). Longer duration of hospital stay, a known risk factor for the development of Candida infections,24,25 is probably responsible for increased candidiasis in these patients with stroke. Both CVC usage (adjusted OR, 2.23; 95%CI, 1.28 to 3.72) and ESRD (adjusted OR, 2.23; 95%CI, 1.28 to 3.72) are known risk factors for invasive candidiasis and invasive mold infections, respectively. Unlike other studies, we did not find any association between sex, age, and severity of COVID-19.9,26,27 As expected, we found poor outcomes associated with IFI. The number of patients studied, and the proportion of patients with diabetes mellitus and end-stage renal disease in our study were similar to the RECOVERY trial. The dose of corticosteroids used were also similar.1 However, the incidence of IFI was higher among our patients. This may be interpreted as a unique susceptibility of Indians to invasive fungal infections and may be due to the high baseline risk of diabetes mellitus,28 and environmental and probable genetic factors.13,29–31\n\nOur institute being one of the COVID care centres, catered to a large population during the epidemic. Thus, despite being a single-center study, we have included a large patient population. To make the study reliable, we have included only those patients with laboratory confirmation of COVID-19. Extensive workup (microbiological, histopathological, and radiological investigations) was done on every patient in whom IFI was suspected to classify based on EORTC guidelines for IFI. In our institute there was no routine screening of patients for fungal colonization was not done as it is not a recommended practice and hence exact prevalence of colonization/infection of IFI could not be estimated in this retrospective case record-based study. Possible confounding due to poor socioeconomic status, drug therapy before hospitalization, seasonal and environmental factors could not be adjusted for.\n\nWhile there is no doubt that higher than the recommended dose or unwarranted use of corticosteroids in COVID needs to be avoided, the possibility that corticosteroid directly or indirectly by inducing hyperglycemia, poses an increased risk of IFI in the Indian population needs to be borne in mind before extrapolating the use of corticosteroid in severe COVID as per Western recommendations. Recently hydrocortisone has shown mortality benefits in severe community-acquired pneumonia.32 Given the high prevalence of IFI in the Indian population especially in the context of steroid usage, extreme caution has to be observed in extrapolating the above findings in the Indian population. This is one of the important implications of our study findings. In the Indian population, the benefits of corticosteroid therapy shown in clinical trials for various indications conducted in Western countries may be offset by fungal infections and may not be applicable. Due caution needs to be exercised before extending corticosteroid use in the Indian population.\n\nThe occurrence of IFI is higher in Indian COVID-19 patients as compared to the Western population. Corticosteroids appear to be a significant predictor of IFI, and methylprednisolone appears to have a slightly higher risk than dexamethasone. We also found that diabetes mellitus, diabetic ketoacidosis, end-stage renal disease, and central venous catheterization as independent risk factors of IFI. Corticosteroid use, though shown to be beneficial, the increased incidence of IFI in the Indian population may negate the beneficial efforts of corticosteroids in the Indian population. To reduce the risk of IFI, we recommend adherence to the rational use of corticosteroids and antibiotics, along with monitoring of serum glucose levels.", "appendix": "Data availability\n\nFigshare: Invasive Fungal Infections in Patients with Recent COVID-19. https://doi.org/10.6084/m9.figshare.24014898.v2. 33\n\nFigshare: Supplementary figure: Modified EORTC based definitions of invasive fungal infections used in the study. https://doi.org/10.6084/m9.figshare.24156471.v1. 34\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nDexamethasone in Hospitalized Patients with Covid-19. N. Engl. J. Med. 2021 Feb 25; 384(8): 693–704. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYajnik CS, Yudkin JS: The Y-Y paradox. Lancet. 2004 Jan; 363(9403): 163. PubMed Abstract \| Publisher Full Text\n\nMohan V: Why are Indians more prone to diabetes? J. Assoc. Physicians India. 2004 Jun; 52: 468–474. PubMed Abstract\n\nChowdhary A, Tarai B, Singh A, et al.: Multidrug-Resistant Candida auris Infections in Critically Ill Coronavirus Disease Patients, India, April–July 2020. Emerg. Infect. Dis. 2020 Nov; 26(11): 2694–2696. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNawaz FA, Yaqoob S, Sharma A, et al.: From black to white: A roadmap to containing the rise of candidiasis amidst COVID-19 and mucormycosis in India. Clin. Epidemiol. Glob. Health. 2021; 12: 100917. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSindhu D, Jorwal P, Gupta N, et al.: Clinical spectrum and outcome of hospitalized patients with invasive fungal infections: a prospective study from a medical ward/intensive care unit of a teaching hospital in North India. Infez. Med. 2019 Dec 1; 27(4): 398–402. PubMed Abstract\n\nBassetti M, Azoulay E, Kullberg BJ, et al.: EORTC/MSGERC Definitions of Invasive Fungal Diseases: Summary of Activities of the Intensive Care Unit Working Group. Clin. Infect. Dis. 2021 Mar 12; 72(Supplement_2): S121–S127. Publisher Full Text\n\nDe Pauw B, Walsh TJ, Donnelly JP, et al.: Revised Definitions of Invasive Fungal Disease from the European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases Mycoses Study Group (EORTC/MSG) Consensus Group. Clin. Infect. Dis. 2008 Jun 15; 46(12): 1813–1821. PubMed Abstract \| Publisher Full Text\n\nGold JAW, Adjei S, Gundlapalli AV, et al.: Increased Hospitalizations Involving Fungal Infections during COVID-19 Pandemic, United States, January 2020–December 2021. Emerg. Infect. Dis. 2023 Jul [cited 2023 Jun 19]; 29(7): 1433–1437. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nWHO fungal priority pathogens list to guide research, development and public health action.[cited 2023 May 15]. 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Microbiol. Infect. 2019 Jan 1; 25(1): 26–34. PubMed Abstract \| Publisher Full Text\n\nPrakash H, Chakrabarti A: Epidemiology of Mucormycosis in India. Microorganisms. 2021 Mar 4; 9(3): 523. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlqarihi A, Gebremariam T, Gu Y, et al.: GRP78 and Integrins Play Different Roles in Host Cell Invasion during Mucormycosis. MBio. 2020 Jun 2; 11(3): e01087–e01020. Publisher Full Text\n\nBerbudi A, Rahmadika N, Tjahjadi AI, et al.: Type 2 Diabetes and its Impact on the Immune System. Curr. Diabetes Rev. 2020; 16(5): 442–449.\n\nGeerlings SE: Clinical Presentations and Epidemiology of Urinary Tract Infections. Microbiol Spectr. 2016 Oct; 4(5). Publisher Full Text\n\nBoelaert JR, Fenves AZ, Coburn JW: Deferoxamine therapy and mucormycosis in dialysis patients: report of an international registry. Am. J. Kidney Dis. 1991 Dec; 18(6): 660–667. PubMed Abstract \| Publisher Full Text\n\nDalili N: An End-Stage Renal Disease Patient with Invasive Fungal Rhinosinusitis. Arch. Clin. Nephrol. 2017 Jan 23; 004–006. Publisher Full Text\n\nBaldin C, Ibrahim AS: Molecular mechanisms of mucormycosis—The bitter and the sweet. Sheppard DC, editor. PLoS Pathog. 2017 Aug 3; 13(8): e1006408. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRamirez J, Guarner F, Bustos Fernandez L, et al.: Antibiotics as Major Disruptors of Gut Microbiota. Front. Cell. Infect. Microbiol. 2020 Nov 24; 10: 572912. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhang Z, Zhu R, Luan Z, et al.: Risk of invasive candidiasis with prolonged duration of ICU stay: a systematic review and meta-analysis. BMJ Open. 2020 Jul 12; 10(7): e036452. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKourkoumpetis TK, Velmahos GC, Ziakas PD, et al.: The Effect of Cumulative Length of Hospital Stay on the Antifungal Resistance of Candida Strains Isolated from Critically Ill Surgical Patients. Mycopathologia. 2011 Feb; 171(2): 85–91. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEgger M, Hoenigl M, Thompson GR, et al.: Let’s talk about sex characteristics—As a risk factor for invasive fungal diseases. Mycoses. 2022 Jun; 65(6): 599–612. PubMed Abstract \| Publisher Full Text\n\nKauffman CA: Fungal Infections in Older Adults. Clin. Infect. Dis. 2001 Aug 15; 33(4): 550–555. Publisher Full Text\n\nChan JCN, Malik V, Jia W, et al.: Diabetes in Asia: Epidemiology, Risk Factors, and Pathophysiology. JAMA. 2009 May 27; 301(20): 2129. Publisher Full Text\n\nSkaria J, John TM, Varkey S, et al.: Are Unique Regional Factors the Missing Link in India’s COVID-19-Associated Mucormycosis Crisis? MBio. 2022 Mar 31; 13(2): e00473–e00422. Publisher Full Text\n\nPourazizi M, Eshraghi B, Azad R, et al.: Father–Son COVID-19-associated mucormycosis: Important role of genetic susceptibility in combination with environmental factors. Clinical Case Reports. 2022; 10(9): e6312. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNaik B, Ahmed SMQ, Laha S, et al.: Genetic Susceptibility to Fungal Infections and Links to Human Ancestry. Front. Genet. 2021 [cited 2023 May 16]; 12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHydrocortisone in Severe Community-Acquired Pneumonia\|NEJM.[cited 2023 May 17]. Reference Source\n\nPari Thenmozhi H, Ramanathan V, Singh R, et al.: Invasive Fungal Infections in Patients with Recent COVID-19. [Dataset]. figshare. 2023. Publisher Full Text\n\nPari Thenmozhi H: Supplementary information (Definitions). figshare. Figure. 2023. Publisher Full Text" }	[ { "id": "251702", "date": "29 Mar 2024", "name": "Prateek Nishant", "expertise": [ "Reviewer Expertise Ophthalmology", "public health", "nanotechnology" ], "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\nCorticosteroids and invasive fungal infections in hospitalized COVID-19 patients – A single-center cross-sectional study: the authors have provided a retrospective analysis of patients admitted during the COVID-19 pandemic and evaluated the association of invasive fungal infections (IFI) with demographic, clinical, and laboratory features of the patients.\nHere are my comments: 1. \"When the epidemic of coronavirus disease 2019 (COVID-19) started, therapeutic options were few and were purported with no evidence.\" Consider revising. 2. \"Though corticosteroid therapy was quite beneficial in the Western world.,,\" Provide a reference showing real-world evidence, or consider revising. 3. \"the unscrupulous use of high-dose corticosteroids...\" and \"Unless the real extent of the benefit of corticosteroid therapy is ascertained in Indian patients, clinicians may tend to use corticosteroids in off-label indications like non-COVID ARDS also.\" Provide references showing real-world evidence, or consider revising. 4. \"Recent immunosuppressive therapy (corticosteroid or other immunosuppressants) was present in\" consider revising. 5. Expand RO, ROC, RC in table 3 6. Sections of the text are repeating the data provided in the table, making it unnecessarily long. Consider revising. 7. \"Among those admitted for active COVID-19, 366 (8%) developed an invasive fungal infection during their hospital stay...\" Do we have information on the association of the severity of illness at presentation with the time interval of onset and causative organism of the IFI? If yes, kindly include this analysis. If not, kindly mention it as a limitation of this report. 8. State the abbreviation IMI from table 5 in the text prior to the table 9. \"There are several reasons for the possible increase in the incidence of fungal infections among Indian patients with COVID-19. Indian people are more susceptible than the Western population to diabetes as indicated by the Y-Y paradox.2,3 Hence, it is possible that corticosteroid therapy, by producing hyperglycemia in non-diabetics, may increase the incidence of fungal infections. Though debatable, other causes like the unscrupulous use of high-dose corticosteroids, climatic conditions favoring fungal spore dissemination, genetic susceptibility, and poor blood sugar control may be leading to an increased incidence of fungal infections in India, especially mucormycosis.\" Consider migrating to discussion section, as well as shortening the paragraph as it does not add much information to what is already known. 10. \"Among patients hospitalized with recent COVID-19, 1.9% had invasive candidiasis. Non-albicans spp. of candida were the predominant species causing candidemia and alarmingly, Candida auris constituted one-third of the entire isolates causing candidemia.\" Avoid repeating results in the discussion section and provide context in the light of which these findings are relevant to the subject matter. The phrase \"causing candidemia\" need not be repeated. 11. Kindly refer to COVID-19 as a pandemic and IFI during COVID-19 as an epidemic. 12. \"Extensive workup (microbiological, histopathological, and radiological investigations) was done on every patient in whom IFI was suspected to classify based on EORTC guidelines for IFI.\" While this is a strength of the study, the implications of this exercise have not been elucidated. 13. It would be helpful to analyse levels of inflammatory markers for risk stratification. 14. The conclusion that \"methylprednisolone appears to have a slightly higher risk than dexamethasone\" needs to be substantiated further in the results. 15. \"In the Indian population, the benefits of corticosteroid therapy shown in clinical trials for various indications conducted in Western countries may be offset by fungal infections and may not be applicable. Due caution needs to be exercised before extending corticosteroid use in the Indian population.\" ... \"Corticosteroid use, though shown to be beneficial, the increased incidence of IFI in the Indian population may negate the beneficial efforts of corticosteroids in the Indian population. To reduce the risk of IFI, we recommend adherence to the rational use of corticosteroids and antibiotics, along with monitoring of serum glucose levels.\" This is apparently the key message of the manuscript, but it does not add anything to the existing literature.\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": [ { "c_id": "11554", "date": "23 Sep 2024", "name": "Hariswar Pari Thenmozhi", "role": "Author Response", "response": "Reviewer Comment: 1. \"When the epidemic of coronavirus disease 2019 (COVID-19) started, therapeutic options were few and were purported with no evidence.\" Consider revising. Author Response: We have revised it as ‘when the pandemic of coronavirus disease 2019 (COVID-19) started, therapeutic options were unavailable and many were recommended without robust evidence’. Reviewer Comment: 2. \"Though corticosteroid therapy was quite beneficial in the Western world.,,\" Provide a reference showing real-world evidence, or consider revising. Author Response: We have revised it as \"Though corticosteroid therapy was quite beneficial, in the Indian population, the real extent of benefit which is probably offset by the increased risk of fungal infections, is not known.\" We have removed the comparison with the Western world. Reviewer Comment: 3. \"the unscrupulous use of high-dose corticosteroids...\" and \"Unless the real extent of the benefit of corticosteroid therapy is ascertained in Indian patients, clinicians may tend to use corticosteroids in off-label indications like non-COVID ARDS also.\" Provide references showing real-world evidence, or consider revising. Author Response: We have revised it as “Though debatable, other causes like the possible overuse of high-dose corticosteroids, climatic conditions favoring fungal spore dissemination, genetic susceptibility, and poor blood sugar control may be leading to an increased incidence of fungal infections in India, especially mucormycosis”. We have removed the statement “Unless the real extent of the benefit of corticosteroid therapy is ascertained in Indian patients, clinicians may tend to use corticosteroids in off-label indications like non-COVID ARDS also”. Reviewer Comment: 4. \"Recent immunosuppressive therapy (corticosteroid or other immunosuppressants) was present in\" consider revising. Author Response: We have revised it as “Ongoing immunosuppressive therapy (corticosteroid or other immunosuppressants) for other indications was present in 113 patients (2.4%) (Table 1)”. Reviewer Comment: 5. Expand RO, ROC, RC in table 3 Author Response: We have made the suggested changes in the table 3. Reviewer Comment: 6. Sections of the text are repeating the data provided in the table, making it unnecessarily long. Consider revising. Author Response: We have revised the Results section as suggested. Reviewer Comment: 7. \"Among those admitted for active COVID-19, 366 (8%) developed an invasive fungal infection during their hospital stay...\" Do we have information on the association of the severity of illness at presentation with the time interval of onset and causative organism of the IFI? If yes, kindly include this analysis. If not, kindly mention it as a limitation of this report. Author Response: We do not have the adequate information on the time interval of onset. Hence, we have included it as a limitation of the study. We have included the following statement “Also, data pertaining to time interval of onset of COVID-19 is not available, its association with severity of illness could not be explored.” Though we have provided the analysis pertaining to the association of severity and organism, we could not stratify based on time interval since onset of COVID-19. Reviewer Comment: 8. State the abbreviation IMI from table 5 in the text prior to the table Author Response: The expansion ‘Invasive mold infections’ to the abbreviation IMI is added within the text prior to table 5. Reviewer Comment: 9. \"There are several reasons for the possible increase in the incidence of fungal infections among Indian patients with COVID-19. Indian people are more susceptible than the Western population to diabetes as indicated by the Y-Y paradox.2,3 Hence, it is possible that corticosteroid therapy, by producing hyperglycemia in non-diabetics, may increase the incidence of fungal infections. Though debatable, other causes like the unscrupulous use of high-dose corticosteroids, climatic conditions favoring fungal spore dissemination, genetic susceptibility, and poor blood sugar control may be leading to an increased incidence of fungal infections in India, especially mucormycosis.\" Consider migrating to discussion section, as well as shortening the paragraph as it does not add much information to what is already known. Author Response: We have moved the elaborate justification for the study to the Discussion section. Reviewer Comment: 10. \"Among patients hospitalized with recent COVID-19, 1.9% had invasive candidiasis. Non-albicans spp. of candida were the predominant species causing candidemia and alarmingly, Candida auris constituted one-third of the entire isolates causing candidemia.\" Avoid repeating results in the discussion section and provide context in the light of which these findings are relevant to the subject matter. The phrase \"causing candidemia\" need not be repeated. Author Response: We have removed the results that have been repeated in the discussion section. We have removed the following statement “Among patients hospitalized with recent COVID-19, 1.9% had invasive candidiasis.” We have removed the phrase \"causing candidemia\". Reviewer Comment: 11. Kindly refer to COVID-19 as a pandemic and IFI during COVID-19 as an epidemic. Author Response: We have corrected the term epidemic to pandemic. Reviewer Comment: 12. \"Extensive workup (microbiological, histopathological, and radiological investigations) was done on every patient in whom IFI was suspected to classify based on EORTC guidelines for IFI.\" While this is a strength of the study, the implications of this exercise have not been elucidated. Author Response: The likelihood of IFI is categorised into three levels based on EORTC guidelines. The major implication of this exercise is in case definition. This would help the readers to appreciate the certainty with which the diagnosis of IFI was made. We do not see any other implications to be mentioned in the article. Reviewer Comment: 13. It would be helpful to analyse levels of inflammatory markers for risk stratification. Author Response: Inflammatory markers were not measured routinely. Since, this is a case record based retrospective study, inflammatory markers could be retrieved for less than 5% of the study participants. Hence, we could not analyse the levels of inflammatory markers. Reviewer Comment: 14. The conclusion that \"methylprednisolone appears to have a slightly higher risk than dexamethasone\" needs to be substantiated further in the results. Author Response: The risk of invasive fungal infections with methylprednisolone, as compared to the baseline risk of dexamethasone was estimated separately using chi-square statistics. The odds ratio can be calculated from the numbers available in Table-2. Reviewer Comment: 15. \"In the Indian population, the benefits of corticosteroid therapy shown in clinical trials for various indications conducted in Western countries may be offset by fungal infections and may not be applicable. Due caution needs to be exercised before extending corticosteroid use in the Indian population.\" ... \"Corticosteroid use, though shown to be beneficial, the increased incidence of IFI in the Indian population may negate the beneficial efforts of corticosteroids in the Indian population. To reduce the risk of IFI, we recommend adherence to the rational use of corticosteroids and antibiotics, along with monitoring of serum glucose levels.\" This is apparently the key message of the manuscript, but it does not add anything to the existing literature. Author Response: In our study, we have clearly documented the frequency of invasive fungal infections in COVID-19 patients and its association with corticosteroid therapy. Though we have not estimated the extent to which fungal infection related mortality offsets the benefit of corticosteroids, we have provided a rough estimation of the burden of fungal infections among hospitalised patients. The estimate of mortality related to fungal infections would help clinicians to appreciate the complication rates, and hence be cautious of this complication and not to be over enthusiastic in the use of corticosteroid therapy." } ] } ]	1	https://f1000research.com/articles/12-1282
https://f1000research.com/articles/13-921/v1	13 Aug 24	{ "type": "Opinion Article", "title": "Key Guidelines for Responding to Reviewers", "authors": [ "Saida Hidouri", "Hela Kamoun", "Sana Salah", "Anis Jellad", "Helmi Ben Saad", "Saida Hidouri", "Hela Kamoun", "Sana Salah", "Anis Jellad" ], "abstract": "Background The process of preparing a scientific manuscript is intricate, encompassing several critical stages, including pre-writing, research development, drafting, peer review, editing, publication, dissemination, and access. Among these, the peer review process (PRP) stands out as a pivotal component requiring seamless collaboration among editors, reviewers, and authors. Reviewers play a crucial role in assessing the manuscript’s quality and providing constructive feedback, which authors must adeptly navigate to enhance their work and meet journal standards. This process can often appear daunting and time-consuming, as authors are required to address numerous comments and requested changes. Authors are encouraged to perceive reviewers as consultants rather than adversaries, viewing their critiques as opportunities for improvement rather than personal attacks.\n\nMethods Opinion article.\n\nAim To equip authors with practical strategies for engaging effectively in the PRP and improving their publication acceptance rates.\n\nResults Key guidelines include thoroughly understanding and prioritizing feedback, maintaining professionalism, and systematically addressing each comment. In cases of significant disagreement or misunderstanding, authors have the option to refer the issue to the editor. Crafting a well-organized and scientific “response to reviews” along with the revised manuscript can substantially increase the likelihood of acceptance. Best practices for writing an effective response to reviews include expressing gratitude, addressing major revisions first, seeking opinions from co-authors and colleagues, and adhering strictly to journal guidelines. Emphasizing the importance of planning responses, highlighting changes in the revised manuscript, and conducting a final review ensures all corrections are properly documented.\n\nConclusion By following these guidelines, authors can enhance their manuscripts’ quality, foster positive relationships with reviewers, and ultimately contribute to scholarly advancement.", "keywords": [ "Academic publishing", "Manuscript evaluation", "Manuscript review process", "Peer assessment", "Peer review", "Research quality", "Review", "manuscript assessment", "Reviewer comments", "Revision guidelines" ], "content": "Introduction\n\nThe process of preparing a scientific manuscript involves eight fundamental steps: pre-writing, research development, drafting, editorial procedures including the peer review process (PRP), editing, publication, dissemination, and access.1–4 A successful PRP typically entails collaboration between editors, reviewers, and authors.4 Authors are responsible for conducting research, analyzing data, and writing the manuscript to present their findings clearly, accurately, and comprehensively.4 Reviewers, on the other hand, evaluate the manuscript’s quality and provide ‘constructive’ feedback.4 Their goal is to ensure that the research meets the journal’s standards and contributes significantly to the field.4 Misunderstandings between authors and reviewers can lead to the frequent rejection of high-quality submissions.4,5\n\nResponding to reviewers’ critiques is one of the most stressful phases of the publication process.4 Therefore, it is crucial to establish strategic methods for authors to handle reviewers’ feedback in alignment with ethical guidelines,6 and to provide thorough protocols for addressing diverse reviewers’ comments and principles for implementing successful revisions.7 Given that a document titled “Responses to Reviewers” is mandatory during the PRP, and recognizing that some authors may struggle with addressing reviewers’ comments, it is essential to develop authors’ skills in resubmitting research and clinical scholarship reports.8 This is critical for the effective dissemination of the authors’ work.\n\nThis opinion article aimed to equip authors with the knowledge needed to engage effectively in the PRP and improve the chances of manuscript acceptance.\n\n\nTips and advices\n\nThe PRP is a cornerstone of scientific publishing, ensuring the rigor and quality of research.4 Authors must navigate this process skillfully to enhance their manuscripts and address reviewers’ feedback.4 According to Day and Gastel,9 “Responding to reviewers’ comments is not just about defending your work; it’s about engaging in a constructive dialogue to improve the manuscript”. To help authors defend their manuscript and engage in constructive dialogue. This paper emphasizes understanding critiques, prioritizing feedback, and maintaining professionalism throughout the process.\n\nTable 1 summarizes the key guidelines and tips for responding to reviewers. The following sections describe these tips to help authors confidently address peer reviewers’ comments and move closer to publication.\n\n\nConsume reviewers’ critiques\n\nGiven that the review report is crucial for the editor’s publication decision,10 authors should:\n\ni) View feedback as a valuable opportunity to improve their work;\n\nii) Not perceive critical remarks from reviewers as personal attacks;\n\niii) Remember that reviewers are critiquing their work, not them as individuals10;\n\niv) Approach negative or major comments with a neutral and objective perspective7; leveraging them for improvement. Some frustrating or adverse comments may hold validity and significantly enhance the research,11–15 and\n\nv) Transcend feelings of frustration, sadness, and perceived unfairness.6\n\nIt is crucial that authors recognize that while the article has not been rejected, the editor has given an opportunity for revision and resubmission.4 To navigate this process effectively, the authors should advocate adhering to some general guiding principles, which are systematic review, patience and reflection, and maintain composure. First, authors should methodically examine comments, categorize them as “major” or “minor,” and store them securely. This structured approach ensures careful consideration and appropriate addressing of all feedback. Second, authors should let feedback sit for a couple of days before responding, and then avoid hastily formulating responses.7 Authors are asked to “sleep on it” before starting the revision process.13 Third, feeling overwhelmed by numerous revision suggestions is natural. However, authors should remain composed and evaluate each comment objectively. Rather than panicking, authors should approach revisions calmly and discern the value of each suggestion.13\n\n\nRead carefully and understand the reviewers’ or editor’s comments/critiques/suggestions\n\nAfter reviewing the comments, authors should:\n\ni) Carefully examine the editor’s letter and consider all remarks provided by the reviewers.7 The goal is to pinpoint the specific points emphasized and address any additional issues raised7;\n\nii) Take sufficient time to understand each comment, ensuring they grasp the reviewers’ perspective and the precise issues highlighted.7,16 If necessary, authors can break down comments into separate points7,16;\n\niii) Distinguish between positive feedback and critiques or requests for revisions7,8,17,18;\n\niv) Open the document where each reviewers’ comments are saved, number each comment, and label them accordingly, attributing each comment to the respective reviewer (e.g., Review 1, comment 1)6; and\n\nv) Evaluate whether the comments can be adequately addressed and whether the revisions align with reviewers’ expectations.16\n\nThe objective is to show the editor and reviewers a commitment to the process by meticulously addressing each comment and implementing necessary changes.\n\n\nSeek opinion\n\nThe PRP can be complex, and addressing reviewers’ comments effectively requires careful consideration and expertise.4 Consulting co-authors and colleagues well-versed in the work can provide valuable insights and perspectives that authors may not have considered on their own.15 Brainstorming with the research group can generate innovative ideas, particularly when addressing complex reviewers’ criticisms. It also helps reach a consensus on how to address the comments.7\n\n\nPrioritize feedback dealing with requests for major revisions\n\nReviewers typically structure their comments with a summary paragraph, followed by detailed constructive feedback and recommendations for refinement.10 They categorize comments as “major” or “minor”.\n\nMajor comments reflect the most concerning issues that must be revised for the paper to be considered for publication.19,20 These comments typically refer to the scientific and methodological aspects of a manuscript.4 Effectively revising and clarifying major issues is fundamental to understanding the manuscript.16,21\n\nMinor issues, while important, do not typically influence the overall conclusions of the manuscript. These may include unclear statements, missing or incorrect references, unclear data presentation, grammatical concerns, and other minor clarifications.7 Authors should make even minor requests and changes without engaging in disagreements with reviewers, even if they do not completely agree.22\n\n\nBe polite and respectful of all reviewers/express gratitude\n\nThroughout the process of responding to reviewers’ reports, authors should remember that reviewers are typically well-meaning colleagues who generously invest their time to assist authors in enhancing their study.4 Therefore, it is essential to regard their comments as constructive feedback and express gratitude for their invaluable contributions.15 Even if authors have reservations about a reviewer’s perceived understanding, it is not advisable to convey such impressions to the reviewer.13 If the reviewers encounter difficulty comprehending certain aspects, it might be due to the authors’ failure to clarify the idea sufficiently.23,24 Authors should remember that readers may vary in expertise, and some may be less experienced than the reviewers.15 Thus, the authors should ensure that their work is clear and accessible to all readers, not just experts.23 Therefore, if the reviewers do not understand certain points, it is appropriate to apologize for not making them clear and to strive to clarify them further. Proceeding with revisions demonstrates to the reviewers that authors take their comments seriously.8\n\nIn some instances, authors may perceive reviewers’ criticisms as discourteous.17 However, this could simply be a case of miscommunication.15 Responding rudely is unwarranted, especially considering the ultimate goal of getting the manuscript published.23,25 It is then strongly advised to maintain a polite tone throughout the response to the reviewers, and to refrain from emotional, confrontational, or defensive expressions, even if the authors disagree with the reviewers or feel that the requested changes are unnecessary.23 Even if it appears that the reviewers are using the review as an opportunity to “teach” them,10 it is important to remain composed and respectful and to welcome reviewers’ recommendations with a positive perspective.8\n\n\nPay attention to details: Respond to every point raised\n\nGenerally, reviews are bulleted.23 If two distinct issues are brought up within one bullet point, authors should ensure that both critiques are explicitly responded to.23 Interspersing responses, breaking up one bullet point with multiple answers, helps maintain clarity and ensures each criticism receives a thorough response.23 If the authors are unable to respond to all points, it is reasonable to:\n\ni) Be specific in the response and address all points raised13;\n\nii) Avoid dodging difficult points by ignoring them;\n\niii) Include additional information; provide requested data or figures that were not in the manuscript if they support the argument;\n\niv) Add or update references and offer a supplementary file if the journal restricts the length of additional data13;\n\nv) Delete unnecessary material, including figures or tables;\n\nvi) Shorten sections of the manuscript if necessary, specifying the extent of the reduction in words or percentage; and\n\nvii) Make minor corrections to the text, such as or revising grammar and typographical mistakes.13,26\n\nThis comprehensive approach demonstrates the authors’ commitment and consideration of the review to both the editor and the reviewers, facilitating a smoother re-evaluation of their manuscript.6,27\n\n\nBe thorough and plan responses\n\nTo enhance the quality of their responses and maintain clarity and professionalism, authors should:\n\ni) Organize responses systematically, addressing each comment with care and politeness, even if they disagree with the reviewers6;\n\nii) Number the reviewers’ points and respond to them sequentially18;\n\niii) Provide specific responses and address all points raised by each reviewer in a formal manner13,23;\n\niv) Ensure that responses are detailed to facilitate better understanding by editors and reviewers;\n\nv) Clearly explain each reviewer’s comments, respond to each criticism individually, point by point, and do not miss any comment4,7,8,15;\n\nvi) Offer clear and concise explanations of revisions where necessary4;\n\nvii) Submit responses directly below the reviewers’ comments, tightening language, correcting any grammatical mistakes or misspellings, and incorporating corresponding changes in the revised manuscript28;\n\nviii) Start each response to each comment with a clear and direct answer to the specific issue raised, providing a “yes” or “no” answer whenever possible.13,23 The objective is to demonstrate to the reviewers that authors have taken their comments seriously and to convey the actions they have taken in response to their critiques promptly23; and\n\nix) Comply, whenever feasible, with the requests of the reviewers.23 Change and modify where it makes sense.\n\nIf authors believe that a particular comment falls outside the scope of their study, they should explain and clarify the reasons for their stance in cases where they disagree with the reviewers or feel that an additional experiment or analysis is unnecessary.13\n\n\nAvoid arguing every single comment\n\nAuthors have the right to engage in discussions regarding reviewers’ comments, but it is best to avoid disputing multiple comments.29 If encountering serious disagreement with reviewers, particularly if a suggestion is deemed unreasonable or requests excessive work that strays from the study’s objectives, authors can refute the suggestion and make no changes.7 In such instances, it is imperative to:\n\ni) Acknowledge the comment;\n\nii) Provide a concise, factual explanation justifying the decision not to implement the suggestion29; and\n\niii) Justify any refusals in the response letter and in the comments.7,13,30,31\n\nIt is worth noting that reviewers may only tolerate one instance of refusal.32 Engaging in a “fight” with the reviewers is unwise, even if the suggestions are flawed or misunderstood.23 Arguing extensively with the reviewers may frustrate them and jeopardize the opportunity to publish the manuscript. If a point of contention is substantial enough to jeopardize the manuscript’s integrity or the arguments presented, authors may appeal to the editor for intervention.23\n\n\nAmbiguous situations\n\nSometimes, authors may encounter ambiguous or conflicting feedback, conflict of interest concerns, or suggested additions that exceed the journal guidelines.4 In such situations, authors should handle reviewers’ comments with careful consideration and diligence. At times, authors may encounter unclear or ambiguous comments. In such situations, authors should seek clarification rather than provide an incorrect response.4 Clarification can be requested in the cover letter or by contacting the editor via email. Sometimes, authors might receive conflicting feedback from two different reviewers.7 In such instances, it is important not to become overwhelmed and to start by thoroughly examining both sets of comments, choosing the one that best matches the authors’ vision for the manuscript.30 Authors should then address this selected feedback by making the required adjustments to their manuscript. Additionally, it is advisable to outline to the editor the two contradictory comments and provide arguments in support of the comment selected by the authors.7,32 This serves to clarify the authors’ rationale behind the decision and helps ensure consistency and coherence in the revision process. In certain instances, suspicions of ethics violations may arise. For instance, a reviewer might reject a manuscript only to later conduct a similar study and publish it.32 Similarly, a reviewer may recommend citing an article that does not align with the study’s scope.32 In such cases, authors may choose to send a separate letter/Email to the editor to clarify the circumstances and possibly suggest a change of reviewer or a reconsideration of the comment.23 This step is crucial for maintaining the integrity of the PRP and ensuring fair and ethical treatment of manuscripts.\n\n\nReviewers’ requests and journal’s guidelines\n\nIf reviewers request additions such as references, tables, or text that exceed the journal’s limits, authors may encounter a dilemma. If they agree to these changes and believe they enhance the manuscript, authors should implement the changes and address the issue in their responses, seeking the editor’s authorization.7 However, if authors find that these changes contradict their vision for the manuscript, they can use the recommendations for authors to justify refusing the change. Authors should then write to the editor to explain why they cannot comply with the reviewers’ request.23,30 This approach ensures that the manuscript remains aligned with the author’s intentions while also respecting the journal’s guidelines and maintaining transparency in the revision process.23,30\n\n\nHighlight changes in the revised manuscript - Use typography to assist the reviewers in navigating through responses\n\nFor the benefit of both reviewers and editors, authors should streamline the revision process and make it as easy as possible for them to navigate. Well-organized responses can reduce confusion and frustration, ultimately increasing the likelihood of acceptance. Here are some recommended practices:\n\n✓ Detail the responses, highlighting significant changes in the revised version, such as new experiments or analyses that modify conclusions.13 This allows the editor to easily track modifications without searching extensively in the revised manuscript;\n\n✓ Address the response directly to the editor, rather than the reviewers. For example, use phrases like “We agree with the reviewer…” instead of “We agree with you …. »\n\n✓ Ensure that every comment is addressed in consecutive order, aligning with the sequence of comments provided by the reviewers. One approach is to copy and paste all comments from reviewers and editors, inserting the response to each point directly below it in a distinct color or font to distinguish between comments and responses.15,16\n\nIf the journal requires identifying changes on a single copy of the manuscript, authors may use Microsoft Word’s track changes feature or highlight with a marker. They may use different colored fonts or highlights to separate corresponding responses to different reviewers and clarify this in the cover letter.7 However, authors should be mindful that this approach might result in a lengthy manuscript that is challenging to read and may not effectively juxtapose the reviewers’ comments with authors” changes.\n\nAnother effective approach to organizing responses to reviewers is to utilize a table format that includes the reviewers’ comments, author responses, and corresponding changes with page and line references in separate columns6,7,13,23,29,32,33 (Appendix 1).34\n\n\nRevise and improve\n\nAfter addressing all comments, authors must ensure any necessary corrections are made to the manuscript.29 It is crucial to meticulously check that all changes made are properly documented. Highlighting the changes is preferable as it makes them easier for reviewers and the editor to verify.4,30 If the journal requires two versions of the revised manuscript - one with highlighted changes and another in a clean format - authors should comply.7,32 It is important to carefully review the journal’s submission requirements for the revised version and adhere to the provided instructions, as they specify how changes should be incorporated.7\n\n\nReview again\n\nIf English is not the authors’ native language, they should consider having the final version corrected by an expert translator.6 Alternatively, authors can use Artificial Intelligence tools to assist with the proofreading process, but it is important to declare the use of such tools.3 Before finalizing the manuscript, it is crucial to perform a final thorough review to ensure that no errors have arisen due to the changes made.7\n\n\nExpress gratitude again\n\nTaking a moment to express gratitude towards the reviewers and the editor demonstrates professionalism and courtesy. Therefore, authors should not forget to reiterate their thanks to them to conclude their cover letter.4,23,30\n\nIn practice, authors are asked to include an introduction and conclusion in their response letter. This provides a comprehensive and respectful response, enhancing the overall impression of the manuscript revision process. Authors should begin the response letter with a brief introductory paragraph expressing appreciation to the reviewers for their time and valuable feedback6 (Appendix 1).34 This introduction sets a positive tone and acknowledges the reviewers’ contributions. For example: “The authors sincerely thank the reviewers for their thorough and insightful feedback on our manuscript. We have carefully considered each comment and made the necessary revisions to address their concerns. We believe these changes have significantly improved the manuscript.” After addressing each comment, the authors should conclude the response letter with a closing paragraph summarizing the major changes made and reiterating gratitude for the reviewers’ input23 (Appendix 1).34 For example, “In conclusion, we have made substantial revisions to the manuscript based on the reviewers’ comments. We believe these changes have strengthened the quality and clarity of our work. We are grateful for the reviewers’ constructive feedback and look forward to your favorable consideration of our revised manuscript.”\n\n\nResubmit promptly\n\nIt is advisable to resubmit the manuscript as quickly as possible, while the reviewers and the editor still have the work fresh in their minds.4 A prompt resubmission, accompanied by a detailed response letter, a clear response table, and highlighted changes, can significantly increase the likelihood of paper acceptance.30 By providing a comprehensive and organized submission, authors demonstrate their commitment to addressing reviewers’ feedback and improving the quality of the manuscript, thereby enhancing its chances of acceptance.\n\n\nConclusion\n\nThe PRP serves dual purposes.32 For publishers, it offers a comprehensive evaluation of manuscripts from diverse perspectives, guarding against potential pitfalls like plagiarism.32 For authors, it offers invaluable external insights, enabling them to refine and enhance their work, thereby improving its prospects for acceptance.32\n\nNavigating reviewers’ critiques can be daunting for authors.23 However, the reviewers’ comments are not personal attacks, but rather constructive contributions aimed at facilitating publication.23 Handling reviewers’ feedback appropriately and ethically significantly enhances the likelihood of manuscript acceptance.23 Therefore, authors should approach the PRP with diligence, carefully considering each comment and making necessary adjustments to strengthen their manuscript. Additionally, maintaining clear and respectful communication with reviewers and editors throughout the process fosters a collaborative and productive environment conducive to scholarly advancement.\n\nResponding to reviewers' comments effectively is crucial for the successful publication of a scientific paper. By following structured guidelines, authors can address critiques thoroughly and respectfully, leading to improved manuscripts and fostering positive relationships with reviewers.\n\n\nEthical approval\n\nThe study design was determined to be exempt from human subjects’ research review, and therefore, formal approval was not required.\n\n\nInformed consent\n\nNo need.", "appendix": "Data availability\n\nNo data associated with this article.\n\nZenodo: Appendix 1: Table format to respond to reviewers. DOI: https://doi.org/10.5281/zenodo.12819228. 34\n\nThe project contains the following extended data:\n\n• [Appendix 1: Table format to respond to reviewers]. 34\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 wish to disclose that artificial intelligence tool ( i.e. , ChatGPT 3.5) was utilized to enhance the manuscript’s wording, readability, and language quality. The tool was used only for language refinement and not for generating text. 3 , 35\n\n\nReferences\n\nBen Saad H: Scientific medical writing in practice: the <<IMR@D(R)>> format. Tunis. Med. 2019 Mar; 97(3): 407–425. PubMed Abstract\n\nBen Saad H: Scientific medical writing in practice: How to succeed the writing style? Tunis. Med. 2019 Feb; 97(2): 273–285. PubMed Abstract\n\nDergaa I, Ben Saad H: Artificial intelligence and promoting open access in academic publishing. Tunis. Med. 2023 Jun 5; 101(6): 533–536. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHiemstra PS: How to write a response to the reviewers of your manuscript. Breathe (Sheff.). 2018 Dec; 14(4): 319–321. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIantorno SE, Andras LM, Skaggs DL: Variability of reviewers’ comments in the peer review process for orthopaedic research. Spine Deform. 2016 Jul; 4(4): 268–271. PubMed Abstract \| Publisher Full Text\n\nOldham MA, Kontos N, Baller E, et al.: JACLP Guide for manuscript peer review: How to perform a peer review and how to be responsive to reviewer comments. J. Acad. Consult. Liaison Psychiatry. 2023 Sep-Oct; 64(5): 468–472. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCuschieri S, Vassallo J: Write a scientific paper (WASP): Editor’s perspective of submissions and dealing with editors. Early Hum. Dev. 2019 Feb; 129: 93–95. PubMed Abstract \| Publisher Full Text\n\nGerwing TG, Allen Gerwing AM, Choi CY, et al.: Re-evaluation of solutions to the problem of unprofessionalism in peer review. Res Integr Peer Rev. 2021 Feb 16; 6(1): 4. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKuper A, O’Sullivan P, Cleland J: Questions and quandaries: How to respond to reviewer comments. Adv. Health Sci. Educ. Theory Pract. 2023 Mar; 28(1): 7–12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nExcellence in peer review: Reviewer training network - editor Resources: (Last visit: July 25, 2024). Reference Source\n\nHow to write a peer review: (Last visit: July 25, 2024). Reference Source\n\nGrech V, Cuschieri S, Eldawlatly AA: Write a scientific paper course - Utility or otherwise? Saudi J. Anaesth. 2022 Oct-Dec; 16(4): 437–439. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJoubert G: A health sciences researcher’s experience of manuscript review comments, 2020-2022. S. Afr. Fam. Pract (2004). 2023 Oct 25; 65(1): e1–e5. Epub 20231025. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNoble WS: Ten simple rules for writing a response to reviewers. PLoS Comput. Biol. 2017 Oct; 13(10): e1005730. Epub 20171012. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTarkang EE, Kweku M, Zotor FB: Publication practices and responsible authorship: A review article. J. Public Health Afr. 2017 Jun 23; 8(1): 723. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCook DA: Twelve tips for getting your manuscript published. Med. Teach. 2016; 38(1): 41–50. PubMed Abstract\n\nOzcakar L, Rizzo JR, Franchignoni F, et al.: Let’s write a manuscript: A primer with tips and tricks for penning an original article. Am. J. Phys. Med. Rehabil. 2022 Jul 1; 101(7): 698–701. PubMed Abstract \| Publisher Full Text\n\nLange CA, Hammes SR: Publish or perish: Five steps to navigating a less painful peer review. Endocrinology. 2021 Mar 1; 162(3). PubMed Abstract \| Publisher Full Text\n\nSakakura K, Fujita H: How to write a revised manuscript in clinical medicine. Cardiovasc. Interv. Ther. 2023 Apr; 38(2): 187–193. PubMed Abstract \| Publisher Full Text\n\n3 top tips for responding to reviewer comments on your manuscript: (Last visit: July 25, 2024). Reference Source\n\nCummings P, Rivara FP: Responding to reviewers’ comments on submitted articles. Arch. Pediatr. Adolesc. Med. 2002 Feb; 156(2): 105–107. PubMed Abstract \| Publisher Full Text\n\nMuchenje V: Editorial: How to respond to reviewers’ comments. S. Afr. J. Anim. Sci. 2017; 47(2): 116. Publisher Full Text\n\nTumin D, Tobias JD: The peer review process. Saudi J. Anaesth. 2019 Apr; 13(Suppl 1): S52–S58. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPerlis RH, Kendall-Taylor J, Hart K, et al.: Peer review in a general medical research journal before and during the COVID-19 pandemic. JAMA Netw. Open. 2023 Jan 3; 6(1): e2253296. Epub 20230103. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBen Saad H: Table format to respond to reviewers (Version 1). Zenodo. 2024. (Last visit: July 25, 2024). Publisher Full Text\n\nDergaa I, Chamari K, Zmijewski P, et al.: From human writing to artificial intelligence generated text: examining the prospects and potential threats of ChatGPT in academic writing. Biol. Sport. 2023 Apr; 40(2): 615–622. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "316501", "date": "26 Aug 2024", "name": "Jeffrey N Love", "expertise": [ "Reviewer Expertise Education Scholarship", "Workplace Based Assessments", "Program Evaluation", "Mentored Peer-Reviews", "Vitality of the Workplace" ], "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\nHidouri et al have used their experience and the literature to develop a comprehensive approach to guidelines and strategies for authors when dealing with the publication peer-review process. From my experience and understanding of the literature, the author’s assessment and approach to issues related to peer-review of a submitted manuscript are accurate and substantiated by appropriate citations from a broad array of fields. This paper is well written and flows nicely. Table 1 does an excellent job of providing a clear understanding of the issues that may arise as well as a balanced, evidence-based approach to effectively deal with each when responding to the peer-review process.\n\nTraditionally, researchers have learned these lessons by trial and error. I believe that the approach the authors recommend would streamline the “budding” scholars learning regarding the peer-review process with the potential to lead to successful publications earlier than would occur otherwise without the “hard knocks”. This is the most comprehensive example of guidelines for responding to the peer review process I have seen. Since these are generally opinion/commentary/perspective publications, a more rigorous approach to evaluating the available literature appears unlikely at this time.\n\nAs a guest editor of a Special Issue in Education with a mentored peer-review program for education fellows, I plan on sharing this paper with our fellows and junior authors.\n\nJeffrey N. Love, MD, MHPE, MSc Professor Emeritus, Emergency Medicine Georgetown School of Medicine CORD Guest Editor Western Journal of Emergency Medicine Special Issue in Educational Research & Practice\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Yes\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Yes", "responses": [ { "c_id": "12377", "date": "06 Sep 2024", "name": "Helmi BEN SAAD", "role": "Author Response", "response": "Dear Dr. Jeffrey N. Love, Thank you for your thoughtful and insightful review of our paper, Key Guidelines for Responding to Reviewers. We are delighted that you found our approach comprehensive and beneficial for both experienced researchers and those new to the peer-review process. Your comments, particularly regarding Table 1, reaffirm our belief that clear, evidence-based strategies can enhance an author’s ability to navigate peer-review successfully. We agree that these lessons are often learned through trial and error, and our goal in sharing these guidelines is to provide a more efficient pathway for emerging scholars. We are honored that you plan to share our paper with your fellows and junior authors in the context of your Special Issue on Educational Research & Practice. It is gratifying to know that our work may contribute to the learning and development of future researchers. Thank you again for your kind words and for your commitment to advancing educational scholarship. Sincerely, Pr Helmi Ben Saad (MD, PhD), On behalf of the co-authors (Hidouri S., Kamoun H., Salah S., Jellad A., Ben Saad H)." } ] }, { "id": "316498", "date": "05 Sep 2024", "name": "Abdelghani Maddi", "expertise": [ "Reviewer Expertise Scientometrics", "Research Evaluation", "Peer Review", "Research Integrity." ], "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. General comment: The manuscript is a well-crafted opinion piece that provides insightful guidance for authors on how to respond effectively to reviewers' comments during the peer review process (PRP). It is particularly valuable for early-career researchers who may be navigating the complexities of peer review for the first time, as well as for more experienced scholars who encounter ambiguous or challenging situations. While the manuscript is commendable for its comprehensive coverage and practical advice, there are several areas where it could benefit from additional clarification and refinement, particularly by addressing some specific issues and minimizing redundancy to enhance readability.\nII. Strengths:\nComprehensive Coverage of PRP Strategies: The manuscript succeeds in presenting a wide array of strategies and practical advice that are relevant to the peer review process. It covers essential aspects of how to respond to reviewer comments, ranging from addressing specific critiques to maintaining a constructive tone throughout the communication. This breadth of coverage provides authors with a robust toolkit to approach various scenarios they may encounter in their scholarly communications. Clear Section Structuring: The logical organization of the manuscript, with well-defined headings and subheadings, greatly aids in its readability. By structuring the content into distinct sections, the authors make it easier for readers to navigate the text and locate the information most relevant to their particular situation. This clarity in organization also helps to highlight the key messages and guidance offered, thereby enhancing the utility of the manuscript as a reference guide. Practical and Applicable Advice: The article excels in offering actionable advice that authors can readily apply when responding to reviewers. For example, the suggestion to break down complex reviewer comments into manageable parts and to address each point methodically helps demystify what can often feel like an overwhelming process. Emphasis on Professionalism and Constructive Dialogue: A key strength of the manuscript is its consistent emphasis on professionalism and the promotion of constructive dialogue. By advocating for a balanced approach that combines firmness in defending one’s scholarly contributions with openness to constructive feedback, the manuscript reinforces the importance of maintaining a respectful and cooperative dynamic between authors and reviewers.\nIII. Areas for Improvement: Despite these strengths, there are several areas where the manuscript could be further enhanced by incorporating additional insights and clarifying certain points. I offer the following suggestions based on my personal experience as both an author and a reviewer:\nAddressing Requests for Non-Citation of Specific Authors in the \"Ambiguous Situations\" Section: It would be beneficial for the manuscript to include guidance on handling situations where reviewers request that specific authors not be cited due to reputational concerns or prior behavior. In such cases, it is vital to determine whether the request pertains to the author as an individual or to the research itself. If the request is directed at the author for personal or ethical reasons, authors should consider contacting the editor privately to discuss the best course of action. This scenario is increasingly relevant in light of the growing prominence of post-publication peer review platforms such as PubPeer, where scholars openly critique the work of their peers. This transparency can sometimes lead to contentious situations, where certain researchers may be effectively \"blacklisted\" due to their public critiques. Addressing this issue would provide authors with a clearer understanding of how to manage such delicate situations. Incorporating a Practice of Acknowledging Reviewers in the \"Express Gratitude Again\" Section: The manuscript could be further enriched by suggesting the inclusion of reviewers in the acknowledgements section of the article when their feedback has substantially contributed to improving the manuscript. Beyond thanking reviewers in the response letter, a formal mention in the acknowledgements section demonstrates the authors’ appreciation for the constructive role reviewers play in refining scholarly work. This practice not only fosters goodwill but also acknowledges the often-overlooked labor of peer reviewers who contribute to the advancement of knowledge through their insights. Highlighting the Issue of Plagiarism of Reviewers' Comments: An additional point worth addressing is the problematic practice of directly copying and pasting reviewers' comments into the manuscript. This practice may be viewed as a lack of originality and could raise concerns regarding academic integrity. It is advisable that if reviewers' comments provide valuable suggestions for improvement, these ideas should be paraphrased and integrated into the manuscript in the authors’ own words. An extreme example can be drawn from my own experience, where authors copied nearly a full page of my comments verbatim to create a new \"Limitations\" section in a paper published by a “gray” publisher. Emphasizing the importance of originality in incorporating reviewer feedback would help maintain the scholarly standards of the work. Reducing Redundancies and Repetition for Greater Clarity: While the manuscript provides many useful insights, there are instances where certain points, such as those concerning professionalism and the manner of responding to reviewers, are repeated multiple times throughout the text. Streamlining these sections by consolidating similar points would help reduce redundancies and improve the overall flow of the manuscript, making it more concise and engaging for the reader.\nTo sum up, this manuscript is a highly valuable resource for authors seeking to effectively navigate the peer review process. The incorporation of the suggested improvements would further enhance its comprehensiveness and clarity, ensuring that it continues to serve as a practical guide for both new and experienced researchers.\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Yes\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Yes", "responses": [ { "c_id": "12378", "date": "12 Sep 2024", "name": "Helmi BEN SAAD", "role": "Author Response", "response": "The authors sincerely thank the reviewer for his thorough and insightful feedback on our manuscript. We have carefully considered each comment and made the necessary revisions to address his concerns. We believe these changes have significantly improved the manuscript. Below are our specific responses to the reviewer positive comments/suggestions. COMMENT 1. I. General comment: The manuscript is a well-crafted opinion piece that provides insightful guidance for authors on how to respond effectively to reviewers' comments during the peer review process (PRP). It is particularly valuable for early-career researchers who may be navigating the complexities of peer review for the first time, as well as for more experienced scholars who encounter ambiguous or challenging situations. While the manuscript is commendable for its comprehensive coverage and practical advice, there are several areas where it could benefit from additional clarification and refinement, particularly by addressing some specific issues and minimizing redundancy to enhance readability. RESPONSE We thank the reviewer for his valuable feedback and for recognizing the potential impact of our manuscript on both early-career and experienced researchers. We appreciate his thoughtful suggestions regarding areas for clarification and the need to minimize redundancy. We agree that enhancing the readability of the paper will strengthen its overall value, and we have refined the manuscript accordingly. By addressing the specific issues highlighted by the reviewer, we aimed to further improve its clarity and utility for all readers. As the reviewer aptly mentioned, together we can achieve more, and we sincerely appreciate the reviewer’ contribution in helping us move towards that goal. We thank the reviewer again for his constructive comments and support. COMMENT 2. II. Strengths: Comprehensive Coverage of PRP Strategies: The manuscript succeeds in presenting a wide array of strategies and practical advice that are relevant to the peer review process. It covers essential aspects of how to respond to reviewer comments, ranging from addressing specific critiques to maintaining a constructive tone throughout the communication. This breadth of coverage provides authors with a robust toolkit to approach various scenarios they may encounter in their scholarly communications. Clear Section Structuring: The logical organization of the manuscript, with well-defined headings and subheadings, greatly aids in its readability. By structuring the content into distinct sections, the authors make it easier for readers to navigate the text and locate the information most relevant to their particular situation. This clarity in organization also helps to highlight the key messages and guidance offered, thereby enhancing the utility of the manuscript as a reference guide. Practical and Applicable Advice: The article excels in offering actionable advice that authors can readily apply when responding to reviewers. For example, the suggestion to break down complex reviewer comments into manageable parts and to address each point methodically helps demystify what can often feel like an overwhelming process. Emphasis on Professionalism and Constructive Dialogue: A key strength of the manuscript is its consistent emphasis on professionalism and the promotion of constructive dialogue. By advocating for a balanced approach that combines firmness in defending one’s scholarly contributions with openness to constructive feedback, the manuscript reinforces the importance of maintaining a respectful and cooperative dynamic between authors and reviewers. RESPONSE We sincerely thank the reviewer for his positive and thoughtful feedback. We are delighted that the reviewer found our manuscript comprehensive and practical, particularly in its coverage of PRP strategies. It is reassuring to know that the breadth of our approach and the actionable advice provided resonated with the reviewer and that the logical structuring of the sections contributed to its readability and utility as a reference guide. We are also pleased that our emphasis on professionalism and fostering constructive dialogue between authors and reviewers was appreciated, as these are core principles we aim to promote. The recognition by the reviewer of these strengths reinforces our belief in the manuscript's potential to support authors in navigating the complexities of the PRP. We thank the reviewer again for his insightful comments and for recognizing the strengths of our work COMMENT 3. III. Areas for Improvement: Despite these strengths, there are several areas where the manuscript could be further enhanced by incorporating additional insights and clarifying certain points. I offer the following suggestions based on my personal experience as both an author and a reviewer: 3.a. Addressing Requests for Non-Citation of Specific Authors in the \"Ambiguous Situations\" Section: It would be beneficial for the manuscript to include guidance on handling situations where reviewers request that specific authors not be cited due to reputational concerns or prior behavior. In such cases, it is vital to determine whether the request pertains to the author as an individual or to the research itself. If the request is directed at the author for personal or ethical reasons, authors should consider contacting the editor privately to discuss the best course of action. This scenario is increasingly relevant in light of the growing prominence of post-publication peer review platforms such as PubPeer, where scholars openly critique the work of their peers. This transparency can sometimes lead to contentious situations, where certain researchers may be effectively \"blacklisted\" due to their public critiques. Addressing this issue would provide authors with a clearer understanding of how to manage such delicate situations. 3.b. Incorporating a Practice of Acknowledging Reviewers in the \"Express Gratitude Again\" Section: The manuscript could be further enriched by suggesting the inclusion of reviewers in the acknowledgements section of the article when their feedback has substantially contributed to improving the manuscript. Beyond thanking reviewers in the response letter, a formal mention in the acknowledgements section demonstrates the authors’ appreciation for the constructive role reviewers play in refining scholarly work. This practice not only fosters goodwill but also acknowledges the often-overlooked labor of peer reviewers who contribute to the advancement of knowledge through their insights. 3.c. Highlighting the Issue of Plagiarism of Reviewers' Comments: An additional point worth addressing is the problematic practice of directly copying and pasting reviewers' comments into the manuscript. This practice may be viewed as a lack of originality and could raise concerns regarding academic integrity. It is advisable that if reviewers' comments provide valuable suggestions for improvement, these ideas should be paraphrased and integrated into the manuscript in the authors’ own words. An extreme example can be drawn from my own experience, where authors copied nearly a full page of my comments verbatim to create a new \"Limitations\" section in a paper published by a “gray” publisher. Emphasizing the importance of originality in incorporating reviewer feedback would help maintain the scholarly standards of the work. 3.d. Reducing Redundancies and Repetition for Greater Clarity: While the manuscript provides many useful insights, there are instances where certain points, such as those concerning professionalism and the manner of responding to reviewers, are repeated multiple times throughout the text. Streamlining these sections by consolidating similar points would help reduce redundancies and improve the overall flow of the manuscript, making it more concise and engaging for the reader. To sum up, this manuscript is a highly valuable resource for authors seeking to effectively navigate the peer review process. The incorporation of the suggested improvements would further enhance its comprehensiveness and clarity, ensuring that it continues to serve as a practical guide for both new and experienced researchers. RESPONSE We thank the reviewer for his valuable feedback and for highlighting the strengths of our manuscript. We greatly appreciate his suggestions for improvement based on his experience as both an author and a reviewer. Almost all the reviewer’ suggestions were considered. We thank again the reviewer for his time and thoughtful review. 3.a. We thank the reviewer for his insightful comment and for highlighting the importance of addressing requests for non-citation of specific authors due to reputational concerns or prior behavior. This is indeed a relevant issue in today’s academic environment, particularly with the increasing transparency brought by platforms like PubPeer. We agree that providing guidance on how to navigate such delicate situations would be valuable for authors, and we have included this in the “Ambiguous Situations” section. We thank again the reviewer for his thoughtful feedback. We have added the following sentence: Finally, when reviewers express concerns about citing specific authors due to their reputation or past behavior, it is crucial to evaluate whether the issue is related to the individual or the research itself. If the request is rooted in personal or ethical concerns, authors should consider discreetly contacting the editor for guidance. With the increasing popularity of post-publication peer review platforms like PubPeer, ScienceOpen, and PREreview, such situations may become more common, necessitating careful consideration by authors. 35 These steps/approaches are crucial for maintaining transparency and professionalism and the integrity of the PRP, and ensuring fair and ethical treatment of manuscripts. 3.b. We thank the reviewer for his thoughtful suggestion regarding the inclusion of reviewers in the acknowledgements section of the manuscript. We agree that acknowledging reviewers, especially when their feedback has significantly contributed to improving the work, is a meaningful way to express gratitude beyond the response letter. This practice not only fosters goodwill but also highlights the important role reviewers’ play in advancing scholarly work. We have incorporated this recommendation into the \"Express Gratitude Again\" section, as it aligns with our goal of promoting a respectful and transparent peer review process. We have also acknowledged the reviewers of our paper in our acknowledgements section (Please see our revised section: Acknowledgments). We have added the following text: Finally, including reviewer acknowledgements in the article's “acknowledgements section” can strengthen the manuscript. When reviewers' feedback has substantially improved the work, formally recognizing their contributions demonstrates appreciation beyond the response letter. 15 This practice not only cultivates positive relationships but also acknowledges the crucial role of peer reviewers in advancing knowledge. 15 By highlighting their efforts, authors recognize the often-underappreciated work that reviewers do to refine scholarly articles. 15 3.c. We thank he reviewer for highlighting the issue of directly copying and pasting reviewers' comments into the manuscript. We agree that this practice undermines originality and raises concerns about academic integrity. The reviewer experience underscores the importance of properly paraphrasing and integrating valuable suggestions from reviewers into the manuscript. We addressed this point in our paper to emphasize the importance of maintaining originality while incorporating feedback. In the section “Pay attention to details: Respond to every point raised” we have highlighted the issue of plagiarism of reviewers' comments and we have added the following sentence : Finally, to uphold scholarly integrity, it is essential to avoid directly copying and pasting reviewers' comments into the manuscript. 8, 28 Instead, valuable suggestions provided by reviewers should be paraphrased and integrated into the manuscript using the author's own words. 8, 28 This practice not only maintains academic standards but also ensures that the incorporation of feedback reflects originality and thoughtful engagement with the review process. 8, 28 Emphasizing this issue reinforces the commitment to academic integrity, 29 and enhances the quality of the work. 3.d. We thank the reviewer for his valuable feedback regarding the reduction of redundancies and repetition in the manuscript. We appreciate the reviewer’ observation that streamlining the sections on professionalism and responding to reviewers will enhance clarity and improve the flow of the text. We carefully reviewed and consolidated similar points to eliminate redundancies and ensure a more concise and engaging manuscript. Your suggestions helped us refining the presentation of our insights, making the content more accessible and impactful for readers. We thank the reviewer again for his constructive input. To sum up, we have made substantial revisions to the manuscript based on the reviewer’ comments/suggestions. We believe these changes have strengthened the quality and clarity of our work. We are grateful for the reviewers and thank him for his positive evaluation of our manuscript and for acknowledging its value as a resource for navigating the PRP. We appreciate the reviewer’s suggestions for further improvements, which will undoubtedly enhance the manuscript’s comprehensiveness and clarity. We have incorporated all his feedbacks to ensure that the guide remains practical and useful for both new and experienced researchers. We thank again the reviewer for his insightful comments and support." } ] }, { "id": "316507", "date": "12 Sep 2024", "name": "Meghit Boumediene Khaled", "expertise": [ "Reviewer Expertise Nutrition and 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\nThis is an interesting article that provides an insightful overview of the Peer Review Process (PRP), emphasizing its critical role in ensuring research quality and rigor. The manuscript highlights the dual benefits of PRP for both publishers, who rely on it to maintain high standards, and for authors, who receive valuable feedback to refine their work.\nThe authors accurately address the significance of responding to reviewers’ critiques, which is indeed one of the most challenging parts of the publication process. Indeed, responding to reviewers can be stressful, as it involves addressing critiques that may challenge the core of the research.\n\nIn section \"Tips and advices\" correct and put advice instead of advices (uncountable noun) Overall, the tips provided are practical and aligned with the goal of enhancing the manuscript through the peer review process. It would be beneficial to expand on specific strategies for prioritizing feedback and provide examples of how to maintain professionalism when responding to particularly challenging critiques.\nConsume reviewers’ critiques Additional tip: - Seeking guidance: If an author is unsure how to address a particular comment, they can reach out to the editor or a mentor for guidance.\nSeek opinion ..... Overall, this section provides a comprehensive overview of the strategies authors should employ when responding to reviewer comments. The text could benefit from incorporating specific examples of major and minor reviewer comments to illustrate the concepts more concretely.\nAmbiguous situations in this paragraph the authors provided solid and actionable advice for authors dealing with ambiguous situations during the peer review process with important guidance on handling ambiguous situations that authors may face during the PRP. However, in Ethical consideration: this section could be strengthened by referencing specific guidelines or policies that journals or organizations like COPE (Committee on Publication Ethics) have in place to handle such situations. This would give authors a clearer path to follow.\nReviewers’ requests and journal’s guidelines This part offers a well-rounded approach to handling reviewers' requests that may conflict with journal guidelines, as well as practical advice on organizing and presenting revisions. Moreover, it provides valuable, practical advice for authors dealing with the peer review process. It balances the need to respect both reviewers' suggestions and the authors' original vision, while also emphasizing the importance of organization and clarity in presenting revisions. Some improvements could be made by simplifying certain recommendations, providing clearer guidance on seeking editorial approval, and streamlining references. The suggestion to use tables to organize responses to reviewers is excellent. This method is often recommended as it allows for a clear, organized presentation of how each comment was addressed, helping both reviewers and editors to easily follow the changes made.\nRevise and improve A solid foundation for authors navigating the manuscript revision process is offered in this section. It covers key areas such as documentation, communication, and final review, with a clear emphasis on professionalism and attention to detail.\nHowever, I recommend reducing repetitive focus on gratitude (A single, well-crafted expression of thanks may be sufficient). The inclusion of a brief discussion on the limitations of AI tools and a more detailed reference to the appendix would also improve the section’s overall effectiveness.\nAI Tool Use: The mention of AI tools for proofreading is timely, but the section could benefit from a brief discussion on the limitations of these tools. Authors should be cautious, as AI tools may not catch all linguistic nuances or contextual errors. A recommendation to use AI tools as a supplementary measure, rather than a primary one, would be more balanced.\nConclusion The authors provide a strong summary of the PRP’s significance for both publishers and authors. The conclusion effectively encapsulates the dual roles of the PRP for both publishers and authors. By highlighting how the PRP not only serves as a quality control mechanism for publishers but also provides authors with valuable feedback, the conclusion underlines the significance of this process in academic publishing.\nI recommend the indexing of this paper after considering the above mentioned comments.\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Yes\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Yes", "responses": [ { "c_id": "12439", "date": "16 Sep 2024", "name": "Helmi BEN SAAD", "role": "Author Response", "response": "The authors sincerely thank the reviewer for his thorough and insightful feedback on our manuscript. We have carefully considered each comment and made the necessary revisions to address his concerns. We believe these changes have significantly improved the manuscript. Below are our specific responses to the reviewer positive comments/suggestions. COMMENT 1. This is an interesting article that provides an insightful overview of the Peer Review Process (PRP), emphasizing its critical role in ensuring research quality and rigor. The manuscript highlights the dual benefits of PRP for both publishers, who rely on it to maintain high standards, and for authors, who receive valuable feedback to refine their work. The authors accurately address the significance of responding to reviewers’ critiques, which is indeed one of the most challenging parts of the publication process. Indeed, responding to reviewers can be stressful, as it involves addressing critiques that may challenge the core of the research. RESPONSE We thank the reviewer for his thoughtful and encouraging feedback. We are pleased that you found our article to provide an insightful overview of the PRP and its essential role in maintaining research quality. We fully agree that responding to reviewers' critiques is one of the most challenging yet vital aspects of the publication process. Our aim was to offer guidance that could ease the stress associated with this task, and your recognition of our efforts is greatly appreciated. No action is needed at this stage. COMMENT 2. In section \"Tips and advices\" correct and put advice instead of advices (uncountable noun). Overall, the tips provided are practical and aligned with the goal of enhancing the manuscript through the peer review process. It would be beneficial to expand on specific strategies for prioritizing feedback and provide examples of how to maintain professionalism when responding to particularly challenging critiques. RESPONSE We thank the reviewer for his positive feedback and valuable suggestion. First, we have changed advices by advice. Second, we have expanded the section on prioritizing feedback and maintaining professionalism in the revised manuscript. Specifically, we included strategies such as: Prioritizing feedback: We have advised authors to categorize reviewer comments into major and minor critiques, focusing on major revisions that directly impact the study’s methodology, results, or conclusions. This approach helps authors address the most critical issues first. For example, if a reviewer requests a clarification on data analysis or the inclusion of additional experiments, these points should be addressed before responding to minor grammatical corrections or stylistic suggestions. Maintaining professionalism: We emphasized the importance of remaining objective and not personalizing critiques. We recommend authors carefully read the reviewer’s comments, take a moment to reflect, and respond thoughtfully, especially to challenging critiques. For example, if a reviewer’s tone seems harsh or overly critical, authors can acknowledge the reviewer’s input, express gratitude, and focus on the content of the critique without addressing the tone directly. For instance, a response might begin with, “We thank the reviewer for their insightful feedback on our methodology,” followed by a detailed explanation of how the comments were addressed or respectfully refuted with supporting evidence. We have added the following sentence in the section “Prioritize feedback dealing with requests for major revisions”: In practice, authors are advised to categorize each reviewer comments into major and minor ones, focusing on major revisions that directly influence the study’s methodology, results, or conclusions. This approach helps authors address the most critical issues first. For example, if a reviewer requests a clarification on data analysis or the inclusion of additional experiments, these points should be addressed before responding to minor grammatical corrections or stylistic suggestions. We have also added the following sentence in the section “Be polite and respectful of all reviewers/express gratitude”: In practice, authors are advised to remain objective and not personalizing challenging critiques. COMMENT 3. Consume reviewers’ critiques Additional tip:- Seeking guidance: If an author is unsure how to address a particular comment, they can reach out to the editor or a mentor for guidance. RESPONSE We thank the reviewer for this thoughtful suggestion. We have incorporated the additional tip on seeking guidance in the \"Seek opinion\" section. Specifically, we highlighted that if authors are unsure about how to address a particular comment, they can seek advice from either the editor or a mentor. This ensures authors are equipped to respond to all comments effectively. We have added the following sentence in the \"Seek opinion\" section: In practice, if authors are uncertain about how to address specific comments, they are encouraged to consult the editor in chief or reach out to a mentor with expertise in the field. This approach provides clarity and helps ensure that responses are well informed and appropriate. COMMENT 4. Seek opinion ..... Overall, this section provides a comprehensive overview of the strategies authors should employ when responding to reviewer comments. The text could benefit from incorporating specific examples of major and minor reviewer comments to illustrate the concepts more concretely. RESPONSE We thank the reviewer for this thoughtful suggestion. We have added the following sentences inside the section “Prioritize feedback dealing with requests for major revisions” Examples of major comments include modifying the central hypothesis, the main algorithm, and redoing an experiment (e.g.; the central hypothesis of the study needs to be revised to better align with the presented data. Specifically, the hypothesis should address the potential impact of variable X on outcome Y, which is currently not considered). Minor remarks may include unclear statements, missing or incorrect references, unclear data presentation, grammatical concerns, reformulation, adding additional references, adding an extra paragraph/table/figure, and adding an appendix (e.g.; the introduction section would benefit from the inclusion of recent references on the topic, particularly those published in the last five years). 7 COMMENT 5. Ambiguous situations in this paragraph the authors provided solid and actionable advice for authors dealing with ambiguous situations during the peer review process with important guidance on handling ambiguous situations that authors may face during the PRP. However, in Ethical consideration: this section could be strengthened by referencing specific guidelines or policies that journals or organizations like COPE (Committee on Publication Ethics) have in place to handle such situations. This would give authors a clearer path to follow. RESPONSE We thank the reviewer for this thoughtful suggestion. We have added the following sentences inside the section “Ambiguous situations” Finally, in case authors suspect that a reviewer has used artificial intelligence -assisted technologies to produce a review report (without acknowledging it), they need to alert the editors. 36 To handle such situations, authors can refer to specific guidelines and policies provided by international organizations (e.g., Committee on Publication Ethics, 37 International Committee of Medical Journal Editors 38). These guidelines provides comprehensive resources and guidelines for ethical practices in publication, including how to handle conflicts of interest and other ethical issues. 37, 38 By following these guidelines, 37, 38 authors can ensure that they handle ambiguous and ethical situations appropriately, maintaining the integrity of the PRP and their research. COMMENT 6. Reviewers’ requests and journal’s guidelines This part offers a well-rounded approach to handling reviewers' requests that may conflict with journal guidelines, as well as practical advice on organizing and presenting revisions. Moreover, it provides valuable, practical advice for authors dealing with the peer review process. It balances the need to respect both reviewers' suggestions and the authors' original vision, while also emphasizing the importance of organization and clarity in presenting revisions. Some improvements could be made by simplifying certain recommendations, providing clearer guidance on seeking editorial approval, and streamlining references. The suggestion to use tables to organize responses to reviewers is excellent. This method is often recommended as it allows for a clear, organized presentation of how each comment was addressed, helping both reviewers and editors to easily follow the changes made. RESPONSE We thank the reviewer for this thoughtful suggestion. No action is needed. COMMENT 7. Revise and improve A solid foundation for authors navigating the manuscript revision process is offered in this section. It covers key areas such as documentation, communication, and final review, with a clear emphasis on professionalism and attention to detail. However, I recommend reducing repetitive focus on gratitude (A single, well-crafted expression of thanks may be sufficient). RESPONSE We thank the reviewer for this thoughtful suggestion. We have reduced the repetitive focus on gratitude. COMMENT 8. AI Tool Use: The mention of AI tools for proofreading is timely, but the section could benefit from a brief discussion on the limitations of these tools. Authors should be cautious, as AI tools may not catch all linguistic nuances or contextual errors. A recommendation to use AI tools as a supplementary measure, rather than a primary one, would be more balanced. The inclusion of a brief discussion on the limitations of AI tools and a more detailed reference to the appendix would also improve the section’s overall effectiveness. RESPONSE We acknowledge the timely mention of AI tools for proofreading. We have added the following sentence inside the “Review again” section: Authors should be cautious, as artificial intelligence tools may not catch all linguistic nuances or contextual errors, which can lead to oversight. Authors are advised to use artificial intelligence tools as a supplementary measure, rather than a primary one. This approach ensures a more balanced and thorough proofreading process. 4, 38, 41 COMMENT 9. Conclusion The authors provide a strong summary of the PRP’s significance for both publishers and authors. The conclusion effectively encapsulates the dual roles of the PRP for both publishers and authors. By highlighting how the PRP not only serves as a quality control mechanism for publishers but also provides authors with valuable feedback, the conclusion underlines the significance of this process in academic publishing. I recommend the indexing of this paper after considering the above mentioned comments. RESPONSE We thank the reviewer for this excellent feedback. No action is needed. COMMENT 10. Is the topic of the opinion article discussed accurately in the context of the current literature? Yes Are all factual statements correct and adequately supported by citations? Yes Are arguments sufficiently supported by evidence from the published literature? Yes Are the conclusions drawn balanced and justified on the basis of the presented arguments? Yes RESPONSE Thank you for your positive feedback and for the 4 “yes”." } ] } ]	1	https://f1000research.com/articles/13-921
https://f1000research.com/articles/13-287/v1	18 Apr 24	{ "type": "Research Article", "title": "A Study about Perceptions of Kimono among College Students and Kimono Enthusiasts: Is It Difficult to Move in a Kimono?", "authors": [ "Kozue Miyashiro", "Kazuya Sasaki", "Tomoharu Ishikawa", "Hiroshi Mori", "Kazuya Sasaki", "Tomoharu Ishikawa", "Hiroshi Mori" ], "abstract": "Background Kimono is being reevaluated for its sustainability aspects, such as having fewer offcuts in the production process due to its structural differences from Western-style clothes and its high reusability due to the adaptability to individuals’ body shapes. On the other hand, once a common attire for daily wear in Japan, kimono has transitioned to being worn only on special events and the kimono-related industry has also shrunk. To stimulate demand for kimono, it is essential to familiarize younger generations with its potential as daily wear.\n\nMethods A questionnaire survey on perceptions of kimono was conducted among two groups in Japan: 211 college students and 50 kimono enthusiasts. The questionnaire included demographic questions and psychometric scales, primarily focusing on their kimono experiences, challenges associated with wearing kimono, their perceptions of kimono and Western-style clothes, and their attitudes towards kimono.\n\nResults The results revealed that a majority of students had worn kimono before, though they found it difficult to move while wearing it. In contrast, kimono enthusiasts evaluated it as easier to move, hard to become disheveled, and casual. They also rated the ease of wearing Western-style clothes lower compared to students, and this tendency intensified with the length of enthusiast experience. Furthermore, the findings indicated that enthusiasts regarded the kimono more as daily wear compared to students, while still deriving enjoyment from it as formal attire in special events.\n\nConclusions These results suggest that the cognition that Western-style clothes are easy to move and kimono is not may change with experiences. Therefore, providing opportunities for people in Japan to acquire how to wear kimono in comfortable ways possibly impacts their perceptions of kimono.", "keywords": [ "Perceptions of kimono", "kimono enthusiasts", "kimono as daily wear", "wearing experience", "challenges when wearing a kimono", "questionnaire" ], "content": "1. Introduction\n\nKimono, a traditional Japanese attire, is being reevaluated for its sustainability aspects, such as having fewer offcuts in the production process due to its structural differences from Western-style clothes and its high reusability due to the adaptability to individuals’ body shapes. In Japan's school education system, there is also a focus on preserving traditional culture. The current Curriculum Guidelines for junior high schools issued in Heisei 29 (Ministry of Education in Japan, 2017) mention the possibility of introducing traditional Japanese clothes and teaching the basics of wearing them.\n\nOn the other hand, kimono is worn less frequently as daily wear in these days. According to a kimono consumer survey (Ministry of Economy, Trade and Industry in Japan, 2015), targeting women aged 20 and over, 76.7% of respondents identified “ceremonial occasions” as situations in which they want to wear kimono in the future. In light of the current situation where there are limited opportunities to wear kimono, Yoshida (2014) claimed that kimono is no longer a fashion worn even in formal settings, but rather positioned as a special costume worn only during specific life events.\n\nThe kimono-related industry has also shrunk, once estimated as much as 2 trillion-yen industry, have fell to approximately 300 billion yen in 2011 (Yoshida, 2014). In terms of the preservation of Japan's traditional heritage, the kimono is currently facing a crisis.\n\nAdachi (2015) discusses the expansion of kimono distancing in modern clothes culture. The catalyst was the rapid proliferation of Western-style lifestyles, leading to a decline in demand for kimono. To compensate for the decrease in kimono sales, the industry pursued a strategy of developing only high-priced formal kimono, neglecting the casual kimono that was once worn in daily life. Consequently, the market became saturated with formal kimono, while casual kimono disappeared. The kimono, which used to be daily wear, became increasingly unaffordable for the average consumer and limited in occasions suitable for wearing. In order to encourage consumers to purchase these products, the industry emphasized their “year-round wearability” and “timelessness” as selling points. However, as a result, seasonal relevance diminished from the kimono displayed in stores, and there has been an increase in conservative classical patterns over more creatively expressive designs.\n\nThe kimono, by its nature, can be both casual and formal, depending on its type and how it is worn. Awareness of this versatility is crucial in recognition of the allure of the kimono. To stimulate demand for kimono, it is necessary to examine how individuals form their impressions of kimonos based on personal experiences. Particularly for women, the comfort of wearing a kimono can vary greatly depending on the position and width of the obi (sash) and the tightness of its tie. If one's past experiences with kimono have been limited to formal occasions, the perception of kimono may become fixed as rigid and cumbersome attire.\n\nTherefore, this study aimed to first investigate the experiences and perceptions regarding kimono among younger generations who may not be familiar with them. Conversely, it explored what aspects of kimono appeal to individuals who are already familiar with them, and how these perceptions differ from those of the younger generation. The study targeted university students (both undergraduate and graduate) as well as kimono enthusiasts (individuals attending kimono classes). By comparing data from these groups, the study also examined the backgrounds of individuals who became kimono enthusiasts, proposing initiatives to stimulate demand for kimono, particularly among the younger generation.\n\nTo understand individuals' involvement with kimono, we utilized questionnaire items concerning their experiences of wearing kimono and the associated challenges, perceptions of kimono and Western-style clothes (Mino & Niwa, 2008), and inquiries into their attitudes towards kimono (Yoshida, 2014).\n\n\n2. Methods\n\nThis study was conducted after obtaining approval from the Research Ethics Committee at Utsunomiya University for research involving human subjects. The survey targeting students was approved on January 12, 2023 (Approval Number H22-0115), and a revised version including enthusiasts as subjects was subsequently approved on March 8, 2023 (Approval Number H22C-0115). The entire study was conducted in adherence with the Declaration of Helsinki (World Medical Association, 2013).\n\nThe survey, titled “survey on kimono among college students” and “survey on kimono among kimono enthusiasts”, respectively, involved distributing paper questionnaires during break times on campus or at kimono classes in the Kanto region. The detailed study hypothesis was not explained in advance to avoid biasing effects on the results.\n\nIt was emphasized that participation was voluntary, and participants were assured that their decision to participate or not would not result in any disadvantages, the survey responses would be used for research purposes only, all responses would be treated anonymously and analyzed statistically, and the survey data would be securely stored. Participants were also informed that they could withdraw from the survey at any time without facing any repercussions, even after agreeing to participate. They were instructed to proceed with the survey only if they agreed to these conditions.\n\nA total of 211 university and graduate students from a university in Japan participated in the survey (79 males, 128 females; 2 respondents chose “no response” and 2 did not select any option; mean age 19.20 ± 1.85 years; 200 Japanese nationals, 2 Mongolian nationals, 9 Chinese nationals). Additionally, 50 individuals attending kimono classes in the Kanto region, participated (4 males, 36 females; mean age 63.00 ± 14.48 years, range 23-80 years, 2 respondents did not provide their age; mean duration of kimono enthusiast 17.42 ± 14.76 years, range 1-60 years, 2 respondents did not provide their duration of being kimono enthusiasts).\n\nThe questionnaire consisted of demographic questions and psychometric scales.\n\n(1) Demographic questions: In the survey targeting students, this section consisted of items asking for gender, age, and nationality. For international students, respondents were also asked about the number of years since they arrived in Japan. In the survey targeting kimono enthusiasts, participants were asked to provide information on gender, age, current occupation, and the duration of their experience as a kimono enthusiast (in years).\n\n(2) Experience with kimono: This section utilized items based on Mino & Niwa (2008; https://www.jstage.jst.go.jp/article/senshoshi1960/49/11/49_11_793/_article/-char/ja/). Participants were presented with ten scenarios with a high likelihood of wearing kimono (e.g., summer festivals, Shichi-Go-San; a traditional Japanese celebration for children who are 3/5/7 years old, Coming of Age ceremonies) as well as an “Other” option, allowing them to select all scenarios in which they had worn kimono. If they chose “Other,” they were provided with a space to specify the specific scenario.\n\n(3) Challenges of wearing kimono: This section utilized items based on Mino & Niwa (2008). Participants were presented with ten options that could be considered challenges while wearing kimono (e.g., difficult to move, hot, cold), along with an “others” option allowing them to specify additional challenges if applicable. Participants were instructed to select all options that applied to them. If they chose “others,” they were provided with a space to specify the specific challenges.\n\n(4) Perceptions of kimono and Western-style clothes: This section utilized items from Mino & Niwa (2008), focusing on the perception of clothes such as Western-style clothes, furisode (long-sleeved kimono for young women), and yukata (casual summer kimono). Participants were instructed to mark their perception on a scale of 0 to 10 for each of 11 adjective pairs (e.g., formal—casual) presented along a continuum. After completing the survey on kimono, participants were instructed to respond to the same 11 adjective pairs regarding Western-style clothes.\n\n(5) Attitudes towards kimono: Participants were asked to respond to 38 items regarding attitudes towards kimono, based on Yoshida (2014; https://www.consortium.or.jp/seisaku/5137). Examples of these items include “I want to wear kimono as casual wear in my daily life.” and “Wearing a kimono turns my mood off.” Responses were solicited using a 7-point scale ranging from “1: Not at all applicable” to “7: Very applicable.”\n\n\n3. Results and Discussion\n\n3.1.1 Experience and occasions of wearing kimono\n\nRegarding students' experiences of wearing kimono, 36 participants (17.06% of the participants) reported that they had never worn kimono. Among them, 9 were female students (7.03% of female students), and 27 were male students (34.18% of male students). It is evident that even among the younger generation of students, the majority have had opportunities to wear kimono. In the case of kimono enthusiasts, all 50 participants reported having experience wearing kimono.\n\nFigure 1 presents the aggregation of occasions for wearing kimono when considering the number of individuals who have worn kimono as 100% for male students, female students, and kimono enthusiasts, respectively.\n\n3.1.2 Challenges of wearing kimono\n\nThe aggregated results of the challenges encountered when wearing kimono for both students and kimono enthusiasts are illustrated in Figure 2. The majority of students (72.2% of males and 82.0% of females) reported experiencing difficulty in movement while wearing kimono. Conversely, among kimono enthusiasts, it is evident that a relatively smaller proportion (52.0%) did so.\n\nWe conducted an exploratory factor analysis on the overall data (students and kimono enthusiasts) regarding the image of kimono. In each item, missing values ranged from one to six participants and they were handled using list-wise deletion. As a result, only one factor was extracted. Two items, “Ease of aligning with fashion trends—Difficulty in alignment with fashion trends” (-.170) and “Fashionable—Not Fashionable” (.084), with factor loadings below .4 were omitted from subsequent analysis.\n\nThe remaining nine items (Table 1) were averaged to calculate the composite score for perceptions of kimono. Basic statistics for each group are presented in Table 2.\n\nWe conducted independent samples t-tests to examine whether there were differences in the composite scores for perceptions of kimono based on participants' attributes (students vs. kimono enthusiasts). Missing values were handled using pair-wise deletion. The results revealed a significant difference between groups (t(258)=-10.314, p<.001), indicating that the kimono enthusiasts rated kimonos as more comfortable to wear, less prone to coming disheveled, and more casual compared to the students (Figure 3).\n\nAdditionally, to explore whether this tendency among kimono enthusiasts was strengthened with a longer duration of enthusiasm, we conducted a correlation analysis between the duration of kimono enthusiasm and the composite score for perceptions of kimono, focusing solely on data from kimono enthusiasts. However, no significant correlation was found (r=.185, p=.213).\n\nWe also conducted an exploratory factor analysis on the scores for perception of Western-style clothes, encompassing all available data. In each item, missing values ranged from one to three participants and they were handled using list-wise deletion. As a result, three factors were extracted. Based on the content of each questionnaire items, we labeled the first factor as “easy to move,” the second factor as “easy to wear in daily life,” and the third factor as “fashionable.” One item, “conspicuous—not conspicuous” (.368), with a factor loading below.4, was omitted from subsequent analysis. The remaining 10 items (Table 3) were averaged to calculate the composite score for perceptions of Western-style clothes.\n\nTo note, for the “fashionable” score for Western-style clothes, we reversed the numerical values to indicate higher scores representing “more fashionable” before calculating the mean. Basic statistics for each group are presented in Table 4.\n\nWe conducted independent t-tests below to examine differences between the groups (students vs. kimono enthusiasts) on each score. Missing values were handled using pair-wise deletion.\n\n3.3.1 Score for “easy to move”\n\nFirst, there was no significant difference in score for “easy to move” between the groups (t(257)=1.299, p=.195).\n\nHowever, a correlation analysis between the duration of being kimono enthusiasts and the score for “easy to move” in Western-style clothes using data only from the kimono enthusiasts revealed a weak but significant negative correlation (r=-.253, p=.090). This suggests that while the evaluation of “easy to move” in Western-style clothes does not differ significantly between the students and kimono enthusiasts overall, those with longer experience in kimono appreciation tend not to perceive Western-style clothes as particularly easy to move. As there is a positive correlation between the duration of being kimono enthusiasts and age (r=.419, p=.004), one interpretation of the above results alone could be that ease of movement in daily life decreases with age. However, as mentioned earlier, no correlation was found between the scores for perceptions of kimono (which also include the evaluation of ease of movement in kimono) and the duration of being kimono enthusiasts. Therefore, it would be more appropriate to interpret that the longer the duration of experience as a kimono enthusiast, the lower the evaluation of ease of movement in Western-style clothes.\n\n3.3.2 Score for “easy to wear in daily life”\n\nNext, when the dependent variable was the score for “easy to wear in daily life,” there was a significant difference between the groups (t(258)=3.174, p=.002), indicating that the kimono enthusiasts rated the ease of wearing Western-style clothes lower than the students (see Figure 4). Furthermore, a correlation analysis was conducted using data only from the kimono enthusiasts to examine the relationship between the duration of being kimono enthusiasts and the score for “easy to wear in daily life” of Western-style clothes. The results showed a weak but significant negative correlation (r=-.264, p=.073). Thus, there is a possibility that the tendency observed in the t-test mentioned above, where the kimono enthusiasts rated the ease of wearing Western-style clothes lower, becomes stronger with a longer duration of kimono enthusiasm.\n\n3.3.3 Score for “fashionable”\n\nThe results, with the “fashionable” score for Western-style clothes as the dependent variable, showed a significant difference between the groups (t(257)=-4.147, p<.001), indicating that the students rated the fashionability of Western-style clothes higher than the kimono enthusiasts (Figure 5). A correlation analysis was conducted using data only from the kimono enthusiasts, examining the relationship between their duration of ”kimono enthusiasm and the “fashionable” score for Western-style clothes, but no significant correlation was found (r=-.136, p=.369).\n\nNext, we conducted an exploratory factor analysis on attitudes towards kimono using the entire dataset (students and kimono enthusiasts). In each item, missing values ranged from one to four participants and they were handled using list-wise deletion. As a result, three factors were extracted. Based on the content of each questionnaire item, the first factor was labeled “kimono as daily wear,” the second factor “kimono as a special day wear,” and the third factor “adviser.” 18 items with factor loadings below. 4 were removed from subsequent analysis.\n\nFor the remaining 20 items (see Table 5), reverse scoring was applied to items as necessary to ensure alignment with the factor names, and composite scores were calculated by averaging scores within each factor. Basic statistics for each group are presented in Table 6.\n\nWe conducted independent t-tests below to compare the scores between the groups (students vs. kimono enthusiasts). Missing values were handled using pair-wise deletion.\n\n3.4.1 Score for “kimono as daily wear”\n\nWe first analyzed the score for “kimono as daily wear” as the dependent variable. The results showed a significant difference between the groups (t(258)=-11.107, p<.001), indicating that kimono enthusiasts perceived kimono more as daily wear than students (Figure 6). Using data only from the kimono enthusiasts, a correlation analysis between the duration of being kimono enthusiasts and the score for “kimono as daily wear” was also conducted, but no significant correlation was found (r=.173, p=.241).\n\n3.4.2 Score for “kimono as a special day wear”\n\nNext, we analyzed the score for “kimono as a special day wear” as the dependent variable. There was no significant difference between the groups (t(258)=1.186, p=.237). This suggests that while enthusiasts may view kimono as more of a daily wear compared to students, they do not necessarily dismiss the enjoyment of wearing it as special attire. It can be inferred from the results that the kimono enthusiasts perceive kimono as adaptable clothes that can serve both daily and formal purposes, depending on the type of kimono and how it is worn.\n\nA correlation analysis was conducted between the duration of being kimono enthusiasts and the score for “kimono as a special day wear” using data exclusively from the kimono enthusiasts, but no significant correlation was observed (r=.155, p=.293).\n\n3.4.3 Score for “adviser”\n\nWe analyzed the “adviser” score as the dependent variable. As the results, there was a significant difference between the groups (t(258)=-6.181, p<.001), indicating that kimono enthusiasts are more likely to have someone they can casually consult about kimono compared to students (Figure 7). Whether this result reflects the need for advice on kimono among enthusiasts, who likely have more opportunities to wear kimono, or conversely, whether the availability of someone to consult about kimono has contributed to becoming an enthusiast, warrants further investigation.\n\nA correlation analysis was conducted between the duration of kimono enthusiasm and the “adviser” score using data exclusively from the kimono enthusiasts, but no significant correlation was observed (r=.074, p=.617).\n\n\n4. Conclusion\n\nIn this study, a questionnaire survey was conducted with Japanese college students and kimono enthusiasts to investigate their experiences with wearing kimono and its challenges, their perceptions of kimono and Western-style clothes, and their attitudes towards kimono.\n\nFirstly, the results indicated that a significant portion of students had opportunities to wear kimono in the past while many students experienced challenges such as difficulty in movement while wearing kimono. This could be attributed to the fact that students' experiences primarily involved wearing kimono for formal occasions or events such as Shichi-Go-San (a traditional rite of passage), where they may have tightly dressed in kimono to prevent them from coming undone. This suggests a consistent trend where students perceive Western-style clothes as more comfortable for movement compared to kimono, reflected across scores for perceptions of kimono, perceptions of Western-style clothes, and attitudes towards kimono. In other words, it seems that the versatility of kimono, which can be casual and easy to move in depending on the type and styling, is not recognized by the younger generation who have only experienced it as formal attire. Adachi (2015) observed that when considering the task of dressing a bedridden individual, it is apparent that kimonos are far more practical than Western-style clothes. Adachi argued that the notion that the popular belief as “Western-style clothes are functional while kimonos are not” stems from the perspective of able-bodied individuals, and negates the inherent flexibility and adaptability of traditional kimono attire.\n\nOn the other hand, it seems that among kimono enthusiasts, the tendency to perceive Western-style clothes as more functionally superior to kimono has been alleviated. The kimono enthusiasts rated kimonos as easier to move, harder to become disheveled, and more casual compared to students. They rated the ease of wearing Western-style clothes lower than college students, with this tendency becoming more pronounced among those with longer experience as enthusiasts. Also, there is a trend for the evaluation of the ease of movement in Western-style clothes to decrease as the duration of enthusiasm increases. Furthermore, while the kimono enthusiasts considered kimonos more of a “daily wear” compared to the college students, they did not deny the enjoyment of wearing them as formal attire.\n\nFrom these results, it can be inferred that the tendency to perceive kimono as more functionally inferior to Western-style clothes may change as individuals accumulate experiences related to kimono. Conversely, to change the negative perceptions of kimono among young people, providing opportunities for them to experience more comfortable ways of wearing kimono could have an impact. Ensuring an adequate number of classes, support systems for dressing in coeducation environments would be key issues to be addressed, creating sufficient opportunities in Japanese school education.\n\nAnother distinction between the students and kimono enthusiasts is the availability of supportive environments for seeking advice about kimonos among the enthusiasts. This implies that newcomers, unfamiliar with kimono attire, could engage with the kimono community through these advisory channels and potentially develop into kimono enthusiasts. Further investigation through interviews will be needed to delve into this process of participation.\n\nCurrently, the inbound demand, which has been severely affected by the COVID-19 pandemic, is gradually recovering. Conducting surveys to understand the perceptions and needs of individuals with cultural backgrounds different from Japanese, regarding kimono, will become increasingly important. From the perspective of Sustainable Development Goals (SDGs), there is also a possibility of growing attention towards kimono as sustainable clothing. Therefore, it is necessary to conduct surveys targeting foreign tourists to Japan and overseas kimono enthusiasts, and comparing the results with those in Japan. The potential confounding between years of kimono enthusiasm and age also needs to be carefully discussed in future studies. By accumulating such insights, we aim to contribute to the expansion of kimono demand in the future.\n\n\nConsent and ethical considerations\n\nThis study was conducted after obtaining approval from the Research Ethics Committee at Utsunomiya University for research involving human subjects. The survey, titled “survey on kimono among college students” (approved on January 12, 2023; Approval Number is H22-0115) and “survey on kimono among kimono enthusiasts” (approved on March 8, 2023; Approval Number H22C-0115), respectively, involved distributing paper questionnaires during break times on campus or at kimono classes in Kanto region. The survey targeting students was conducted from January to June 2023, while the survey targeting enthusiasts was conducted from April to May 2023. All participants were confirmed to be adults in Japan at the time of participation. The entire study was conducted in adherence with the Declaration of Helsinki.", "appendix": "Data availability\n\nUtsunomiya University Academic Institutional Repository: Is It Difficult to Move in a Kimono? A Study about Perceptions of Kimono among College Students and Kimono Enthusiasts. https://doi.org/10.24565/0002000161 (Miyashiro et al., 2024).\n\nThis project includes the following underlying data:\n\n• Kimono_survey.xlsx (Responses from participants used in this study)\n\nUtsunomiya University Academic Institutional Repository: Is It Difficult to Move in a Kimono? A Study about Perceptions of Kimono among College Students and Kimono Enthusiasts. https://doi.org/10.24565/0002000161 (Miyashiro et al., 2024).\n\nThis project contains the following extended data:\n\n• Kimono Questionnaire for Enthusiasts (A complete questionnaire for kimono enthusiasts translated into English)\n\n• Kimono Questionnaire for Students (A complete questionnaire for students translated into English)\n\n• STROBE_checklist_cross-sectional-F1000.docx (A reporting checklist according to STROBE cross-sectional research guidelines)\n\n• Flow chart.pptx (Diagram showing the relationship between research content and procedures)\n\nThe data is available under the terms of the Creative Commons Zero “No Rights Reserved” data waiver (CC0 1.0 Public Domain Dedication).\n\n\nAcknowledgments\n\nWe extend our sincere gratitude to Akiko Imaizumi, a tsumugi weaver associated with the Yuuki Tsumugi Sensibility Kansei Information Technology Council at the Industrial Tourism Division of Oyama City Office, and Junko Nagata, a traditional craftsperson from the NPO preserving the traditional techniques of making floss silk and its hand spinning, for their understanding and cooperation in this research, as well as to all other parties involved.\n\n\nReferences\n\nAdachi T: Is the Revival of Kimono Authentic? Textile Trends. 2015; 113: 58–72. (in Japanese).\n\nMinistry of Economy, Trade and Industry in Japan, Textile Division: Report from the Secretariat (Questionnaire Survey Results).2015. (in Japanese). Retrieved March 2, 2024. Reference Source\n\nMinistry of Education in Japan: Curriculum Guidelines for junior high schools (issued in Heisei 29).2017. (in Japanese). Retrieved March 2, 2024. Reference Source\n\nMino T, Niwa H: Positioning for Yukata in clothing life of young women: in special reference to an image of women college students in Nagano-city. Journal of the Japan Research Association for Textile End-uses. 2008; 49: 793–802. (in Japanese)\n\nMiyashiro K, et al.: Data from: Is It Difficult to Move in a Kimono? A Study about Perceptions of Kimono among College Students and Kimono Enthusiasts. [Dataset]. Utsunomiya University Academic Institutional Repository; 2024. Publisher Full Text\n\nWorld Medical Association: WMA Declaration of Helsinki: Ethical principles for medical research involving human subjects. JAMA. 2013; 310(20): 2191–2194. Retrieved March 28, 2024. Reference Source\n\nYoshida M: Analysis of new segments and their characteristics in the kimono-related market. Research Report on the Project of Future Kyoto Creation. 2014; 2013(1): 81–104. (in Japanese). Retrieved March 28, 2024. Reference Source" }	[ { "id": "270665", "date": "22 May 2024", "name": "Ellen McKinney", "expertise": [ "Reviewer Expertise Japanese fashion", "Kimono", "Zero-waste apparel 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\nThis study illuminates the occasions on which young people wear kimono and how they perceive the practice. It also compares this with the experiences of older people who regularly wear kimono.\nThe literature review establishes the problem under investigation and serves as a foundation for this study. To provide a comprehensive context, it may be beneficial to incorporate the findings of previous related studies, including the one from which the survey questions are derived. These findings can then be compared and discussed at the conclusion of the paper, offering a more comprehensive understanding of the cultural significance of kimono wearing in Japan.\nThe study method is robust and comprehensive. However, it is important to note that the statistical analysis is beyond the scope of my expertise, therefore, I am unable to provide detailed commentary on this aspect.\n\nThe conclusions and discussion provide good ideas for increasing students' interest in kimonos for daily wear and good ideas for future research, such as interviews.\nThere are a few minor suggestions: The introduction should clearly list all hypotheses and research questions and serve as a reliable guide for our readers, ensuring a smooth navigation through the study.\nThis link needs to be fixed. Please correct the following: Ministry of Economy, Trade and Industry in Japan, Textile Division: Report from the Secretariat (Questionnaire Survey Results).2015. (in Japanese). Retrieved March 2, 2024. Reference Source\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "11805", "date": "18 Jun 2024", "name": "Kozue Miyashiro", "role": "Author Response", "response": "We apologize for the delayed response. We have received your review and sincerely appreciate the time and effort you have dedicated on our behalf." }, { "c_id": "11820", "date": "27 Jun 2024", "name": "Kozue Miyashiro", "role": "Author Response", "response": "In accordance with your suggestions, we have revised the paper to include a list of the hypotheses and research questions in the introduction and have submitted version 2 to the editor. Additionally, I apologize for the broken link in the references. I have updated the link to the correct website." } ] }, { "id": "293693", "date": "27 Jun 2024", "name": "Lasni Buddhibhashika Jayasooriya", "expertise": [ "Reviewer Expertise Female schoolteachers' dress code", "society and culture", "school curriculum" ], "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 adopts a quantitative approach to explore the experiences, challenges, perceptions, and attitudes towards wearing kimono among college students and kimono enthusiasts. The methodology employed is clearly articulated, and the paper presents the data and results appropriately. However, I find my statistical knowledge insufficient to provide detailed comments on the chosen statistical tests and their usage.\nThe authors discuss literature, highlighting the decline in kimono wearing. It would have been more informative if the distinction between wearing kimono in \"daily life\" and at work had been elaborated. Before World War II, it was common for schoolteachers to wear kimono, but this practice shifted to Western-style attire. While Westernization significantly contributed to this shift, other factors such as economic considerations, safety, and productivity-related issues also played a role (See T, Namba,2008 [Ref 1]] and UGLB, Jayasooriya, et. al., 2020 [Ref 2]).\nThere is a considerable difference between the mean age of the college student group and that of kimono enthusiasts, which may influence their daily activities and preferences for \"daily wear\". Additionally, age differences might affect exposure to cultural values and knowledge, resulting in varying attitudes towards kimono. These showcase limitations of comparison between the two groups, which would be appropriate to mention. On the other hand, the perceptions of kimono enthusiasts are biased in favor of kimono. Therefore, in the conclusion section of the abstract, it would be appropriate to specify that 'the ease of movement in Western clothing is alleviated as the experience of wearing kimono increases' is a perception that may not be shared by college students since that finding is based on kimono enthusiasts' data. Moreover, understanding what inspires kimono enthusiasts to embrace kimono culture would be valuable information to explore more (especially through interviews as authors have suggested) in future research to find how to popularize kimono.\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": "12468", "date": "19 Sep 2024", "name": "Kozue Miyashiro", "role": "Author Response", "response": "We would like to sincerely thank you for taking the time to carefully review our manuscript and for providing such valuable feedback. Regarding your first suggestion, to distinguish between wearing kimono in everyday life and in the workplace, we have addressed this by adding the following footnote in the Introduction. we have also included citations for the two references you kindly recommended. Thank you again for your assistance. ------------------------------------------------------------- It may be beneficial to distinguish between wearing kimono in daily life and wearing it in the workplace. Jayasooriya et al. (2020) conducted an interview-based study with Japanese female teachers, examining how the relaxation of dress codes in the workplace affected their professional performance. The findings suggest that while the duties of Japanese teachers are diverse, including not only teaching but also tasks such as supervising school-wide cleaning and assisting with school meals, the ability to wear casual attire facilitates their dynamic roles. Additionally, Namba (2008) argued that the transition from traditional Japanese clothing to Western-style attire in modern Japan has been obscured by preconceived notions. Namba's study investigates in detail the shifts in gender perspectives and aesthetic values, as well as the growing appreciation of the functionality of Western attire, which contributed to the change in clothing norms among female teachers. ------------------------------------------------------------- Regarding your second suggestion—that the difference in age between the enthusiast group and the student group, in addition to the distinction of being an enthusiast or not, may introduce significant confounding factors—we have addressed this by incorporating the following revisions into the Conclusion as a limitation of this study. We believe this clarification has enhanced the paper by clearly outlining its limitations as well as its contributions. Thank you once again for your valuable insights. ------------------------------------------------------------- The potential confounding between years of kimono enthusiasm and age also needs to be carefully treated: A significant disparity exists between the mean age of the college student group and that of the kimono enthusiasts, which may impact their daily routines and preferences for everyday attire. Moreover, age differences could influence their exposure to cultural values and knowledge, potentially leading to divergent attitudes towards kimono. Similarly, the finding that \"the ease of movement in Western clothing becomes less significant as the experience of wearing kimono increases\" must be carefully examined in future research to determine whether this applies more broadly to populations beyond kimono enthusiasts. -------------------------------------------------------------" } ] } ]	1	https://f1000research.com/articles/13-287
https://f1000research.com/articles/12-383/v1	12 Apr 23	{ "type": "Clinical Practice Article", "title": "Satisfactory result of great saphenous vein endovenous laser ablation until below the knee on active venous leg ulcer: a case series", "authors": [ "Taofan Taofan", "Iwan Dakota", "Achmad Hafiedz Azis Kartamihardja", "Jonathan Edbert Afandy", "Suci Indriani", "Suko Adiarto", "Iwan Dakota", "Achmad Hafiedz Azis Kartamihardja", "Jonathan Edbert Afandy", "Suci Indriani", "Suko Adiarto" ], "abstract": "Background: Active venous leg ulcer (VLU) is the most severe manifestation of chronic venous disease which not only affects patients’ health, but also decreases the quality of life, and delivers economic burdens. Treatment of superficial venous reflux with early endovenous laser ablation (EVLA) has been proven to reduce ulcer recurrence levels and promote faster VLU healing. We reported three cases of patients with active VLU undergoing EVLA with different approaches. Case illustration: Three patients came with complaint of leg ulcer, diagnosed with C6sEpAsdPr, with venous clinical severity scores (VCSS) of 15, 23, and 22 respectively. Severe great saphenous veins (GSV) reflux was found in all patients by duplex ultrasound examination. The second patient had undergone above-the-knee EVLA. All patients underwent EVLA using 1470-nano meter wavelength laser device and ELVeS radial fiber (Biolitec, Bonn, Germany). The laser energy protocol used was 6 W linear endovenous energy density (LEED) 50 J/cm for proximal until media ATK GSV ablation, 5 W LEED 40 J/cm for media ATK until proximal below-the-knee (BTK) GSV, and 2 W LEED 20 J/cm for proximal until distal BTK GSV. The third patient was also treated with EVLA for small saphenous vein severe reflux. Follow-up until 6 months post-EVLA showed significant healing of the ulcer with 14, 16, and 17 VCSS reduction consecutively without any complication. Conclusion: We’ve reported three cases of patients with active VLU undergoing EVLA until BTK with significant results. The EVLA of GSV until BTK is safe and provides satisfactory results in patients with VLU.", "keywords": [ "venous leg ulcer", "endovenous laser ablation", "below the knee", "laser power", "outcome", "complication" ], "content": "Introduction\n\nActive venous leg ulcer (VLU) is the most severe manifestation of chronic venous disease (CVD), classified as clinical C6 on clinical, etiological, anatomical, and pathophysiological (CEAP) classification with several contributing factors including venous reflux, obstruction outflow, pump failure of calf muscles, and obesity that causes chronic venous hypertension.1 The prevalence ranges between 0.8 to 2.2 patients for every 1000 people/year and with 19.0±12.1 weeks healing time.2 Active VLU alone represents 3.5% of patient populations with CVD.3 Despite the small number, the quality of life of patients with active VLU is affected in various dimensions, especially on the emotional level and regarding body image, with pain and ulcer severity contributing to a decrease in patients’ quality of life.4 VLU not only impacts patients’ health but also delivers an economic burden with approximately £7706 per patient per year direct cost to manage VLU patients, and more than £2 billion annually (representing 1.2% of the annual budget) in a study on the British population.5 Patients with an advanced form of chronic venous insufficiency (CVI), including lipodermatosclerosis, healed VLU, and active VLU have a complex venous disease with a superficial, perforator, and deep vein involvement.6 Treatment of superficial venous reflux with early endovenous laser ablation (EVLA) has been proven to reduce ulcer recurrence levels and promote faster VLU healing.7 In a study by Montminy et al.,8 the VLU healing rate after 12 months in the patient group treated with EVLA was 82% versus 36% in the compression therapy only group. Here we report three cases of patients with active VLU undergoing EVLA using 1470-nano meter (nm) wavelength laser device and ELVeS radial fiber (Biolitec, Bonn, Germany) in National Cardiovascular Center Harapan Kita, Jakarta, Indonesia with different approaches.\n\n\nCase illustration\n\nA 60-year-old woman, who worked as a baker, presented with a complaint of a wound in her right ankle accompanied by pain (visual analog scale (VAS) 3/10) in the past three months. The complaint began with swelling in both lower limbs that got worse one year earlier. There was a change of skin color on both the patient’s leg and foot which became darker over time. The patient had a history of hypertension. On physical examination of the malleolus medial dextra region, there was a solitary ulcer, sized 3×4 cm with irregular edges, erythema ulcer base accompanied by purulent discharge, dry distant tissue, edema (+), and hyperpigmentation on 1/3 medial cruris until dorsum pedis (Figure 1A). There was severe CVI in above the knee (ATK) and below the knee (BTK) great saphenous vein (GSV) and moderate CVI in the deep vein of both lower limbs from duplex ultrasound (DUS) examination of the lower extremity. The patient was diagnosed with CVI on both lower limbs with active VLU on malleolus medial dextra (C6sEpAsdPr). The venous clinical severity score (VCSS) was 15. The patient agreed to EVLA treatment on the right lower limb and received ceftriaxone antibiotics for five days. The procedure was done after the patient finished the antibiotics course.\n\nEVLA was performed under spinal anesthesia. Mapping was done on the right GSV. The diameter of the saphena-femoral junction (SFJ) was au11.0 mm, proximal ATK GSV 9.2 mm, medial ATK GSV 6.0 mm, distal ATK GSV ATK 6.1 mm, proximal GSV BTK GSV 5.2 mm, media BTK GSV 4.5 mm, and distal BTK GSV 3.0 mm. Double puncture was used on distal BTK and distal ATK GSV because of tortuosity and branching at distal ATK. Puncture and application of tumescent anesthesia were done by guided DUS. EVLA started 3 cm from SFJ with laser power of 6 W linear energy density (LEED) 50 J/cm at proximal until media ATK, 5 W LEED 40 J/cm at media ATK until proximal BTK, and 2W LEED 20 J/cm at proximal until distal BTK. The total ablated GSV length was 60 cm with a total of 850 mL tumescent. Lower extremity DUS showed perfectly obliterated ablated GSV, no thrombus found in the deep vein, and a patent epigastric vein. The patient was discharged one day after the procedure.\n\nThe patient’s condition was assessed one week after EVLA, and she reported no more pain, significant rapid improvement of the ulcer, granulation tissue (+), and no more discharge (Figure 1B). At follow up six months post-EVLA, the patient didn’t have any complaints and had a healed ulcer. There was a 14-point improvement in VCSS score down to a score of 1.\n\nA. pre-EVLA; B. 1-week post-EVLA.\n\nA 50-year-old male chef presented with complaints of wounds on his left ankle in the last two years accompanied by pain aggravated by walking (VAS 4/10). The patient had undergone EVLA on the left ATK GSV with phlebectomy eight months earlier, but there wasn’t any improvement of the ulcer. The patient had wound care with a surgeon who suggested doing a lower extremity vessel evaluation. The patient had a history of hypertension, type 2 diabetes mellitus, and obesity with body mass index (BMI) of 39.45 kg/m2. Physical examination of the malleolus sinistra region showed multiple ulcers sized 18×10 cm on the medial side, 8×5 cm, and 4×2 cm on the lateral side with irregular edges (Figure 2A). The ulcer had an erythema base, purulent discharge, dry distant tissue, and edema (+). Hyperpigmentation of 1/3 of the medial cruris sinistra until dorsum pedis sinistra. Lower extremity DUS revealed perfectly obliterated proximal until distal ATK left GSV, severe CVI on BTK left GSV, deep veins and accessory veins of both lower limbs, and moderate CVI in right GSV (Figure 3). The patient was diagnosed with CVI on both lower limbs and active VLU on malleolus medial and lateral sinistra (C6sEpAsdPr) with VCSS 23. The patient decided to undergo EVLA on the left lower limb. A culture of the ulcer base swab reported Pseudomonas aeruginosa (which is resistant to cefazoline). The patient received ceftriaxone and metronidazole for five days. The procedure was done after the patient finished the antibiotics course.\n\nA. pre-EVLA; B. 6-months post EVLA.\n\nA. Obliterated segment of above-the-knee left GSV;\n\nB. persistent reflux of below-the-knee GSV (968 ms).\n\nEVLA was done under spinal anesthesia. Mapping of left GSV and accessory vein was done resulting in proximal ATK accessory vein diameter 6.0 mm, medial ATK 8.3 mm, and distal ATK 6.5 mm. The diameter of distal ATK GSV was 8.00 mm, proximal BTK GSV 7.4 mm, and media BTK GSV 5.4 mm. The puncture was initially started from distal ATK GSV retrogradely, but the laser catheter couldn’t pass because of branching in the proximal BTK area. Access was moved to the left dorsalis pedis, and a laser catheter was introduced until distal ATK. The total tumescent amount was 350 mL. EVLA was started in distal ATK GSV until proximal BTK with laser power of 5 W LEED 40 J/cm, followed by 2 W LEED 20 J/cm in proximal until media BTK GSV. The second puncture was done on distal ATK accessory veins with laser power 6 W LEED 50 J/cm from proximal until distal ATK of the left accessory vein. The total amount of the tumescent was 500 mL. The total ablated GSV length was 33 cm and the accessory vein was 29 cm. Lower extremity DUS showed ATK until BTK left GSV and accessory vein were perfectly obliterated, no DVT found, and patent epigastric vein.\n\nThe patient was discharged two days after the procedure with optimal medical treatment and wound care by the nursing team with modern wound dressing. At follow up after six months, the patient did not have any complaints. Skin condition on malleolus sinistra region showed healed ulcer with granulation tissues, no purulent discharge, minimal swelling until below the knee, and hyperpigmentation (Figure 2B). There was a 16-point reduction of VCSS down to 7.\n\nA 65-year-old male farmer presented with complaints of ulcers with smelly discharge at the right ankle accompanied by pain (VAS 4/10) in the past two years which became worse and enlarged in the past six months. Complaints begin with swelling of both lower limbs for 11 years. The patient had undergone various traditional treatments before such as the use of a flour mixture. The patient had a history of hypertension and diabetes mellitus, was an ex-smoker, and was obese with a BMI of 33.3 kg/m2. Physical examination showed multiple ulcers sized 10×8 cm at malleolus lateral dextra and 8×3 cm at malleolus medial dextra with irregular edge, wet base with purulent discharge, erythema, edema (+), and hyperpigmentation from 1/3 proximal cruris dextra until dorsum pedis dextra (Figure 4A). Lower extremity DUS showed severe CVI of bilateral GSV, small saphenous vein (SSV), and deep vein. The patient was diagnosed with bilateral CVI with active VLU at malleolus medial and lateral dextra (C6sEpAsdPr), and VCSS was 22. The patient decided to undergo EVLA on right lower limb first and received ceftriaxone and metronidazole five days before the procedure. The procedure was done after the patient finished the antibiotics course.\n\nEVLA was done under spinal anesthesia. Mapping was done along the right GSV and SSV. The diameter of SFJ was 12.0 mm, proximal ATK GSV was 7.5 mm, media ATK GSV was 7.0 mm, distal ATK GSV was 7.8 mm, proximal BTK GSV was 6.0 mm, media BTK GSV was 4.0 mm, and distal BTK GSV was 3.0 mm. The proximal SSV diameter was 7.0 mm, and the media SSV was 6.5 mm. Puncture by guided DUS was done at three locations for GSV: medial side of dorsalis pedis (distal from the ulcer), proximal BTK GSV with laser catheter introduced retrogradely, and proximal BTK GSV with laser catheter introduced until 3 cm passed SFJ. EVLA was done with laser power 6 W LEED 50 J/cm in proximal until media ATK GSV, 5 W LEED 40 J/cm in media ATK GSV until proximal BTK GSV, and 2 W LEED 20 J/cm in proximal until distal BTK. Puncture for SSV was done at media BTK, laser catheter was introduced until 5 cm passed Sapheno-poplitea Junction. EVLA at proximal until media SSV was done with laser power 4 W LEED 30 J/cm. The total ablated GSV length was 64 cm and the SSV length was 10 cm with a total of 850 mL of tumescent amount. Lower extremity DUS showed the ablated GSV and SSV were perfectly obliterated, no thrombus found, and a patent epigastric vein. Wound dressing of the ulcer and an elastic bandage was applied to the patient’s right lower limb.\n\nThe patient was discharged two days after the procedure with optimal medical therapy and the wound care was done by the nursing team with modern wound dressing. At follow up after six months, the patient did not have any complaints and the ulcer and skin condition had significantly improved. There was no ulcer left, hyperpigmentation was limited to 1/3 proximal cruris dextra, and there was a scar (+) on the previously ulcerous region (Figure 4B). There was a 17-point reduction of VCSS down to 5.\n\nA. pre-EVLA; B. 6-months post EVLA.\n\n\nDiscussion\n\nAccording to the European Society for Vascular Surgery (ESVS) 2022 Clinical Practice Guidelines on the Management of Chronic Venous Disease of the Lower Limbs, it is recommended to do early endovenous ablation in patients presenting with active VLU and superficial vein incompetence to accelerate ulcer healing (Class 1 Recommendation with Level of Evidence).1 But the topic of how to do EVLA in active VLU patient remains to be discussed.\n\nAll of the patients we have reported here were classified as C6 CEAP clinical criteria with DUS examination revealing reflux of both ATK and BTK GSV, and one case each with accessory vein and SSV involvement. This clinical finding was correlated with superficial vein as mentioned in García-Gimeno et al.’s9 study that in CVD patients, involvement of ATK and BTK GSV without SSV (odds ratio (OR) 1.72, P<0.05) or with SSV (OR 2.62, P<0.05) significantly increases the possibility of the patient to be in C4 – C6 clinical class.\n\nNumerous incidences of BTK GSV reflux after ATK GSV EVLA have been reported. A study by de Arujo et al.10 showed a 70% incidence of BTK reflux one year after ATK GSV ablation. The study was consistent with our second case which presented persistent symptoms and delayed ulcer healing even after the treatment of ATK GSV EVLA. Pihlaja et al.11 stated that persistent reflux of superficial vein after ablation was the main factor of delayed ulcer healing (multivariate hazard ratio (HR) 0.123, 0.0051-0.295 95% CI, P<0.001) with multifactorial etiology including missed reflux segment and incomplete therapy, reflux sources (GSV/SSV/perforator) which were normal at the earlier examination, recanalization of the treated segment, and history of deep vein thrombosis.\n\nThe decision to do GSV EVLA until BTK is preferred because it is supported by numerous pieces of evidence that provide significantly more advantages than only ATK GSV EVLA. Elimination of reflux throughout the length of the incompetent GSV segment from the SFJ to the most distal point will lead to significant clinical improvement and reduce the need for adjuvant therapy.10 A systematic review by Sussman et al.12 mentioned that in CVI with C4 to C6 disease, more aggressive treatment of the ATK and BTK GSV is justified if the DUS findings demonstrate groin to ankle reflux. These pieces of evidence support our decision to treat our patient with EVLA until BTK GSV.\n\nHowever, there is another factor that should be taken into consideration which is the risk of complications. Reported complications of EVLA procedure are infection (0.5%), thromboembolic events such as deep vein thrombosis and endovenous heat-induced thrombosis (0.85%), hematoma (2.1%), skin burn (2.1%), short term paraesthesia (3.8%), superficial thrombophlebitis (5.6%), and bruising (39%).13 Nerve injury risk in EVLA is directly related to the distance of the ablated vein with the nerve through the needle stick mechanism or burn due to laser energy transfer. This means that BTK GSV EVLA had a higher risk of causing nerve injury since the saphenous nerve runs medially towards the GSV at the level of the upper calf to the ankle.14 Sinabulya et al.15 demonstrated a non-clinically significant permanent sensory loss at 8% of limbs that underwent BTK GSV EVLA after a mean of 41 months follow-up duration in VLU patients without any major nerve injury reported. Utoh and Tsukamoto observed the effect of ablation length on the incidence of post-EVLA neuropathy with an incidence of 0.8% if the ablation length was less than 40 cm from the SFJ and 4.6% if it was more or equal to 40 cm.16 All of the patients in our cases did not show any nerve injury symptoms after follow-up at six months.\n\nVarious efforts need to be made to minimize complications from EVLA. Tumescent anesthesia is used in EVLA to prevent thermal-induced tissue damage, compressing the size of the vein to be treated to allow better energy absorption, as well as allowing early mobilization and reducing the risk of DVT where EVLA without tumescence has an incidence of approximately 36.5% of nerve-related paresthesia.14,17,18 Reducing the number of punctures while administering tumescent anesthesia also logically reduces the incidence of nerve injury.10 We administered DUS-guided tumescent anesthesia in our patients and at follow-up, our patients did not show any signs or symptoms of nerve injury.\n\nIt’s hard to determine the cut-off of laser power in EVLA to perfectly obliterate the vein without complication. Reducing the laser energy along the distal segment of BTK GSV may reduce the incidence of paresthesia, but with consequences of decreased treatment success.10 The newer generation of EVLA with 1470-nm wavelength has more advantages with chromophore targeting only water in the endothelium compared to earlier laser generations with 940-nm and 980-nm wavelengths that targeted hemoglobin molecules.19,20 EVLA with higher wavelength is related to lower energy levels and minimal side effects.20 A study by Arslan et al.20 showed recanalization numbers were significantly lower (P=0.017) after 48 months of follow-up in a group of EVLA with 1470-nm radial-tip laser catheters using laser power LEED 45–120 J/cm (8.3%) compared to the group with 980-nm bare-tip laser catheter using laser power LEED 60–120 J/cm (15.9%). Post-procedural complications such as pain, induration, ecchymosis, paresthesia, and DVT were significantly lower in the 1470-nm group. In another study by Doganci and Demirkilic, 3.33% of the 1470-nm group reported paresthesia compared to 30% in the 980-nm group (P<0.0001). The symptoms experienced tended to be minor with an average duration of less than four weeks in both groups.21\n\nAlthough a systematic review and meta-analysis by Malskat et al.22 showed that the commonly used EVLA parameters (wavelength, delivered energy, and outcome) did not affect the high success rate of the therapy (92%), the laser energy used in this study has a cut off of 50 J/cm. Mendes-Pinto et al.23 showed that closure rates at one year follow-up were lower in a group of 1920-nm EVLA with LEED 17.8±0.6 J/cm (87.5%) compared to the 1470-nm group with LEED 24.7±0.8 J/cm (94.7%) whereas Park et al.19 performed EVLA using 1470-nm laser with laser energy 6W LEED 30 J/cm on 267 limbs and obtained 84.5% completely obliterated GSV results in one month and 100% after six months. Utoh and Tsukamoto proposed EVLA with two-step ablation protocol in their trial that involved 90 limbs, using 1470-nm laser with energy 7W in ATK GSV (LEED 50 – 70 J/cm) and 5W in BTK GSV (LEED 20-25 J/cm) with mean ablated GSV length of 50.4 cm. The DUS follow-up resulted in perfect obliteration of the ablated vein without any saphenous nerve injuries.24 In our case, we were using a protocol with lower laser energy than some past literature because of anatomical consideration that the average GSV diameter of an Asian population was significantly lower than a Caucasian population (Median 2.9 mm vs 5.7 mm; P<0.01).25\n\n\nConclusion\n\nWe’ve reported three cases of patients with active VLU undergoing EVLA until BTK with significant results. The EVLA of GSV until BTK provides satisfactory results in patients with VLU. A combination of DUS-guided procedure, administration of tumescent anesthesia, use of newer generation device, minimal laser energy, and post-procedural management could minimize the risk of complications and produce a maximal outcome.\n\n\nResearch ethics and patient consent\n\nWritten informed consent has been obtained from the patients for publication of the case report 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\n\nAcknowledgements\n\nWe would like to thank the patients for allowing us to have their cases published.\n\n\nReferences\n\nMaeseneer MGD, Kakkos SK, Aherne T, et al.: Editor’s Choice – European Society for Vascular Surgery (ESVS) 2022 Clinical Practice Guidelines on the Management of Chronic Venous Disease of the Lower Limbs. Eur. J. Vasc. Endovasc. Surg. 2022 Feb 1; 63(2): 184–267. PubMed Abstract \| Publisher Full Text\n\nBerenguer Pérez M, López-Casanova P, Sarabia Lavín R, et al.: Epidemiology of venous leg ulcers in primary health care: Incidence and prevalence in a health centre—A time series study (2010-2014). Int. Wound J. 2019; 16(1): 256–265. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHoms-Romero E, Romero-Collado A, Verdú J, et al.: Validity of Chronic Venous Disease Diagnoses and Epidemiology Using Validated Electronic Health Records From Primary Care: A Real-World Data Analysis. J. Nurs. Scholarsh. 2021; 53(3): 296–305. Publisher Full Text\n\nFolguera-Álvarez C, Garrido-Elustondo S, Rico-Blázquez M, et al.: Factors Associated With the Quality of Life of Patients With Venous Leg Ulcers in Primary Care: Cross-Sectional Study. Int. J. Low Extrem. Wounds. 2020 Oct 26; 21: 521–528. Publisher Full Text\n\nPhillips CJ, Humphreys I, Thayer D, et al.: Cost of managing patients with venous leg ulcers. Int. Wound J. 2020; 17(4): 1074–1082. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSermsathanasawadi N, Pruekprasert K, Pitaksantayothin W, et al.: Prevalence, risk factors, and evaluation of iliocaval obstruction in advanced chronic venous insufficiency. J. Vasc. Surg. Venous Lymphat. Disord. 2019 May 1; 7(3): 441–447. PubMed Abstract \| Publisher Full Text\n\nRen SY, Liu YS, Zhu GJ, et al.: Strategies and challenges in the treatment of chronic venous leg ulcers. World J. Clin. Cases. 2020 Nov 6; 8(21): 5070–5085. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMontminy ML, Jayaraj A, Raju S: A systematic review of the efficacy and limitations of venous intervention in stasis ulceration. J. Vasc. Surg. Venous Lymphat. Disord. 2018 May 1; 6(3): 376–398.e1. PubMed Abstract \| Publisher Full Text\n\nGarcía-Gimeno M, Rodríguez-Camarero S, Tagarro-Villalba S, et al.: Reflux patterns and risk factors of primary varicose veins’ clinical severity. Phlebology. 2013 Apr; 28(3): 153–161. PubMed Abstract \| Publisher Full Text\n\nde Araujo WJB , Timi JRR, Nejm CS, et al.: Persistent below-knee great saphenous vein reflux after above-knee endovenous laser ablation with 1470-nm laser: a prospective study. J. Vasc. Bras. 2016; 15(2): 113–119. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPihlaja T, Vanttila LM, Ohtonen P, et al.: Factors associated with delayed venous ulcer healing after endovenous intervention for superficial venous insufficiency. J. Vasc. Surg. Venous Lymphat. Disord. 2022 Nov 1; 10(6): 1238–1244. PubMed Abstract \| Publisher Full Text\n\nSussman MS, Ryon EL, Bahga A, et al.: A systematic review of the treatment of residual below the knee venous reflux after endovenous thermal ablation of the great saphenous vein. J. Vasc. Surg. Venous Lymphat. Disord. 2022 Jan 1; 10(1): 233–240. PubMed Abstract \| Publisher Full Text\n\nDermody M, O’Donnell TF, Balk EM: Complications of endovenous ablation in randomized controlled trials. J. Vasc. Surg. Venous Lymphat. Disord. 2013 Oct 1; 1(4): 427–436.e1. Publisher Full Text\n\nDexter D, Kabnick L, Berland T, et al.: Complications of Endovenous Lasers. Phlebology. 2012 Mar 1; 27(1_suppl): 40–45. Publisher Full Text\n\nSinabulya H, Östmyren R, Blomgren L: Editor’s Choice – Mid-term Outcomes of Endovenous Laser Ablation in Patients with Active and Healed Venous Ulcers: A Follow-up Study. Eur. J. Vasc. Endovasc. Surg. 2017 May 1; 53(5): 710–716. PubMed Abstract \| Publisher Full Text\n\nUtoh J, Tsukamoto Y: Incidence of Nerve Injury after Endovenous Thermal Ablation for Incompetent Great Saphenous Veins. Jpn. J. Phlebol. 2021 Nov 25; 32(3): 337–341. Publisher Full Text\n\nGunes T, Altin F, Kutas B, et al.: Less Painful Tumescent Solution for Patients Undergoing Endovenous Laser Ablation of the Saphenous Vein. Ann. Vasc. Surg. 2015 Aug 1; 29(6): 1123–1127. PubMed Abstract \| Publisher Full Text\n\nMemetoglu ME, Kurtcan S, Kalkan A, et al.: Combination technique of tumescent anesthesia during endovenous laser therapy of saphenous vein insufficiency. Interact. Cardiovasc. Thorac. Surg. 2010 Dec 1; 11(6): 774–778. PubMed Abstract \| Publisher Full Text\n\nPark YS, Kim YW, Park YJ, et al.: Clinical results of endovenous LASER ablation (EVLA) using low linear endovenous energy density (LEED) combined with high ligation for great saphenous varicose veins. Surg. Today. 2016 Sep; 46(9): 1019–1023. PubMed Abstract \| Publisher Full Text\n\nArslan Ü, Çalık E, Tort M, et al.: More Successful Results with Less Energy in Endovenous Laser Ablation Treatment: Long-term Comparison of Bare-tip Fiber 980 nm Laser and Radial-tip Fiber 1470 nm Laser Application. Ann. Vasc. Surg. 2017 Nov 1; 45: 166–172. PubMed Abstract \| Publisher Full Text\n\nDoganci S, Demirkilic U: Comparison of 980 nm Laser and Bare-tip Fibre with 1470 nm Laser and Radial Fibre in the Treatment of Great Saphenous Vein Varicosities: A Prospective Randomised Clinical Trial. Eur. J. Vasc. Endovasc. Surg. 2010 Aug 1; 40(2): 254–259. PubMed Abstract \| Publisher Full Text\n\nMalskat WSJ, Engels LK, Hollestein LM, et al.: Commonly Used Endovenous Laser Ablation (EVLA) Parameters Do Not Influence Efficacy: Results of a Systematic Review and Meta-Analysis. Eur. J. Vasc. Endovasc. Surg. 2019 Aug 1; 58(2): 230–242. PubMed Abstract \| Publisher Full Text\n\nMendes-Pinto D, Bastianetto P, Cavalcanti Braga Lyra L, et al.: Endovenous laser ablation of the great saphenous vein comparing 1920-nm and 1470-nm diode laser. Int. Angiol. 2016 Dec; 35(6): 599–604. PubMed Abstract\n\nUtoh J, Tsukamoto Y: Prevention of Saphenous Nerve Injury after Endovenous Laser Ablation of Incompetent Great Saphenous Veins: 2 Step Ablation. Jpn. J. Phlebol. 2021 Dec 24; 32(3): 355–357. Publisher Full Text\n\nLee Q, Gibson K, Chan S, et al.: A comparison between Caucasian and Asian superficial venous anatomy and reflux patterns – Implications for potential precision endovenous ablation therapy. Phlebology. 2020 Feb 1; 35(1): 39–45. Publisher Full Text" }	[ { "id": "202935", "date": "24 Oct 2023", "name": "Windsor Ting", "expertise": [ "Reviewer Expertise Venous 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\nThis manuscript reports on three cases of active venous ulcers from superficial venous insufficiency treated with endovenous laser ablation.\n\nThe efficacy and safety of endovenous thermal ablation in patients with an active venous ulcer from superficial venous insufficiency have been reported. Nevertheless, there is an important role for case reports of these patients because it provides a picture of these patients in the real world.\nThis manuscript is overall well-written and potentially suitable for indexing.\n\nSeveral comments:\nThere are numerous grammatical errors in the manuscript. The authors should try to correct these errors before indexing of the manuscript.\n\nThe term \"chronic venous insufficiency (CVI)\" is used throughout the manuscript. CVI means different things to different people. Please define CVI so it is clear what exactly is CVI.\n\n\"Treatment of superficial venous reflux with early endovenous laser ablation (EVLA) has been proven to reduce ulcer recurrence levels and promote faster VLU healing.\"\nIt has been shown or associated with. \"Prove\" is too strong a statement.\n\n\"and received ceftriaxone antibiotics for five days\"\nWhy antibiotic? Did the patient have a positive wound culture? Does the author use antibiotic routinely in these cases?\n\"EVLA was performed under spinal anesthesia.\"\n\nWhy spinal anesthesia? These cases can be done with with just tumescence.\n\n\"Lower extremity DUS showed perfectly obliterated ablated GSV, no thrombus found in the deep vein, and a patent epigastric vein.\"\nWhen was this performed? What is the authors' recommendation regarding postoperative ultrasound?\n\"The patient was discharged one day after the procedure.\"\nWhy was the patient hospitalized?\n\"The patient had a history of hypertension, type 2 diabetes mellitus, and obesity with body mass index (BMI) of 39.45 kg/m2.\"\nDid any of these patients have peripheral artery disease? At least one patient was a smoker. How was PAD ruled out? Is it necessary to rule out PAD?\n\"The patient was discharged two days after the procedure with optimal medical treatment and wound care by the nursing team with modern wound dressing.\"\nWhat is optimal medical treatment?\nWhat did the wound care consist of?\nWhat is modern wound dressing?\n\"smelly discharge\"\nMalodorous discharge is a better medical term.\n\n\"The decision to do GSV EVLA until BTK is preferred because it is supported by numerous pieces of evidence that provide significantly more advantages than only ATK GSV EVLA.\"\nHow far below the knee?\n\n\"Various efforts need to be made to minimize complications from EVLA. Tumescent anesthesia is used in EVLA to prevent thermal-induced tissue damage,\"\nWhat about foam sclerotherapy for the GSV below the knee?\n\"the average GSV diameter of an Asian population was significantly lower than a Caucasian population (Median 2.9 mm vs 5.7 mm; P<0.01).25\"\nIs that really true? GSV reflux is diagnosed much earlier in Caucasian population whereas in the Asian population, saphenous vein reflux is usually diagnosed late as demonstrated in your three cases.\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? Yes", "responses": [ { "c_id": "10568", "date": "29 Nov 2023", "name": "Taofan Taofan", "role": "Author Response", "response": "Thank you very much for the wonderful insights from Dr. Windsor Ting regarding our manuscript. He gave us constructive comments to improve our manuscript. Here we will try to answer several comments from him. 1. There are numerous grammatical errors in the manuscript. The authors should try to correct these errors before indexing the manuscript. Thank you for the comments, we try our best to revise the grammatical errors in our manuscript. 2. The term \"chronic venous insufficiency (CVI)\" is used throughout the manuscript. CVI means different things to different people. Please define CVI so it is clear what exactly is CVI. Chronic venous disease (CVD) is defined as a long-term morphological and functional abnormality of the venous system that manifests as symptoms or signs requiring treatment or examination. Chronic venous insufficiency (CVI), which correlates with clinical, etiological, anatomical, and pathophysiological (CEAP) classification as C3 through C6, is reserved for advanced CVD and applied to functional anomalies of the venous system that result in edema, skin changes, or venous ulcers. 3. \"Treatment of superficial venous reflux with early endovenous laser ablation (EVLA) has been proven to reduce ulcer recurrence levels and promote faster VLU healing.\"It has been shown or associated with. \"Prove\" is too strong a statement. Thank you for the advice. We have changed the statement to “Treatment of superficial venous reflux with early endovenous laser ablation (EVLA) has been associated with reducing ulcer recurrence levels and promoting faster VLU healing.” 4. \"and received ceftriaxone antibiotics for five days\"Why antibiotic? Did the patient have a positive wound culture? Does the author use antibiotic routinely in these cases? Although the current ESVS chronic venous disease guideline doesn’t advise routine use of systemic antimicrobials for venous leg ulcers, in our practice, we usually still use it as an empirical antibiotic in our hospital. 5. \"EVLA was performed under spinal anesthesia.\" Why spinal anesthesia? These cases can be done with just tumescence. We believe these cases can be done with tumescence anesthesia alone, but spinal anesthesia showed significantly lower pain scores compared to tumescence alone. Our patients already experienced pain related to their VLU so we assumed it would be better to minimize their pain-related procedure with the choice of spinal anesthesia despite the longer preparation time and spinal anesthesia-related complications which fortunately didn’t happen in our patients. For that reason, we also prefer to hospitalize our patients. 6. “Lower extremity DUS showed perfectly obliterated ablated GSV, no thrombus found in the deep vein, and a patent epigastric vein.”When was this performed? What is the authors’ recommendation regarding postoperative ultrasound? The lower extremity DUS was performed one day after the procedure. After that, routine DUS follow-up was performed within 3 – 6 months after the procedure, according to the Guidelines of the First International Consensus Conference on Endovenous Thermal Ablation for Varicose Vein Disease. 7. “The patient was discharged one day after the procedure. ”Why was the patient hospitalized? The patient was hospitalized to perform the post-procedural lower extremity DUS. Another consideration was the patient traveled quite far away to our center so it would be harder to monitor the patient’s post-procedural condition. Although we believe that EVLA can be done in outpatient settings in certain conditions. 8. “The patient had a history of hypertension, type 2 diabetes mellitus, and obesity with body mass index (BMI) of 39.45 kg/m2.”Did any of these patients have peripheral artery disease? At least one patient was a smoker. How was PAD ruled out? Is it necessary to rule out PAD? We ruled out PAD by performing an ankle-brachial index examination and lower extremity DUS examining the arteries flow. We believe that significant PAD (with ABI <0.5) was a relative contraindication for EVLA that prevented the use of post-procedural compression therapy. 9. “The patient was discharged two days after the procedure with optimal medical treatment and wound care by the nursing team with modern wound dressing.” What is optimal medical treatment? Optimal medical treatment here means adequate medical treatment to control our patient’s risk factors. What did the wound care consist of? What is modern wound dressing? Wound care was done by following the TIME concept that was proposed by Schultz et al.4 with a combination use of modern wound dressing. The tissue component provides viable wound tissue by debridement. In our case, we used a combination of chemical, autolytic, and sharp debridement. The debridement process was done until granulation tissue was formed in approximately less than 2 weeks. The infection/inflammation control was done with combination use of cadexomer iodine, octenidine dihydro-chloride, polyhexamethylenebiguanide, and concentrated surfactant gels. Moisture should be balanced, and, in our case, we reduce the excessive fluid that causes maceration of the wound margin by using calcium alginate and hydrofoam. The edge of the wound was assessed with the target of advancing epidermal margin and decreased wound stage. The wounds were then covered with transparent film and collagen dressing. Another important component is the use of a 3-layer tubular compression bandage to achieve 40 – 50 mmHg pressure which is known to be useful in promoting VLU healing. 10. \"smelly discharge\"Malodorous discharge is a better medical term. Thank you for the advice, we have changed this term. 11. \"The decision to do GSV EVLA until BTK is preferred because it is supported by numerous pieces of evidence that provide significantly more advantages than only ATK GSV EVLA.\"How far below the knee? Until the lowest part where there is still significant reflux. 12. \"Various efforts need to be made to minimize complications from EVLA. Tumescent anesthesia is used in EVLA to prevent thermal-induced tissue damage, \"What about foam sclerotherapy for the GSV below the knee? We believe that foam sclerotherapy has a higher recurrence rate, so in our cases, foam sclerotherapy is not an option.6–8 13. \"the average GSV diameter of an Asian population was significantly lower than a Caucasian population (Median 2.9 mm vs 5.7 mm; P<0.01).25\"Is that really true? GSV reflux is diagnosed much earlier in Caucasian population whereas in the Asian population, saphenous vein reflux is usually diagnosed late as demonstrated in your three cases. We and the authors of the article believe that the result can be biased since those Caucasian patients may have been presented earlier. But we can’t conclude that the result didn’t represent the actual condition since 1) Singapore is a highly developed country so we believe that the diagnosis that was made won’t be too late. 2) If the diagnosis was made later, we believe that the GSV diameter of the Asian population would be larger than the Caucasian population that was diagnosed earlier. Once again, we would like to thank you for the opportunity for our manuscript to be reviewed by such an experienced doctor in the field. Hope our answers and revision can satisfy him and please let us know if further revision is needed." } ] } ]	1	https://f1000research.com/articles/12-383
https://f1000research.com/articles/13-736/v1	03 Jul 24	{ "type": "Opinion Article", "title": "Life should be redefined", "authors": [ "Zheng Liu" ], "abstract": "Understanding the nature of life and its propensity for reproduction has long been a question that humans aspire to answer. Reproduction, a defining characteristic of life, fundamentally involves the replication of genetic material, be it DNA or RNA. The driving force behind this replication process has always intrigued scientists. In recent years, theories involving selfish genes, the RNA world, and entropic forces have been proposed by some scholars. These theories seem to suggest that life, as we know it, exists solely in Earth’s environment and is based on a single type of genetic material, either DNA or RNA. However, if we broaden our definition of life to include any replicable molecules, we might be able to transcend traditional thought. This could potentially enhance our understanding of the impetus behind DNA replication and provide deeper insights into the essence of life.", "keywords": [ "DNA replication", "reproduction", "RNA world", "entropic forces", "self-replicating molecules" ], "content": "Introduction\n\nThe quest for understanding the existence of life has always captivated people. Currently, it’s challenging to define what life is. Traditionally, Life is defined as an extension of being into the next generation and into the next species in evolutionary time (Chatterjee, 2023). Reproduction, the process of passing on genetic material (DNA or RNA) to the next generation, is a fundamental characteristic of life. This phenomenon prompts the question: why is the replication of DNA or RNA necessary for life and what drive DNA or RNA replication? Over the years, scientists have deepened their understanding of life. Some have proposed the theory of selfish genes (Noble and Noble, 2022), while others argue that RNA is the origin of life (Higgs and Lehman, 2015). A particularly innovative perspective comes from Professor Jeremy England, who posits that entropic forces drive the replication of DNA or RNA (England, 2013). His theory, grounded in the second law of physics, suggests that life arises from the increase in the universe’s entropy. This provides a physical explanation for the reproduction and continuation of life. Building on these theoretical foundations, I think the life and genetic materials should be redefined. Given that DNA or RNA, as genetic material, can replicate and generate life, I hypothesize that any molecules with replication capabilities, regardless of their environment, could potentially evolve into life. This speculation opens up possibilities for the discovery of new life forms in the universe.\n\n\nThe expectation for reproduction of organisms\n\nWhy is there such a vast diversity of life on Earth? The prevailing understanding is that given varying environmental pressures and ample time, a single species can evolve into distinct species. Each species has a natural desire to reproduce and pass on its genes. As Charles Darwin elucidated, individuals possessing traits that better suit their environment have a higher likelihood of reproducing. This allows them to pass on these advantageous traits to their offspring, thereby enhancing the organism’s reproductive success and allowing the organism to reproduce more. Over time, this process results in the evolution of species that are well-adapted to their specific environments. The innate drive to survive and reproduce is fundamental to the perpetuation and diversity of life on Earth. But what exactly is the purpose behind the reproduction of species? Humans have established complex societies, systems of relationships and norms, to fulfil their social, emotional, and cultural needs. Naturally, human reproduction encompasses these needs, including sexual maturation, social support, and the continuation of the family line. In today’s world, there is no doubt that social and emotional needs have become paramount. However, these needs are not present in viruses, bacteria, or insects. Although viruses and bacteria seem to lack self-consciousness, they still carry out self-replication. A fascinating example is the male mayfly, which has a lifespan of only 24 hours (Araújo et al., 2021). Its sole purpose from birth is to mate. What is the objective of this replication in bacteria and viruses and what drives male mayflies to behave in such a way?\n\n\nSelfish genes drive reproduction\n\nOne theory suggests that genes choose us, and they are selfish (Gardner and Welch, 2011). In his book, ‘The Selfish Gene’, Richard Dawkins posits that genes, rather than individuals or species, are the primary units of selection in evolution. Consequently, genes have propelled the reproduction of all species. According to this theory, genes are the fundamental unit of natural selection, acting in a manner that ensures their own survival. Organisms serve as carriers of these genes, with reproduction being the ultimate goal (Figure 1). Reproduction is the prize for living organism with or without self-consciousness. Numerous instances of this theory are evident in nature, and recent studies have further validated it. A study found that individuals with specific variants of the ERAP2 gene had a higher survival rate during the Black Death, a catastrophic pandemic in the 14th century (Klunk et al., 2022). This pandemic, from another perspective, is that ERAP2 gene with specific variants, selectively replicated itself within certain individuals. Such events have recurred throughout human history, exerting substantial selective pressure on the human population. This altered the prevalence of certain genetic variants, thereby influencing our disease susceptibility today. From this perspective, it appears as though the ERAP2 gene with specific variants is driven by its survival instinct. However, this theory does not address the question of why genes, despite their lack of self-consciousness, need to replicate and ensure their survival. In other words, what is the purpose of gene replication?\n\nOn Earth, inorganic molecules capable of self-replication spontaneously synthesize organic molecules, including RNA. Influenced by the entropic forces, RNA serves as the genetic material, leading to the emergence of life, irrespective of whether the organisms possess self-consciousness. In environments distinct from Earth, any molecules with self-replication capabilities could potentially evolve into genetic material, thereby initiating new forms of life.\n\n\nLife begins with RNA\n\nIn order to address the aforementioned questions, it is essential to determine what the first gene or genetic material on Earth was and understand how it initiated replication. The RNA world hypothesis suggests that life on Earth have begun with a simple self-replicating RNA molecule, with DNA only appearing later as a result of RNA evolution. Gerald Joyce team discovered that a highly evolved RNA polymerase ribozyme has the ability to function as a reverse transcriptase (Samanta and Joyce, 2017). This reverse transcriptase ribozyme can incorporate all four types of dNTPs and can produce products containing up to 32 deoxynucleotides. Recently, significant progress has been made by the team led by Clemens Richert. They managed to replicate RNA sequences of up to 12 nucleotides in a dilute aqueous solution of an unactivated dinucleotide, without the involvement of any enzymes (Welsch et al., 2023). The RNA world hypothesis offers a persuasive explanation for the early stages of life on Earth. However, is RNA an organic molecule that can be directly synthesized from inorganic substances? The Miller-Urey experiment in 1953 was provided evidence that essential organic molecules, fundamental to life, could be synthesized from inorganic substances. In fact, scientists have developed more methods in recent years to synthesize organic molecules from hydrogen and oxygen under different conditions (Hudson et al., 2020). Studies have demonstrated that all four of RNA’s major components can be efficiently assembled from simple chemicals under certain conditions (Figure 1). A paper published in Science presents a straightforward chemical pathway to the formation of ribonucleotides (Becker et al., 2016). These studies underscore the remarkable ability of the natural environment to transform simple inorganic molecules into complex organic ones, such as RNA, a key characteristic of life on Earth. It suggests that the emergence of life could be a random event in nature, rather than being designed. However, what drives RNA to replicate itself?\n\n\nEntropic forces drive life\n\nJeremy England, a professor at Massachusetts Institute of Technology, has put forth a theory suggesting that life arises because the principle of increasing entropy compels matter to adopt life-like physical properties (England, 2015). It would suggest that the replication of genes is driven by entropic forces (Figure 1). This theory has been employed to elucidate the impetus behind evolution and the replication of DNA/RNA. DNA/RNA molecules prefer to be in their lowest energy conformation (the resting position with high entropy). Replication of DNA or RNA is a process that facilitates the attainment of this state. Interestingly, this theory is a manifestation of the renowned Big Chill hypothesis (or the heat death of the universe) in the context of human evolution. The Big Chill hypothesis posits that all entities in the universe are transitioning from a state of uniform high energy to one of high entropy based on the second law of thermodynamics (Fleck, 2023). Therefore, it can be inferred that every living organism will attain a state of high entropy. Molecules with high entropy are both disordered and disorganized. A study discovered that an increase in entropy leads to a more random replication process, potentially resulting in a higher rate of errors or mutations (Arias-Gonzalez., 2012). Actually, gene mutations are essential for the survival of genes under stress. If a mutation provides an organism with an environmental advantage, that organism has a higher likelihood of survival and reproduction. This phenomenon is evident in the continuous mutation of the SARS-CoV-2 virus as it attempts to coexist with humans (Markov et al., 2023).\n\n\nRNA and DNA are not the only genetic materials\n\nIf all the theories mentioned above are proven correct, it leads us to several intriguing questions. Why is life, as we know it, only discovered on Earth so far? To date, there are no known types of genetic material fundamentally different from DNA and RNA. Since anywhere in the universe will transit from a state of low entropy to high entropy, does this imply that only Earth’s environment is suitable for DNA/RNA replication? In other words, does life in the universe require an environment similar to Earth’s to exist? If we assume that the only genetic material for life is DNA or RNA, then it implies that there is only one form of life in the universe, akin to life on Earth. It suggests that only another planet with similar conditions - air, water, temperature, pressure, and so on - could give rise to DNA or RNA, and subsequently, organisms resembling those on Earth. Do we increasingly believe that there is only life on Earth in the universe, or that only environments similar to Earth can produce life? Moreover, life has only one form, which is a living organism with DNA or RNA as genetic material. I disagree with this viewpoint. This perspective is inherently flawed as it habitually considers DNA and RNA as the sole genetic materials. The crux of the matter is that DNA or RNA may be the only genetic materials suitable for Earth’s environment.\n\n\nAny molecules with self-replicating ability can be genetic material\n\nPerhaps a shift in our perspective could provide a better answer to this question. We could redefine the genetic material of life (or living organisms) as any molecules capable of self-replication, not limited to DNA or RNA (Figure 1). In this way, life needs to be redefined. Actually, self-replicate has been seen in very different looking chemical systems, for example in rotaxanes, a self-assembling rotaxane that can replicate itself discovered by the scientists (Tamara et al., 2015). Ignacio Colomer et al. discovered a self-replicator consists of a system of small molecules composed of hydrogen and carbon (Colomer et al., 2018). This process of self-replication could occur anywhere in the universe, which encompasses a vast range of environments distinct from Earth. For instance, envision this process taking place in an atmosphere with a temperature of -63 degrees Celsius, a pressure of 600 Pa, and a composition of 95% carbon dioxide - conditions naturally found on Mars. Currently, the laboratory possesses the capability to simulate the self-replication of substances under such conditions. Actually, Schulze-Makuch et al., has already proposed alien life could be based on different chemistries, solvents, and energy sources (Schulze-Makuch and Irwin, 2006). Given sufficient time, these simple organic molecules, capable of self-replication, could give rise to other forms of life, similar to the original genetic material RNA on Earth. In other words, the genetic material of life elsewhere in the universe may not necessarily be DNA or RNA, as these replicable molecules could potentially form other new life forms.\n\n\nConclusions\n\nThis paper presents a novel opinion by reviewing recent studies and theories concerning the biological reproduction, drawing from the fields of biology (with a focus on theories of selfish genes and the RNA world), physics (specifically the second law of thermodynamics and entropy theory), and chemistry (emphasizing self-replicating systems). It suggests that molecules capable of self-replication may, under certain conditions, evolve into various forms of life. This perspective represents a departure from traditional concepts that identify DNA and RNA as the sole genetic materials. It provides a new insight into the origins and implications of life’s existence in the universe, providing a theoretical basis for searching for other diverse forms of life in the universe.\n\nEthical approval and consent were not required.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nAraújo VA, Dias LG, Serrão JE: Rapid and efficient mating in mayflies (Ephemeroptera): morphological and reproductive strategies in primitive winged insects. Naturwissenschaften. 2021; 108(2): 10. PubMed Abstract \| Publisher Full Text\n\nArias-Gonzalez JR: Entropy involved in fidelity of DNA replication. PLoS One. 2012; 7: e42272. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBecker S, Thoma I, Deutsch A, et al.: A high-yielding, strictly regioselective prebiotic purine nucleoside formation pathway. Science. 2016; 352(6287): 833–836. PubMed Abstract \| Publisher Full Text\n\nColomer I, Morrow SM, Fletcher SP: A transient self-assembling self-replicator. Nat. Commun. 2018; 9(1): 2239. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChatterjee S: Defining Life. From Stardust to First Cells. Cham: Springer; 2023. Publisher Full Text\n\nEngland JL: Statistical physics of self-replication. J. Chem. Phys. 2013; 139(12): 121923. PubMed Abstract \| Publisher Full Text\n\nEngland JL: Dissipative adaptation in driven self-assembly. Nat. Nanotechnol. 2015; 10(11): 919–923. PubMed Abstract \| Publisher Full Text\n\nFleck R: The Laws of Thermodynamics. Entropy and the Second Law of Thermodynamics. Cham: Springer; 2023. Publisher Full Text\n\nGardner A, Welch JJ: A formal theory of the selfish gene. J. Evol. Biol. 2011; 24: 1801–1813. PubMed Abstract \| Publisher Full Text\n\nHiggs PG, Lehman N: The RNA World: molecular cooperation at the origins of life. Nat. Rev. Genet. 2015; 16(1): 7–17. PubMed Abstract \| Publisher Full Text\n\nHudson R, de Graaf R , Strandoo Rodin M, et al.: CO2 reduction driven by a pH gradient. Proc. Natl. Acad. Sci. USA. 2020; 117(37): 22873–22879. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKlunk J, Vilgalys TP, Demeure CE, et al.: Evolution of immune genes is associated with the Black Death. Nature. 2022; 611: 312–319. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKosikova T, Hassan NI, Cordes DB, et al.: Orthogonal Recognition Processes Drive the Assembly and Replication of a [2]Rotaxane. J. Am. Chem. Soc. 2015; 137(51): 16074–16083. PubMed Abstract \| Publisher Full Text\n\nMarkov PV, Ghafari M, Beer M, et al.: The evolution of SARS-CoV-2. Nat. Rev. Microbiol. 2023; 21: 361–379. Publisher Full Text\n\nNoble D, Noble R: Origins and demise of selfish gene theory. Theor Biol Forum. 2022; 115(1-2): 29–43. PubMed Abstract \| Publisher Full Text\n\nSamanta B, Joyce GF: A reverse transcriptase ribozyme. elife. 2017; 6: e31153. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSchulze-Makuch D, Irwin LN: The prospect of alien life in exotic forms on other worlds. Naturwissenschaften. 2006; 93(4): 155–172. PubMed Abstract \| Publisher Full Text\n\nWelsch F, Kervio E, Tremmel P, et al.: Prolinyl Nucleotides Drive Enzyme-Free Genetic Copying of RNA. Angew. Chem. Int. Ed. Engl. 2023; 62(41): e202307591. PubMed Abstract \| Publisher Full Text" }	[ { "id": "312177", "date": "21 Aug 2024", "name": "Denis Noble", "expertise": [ "Reviewer Expertise Cardiac electrophysiology", "evolutionary 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\nThis Review article proposes that there could be other self-replication molecules in addition to DNA & RNA. It also supports England's (2015) hypothesis that entropic forces are responsible for making matter adopt life-like physical properties. It justifies this speculation using recent work by other authors. The review will be of most use to students searching for new leads on current thinking about the origin of life.\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Yes\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Partly", "responses": [ { "c_id": "12423", "date": "17 Sep 2024", "name": "Zheng Liu", "role": "Author Response", "response": "Thank you very much for recognizing the viewpoints presented in this paper. The open new mode of F1000Research allows me to express novel viewpoints and share them with other academic scholar. These viewpoints are often difficult to get accepted by traditional journals, but I believe that the emergence of any novel viewpoint will drive progress in science and thought." } ] }, { "id": "299580", "date": "23 Aug 2024", "name": "Kevin S. Lang", "expertise": [ "Reviewer Expertise DNA Replication", "transcription", "translation", "microbiology", "molecular biology", "evolution." ], "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 intriguing essay that urges for the reassessment of what is considered “life”. The author makes a case for refining definitions of “life” to aid in the pursuit of identifying lifeforms on planets other than Earth. They highlight existing frameworks, such as the selfish gene theory, in the context of replication of biological molecules, suggesting that lifeforms may have some fluidity beyond historical definitions. These ideas have significant value for shaping the perceptions of what life could look like beyond what is observed on Earth. In my opinion the essay could be improved significantly by the following considerations:\nThe author should consider providing a more explicit suggestion of what they think the definition should be tailored to. For example, is life strictly constrained by the replication of only organic molecules? Could replication of inorganic molecules be considered “life”? This is important as the author highlights that some organic molecules (ie genes) utilize organisms for their own replication. Parallel to this framework, things like limestone could be considered to replicate by utilizing marine life for its replication. Would this then be considered life? In line with the above comment, would the new definition of life pertain to molecules that template their own replication or self-assembly? The author discusses the generation of biomolecules from inorganic substrates, citing the RNA theory of the origin of life. This is an example of self-assembly. Other examples of this beyond RNA and DNA exist on Earth, for example, prions and viral capsids. The distinction of these molecules is that they don’t necessarily involve templating their own replication. Rather, they drive their own self-assembly from simple substrates to more complex biomolecules. A clearer definition would enhance this essay from being a simple review of existing ideas to proposing a novel definition. Lastly, the author highlights indexed essays that discuss the relationship between life and entropic forces. However, the way the author discusses the relationship between life and entropy is unclear. For example, the author states that DNA and RNA are in a state of high entropy. This is perplexing, given that these biomolecules are highly ordered, and thus fighting against entropy. Therefore, is the author stating that the new definition of life should be any molecules that are moving to a state of low entropy, and thus, driving themselves away from natural tendency of the 2nd law of thermodynamics to increase entropy?\nIn summary, this is an intriguing essay that will benefit by a more explicit definition of what should be considered “life”.\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": "12424", "date": "20 Sep 2024", "name": "Zheng Liu", "role": "Author Response", "response": "Authors' point by point response to the Reviewer comments is as follows - 1. I have considered this issue while writing my paper, but I have been very cautious. I am also concerned that my viewpoint may be too radical and difficult to accept. However, with the help of the F1000Research platform and the opportunity to answer questions, my response is: Yes. Traditional thinking defines life as having certain perceptions or consciousness, such as in humans, animals, and plants. However, the emergence of viruses has challenged this common understanding. A virus is merely a sequence of DNA or RNA, and although it is an organic substance (without consciousness, is it different from inorganic substances?), it constantly replicates and is also a form of life. I believe we can be bolder. In my article, I speculate that inorganic substances capable of self-replication can also be considered life, which is a novel viewpoint in this paper. Regarding the statement 'limestone could be considered to replicate by utilizing marine life,' I disagree because limestone is not self-replicating; its production results from the accumulation of products from marine biological activities. I think it is essential to emphasize self-replication, which involves actively replicating oneself. 2. This question is very interesting. The main point of the paper is that molecules capable of self-replication can be defined as life, similar to a piece of DNA (virus) that can self-replicate. If a molecule only drives its own self-assembly from simple substrates to more complex biomolecules, I believe this is growth, not replication, and therefore not life. I think the example of prions is also a form of life. Prion protein is coded by the PRNP gene. Prion proteins cannot self-replicate and cannot be considered life. However, while prions are composed of misfolded protein aggregates, they propagate by inducing conformational changes in normal prion proteins (PrP^C) to transform them into the abnormal, disease-causing form (PrP^Sc). The misfolded prion acts as a template, guiding the normal proteins to adopt the abnormal structure, exhibiting characteristics of life. This precisely supports the viewpoint of this paper that any self-replicating molecule, including misfolded prions, can serve as genetic material and ultimately become life. Additionally, I have included examples of prions in the revised version of my paper. Viral capsids are part of a virus and are composed of proteins encoded by viral genes. To my knowledge, I have not seen viral capsids self-replicate. If there were independent viral capsids that could self-replicate (no need for DNA or RNA), I would also define them as life. Thank you very much for your suggestion. I have added a clearer definition of life to my paper in the conclusion section and changed the title to \" Life should be redefined: Any molecule with the ability to self-replicate should be considered life \". Additionally, it should be emphasized that self-replication should also include one molecule inducing another molecule to become itself (such as a misfolded prions induce prions). 3. I believe there may be a misunderstanding. According to England's theory, DNA or RNA molecules exist in a high-energy (low entropy, ordered and organized) state, which makes them ordered. The replication of DNA or RNA molecules progresses towards a lower energy state, ultimately leading to a low-energy (higher entropy, disordered and disorganized). This process is driven by the second law of thermodynamics, which governs the behavior of all matter in the universe, including life. However, an increase in entropy driven by the second law of thermodynamics does not necessarily indicate life; only molecules with active self-replication functions are considered life. The second law of thermodynamics drives all matter in the universe towards disorder and heat death. For example, if a drop of ink is added to a cup of water, the ink will eventually distribute evenly among the water molecules due to the second law of thermodynamics, which is unrelated to life, vice versa. I am very grateful for your suggestions on my paper. I have been contemplating new perspectives on life during this period, and I have added new paragraph accordingly." } ] } ]	1	https://f1000research.com/articles/13-736
https://f1000research.com/articles/13-1078/v1	19 Sep 24	{ "type": "Research Article", "title": "Examining the relationship between health literacy and pesticide protective behaviors among farmers in Thailand", "authors": [ "Thiwakorn Rachutorn", "Thawatchai Aeksanti", "Chamroen Pall", "Varavut Tanamool", "Anake Srisuwan", "Somany Mok", "Rebecca S Dewey", "Samphors Sim", "Malika Kong", "Pisey Vong", "Thiwakorn Rachutorn", "Thawatchai Aeksanti", "Varavut Tanamool", "Anake Srisuwan", "Somany Mok", "Rebecca S Dewey", "Samphors Sim", "Malika Kong", "Pisey Vong" ], "abstract": "Background The use of chemical pesticides without proper health literacy (HL) and necessary pesticide protective behaviors (PPB) can result in adverse effects on human health.\n\nMethods This study aims to determine if there is a correlation between HL and PPB among farmers in the Nakhon Ratchasima province, using a random sample of 464 farmers. Structured interviews consisted of three parts: 1. General information, 2. Health literacy (including knowledge, understanding, and other sub-aspects), and 3. Protective behaviors against chemical exposure. Each part of the questionnaire had a reliability index of 0.60 or higher. The reliability of the 2nd and 3rd parts of the questionnaire were as follows: sub-sections of part 2 had a Kuder-Richardson (KR-20) coefficient of 0.79 and Cronbach’s alpha (α) coefficient of 0.85-0.86, while part 3 had an α of 0.88. Risk of chemical exposure was assessed using a Cholinesterase Reactive Paper test administered by a finger-prick blood test. Data was analyzed using the Spearman correlation and binary logistic regression. The study was reviewed by the Human Research Ethics Committee with the approval date: August 9, 2021, and expiry date: August 9, 2022.\n\nResults Most participants had moderate levels of overall HL (48.8%) and PPB (44.6%). There was a statistically significant positive correlation between HL and PPB (rs(478) = 0.70, p<.005). Logistic regression analysis demonstrated that HL had a statistically significant positive association with PPB (p<.001, OR = 6.57, 95% CI 3.95, 10.94) and was associated with blood cholinesterase levels.\n\nConclusions These findings highlight the need for increased health literacy among farmers in Thailand to ensure correct protective behaviors against chemical exposure and reduce the adverse effects of pesticide exposure on human health.", "keywords": [ "health literacy", "pesticide exposure", "chemical exposure", "farming" ], "content": "Introduction\n\nCurrently, the agricultural industry in Thailand uses a variety of chemicals to prevent and control pests, weeds, grasses, and plant diseases, as well as to stimulate production. Thai farmers have reported the use of agricultural chemicals in various cultivation processes.1 Furthermore, 69.9% of farmers use a moderate level of dangerous chemicals, 3.1% of farmers use a high level of dangerous chemicals, while only 19.9% of farmers use a low level of dangerous chemicals.2 The most used pesticides are organophosphates and carbamates.3 Inappropriate and unsafe behaviors around pesticide use are likely to result in negative impacts on human health. Such inappropriate pesticide uses behaviors include mixing chemicals, poor storage, and spraying.4 Other unsafe behaviors include using multiple types of pesticides together in spraying, taking breaks during spraying to smoke, eat, and drink, opening pesticide bottles using one’s teeth, blowing, or sucking the spray nozzle to remove a blockage, and not wearing rubber gloves.3,5 These high-risk behaviors may result in toxic chemical exposure, lead to negative impacts on human health, and result in acute and chronic health concerns. Acute symptoms range from mild to severe, including death, and depends on the chemical concentration and toxicity, as well as the amount ingested or absorbed. Chronic symptoms can result from the accumulation of toxins in the body over time, causing abnormalities in the nervous system.6 Farmers who practice poor pesticide use are at risk for both acute incidents during spraying and chronic effects from long-term contamination. Exposure to pesticides for more than three years increases the risk for cardiovascular and heart diseases.7 Thus, if farmers fail to protect themselves from pesticide exposure and contamination, they are more likely to experience both acute and chronic health conditions.\n\nIn 2020, Thailand’s Ministry of Public Health released a report on occupational and environmental diseases which revealed a morbidity rate from pesticide poisoning of 13.75 per 100,000 population, a value which is higher than the rate reported in 2019.\n\nIn 2020, Thailand’s Nakhon Ratchasima province reported a morbidity rate as high as 64.26 per 100,000 population, which is over twice the rate of 31.8 per 100,000 population reported in 2019.8 This data reflects an increase in the morbidity rate at both the national and provincial levels. Moreover, a biological risk assessment of pesticide exposure among rice farmers in the Kaeng Sanam Nang sub-district, Kaeng Sanam Nang district, Nakhon Ratchasima province, found that the sample group was at risk and unsafe, with exposures being found in up to 60.0% of sample groups.9 Another study reported that rice farmers were at increased risk of adverse health effects when compared to farmers growing other crops.10 Based on this study, rice farmers can be assumed to have the greatest risk of pesticide exposure.\n\nSustainable Development Goals (SDGs) rely on the availability of human resources. Therefore, promoting health literacy is crucial as it fosters and enhances individuals’ abilities to sustainably manage their own health, and adopt desirable health behaviors. In the available literature describing past research, health literacy has been associated with improved health outcomes, self-evaluation of health, and informed decision-making. These individuals are also more susceptible to illnesses or health problems, and more at risk to make inappropriate health decisions.11 People with low health literacy are likely to encounter more health issues, while those with high health literacy tend to make better decisions regarding their health.12 Health literacy can be described as consisting of the following six components13,14 across three levels, Level 1: Basic Health Literacy (Functional literacy), including Access to Health Information and Services (Access) and Knowledge and Understanding (Cognitive), Level 2: Interactive Health Literacy, including Communication, Inquiry, Exchange (Communication), and Self-Management, and Level 3: Critical Health Literacy, including Media Literacy and Decision-making. This model of health literacy is used in this study’s design.\n\nPrevious research has yet to characterize health literacy among Thai farmers, a group more closely involved with, and more often exposed to plant pest control chemicals than other groups. Previous studies have reported that farmers display incorrect behaviors around the prevention of exposure to pest control substances, such as not reading the labels or instructions before use, not wearing a mask, or covering their nose during pesticide use, not wearing eye protection or protective gloves, inhaling chemicals during spraying, or drinking water while working. Furthermore, improper storage of substances and incorrect disposal of chemical containers in violation of public health principles have also been observed.15 The most reported unsafe behaviors included mixing multiple types of chemicals into a single spray, followed by not wearing protective gloves while working with chemicals, and not having a specific safe storage place for plant pest control chemicals.16 The negative health impact on farmers exposed to plant pest control chemicals is significant. Exposures to plant pest control chemicals over a period of three years or more has been associated with a risk of cardiovascular and heart diseases.7 In summary, poor protective behaviors of rice farmers to pest control chemicals will result in exposure to plant pest control chemicals and endanger human health. Therefore, this study aims to investigate health literacy in Thai farmers and explore the association between health literacy and exposure-preventing behaviors, especially in farmers who are responsible for spraying plant pest control chemicals. This research is conducted at key farming areas in Thailand, so as to provide an understanding of the problem in the community context and aid in the development of a health literacy promotion program to improve the health literacy and behaviors of farmers. This research aims to ultimately prevent exposure to plant pest control chemicals, improve work safety, and reduce the risks to, and impacts on, farmers’ health.\n\nThis study aims to describe health literacy and to determine the relationship between health literacy and behaviors aimed at preventing exposure to plant pest control chemicals among Thai farmers.\n\n\nMethods\n\nA cross-sectional analytical study was conducted to study the association between health literacy and behaviors aiming to prevent exposure to plant pest control chemicals among Thai farmers. The variables measured include general information characterizing the sample group, health literacy, and behaviors aimed at preventing exposure to plant pest control chemicals.\n\nThe population consists of men and women farmers aged 18 and over engaged in agriculture with agricultural households registered with the agriculture office totaling 521,593 people.17 The required sample size was calculated using GPower software,18 which was created from Cohen’s (1988) formula.19 The calculation was performed according to the statistics used in data analysis, with a 95% confidence level, a margin of error of .05, test power of .80, and an effect size of .05.18 This resulted in a required sample size of 464 people. Multi-stage stratified cluster random sampling was used and divided according to the characteristics of agricultural areas in a stratified random sampling method, which resulted in 3 groups: 1) paddy farming only, 2) paddy and upland rice farming, and 3) paddy farming and cash crop growing.\n\nWe obtained ethical approval from the Ethical Review Committee of the Public Health Office of Nakhon Ratchasima Province, Thai Ministry of Public Health (Reference No: NRPH 053). The Ethics in Human Research Committee of the Nakhon Ratchasima Public Health Provincial Office. The research was reviewed and approved on August 9, 2021, and the approval expires on August 9, 2022. The research is conducted in compliance with the Declaration of Helsinki, The Belmont Report, and the CIOMS Guideline International Conference on Harmonization in Good Clinical Practice (ICH-GCP). The research team is led by Thiwakorn Rachutorn from Nakhon Ratchasima Rajabhat University.\n\nThe research has been approved with an expedited review, which means that it is considered to be a low-risk study. The documents reviewed include the full protocol, participant information sheet, informed consent form, and questionnaire. In addition to research consent form was provided to participants with volunteer consent with type of written consent obtained before collecting data. All the participants was provided read and understood the objectives of research and signs consent form willingly.\n\nInformed consent: The form ensures that participants are fully informed about the research objectives, procedures, and potential risks and benefits.\n\nConfidentiality: It explicitly states that the researcher will treat participant responses as confidential, protecting their personal information.\n\nVoluntary participation: Participants are free to choose whether or not to participate and can withdraw at any time.\n\nWitness signatures: The requirement for two witnesses to sign the form adds a layer of assurance that the participant’s consent is voluntary and informed.\n\nData aggregation: The research findings will be presented in an aggregated form, protecting individual participant identities.\n\nThese elements together contribute to a consent form that aligns with ethical principles for research involving human subjects.\n\nThe study included a questionnaire and risk screening, which was conducted using a finger-prick blood test. The details are as follows:\n\nThe questionnaire consisted of three parts:\n\nPart 1: General information. Questions included gender, age, education, average annual household income, history of using chemical pest control substances, sources of information about using chemical pest control substances, use of chemical pest control substances in rice cultivation, history of exposure to chemical pest control substances, and history of training on the use of chemical pest control substances.\n\nPart 2: A questionnaire to measure health knowledge for using chemical pest control substances across six aspects, which was divided into two sub-sections:\n\nPart 2.1 covered one aspect: knowledge and understanding. This portion consists of 13 questions with closed-ended response options yes, no, and unsure. The correct answer scored 1 point, while wrong or unsure answers scored 0 points. A participant’s total score in the area of health knowledge could be classified as high (a score above 80%), moderate (a score between 60% and 80%), or low (a score below 60%) using Bloom’s cut-off point.20,21\n\nPart 2.2 covered five aspects: access to information and services (7 items), communication (8 items), self-management (6 items), media and information literacy (6 items), and decision-making (10 items). Responses were closed-ended with five answer choices describing the frequency with which the participant performed that behavior: regularly (all seven days in a week), frequently (5-6 days in a week), sometimes (3-4 days in a week), infrequently (1-2 days in a week), or never (not at all). For the 30 positive questions, responses were scored from 5-1 respectively, and for the seven negative questions, responses were scored from 1-5 respectively.\n\nPart 3: covered preventive behavior aiming to reduce exposure to chemical pesticides, consisting of 30 items divided as follows: behaviors performed in the preparation for (10 questions), during (9 questions), and after (11 questions) the spraying of chemical pesticides. Responses were closed-ended with five answer choices, with 13 questions scored positively and 17 questions scored negatively. Response options and scoring were as described in part 2.2. Scores from parts 2.2 and 3 were used to interpret the level of health knowledge or behavior. Total scores could be classified as either high (75-100 %), medium (26-74 %), or low (0-25 %) using quartile calculation.\n\nThe risk of exposure to chemical pesticides was determined by finger-prick blood tests using cholinesterase reactive paper on farmers following the procedure set in place by the Bureau of Occupational and Environmental Diseases, within Thailand’s Ministry of Public Health.22 The blood test results of farmers were divided into four groups by the level of AChE: safe (≥ 100.0 U/ml), normal (87.5 – 99.9 U/ml), at-risk (75.0 – 87.4 U/ml), and unsafe (< 75.0 U/ml).23\n\nThe research tool used in this study underwent examination for accuracy and content coverage by three qualified experts, namely a health knowledge expert, an occupational health and safety professional, and a researcher specializing in the health of farmers. Only questions with an index of item objective congruence (IOC) of greater than 0.60 were selected. Suggestions were then implemented, and the tool was piloted in a group of 30 farmers similar to the research sample group. The reliability of each questionnaire item and part was evaluated separately. The knowledge and understanding part were analyzed using the Kuder-Richardson 20 (KR20) method and yielded a reliability of r = 0.79. The parts covering access to information and services, communication, self-management, and media literacy, yielded a Cronbach’s alpha coefficient (α) of α = 0.86. For decision-making, the reliability was α = 0.85, and for the questionnaire on behaviors aimed at avoiding exposure to chemical pesticides, the reliability was α = 0.88.\n\n\n\n1. Field research assistants were trained to collect data in the communities where the sample group resided. The lead investigator distributed a data collection manual for the study, which included the details of the research project, the purpose of the research, the guidelines for introducing the data collectors, an explanatory letter and research consent form, the characteristics of the sample group for data collection, the content of each part of the tool, and steps on how to use the tool to collect data. To ensure that the data collectors understood and could correctly use the tool according to the research procedures, the lead investigator organized a practical training session and demonstrated how to collect data in the field. This training included information on how to introduce themselves, how to explain the purpose of seeking cooperation when providing information, how to correctly record data and how to check for complete responses. The data collectors also practiced actual data collection with farmers who were like the research sample group, and their performance was evaluated until they could fully follow the study procedures.\n\n2. A letter was sent to the Subdistrict Administrative Organization leader to request permission for data collection within the chosen area. Once approval was received, the researchers met with the village leader and village health volunteers (VHV) to explain the details of the research, emphasizing the ethical principles of research to protect the rights of the sample group throughout the study period.\n\n3. The date, time, and location of each visit to the area for data collection were coordinated and agreed upon with the sample group of farmers.\n\n4. Each data collector proceeded to the field and collected data from the sample. If a member of the sample group was unable to read the questionnaire by themselves, the data collector would read the questionnaire and let the participants respond by themselves.\n\n5. The lead investigator checked the accuracy of the collected data again and digitally inputted the obtained information into the database for analysis.\n\nThe analysis was performed using SPSS version 16 https://www.ibm.com/products/spss-statistics to present the results. Descriptive statistics were used to present values, frequency distributions, percentages, averages, standard deviations, and minimum and maximum values. Inferential statistics were used to assess the association between health knowledge and exposure prevention behaviors using the Spearman rank correlation coefficient (or Spearman’s rho [rs]). As the data obtained from the questionnaire was found not to be normally distributed, binary logistic regression was performed using the stepwise method, which consisted of selecting the independent variable with the highest correlation value for the first analysis, followed by variables with successively lower correlation values.\n\n\nResults\n\nThe results describe the participant cohort of 464 individuals, and include their general information, health awareness, exposure prevention behaviors, the association between health awareness and exposure prevention behaviors, and binary logistic regression associations between variables of interest.\n\nMost of the sample group of farmers were women, accounting for 62.3%, with an average age of 55.3 years. 65.1% had completed secondary education, and 59.3% had an annual average household income of less than 60,000 THB in USD is 1,700 USD. Regarding the use of chemical pesticides by the sample group, 73.6% reported a history of using chemical pesticides for 1-5 years. Information about chemical pesticides was obtained mainly from sellers (42.8%), followed by public health officials and fellow farmers (14.6% each). In past growing seasons, 73.5% had used pesticides, 68.3% had used herbicides, and most had used up to five types of chemical pesticides. Only 10.3% had received training in the use of chemical pesticides in the past year.\n\nThe assessment of health awareness covered the following six components: 1) Understanding and knowledge were low in 40% of the sample. When considered on a per-item basis, the highest level of knowledge was in reading and understanding the label each time before using the chemical pesticides (91%). The least amount of knowledge was in using chemicals in quantities different from those specified on the label (52.7%). 2) Access to information and services was moderate in 44.4% of the sample. The highest level of knowledge was in farmers accessing services when they experienced health problems resulting from the use of chemical pesticides (45.6%), while the lowest was in searching for and choosing information sources detailing the use of chemical pesticides (39.1%). 3) Communication was moderate in 46.6% of the sample. The highest level of knowledge was in farmers asking public health personnel how to better take care of their health (40%), while the lowest was in reading and listening to information about chemical pesticides from others and understanding the content (44%). 4) Self-management was moderate in 42.9% of the sample. The ability to self-monitor for health conditions that may result from the use of pesticides was highest 45%, while the use of personal protective equipment such as helmets, glasses, masks, gloves, shoes, and tight clothes at all times, even when not expecting to experience an allergic reaction to the pesticides, was lowest (28.7%). 5) Information literacy was moderate in 44.2% of the sample. Knowledge of comparing products from multiple sources to confirm and verify their accuracy and reliability before buying pesticide products was the highest (37.1%), while knowledge around trusting the promotional marketing materials of pesticide sales without reconsideration was the lowest (29.4%). 6)Decision-making was moderate in 43.8% of the sample. Wearing masks and rubber gloves to protect oneself from contact with pesticides when spraying pesticides was highest (39.0%), while knowledge around trusting information about pesticides received from friends or acquaintances without doubt was lowest (52.9%). Overall, it was found that the majority of the sample had a moderate level of health knowledge (48.8%), followed by a high level (26.0%), and a low level (25.2%).\n\nAssessing the frequencies of farmers reported self-protective behaviors in the past month, it was found that the majority performed behaviors overall at a moderate level (44.6%). When looking individually at behaviors performed before, during, and after pesticide use, it was found that: 1) In preparation for using pesticides, most reported performing behaviors at a moderate level (47.1%), with wearing rubber gloves to prevent contact with pesticides (29.2%) as the most frequently reported behavior, and checking the condition of the spray head, spray line, container, and equipment used for spraying chemicals before use (34.4%)as the least frequently reported behavior. 2) During the spraying of pesticides, most participants reported performing self-protective behaviors at a low level (53.7%), with wearing rubber gloves to prevent contact with pesticides (36.7%) as the most frequently reported behavior and wearing a mask as the least frequently reported behavior (31.9%). 3) After spraying pesticides, most reported performing self-protective behaviors at a moderate level (42.5%), with storing pesticides and equipment in a safe place out of the reach of children (39.2%) as the most frequently reported behavior and placing warning signs to alert others of pesticide use in the area as the least frequently reported behavior (48.3%).\n\nThere was a positive and significant association between health knowledge and exposure prevention behaviors in all aspects (rs between.64 and.75, p < .001). However, it was found that the health knowledge and understanding aspect had the lowest correlation with exposure prevention behaviors (rs (478) = .14, p < .05). Details are shown in Table 1.\n\n p-value <0.014 indicates a strong significant relationship.\n\n p-value <0.001 indicates a very strong relationship among groups.\n\nThe Binary logistic regression analysis provided adjusted odds ratios (ORs) with 95% confidence intervals (CIs), indicating that the level of knowledge has a statistically significant relationship with exposure prevention behaviors at a level of.001 (Adjusted OR = 6.57, 95% CI = 3.95-10.94), as shown in Table 2.\n\n p-value <0.001, adjusted for gender, age, education, average annual household income, history of using pesticides in rice cultivation, history of exposure to pesticides, experience in pesticide use, training.\n\nMultiple Logistic Regression analysis provided the adjusted OR and 95%CI. It was found that the level of health knowledge was significantly associated with the frequency at which farmers performed behaviors to prevent exposure to pesticides (p < 0.001, Adjusted OR = 6.57, 95% CI = 3.95-10.94), as shown in Table 3.\n\na Adjusted for gender, age, education, family income, history of using chemicals, history of attending training, history of chemical testing.\n\n\nDiscussion\n\nFarmers in this study reported that they had been using pesticides for between 1 and 5 years, with an average of 3.65 years, which is consistent with findings in a study by Suwanrattanat and Panyasophon,24 that reported 83.3% of farmers hade been using chemicals for between 1 and 5 years. The present study found that farmers reported obtaining the majority of their information from pesticide sellers, again consistent with a study by PewKluang, and Hunniran25 that too reported most farmers as having received information from chemical sellers (81.6%) and pesticide distributors (62.1%). The most commonly used pesticides in the recent growing season were, in order of frequency, those for eliminating snails, rats, aphids, insects, and controlling weeds or grass. Most farmers reported using all types of pesticides, indicating that farmers are feeling the need to control a wide and increasing number of pests, especially cherry snails, which continue to increase rapidly in population.26\n\nThis study found that overall levels of health knowledge across all components were at a moderate level. When considering each component individually, these findings are consistent with those of a study by Suwanrattanat and Panyasophon,24 which found that most farmers in the Nong Bunmak District in the Nakhon Ratchasima Province, had moderate levels of health knowledge across all aspects. Additionally, this is in agreement with the findings of a study by Suwanphan and Sridaket27 that found farmers to have moderate levels of knowledge about accessing information and services, decision-making, and self-management, but not in the aspect of understanding knowledge and communications, which was found to be at a low level. Considering the results of this study in the context of previous studies, it is clear that the overall level of health knowledge of most farmers still needs improvement. Consequently, all relevant sectors should be compelled to promote the importance of health knowledge to farmers, in addition to taking measures to improve the levels of health knowledge among sellers and distributors of pesticides, due to the reliance of farmers on pesticide sellers for this information, as revealed in the present study.\n\nThis study found that farmers’ practices of preventive behaviors aiming to reduce and prevent exposure to chemical pesticides were at a moderate level. A previous study reported that 64.80% of workers had a good level of using Respiratory Protective Equipment (RPE).27 When divided into the different intervals at which these behaviors were practiced (i.e., before, during, and after pesticide use), we found that 1) behaviors around the preparation for the use of chemical pesticides were practiced at a moderate level, 2) behaviors during the spraying of chemical pesticides were practiced at a low level, and 3) behaviors after spraying chemical pesticides were practiced at a moderate level. This is consistent with the findings of Chantaphao, Pandee, and Nuwatthana,28 who reported moderate levels of self-protective behaviors around the use of chemical pesticides among most rice farmers (95%). Moreover, studies by Suanmuang, Kongtaveelert, Sombhopjaroen, and Sujirarat29 and by Thaioou, Thiphom, Yasak, and Chanthorn30 both reported farmers as having moderate levels of self-protective behaviors against exposure to chemical pesticides (63.3% and 58.9%, respectively). This indicates that most rice farmers have some preventive behaviors against exposure to chemical pesticides, but that the frequency with which they practice these behaviors leaves room for improvement. It is of paramount importance that self-protection against chemical pesticide exposure is promoted to reduce the risks to and impact on the health of rice farmers.\n\nHealth literacy levels were found to be closely associated with the reported frequency of preventive behaviors in regard to chemical pesticide exposure. While each of the six components of health literacy individually correlated with behaviors at a level that was found to be statistically significant, the knowledge understanding component had the weakest correlation with behaviors aiming to prevent exposure to chemical pesticides in comparison to the other components. This indicates that understanding of information about preventive measures alone is not sufficient to promote good self-protection practices, and that consequently, more training is needed to provide and maintain sufficient levels of knowledge and understanding about chemical pesticides for farmers. Other activities should also be aimed at improving skills in accessing information and services, communication, self-management, media literacy, and decision-making skills, which are components of health literacy that farmers need for effective self-preservation. These suggested interventions are likely to improve farmers’ efficiency at preventing exposure to pesticides, and consequently improve health and quality of life.\n\nCholinesterase reactive paper screening of finger-prick blood samples taken from farmers demonstrated that the majority of farmers (72.2%) had normal and safe levels of cholinesterase enzyme levels, which is an improvement from the findings of previous studies, where percentages of farmers as low as 24.7% had cholinesterase enzyme levels in the safe range.31 However, the study still found 27.8% of farmers had levels that indicated that they were at risk or unsafe, consistent with inadequate exposure prevention behaviors. While the majority of farmers report behaviors consistent with providing a moderate level of protection, there is research suggesting that the risks to farmers’ health decrease with increased self-protective behaviors. The majority of participants in the present sample reported using personal protective equipment regularly (36.9%) or sometimes (50.8%), which may indicate that the risk to their health has decreased over the course of the past year.31\n\n\nConclusion\n\nThese findings suggest that, overall, the level of farmers’ health knowledge needs to be improved. As the majority of farmers reported receiving their information primarily from the sellers and distributors of chemical pesticides, individuals working in those industries must also improve their level of health knowledge, so as to promote good practices. We found that most farmers do practice behaviors to prevent exposure to chemical pesticides at a moderate level, but this also requires improvement to decrease the severity and frequency of exposures. Health knowledge was found to be strongly associated with the frequency of self-protective behaviors. As such, the importance of maintaining high levels of health knowledge must be emphasized to rice farmers, in order to modify behavior and increase levels of self-protection against chemical pesticide exposure.\n\n\nRecommendations\n\nThis article represents a call to the relevant agencies to capitalize on these research findings when planning and making agricultural policy. Action must be taken to reduce the risks to and impacts on farmers’ health resulting from the improper use of chemical pesticides. This requires the promotion of health knowledge, especially health knowledge relating to the understanding of the use of chemical pesticides. The insufficient levels of health knowledge and understanding demonstrated within this sample indicate an urgent need for improvement in this area.\n\n\n\n1. Future research should investigate farmers growing economic crops other than rice, while using chemical pesticides that are severely harmful to health, including, but not limited to, cassava, sugarcane, and feed corn.\n\n2. It is necessary to investigate individuals who work as hired pesticide sprayers. This group is exposed to chemical pesticides continuously and it would be valuable to measure the risks to and impact on health, both acute and chronic.\n\n3. Qualitative research is needed to understand the real causal mechanisms that relate health literacy, preventive behaviors, and cholinesterase enzyme levels. This research should be conducted in targeted and contextually appropriate sectors of the industry such that the findings will have the maximum utility for problem-solving and planning for farmers and policymakers in the most needed areas.\n\n\nEthics and consent\n\nWe obtained ethical approval from the Ethical Review Committee of the Public Health Office of Nakhon Ratchasima Province, Thai Ministry of Public Health (Reference No: NRPH 053). The Ethics in Human Research Committee of the Nakhon Ratchasima Public Health Provincial Office. The research was reviewed and approved on August 9, 2021, and the approval expires on August 9, 2022. The research is conducted in compliance with the Declaration of Helsinki, The Belmont Report, and the CIOMS Guideline International Conference on Harmonization in Good Clinical Practice (ICH-GCP). The research team is led by Thiwakorn Rachutorn from Nakhon Ratchasima Rajabhat University.\n\nThe research has been approved with an expedited review, which means that it is considered to be a low-risk study. The documents reviewed include the full protocol, participant information sheet, informed consent form, and questionnaire\n\nIn addition to research consent form was provided to participants with volunteer consent with type of written consent obtained before collecting data. All the participants was provided read and understood the objectives of research and signs consent form willingly.\n\n\nInformed consent\n\nThe form ensures that participants are fully informed about the research objectives, procedures, and potential risks and benefits.\n\n\nConfidentiality\n\nIt explicitly states that the researcher will treat participant responses as confidential, protecting their personal information.\n\n\nVoluntary participation\n\nParticipants are free to choose whether or not to participate and can withdraw at any time.\n\n\nWitness signatures\n\nThe requirement for two witnesses to sign the form adds a layer of assurance that the participant’s consent is voluntary and informed.\n\n\nData aggregation\n\nThe research findings will be presented in an aggregated form, protecting individual participant identities.\n\nThese elements together contribute to a consent form that aligns with ethical principles for research involving human subjects.", "appendix": "Data availability statement\n\nFigshare: Dataset for analysis: https://doi.org/10.6084/m9.figshare.26934202.v2 32\n\nThis project contains following datasets:\n\n1. Dataset - Copy.xlsx\n\n2. Volunteer Consent Form (1).pdf\n\n3. Explanatory Document for Volunteers (1).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\nAroonsrimorakot S, Sangnate V, Pradabphetrat P: The chemical application in rice production of farmers in Nong-Sue District. Pathum Thani Province. Prawarun Agricultural Journal. 2017; 14(2): 173–180. Reference Source\n\nPromnon S, Nathapindhu G: The situation of pesticide usage in Dongklang Sub-district, Khonsan District, Chaiyaphum Province. Thailand Journal of Health Promotion and Environmental Health. 2018; 41(2): 116–128. Reference Source\n\nJawjit S, Kwanhian W, Vattanasit U, et al.: A comparison of knowledge, attitudes, and practices of rice farmers and levels of pesticide residues in the environment in Nakhon Si Thammarat Province. Journal of Safety and Health. 2017; 37(4): 10–20. Publisher Full Text\n\nPetchchuay C: The situation of agricultural chemical use in the lower Mekong Basin region. Science and Technology Journal Ubon Ratchathani University. 2017; 9(1): 111–122. Reference Source\n\nChantaramanee N: Behaviors of Chemical Pesticide Uses and the Effectiveness of an Occupational Health Education Program of Safety Knowledge among Farmers in Upriver Area, Phayao Province. Journal of Safety and Health. 2017; 10(37): 35–45. Reference Source\n\nThetkathuek T: Occupational health in agriculture on pesticides in occupational health and safety. 5th ed. Vol. 25. . Bangkok: Odeon Store Publisher; 2013; pp. 102–120. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHung DZ, Yang HJ, Li YF, et al.: The long-term effects of organophosphates poisoning as a risk factor of CVDs: a nationwide population-based cohort study. PLoS One. 2015 Sep 4; 10(9): e0137632. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMinistry of Public Health: Epidemiological Surveillance Report 2019-2020.Reference Source\n\nChaiklieng S, Praengkrathok S: Risk Assessment on Pesticide Exposure by Biological Monitoring among Farmers: A Case Study in Tambon Kangsanamnang, Nakhonratchasima Province. SRIMEDJ. 2013 Nov. 11 [cited 2023 Jul. 20]; 28(3): 382–389. Reference Source\n\nRivera EP, Siriwong W, Taneepanichskul N, et al.: Health risk related to pesticide exposure in the agriculture system in Thailand: A systematic review. Journal of Health Research. 2016; 30(Suppl. 1): S71–S80.\n\nBrabers AE, Rademakers JJ, Groenewegen PP, et al.: What role does health literacy play in patients’ involvement in medical decision-making? PLoS One. 2017 Mar 3; 12(3): e0173316. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChesser AK, Keene Woods N, Smothers K, et al.: Health literacy and older adults: A systematic review. Gerontology and Geriatric Medicine. 2016 Feb 17; 2: 233372141663049. Publisher Full Text\n\nNutbeam D: Defining, measuring and improving health literacy. Health Evaluation and Promotion. 2015; 42(4): 450–456. Publisher Full Text\n\nDivision of Health Education, Department of Health Service Support: Strengthening and evaluating health literacy and health behaviors among children and youth (ages 7-14), people aged 15 years and over, updated version.2018; pp. 52–64.\n\nPremapree P: Disease situation and illness from chemical pesticides.2016. Reference Source\n\nSirirattanapruek S: Occupational Health and Environment Threat Surveillance System Development Project.2002. Reference Source\n\nDepartment of Agricultural Extension: Farmer Registration Improvement.2019. Reference Source\n\nFaul F, Erdfelder E, Buchner A, et al.: Statistical power analyses using G* Power 3.1: Tests for correlation and regression analyses. Behav. Res. Methods. 2009 Nov; 41(4): 1149–1160. PubMed Abstract \| Publisher Full Text\n\nCohen J: Statistical power analysis for the behavioural sciences. Vol. 56. . Hillsdale, New Jersey: L. Lea; 1988; p. 102.\n\nBloom BS: Taxonomy of Educational Objectives: Handbook II. David McKay; 1956.\n\nKangkhetkron T, Juntarawijit C: Factors influencing practice of pesticide use and acute health symptoms among farmers in Nakhon Sawan, Thailand. International Journal of Environmental Research and Public Health 2021 Aug 20; 18(16): 8803. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBureau of Occupational and Environmental Diseases, Ministry of Public Health: Knowledge of pesticide exposure risk screening by cholinesterase test paper Cholinesterase reactive paper for health workers in primary care. Department of Disease Control, Ministry of Public Health; 2017.\n\nHughes D, Thongkum W, Tudpor K, et al.: Pesticides use and health impacts on farmers in Thailand, Vietnam, and Lao PDR: Protocol for a survey of knowledge, behaviours and blood acetyl cholinesterase concentrations. PLoS One. 2021 Sep 30; 16(9): e0258134. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSuwannarat J, Panyasophorn T: Research and development of health knowledge model for behavior to prevent chemical pesticides in farmers. Nursing and Health Care Journal. 2022; 40(1): 84–93. Reference Source\n\nPewKluang K, Hunniran P: Development of a model to prevent health impacts and safety from the use of pesticides by farmers with community participation in Suphan Buri Province. Journal of Buddhist Social Sciences and Anthropolog. 2022; 7(5): 158–174.\n\nPradubpetcharat P, Arunsrimorakot S, Piyapong C, et al.: Analysis of apple snail outbreak areas in Thailand. Pravarun Agricultural Journal. 2017; 14(2): 247–257.\n\nPanakobkit W, Sakunkoo P, Chamroen P: Health Belief Model and Behavioural Usage of Respiratory Protective Equipment among Sugarcane Workers in Northeast of Thailand: A Cross-sectional Analytical Study. Journal of Clinical and Diagnostic Research. 2019 Dec 1; 13(12). Publisher Full Text\n\nChantaphao K, Pundee R, Nuwatana W: Comparison of knowledge. Pesticide use prevention and behavior between rice farmers and watermelon farmers, Nong Luang Sub-district, Thatako District, Nakhon Sawan Province. Thai Journal of Health Sciencesm. 2021; 3(3): 52–63.\n\nSuanmuang M, Kongtaveelert A, Sombhopjaroen M, et al.: Knowledge and behavior in using chemical pesticides of hired sprayers. Journal of Health Education. 2021; 2(2): 42–47. Publisher Full Text Reference Source\n\nThaioou T, Thiphom S, Yasak S, et al.: Factors related to behaviors on pesticide protection of pesticide spraying workers in Dong Prakham Sub-District, Phrom Phiram District. Phitsanulok Province. Disease Control Journal. 2017; 43(3): 293–305.\n\nKetbumroong V, Photipim M, Prathumyo J: Health Situation of Farmers from the use of Pesticides in Group T60.0, Mueang District, Nakhon Ratchasima Province. journalkorat. 2020 Dec. 28 [cited 2023 Jul. 8]; 6(2): 76–91. Reference Source\n\nPall C: Dataset for analysis. Dataset. figshare. 2024. Publisher Full Text" }	[ { "id": "329000", "date": "08 Nov 2024", "name": "Andrew Povey", "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\nIn this manuscript, the authors describe a cross-sectional study of health literacy and pesticide protective behaviours in Thai farmers. They report significant associations between health literacy and those behaviours aimed at preventing pesticide exposure. This is an interesting paper but the manuscript needs additional detail and clarification in a number of areas. In addition, the presentation could be improved and the paper may benefit from an English Language edit.\n\nSuggestions for the authors include the following\nAbstract\n\nThe abstract lacks a clear aim and a description of the analysis that was carried out in the methods section.\n\nThe abstract contains a number of sentences that don’t really belong in the abstract and should be deleted. These include\n\n“Each part of the questionnaire had a reliability index of 0.60 or higher. The reliability of the 2nd and 3rd parts of the questionnaire were as follows: sub-sections of part 2 had a Kuder-Richardson (KR-20) coefficient of 0.79 and Cronbach’s alpha (α) coefficient of 0.85-0.86, while part 3 had an α of 0.88”\n“The study was reviewed by the Human Research Ethics Committee with the approval date: August 9, 2021, and expiry date: August 9, 2022.”\n\nIntroduction\nPlease clarify what is meant by “Chronic symptoms can result from the accumulation of toxins in the body over time, causing abnormalities in the nervous system” Most, but not all pesticides are excreted from the body and don’t accumulate in the body. Please provide extra detail for the following sentence “… found that the sample group was at risk and unsafe, with exposures being found in up to 60.0% of sample groups..” What were the exposure levels and who were the sample groups? It is best not to have single sentence paragraphs such as “In 2020, Thailand’s Ministry …… reported in 2019.” The whole paragraph starting with “Sustainable Development Goals….” appears out of place and with little relevance to pesticides. It should be rewritten to make more relevant. The paragraph starting with ” Previous research ….” should be merged with the first paragraph as there is a significant element of repetition as the same ideas and information are present in both paragraphs.\n\nMethods\nA sample size calculation is provided but on what basis was this calculation undertaken e.g. regression analysis between what variables? Please provide that information. Please provide more details of the multi-stage stratified cluster random sampling (e.g. what were the clusters). What were the eligibility and ineligibility criteria used for the participants? For example, was there an age range or level of literacy? How were the scores in Part 2.2 of the questionnaire categorised? How does the “Cholinesterase Reactive Paper test” assess the risk of exposure? How were the levels for the “safe, normal, at-risk and unsafe” categories chosen? The reference provided is for a protocol of a study and doesn’t seem to provide that information. “the approval expires on August 9, 2022” should be “the approval expired on August 9, 2022”. The material describing the consent process and form i.e. “The research has been …………. involving human subjects” is not required and should be deleted from both the main text and the section on Ethics and Consent. The section on Data collection process should be shortened considerably as it contains material that isn’t really relevant for a paper.\n\nResults\nThere should be a Table that provides information on Part 1 of the questionnaire (“General Information”) that describes clearly the population studied. In addition, how many farmers were approached and how many refused to take part?\n\nWhat were the actual values of the “Cholinesterase Reactive Paper test”? Were these values associated with the use of organophosphates? Why was no comparison carried out on the three separate farming groups as the use of pesticides is likely to differ between them? It would be useful to see the actual results for each individual health knowledge aspect (as additional data) so that the reader can view the range of results obtained. The authors use the term “Health Awareness” but only in the results. Is this the same as “Health Knowledge”? Table 2 uses the term “strong protective behaviours”? What are they as “strong protective behaviours” do not appear to have been defined in Part 3 of Research Tools. Why were “moderate” and “low” levels of health knowledge combined? The ORs are adjusted for a number of variables – why were these variables chosen? Rather than including in Table 2 the “ % of strong protective behaviours” the authors should put in the actual numbers of participants with and without such behaviours In Table 3, the variables chosen for adjusting the ORs differ from those in Table 2. How were these variables chosen? Did the authors not collect data on the last time pesticides were used (and which pesticides were used) as this presumably is an important determinant of AChE levels?\n\n•\n\nThe authors describe their results in terms such as “ Access to information and services was moderate in 44.4% of the sample” whereas a more accurate way of describing this would be “44.4% of the sample had a moderate score for questions on access to information and services”. I would recommend rewriting the results to present them more clearly.\nDiscussion\nThe authors should use the first paragraph of the discussion to clearly identify what they consider to the key results of the study. The discussion should not introduce new results that have not been presented in the actual results section e.g. the data in the last sentence “The majority of participants in the present sample reported using personal protective equipment regularly (36.9%) or sometimes (50.8%), which may indicate that the risk to their health has decreased over the course of the past year.” does not appear in the 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? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "332728", "date": "25 Nov 2024", "name": "Nurul Izzah Abdul Samad", "expertise": [ "Reviewer Expertise Environmental Health", "occupational health and safety", "ergonomics", "chemical assessments and biomonitoring" ], "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 interesting study discusses the relationship between health literacy and pesticide protective behaviors among farmers. As we all know, health literacy is an important indicator of someone's view and practice toward exposure and risks. Furthermore, this relationship can impact the foundation of occupational health and safety among farmers, particularly in improving public health in Thailand. However, some improvements need to be addressed.\nAbstract:\nThe abstract contains details, but some of the information should be included in the main text, not in the abstract. For example, details on the reliability test results and the information on the expiry date of the ethics approval. Please include the analysis of the cholinesterase reactive paper test in this section.\n\nIntroduction:\nPlease explain properly the contribution of SDG towards health literacy and pesticide-related health risks. Other than that, please include the basic course/ program/ training regarding health literacy of pesticide exposure and health risks that the workers participate in, whether it is provided by a government or from any private agency. Please explain more about the concept of health literacy from the authors' perspective.\n\nMethodology:\nPlease elaborate on the multi-stage stratified cluster random sampling, what do you mean by each of the processes involved. Is the interview/ questionnaire conducted in the Thai language, and what about the questions in the questionnaire? in English or Thailand language? Other than that, please explain the inclusion/ exclusion criteria for the study location and respondents. Other than that, please discuss more on the questionnaire, whether it was self-developed or adopted from another study. Please do the correct citations for the questionnaire. On another note, I am not sure whether health knowledge carries the same definition as health literacy. Please use consistent wording. the biological analysis was left out of the write-up. Please explain in detail the analysis performed. Will the total scoring be 100 points? Please elaborate more on the scoring.\n\nResults: For the section on health awareness, does this section represent health literacy? if so, consider changing the title. Similarly, please look at the title of the section 'Behavior aimed at ..'. Consider revising the paragraphs to be more readable. The result for AChE is missing. Explain why the authors choose to combine the results for low and moderate levels of health knowledge, and not measure them separately. Please also explain why the authors choose several parameters for Table 2 and Table 3 as controlled parameters. Explain whether the authors run any comparative analysis for the 3 groups (paddy farming, paddy and upland rice, and cash crop).\n\nDiscussion: Some data was presented in this section but was not depicted in the result section (AChE, PPE result).\n\nOther comments: Several typing errors were observed and please seek English editing for better readability.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-1078
https://f1000research.com/articles/13-1077/v1	19 Sep 24	{ "type": "Research Article", "title": "A survey measuring employee’s inclusion in Malaysia", "authors": [ "Yuen Yee Yen", "Ong Jun Wei", "Ong Jun Wei" ], "abstract": "Background Organizations recognized the importance of workplace inclusion. However, up to date, few organizations had developed strategic initiatives to improve workplace diversity. This research examines the impact of awareness of inclusion, inclusive leadership, psychosocial capital, and meaningful engagement on employee’s inclusion in the context of Malaysia.\n\nMethods The study employed a quantitative survey approach and collected data through a questionnaire survey administered to 204 participants. Descriptive analysis, reliability analysis and multiple linear regression analysis were utilized to explore the relationships between the independent and dependent variables.\n\nResults The findings indicate a significant correlation between awareness of inclusion and psychosocial capital with employee’s inclusion. However, no significant correlations were found between inclusive leadership and meaningful engagement with employee’s inclusion. These results underscore the importance of fostering an inclusive culture and nurturing psychosocial support to enhance employee’s inclusion experiences in the workplace.\n\nConclusion This study contributes to the knowledge by being one of the pioneer research in Malaysia that provides insights into the factors influencing employee’s inclusion in Malaysia. The findings is important for organizations, particularly small and medium enterprise in Malaysia to promote employee inclusion in a multi-racial diversity society.", "keywords": [ "Awareness of inclusion", "psychosocial capital", "employee's inclusion", "inclusive leadership", "meaningful engagement" ], "content": "1. Introduction\n\nInclusion remains a significant amount of uncertainty, like the lack of an obvious sense and its applications within an organizational context (Gardner, Love, & Waller, 2023). Developing an organizational culture that prioritizes inclusion is one of the most efficient methods for attracting skilled and diverse employees even while building a sustainable workforce (Heitner, Kahn, & Sherman, 2013). Organizations strive to provide their customers with the highest quality products and services while remaining competitive. The most successful organizations prioritize inclusive environments and link diversity programs to strategic planning efforts. (Heitner, Kahn, & Sherman, 2013). Therefore, an organizational goal would be to retain the benefits of an inclusive workplace to nurture a culture that produces engaged and positive performers. Consequently, by identifying and eliminating barriers to full participation, the above like those increases the involvement of all employees (Roberson, 2006; Sturm, 2006).\n\nThis study aims to investigate the environment where employees interact with the social and psychological resources that are given to them on an individual basis. The study is measured by an employee’s psychosocial capital, which combines social and psychological capital. An individual’s social capital is tied to his or her connections with others, social media sites, and connect to the information and assets owned by the people in his or her network (Im & Chung, 2023; Thompson et al., 2015). Positive psychology and organizational behaviour have influenced the concept of psychological capital, which emphasizes an individual’s internal resources that can be used to succeed. Hope, efficacy, resilience, and optimism are psychological capital constructs and how they affect an individual’s approach to work (Ince, 2023; Thompson et al., 2015).\n\nOrganizations recognized the importance of workplace inclusion (Ince, 2023). However, up to date, few organizations had developed strategic initiatives to improve workplace diversity (Jejeniwa, Mhlongo, & Jejeniwa, 2024). As a result, this research will assist businesses in expanding their value of diversity to include inclusion strategies that extend to organizational practices and cultures. In addition, this research will fill knowledge gaps about current inclusion initiatives. Therefore, the study’s findings will be critical for organizations seeking to capitalize on the benefits of a diverse workforce through inclusion. This research aims to provide insights to help organizations, particularly organizations from a multi-racial collectivist society to create an inclusive organizational culture for employees with diverse background.\n\nBecause there is no universal agreement on inclusion theory in the published literature (Jejeniwa, Mhlongo, & Jejeniwa, 2024; Madera, Yang, Wu, Ma, & Xu, 2023), this study suggests a comprehensive approach to operational and sociocultural factors of inclusion. Furthermore, no research has been done to date on employee inclusion, inclusive leadership, psychosocial capital, and meaningful engagement in relation to employee inclusion.\n\nThe research bridges the theoretical gaps by being one of the pioneer study in Malaysia that investigates employee’s inclusion im a diverse multi-racial working environment post-COVID-19 pandemic. This study performs a holistic evaluation on employee’s psychological capital and awareness in determining employee’s inclusion at workplace. The study is important in building significant connections between meaningful engagement, inclusive leadership and.\n\nThe emergence of multicultural organizations gave rise to the concept of inclusion (Okatta, Ajayi & Olawale, 2024). Inclusion is also still being researched, even though it is openly discussed in practice. There is no consensus on what constitutes inclusion. It is limited for some to include disabled students in school environments (Park, Park, & Shryack, 2024).\n\n\n2. Literature reviews\n\nEmployee inclusion in an organization refers to creating a working environment where all employees feel valued, respected, and empowered to contribute fully to their jobs, regardless of their diverse backgrounds Okatta, Ajayi & Olawale, 2024). Organizations with a diverse workforce encourage employee’s inclusion through constructive conflict-resolution processes (Baumeister et al., 2002). These processes can help employees explore conversations with brainstorming sessions and various views (Moon, 2018). Employee’s inclusion at workplace have continued to evolve over time, with greater job involvement of employees with different education, socio-economic status, religion, marital status\\,values, personality, and skills (Heitner, Kahn, & Sherman, 2013).\n\nAwareness of inclusion refers to the subjective belief that we are effective in the lives of others (Okatta, Ajayi & Olawale, 2024). As a result, when others notice one’s presence and validate one’s actions, the individual perceives and interprets that they matter. Attention, importance, and dependence are the three dimensions of the awareness of inclusion (Im & Chung, 2023).\n\nThe feeling that one commands the interest or notice of another person is the recognition of one’s own presence (Im & Chung, 2023).\n\nPrevious research has found that employee’s inclusion in an organization is predicted by awareness of inclusion, and commitment and engagement are linked to organizational behaviour (Mor Barak, 2018). By examining perceptions of inclusion and meaningful engagement, researchers can develop approaches that consist of the overall organisational environment and culture that purposefully facilitate greater integration of the organisation with the communities and society it serves (Mor Barak, 2015; Okatta, Ajayi & Olawale, 2024).\n\nInclusive leadership is concerned with the relationship that exists between leaders and followers to achieve a goal, in which diversity of thought and perspective is actively sought, valued, and incorporated into the discussion and decision. Leaders must advocate for and represent the diverse needs and values of their followers (Madera, Yang, Wu, Ma, & Xu, 2023). Leaders will create space for followers to feel safe, respected, and appreciated so that they can contribute fully without having to suppress or sublimate their identity (Okatta, Ajayi & Olawale, 2024). By removing barriers that cause exclusion and marginalization, it broadens members to think beyond assimilation strategies or organizational demography to empower and participate in activities (Park, Park, & Shryack, 2024).\n\nInclusive leadership has an impact on inclusion. Valuing others for their individuality enables the exchange of varied viewpoints, which results in diverse viewpoints being incorporated into decision-making as well as problem-solving processes (Sabharwal et al., 2019). Allowing employees, a voice and involvement in decision-making demonstrates a delegation of power which not only nurtures a feeling of belonging but also generates value in various voices and points of view (Mor Barak, 2018; Sabharwal et al., 2019). It is widely accepted to include uniqueness in the definition of inclusion; experts of this framework believe that employees do not need to surrender their distinctive characteristics to become valued members of the in-group (Mor Barak, 2015). Employees will have the assumption that their special contributions are appreciated and that they are motivated to participate fully because of this (Mor Barak, 2015). Inclusion is the major factor to innovativeness in heterogeneous workgroups since it fulfils employee’s need for uniqueness (Moon, 2018).\n\nEmployees in work environments who perceive their performance as a reflection of a higher power, such as their supervisor or the organization, feel as if they matter to their supervisor or the organization. Finally, dependence is defined as the belief that others rely on us (Simons et al., 2015). Employees can perceive success when others rely on their work or are a part of the team’s achievement. Employees can perceive they matter when others rely on their work or are a part of a team accomplishment because they are held accountable to the team and are expected to do their part and come through for the group. Madera, Yang, Wu, Ma, and Xu (2023) expands on the concepts of ego extension which is overlooked in his later work. The feeling that others are proud of another’s accomplishments or saddened by their failures is referred to as ego extension (Madera, Yang, Wu, Ma, & Xu, 2023). Ego extension is an increase in importance. Others become invested in one’s successes and failures when they care about their needs, thoughts, and behaviours.\n\nResearchers have also discovered psychosocial capital at different levels, including the individual (micro), the organisation as well as the society or the community (macro) (Gardner, Love, & Waller, 2023). Individually, social capital emphasizes interpersonal relationships.\n\nAccording to Heitner, Kahn, and Sherman (2013), social capital in the workplace can be used in three ways: obligations and expectations, information flow, and uncertainty. Obligations and expectations are dependent on the working environment’s trust to expand relationships and resources (Ince, 2023). To provide a foundation for action, information must flow through the network structure. To achieve group efficacy, the presence of norms and sanctions must coexist to reduce the risk of uncertainty (Heitner, Kahn, & Sherman, 2013).\n\nIn social and psychological descriptions of inclusion, the concept of a feeling of belonging is an essential element of agreement. The fundamental need to belong, according to Baumeister and Leary, refers to the desire for individuals to establish interpersonal relationships with the others, which resulted in the desire to belong to social groups (Im & Chung, 2023). According to Madera, Yang, Wu, Ma, and Xu (2023), belonging happens when a person has frequented pleasant interactions with others that occur inside the sense of a long-term and stable framework of concern for the welfare of others.\n\nPsychosocial capital is a key motive for employees perceived organisational membership, according to Gardner, Love, and Waller (2023). In an organisational context, a feeling of belonging is defined as the extent to which a worker sees themselves as one of the “in-groups” instead of the “out-group”. The in-group is the organization’s insiders, and treating employees differently inside this group generates the view that certain employees are more valuable to the organisation. Employees’ perceptions of out-group members, in contrast, are more expendable (Park, Park, & Shryack, 2024).\n\nA lack of psychosocial capital has an adverse effect on cognitive processes and affects consciousness (Baumeister et al., 2005). Based on the literature, focusing solely on belongingness raises the risk of conformity and assimilation, especially among members of minority groups who feel compelled to conform to be accepted at work (Ince, 2023). Employees that engage in conforming behaviors are at odds with the values or demographics of the organisation or their work team. Individually, this will frequently result in emotional tiredness and a desire to leave. Furthermore, hostile work environments to diverse perspectives, behaviors, or beliefs; perceptions or minority status; and collectivism are the origin of unification and uniformity (Moon, 2018).\n\nThe work engagement approach recognizes engagement as a psychological state, but it has also begun to examine engagement as the inverse of burnout to create a continuum of workplace well-being (Jejeniwa, Mhlongo, & Jejeniwa, 2024), where burnout was defined as tiredness, cynicism, and inefficacy, whereas engagement was described as energy, involvement, and satisfaction, as well as efficacy (Okatta, Ajayi & Olawale, 2024).\n\nMeaningful engagement is an important concept that has been overlooked in the inclusion literature. Park, Park, and Shryack (2024) applies meaningful engagement by empowering oppressed groups and reducing discriminatory beliefs and practices among those with greater privilege and power (Kenny et al., 2018). Consciousness is made up of experiences that shape people’s behavior and attitudes as they encounter various circumstances, situations, or conditions. Employee behaviors are influenced by various levels of awareness of one’s own experience, policies, biases, and the behavior of others.\n\nEmployees with a high level of inclusive consciousness are expected to want to improve and maintain a sense of meaningful engagement for others. Inclusion necessitates deliberate choices and actions, which result in the ability to increase inclusion for others through meaningful engagement (Sabharwal et al., 2019). It influences how managers interact with employees in addition to making conscious choices and implementing decision-making processes. Simmons and colleagues discovered in a recent study that leaders who promote meaningful engagement can retain employees and interact in ways that go beyond the avoidance of discrimination and bias (Simons et al., 2015). As a result, meaningful engagement can be defined as being aware of mutual interaction concepts and practices at the workplace, as well as how they influence individual attitudes and behaviors (Brimhall & Mor Barak, 2018).\n\nMeaningful engagement is important to because of its obvious benefits to an organization, which include productivity improvements, lower costs associated with lower turnover rates, as well as stronger customer connections (Park, Park, & Shryack, 2024). A higher level of employee engagement leads to higher quality work and enhances organisational commitment, resulting in a lower rate of turnover. Employees are more likely to go beyond for the organization (Thompson et al., 2015).\n\nBased on the literature reviews above, the following research questions and research hypotheses were formed and evaluated in this study:\n\nResearch questions\n\nRQ1: Is there a relationship between the awareness of inclusion and employee’s inclusion in Malaysia?\n\nRQ2. Is there a relationship between inclusive leadership and employee’s inclusion in Malaysia?\n\nRQ3. Is there a relationship between psychosocial capital and employee’s inclusion in Malaysia?\n\nRQ4: Is there a relationship between meaningful engagement and employee’s inclusion in Malaysia?\n\nHypothesis\n\nH1: There is a positive relationship between awareness of inclusion and employee’s inclusion in Malaysia.\n\nH2: There is a positive relationship between inclusive leadership and employee’s inclusion in Malaysia.\n\nH3: There is a positive relationship between psychosocial capital and employee’s inclusion in Malaysia.\n\nH4: There is a positive relationship between meaningful engagement and employee’s inclusion in Malaysia.\n\nResearch framework, which was developed based on literature reviews of the most recent research, was exhibited in Figure 1 below.\n\n\n3. Methods\n\nEthical clearance was approved from the Multimedia University Ethics Committee before the survey questionnaire was distributed to the respondents of this research (Ethical approval number: PD20220284). Written informed consent was obtained from all respondents before their data and response were collected with an assurance of data anonymity and data confidentiality.\n\nEthics statement (Approved date: 20 September 2022)\n\nMMU respects your privacy and is committed to protecting your personal data.\n\nThe survey included five items measuring employee’s inclusion, five items measuring awareness of inclusion, five items measuring inclusive leadership and five items measuring meaningful engagement. All questions in the survey were measured using 5-point Likert scales, denoted by 1: strongly disagree, 2-Disagree, 3-Neither Agree or Disagree, 4-Agree and 5-Stongly agree.\n\nThe survey was pretested by two academics and two industry experts from small and medium enterprises to validate the consistency of the survey items. Based on the reviews of the two academics and two industry experts, amendments were made to the format, questions, and instructions to improve the ease of understanding of the survey items. Thereafter, a pilot study was conducted in which surveys were distributed to 100 employees in Klang Valley Malaysia.\n\nPurposive Sampling technique was being used in this research. A total of 300 employees who worked in small and medium enterprises in Klang Valley for at least 2 years were selected as respondents. Respondents were approached face-to-face for data collection. A question “How many years have you been serving your organization?” were asked and only respondents who worked in small and medium enterprises in Klang Valley for at least 2 years were selected as the respondents.\n\nFrom 15 October 2022 to 14 April 2023, data collection for this study was conducted to examine factors affecting employee’s inclusion in Malaysia. Klang Valley region was selected as the target region for this research as Klang Valley Klang Valley, is the economic heartbeat of Malaysia. Klang Valley contributes a substantial portion of Malaysia’s GDP, driven by a diversified workforce, who worked in manufacturing, technology, and service small and medium enterprises. The purpose of this research and the meaning of each question in the survey were clearly explained to the respondents before the start of data collection. Over a six-month period of data collection, out of three hundred participants approached, 204 agreed to participate in this research.\n\nStatistical Package for the Social Sciences (SPSS) software was used to analyze the survey responses’ results. Descriptive statistics were used to determine the frequency of demographic data. This study used Cronbach’s alpha to evaluate the reliability and determine the internal consistency. Multiple regression was the primary statistical test used to analyze the outcomes of research questions 1, 2 3, and 4. Multiple regression analysis is used to analyze data in this research as it allows researchers to assess the strength of the relationship between the dependent variable (Employee’s Inclusion) and several predictor variables (awareness of inclusion, inclusive leadership, psychosocial capital, and meaningful engagement).\n\n\n4. Results\n\nTable 1 exhibited analysis of reliability in this study encompassed 5 variables, namely employee’s inclusion in Malaysia as the dependent variable (DV), and awareness of inclusion, inclusive leadership, psychosocial capital, and meaningful engagement as independent variables (IV). The dependability of these variables towards employee’s inclusion in Malaysia was examined using Cronbach’s Alpha Coefficient. The SPSS software revealed Cronbach’s Alpha Coefficient values for the dependent variable, employee’s inclusion in Malaysia, as 0.916, indicating a high level of dependability. Similarly, the independent variables, awareness of inclusion (0.916), inclusive leadership (0.905), psychosocial capital (0.922), and meaningful engagement (0.902), also exhibited strong levels of dependability. Notably, all variables demonstrated Cronbach’s Alpha Coefficient values exceeding 0.70, signifying high levels of internal consistency and reliability. In summary, these findings attest to the consistency and reliability of the methods employed to assess these variables, thereby establishing a solid groundwork for examining the relationship between employee’s inclusion and the independent variables.\n\nTable 2 exhibited the comprehensive descriptive analysis outcomes encompassing both the dependent and independent variables investigated in this study. The results for each variable were conveyed in terms of the mean and standard deviation. It was important to note that a total of 204 respondents actively participated in the survey, utilizing a 5-point Likert Scale. The scale employed ratings ranging from “1” representing strong disagreement to “5” indicating strong agreement.\n\nawareness of inclusion, the respondents exhibited a moderate level of agreement towards inclusion, with an average adoption rate of 3.2510. The overall standard deviation of 1.07132 suggests that, overall, respondents tended to have a neutral stance, neither strongly agreeing nor disagreeing with this aspect.\n\nPsychosocial capital displayed a higher overall mean of 3.3647, indicating that, on average, respondents found it easy to accept psychosocial capital. However, the overall standard deviation of 1.07508 highlights some variability in respondents’ perceptions of psychosocial capital. Nevertheless, the neutral overall mean suggested that there are diverse perspectives among most respondents regarding inclusion. Furthermore, meaningful engagement exhibited the second highest overall mean at 3.3118, suggesting that respondents considered it valuable and beneficial. The low overall standard deviation of 1.04935 indicated a moderate level of agreement among respondents regarding meaningful engagement. Moving on, the overall mean for inclusive leadership was 3.2608, indicating a moderate influence on respondents’ “employee’s inclusion,” falling within the “Neutral” to “Agree” range on the 5-point Likert Scale. The overall standard deviation of 1.10057 implied variations in the extent of inclusive leadership among respondents. Finally, awareness of inclusion yielded an overall mean of 3.2559, indicating a modest level of agreement among respondents. The standard deviation of 1.10164 signified that respondents’ levels of agreement vary, with some expressing higher levels of acceptance compared to others.\n\nIt can be observed in Table 3 that the multiple linear regression result shows that awareness of inclusion (Standardized Beta Coefficient = 0.322) and psychosocial capital (Standardized Beta Coefficient = 0.403) displayed highly significant p-values, both falling below 0.001, demonstrated a statistically significant relationship with employee’s inclusion. On the other hand, inclusive leadership and meaningful engagement can be considered as having an insignificant relationship with employee’s inclusion (p-value >0.05). Therefore, Hypothesis 1 and Hypothesis 3 are supported while Hypothesis 2 and Hypothesis 4 are not supported. The regression analysis within the model summary table revealed an R-Square value of 0.954, indicating that the independent variables developed by the researchers can explain 95.4% of the variance in the dependent variable.\n\n\n5. Discussion and implications of study\n\nThe primary objective of the researcher conducting this study was to identify the factors influencing employee’s inclusion in Malaysia. To delve deeper into this subject, 4 independent variables were employed, namely awareness of inclusion, inclusive leadership, psychosocial capital, and meaningful engagement.\n\nThis research contributes to the existing knowledge base in several ways. Firstly, it expands our understanding of the factors that influence employee’s awareness of inclusion in the context of Malaysia. By examining the impact of awareness of inclusion, inclusive leadership, psychosocial capital, and meaningful engagement, this study provides insights into the specific dynamics that shape employee’s inclusion within organizations.\n\nThe findings of this research highlight the importance of awareness of inclusion as a crucial factor in fostering an inclusive work environment. It emphasizes the need for organizations to go beyond surface-level diversity and focus on creating an inclusive culture that values and embraces diversity at all levels. This contributes to the growing body of literature on diversity and inclusion by emphasizing the significance of employee’s inclusion experiences.\n\nFurthermore, the study sheds light on the role of inclusive leadership in driving employee’s inclusion. It deepens our understanding of the specific leadership behaviors and skills that contribute to creating an inclusive work environment. This knowledge can inform leadership development programs and practices, enabling organizations to cultivate inclusive leaders who can effectively manage diverse teams and promote a culture of employee’s inclusion.\n\nThe research also highlights the importance of psychosocial capital in influencing employee’s inclusion. By recognizing the significance of social support, trust, and shared values, the study contributes to our understanding of the social and psychological aspects of inclusion. This knowledge can help organizations create supportive and trusting work environments that enhance employee well-being and foster a sense of inclusion.\n\nMoreover, the study underscores the importance of meaningful engagement in shaping employee’s awareness of inclusion. It emphasizes the need for organizations to provide employees with opportunities for meaningful work, involvement in decision-making processes, and avenues for personal and professional growth. This contributes to the literature on employee engagement and underscores the relationship between employee’s engagement and inclusion.\n\nThis research’s primary goal is to provide a thorough understanding of the importance and influencing factors that Malaysia employees face when deciding whether to embrace and accept employee’s inclusion. After further exploration, this research report will also give useful information to the organizations and companies regarding the implementation of employee’s inclusion in their workplace. This is because the findings of this research will help them develop a more thorough knowledge of the employee’s fundamental demand in a newly inclusive environment, allowing them to improve their workplace more effectively. It is worth noting that, based on the findings of the preceding chapter’s analysis, the awareness of inclusion and psychosocial capital are all strongly associated with the employee’s inclusion in Malaysia, but not inclusive leadership and meaningful engagement. As a result, the acceptance of employee’s inclusion is essential in the overall picture.\n\nThe findings of this research have several important managerial implications for organizations in Malaysia. Firstly, organizations need to prioritize creating a culture of inclusion that values diversity and fosters a sense of belonging among employees. By enhancing employee’s awareness of inclusion, organizations can reap numerous benefits, including improved employee engagement, job satisfaction, and overall performance.\n\nInclusive leadership plays a crucial role in fostering an inclusive work environment. Managers and leaders should be trained to develop inclusive leadership skills, such as active listening, empathy, and promoting diversity. These leaders should function as role models by embracing diversity, treating all employees fairly, and providing equal opportunities for growth and development.\n\nPsychosocial capital, which encompasses social support, trust, and shared values, should be nurtured within organizations. Building positive relationships among employees, encouraging teamwork, and promoting a supportive work culture can enhance psychosocial capital. This, in turn, contributes to higher levels of employee well-being, trust, and commitment.\n\nMeaningful engagement is another key aspect highlighted by this research. Organizations should focus on providing employees with opportunities for meaningful work, involvement in decision-making processes, and opportunities for personal and professional growth. By involving employees in decision-making and goal setting, organizations can enhance their sense of ownership and commitment.\n\nManagers and leaders should also invest in training programs that promote employee’s diversity and inclusion, develop inclusive leadership skills, and create awareness about the benefits of employee’s inclusion. This can lead to a more inclusive and harmonious work environment.\n\nFurthermore, organizations need to regularly assess and monitor employee’s inclusion climate within their workplaces. This can be done through employee surveys, focus groups, and regular feedback mechanisms. By understanding employee’s perceptions of inclusion, organizations can identify areas for improvement and take appropriate actions to address any issues or concerns.\n\n\n6. Conclusion and limitation of study\n\nIn summary, the managerial implications of this research suggest that organizations in Malaysia should prioritize creating an inclusive culture, develop inclusive leadership skills, nurture psychosocial capital, promote meaningful engagement, and regularly assess the inclusion climate. By implementing these practices, organizations can enhance employee’s awareness of inclusion, leading to improved employee outcomes and organizational success.\n\nWhile this study contributes valuable insights, it is important to acknowledge its limitations. This research focuses specifically on the context of Malaysia, which may limit the generalizability of the findings to other cultural and organizational settings. Cultural factors, local norms, and specific organizational contexts in other countries may influence employee’s awareness of inclusion differently. Therefore, caution should be exercised when extrapolating the results to other contexts.\n\nFuture research should focus on conducting comparative studies across different cultural contexts to examine how the factors influencing employee’s inclusion vary across countries. This would provide a more comprehensive understanding of the cultural dynamics at play and contribute to the development of context-specific strategies for promoting employee’s inclusion.\n\n\nEthics and consent\n\nEthical clearance was approved from the Multimedia University Ethics Committee before the survey questionnaire was distributed to the respondents of this research (Ethical approval number: PD20220284). Written informed consent was obtained from all respondents before their data and response were collected with an assurance of data anonymity and data confidentiality.\n\nFull ethics statement (Approved date: 20 September 2022).", "appendix": "Data availability\n\nFigshare: Yee Yen, Yuen (2024). A Survey Measuring Employee’s Inclusion in Malaysia. figshare. Dataset. https://doi.org/10.6084/m9.figshare.26926900 (Yuen, 2024).\n\nThis project contains the following underlying data:\n\n• Data Measuring Employee’s Inclusion in Malaysia.xlsx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nFigshare: Yee Yen, Yuen (2024). A Survey Measuring Employee’s Inclusion in Malaysia. figshare. https://doi.org/10.6084/m9.figshare.26926900 (Yuen, 2024).\n\nThis project contains the following extended data:\n\n• Questionnaire Measuring Employee’s Inclusion in Malaysia.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\nBaumeister RF, DeWall CN, Ciarocco NJ, et al.: Social exclusion impairs self-regulation. J. Pers. Soc. Psychol. 2005; 88(4): 589–604. Publisher Full Text\n\nBaumeister RF, Twenge JM, Nuss CK: Effects of social exclusion on cognitive processes: Anticipated aloneness reduces intelligent thought. J. Pers. Soc. Psychol. 2002; 83(4): 817–827. PubMed Abstract \| Publisher Full Text\n\nBrimhall K, Mor Barak ME: The Critical Role of Workplace Inclusion in Fostering Innovation, Job Satisfaction, and Quality of Care in a Diverse Human Service Organization. Hum. Serv. Organ. Manag. Leadersh. Gov. 2018; 42(1): 474–492. Publisher Full Text\n\nGardner A, Love A, Waller S: How do elite sport organizations frame diversity and inclusion? A critical race analysis. Sport Manag. Rev. 2023; 26(3): 339–360. Publisher Full Text\n\nHeitner K, Kahn A, Sherman K: Building consensus on defining the success of diversity work in organizations. Consult. Psychol. J.: Pract. Res. 2013; 65(1): 58–73. Publisher Full Text\n\nIm J, Chung YK: Exploring diversity, equity, and inclusion in hospitality and tourism firms through the organizational justice and stakeholder theories. Tour. Manag. 2023; 95(1): 104662. Publisher Full Text\n\nInce F: Transformational leadership in a diverse and inclusive organizational culture. Handbook of Research on Promoting an Inclusive Organizational Culture for Entrepreneurial Sustainability. 2023; pp. 188–201.\n\nJejeniwa TO, Mhlongo NZ, Jejeniwa TO: Diversity and inclusion in the workplace: a conceptual framework comparing the USA and Nigeria. International Journal of Management & Entrepreneurship Research. 2024; 6(5): 1368–1394. Publisher Full Text\n\nKenny A, Power M: Social inclusion and intellectual disability in Ireland: social inclusion coordinators' perspectives on barriers and opportunities. Scott. J. Resid. Child Care. 2018; 17(4): 1–23.\n\nMadera JM, Yang W, Wu L, et al.: Diversity and inclusion in hospitality and tourism: bridging the gap between employee and customer perspectives. Int. J. Contemp. Hosp. Manag. 2023; 35(11): 3972–3989. Publisher Full Text\n\nMoon KK: Examining the relationships between diversity and work behaviors in US federal agencies: Does inclusive management have an effect? Rev. Public Pers. Adm. 2018; 38(2): 218–247. Publisher Full Text\n\nMor Barak ME: Social Psychological Perspectives of Workforce Diversity and Inclusion in National and Global Contexts. Thousand Oaks, CA: Sage Publications; 2018.\n\nMor Barak ME: Inclusion is the key to diversity management but what is inclusion? Hum. Serv. Organ. Manag. Leadersh. Gov. 2015; 39(2): 83–88.\n\nOkatta CG, Ajayi FA, Olawale O: Enhancing organizational performance through diversity and inclusion initiatives: a meta-analysis. Int. J. Appl. Res. Soc. Sci. 2024; 6(4): 734–758. Publisher Full Text\n\nPark S, Park S, Shryack J: Measures of climate for inclusion and diversity: Review and summary. Hum. Resour. Dev. Q. 2024; 34(4): 463–480. Publisher Full Text\n\nRoberson QM: Disentangling the meanings of diversity and inclusion in organizations. Group Org. Manag. 2006; 31(1): 212–236. Publisher Full Text\n\nSabharwal M, Levine H, D’Agostino M, et al.: Inclusive Work Practices: Turnover Intentions Among LGBT Employees of the US Federal Government. Am. Rev. Public Adm. 2019; 49(4): 482–494. Publisher Full Text\n\nSimons T, Leroy H, Collewaert V, et al.: How leader alignment of words and deeds affects followers: A meta-analysis of behavioral integrity research. J. Bus. Ethics. 2015; 132(1): 831–844. Publisher Full Text\n\nSturm S: Architecture of Inclusion: Advancing Workplace Equity in Higher Education. The. Harv. J. Law Gend. 2006; 29(1): 247.\n\nThompson KR, Lemmon G, Walter TJ: Employee engagement and positive psychological capital. Organ. Dyn. 2015; 44(3): 185–195. Publisher Full Text\n\nYuen YY: A Survey Measuring Purchase Intention towards Environmentally Friendly Products. Dataset. figshare. 2024." }	[ { "id": "325419", "date": "28 Oct 2024", "name": "Yasser F Hendawy Al-Mahdy", "expertise": [ "Reviewer Expertise Leadership", "Management", "Administration", "Psychology", "Quantitative 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 study provides a valuable contribution to understanding the factors influencing employee inclusion in Malaysia, especially within SMEs. The authors successfully highlight the significance of awareness of inclusion and psychosocial capital as factors contributing to workplace inclusion. However, to enhance the paper’s rigor and ensure it meets the standards of replicable research, the following revisions are suggested:\n1. Literature and Theoretical Framework:\n\n- Expand the literature review, particularly for the variables of meaningful engagement and inclusive leadership. Citing more recent and relevant studies will strengthen the foundation for selecting these variables and align the study more closely with current research in organizational behavior and employee inclusion.\n2. Methodology Details:\n\n- Provide the full list of survey items used to measure each variable. This addition will improve the transparency of the research tools and support replicability. Additionally, including more specifics on the modifications made after the pre-test would clarify how the final instrument was refined.\n3. Source of Measurement Tools:\n\n- The article does not indicate whether the measurement tools used for each variable were created by the researchers or adapted from established tools. This detail is crucial for assessing the validity and reliability of the findings. If the instruments were developed specifically for this study, the authors should describe the validation process. Conversely, if established tools were used, they should cite the original sources to support methodological rigor and transparency.\n4. Data Availability:\n\n- For full reproducibility, include the source data, if possible, or a detailed data availability statement explaining how interested researchers might access the data. This step is essential to support the scientific community in validating and building upon the findings presented.\n5. Interpretation of Findings:\n\n- While the study interprets significant findings well, the discussion around non-significant findings could be expanded. The authors could explore potential explanations for why inclusive leadership and meaningful engagement did not significantly impact employee inclusion. Discussing moderating factors or suggesting further research could enhance the study's applicability and depth.\n6. Scope and Limitations:\n\n- To avoid overgeneralization, discuss the limitations of focusing on SMEs in Klang Valley and how these findings might vary in different organizational or regional contexts. This clarification will help readers understand the boundaries within which the study's conclusions are applicable.\nIn conclusion, this paper provides a promising examination of employee inclusion in Malaysia but would benefit from additional literature support, methodological transparency, and a deeper analysis of certain findings. Addressing the above points will significantly enhance the study's clarity, rigor, and contribution to the field.\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\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "336074", "date": "23 Nov 2024", "name": "Rebecca J Evan", "expertise": [ "Reviewer Expertise diversity", "equity", "and inclusion initiatives and strategies in workplaces", "leadership" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the opportunity to review this paper. This topic remains relevant in workplaces and understanding the global implication is incredibly beneficial for the modern day workplace. My comments below are offered to enhance your current paper:\n1. In both the background section and on page 2, there is a connection between \"workplace inclusion\" and \"workplace diversity.\" I recommend defining the distinction between these two concepts since they are frequently used interchangeably. It sounds as if diversity is being used in the paper as diversity of point of view - is this accurate? Or perhaps a connection between diversity and inclusion can be beneficial to connect to the strategic initiatives a corporation might engage in.\n2. On page 4, section 2.4, the connection between ego extension and inclusive leadership is unclear. Is ego extension related to psychological capital or belonging? A sentence connecting the concepts will help to clarify.\n3. On page 4, section 2.4, the concept of belonging is introduced. What is the connection of belonging to this research. Are you measuring belonging? Belonging is a different concept, as defined in your paper, but on page 5 you recommend to not focus only on belonging. My question is how is focusing on belonging different and/or the same as belonging?\n4. Why was Malaysia selected as the focus of the research? How might diversity and inclusion be different in Malaysia compared to where other inclusion studies have been done? Although it might not be generalizable, understanding the context could lend to being applicable to companies or areas of the world that have similar contexts.\n5. In section 3.2, where did you source the questions? I see Mor Barak cited in the paper - was Mor Barak's Inclusion-Exclusion model utilized for this research? Understanding where the questions were sourced could help explain the measurement.\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": [] } ]	1	https://f1000research.com/articles/13-1077
https://f1000research.com/articles/13-1076/v1	19 Sep 24	{ "type": "Research Article", "title": "Prevalence, satisfaction and preference of tooth shades and their correlation with age, gender and skin shade: A cross sectional study", "authors": [ "Tanay Chawda", "Prashanth Bajantri", "Srikant Natarajan", "Alisha Ono", "Thilak Shetty", "Shobha Rodrigues", "Umesh Pai", "Mahesh M", "Sharon Saldanha", "Puneeth Hegde", "Sandipan Mukherjee", "Ann Sales", "Vignesh Kamath", "Tanay Chawda", "Srikant Natarajan", "Alisha Ono", "Thilak Shetty", "Shobha Rodrigues", "Umesh Pai", "Mahesh M", "Sharon Saldanha", "Puneeth Hegde", "Sandipan Mukherjee", "Ann Sales", "Vignesh Kamath" ], "abstract": "Shade selection is one of the most important factors that determines the satisfaction of the patient with the dental prosthesis and thus the overall success of the treatment. Conventional methods of shade selection require the presence of existing teeth or past dental/photographic records. In the absence of these, shade selection becomes challenging and must be done subjectively and arbitrarily based on the patient’s age and sex. This study aims to assess the prevalence, satisfaction, and preference of tooth shades, investigating their correlation with age, sex, and skin shade in a diverse sample of 120 participants.\nMethods A total of 120 participants, evenly distributed among 60 males and 60 females, were surveyed. Participants were categorized into age groups (n=15) and asked about their satisfaction with existing tooth shades and their preferences.\n\nResults The most common existing tooth shade was Value 2 (52.5%). Statistical analysis using Chi-square tests revealed that Value 2 was the most desired shade among males and females alike, particularly in the age group of 41 to 50 years (p < 0.001). Shade 2L1.5 was the most prevalent (n=26), with Value 2 (59.16%) being the most sought-after shade, followed by Shade 2L1.5 (n=21), Shade 2M1 (n=18), Shade 1M1 (n=15), and Shade 2R1.5 (n=14). Existing tooth shades of Value 0 were the least common. The highest satisfaction with existing shades was observed in males aged 41 to 50 (n=15), followed by males aged 51 to 60 (n=14) and females aged 31 to 40 (n=12) and 41 to 50 (n=12). Significant differences in satisfaction were noted among males (p < 0.001).\n\nConclusions This study reveals a consistent and strong preference among both males and females for tooth shades classified as Value 2, following the VITA Tooth-Guide 3D Master shade guide. This universal preference suggests the relevance and acceptance of this shade category across diverse patient groups.", "keywords": [ "Shade selection", "VITA Tooth-Guide 3D Master", "esthetics" ], "content": "Introduction\n\nFacial esthetics have become important in modern society as they seem to define one’s character. Dental appearance is one of the main features that determines the attractiveness of our face and plays a key role in our social interactions.1 It has been found that the most important factors that influence the perception of beautiful teeth are age, gender, and skin color.2,3\n\nShade selection is an important procedure for providing patients with an esthetic restoration that harmoniously blends with the patient’s existing dentition.4 The selection of teeth with proper shade positively influences the patient’s aesthetic perception and improves prosthesis acceptance.5\n\nThe selection of artificial teeth to replace missing natural teeth is a relatively straightforward procedure when natural anterior teeth remain. Various tooth-shade guides have been developed for use in patients with natural teeth. However, the choice of tooth shade is problematic for edentulous individuals with no preextraction records.6\n\nVarious factors such as age, sex, and skin color have been proposed as aids for artificial tooth shade selection.7 Some dentists have even suggested the color of hair and eye color, but most authors favor the use of facial skin tone as a guide for tooth shade selection.8\n\nThere is limited scientific information on the relationship between facial skin complexion and tooth color in the Indian population. This lack of knowledge may impact the ability of prosthodontists to provide better aesthetics to the patient.\n\nThe perception among dentists is that individuals with darker skin color have lighter shades of teeth. This perception is commonly explained by the illusion of a greater contrast between skin color and tooth shade.3\n\nThe age of the patient was found to have a definite relationship with the tooth shade value, which has been corroborated by many studies that have shown darker tooth shade values with an increase in age and vice versa.3,6\n\nSex is another factor significantly associated with tooth shade values. Men were more likely to have darker tooth shade values, whereas women of the same age group were more likely to have lighter tooth shade values.9\n\nVarious studies have been conducted to establish a relationship between age, sex, and skin color in individuals with tooth shades, but contrasting results have been reported. One reason for the varying results can be attributed to the ethnic origin of the study samples.8,9\n\nIndividual studies conducted by Ajayi et al. (2011), Albashaireh et al., Hamamci et al. (2009), and Afshar MK et al. (2019) had reported satisfaction with dental appearance of 79.4% in Nigeria,10 67.6% in Jordan,11 71.1% in Turkey,12 and 47.2% in Malaysia.13\n\nA study conducted by Maghaireh et al. (2016) found that most people were not satisfied with their tooth color, and the sought-after treatment was tooth whitening. They also reported that women are significantly more likely to seek cosmetic and orthodontic restorations.14\n\nIn a study by Tin-Oo (2011), satisfaction with tooth color was significantly lower in women, and tooth whitening was the most preferred treatment.15\n\nResearch in the field of esthetics and shade matching has predominantly been conducted in Western populations. However, with increasing dental awareness and demand for esthetics in developing countries, such as the Indian subcontinent, research in the field of esthetics based on the local population has become the need of the hour.\n\nThis study aimed to determine the prevalence, satisfaction, and preference of tooth shades and their correlation with sex, age, and skin color.\n\nThe null hypothesis was that there would be no difference in the prevalence, preference, and satisfaction of tooth shades between the age class, gender, and skin shade patterns.\n\n\nMethods\n\nThis study was conducted in the Department of Prosthodontics and Crown and Bridge, Manipal College of Dental Sciences, Mangalore.\n\nA Pilot study was conducted which showed a prevalence of satisfaction of 56.52% with an alpha of 5 % the corresponding z value was Z=-1.95996398454005.\n\nUsing the formula n=(Z(α/2)/d) 2^ “p(1-p)” the minimum percentage difference to be deemed clinically significant at 10%, the minimum sample size required would be 95 for the study. A method of matched quota sampling was employed to recruit an equal number of participants in each age group and sex. For the easy divisibility of the groups, a sample size of 120 was selected.\n\n120 participants were included in this study using the following inclusion criteria:\n\n1) All six maxillary anterior teeth (canine-to-canine) (13, 12, 11, 21, 22, 23) should be present.\n\n2) Teeth should be no external discoloration or staining\n\n3) All the 6 maxillary anterior teeth should have similar shades\n\nThe 120 participants were then equally divided into eight groups based on their age and gender, as follows:\n\nQuestionnaire\n\nThe participants were then asked to complete a questionnaire on their age, gender, and ethnic origin. They were then shown a face mirror and asked if they were satisfied with the shade of their upper front teeth.\n\nShade selection\n\nThe investigators then selected the most common tooth shade among the maxillary anterior teeth using a shade guide (3D Master, VITA Zahnfabrik H. Rauter GmbH & Co. KG Postfach 1338 D-79704 Bad Säckingen), as per manufacturer instructions (Figure 1A).\n\nIf the test subjects were not satisfied with their existing tooth shade, they were guided to find the preferred tooth shade using the “VITA Tooth-Guide 3D Master” shade guide.\n\nThe participants’ skin color was recorded using the L’Oreal skin shade guide (Figure 1B).\n\nAfter collecting the data from all 120 participants, statistical analysis was done using χ2 test to correlate Tooth shade, skin shade, age and gender. Odds ratios were calculated using a logistic regression. Statistical significance was considered at 95% confidence interval, and p values less than 0.05 were considered significant. IBM SPSS Statistics version 20.0 was used for these statistical calculations.\n\n\nResults\n\nA total of 120 participants were grouped based on their age and sex to evaluate the prevalence, satisfaction, and preference of tooth shade and their correlation with age, sex, and skin shade using questionnaires along with the VITA Tooth-Guide 3D Master shade guide and L’Oreal skin shade guide.\n\nAs can be seen in Table 1, the most common existing among the participants was Value 2 (52.5%) of VITA Tooth-Guide 3D Master shade. Shade 2L1.5 (n=26) was the most common, followed by 3L1.5 (n=14), 2M1 (n=12), 2R1.5 (n=10), and 2M2 (n=9).\n\nThe least common existing tooth shades were of value 0, with no participants showing any existing shade.\n\nThe most commonly desired tooth shade was of value 2 (58.33%). Shade 2L1.5, the most commonly preferred tooth shade (n=21), followed by 2M1 (n=18), 1M1 (n=15), 2R1.5 (n=14), and 1M2 (n=9).\n\nChi-square tests revealed that value 2 was the most preferred shade among males and females equally in the age group of 41–50 years, and this was statistically significant (p<0.001) (Table 2).\n\nAmong the shades present, highest satisfaction was observed with people having shades of value 1 (90%), followed by values 2 (82.25%), value 3 (44.44%), and value 4 (33.33%).\n\nAs shown in Figure 2, the highest satisfaction with existing shade was seen in males aged 41–50 years (n=15), followed by males aged 51–60 years (n=14), and females aged 31–40(n=12) and 41–50 (n=12). The lowest satisfaction was observed in males aged 20-30 (n=12), followed by males aged 31–40 years (n=10), and females aged 20-30 (n=5).\n\nA) Males. B) Females.\n\nThe differences in satisfaction with tooth shades among the males were statistically significant (p<0.001) (Table 3).\n\nNo statistically significant correlations or differences were found between participants with different skin shades concerning shade present, shade wanted, and satisfaction with existing shades.\n\n\nDiscussion\n\nVarious methods of dental shade selection can be broadly categorized into visual and digital methods. Visual methods include the use of stocks and custom shade guides. Digital methods include digital cameras, color-measuring software, colorimeters, spectrophotometers, and intraoral scanners. Despite developments in dental shade selection methods, shade selection remains a challenge that affects esthetic outcomes.16\n\nThis challenge is augmented when patients are edentulous and lack any prior photographic or dental records of the shade of their original teeth, and conventional dental shade selection tools cannot be used.\n\nAccording to the protocols, the age, sex, and complexion of the patient should be taken into consideration while choosing the dental shade for completely edentulous patients. There are several recommendations for selecting the shape and size of artificial teeth, which are supported by rationale and empirical data.17–20\n\nHowever, shade selection for completely edentulous patients follows vague and broad criteria and is therefore more subjective and arbitrary. These add complexities to complete dentures and full-mouth rehabilitation.17–22\n\nThe current study demonstrated that the age and sex of the patient affect their satisfaction with existing dental shades and their shade preferences. No correlation was observed between skin shade and existing or desired shade in the observed test subjects. These observations are similar to those of a previous study. Esan TA, et al.23\n\nOverall, 67.5% of participants were satisfied with their existing dental shades, while 32.5% people wanted to change their dental shades.\n\n8.3% of the test subjects had dental shade of Vita 3D master value 1. Ninety% of these people were satisfied with their existing dental shade, while 10% of the people wanted to change their shade to value 3.\n\n51.6% Of the test subjects had dental shade with vita 3d master value 2. 82.25% Of these people were satisfied with their existing dental shade, while 11.2% of the people wanted to change their shade to value 1.\n\n37.5% Of the test subjects had dental shade with vita 3d master value 3. 44.44% Of these people were satisfied with their existing dental shade, while 37.77% of the people wanted to change their shade to value 2.\n\n2.5% of the test subjects had dental shade of vita 3d master value 1. 33.33% Of these people were satisfied with their existing dental shade, while 66.66% of the people wanted to change their shade to value 2.\n\nTherefore, shades of value 2 were the most desired shades among the Vita 3D master shades.\n\nThe most wanted/liked shades by the test subjects were 2L1.5 (17.5%), 2M1 (15%), 1M1 (12.5%), 2R1.5 (11.67%), 1M2 (7.5%), 2M2 (6.67%), and 2L2.5 (5.83%).\n\nIn the age group of 20 to 30 years, 53.3% of the female participants had shades of value 2, while 40% had shades of value 3. 66.7% were satisfied with their existing shade. 46.7% liked shades of value 2 and 26.7% liked value 3.\n\n53.3% Of the male participants had shades of value 2, while 33.3% had shades of value 3. Twenty% were satisfied with their existing shade. 46.7% liked value 2 and 33.3% liked value 1.\n\nIn the age group of 30 to 40 years, 46.7% of the female participants had shades of value 3, while 40% had shades of value 2. Eighty% were satisfied with their existing shade. 53.3% liked value 2, and 26.7% liked value 3.\n\n46.7% Of the male participants had shades of value 2, while 46.7% had shades of value 3. 33.3% were satisfied with their existing shade. Sixty% liked value 2, and 33.3% liked value 1.\n\nIn the age group of 40 to 50 years, 53.3% of the female participants had shades of value 2, while 40% had shades of value 3. Eighty% were satisfied with their existing shade. 73.3 % liked value 2, and 20% wanted to liked value 3.\n\n66.7% Of the male participants had shades of value 2, while 20% had shades of value 3. 80% were satisfied with their existing shade.\n\nIn age group 50 to 60, 40% of the female participants had shades of value 3, while 40% had shades of value 4. 66.7% were satisfied with their existing shade. 53.3% liked value 2, and 26.7% liked value 1.\n\n66.7% Of the male participants had shades of value 2, while 26.7% had shades of value 3. 93.3% were satisfied with their existing shade. 73% liked value 2 and 20% liked value 3.\n\nMales in the higher age groups were more satisfied with their teeth than younger age groups and females. This was also observed in studies conducted by Tin-Oo et al. and Maghaireh et al.14,15\n\nThe results of this study showed that people become more satisfied with their shade as age advances. In addition, shades of value 2 were the most common and the most liked shade by males and females of all genders as compared to shades of other values.\n\n\nConclusions\n\nWithin the limitations of this study, the following conclusions can be drawn:\n\n1. Satisfaction with existing shade increases in males, especially in the age group of 41–50 years.\n\n2. The most desired tooth shades by both males and females were of value 2, as per the VITA Tooth-Guide 3D Master shade guide.\n\n\n\n1. In this study, participants with different skin shades were not evenly selected. Light shade (n=5), fair shade (n=14), medium shade (n=45), Medium Dark shade (n=37), or dark shade (n=19). This can influence the results with respect to the relationship between skin shade and the satisfaction of existing tooth shades, along with tooth shades preferred by the participants of different skin shades.\n\n2. A larger sample size may reveal further correlations between the hue, value, and chroma of existing and preferred tooth shades.\n\n\n\n1. In the case of the unavailability of dental photographic records in edentulous patients, age and sex can act as a guide for shade selection.\n\n2. If the patient or dentist is unsure about the shade of complete dentures and full-mouth rehabilitations, shades of value 2 can be selected, as they are the most liked shades according to the present study.\n\n3. Older men may prefer darker shades of teeth, whereas women of all ages may prefer lighter shades.\n\nAll observations were performed in conformity with the ethical standards of the Institutional Ethics Committee, Manipal College of Dental Sciences Mangalore, after receiving approval from the committee (ref:22007 dated:12/02/2022). Each individual assigned to participate in the study gave written informed consent to participate in the study.", "appendix": "Data availability\n\nFigshare: prevalence, satisfaction and preference of tooth shades and their correlation with age, gender and skin shade: a cross sectional study, DOI: https://doi.org/10.6084/m9.figshare.24903114.v3. 24\n\nThis project contains the following:\n\n• Raw data\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nFigshare: prevalence, satisfaction and preference of tooth shades and their correlation with age, gender and skin shade: a cross sectional study, DOI: https://doi.org/10.6084/m9.figshare.24903114.v3. 24\n\nThis project contains the following:\n\n• Questionnaire\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nFigshare: prevalence, satisfaction and preference of tooth shades and their correlation with age, gender and skin shade: a cross sectional study, DOI: https://doi.org/10.6084/m9.figshare.24903114.v3. 24\n\nThis project contains the following:\n\n• STROBE CHECK\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nSamorodnitzky-Naveh GR, Geiger SB, Levin L: Patients’ satisfaction with dental esthetics. J. Am. Dent. Assoc. 2007; 138: 805–808. Publisher Full Text\n\nJahangiri L, Reinhardt SB, Mehra RV, et al.: Relationship between tooth shade value and skin color: an observational study. J. Prosthet. Dent. 2002; 87: 149–152. PubMed Abstract \| Publisher Full Text\n\nMcAndrew R: Contemporary Fixed Prosthodontics. 3rd ed. Vol. 29. . Sage; 2014 Dec; pp. 328–329. Publisher Full Text\n\nAzad A, Ahmad S, Zia M, et al.: Relationship of age, gender and skin tone to shades of permanent maxillary central incisors. Pak. Oral Dent. J. 2007; 27: 119–125.\n\nMoon RJ, Millar BJ: Dental Aesthetics: A Study Comparing Patients’ Own Opinions with Those of Dentists. Open J. Stomatol. 2017 Apr 17 [cited 2022 Jan 6]; 07: 225–233. Publisher Full Text\n\nMarcucci B: A shade selection technique. J. Prosthet. Dent. 2003; 89: 518–521. Publisher Full Text\n\nHammad IA: Intrarater repeatability of shade selections with two shade guides. J. Prosthet. Dent. 2003; 89: 50–53. PubMed Abstract \| Publisher Full Text\n\nZarb G, Bolender CL: Prosthodontic treatment for edentulous patients: complete dentures and implant-supported prostheses. 12th ed.St. Louis: Mosby Inc.; 2004; pp. 190–207.\n\nBauer J, Vasilache I, Schlegel AK, et al.: Esthetics and Psyche—Part 1 Assessment of the Influence of Patients’ Perceptions of Body Image and Body Experience on Selection of Existing Natural Tooth Color. Int. J. Prosthodont. 2012; 25: 36–43. PubMed Abstract\n\nAjayi EO: Dental aesthetic self-perception and desire for orthodontic treatment among school children in Benin City, Nigeria. Nig. Q. J. Hosp. Med. 2011; 21(1): 45–49. PubMed Abstract\n\nAlbashaireh ZSM, Alhusein AA, Marashdeh MM: Clinical assessments and patient evaluations of the esthetic quality of maxillary anterior restorations. Int. J. Prosthodont. 2009; 22(1): 65–71. PubMed Abstract\n\nHamamci N, Baaran G, Uysal E: Dental Aesthetic Index scores and perception of personal dental appearance among Turkish university students. Eur. J. Orthod. 2009 Apr; 31(2): 168–173. PubMed Abstract \| Publisher Full Text\n\nAfshar MK, Eskandarizadeh A, Torabi M, et al.: Patient Satisfaction with Dental Appearance and Related FactorsA Cross Sectional Study. J. Evol. Med. Dent. Sci. 2019; 8: 3569–3574. Publisher Full Text\n\nMaghaireh GA, AIzraikat H, Taha NA: Satisfaction with Dental Appearance and Attitude toward improving Dental Esthetics among Patients attending a Dental Teaching Center. J. Contemp. Dent. Pract. 2016; 17: 16–21. PubMed Abstract \| Publisher Full Text\n\nTin-Oo MM, Saddki N, Hassan N: Factors influencing patient satisfaction with dental appearance and treatments they desire to improve aesthetics. BMC Oral Health. 2011 Feb 23; 11: 1–8. Publisher Full Text\n\nTabatabaian F, Beyabanaki E, Alirezaei P, et al.: Visual and digital tooth shade selection methods, related effective factors and conditions, and their accuracy and precision: A literature review. J. Esthet. Restor. Dent. 2021; 33: 1084–1104. PubMed Abstract \| Publisher Full Text\n\nSharry JJ: Complete denture prosthodontics. 3rd ed.New York: McGraw-Hill; 1974.\n\nJohnson DL, Stratton RJ: Fundamentals of removable prosthodontics. Chicago: Quintessence; 1980; pp. 289–307.\n\nPound E: Applying harmony in selecting and arranging teeth. Dent. Clin. N. Am. 1962; 6: 241–258.\n\nLanda LS: Practical guidelines for complete denture esthetics. Dent. Clin. N. Am. 1977; 21: 285–298. PubMed Abstract \| Publisher Full Text\n\nHeartwell CM, Rahn AO: Syllabus of complete dentures. 3rd ed.Philadelphia: Lea & Febiger; 1980; pp. 293–306.\n\nZarb GA, Bolender CL, Hickey JC, et al.: Boucher’s prosthodontic treatment for edentulous patients. 10th ed.St Louis: CV Mosby Co; 1990; pp. 330–342.\n\nEsan TA, Olusile AO, Akeredolu PA: Factors Influencing Tooth Shade Selection for Completely Edentulous Patients. J. Contemp. Dent. Pract. 2006; 7: 80–87. PubMed Abstract \| Publisher Full Text\n\nBajantari P: Prevalence, satisfaction, and preference of tooth shades and their correlation with age, gender, and skin shade: a cross-sectional study. Dataset. figshare. 2023. Publisher Full Text" }	[ { "id": "339847", "date": "28 Nov 2024", "name": "Stephen Westland", "expertise": [ "Reviewer Expertise Specialist in colour and appearance of teeth" ], "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 manuscript that explores the relationship between prevalence, satisfaction and preference for shades and age, gender and skin shade. I believe that the work was carried out with Indian participants. With that in mind I think it would be sensible to specify this in the abstract. In the Methods section a Z value of Z=-1.95996398454005 is reported. I don't think this number of decimal places is justified. I suggest this be changed to 1.96. In terms of the pilot study conclusions, are the authors satisfied that 120 participants in total should be recruited rather than 120 in each of the age age/gender categories? Under Eligibility Criteria point 2 should be changed from\n\n\"Teeth should be no external discoloration or staining\" to\n\n\"Teeth should have no external discoloration or staining.\" In the Grouping section, shouldn't the table have a title, e.g. Table 1: blah blah. Under Procedure the authors write:\n\"The investigators then selected the most common tooth shade among the maxillary anterior teeth\" Is this really what the mean? In which case, what was the most common tooth shade. I think they might mean to write that they selected the tooth shade that best matched the participant's teeth.\n\nUnder Wanted tooth shades, I think this would be better expressed as Desired tooth shades. Under wanted shade section, I do find it confusing. For example, in Table 1 it is evident that Value 2 is most prevalent and most preferred. Later, in the statistical analysis in Table 2 it is reported that there is significance for the the 41-50 age group. But what is significant? It is not clear. The way the Discussion is presented is not very engaging. It is simply a list of observations with very little discussion involved. Ultimately, although satisfaction and preference is interesting, I think prevalence is most important. The finding is that most people have teeth of Value 2. Is there any correlation of tooth shade prevalence with age or gender? I think a clearer Discussion is needed. Factual observations should be moved to the Results section. The list of observations in the Discussion is too long. A proper discussion of what the results mean clinically is needed.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "339854", "date": "12 Dec 2024", "name": "Dr. Gbenga Emmanuel Adebayo", "expertise": [ "Reviewer Expertise Aesthetic Restorative Dentistry", "Endodontics and Dental implantology" ], "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 focused on the prevalence, satisfaction of patients and their preference for tooth shade and how it correlate with their age gender and skin color. This is a very good research topic as it addresses the aesthetic need and satisfaction of patient. The demand of patient for dental prosthesis that meet their aesthetic quest is on the rise, and tooth shade matching is a significant factor in meeting this demand. However, having read through the article thoroughly, there are things I observed and these are pointed out under the different sections of the article as follows: Title The title of the research is clear and objectives well captured, although “skin color” would have been more appropriate than “skin shade”\nAbstract The author made mention in the abstract that in the absence of teeth and dental photograph, tooth shade selection becomes challenging and subjective. But I want to say that whether teeth and dental photograph are available or not, tooth shade matching is still challenging and subjective if conventional visual method of tooth shade selection is used. Subjectivity of shade selection primarily has to do with the method of shade matching used, whether it is visual or machine aided such as spectrophotometer. I feel the sentence can be rephrased for better understanding.\nIntroduction Introduction seems good and past studies were referenced. However, the author is not consistent with the use of “esthetic and ‘aesthetic”, he should have stuck to one. Also, the introduction has too many small paragraphs that can be combined.\nMethod - Sampling technique used for this study not appropriate in my own opinion as it might have introduced bias, although it has the advantage of making grouping into equal male and female easy. - Procedure for the study is not detailed. For example, the tooth shade matching steps was not stated clearly, were the investigators screened for eye anomaly or not, was it done under natural light or not, were the teeth wet or dry etc. For the skin shade matching, which part of the body skin was used, how was the matching done etc. - Age bracket of the participants and the reason should have been included in the selection criteria not just showing it in the grouping. - The description of the shade value should have been presented for better understanding of the results.\nResult Result well presented in my own view and breaking it into sections made it clearer\nDiscussion Discussion is not adequate, nearly repetition of the result earlier presented, not much reference was made to other studies to corroborate the findings. I feel the discussion can be worked on to make it more robust.\nConclusion Well concluded\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "13054", "date": "02 Jan 2025", "name": "Dr Prashanth Bajantri", "role": "Author Response", "response": "We thank both the reviewers and the Editorial for the time and effort invested in our manuscript and we are most happy to make the changes suggested by the reviewers. All the recommendations made by the reviewers have been humbly accepted and the necessary rectifications have been made in the document. However, if the reviewers feel the need for any more corrections we are happy to do so kind regards, Shobha Rodrigues shobha.j@manipal.edu corresponding Author" } ] } ]	1	https://f1000research.com/articles/13-1076
https://f1000research.com/articles/13-98/v1	16 Feb 24	{ "type": "Research Article", "title": "Metabolomic characterization of human glioblastomas and patient plasma: a pilot study", "authors": [ "Yin Allison Liu", "Orwa Aboud", "Lina A. Dahabiyeh", "Orin Bloch", "Oliver Fiehn", "Orwa Aboud", "Lina A. Dahabiyeh", "Orin Bloch", "Oliver Fiehn" ], "abstract": "Background Glioblastoma (GBM) is a clinically challenging primary brain tumor with poor survival outcome despite surgical resection and intensive chemoradiation. The metabolic heterogeneity of GBM can become biomarkers for treatment response, resistance, and outcome prediction. The aim of the study is to investigate metabolic distinctions between primary and recurrent GBM tissue and patient plasma to establish feasibility for metabolic profiling.\n\nMethods A single-center cohort study analyzed tissue and blood samples from 15 patients with GBM using untargeted metabolomic/lipidomic assays. Metabolomic, lipidomic, and biogenic amine analyses were conducted on GBM tissue and patient plasma at diagnosis and recurrence using untargeted mass spectrometry. The study utilized a small but longitudinally collected cohort to evaluate alteration in metabolites, lipids, and biogenic amines between specimens at diagnosis and recurrence.\n\nResults Exploratory analysis revealed significant alteration in metabolites, lipids, and biogenic amines between diagnostic and recurrent states in both tumor and plasma specimens. Notable metabolites differed at recurrence, including N-alpha-methylhistamine, glycerol-3-phosphate, phosphocholine, and succinic acid in tissue, and indole-3-acetate, and urea in plasma. Principal component analysis revealed distinct metabolomic profiles between tumor tissue and patient plasma. Distinct metabolic profiles were observed in GBM tissue and patient plasma at recurrence, demonstrating the feasibility of using metabolomic methodologies for longitudinal studies. One patient exhibited a unique tumor resistance signature at diagnosis, possibly indicating a high-risk metabolomic phenotype.\n\nConclusions In this small cohort, the findings suggest the potential of metabolomic signatures of GBM tissue and patient plasma for risk stratification, outcome prediction, and the development of novel adjuvant metabolic-targeting therapies. The findings suggest metabolic discrepancies at diagnosis and recurrence in tissue and plasma, highlighting potential implications for evaluation of clinical response. The identification of significant changes in metabolite abundance emphasizes the need for larger studies using targeted metabolomics to validate and further explore these profiles.", "keywords": [ "glioblastoma", "untargeted metabolomics", "biomarker", "feasibility", "pilot" ], "content": "Introduction\n\nGlioblastoma (GBM) is a fatal tumor with a median survival of less than two years.1 Most GBMs respond to initial therapeutic interventions of surgical resection and chemoradiation2,3 but eventually, all patients will relapse. The range of progression free survival is wide, from a few months to more than two years. Understanding the differences in molecular features of GBM and its microenvironment at diagnosis and at recurrence can help identify biomarkers to monitor for treatment response, understand pathogenesis of treatment resistance, and predict outcome. It may also help identifying new therapeutic targets.\n\nSurgical resection and standard chemoradiation improve survival but this initial effect is limited by the development of resistance.4 While therapy resistance and the aggressiveness of GBM have been investigated at the genomic and transcriptomic levels, less is known about the metabolic phenotypes. Altered metabolism is a hallmark of cancer.5 Metabolomic changes are critical for tumor cells to undergo conversion to aggressive and treatment-resistant phenotypes.6 Recurrent, therapy resistant tumors develop within the high dose radiation field, and the ability of recurrent tumors to resist therapy is, in part, due to metabolomic alternation within the tumor.7 Tumor metabolism is influenced by both cancer cell-intrinsic information (genome, epigenome, proteome, post-translational modifications) and cell-extrinsic cues from the tumor microenvironment.\n\nTargeting the metabolome has succeeded in a number of cancers including high-grade gliomas.7 Glucose uptake can inform prognosis in a variety of cancers including glioma.8 Metabolomic profiling in GBM tissue may provide important information on the differences in tumor responses to initial standard of care therapies and for understanding the differences between tumors at diagnosis and at recurrence. This may help predict tumor aggressiveness and patient prognosis. Early data from several metabolomic studies in small cohorts of patients with GBM have yielded promising results.9,10 GBM is a heterotrophic tumor but is also known to have highly heterogeneous lipid metabolism11 and favors heterotrophy.12,13 However, the comprehensive metabolomic profile including metabolites, biogenic amines, and lipidomes have not been studied. The comparison between GBM tissue and patient blood specimens has not been performed. Therefore, it is unclear if patient blood can be used as a surrogate to predict tumor status in the brain.\n\nWe performed a study to test the hypothesis that recurrent GBMs are metabolically distinct from GBM at initial diagnosis, and patient plasma can be used as a liquid biopsy to reflect this difference. Using untargeted mass spectrometry, we profiled the metabolomes, lipidomes, and biogenic amines of human glioblastoma tissue and patient plasma both at diagnosis and at recurrence, and correlated metabolomic information with clinical data. We identified patterns of metabolomic remodeling in tumor tissue and patient plasma. These changes can pave the way for metabolomic signature identification for treatment response monitoring, risk stratification, and outcome prediction.\n\n\nMethods\n\nAll subjects gave their written informed consent for inclusion before they participated in the study. The study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Ethics Committee of the University of California, Davis (Tissue collection project identification code 218204, original approval date 06/01/2005; plasma collection project identification code 1412052-2, approval date 4/16/2019).\n\nThe UC Davis Pathology Biorepository at the Comprehensive Cancer Center provides high quality and well-characterized human brain tumor tissue specimens. In this centralized biorepository, all samples were collected after patients’ informed consents and underwent quality control by a clinical neuropathologist. From January 2010 to July 2022, a total of 12 fresh frozen GBM specimens were identified and obtained from the biorepository for metabolomic analysis. Limited deidentified clinical information was abstracted from the medical records within the scope of the approved IRB protocol of the biorepository. All patients underwent the standard Stupp protocol2 for glioblastoma treatment.\n\nThe UC Davis Department of Neurosurgery (Dr. Orin Bloch Laboratory) has an IRB approved protocol to collect blood samples from patients with GBM at diagnosis and throughout treatment, along with access to clinical information of these patients. All procedures performed in this study were in accordance with the 1964 Helsinki Declaration and its later amendments or comparable ethical standards. From August 2019 to July 2022, a total of 12 plasma specimens were selected for metabolomic analysis.\n\nAll patients underwent the standard Stupp protocol2 for glioblastoma treatment. Blood specimens were collected before surgery during the hospitalization. No anesthesia was administered at the time of the blood collection, but all patients were on high dose oral steroids in the peri-operative periods. Untargeted metabolomic, biogenic amine, and lipidomic analyses for GBM tissue and patient plasma were performed.\n\nSample preparation and extraction\n\nMetabolites and biogenic amines were extracted as previously described.14 Blood plasma or serum was extracted following the protocols first published by V. Matyash et al.15 In detail, methanol (1.5 ml) was added to a 200 ml sample aliquot, which was placed into a glass tube with a Teflon-lined cap, and the tube was vortexed. Then, 5 ml of MTBE was added, and the mixture was incubated for 1 h at room temperature in a shaker. Phase separation was induced by adding 1.25 ml of MS-grade water. Upon 10 min of incubation at room temperature, the sample was centrifuged at 1,000 g for 10 min. The upper (organic) phase was collected, and the lower phase was reextracted with 2 ml of the solvent mixture, whose composition was equivalent to the expected composition of the upper phase [obtained by mixing MTBE/methanol/water (10:3:2.5, v/v/v) and collecting the upper phase]. Combined organic phases were dried in a vacuum centrifuge. To speed up sample drying, 200 ml of MS-grade methanol was added to the organic phase after 25 min of centrifugation. Extracted lipids were dissolved in 200 ml of CHCl3/methanol/water (60:30:4.5, v/v/v) for storage.\n\nUsing this protocol, lipid extracts in methyl tert-butyl ether phase (MTBA) were separated from proteins and polar hydrophilic small molecules (in the methanol/water phase) in a way that the lipids were found in the top layer of liquid-liquid separations, rather than in the bottom layer.\n\nDecanting the top layer therefore ensured that the extracts were not contaminated by proteins or polar compounds. The top layer was used for lipidomics while the bottom layer (methanol/water phase) was very suitable for the hydrophilic interaction liquid chromatography-mass spectrometry (HILIC-MS) investigations.\n\nData acquisition\n\nMetabolite profiling using HILIC-MS was performed on the Agilent 1290 UHPLC/Sciex TripleTOF 6600 mass spectrometer. Metabolites (5 μL) were separated using Waters AcquityUPLC BEH amide column (1.7 μm, 2.1 × 50 mm) and a binary mobile phase. Mobile phase A: 100% H2O +10 mM Ammonium Formate + 0.125% Formic acid; B: 95:5 ACN/H2O + 10 mM Ammonium Formate + 0.125% Formic acid. Chromatographic data acquisition was 15 min long. Data were acquired in data-dependent acquisition mode with a mass range 50-1,500 m/z for MS1 and 40-1,000 m/z for MS2.\n\nLipidomic data were acquired using the Agilent 1290 UHPLC/Agilent 6530 QTOF (for positive mode) and 6550 QTOF (for negative mode) mass spectrometer. Waters Acquity Premier BEH C18 column (1.7 μm, 2.1 × 50 mm) was used for chromatographic separation applying binary mobile phase system (Positive mode: mobile phase A: 60:40 v/v acetonitrile:water + 10 mM ammonium formate + 0.1% formic acid; mobile phase B: 90:10 v/v isopropanol:acetonitrile + 10 mM ammonium formate + 0.1% formic acid. Negative mode: mobile phase A: 60:40 v/v acetonitrile:water + 10 mM ammonium acetate; mobile phase B: 90:10 v/v isopropanol:acetonitrile + 10 mM ammonium acetate). MS scan range and mass resolution for positive mode were 120-1,200 m/z and 10,000, respectively, and 60-1,200 m/z and 20,000 for negative mode.\n\nPrimary metabolism data were acquired by gas chromatography (GC)-MS using an Agilent 7890A GC coupled to a Leco Pegasus HT TOF mass spectrometer. Extracts were dried down, derivatized by methoxyamination and trimethylsilylation, and injected in spitless mode with a temperature gradient from 50-330°C. Mass spectra were acquired at 17 Hz from 85-500 Da.14\n\nRaw data processing and metabolite annotation\n\nAcquired raw LC-MS and LC-MS//MS data were processed using the following steps: Raw CSH-C18-TOF (for lipidomics) and HILIC-TTOF (for polar metabolites profiling) MS data were processed using MS-Dial (version 4.9). Data-independent MS/MS deconvolution was performed for comprehensive metabolome analysis.14 Raw GC-TOF MS data files were processed using ChromaTOF and metabolomics BinBase database.14 Peak heights were used for analysis given the strong correlation between extracted ion peak area and peak height across a wide range of concentrations. For very abundant peaks, ion saturation may occur, and in such cases, peak area may be a slightly better measure than peak height. However, in metabolomics, most compounds are low in abundance. Therefore, peak height is a more robust way to measure metabolite levels because the nose baseline has less impact (e.g., for peak start/end) on peak height compared to peak area.\n\nDescriptive statistics were used to characterize baseline patient and treatment characteristics. Individual metabolite abundance comparisons at diagnosis and at relapse were performed using GraphPad Prism 9 (version 9.5, San Diego, CA). MetaboAnalyst 5.0 (version5.0, McGill University, Montreal, QC, Canada)16 was used to generate principal component analysis (PCA), score plots, heat maps and volcano plots. The processed peak heights with their annotation were imported to MetaboAnalyst, normalized to the total sample median and auto scaled. Paired or unpaired Student’s t-Test was used to identify significantly altered metabolites between the compared groups (p-value of less than 0.05 was considered significant). ChemRICH (version 2023), a statistical enrichment approach based on chemical similarity rather than sparse biochemical knowledge annotations was used to group the metabolites. ChemRICH sets have a self-contained size where p-values do not rely on the size of a background database.\n\nThe protocols are deposited at Protocol IO: https://dx.doi.org/10.17504/protocols.io.n92ldmjkol5b/v1.\n\n\nResults\n\nPatient demographics are described in Table 1.29 In the tissue cohort, a total of 12 specimens from nine patients were analyzed (nine specimens at diagnosis, three of which had paired specimens at recurrence). The mean age at diagnosis was 49 years old. There was a male predominance of 67%. Most of this cohort was non-Hispanic White in race/ethnicity.\n\nGBM, glioblastoma; IDH, Isocitrate Dehydrogenase; EGFR, epidermal growth factor receptor; MGMT, O6-methylguanine-DNA methyltransferase; ATRX, Alpha thalassemia/mental retardation syndrome X-linked; PFS, progression-free survival; OS, overall survival.\n\nIn the plasma cohort, a total of 12 paired specimens (diagnosis and at recurrence) from six patients with GBM were analyzed. The mean age was 54 years old. There was a male predominance of 67%. The original GBM tissue pathology all showed Isocitrate Dehydrogenase (IDH) wild type. Additional pathology features including epidermal growth factor receptor (EGFR), O6-methylguanine-DNA methyl-transferase (MGMT), and Alpha thalassemia/mental retardation syndrome X-linked (ATRX) status are shown in Table 1. The mean progression free survival of this cohort was 14 months. The mean overall survival was 17 months.\n\nThe GBM tissue cohort included nine tumor tissue specimens at diagnosis, three of which had paired tissue specimens at recurrence. A complete list of significantly altered metabolites is available in Table 2. A summary of these changes is shown in Figure 1. Principal component analysis (PCA) showed two grouped clustering trends with significant overlap (Figure 1A). A heat map of the top 50 significantly altered metabolites, lipids, and biogenic amines, showed differences in cluster trends between tissue samples at diagnosis and at recurrence (Figure 1B). There were several significantly upregulated compounds (Figure 1C) in the lipidomic and biogenic amine analysis. Also included in Figure 1 are scattered column plots for compounds with significant change in abundance at diagnosis and at recurrence (Figure 1D), which included N-alpha-methylhistamine (P=0.037), 2,3-dihydroxypropyl dihydrogen phosphate with (P=0.029), CE22:6 (P=0.021), LPE 20:4 (P=0.004), LPE 22:6 (P=0.011), LPE 22:4 (P=0.041), CE 20:3 (P=0.031), CE 16:1 (P=0.003), phosphocholine with a (P=0.045), and succinic acid (P=0.025).\n\nComparison of the metabolomic profiles from nine tissue specimens at diagnosis, and three tissue specimens at recurrence. GBM, glioblastoma.\n\n(A) Principal component analysis (PCA) plot showing different trends of metabolomic characteristics between tissues at diagnosis (purple) and tissue at recurrence (light blue). (B) Heatmap of the top 50 altered metabolites at diagnosis and at recurrence. Blue indicates decreased peak value and maroon indicates increased peak value of each compound listed. (C) Volcano plot of up regulated metabolites in red and down regulated metabolites in blue in glioblastoma tumor tissue specimens at recurrence comparing to at diagnosis using p-value of <0.05 and fold change cutoffs of 1.5. (D) Plots of individual values for each metabolite demonstrating peak value changes at diagnosis and at recurrence in brain tumor tissue. Values were determined as peak heights from LC/MS analysis. Single asterisk indicates a p value of <0.05. Double asterisks indicate a p value of <0.01.\n\nWhen analyzing the three paired tissue specimens at diagnosis and at recurrence, again the PCA plot demonstrated two overlapping clusters (Figure 2A). The heat map showed more visible separation between tissue samples at diagnosis and at relapse (Figure 2B). We found 19 compounds that were significantly altered. Volcano plot (using p-value <0.05 and Fold Change cutoff 1.5) revealed that three metabolites were upregulated, and six metabolites were down regulated (Figure 2C). A complete list of significantly altered metabolites is available in Table 3. Among these metabolites, we found that the levels of the 2-methylbutyryl-L-carnitine (P=0.02) and an unknown compound eluting at 1.84 minutes with an accurate mass of 186.1075 Da (P=0.04) were significantly higher in primary tumors than recurrent GBMs (Figure 2D).\n\n(A) Principal component analysis (PCA) plot showing different trends of metabolomic characteristics between tissues at diagnosis (purple) at tissue at recurrence (light blue). (B) Heatmap of the top 50 altered metabolites. Blue indicates decreased peak value and red indicates increased peak value of each compound listed. (C) Volcano plot of upregulated metabolites in red and downregulated metabolites in blue in glioblastoma tumor tissue specimens at recurrence comparing to at diagnosis using p-value of <0.05 and fold change cutoffs of 1.5. (D) Plots of individual values for each metabolite demonstrating peak value changes at diagnosis and at recurrence in brain tumor tissue. Values were determined as peak heights from LC/MS analysis. Single asterisk indicates a p value of <0.05. Double asterisks indicate a p value of <0.01.\n\nGBM, glioblastoma.\n\n* For paired analysis, Metaboanalyst calculates fold changes (FC) by computing the ratio between paired samples (i.e., one FC per pair), and then computing their means (i.e., pair means). Super class and main class were defined in the metabolomics workbench https://www.metabolomicsworkbench.org/databases/refmet/refmet.php.\n\nAll six patients enrolled in this cohort had paired plasma specimens at diagnosis and at recurrence. However, these were not the same patients whose GBM tissue were studied in the cohort above. PCA analysis showed evident separation between the metabolomic profiles at diagnosis and at recurrence, except for patient one, whose metabolomic profiles were similar at diagnosis and at recurrence (Figure 3A). The heatmap of the top 50 altered metabolites showed visible differences between plasma at diagnosis and at recurrence (Figure 3B). Again, the metabolite profile of patient one at recurrence was similar to its status at diagnosis, while the other patients’ profiles demonstrated differences.\n\n(A) Principal component analysis (PCA) plot showing different trends of metabolomic characteristics between tissues at diagnosis (purple) at tissue at recurrence (light blue). (B) Heatmap of the top 50 altered metabolites. Blue indicates decreased peak value and red indicates increased peak value of each compound listed. (C) Volcano plot of up regulated metabolites in red and down regulated metabolites in blue in glioblastoma tumor tissue specimens at recurrence comparing to at diagnosis using p-value of <0.05 and fold change cutoffs of 1.5. Single asterisk indicates a p value of <0.05. Double asterisks indicate a p value of <0.01. (D) Progression free survival of six patients whose plasma samples were analyzed. (E) Significantly altered metabolite clusters by ChemRich, a statistical enrichment approach based on chemical similarity. The size of the dots is in proportion with the level of alteration in each cluster of metabolites. Red indicates increased peak value and blue indicates decreased peak value. (F) Box plots demonstrating metabolite peak value changes at diagnosis and at recurrence in brain tumor tissues. Values were determined as peak height from LC/MC analysis. Single asterisk indicates a p value of <0.05. Double asterisks indicate a p value of <0.01.\n\nThere were 61 compounds that were altered significantly between diagnosis and recurrence in the patient plasma. The representatives were shown in Figure 3C. A complete list of significantly altered metabolites is available in Table 4. The progression free survival of these six patients was shown in Figure 3D. Using ChemRich, we were able to identify that based on chemical structural similarity, amino acids and unsaturated phosphatidylcholines were significantly up regulated and unsaturated fatty acids and phosphatidylethanolamines were downregulated (Figure 4E). The compounds with significantly increased abundance at recurrence included 2,4-difluorotoluene (P=0.031), diatrizoic acid (P=0.032), indole-3-acetate with (P=0.029), urea (P=0.025), pseudo uridine (P=0.042), and maltose (P=0.035). The compounds with significantly decreased abundance included FA 20:1 (eicosenoic acid) (P=0.017), glucose-1-phosphate (P=0.017), FA 18:2 (linoleic acid) (P=0.017), arginine (P=0.036), FA 20:3 (homo-gamma-linolenic acid) (P=0.036), galactosamine (P=0.007), and FA 18:3 (linolenic acid) (P=0.012) (Figure 3F).\n\nGBM, glioblastoma.\n\n* For paired analysis, Metaboanalyst calculates fold changes (FC) by computing the ratio between paired samples (i.e., one FC per pair), and then computing their means (i.e., pair means). Super class and main class were defined in the metabolomics workbench https://www.metabolomicsworkbench.org/databases/refmet/refmet.php.\n\n(A, C, E) Principal component analysis plots comparing tissue vs. plasma specimens at diagnosis, tissue vs. plasma at recurrence, and all four specimen groups. (B, D, F) Heatmaps of the top 50 significantly altered metabolites in the comparisons correlating with A, C, and E, respectively.\n\nBoth the PCA and heatmap analyses showed separate metabolic profiles from tissues at diagnosis and plasma at diagnosis (Figure 4A and B). Similarly, the metabolomic profile from tissue at recurrence separated from plasma at recurrence (Figure 4C and D). When placing all four groups of data in one plot (Figure 4C and D), we again saw inter-specimen differences between the metabolomic profiles in tissue and plasma, but there were no intra-specimen differences at diagnosis and at recurrence.\n\n\nDiscussion\n\nIn this study, we investigated the comprehensive untargeted metabolomic, lipidomic, and biogenic amine profiles of GBM tissue and patient plasma specimens at diagnosis and at recurrence. Despite a small overall cohort size, our result showed that many metabolites were altered in GBM tissue and patient plasma at recurrence when compared to diagnosis. Our study demonstrated the feasibility of studying GBM tissue and patient blood specimen longitudinally using metabolomic methodology.\n\nGBM display marked metabolic heterogeneity in their microenvironments.17 Both glucose and lipid metabolisms are abnormally regulated in GBM tissues.18,19 In our study, we observed several metabolites that had changed in abundance at recurrence when compared to diagnosis. Many of these metabolites were also identified in a recently published study on the metabolic hallmarks of gliomas.20 Specifically, we identified 2-methylbutyryl-L-carnitine that was known to reflect tumor metabolic flexibility in brain tumor tissues at diagnosis and at recurrence. Carnitine serves as a “shuttle-molecule” that allows fatty acid acyl moieties to enter the mitochondrial matrix for oxidization via the beta-oxidation pathway.21 We found that the 2-methylbutyryl-L-carnitine level was significantly reduced in recurrent tumors compared to initial GBM tissue. Carnitine transporter modulation has been thought to be a potential target for cancer treatment.21 In addition, we also found many altered levels of lipids in GBM tissue at recurrence when compared to initial diagnosis. Our findings are in line with previously published data suggesting lipid metabolic alterations in GBM.22 In addition, mannitol was upregulated in recurrent tissue compared to the original tumor, suggesting BBB permeability changes after surgical resection and chemoradiation. This may suggest mannitol as a vehicle to guide targeted treatment.\n\nNotably, the list of metabolites with significantly altered abundance and fold changes differ when comparing the unpaired samples (nine tissue samples at diagnosis vs. three tissue samples at recurrence) and the paired samples (three tissue samples from the same patients at diagnosis and at recurrence). Despite a small sample size, the paired tissues samples demonstrated a clearer trend in the differences in compound abundance at diagnosis and at recurrence (Figure 1A compared with Figure 2A). It is likely that the effect size was reduced because of the heterogeneity of unpaired samples. Based on these findings, we recommend that future studies utilize paired samples due to their superior ability to serve as an internal control. The paired samples offer a more reliable basis for assessing changes in metabolite abundance between diagnosis and recurrence, providing greater confidence in the observed differences.\n\nIn both the PCA plot from patient plasma and the heatmap generated from the top 50 altered metabolites, we found that the metabolomic profiles differed between specimens at diagnosis and at recurrence, except for one patient with early recurrence. The metabolomic profile of this patient’s plasma at diagnosis was different from the rest of the plasma specimens at diagnosis and was similar to the group pattern at recurrence. This notable finding needs to be validated in a larger cohort of patients with treatment refractory tumors and early recurrence. This metabolomic signature may indicate a high risk and poor prognosis.\n\nIn the plasma cohort, we found several significantly altered metabolites with large fold changes. For example, 2,4-difluorotoluene increased in patient plasma at recurrence; this metabolite is incorporated into DNA and undergoes replication by DNA polymerase enzymes.23 The observed change may suggest rapid growth of recurrent tumors. However, it is worth noting that this compound is also used as an intermediate in the production of pharmaceuticals and dyes. Therefore, it is crucial to validate this finding through further investigation in future studies. Diatrizoic acid also increased at recurrence. This compound is a contrast agent used during imaging and can be attributed to a previous injection for neuroimaging prior to blood sample collection. Indole-3-acetate is an indol-3-yl carboxylic acid anion and has a role as a human metabolite. We again found several other compounds involved in glucose and lipid metabolism. The overall pattern changes of these compounds need to be validated in targeted metabolomics for their potential candidacy as biomarkers for treatment response and tumor recurrence. The enrichment of these metabolites in recurrent GBM tissue may suggest that targeting metabolic activity can be a potential adjuvant targeted treatment for patients with GBM.\n\nOf note, when plotting all four groups in the same PCA plot, the brain tissue and plasma specimens separated distinctly from each other regardless of disease status (Figure 4). There was no overlap between specimen types, while the intra-specimen comparison at diagnosis and at recurrence became smaller. This suggested that plasma metabolite patterns are not reflective of brain tumor tissue, and therefore, two sets of biomarker panels are necessary for tissue and plasma. The pattern of tumor microenvironment can be further altered through end organ metabolism in the plasma. Also, plasma is affected by systemically administered medication for peri-operative care.\n\nOur study has limitations. First, we must acknowledge that the sample size in this pilot study is small. Second, although we have paired data within the brain tissue and plasma cohorts at diagnosis and at recurrence, we were unable to identify if the tissue and plasma specimens were from the same patients due to the restrictions of the UC Davis biorepository consents for GBM tissue. In addition, we did not have normal brain tissue or plasma for comparison for ethical reasons. We also recognized that the blood metabolomic profiles of healthy volunteers vary24–26 and the metabolic signatures of normal controls can also indicate early states of certain diseases,27 drug effects,24 and dietary composition.28 We will obtain age, sex, and ethnicity matched controls in the future study to minimize potential confounding effects. These limitations prevented us from identifying small changes in metabolite abundance. Therefore, only significant and large fold changes were analyzed. A bigger cohort with paired specimens will be emphasized in future studies. The current study paved the way for the next targeted metabolomics, lipidomic, and biogenic amine studies validating and further investigating these profiles.\n\n\nConclusions\n\nOur data suggest that metabolomic profiles of human GBM tissue and patient plasma differ at diagnosis and at recurrence. Many metabolites involved in tumorigenesis and metabolomic flexibility were identified. A larger study using target metabolomic assay is warranted to measure the levels of these metabolites, which will help identify the metabolomic signatures in both GBM tissue and patient plasma for risk stratification, clinical outcome prediction, and development of new adjuvant metabolomic-targeting therapy.\n\n\nAuthor contributions\n\nAll authors contributed to the study conception and design. Material preparation, data collection and analysis were performed by Yin Allison Liu, Orwa Aboud, Lina Dahabiyeh, Orin Bloch, and Oliver Fiehn. The first draft of the manuscript was written by Yin Allison Liu, and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.", "appendix": "Data availability\n\nFigshare: Brain tissue Biogenic Amines 10.9.22.xlsx/. https://doi.org/10.6084/m9.figshare.24769668.v2. 29\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 would like to thank Dr. Robert O’Donnell for his critical review of this manuscript. An earlier version of this article can be found on Research Square (doi: https://doi.org/10.21203/rs.3.rs-2662020/v1).\n\n\nReferences\n\nOstrom QT, Cioffi G, Waite K, et al.: CBTRUS Statistical Report: Primary Brain and Other Central Nervous System Tumors Diagnosed in the United States in 2014-2018. Neuro-Oncology. Oct 5 2021; 23(12 Suppl 2): iii1–iii105. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStupp R, Mason WP, van den Bent MJ , et al.: Radiotherapy plus concomitant and adjuvant temozolomide for glioblastoma. N. Engl. J. Med. 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Publisher Full Text\n\nParik S, Fernandez-Garcia J, Lodi F, et al.: GBM tumors are heterogeneous in their fatty acid metabolism and modulating fatty acid metabolism sensitizes cancer cells derived from recurring GBM tumors to temozolomide. Front. Oncol. 2022; 12: 988872. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChinnaiyan P, Kensicki E, Bloom G, et al.: The metabolomic signature of malignant glioma reflects accelerated anabolic metabolism. Cancer Res. Nov 15 2012; 72(22): 5878–5888. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPrabhu AH, Kant S, Kesarwani P, et al.: Integrative cross-platform analyses identify enhanced heterotrophy as a metabolic hallmark in glioblastoma. Neuro-Oncology. Feb 19 2019; 21(3): 337–347. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBarupal DK, Zhang Y, Shen T, et al.: A Comprehensive Plasma Metabolomics Dataset for a Cohort of Mouse Knockouts within the International Mouse Phenotyping Consortium. Metabolites. May 22 2019; 9(5). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMatyash V, Liebisch G, Kurzchalia TV, et al.: Lipid extraction by methyl-tert-butyl ether for high-throughput lipidomics. J. Lipid Res. May 2008; 49(5): 1137–1146. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPang ZQ, Chong J, Zhou GY, et al.: MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights. Nucleic Acids Res. Jul 2021; 49(W1): W388–W396. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShakya S, Gromovsky AD, Hale JS, et al.: Altered lipid metabolism marks glioblastoma stem and non-stem cells in separate tumor niches. Acta Neuropathol. Commun. May 31 2021; 9(1): 101. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGuo D, Bell EH, Chakravarti A: Lipid metabolism emerges as a promising target for malignant glioma therapy. CNS Oncol. May 2013; 2(3): 289–299. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDelle Donne R, Iannucci R, Rinaldi L, et al.: Targeted inhibition of ubiquitin signaling reverses metabolic reprogramming and suppresses glioblastoma growth. Commun. Biol. Aug 2 2022; 5(1): 780. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBjorkblom B, Wibom C, Eriksson M, et al.: Distinct metabolic hallmarks of WHO classified adult glioma subtypes. Neuro-Oncology. Sep 1 2022; 24(9): 1454–1468. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nConsole L, Scalise M, Mazza T, et al.: Carnitine Traffic in Cells. Link With Cancer. Front. Cell. Dev. Biol. 2020; 8: 583850. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKou Y, Geng F, Guo D: Lipid Metabolism in Glioblastoma: From De Novo Synthesis to Storage. Biomedicines. Aug 11 2022; 10(8). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPallan PS, Egli M: Pairing geometry of the hydrophobic thymine analogue 2,4-difluorotoluene in duplex DNA as analyzed by X-ray crystallography. J. Am. Chem. Soc. Sep 9 2009; 131(35): 12548–12549. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGuo L, Milburn MV, Ryals JA, et al.: Plasma metabolomic profiles enhance precision medicine for volunteers of normal health. Proc. Natl. Acad. Sci. U. S. A. Sep 1 2015; 112(35): E4901–E4910. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChen L, Zhernakova DV, Kurilshikov A, et al.: Influence of the microbiome, diet and genetics on inter-individual variation in the human plasma metabolome. Nat. Med. Nov 2022; 28(11): 2333–2343. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSato S, Parr EB, Devlin BL, et al.: Human metabolomics reveal daily variations under nutritional challenges specific to serum and skeletal muscle. Mol. Metab. Oct 2018; 16: 1–11. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWittenbecher C, Guasch-Ferre M, Haslam DE, et al.: Changes in metabolomics profiles over ten years and subsequent risk of developing type 2 diabetes: Results from the Nurses’ Health Study. EBioMedicine. Jan 2022; 75: 103799. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEsko T, Hirschhorn JN, Feldman HA, et al.: Metabolomic profiles as reliable biomarkers of dietary composition. Am. J. Clin. Nutr. Mar 2017; 105(3): 547–554. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLiu A: Brain tissue Biogenic Amines 10.9.22.xlsx. [Dataset]. figshare. 2023. Publisher Full Text" }	[ { "id": "251328", "date": "20 Mar 2024", "name": "Joseph Chen", "expertise": [ "Reviewer Expertise GBM tumor microenvironment", "biomaterials", "mechanobiology", "proteomics", "extracellular matrix", "cell migration" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nCOMMENTS TO AUTHORS\nIn this report, the authors present a pilot study to explore the utility of metabolomic characterization as a tool for risk stratification, outcome prediction, and the identification of new metabolic-targeting therapies. The authors use untargeted assays to analyze metabolomic, lipidomic, and biogenic amine profiles of GBM tissue and plasma from a mixed cohort of 15 patients. The investigation revealed distinct metabolic, lipidomic, and biogenic amine profiles between primary and recurrent states in both tissue and plasma. Additionally, the data revealed that metabolomic profiles also differed from tissue and plasma samples. This study identifies several metabolites in the tissue that corroborate findings in the literature; however, the plasma data appears to identify secondary metabolites from peri-operative care that may confound the interpretation. Although this report indicates the possibility of leveraging metabolomic tools to inform patient prognosis, this study has many limitations that hamper these conclusions. These include includes the small sample size, the lack of controls, and the inability to directly analyze tissue and plasma from the same patient. Additionally, the clearer separation in metabolite data in the patient matched tissue cohort (n=3) highlights the limitation of their bulk/combined analysis and reduces the confidence in their results. Given these limitations, it is unclear whether there is sufficient data to support the author’s conclusions.\nMAJOR COMMENTS:\nDetails on the patient demographics in the GBM tissue cohort is limited. Why are there no details on IDH, EGFR, or MGMT status in the patient tissue? Which three patients were part of the matched groups? Where is the prognosis data for this group? With such small sample sizes, the addition of patient data is needed and may identify new insights and interpretations. With the list of altered metabolites being different (Table 2 and Table 3), how do the authors parse out the relevant metabolic alterations that occur during recurrence? Is the bulk primary tumor comparison with 3 recurrent tumors useful or does it confound the patient-matched analysis? Interpretation of the 1 plasma sample that showed similar metabolic profiles is premature. The authors’ conclusion that this sample may be evidence of an aggressive signature seems unwarranted as it would suggest that no metabolic alterations at the plasma level leads to early recurrence and patient death. Alternatively, the data may point to a temporal effect of plasma analysis, where in early recurrence, only a short time has elapsed and thus plasma levels are more similar. If this were true, additional analysis would be needed to detail the duration of time between measurements and may suggest strong variance in plasma level analysis.\nMINOR COMMENTS:\nThere are several reports within recent years that have investigated the metabolome in GBM. A more exhaustive survey of the literature is needed. Figure 1D lists N-alpha-methylhistamine twice\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "11791", "date": "25 Jun 2024", "name": "Yin Allison Liu", "role": "Author Response", "response": "MAJOR COMMENTS: Details on the patient demographics in the GBM tissue cohort is limited. Why are there no details on IDH, EGFR, or MGMT status in the patient tissue? Which three patients were part of the matched groups? Where is the prognosis data for this group? With such small sample sizes, the addition of patient data is needed and may identify new insights and interpretations. Response: The current biobank has an IRB protocol that limits access to information beyond general tumor pathology diagnosis, age at diagnosis, sex, and ethnicity. We have included the details of matched patients in Table 1. Our aim is to use this study as a basis for justifying a grant that would enable the establishment of a biobank with comprehensive clinical information. This initiative reflects a valuable lesson learned by our team. With the list of altered metabolites being different (Table 2 and Table 3), how do the authors parse out the relevant metabolic alterations that occur during recurrence? Is the bulk primary tumor comparison with 3 recurrent tumors useful or does it confound the patient-matched analysis? Response: Thank you for this insightful question. While we have been exploring both approaches to analyze the data, we also realized that while the bulk comparison provides an initial perspective on metabolic changes throughout glioblastoma progression, it may potentially confound patient-matched analyses. Moving forward, we will focus on patient-matched analyses to pinpoint precise metabolic alterations associated with recurrence within individuals. This approach aims to uncover unique metabolic profiles that play a role in tumor progression and resistance to treatment. We listed this in the limitation section. Interpretation of the 1 plasma sample that showed similar metabolic profiles is premature. The authors’ conclusion that this sample may be evidence of an aggressive signature seems unwarranted as it would suggest that no metabolic alterations at the plasma level leads to early recurrence and patient death. Alternatively, the data may point to a temporal effect of plasma analysis, where in early recurrence, only a short time has elapsed and thus plasma levels are more similar. If this were true, additional analysis would be needed to detail the duration of time between measurements and may suggest strong variance in plasma level analysis. Response: We agree that the interpretation based on n=1 was premature. We have revised the interpretation in the discussion section according to the reviewers' suggestions. MINOR COMMENTS: There are several reports within recent years that have investigated the metabolome in GBM. A more exhaustive survey of the literature is needed. Response: We have conducted additional literature reviews and incorporated new references into both the introduction and discussion sections. Figure 1D lists N-alpha-methylhistamine twice Response: We have removed the repeated graph." } ] }, { "id": "260753", "date": "23 May 2024", "name": "Andrew J Scott", "expertise": [ "Reviewer Expertise Cancer and brain metabolism", "metabolomics", "therapy resistance" ], "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\nGlioblastoma (GBM) is one of the most difficult to treat cancers, and the investigation of metabolites in patients may represent a potential strategy to develop new stratification, prediction and treatment modalities. In this study, a small panel of tumor tissue and plasma samples from GBM patients are subjected to metabolomic analysis in an effort to determine if metabolites differ between primary and recurrent GBM. Plasma samples are also investigated, although these samples were from a different cohort of patients. Several differences are noted in select metabolites, although sample size is small (n=3 recurrent tumors compared with n=3 matched primary tumors, or n=3 recurrent tumors compared to the 3 matched primary + additional unmatched samples). For this reason the conclusions regarding metabolite differences between primary and recurrent GBM tumors may not be reliable. Moreover, further details regarding methodological and analytical descriptions are needed. Concerns are described below.\n1) Acquisition of patient-matched primary and recurrent tumors is important for determining new prognostic/therapeutic approaches and is a strength of the study, but sample number is a major concern. It is difficult to draw reliable conclusions and interpretations from an n=3 group of patients, in particular with regard to conclusions about changes in individual metabolite levels between primary and recurrent tumors. How reliable are these findings when false discovery rates are considered?\n2) While analyses of individual metabolites (e.g., Figs 1D, 2D, 3B) lack sufficient statistical power, pathway-level (rather than metabolite-level) analysis tools are available in MetaboAnalyst that incorporate comprehensive metabolomic data (such as pathway analysis or MSEA, somewhat analogous to GSEA of geneset data) to generate metabolite enrichment and pathway predictions. These tools may be useful to more reliably and repeatably inform about metabolic states of tumors.\n3) The authors understate the current literature on GBM metabolomic profiling and imply this has not been done before. Several larger scale studies have already performed metabolomic profiling of GBMs and other high-grade gliomas and identified unique metabolic signatures, including (unmatched) primary vs. recurrent analyses. These datasets included stratification into various subgroups and correlations with patient medical and outcome data. Relevant DOIs are: a.) Scott AJ . et.al., 2023 b.) Chinnaiyan P. et.al., 2012 c.) Kesarwani P .et.al., 2019 Further expansion into the literature and contextualization of the authors' findings with these existing data are necessary.\n4) In Table 1, further clarification on which patients were used in the different matched vs. unmatched analyses is needed.\n5) Throughout the text and figures, the authors use phrases such as “top 50 altered metabolites,” “significantly altered/different abundance/fold change,” etc. These are vague and statistically undefined, unclear.\nMinor comments 6) Description of clustering methods/algorithms used to produce dendrograms for the heatmaps were not found. 7) More contrast or use of color-blind palettes would assist readability of figure panels (Figs 1A, 1B, 2A, 2B, 4C, 4D).\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? No", "responses": [ { "c_id": "11792", "date": "25 Jun 2024", "name": "Yin Allison Liu", "role": "Author Response", "response": "1) Acquisition of patient-matched primary and recurrent tumors is important for determining new prognostic/therapeutic approaches and is a strength of the study, but sample number is a major concern. It is difficult to draw reliable conclusions and interpretations from an n=3 group of patients, in particular with regard to conclusions about changes in individual metabolite levels between primary and recurrent tumors. How reliable are these findings when false discovery rates are considered? Response: Thank you for the feedback. We acknowledge that the small sample size may compromise the reliability of our conclusions, making it challenging to draw definitive results. This study serves as a pilot based on the availability of specimens in the biobank, and we intend to use these preliminary findings to support our application for a larger grant to fund expanded biospecimen collection. Following FDR batch correction, we found no significant compounds, which we must acknowledge. We have submitted grant proposals with the intention that, if funded, we will have access to a substantial collection of specimens and plasma for comprehensive analysis. 2) While analyses of individual metabolites (e.g., Figs 1D, 2D, 3B) lack sufficient statistical power, pathway-level (rather than metabolite-level) analysis tools are available in MetaboAnalyst that incorporate comprehensive metabolomic data (such as pathway analysis or MSEA, somewhat analogous to GSEA of geneset data) to generate metabolite enrichment and pathway predictions. These tools may be useful to more reliably and repeatably inform about metabolic states of tumors. Response: We used ChemRICH (ChemRICH (ucdavis.edu)), a tool developed in our core lab and a statistical enrichment approach based on chemical similarity to classify our data, and the results are shown in Figure 3(E). We did not perform this enrichment analysis for the tissues demonstrated in Figures 1 and 2 due to the very small sample size. 3) The authors understate the current literature on GBM metabolomic profiling and imply this has not been done before. Several larger scale studies have already performed metabolomic profiling of GBMs and other high-grade gliomas and identified unique metabolic signatures, including (unmatched) primary vs. recurrent analyses. These datasets included stratification into various subgroups and correlations with patient medical and outcome data. Relevant DOIs are: a.) Scott AJ . et.al., 2023 b.) Chinnaiyan P. et.al., 2012 c.) Kesarwani P .et.al., 2019 Further expansion into the literature and contextualization of the authors' findings with these existing data are necessary. Response: Thank you for the suggested references. We have expanded our discussion and added the references. 4) In Table 1, further clarification on which patients were used in the different matched vs. unmatched analyses is needed. Response: We have added a column to indicate the matched tissue specimens and also included notation on whether the specimens are paired or unpaired for each specimen type. 5) Throughout the text and figures, the authors use phrases such as “top 50 altered metabolites,” “significantly altered/different abundance/fold change,” etc. These are vague and statistically undefined, unclear. Response: “Top 50 altered\" denotes the top 50 metabolites with significantly altered abundance in each comparison, exhibiting fold changes greater than 1.5. This includes both metabolites with increased and decreased fold changes. We have added this in the result section. Minor comments 6) Description of clustering methods/algorithms used to produce dendrograms for the heatmaps were not found. Response: Dendrogram and heat map were produced from MetaboAnalyst version 4.0 using the default Euclidean distance and Ward linkage. We have added this in the result section. 7) More contrast or use of color-blind palettes would assist readability of figure panels (Figs 1A, 1B, 2A, 2B, 4C, 4D). Response: We have regenerated the figures with improved contrast resolution. Additionally, we have selected colors that are friendly for individuals with color blindness." } ] } ]	1	https://f1000research.com/articles/13-98
https://f1000research.com/articles/13-1075/v1	19 Sep 24	{ "type": "Research Article", "title": "More value and less waste in research on primary cam morphology and its natural history: a qualitative interview study of stakeholders' perspectives", "authors": [ "H Paul Dijkstra", "Sean McAuliffe", "Jolanda Boersma", "Mike Clarke", "Karim Khan", "Sion Glyn-Jones", "Trisha Greenhalgh", "Sean McAuliffe", "Jolanda Boersma", "Mike Clarke", "Karim Khan", "Sion Glyn-Jones", "Trisha Greenhalgh" ], "abstract": "Background Primary cam morphology, an acquired bony prominence at the head-neck junction of the femur, is highly prevalent in athlete populations, and causally associated with femoroacetabular impingement syndrome and early hip osteoarthritis. Experts agreed on key elements for primary cam morphology and a prioritised research agenda for the field. This research agenda will require higher-quality research to achieve meaningful progress on the aetiology, prognosis and treatment of primary cam morphology in athletes.\n\nAim To explore stakeholders’ perspectives of high-quality research in the research field of primary cam morphology and its natural history.\n\nMethods Grounded in interpretive description, we used semi-structured interviews to explore stakeholders’ perspectives of high-quality research in the primary cam morphology research field. The framework for INcreasing QUality In patient-orientated academic clinical REsearch (INQUIRE) informed the interview guide. Audio-recorded interviews were transcribed and analysed using thematic analysis. We recruited a heterogenous and purposive maximum variation sample, drawing from a network of research contacts.\n\nResults Fifteen individuals, several with multiple perspectives on research quality in the field, participated. Exploring stakeholders’ perspectives on research quality through an established research quality framework (INQUIRE) illuminated areas for immediate action for research communities in the field of primary cam morphology and its natural history. We crafted five action inviting themes: research communities should: partner with athletes/patients; champion equity, diversity and inclusion; collaborate with one another; pursue open science; and nurture young scholars.\n\nConclusion The findings of this study could inform concrete actions by research communities to pursue higher quality research—more research value and less waste—in the field of primary cam morphology and its natural history. Although the five action-inviting themes reflect contemporary trends in research, and could therefore be transferable to other areas of research, their practical application remains context- and field-specific.", "keywords": [ "research value", "research waste", "qualitative research", "high-quality research", "femoroacetabular impingement syndrome", "primary cam morphology" ], "content": "Introduction\n\nPrimary cam morphology develops as a largely benign prominence at the head-neck junction of the hip in many young athletes.1 The risk of developing primary cam morphology is associated with the level of athletic activity during skeletal growth.2–4 Although largely benign, this morphology is associated with femoroacetabular impingement (FAI) syndrome,5 and causes early hip osteoarthritis, with potentially significant consequences for hip-health and athletic careers.6–9 Despite the morphology’s high prevalence (up to 80% in many athletic populations10), many questions remain unanswered. For example, to date, no prospective studies have examined this morphology’s formation and/or prognosis in girls or in populations from the Global South. Scientists cannot yet predict the individuals who might develop the morphology or its hip disease consequences, or who might need their hips replaced. Multi-centre and multi-profession collaboration to produce higher quality research with impact is paramount when promoting research value and avoiding research waste.11\n\nA concept analysis of primary cam morphology was an important first milestone towards more clarity on the morphology and its natural history.1 In addition, the Young Athlete’s Hip Research (YAHiR) Collaborative’s Aspetar-Oxford-La Trobe Young Athlete’s Hip Webinar Series, which delivered 11 webinars during the Covid-19 pandemic, contributed to mobilising an international community of athletes, patients, clinicians, and researchers interested in improving clinical outcomes through coproducing knowledge in the field. This collaboration paved the way for the Oxford Consensus Study on primary cam morphology definitions, terminology, taxonomy, and imaging outcomes as well as a prioritised research agenda on conditions affecting the young person’s hip.12,13 However, at the time of the empirical work described below, no peer reviewed evidence existed on the perspectives of stakeholders in this research field on factors contributing to high quality research. Informed by the comprehensive framework for INcreasing QUality In patient-orientated academic clinical REsearch (INQUIRE),14 we aimed to address this gap.\n\nThis study aimed to explore research quality on primary cam morphology and its natural history through the perspectives of athletes, patients, parents and coaches, clinicians, and researchers. Exploring stakeholders’ diverse perspectives on high-quality research through the lens of an existing research quality framework (INQUIRE) could pave the way for authentic collaboration to enhance research quality on primary cam morphology and its natural history.\n\n\nMethods\n\nIn this section, we discuss the ontological and epistemological orientation, study design, ethical considerations, sampling strategy, data collection and analysis, and research team reflexivity for this study.\n\nThis was a descriptive qualitative study,15,16 situated within a pragmatism-informed interpretive description research paradigm.17–19 By ‘pragmatism-informed’ in this context, we mean drawing on the practical wisdom of practitioners and oriented to informing their practice in concrete situations. An interpretative orientation acknowledges that human experience is both constructed and contextual.\n\nWhile some qualitative methodologies have a primary aim of developing theory, interpretive description emphasises the need for ‘informed action’:\n\nInterpretive description is an approach to knowledge generation that straddles the chasm between objective neutrality and abject theorizing, extending a form of understanding that is of practical importance to the applied disciplines within the context of their distinctive social mandates. It responds to the imperative for informed action within the admittedly imperfect scientific foundation that is the lot of the human sciences (Ref. 20, p26).\n\nInterpretative description, responding to the needs within applied health sciences to address pragmatic questions,21 seeks to describe and understand a process or phenomenon (in this case, research on primary cam morphology and its natural history) through the subjective perspectives of research participants and, importantly, intends to use this knowledge to inform practice.22,23\n\nThis study’s pragmatic orientation manifests at different stages of the research process. For example, the research team’s expert clinical knowledge is seen as solid grounding for research design. It is this practical knowledge, tested and validated in the clinic, which is emphasised in interpretive description and used as a way to provide answers to solve real-world problems.23 Particularly in areas where there is little prior research or empirical data about a health phenomenon, such foreknowledge and expertise are viewed as a useful starting place for orienting research.21\n\nAlongside the foreknowledge that the researcher brings to the study, interpretative description aims to explore the subjective experiences of participants relevant to this study: the experiences and perspectives of doing research on primary cam morphology and its natural history. Participants should therefore be a purposive sample representing the full breadth of different kinds of knowledge and experience of the topic being researched.24,25 Within interpretive description research, this knowledge and understanding is constantly revised in a continuous process of (re) negotiating, where both researchers and participants co-construct a coherent narrative that can inform clinical—and research—practice.26\n\nIn summary, interpretive description suits the research question for this study. It facilitates straightforward and pragmatic answers to questions that are relevant to researchers, clinicians, patients, and policy makers15,16 and helps to improve understanding of what works (or might work) best to promote high-quality research in the field of primary cam morphology and its natural history.\n\nEthical approval was received from the University of Oxford’s Medical Sciences Interdivisional Research Ethics Committee (Project ID R66281) and Qatar University Institutional Review Board (QU-IRB 1239-EA/20) prior to conducting the study. We followed the ‘Standards for Reporting Qualitative Research: A Synthesis of Recommendations’ for this report.27\n\nWe developed, piloted, and adapted an interview guide based on the INQUIRE framework to explore participants’ perspectives of research quality on primary cam morphology and its natural history. The INQUIRE framework provides a guide for the practical assessment of clinical research quality at all stages of a research project, and for developing quality enhancement initiatives (Figure 1).14\n\nThis framework was a useful scaffold for developing quality enhancement initiatives (Figure 1), addressing five study stages (concept, planning and feasibility, conduct, analysis and interpretation, and reporting and knowledge translation), and six dimensions: (1) protection of patient safety and rights, (2) relevance/patient centredness and involvement, (3) minimisation of bias [1] (internal validity), (4) precision, (5) transparency/access to data, and (6) generalisability [2] (external validity) of the study results.\n\nThe six dimensions interact with two promoters, a set of factors that may enhance all quality dimensions at a research institution: (1) an established research infrastructure (e.g. well-trained personnel and functional facilities on-site: 3T MRI with trained radiographer and radiologist for serial hip joint imaging), and (2) sustainability through education (the structures and systems to support young researchers and build capacity through mentoring and developing the next generation, and continuous education of all study personnel to secure a long term productive clinical research environment). The Interview Protocol Refinement (IPR) Framework28 was then used to develop and refine the interview guide (Figure 2).\n\nA purposive and structured variation approach was used to select the sample for this study. This method allowed us to select a sample of stakeholders representing a wide range of expertise and experience. Participants were purposively identified. Most were clinician-researchers who have published in the field between 2010 and 2021; (n=9). Other participants (n=6) were identified from the first author’s collegial, athlete and patient networks, and that of co-researcher Dr Sean McAuliffe (SMA) with oversight by the first author’s DPhil supervisors: Professors Trisha Greenhalgh (TG), Siôn Glyn-Jones (SGJ), Karim Khan (KK) and Mike Clarke (MC). The professional background of the research team allowed us to reach a large population of primary cam morphology research stakeholders, guarding against over-representation of one group. We invited all potential participants through e-mail. This sampling strategy is common in interpretive description and rests on the premise that researchers’ knowledge of the topic area enables them to identify participants who are especially knowledgeable about or experienced with the topic of interest.17,18,22,26,29 Potential participants included clinicians, researchers, patients, athletes, sports coaches, and parents of competitive adolescent athletes. Most participants had more than one role, ‘researcher, clinician, and parent’, for example. This often allowed the first author to explore a multiplicity of perspectives in each individual interview.\n\nThe sampling strategy, aimed at maximum variation in stakeholder background and expertise, was informed by literature and the ‘closeness continuum’ model.30 According to this model, participants can have different types of expertise, based on closeness to the topic of interest. Some individuals have a degree of ‘subjective closeness’ to a topic, which involves deep experiential knowledge or real-life experiences. Patients may have this kind of subjective closeness. Participants with professional and/or legal (ethical) responsibility represent a ‘mandated closeness’. Finally, individuals can have a degree of ‘objective closeness’ to a topic, because of their profession or occupation.30 To represent a wide range of experience and expertise in our sample, we purposively included participants from all three categories.\n\nFifteen individuals participated: six physiotherapists, five physicians, a sport scientist, and three athletes/patients (Table 1). Two physiotherapists were also patients, four participants had adolescent children playing competitive sport, while three were sports coaches. The lead author conducted semi-structured online interviews during the Covid-19 pandemic between June 2020 and February 2022. The interviews lasted on average 60 minutes (range 44:32 to 68:08 minutes).\n\nUsing video conferencing technology (Zoom®), all interviews were audio-recorded with permission. Informed oral consent was recorded during the first part of each interview after confirming that participants understood the research project and their rights. Co-researcher (SMA) attended 14 of 15 interviews and kept field notes that provided further interview context for analysis.31 Audio-recorded interviews were transcribed by a third member of the research team, Ms Jolanda Boersma (JB), a research assistant experienced in conducting and transcribing qualitative research, before being imported to qualitative data analysis software NVivo® (QRS international Pty Ltd, Burlington, Massachusetts, United States). To protect their privacy, we assigned a unique number to each participant and deleted identifying information from the transcript.\n\nGiven the semi-structured nature of the interview guide, we had the flexibility to invite participants to elaborate on their responses; they could discuss their perspectives in whatever direction, and in as much depth as they wished. We were therefore able to probe beyond the specific questions of the interview guide, exploring participants’ unique personal experiences, practices, and preferences, which shaped their perspective on primary cam morphology research.32 These included, for example, concerns about the morphology that competitive athletes, who were worried about their future sporting careers, might have. We also asked parents and coaches of adolescent athletes how they perceived high load training and competition that might put young athletes at risk of primary cam morphology and future hip disease (Figure 2).\n\nConsistent with interpretive description, we used thematic analysis to analyse the data.33–35 Thematic analysis is an approach that seeks to develop themes across cases, through reading, re-reading, and charting of data.34 It is a form of pattern recognition where identified themes become the categories for analysis.32 Often misunderstood as a single method with one set of procedures, thematic analysis is best thought of as a continuum of methods—from types that place prominent emphasis on developing codes and categories and demonstrating their reliability (both within and between different coders), to more reflexive approaches which place more emphasis on a single researcher developing a plausible and coherent account of the data.34,35\n\nIn this study, we chose not to prioritise ‘coding reliability’ since this notion rests to some extent on positivist philosophical assumptions (e.g. that the data are ‘out there’ waiting to be collected and that every researcher analysing the same data should get identical findings). Rather, we sought to use a structured coding framework to support and inform reflexive thematic analysis.34\n\nThe analysis therefore incorporated both a deductive coding approach (based on a priori codes generated from the quality dimensions and promoters of the INQUIRE framework14) and a data-driven inductive approach. Early analysis of the transcripts was guided but not constrained by the preliminary codes derived from the INQUIRE framework: we populated codes according to the coding framework, but we also flagged instances in the data that did not fit. Consistent with thematic analysis, two co-researchers (SMA and JB) and the lead author immersed themselves in the data to become familiar with the depth and breadth of the content. We read interview transcripts several times. Based on the INQUIRE framework, JB and the lead author independently coded all interviews and SMA coded half of the interviews. The lead author regularly met with both co-researchers to discuss and reflect on our perspectives that shaped how we identified primary patterns in the data. Once initial coding was complete, discussions among the research team and further analytic work allowed us to identify underlying patterns of shared meaning that drew together several of the initial ‘domain summary’ codes into richer and more complex themes (more ‘fully realised themes’) that revealed multiple facets of a particular meaning or experience.34,35\n\nFor example, the initial coding framework emphasised ‘Protection of patient safety & rights’ and ‘Relevance/Patient centeredness and involvement’ as possible ‘domain summary’ themes. This evolved into ‘Research communities should partner with patients/athletes’ to better represent authentic involvement—athletes/patients co-driving research. The process of coding and theme development had both descriptive and interpretive elements, representing what participants said and subjective considerations by the research team of patterns that were not directly evident. Here we aligned with the notion that themes are not ‘discovered’ nor do they represent pre-existing forms of knowledge waiting to ‘emerge’.33–35 Thematic analysis is seen as an active process of knowledge production by the researcher—themes are patterns that a researcher identifies through their perspective of the data.\n\nInterpretive description also draws attention to researchers’ disciplinary orientations and subjectivity. To account for their perspectives, researchers should engage in reflexivity. Reflexivity involves recognising that researchers are part of the process of producing data and their meanings—a ‘sensitivity to the ways in which the researcher and the research process have shaped the collected data, including the role of prior assumptions and experience …’(Ref. 36, p51). The researcher is a ‘valuable instrument’ of the research in interpretive description; their technical knowledge, research background and personal experience are ‘major sources of insight’.22 Findings do not ‘emerge’ from the data, nor do data ‘speak for themselves’. The researcher ultimately determines what constitutes data, which data are relevant, how the final dataset will be presented and structured, and how and to whom the findings will be disseminated—no matter how participatory and collaborative the method.37 Therefore, although we acknowledge the influence of our preconceptions, we perceived our subjective clinical experience and prior knowledge (particularly HPD, SMA) to be a resource in this study.38\n\nThis study’s research team consisted of the following: HPD, lead researcher, a practising sport and exercise medicine physician, director of medical education, and DPhil candidate responsible for the overall design of the study, participant recruitment, data collection and analysis; SMA, a practising sports physiotherapist, and PhD-trained qualitative researcher, acted as Qatar-based co-principal investigator, attended 14 of 15 online interviews as an observer and contributed to the analysis; JB, a medical anthropologist with experience in qualitative research (sociology and anthropology) but no clinical experience or prior knowledge of the topic, aided in transcribing and analysing data; TG, a professor of primary healthcare with extensive experience in qualitative and mixed-method research, supervised on all aspects of the study as DPhil supervisor to HPD; SGJ, a practicing orthopaedic surgeon, professor of orthopaedic surgery and experienced researcher, oversaw all aspects of the study as principal investigator and DPhil supervisor to HPD; MC, experienced researcher and DPhil supervisor to HPD, provided oversight to all aspects of the study; KK, sport and exercise medicine physician, and previous journal editor, provided oversight to all aspects of the study as an experienced researcher and DPhil supervisor to HPD. HPD and SMA, SGJ and KK had working relationships with some of the participants.\n\nThe research team’s diverse academic training and experiences set the foundations for interdisciplinary dialogue and helped to promote reflexivity throughout the project.25 Olmos-Vega and colleagues (2022, p6) put it thus: ‘… assumptions become most evident when viewed from the point of view of others who do not share them’.39 Several discussions, for example, brought together an anthropological, non-clinical perspective (JB) to theme development with that of a physician with intimate knowledge of the field (HPD), and a PhD physiotherapist working in research and elite sport (SMA). In addition, TG, with vast clinical and (qualitative) research experience, shaped how the lead author approached the complicated deductive-inductive coding dance. An excerpt from his research and DPhil supervision diary provides nuance: ‘Don’t get boxed-in by your (INQUIRE-informed) coding framework. Dive deeper and search for meanings and insightful, new patterns/themes to inform future (research) practice’.\n\nIt is important to consider how professional identity and positionality might have influenced aspects of this study, including the research topic, research design, context and process, participants, data collection and analysis.40,41\n\nWhen selecting a sample, we recruited participants who could contribute meaningfully to the aims of the study, either through their research experience, professional involvement, or personal experience with primary cam morphology. Participants were purposively identified, including from the lead author’s collegial network (research and clinical), as described. Although diverse to a certain extent (clinicians, researchers, athletes, patients, parents), the ten men and five women participants were all white and from the Global North. Participants representing research teams and athletes from the Global South could have shared different perspectives on research quality.\n\nIt is important to reflect on the prior relationship with some interviewees, as this ultimately shaped the data collected during this study. Garton and Copland refer to such interviews as ‘acquaintance interviews’.42 Data are generated in a particular way because participants may invoke prior relationships (most often implicitly, but at times explicitly) in these interviews.42\n\n‘Insider status’ offers affordances and challenges. Insider status can often lead to valuable and even unique insights.43 A certain social or professional proximity often allows researchers access to resources that are not always available in more traditional interviews and might not be available to researchers who do not share this familiarity with their participants.42 Thus, some participants could have regarded the lead author as a professional or social proximate rather than an outsider; they might therefore have been more comfortable sharing their perspectives. In keeping with interpretive description, it is through this deep involvement with a small number of individuals familiar with the researcher and willing to share their experiences that it is possible to build trust and gather valuable data.23\n\nCognisant of the fact that insider status could also be a challenge—participants might feel obliged to assist the researcher because of their prior relationship—we ensured participants knew their rights, including the right to change consent or retract completely.44 Participants received an email explaining the study, their rights, and the informed consent process. They were able to ask questions or raise concerns at any time before or during the interview. Before starting the formal interview, the lead author briefly explained the aim and background of the study again, including participants’ rights. As mentioned earlier, the interview started after verbal consent was recorded and documented in the presence of a second member of the research team (SMA).\n\n\nResults\n\nBelow, we set out the findings on stakeholders’ perspectives of high-quality research on primary cam morphology and its natural history, structured according to five themes (informed by the INQUIRE framework’s six dimensions and two promotors). These action-inviting themes could bolster efforts by research communities to perform higher quality research in this field: research communities should (1) partner with athletes/patients; (2) collaborate with one another; (3) pursue open science; (4) champion equity, diversity, and inclusion; and (5) nurture young scholars. Each theme is described and illustrated with excerpts from one or more participant interviews. Where appropriate, we refer to intersectionality, for example, an athlete-patient and clinician (P8) describing how her experiences and perspectives as an athlete-patient informed clinical practice. As a result, some quotations are longer when we desired to communicate the way a participant illustrated or described a specific situation.\n\nThis theme combines and extends two INQUIRE dimensions: protection of patient safety and rights and relevance/patient centeredness and involvement. Our interviewees reported that athlete/patient-centred research is important and multifaceted. The athlete/patient distinction is important—most athletes with primary cam morphology will never become patients. Athletes are at risk of developing primary cam morphology but ‘we know that obviously only a small percentage of people, even if they have primary cam morphology, develop symptoms’. (P5)\n\nMore than just being involved, athletes/patients should co-drive research as equal partners. Athletes/patients in this study expressed keenness to get involved in research. This was especially true ‘if patients are aware that the ultimate goal is to help people to get better and to utilise the information in a way that’s going to help people’. (P8 – physiotherapist, athlete, patient) She continued to explain:\n\nI think patients will be willing to help. I think a lot of people want to share their story. And I think it’s actually like a therapeutic part of the journey as well. At least I noticed that for me, when I’m able to, even now, kind of reflect on how far I’ve come. There’s a benefit of that. And you realize that: ‘Okay, my struggle is actually helping other people.’ (P8)\n\nInvolvement, however, could be therapeutic at more than one level. Another athlete-patient (P10), discussing how involvement helped her ‘own learning about the condition’, also felt proud to contribute to research (Table 2, quote 1). Educating research teams and other stakeholders ‘can provide valuable input that other people might not be able to give’. (P10)\n\n\n\n1. ‘This injury has had a massive impact on my life, whether I sort of accepted it until now is a different story. … So being able to contribute to maybe the future planning and research and things like that, I think, for me is a very proud moment. And it's something that, like I said, I do feel strongly about.’ (P10)\n\n\n\n2. ‘And I think it's key [involving children/parents], you know, you might plan a great study, but then the parent tells you: “This is impossible, because …” for example: “I drive my son from school to this place. So, in the meantime, I can't get him on this device” or “I can't charge the device, because…” or “He doesn't wear these shoes, because…” you know, all the practicalities of what is realistic only come out when you speak to the relevant people. And the relevant people in that case, are the parents and the kid. You know, like, no one asks the kids: “do you like to wear this? Do you like to put this in your shoes?” And then they go: “Well, I don't like those, because they're too big you or I don't like the colour”.’ (P4)\n\n\n\n3. ‘… what we find is important isn't important for some patients. … We want to look at the alpha angle and measuring, but the patient doesn’t care about the size of the alpha angle. They're concerned about getting back to football.’ (P11)\n\n\n\n4. ‘I think the first thing is in plain language. Because that's the biggest mistake we make, in language that even clinicians and other researchers don't understand. So, I'm taking some time to, again, involve the stakeholders, people, end-users, the knowledge-users, and actually involve them right from the beginning. In terms of, how you're going to communicate your findings, and is it meaningful to the people [who] are going to use it?’ (P7)\n\n\n\n5. ‘… there’s still a lot of hysteria and alarming language being used in conjunction with things like cam morphology, cam lesions and femoroacetabular impingement syndrome. So, I think, to a certain extent, we need to make sure we don’t use that kind of inflammatory language in any kind of education of cam.’ (P1)\n\n\n\n6. ‘So, I've been much more inclined to say somebody has hip pain and maybe associated with cam morphology rather than telling somebody: ‘You've got a syndrome, you've got FAI syndrome.’ … you've got to be really careful what your wording is, especially in young people … 16-year-olds are usually really worried about their future …’ (P15)\n\n\n\n7. ‘… I had the experience of a player whose … older brother ends up having bilateral hip surgery over the course of a number of years and has to retire from football. And the younger brother … had fixated in his head that he had to have surgery. And the way he described his hip to us, he was using all those words that were scary words, in his mind. About this impingement, and his bone rubbing on bone, and his cartilage wearing off … And he said: ‘I’ve got to be shaved back; it’s got to be smoothened out. So, I got a smooth surface that rubs against a smooth surface’ that sort of talk. And I was like, if there's anything I learned from this … I have to be really careful on the terminology that I use, because they will create a picture in their mind. And this poor fella ended up having surgery; the surgery didn't go to plan. He’s back playing but he's not at the level that he could've been.’ (P3)\n\n\n\n8. ‘Look I don’t have any concerns about my children participating in research. The only concern I would have, is if their photos somehow identify them as individuals, and they were available on the web without us knowing it. … A sort of breach of confidentiality.’ (P1)\n\n\n\n9. ‘The other concern that I would have, is exposure to radiation. I wouldn’t be too keen on my children being exposed to CT-scans and repeated radiation.’ (P1)\n\n\n\n10. ‘The problem being - as the level increased and I got onto the senior team - the training increased, the volume in terms of the sessions and intensity on top of the gym work and not having anyone kind of looking out for me … I was trying to juggle four or five different managers. But if they [sport scientist, ‘strength conditioner’, physio and doctor] are not strong enough to speak up to the manager, then who's held accountable? So, then it goes back to the county boards. If the county board is employing a manager to manage a team, they're there to get results. But the players are the people that are being mismanaged. … So, until the manager has a guideline to say: “You're only allowed to do this much training in a week, and that's your responsibility. And if you break this, you're held liable, as is your medical team”.’ (P9)\n\n\n\n11. ‘Is it something that they can provide really valuable insight into? … we're almost asking someone's input about a condition [primary cam morphology] that they may be completely asymptomatic for their whole life … if you have a problem, which is already there, like, for example, knee OA … and you're trying to get participant involvement, there's so many people living with knee OA that have really good insight about the burden that it gives them in their life, their health care …’ (P5)\n\nDiscussing his ‘passion to try and create change’ and ‘to try and educate’ (especially parents of young athletes) about the morphology and its hip-disease consequences, another athlete (P9) shared how his ‘whole life was changed because of [his] hips’:\n\nI think that’s where my story, me speaking and educating the parents, and showing them: ‘If this resource was available to my family, and this testing or research project, whatever you want to call it, was there … it would have stopped me going through a year of operations. Untold pain, untold misery, sadness, heartache, you know, financial.’ The list goes on. I think, one thing that we can do, as people who have a voice is to make sure that these parents [are educated]. (P9)\n\nOur interviewees gave several examples of how a partnership approach could facilitate more value and less waste in research. First, engagement pivots on and promotes the relevance of research:\n\nI think, to really explore your question beforehand, and spend quite a lot of time doing that [is important]. So, refining your research question by involving stakeholders, involving clinicians, involving athletes … seeing what is meaningful to them, what do they want to know. (P7)\n\nSecond, athletes/patients (including adolescents, their parents, and coaches) could enlighten, not only researchers, but also the research process by illuminating blind spots in their research plans (Table 2, quote 2). In addition to gaining such insight to ‘the practicalities of what is realistic’, professionals also learned that patients ascribe importance to different things than researchers do (Table 2, quote 3). Additionally, patients can help in planning research; ‘they give us ideas that we wouldn’t have if we just think with our research hat on’. (P14)\n\nThird, athlete/patient partnerships change how research communities communicate about research and research findings. A recurring theme in our interviews was the need to avoid jargon and use a language that everyone understands. The way to achieve this, they felt, was to involve all stakeholders from the outset, as illustrated by quote 4 (Table 2). Clinician-researchers and parents of competitive adolescent athletes, in particular, stressed the importance of avoiding alarming and inflammatory language (Table 2, quote 5). A former elite athlete and now sports coach warned that ‘things like “abnormality” perhaps trigger a lay person to automatically think that this is something damaging and negative, and will be inhibiting: so, “lesion”, when you say to me “lesion”, I’m thinking of something more like a scar or an abrasion’. (P12) Although femoroacetabular impingement (FAI) syndrome is the agreed term, ‘syndrome is a negative thing’ (Table 2, quote 6).\n\nSharing their experiences, several participants were concerned that language and communication style—in research and in the clinic—could create the need for (unnecessary) interventions. A clinician-researcher shared how a patient’s expectations had been shaped by an older footballer-brother who had bilateral hip surgery. The older brother framed the problem based on his own surgical experience (Table 2, quote 7). An athlete-patient and clinician shared her experience as a patient—how the language used and framing of the condition by a surgeon in a position of power left her vulnerable, confused, and distressed:\n\nAnd so, I ended up going to this surgeon who’s pretty well-known … And I remember, I had not tried physical therapy yet. This was before starting physical therapy. I go in, and I remember, he takes my imaging out that I had, puts it up on the screen and says: ‘Oh, you have a large labral tear, you have a cam and pincer lesion. And if you don’t have a hip arthroscopy, you’re going to get hip arthritis, and end up needing a hip replacement.’ And I remember I just sat there, and I was just crying, and I was alone … I didn’t know much about cam or pincer or labral tear. And then I remember asking: ‘Well, if I don’t get the surgery, and I keep running, what will happen?’ and I remember him saying like, feeling very, you know, definitive in his wording: ‘well, you’ll get hip arthritis.’ … The appointment ended with him saying: ‘Okay, well, you can schedule the surgery on your way out and then we’ll be in touch.’ … I remember leaving there and I just thought, like: ‘Wow!’ Like ‘this is terrible.’ I remember I just was crying because here I was an athlete my whole life. I played college soccer, running was a huge part of my life and to then just be told that I have this condition in my hip. And if I don’t get the surgery, I’m going to end up with hip arthritis. And I have to stop running. And it really just led me down that spiral of catastrophising. (P8)\n\nFourth, our participants, including parents of young competitive athletes, raised the importance of safe research, particularly when children, female athletes, and competitive athletes are involved. Research communities should guard against breaches of confidentiality (Table 2, quote 8), and protect, especially children, from unnecessary exposure to imaging-related radiation (Table 2, quote 9). Protecting athletes’ health, including those participating in long-term research, and the influence of power-dynamics in competitive sport—especially when ‘juggling’ several managers at the same time—was raised as a safety concern by participant 9. Medical teams, particularly those involved in long-term research, must be empowered to protect athletes, and should, with club managers, be accountable to a higher management (Table 2, quote 10).\n\nFinally, engagement could also be a challenge for athletes/patients, given that it requires them to share knowledge of living with primary cam morphology, which, in most, is an asymptomatic, benign morphology—unlike, for example, knee osteoarthritis (OA) (Table 2, quote 11).\n\nIn sum, when athletes/patients are equal partners in research—when they share their experiences and expertise—research would likely be more relevant, safer, and more ethical. Athlete/patient partners, as people who have a voice, could help to shape clearer and less threatening communication in research and in the clinic, and expressed eagerness to share their stories and struggles—to get involved in research and education to help others. Healthcare professionals and researchers seemed equally keen to involve and learn from athlete/patient partners.\n\nThis theme combines and extends elements from several INQUIRE dimensions and promotors, including minimisation of bias (internal validity), precision, infrastructure, and sustainability.\n\nInterviewees discussed the need for coordinated efforts to plan and deliver multi-centre and multidisciplinary research on, for example, primary cam morphology aetiology and prognosis (Table 3, quote 12). To strengthen large-scale multi-centre research collaborations—‘helping each other’—research teams should agree on research questions (Table 3, quote 13). Such studies should use the same methodology and capitalise on transparent research centre-specific expertise to facilitate high quality data sharing (Table 3, quote 14).\n\n\n\n12. ‘So we need to identify groups around the world that at are working particularly with adolescent football players and try to link data between athletes that are playing without developing hip and groin pain and without developing cam morphology and those who are developing hip and groin pain and cam morphology … and then to be able to track these over time and determine some of the differences that exist between players that go on to develop hip and groin pain, so we can intervene better at earlier stages.’ (P1)\n\n\n\n13. ‘So, it's more interesting, if you are collaborating with each other and defining exactly what you're doing. What more research do we need to have in this kind of field of area? And if you have the same participants at different hospitals. You don't need to do it all by yourself. No, you can ask each other, helping each other and getting large cohorts and groups with the same questions we want to have answered.’ (P11)\n\n\n\n14. ‘Some groups in the world are dedicated in studying this topic [primary cam morphology formation], of whom some already have some collaborations. But I think that is one of the most important aspects, to collaborate in studies, multi-centre studies … Using the same methodology, so using the same type of clinical examination, questionnaires, imaging, and stuff like that. So that you can also interchange the data. And more in detail also, quantifying things. So, how do you quantify when somebody has cam morphology? I mean, we talk a lot about that. But I think all the quantitative measures we have to date, they're okay, but they can be improved … So also, that is a field where we can improve and where we preferably use the same methodology as well.’ (P6)\n\n\n\n15. ‘In terms of infrastructure, it is very important that well, in practical ways, the centre where the expertise is, probably does their part of the study. So, the participants come from everywhere, but the imaging analysis might be done somewhere, where they have a lot of expertise and statistical analysis might be done somewhere else … But what I find really important, especially with the imaging analysis, and software techniques used for that, is that people should be very transparent in what they use, how to use it, and everybody should have the possibility to use it.’ (P6)\n\n\n\n16. ‘I think the infrastructure is also the internet. Databases. So, I think, if that infrastructure is to improve, we have connection … using the same DICOM images … then connecting them with the same server. I think that infrastructure would be the most important thing to improve on, then we can have large cohorts and large studies. And then you don't need to travel because you're in Australia or somewhere else. And then you can combine it with the same protocol, with the same images, and maybe a computer helping you to investigate the things you want to see.’ (P11)\n\n\n\n17. ‘… to really have a meaningful impact, this kind of work would need to involve an international collaboration. Some sort of registry, a large database, and that will make a really big impact. So this is the challenge, to actually make sure that there are various stakeholders. But I think there is the possibility to do that, because there’s a wide interest, there is no competitive advantage anywhere. … because everyone can gain something, you know. If research shows better, kind of procedures to reduce the risks and better clinical outcomes, that's going to save money anyway on the healthcare system as well. So there should be a vested interest, and the financial return for the investing, by doing wider type of collaborations.’ (P4)\n\n\n\n18. ‘… collaboration, international collaboration, and you know, we're always competitive. I'm not particularly competitive; I suppose … because we're smaller, there's not a lot of money, we're really, really good at being collaborative, because we need each other. But I think in in other areas of research, it can be a little bit competitive. So, I think … we're stronger together; that [collaboration] needs to be driven probably by very global bodies, like the IOC, or FIFA or whatever.’ (P7)\n\n\n\n19. ‘Data sharing is my biggest problem and has always been. And it has never been solved. And it needs to be solved. And I think now there is the technology to do it. So there is a plethora of studies, that are conducted on 10 subjects, 15 subjects, 20 subjects, 30 subjects at best. And none of these actually contribute to really a consensus. So usually, the consensus comes 10 to 15 years later, when there is a big systematic review and meta-analysis that says: ‘This thing works, and this thing doesn't work.’ And to me, it's a waste of time. Because you have to wait 15 years and a lot of effort from various research groups. While, in a couple of years with the right structure in place, it could be possible to interrogate it.’ (P4)\n\n\n\n20. ‘We’re doing a multi-disciplinary approach of orthopaedic surgeons, sports medicine physicians and the radiology department. So that we can have a collaborative team of three different medical specialties, and I think we’re all good at one part. So, the orthopaedic surgeon knows how to carry on when it’s symptomatic and probably do surgery or something like that. The sports medicine physician is probably the more conservative part, and the radiologist can give information on how to image those hips for example. I think that might work together really well.’ (P2)\n\n\n\n21. And I know that it's that word, it's used all the time, but ‘stakeholders’. So, it's multiple stakeholder-involvement, I think, really makes a difference. Because each person is going to add a different dimension to it. The challenge comes in integrating all of that into your outputs. But it can be done. And I think we're seeing a move in sports medicine to do that. … And I think that's one of the things where there is that disconnect between researchers and clinicians. Now because … research is often done in a sterile environment, and clinicians go: ‘Well that doesn't work for me.’ (P7)\n\n\n\n22. ‘… understand the rationale. And converting that into a performance- and a financial rationale. So, for me, just to say: ‘Do you want to do a hip study, to find out how hips grow?’ That’s not going to land. But to map it out: ‘This is the performance-challenge we have. This is a financial challenge we currently have and this is what the future could look like, financially-performance wise.’ You have to convert that. So that's number one. The internal messaging has to be: What’s in it for the coach. What’s in it for the finance director. What’s in it for everyone.’ (P3)\n\n\n\n23. ‘And the questions were determined initially by the medical staff, but ultimately, we had coaches starting to determine the questions, going: ‘Here's my performance challenge, how do we unpick that?’ So, when you come to find the question and then go to the right university and the right group of people, that understand the landscape of professional sport, that's the easiest mix.’ (P3)\n\n\n\n24. ‘So, you're getting your question answered. Gone are times … where the University determines the question. And if they did offer a question, it would have to be twisted to be beneficial for the football club. But that went really well actually, us going to university with a series of questions. … So, both sides need to work collaboratively to the same solution. And it's just communication, isn’t it? It’s really, really trying to understand, what does success look like and how long does it take to do it. I think that's a key one. Because Universities work at such a slow pace, in comparison to a football club, that works so quick.’ (P3)\n\nTo reduce attrition and measurement bias, research centre-specific expertise is particularly important when performing and analysing imaging. Long-term prospective studies (with serial hip imaging over time—every five years, for example) could benefit from an international network of collaborating imaging units to accommodate elite athletes who are often contracted to live and play around the world. They could be accommodated at an imaging centre close to them. Imaging collaboration could include shared (online) infrastructure like Digital Imaging and Communications in Medicine (DICOM) (Table 3, quotes 15 and 16).\n\nInternational collaboration on a registry or large database could have a ‘really big impact’ on this field, benefitting research teams, patients, and healthcare systems (Table 3, quote 17). Collaboration could be bolstered when—with a ‘we need each other’-approach—coordinated by global sporting bodies like the International Olympic Committee (IOC) or FIFA (Table 3, quote 18). Participants commented on data sharing, including their frustration with it. Meaningful data sharing was acknowledged as ‘my biggest problem’ (P4). However, if done well, for example through the 11 IOC Research Centres [3], such data sharing could improve small sample bias and result in large datasets ‘that could be interrogated with better techniques, and with better statistical knowledge’ (Table 3, quote 19).\n\nA common theme was also multidisciplinary team approach to intra-team collaboration, including with academic partners. Multidisciplinary team collaboration should involve athletes, coaches, different medical specialties and topic experts, researchers, and methodologists, for example (Table 3, quote 20 and 21). Some participants described their perspectives and experiences on multi-stakeholder collaboration to facilitate research buy-in. Buy-in could make or break research in this field. How researchers frame their research question, especially in elite sport, is key for engaging with management, big stakeholders, and decision-makers, including finance decision-makers (Table 3, quote 22).\n\nEffective research collaboration among academia and professional sports clubs is important in this field.4,45–47 Researchers working with football clubs benefit when clubs, especially the coaches in the clubs, determine the research questions before engaging ‘the right university’ (Table 3, quote 23). However, such a collaboration could often be a slog, and someone needs to ‘kind of steer the university’ on what is possible and what is not impossible (Table 3, quote 24).\n\nIn sum, participants discussed how ‘we are stronger together’ when aligning to pursue large-scale, multi-centre and international collaborations to answer research questions that matter to all. Effective multidisciplinary intra-team collaboration resonated with our interviewees too.\n\nThis theme includes and extends the INQUIRE dimension, transparency/access to data. Access—for everyone—to as much information as possible, and translated to lay people’s language, resonated with our interviewees (Table 4, quotes 25 and 26). All stakeholders, including athlete/patients and coaches, should have access to research—in ‘plain language’:\n\n\n\n25. ‘… everyone should have access to as much information as possible, in the most accurate up to date information, where possible. But at least to have the summary or the breakdown, if not the whole thing. To still be able to have access to that information and understand what the study was and what the concluding things were from it.’ (P10)\n\n\n\n26. ‘Everyone. Everyone should have access. And study results should be translated to lay people’s language, for access to the information for the community. So, using things like infographics or factsheets etcetera is absolutely essential. And that’s the kind of thing that can help educate parents and football clubs, and coaches.’ (P1)\n\n\n\n27. ‘Once I stopped studying, obviously, you stop having access to all the database and the resources that the university provides. … Even for my work now, I regularly quote journal articles and research to back up what I’m saying. And so, it is important to have more access to that, to be able to better justify and explain or backup what we’re recommending.’ (P2)\n\n\n\n28. ‘… it is basic methodological practice that is going to improve the quality … having protocols, being registered and available in open forums so that people are aware of studies that are happening.’ (P1)\n\n\n\n29. ‘Most of the bigger studies will publish their protocol, specified which analysis they will do, the outcome measures, the factors they study… So that’s the first thing and the other thing might be to publish your database open access.’ (P6)\n\n\n\n30. … you have to publish your data set open access. I’m a fan of that, but there are quite some issues involved in that. And probably journals in the future will require that much more. … for me, it’s a no-brainer. I think everybody should do that [share anonymised patient data between research groups]. Even for the grants we apply for now, it’s even, how you say, necessary to do that. To have your data open access. And I think it’s moving more like that. And it might be difficult, what I experienced with other consortia that I worked in, with cohorts that are already established. Because participants did not already give their informed consent for sharing the data outside the centre or whatever. So that might be sometimes a problem. But for newly studies, that should certainly be the case. And for us, we can only run studies if we do that. (P6)\n\n\n\n31. An early career researcher, trying to get his name out there a little bit, is probably … more inclined to go with the high impact, high ranking journal, because it’s important for, whatever you’re trying to do, whether it be your next job. But I’m aware that that is not great for the dissemination of research, more often than not, because then you’ve got to drive that separately. On top of the fact that it's already in that journal, you’ve got to drive it to other people that need to know about it. That creates a lot of work for the researcher. (P5)\n\n\n\n32. ‘We had a clear protocol that we discussed with players beforehand: “This will be the approach, this is what you need to sign off, the club doc needs to sign off. And then we release the scans” and so on.’ (P15)\n\n\n\n33. ‘I would say that there’s nothing to share. I mean, I would say that you really don’t know enough about that [primary cam morphology]. Because we know that this is, frankly, probably pretty typical development. I don’t think you can sit here and say that this is atypical. And I would say, unless you see something that is not something you’re looking for, like an osteosarcoma or something like that, I don’t think it’s warranted to share that with them, other than saying: ‘we’re in the data collection process and we’re trying to understand these things. And we just don’t know enough about this.’ And I think that would be where I would leave it.’ (P13)\n\n\n\n34. ‘We also asked them if they wanted their medical staff to be involved or not. Because they are the participants and scientifically seen and ethically seen, their medical staff does not have any right to know their personal information.’ (P2)\n\n\n\n35. ‘What I’m not in favour of, is the extortionate costs of open access. … the production costs are a lot less. And I’m also a reviewer and an editor that doesn’t get paid to do any editing or reviewing. So that is the thing I can’t get my head around, you know, we are all doing this work for free.’ (P4)\n\n\n\n36. Well, I would say that open access research is paramount. And the basis of research, as we know it nowadays, is completely crazy. So, what we do is that we publish, sometimes with our effort and with our money, and then we transfer our copyrights to an editor and then the editor will ask for money from the universities. … So, this is completely crazy. Right? (P14)\n\n\n\n37. … the problem with open access now, in science in general, is that there is a plethora of low-quality journals that pretty much pay - publish anything, provided that you pay. And the scary thing is that, even researchers don’t know what’s the difference between a good journal and a bad journal. You know, I had staff in the past that approached me to say: ‘Oh, I've been invited to write a paper for this journal.’ And I’m thinking about writing it. And I have to explain them what a predatory journal is. And that’s people with PhDs and years of experience, and you think: ‘Wow, we’ve got it wrong here.’ (P4)\n\n\n\n38. ‘I think that Open Access papers are probably not that important. And I say that because there’s a fee that’s associated with that. And when you do that, then that makes things more difficult to get papers published, because it takes more money to do that, and it pulls money away from doing other research efforts.’ (P13)\n\nSo, it’s going to be athletes and coaches. A lot of scientific language isn’t particularly meaningful to them. And even clinicians, who would have been taught in that area, they still have moved into an environment where they don’t use that language anymore. So, I think, I think Open Access is good, but I think it still needs plain language. (P7)\n\nAn athlete/patient participant warned that financial and career benefits for researchers should not trump end users’ access to research —‘it’s silly and very naïve in this day and age that it’s happening’! (P9):\n\nIf a person is paid to do this research and is then publishing papers on their own study, it’s again for their benefit. And it’s for the benefit of the financier. So why, even though they’re doing it for themselves, why should we [athletes/patients] not have access to that? (P9)\n\nPeer reviewed publications buried behind paywalls are problematic for young scholars and clinicians alike (Table 4, quote 27). Access should be easy—‘simply click on a button’—and include study protocols to reduce research waste (Table 4, quote 28) and data (Table 4, quote 29). Although open access to data resonated with our interviewees—even if it becomes a future journal requirement for new studies—there are important considerations, including informed consent from participants for anonymised patient data to be shared among research groups (Table 4, quote 30).\n\nSome participants felt that prioritising open access was easier said than done. For example, particularly for early career researchers, impact factor might trump open access; an approach that could disrupt effective dissemination of results (Table 4, quote 31).\n\nResearchers should think carefully when sharing test results with individual research participants (and, in the professional football club context, their sports club medical teams and managers): they should have an agreed protocol for this (Table 4, quote 32) and be comfortable to say: ‘there’s nothing to share’. Particularly when sharing, for example, ‘normal’ imaging results of ‘frankly, probably a pretty typical development [primary cam morphology]’ in athletes (Table 4, quote 33). Research teams should also give athletes/patients ownership of the decision to share, or not to share, their results with club medical staff (Table 4, quote 34).\n\nFinally, participants also expressed concern about, or questioned the need for, open access. They discussed: the high (‘extortionate’) cost of open access publication (Table 4, quote 35); the ‘completely crazy’ academic publication system—paying to sign away copyright (Table 4, quote 36); the problem of predatory or low-quality open access journals (Table 4, quote 37); and their perspective that open access papers are ‘not that important’ as the average clinician ‘don’t really read research papers’—the cost of open access publication ‘pull money away’ from research (Table 4, quote 38).\n\nIn sum, our study participants discussed how research communities could pursue open science to improve research quality. Clinicians, researchers, and athletes/patients need to have easy access to important findings. There are perverse incentives (e.g. researchers seeking publication in a high impact factor journal that is only available to readers via a paywall). Finally, the cost of making publications open access could be prohibitive.\n\nThis theme includes and extends the INQUIRE dimensions: generalisability (external validity), and relevance/patient centredness & involvement. Our interviewees highlighted several equity, diversity, and inclusion (EDI) elements of high-quality research relevant to the steps of a research project in the hip-and-groin research field.\n\nFirst, as described in theme 1, research communities should partner with athletes/patients. Such partnerships, to inform research questions, for example, should focus on racial/ethnic and sex/gender minoritised individuals and groups in the EDI context of this research field (e.g. girls, women, Black people, and people from the Global South).\n\nSecond, considering study populations, the primary cam morphology research field is largely void of research involving girls and women, and people from the Global South—particularly athletes. This was emphasised by our interviewees too (Table 5, quote 39). To engage more diverse populations, research should not only consider the different impact on males and females, but also involve people of different ages, people with disabilities, and people with different ethnicities (P12). To date, very little research in this field is done in the Global South, for example. A clinician-researcher and patient warned that ‘to understand the injury or morphology well’ it is important not to ‘shut out certain geographical areas’ (P13). Participant 7 confirmed this perspective, discussing research that involved diverse populations with ‘genetic variation’ and different athletic backgrounds (Table 5, quote 40).\n\n\n\n39. ‘A major thing is to include women, which I think there's a bit of a void. So that’s very underrepresented across everything, and particularly across elite athletes. To look at the complexities of researching elite athletes. … listening to the athlete voice … And not just take them as this commodity, with, let's say, a combination of anatomy, physiology - but actually bringing in the bio-psychosocial. So, making it a lot more multi-dimensional, making a lot more inclusive in terms of beyond the elite.’ (P7)\n\n\n\n40. ‘Having inclusions throughout the world, throughout genetic variation, I guess. So, most of the studies done so far … are in Caucasians. And I think it's important to have people involved as well with different genetic backgrounds. I’m especially interested as well in Asia. Because we know already that their hip morphology is way different than people with other genetic backgrounds. And well, just having enough numbers in different age groups from different athletic backgrounds … (P6)\n\n\n\n41. ‘I think the primary [female participant recruitment issue] was, that there were three male researchers that were doing the recruitment. And that required a physical examination of the hip-groin area, which is obviously a sensitive area …’ (P5)\n\n\n\n42. ‘Move that [meeting] around the world, to try to make it as accessible as possible. And I think doing it via zoom, is really probably the best way to do it. … so you reduce those costs as well. … I think the other part of it, is to include all stakeholders in it. So, the researchers, I think clinicians, and coaches. That is going to be really important. Parents.’ (P13)\n\n\n\n43. ‘For different countries, it's access to the same resources that we have. So, a good way of trying to encourage this, is getting competent people from other countries, and trying to link up. Try and make links, and then helping provide resources. You know, so developers together and making sure that - maybe an academic unit, where things are more set up, can help. But then you have things like visitation. So it could be that somebody doesn't have much research experience, then comes visits for a few weeks and get some experience and just develops these links that way.’ (P15)\n\nThird, research team-specific EDI considerations include fostering an inclusive and equitable research climate within teams and their collaborative networks. Our interviewees discussed: (1) team diversity (e.g. female research participants might feel uncomfortable when male researchers perform a groin evaluation, as illustrated in quote 41 (Table 5)); (2) access for team members who live remotely (e.g. accessible and inclusive online meetings, as illustrated in quote 42 (Table 5)); (3) building capacity (e.g. team member compensation and mentoring ensuring socioeconomic status and knowledge about the research topic do not exclude certain team members, as illustrated in quote 43 (Table 5)).\n\nFinally, EDI in knowledge translation include, as discussed above, easy access to research reports written in lay language, ideally with patient partners (Table 4, quote 26).\n\nThis theme includes and extends the INQUIRE promotor: sustainability/education. Mentoring seems to be key for scholarly growth and has been defined as ‘a dynamic, reciprocal relationship in a work environment between and advanced career incumbent (mentor) and a beginner (protégé) aimed at promoting the career development of both.’ (Ref. 48, p17). Four archetypes of mentorship have been proposed: the traditional mentor, the coach, the sponsor, and the connector.49\n\n… the mentor guides, the coach improves, the sponsor nominates, and the connector empowers, but always the mentee benefits. (Ref. 49, pE2)\n\nInterviewees illuminated how research communities could nurture young scholars through mentoring, deconstructed here using the four archetypes above. First, through careful mentoring by humble mentors. Humble mentors model imperfection—they are willing to say, ‘I don’t know’.50 They seem to carefully guide young scholars to pursue relevant research questions ‘as part of something bigger’, as quote 44 (Table 6) illustrates. Second, through mentors that challenge mentees in safe spaces (the coach or supervisor-type mentorship), as quote 45 (Table 6) illustrates. Third, through mentors that create opportunities – the sponsor-type mentorship. Scholars should not be ‘dumped’ into research with a ‘good luck, my friend’ approach (P2). Rather, research teams—especially senior researchers and mentors—should create opportunities for young scholars to lead (Table 6, quote 46). Finally, through mentors that empower. Clinician-researcher (P3) described his role (as a connector-type mentor) in creating a stable and sustainable environment for young scholars, connecting them with a professional sporting organisation (football club) as employer and a university for academic training:\n\n\n\n44. ‘… one of the things that really helped me was having mentors that were able to represent what we don’t know, rather than saying that we have all the answers; we just need you to prove them. To be very open to the fact that there’s so much unknown in this area and we would like you to [focus on] this particular aspect of it, so we can built on that and I think that’s a really important thing as a PhD-student but also mentoring a PhD-student, that you are part of something that’s much, much bigger and you’re coming into a team that are trying to answer a bunch of questions that is going to move the field forward and reduce the burden of these injuries to help society. So, I think putting it in perspective of what’s happened before and what will happen in the future is very beneficial.’ (P1)\n\n\n\n45. ‘In the beginning he was very strict, and we had. some really strict deadlines, and there were sometimes that I really hated him, but afterwards that probably was a good lesson for me. So, I think it's really important to have a good supervisor, to have the opportunity to ask questions, to not have a really strict hierarchy. So, we have a professor that is really easy to go to, to talk to, to ask questions to, not only on scientific basis, but also financially and things like that. So that also makes it a really safe environment for scientific research.’ (P2)\n\n\n\n46. ‘… as a student, I provided most of the education for the other researchers. Not the junior researchers, because I was the first one on there. And I set up the protocol and all that sort of thing. So, I was sort of leading that and like, I was thrown in the deep end effectively, but a great learning experience.’ (P5)\n\n\n\n47. ‘So, providing positions that will facilitate the collection of data would be really beneficial. … at the moment a lot of our positions are very short term and tied to external funding, so that creates considerable stress and lack of certainty about the long-term job and continuity. And that’s a problem if you’re trying to do long-term prospective studies. And we’re already seeing that with our prospective studies, which is now up to five years, that the PhD-students are starting to finish and if we don’t have positions available then we lose all the intellectual property that’s been developed with this cohort, that incredibly deep and rich intellectual property with that cohort if we can’t ensure positions for those PhD-students once they finish. So that is a problem, yes.’ (P1)\n\n\n\n48. ‘When they go into postgrad, funding is a huge thing. Just trying to support themselves and live as a postgraduate student can become a big issue, getting funding for their research, it tends to be specific areas that are probably over funded. So, things like cancer are hugely funded. Arthritis isn't as well funded, considering it's one of the biggest problems.’ (P7)\n\n\n\n49. ‘So, until someone has longevity, in a sense of ‘Ok, I’m going to do a project that, I’m comfortable I can put 3 to 5 years PhD focus on, and it's protected.’ So, we ended up creating agreements for a member of staff, who was doing a PhD, saying, even if you leave the club, you can have access to the data, you can use the data, publish data, right off the bat, to protect him. Because it was ridiculous otherwise. But that insight doesn't really exist in many clubs.’ (P3)\n\n\n\n50. ‘We had a big group, with probably ten or twelve different scientific researchers from different fields, and we had education every week and we discussed our own progress, our pitfalls, our positive sides, suggestions for others. That was really useful as well in my opinion. So, every week, one or two hours a week, just to evaluate and discuss every project. And that gave me a lot of good ideas, to include in my own research. So, if you stick ten smart heads together, you might create some good thoughts on performing research in the future.’ (P2)\n\n\n\n51. ‘Because a PhD has a lot of downsides, again a rejection, again a wrong interpretation of the data, again a manuscript that had major revisions but got rejected afterwards, again congresses in corona-time that just don’t go on … But if you stick your heads together and just discuss those downsides and positive sides, that might be really useful.’ (P2)\n\nWhy don’t we ask the real - performance, injury, whatever it is – questions? Why don’t we generate the questions and then go to the Universities? Get the contract which [is] always the most painful bit. But get the contract sorted out and then doing. If it’s a PhD, we do an interview to find the right student that would fit the University and also our needs. Because they’ll be imbedded for three years within our program, became effectively a member of staff for us, the players knew no difference, they just saw a member of staff and it went really well. (P3)\n\nA clinician-researcher and young scholar (P2) stressed the importance of ‘insight in the ethical way of things’ when creating opportunities for young scholars, and warned against research for the sake of research:\n\nYou cannot just only say: ‘I want to do research as quick as possible and get the highest paper with the best impact-factor’ but also think of sustainable quality research … (P2)\n\nSeveral participants mentioned lack of sustainable employment and funding as a problem, creating ‘considerable stress and lack of certainty about the long-term job and continuity’ (P1), as quote 47 (Table 6) illustrates. Research in this field (‘arthritis’) seems to struggle for funding compared to other fields like cancer (Table 6, quote 48). However, protected employment seems not enough; financial and collegial support for relevant research, with continued access to data after employment, should be cemented in employment contracts (Table 6, quote 49).\n\nIn addition to mentoring, participants discussed personal growth when well-organised research teams created opportunities for structured education, for discussing ideas (Table 6, quote 50), and for sharing the struggles of being a young scholar (Table 6, quote 51). Participants emphasised structured education programmes for young scholars. One participant urged education on ‘the rules and the processes of research.’ (P4). Although important, this element is often missing in education; ‘that a lot of people, despite the fact that they have PhDs, still don’t understand the research process, is fascinating to me.’ (P4). Participant 2 agreed, advocating for a structured education programme: ‘We had like a course of two weeks on biomedical statistics, but to be honest, how can you learn biomedical statistics in two weeks?’ (P2). Another participant advocated for ‘having the right people in the right positions to educate the team’ on more field-specific knowledge and skills (P5).\n\nIn sum, creating opportunities for young scholars to learn, teach, and lead even large-scale studies in well-supported teams, resonated with participants. Participants agreed that stable and sustainable research environments are key for supporting young scholars’ development into independent researchers.\n\n\nDiscussion\n\nThe findings of this study show that, for higher quality research in the field of primary cam morphology and its natural history, research communities should: partner with athletes/patients; foster collaboration; pursue open science; champion equity, diversity and inclusion, and nurture young scholars (Figure 3). Informed by the INQUIRE framework, these action-inviting themes provide important insights for higher quality research—more value, less waste—on primary cam morphology and its natural history, including hip-disease consequences.\n\nHigh quality research on primary cam morphology and its natural history is ultimately aimed at benefitting athletes/patients. It is therefore important to keep their preferences, experiences and needs at the centre of research (Figure 3). This approach to research in the field of primary cam morphology and its natural history is supported by the results of the Oxford Consensus Study12,13: athletes/patients should be ‘in charge as partners with power—exerting some control over all decisions’.13\n\nOur first theme echoed that authentic patient and public involvement (PPI) in research—partnering with athletes/patients—could facilitate more relevant, safer, and more ethical research.51 Patient-centred research could help to identify unmet needs and gaps for research communities to prioritise—research questions that are relevant to athletes/patients with primary cam morphology or a related hip disease. These include qualitative research to explore experiences, preferences, and perspectives. It goes without saying that athlete/patient-centred research must be safe and ethical. In the context of primary cam morphology and its natural history, this means, for example, avoiding radiographs when researching aetiology in maturing athletes, protecting participants’ personal information, prioritising general and research-specific ethics and integrity, and valuing methodological rigour.\n\nA haphazard approach to language (including terminology and definitions) could confuse patients.52 This gap was addressed when the research community agreed on primary cam morphology terminology, definitions, taxonomy, and imaging outcomes for research.12 The YAHiR Collaborative and others are working to implement this agreement and to address areas of tension and dissent. This will take time; many clinicians and researchers still use cam ‘lesion’, ‘deformity’ or ‘impingement’ instead of the agreed ‘morphology’.5,12 With athletes/patients as partners, research communities would likely be more inclined to prioritise clear and non-threatening language when stakeholders communicate about the morphology and its hip-disease consequences.\n\nSecond, high-performing research teams should collaborate with one another—a key INQUIRE element of high-quality research.14 Such collaborations could catalyse, among other benefits, larger data sets (through well-planned multi-centre research projects on primary cam morphology aetiology and prognosis, for example), increased methodological rigour (by involving, for example, methodologists and specialist radiologists from the outset), and better framing of research questions to secure wider buy-in (of football club managers, for example). Professor Trish Greenhalgh shared ‘3 tips for authentic research collaboration from interdisciplinary health research’ in Session 4 of the 2022 Oxford Young Athlete’s Hip Symposium: ‘build relationships and trust’, ‘foster tolerance of uncertainty’, and ‘harness conflict productively’.53\n\nThird, the research community should pursue open science. Participants emphasised access for everyone to as much information as possible—including protocols, datasets, and summaries of results in non-scientific language. Several participants discussed ‘extortionate’ costs of open access publishing and warned against predatory and low-quality open access journals. These problems are not unique to the hip-and-groin research field. With an estimated annual turnover of $2 billion, the open access publishing model has become the ‘mainstream approach to delivering scientific knowledge with Article Processing Charges as driving force’.54 Predatory journals and publishers, a problem in all research fields,55 were defined as ‘entities that prioritize self-interest at the expense of scholarship and are characterized by false or misleading information, deviation from best editorial and publication practices, a lack of transparency, and/or the use of aggressive and indiscriminate solicitation practices’.56 This consensus definition is likely to contribute to a coordinated strategy aimed at eradicating the plague of predatory journal and publishers.\n\nFourth, high-quality research on primary cam morphology champions EDI. An EDI-conscious research community at each stage of the research process, would be more aware of possible blind spots, including a tokenistic, tick-box approach to EDI.57 Similar to other research fields, there is a lack of diversity and inclusion in sport and exercise medicine, science and rehabilitation in general, but specifically Black female athletes.58–60 Other fields have prioritised efforts to improve EDI, including in academia61 and nursing.62 An EDI lens should not only inform research populations but also research teams. Our findings suggest such a research community would likely (1) prioritise more diverse research populations and research teams with an immediate focus on girls and women, and the Global South (diversity); (2) secure access to equal and fair opportunities to minoritised individuals and populations (equity); and (3) emphasise inclusion as ‘a sense of belonging: feeling respected, valued, and seen for who we are as individuals’.63\n\nFinally, participants in this study emphasised young scholars, in high-quality research, should be nurtured. This echoed the move away from an ‘unhealthy reliance on impact factors’ to assessing scientific research quality,64 to rather focus on nurturing and mentoring the next generation of scholars.65 They are carefully mentored, share, and learn together, benefit from opportunities created by their mentors and seniors, and thrive when employed with funding—creating a stable and sustainable research environment.\n\nThe findings of this study, informed by the six dimensions and two promotors of the INQUIRE framework, are consistent with current trends in assessing research. However, what research quality in health care is, also depends on context and research type. The INQUIRE framework’s dimensions—minimisation of bias, precision, and generalisability—illuminate a predominantly positivist lens to assessing research quality. For example, we don’t trust results of cohort studies plagued by researcher bias and imprecision. ‘Confirmability’, ‘credibility’, and ‘transferability’, on the other hand, are concepts for defining and investigating rigorous qualitative research.66–68 A carefully constructed conceptual framework for research quality in health care can inform efforts to improve research in a specific field. A new, more inclusive framework could, for example, be the catalyst to moving a field beyond the ‘impact-factor-is-king’ approach to assessing research quality, to embracing a more contemporary approach. In this study, our analysis started with the INQUIRE framework but also explored research quality beyond the positivist frame of enquiry.\n\nDespite worldwide quests, a uniform approach to describing and assessing research quality and impact is still contested. The 2014 ‘Increasing Value, Reducing Waste’ series in The Lancet69–74 spotlighted waste in biomedical research and made 17 recommendations to increase research value, addressed to five main stakeholders—funders, regulators, journals, academic institutions, and researchers. The authors of this series formed an alliance (the Reduced Research Waste and Reward Diligence [REWARD] campaign),75 emphasising five principles—several echoed in our findings—to maximise research potential, including (1) the right research priorities; (2) robust research design, conduct and analysis; (3) regulation and management that are proportionate to risks; (4) access to all information on research methods and findings; and (5) complete and usable reports of research. However, a follow-up article in 2016, providing an overview of the effects of The Lancet’s Series and REWARD campaign, concluded that, overall, and despite early corrective actions by some stakeholder groups, further work was needed to increase research value.11 Six years later, the tide continues to turn against research waste and, importantly, the narrow notion that high quality research and impact can only be ‘measured with a number’.65,76\n\nThe findings of this study resonate with the key quality concepts of the Agreement on Reforming Research Assessment [4]. This agreement emphasises research (quality) assessment based primarily on qualitative judgement and more-inclusive assessment systems.76 Commendably, this agreement was co-produced ‘bottom-up’ by research stakeholders from 350 research organisations and 40 countries as ‘an exercise of consensus’, based on a ‘common vision, and shared responsibility and direction.’.77 This inclusive approach is a foundation to collaborate—a call for collective action. To date (31 July 2023) and supported by the Coalition for Advancing Research Assessment initiative,78 608 organisations worldwide have signed the agreement.79 Others have paved the way for this approach, notedly in the transdisciplinary research context,80 and patient-orientated academic clinical research’ (the INQUIRE framework described earlier).14\n\nBelcher et al. (2016) proposed a framework of four main principles when assessing research quality in transdisciplinary research.80 These principles are (1) relevance (the importance, significance, and usefulness of the research problem, objectives, processes, and findings to the problem context); (2) credibility (the research findings are robust, and the sources of knowledge are dependable. This includes a clear demonstration of the adequacy of the data and the methods used to procure the data including clearly presented and logical interpretation of findings); (3) legitimacy (the research process is perceived as fair and ethical, including ethical and fair representation of all involved, and the appropriate and genuine inclusion and consideration of diverse participants, values, interests, and perspectives); and (4) effectiveness (the research generates knowledge and stimulates actions that address the problem and contribute to solutions and innovations).\n\nIn sum, there are no shortage of research quality frameworks; however, how these frameworks are applied to inform research practice depends on several factors, including context. Nevertheless, there seems to be a world-wide movement towards a more qualitative assessment of research quality.\n\nTo our knowledge, this is the first study in the hip-and-groin research field exploring research stakeholders’ perspectives on research quality. In light of these efforts to articulate research quality, limitations of this study deserve particular attention. Although our aim was to explore (describe and understand) perspectives on research quality of a diverse stakeholder group (rather than a deep case-by-case phenomenological analysis of a smaller homogenous group) the study population could have been even more diverse—we did not, for example, recruit any participants from the Global South or Black female athletes. This was perhaps a blind spot – patients, particularly in this research field, are not only middle-aged white males. Participants from the Global South at the intersection of race and gender, compared to their white Global North counterparts, would likely have different perspectives on participation and access to three-dimensional imaging, for example.\n\nAlthough the data in this study provided a rich and complex picture of a diverse group of participants’ experiences and perspectives on research in the field of primary cam morphology and its natural history, it did not aim to completely capture the phenomenon under scrutiny.81 Our interviewees emphasised language and communication about the morphology, referring to ‘inflammatory’ language, for example. What ‘inflammatory’ is, however, depends on the hearer. Research communities might therefore choose to adopt a more flexible approach to defining ‘inflammatory’ language. We need more research on the perspectives and needs of subgroups living with primary cam morphology and its hip disease consequences, focussing on women, adolescents and the Global South. Village-born Kenyan long-distance runners who pad 25 miles a day barefoot, for example, or youngsters playing football for many hours per week in rural villages in South Africa: do they develop primary cam morphology or its hip disease consequences? what are their challenges, priorities and concerns? These and other gaps in current research should be addressed by the YAHiR Collaborative and collaborators.\n\nThe research team reflected on two aspects of our sampling strategy. First, the structured variation approach to sampling (informed by the ‘closeness continuum’) resulted in breadth, rather than individual depth, of perspectives. However, our purpose was not an in-depth phenomenological analysis; we were interested in multiple perspectives on research quality from a diverse stakeholder group. Second, the role of prior relationships between researchers and some participants. The familiar nature of some ‘acquaintance interviews’ might have shaped the data gathered during this study.42 For example:\n\n… But you know better than anybody, that some of the athletes may feel that osteoarthritis in 10 years’ time is much less important than what their pain-and-function is the season. (P15)\n\nStarting the sentence with ‘you know better than anyone’, the participant aligned himself with the lead investigator and interviewer, drawing upon their shared knowledge. The participant was still the interviewee, but it could be seen that he also invoked the professional relationship with the lead investigator.42 Some participants might have assumed the lead investigator knew the answer anyway, limiting the extent to which the interviewee elaborated on their responses. For that reason, we had a third person (SMA) present during the interview allowing the lead investigator the opportunity to ask, for example: ‘For SMA’s benefit, could you just explain why?’\n\nFinally, we briefly mention critical orientations like power and equity. Epistemologically, were our orientation more ‘critical theory’ than pragmatism-informed interpretivist, we would have paused to unpack these constructs more.\n\n\nConclusion\n\nExploring stakeholders’ perspectives on research quality through an established research quality framework (INQUIRE) illuminated areas for immediate action in the research field of primary cam morphology and its natural history. Research communities in this field should: partner with athletes/patients; collaborate authentically with one another; champion equity, diversity, and inclusion; pursue open science, and nurture young scholars. Such an approach would ultimately benefit athletes and patients.\n\nThe findings of this study could inform concrete actions by research communities to pursue higher quality research—more research value and less waste—in the field of primary cam morphology and its natural history. Although the five action-inviting themes reflect contemporary trends in research, and could therefore be transferable to other areas of research, their practical application remains context- and field-specific.\n\n\nEthical approval\n\nEthical approval was received from the University of Oxford’s Medical Sciences Interdivisional Research Ethics Committee (Project ID R66281) and Qatar University Institutional Review Board (QU-IRB 1239-EA/20) prior to conducting the study.", "appendix": "Data availability statement\n\nThe research team carefully considered open access to all research data (transcribed interviews). However, we decided not to publish the transcribed interviews in an open access repository for three main reasons: First, the hip-and-groin in athletes research field is small. The research field on femoroacetabular impingement syndrome and related bony morphologies in athletes is even smaller. Our research participants - 15 elite athletes, coaches, clinicians and researchers in this small field - could therefore be easily identified even with complete anonymization of interview transcripts. Second, although verbal informed consent was recorded as part of each interview, we did not seek explicit informed consent from participants to publish de-identified transcripts nor did me get University of Oxford Institutional Review Board permission to do so. Finally, to help the reader and support our research findings, we provide very extensive quotations to underpin our study results (in the manuscript text but also as results tables). Upon reasonable request (e.g. for peer review or further research), the research team would consider to provide full access to the data (transcribed interviews). Such requests should be directed to the corresponding author: Dr HP Dijkstra.\n\nInformed consent by research participants: Due to COVID-19 restrictions at the time, all interviews were conducted online and recorded after obtaining (and recording) verbal informed consent at the beginning of each interview. This process was clearly outlined in our Ethical Approval documents and approved by the University of Oxford’s Medical Sciences Interdivisional Research Ethics Committee and the Qatar University Institutional Review Board as detailed above.\n\n\nAcknowledgement\n\nThis manuscript has been published as Chapter 6 (More value and less waste in research on primary cam morphology and its natural history: a qualitative interview study of stakeholders’ perspectives) of the lead author’s DPhil Evidence-Based Health Care thesis: Improving research quality on primary cam morphology. The full thesis can be accessed here (Oxford University Research Archive): https://ora.ox.ac.uk/objects/uuid:288081e3-b59b-4488-af49-45a510a76dfc\n\n\nReferences\n\nDijkstra HP, Ardern CL, Serner A, et al.: Primary cam morphology; bump, burden or bog-standard? A concept analysis. Br. J. Sports Med. 2021; 55: 1212–1221. 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COARA; (accessed 19 Jan 2023). Reference Source\n\nSignatories: CoARA. (accessed 24 Aug 2023). Reference Source\n\nBelcher BM, Rasmussen KE, Kemshaw MR, et al.: Defining and assessing research quality in a transdisciplinary context. Res. Eval. 2016; 25: 1–17. Publisher Full Text\n\nTracy SJ: Qualitative Quality: Eight “Big-Tent” Criteria for Excellent Qualitative Research. Qual. Inq. 2010; 16: 837–851. Publisher Full Text\n\n\nFootnotes\n\n1 The term ‘bias’ is usually used in relation to quantitative research. A related term in qualitative research is ‘perspective’. Interpretive qualitative researchers consider that there is no such thing as an unbiased sample, but that it is important to include a wide range of perspectives. This is how we interpreted this criterion in the framework when exploring stakeholders’ perspectives on qualitative research.\n\n2 The term ‘external validity’ is usually in relation to quantitative research. ‘Transferability’ refers to the generalisability of inquiry in qualitative research.\n\n3 International Olympic Committee (IOC) Research Centres for the Prevention of Injury and Illness. Eleven IOC Research Centres are supported by a four-year grant for 2023-2026: https://olympics.com/ioc/medical-research/research-centres\n\n4 Work on this Agreement, drafted by Science Europe, the European University Association, and Dr Karen Stroobants, supported by the European Commission, started in January 2022. This agreement ‘… set a shared direction for changes in assessment practices for research, researchers, and research performing organisations, with the goal to maximise the quality and impact of research. It includes principles, commitments, and timeframes for reforms and lays out principles for a Coalition of organisations willing to work together in implementing the changes.’ - https://www.scienceeurope.org/our-resources/agreement-reforming-research-assessment/" }	[ { "id": "341285", "date": "21 Nov 2024", "name": "Samantha Bunzli", "expertise": [ "Reviewer Expertise Musculoskeletal pain", "Qualitative research", "Equity" ], "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 qualitative study explored the perspectives of clinician-researchers, parents, patients and sports coaches on research quality in the field of primary cam morphology. I think the rationale for this study is good. I have some overall comments related to the study methods, interpretations of results and structure of the manuscript.\nMethods: I understand that the interview guide was flexible, however I have queries about how the example questions provided in Figure 2 were selected. For example, the question about clinician-researcher perspectives on ‘spinning of results’ could be leading and open to social desirability bias – would we expect any of the participants to perceive this as acceptable? Would it not have been relevant to ask the clinician-researchers “How can we improve research quality in the field?”\nFollowing on from this comment, the authors acknowledge the pre-existing relationship between the interviewer and some of the participants and consider the potential impact of this in the limitations. However, I would like to see a discussion around the potential for social desirability bias in the participants responses.\nThe authors acknowledge that their participants lacked diversity, and I note that only 5/15 participants were women. Why wasn’t a better attempt to include more diverse voices in this project? This seems to me in direct contrast with findings presented in Theme 4.\nThe methodology is detailed and the inclusion of specific examples throughout (e.g. how reflexivity was enacted) can be helpful for readers less familiar with qualitative research.\nHowever, this manuscript is very long. As a qualitative researcher, I can appreciate that, in general, manuscripts of qualitative studies benefit from a more generous word count than that of quantitative studies, however the discussion section of this manuscript alone is >2000 words. The authors present data in Theme 3 from participants suggesting that the: “average clinician ‘doesn’t really read research papers’”. I would speculate that the length of this article may act as a barrier to access for some readers. I believe it would be possible to shorten this manuscript without losing richness.\nResults: There is some detail in the results section which I believe would be better placed in the discussion. For example, the results section for Theme 5 opens with a description of existing mentorship frameworks.\nI like the inclusion of Figure 3. I suggest that the quote for Theme 5 could be replaced with a more meaningful (actionable) quote.\nDiscussion: I think there is an opportunity to discuss the problem of gender bias in orthopaedics more broadly. For example, data in US shows 7.4% of practicing orthopaedic surgeons are female. In the field of orthopaedic research, a 2024 systematic review by Sonnier et al. showed that among studies involving athletes, 19.9% of studies included women in the authorship team; 21.5% of studies had a woman first author and 16.7% had a woman as senior author. Studies which included women in the author team were significantly more likely to isolate female athlete participants.\nMight the authors like to comment on the specific need to nurture young scholars who represent voices other than that of men from WEIRD (Western, Educated, Industrialized, Rich, and Democratic) backgrounds?\n\nRelevant to discussion related to patient-centred research, I would like to see a discussion around the contribution that qualitative research (such as this study!) can make in the field. Given the field of orthopaedics has traditionally been dominated by researcher-driven priorities and positivist research paradigms, it would be relevant to reflect on the value of building capacity among junior researchers in consumer-engaged, qualitative approaches.\nOn the topic of qualitative research – I find it noteworthy that the authors decided not to provide access to transcribed interviews despite their recommendations around open access in Theme 3. Perhaps in the main text, the authors could acknowledge the ethical considerations around the sharing of qualitative 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? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "344630", "date": "20 Dec 2024", "name": "Jinchi Tang", "expertise": [ "Reviewer Expertise Orthopedics", "hip morphology", "cam morphology" ], "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 study explored stakeholder perspectives on research quality in primary cam morphology and its natural history using the INQUIRE framework, identifying five actionable themes: partnering with athletes/patients, fostering authentic collaboration, championing equity, promoting open science, and nurturing young scholars. These findings contribute significantly to advancing the field by offering concrete recommendations to enhance research relevance, inclusivity, and impact while reducing waste. This study presents a meaningful contribution to the readership. However, some issues require attention and further work. Please find below a summary of suggestions for each section of the manuscript. Abstract: - Background: “Experts agreed on key elements for primary cam morphology and a prioritised research agenda for the field.” Improved: \"Experts have reached consensus on key elements of primary cam morphology and established a prioritized research agenda for the field.\" - Background: There is not a clear transition from discussing the general condition to the specific focus of the study. A sentence may be added to explain why this research is critical at this time. - Aim: The aim is not a complete sentence. It could be reframed to directly state the study’s purpose, e.g., \"This study aims to investigate stakeholders' perspectives on high-quality research within the field of primary cam morphology to identify areas of research value and potential waste.\" - Method: Provide more information about the sample, such as specifying the geographic scope of the research, if applicable. Introduction: - P1: Maybe add a sentence about the broader impact of primary cam morphology on public health to justify the importance of the research. - P1: While the introduction discusses the condition, it could more directly tie these details to the necessity for further research. For example, explain why gaps in research exist despite the high prevalence of the condition. - P2: You only mentioned the research gap, but what are current studies on primary cam morphology aiming to achieve? Aim: - P1: \"This study aimed to explore research quality on primary cam morphology and its natural history...\" The use of \"explore\" could be more specific. What aspects of research quality are being examined? Is the study evaluating methods, outcomes, participant satisfaction, or something else? Can you specify which elements of research quality are being addressed to provide a clearer picture of the study’s objectives. Methods: Although the methods section is well-structured, consider whether the report should follow certain standardized criteria to make it more robust, such as the Consolidated Criteria for Reporting Qualitative Research (COREQ) or Standards for Reporting Qualitative Research (SRQR). Ontological and epistemological orientation, and study design: - P1: The use of specialized terminology (e.g., \"ontological and epistemological orientation\") is appropriate for the audience but could benefit from brief definitions or explanations for clarity. - P1&P2: Maintain consistent terminology, especially when referring to the research approach (e.g., \"interpretative\" vs. \"interpretive\"). Instrument Development: - P1: Can you add more details of the piloting process of the interview guide? Who was involved in the pilot testing? What changes were made as a result of this testing? Specify any adaptations made to the interview guide based on feedback from the piloting process or during the actual data collection phase. - P2: \"This framework was a useful...\" Improved: \"The INQUIRE framework was a useful...\" Sample: - P1: How was the number of stakeholders in each group determined? Was it random? - P2: Provide more context or a brief explanation of the \"closeness continuum\" model to help readers understand why it is particularly suited to your study. This could include its advantages over other models. Data Collection: - P1: Since most participants had multiple roles (e.g., researcher, clinician, and parent), could these overlapping roles have influenced the data and interpretations? Analysis: - P3: SMA and JB are mentioned in the coding process, but how were disagreements or differences in coding resolved? Was there a specific process for reconciliation? - P4: Expand on the transition from \"domain summary codes\" to \"fully realized themes.\" This is an important methodological step that could benefit from more concrete examples to show how it was achieved. Research Team and Reflexivity: - How exactly was reflexivity operationalized? For example, were there formal steps or reflective practices (e.g., journaling, team discussions) to identify and address biases? - Can you provide more specific instances where reflexivity influenced decisions during the study (e.g., changes in coding, themes, or interpretation)? Results: Theme 1: - Can you explore whether there were disagreements or variations in perspectives among stakeholders? For instance, did clinicians and athletes/patients view partnerships differently? Theme 2: - Maybe expand on why collaboration is challenging. For example, discuss logistical, financial, or cultural barriers that prevent multi-center studies. - What are the barriers to meaningful data sharing? (e.g., Table 3, quote 19). Is it a lack of standardization, infrastructure, or trust among research centers? Theme 4: - Maybe elaborate on the lack of representation in existing studies and how it affects the generalizability of findings. For example: \"The absence of research on athletes from the Global South limits our understanding of how genetic variation or socio-environmental factors influence primary cam morphology.\" Discussion: Summary of Findings and Implications for Research and Practice: - This section could be more impactful by directly stating how these findings advance the field or address specific gaps identified earlier in the document. - The summary is somewhat lengthy. Consider focusing more on implications, such as explicit, actionable recommendations for each finding. For example: Theme1: Encourage collaboration with patient advocates to develop non-inflammatory language guidelines. Comparison to the Research Quality Literature: - Can you briefly explain the unique contributions of each framework to the field of primary cam morphology research? For example, how does Belcher et al.’s framework address gaps in the INQUIRE model? - Can you discuss the global applicability of these frameworks? How can they be adapted for underrepresented populations or resource-limited settings?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\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": [] } ]	1	https://f1000research.com/articles/13-1075
https://f1000research.com/articles/13-1074/v1	19 Sep 24	{ "type": "Case Report", "title": "Case Report: Emergency endovascular management of a ruptured giant abdominal aortic aneurysm with severely angulated and conical shaped neck using novel multiple stiff wire technique", "authors": [ "Taofan Taofan", "Iwan Dakota", "Suko Adiarto", "Suci Indriani", "Ruth Grace Aurora", "Rendra Mahardhika Putra", "Bagas Adhimurda Marsudi", "Jonathan Edbert Afandy", "Melani Limenco Benly", "Kanya Paramastri", "Macmilliac Lam", "Muhammad Rafli Iqbal", "Keviano Bobby Saputro", "Sung Gwon Kang", "Bambang Widyantoro", "Iwan Dakota", "Suko Adiarto", "Suci Indriani", "Ruth Grace Aurora", "Rendra Mahardhika Putra", "Bagas Adhimurda Marsudi", "Jonathan Edbert Afandy", "Melani Limenco Benly", "Kanya Paramastri", "Macmilliac Lam", "Muhammad Rafli Iqbal", "Keviano Bobby Saputro", "Sung Gwon Kang", "Bambang Widyantoro" ], "abstract": "Background Ruptured abdominal aortic aneurysm (rAAA) is commonly fatal, with an overall mortality rate of nearly 90%, and the risk of subsequent rupture remains high, especially in large aneurysm diameters or progressive disease. Unfavorable neck anatomy in EVAR is linked to early graft failure and long-term complications. Recently, a novel multiple stiff wire (MSW) technique has been developed to overcome the challenges of hostile neck anatomy without introducing additional devices and procedural complexity. It has also been feasible in a series of elective cases. In this case, we report the first-ever utilization of the MSW technique in an emergency case of an acute contained rAAA with a conical-shaped, severely angulated neck who underwent Endovascular Aortic Repair (EVAR).\n\nCase presentation A 61-year-old man came with intermittent sharp stomach pain radiating to his back since three weeks ago. Physical examination showed elevated blood pressure and anemic conjunctiva. Laboratory examinations showed anemia, leukocytosis, elevated D-dimer level, high creatinine level, and low eGFR. CT-Scan Angiography (CTA) revealed severely hostile anatomy, a conical-shaped abdominal aorta aneurysm with a length of 13.2 cm and a maximum diameter of 9.3 cm with angulation of 90.1°. The patient was diagnosed with Ruptured AAA with a conical-shaped, severely angulated neck. Endovascular Aortic Repair (EVAR) management with MSW technique was planned for him. After four days, The patient was discharged in a clinically stable condition with optimal medical treatment and education.\n\nConclusion The endovascular approach could be performed in emergency settings and has been proven to reduce length of stay, mortality, and morbidity rates. In this case, the endovascular approach with the MSW technique showed promising results for the patient.", "keywords": [ "Abdominal Aortic Aneurysm", "Endovascular Aortic Repair", "Multiple Stiff Wire Technique", "Hostile Neck", "Conical-Shaped Neck", "Ruptured Giant AAA" ], "content": "Introduction\n\nAbdominal Aortic Aneurysm (AAA) is increasing worldwide, ranging from 4.2% to 11% per year, as it is a degenerative process and almost exclusively occurs in the infrarenal region and can present as asymptomatic (majority of cases), symptomatic non-ruptured, and ruptured AAA (rAAA). When ruptured, AAA is commonly fatal, with an overall mortality rate of nearly 90%.1 Rarely, the surrounding peritoneum can effectively seal off and contain the rupture, but the risk of subsequent rupture remains high especially in large aneurysm diameters or progressive disease.2\n\nEndovascular Aortic Repair (EVAR) remains the cornerstone of AAA management and is generally favored over open surgical repair. However, EVAR presents many challenges, one of which is limited due to challenging anatomy. A hostile neck remains one of the most common reasons a vascular specialist might not recommend EVAR.3 Studies have found unfavorable neck anatomy to be linked to early graft failure and long-term complications such as stent graft collapse, migration, type I endoleak, and late aneurysm rupture.4\n\nRecently, a novel multiple stiff wire (MSW) technique has been developed to overcome the challenges of hostile neck anatomy without introducing additional devices and procedural complexity. It has also been feasible in a series of elective cases.5 In this case, we report the first-ever utilization of the MSW technique in an emergency case of an acute contained rAAA with a conical-shaped, severely angulated neck who underwent EVAR.\n\n\nCase report\n\nA 61-year-old man came with intermittent sharp stomach pain that was referred to his back for three weeks. The patient had no prior history of abdominal, flank, or lower back pain before his presentation at our hospital. Other complaints, such as chest pain, shortness of breath, coughing, fever, and bloody stool, were denied.\n\nPhysical examination showed elevated blood pressure (148/90 mmHg), regular heart rate (73 bpm), elevated respiratory rate (22×/min), and normal oxygen saturation (98%). Anemic conjunctiva was found, although other physical examinations appeared within normal range. Laboratory examinations showed anemia (Hb 7.7 g/dL), leukocytosis (10.920 cells/μL), elevated D-dimer level (12.410 μg/mL), high creatinine level (2.01 mg/dL), and low eGFR (37 mg/mL/min/1.73 m2). CT-Scan Angiography (CTA) revealed a ruptured (Figure 1B) and conical-shaped abdominal aorta aneurysm with a length of 13.2 cm, maximum diameter of 9.3 cm (Figure 1A), and 90.1° angulation (Figure 1C).\n\nA. Pre-procedural axial slice CT Scan angiography showing giant abdominal aortic aneurysm; B. Axial CT Scan angiography showing ruptured aneurysm; C. Maximum Intensity Projection of CT Scan showing anatomy features of the conical neck and severe angulation (90.1°)\n\nThe patient was diagnosed with Ruptured AAA with a conical-shaped, severely angulated neck, alongside anemia due to gastrointestinal bleeding, controlled hypertension, and CKD. EVAR management with multiple stiff wire techniques was planned for him.\n\nThe EVAR procedure was done using the MSW technique.5 After general anesthesia, vascular access to the right femoral artery (RFA) and left femoral artery (LFA) was established, followed by the insertion of a guidewire with a support catheter through both femoral arteries, which was then positioned in the descending thoracic aorta. Wire exchanges with 0.035″ × 260 cm Extra Stiff Wire (Cook, Bloomington, USA) were done in both accesses. Initial aortography from right brachial artery access revealed a contained rupture of the infrarenal aorta. The proximal neck angulation was decreased to 45.4° (Figure 2A). A SEAL Novus Main Body Stent Graft® sized 26 mm × 50 mm main body (S&G Biotech, Yongin, Korea) was deployed via the RFA (Figure 2B). Then, a wiring attempt for intragraft cannulation via RFA was done but failed, so it was decided to do wire snaring from brachial artery access to the LFA access (Figure 2C). Aortography with a pigtail catheter via LFA was done to confirm the wire position (Figure 2D). Wire exchange with 0.035″ × 260 cm Extra Stiff Wire (Cook, Bloomington, USA) was done, and SEAL Novus Limb Stent Graft® sized 12 mm × 80 mm (S&G Biotech, Yongin, Korea) was deployed from abdominal aorta until left common iliac artery. Another SEAL Novus Flared Limb Stent Graft® 12 mm × 100 mm (S&G Biotech, Yongin, Korea) was deployed until the left external iliac artery overlapped with the previous stent. For the right common iliac artery, SEAL Novus Limb Stent Graft® 12 mm × 120 mm (S&G Biotech, Yongin, Korea) was deployed, overlapping with the previous stent. Final aortography revealed an excellent position of the stent grafts. The contrast filled the whole cover stent without a sign of endoleak (Figure 2E). A 270 mL Iodixanol 370 mg/mL contrast was used, dose area product 180.68 Gy.cm2, and fluoroscopy time was 1 hour 05.54 minutes.\n\nA. Proximal Neck Angulation; B. Main Body Deployment; C. Wiring Attempt; D. Aortography; E. Final Aortography.\n\nAfter the procedure, the patient was observed in the intensive cardiovascular care unit. Upon laboratory testing, the patient’s hemoglobin went up to 11 mg/dL. The evaluation CTA indicated an optimal stent location without migration, no endoleak was detected, and a decreased proximal neck angulation of 41.0° (Figure 3). After four days, the patient was discharged in a clinically stable condition with optimal medical treatment and education. The patient was prescribed spironolactone, bisoprolol, candesartan, rosuvastatin, sucralfate, lansoprazole, and ibuprofen as pharmacotherapy.\n\nA. volume rendering shows the stent graft position with no evidence of endoleak; B. Maximum Intensity Projection of CT scan shows anatomy features of the conical neck and angulation of the abdominal aorta.\n\n\nDiscussion\n\nThe emergency EVAR approach for rAAA was initially implemented in 2004, with published findings indicating a reduction in the 30-day postoperative death rate (17.9% vs. 30.0%).6 Compared to open surgery, a US database cohort found in-hospital mortality was significantly lower for EVAR (23.8% vs. 36.3%), and similar results were found after analysis of the Vascular Quality Initiative database (23% vs. 35% for EVAR vs. open repair).7,8 Endovascular repair provides a superior option, particularly in patients of advanced age with chronic pulmonary disease, cardiovascular disease, and renal dysfunction. It is associated with a threefold reduction in perioperative mortality, even in younger patients with fewer comorbidities.9\n\nThe clinical profile of this patient was all in favor of the emergency EVAR procedure. The patient had old age, cardiovascular disease, and renal dysfunction, which were determinants of periprocedural mortality and morbidity, as well as worse outcomes if open surgical repair was attempted.\n\nIn our case, the momentous challenge of the hostile neck anatomy with severe neck angulation remains. Endovascular aneurysm repair (EVAR) with pronounced neck angulation, in contrast to mild neck angulation, exhibited a markedly elevated incidence of type 1a endoleak over three years (5.6% versus 2.6%), neck-related secondary interventions over three years (13.1% versus 9%), migration rates within one year (5.4% versus 4.0%), and both aneurysm-related and all-cause mortality within one year (6.4% versus 4.3%).10\n\nSeveral techniques have been proposed to overcome the anatomical challenges of severe neck angulation. The Kilt technique was recently developed to modify AAA neck angulation and proved effective with 100% technical success and without any development of endoleaks during long-term follow-up.11 Our cohort developed the MSW technique and involved a similar method, introducing additional wires to further control and modify the neck angle. The MSW technique demonstrated promising results in the number of thoracic and abdominal endovascular repairs. It enables neck angulation modification of the aortic neck without added procedure complexity, the need for specialized devices, or special training for the operator. It also comes with the benefit of reduced cost compared to specialized devices.5 The MSW technique is the perfect solution for emergency cases in developing countries where specialized devices are limited. With the MSW technique, there’s no need for expensive equipment, which makes it an affordable and practical choice.\n\nThis case report represents the first-ever application of the MSW technique in an emergency EVAR protocol in a contained ruptured giant AAA with a hostile neck. The patient was at high intraoperative risk because of the severe angulation and conical-shaped neck anatomy.\n\n\nConclusion\n\nOur case illustrates the successful application of the MSW technique in an emergency EVAR for a challenging anatomical scenario. This approach highlights the potential of innovative methods in improving outcomes for patients with ruptured AAAs, underscoring the importance of continued advancements in endovascular interventions.\n\n\nConsent\n\nInformed consent has been obtained from the patient to publish the case report and accompanying images.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nFigshare: CARE checklist for “Emergency endovascular management of a ruptured giant abdominal aortic aneurysm with severely angulated and conical shaped neck using novel multiple stiff wire technique”. https://doi.org/10.6084/M9.FIGSHARE.26976100.V1. 12\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 thank the patient for allowing us to publish their case and the cardiothoracic surgery and anesthesia teams for their involvement in managing these patients.\n\n\nReferences\n\nBooth MI, Galland RB: Chronic contained rupture of an abdominal aortic aneurysm: a case report and review of the literature. Ejves Extra. 2002; 3(2): 33–35. Publisher Full Text\n\nLederle FA, Johnson GR, Wilson SE, et al.: Rupture rate of large abdominal aortic aneurysms in patients refusing or unfit for elective repair. JAMA. 2002; 287(22): 2968–2972. Publisher Full Text\n\nAntoniou GA, Georgiadis GS, Antoniou SA, et al.: A meta-analysis of outcomes of endovascular abdominal aortic aneurysm repair in patients with hostile and friendly neck anatomy. J. Vasc. Surg. 2013; 57(2): 527–538. PubMed Abstract \| Publisher Full Text\n\nPitros C, Mansi P, Kakkos S: Endografts for the treatment of abdominal aortic aneurysms with a hostile neck anatomy: A systematic review. Front. Surg. 2022; 9: 872705. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTaofan T, Adiarto S, Dakota I, et al.: Endovascular management of aortic aneurysm with severe neck angulation and/or iliac artery tortuosity using multiple stiff wire technique: a case series. F1000Res. 2023; 12: 12. Publisher Full Text\n\nMoore R, Nutley M, Cina CS, et al.: Improved survival after introduction of an emergency endovascular therapy protocol for ruptured abdominal aortic aneurysms. J. Vasc. Surg. 2007; 45(3): 443–450. PubMed Abstract \| Publisher Full Text\n\nGupta AK, Dakour-Aridi H, Locham S, et al.: Real-world evidence of superiority of endovascular repair in treating ruptured abdominal aortic aneurysm. J. Vasc. Surg. 2018; 68(1): 74–81. PubMed Abstract \| Publisher Full Text\n\nRobinson WP, Schanzer A, Aiello FA, et al.: Endovascular repair of ruptured abdominal aortic aneurysms does not reduce later mortality compared with open repair. J. Vasc. Surg. 2016; 63(3): 617–624. Publisher Full Text\n\nSchermerhorn ML, O’Malley AJ, Jhaveri A, et al.: Endovascular vs. open repair of abdominal aortic aneurysms in the Medicare population. N. Engl. J. Med. 2008; 358(5): 464–474. 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; 17(2): e0264327. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKim T-H, Jang H-J, 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\nLam M: CARE checklist for ‘Emergency endovascular management of a ruptured giant abdominal aortic aneurysm with severely angulated and conical shaped neck using novel multiple stiff wire technique.’. figshare. 2024. Publisher Full Text" }	[ { "id": "329304", "date": "31 Oct 2024", "name": "Muhamad Taufik Ismail", "expertise": [ "Reviewer Expertise vascular medicine", "peripheral intervention", "coronary intervention", "neovascularization", "nanomedicine", "molecular", "regenerative", "and precision medicine" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI have reviewed the case report titled \"Emergency Endovascular Management of a Ruptured Giant Abdominal Aortic Aneurysm with Severely Angulated and Conical-Shaped Neck Using a Novel Multiple Stiff Wire Technique\" and have identified several areas for improvement:\nBackground and Introduction: The background effectively emphasizes the significance of ruptured abdominal aortic aneurysms (rAAA) and the technical challenges associated with endovascular aneurysm repair (EVAR) in anatomically complex cases, such as those with severely angulated necks. The inclusion of information about abdominal aortic aneurysms, their prevalence, and associated healthcare burdens provides a strong foundation for discussing this case. However, a specific description of the multiple stiff wire (MSW) technique and the rationale for selecting this technique over other alternatives is missing. Please include a brief overview of other commonly used techniques in the introduction, especially those applicable to EVAR in cases with hostile neck anatomy, like the triple wire technique, which also does not require additional devices. Technical Details and Illustrative Aids: Given that the multiple stiff wire technique is relatively novel, it would enhance reader comprehension to provide a more comprehensive explanation of this method in the case section. Consider including a detailed step-by-step description of the procedure or summarizing it with images to aid visualization. Additionally, an explanation of its advantages and disadvantages would be valuable. Terminology: Instead of using “first ever utilization,” consider a more nuanced phrasing such as, “To our knowledge, there are no reported or published articles regarding the use of the multiple stiff wire technique in the emergency management of ruptured abdominal aortic aneurysm.” This wording preserves the novelty of the approach while avoiding overly definitive claims. Post-Procedure Outcomes: The post-procedure assessment should include a detailed evaluation of potential adverse events, especially the impact on renal function, as this patient had an initially abnormal renal function test, which may be affected by contrast administration. Additionally, consider including other clinical outcomes, such as cardiovascular or cerebrovascular complications, and provide longer follow-up data where possible. A follow-up CTA at 1 month (or longer if available) is recommended to assess complications such as endoleak, possible shortening or migration etc.\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? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-1074
https://f1000research.com/articles/13-1073/v1	19 Sep 24	{ "type": "Research Article", "title": "A novel hybrid genetic algorithm and Nelder-Mead approach and it’s application for parameter estimation", "authors": [ "Neha Majhi", "Rajashree Mishra", "Neha Majhi" ], "abstract": "Background Traditional optimization methods often struggle to balance global exploration and local refinement, particularly in complex real-world problems. To address this challenge, we introduce a novel hybrid optimization strategy that integrates the Nelder-Mead (NM) technique and the Genetic Algorithm (GA), named the Genetic and Nelder-Mead Algorithm (GANMA). This hybrid approach aims to enhance performance across various benchmark functions and parameter estimation tasks.\n\nMethods GANMA combines the global search capabilities of GA with the local refinement strength of NM. It is first tested on 15 benchmark functions commonly used to evaluate optimization strategies. The effectiveness of GANMA is also demonstrated through its application to parameter estimation problems, showcasing its practical utility in real-world scenarios.\n\nResults GANMA outperforms traditional optimization methods in terms of robustness, convergence speed, and solution quality. The hybrid algorithm excels across different function landscapes, including those with high dimensionality and multimodality, which are often encountered in real-world optimization issues. Additionally, GANMA improves model accuracy and interpretability in parameter estimation tasks, enhancing both model fitting and prediction.\n\nConclusions GANMA proves to be a flexible and powerful optimization method suitable for both benchmark optimization and real-world parameter estimation challenges. Its capability to efficiently explore parameter spaces and refine solutions makes it a promising tool for scientific, engineering, and economic applications. GANMA offers a valuable solution for improving model performance and effectively handling complex optimization problems.", "keywords": [ "Genetic Algorithm", "Maximum Likelihood Estimation", "Nelder-Mead algorithm", "Power Density", "Weibull Distribution", "Wind speed analysis" ], "content": "1. Introduction\n\nIn the continuous pursuit of optimization, where achieving the finest possible outcomes with utmost efficiency and accuracy is crucial, the fusion of diverse methodologies frequently yields superior solutions. Optimization algorithms are always looking for ways to improve efficiency and robustness, encouraging professionals and scholars to investigate novel ideas that happen to be mostly inspired by nature or mathematical concepts. Hybridization in optimization algorithms has garnered significant attention in recent years, offering a potent means to enhance efficacy and efficiency. Among these methodologies, Genetic Algorithms (GA) and the Nelder-Mead Simplex Algorithm (NM) emerge as prominent contenders, each boasting distinct advantages and applications. However, the fusion of these theories has recently proven to be an enticing strategy for enhancing optimization capabilities across various domains.\n\nInspired by evolution and natural selection, genetic algorithms operate by repeatedly developing a population of potential solutions over a series of generations. The concepts of genetic recombination and survival of the fittest are collectively mirrored by the selection, crossover, and mutation operators involved in this evolutionary process. GAs are a popular choice in various industries, including engineering, finance, and biology, because of their impressive effectiveness in solving complicated, high-dimensional optimization problems with non-linear and multimodal objective functions.\n\nThe Nelder-Mead Simplex Algorithm, on the other hand, provides a geometric method for repeatedly refining a simplex—a multi-dimensional geometric shape in the direction of the ideal solution. Its foundation is mathematical optimization. Nelder- Mead algorithms are especially well-suited for problems with few variables or smooth objective functions because, in contrast to GAs, which rely on a population-based approach, they operate on a single point or simplex at each iteration. Due to its ease of use, simplicity, and speedy convergence to local optima, it now has a deserving place within the optimization toolbox.\n\nIndividually, both GA and NM have strengths and limits that make them appropriate for specific optimization scenarios. GA excels in global exploration, utilizing population variety to explore large solution spaces and avoid local optima. On the other hand, NM excels at local refinement, expertly traversing convex and smooth terrain to locate specific optima. By fusing two different but complementary methods, the hybridization of GA and NM aims to get the best of both worlds and encourage synergy in optimization techniques.\n\nMany GA combinations have been proposed in the literature before our study; we briefly mention a few of them below. A hybrid algorithm for the collocation approach of boundary value problem-solving was presented by Nikos E. Mastorakis.1 A combined NM and GA was proposed by Durand and Alliot,2 and evaluated on two benchmark functions where the employment of either technique alone is useless. Their research demonstrates the speed boost that NM provides. The trade-off in global optimization between computing time, precision, and dependability was initially noted by Renders and Flasse.3 By fusing a genetic algorithm, particle swarm optimization, and the Nelder-Mead simplex search methodology, Fanetal.4 have created a revolutionary strategy. Their research was focused on determining the global best solution for non-linear continuous variable functions. They have shown how their technique performs comparably on 10 test issues in their study article. Hwang and He5 have presented an inventive adaptive real-parameter simulated annealing genetic method in a similar spirit. The benefits of simulated annealing and genetic algorithms are both effectively maintained by this approach. A comparative examination of the algorithm’s performance on two engineering design issues and sixteen benchmark problems has been provided by the authors.\n\nMany industries are interested in using the Nelder-Mead Simplex Algorithm (NM) working together with Genetic Algorithms (GA), including bioinformatics, finance, and engineering. Combining these methods provides a potent method of resolving challenging optimization issues in engineering, where designs are complicated and rules are demanding. Combining GA with NM helps improve portfolio management and risk assessment in the financial industry, where on-time and correct choices are essential. Similarly, in bioinformatics, where understanding biology relies on smart computer methods, hybrid algorithms speed up tasks like genomic analysis and drug discovery. This article explores how combining NM and GA enhances both, highlighting how they work together to solve real-world issues. In this paper, the GANMA algorithm has been tested on fifteen benchmark problems on three different dimensions (10, 20, and 30). According to the results from the experiment, the suggested GANMA algorithm is a promising one that can quickly find the best or almost the best solution for the majority of the functions that were examined.\n\nThe remaining portion of the research study is structured as follows: Section 2 covers the fundamentals of the Genetic Algorithm and Nelder-Mead simplex search; comprehensive information about the suggested techniques is provided in Section 3; and the performance and result analysis of the proposed algorithm is offered in Section 4. Information about parameter estimation and the Weibull distribution is shown in Section 5, information regarding estimation techniques is presented in Section 6, and a simulation test and result regarding an estimation approach is shown in Section 7. Two real-world Wind speed data sets are provided as examples in Section 8 to show how effective the suggested technique is. Section 9 finally has some concluding observations.\n\n\n2. Overview of GA, and NM\n\nA brief overview of GA, and NM have been described below.\n\nGA is an approach to heuristic search. The ideas of the biological evolution of species serve as its inspiration. In contrast to traditional optimization methods, GA6,7 starts with a collection of starting solutions known as chromosomes.\n\nGenetic algorithms (GAs) work by continually improving solutions based on their fitness, which measures how well they solve a problem. Unlike some traditional methods, GAs don’t assume anything about the problem, like whether it’s smooth or has just one best solution. Instead, they explore different possibilities to find good solutions, even in complex situations where there might be many equally good answers. GAs have been used successfully in many difficult optimization problems. They often work better than traditional methods, especially when there are multiple equally good solutions. This flexibility and ability to handle complex situations make GAs a valuable tool for solving optimization problems in various fields.\n\nFollowing is a summary of the GA stages in this study:\n\nI. Initialization:\n\n• First, create a vector of real values for each variable between predefined ranges. This vector will represent the initial population of individuals.\n\nII. Evaluation:\n\n• Evaluate the fitness of each individual using an objective function.\n\nIII. Selection:\n\n• Select individuals from the population to create a mating pool based on their fitness values.\n\nIV. Crossover (Recombination):\n\n• Pair selected individuals and perform crossover to create offspring by blending or combining their real values.\n\nV. Mutation:\n\n• Introduce random changes to the real values of offspring to promote exploration of the search space.\n\nVI. Combining Populations:\n\n• Combine the offspring generated from crossover and mutation with the initial population.\n\nVII. Sorting:\n\n• The combined population is sorted based on their fitness levels, with the most fit people having the lowest fitness values.\n\nVIII. Elitism:\n\n• Keep only the top half of the sorted population, discarding the bottom half. This ensures that the best-performing individuals from the previous generation are preserved for next generation.\n\nIX. Termination:\n\n• Steps 2 through 8 should be repeated for the designated number of generations or until a termination criterion—such as achieving a maximum number of iterations or reaching a certain fitness level is satisfied.\n\nThis approach with elitism helps maintain diversity in the population while ensuring that the best individuals are preserved across generations, ultimately leading to the discovery of better solutions in the optimization process. Real-coded genetic algorithms are suitable for optimization problems with continuous decision variables and offer advantages such as direct representation of real-valued solutions, robustness, and ability to handle high-dimensional search spaces.\n\nThe simplex search technique addresses basic unconstrained minimization cases like Olsson & Nelson,8 nonlinear least squares, nonlinear simultaneous equations, and function minimization. Spendley, Hext, and Himsworth9 initially suggested the simplex search technique, which was later improved upon by Nelder and Mead.10\n\nThe steps of the Nelder-Mead10,11 algorithm are summarized in as follows:\n\nI. Initialization:\n\n• A simplex is a collection of n + 1 vertices in a n dimensional space. These vertices can be deliberately selected or created at random.\n\n• At every simplex vertex, evaluate the objective of the function.\n\nII. Ordering:\n\n• Order the vertices based on their corresponding function values.\n\n• Let x1, x2, …, xn+1 denote the vertices such that f (x1) ≤ f (x2) ≤ … ≤ f (xn+1).\n\nIII. Centroid:\n\n• Calculate the centroid of each vertex, except the worst (highest) one:\n\nIV. Reflection:\n\n• Reflect the worst vertex (highest) through the centroid to obtain a trial point\n\nwhere α is a reflection coefficient, typically set to 1\n\n• Evaluate the objective function at xr.\n\nV. Expansion:\n\n• Expanding further should be considered if the reflected point xeis superior to the second-worst vertex:\n\nwhere γ is an expansion coefficient, usually γ>1\n\n• Evaluate the objective function at xe.\n\nVI. Contraction:\n\n• Contraction should be done if the reflected point xris worse than the worst vertex:\n\n– Outside contraction: xc=xcentroid+ρ(xr−xcentroid)\n\n– Inside contraction: xc=xcentroid+ρ(xr−xcentroid)\n\nwhere ρ is a contraction coefficient, typically 0 < ρ <1 (typically 0.5).\n\n• Evaluate the objective function at xc.\n\nVII. Update simplex:\n\n• Replace the worst vertex with the new trial point if it improves the function value.\n\nVIII. Termination:\n\n• Till a termination criterion such as a maximum number of iterations, a small modification in step size, or a slight modification in the function value is satisfied, repeat the steps described above.\n\nThe algorithm converges when the simplex becomes sufficiently small or when the function values at the vertices are close to each other. The choice of parameters α, γ, and ρ can significantly affect the performance of the algorithm and may need to be tuned based on the problem characteristics.\n\n\n3. Methods\n\nThe combination of Genetic Algorithms (GA) with the Nelder-Mead simplex algorithm (NM) is driven by their supportive characteristics in both global exploration and local exploitation. GA is a population-based technique that effectively explores diverse sections of the search space, although fine-tuning solutions at local optima may provide issues. In contrast, it requires greater capacity for worldwide investigation. Combining both methods intends to take advantage of the characteristics of both algorithms, resulting in a more balanced and efficient optimization process. This hybridization method has the potential to improve convergence rates, solution quality, and robustness, making it a compelling choice for handling complicated optimization problems across several domains.\n\nThe suggested algorithm’s (GANMA) stages are summed up as follows:\n\nI. Initialization:\n\n• Generate an initial population of solutions for the GA.\n\nII. Evaluation:\n\n• Analyze each solution’s objective function within the population.\n\nIII. Genetic Algorithm (GA) Cycle:\n\n• Selection: Select a parent from the current population. Selection techniques that are often used include rank-based, roulette wheel, and tournament selection.\n\n• Crossover: Perform crossover to create offspring solutions. Since this is a real coded GA, a common method is the arithmetic crossover or simulated binary crossover.\n\n• Mutation: Apply mutation operators to the offspring solutions. Here is where the Nelder-Mead simplex algorithm comes into play. After mutation, the simplex is formed around the mutated solutions.\n\n• Elitism: Combine the initial population and offspring after mutation, then calculate the mean combination. Sort the combined population according to their fitness and keep the first half population while rejecting the other half.\n\n• Replacement: Replace the initial population with the best half from the previous step.\n\nIV. Nelder-Mead Simplex Algorithm:\n\n• Define the simplex for the NM algorithm. This can be done by selecting a set of initial points around the best solution found by the GA so far.\n\n• Reflection: Take the centroid of the remaining points and reflect the worst point of the simplex.\n\n• Expansion: Attempt to extend the simplex in that direction if the reflected point is superior to the second-worst but not superior to the greatest.\n\n• Contraction: If neither reflection nor expansion produces a better point, contract the simplex towards the best point.\n\n• Update the simplex based on the chosen operation (reflection, expansion, contraction, or shrinkage).\n\n• Repeat the above steps until convergence criteria are met.\n\nV. Termination:\n\n• Repeat the GA cycle and NM algorithm until a termination criterion is satisfied. This could be a maximum number of iterations, reaching a specific fitness threshold, or convergence of the simplex.\n\nVI. Output:\n\n• The best solution found after the termination criterion is met.\n\n• Apply the Nelder-Mead simplex algorithm to the best solution.\n\nVII. Optimal:\n\n• The best solution found after the NM algorithm.\n\nBy combining GA with NM in this way, you leverage the global exploration capability of the GA with the local refinement ability of the NM algorithm, potentially leading to improved convergence and robustness in optimization tasks.\n\nThe pseudo-code for the hybridization of the GA and Nelder-Mead simplex algorithm is presented in Algorithm.12\n\n1: Initialize GA parameters (size of population, rate of mutation, rate of crossover, number of generations)\n\n2: Initial population\n\n3: while termination condition is not met do\n\n4: Evaluate each individual’s current level of fitness\n\n5: Select parents (using tournament selection) for crossover\n\n6: for each pair of parents do\n\n7: Apply one-point crossover\n\n8: Apply uniform mutation\n\n9: end for\n\n10: Combine initial population with offspring\n\n11: Evaluate the fitness of the combined population\n\n12: Sort the combined population by fitness\n\n13: Keep the top half of the sorted population\n\n14: Create a simplex from the best individuals (e.g., top 2)\n\n15: Perform Nelder-Mead steps on the simplex:\n\n16: - Reflection\n\n17: - Expansion\n\n18: - Contraction\n\n19: - Shrink\n\n20: Update the simplex\n\n21: Replace the worst individuals with the simplex’s best individuals\n\n22: Evaluate the fitness of the updated population\n\n23: end while\n\n24: From the final population, choose the best solution\n\n25: Perform Nelder-Mead steps on the best solution\n\n26: Find the optimal solution\n\n\n4. The performance of GANMA\n\nThis study analyzes 15 benchmark test functions for simulation tests to fully investigate the feasibility as well as the effectiveness of GANMA. Windows is used as the experimental environment, while Python 3.11 is used as the programming environment. The 15 benchmark test functions (denoted as f1 to f15), cover different types. The unimodal functions f1 through f4 are included in the first kind. Multimodal functions f5 through f9 are included in the second category. Shifted unimodal and multimodal functions, f10 - f15, are included in the third category. Table 1 displays the expressions, ranges, and global minimum values of the 15 test functions. The function’s dimensions (n) are 10, 20, and 30, in that order. The GANMA method was compared to two well-known algorithms, the GA and NM algorithms. To ensure fair and reliable test results, the population size is uniformly set to 100, the number of iterations is set to 300, 400, and 600 for n = 10, 20, and 30, respectively, and the three algorithms are run 30 times independently for each of the three dimensions. The probability of crossover and mutation are (Pc = 0.8) and (Pm = 0.05) respectively, γ = 1.5, β = 0.5, and η = 0.5 have been chosen as the hybrid algorithm’s parameter values. The NM algorithm has a step size of 1.0 and a termination threshold of 1E-5.\n\nTable 2 demonstrates how the performance of the GANMA, GA, and NM algorithms for dimensions (n) 10, 20, and 30 have been evaluated by comparing the mean value (Mean), standard deviation (Std), and best value (Best) of the final solutions for each benchmark function throughout 30 trials. The algorithm achieves the best optimization performance with the least standard deviation, optimal value, and average value closer to the theoretical ideal value. Any value less than 10−6 in terms of mean, standard deviation, and best value will be regarded as zero. The ideal experimental outcomes are truncated.\n\nThe statistical results of GANMA’s performance on 15 benchmark functions with dimensions (n) of 10, 20, and 30 are shown in Table 2. It also contains the final solutions’ best (Best), mean (Mean), and standard deviation (Std) across a 30-run period for each benchmark function. All benchmark functions for unimodal functions (f1 - f4) have been solved in all three dimensions (10, 20, and 30). For the multimodal functions (f5 – f9), the solutions for f5 and f9 occur in 10, 20, and 30 dimensions, whereas the solutions for f6 and f7 in 10 and 20 dimensions are almost optimal. The standard deviation range is 1.62E − 13 ∼ 7.89E + 00, 1.45E − 11 ∼ 1.57E + 01, and 1.29E − 11 ∼ 2.95E + 01, respectively, while the mean value’s variations range in the 10, 20, and 30 dimensions is 3.18E − 13 ∼ 1.46E − 01, 1.11E − 11 ∼ 2.52E − 01, and 4.39E − 11 ∼ 2.84E + 00.\n\nSix shifted test functions have been chosen for this study to validate the performance of GANMA: three shifted multimodal test functions, denoted as f13 to f15; and three shifted unimodal test functions, denoted as f10 to f12, Sphere, Elliptic, and Rosenbrock. On functions f10, f11, f12 (in 10, 20, and 30), and f15 (in 10), GANMA achieved optimum solutions; on functions f13 (in 10) and f14 (in 10, 20, and 30), the solutions are nearly optimal. Even while GA is outperformed by the solutions of f13 and f15 (in 20 and 30) in GANMA, the solutions are still far from the optimal ones. Furthermore, the Std that GANMA found on five test functions is not too high, suggesting that GANMA’s performance on shifted test functions is steady.\n\nTherefore, for all unimodal functions (in 10, 20, and 30 dimensions), GANMA can obtain the global optimum. GANMA can identify outcomes with negligible deviations from the global optimal value for multimodal functions. Except for f5 and f9 in dimensions 10, 20, and 30, the results of f6, and f7 in dimensions 10 and 20 are quite near to the optimal value. The outcomes produced by GANMA algorithms for shifted unimodal and multimodal functions are optimal or extremely near-optimal in all functions for all three dimensions, except f13 and f15 (in 20 and 30). The benefits of the GANMA algorithm include excellent robustness, high convergence accuracy, and steady performance in all scenarios, whether they involve multimodal functions, unimodal functions, or shifting unimodal and multimodal functions. This is shown in Table 2 under the various numbers of iterations for the corresponding dimensions, which are 300, 400, and 600 for the dimensions 10, 20, and 30, respectively.\n\nTo help further investigate the evolutionary behavior of various methods, the convergence curves of GANMA and GA for a few chosen benchmark functions are displayed in Figure 2, Figure 3, and Figure 4 for dimensions (n) = 10, 20, and 30, respectively. These graphs demonstrate the convergence behavior of methods that can help to analyze the evolutionary behavior of various algorithms. The y- and x-axes, respectively, represent the values of the fitness function and the number of iterations. The blue solid line shows the genetic algorithm (GA), while the suggested method GANMA is shown by the solid orange line.\n\nUntil the ideal solution is discovered, GA shows a decreasing trend for unimodal functions like f1, f2, f3, and f4. In contrast, GANMA presents a straight line for all three dimensions (n = 10, 20, and 30). Similar to this, for multimodal functions other than f5 and f7 (in 30), there is a greater similarity between the global optimum solution and the GANMA optimal solution in f5, f7 (in 10, and 20), and f6, f8 (in 10, 20, and 30). As a result, of these two algorithms, the lowest optimum solution and the fastest rate of convergence are found through GANMA. The curves for shifted functions, except f15 (in 20 and 30), demonstrate how well the proposed method was able to obtain the ideal solution for other functions like f10, f11, and f12 (in 10, 20, and 30). Out of these two methods, GANMA yields the lowest optimum solution and has the fastest convergence rate than GA’s in both the multimodal and shifted functions.\n\nExamining the convergence curve and experimental results, it can be shown that GANMA generally performs exceptionally well on the 15 test functions, with a proportion of correct convergence to the global optimal solution that approaches 90%. When compared to GA and the NM algorithm, GANMA outperforms both in terms of exploration and exploitation. As a result, GANMA can meet the requirements for addressing diverse optimization issues, increasing its competitiveness.\n\n\n5. Application of proposed algorithm (GANMA) for Weibull-Parameter Estimation\n\nThe Weibull distribution is a probability distribution that is often used in reliability and survival research. Weibull et al.13 had shown that the Weibull distribution fit many different datasets and offered satisfactory results, even for small samples. The Weibull distribution, known for its flexibility in modeling various failure and survival scenarios, is defined by two parameters: the shape (β) and scale (η) parameters. In some cases, a location (α) parameter is added to create a three-parameter Weibull distribution, allowing for greater flexibility in fitting data with location shifts. The three-parameter probability density function (pdf) will have only two parameters14 when the location parameter (α) is equal to zero. Because no failure may occur before or after the time is zero, the two Weibull parameters are frequently utilized in failure analysis.15\n\nWeibull parameter estimation employs a variety of methods. Method of Moments (MOM), the maximum likelihood (ML) approach, and modified maximum likelihood (MML) methods were all used by Seguro and Lambert.16 They discovered that the time series data sets are more suited for the ML approach. They advised utilizing the MML technique for data sets that were formatted as frequency distributions. The least squares approach, the ML method, and the MML method were contrasted by Akgül et al.17 ML was shown to be the most effective approach overall, but they also noted that MML and ML are equally effective for big data sets, despite MML’s lower computational complexity. The ML technique was used in the studies of Kollu et al.18 and Akpnar and Akpnar19 to estimate the Weibull parameters. Teimouri et al.20 investigated the MoM using their proposed L-moment estimator, the ML approach, the logarithmic moment method, and the percentile method. They discovered that the ML method and their suggested approach are the most effective estimators. The power density approach was proposed by Akdağ and Dinler.12 They concluded that it outperformed popular techniques like MoM and ML techniques. After evaluating five different methods for approximating the Weibull distribution, Saleh et al.21 recommended the mean wind speed methodology and the ML method. Azad and colleagues22 discovered that the MoM and ML techniques were more effective than other approaches.\n\nConsidering the Weibull distribution has a nonlinear log-likelihood function and is compatible with numerical optimization techniques like Newton-Raphson (NR) and Nelder-Mead (NM), previous studies have often used MLE approaches for parameterizing the Weibull distribution. However, the effectiveness of these iterative methods heavily relies on the initial value chosen. In a departure from traditional approaches, this study employs Genetic Algorithms (GAs) as a heuristic search method, considering a set of solutions within the search space rather than individual points, to address the initial value problem in Weibull parameter Maximum Likelihood estimation.23,24 GAs have been successfully applied in various optimization contexts, ranging from optimizing mixing parameters for high-performance concrete to signal control optimization. Parameterization of distributions such as the skew-normal distribution,25 nonlinear regression,26 and negative binomial gamma mixed distribution27 have all been applied previously. Notably, Thomas et al.28 pioneered the use of GA for Weibull distribution parameter estimation in the context of break-down periods of insulating fluid data, achieving performance comparable to traditional methods based on maximizing the log-likelihood function.\n\nA versatile continuous probability distribution, the Weibull distribution is frequently used in survival analysis and reliability engineering. It is characterized by its ability to model the distribution of time until an event occurs. Named after Wallodi Weibull, who described it in the 1950s, the distribution is flexible and can take different shapes depending on its parameters. The shape parameter affects the structure of the Weibull distribution curve resulting in whether the distribution appears to be a Rayleigh distribution (β = 2), an exponential distribution (β = 1), or another shape. The scale parameter determines the distribution’s scale or size. Together, these factors enable the Weibull distribution to simulate a wide range of events with varying shapes and sizes.\n\nThe following is the Weibull two-parameter distribution’s probability density function (PDF):\n\n• x is the random variable,\n\n• β is the shape parameter,\n\n• ηis the scale parameter.\n\nThe following represents the Weibull distribution’s cumulative distribution function (or CDF):\n\nProbability density and cumulative distribution plots for some different parameter values are given in Figure 1.\n\nTwo-Parameter Weibull is Commonly applied in reliability engineering for modeling time until the failure of components. Whereas, Three-Parameter Weibull is Useful when considering scenarios where the event initiation may not be at zero, such as analyzing the time until an event occurs after a certain threshold.\n\n\n6. Methods for estimating parameters\n\nEstimating the parameters of the Weibull distribution poses a significant challenge due to the intricacies involved in utilizing sample data for accurate estimation. Parameter estimation involves the process of determining the distribution’s parameters using available sample data, aiming to derive optimal values that provide meaningful insights into the underlying data. Making incorrect parameter choices can lead to misleading results, underscoring the importance of analyzing and selecting appropriate estimation techniques for accurate modeling. Therefore, a thorough evaluation of estimation methods is essential to determine the most suitable approach for a given dataset and analysis context.\n\nThe statistical method known as Maximum Likelihood Estimation (MLE) is used to estimate Weibull parameters by maximizing the likelihood function, which determines how well the distribution fits the observed data. MLE is known for its efficiency, but its optimization can be complex due to non-linear equations and numerical stability issues. The PDF of the Weibull distribution is given by Equation (1). Given a sample x1, x2, … xn from a Weibull distribution, the likelihood function is given by:\n\nThe Weibull distribution’s log-likelihood function is as follows:\n\nThe log-likelihood function is differentiated with respect to β and η, the derivatives are set to zero, and the resultant system of equations is solved to get the MLE.\n\nBy eliminating α from the above equations and simplifying the equations we get,\n\nEqn. (8) may be used to calculate the estimate η̂. However, because of Eqn. (9) did not give an analytical solution, the estimate β̂ must be calculated numerically. This is possible by using the optimization strategy. The Nelder-Mead, Newton Rapson, simulated annealing, or GA algorithms can all be used to solve the nonlinear function that the ML estimator of the shape parameter β contains. In this study, the suggested method, GA, and NM were all used to optimize the log-likelihood function. Nelder-Mead is a powerful algorithm that converges quickly, but its performance is dependent on the initial guess. As a result, we took into account the GA while maximizing the Weibull distribution’s loglikelihood function. Eqn. (5) is considered a fitness function for GA and NM methods.\n\nBelow the proposed method on MLE of Weibull Distribution has been described briefly.\n\n6.1.1 Proposed method\n\n(Genetic and Nelder -Mead Algorithm (GANMA))\n\nTo improve the precision and reliability of parameter estimation, we proposed a hybrid approach GANMA that integrates the GA and the NM method with MLE for two-parameter Weibull distributions. The GA aids in exploring the parameter space globally, generating diverse candidate solutions, while the NM fine-tunes these solutions through local search, aiming for optimal parameter estimates. To the best of our knowledge, this is the first instance where the GANMA is being utilized to estimate the Weibull distribution’s parameters.\n\nThe steps of the proposed method in this study are summarized as follows:\n\nStep 1: Problem Formulation - We aim to find the MLE parameters β (shape) and η (scale) for a Weibull distribution.\n\nStep 2: Genetic Algorithm (GA) Phase -\n\n• Generate an initial population (P) of possible solutions. For the Weibull distribution, each solution indicates a collection of parameters (β, η).\n\n• Define the fitness function f(β, η) that measures the goodness of fit between the observed data and the Weibull distribution with the given parameters. A suitable fitness function could be the log-likelihood shown in Equation 5.\n\n• Select individuals within the population according to their fitness by using a selection process (tournament selection). Higher fitness levels increase the probability of selection.\n\n• Apply crossover operations (one-point crossover) to pairs of selected individuals to create new candidate solutions.\n\n• Introduce small random changes (mutations) to the parameters of some individuals to add diversity to the population.\n\nStep 3: Nelder-Mead Algorithm (NM) Phase -\n\n• Take the best individual from the final population of the GA as an initial guess for the parameters (β1, η1).\n\n• Define the log-likelihood function L(β, η) for the Weibull distribution shown in equation 5.\n\n• To minimize the log-likelihood function and improve the parameter estimations (i.e., reflection, expansion, contraction, and shrinkage), apply the Nelder-Mead method.\n\n• Repeat the iterations until convergence criteria are met (e.g., small changes in parameters or a maximum number of iterations).\n\nStep 4: Repeat the selection, crossover, and mutation steps for several generations until convergence is met (i.e. end of GA phase).\n\nStep 5: Apply the NM method to the best GA solution once again after the GA phase.\n\nStep 6: Result - The final parameters (β̂, η̂) obtained from the Nelder-Mead optimization represent the Maximum Likelihood Estimates (MLE) for the Weibull distribution.\n\n\n7. Monte Carlo simulations\n\nThe two-parameter Weibull distribution parameter estimation methods were investigated using a Monte Carlo simulation. The scale parameter was set to 1, while the other shape parameters were set to 0.5, 1, 3, and 6. The simulation has been repeated 1000 times for sample sizes of 20, 100, and 500 respectively. With a population size of 100, the GA and GANMA have corresponding crossover and mutation rates of 0.1 and 0.8. The parameters that are used to compare the goodness-of-fit of different parameter estimating methods are mean absolute error (MAE) and bias. For the parameters β (shape) and η (scale), MAE and bias are computed using the formula provided by:\n\n(For shape parameter)\n\n(For scale parameter)\n\nGreater efficiency is implied by lower absolute values of the bias and MAE. For various data sizes and shape parameters, Tables 3-5 displays the parameter estimates, bias, and MAE for each parameter estimation method. The results of the simulation demonstrate that the GANMA approach performed better than NM and GA when estimating shape and scale parameters based on MAE and bias criteria. The best results are highlighted in bold.\n\nFigures 5-7 illustrate the outcome across various shape parameters while keeping the scale parameter constant—as well as various data sizes by plotting the convergence graph of the PDF of Weibull parameters and the PDF of MLE of parameters using NM, GA, and GANMA. The solid black line depicts the PDF of parameters (β, η), whilst the usual genetic algorithm is illustrated by the solid green line, the yellow solid line shows the Weibull PDF using NM, and the suggested method GANMA is shown by the solid red line. It has been found that parameter estimation using the suggested technique converges with the original PDF as the shape parameter and data size increase. GANMA, the suggested algorithm, performs better than GA and NM in all types of situations.\n\nBased on MAE and bias criteria, the simulation results demonstrate that the GANMA technique outperformed NM and GA in the estimation of shape and scale parameters. In each simulated scenario, the GANMA technique yielded the best shape parameter efficiency in terms of bias and MAE for sample sizes of 20, 100, and 500 respectively.\n\nThroughout almost every simulated scenario, GANMA achieved the maximum efficiency in the estimate of scale parameters for sample sizes of 20, 100, and 500, based on at least one decision criterion. By analyzing MAE and bias for each simulation scenario, GANMA proved to be the most effective approach for the data size 20. For small, moderate, and high sample sizes, GANMA is a fairly effective strategy overall. Additionally shown in Figures 8-11 are the absolute values of the biases and the MAE.\n\nThe MAE values for the shape parameter β are shown in Figure 8. In every simulated scenario, GANMA outperformed NM and GA in terms of efficiency. The second-best approach is NM. An increase in sample size resulted in lower MAE values. On the other hand, MAE values increased along with an increase in the form parameter value.\n\nThe scale parameter η’s MAE values are displayed in Figure 9. For sample sizes of 20, 100, and 500, GANMA proved to be the most effective approach. When the shape parameter is set to a higher value, the MAE values drop. Likewise, as the sample size is raised, the MAE values drop.\n\nThe shape parameter β’s absolute bias value is displayed in Figure 10. The most efficient results were obtained using GANMA. NM outperformed GA on some occasions. As with MAE values, larger sample sizes resulted in lower absolute bias levels. Increasing the parameter value resulted in higher absolute bias levels.\n\nThe absolute bias for the scale parameter η is shown in Figure 11. Most of the time, GANMA outperformed other methods in terms of efficiency. The second-best approach is NM. Increasing the shape parameter and sample size leads to lower absolute bias levels.\n\n\n8. Estimation of Weibull-Parameter in Wind speed analysis\n\nThe decrease in fossil fuel supplies and their lack of reliability in meeting future energy demands have made renewable energy a hot topic for academics. Wind is one of the main sources of renewable energy, and wind speed modeling has been studied in great detail. In wind power applications, the most popular Weibull distribution is two parameters. It has been discovered that this PDF is correct for the majority of wind regimes observed in nature, is easy to use, and is adaptable. In several research, it has been noted that the wind speed data cannot be adequately represented for specific applications, including those with bimodal distributions, short time horizons, low and high wind speeds, and domains with a high frequency of nulls.12,29,30 The given equation may be used to determine the probability density function.\n\nPower density\n\nPower density in wind speed analysis refers to the amount of power that can be obtained from the wind per unit area. This statistic is critical when evaluating the feasibility and potential viability of wind energy projects since it quantifies the energy available from the wind at a given place. The power density (PD) may be easily calculated using the following equation once β and η have been established.\n\nIn this challenge, two real-world data sets have been used to examine wind-speed analysis. The very first set of data came from the seas surrounding the Maluku Islands and Sulawesi. The data under analysis were gathered by the satellite Quikscat, which measured the ocean wind 10 meters above sea level using a scatterometer. The measurement’s horizontal and vertical spatial resolution is 0.25°earth grid. The information from the January measurement point at latitude 116° and longitude 85.5° is included in the accessible data.31\n\nTarama Island and Iriomote Island, which are close to northern Taiwan, had their wind speeds recorded in the second data set. At Iriomotejima Meteorological Station, the maximum daily wind speed and direction were recorded in March 2012.32\n\nThe Kolmogorov-Smirnov (K-S) test is a nonparametric statistical test used to compare two distributions. The K-S test calculates the maximum absolute difference between the empirical cumulative distribution functions (ECDFs) of the distributions being compared, providing a test statistic (D). A p-value derived from this statistic indicates the significance of the difference, helping in goodness-of-fit testing, comparing sample distributions, and model validation without assuming any specific distribution for the data.\n\nThe statistical confirmation that the monthly data sets come from the Weibull distribution can be obtained by doing the K-S test separately for each data set. The most significant difference between the theoretical distribution, SN(x), and the observed distribution, F0(x), is the K-S test statistic.33\n\nMonthly distributions from the Weibull distribution are selected for further investigation following the K-S test (p−value≥0.05), which indicates the probability of observing a discrepancy as large as the one computed if the two distributions were the same.\n\nResults across shape and scale parameters were obtained by plotting the convergence graph between the PDF and CDF of MLE of parameters using NM, GA, and GANMA, as shown in Figures 12 and 13. The solid green line and dotted green line represent the PDF and CDF of the standard genetic algorithm, the yellow solid line, and dotted yellow line represent the Weibull PDF and CDF using NM, and the solid red line and dotted red line represent the suggested method for both the PDF and CDF, respectively. Figure 12 illustrates that the PDF and CDF for both GANMA and NM convergence are on the same line.\n\nTables 6 and 7 present the shape and scale parameters, k-s value, p-value, and power density for the first and second data sets, respectively, for all three estimation techniques. The greatest p-value and the lowest k-s statistic for both data sets are produced by the suggested approach (GANMA) out of the three estimation techniques. The Weibull distribution and the actual wind speed data seem similar, as indicated by the p-value exceeding the selected significance threshold (e.g., 0.05). In other words, the data is well-fitted by the Weibull distribution. The parameters estimated using GANMA are considered the best fit for describing the wind speed data, based on the K-S test findings. The observed wind speed data and the predicted Weibull distribution with these parameters were well recognized, as evidenced by the low K-S statistic and high p-value.\n\nThe maximum power density is demonstrated by the parameters estimated through MLE implementing NM, as shown in Table 6. This suggests that the parameters possess greater absolute performance in terms of power generation. Despite the slightly lower power density value of the parameters estimated by MLE using GANMA compared to NM, they are nevertheless selected as the best fit since they have the greatest p-value and the least k-s statistic. This suggests that for wind speed data set 1, parameters calculated by MLE using GANMA offer the best match.\n\nThe parameters that are estimated by MLE using GANMA are found to provide the best fit in Table 7, as shown by their lowest K-S statistic and highest p-value. Additionally, superior performance in terms of power generation is indicated by the higher power density value associated with these parameters.\n\n\n9. Conclusion\n\nTo improve the exploitation capabilities of GA, this study presents a unique hybridized approach called the Genetic and Nelder-Mead Algorithm (GANMA), in which NM is included. GANMA has been employed to verify the robustness and efficiency of the suggested technique on fifteen benchmark problems for three separate dimensions. Because of its high level of accuracy and stability, GANMA performs very well in improving unimodal, multimodal, and shifting unimodal/multi-modal functions, as shown by the test function comparison experiment table. According to the testing results, the suggested method is strong and has the potential to solve benchmark issues more quickly than the other two algorithms in the majority of situations.\n\nFurthermore, estimating the Weibull distribution’s scale (η) and shape (β) parameters, this study aims to assess the efficacy of three estimation methods: ML estimators employing GA, NM, and GANMA. The MAE and bias criteria are used to assess the efficiency of the parameter estimating techniques. Based on the conclusions drawn from the Monte Carlo simulation and the examination of real-world wind speed data, the ML estimator using GANMA performs better in Weibull parameter estimation than the ML estimator using NM and GA estimator. We used the K-S test to compare three sets of parameters for two fitting wind speed data sets with a Weibull distribution and selected the set of parameters that minimized the K-S statistic and maximized the associated p-value, indicating the best fit. Moreover, it may be said that the two sets of data were collected in two different geographic locations with different meteorological conditions. In these data sets, which included a variety of meteorological situations, GANMA demonstrated superiority.\n\n\nCompliance with ethical standards\n\nWe certify that the submitted manuscript is our original work that is not currently being considered elsewhere. The paper is an unfunded independent piece of labor.\n\nThis article does not include any research that any of the authors conducted using humans or animals.", "appendix": "Data availability\n\nAll data supporting the findings of this study, including figures and tables, have been deposited in the given link; https://doi.org/10.5281/zenodo.13309711 34\n\nThe files are as follows:\n\n[Data Sets] data has been obtained from a third party for two real-life problems, which are available at data sets.docx\n\nThe extended data files are available in Zenodo at the following DOI: [https://doi.org/10.5281/zenodo.13309711.v3] 34\n\n[Algorithm] The algorithm described in the manuscript available at algorithm.docx\n\nThe files included: raw data of functions.docx and raw data of functions(generation wise).docx Contains data analysis that supports the study but are not included in the main manuscript.\n\n[Tables] This file contains all the tables referenced in the manuscript. tables.docx\n\n[Figures] This file contains all the figures referenced in the manuscript, including detailed captions. figures.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\nMastorakis NE: On the solution of ill-conditioned systems of linear and non-linear equations via genetic algorithms (gas) and nelder-mead simplex search nikos e. mastorakis. WSEAS Trans. Inf. Sci. Appl. 2005; 2(5): 460–466.\n\nDurand N, Alliot J-M: A combined nelder-mead simplex and genetic algorithm. HAL. 1999; 1999.\n\nRenders J-M, Flasse SP: Hybrid methods using genetic algorithms for global optimization. IEEE Trans. Syst. Man Cybern. B Cybern. 1996; 26(2): 243–258. Publisher Full Text\n\nFan S-KS, Liang Y-C, Zahara E: A genetic algorithm and a particle swarm optimizer hybridized with nelder–mead simplex search. Comput. Ind. Eng. 2006; 50(4): 401–425. Publisher Full Text\n\nHwang S-F, He R-S: A hybrid real-parameter genetic algorithm for function optimization. Adv. Eng. Inform. 2006; 20(1): 7–21. Publisher Full Text\n\nBeasley D: An overview of genetic algorithms. University Computing. 1993; 15: 170–181.\n\nHolland JH: Adaptation in natural and artificial systems. Ann Arbor: univ. of mich. press; 1975; vol. 7. ; 390–401.\n\nOlsson DM, Nelson LS: The Nelder-mead simplex procedure for function minimization. Technometrics. 1975; 17(1): 45–51. 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Publisher Full Text\n\nYalçınkaya A, Şenoğlu B, Yolcu U: Maximum likelihood estimation for the parameters of skew-normal distribution using genetic algorithm. Swarm Evol. Comput. 2018; 38: 127–138. Publisher Full Text\n\nAltunkaynak B, Alptekin ESİN: The genetic algorithm method for parameter estimation in nonlinear regression. Gazi Univ. J. Sci. 2004; 17(2): 43–51.\n\nGençtürk Y, Yiğiter A: Modelling claim number using a new mixture model: negative binomial gamma distribution. J. Stat. Comput. Simul. 2016; 86(10): 1829–1839. Publisher Full Text\n\nThomas GM, Gerth R, Velasco T, et al.: Using real-coded genetic algorithms for weibull parameter estimation. Comput. Ind. Eng. 1995; 29(1-4): 377–381. Publisher Full Text\n\nKusiak A, Zheng H, Song Z: On-line monitoring of power curves. Renew. Energy. 2009; 34(6): 1487–1493. Publisher Full Text\n\nMorgan EC, Lackner M, Vogel RM, et al.: Probability distributions for offshore wind speeds. Energy Convers. Manag. 2011; 52(1): 15–26. Publisher Full Text\n\nMahmuddin F: Analysis of wind energy potential with a mobile floating structure around sulawesi and maluku islands of indonesia. International Conference on Offshore Mechanics and Arctic Engineering. American Society of Mechanical Engineers; 2015; volume 56574. : p. V009T09A064.\n\nKomatsu T, Mizuno S, Natheer A, et al.: Unusual distribution of floating seaweeds in the east china sea in the early spring of 2012. J. Appl. Phycol. 2014; 26: 1169–1179. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMassey FJ Jr: The kolmogorov-smirnov test for goodness of fit. J. Am. Stat. Assoc. 1951; 46(253): 68–78. Publisher Full Text\n\nMishra R, Majhi N: Python code and raw data for our proposed algorithm (GANMA).2024. Publisher Full Text" }	[ { "id": "329147", "date": "28 Oct 2024", "name": "HABBI FATIHA", "expertise": [ "Reviewer Expertise Optimization methods", "meta-heuristics", "identification", "induction machine", "synchrounous generator", "Automatic Voltage Regulation", "Photovoltaic systems" ], "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 aims to present a novel hybrid GA and NMA. It should make a contribution to enhance the exploitation capabilities of GA by using NMA. To highlight the performance of GANMA, it is tested across various benchmark functions and parameter estimation tasks. There are a number of issues with the methods and analysis that need to be clarified. The comments for authors are listed below 1- The authors should firstly focus on the necessity to hybrid the GA with NMA. This is followed by highlighting the problem that is still not covered by other researchers. 2- In the overview section, the authors mention that: GA is an approach to heuristic search. So, what is the difference between metaheuristic optimization method and heuristic search approach? 3- In Nelder–Mead Simplex Search Method section, the equations must be numbered. There is a sign error in one of the contraction equations of NMA. Equations 5 and 7 must be verified 4-The justification of using NMA in this paper is not clear. What is the merit of using NMA, while there are thousands of optimization algorithms? 5-The theoretical explanation on why the NMA tends to provide local solution, is not clearly explained. Please show a detail explanation on the demerit of the NMA. The author may support with some preliminary experiments 6-The authors define the simplex for the NM algorithm by selecting a set of initial points around the best solution found by the GA so far in the suggested algorithm’s (GANMA). Please show a detail explanation on the initial conditions choice of NMA 7-The authors must clarify what makes after mutation; just the mutated solutions are affected by NM algorithm. Or, the NM algorithm is applied to only the best solution after reproduction and when the end of the main loop is met. 8- When checking the Table 2, it shows less performance of GANMA for f8 in three dimensions (-1.97E+01 (Best solution for n=10), -3.94E+01(Best solution for n=20), -9.86E+01(Best solution for n=30)). Please comment on these numbers. Therefore, the authors must clarify what makes the proposed method superior. 9- In conclusion, the authors mention that: To improve the exploitation capabilities of GA, this study presents a unique hybridized approach called the GANMA, in which NM is included. Please explain the point of a unique hybridized approach 10- The literature for the Weibull-parameter estimation methods is too old. The authors are required to use the most recent ones. Additionally, please put recent optimization algorithms Ref 1 Ref 2 Ref 3 Ref 4 Ref 5\nThe comments of co-reviewer This paper is an interesting study about parameter estimation using a hybrid genetic algorithm and Nelder Mead approach. Below, I give some major comments for improving it: 1. The authors need to mind the proper use of abbreviations and switching between them and their original terminologies. 2. Added reference to formulas. 3. An flowchart for proposed GANMA may be given by the authors in the paper for better understanding of the readers. 4. What is the role of benchmark function for an optimization technique? 5. In Table 2 on page 10 (f8 function), the GA gives best results than the GANMA in 10, 20 and 30 dimensions. Please comment on these numbers. 6. In page 7 (fourth section), the chosen reflected value α is not given in the paper. Also, the reason for the selected values of: γ=1.5, β=0.5 and η=0.5must be listed. Why didn’t you use the standard NMA values (α=1, β=2 and γ= η=0.5). In addition, these values (α, β,γ and η) are the same values used for Weibull-Parameter Estimation. 7. In Figures 3 (f15), 4 (f5, f15) why there is a zigzag in the fitness graph. 7. In order to check the performance of the proposed GANMA, it is suggested to compare the proposed GANMA with another way of hybridization, which is explained below. - Apply the GA to locate the interval, which likely contains the global minimum. - Then, switch to the NMA assuming the final solution of the GA as a starting solution for NMA. 8. The literature for the Weibull-parameter estimation methods seems too old. Please put the recent optimization algorithms.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "343361", "date": "06 Dec 2024", "name": "Olympia Roeva", "expertise": [ "Reviewer Expertise metaheuristic algorithms for mathematical modelling and optimization" ], "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\nIs the work clearly and accurately presented and does it cite the current literature?No. The paper structure should be reconsidered. First, all used/known methods and knowledge used in the research should be presented and then the proposed new techniques, the new results obtained – only results and experiments made by the authors. The presented results should be discussed and compared with similar published results.\nThe references are not up to date. Recent titles should be added. 1/3 of the references are related to Weibull-Parameter Estimation and at the same time there is no deep analysis of the hybrids based on GA – their advantages and disadvantages, the existing gaps, and the role of the proposed hybrid in the current state of the art. The figures should appear after their introduction in the text. Figure 1 is mentioned on page 19, but appears on page 12.\nIs the study design appropriate and does the work have academic merit?\nYes.\nAre sufficient details of methods and analysis provided to allow replication by others?\nNo. For example, the applied GA selection operator is not given. The GA parameter, ggap, is not given. The fitness function is unknown.\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes.\nAre all the source data underlying the results available to ensure full reproducibility?\nYes.\nAre the conclusions drawn adequately supported by the results?\nYes.\nI have a few questions:\nWhy reference 12 is cited in the sentence “The pseudo-code for the hybridization of the GA and Nelder-Mead simplex algorithm is presented in Algorithm.12”? The NM algorithm works with a single solution and GA works with a population of the solutions. How is it performed the following step in pseudo-code 21: “Replace the worst individuals with the simplex’s best individuals”? The NM algorithm returns/gives only one solution, so only one worst individual can be replaced. How the GA and NM algorithm parameters are set? Are these parameters optimal?\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-1073
https://f1000research.com/articles/13-1072/v1	19 Sep 24	{ "type": "Study Protocol", "title": "Protocol for a pilot clinical trial of the senolytic drug combination Dasatinib Plus Quercetin to mitigate age-related health and cognitive decline in mental disorders", "authors": [ "Abigail Schweiger", "Breno Diniz", "Ginger Nicol", "Julie Schweiger", "Andes E. Dasklakis-Perez", "Eric J Lenze", "Abigail Schweiger", "Ginger Nicol", "Julie Schweiger", "Andes E. Dasklakis-Perez" ], "abstract": "Background Major depressive disorder (MDD) and schizophrenia are linked to accelerated aging leading to reduced lifespan, health span and cognitive decline. Cellular senescence, in which cells lose proliferative capacity and develop a senescence-associated secretory phenotype (SASP), plays a role in this process. Emerging research suggests that the senolytic regimen of dasatinib+quercetin (D+Q) reduces senescent cells, potentially mitigating age-related health and cognitive decline. This pilot study aims to assess the feasibility and safety of D+Q in older adults with schizophrenia, schizoaffective disorder, and treatment-resistant depression (TRD).\n\nMethods This single-center study will recruit 30 participants total aged 50 years or older with schizophrenia/schizoaffective disorder or 60 years or older with TRD; the difference in age limits is because individuals with schizophrenia are biologically about 10 years older than general population owing to metabolic burden. Each participant will receive two consecutive days of 100 mg oral dasatinib plus 1250 mg oral quercetin at baseline and weeks one through three, (i.e., two days on, five days off) along with lifestyle risk management education. Questionnaires and assessments will measure health and cognitive function as well as psychiatric function at baseline, week 10, and one year. Magnetic Resonance Imaging (MRI) will measure structural and functional brain health at baseline and 10 weeks. Blood sampling for SASP testing will occur at seven time points: baseline, weeks one through four, week 10, and one year.\n\nConclusion This pilot aims to evaluate the safety and feasibility of the senolytic regimen and D+Q’s potential to counteract accelerated aging in adults with schizophrenia/schizoaffective disorder and TRD.\n\nTrial registration Dasatinib Plus Quercetin for Accelerated Aging in Mental Disorders is registered on ClinicalTrials.gov: NCT05838560; posted May 1, 2023.", "keywords": [ "Aging", "cognitive decline", "schizophrenia", "depressive disorder", "major", "cellular senescence", "geriatrics" ], "content": "Introduction\n\nAccelerated biological aging has been proposed as a general pathological mechanism with similarities across mental and physical disorders, necessitating a “convergence” approach to precision medicine that leverages links between physical and mental health. This approach requires new scientific methods that span individual medical conditions with potential overlapping etiologies. Patients with SMDs die younger than non-mentally ill individuals due to earlier onset of cardiometabolic risk conditions like obesity and diabetes, disorders of immune functioning and neurocognitive decline. While mortality in persons with mental disorders is often tied to poverty and associated environmental toxicity that disproportionately effect people with SMDs, the 15-20-year mortality gap is not fully explained by lifestyle and socioeconomic factors alone. Thus, biological aging as a treatment target is particularly relevant in disorders like depression and schizophrenia, which are prevalent and cause significant disability worldwide.\n\nIndividuals with schizophrenia experience a greatly reduced lifespan and health span, primarily due to earlier onset of conditions commonly associated with aging, such as diabetes, heart disease, and cognitive decline.1 The causes of cellular aging in schizophrenia are most certainly multifactorial, but in particular, biological risk for the condition itself has been associated with aggressive forms of insulin resistance, for example, which has been proposed as a potential target for new treatments. In Major Depressive Disorder, a subset of individuals – particularly those with TRD, defined as having at least two adequate failed antidepressant trials – exhibit a cellular SASP that can be measured via a simple proteomic test performed on peripheral blood.2 People with depression and a high SASP index value have greater age-related medical comorbidities,3 and their depression is more treatment-resistant.4 These findings coincide with increasing evidence that older adults with TRD are more likely to exhibit signs of accelerated cognitive decline and multiple age-related medical comorbidities.5–7\n\nThe field of geroscience has proposed that biological aging, underlying age-related mortality and illnesses (such as dementia), is due to a discrete number of aging pathways that are targets for intervention. Of these, cellular senescence has arisen as a key focus for novel interventions (both pharmacological and lifestyle). Cellular senescence is one of the hallmarks of biological aging8 and is characterized by a state of irreversible cell cycle arrest, loss of proliferative capacity,9 resistance to apoptosis, and a shift in the cellular secretory profile, named as the SASP.3,10 The SASP is a set of signaling proteins and other biomarkers (e.g., microRNAs, extracellular vesicles) pivotal in governing cellular pathways involved in immune-inflammatory responses, cell cycle control, intercellular communication, and tissue remodeling.11,12 The SASP is very heterogeneous and probably dependent on the cell type and senescence stimuli. However, prior studies have suggested that few markers are commonly secreted from most senescent cells, such as the interleukin (IL)-6, IL-8, intercellular adhesion molecule (ICAM), FAS-ligand, CXCL-20, MIP-3a, MIF, IGFBPs, among others. Senescent cells are typically cleared from the body by its immune system. The accumulation of senescent cells with advancing age is attributed, in part, to age-related immunological shifts compromising the efficient recognition and clearance of senescent cells. This accrual precipitates detrimental consequences as heightened SASP secretion exacerbates various age-related conditions including cardiac disease, osteoporosis, kidney disease, osteoarthritis, and cancer.8,13–17 Moreover, heightened SASP levels have been associated with prevalent aging-related syndromes such as obesity, cardiometabolic syndrome, and frailty, which are also at elevated rates in individuals with mental disorders.18 Notably, the ramifications of cellular senescence and elevated SASP extend to the brain, evidenced by the senescent phenotype exhibited by aged microglia, astrocytes, and neurons in Alzheimer disease affected brains.19–21\n\nThe SASP proteins reflect interrelated biological functions; examining them as a composite index (SASP index) might provide a biomarker for assessing cellular senescence and its response to therapeutics. Our group established a peripheral SASP index comprising 22 proteins. We validated the SASP index and examined it in older adults with depression,22 finding a positive correlation between higher SASP levels and higher comorbid physical health conditions and cognitive impairment in major depression across the lifespan. Although similar studies of SASP have not been conducted in schizophrenia/schizoaffective disorder, existing studies have implicated analogous cellular pathways (e.g., inflammation, oxidative stress) in features of accelerated aging, including advanced brain age.\n\nSenotherapeutics as treatments for mental disorders – in geroscience and across the age-span. Senotherapeutic interventions fall into two categories: senomorphics, which reduce the SASP Index value, and senolytics, which selectively hasten the death of already senescent cells. A range of senolytic therapies currently exist, spanning behavioral lifestyle interventions (e.g., intermittent fasting) and drugs (e.g., metformin, rapamycin, azithromycin). SASP index levels might both identify individuals most likely to benefit from senolytics and track treatment response (i.e., as senolytics clear out senescent cells from the body, SASP score decreases).\n\nPreclinical studies have found that senolytic therapies can enhance lifespan, health span, and brain function in mice.23 Many of these studies used the combination of dasatinib (a cancer drug) and quercetin (a supplement).24 Both dasatinib and quercetin have shown senolytic effects in different tissues, and it is thought that their combination provides a synergistic senolytic effect.25 These promising results have led to several early-phase clinical trials in various accelerated aging-related conditions, including kidney disease26 and idiopathic pulmonary fibrosis,27 as well as an ongoing study in Alzheimer disease.28 Importantly, it appears that only brief boluses (e.g., two days of dasatinib+quercetin) are necessary for this senolytic effect; in this dosage, these drugs have been safe and well tolerated in the clinical trials conducted to-date.\n\nSenolytics may be particularly relevant to these mental illnesses, given that accelerated brain aging and increased age-related comorbidities are responsible for much of the reduced lifespan and health span. Both dasatinib and quercetin have demonstrated blood-brain barrier penetrance in rodent models, and there are supportive in human studies; further, preclinical research has demonstrated the efficacy of senolytic agents for neurodegenerative disease.28\n\nIn this study, we aim to examine the effects of a combination of dasatinib plus quercetin (D+Q) – two drugs with known senolytic properties – on physiological aging parameters in older individuals with schizophrenia/schizoaffective disorder and TRD. To our knowledge, this preliminary study will be the first to test senolytic treatment within the cohort of individuals contending with mental illnesses associated with accelerated aging.\n\n\nAims\n\nAim 1: Evaluation of Safety and Feasibility of D+Q in Schizophrenia/Schizoaffective Disorder and TRD. This aims to assess the safety and feasibility of the combination of D+Q in individuals with schizophrenia/schizoaffective disorder and TRD. Specifically, we will collect data on the rates of adverse events (AEs), serious adverse events (SAEs), treatment discontinuation due to AEs, and treatment completion. Furthermore, overall recruitment numbers will be documented to determine the feasibility of the proposed treatment approach.\n\nAim 2: Examination of Changes in SASP with D+Q Treatment. This aims to evaluate the effect of the combination of D+Q on the SASP in individuals with schizophrenia/schizoaffective disorder and TRD. SASP will be assessed at baseline and weeks one through four to determine acute changes in SASP with each weekly dosing of D+Q, testing the engagement of the treatment target. SASP will also be assessed at week 10 and one year to measure persistence of the treatment effect.\n\nAim 3: Investigation of Acute and Long-term Changes in Neuropsychological Functioning, Functional Status, Brain Markers of Aging, and Clinical Symptoms of Schizophrenia/Schizoaffective Disorder and TRD. This study aims to explore the acute and long-term effects of the combination treatment of D+Q on various aspects of neuropsychological functioning, functional status, brain markers of aging, and clinical symptoms in individuals with schizophrenia/schizoaffective disorder and TRD. Measures of these domains will be assessed at baseline, the end of the acute treatment period (10 weeks for clinical/functional/neuropsychological measures), and the end of one year (all measures) to provide a comprehensive understanding of the treatment outcomes.\n\nThe focus for Aims 2 and 3 will be largely descriptive. We do not anticipate inferential testing but plan to examine effect size and 95% confidence interval for effects.\n\n\nProtocol\n\nThis single-center, open-label pilot study will be conducted locally through Washington University in St. Louis School of Medicine/Barnes-Jewish Hospital, an academic medical center located in St. Louis, Missouri. The comprehensive trial framework is depicted in Figure 1. The protocol relies on the Standard Protocol items: Recommendations for Interventional Trials (SPIRIT) guidelines.\n\nAbbreviations: TRD = treatment-resistant depression; NIH = National Institutes of Health; MRI = magnetic resonance imaging; SASP = senescence-associated secretory phenotype.\n\nOur recruitment strategy will draw from successful approaches utilized in previous clinical trials conducted in our laboratory, leveraging electronic health records (EHR) and the Volunteer for Health platform (VFH). Additional recruitment techniques may include advertisements, media, word-of-mouth/snowballing, and VFH social media. After discussion and pre-screening with the potential participant either by phone or in person, and possibly medical records review or meeting with the patient’s physician, the research team will screen for eligibility per the inclusion/exclusion criteria below. All recruitment materials will be submitted to the IRB for approval.\n\nEligibility criteria\n\nInclusion criteria will include participants (1) diagnosed with either TRD, defined as major depressive illness with current depressive symptoms despite undergoing at least two adequate trials of antidepressants in this or the previous episode, or schizophrenia/schizoaffective disorder. The rationale for criterion 1 is to ensure that participants have a well-established diagnosis resistant to standard treatments, and the requirement of treatment resistance for depression is due to the findings of elevated SASP and accelerated cognitive decline in older adults with TRD, (2) aged 50 years or older for those with schizophrenia/schizoaffective disorder and 60 years or older for those with TRD. The age criterion is set based on association of reduced health span in these conditions: individuals with schizophrenia have significant age-related pathologies beginning in their 50s or earlier, while individuals with TRD have been shown to have elevated SASP at age 60+,29,30 (3) presenting with at least three conditions commonly associated with aging which are at least moderate but not end-stage, such as hypertension, diabetes, metabolic syndrome, cardiac disease, non-asthmatic lung disease, adult-onset cancer, arthritis, and other inflammatory diseases typically seen with advancing age. This criterion of multiple aging-related conditions may enrich the sample for elevated SASP, accelerated aging, or benefits from senolytics, and (4) currently receiving an adequate dose of medication tailored for their condition, be it schizophrenia, schizoaffective disorder, or TRD; this ensures that participants are already on a therapeutic regimen, providing a stable baseline for the study.\n\nExclusion criteria will include (1) contraindications for dasatinib or quercetin, as these are the primary investigational drugs, (2) active suicidal ideation to a degree where outpatient clinical trial management is deemed unsafe; the safety of participants is paramount, and those with severe suicidal tendencies are not suitable for an outpatient setting, (3) dementia, which is both an end-stage condition and would impede the outcomes and assessments, (4) medications known to be potent CPY3A4 inhibitors or inducers, or those known to induce senescence, such as alkylating agents, anthracyclines, platins, and other chemotherapy drugs, as well as everolimus and topotecan due to their interactions with quercetin. These medications can significantly influence the primary outcomes of the study, and (5) active inflammatory, infectious, or malignant diseases, sensory deficits, recent heart attacks or strokes, severe bleeding disorders, uncontrolled hypertension or diabetes mellitus, active liver diseases, cirrhosis, and current usage of systemic steroids, quinolone antibiotics, hydroxychloroquine, or chloroquine. These conditions will either impair the ability to measure SASP or reflect end-stage conditions unlikely to benefit from senolytics.\n\nThe Washington University Institutional Review Board (IRB) on April 5, 2023 (IRB ID# 202302203) determined that the study should be designated greater than minimal risk because of the risks associated with the investigational drugs requiring written documentation of consent prior to study participation. The IRB approved a waiver of the requirement to obtain documentation of consent for the phone screen. The principal investigator will conduct and supervise all procedures to recruit participants for the protocol and obtain their verbal informed consent for the telephone prescreening and their written informed consent for all study procedures. Trained study staff will discuss the study, including the risks and benefits of participation, with potential participants and relevant members of their treatment team as needed to provide informed consent for interested individuals. Informed consent will be obtained from all participants before any study procedures are initiated. The consent form, which incorporates The Health Insurance Portability and Accountability Act (HIPAA) authorization, describes the purpose, processes, risks, strategies to minimize them, and possible benefits. Participants will be assured that participation in the study is entirely voluntary and that they are free to withdraw consent at any time and discontinue participation without prejudice to their current or future medical care. The study was approved and received a waiver of documentation of consent from the Washington University Institutional Review Board (IRB) on April 5, 2023 (IRB ID# 202302203).\n\nSenolytic treatment overview\n\nThe medication regimen for this trial involves the administration of D+Q. Participants will receive two consecutive days of dasatinib 100mg orally plus quercetin 1250mg orally at baseline and weeks one, two, and three (i.e., two days on, five days off). Thus, each person will receive a total of eight doses of each medication. The D+Q will be self-administered or administered in person. The rationale for this dosing is that brief, pulsed regimens of D+Q have been shown to significantly clear senescent cells and reduce them in the body without causing the toxicity that could be seen with a longer or continuous dosing of dasatinib.\n\nLifestyle risk management\n\nParticipants assigned to the D+Q arm will be provided with lifestyle risk management during weeks one through 10 of the trial, in a manner like that conducted in the concurrent study at Washington University.31 To ensure adherence, participants will be brought in weekly to receive their study medication and receive tailored lifestyle education, emphasizing strength, balance, and nutrition. Continuous communication with participants will be maintained to provide support, address concerns, and help navigate obstacles to engaging in the prescribed activities. The rationale for this lifestyle risk management is a necessary element to realize the benefits of D+Q; for example, senolytics may not be expected to show beneficial effects on age-related domains if the participant is highly sedentary and/or eating mainly high-sugar, pro-inflammatory foods.\n\nWe acknowledge the potential need for clinical interventions among some participants, such as optimizing psychiatric medications or intensifying psychiatric treatment. In such cases, recommendations will be made by the study team on a case-by-case basis, prioritizing participant safety. Our specialized knowledge, particularly in psychiatry, will ensure the effective execution of this plan:\n\n1. Participants receiving ongoing care from a provider (PCP, psychiatrist, therapist): We will advise these participants to continue their current care, while being available to address any inquiries regarding their ongoing management.\n\n2. Participants who report to us that they are in crisis, such as severe worsening of symptoms: We will assess the severity of the crisis and implement measures necessary to ensure their safety and proper management.\n\nWhile participant compliance with data collection at all time points is anticipated, non-completion of certain assessments will not be grounds for exclusion. Furthermore, to promote participant retention and follow-up completion, we will have inpatient as well as telephone contact with participants throughout the acute phase and until the one-year mark.\n\nNeuroimaging\n\nParticipants will undergo neuroimaging assessments at baseline and 10-week. These assessments involve a brain MRI lasting approximately one hour, administered on a Siemens 3T Prisma Scanner at Washington University. The imaging protocol will include both anatomic-related brain structures (e.g., hippocampal volume) and functional (resting state fMRI) modalities. Structural MRI will assess brain health and aging, while resting state fMRI will assess whether brain connectivity changes are seen with D+Q (providing a CNS measure of target engagement or treatment mechanism). In addition, diffusion MRI will be conducted, comprising two scans per sequence with b values of 1500 and 3000, featuring 2.0mm voxels, TR=3500ms, TE=83ms. Should any clinically meaningful abnormality arise or necessitate further medical attention, workflows have been established for sharing the MRI images and reports with the participant’s healthcare provider.\n\nSASP index\n\nParticipants will provide blood samples at seven time points: baseline, weeks one through four, week 10, and one year (for those completing D+Q regimen). Blood draws for weeks one through four will be scheduled for subsequent week post-dosing. For instance, if a participant initiates their study medication on Monday, their week one blood draw will occur the following Monday. Each subject will contribute approximately 10 ml of blood, with accompanying measurements of weight, height, and vital signs. These blood samples will undergo analysis for SASP and other yet-to-be-determined blood-based markers. SASP proteins hold promise as diagnostic markers for the accumulation of senescent cells and subsequently age-related pathologies. Reflecting interrelated biological functions, SASP proteins, when evaluated as composite biomarker index (SASP index), present a robust measure for assessing cellular senescence and therapeutic responses. While SASP expression is cell-dependent, a core set of SASP proteins is commonly expressed by senescent cells. Our research team has developed a peripheral SASP index comprised of 22 proteins. If we find changes in SASP with dosing of D+Q, this may indicate that SASP levels can be used to track response to treatment.\n\nNeuropsychological testing\n\nThe neuropsychological evaluation encompasses the NIH Toolbox Cognition Battery, supplemented by paragraph recall, alongside two psychological well-being assessments from the NIH Toolbox Emotion Battery. These assessments are slated for three specific intervals: baseline, week 10, and study endpoint. While the Cognitive Battery is specifically tailored to assess participants’ cognitive functions and memory recall capabilities, the psychological well-being assessments aim to gauge their mental health and overall well-being. The results of these assessments will serve to establish a neuropsychological baseline and subsequently monitor the participants’ cognitive functions and psychological well-being throughout the study. This approach aims to discern the intervention’s impact on the participants’ cognitive abilities and emotional wellness.\n\nBehavioral questionnaires and assessments\n\nThroughout the study duration, participants will be tasked with completing a series of questionnaires aimed at assessing their health status and mood. These assessments will be administered at baseline, week 10, and the study’s endpoint. The schedule of assessments is shown in Table 1. The subjective data from the questionnaires, along with the objective findings of the neuroimaging and biomarker analyses, will present a holistic understanding of the intervention’s impact across common mental and physical health domains.\n\n+Subset of SCID-5 will be administered to assess Bipolar and Related Disorders, Depressive Disorders, Schizophrenia and Other Psychotic Disorders.\n\nTreatment with D+Q\n\nD+Q in tandem have potential adverse effects. While prolonged daily use of dasatinib carries potential for several serious adverse effects, this study administers only eight doses intermittently, like other studies of these drugs as senolytics. Furthermore, the dose that will be used in this study is considered safe and there are no interactions between quercetin with dasatinib.32,33 From the three clinical trials that have employed intermittent D+Q dosing, only one instance of a SAE has been documented: edema and pleural effusion. However, the causal relationship between the medication and the SAE remains inconclusive. Non-SAE reported during these trials included respiratory symptoms, skin irritation and ecchymosis, as well as gastrointestinal discomfort.26,27,34 These known risks associated with this therapeutic combination are categorized as follows:\n\n• Likely: Cough, nausea, and headaches.\n\n• Less likely (1-10%): Shortness of breath, runny nose, respiratory infection, fatigue, dizziness, anxiety, sleeplessness, skin irritation, bruising, appetite changes, constipation, diarrhea, heartburn, joint pain, either dry or watery eyes, as well as mouth soreness.\n\n• Rare (<1%): Edema and pleural effusion.\n\nTo mitigate the associated risks of D+Q, the study adopts an intermittent dosing regimen, administering eight doses over a four-week period. Oversight by expert medical personnel ensures participant safety and appropriate medication management. It is pertinent to note the potential fetal toxicity linked to dasatinib.35 Despite the study’s inclusion criteria stipulating an age threshold of 50+ for the schizophrenia/schizoaffective group and 60+ for the TRD group, all participants will receive comprehensive information regarding the fetal risks associated with dasatinib. Women of child-bearing potential and their male counterparts are strongly advised to employ effective contraception measures, such as condoms, throughout the study and for 90 days following the final dose.\n\nDose adjustment\n\nIn the event a participant becomes pregnant or develops intolerable side effects during the treatment phase of the study, we will discontinue the study medication. Participants can continue with the other study assessments that are not contraindicated by pregnancy.\n\nLifestyle intervention\n\nThe content of the healthy lifestyle intervention includes weekly health coaching content with information on healthy diet and physical activity adapted from an existing intervention developed for delivery in community clinical settings.\n\nPeripheral biomarker collection\n\nWhile generally safe, peripheral biomarker collection sometimes results in discomfort or minor complications at the venipuncture site. To optimize outcomes, only qualified personnel are authorized to conduct blood draws, adhering rigorously to sterile techniques and institutional policies to ensure participant safety.\n\nNeuroimaging procedures\n\nNeuroimaging procedures, particularly MRIs and fMRI scans, carries inherent risks for participants, including potential discomfort and feelings of claustrophobia during the scan. Additionally, certain metal implants or medical devices may impede the imaging process, posing a risk to the participant. To ensure participant safety, individuals with MRI contraindications are excluded from this aspect of the study. Pre-scan screening is conducted to identify any metallic objects within the body, with their presence warranting exclusion from the imaging procedure. Participant comfort is paramount, with provisions made for pauses, rests, or opt-outs should discomfort arise. Earplugs are provided to mitigate scanner noise. In the event of significant abnormalities detected during the scan, participants will be promptly referred to their primary care physician for further evaluation and treatment.\n\nRisk-benefit assessment\n\nThe study’s significance lies in its potential to inform future research. By investigating potential treatments aimed at counteracting accelerated aging in individuals with mental illness, the study aims to bridge a critical knowledge gap regarding accelerated aging in mental illnesses. Direct clinical benefits to individual participants are not guaranteed. However, participants will undergo comprehensive assessments at the study’s initiation and regular intervals thereafter. These assessments hold the potential to reveal previously unidentified conditions, such as acute medical or psychiatric illnesses. Addressing these conditions could lead to enhanced health management strategies for participants, thereby offering avenues of care that may have otherwise remained unexplored without the study’s intervention. Low risks associated with participation juxtaposed against the potential for both scientific advancement and individual benefits suggest a favorable risk-to-benefit profile.\n\nThe overall aim of this randomized pilot and feasibility study is to determine safety, tolerability, and detection of early treatment effects in\n\n1. Safety and feasibility of D+Q: The primary aim of the study is to evaluate the safety and feasibility of D+Q in two mental illnesses associated with accelerated aging: schizophrenia/schizoaffective disorder and TRD. To achieve this, the study will collect data on rates of AEs, SAEs, treatment discontinuation due to AEs, treatment completion, and overall recruitment numbers.\n\n2. Changes in SASP with D+Q treatment: The study seeks to examine changes in the SASP consequent to D+Q administration. SASP dynamics will be examined at multiple time points to discern acute and long-term changes.\n\n3. Neuropsychological functioning, functional status, and brain markers of aging: The study will investigate acute and long-term changes in neuropsychological functioning, functional status, brain markers of aging, and clinical symptomatology across illnesses. These parameters will be assessed at baseline, the conclusion of the acute period (10 weeks) for clinical, functional, and neuropsychological measures, and at the end of one year, allowing a preliminary view of the intervention’s impact.\n\nAnalytical approach\n\nThe analysis for Aims 2 and 3 will be primarily descriptive in nature. The study does not anticipate inferential testing. Instead, the focus will be on examining the effect (in terms of changes in measures) and providing a 95% confidence interval for the observed effects.\n\nThis approach ensures that the data analysis is aligned with the study’s primary objectives and provides a comprehensive understanding of the impact of D+Q on the mental illnesses of interest. Using multiple time points for assessment ensures that immediate and long-term effects are captured, providing a holistic view of the treatment’s efficacy.\n\nThe findings from this trial will be disseminated through scientific forums, such as conferences and peer-reviewed journals. Target audience includes primary care physicians and psychiatrists. Furthermore, the main outcomes will be made publicly available through ClinicalTrials.gov, adhering to the International Committee of Medical Journal Editors’ guidelines on authorship for published articles.\n\nThe study is ongoing, and no data analysis has been performed.\n\n\nDiscussion\n\nThis study will be the first to test a senolytic strategy for mitigating accelerated aging effects in older adults with schizophrenia/schizoaffective disorder and TRD, who are at high risk for reduced lifespan, health span, and accelerated cognitive decline. Owing to its first-in-kind nature, this clinical trial takes an important first step in exploring the effects of senolytic therapy on a known biomarker of cellular senescence and clinical outcomes. However, for the same reasons, the study will be subject to important limitations. First, the study is open-label and has a small sample size; results will be preliminary, and future studies will need a control group and likely more statistical power to measure treatment effects. Moreover, in an open-label study the awareness of both participants and investigators regarding the administered treatment raises the risk of expectancy biases. Also, the participant cohort recruited for this study may not entirely represent the broader population of individuals with the targeted conditions. Another salient limitation is the duration of follow-up. Despite the inclusion of multiple assessment time points, including a one-year follow-up, the long-term effects of D+Q remain largely unexplored; Therefore, we do not know the best duration of study to assess treatment effects.\n\nLooking forward, several avenues for future research emerge. For example, some have argued that clinical benefits of senolytics may be transient at best if biological mechanisms that extend the life and function of remaining healthy cells, like telomerase activity, are not simultaneously addressed, potentially accelerating degenerative processes in the long-term.36,37 Similarly, when we focus on suppressing biomarkers of senescence, we risk conflating biomarkers with aging when they are simply signs of illness in the face of impaired maintenance.38 Thus, larger randomized controlled trials that measure cellular mechanisms associated with senescence and with maintenance of cellular functioning together with clinical outcomes, would provide more robust evidence concerning the efficacy of D+Q as a senolytic and/or senomorphic treatment. Extended observational follow-up of clinical trials and observational examination of health systems data tracking relevant outcomes across relevant age and diagnostic cohorts spanning several years will also be needed to elucidate the long-term safety and efficacy of the intervention.\n\nSenolytics are not going to cure death but administered with precision (given to the right person for the right problem at the right time), they could extend healthy lifespan to a degree that allows middle-aged and older adults to lead longer and more productive lives. This is of increasing public health importance, as birth rates decline and the proportion of the population that is aging continues to grow. This study lays the groundwork for understanding the effects of D+Q. Exploring D+Q in combination with other pharmacological and non-pharmacological therapies may yield synergistic benefits. Future studies will benefit from the inclusion of a diverse participant pool, considering factors like age, gender, ethnicity, and comorbidities. This inclusivity offers insights into the differential treatment effects across various population subgroups. Such studies would allow enhanced generalizability of results while also appropriately interrogating mechanisms of illness and health across conditions and ages. Beyond clinical and neuropsychological outcomes, future research should incorporate considerations of the treatment’s impact on participants’ overall quality of life and health span.\n\n\nConclusions\n\nThis study probes safety, feasibility, and prospective therapeutic effects of D+Q for individuals with schizophrenia/schizoaffective disorder and TRD. By examining treatments to mitigate the relationship between accelerated aging and mental disorders, we aim to provide insights into the reduced health span and lifespan in these disorders. This provides a novel path for reducing the morbidity of common mental disorders.\n\nAll personnel involved in the design and conduct of the research involving human participants will receive the required education on protecting human research participants before the start of the project. This study has been approved by the Human Research Protection Office at Washington University (approval #202302203) on April 5, 2023. All study procedures will comply with the Washington University IRB informed consent standards. Any protocol modifications will be approved by this IRB, and significant modifications will be communicated by updates to the trial registration and/or direct communication with participants. The study has also been registered at ClinicalTrials.gov (NCT05838560, posted May 1, 2023). Informed consent will be verified in writing with all participants prior to their enrollment in the study. Through the consent process, those being enrolled will receive education on the voluntary nature of their participation as well. The informed consent form that will be used and the completed SPIRIT checklist are available as Extended data. The Washington University Institutional Review Board (IRB) determined that the study should be designated greater than minimal risk because of the risks associated with the investigational drugs requiring written documentation of consent prior to study participation. The IRB approved a waiver of the requirement to obtain documentation of consent for the phone screen.\n\nData confidentiality\n\nWhile rigorous precautions are enforced, the study acknowledges the potential for inadvertent breaches of electronic or paper records breaches. To counteract such vulnerabilities, stringent data management protocols are employed. These protocols include utilization of locked storage facilities, the implementation of restricted data access controls, and the adoption of anonymized participant identification numbers. Such measures are thoughtfully designed to safeguard the integrity and confidentiality of participant data throughout the study.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nOpen Science Framework: ‘Protocol for a pilot clinical trial of the senolytic drug combination Dasatinib plus Quercetin to mitigate age-related health and cognitive decline in mental disorders,’ https://doi.org/10.17605/OSF.IO/92GMQ. 39\n\nThis project contains the following extended data:\n\n- Senolytics Informed Consent.pdf\n\n- SPIRIT checklist for ‘Protocol for a pilot clinical trial of the senolytic drug combination Dasatinib plus Quercetin to mitigate age-related health and cognitive decline in mental disorders.pdf’\n\n- Study forms and assessments\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\nA special thank you to Stephanie Brown’s assistance with manuscript preparation. The authors would also like to acknowledge the contributions of the clinical trial team (Leonard Imbula, BA - all were compensated for their role), and the research participants without whose cooperation this study would not have been possible.\n\n\nReferences\n\nSeeman MV: Subjective Overview of Accelerated Aging in Schizophrenia. Int. J. Environ. Res. Public Health. Dec 31 2022; 20(1). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLaursen TM: Causes of premature mortality in schizophrenia: a review of literature published in 2018. Curr. Opin. Psychiatry. Sep 2019; 32(5): 388–393. Publisher Full Text\n\nSeitz-Holland J, Mulsant BH, Reynolds CF III, et al.: Major depression, physical health and molecular senescence markers abnormalities. Nat. Mental Health. 2023/03/01 2023; 1(3): 200–209. Publisher Full Text\n\nTessema T, Diniz BS, Vieira EM, et al.: Elevated senescence-associated secretory phenotype index in late-life bipolar disorder. J. Affect. Disord. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nForman DE, Racette SB, Toto PE, et al.: Modified Application of Cardiac Rehabilitation in Older Adults (MACRO) Trial: Protocol changes in a pragmatic multi-site randomized controlled trial in response to the COVID-19 pandemic. Contemp. Clin. Trials. Jan 2022; 112: 106633. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKonrad M, Nieman DC: Evaluation of Quercetin as a Countermeasure to Exercise-Induced Physiological Stress. In: Lamprecht M, ed. Antioxidants in Sport Nutrition. 2015. Publisher Full Text\n\nPelletier DM, Lacerte G, Goulet ED: Effects of quercetin supplementation on endurance performance and maximal oxygen consumption: a meta-analysis. Int. J. Sport Nutr. Exerc. Metab. Feb 2013; 23(1): 73–82. PubMed Abstract \| Publisher Full Text\n\nTkemaladze J, Apkhazava D: Dasatinib and Quercetin: Short-Term Simultaneous Administration Improves Physical Capacity In Human. J. Med. 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PubMed Abstract \| Publisher Full Text\n\nOpen Science Framework: Protocol for a pilot clinical trial of the senolytic drug combination Dasatinib plus Quercetin to mitigate age-related health and cognitive decline in mental disorders.Publisher Full Text" }	[ { "id": "325468", "date": "24 Sep 2024", "name": "Amer Burhan", "expertise": [ "Reviewer Expertise geriatric psychiatry", "dementia", "treatment resistant depression", "brain stimulation and ketamine" ], "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 manuscript describes a protocol for a pilot study investigating the safety and preliminary efficacy of a senolytic intervention (D+Q), that has evidence in animal models and preliminary evidence of safety in human clinical conditions, in patients with schizophrenia/schizoaffective disorder and treatment resistant depression, at one center in the US. The rationale is well articulated and is sound building on this group's already established work on cell senescence proteomic biomarkers, that is done mainly in late life depression. The design is sound and will likely answer the safety question in this population and preliminary evidence of target engagement. The clinical variables and brain imaging are not likely to be adequately explored given the small sample and the mixed population to be recruited. It would have been more likely to achieve some of the third objective in terms of estimating effect size, if the authors focused on one of the populations at a time, in this case late life treatment resistant depression as better fit for with the previous results form this group. I suggest trying to recruit 30 participants with late life depression, which would make this more useful, that doesn't mean the group can't do preliminary assessment of the safety and target engagement in schizophrenia and schizoaffective disorder, but would allow better conclusions from each of the studies thanks you for inviting me to review this interesting protocol\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": "335596", "date": "29 Oct 2024", "name": "Pierfelice Cutrufelli", "expertise": [ "Reviewer Expertise My primary area of expertise lies in clinical psychiatry", "with a particular focus on schizophrenia and mood disorders. I specialize in evaluating the efficacy", "safety", "and pharmacological profiles of psychiatric drugs", "including innovative pharmacological interventions. I also possess a strong background in conducting systematic reviews and meta-analyses", "which allows me to critically assess evidence-based practices in psychiatric care." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis protocol describes an interesting pilot study investigating the potential of senolytic therapy in mental disorders associated with accelerated aging, using drug combination Dasatinib Plus Quercetin. While the overall design is thoughtful and the rationale well-presented, several methodological concerns and omissions need to be addressed.\nLiterature Review\nThe literature review regarding nutraceutical interventions in severe mental illness appears insufficient. While the authors focus on the senolytic properties of dasatinib plus quercetin (D+Q), they fail to adequately review the existing literature on quercetin and other nutraceuticals in psychiatric conditions. The protocol's review of dasatinib is insufficient, lacking comprehensive discussion of its pharmacological properties as a tyrosine kinase inhibitor, its established safety profile in oncological and non-oncological conditions, and potential interactions with psychiatric medications and other commonly used drugs in the target population. Furthermore, while the authors cite its senolytic properties, they should provide a more thorough review of previous clinical trials using dasatinib as a senolytic agent. The protocol provides insufficient justification for the specific combination of dasatinib plus quercetin (D+Q), lacking detailed mechanistic explanation of how these compounds work individually (particularly dasatinib's role as a tyrosine kinase inhibitor and quercetin's anti-inflammatory and antioxidant properties) and the molecular basis for their proposed synergistic action in senolytic effects. The authors should thoroughly review both the pharmacological properties and existing clinical evidence for this combination, including potential interactions with psychiatric medications and the rationale for their specific dosing regimen, which is crucial for interpreting study outcomes and identifying relevant biomarkers. Additionally, the protocol should clearly explain why this particular combination might be especially beneficial in psychiatric populations, as opposed to other senolytic approaches. The protocol would benefit from a more comprehensive literature review and methodological considerations drawn from recent research in nutraceutical interventions for psychiatric and aging-related conditions. Several key studies have demonstrated the potential of natural compounds in these fields: Grosso et al. (2014) showed through meta-analysis that omega-3 supplementation significantly improves depressive symptoms, particularly as adjuvant therapy; Pivari et al. (2022) demonstrated how targeted nutraceutical interventions like curcumin can effectively modulate inflammation and oxidative stress pathways in chronic conditions; and Fusar-Poli et al. (2022) established that even simple interventions like cocoa-rich products can significantly impact depression and anxiety symptoms. Incorporating these and other relevant findings into your review could better consolidate your aims, making them plausible, relevant, and achievable.\n\nSASP Definition and Measurement:\nThe manuscript fails to clearly define the SASP (Senescence-Associated Secretory Phenotype) acronym at first use and does not adequately explain its biological significance The methodology for SASP measurement and evaluation, although mentioned, needs more details for clarity and transparency. The correlation between proposed outcome measures and SASP levels is not clearly explained\nAssessment Procedures:\nThe protocol lacks specificity regarding who will conduct the various assessments No information on rater training or inter-rater reliability measures Distinction between self-report and clinician-administered scales is not clear The rationale for selecting specific psychological/psychiatric measures is inadequately explained; a detailed description of the scales and their rationale is required\nConfounding Factors:\nThe concurrent lifestyle intervention could mask the effects of D+Q treatment. Address this, since no clear plan is explained for controlling or analyzing this potential confounding variable Exclusion criteria should address concurrent use of other nutraceuticals that might affect outcomes\nStatistical Analysis:\nThe statistical analysis plan is insufficiently detailed; while the authors state that \"analysis for Aims 2 and 3 will be primarily descriptive in nature,. this appears insufficient as even pilot studies should include preliminary hypothesis testing to identify promising trends and guide future research. Moreover, the complex nature of longitudinal data with multiple outcomes and two distinct diagnostic groups (TRD vs. schizophrenia/schizoaffective disorder) demands more sophisticated statistical modeling, including mixed-effects models and interaction analyses, to properly inform future trial design. Effect size calculation is particularly crucial in biomedical research as it quantifies the magnitude of treatment impact, enables comparison across different interventions and studies through standardized measures, and provides essential information for determining sample sizes in future clinical trials - aspects that are especially relevant when testing novel compounds like senolytics where establishing clinical significance is as important as statistical significance.While the authors mention they will examine \"effect size and 95% confidence interval for effects,\" they fail to specify which effect size measures will be used (e.g., Cohen's d, Hedges' g, or partial eta-squared for repeated measures), how these will be calculated for their longitudinal data structure, and what methods will be employed to handle the multiple comparison problem in effect size estimation across different outcomes. No clear strategy for handling missing data Lack of power calculations even for pilot study effect size estimation More detail is needed on your statistical approach to prevent reporting bias, such as multiple test corrections.\nAssessment Tools:\nBetter explanation needed for choice of specific scale. E.g. the authors will use the WHO Disability Assessment Schedule (WHODAS) but provide limited justification for this choice and lack detail in their analysis strategy. Recent research by Rodolico et al. (2024) demonstrated both the utility of WHODAS in evaluating disability in patients with severe mental illness and its significant correlation with medication side effects, providing a methodological framework that could inform this protocol. Given the potential interaction between existing antipsychotic medications and the proposed senolytic intervention, the authors could read and consider this recent evidence to strengthen their assessment approach and explain how WHODAS specifically relates to their intervention outcomes. This is particularly relevant as their protocol involves similar patient populations and could benefit from established methods for analyzing disability outcomes in the context of medication effects. A similar evaluation and reference standard should be conducted for each scale and measure, where necessary. Unclear how screening assessments will be integrated into analysis. Validation status of measures for the target populations not addressed.\n\nConclusion: While this protocol addresses an important research question with potential clinical significance, several methodological issues need to be addressed before implementation. The primary concerns relate to measurement protocols and scale measures description, potential confounding factors, and statistical analysis planning. A more comprehensive literature review is also needed. Addressing these issues would strengthen the study's scientific rigor and potential contribution to the field.\n\nIs the rationale for, and objectives of, the study clearly described? Partly\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] } ]	1	https://f1000research.com/articles/13-1072
https://f1000research.com/articles/11-918/v1	10 Aug 22	{ "type": "Research Article", "title": "Physical therapists’ use of personal protective equipment during the COVID-19 pandemic: a cross-sectional study in Saudi Arabia", "authors": [ "Walaa Elsayed", "Faisal Albagmi", "Mohammed Alghamdi", "Ahmed Farrag", "Walaa Elsayed", "Mohammed Alghamdi", "Ahmed Farrag" ], "abstract": "Background: Physical therapy (PT) services can be essential for recovery from coronavirus disease 2019 (COVID-19) infection. Maintaining an efficient healthcare service is achieved by ensuring the safety of a well-informed healthcare practitioner. This study aimed to assess the sources of knowledge, attitude, experience, and accessibility to the personal protective equipment (PPE) of the physical therapists working in Saudi Arabia. Methods: A cross-sectional study was conducted to survey on-duty PT practitioners using a web-based questionnaire. Licensed PT practitioners were invited to participate, and a sample of 424 therapists responded. The questionnaire comprised of 22 questions covering the demographic data and the following domains: sources of knowledge regarding the pandemic, experience, and attitude of the therapists during the pandemic, and accessibility to the PPE. Results: Around 83% of the participants (352) completed all the survey questions. Governmental websites were the most used source of knowledge (39%). Hand sanitization was implemented by the majority of participants (81%). Participants, mainly males and experienced therapist, were willing to treat COVID-19 patients. The COVID-19 complications of prolonged ventilation and immobilization were successfully treated by 91.2% of participants who treated positive cases. About a third of the participants were part of COVID-19 management planning teams or received training to deal with the pandemic. Most of the necessary PPE was adequately accessible during the pandemic. Conclusions: Therapists implemented the recommended hygienic practices and had no problems accessing the necessary PPE. More efforts should target therapists’ education about the social media misleading information and involving the therapists in the pandemic management planning teams.", "keywords": [ "COVID-19", "Attitude", "Protection", "Physical Therapy", "patient care", "Rehabilitation" ], "content": "Introduction\n\nSince the emergence of the coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), in China in December 2019,1 the world has been encountering unprecedented challenges and COVID-19 was declared a global pandemic in March 2020.2 Numbers of infected cases have been escalating rapidly worldwide, and the governments across the world have had to impose stringent measures to control the rapid spread of the disease. These measures included lockdown, social distancing, travel limitations, public use of personal protective equipment (PPE) and rearrangement of health administrations.3\n\nThe crisis the world has been facing because of the pandemic is attributed to the fast and vast spread of the disease among the population.4,5 This resulted in overloaded healthcare systems and an extensive burden being placed on healthcare workers all over the world.6–8 Reports have shown increased stress and anxiety of the healthcare providers due to increased workload and fear of contracting and transmitting the disease to family and friends.9–12 This may impact the attitude and performance of the healthcare provider and accordingly, the efficiency of the whole healthcare system.13,14\n\nDuring such a crisis, it is important to maintain an efficient healthcare system. This could be achieved by providing training to, updating the knowledge of, and protecting the healthcare providers. Unfortunately, some reports revealed a shortage of knowledge in healthcare workers regarding the COVID-19 pandemic in Saudi Arabia, with estimates that only about 45% of healthcare workers have a good awareness of COVID-19 when measured in March and April 2020.15 Misleading information and myths about the pandemic have gone viral across the different media channels, contributing further to limiting the knowledge of the healthcare workers.16 Furthermore, protection of the healthcare providers should be ensured by sufficient supplies and ease of accessibility to the PPE. Recent reports showed that shortage of the PPE supplies is associated with increased risk of infection and severity of symptoms and elevated anxiety among the healthcare providers.17\n\nPhysical therapy (PT) services are essential for the comprehensive recovery of some COVID-19 patients. Cardiopulmonary rehabilitation in acute and post-acute settings can significantly maintain and improve the pulmonary functions.18,19 Physical therapists also manage patients recovering from a COVID-19 infection to help them restore mobility and lung functions. This exposes the physical therapists to a high risk of contracting the infection, considering that the physical therapy practice requires prolonged physical contact with the patients.20\n\nTherefore, collecting information regarding healthcare workers’ sources of knowledge and their attitude and experience during the COVID-19 pandemic and accessibility to the PPE is important to assess and maintain the efficiency of healthcare systems. Findings retrieved from such information could help decision makers find weaknesses and strengths in order to improve the services provided to the patients. To the authors’ knowledge, no studies have assessed such information among physical therapists working in the Saudi healthcare system. Thus, the purpose of this study is to assess and report the sources of knowledge, attitude, experience and accessibility of PPE for physical therapists working in Saudi Arabia.\n\n\nMethods\n\nThis study implemented a cross-sectional design that was based on an online questionnaire to survey physiotherapists in Saudi Arabia in September 2020 during the COVID-19 pandemic. We surveyed the participants’ sources of knowledge, attitude, experience, and accessibility of PPE during the pandemic.\n\nThis study was approved by the Institutional Review Board of the Prince Sultan Military College of Health Sciences, Saudi Arabia (IRB No: IRB-2020-PT-032). Written informed consent was obtained from all participants before proceeding to the survey by providing it at the cover letter and having each participant accepting it by clicking start to proceed to the survey. Anonymity of the participants was ensured and no personal identifier was obtained.\n\nPhysical therapy practitioners working in the Saudi healthcare system (including governmental and private sectors hospitals and clinics) were invited through emails and professional social media groups to fill an anonymous web-based questionnaire. Data were collected during September 2020 by sending the survey to professional physiotherapy groups on social media channels to cover the five geographical regions of Saudi Arabia. Social network channels used were Twitter, Facebook, WhatsApp, Instagram, LinkedIn, and Snapchat.\n\nUsing the Raosoft calculator, a sample size of 257 therapists was targeted. This was based on an estimated population size of 5000 licensed physical therapists, according to the data available through the World Physiotherapy website,21 and using a confidence level of 90%, and P-value of 0.05. The inclusion criteria were licensed physical therapy practitioners working inside Saudi Arabia only. Participants were excluded if they were not working in Saudi Arabia, or if they were any health care providers other than physical thrapy practiotioners.\n\nThis study used a web-based survey (QuestionPro) comprised of 22 questions. It covered the participant’s demographic data and the following areas: sources of knowledge regarding the pandemic, experience, and attitude of the therapists during the pandemic, and accessibility to the PPE. The survey tool was developed by the authors in accordance with the guidelines of the World Physiotherapy regarding the PT services during the COVID-19 pandemic,22 and based on a questionnaire for spine surgeons,23 and a study that assessed the PT practice during the pandemic.24\n\nThe sources of knowledge about the COVID-19 pandemic was assessed by one question that had four answer categories including news, social media, official websites (e.g. World Health Organization), and family and friends. Each category had a 4-point Likert scale (least used to most used). The attitude topic was assessed by two questions concerned with the type of precautionary measures implemented at home, and willingness of participants to treat a positive COVID-19 patient. Regarding the topic of experience, nine questions were developed to assess training of the participants during the pandemic, their involvement in pandemic management teams, actual treatment of positive cases, and their feedback about the efficacy of the treatment they provided for those cases. Accessibility to the PPE was assessed by one question with six answer categories in order to identify accessibility. The questionnaire can be found as Extended data.52\n\nThe authors reviewed and confirmed the face and content validity of the questionnaire items. Then, the questionnaire was pilot tested by ten respondents who volunteered to take part of the survey that was announced through professional social networks. They completed the questionnaire online, and their comments about the questions and the cover letter were recorded. Then, the respondents were interviewed via phone and requested to provide responses to the survey items that were rephrased using alternative wording. Their responses were checked against what they provided in the web-based questionnaire. Afterwards, the questionnaire was amended accordingly based on the pilot study results. The formal questionnaire was constructed using QuestionPro software and disseminated during September 2020 through emails and social media. We used various professional social media groups through Twitter, Facebook, WhatsApp, Instagram, LinkedIn, and Snapchat.\n\nData were analyzed using SPSS version 26 (SPSS, Chicago, IL). Completed responses for each variable were examined. Descriptive statistics were performed for all the variables in the form of frequency (percentages) distribution. Univariable analyses were performed to examine the significant differences between the defined parameters among different demographic characteristics. Chi-square test was used for the categorical parameters. The significance level (α) was set at P≤0.05. Variables with significant univariable effects were further processed using multivariable analysis. Logistic regression was performed to estimate the association between the demographic characteristics and study parameters.\n\n\nResults\n\nOf the 2021 subjects who viewed the survey, 795 participants started it. A total of 425 physical therapy practitioners completed the knowledge and attitude sections, and only 352 (83%) participants completed the entire survey including the PPE.52 The demographic data are presented in Table 1.\n\nPT=physical therapist.\n\nThe participants reported that the sources of knowledge they used the most were the official governmental websites e.g. Ministry of Health (n=165, 39%), followed by the social media including Twitter, Facebook, WhatsApp, and Snapchat (n=113, 26.7%). Knowledge obtained through colleagues and family members were the least used (n=16, 3.8%). Although not being the most used source of knowledge (n=69, 16.3%), print and broadcast media were significantly associated with age (P=0.016) and years of experience (P=0.043), as older (n=28, 20.4%) and more-experienced (n=32, 20.5%) participants reported using it as the most used source of knowledge, more than their younger (n=41, 14.3%) and less-experienced (n=37, 13.8%) counterparts.\n\nHand sanitization and washing clothes were the most commonly implemented precautionary measures reported by 81.1% and 80.9% of participants, respectively. Self-isolation was implemented by 26.8% of participants, and about 8.0% reported implementing other additional measures, which were implemented by women more than men (P=0.037) (Table 2).\n\nValues indicate number (%) of participants who reported implementing those precautionary measures (n=425).\n\nFurthermore, about half of the participants (52.1%) reported their willingness to manage and treat COVID-19 patients. This positive attitude towards the COVID-19 patients was significantly associated with gender (P<0.001) and experience (P=0.027). Male and more-experienced therapists were more willing to manage positive COVID-19 patients than their female and less-experienced counterparts (Table 3).\n\nValues indicate number (%) of participants who answered “yes” to the questions (n=425).\n\nAt the institutional level, participants reported that they were involved in management teams of the COVID-19 pandemic (30.9%). However, this was associated with age ((P=0.036), gender (P<0.001), experience (P<0.001), and type of institution (P<0.001). The results revealed that older and more experienced male therapists working in governmental institutions were more involved in the pandemic management teams. Unexpectedly, only 134 participants (31.6%) received training to deal with the pandemic (Table 3).\n\nIn total, 99 participants (23.6%) reported treating positive COVID-19 patients. Managing infected patients was significantly associated with gender (P=0.007), experience (P<0.001) and type of the institution (P<0.001). Around 47.8% of participants who treated infected patients handled five or less patients, while around 63.3% treated more than ten patients. The number of COVID-19 cases treated by participants was associated with gender (P=0.008) as male therapists reported managing more infected patients than female therapists. Only 7% of them felt unconfident treating COVID-19 patients (Table 4). About 28.4% of participants treated the complications of prolonged ventilation and immobilization associated with the COVID-19 infection, and 91.2% of them reported a positive impact on the patient’s condition. The reported data regarding the impact of the physical therapy treatment were associated with the participant’s gender (P=0.041).\n\nValues indicate number (%) of participants who reported treating COVID-19 patients (n=91).\n\nParticipants reported that accessibility to most of the protective equipment and sanitization supplies was not problematic during the pandemic. Availability of hand sanitizer, gloves, surgical masks, and gowns was of no or little problem for 93.5%, 93.5%, 89.8%, and 87.2% of participants, respectively. However, accessibility to respiratory masks and face shields/goggles was a huge problem for 23.3%, and 16.8% of participants, respectively (Table 5).\n\nValues indicate number (%) of participants (n=352).\n\n\nDiscussion\n\nDuring the past year, several studies examined how the healthcare practitioners handled the COVID-19 pandemic.9,15,25–30 However, studies focusing on the PT profession were scarce.24,31–33 Physical therapists typically spend extended periods of time treating patients through prolonged and direct physical interaction with patients.20 In the current pandemic, physical therapists play an important role providing respiratory support and active mobilization to COVID-19 patients both inside and out of an acute care setting.18,19,34,35\n\nThe COVID-19 pandemic is an unprecedented medical situation that has been associated with extreme measures imposed worldwide. Accordingly, it was essential to assess the knowledge of physical therapists about the new viral infection. Our results showed that nearly 40% of the physical therapists were responsible enough to seek knowledge about the new pandemic from trusted sources such as the official websites. Meanwhile, more than one quarter (26.7%) of the participants used social media as their main source of information. This may suggest that the physical therapists may have developed misconceptions about the pandemic because of the invalid information about how the virus spreads and any myths about the virus symptoms through the social media.16,36 Other studies investigated the community knowledge about the pandemic and found a significant knowledge gap among the public37,38 and healthcare providers.15\n\nThe current results indicate commitment from most of the physical therapists to apply the recommended precautionary measures. More than 80% of the participants reported using hand sanitizers and washing clothes once they return home. Previous reports revealed an increased anxiety among healthcare providers in Saudi Arabia during April 2020 because of the pandemic.28 One of the main reasons for increased anxiety was the fear of contracting the infection and transmitting it to family and friends.15,39 In the current study, women were more inclined than men to apply additional precautionary measures, which reflects a greater protective attitude. This is in accordance with previous studies that showed hygienic practices were positively associated with women,37,40 and they were more compliant than men with the imposed public policy measures while dealing with COVID-19 pandemic as mandating the use of face masks, quarantine the infected cases, etc.41\n\nIn the current study, physical therapists showed a positive attitude towards managing COVID-19 positive cases. Despite of the documented concern and anxiety among healthcare providers regarding the pandemic,15,39 more than half of the participants were willing to treat a COVID-19 patient. Physical therapy services by nature require extended and direct physical interaction between the therapist and the patient, which would potentially significantly increase the risk of contracting a highly contagious infection such as COVID-19. Thus, it is expected that physical therapists might be hesitant to manage a positive case, which was reported by almost half of the study participants. Meanwhile, men as well as more experienced therapists, were more motivated to treat COVID-19 patients. This finding is counterintuitive considering the reported fact that older adults and males are more likely to be at greater risk of serious morbidity and higher mortality.42–44 However, this interesting finding could be explained by reports of the gender-based differences regarding attitude and risk perception during the COVID-19 pandemic. Women reported greater fear and health-related negative expectations than men.41,45 Additionally, experienced therapists are commonly assigned to higher administrative positions that limit direct interaction with patients. Furthermore, they are typically older than less experienced therapists. Therefore, they are considered amongst the high-risk group for contracting infection and experiencing serious health consequences. Thus, they had limited or no interaction with patients, which may explain their positive attitude and limited concern regarding treating patients diagnosed with COVID-19.\n\nUnfortunately, only about one third of the participants (30.9% and 31.6%, respectively) reported being involved in management and planning teams of the pandemic or receiving training to deal with the pandemic. This surprisingly low percentage indicating the need to provide more training programs for rehabilitation professionals by the governing authorities. However, it could be justified by the fact that COVID-19 is a life-threatening disease for which, the first line of treatment is medical rather than rehabilitative. Thus, it is reasonable that physicians and nurses become the focus group for treatment planning and training efforts during the pandemic. This should not underestimate the valuable role physical therapists have in acute settings for treating COVID-19 patients.19 Our findings also indicate that involvement in management teams was positively associated with male, older and more experienced therapists working in governmental institutions. This further corroborates the finding discussed here above regarding gender-based differences about worries, fear and negative expectations toward the pandemic that are more associated with women. This could potentially be a barrier for female therapists to participate in management and planning teams. Additionally, the measures imposed by the Saudi Ministry of Health targeted primarily the governmental medical institutions that are more capable to accommodate the increased number of COVID-19 cases.46 This may explain the interesting finding favoring therapists working in governmental institutions. This argument is supported by the reported data regarding actual treatment of positive cases. The majority of therapists who reported treating COVID-19 cases were mostly working in governmental institutions, and male therapists treated higher numbers of patients compared with female therapists.\n\nThe results revealed that accessibility to the PPE was not a problem for the majority of the participants. This indicates the preparedness of the Saudi healthcare system to face the pandemic and equip the healthcare providers with the necessary protective equipment.46 This is particularly important considering that more than 60% of the participants work in governmental institutions. Protection of healthcare providers during a pandemic is crucial for the quality and efficiency of the service provided. Reports have shown a significant shortage of PPE in some healthcare systems. In Italy, only 13% of physicians reported to have access to PPE every time they needed to.47 Another study in Ethiopia identified a critical shortage of PPE that is significantly associated with high levels of dissatisfaction amongst healthcare workers.48 This should be a warning to the governing authorities to continuously provide sufficient supplies of PPE and avoid shortage using different resources,49,50 given the findings revealing that limited access to or shortage of PPE is significantly associated with increased risk of contracting the COVID-19 infection and increased severity of symptoms among the health care workers.17\n\nThe current study has some limitations that should be noted. The data collection process was not carried out at the time of the lockdown during the peak of the COVID-19 pandemic during March to June 2020.51 Therefore, the data obtained were collected retrospectively. Thus, it may likely suffer the recall bias inherent with retrospective self-reported data. The five geographical regions of the Saudi Arabia were not equally represented, which may limit the generalizability of the obtained findings. However, successfully recruiting participants more than the required minimal sample size could provide credible data.\n\nIn conclusion, the current study showed that physical therapists were knowledgeable about best hygienic practices. Furthermore, sufficient supplies of the PPE were available through the Saudi healthcare system, which indicates appropriate planning by the authorities. Physical therapists showed a positive attitude towards COVID-19 patients. Yet, this could be improved significantly by implementing a stringent plan to educate the physical therapy practitioners about misleading information on social media as a source of information and involving them more in management planning teams.\n\n\nData availability\n\nOpen Science Framework: COVID-19 influence on rehabilitation service providers in Saudi Arabia. https://doi.org/10.17605/OSF.IO/4M7GV.52\n\nThis project contains the following underlying data:\n\n• Raw Data with codebook.csv (dataset)\n\n• CodeBook-Raw Data.csv (codebook)\n\nOpen Science Framework: COVID-19 influence on rehabilitation service providers in Saudi Arabia. https://doi.org/10.17605/OSF.IO/4M7GV.52\n\nThis project contains the following extended data:\n\n• Questionnaire.pdf\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).", "appendix": "Acknowledgement\n\nThe authors would like to acknowledge the physical therapists who participated in the current study.\n\n\nReferences\n\nZhu N, Zhang D, Wang W, et al.: A Novel Coronavirus from Patients with Pneumonia in China, 2019. 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Publisher Full Text\n\nPeckham H, de Gruijter NM , Raine C, et al.: Male sex identified by global COVID-19 meta-analysis as a risk factor for death and ITU admission. Nat. Commun. 2020; 11(1): 6317. PubMed Abstract \| Publisher Full Text\n\nGebhard C, Regitz-Zagrosek V, Neuhauser HK, et al.: Impact of sex and gender on COVID-19 outcomes in Europe. Biol. Sex Differ. 2020; 11(1): 29. PubMed Abstract \| Publisher Full Text\n\nAlsharawy A, Spoon R, Smith A, et al.: Gender Differences in Fear and Risk Perception During the COVID-19 Pandemic. Front. Psychol. 2021; 12: 689467. PubMed Abstract \| Publisher Full Text\n\nAlgaissi AA, Alharbi NK, Hassanain M, et al.: Preparedness and response to COVID-19 in Saudi Arabia: Building on MERS experience. J. Infect. Public Health. 2020; 13(6): 834–838. PubMed Abstract \| Publisher Full Text\n\nSavoia E, Argentini G, Gori D, et al.: Factors associated with access and use of PPE during COVID-19: A cross-sectional study of Italian physicians. PLoS One. 2020; 15(10): e0239024. PubMed Abstract \| Publisher Full Text\n\nDeressa W, Worku A, Abebe W, et al.: Availability and use of personal protective equipment and satisfaction of healthcare professionals during COVID-19 pandemic in Addis Ababa, Ethiopia. Arch. Public Health. 2021; 79(1): 146. PubMed Abstract \| Publisher Full Text\n\nLivingston E, Desai A, Berkwits M: Sourcing Personal Protective Equipment During the COVID-19 Pandemic. JAMA. 2020; 323(19): 1912–1914. PubMed Abstract \| Publisher Full Text\n\nBauchner H, Fontanarosa PB, Livingston EH: Conserving Supply of Personal Protective Equipment-A Call for Ideas. JAMA. 2020; 323(19): 1911. PubMed Abstract \| Publisher Full Text\n\ncontributors W: COVID-19 pandemic in Saudi Arabia.2022.Reference Source\n\nElsayed WH, Farrag A, Albagmi F, et al.: COVID-19 influence on rehabilitation service providers in Saudi Arabia. [Dataset].2022, June 30. Publisher Full Text" }	[ { "id": "293151", "date": "12 Jul 2024", "name": "Matthew R. Hyland", "expertise": [ "Reviewer Expertise Impacts on the profession of physical therapy that are not directly intervention based (ie impacts of COVID-19", "health policy such as predicting outcomes of care", "injuries in physical therapists." ], "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\nIt is interesting the authors chose not to site any published research in the United States during that period when the Northeast was the epicentre at that time. In the abstract and in the manuscript, they reference physical therapy services with the abbreviation PT. PT is a licensed designation for physical therapists or physiotherapists not for the profession. I suggest these changes be made throughout. In the abstract and early in the manuscript the authors identify “experience” as a domain. It is not clear until much later in the manuscript that they are referring to experience as years in the profession, not experience in working with COVID-19 patients. I would state that earlier on. When reporting statistics it should be a fact, 83%, not “around 83%.” In the introductions the authors state, “Therefore, collecting information regarding healthcare workers’ sources of knowledge and their attitude and experience during the COVID-19 pandemic and accessibility to the PPE is important to assess and maintain the efficiency of healthcare systems” I think it is important to add, after healthcare systems, “and to protect the health of their workforce and patients they serve.” I don’t think this research is about the healthcare systems, rather the healthcare workers and patients they serve. Big distinction in my opinion. Significant at the end of the section of “study settings and participants.” Under results “Sources of knowledge about the COVID-19 Pandemic” I would suggest an associated table. Enhancing the conclusion would add to the manuscript such as what does this mean for the future, if another pandemic hits, why is the research important.\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? Partly", "responses": [ { "c_id": "12386", "date": "18 Sep 2024", "name": "Faisal Albagmi", "role": "Author Response", "response": "We would like to thank the reviewer for their thoughtful comments and suggestions. Below is a detailed response to each of the issues raised, along with the corresponding corrections made in the manuscript: Citing Published Research in the United States Comment: It is interesting that the authors chose not to cite any published research in the United States during that period when the Northeast was the epicenter at that time. Response: We have cited the work of Miller et al. (2020) in reference no. 7 to address this concern. Please see page 2 for the citation. Use of \"PT\" for Physical Therapy Comment: PT is a licensed designation for physical therapists or physiotherapists, not for the profession. I suggest these changes be made throughout. Response: We have corrected this issue throughout the manuscript. PT is now used to refer to \"physical therapist\" and not \"physical therapy.\" Please see pages 3, 5, and 7 for the changes. Clarifying \"Experience\" Comment: In the abstract and early in the manuscript, the authors identify “experience” as a domain. It is not clear that they are referring to years in the profession, not experience in working with COVID-19 patients. Response: We have clarified this in the abstract by adding “years in the profession.” Please refer to page 1, fifth line in the abstract, and throughout the manuscript for consistency. Accuracy in Reporting Statistics Comment: When reporting statistics, it should be a fact (83%) not “around 83%.” Response: This issue has been corrected. We have used the precise figure “83%” in both the abstract and results sections. Please see page 1 (abstract) and page 6 (results section). Revision to Introduction Comment: The introduction should focus more on the healthcare workers and the patients they serve, not just healthcare systems. Response: We revised the last paragraph of the introduction to reflect this distinction by adding: “and to protect the health of their workforce and the patients they serve.” Please see page 4. Typo Correction Comment: Significant at the end of the section of \"study settings and participants.\" Response: The typo has been corrected to \"therapy practitioners.\" Please refer to page 5. Table Addition for \"Sources of Knowledge\" Comment: Under results, a table is suggested for “Sources of knowledge about the COVID-19 Pandemic.” Response: We have added Table 2 to represent the sources of knowledge about the COVID-19 pandemic. Please see page 8 for the new table. Enhancing the Conclusion Comment: Enhancing the conclusion would strengthen the manuscript, discussing what this means for the future if another pandemic hits. Response: We have enhanced the conclusion by stating: “Developing better physical therapists’ awareness about the COVID-19 pandemic would help establish more efficient management strategies during pandemics. In doing so, appropriate and immediate responses could be implemented to ensure the continuity of service provision and limit economic burden.” Please refer to page 10. We believe these revisions have significantly improved the clarity and impact of the manuscript, and we appreciate your feedback. Thank you for your careful review." } ] } ]	1	https://f1000research.com/articles/11-918
https://f1000research.com/articles/10-1053/v1	18 Oct 21	{ "type": "Research Article", "title": "Prediction of the Effects of Synonymous Variants on SARS-CoV-2 Genome", "authors": [ "Wan Xin Boon", "Boon Zhan Sia", "Chong Han Ng", "Wan Xin Boon", "Boon Zhan Sia" ], "abstract": "Background: The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had led to a global pandemic since December 2019. SARS-CoV-2 is a single-stranded RNA virus, which mutates at a higher rate. Multiple studies had been done to identify and study nonsynonymous mutations, which change amino acid residues of SARS-CoV-2 proteins. On the other hand, there is little study on the effects of SARS-CoV-2 synonymous mutations. Although these mutations do not alter amino acids, some studies suggest that they may affect viral fitness. This study aims to predict the effect of synonymous mutations on the SARS-CoV-2 genome.\n\nMethods: A total of 30,229 SARS-CoV-2 genomic sequences were retrieved from Global Initiative on Sharing all Influenza Data (GISAID) database and aligned using MAFFT. Then, the mutations and their respective frequency were identified. A prediction of RNA secondary structures and their base pair probabilities was performed to study the effect of synonymous mutations on RNA structure and stability. Relative synonymous codon usage (RSCU) analysis was also performed to measure the codon usage bias (CUB) of SARS-CoV-2. Results: A total of 150 synonymous mutations were identified. The synonymous mutation identified with the highest frequency is C3037U mutation in the nsp3 of ORF1a, followed by C313U and C9286U mutation in nsp1 and nsp4 of ORF1a, respectively.\n\nConclusion: Among the synonymous mutations identified, C913U mutation in ORF1a and C26735U in membrane (M) protein may affect RNA secondary structure, reducing the stability of RNA folding and possibly resulting in a higher translation rate. However, lab experiments are required to validate the results obtained from prediction analysis.", "keywords": [ "COVID-19", "SARS-CoV-2", "Synonymous mutations", "RNA secondary structure" ], "content": "Introduction\n\nIn December 2019, coronavirus disease 2019 (COVID-19) cases first emerged from Wuhan, China1. Soon after, rapid spread of COVID-19 has resulted in a serious global outbreak. COVID-19 is an infectious and potentially lethal disease caused by a newly found coronavirus strain, known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The virus causes clinical manifestation ranging from asymptomatic to severe pneumonia and eventually death2. SARS-CoV-2 seems to have a higher transmission rate3 but lower mortality rate2 in comparison to Middle East respiratory coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus (SARS-CoV).\n\nSARS-CoV-2 is a single-stranded RNA virus with a genome size of 29,903 bases. In general, RNA viruses have a higher mutation rate than DNA viruses and this allows them to evolve rapidly, escaping the host immune defence response4. A study by Kim et al. (2020) identified a total of 1,352 nonsynonymous and 767 synonymous mutations from 4,254 SARS-CoV-2 genomes5. While in another study done by Khailany et al. (2020), 116 mutations had been identified from 95 SARS-CoV-2 genomes6.\n\nIn this study, we focus on synonymous mutations instead of nonsynonymous mutations as researchers often overlook their biological importance. Synonymous mutations are also known as silent mutations because the nucleotide mutations result in a change in the RNA sequence without altering the amino acid sequence7. Synonymous mutations have been suggested to have no functional consequence on the fitness of organisms and their evolution in long term8. However, numerous recent studies had showed that synonymous mutations may affect the folding and stability of RNA structures9. For RNA viruses, even though synonymous mutations generally do not change their pathogenicity, some studies reveal that synonymous mutations may affect the RNA secondary structure of the virus10 and also change the codon usage bias of the genes in the virus11,12.\n\n\nMethods\n\n30,229 SARS-CoV-2 genomic sequences were retrieved from GISAID database (Global Initiative on Sharing All Influenza Data, RRID:SCR_018251)13 ranging from 31 December 2019 to 22 March 2021. SARS-CoV-2 genomic sequences were filtered by setting parameters to keep only sequences with complete genome and high coverage. The reference sequence of SARS-CoV-2 genome (NC_045512.2)14 was retrieved in fasta format from NCBI database (NCBI, RRID:SCR_006472). It is a Wuhan isolate with a complete genome which comprises of 29,903 bases.\n\nThe rapid calculation available in MAFFT online server (MAFFT, version 7.467, RRID:SCR_011811)15 was used to perform multiple sequence alignment (MSA) for 30,229 SARS-CoV-2 genomes. This option supports the alignment of more than 20,000 sequences with approximately 30,000 sites. The alignment length was kept, which means the insertions at the mutated sequences were removed, to keep the alignment length the same as the reference sequence. While other parameters were left as default.\n\nA simple Python script was written to identify the mutations in 30,229 SARS-CoV-2 genomes. To determine whether the identified mutations are synonymous or nonsynonymous, MEGA X software, version 10.2.5 build 10210330 (MEGA Software, RRID:SCR_000667)16 was utilized to perform the translation for inspection purposes. The presence of amino acid changes was identified by referring to the genomic position of the nucleotide mutations. Synonymous mutations with the top 10 highest frequencies were generated.\n\nThe RNA secondary structure of wild type and mutant sequences were predicted using RNAfold program, version 2.4.18 (Vienna RNA, RRID:SCR_008550) to show how mutations affect RNA secondary structure. The RNA secondary structure prediction was performed using a sequence length of 250 nucleotides upstream and downstream of the mutation site. The minimum free energy (MFE) was also calculated in the RNAfold program for both wild type and mutant sequences to show comparison of the RNA folding stability between them. The comparison on the value of minimum free energy (MFE) is important to indicate whether the mutations affect the folding stability of the respective RNA structure.\n\nTo predict how the mutations affect RNA local folding, base pair probability was estimated by utilizing MutaRNA, version 1.3.0 (MutaRNA, RRID:SCR_021723)17. MutaRNA is a web-based tool that allows prediction and visualization of the structure changes induced by a single nucleotide polymorphism (SNP) in an RNA sequence. It includes the base pair probabilities within RNA molecule of both wild type and mutant. The parameters used in MutaRNA were set as default, in which the window size is 200nt and the maximal base pair span is 150nt.\n\nRelative synonymous codon usage (RSCU) represents the ratio of the observed frequency of codons appearing in a gene to the expected frequency under equal codon usage. RSCU is calculated using the formula:\n\n\n\nwhere Xi implies the number of occurrences of codon i and n stands for the number of synonymous codons encoded for that particular amino acid.\n\n\nResults and discussion\n\nA synonymous mutation is a change in the nucleotide that does not cause any changes in the encoded amino acid. Synonymous mutations were previously considered to be less important, but they are now proven to have some effects on RNA folding, RNA stability, miRNA binding and translational efficiency18. Synonymous mutations may have significant effects on the adaptation, virulence, and evolution of RNA viruses19. Another study done also indicated that synonymous mutations have association with more than 50 human diseases such as hemophilia B, tuberculosis (TB), cystic fibrosis (CF), Alzheimer, schizophrenia, chronic hepatitis C and so on20. All these studies show that increasing importance has been associated with synonymous mutations over these years. Hence, it is necessary for us to study the effects of synonymous mutations of SARS-CoV-2 genome.\n\nA total of 381 mutations were found in SARS-CoV-2 genomes by using python script, in which 150 of them are synonymous mutations. The distribution of synonymous mutations in 11 coding regions is shown in Figure 1. Among these mutations, ORF1a and ORF1b have a higher number of synonymous mutations at 76 and 33, respectively, which might be due to their longer sequence length. Besides that, our findings also show high C to U mutation rate in SARS-CoV-2 genetic variation and this mutational skews are in line with the studies done by Rice et al. (2021) and Simmonds (2020)21,22. These mutational skews are necessary to be considered when deducing the selection acting on synonymous variants in SARS-CoV-2 evolution23.\n\nThe synonymous mutations in SARS-CoV-2 genomes with the top 10 highest frequency were listed in Table 1. As shown in Table 1, synonymous mutations with the highest frequency identified from SARS-CoV-2 genomes is C3037U mutation located in nsp3 of ORF1a, followed by C313U mutation in nsp1 of ORF1a and C9286U mutation in nsp4 of ORF1a. Mutations with higher frequency are mostly found in ORF1a and ORF1b. It is of great interest to find out the effect of these top 10 synonymous mutations on SARS-CoV-2 genome.\n\nSARS-CoV-2 virus can form highly structured RNA elements, which may affect viral replication, discontinuous transcription and translation24–28\n\nThe RNA secondary structures of wild type and mutant sequences were predicted using RNAfold program. Minimum free energy (MFE) of each structure was also calculated to show the folding stability of the respective RNA structure. Among all, C913U mutation and C26735U mutation were found to have a more obvious effect on the predicted RNA secondary structure compared to the wild type.\n\nAs shown in Figure 2(A), a single hairpin is formed around the mutant with C913U mutation instead of a multiloop in the wild type. The minimum free energy value of the mutant (- 146.90 kcal/mol) is slightly less negative than that of the wild type (- 147.40 kcal/mol), which makes it a less thermodynamically stable structure compared to the wild type.\n\n(A) RNA secondary structure of wild type C913 and mutant U913. (B) Circular plots showing the base pairing probabilities with darker shades indicating higher base pairing probabilities and a red arrow pointing to the mutation site.\n\nTo visualize the differences in the base pairing potential induced by the mutation, base pairing probability was estimated using MutaRNA. The circular plots in Figure 2(B) show the base pairing probabilities of both wild type and mutant. As shown in the circular plots, C913U mutation decreased the Watson–Crick base pairing probability near the mutation site, which led to a less stable predicted RNA secondary structure. C913U mutation is found in the nsp2 of ORF1a in SARS-CoV-2 genome. Nsp2 in SARS-CoV interacts with two human host proteins specifically, which are prohibitin 1 (PHB1) and prohibitin 2 (PHB2)29. This interaction may disrupt the intracellular host signalling during the viral infections, rather than taking part in the viral replication29. It is yet to see if nsp2 of SARS-CoV-2 shares same or similar function as that of SARS-CoV.\n\nC26735U mutation is located at the membrane (M) protein. M protein may suppress host immune responses via the interference of Type I interferon production30. C26735U mutation induces changes in the predicted RNA secondary structure by forming an extra multibranch loop at the mutation site as shown in Figure 3(A). The RNA secondary structure formed by the mutant (-134.50 kcal/mol) has a less negative minimum free energy value compared to the wild type (-136.30 kcal/mol), which makes it a less stable structure. While for the circular plots in Figure 3(B), C26735U mutation decreases the base pairing probabilities in flanking regions, which again predicted that the mutation decreases the folding stability of the RNA secondary structure.\n\n(A) RNA secondary structure of wild type C26735 and mutant U26735. (B) Circular plots showing the base pairing probabilities with darker shades indicating higher base pairing probabilities and a red arrow pointing to the mutation site.\n\nIn short, both C913U and C26735U mutations cause a more drastic change in RNA secondary structure. Given the shortcomings of prediction tools, it is necessary to check if the changes in RNA secondary structure affect the pathogenicity of SARS-CoV-2 using experimental approaches. Besides that, these two mutations also reduce the folding stability of the RNA secondary structure, which then affects the polypeptide translation and folding. There is evidence suggesting that stable RNA structures play a key role in reducing the translation speed to prevent “ribosomal traffic jams” so that the newly translated polypeptides can fold properly31. Hence, both C913U and C26735U mutations increase the translation speed of SARS-CoV-2 RNA but they might cause the nascent polypeptide folding more prone to error during translation.\n\nCodon usage bias (CUB), which is non-random usage of synonymous codons, is common in all species. It is a phenomenon where some codons are preferred over others for a specific amino acid. SARS-CoV-2 replicates using host cell’s machinery and synthesizes its protein by utilizing host cellular components. Hence, codon usage bias may affect the replication of viruses32.\n\nRelative synonymous codon usage (RSCU) is a widely used statistical approach33 that can be used to measure codon usage bias in coding sequences. The RSCU values of SARS-CoV-2 are shown in Table 2 and the most preferred codons for each amino acid are marked in bold. Stop codons (UAA, UAG, UGA) and codons which code for an amino acid uniquely (AUG, UGG) are excluded from RSCU analysis.\n\nBased on the RSCU values, the synonymous codons can be classified into five groups: i) codons with RSCU value equals to 1.0 are unbiased codons; ii) codons with RSCU value > 1.0 are codons preferred in a genome; iii) codons with RSCU value < 1.0 are codons less preferred in a genome; iv) codons with RSCU value > 1.6 are codons which are over-represented in a genome; v) codons with RSCU value < 1.6 are codons which are under-represented in a genome32. There are 15 preferred codons (RSCU value > 1.0) and 11 over-represented codons (RSCU value > 1.6) in SARS-CoV-2 genome as shown in Table 2. The preferred codons in SARS-CoV-2 genome are GCA (Ala), CGU (Arg), AAU (Asn), GAU (Asp), UGU (Cys), CAA (Gln), GAA (Glu), CAU (His), AUU (Ile), UUG (Leu), AAA (Lys), UUU (Phe), CCA (Pro), AGU (Ser) and UAU (Tyr) while the over-represented codons are GCU (Ala), AGA (Arg), GGU (Gly), CUU (Leu), UUA (Leu), CCU (Pro), UCA (Ser), UCU (Ser), ACA (Thr), ACU (Thr), and GUU (Val). The presence of the preferred and over-presented codons in a genome increases the protein synthesis rate.\n\nTable 3 shows the RSCU analysis of the top 10 synonymous mutations. The codons in bold in the ‘codon change’ column are the codons with higher RSCU value, which means they are more preferred in SARS-CoV-2 genome. Most of the mutations change the codon to a more preferred codon as shown in Table 3. Since it is presumed that preferred codons have a higher translation rate compared to nonpreferred codons34, it is possible that most of the mutations may increase the translation efficiency of SARS-CoV-2, which may affect virus replication, transmission, and evolution.\n\n\nConclusions\n\nThe effects of SARS-CoV-2 synonymous mutations in various aspects such as RNA folding and RNA stability of the virus were studied, even though they do not cause changes in amino acid residue of the protein. Most of the synonymous mutations identified in the SARS-CoV-2 genome are found to have a minor effect on RNA folding and RNA stability of the virus except for C913U and C26735U mutations. Due to the shortcomings of prediction tools, experimental studies are needed to give a more comprehensive understanding of the biological consequences of synonymous mutations on SARS-CoV-2 virus.\n\n\nEthics and dissemination\n\nNo ethical approval is required for data analysis in this study (EA2702021).\n\n\nData and software availability\n\nSARS-CoV-2 virus genome sequence data were obtained from the GISAID Database. The multiple alignment data can be assessed through FigShare.\n\nFigshare: MSA (SARS-CoV-2). https://doi.org/10.6084/m9.figshare.16681900.v135\n\nThis project contains the following underlying data.\n\n• MSA_0.fasta (multiple sequence alignment of SARS-CoV-2 sequences obtained between 31-12-2019 and 31-05-2020.)\n\n• MSA_1.fasta (multiple sequence alignment of SARS-CoV-2 sequences obtained between 01-06-2020 and 15-10-2020.)\n\n• MSA_2.fasta (multiple sequence alignment of SARS-CoV-2 sequences obtained between 16-10-2020 and 31-01-2021.)\n\n• MSA_3.fasta (multiple sequence alignment of SARS-CoV-2 sequences obtained between 01-02-2021 to 22-03-2021.)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nThe python code for the identification of SARS-CoV-2 genome mutations can be assessed through GitHub.", "appendix": "Author contributions\n\n\n\nCHN contributes to the concept, design, supervision of the project. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKelly JA, Olson AN, Neupane K, et al.: Structural and functional conservation of the programmed −1 ribosomal frameshift signal of SARS coronavirus 2 (SARS-CoV-2). J Biol Chem. 2020; 295(31): 10741–10748. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCao C, Cai Z, Xiao X, et al.: The architecture of the SARS-CoV-2 RNA genome inside virion. Nat Commun. 2021; 12(1): 3917. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCornillez-Ty CT, Liao L, Yates JR 3rd, et al.: Severe Acute Respiratory Syndrome Coronavirus Nonstructural Protein 2 Interacts with a Host Protein Complex Involved in Mitochondrial Biogenesis and Intracellular Signaling. J Virol. 2009; 83(19): 10314–10318. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSui L, Zhao Y, Wang W, et al.: SARS-CoV-2 Membrane Protein Inhibits Type I Interferon Production Through Ubiquitin-Mediated Degradation of TBK1. Front Immunol. 2021; 12: 662989. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFaure G, Ogurtsov AY, Shabalina SA, et al.: Role of mRNA structure in the control of protein folding. Nucleic Acids Res. 2016; 44(22): 10898–10911. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWong EH, Smith DK, Rabadan R, et al.: Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus. BMC Evol Biol. 2010; 10(1): 253. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSharp PM, Tuohy TM, Mosurski KR: Codon usage in yeast: Cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res. 1986; 14(13): 5125–5143. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKomar AA: The Yin and Yang of codon usage. Hum Mol Genet. Oxford University Press, 2016; 25(R2): R77–R85. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWx B: MSA (SARS-CoV-2). figshare. Dataset. 2021. http://www.doi.org/10.6084/m9.figshare.16681900.v1" }	[ { "id": "97299", "date": "02 Nov 2021", "name": "Takahiko Koyama", "expertise": [ "Reviewer Expertise Genome Analysis", "SARS-CoV-2", "Cancer", "Immunology", "Stem cell" ], "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\nBoon et al. made an investigation of synonymous mutations of SARS-CoV-2 genomes. Authors first identified common synonymous mutations such as 3037C>T followed by secondary structure predictions using RNAfold.\n\nFirst, the number of genomes authors used is too small and too old. Currently, nearly 5 million genomes are uploaded at GISAID; however, authors used only 30,229. The set does not represent the current mutational landscape of SARS-CoV-2. Authors need to update the data. I have 3 million genomes analyzed and 18108 distinct synonymous mutations identified. The list of highest frequency in Table 1 looks completely different with the latest dataset.\nSecondly, authors employed RNAfold for RNA secondary structure prediction. Although RNAfold is a standard software for the task, the accuracy of the prediction is not impressive. Authors need to explore various other tools for the secondary structure or justify the usage of RNAfold.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "7389", "date": "08 Nov 2021", "name": "Chong Han Ng", "role": "Author Response", "response": "Boon et al. made an investigation of synonymous mutations of SARS-CoV-2 genomes. Authors first identified common synonymous mutations such as 3037C>T followed by secondary structure predictions using RNAfold. First, the number of genomes authors used is too small and too old. Currently, nearly 5 million genomes are uploaded at GISAID; however, authors used only 30,229. The set does not represent the current mutational landscape of SARS-CoV-2. Authors need to update the data. I have 3 million genomes analyzed and 18108 distinct synonymous mutations identified. The list of highest frequency in Table 1 looks completely different with the latest dataset. RE: Thank you for the comments and feedbacks. We downloaded SARS-CoV-2 virus genome data submitted from 31 December 19 to 22 March 21 on 23 March 21. There were about a total of 842,603 SARS-CoV-2 virus genomes sequences before applying filters. SARS-CoV-2 genomic sequences were filtered by setting parameters to keep only sequences with complete genome, high coverage, low coverage excluded and patient status options. The use of the low coverage excluded and patient status filters were unintentionally left out in the manuscript and they will be added later. In our study, the use of these filters allows us to analyze high quality data to identify SARS-CoV-2 mutations without the requirement of high computing power. Our data is representative of the mutational landscape of SARS-CoV-2 for this specified period. Same synonymous mutations, including C913T, C3037T, C5986T, C14676T, C15279T and T16176C were identified in alpha strain by other research groups (https://covariants.org/variants/20I.Alpha.V1) and (https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/959438/Technical_Briefing_VOC_SH_NJL2_SH2.pdf). The frequency of alpha strain peaked in April-May 21 and subsequently it has been quickly replaced by delta strain. Interestingly the defining synonymous mutations of delta strain (https://covariants.org/variants/21A.Delta) are very different from those of alpha strain. The mutational landscape of SARS-CoV-2 genome is very dynamic as shown by other research groups. Bear in mind that the main objective of our paper is not to monitor the mutational changes of SARS-CoV-2 genome. Although it is useful to get more recent dataset, it is out of the scope of our study to update the data. Both identification of the SARS-CoV-2 mutations and the prediction analysis of the biological consequences of these mutations are very time-consuming processes. The first draft of the manuscript was prepared in late June 21 and submitted in late August 21. Since different SARS-CoV-2 variants may have different sets of mutations, we will gain more insight to study the effects of different mutations in different SARS-CoV-2 variants. In our follow-up study, we plan to predict and compare the effect of the mutations of different variants. These analyses may provide some plausible explanation why some variants are replaced by other variants eventually. Secondly, authors employed RNAfold for RNA secondary structure prediction. Although RNAfold is a standard software for the task, the accuracy of the prediction is not impressive. Authors need to explore various other tools for the secondary structure or justify the usage of RNAfold. RE: We chose RNAfold because it is the most commonly used tools to predict the RNA secondary structure. Other than RNAfold, we also considered using Mfold to perform the RNA secondary structure prediction as well. However, the Mfold server was down during the time of the study. RNAfold computes an optimal structure over the whole sequence length, which means its performance and accuracy can be affected as the sequences used get longer. However, in our case, the accuracy of the prediction is still acceptable since the sequence we used to do the structure prediction is relatively short. Besides, the prediction results we obtained from RNAfold is further supported with the prediction results obtained from MutaRNA, which predicts the structural changes induced by the mutation by estimating the base pairing probabilities. In our results, the circular plot from MutaRNA shows the changes in the base pairing probabilities near the mutation site correlates well with the RNA secondary structure predicted by RNAfold." }, { "c_id": "9047", "date": "30 Nov 2022", "name": "Chong Han Ng", "role": "Author Response", "response": "First, the number of genomes authors used is too small and too old. Currently, nearly 5 million genomes are uploaded at GISAID; however, authors used only 30,229. The set does not represent the current mutational landscape of SARS-CoV-2. Authors need to update the data. I have 3 million genomes analyzed and 18108 distinct synonymous mutations identified. The list of highest frequency in Table 1 looks completely different with the latest dataset. RE: We submitted a revised version in Sep 2022. Although we didn’t use the latest dataset, we provide some justification in the discussion to explain why our data may remain relevant. We hope you will consider to review our manuscript again. The landscape of mutational profile of SARS-CoV-2 genome is very dynamic, changing rapidly. It is far beyond the scope of this study to include all variants reported. Based on the timelines of emergence of different variants, the cut-off date of our data collection overlaps with the period when the frequency of the alpha variant peaked. All the synonymous mutations except C241T reported in the alpha strain have been identified in our study as well. Although the alpha variant has been replaced by other variants in human population, it is detected from wildlife animals based on a few recent genomic surveillance analysis. It is possible that these alpha variant from wildlife animal may jump back to human, hence it remains relevant to predict the biological consequences of these synonymous mutations. The title of the paper has been revised accordingly. The limitation of the dataset was included in the discussion. Secondly, authors employed RNAfold for RNA secondary structure prediction. Although RNAfold is a standard software for the task, the accuracy of the prediction is not impressive. Authors need to explore various other tools for the secondary structure or justify the usage of RNAfold. RE: In the revised version, we used 3 RNA secondary prediction analysis tool, namely RNAfold, IPknot++, to improve the outcome of the analysis. The prediction results for all top 10 synonymous mutations using these 3 tools and the base pair probability estimation results are summarized in the Table 2." } ] }, { "id": "101828", "date": "20 Dec 2021", "name": "Leyi Wang", "expertise": [ "Reviewer Expertise Clinical Virology Diagnosis" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript entitled “Prediction of the Effects of Synonymous Variants on SARS-CoV-2 Genome” reports an analysis of the SARS-CoV-2 genome obtained in the GISAID database. The authors analyzed synonymous changes of the 30,229 SARS-CoV-2 sequences available online, and the effects of these changes on RNA secondary structures and base-pair probability. They identified 150 synonymous mutations in 11 coding regions. Mutations with higher frequency are mostly found in ORF1a and ORF1b and two mutations (C913U and C26735U) found with effect on the predicted RNA secondary structure are not those with higher frequency.\nThis study collected 30,229 sequences in the database in the period of 31 Dec 2019 to 22 March 2021. As of 17 Dec 2021, there are over 4.4 million complete genomes with high coverage. Will these sequences used in the study include all variants reported or what sequences of variants are included? A table to summarize all variants with these mutations or not is needed.\nA major concern is that the sequences even filtered by setting parameters to keep only sequencing with complete genome and high coverage still contain bad sequences, how did the authors exclude those sequences?\nIn the abstract section, the results part only included those mutations with high frequency but did not contain results of other analyses. Instead, they included the results of RNA secondary structure analysis in the 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? 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": "8660", "date": "05 Sep 2022", "name": "Chong Han Ng", "role": "Author Response", "response": "The manuscript entitled “Prediction of the Effects of Synonymous Variants on SARS-CoV-2 Genome” reports an analysis of the SARS-CoV-2 genome obtained in the GISAID database. The authors analyzed synonymous changes of the 30,229 SARS-CoV-2 sequences available online, and the effects of these changes on RNA secondary structures and base-pair probability. They identified 150 synonymous mutations in 11 coding regions. Mutations with higher frequency are mostly found in ORF1a and ORF1b and two mutations (C913U and C26735U) found with effect on the predicted RNA secondary structure are not those with higher frequency. This study collected 30,229 sequences in the database in the period of 31 Dec 2019 to 22 March 2021. As of 17 Dec 2021, there are over 4.4 million complete genomes with high coverage. Will these sequences used in the study include all variants reported or what sequences of variants are included? A table to summarize all variants with these mutations or not is needed. Response: We downloaded the raw data on 23rd March 2021 and completed the data analysis in late June 2021. We submitted the manuscript in late August 2021. The landscape of mutational profile of SARS-CoV-2 genome is very dynamic, changing rapidly. It is far beyond the scope of this study to include all variants reported. Based on the timelines of emergence of different variants, the cut-off date of our data collection overlaps with the period when the frequency of the alpha variant peaked. All the synonymous mutations except C241T reported in the alpha strain have been identified in our study as well. We added new paragraph in the discussion section to discuss the impact of our findings and to explain why the study of alpha variant remains relevant now. In addition, we used 3 RNA secondary prediction analysis tool, instead of one, to improve the outcome of the analysis. The prediction results for all top 10 synonymous mutations using these 3 tools and the base pair probability estimation results are summarized in the Table 2. A major concern is that the sequences even filtered by setting parameters to keep only sequencing with complete genome and high coverage still contain bad sequences, how did the authors exclude those sequences? Response: In our original method, we used the high coverage filter when downloading from GISAID database, in which only entries with less 1% N and 0.05% unique amino acids mutations are included. To further reduce bad sequences, we filtered to remove those sequences with higher than 0.1% N unresolved nucleotides and ambiguous letters. A total of 3584 sequences were removed by applying this filter. The list of the synonymous mutations remains unchanged despite of the revision of the mutation frequency. In the abstract section, the results part only included those mutations with high frequency but did not contain results of other analyses. Instead, they included the results of RNA secondary structure analysis in the conclusion. Response: The abstract has been revised to update the results and conclusion." } ] }, { "id": "135257", "date": "28 Apr 2022", "name": "Chandran Nithin", "expertise": [ "Reviewer Expertise RNA structure prediction", "Computational Structural Biology", "RNA-protein complexes." ], "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 titled \"Prediction of the Effects of Synonymous Variants on SARS-CoV-2 Genome\" analyzes 30,299 SARS-CoV-2 genomes retrieved from GISAID for the period between 31st December 2019 and 22nd March 2021. The study identifies 381 mutations in the genome, of which 150 are synonymous. The study discusses two mutations, C913U and C26735U.\nThe dataset used in this study is outdated and represents only a short period between 31st December 2019 and 22nd March 2021. It will be necessary to update the data to include more sequences from a wider time frame.\nThe authors had indicated (through the editorial manager) that they are unwilling to update the dataset; the authors need to indicate the same in the title and detail the limitations of the dataset in the introduction section.\n\nThe authors have used the RNAfold program to predict the secondary structure of wild-type and mutant sequences. The authors need to use additional prediction tools and check for consensus between the predicted structure. Moreover, authors need to employ prediction tools to predict pseudoknots in the RNA secondary structure.\n\nThe secondary structure of SARS-CoV2 determined with the help of data from SHAPE-MaP, icSHAPE, and DMS-MaPseq experiments is available in the literature.1,2,3 The authors should utilize this data to augment this study.\n\nThe study requires the inclusion of appropriate controls which quantify the effect of mutations on the stability of the RNA structure. The authors state that \"The minimum free energy value of the mutant (- 146.90 kcal/mol) is slightly less negative than that of the wild type (- 147.40 kcal/mol), which makes it a less thermodynamically stable structure compared to the wild type.\" This claim needs to be explored in detail and supported with evidence from experimental data and literature.\n\nThe authors state that C26735U mutation induces changes in the predicted RNA secondary structure by forming an extra multibranch loop at the mutation site. The authors should compare the same with secondary systems mentioned in point 3 (See Ref 1, 2, and 3). The authors need to perform a similar analysis for C913U.\n\nThe study identifies 381 mutations in the genome, of which 150 are synonymous; however, it discusses only two. The authors need to provide the data on the remaining 148 synonymous mutations and briefly discuss some of them in the manuscript.\n\nThe authors need to expand and include relevant literature in the introduction section.\n\nThe manuscript needs to be edited for language errors.\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? No", "responses": [ { "c_id": "8661", "date": "05 Sep 2022", "name": "Chong Han Ng", "role": "Author Response", "response": "The manuscript titled \"Prediction of the Effects of Synonymous Variants on SARS-CoV-2 Genome\" analyzes 30,299 SARS-CoV-2 genomes retrieved from GISAID for the period between 31st December 2019 and 22nd March 2021. The study identifies 381 mutations in the genome, of which 150 are synonymous. The study discusses two mutations, C913U and C26735U. The dataset used in this study is outdated and represents only a short period between 31st December 2019 and 22nd March 2021. It will be necessary to update the data to include more sequences from a wider time frame. The authors had indicated (through the editorial manager) that they are unwilling to update the dataset; the authors need to indicate the same in the title and detail the limitations of the dataset in the introduction section. Response: The landscape of mutational profile of SARS-CoV-2 genome is very dynamic, changing rapidly. As of 14 August 2022, there are more than 12 million SARS-CoV-2 virus genomes sequences deposited in GISAID database. Although it is useful to get more recent dataset, it is out of the scope of our study to update the data. Both identification of the SARS-CoV-2 mutations and the prediction analysis of the biological consequences of these mutations are very time-consuming processes. Based on the timelines of emergence of different variants, the cut-off date of our data collection overlaps with the period when the frequency of the alpha variant peaked. All the synonymous mutations except C241T reported in the alpha variant have been identified in our study as well. Although the alpha variant has been replaced by other variants in human population, it is detected from wildlife animals based on a few recent genomic surveillance analysis. It is possible that these alpha variant from wildlife animal may jump back to human, hence it remains relevant to predict the biological consequences of these synonymous mutations. The title of the paper has been revised accordingly. The limitation of the dataset was included in the discussion. The authors have used the RNAfold program to predict the secondary structure of wild-type and mutant sequences. The authors need to use additional prediction tools and check for consensus between the predicted structure. Moreover, authors need to employ prediction tools to predict pseudoknots in the RNA secondary structure. Response: To improve the outcome of the RNA secondary structure analysis, 3 prediction tools, namely RNAfold, IPknot++ and MXfold2 are used in our study. Of these, IPknot++ predicted some synonymous mutations may affect the pseudoknot formation. The prediction results for all top 10 synonymous mutations using these 3 tools are summarized in the Table 2 The secondary structure of SARS-CoV2 determined with the help of data from SHAPE-MaP, icSHAPE, and DMS-MaPseq experiments is available in the literature.1,2,3 The authors should utilize this data to augment this study Response: To improve the outcome of the prediction analysis, the RNA secondary structure of wild type and mutant sequences were predicted using RNAfold program with the incorporation of SHAPE reactivity data obtained from the study done by Manfredonia et al. (2020). The study requires the inclusion of appropriate controls which quantify the effect of mutations on the stability of the RNA structure. The authors state that \"The minimum free energy value of the mutant (- 146.90 kcal/mol) is slightly less negative than that of the wild type (- 147.40 kcal/mol), which makes it a less thermodynamically stable structure compared to the wild type.\" This claim needs to be explored in detail and supported with evidence from experimental data and literature. Response: Instead of comparing minimum free energy between the wild type and mutant, we applied three RNA secondary structure prediction tools to predict the effect of the mutation on RNA secondary structure. The authors state that C26735U mutation induces changes in the predicted RNA secondary structure by forming an extra multibranch loop at the mutation site. The authors should compare the same with secondary systems mentioned in point 3 (See Ref 1, 2, and 3). The authors need to perform a similar analysis for C913U. Response: The results of the 4 mutations showing changes in all 3 prediction tools are included in Figure 2-5. The study identifies 381 mutations in the genome, of which 150 are synonymous; however, it discusses only two. The authors need to provide the data on the remaining 148 synonymous mutations and briefly discuss some of them in the manuscript. Response: The RNA secondary structures prediction results using 3 prediction tools for the top 10 synonymous mutations have been included in Extended data 1-3. There were 4 mutations showing changes in all 3 prediction tools and the results are discussed in the manuscript. The authors need to expand and include relevant literature in the introduction section. Response: The relevant literature in the introduction section has been updated. The manuscript needs to be edited for language errors. Response: The language errors have been edited accordingly." } ] } ]	1	https://f1000research.com/articles/10-1053
https://f1000research.com/articles/13-1069/v1	18 Sep 24	{ "type": "Research Article", "title": "Simplification of clean development mechanism to measure CO2 emission reductions from shifting private transportation to mass rapid transit: a case study of MRT Jakarta Phase 1", "authors": [ "Nunuj Nurdjanah", "Tri Edhi Budhi Soesilo", "Kosuke Mizuno", "Raldi Hendro Koestoer", "Tri Edhi Budhi Soesilo", "Kosuke Mizuno", "Raldi Hendro Koestoer" ], "abstract": "Background The Indonesian government built the Mass Rapid Transit (MRT) in Jakarta to reduce traffic congestion and carbon dioxide (CO2) emissions. The objective of this study is to estimate the CO2 emissions reductions from switching from private transport to MRT by using a methodology proposed by the United Nations Convention on Climate Change (UNFCCC) for developing countries, namely the Clean Development Mechanism (CDM) methodology, which generates Certified Emission Reductions (CERs). This methodology is more comprehensive than other available methodologies. However, this method has not been widely used to calculate greenhouse gas (GHG) emission reductions in mass transit projects because it is complex enough to require a lot of data based on primary surveys. Therefore, this research simplifies the CDM formula to make it easier and applicable in Indonesia.\n\nMethods The primary data were collected using a questionnaire distributed to 480 MRT Jakarta Phase 1 user respondents in September 2019 (baseline); the secondary data were obtained from The MRT Jakarta. The data were processed using IBM SPSS Statistics 27. The simplified Clean Development Mechanism Approved Consolidated Methodology 0016 (CDM ACM 0016) was the analysis method used.\n\nResult The results of this study indicate that 53.75% of MRT Jakarta Phase 1 users are shifting from private transportation, which has reduced CO2 emissions by 2,732.7 tons in 2019 and 6,043.9 tons in 2023. Increasing the number of MRT passengers who switch from private transportation will further reduce CO2 emissions.\n\nConclusion and implications The simplified CDM ACM 0016 formula may be suitable for use in Indonesia. This would enable the measurement of CO2 emission reductions through mitigation actions through MRT development to be certified by the UNFCCC. Applying this method in calculating CO2 emission reductions, implementing strategies to increase MRT passengers, and using renewable energy electricity sources would increase CO2 emission reductions.", "keywords": [ "Mass Rapid Transit (MRT)", "Greenhouse Gas", "Shifting", "Private Transportation", "Clean Development Mechanism" ], "content": "Introduction\n\nThe world’s highest greenhouse gas contributor is CO2 emissions in the transportation sector, which account for approximately 20% of global emissions, with the majority of these emissions resulting from land transportation (Albuquerque, Maraqa, Chowdhury, & Mauga, 2020). It is estimated that as much as 91% of transport emissions originate from road transport (Sekaryadi & Santosa, 2017). Projections indicate that transportation will be the most rapidly growing source of emissions over the next three decades, particularly in developing countries. The proportion of greenhouse gas (GHG) emissions from transportation in developing countries is projected to increase from approximately 35% in 2000 to 52% to 63% by 2030. Therefore, measures must be taken to reduce carbon dioxide and related greenhouse gas emissions. In this sector, several options are available for consideration, including the promotion of vehicles that use clean technologies and fuels, demand management, the implementation of more efficient public transportation systems, and the transition to cleaner modes of transportation (Asian Development Bank, 2013). However, countries’ patterns and behaviors vary considerably in implementing CO2 emission reduction efforts and targets (Nihayah, Gravitiani, & Tri Rahayu, 2021).\n\nAccording to data published by the World Resource Institute (WRI), Indonesia became the sixth most significant carbon GHG emitter in the world in 2018, followed by China, the United States, the European Union, India, and Russia (WRI, 2019). The results of the calculation of national carbon dioxide (CO2) emissions indicate that Indonesia’s greenhouse gas (GHG) emission level in 2018 was 1,615,569 Gg CO2e (Central Bureau of Statistics, 2020). A total of 144,169 Gg tons of CO2 were produced by the transportation sector, comprising the land and rail transportation subsectors, which collectively emitted 130,748 Gg tons of CO2 (90.7%), the sea transportation subsector, which emitted 131 Gg tons of CO2 (0.1%), and the air transportation subsector, which emitted 13,291 Gg tons of CO2 (9.2%). The land transportation and railway sectors are the primary contributors to greenhouse gas emissions (Directorat General Climate Change, Ministry Environment and Forestry, Republic Indonesia, 2019).\n\nBased on these considerations, the Government of Indonesia took the initiative to begin construction of the first MRT line to be operational in Jakarta in 2019. The initial project, called MRT Jakarta Phase 1, was designed to facilitate transitioning from private transportation to public transportation. The city of Jakarta was chosen as the location of the MRT project due to its status as the capital of Indonesia, with the highest concentration of private vehicles. This factor contributes to congestion and increased greenhouse gas emissions. Data from the DKI Jakarta Environment Agency show that greenhouse gas (GHG) emissions by the DKI Jakarta reached 38.03 million tons CO2 in 2010 and increased to 57.6 million tons CO2 in 2018. This represents a 51.3% increase in GHG emissions during the observed period. The main source of GHG emissions in DKI Jakarta is the combustion of fuel oil for transportation purposes, followed by emissions from the energy sector, especially power plants. The level of greenhouse gas (GHG) emissions in the transportation sector in DKI Jakarta was 7,776,000 tons CO2 (DKI Jakarta Provincial Environmen Agency, 2019).\n\nOne of the primary causes of the elevated GHG emissions in DKI Jakarta can be attributed to the prevalence of motorized vehicles, particularly private cars. According to data from the Central Bureau of Statistics of the DKI Jakarta Province (2019), the number of motorized vehicles in DKI Jakarta in 2019 was 11,839,921. Of these, 8,194,590 units were motorcycles (69.2%), 2,809,989 units were passenger cars (23.7%), 295,370 units were busses (2.5%), and 543,972 units were trucks (4.6%). According to data from the Jakarta Bogor Depok Tangerang Bekasi (Jabodetabek) Urban Transportation Policy Integration (JUTPI) Phase 2, the utilization of public transportation in DKI Jakarta in 2018 remains relatively low at 10%, inclusive of the usage of public busses, TransJakarta, electric rail trains (KRL), taxis, and bajaj (Coordinating Ministry of Economic Affairs collaboration with JICA, 2019). This is because the individual ownership and use of motorized vehicles often results in single-passenger trips, in which the vehicle typically carries only one person. This scenario results in the movement of vehicles rather than the efficient transportation of people and thus contributes to transportation inefficiencies. These inefficiencies manifest in the form of increased time and fuel wastage due to traffic congestion, resulting in increased levels of environmental pollution from exhaust emissions (Anususanto, Priyanto, Munawar, & Wibisono, 2014). It is therefore imperative to reduce the consumption of natural resources, particularly physical space and energy, while also mitigating the associated environmental impacts. Non-motorized modes of transportation, such as walking and bicycles, should be prioritized for short distances. For certain distances that require motorized transportation, it is preferable to utilize modes of transportation with higher capacity and superior energy efficiency, such as high-capacity collective transportation modes, including urban railways, subways, and busses (D’Agosto, 2019). There is potential for CO2 reduction from shifting the use of private transportation to mass transportation (Hirota, Poot, & Minato, 2003). MRT projects have a good impact on carbon dioxide (CO2) reduction, mainly in developing cities where the transport demand has increased rapidly. The existing assessment to reduce CO2 emissions, however, is hardly applicable to urban transportation projects because of limited data (Luathep, Fukuda, Jaensirisak, & Fillone, 2013). Therefore, if MRT development is able to replace the use of private transportation by 2%, it will result in savings of 6.77 Barrels of Oil Equivalent (BOE) per vehicle per year. Similarly, a 0.1% shift from motorcycle users to public transportation would result in savings of 1.17 BOE per vehicle per year (Directorate General of New, Renewable Energy and Energy Conservation, 2020). Furthermore, the substitution of private transportation with MRT will reduce CO2 emissions (Maimunah & Kaneko, 2016).\n\nIt is for this reason that MRT is a mode of transport that has been identified as a potential candidate for inclusion in the CDM project. The emission reductions that can be attributed to this mode of transport can be certified and traded. The impact of MRT Jakarta phase 1 operations on CO2 emissions has been quantified in several studies in Indonesia. It is important to note, however, that the aforementioned calculations did not employ the CDM methodology proposed by the UNFCCC for obtaining Certified Emission Reductions (CERs). This methodology is more comprehensive than other available methodologies. Nevertheless, it has not been widely employed in the calculation of greenhouse gas (GHG) emission reductions in mass transit projects, primarily because of its complexity and the necessity for extensive primary data. Accordingly, this study presents a simplified version of the CDM formula, adapted to the Indonesian context, for estimating CO2 emission reductions resulting from the shift from private transportation to MRT. The objective of this approach is to facilitate the accounting of CO2 emission reductions from MRT projects in Indonesia with a view to carbon certification and trading.\n\n\nLiteratur review\n\nCDM is one of the flexible mechanisms outlined in the Kyoto Protocol that provides emission reduction projects that generate Certified Emission Reductions (CERs), derived from the mitigation activities of CDM Projects (UNFCCC, 2022). The objective is to facilitate the reduction of carbon emissions in developing countries through the implementation of carbon markets, thereby enabling the realization of sustainable development (Zegras, Chen, & Grütter, 2009). The CDM methodology is a methodology that the Intergovernmental Panel on Climate Change (IPCC) uses to estimate CO2 emission reductions within the transportation sector. It is a sophisticated method that is flexible and depends on data requirements, such as vehicle technology and vehicle type, and can be combined with fuel consumption and average mileage. It is a considerably more rigorous approach than other methodologies of a similar nature (Dharmowijoyo & Tamim, 2010). However, the CDM methodology is challenging to implement, its formula is intricate, the amount of data required is vast, and its costs are considerable. As a result, only 0.3% of the transportation sector is included in the CDM and certified, despite the sector’s contribution of 20% to emissions (Asian Development Bank, 2013). Nevertheless, the CDM methodology offers certain advantages, including the potential to enhance international climate cooperation in climate change mitigation efforts (Wan, Zhang, & Chen, 2024). The United Nations Framework Convention on Climate Change (UNFCCC) has approved more than 250 CDM methodologies for measuring baseline emissions, monitoring emissions, and awarding carbon certificates. While these methodologies are not yet mandatory, they can be adapted in a way that does not undermine the country’s own emission reduction calculations (Michaelowa et al., 2020). Although the CDM methodology is not yet a mandatory requirement of the UNFCCC, particularly for developing countries in measuring CO2 emissions, the utilization of this method can result in global recognition through the issuance of emission certificates. The existence of comparable emission measurement standards between countries will facilitate the comparison of carbon emissions and facilitate international trade. Nevertheless, the implementation of the CDM methodology in each country is constrained by inherent discrepancies that can be mitigated through adaptations contingent on the completeness of the data requirements and transportation conditions in each country. One potential solution is to simplify the methodology to facilitate its application to CDM projects in each country. Nevertheless, any proposed simplification must be supported by scientific evidence and deemed reasonable.\n\nOne of the approved CDM methodologies for the transportation sector is ACM 0016, which was developed for calculating emission reductions from mass transit projects and came into effect in 2010 (Institute for Global Environmental Strategies (IGES), 2011). Nevertheless, this approach presents a significant challenge in practice due to the difficulty of obtaining data to establish an emissions baseline in the absence of mitigation initiatives such as MRT. Consequently, only a limited number of MRT projects can be included in the CDM list (Sharma, Dhyani, & S. Gangopadhyay, 2010). Thus, it is imperative to establish the baseline in a manner that aligns to construct the MRT. For instance, the rationale behind the establishment of MRT Jakarta is to alleviate congestion and curtail CO2 emissions by encouraging the transition from private vehicle usage to MRT. The baseline for the MRT Jakarta project is therefore the emissions from private vehicle users who have switched to MRT. In order to facilitate implementation and provide greater clarity in determining baseline emissions, emissions from the MRT project, and resulting emission reductions, this study employs simplifications of the ACM 0016 methodology.\n\n\nMethods\n\nThis research project has been approved by the Head of the Research and Development Center for Road Transportation and Railways, Transportation Research and Development Agency, Ministry of Transportation of the Republic of Indonesia, through an approval letter (number 201/KU.004/VIII/BLTD-2019) dated August 21, 2019, issued in Jakarta. The aforementioned approval letter permits the collection of primary data from users of the Jakarta MRT Phase 1 in Jakarta, Indonesia.\n\nA consent form was included in the questionnaire on the opening page, before respondents answered the questions. Due to the limited survey time on the train, participants gave verbal consent to participate in the study, which was approved by the ethics committee. There was no external influence or coercion on participants to participate in this study. In addition, all data collected will be kept confidential to maintain the privacy of the participants.\n\nThis research was conducted on the MRT Jakarta Phase 1 operational line, which has a length of 16 km, starting from HI Bundaran Station and ending at Lebak Bulus Station. The MRT Jakarta Phase 1 line includes elevated structures and underground lines, which comprise 13 stations. Of these, seven are elevated stations and six are underground stations. In Figure 1 shows The elevated MRT line consists of the following stations: Lebak Bolus, Fatmawati, Cipete Raya, Haji Nawi, Blok A, Blok M, and Sisingamangaraja. The underground line consists of the following stations: Senayan, Istora, Bendungan Hilir, Setiabudi, Dukuh Atas, and Bundaran HI (PT. MRT Jakarta, 2024).\n\nSource: PT. MRT Jakarta (2024).\n\nThe survey was conducted over 7 days, including weekdays and weekends. The travel patterns of MRT users on weekdays differ from those observed on weekends. On weekdays, the MRT is primarily used for work-related commutes, whereas on weekends, it is used more frequently for non-work purposes.\n\nThis study employed a combination of primary and secondary data sources. Secondary data were obtained through a comprehensive review of relevant literature and information from relevant agencies. Primary data were collected by administering questionnaires to MRT users and by direct observation. The sample was determined in accordance with the Isaac and Michael formula, which is a statistical method for calculating the minimum sample size for a given population.\n\nIn this context, variable S represents the number of samples to be determined, and N denotes the known population size. The chi-squared statistic, denoted by χ2, is a function of the level of freedom and error rate. The variable d represents the difference between the sample and the population means. The probability of being correct (P) is a function of the aforementioned variables, whereas the probability of being wrong (Q) is a function of the variables N and S (Sugiyono, 2016).\n\nIn 2019, the daily ridership of the MRT system was 86,270 passengers. The calculated value of the chi-square statistic, with one degree of freedom 1 and a 5% margin of error, is 3.841. This indicates that the probability of the observed result is 0.5. Based on this parameter, a minimum sample size of 382 was determined for statistical significance. The survey was conducted inside the train due to the relatively short waiting time of only 5 minutes at the station. To ensure accurate data collection, respondents were marked as passengers boarding from the station where they first boarded the train. Furthermore, the data obtained was processed using IBM SPSS Statistics 27 software (IBM, 2024).\n\nIn this study, validity and reliability tests were conducted on the variables included in the questionnaire distributed to MRT user respondents. The trial was conducted with a sample of 50 MRT users. The variables addressed in this study encompass respondents’ profiles and those related to using MRT Jakarta Phase 1. The questionnaire included questions regarding the respondents’ characteristics, including age, education level, current occupation, and income. The variables pertaining to the use of the MRT system encompass the preceding modes of transportation used by respondents before they adopted the MRT, the rationale behind their chosen mode of transport, the frequency of their weekly trips, and the number of daily trips.\n\nThe instrument reliability test uses the Cronbach’s alpha value as the reliability coefficient. If the reliability coefficient value is equal to or greater than 0.6, the instrument has good reliability; if the reliability coefficient value is <0.6, then the tested instrument is not reliable (Arikunto, 2017).\n\nTable 1 showing The validity test results indicate that all variables were statistically significant at a significance level of 0.05 or below. The reliability test results for the variables in question indicate that a Cronbach’s alpha value of 0.69 is more significant than 0.6, demonstrating reliability\n\nThis study employed a descriptive analytical methodology, whereas the calculation of CO2 emission reductions was based on the simplified CDM ACM 0016 methodology. A descriptive approach was employed to examine the demographic and socioeconomic characteristics of MRT users, including gender, age, income, and occupation. The methodology employed to quantify CO2 emission reductions resulting from the switching of private transportation to MRT systems is that delineated in the simplified Clean Development Mechanism (CDM) ACM 0016 (UNFCCC, 2015).\n\nThe CDM ACM 0016 methodology was designed for the development and operation of rail- or bus-based mass transit systems (MRTS) in urban or suburban areas. This is achieved through the following formula:\n\nWhere:\n\nERy = Emission reduction in year y (tons of CO2)\n\nBEy = Baseline emissions in year y (tons CO2)\n\nPEy = Emission reduction by MRT Project in year y (tons CO2)\n\nThe calculation of emission reductions excludes the consideration of the linkage of emissions in the year in question (LEy) due to the substantial resources required for such a survey. The baseline scenario considers the emissions resulting from using road transportation modes, specifically cars and motorcycles, in the absence of MRT. These emissions are differentiated according to the type of road transportation mode and are calculated based on data from surveyed passengers.\n\nThe baseline emissions were calculated using the following formula:\n\nWhere:\n\nBEy = Baseline emissions in year y (t CO2)\n\nBEp,y = Baseline emissions per surveyed passenger in year y (t CO2)\n\nFEXp,y = Expansion factor per surveyed passenger per year (y)\n\nPy = Total number of passengers per year y\n\nPSPER = Number of passengers during the survey period (1 week)\n\np = Passenger survey (per passenger)\n\ny = Year\n\nThe baseline emissions per passenger were calculated using the following formula:\n\nWhere:\n\nBEp,y = Baseline emissions per surveyed passenger in year y (t CO2)\n\nEFpkm,i,y = Emission factor per passenger kilometer per transport mode in year y (g CO2/pkm)\n\nBTDp,i,y = Baseline mileage per surveyed passenger using transit mode I in year y (pkm)\n\nThe vehicle categories identified use fuel oil and operate on roads parallel to the MRT Jakarta Phase 1 line.\n\nThe emissions generated by the MRT project were calculated using the following formula:\n\nWhere:\n\nPEy = projected emissions in year y (t CO2)\n\nDPEy = Project direct emissions in year y (t CO2)\n\nIPEy = Indirect emissions of the project in year y (t CO2)\n\nThe direct emissions of the project in year y (t CO2) are calculated using the following formula:\n\nWhere:\n\nDPEy = Direct project emissions in year y (t CO2)\n\nECy = Electricity consumption (only for MRT traction) per year y (MWH)\n\nEFEl,y = Electricity Grid Emission Factor (kg CO2/kWh).\n\nIndirect project emissions (IPEy) are calculated using the following formula:\n\nWhere:\n\nIPEy = Project indirect emissions in year y (t CO2)\n\nIPEp,y = Project indirect emissions per surveyed passenger p in year y (g CO2)\n\nFEXp,y = Expansion factor for each surveyed passenger (p) in year y\n\nPy = Total number of passengers per year y\n\nPSPER = Number of passengers during the survey period (one week)\n\nP = surveyed passengers (each individual)\n\ny = year of the credit period\n\nThe mitigation action strategy implemented in this methodology is to reduce GHG emissions by enhancing energy efficiency and redirecting users of high-GHG transportation modes to those that produce fewer GHG emissions (UNFCCC, 2015). In this study, the methodology is streamlined to facilitate its implementation in accordance with the availability of data and traffic conditions on the road sections where the MRT Jakarta is constructed. This is detailed in the Results and Discussion section.\n\n\nResults and discussion\n\nTable 2 presents the socioeconomic characteristics of MRT users as revealed by the survey results. As can be seen, the age range of respondents is 15-25 years, representing 32.7% of the total sample. Additionally, users aged 65 years and older constitute 1% of the total sample. Most MRT users have obtained a bachelor’s degree, representing 58% of the total sample. The gender distribution of respondents revealed that 47.1% were male and 52.9% were female. The largest occupational group among respondents was private employees (49% of the total sample. The largest proportion of respondents with incomes above Rp 14,000,000 was 20.8%.\n\nTable 3 shows the results of the MRT usage survey as follows: the most used transportation before switching to MRT was TransJakarta BRT at 32.2%, private cars at 25.21%, and motorcycles at 28.54%. The total number of private transportation users was 258 of 480 respondents, representing 53.75% of the sample. Regarding travel purpose, 52.8% of respondents traveled for work, 24.2% for sightseeing, and 8.85% for business. Based on the daily travel frequency is presented, 83.7% traveled by MRT to go and return, 11.3% traveled, and 5% traveled back.\n\nThe profile of MRT Jakarta Phase 1 users indicates that the MRT is a mode of transportation that has been able to attract individuals belonging to the upper-middle-class economy, as evidenced by the responses of respondents who were predominantly those with high levels of education and income. Most respondents use MRT for their daily commutes, with the primary objective being work-related.\n\nThis study’s estimation of CO2 emission reductions by the CDM approach for mass transit without feeder transport. This is because during the study period, the MRT system was not integrated with the feeder transportation network. The analysis is primarily concerned with emissions from road transportation, focusing on reducing emissions from private vehicles due to a shift in modal preference toward MRT. The scope of the emission calculation covers a range of private transportation modes, including motorcycles and cars. The study did not analyze public transportation users opting to use MRT. This is because mass transit operations, such as MRT, alleviate congestion by incentivising individuals to transition from private vehicle use. This is particularly relevant given that private vehicles are associated with increased vehicle exhaust emissions due to prolonged low vehicle speeds.\n\nIn this study, the calculation of emission reduction using the CDM ACM 0016 method was simplified by excluding three variables for the following reasons:\n\n1. Indirect emissions reductions derived from carbon dioxide (CO2) emissions from the point of origin to the railway station and from the station to the final destination are not included in the calculation because they have no impact on emissions reductions along roads parallel to MRT operations. The CO2 emission reductions calculated in this study are exclusively associated with emissions reductions along roads parallel to the MRT corridor.\n\n2. The analysis does not incorporate leakage from public conveyance or other road segments. Leakage in public transportation is defined as a reduction in passenger occupancy (load factor) resulting from migrating other public-transport users to the MRT system. This study did not include surveys to assess the dynamic load factor of other public transportation modes, such as Bus TransJakarta, micropet, metrodin, and other public vehicles operating along routes parallel to the MRT. Moreover, speed and travel time surveys were not conducted on alternative road sections running parallel to the MRT corridor.\n\n3. The passenger expansion factor was assumed to be 1 (one) due to the unfeasibility of sampling at the station using the systematic method of calculating the line length. This is because the station-waiting time is only 5 min, which is insufficient for the application of the proposed methodology. Sampling of passengers was conducted on the vehicles themselves using incidental sampling techniques.\n\nThe simplified ACM 0016 CDM formula used in this study is outlined in Table 4.\n\nIt is also noteworthy that there is no measurement of carbon emissions at the upstream level, which refers to emissions originating from power plants. This study focused exclusively on emissions along the MRT route and the electricity consumption attributed to MRT operations along this route.\n\nIn calculating the baseline CO2 emissions, the following factors were considered: the CO2 emissions generated by private transportation users who switch to MRT Jakarta Phase 1. Table 5 showing the onboard survey results indicate that 53.75% (or 258 respondents) of private transportation users switched to using the MRT in the road corridor parallel to the MRT. This figure shows 50 private car users, 25 motorcycle users, 71 online car users, and 112 online motorcycle taxi (Ojek Online) users. Online one and online cars are included in the category of private transportation, as they represent the conversion of private vehicles into online public transportation. The derived baseline accounts for emissions generated by private transportation in scenarios where MRT is not used, based on data obtained from surveyed passengers.\n\nThe calculation in Table 5 assumes that private transportation users use premium fuel, which has a local emission factor of 72,967 kg CO2/TJ (72,967 g CO2/TJ). The baseline emissions for the use of private transportation that switches to using MRT, as calculated from the survey data, are 169,625.6 g CO2 per day or 169.8 kg CO2 per day for one trip. If two round trips are completed, the baseline emissions for the MRT corridor are 339.3 kg CO2 per day.\n\nIt is assumed that the percentage of private transport users (53.8%) represents the percentage of the population that transfers to MRT. In 2019, the total number of MRT users during the 9-month period or 275 days) was 23,637,960 passengers. This figure can be used to calculate the number of private transportation users who moved to MRT, which comprised 12,705,404 passengers per year. Based on these assumptions, the baseline emissions of all private transport users who shifted to MRT in 2019 were 16,706,684.4 kg CO2 or 16,706.7 tons CO2 (equivalent to 16,706,700 kg CO2) as shown in Table 6.\n\nThe data from P.T. MRT Jakarta indicate that the electricity consumption for MRT traction over the eight-month period from May to December 2019 was 14,448,000 kWh, which is equivalent to 14,448 MWh. This equates to an average consumption of 0.6795 kWh per passenger, resulting in a total electricity consumption of 16,062,106 kWh for 2019. It has been established that the electricity network emission factor for the DKI Jakarta area in 2019, as calculated by the Ministry of Energy and Mineral Resources, is 0.87 tons of CO2 per MWh (ESDM, 2019). Based on these calculations, the direct emissions of the MRT project in 2019 were 13,974.03 tons of CO2. This is shown in Table 7.\n\nThe reduction in CO2 emissions resulting from the start of operations for MRT Jakarta Phase 1 can be quantified by subtracting the baseline emissions from the emissions associated with the MRT Jakarta Phase 1 project. This reduction can be achieved through a transition from private transportation to MRT use. The baseline emissions of 16,706.7 tons of CO2 are subtracted from the MRT project emissions of 13,974.03 tons of CO2, resulting in a reduction value of 2,732.7 tons of CO2 in 2019. Thus, the reduction in CO2 emissions resulting from the shift from private transportation to MRT averaged 227.7 tons of CO2 per month, with a daily average of 9.9 tons of CO2 in 2019. This is shown in Table 8.\n\nIn this study, the authors predicted 2023 using the above formula and leveraging data derived from the 2019 survey outcomes. Predictions are made to determine the emission reduction impact of MRT construction and operation if there is an increase in private vehicles that switch to using MRT. The following assumptions are used:\n\na. The average mileage of private cars using the survey results was 19.7 km and that of motorcycles was 17.3 km.\n\nb. The passenger emission factor using the premium was 72,600 kg CO2/TJ (Ministry of Energy and Mineral Resources, 2019).\n\nc. MRT daily average electricity consumption based on the analysis of secondary data obtained from MRT.\n\nd. The electricity network emission factor is 0.87 tons CO2\n\ne. The passenger expansion factor was assumed to be 1 because sampling was not carried out at the station node but was carried out onboard, did not use queues, and was not categorized in clusters.\n\nf. Leaked emissions were not considered because the shifting included in the calculation only included shifting private transportation to MRT and not shifting from other public transportation modes.\n\ng. Indirect error is not considered because the travel pattern from origin to destination generally still uses fossil fuel transportation.\n\nIn this study, the aforementioned formula is used to project emission reductions in 2023 using data derived from the 2019 survey results. 2023 represents the normalization period after the COVID-19 pandemic in Indonesia. As a result, there is a significant increase in MRT ridership in 2023, as the previously imposed capacity restrictions have been lifted. Therefore, a growth in CO2 emission reduction resulting from the operation of MRT Jakarta Phase 1 can be observed compared with the 2019 data. The following assumptions were used to estimate CO2 emission reductions in 2023:\n\na. The mean distance traveled by private car passengers was 19.7 km, while the mean distance traveled by ‘car online’ passengers is 17.8 kilometers. The mean distance traveled by motorcycle passengers was 17.3 km, and the mean distance traveled by ‘ojek online’ passengers is 17.2 kilometers. These figures are derived from the findings of a survey conducted in 2019.\n\nb. The emission factor for premium car users is 72,600 kg CO2/TJ (Directorate General of New Renewable Energy and Energy Conservation, 2020).\n\nc. The daily average MRT electricity consumption was based on the results of secondary data analysis obtained from MRT.\n\nd. The emission factor of the power grid is 0.87 tons of CO2.\n\ne. Passenger growth factor was assumed to be 1 because sampling was not performed at station nodes but on trains without using queues and not categorized in clusters.\n\nf. Emissions leaked due to the transfer of other public transportation to the MRT were not included in the analysis, as it only included transfers from private vehicles to the MRT and not transfers from other public vehicles.\n\nTo establish a baseline for prediction, the shifting of private vehicles in 2019 was taken as the point of departure. A review of the survey data indicates that the shift toward private transportation totaled 53.75%. If 2023 is assumed to have the same shifting conditions as 2019, then the emission reduction can be estimated as follows:\n\n1. The baseline carbon dioxide emissions per day, calculated based on survey data, were found to be 339.3 kg CO2 per day.\n\n2. The baseline emissions per passenger is 1.3 kg CO2, i.e. 339.3 kg CO2 divided by the number of respondents.\n\n3. The baseline calculation for a given year is obtained by multiplying the baseline per passenger by the number of passengers in the observed year (in 2023).\n\n4. The next step is to calculate the emissions generated by the MRT project.\n\nAccording to data provided by PT MRT Jakarta, the total number of passengers using the MRT system during the nine months from January to September 2023 was 24,020,222. The calculation indicates that 12,860,877 individuals use private transportation users is 12,860,877 individuals. Furthermore, it can be established that the baseline emission in 2023 is 16,976.9 tons of CO2 as shown in Table 9.\n\nIt is established that the electric traction power in 2023 is 12,567 MWH. When this figure is multiplied by the power grid emission factor of 0.87, the direct emissions of the MRT project in 2023 are 10,932.99 tons of CO2, as shown in Table 10. The reduction in baseline emissions, in conjunction with the project emissions, resulted in an overall reduction of 6,043.9 tons of CO2 in 2023, as illustrated in Table 11. Subsequent calculations can be performed using the same assumptions by first predicting the number of users and the electric traction power for each year. This methodology allows the projection of the total number of users and electric traction power for each year in the future.\n\nThe results of this study indicate that 53.75% of MRT Jakarta Phase 1 users transitioned from private transportation, leading to a reduction in CO2 emissions of 2,732.7 tons in 2019 and 6,043.9 tons in 2023. The value of CO2 emission reductions produced in this study are comparatively lower than those reported by the DKI Jakarta Provincial Environment Office, which documented emission reductions from the MRT Jakarta Phase 1 project resulting from the transition of private transportation to MRT in 2019, amounting to 6,151 tons of CO2 (DKI Jakarta Provincial Environment Office, 2019). Ini 2022, the implementation of MRT Jakarta Phase 1 resulted in a reduction of 2,104 tonnes of CO2 emissions (DKI Jakarta Provincial Environment Agency, 2023).\n\nThe discrepancy can be attributed to the different methodologies used in the calculations. The emission calculations reported by the DKI Jakarta Environment Agency employ the Tier I approach. This approach only considers vehicle fuel consumption, assuming that MRT users switch from private transportation. It does not account for the emissions generated by MRT operations. Various methodologies are employed to quantify CO2 emissions associated with mass transportation, with notable discrepancies in specific factors incorporated into calculations. Accordingly, Fontaras et al. stated that In order to determine the quality of monitoring, reporting, and reported emissions reductions, CO2 certification procedures are required (Fontaras, Zacharof, & Ciuffo, 2017).\n\nThis research shows that not all MRT Jakarta Phase 1 users replaced private transport with public transport. Many also switched from other public transportation modes. Therefore, it is not appropriate to calculate CO2 emissions reductions by assuming that all MRT passengers will replace private transport with public transportation. Calculating emissions reductions using CDM ACM 0016 shows that the greater the number of private transport users who switch to MRT, the greater the potential CO2 reductions. Conversely, if the number of MRT users decreases, the MRT project may increase CO2 emissions. This phenomenon is due to an increase in electricity consumption per passenger, resulting in an increase in emissions associated with electricity generation. The operation of MRT Jakarta Phase 1 still relies on electricity from coal-fired power plants, which have high emission factors. These findings are in agreement with the finding that switching from private transport to MRT does not result in CO2 benefits. Therefore, efforts to increase MRT ridership and energy conservation initiatives are needed (Sharma, Singh, Dhyani, & Gaur, 2014). It is also recommended that non-motorized modes of transport, such as walking and cycling, be prioritized for short distances, in line with research that suggests reducing the consumption of natural resources, especially physical space and energy and their environmental impacts. For certain distances that require motorized transport, modes that offer higher capacity and better energy efficiency, such as high-capacity collective transport modes, such as urban trains, subways, and busses, should be used (D’Agosto, 2019). Therefore, the construction of MRT in Jakarta is very appropriate, as evidenced in this study that more than 50% can attract private transport users to switch.\n\nThe paradigm of using the CDM methodology, which is quite difficult because it requires a lot of data (Asian Development Bank, 2013), and the difficulty of determining the baseline in the transport sector (Michaelowa, et al., 2020), especially for the MRT project, can be overcome by simplifying the CDM ACM 0016 in this study. However, there is still a need for a primary survey to obtain factual data on the modes of transport switching to MRT.\n\nThe strength of this research is that the calculation of CO2 emission reductions from the operational impacts of MRT Jakarta Phase 1 used the CDM ACM 0016 method, which is a calculation used by the IPCC and recommended by the UNFCCC to obtain carbon certification that can be used in world carbon trading. This method is simplified for use in Indonesia. The advantage of using this method is that the calculation of CO2 emission reductions from MRT operations is carried out using primary surveys; thus, private transportation users who switch to MRT can be identified. Second, the calculation also includes the distance traveled for each type of vehicle and fuel consumption. Third, the calculation also includes the electricity emissions generated from MRT operations.\n\nIn this study, the CDM ACM 006 method is simplified because it does not include measuring emission reductions that occur from the origin to the starting station and from the end station to the final destination, shifting MRT users from other modes of public transportation, and emission reductions on other roads affected by MRT operations. Future research can address these shortcomings to improve the results of this study.\n\n\nConclusion\n\nThe results of the primary survey conducted in this study indicate that 53.75% of MRT users have transitioned from private transportation. Moreover, the simplified CDM ACM 0016 method yielded a CO2 emission reduction calculation of 2,732.7 tons of CO2 in 2019 and 6,043.9 tons of CO2 in 2023. It should be noted that the reductions in CO2 emissions in 2020, 2021, and 2022 were not calculated in this study due to the ongoing impact of the Corona Virus Disease 19 (Covid-19) pandemic, which has resulted in significant restrictions on passenger capacity in vehicle transportation, with reductions ranging from 50% to 75%.\n\nThis study demonstrates that the CDM method for measuring CO2 emission reductions can be applied in Indonesia. However, the formula must be simplified to align with the transportation sector’s characteristics and data availability to ensure its effectiveness. The CDM ACM 006 formula streamlining is anticipated to be implemented in Indonesia. This would facilitate the certification of CO2 emission reductions through mitigation actions through MRT development by the UNFCCC.\n\nIt is crucial to cultivate greater interest among private transportation users in opting for MRT, thereby augmenting the number of MRT passengers. This can be achieved by implementing strategies such as offering incentives to private transportation users to transition to MRT, expanding the operational scope of MRT, enhancing integration facilities, improving accessibility to MRT stations, and developing a feeder ecosystem around stations. Furthermore, to augment the quantity of emission reductions generated from MRT operations, it is imperative to transition the utilization of energy sources for MRT operations toward renewable energy sources, such as solar power, hydropower, and nuclear power. Low emission factors characterize these energy sources and have considerable potential to curtail future greenhouse gas emissions.\n\nThis research project has been approved by the Head of the Research and Development Center for Road Transportation and Railways, Transportation Research and Development Agency, Ministry of Transportation of the Republic of Indonesia, through an approval letter (number 201/KU.004/VIII/BLTD-2019) dated August 21, 2019, issued in Jakarta. The aforementioned approval letter permits the collection of primary data from users of the Jakarta MRT Phase 1 in Jakarta,Indonesia.\n\nA consent form was included in the questionnaire on the opening page, before respondents answered the questions. Due to the limited survey time on the train, participants gave verbal consent to participate in this study which was approved by the ethics committee. There was no external influence or coercion on participants to participate in this study. In addition, all data collected will be kept confidential to maintain the privacy of the participants.", "appendix": "Data availability\n\n\n\n1. Figshare: Primary Survey Data in the MRT https://doi.org/10.6084/m9.figshare.26824318.v3 (Nurdjanah, Primary_Survey_Data_in_the_MRT, 2024a)\n\nThis project contains following dataset:\n\n• Primary Survey Data in the MRT.xls.\n\n\n\n2. Descriptive of Respondent’s Answer: https://doi.org/10.6084/m9.figshare.26826532 (Nurdjanah, Descriptive of Respondent’s Answer, 2024b)\n\nThis project contains following dataset:\n\n• Descriptive of MRT Respondent Answer,xls\n\nData are avalilable under the terms of the Creative Commons Attribution 4.0 Internasional license (CC-BY 4.0)\n\nFigshare: Survey form of mrt users: https://doi.org/10.6084/m9.figshare.26889658.v1 (Nurdjanah, SURVEY_FORM_OF_MRT_USER, 2024c)\n\nThis project contains following dataset:\n\n• SURVEY FORM OF MRT USERS.PDF\n\nData are avalilable under the terms of the Creative Commons Attribution 4.0 Internasional license (CC-BY 4.0)\n\n\nReferences\n\nAlbuquerque F, Maraqa M, Chowdhury R, et al.: Greenhouse gas emissions associated with road transport projects. Transportation Research Procedia. 2020; 48: 2018–2030. Publisher Full Text\n\nAnsusanto J, Priyanto S, Munawar A, et al.: Charakteristics of Travel Patterns in Yogyakarta City. Jurnal Transportasi. 2014; 61–68.\n\nArikunto S: Pengembangan Instrumen Penelitian dan Penilaian Program. Yogyakarta: Pustaka Pelajar; 2017.\n\nAsian Development Bank: South Asia Operational Knowledge Working Paper Series: The Clean Develompent Mechanism Afield Guide for Transport Project. Manila: ADB; 2013.\n\nCentral Bureau of Statistics of DKI Jakarta Province: DKI Jakarta Transportation Statistics. Jakarta: Central Bureau of Statistics of DKI Jakarta Province; 2019.\n\nCentral Bureau of Statistics: Greenhouse Gas Emissions by Sector Type (thousand tons CO2e), 2000-2019. Jakarta: Central Bureau of Statistics, Republic of Indonesia; 2020.\n\nCoordinating Ministry of Economic Affairs collaboration with JICA: Jabodetabek Urban Transportation Policy Integration Project Phase 2 in the Republic of Indonesia. Jakarta: JICA Almec Coorporation; 2019.\n\nD’Agosto.: Transportation, Energy Use and Environmental Impacts. Amsterdam: Elsevier; 2019.\n\nDharmowijoyo DB, Tamim OZ: Selection of Carbon Dioxide Emission Reduction Calculation Method in The Transportation Sector. Jurnal Transportasi. 2010; 10: 245–252.\n\nDirectorat General Climate Change, Ministry Environment and Forestry, Republic Indonesia: Report of GHG and Monitoring, Reporting and Verification 2018. Jakarta: Ministry Environment and Forestry, Republic Indonesia; 2019.\n\nDirectorate General of New Renewable Energy and Energy Conservation: Energy Conservation Roadmap. Jakarta: Ministry of Energy and Mineral Resources; 2020.\n\nDKI Jakarta Provincial Environment Agency: Inventory of Emission Profile and Reporting of Greenhouse Gas Emission Reduction in DKI Jakarta Province. Jakarta: DKI Jakarta Provincial Environment Agency; 2019.\n\nDKI Jakarta Provincial Environment Agency: Inventory of Emission Profile and Reporting of Greenhouse Gas Emmision Reduction of DKI Jakarta Province in 2023. Jakarta: DKI Jakarta Provincial Agency; 2023.\n\nFontaras G, Zacharof N, Ciuffo B: Fuel consumption and CO2 emissions from passenger cars in Europe – Laboratory versus real-world emissions. Progress in Energi and Combustion Science. 2017; 60: 97–131. Publisher Full Text\n\nHirota K, Poot J, Minato K: Do Policy Incentives Affect The Environmental Impact of Private Car Use? Evidence from a Sample of Large Cities. IDEAS/RePEc search. 2003; pp. 1–19.\n\nIBM: 2024, August Wednesday. Reference SourceReference SourceReference Source\n\nInstitute for Global Environmental Strategies (IGES): CDM in Charts. Tokyo: Ministry of The Environment of Japan; 2011.\n\nLuathep P, Fukuda A, Jaensirisak S, et al.: Measuring Emission Reduction Impacts of Mass Rapid Transit in Bangkok: the Effect of A Full Network. 13th WCTR. Rio De Janeiro: WCTRS; 2013; pp. 1–18.\n\nMaimunah S, Kaneko S: MRT as Climate Policy in Urban Transportation. Climate Change Policies and Challenges in Indonesia. 2016; pp. 243–264. Publisher Full Text\n\nMichaelowa A, Brescia D, Wohlgemuth N, et al.: CDM method transformation: updating and transforming CDM methods for. Freiburg, Germany: University of Zurich; 2020.\n\nMinistry of Energy and Mineral Resources: Electricity System Greenhouse Gas Emission Factor 2019. Jakarta; 2019.\n\nNihayah DM, Gravitiani E, Tri Rahayu SA: Does The Clean Development mechanism Exist in Developing Countries After an International Agreement. International Journal of Energy Economics and Policy. 2021; 11: 409–417. Publisher Full Text\n\nNurdjanah N: Descriptive of Respondent’s Answer.2024a, August 31. Reference SourceReference Source\n\nNurdjanah N: Primary_Survey_Data_in_the_MRT.2024b, August 31. Reference SourceReference Source\n\nNurdjanah N: SURVEY_FORM_OF_MRT_USER.2024c, September 02. Publisher Full Text Reference Source\n\nPT. MRT Jakarta: peta-jalur-mrt-jakarta.2024, August 31. Reference SourceReference Source\n\nSekaryadi Y, Santosa W: Vehicle Emissions on West Java Provincial Roads. Journal HPJI. 2017; 29–36.\n\nSharma N, Dhyani R, Gangopadhyay S: Methodology for Estimation of CO2. Journal of Scientific and Industrial Research. 2010 August 2010; 69: 586–593.\n\nSharma N, Singh A, Dhyani R, et al.: Emission Reduction from MRTS Projects A case Study of Delhi metro. Atmospheric Pollution Research. 2014; 5: 721–728. Publisher Full Text\n\nSugiyono: Metode Penelitian Kuantitatif, Kualitatif dan R&D. Bandung: P. T Alfabet; 2016.\n\nUNFCCC: Approved consolidated baseline and monitoring methodology ACM0016. Bonn: UNFCCC/CCNUCC; 2015.\n\nUNFCCC: CDM Methodology Booklet. Bonn: UNFCC; 2022.\n\nWan P, Zhang ZX, Chen L: Environmental co-benefits of climate mitigation: Evidence from clean development mechanism projects in Chin. China Economic Review. 2024; 85: 102182. Publisher Full Text\n\nWRI: Indonesia Annual Report 2019. Jakarta: WRI; 2020.\n\nZegras P, Chen Y, Grütter J: Behavior-Based Transportation Greenhouse Gas mitigation Under the Clean Development Mechanism. Transport Effiecient Development in Nanchang China. Transportation Research Record: Journal of the Transportation Research Boar. 2009; 2114: 38–46. Publisher Full Text" }	[ { "id": "331896", "date": "17 Oct 2024", "name": "Qing Yu", "expertise": [ "Reviewer Expertise Transportation data science", "Transportation energy and emissions", "Electric vehicles", "Public transportation", "Urban planning & mobility", "Agent-based 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\nThis paper is well organized and easy to understand. Through its research on the Jakarta MRT Phase 1 project, the article proposes a simplified CDM model and provides a detailed carbon emission estimation, offering significant policy implications and practical value. However, the paper can be further improved in the following areas: 1. Figure 1 is too blurry: The clarity needs to be improved. 2. Data details: The paper only provides an overview of the survey information but does not explain what specific data was collected. Does it include passenger travel OD information for each trip? If not so, what kind of travel information is included? This is crucial for the carbon emission calculations, and I suggest adding more details in the data description section. 3. Simplified vs. original CDM ACM 0016 method: The paper mentions that a simplified version of the CDM ACM 0016 method is used to calculate the carbon emissions and reductions for the MRT project. However, there is no error analysis or quantitative comparison between the simplified and original versions. While the simplification makes the CDM ACM 0016 method more practical for application, there is no sensitivity analysis or uncertainty assessment to evaluate the accuracy of the simplified results. This is a notable shortcoming of the paper. 4. Comparison between 2019 and 2023 emissions: Why does the paper compare emissions for 2019 and 2023 specifically? Why were these two years chosen, and how are future scenarios considered? The 2023 data is not based on direct observations but is predicted and assumed based on 2019 data. The paper assumes that future travel patterns and passenger growth rates will be similar to 2019. Is there any real data available for some level of validation of these predictions? 5. Policy recommendations: I suggest adding more policy recommendations based on the results to enhance the practical reference value of this study for urban carbon reduction strategies in transportation policy.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-1069
https://f1000research.com/articles/12-41/v1	11 Jan 23	{ "type": "Research Article", "title": "A Fondrakö text: Cultural religious tradition and social integration of community", "authors": [ "Sonny E. Zaluchu" ], "abstract": "Fondrakö is the local wisdom of the Nias ethnic community and has two functions. First are the oral religious holy book teaching ancestors' values and philosophy. Second is the highest consensus institution of the traditional society formulating and making decisions on the socio-religious law to guarantee the order of the community. This paper explains that social differentiation has happened in the modern era; philosophical values of fondrakö remain to live up to this day and experience the proliferation of rites. The argumentation built through this paper is that primitive culture will not simply disappear in the modern community just because it experiences accommodation and the decrease of emotional intensity into new forms. Social laws of primitive religion are not always contradictory and can run parallel with civilization.", "keywords": [ "local wisdom", "fondrakö", "sociology", "social binding", "Durkheim", "community" ], "content": "Introduction\n\nThe ethnic religious texts, in the beginning, did not have the early written form. The contemporary final form is the transformation from the traditional format of oral products or oral law collection. The research results of Tsuria, Bellar, Campbell, and Cho (2021) conclude that, along with time, holy books and religious texts experienced the shift from oral composition uttered in religious meetings and rites to become written texts in a form of copies on animal skin or papyrus paper and last to be written in a book format after the revolutionary invention of a printing device. In other words, the ancient religious texts were built in the oral tradition (Clark, 2005) and then developed to become written documents as long as the advanced printing technology (Long & Long, 2017). Although text transmission change has happened, Widder (2017, p. 2) emphasized that the power of those texts relies on the linguistic aspect more than its form. According to Widder (2017), language becomes the best media in delivering religious messages by listening to what is talked about or delivered orally. Therefore, in various traditions, the transmission of religious messages and teachings has started in a form of the oral method. Especially before the writing and printing technology took over, oral tradition was rooted deeply in the way the community built their spirituality. Through language, communities define their belief system and build symbols to communicate in the system horizontally.\n\nFondrakö is one of the oral traditions developed in the ancient Nias ethnic community but is still influential in the contemporary community life. The values and teachings in this tradition still remain as local wisdom in the social life order of the Nias community, even though the majority of Nias people have converted into Christian followers and have abandoned their ethnic religion (Harefa, 2013; Mendrofa, 1981). The reality is the laws of fondrakö are in line with the teachings of Christianity and is even feared and obeyed more than religious instructions. This is a crucial matter because the values of fondrakö rely on ethnic religion and customs, not on the teachings of Christian religion sourced from Divine revelations. Fondrakö is the cultural product from a primitive community, which at the beginning took root in myths, traditions, rituals, natural power, and is pagan in the animism-dynamism perspective. Because the community tend to give more attention to traditional values than to the teachings of the holy book, on the one hand, the clashes of values and behavior often happen, and there will be the combination of teachings or there appears syncretism, on the other. This occurs because in the perspective of the local inhabitants, fondrakö is not merely the values arranging social relationship and kinship but also inclusive as spiritual teachings from an oral ‘religious text’. The relationship of both is inseparable. Since Nias people live and actualize as a community, fondrakö becomes the referent values side by side with the spiritual aspect.\n\nThis paper aims to comprehend deeply why fondrakö becomes a discourse power that keeps surviving in the modern era. Exploration toward values and power of fondrakö is expected to provide contribution for the anthropological studies of culture and religious sociology, which will complete the literature on unification of culture and religion. For that, the first thing to do is to introduce the origin of fondrakö with two approaches, myths and sociology. Then the discussion will dig out the power of fondrakö in its tradition root as it became a covenant, social binding, and its integration in a belief system or ethnic religious spirituality. There are not many that have conducted specific exploration on the law of fondrakö and analyzed it in the concept of sociology. Several research results reported are more about the practical implementation of fondrakö in various fields of life and do not touch the socio-religious approach as discussed in this paper. The research of Harefa (2013), for instance, only descriptively explained the concept of fondrakö as a customary product. The power of fondrakö is seen as a tradition producing local wisdom. Therefore, the research of Zega (2019) elaborated the implementation of the cooperation workshop as arranged in fondrakö and in the modern leadership management. Markus (2004), although not specifically reviewing fondrakö, in his thesis on intercultural mission related to arts and handicraft mentioned that fondrakö is related to the initiation of a clan leader in Nias. The quite complete research was conducted by Gulo (2011) writing a thesis on the relationship between fondrakö and the concept of böwö, namely customary dowry in the Nias wedding scheme. The research on fondrakö as social binding and spiritual construction as the gap that will be addressed in this paper. The temporary belief is that fondrakö is not only a customary entity but also part of a belief system that moves various strata of the community social life in a consensus.\n\n\nMethods\n\nThis article followed all ethical standards for research without direct contact with human or animal subjects.\n\nThis paper will be arranged in four steps to achieve the research objectives. First, theoretically explaining sacred texts and books in a cultural context. Then explaining the relationship between fondrakö and Nias people's religiosity. A more specific discussion in the third part concerns the blessing and curse of fondrakö as moral and supernatural force that builds people’s fear of not violating it. The last section is an analysis of how fondrakö plays a role in the formation of social binding and modernity challenges. Discussions rely on primary data from the literature on Nias in the form of books and research results published in journals. Web searches and library studies were conducted to collect these books. All of these sources have become references cited in the article.\n\nThus all of this research is qualitative Marying (2004), which is carried out with a literature study to construct a theory about fondrakö. There are still very few references to fondrakö and Nias culture, so all books and articles researched on Nias topics must be used. Several parts of that research provide data and notes about fondrakö. The research began with initial observations in a traditional Nias village. The researcher unilaterally decided on a traditional village chosen as the object of observation and observed social behavior in joint decision-making based on fondrakö values. Observations were also focused on seeking answers as to whether fondrakö was still valid and to what extent it had influenced community decision-making. The observation results become a phenomenon analyzed and constructed using the sociology of religion approach. This approach was chosen because the observation group is a Christian community. However, they still practice fondrakö traditional values even though they are aware that the values of the two have mixed in the people's perspective. Decisions taken within the group are universal and binding and affect the social dynamics of society. The sociology of religion approach was chosen because fondrakö directly impacts social interaction in society and is part of a belief system. As is known, sociology looks at religion, not from the point of view of human relations with God (theology). In contrast, sociology sees religion as about society and its impact on society. From this perspective, the sociology of religion will explain how religion, both primitive religion through fondrakö and mainstream religion, collaborate in shaping culture, behavior, and social interactions. Fondrakö is part of the culture of the inclusive Nias people, which is directly related to religious life.\n\n\nResults\n\nEvery religion has its own religious holy book. Through the religious holy book, the followers have doctrinal guidance on the principles of belief, values, and statements on what they believe in, the teachings that are believed in and considered holy, the wisdom to live well both individually and in community, and the guidance to approach or understand the transcendent God (Wilson, 1991). Basically, the religious holy books are not far different from the texts born in a form of oral literary works which are then written in a book. What makes them different, according to Madigan (2013), is the attitude and treatment toward the text. Madigan (2013) stated that when a community of the believers considers and admits a text has sacredness, dignity, and can be accepted as a truth to strengthen faith and religious life, the text by itself is categorized as a religious holy book. If it has been accepted as holy writing, the influence of the text spreads, not only reaching the religious area but also covering the political, social, and economic life of the community. Furthermore, Madigan explained that the texts in a holy book are important elements in a complex process of religious follower identity formation (Madigan, 2013). Through the texts in a holy book, religious followers can hear God in the middle of the community (Siddiqee, 2013). In other words, the religious holy book texts, are on one hand informative, and on the other, performative because they are related directly in the religious follower community identity formation. The relation of both forms the locus of belief in the middle of the community. Therefore, the religious holy books always correlate with the way religious followers express their social life (Ritzer & Stepnisky, 2019a, p. 111).\n\nAt the beginning, religious holy books did not appear in a contemporary form. The information contained inside them as the content of a holy book took the more primitive form when first introduced in society, namely utterances and oral communication. Durkheim stated that analyzing the religious contemporary form only manages to be done when that religion is learned in its most primitive form (McKinnon, 2014). In the religious holy book context, the thinking of Durkheim can be accepted because the truth is the religious holy books that we receive today are the transformation results from their primitive form sourced from animism, naturism, and totemism (Durkheim, 2011). In that primitive form, the religious holy books did not have their current form. The informative and performative form of religious holy books is stated in symbols, abstraction, rituals, and other oral forms. As time went by, the texts experienced shifts and form change. In the beginning they were delivered in the oral and verbal composition, then they were written and stated in a form of reading, and then transferred in various forms of manuscript copies and finally arrived in a contemporary form in a book or digital application (Tsuria et al., 2021).\n\nBy taking the examples of the dichotomy of holy-forbidden, holy-unholy from the context of The Old Testament, Hundley explained that religious texts in general play a role in providing clues to the followers on sacrality (Hundley, 2013). Sacred space formed from religious texts become direction and guidance in living a pious life and on how to behave religiously in a secular world. This is inseparable from the way the group of community interpret religious texts and apply them in their life. According to Sanders, the hermeneutic pattern always relies on two points. The first reference is a text as tradition that then becomes the behavior pattern in a context and situation (Sanders, 1987, p. 173). In this case, it is seen that religious behavior and social behavior are also influenced by how far a group of community interprets their religious texts. In regard to this, Shillington (Shillington, 2002, p. 63) revealed that religious texts are from the unity of language, texts, and oral utterances that encourage intention inside the religious followers to behave according to the content of their holy book. Therefore, religious holy books can be seen as a rule that internalizes and binds the religious followers to carry out their role in the social order. Berger & Luckmann (2018, p. 21) supported this conclusion through his theory on social construction. Religious holy book texts can become an individual knowledge potential that can be developed to form reality in the middle of the community. We can conclude from that statement that social behavior basically runs parallel with the community religiosity aspect itself. Both exist in the dialectical relationship. Practically, that social behavior is the reflection of interpretation and internalization of religious values through religious holy books.\n\nValidation of fondrakö was conducted in a rite led by ere. In the ancient Nias belief, ere was the religious imam (Laiya, 1983, p. 24). The meaning of ere as the local religion imam was also introduced by the missionaries that came to Nias when they spread the Christian religion (Hummel & Telaumbanua, 2007; Sundermann, 1905; Zaluchu, 2021). The original meaning of ere is an expert or specialist in a certain field. Therefore, the function of ere was often associated with religious rites and rituals, so the position was made to be specific in the field of religion.\n\nThe activity center of ere was a meeting house named osali. In osali, ere led the ceremonies and rituals in front of the inhabitants and provided explanation and interpretation on the laws of the custom and religion. Osali did not only become a public space but also functioned as a religious space. This idea was then adopted by the Western missionaries when they changed the function of osali to become the worship place for Christians. Therefore, ere had the key role in the rite management for the need of the custom and religion of the community. Its position was equal with a ruler and was very respected. Ere was even considered as a holy person because he had the supernatural ability, namely as a mediator to enter the spirit world. The imam was believed as the traffic media of the ancestor spirits that had passed away to communicate with the livings (Sundermann, 1891).\n\nThe existence of ere (imam) in the ceremony of fondrakö was not just symbolical or as the executor but also as the religion legitimation that confirmed that fondrakö was not just the product arranging customs, but it also covered spiritual cosmology involving the real world and the spirit world. The ancient Nias people believed that the world of the living was always overlapped with the world of the dead, inhabited by the spirit of ancestors. They believed that the supernatural power in the world was also related with the activities of the supernatural spirits. In the animism perspective, the spirits are believed to have power and always wish to communicate with those who are still alive through the mediation of an imam or a shaman (Harrison-Buck & Freidel, 2021; Strijdom, 2021). The legitimation of ere in a ceremony confirms that all law provisions agreed upon on earth have the supernatural world consequences through the presence of ancestor spirits as witnesses, consent grantors, and also supervisors or punishers. MacGregor (2019) explained that community basically builds a system of belief through narrations explaining how the physical world was formed and how humans live in that world. The narrations are always accompanied with rituals and concepts that describe that humans do not live alone and require harmony with the supernatural world for their current and future lives. Based on this thinking, it is seen that the religious values of fondrakö are very strong because of its role in forming the system of belief of the community.\n\nThe main law contained in fondrakö is not far different from the provisions of the Book of Leviticus in the Moses’s Torah. The laws set forth contain the custom aspect (social rules) on one hand, and the Leviticus aspect (ritual and religious rules) on the other. Therefore, fondrakö can be seen as a doctrinal theological construction that is integrated into the social system. Referring to the explanation of Smart (1984, p. 9), doctrine is an effort to provide a system, explanation, and intellectual power toward the language of mythology and symbolism deriving from the belief and religious ritual. Relying on that opinion, fondrakö of Nias people is not only understood at the level of myths, symbolism, and rituals but also a doctrinal system at the practical level in the middle of the community (Potapova, Danilova, Prasolov, Makarova, & Kryukova, 2018). This is the reason why fear and obedience toward the values of fondrakö survive in every generation of Nias people. Even though Christianity has taken over the belief system of the Nias, the doctrinal power of fondrakö in the social order of the community has never really disappeared. Up to this day, although the villages have changed their form, the relationship between them fuses in civilization, and although the village power shifts to modern government and the ethnic religion has been abandoned, the doctrinal values of fondrakö remain to the foundation in the social interaction and the way the community lives.\n\nThe content fragment of fondrakö Maenamolo, found at Gomo, the oldest of the megalithic area that became the first human community civilization witnessed in Nias, is one of the evidences parallel with the teachings of Christianity (Hammerle, 2010). This content of fondrakö was read to public by ere as many as 27 times with a purpose, and the content could linger and was memorized by listeners. That fragment of fondrakö is as follows (Gulo, 2011):\n\n“A tiger, sir\n\nOn the land split stands fire as big as a sago tree\n\nBecoming small, then disappearing\n\nThis is the seat of the child of Lawalani Sanetua (the determiner of all things)\n\nThis is the law, this is Fondrakö\n\n1. Do not fornicate\n\n2. Do not steal\n\n3. Do not deviate\n\n4. Do not kill the living beings\n\n5. Do not take the property of your own people\n\n6. The ancestor spirits from your father (lahu zanalawa ama)\n\nThe ancestor spirits from your mother (lahu zanebua ono)\n\nFather, money existing in heavens is floating\n\nHere is our real father\n\nHis substitution is here, a person called father,\n\nHe is the leader of the village, an imam, and a counselor”\n\nWhen it is observed, the content of fondrakö is not far different from some of the law received by Moses for Bani Isra’il at the foot of Mount Sinai and known as The Ten Commandments (Sailhamer, 2009). The first fondrakö is parallel with the seventh commandment that forbids fornicating, the second fondrakö is parallel with the eighth commandment that forbids the act of stealing, the fourth fondrakö is parallel with the sixth commandment that forbids murder, the fifth fondrakö is parallel with the tenth commandment that forbids the desire to keep the public property, and the sixth fondrakö is parallel with the obligation to respect parents, which is the content of the fifth commandment. That is why fondrakö reflects moral formation (Sahidah, 2020) among those who accept and implement the law.\n\nThe hybridization concept is explained very well by Hedges (2021). According to Hedges (2021), the lived religion always has the chance to experience the hybrid process. The main emphasis does not lie in the belief system and religious texts but focuses on the activities and behavior that are more real, where the moral values are seen and practiced together (Ganzevoort & Roeland, 2014). This is the reason behind the description of Hedges on the existence of a very significant relationship between transcendent matters (texts and the system of belief) and the reality (practice and behavior). According to this concept, a very good relationship can last between an institution and an individual to make it happen (Hedges, 2021), which in this case is fondrakö as an institution and community as the gathering of individuals. Based on that thinking, it can be concluded that fondrakö as the highest consensus institution of Nias community is not an elite hegemonial institution or an institution separated from its supporting community. On the contrary, the concept of fondrakö introduces how an institution is formed from the wish of the community themselves in realizing sacrality and the relations that must be maintained both personally and related to worldly matters (Ritzer & Stepnisky, 2019b). In this case, fondrakö can be positioned as a religious language in the social life order (Alston, 2005). Therefore, drawing a firm line between social content and religious content in fondrakö cannot be done because they are mutually integrated. Both are united in the text and in the spirit forming them.\n\nFondrakö is ritual-constitutional. In its legitimation, a colossal custom party (owasa) was held, and the feast was made for all the inhabitants of the village. This is the characteristic of fondrakö as the highest constitutional institution of the community (Beatty, 2013). The peak of owasa is a stipulation. First are the stipulation and enforcement of law for the next generation (fondrakö fanotou). This is done because the laws of fondrakö are binding and generational. Fondrakö fanotou also functions as the effort to preserve law for their children and grandchildren as the next generation. Second is the stipulation of the revised law (fondrakö fawuluni). This law is stipulated with the awareness that the community, challenges, and needs experience development. In a different time and a new generation, law adjustment is required by making null and void the previous laws that are no longer relevant and new laws are formulated so that they become adaptive with the demand of the era (Zebua, 1996).\n\nAs the constitutional institution, fondrakö has a legal aspect (which has to be complied with) and punishment (the consequence due to violation). Its position is equal with the senate in a political institution that holds the power and highest sovereignty in the community behavior control (Bond, 2015) and the people democracy (Kosmin, 2015). All legal products that have been stipulated in fondrakö are binding in the macro and micro level, and demand high compliance. Even though the laws are not present in writing, its complete content is considered as a convention. Although realizing the very grave legal consequences due to violation, the community fight to maintain the convention and guard it as a cultural heritage. This occurs because the customary law has been integrated into the social structure so that it can survive as the power of values since the birth of someone until the person’s demise (Zaluchu, 2020). Hedges (2021, p. 25) defines this pattern characteristic as a ‘sui generis’ deriving from a Latin term meaning of its own kind. As an independent law, its existence becomes very strong, personal, and indispensable. Stipulation is as the final provision where none can refute, change, or reduce it. Fondrakö becomes the highest law that does not depend on or is influenced by other things, except by the group of the community where the law itself has been established.\n\nThe main philosophy behind the implementation of fondrakö is as a blessing and a curse. The dimension of blessing and curse can be seen from its name. Fondrakö comes from the word rakö meaning ‘stipulated through oath and bound with a curse’ (Mendrofa, 1981). Zebua explained that that philosophy becomes one of the effective powers based on the compliance of the community. For those who implement and obey it, they will obtain a blessing passing down to their children and grandchildren. On the contrary, those who violate it will receive social sanction, and they and their descendants will be mocked and cursed in their entire life (Zebua, 1996).\n\nThe stipulation of this fondrakö law resembles the ways of agreement stipulation occurring in the ancient Middle East area, where the parties agreeing stipulated an agreement by sacrificing an animal cut in certain ways (Beaumont, 2012). The animal was cut equally, and the left part was separated from the right part. The parties entering into an agreement passed the animal body by continuing saying a blessing and a curse. It is a blessing when they obey the agreement, and it is a curse like the sacrificed animal being cut half if they violate the agreement. This rite was done with full awareness toward the obligation to maintain the law and its consequences. A similar thing happens with the stipulation of fondrakö. All village inhabitants gathered together outside the meeting hall (ahe gosali). In the Middle East, the agreement stipulation only involves the parties in the agreement, but fondrakö involves more mass, takes place communally, and is under the supervision of the customary elders and an imam. The covenant was conducted together by the community (adults and children) that inhabit one village. The peak of the ceremony is the stipulation with the blessing-curse symbolism. In that ceremony, several sticks, a cock, and liquid tin were provided. The ceremony was led by ere, where the sticks were broken in front of public. Then the chicken was sacrificed with an unusual way. Its legs and wings were broken and was killed by twisting its neck. The hot tin liquid was then poured inside the animal. The ere then shouted loudly and declared to public, “whoever violates whatever has been stipulated in this Mondrakö, they will soon die (broken like the sticks), or tortured like the chicken whose legs and wings are broken and everything eaten by them will feel hot like the hot tin poured into the mouth of the chicken.” The sentence is also equipped with the curse “Lö mowa’a ba danö ba lö molehe ba mbanua” meaning that they (who violate) will never have their offspring (Gea, 2013).\n\nCreating collective compliance with the approach of ‘blessing and curse’ is the characteristic of the society that builds its community with myths. Tylor (2010) called this as the characteristic of primitive culture that relies on animism and has the existential function for humans (Dhavamony, 2016). In such a community, the members build social participation with magical elements so that interpretation is created. Therefore, myths are required as the active power in the community life, but they are also a reality lived by in the daily life (Malinowski, 1948) and a part of primitive esthetics. In some certain cultures, and it is equipped with dances with magic nuance (Weir, 2013). Actually, there is no logical relationship between fondrakö law violation and the symbolism of broken sticks or the sacrificed animal, even including also the consequence aspect to the offspring. This can be explained from the thinking of Eliade (2002) on ancient community. Rites and rituals are not just a procedure but also inclusive with the effort to provide in-depth meaning for the sake of accomplishing the purposes of the rites and rituals. The words a curse and a blessing are considered as the effort to materialize supernatural things believed in the cosmology and can sublimize in the real world (Dufour & Boutaud, 2013; Eliade, 2002). Therefore, everyone bound in the covenant will build awareness to completely comply with the law on one hand, and on the other, maintain fear as a way to avoid a curse due to violation.\n\nThe survival of the ancient law of fondrakö in the middle of Nias community is caused by its function in the social binding formation. Although it is a legal rule and a socio-religious law, the community treat fondrakö as the glue for social life. Zebua (1996, p. 46) clarified the fondrakö law in two parts. The first part is the provisions that govern customs. In this first part, everything on a human life cycle that starts from birth to the demise of the humans is arranged in the law and customary provisions - including arrangements regarding honor and social stratification in the community. Meanwhile, the second part of fondrakö is the arrangement on the law covering the marriage customary law, the law governing the economic life, the rules on crimes, criminal and civil laws, and the law on civics (arranging the governance and decision making in the power structure in a village). The classification shows that fondrakö plays a role in forming social structure, making every member of the community bound in a contract. As in a contract, its success is determined by the awareness of the community members to mutually bind each other and mutually have solidarity toward each other. The thinking of Durkheim on community formation in the social eye perspective (Durkheim, 2018, p. 130; Ritzer & Stepnisky, 2019a, pp. 92–95; Strenski, 2015, p. 129) can be used to understand how fondrakö is seen as norms, faith, and values functioning to form community collective awareness. The main objective of this awareness is as the cohesion and social integration. Every individual is demanded to be an agent to create wholeness, unity, and order of the community to comply with the law. For Durkheim (1965), the formation of collective awareness only happens if every individual acts as an agent for the collective interest. The results are social and economic resistance, stability, and security of the group.\n\nThe research of Puccioni (2016) discovered a fact that ancient Nias community lived in the community groups called öri. Every öri was separated from each other and had a legal system, customs, and the autonomous government under the leadership of an elder named tuhenöri. The bilateral relationship among öri was basically bad. The competition in economy, customs, and area influence could lead to the act of conquering each other, ethnic war, and open hostility. If an öri failed to build social binding in its community, that village would be vulnerable toward internal disunity and would be easily conquered by other enemies of öri. Therefore, every tuhenöri was obliged to guard the wholeness of each öri using fondrakö. With it, dialectics occurred between collective awareness and individual awareness in producing social binding leading to the formation of social integration in an öri. The problem is that villages are no longer öri in the modern era and the government in a community has been taken over by a different elite. Will fondrakö become only a cultural heritage and has it been replaced with the values of modernity?\n\nNielsen (2003) that relied on the thinking of Durkheim (1995) and Martins & Guerra (2013) formulated an argument to answer those questions. The past community rites could experience a number of form changes in the modern religious practice through a rite proliferation. A number of shifts and adjustments happened without changing the meaning. Demerath (2003) specifically defined the shifts and adjustments as the sacrality process due to the occurrence of religious myth transformation to become a habit in a cultural commonplace. Simultaneously, the number of rites and the rituals of early forms can just change anytime. Their emotional intensity decreases due to social contour changes and other factors from the era because of complex social differentiation. Hence, it can be concluded that in the modern community, both in the religious scope and in the culture, proliferation is a natural thing happening as a way of the community to maintain the self-existence and group identity (Buzan & Albert, 2010). Although at the beginning the rites only involved certain groups and did not play a role in the community widely (Hirschle, 2012), the acceptance in the context of cultural commonplace kept taking place. Adaptation and modification happened in the form of the ritual and philosophical values integrated into the social order involving family, the state, workplaces, markets, and ethnic groups.\n\nThe Nias’s fondrakö experienced a similar process. The modern Nias community life can never be separated from the fondrakö philosophical values. In every social, cultural, and religious practices, specifically seen in the social decision making, community interest, consensus and agreement, life cycle initiation (birth, adult initiation, marriage, death), warning implementation, kinship relationship and social action, and moreover the religiosity aspect, the values of fondrakö are still maintained and practiced. This proves that fondrakö has changed from the rites and rituals of ethnic religion to become life philosophy that keeps living in every generation. Even though the face of the world has been colored by digitalization and the internet, the signs of contemporary progress do not reduce or get rid of the local wisdom of the modern Nias community. In the marriage initiation, for example, ere as the ethnic imam no longer plays a role and is replaced with a priest. However, the procession essence and the meaning of marriage are still maintained according to the fondrakö’s strict customary provisions (Saputra, 2018; Zaluchu, 2020).\n\n\nConclusion\n\nIt can be concluded that fondrakö for the modern Nias community is not merely a rite or a primitive cultural product. Traditional practice has experienced transformation to become point of view of life and a philosophical product integrated into the way to behave, social structure, and community spirituality. This is why the modern Nias people cannot be separated from their local wisdom values. This also refutes the general point of view that the world change into the digital culture that is free of values has shifted the existence of traditional values. What has happened in Nias becomes an example of how the local wisdom is able to survive and experience adaptation because of the decisions of the community themselves. The contemporary Nias community are capable of drawing a line of when to interact with the modern lifestyle that is all digitalized and when they must hold the fondrakö’s philosophical principles as the foundation of the way of life. Hybridization requires thinking as an adaptive solution in accommodating the local wisdom into modernity without making them contradictory to each other. Through the philosophy of fondrakö keeps on living in the contemporary Nias community, it can be seen that modern humans will tend to have orientation toward primitive forms both in the social context and in religion to maintain values and morality.", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nAcknowledgements\n\nThank you to Yusak Setiawan, Ph.D. from Universitas Kristen Satya Wacana Salatiga that has read and provided suggestions from his expertise to sharpen this paper analysis!\n\n\nReferences\n\nAlston WP:Religious Language. Wainwright WJ, editor. The Oxford Handbook of Philosophy of Religion2. New Yok:Oxford University Press;2005; (pp. 220–244).\n\nBeatty A: Ovasa; Feasts of merit in Nias. Bijdragen Tot de Taal-, Land- En Volkenkunde/Journal of the Humanities and Social Sciences of Southeast Asia. 2013; 147(2): 216–235. 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P., editor.Yogyakarta:Pustaka Pelajar;1st ed.2019b.\n\nSahidah A: Agama Sipil Roberth N. Bellah [Civil Religion of Robert N. Bellah]. Yogyakarta:Cantrik Pustaka;2020.\n\nSailhamer JH: The Meaning of Pentateuch. Downer s Grove, Illionis, Illionis:IVP Academic;2009.\n\nSanders JA: From Sacred Story to Sacred Text - Canon as Paradigm. Eugeren, OR:Wipf and Stock Publishers;1987.\n\nSaputra A: Deskripsi Analitik Pertunjukan Maena dalam Upacara Adat Perkawinan Pada Masyarakat Nias di Desa Hili Waele I Kecamatan Boto Muzoi Nias Induk. Universitas Sumatera Utara;2018.Reference Source\n\nShillington VG: Reading the Sacret Text - An Introduction to Biblical Studies. London, UK:T&T Clarck Ltd;2002.\n\nSiddiqee S: Listening to God in Community. Explor3, Spring. 2013; 28–31.\n\nSmart N: The Religious Experience of Mankind. New Yok:Charles Scribner’s Sons;1984.\n\nStrenski I: Understanding Theories of Religion: An Introduction. 2nd ed.2015.Reference Source\n\nStrijdom JM: Animism: Comparing Durkheim and Chidester’s analyses of EB Tylor’s theory of religion. HTS Teologiese Studies/Theological Studies. 2021; 77(2). Publisher Full Text\n\nSundermann WH: Des Kultus der Niasser. RMG;1891; 1025.\n\nSundermann WH: Niassich-Deutsches Worterbuch. Moers:Bataviaasch Genootschap van Kunsten en Wetenschappen;1905.\n\nTsuria R, Bellar W, Campbell H, et al.: Transferred, mediated or transformed: considering the design, features, and presentation of sacred text mobile applications. J. Contemp. Relig. 2021; 36(1): 57–78. Publisher Full Text\n\nTylor EB: Primitive culture: Researches into the development of mythology, philosophy, religion, art, and custom. Primitive Culture: Researches into the Development of Mythology, Philosophy, Religion, Art, and Custom. 2010; 2. Publisher Full Text\n\nWeir L: Primitive rituals, contemporary aftershocks: Evocations of the orientalist “other” in four productions of le Sacre du printemps. Avant. 2013; 4(3): 111–143. Publisher Full Text\n\nWidder W:Introduction to Linguistic and the Bible.Magum D, Westbury J, editors. Lingustic and Biblical Exegesis. Bellingham, WA:Lexham Press;1st ed.2017.\n\nWilson A, editor.Scripture and Tradition. World;s Scripture: A Comparative Anthology of Sacred Texts. 1st ed.1991.Reference Source\n\nZaluchu SE: Perspektif antropologi dan religi perkawinan suku nias. Sejarah Dan Budaya: Jurnal Sejarah, Budaya, Dan Pengajarannya. 2020; 14(2): 108–119. Publisher Full Text Reference Source\n\nZaluchu SE: Lowalangi: From the name of an ethnic religious figure to the name of god. HTS Teologiese Studies/Theological Studies. 2021; 77(4): 1–6. Publisher Full Text\n\nZebua F: Kota Gunungsitoli: Sejarah Lahirnya dan Perkembangannya [The City of Gunungsitoli: History and Development]. Waruwu M, editor. Gunungsitoli:Nias;1st ed.1996.\n\nZega PD: Budaya Fondrako Dalam Kepemimpinan Kepala Ruangan Di Rumah Sakit. Universitas Sumatera Utara;2019. Publisher Full Text" }	[ { "id": "185544", "date": "28 Jul 2023", "name": "Oinike Natalia Harefa", "expertise": [ "Reviewer Expertise Indonesia" ], "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. There are many kinds of fondrakö in Nias that are established based on the area (villages). It is better to make it clear from the beginning that each fondrakö is not for the whole Nias people.\n2. In the past, fondrakö delivered with oral tradition. Today, some fondrakö have been written. What do you think about this? I suggest that the author emphasize this relation in the section of the holy book.\n\n3. Does decision-making through the fondrakö deal with justice for the victims of violence? Or is it more for the social interest rather than a preference for individual well-being? For instance, in the case of violence against women.\n4. The author mentions about \"dowry\" in Nias. Please check the right terminology for this, is it dowry or bride price? It is two different things.\n\n5. The author mentions how fondrakö affects the relationship with God, this tradition is more judgemental rather than a grace-based approach, as the soul of Christianity. Even, the author also writes, \"This is the reason why fear and obedience toward the values of fondrakö survive in every generation of Nias people\". How does the author deal with this?\n6. Is the fondrakö still relevant today for the younger generation in Nias? The author seems too optimistic about fondrakö but less in criticism, especially at the point of blessing or curse.\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?\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": [] }, { "id": "159966", "date": "12 Sep 2024", "name": "Fransiskus Irwan Widjaja", "expertise": [ "Reviewer Expertise Missiology", "Ethnography and Theology of Mission" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe author is courageous to expose and lift the fondrakö as a central research topic. This primitive oral culture still exists today and is very important to dig up and valuable for others concerned with ethnography or contextualizing the local culture using ancient history to study further. Zaluchu ‘s conclusion of the Social laws of primitive religion is not always contradictory. It can run parallel with civilization, and primitive culture will not simply disappear in the modern community is an audacious statement that should get two thumbs for appreciation. The author may look at other articles for comparison and additional citations attached.\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": [] } ]	1	https://f1000research.com/articles/12-41
https://f1000research.com/articles/13-1061/v1	17 Sep 24	{ "type": "Data Note", "title": "A guide to selecting high-performing antibodies for Rab10 (UniProt ID: P61026) for use in western blot, immunoprecipitation, and immunofluorescence", "authors": [ "Vera Ruíz Moleón", "Charles Alende", "Maryam Fotouhi", "Kathleen Southern", "Riham Ayoubi", "Carl Laflamme", "NeuroSGC/YCharOS/EDDU collaborative group", "ABIF consortium", "Vera Ruíz Moleón", "Charles Alende", "Maryam Fotouhi", "Kathleen Southern", "Riham Ayoubi" ], "abstract": "Rab10 is a small GTPase involved in cargo transport from the trans-Golgi network to the plasma membrane and endocytic recycling back to the cell membrane. It has garnered significant interest in neurodegenerative disease research, particularly due to its phosphorylation by the LRRK2 kinase. This relationship underscores the importance of Rab10 in cellular processes related to disease pathology, specifically Parkinson’s disease. The accessibility of renewable and selective antibodies against Rab10 would advance research efforts, enabling further understanding of its function and implications in disease. Here, we have characterized eight Rab10 commercial antibodies 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 larger, collaborative initiative seeking to address antibody reproducibility issues by characterizing commercially available antibodies for human proteins and publishing the results openly as a resource for the scientific community. While use 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: P61026", "RAB10", "Rab10", "antibody characterization", "antibody validation", "western blot", "immunoprecipitation", "immunofluorescence" ], "content": "Introduction\n\nThe family of small GTPase Rabs are regulators of membrane trafficking, cycling between an active GTP-bound form and inactive GDP-bound form to recruit effector proteins and monitor vesicle formation and fusion with membranes. Rab10 is involved in the process of membrane trafficking from the trans-Golgi network to the plasma membrane.1 Moreover, it regulates the transport of GLUT4 glucose-transport enriched vesicles to the plasma membrane.2–4\n\nPhosphorylation of Rab10 at Thr73 by Leucine-rich repeat kinase 2 (LRRK2)5 regulates its activity. The characterization of phospho-Rab antibodies, including those targeting Rab10, has been conducted elsewhere.6 LRRK2, a protein kinase associated with Parkinson’s disease,7,8 has been shown to have increased kinase activity when subject to pathogenic mutations.9 Elevated levels of phospho-Rab10 have been identified in neutrophils from Parkinson’s disease patients with LRRK2 mutations.10 While inhibiting Rab10 is being explored as a potential therapeutic strategy, a deeper understanding of its mechanism is needed. This understanding could be greatly enhanced by the availability of selective and renewable Rab10 antibodies.\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.11–13 Here we evaluated the performance of eight commercial antibodies for Rab10 for use in western blot, immunoprecipitation, and immunofluorescence, enabling biochemical and cellular assessment of Rab10 properties and function. The platform for antibody characterization used to carry out this study was endorsed by a committee of industry academic representatives. It consists of identifying human cell lines with adequate target protein expression and the development/contribution of equivalent knockout (KO) cell lines, followed by antibody characterization procedures using commercially available antibodies against the corresponding protein. The standardized consensus antibody characterization protocols are openly available on Protocol Exchange, a preprint server (DOI: 10.21203/rs.3.pex-2607/v1).14\n\nThe authors do not engage in result analysis or offer explicit antibody recommendations. 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. Guidelines on how to interpret antibody characterization data found in this study are featured on the YCharOS gateway.15\n\n\nResults and discussion\n\nOur standard protocol involves comparing readouts from WT (wild type) and KO cells.16,17 The first step was to identify a cell line(s) that expresses sufficient levels of a given protein to generate a measurable signal using antibodies. To this end, we examined the DepMap (Cancer Dependency Map Portal, RRID:SCR_017655) transcriptomics database to identify all cell lines that express the target at levels greater than 2.5 log2 (transcripts per million “TPM” + 1), which we have found to be a suitable cut-off.11 The HAP1 expresses the Rab10 transcript at 7.9 log2 (TPM+1), which is above the average range of cancer cells analyzed. A RAB10 KO HAP1 cell line was obtained from Horizon Discovery (Table 1).\n\nFor western blot experiments, WT and RAB10 KO protein lysates were ran on SDS-PAGE, transferred onto nitrocellulose membranes, and then probed with eight Rab10 antibodies in parallel (Table 2, Figure 1).\n\n* Monoclonal antibody.\n\n** Recombinant antibody.\n\nLysates of HAP1 WT and RAB10 KO were prepared, and 40 μg of protein were processed for western blot with the indicated Rab10 antibodies. 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. All antibodies were used at 1/1000. Predicted band size: 22.5 kDa. Monoclonal antibody, Recombinant antibody.\n\nWe then assessed the capability of all eight antibodies to capture Rab10 from HAP1 protein extracts using immunoprecipitation techniques, followed by western blot analysis. For the immunoblot step, a specific Rab10 antibody identified previously (refer to Figure 1) was selected. Equal amounts of the starting material (SM) and unbound fraction (UB), as well as the whole immunoprecipitate (IP) eluates were separated by SDS-PAGE (Figure 2).\n\nHAP1 lysates were prepared, and immunoprecipitation was performed using 1 mg of lysate and 2.0 μg of the indicated Rab10 antibodies pre-coupled to Dynabeads protein A or protein G. Samples were washed and processed for western blot with the indicated Rab10 antibody. For western blot, ab237703* and MA5-15670* were used at 1/500 and 1/1000, respectively. The Ponceau stained transfers of each blot are shown. SM = 4% starting material; UB = 4% unbound fraction; IP = immunoprecipitate. Monoclonal antibody, Recombinant antibody.\n\nFor immunofluorescence, eight antibodies were screened using a mosaic strategy. First, HAP1 WT and RAB10 KO cells were labelled with different fluorescent dyes in order to distinguish the two cell lines, and the Rab10 antibodies were evaluated. Both WT and KO lines imaged in the same field of view to reduce staining, imaging and image analysis bias (Figure 3). Quantification of immunofluorescence intensity in hundreds of WT and KO cells was performed for each antibody tested, and the images presented in Figure 3 are representative of this analysis.14\n\nHAP1 WT and RAB10 KO cells were labelled with a green or a far-red fluorescent dye, respectively. WT and KO cells were mixed and plated to a 1:1 ratio on coverslips. Cells were stained with the indicated Rab10 antibodies and with 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 an antibody was recommended for immunofluorescence by the supplier, we tested it at the recommended dilution. The rest of the antibodies were tested at 1 and 2 μg/ml and the final concentration was selected based on the detection range of the microscope used and a quantitative analysis not shown here. Antibody dilution used: ab104859 at 1/200, ab181367 at 1/100, ab237703 at 1/500, A22746 at 1/600, 8127 at 1/50, 11808-1-AP at 1/400, 27094-1-AP at 1/600 and MA5-15670* at 1/500. Bars = 10 μm. Monoclonal antibody, Recombinant antibody.\n\nIn conclusion, we have screened eight Rab10 commercial antibodies by western blot, immunoprecipitation, and immunofluorescence by comparing the signal produced by the antibodies in human HAP1 WT and RAB10 KO cells. To assist viewers in interpreting antibody performance, Table 3 outlines various scenarios in which antibodies may perform in all three applications. Several high-quality and renewable antibodies that successfully detect Rab10 were identified in all applications. Researchers who wish to study Rab10 in a different species are encouraged to select high-quality antibodies, based on the results of this study, and investigate the predicted species reactivity of the manufacturer before extending their research.\n\nThe underlying data for this study can be found on Zenodo, an open-access repository for which YCharOS has its own collection of antibody characterization reports and corresponding dataset.18,19\n\nInherent limitations are associated with the antibody characterization platform used in this study. Firstly, the YCharOS project focuses on renewable (recombinant and monoclonal) antibodies and does not test all commercially available Rab10 antibodies. YCharOS partners make up approximately 80% of all renewable antibodies, but some top-cited polyclonal antibodies may not be available through these partners.\n\nSecondly, the YCharOS effort employs a non-biased approach that is agnostic to the protein for which antibodies have been characterized. The aim is to provide objective data on antibody performance without preconceived notions about how antibodies should perform or the molecular weight that should be observed in western blot. As the authors are not experts on the Rab family of proteins or vesicle trafficking, only a brief overview of the protein’s function and its relevance in disease is provided. Rab10 experts are responsible for analyzing and interpreting observed banding patterns in western blots and subcellular localization in immunofluorescence.\n\nThirdly, YCharOS experiments are not performed in replicates primarily due to the use of multiple antibodies targeting various epitopes. Once a specific antibody is identified, it validates the protein expression of the intended target in the selected cell line, confirming the lack of protein expression in the KO cell line and supports conclusions regarding the specificity of the other antibodies. Moreover, some antibody clones are donated by 2-3 manufacturers (cross-licensed antibodies), effectively serving as replicates and enabling the validation of test reproducibility. All experiments are performed using master mixes, and meticulous attention is paid to sample preparation and experimental execution. In immunofluorescence, the use of two different concentrations serves to evaluate antibody specificity and can aid in assessing assay reliability. In instances where antibodies yield no signal, a repeat experiment is conducted following titration. Additionally, our independent data is performed subsequently to the antibody manufacturers internal validation process, therefore making our characterization process a repeat.\n\nLastly, as comprehensive and standardized procedures are respected, any conclusions remain confined to the experimental conditions and cell line used for this study. The use of a single cell type for evaluating antibody performance poses as a limitation, as factors such as target protein abundance significantly impact results.14 Additionally, the use of cancer cell lines containing gene mutations poses a potential challenge, as these mutations may be within the epitope coding sequence or other regions of the gene responsible for the intended target. Such alterations can impact the binding affinity of antibodies. This represents an inherent limitation of any approach that employs cancer cell lines.\n\n\nMethods\n\nThe standardized protocols used to carry out this KO cell line-based antibody characterization platform was established and approved by a collaborative group of academics, industry researchers and antibody manufacturers. The detailed materials and step-by-step protocols used to characterize antibodies in western blot, immunoprecipitation and immunofluorescence are openly available on Protocol Exchange, a preprint server (DOI: 10.21203/rs.3.pex-2607/v1).14 Brief descriptions of the experimental setup used to carry out this study can be found below.\n\nCell lines used and primary antibodies tested in this study are listed in Tables 1 and 2, respectively. To ensure that the cell lines and antibodies are cited properly and can be easily identified, we have included their corresponding Research Resource Identifiers, or RRID.20,21 HAP1 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-glutamine (Wisent cat. number 609-065, 100 IU penicillin and 100 μg/ml streptomycin (Wisent cat. number 450201).\n\nPeroxidase-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 A-21429 and A-21424). Peroxidase-conjugated Protein A for IP detection is from MilliporeSigma, cat. number P8651. Peroxidase-conjugated anti-mouse IgG for IP detection is from Abcam, cat. number ab131368.\n\nHAP1 WT and RAB10 KO cells were collected in RIPA buffer (25 mM Tris-HCl pH 7.6, 150 mM NaCl, 1% NP-40, 1% sodium deoxycholate, 0.1% SDS) (Thermo Fisher Scientific, cat. number 89901) supplemented with 1× protease inhibitor cocktail mix (MilliporeSigma, cat. number P8340). Lysates were sonicated briefly and incubated 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 (GeneDireX, cat. number PM008-0500) was used.\n\nWestern blots were performed with 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) 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 (Thermo Fisher Scientific, cat. number 32106) or Clarity Western ECL Substrate (Bio-Rad, cat. number 1705061) prior to detection with the iBright™ CL1500 Imaging System (Thermo Fisher Scientific (cat. number A44240).\n\nAntibody-bead conjugates were prepared by adding 2 μg to 500 μl of Pierce IP Lysis Buffer (Thermo Fisher Scientific, cat. number 87788) in a microcentrifuge tube, together with 30 μl of Dynabeads protein A - (for rabbit antibodies) or protein G - (for mouse antibodies) (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 cells were collected 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. Protein A: HRP was used as a secondary antibody at a dilution of 2 μg/ml when the rabbit antibody ab237703* was used for western blot to detect the IP. Anti-mouse IgG for IP: HRP was used as a secondary antibody at a concentration of 0.3 μg/ml when the mouse antibody MA5-15670* was used for western blot to detect the IP.\n\nHAP1 WT and RAB10 KO cells were labelled with a green and a far-red fluorescence dye, respectively (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 on 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 37oC, 5% CO2. Cells were fixed in 4% paraformaldehyde (PFA) (VWR, cat. number 100503-917) in phosphate buffered saline (PBS) (Wisent, cat. number 311-010-CL). 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% BSA, 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 Rab10 antibodies overnight at 4°C. Cells were then washed 3 × 10 min 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 confocal high-content microscopy system (Molecular Devices), using a 20x NA 0.95 water immersion objective and scientific CMOS cameras, equipped with 395, 475, 555 and 635 nm solid state LED lights (lumencor Aura III light engine) and bandpass filters to excite DAPI, Cellmask Green, Alexa-555 and Cellmask Red, respectively. Images had pixel sizes of 0.68 x 0.68 microns, and a z-interval of 4 microns. For analysis and visualization, shading correction (shade only) was carried out for all images. Then, maximum intensity projections were generated using 3 z-slices. Segmentation was carried out separately on maximum intensity projections of Cellmask channels using CellPose 1.0, and masks were used to generate outlines and for intensity quantification.22 Figures were assembled with Adobe Illustrator.", "appendix": "Data availability\n\nZenodo: Antibody Characterization Report Rab10, https://doi.org/10.5281/zenodo.13684961. 18\n\nZenodo: Dataset for the Rab10 antibody screening study, https://doi.org/10.5281/zenodo.13685286. 19\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgment\n\nWe 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 KO cell line suppliers, for the development of community-agreed protocols, and for their shared ideas, resources, and collaboration. Members of the group can be found below. 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, Peter S. McPherson, 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 your support on 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\n\nReferences\n\nHutagalung AH, Novick PJ: Role of Rab GTPases in membrane traffic and cell physiology. Physiol. Rev. 2011; 91(1): 119–149. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLarance M, Ramm G, Stöckli J, et al.: Characterization of the role of the Rab GTPase-activating protein AS160 in insulin-regulated GLUT4 trafficking. J. Biol. Chem. 2005; 280(45): 37803–37813. PubMed Abstract \| Publisher Full Text\n\nKhan TG, Ginsburg D, Emmer BT: The small GTPase RAB10 regulates endosomal recycling of the LDL receptor and transferrin receptor in hepatocytes. J. Lipid Res. 2022; 63(8): 100248. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChen CC, Schweinsberg PJ, Vashist S, et al.: RAB-10 is required for endocytic recycling in the Caenorhabditis elegans intestine. Mol. Biol. Cell. 2006; 17(3): 1286–1297. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSteger M, Tonelli F, Ito G, et al.: Phosphoproteomics reveals that Parkinson’s disease kinase LRRK2 regulates a subset of Rab GTPases. elife. 2016; 5: 5. Publisher Full Text\n\nLis P, Burel S, Steger M, et al.: Development of phospho-specific Rab protein antibodies to monitor in vivo activity of the LRRK2 Parkinson’s disease kinase. Biochem. J. 2018; 475(1): 1–22. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYan T, Wang L, Gao J, et al.: Rab10 Phosphorylation is a Prominent Pathological Feature in Alzheimer’s Disease. J. Alzheimers Dis. 2018; 63(1): 157–165. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEguchi T, Kuwahara T, Sakurai M, et al.: LRRK2 and its substrate Rab GTPases are sequentially targeted onto stressed lysosomes and maintain their homeostasis. Proc. Natl. Acad. Sci. USA. 2018; 115(39): E9115–E9124. PubMed Abstract \| Publisher Full Text\n\nLeandrou E, Markidi E, Memou A, et al.: Kinase activity of mutant LRRK2 manifests differently in hetero-dimeric vs. homo-dimeric complexes. Biochem. J. 2019; 476(3): 559–579. PubMed Abstract \| Publisher Full Text\n\nKarayel O, Tonelli F, Virreira Winter S, et al.: Accurate MS-based Rab10 Phosphorylation Stoichiometry Determination as Readout for LRRK2 Activity in Parkinson’s Disease. Mol. Cell. Proteomics. 2020; 19(9): 1546–1560. PubMed Abstract \| Publisher Full Text \| Free 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. elife. 2023; 12: 12. Publisher Full Text\n\nCarter AJ, Kraemer O, Zwick M, et al.: Target 2035: probing the human proteome. Drug Discov. Today. 2019; 24(11): 2111–2115. PubMed Abstract \| Publisher Full Text\n\nLicciardello MP, Workman P: The era of high-quality chemical probes. RSC Med. Chem. 2022; 13(12): 1446–1459. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAyoubi R, Ryan J, Bolivar SG, et al.: A consensus platform for antibody characterization (Version 1). Protocol Exchange. 2024.\n\nBiddle MS, Virk HS: YCharOS open antibody characterisation data: Lessons learned and progress made. F1000Res. 2023; 2023(12): 1344.\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\nRuiz Moleon V, Alende C, Fotouhi M, et al.: A guide to selecting high-performing antibodies for Rab10 (UniProt ID: P61026) for use in western blot, immunoprecipitation and immunofluorescence. Zenodo. 2024. Publisher Full Text\n\nAyoubi R, Laflamme C: Dataset for the Rab10 antibody screening study [Data set]. Zenodo. 2024. 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": "325289", "date": "10 Oct 2024", "name": "Jan Voskuil", "expertise": [ "Reviewer Expertise Life-time career expertise on antibody characterisation and validation in all immunoassays. Both experience as an academic scientist", "and as a commercial provider." ], "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\nTable 3 was not visible, broken images. The authors delivered an excellent approach to validate commercial antibodies by comparing their generated signals from a suitable cell line, proven to express the target gene sufficiently for antibody detection, with its cognate knock-out derivative cell line. In their approach, they analysed the antibody performance in Western blot (WB), in immuno-precipitation (IP), and in immunocytochemistry (staining of entire cells detected by immunofluorescence, IF). Although the objective of the authors are to present their approach as a method of finding high performing antibodies from the market, the data themselves are left without scientific assessment. I think this paper will benefit from an extra paragraph to discuss the quality of the individual data. For example, some antibodies show extra bands in WB, and it is not clear whether these bands would disappear upon further antibody dilution (without loss of specific signal), or that all the bands, the correct and the wrong ones, would equally fade by further antibody dilution. The target Rab10 is located in vesicular membranes and perinuclear. Its location in the IF data is not very clear in many cases. A few sentences on the quality of the data would be desirable and put some extra scientific weight to the article. The authors suggest that several antibodies worked well across all three applications, but I could only find one of them. Table 3 was inaccessible to me. This paper is extremely useful for scientists needing a good Rab10 antibody for either WB, IP or ICC. I highly commend this paper for indexing, and I hope my remarks will be addressed in the final version.\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? Partly", "responses": [] }, { "id": "325290", "date": "10 Oct 2024", "name": "Sian E. Evans", "expertise": [ "Reviewer Expertise Oncology", "Western Blotting", "ELISA", "Immuno-fluorescence", "Cell-based assays." ], "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 data note provides a detailed description of the characterisation of eight commercial antibodies targeting Rab10. The study evaluates their suitability for western blot, immunoprecipitation, and immunofluorescence using a standardised experimental protocol.\nThe aim is to assess antibody performance for Rab10 using a wild-type and knock-out cell line. The materials and methods are well-documented, and a link to the standardised antibody characterisation protocols is provided for further reference (DOI: 10.21203/rs.3.pex-2607/v1).\nThe results and discussion section is concise and coherent. The authors justify their choice of using the HAP1 cell line and reference the database they utilized, which will be beneficial for other researchers. All images and tables are presented clearly. The inclusion of Table 3, which demonstrates the distinction between successful and unsuccessful antibody performance, is particularly helpful for researchers in interpreting the data.\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": [] } ]	1	https://f1000research.com/articles/13-1061
https://f1000research.com/articles/13-674/v1	21 Jun 24	{ "type": "Opinion Article", "title": "The gamma-band activity model of the near-death experience: a critique and a reinterpretation.", "authors": [ "Nigel A Shaw" ], "abstract": "Near-death experience (NDE) is a transcendent mental event of uncertain etiology that arises on the cusp of biological death. Since the discovery of NDE in the mid-1970s, multiple neuroscientific theories have been developed in an attempt to account for it in strictly materialistic or reductionistic terms. Therefore, in this conception, NDE is at most an extraordinary hallucination without any otherworldly, spiritual, or supernatural denotations. During the last decade or so, a number of animal and clinical studies have emerged which reported that about the time of death, there may be a surge of high frequency electroencephalogram (EEG) at a time when cortical electrical activity is otherwise at a very low ebb. This oscillatory rhythm falls within the range of the enigmatic brain wave-labelled gamma-band activity (GBA). Therefore, it has been proposed that this brief, paradoxical, and perimortem burst of the GBA may represent the neural foundation of the NDE. This study examines three separate but related questions concerning this phenomenon. The first problem pertains to the electrogenesis of standard GBA and the extent to which authentic cerebral activity has been contaminated by myogenic artifacts. The second problem involves the question of whether agents that can mimic NDE are also underlain by GBA. The third question concerns the electrogenesis of the surge in GBA itself. It has been contended that this is neither cortical nor myogenic in origin. Rather, it arises in a subcortical (amygdaloid) location but is recorded at the cortex via volume conduction, thereby mimicking standard GBA. Although this surge of GBA contains genuine electrophysiological activity and is an intriguing and provocative finding, there is little evidence to suggest that it could act as a kind of neurobiological skeleton for a phenomenon such as NDE.", "keywords": [ "Amygdala", "Consciousness", "Electroencephalogram", "Electromyogram", "Gamma oscillations", "Near-death Experience" ], "content": "Introduction\n\nThe near-death experience (NDE) is a constellation of mental events often of a mystical or transcendental quality which uniquely arise on the precipice of biological death. A subject, victim, or patient is typically unconscious or semi-conscious. What also distinguishes NDE is its recurring nature. Once recovered, survivors tended to report remarkably similar sensations, perceptions, and usually (although not invariably) positive feelings. Although recorded for millennia in almost every society, culture, and religion, formal contemporary studies of the NDE did not begin until the mid-1970s. The catalyst was the publication of psychiatrist Raymond Moody’s book “Light After Light” (Moody, 1975). When considering NDE, it is probably not useful to conflate it with other near-death phenomena such as the deathbed vision and the anticipated or fear of death experience, even though their features may overlap.\n\nThere is little doubt that NDE is a bona fide experience (Fischer and Mitchell-Yellin, 2016; Sartori, 2016). The principal question is what the ontological status is. Sometimes, the sequence of NDE components unfolds in a manner that creates the impression of an other-worldly journey. This has been interpreted by some as the first step towards a post-mortem existence and, therefore, a glimpse of life after death (Wheeler, 1977; Blackmore, 1993). Prima facie, the NDE might, therefore, provide a kind of empirical confirmation of the dualist notion that mind, spirit, soul, or consciousness are quite separate entities with a distinct existence or at least independence from the corporeal body or brain.\n\nContrary to this, a survivalist or supernatural paradigm is a naturalistic or materialistic explanation that maintains that the NDE is, at most, a complex and fantastic hallucination (Sacks, 2012). The primary difficulty with this proposal is accounting for how phantasmagoria could arise under such inauspicious circumstances. During the past half-century, at least two dozen neuroscientific theories have been proposed. There are many variations in one another.\n\nEarlier models tended to rely on seemingly simple modes of action involving, for example, endorphins, birth memories, hypoxia, autoscopy, hypercapnia, and pharmacology. More elaborate and sophisticated theories have relied on advances in neuroscience (e.g. Saavedra-Aguilar and Gomez-Jeria, 1989; Jansen, 2001; Strassman, 2001). To date, however, no single neuroscientific theory has proved entirely satisfactory. This failure has sometimes been used as de facto evidence in favor of a paranormal explanation. Multiple accounts of these theories are available, and some are more sympathetic to a neuroscientific explanation than others. The selection includes Moody (1975), Ring (1980), Sabom (1982), Zaleski (1987), Morse and Perry (1992), Blackmore (1993), Fenwick and Fenwick (1995), Kellehear (1996), Ritchie and Sherrill (2007), Greyson (1998), Jansen (2001), Fox (2003), Mobbs and Watt (2011), Alexander (2012), Sacks (2012), and Michael et al. (2023). The majority of these are critical surveys of extant models, although there are some exceptions (e.g. Blackmore, 1993; Jansen, 2001; Michael et al., 2023).\n\nIn the present century, two new neuroscientific models have emerged. As a measure of popular interest in this subject, both have attracted a good deal of attention in general news media. The first is the rapid eye movement (REM) sleep-intrusion theory (Nelson et al., 2006). More recently, the gamma oscillation model was proposed by George Mashour et al. at the University of Michigan (Borjigin et al., 2013a). For the present purposes, this model is referred to as the gamma band activity (GBA) theory, although this was never a term formally adopted by the authors. This is also known as the end-of-life electrical surge (ELES) model (Chawla et al., 2009). Unlike the REM-intrusion model, the GBA theory is essentially new and, in some respects, quite startling material. This was recently described as a “landmark” discovery (Shlobin et al., 2023).\n\nAs an example of worldwide attention, the GBA model almost immediately attracted, on August 14, 2013, The New Zealand Herald ran a headline entitled “Brain kicks in as heart fails”. The article then began “Scientists believe they may have solved the mystery behind the shining light people often talk about after having near-death experiences.”\n\nThe starting point of the investigation by Borjigin et al. was an attempt to solve a neurophysiological puzzle. A significant minority of patients who suffer cardiopulmonary arrest (CPA) and survive also report having NDE (Parnia et al., 2001; van Lommel et al., 2001). With cerebral blood flow failing, the acute loss of O2 supply and depletion of glucose reserves means that cortical function, as reflected in electroencephalographic (EEG) activity, will rapidly cease. The characteristic pattern consists of a continuous slowing of frequency and loss of amplitude, which rapidly deteriorates towards a complete loss of electrical activity, that is, to an isoelectric EEG (Clute and Levy, 1990; van Lommel 2004). However, if NDE is a genuine type of brain hallucination, it would be predicted that there should still be at least a transient neural correlate of such an event that might be detectable in the unconscious brain despite the state of cerebral ischemia. Throughout this review, amplitude refers to activity measured in microvolts.\n\nTherefore, the authors focused their attention on an enigmatic high-frequency EEG rhythm known as gamma oscillation. This activity has long been considered to be related to the maintenance of consciousness and states of alertness (Thompson, 1975). Borjigin et al. reasoned that a brief paroxysmal burst of gamma oscillations in the dying brain might plausibly represent what they described as the neural signature of NDE.\n\n\nFunctional significance and generation of gamma waves\n\nHans Berger, the discoverer of human EEG, defined low-voltage fast cortical oscillations with a frequency greater than alpha as beta activity, that is, 14 Hz or greater. However, pioneering electroencephalographer Herbert Jasper soon identified an even higher frequency EEG, which was labelled as gamma rhythm (Jasper and Andrews, 1938). The exact constituent gamma frequency is unclear, but most contemporary research studies define it as oscillatory neural activity with a frequency range of 30–100 Hz, which is normally split into low, medium, and high gamma (Herrmann et al., 2004; Hoogenboom et al., 2006; Jensen et al., 2007; Buzsaki and Wang, 2012).\n\nAll types of higher cognitive processes have now been partially attributed to synchronized high-frequency GBA. Nonetheless, even most partisan advocates of such a role usually acknowledge that the current understanding is still fundamentally speculative and tentative. Among the cognitive operations frequently thought to be involved with GBA are perception (Tallon-Baudry and Bertrand, 1999; Lee et al., 2003; Kaiser and Lutzenberger, 2005; Hoogenboom et al., 2006; Uhlhass and Singer, 2006; Hughes, 2008; Ahmed and Cash, 2013; Bosman et al., 2014) selective attention (Kaiser and Lutzenberger, 2005; Uhlhass and Singer, 2006; Jensen et al., 2007; Fries, 2009; Ahmed and Cash, 2013; Bosman et al., 2014), long and short-term memory encoding and formation (Kaiser and Lutzenberger, 2003, 2005; Herrmann et al., 2004; Uhlhass and Singer, 2006; Jensen et al., 2007; Hughes, 2008; Bosman et al., 2014), sensory-motor control (Lee et al., 2003; Uhlhass and Singer, 2006; Schroeder and Lakatos, 2009; Ahmed and Cash, 2013; Bosman et al., 2014) and language acquisition (Lee et al., 2003). In addition to the long-standing view, GBA is involved in arousal and conscious awareness (Lee et al., 2003; Hughes, 2008; Ahmed and Cash, 2013) Most notably, oscillatory gamma rhythms are considered to play a crucial role in sensory processing, particularly regarding the so-called perceptual binding problem (Tallon-Baudry and Bertrand, 1999; Lee et al., 2003; Jensen et al., 2007; Hughes, 2008; Schroeder and Lakatos, 2009). This involves a mechanism by which separate features, elements, or components are successfully combined, coordinated, and processed to form a coherent and integrated percept. According to the current doctrine, this is accomplished by synchronized gamma – frequency rhythms activating separated, distributed, and diverse neuronal networks, assemblies, and regions. This facilitates successful perception or internal representation of a particular object or image.\n\nIn addition to controlling and recruiting neuronal ensembles, gamma frequency synchronization plays a role as a timekeeper (Buzsaki and Wang, 2012). In this sense, it provides a temporal framework for information processing and communication within the brain, which acts as a neural clock.\n\nIn addition, there is still no definitive understanding of the cellular mechanisms responsible for GBA electrogenesis of GBA (Traub et al., 1999; Lee et al., 2003; Traub et al., 2004; Uhlhass and Singer, 2006; Bartos et al., 2007; Fries, 2009; Traub and Whittington, 2010; Buzsaki and Wang, 2012; Ahmed and Cash, 2013). Both excitatory and inhibitory chemical neurotransmissions are likely involved in this process.\n\nHowever, the omnipresence of GABAergic interneurons in networks and regions where gamma waves typically arise has encouraged the idea that these are the basic functional units of high-frequency oscillations. Fast spiking inhibitory interneurons may interact and interconnect with excitatory pyramidal cells to produce and drive the GBA. Furthermore, continual mutual inhibition among the interneurons may set up recurrent feedback loops that autonomously maintain the periodicity, synchronicity, and frequency of the gamma rhythms. Moreover, gamma oscillations may be partially regulated via electrotonically coupled gap junctions between the interneurons.\n\nNeurophysiological models, such as those outlined above, have been developed primarily to account for cortical gamma waves. Therefore, they should provide a framework for or background to the GBA model of NDE generation.\n\n\nEvidence for the GBA model\n\nBorjigin et al. (2013a) used an adult rat model. In advance, bilateral skull-screw electrodes were implanted over the frontal, parietal, and visual cortices. On the experimental day, EEG activity was recorded sequentially from animals while awake, while anesthetized with a standard ketamine and xylazine combination, and during a state of cardiac arrest (induced by intracardiac injection of potassium chloride). Initially, the amplitude of the EEG was preserved and then decreased. However, beginning approximately 10 s after the onset of cardiac arrest and before the onset of suppression and essentially permanent isoelectricity, there was a brief interregnum consisting of mostly tightly synchronized, relatively high-amplitude, diffusely distributed GBA with a dominant frequency of approximately 40 Hz and a range of 25-50 Hz. This paroxysmal activity persisted for up to 20 s. Both the generalized coherence and power of these oscillations were significantly enhanced on the brink of death when compared with those in animals who were awake or anesthetized.\n\nBased on assumptions regarding the normal role of cortical gamma oscillations in mediating cognitive and perceptual function as summarized above, the authors interpreted their findings as evidence that there exists a transitory period of intensified alertness in the acutely dying brain where complex multi-faceted information processing may still occur. They conclude their paper with the provocative suggestion that this apparent discovery of high-level conscious activity on the cusp of death might provide the neurophysiological foundation for a novel naturalistic explanation of NDE.\n\n\nCritique of the GBA model\n\nThe prima facie weakness of the GBA theory is that it provides only the barest and most inchoate notion of how NDE might have been triggered under such conditions. Borjigin et al. made little or no attempt to advance or expand their model beyond the observation that this anomalous surge in electrical activity can be reliably recorded from the rodent brain almost immediately following cardiac arrest. Otherwise, it is not at all obvious how or why a state of comparatively high-voltage GBA generated ephemerally at the brink of biological death could ultimately sculpt an NDE. Vague statements such as the data providing “strong evidence for the potential of heightened cognitive processing in the near-death state” are not especially edifying. However, if investigators observe such an evident and unmistakable pattern of activity in the near-death state of a mammalian brain, then this is precisely what might be expected if there were indeed some neurobiological processes underlying NDE in humans. In a subsequent rebuttal, the authors expanded upon these questions (Borjigin et al., 2013c).\n\nNevertheless, if the current theories regarding the focal role that GBA is expected to play in the neuronal processing of perception, sensation, and memory ultimately turn out to be correct, then these activities might at least partially evoke the complex imagery and other phenomena of the NDE. It is more difficult to account for the invariant nature of much of the content and the apparent serial ordering of individual elements of the NDE (Michael et al., 2023). However, more recent investigations have strongly suggested that such temporal ordering is not a common feature of most NDEs (Martial et al., 2017). Unfortunately, any attempt to extend, develop, or expand the GBA theory would inevitably be stymied because the body of evidence concerning the role of gamma oscillations in any higher-level cognitive function is convincing in many respects but not entirely conclusive (Buzsaki, 2006).\n\nA second difficulty concerns the status of gamma rhythm as a measure of CNS arousal. Borjigin et al. seem to take for granted the standard doctrine that GBA is “associated with waking consciousness” and their model is largely predicated on this relatively long-standing assumption. There is little direct evidence linking GBA to conscious experiences. Perhaps the most persuasive argument is that gamma frequency EEG is more prevalent during states of wakefulness and REM sleep than during non-REM (slow wave) sleep or general anesthesia (Lee et al., 2003). Borjigin also appears to endorse this straightforward and intuitive view. Nevertheless, the ubiquitous presence of gamma waves means that there is a lack of clear, consistent, and exclusive associations between gamma activity and alertness (Vanderwolf, 2000; Buzsaki and Wang, 2012). This apparent independence tends to undermine the potential role of GBA as a mediator or reliable index of CNS arousal. Thus, if there is a functional disconnect between GBA and levels of consciousness, this would mean that any apparent relationship between them would be merely accidental or fortuitous. This raises the apostatic possibility that GBA has little, if anything, to do with the maintenance and regulation of states of awareness. The extent to which this would represent the integrity and feasibility of the GBA model for NDE generation is uncertain. However, a central tenet is that high-voltage gamma signals are an indication of a hyperaroused brain even in the context of rapidly deteriorating and irreversible cerebral function.\n\nThe authors formally analyzed the absolute and relative power of GBA for both wakefulness and ketamine-xylazine anesthesia. For absolute power, little difference could be detected between the conscious and unconscious states for any of the four GBA subbands. Regarding relative power, there was a tendency for activity to increase during the waking period, but only in the medium and higher gamma bands. Such findings do not resolve the relationship between GBA and the level of arousal. Of course, it is possible that GBA may subserve separate roles or functions depending on the state of consciousness.\n\nShortly after Borjigin’s article was published, Greyson et al. produced a brief but skeptical review of its relevance for understanding the origins of NDE (Greyson et al., 2013). This elicited a forceful rebuttal by Borjigin (Borjigin et al., 2013c). Four of the most pertinent questions are summarized below:\n\nFirst, Greyson questioned how the authors could claim that there was evidence of a hyperaroused brain in the post-cardiac arrest state when total electrical energy was drastically dissipated. Borjigin’s rejoinder reiterated the dogma that gamma oscillations play a central role in regulating wakefulness and alertness. This implies that concentrating on the overall undifferentiated EEG is misleading and immaterial in assessing the level of consciousness after cardiac arrest. Instead, they insisted that the appropriate index of conscious experience under these circumstances was the power, synchrony, connectivity, and coupling of the gamma oscillations. Judging by these findings, it stands to reason that the rodent brain must have been in a state of high alertness, albeit for a relatively fleeting period post cardiac arrest.\n\nSecond, Greyson identified a complication inherent in rodent data. All rats displayed a burst of high-frequency electrical activity; however, only a minority of patients surviving cardiac arrest subsequently reported an NDE. If the surge of EEG was really responsible for the NDE, this implies that an NDE should be a near-universal event in such patients, not an occasional one. Borjigin dealt with this objection by pointing out that their animal subjects were a very homogeneous group, in contrast to patients who reported having had an NDE. Differences among the latter with regard to genetics, physiology, and clinical conditions might account for the discrepancy in the predicted rate of NDE reporting. In addition, Borjigin also raised the possibility that many cardiac arrest patients have an NDE, but the remembrance of it is forgotten by the time consciousness is regained.\n\nThird, Greyson was also curious as to why a burst of postcardiac arrest EEG had never been detected in earlier clinical studies. It was pointed out that EEG characteristically deteriorates and rapidly disappears within approximately 20 s after cardiac arrest (van Lommel, 2004). Greyson claimed that there is no evidence of this surprising and incongruous EEG surge that there should otherwise have been in at least some patients. In response, Borjigin et al. suggested that the different techniques for recording and more complex processing and analysis that they employed in their own studies might account for the failure to observe and quantify any such EEG surge during clinical studies. In particular, they call attention to the fact that patient EEG recordings are performed using scalp electrodes. In contrast, animal studies used epidural electrodes, which meant that EEG signals were not attenuated or vitiated via passage through the skull and scalp. Therefore, more detailed and sensitive information about cortical function could be expected to be obtained under such conditions.\n\nFourth, Greyson claimed that many (possibly a quarter) NDEs arose during general anesthesia. If this estimate is correct, then the question may be raised as to why there was no evidence of post -arrest surges of GBA during the previous anesthetic state. Borjigin does not explicitly address this concern.\n\n\nClinical studies of GBA activity\n\nSubsequently, an activity analogous to that found in rodents was also discovered in a number of clinical recordings. The detection of these high-frequency EEG bursts during the perimortem period strengthened the idea of a putative role for gamma oscillations in the induction of NDE. In fact, Mashour et al. in 2013 were not the first to suggest that a surge in EEG activity at the moment of death might be linked to NDE. Four years earlier, Chawla et al. (2009) conducted a study that anticipated much of Borjigin’s research (Chawla et al., 2009). Instead of rodents, the subjects were seven terminally ill patients. EEG activity was measured using either a Bispectral Index Monitor (n=6) or Sedline Monitor (n=1). These produce an integrated numerical value, thereby providing only a relative gross measure of the level of consciousness or depth of anesthesia.\n\nAll patients exhibited a brief surge in electrical energy just prior to death and immediately after the loss of blood pressure. The authors described this phenomenon as a spike that typically lasted for just 30 – 80 s. It was assumed that the spike was composed of genuine EEG activity, but raw data were only available for a single case using the Sedline Monitor. A retrospective analysis of this recording revealed that the spike was composed of high-frequency EEG signals within the gamma range. Such a finding is congruent with the rodent study, and the authors also emphasized the supposed association between gamma waves and cerebral arousal. Nonetheless, it remains uncertain whether the spikes in the other six patients also contained GBA. The authors also devoted some effort to trying to exclude sources other than the EEG particularly electromyographic (EMG) artefact and electrical interference.\n\nSubsequently, Chawla and Seneff (2013) positively wrote about rodent findings, claiming that they confirmed their original human observations. In contrast, Borjigin et al. (2013b) did not seem enthusiastic about the possible relevance of these ELES (as Chawla described them) recorded from human patients to their animal research. They listed several reasons for remaining wary. These caveats include the different methodologies used to collect and analyze the EEG and the possible neurological impairment of critically ill patients.\n\nSimilar to Borjigin, the authors also speculated that the ELES could represent the psychophysiological basis of NDE. Similar to the rodent model, scant attention has been paid to how the EEG spike might actually induce an NDE. According to the authors, this could involve anoxic depolarization of the neuronal membrane, creating a temporary flood of gamma-frequency EEG signals. By some unspecified operation, this activity interferes with or destabilizes synaptic connections underlying memory circuits leading to the release of key components of the NDE.\n\nTo further investigate and quantify ELES, the authors analyzed the terminal EEG of a much larger group of critically ill palliative care patients (n=35) (Chawla et al., 2017). In this case, they employed only a Sedline Monitor to provide a measure of cerebral activity. The output from this device is labelled the patient state index (PSI). The PSI has a 1 – 100 scale and, therefore, provides an objective index of the level of consciousness. A significant increase in PSI after the cessation of cardiac function was used to classify episodes in which there was a spike or surge in EEG (i.e., an ELES). None of the patients diagnosed with brain death generated an ELES. However, almost half of the remaining participants displayed a robust spike shortly after death. The authors inferred that this surge was composed of high-frequency oscillatory signals that they implied resided within the gamma band range and was compatible with rodent findings. They also argued that bursts are unlikely to reflect high-frequency myogenic activity. It was concluded that the ELES was not an unusual event under such circumstances, but no comment was made regarding its relevance to the NDE or any other near-death phenomena.\n\nApart from Chawla et al. (2009), there are other potentially relevant clinical studies that predate Borjigin’s animal research. For example, Auyong et al. (2010) recorded processed EEG from three terminally ill patients using a Bispectral Index Monitor. Two of these were processed for donations after cardiac death. The Monitor generates a bispectral index score (BIS) between 0 (brain death) and 100 (total consciousness). Therefore, this is equivalent to the PSI method employed by Chawla et al. (2017). In all three patients analyzed, it was found that the BIS roughly doubled within minutes after withdrawal of life support and remained elevated until just prior to cardiac death when it dropped precipitously. The maximum scores recorded for the patients were 95, 84, and 83, respectively. In the face of this, it could be inferred that such values should reflect a reasonably high level of consciousness in patients despite their end-of-life status.\n\nThe authors were uncertain what to make of their findings, but did suggest that a “distinct change in cortical electrical activity may have occurred.” Notably, in one patient, the raw EEG consisted of low-amplitude fast activity during the period when the BIS was paradoxically high. The authors also draw attention to the similarity of their findings to those of Chawla et al. (2009).\n\nAnother example of a clinical recording of GBA is a single case study (Vicente et al., 2022). The subject was an 87-year old male who suffered a traumatic brain injury, underwent a craniotomy to evacuate a subdural hematoma, and subsequently developed seizures. He experienced a heart attack and died while being continuously monitored using EEG. Fortuitously, the neurophysiological events immediately surrounding death were therefore able to be captured. The authors claimed that this was an unprecedented and unique recording. By this, they mean “the first continuous EEG recording from the human brain in the transition phase to death.”\n\nEpochs of EEG activity, each of 30 s duration, were analyzed. During the final 900 s following the last seizure, the overall EEG activity deteriorated. However, what was most striking was the huge intensification of gamma waves in the 30 s prior to cardiac arrest. This transition period immediately before cardiac arrest was otherwise characterized by bilateral suppression of cerebral rhythms. The surge of high-frequency activity did not persist in the post-cardiac arrest period but remained relatively higher than in the interictal interval some 15 min earlier. This is in marked contrast to EEG in the other frequency bands.\n\nVicente et al. stressed the similarity between their findings and those of other rodents. However, there was one significant difference between the animal data and other human studies of ELES (Auyong et al., 2010; Chawla et al., 2017). In all such cases, the onset of gamma waves did not begin until after cardiac arrest or withdrawal of support. By contrast, Vicente et al. are outliers in this respect. A burst of gamma activity occurred immediately before the cardiac arrest. It is assumed that the same basic pathobiological mechanisms are responsible for the surge, regardless of timing. However, the authors made no categorical comments on this discrepancy.\n\nThe authors acknowledged that the EEG findings of heightened power and connectivity of their elderly and critically ill patients with healthy rodents must be performed cautiously. Nonetheless, they believed that the high-frequency surge recorded in both species might be legitimately interpreted as a neural signal that high-level cerebral function had been preserved, albeit briefly. Further, this could therefore constitute evidence that memory, perception, information processing, and dreaming networks and circuits might still be able to operate, and therefore could possibly represent the neural substrate of an NDE. Indeed, their implicit enthusiasm for such a notion led them to make quite unjustifiably premature statements such as “to investigate oscillatory changes during near-death experiences”. It takes for granted that the two are temporally related, for which there is currently no direct evidence.\n\nAs with animal data, Greyson also provided a critical commentary on these human findings (Greyson et al., 2022). First, it was pointed out that there was little gamma power in the post-cardiac arrest period. What was observed was that gamma oscillations were relatively more prominent than the even more depressed alpha, beta and delta rhythms. Second, it was argued that identifying the exact time of cardiac arrest was a somewhat arbitrary and uncertain decision. Electrocardiographic (ECG) activity was still present, even after it was assumed that the heart had stopped beating. The remaining challenge posed by Greyson is potentially the most serious. This raises the question of whether gamma oscillations are partially artifactual rather than authentic. This controversy will be discussed later in this review.\n\nThe most recent study of the gamma surge in terminally ill patients was conducted by the same group that had carried out the original rodent investigation (Xu et al., 2023). EEG was recorded in four critically ill comatose patients before and after mechanical ventilatory support was withdrawn. In two of these cases, there was a characteristic burst in gamma power that appeared within seconds of the loss of breathing support. As the hypoxic state worsened, the high-frequency activity waxed in strength, but then waned and eventually ceased after approximately five minutes. The authors concluded that their findings provided compelling evidence for a brief period of heightened sentience in the dying human brain. Although based on a small number of subjects, it is also notable that approximately the same percentage of patients exhibited a perimortem spike as did the much larger cohort studied by Chawla et al. (2017).\n\n\nEEG activity underlying mystical states\n\nComputational neuroscientist Christof Koch (2023) provided a commentary on the work of Xu et al. He suspected that high-frequency high-amplitude oscillations were contaminated by muscle and/or seizure activity. However, such skepticism is really just a reiteration of the concerns that the authors themselves have proactively dealt with. In fact, Koch’s most useful contribution to this debate was his insight that if gamma oscillations underlie mystical states, such as the NDE, then similar activity should also be recorded after intoxication with a psychedelic agent that can mimic the NDE.\n\nInformation directly relevant to this observation has recently become available, although this was not mentioned by Koch. It is well known that the classical hallucinogen N,N-dimethyltryptamine (DMT) (aka ayahuasca) can rapidly conjure up a mystical state virtually identical to the NDE. As such, it provides the foundation for Strassman’s “Spirit Molecule” model of NDE generation (Strassman, 2001). Another formal study recently confirmed the finding that DMT can virtually simulate the entire phenomenology of the NDE (Timmermann et al. 2018). In his original research, Strassman abandoned EEG recordings during the DMT state after only three attempts. However, Timmermann et al. (2019) successfully recorded brain activity in healthy adults during the intense hallucinatory phase of DMT intoxication. What was discovered was The dominance of slow delta and theta oscillations was accompanied by a striking loss of spectral power in the faster rhythms. Such findings are, of course, quite contrary to the expectations of the GBA model. Assuming that the high-frequency burst of activity is actually associated with the induction of an NDE, it would be predicted that fast oscillations underlie the action of an agent such as DMT. This is strong implicit evidence that the surge in GBA at the moment of death is unlikely to be responsible for NDE.\n\nLittle attention was paid to gamma activity, but what there was suggests that it did not share the same drop in absolute power as the alpha and beta waves during the DMT state. This may slightly confound the matter, but it is clear that the lower frequencies are most functionally relevant. Therefore, it follows that if the post-arrest surge was related to the NDE, it should have consisted predominantly of delta and theta waves, albeit with a contribution from gamma. In the current study, where EEG and functional MRI activities were simultaneously recorded (Timmermann et al., 2023), essentially the same findings were obtained.\n\nThis relationship between hallucinatory experience closely resembling NDE and low-frequency EEG is even more striking with dissociative anesthetics. Rogo (1989) provided multiple illustrations of how intoxication with phencyclidine (PCP) and ketamine can reproduce the imagery and phenomenology of NDE. Similarly, Jansen’s NMDA model of NDE generation relies on the assumption that a congener of ketamine is intrinsically synthesized (Jansen, 2001). This mode of action is similar to that of endogenous DMT (Strassman, 2001). However, unlike DMT, there are numerous examples of raw unprocessed EEG that underlie ketamine or PCP anesthesia. Without exception, they are characterized by slow diffuse activity within the theta range (e.g. Rodin et al., 1959; Corssen et al., 1974; Stockard et al., 1976).\n\nThis appears to be a general principle. In his essays on his personal experience with the classical hallucinogen mescalin, Huxley drew attention to the similar visionary properties of carbon dioxide therapy (CDT) and carbogen (Huxley, 2004). This treatment for mild personality disorders was introduced by the Hungarian-American psychiatrist, L.J. von Meduna, in the 1950s (Meduna, 1950). Meduna demonstrated that after a little more than two dozen inhalations of the carbogen mixture, an ecstatic, otherworldly state almost indistinguishable from NDE could be rapidly induced in his subjects. Subsequently, Morrice (1956) recorded the EEG during the CDT and reported that it was also associated with a widespread theta rhythm.\n\nThe EEG findings of these three distinct hallucinogenic agents are therefore totally incompatible with the concept and expectation that a burst of high-frequency gamma waves might represent the psychophysiological basis of a mystical experience, such as the NDE.\n\nIt should also be acknowledged that the notion of the advantages of a psychedelic model of NDE generation had already been exhaustively canvassed by Michael before Koch’s rather inchoate suggestion (Michael, 2021a, 2021b). This was within the context of two commentaries on Bruce Greyson’s book After (Greyson, 2021). This work is not sympathetic to psychedelic explanations or perspectives. Michael has argued, however, that psychedelic agents can not only simulate NDE but may also provide insights into their neurobiological substrate, which potentially may play a role in endogenous hallucinogens.\n\n\nSummary of clinical studies\n\nAs discussed above, the trajectory of EEG activity following cardiac arrest is both well defined and simple. It consists of an almost immediate decline in EEG power, which culminates in a state of isoelectricity within 20 s. During the last decade, however, it has become increasingly clear that in a subset of such patients, there is a sequence of fast, relatively high-amplitude activity within the frequency range of gamma oscillations superimposed on this basic pattern. Although originally described in rodents, this neurophysiological event that may arise during the perimortem period has now been reported in at least five clinical studies, as summarized in the present section. This surge, spike, or burst of activity in both rodents and humans suggests that it is probably a universal feature of the dying mammalian brain. While common in critically ill humans, it is not invariably present, probably because of the heterogeneous conditions of such patients.\n\nAnother slightly anomalous feature is that the onset of a burst or surge tends to vary among studies. This discrepancy is most likely due to the criteria used to define the moment of death (Greyson et al., 2022). These could include undetectable blood pressure, cessation of heartbeat, loss of ECG activity, or withdrawal of life support. This is a crucial problem, as it relates to the perennial question of exactly determining when the NDE occurred.\n\nDespite much speculation, these seemingly paradoxical surges in electrical energy about the time of death remain a phenomenon in the search for a function, origin, and significance.\n\n\nAre gamma oscillations a homogeneous type of cerebral rhythm?\n\nThe first part of this appraisal dealt with the evidence for the GBA model of NDE and some of the shortcomings, limitations, and questions raised by the theory. However, none of these matters are necessarily fatal objections nor are they inherently insoluble or irrefutable. Regrettably, a more fundamental problem also exists that could pose an existential threat to the viability of the model. This is the question of the exact origin of the gamma oscillations. In particular, they are contaminated by artifacts from various sources. Recently, several of these so-called gamma skeptic papers have investigated this possibility. Three such studies are considered here.\n\nFirst, Whitham et al. (2007) used neuromuscular blockade in two male subjects to quantify the contribution of EMG artifacts to higher-frequency scalp-recorded EEG. When the subjects were paralyzed with arrested skeletal muscle activity, the power of the frequencies within the gamma range decreased 10 – 200 fold. However, the precise amount depends on the particular subject, the frequencies examined, and the position of the electrodes. Nonetheless, the authors estimated that EMG activity arising from the cervical, scalp, jaw, and cranial musculature had a significant impact on the activity in the gamma frequency band. They concluded that studies of GBA recorded via scalp electrodes need to be treated cautiously because of the amount of EMG activity they appear to contain.\n\nAnother study also implicated myogenic rather than neuronal activity in the generation of GBA (Yuval-Greenberg et al., 2008). In this instance, ocular muscle activity is reflected in fast involuntary miniature eye movements or microsaccades. The normal and essential role of saccadic movements in perception is to maintain the viability of a static retinal image. In their absence, optically stabilized images rapidly fade.\n\nFollowing a period of fixation, young adult subjects were presented with an image and the induced gamma-band response (iGBR) was measured. This is an augmented train of GBA occurring approximately 200-300 milliseconds the visual stimulus. iGBR is considered a crucial neural correlate of memory, perception, and other cognitive processes. Concurrent with EEG recording, binocular eye-tracking technology was employed, thereby demonstrating a strong association between the occurrence of saccadic movements and iGBR. The authors concluded that evoked GBA was slightly greater than the far-field reflection of microsaccades. However, they were careful about extrapolating their findings beyond the scalp EEG recordings.\n\nDespite the matter discussed above, which suggests that much of the GBA can be accounted for by non-cerebral activity, it has usually been presumed that there remains a residue or core of such activity, which reflects a genuine cerebral cortical rhythm. However, even this qualified and restricted claim has been cast into doubt. For example, Burns et al. (2011) investigated the possibility that gamma oscillations are merely a filtered neural noise.\n\nEEG recordings were obtained from several electrode positions within the primary visual cortex of curarized and anesthetized macaque monkeys, following full-field drifting grating stimulation. This consists of brief presentations of sine wave gratings moving at right angles relative to the orientation of the gratings. Bursts of post-stimulus GBA were analyzed for their degree of autocoherence. Autocoherence is defined as the constancy and regularity of the frequency and phase synchronization of the oscillations. A high level of autocoherence is a necessary property of a cerebral rhythm if it is to perform usefully and reliably as a timekeeper and therefore to subserve higher cognitive functions such as those currently attributed to GBA.\n\nThe visual cortex recordings were compared to two sets of manufactured data labelled as the noise model and the burst model. The noise model consisted of bursts of gamma activity, independent of any visual stimulation. The burst model had epochs of autocoherent gamma (or time signals) embedded in an otherwise spontaneous non-evoked activity. Burst frequency-burst duration distributions were computed for each of the three conditions. The distribution of actual cortical recordings was nearly identical to that of the simulated noise model. However, both visually and statistically, the distribution of the actual data appeared to be markedly different from that of the simulated burst model. The authors concluded that the autocoherence in GBA recorded from the visual cortex was no greater than chance; therefore, no genuine clock signals could be detected in gamma oscillations. This means that the popular concept of gamma oscillations is a type of clock-like temporal regulator; therefore, the synchronizing agent is unlikely to be correct and should be abandoned. Intrinsic network filters operating on neural noise were presumably responsible for recruiting and generating a prevailing gamma rhythm of approximately 40 Hz.\n\nThe authors were specifically concerned with the relevance of their findings to the binding problem and the related cognitive and perceptual functions. However, there is a broader and possibly more important message in the data. It is possible that even so-called bona fide gamma oscillations arising unequivocally within the CNS may be nothing more significant or meaningful than the fortuitously created by-product of spontaneous firing and other random neuronal processes. In a subsequent experiment, Burns et al. replicated their findings in awake and anesthetized monkeys (Xing et al., 2012).\n\nIn summary, these three studies represent an extreme position where gamma oscillations are essentially or mostly artifactual and non-functional biorhythms masquerading as authentic EEG signals. Although not mainstream, such studies are nonetheless useful in reiterating that gamma activity is not a pure cerebral rhythm. A much less controversial and nuanced perspective is that GBA is best conceived as an amalgam of genuine EEG plus EMG artifacts and/or eye movements and/or routine neural litter accidentally organized into an approximate 40 Hz pattern. The relative contribution of each to a specific or individual gamma oscillation probably varies depending on the recording conditions, nature of the subject, and their behavioral state. If this analysis is correct, then a mysterious burst of GBA occurring at the time of death must be treated cautiously and interpreted carefully. The more the GBA has been contaminated by artifacts, the less likely it is to fulfill its purported role as a kind of neural blueprint for NDE. It is a concern that those who propose a link between GBA and NDE choose to turn a proverbial blind eye to such a potential flaw or weakness in their argument.\n\nAdditional information on the likely contamination of the bursts of GBA by EMG activity was discussed by Greyson et al. (2022). A review of the difficulty in distinguishing EMG activity from high-frequency EEG is available in Muthukumaraswamy (2013).\n\n\nThe canine model of alpha coma pattern\n\nIrrespective of whether gamma activity is of myogenic or neurogenic origin, it seems very unlikely that the surge in GBA in the perimortem period reflects muscle activity. The reasons for this lack of EMG contamination have not been reported previously (Chawla et al., 2017; Xu et al., 2023). The evidence for this includes studies where animals were killed by decapitation, analysis of high PSI scores in patients in whom an ELES was observed, and complete absence of movement or EMG artifacts in unconscious subjects. This implies that the GBA surge must represent genuine brain activity; however, when it is also considered that the EEG is at such a low ebb, it suggests that the surges are composed of neither cortical EEG nor EMG activity, but rather represent activity from a third source. The question might, therefore, be asked about their actual origin. Thus, there may be a suitable candidate.\n\nDespite this claim, Borjigin’s rodent study is not unique. Three decades ago, a group of Russian physiologists performed an experiment that, in important ways, anticipated much of the later investigation (Gurvitch et al., 1984) although with two chief methodological differences. First, the Russian study used canines, rather than rodents. Second, the dogs were temporarily revived after circulatory arrest. Notwithstanding these differences, the findings are consistent. It should also be noted that the present explanation of Gurvitch’s research findings differs somewhat from that in their paper. It is uncertain whether such an experiment can be performed. However, the authors affirmed that the animals were either anesthetized or comatose throughout all procedures.\n\nThe primary aim of this study was to develop a canine model of alpha coma pattern (ACP) (Vignaendra et al., 1974; Chokroverty, 1975; Westmoreland et al., 1975; Alving et al., 1979; Austin et al., 1988). In particular, the identification of a subcortical pacemaker could be responsible for generating such a puzzling EEG rhythm during post-anoxic coma. Clinical coma is normally associated with a standard EEG pattern consisting of predominantly generalized semi-regular high-voltage delta activity. In contrast, ACP is a comparatively rare EEG coma pattern consisting of diffuse sinusoidal rhythms, usually within the alpha or theta frequency bands, and is often a bad prognostic sign. Since alpha activity is normally correlated with a state of relaxed wakefulness, ACP may paradoxically give an erroneous impression that comatose patients may be conscious. It should be noted that while ACP helped inspire the current re-interpretation of the GBA model, it is not claimed that it plays any role in the induction of NDE.\n\nThe dogs were anesthetized with ether and implanted at various subcortical and cortical locations. CPA was induced by ventricular fibrillation and aggressive resuscitation (cardiac massage and artificial lung ventilation), followed by various intervals. During the post-anoxic coma period, characterized by a near isoelectric EEG, bursts of high-voltage activity began to arise in the amygdaloid nuclei. This activity typically commenced approximately 30 min after resuscitation began, and individual bursts could last for several seconds. Amygdaloid discharges were reflected in closely time-locked, widely generalized oscillations recorded from the cortex. However, the amplitude of the cortical rhythms was only a fraction of that generated in the amygdala. The authors analyzed the activity recorded from other subcortical structures and established that the oscillations originated in the amygdala and were then presumed to be sequentially propagated to and distributed throughout the cortex via diffuse thalamocortical pathways. As the EEG was always within the alpha frequency band, it was also supposed that this activity could be the canine analog of ACP and, therefore, could be a prototype for the generation of ACP in human patients. In addition, Gurvitch demonstrated that if the amygdala was unilaterally or bilaterally destroyed, the alpha-like oscillatory potentials either attenuated or disappeared completely from all EEG monitoring sites. This confirmed that the amygdala was the primary site for the generation of alpha-frequency oscillations. Destruction of the amygdala was carried out by injections of Novocaine or ablation, and the location of the damage was confirmed histologically.\n\nWhether abnormal discharges from amygdaloid pacemakers constitute the pathophysiological basis of ACP remains speculative and problematic. Also contentious is the question of how oscillatory activity is transmitted to the cortex. Considering their diminutive amplitudes, it seems most likely that the apparent alpha-range cerebral rhythms reflect far-field amygdaloid activity, which is conveyed to the surface of the brain via volume conduction. Such an origin would be much more compatible with their small size than if the amygdaloid signals had been propagated by afferent impulses through thalamocortical axonal tracts and relay stations. With the latter type of conduction and secondary generation, it might have been expected that the original high voltage of amygdaloid emissions would still have been preserved and therefore replicated at the cortical level.\n\nIf cortical oscillations represent only remotely recorded amygdaloid discharges, then one reason why they can be successfully observed during the post-resuscitation period is a lack of competition from the usually dominant cortical EEG rhythms. During cerebral ischemia, normal cortical rhythms are at least transiently suppressed, although neuronal tissue can remain reactive. However, once the cortical EEG starts to re-establish and re-assert itself, minute far-field emissions would become swamped or masked. In Gurvitch’s recordings during the post-resuscitation period, oscillatory bursts eventually began to wane, and the EEG became increasingly dominated by high-amplitude delta rhythms.\n\n\nThe relevance of the canine model of alpha coma pattern to the electrogenesis of the GBA surge\n\nWhether the canine model proposed by Gurvitch et al. can function as a viable analog of ACP in human patients remains controversial. Be that as it may, it is also possible that their findings do provide an insight into the equally baffling nature of the post-cardiac arrest burst of GBA.\n\nBased on their paroxysmal behavior, small amplitude, and widespread cortical location, it seems reasonable to assume that the eruptions of oscillatory EEG activity recorded from both the rodent and canine cortices share a common mode and site of generation. As discussed above, the source of alpha frequency band activity was localized to the amygdaloid nuclei. Therefore, it seems logical that the bursts of GBA recorded after cardiac arrest in rodents have the same origin. Furthermore, in both instances, it is the context of cerebral ischemia or hypoxia, which allows this stream of volume-conducted amygdaloid activity to temporarily appear in cortical recordings. In addition, if far-field oscillatory activity is diffusely broadcast from the amygdaloid nuclei, this means that essentially the same signal should be received and recorded from all cortical locations. This largely accounts for the significant degree of coherence, connectivity, and synchronicity reported in both experiments.\n\nIf the preceding interpretation is correct, Borjigin’s investigation may have mistaken far-field subcortical amygdaloid activity for cortical gamma oscillations. Therefore, any comparison these investigators made between the relatively high-amplitude post-cardiac arrest EEG surge and the genuine GBA recorded during states of wakefulness and anesthesia would be quite spurious and misleading. This would also mean that no matter what the electrogenesis of gamma activity ultimately turns out to be, this would remain an irrelevant consideration. The apparent discrepancy between alpha-frequency activity generated in the amygdala and gamma-frequency activity recorded at the cortex is discussed and potentially reconciled in a later section.\n\nIn summary, it seems possible that Borjigin and co-workers dealt with two separate rhythms that superficially resembled gamma oscillations. One is a veritable gamma rhythm with a characteristically small amplitude. In contrast, the second comprised amygdaloid activity disguised as abnormally high-amplitude fake gamma waves. The failure to recognize this flaw may have compromised their research. In particular, the increased power of the post-cardiac arrest burst of electrical energy cannot be considered a sign of heightened consciousness or alertness. Thus, if it turns out that the EEG burst is nothing more than fake cortical activity, then the question of the precise origins of gamma oscillations becomes largely redundant. This also makes it even more unlikely that GBA could serve as the pathophysiological basis of NDE.\n\n\nThe origin and nature of the amygdaloid oscillations\n\nParoxysmal amygdaloid discharges, identified as the origin of alpha band cortical waves, have been investigated for decades (Eidelberg and Woodbury, 1972). They have been reported in humans (Lesse et al., 1955), chimpanzees (Delgado et al., 1970), monkeys (Domino and Ueki, 1960), dogs (Domino and Ueki 1959,1960), rabbits (Bressler and Freeman, 1980), cats (Pagano and Gault, 1964; Kato et al., 1964, Gault and Coustan, 1965; Knapp and Lubar, 1976, Bressler and Freeman, 1980, Bauer et al., 2007, Popescu et al., 2009), rats (Kanta et al., 2019) and mice (Stujenske et al., 2014). Therefore, it can be assumed that they are common properties of the mammalian limbic system.\n\nThese intermittent oscillatory emissions or signals arise in the basolateral amygdala (BLA) and consist of spindle-like bursts of high-frequency high-amplitude activity, typically lasting from seconds to minutes. They are endogenous but not strictly spontaneous because they can be evoked by a variety of stimuli. These included states of arousal, threat, learning, emotion, fear, stress, anticipation, pain, and noise. It might be predicted Therefore, conditions such as hypoxia, ischemia, or cardiac arrest would provide an optimal milieu for the enhancement and/or appearance of the BLA rhythm. Nonetheless, it is in no way implied that these amygdaloid oscillations recorded from the cortex possess any mystical or psychedelic properties and, therefore, could be responsible for the NDE.\n\nThis fast BLA activity also involves a number of monickers. Sometimes, it has been labelled the 40 Hz amygdaloid rhythm after its focal frequency, or else fast oscillations of the amygdala or 40 Hz burst phenomena in the amygdala. It has also been described as amygdaloid spindling because of its waxing and waning appearance. Because its frequency normally falls within the gamma range, it has also been defined as an amygdaloid gamma oscillation.\n\n\nTHe effects of ether on the amygdaloid discharges\n\nThe Achilles heel of the present reinterpretation of Borjigin’s data must lie in the discrepancy in the frequency between the post-cardiac arrest bursts of electrical activity. In a Russian study, this value was mostly within the alpha band. In contrast, the American study had a dominant frequency of approximately 40 Hz, which is representative of gamma-frequency oscillations. On the face of it, this comparison exposes a difficulty which is at variance with the amygdaloid generator model proposed above. Nonetheless, this conundrum may be satisfactorily solved by one or more of the three possible factors. An interaction between these and other variables might account for the incongruity in frequencies; therefore, it is not necessarily an intractable problem.\n\nFirst, the animals were subjected to opposite treatments, with the dogs being aggressively resuscitated. The second limitation is the use of different animal species. The 40 Hz central rhythm is not fixed, but is rather an average. Individual species may exhibit considerable variability (Knapp and Lubar, 1976; Eidelberg and Woodbury 1972). This may range from a high frequency of approximately 50 Hz (e.g., rabbits) to a low frequency of approximately 30 Hz (e.g., humans, chimpanzees, and dogs).\n\nThe third factor is the anesthetic used. This was also a preference favored by Gurvitch. Limited information exists on the effects of ether on amygdaloid function (Kato et al., 1964; Domino and Ueki, 1959; Gurvitch, 1964). However, it has been suggested that the amygdala is ultrasensitive to this gas. This was manifested most clearly by a reduction in the frequency of the intrinsic (40 Hz) rhythm. However, these findings are sometimes difficult to quantify. Nonetheless, overall, they indicate that even a moderate level of ether anesthesia is sufficient to reduce the frequency to within the alpha range. This would also have been a reasonable expectation, assuming that the endogenous canine rhythm is at the lower end of the mammalian scale, as discussed above. It may also be relevant that the effects of ether on rhinencephalic (although not specifically amygdaloid) function may linger for long after active inhalation has ceased (Gault and Coustan, 1965). It can therefore be confidently asserted that the bursts of slower canine alpha activity in the cortical EEG were fundamentally and functionally equivalent to the faster bursts of the so-called gamma activity in the rodent EEG. There seems to be no essential difference once the anesthetic influence, in particular, is taken into account.\n\n\nConclusions\n\nThe purpose of the present review was to investigate the claim that a surge in fast EEG activity during the perimortem period could serve as a neurobiological substrate for NDE. Establishing such a relationship is fraught with methodological and conceptual difficulties. Nevertheless, this paradoxical and abnormal rhythm has been detected in humans, dogs, and rats. Therefore, it can be tentatively assumed as a universal feature of the dying mammalian brain. Furthermore, it is well established that this burst of activity has an electrophysiological origin. This is not merely an artifact. However, the question persists as to not only its significance, but more fundamentally, what its electrogenesis is. If it cannot be established that it is a type of high-frequency EEG, then it is difficult to justify or understand how it could conceivably spawn an NDE.\n\nA very fast EEG with diminutive amplitude has conventionally been labelled as the gamma rhythm. However, the present analysis has revealed that, in principle, there are multiple waveforms that superficially share most of the gamma wave characteristics. However, despite their common appearance, they possess distinct electrogenesis and therefore significance. One possible subtype of gamma oscillations is cortico-genic, consisting of genuine EEG activity. The second type could be of largely myogenic origin and composed of far-field muscle activity. However, the third type can be generated by volume-conducted amygdaloid discharges. Superficially, it could be difficult to distinguish between these three near-identical potential variations or subtypes of GBA. Recognizing that the gamma rhythm may best be conceived as a generic waveform may be key to understanding the nature and origin of the high-frequency surge at the time of death.\n\nIf amygdaloid signals are the source of the perimortem cortical paroxysms, the problem of how the transient bursts of their high-frequency activity could actually generate an NDE becomes superfluous. They could not conceivably cope with the often complex and multifarious nature of NDE with its otherworldly sights, sounds, and emotions, and dependence upon an altered state of consciousness. There seems to be little point to gain by pursuing such an unrewarding explanation.\n\nThe question of whether cortical gamma bursts reflect far-field amygdaloid activity could be definitively answered by systematic destruction of the amygdaloid nuclei in a manner similar to that employed in Gurvitch’s experiment. The preservation of the transient electrical surges under such conditions would unequivocally discredit this explanation. Nevertheless, even if an origin in the amygdala is ruled out, this would do little to improve the chances that a fleeting eruption of the GBA could underlie the NDE. This is because the genesis and relevance of the actual gamma cortical oscillations remain uncertain and disputed. It is therefore difficult to disagree with Greyson’s prescient initial verdict that the mysterious EEG burst after cardiac arrest “is unlikely to contribute to an understanding of near-death experiences” (Greyson et al., 2013).\n\nNevertheless, any consideration as to whether the mysterious gamma oscillations at about the time of death are of myogenic, cortical, or amygdaloid origin may be a futile or unnecessary exercise. This is because multiple investigations have revealed that the EEG activity underlying visionary experience near- identical to the NDE lies at the opposite end of the EEG frequency spectrum to the fast gamma waves. Regardless of what the electrogenesis of the gamma spikes ultimately turns out to be, it is highly unlikely that they could be responsible for generating an NDE.\n\nThe present re-interpretation of the significance of the surges in GBA is obviously somewhat routine and quotidian, especially when compared with the more exotic, intriguing, and tantalizing alternative. It is unlikely to attract the same amount of attention from media. Nonetheless, it has the virtue of being parsimonious. As Ockham’s principle reminds us, simplicity is often a useful guide for scientific truth.\n\n\nEthics and consent\n\nEthical approval and consent were not required.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nAcknowledgements\n\nThe authors thank Professor Maurice Curtis, Department of Anatomy, University of Auckland, for the opportunity to write this review.\n\nThe authors thank Dr. Pascal Michael, University of Greenwich, for his extensive review of an earlier version of this article.\n\n\nReferences\n\nAhmed OJ, Cash SS: Finding synchrony in the desynchronized EEG: The history and interpretation of gamma rhythms. Front. Integr. Neurosci. 2013; 7: 58. Publisher Full Text\n\nAlexander E: Proof of Heaven: A Neurosurgeon’s Journey into the Afterlife. New York: Simon and Schuster; 2012.\n\nAlving J, Moller M, Sindrup E, et al.: Alpha pattern coma following cerebral anoxia. Electroenceph. Clin. Neurophysiol. 1979; 47: 95–101. 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Cambridge, MA: MIT Press; 1999.\n\nTraub RD, Whittington MR: Cortical Oscillations in Health and Disease. Oxford: Oxford University Press; 2010.\n\nUhlhass PJ, Singer W: Neural synchrony in brain disorders: relevance for cognitive dysfunctions and pathophysiology. Neuron. 2006; 52: 155–168. PubMed Abstract \| Publisher Full Text\n\nVanderwolf CH: Are neocortical gamma waves related to consciousness? Brain Res. 2000; 855: 217–224. PubMed Abstract \| Publisher Full Text\n\nVan Lommel P: About the continuity of our consciousness. Adv. Exp. Med. Biol. 2004; 550: 115–132. Publisher Full Text\n\nVan Lommel P, van Wees R , Meyers V, et al.: Near-death experience in survivors of cardiac arrest: a prospective study in the Netherlands. Lancet. 2001; 358: 2039–2045. PubMed Abstract \| Publisher Full Text\n\nVicente R, Rizzuto M, Sarica C, et al.: Enhanced interplay of neuronal coherence and coupling in the dying human brain. Front. Aging Neurosci. 2022; 14: 80. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVignaendra V, Wilkus RJ, Copass MK, et al.: Electroencephalographic rhythms of alpha frequency in comatose patients after cardiopulmonary arrest. Neurology. 1974; 24: 582–588. PubMed Abstract \| Publisher Full Text\n\nWestmoreland BF, Klass DW, Sharbrough FW, et al.: Alpha coma: electroencephalographic, clinical and etiologic correlations. Arch. Neurol. 1975; 32: 713–718. Publisher Full Text\n\nWheeler DR: Journey To the Other Side. New York: Ace Books; 1977.\n\nWhitham EM, Pope KJ, Fitzgibbon SP, et al.: Scalp electrical recording during paralysis: quantitative evidence that EEG frequencies above 20 Hz are contaminated by EMG. Clin. Neurophysiol. 2007; 118: 1877–1888. PubMed Abstract \| Publisher Full Text\n\nXing D, Shen Y, Burns S, et al.: Stochastic generation of gamma-band activity in primary visual cortex of awake and anesthetized monkeys. J. Neurosci. 2012; 32: 13873–13880a. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nXu G, Mihaylova T, Li D, et al.: Surge of neurophysiological coupling and connectivity of gamma oscillations in the dying human brain. Proc. Natl. Acad. Sci. USA. 2023; 120: e2216268120. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYuval-Greenberg S, Tomer O, Keren AS, et al.: Transient induced gamma-band response in EEG as a manifestation of miniature saccades. Neuron. 2008; 58: 429–441. PubMed Abstract \| Publisher Full Text\n\nZaleski C: Otherworld Journeys: Accounts of Near-Death Experience in Medieval and Modern Times. New York: Oxford University Press; 1987." }	[ { "id": "300181", "date": "29 Jul 2024", "name": "Matthew R. Hudson", "expertise": [ "Reviewer Expertise Electrophysiology", "neuronal oscillations", "neuropsychiatry" ], "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\nAn interesting and comprehensive review which aimed to critically investigate evidence/suggestions that GBA is involved in near death experience, as well as provide alternative explanations for this phenomenon. In its current state, my opinion is that this article is acceptable for indexing. I do however have one comment below which the author might like to consider:\nThe author describes gamma oscillatory changes following administration of hallucinogenic drugs such as ketamine and PCP and describes that these are characterised by \"slow diffuse activity within the theta range\", however, for both these compounds, pronounced augmentation of gamma band power has been demonstrated. Therefore, this could be considered to be compatible with the suggestion high-frequency gamma might be linked to mystical experience/NDE.\nKao HY, Dvořák D, Park E, Kenney J, Kelemen E, Fenton AA. Phencyclidine Discoordinates Hippocampal Network Activity But Not Place Fields. J Neurosci. 2017 Dec 6;37(49):12031-12049. doi: 10.1523/JNEUROSCI.0630-17.2017. Epub 2017 Nov 8. PMID: 29118102; PMCID: PMC5719978.\nJones, Nigel C., et al. \"Effects of aberrant gamma frequency oscillations on prepulse inhibition.\" International Journal of Neuropsychopharmacology 17.10 (2014): 1671-1681.\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Yes\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Yes", "responses": [] }, { "id": "295790", "date": "26 Aug 2024", "name": "Pascal Michael", "expertise": [ "Reviewer Expertise BSc and MSc in neuroscience and psychology. PhD in near-death experiences and psychedelics." ], "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 interesting article on reframing prior findings of gamma activity in the dying brain, with implications for the NDE, mainly by deconstructing these prior studies' interpretations and reviewing the evidence of gamma's contribution to consciousness. It is also written extremely clearly and coherently. I reviewed a previous version of this manuscript, many points of which the author has evidently incorporated well into this new one. However, there are a number of - mostly minor - strong recommendations I would finally integrate, listed below. I trust these will also be duly reflected somehow in the final version, and thus would endorse its publication.\n\"confirmation of the dualist notion that mind, spirit, soul, or consciousness are quite separate entities\" - I don't think that 'dualist' is justified as the only non-materialist ontology that NDEs suggest. We don't know what the specific ontological model would be, where dualism is just one (e.g. idealism, neutral monism etc)\n\"an event that might be detectable in the unconscious brain despite the state of cerebral ischemia.\" - I wouldn't say 'unconscious', as the point of this article is that there may be such transient activity, which could be linked to the NDE event. And so, NDErs become conscious, only unconscious to external observers. Thus, 'in a state of disconnected consciousness' would be the more accurate term\n\"Fast spiking inhibitory interneurons may interact and interconnect with excitatory pyramidal cells to produce and drive the GBA.\" - Clarify the sentence to explain how inhibitory interneuron input to the excitatory pyramidal neurons produces the GBA, if youre implying an inhibition* of the excitatory neurons Also this whole paragraph requires more substantiation by citations\n\"It is more difficult to account for the invariant nature of much of the content \" - Id put 'qualitative* content' here, and even better, 'distinguished from the phenomenological features', to drive home that such neural correlates can account for the feature invariance, but not so easily the content invariance\n\"However, more recent investigations have strongly suggested that such temporal ordering is not a common feature of most NDEs (Martial et al., 2017)\" In fact, this same paper does show a definite ordering in a minority* of NDEs, approximately encompassed by sense of peace, OBE and a sense of returning\n\"A second difficulty concerns the status of gamma rhythm as a measure of CNS arousal.\" - This whole paragraph should consider carefully if there are any conflations between 'arousal / alertness' and 'consciousness' (Seems borjigin is emphasising gamma effects on the latter)\n\"The authors also devoted some effort to trying to exclude sources other than the EEG\" - 'effort to try to'*\n\"The Monitor generates a bispectral index score (BIS) between 0 (brain death) and 100 (total consciousness).\" - Clarify if 100 ie 'total consciousness' is the average expected level for any person in a normal waking state, as this is relevant for the ELEs findings\n\"By contrast, Vicente et al. are outliers in this respect. A burst of gamma activity occurred immediately before the cardiac arrest\" - Clarify that you're being consistent in terms of the difference between cardiac arrest, and the onset of heart attack ie including pre-arrest fibrillation - which would weigh on this potential discrepancy\n\n\"The most recent study of the gamma surge in terminally ill patients was conducted by the same group that had carried out the original rodent investigation (Xu et al., 2023).\" - It would be nice to have some more sentences directly comparing findings to the previous studies, as you did more completely with said previous studies\n\"N,N-dimethyltryptamine (DMT) (aka ayahuasca) can rapidly conjure up a mystical state virtually identical to the NDE.\" - This is definitely an over-statement. 'very similar in terms of phenomenological features' would be more appropriate (see Michael et al, 2023 [already cited] & Michael et al, 2024: \"Smokable \"Vine of the Dead\": Two Case Studies of Experiencers of Both \" by Pascal Michael, David Luke et al. (ciis.edu) )\n\"What was discovered was The dominance of slow delta and theta oscillations was accompanied by a striking loss of spectral power in the faster rhythms. Such findings are, of course, quite contrary to the expectations of the GBA model\" --> In fact, increased low gamma was found over the posterior cingulate after psilocybin administration [also shown to be very NDE resembling, see (PDF) The Death Trip: A Case Study of Psilocybin's Simulation of the Phenomenology and Long-term changes of the Near-death Experience (researchgate.net)] (Kometer et al, 2015) And increased low/high gamma was found in the Frontal, temporal, parietal-occipital regions, under Ayahuasca (Schenberg et al, 2015) Also, increased power & synchrony of gamma was found under DMT specifically, which correlated with mystical experience (Pallivicini et al, 2020)\n\"Without exception, they are characterized by slow diffuse activity within the theta range (e.g. Rodin et al., 1959; Corssen et al., 1974; Stockard et al., 1976).\" - In fact, the literature suggests that, although mixed due to other factors, psychoactive ketamine doses generally lead to increases in gamma --> \"Ketamine amplifies induced gamma frequency oscillations in the human cerebral cortex\" by Shaw et al. (2015) \"Ketamine can produce oscillatory dynamics by engaging mechanisms dependent on the kinetics of NMDA receptors\" by Nicolás-Alonso and Andrade-Valenc (2024) \"The neurophysiology of ketamine: an integrative review\" by McMillan and Muthukumaraswamy (2020)\n\"This activity typically commenced approximately 30 min after resuscitation began, \" - Clarify why this canine alpha pattern is relevant, given that this statement suggests it didnt even occur during (anaesthetic) coma\n\"the second comprised amygdaloid activity disguised as abnormally high-amplitude fake gamma waves\" - You may clarify this later, but make clear why amygdala-derived alpha diffusing to the cortex may appear as gamma (conflated with, or in addition to cortical GBA)\n\" It might be predicted Therefore, conditions such as hypoxia, ischemia, or cardiac arrest... etc\" + \"THe effects of ether\" - correct phrasing\n\"Because its frequency normally falls within the gamma range, it has also been defined as an amygdaloid gamma oscillation.\" - Clarify why this fast BLA may simultaneously be in the gamma range but also be the origin of alpha\n\"There seems to be no essential difference once the anesthetic influence, in particular, is taken into account.\" - May this also weigh in on Borjigin's findings that there was no GBA in the anesthetised rodents (ie anaethesia-induced significant slowing to point of gamma not being detected)?\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? Yes\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Yes", "responses": [] }, { "id": "316189", "date": "04 Sep 2024", "name": "Duan Li", "expertise": [ "Reviewer Expertise computational neuroscience", "EEG", "consciousness", "anesthesia" ], "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 provides a great review of recent EEG studies on dying animals and patients and proposed alternative interpretations of gamma brain activity that was associated with near-death experiences in those studies. The article is well-written, with its conclusions supported by evidence from the referenced publications. However, I would like to suggest a few areas for improvement to further enhance the discussion and scope of the review:\nAs noted by other reviewers, several studies have reported enhanced gamma activity following the administration of hallucinogenic drugs. These findings imply that the EEG signatures of hallucinogenic agents are not entirely incompatible with the gamma surge hypothesis of NDE. The author might consider exploring this connection. In addition to the work by Borjigin et al 2013, other studies have also found synchronized gamma activity in diverse rodent models, e.g. asphyxia (Li et al. 2015; Lee et al 2017, Schramm et al 2020; Carton-Leclercq et al 2023) and drug intoxication (Zhang et al 2019, in rat hippocampus). A recent review on this topic by Mashour et al. (2024) may also provide additional context. Compared to cardiac arrest model in Borjigin et al. 2013, the models of circulatory arrest, especially the asphyxia and resuscitation model in Schramm et al 2020, may offer more relevant comparisons to the canine ACP model. The author might consider including a discussion on potential neurophysiologic and neurochemical mechanisms underlying the gamma surge. For example, Schramm et al 2020 have investigated the neuronal origins of the EEG changes during the dying-to-recovery process. Li et al 2015 reported significant increases in the cortical release of several neurotransmitters following asphyxia. Schramm et al 2020 proposed that NDE might be generated during resuscitation based on the resemblance of EEG patterns observed in hallucinatory diseases such as schizophrenia. Including a discussion on this alternative hypothesis could enrich the paper's exploration of NDE mechanisms.\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? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-674
https://f1000research.com/articles/11-41/v1	13 Jan 22	{ "type": "Research Article", "title": "Desired support system to eradicate urban homelessness: an exploratory descriptive study", "authors": [ "Noor Ashikin Mohd Rom", "Nurbani Md. Hassan", "Al-Mansor Abu Said", "Burhanuddin Bachik", "Nurbani Md. Hassan", "Al-Mansor Abu Said", "Burhanuddin Bachik" ], "abstract": "Background - The new increasing homeless lately consist of women, children, youth, the elderly and marginalized ethnic or migrant groups. Some of them are working and earn salaries, however, the income is not sufficient to live modestly. Purpose – The purpose of this research is to establish a desired support system to eradicate urban homelessness in the country. Design/methodology/approach – This is an exploratory descriptive method study which employed quantitative techniques. The study employed a social ecological model to investigate behavior of homeless via multiple levels of influences including intrapersonal, interpersonal, organizational, community and public policy. Surveys have been conducted on sixty-five homeless individuals. Findings – It was found that support systems and structures should be derived from the whole streams from families, communities, organizations and government. Employment opportunities, long-term shelters within the community places and highly demanded skills are needed to improve their living condition. Research limitations – This study is only focused on the socio-economic structures of the homeless in a capital city. Originality/value – This is an empirical research using a social ecological model for the homeless in the Kuala Lumpur area. Research on homeless study has received little attention and has yet to be fully explored.", "keywords": [ "Homeless", "vagrants", "social-ecological model", "government policy", "support system" ], "content": "Introduction\n\nAccording to the Malaysian National Key Result Area (NKRA), every citizen should have access to necessities, including a home. Homeless people are often portrayed as causing inconvenience and annoyance to the public. The living conditions of the homeless people and surrounding environments may tarnish the image of the capital city, Kuala Lumpur. It was reported that homeless people have not been fully accepted by the authorities and are perceived as a public nuisance.1\n\nThe welfare department, Jabatan Kebajikan Masyarakat (JKM) reported approximately 2,472 homeless people comprising 3,117 adults and 355 children. In terms of ethnicity, 48.9% are Malay, 15.6% are Indian, 13.4% are Chinese, and 1.8% are other ethnicities. Nonetheless, 20.4% of homeless people are non-Malaysians. The Malaysian government has established the Desa Bina Diri (DBD) for homeless and impoverished people. The DBD offers protection, provides rehabilitation, and equips them with essential skills to be productive, independent, secure a job, and adapt to the community. In addition, homeless individuals can join DBD voluntarily or by court order following the provisions of the Destitute Persons Act 1977.1\n\nThe number of homeless people is increasing due to the global economic uncertainty of the COVID-19 pandemic worldwide. This phenomenon is worrying and should not only be the responsibility of policymakers, but the whole structure consisting of the family, society, and organisations to collaborate to curb the desperate living conditions of unfortunate individuals. Therefore, this study aims to establish a desired support system to eradicate urban homelessness in the country.\n\n\nRelated works\n\nA home is a place that provides shelter, privacy, warmth, love, relaxation, health, happiness, stability, and paradise2 and is essential for the wellbeing of man.3,4 Economic uncertainty and the increased living costs contribute to the increase of homeless people in Malaysia.5 One common perception is that homeless people worldwide are deprived of fundamental human needs and are often poor and financially insecure.5–7 Homeless' lives becoming worsen due to lack of family and social support. They felt abandoned and lost hope.8\n\nHousing costs and food prices have been increasing rapidly over the years, leading to an increase in beggars and vagrants.9 The cause of homelessness varies and is linked to unemployment, low income, unable to afford a proper house, lack of affordable housing, and unavailability of transport to work.7,9 In addition, the unemployment issue among the homeless can be prevented through training and equipping them with essential skills, including reading, grooming, and job interview skills.6,10,11 Policymakers should comprehend the various perspectives that influence homelessness, such as the socio-economic systems, inadequate housing, and inequitable welfare that have dire consequences for families and individuals.7,10\n\nThe Social Ecological Model describes that the behaviour of individuals is influenced and encouraged by their surroundings. There are five influence levels: intrapersonal, interpersonal, organisational, community, and public policy.12,13 Homelessness is influenced by circumstances, socio-economy, and environmental conditions.13,14 A framework that incorporates the five crucial levels of the Social Ecological Model has been established. The first level consists of the individual’s demography and economic status, and the second level is the interpersonal relationship with family, peers and network. Additionally, the third level consists of the relationship between the individual and the community, including associations and informal networks. The fourth level is organisations that deal with rules and regulations, and the fifth level is policy which comprises local, state, and national policies for citizens.15\n\n\nMethods\n\nThis study employed an exploratory descriptive study using the Statistical Package for the Social Sciences (SPSS Statistics 26) to investigate the behaviour of homeless via multiple influences, such as intrapersonal, interpersonal, organisational, community, and public policy. The study employed a social ecological Model to survey sixty-five (65) homeless people. The survey respondents were identified from soup kitchens organised by numerous non-governmental organisations (NGOs) around Kuala Lumpur.\n\nThe interviews were conducted at the respondent’s location with their full consent. The Ethical Approval No.: EA1042021 was obtained from Technology Transfer Office (TTO), Multimedia University, to conduct this study. Prior to the interview session, the objectives of this study and respondents’ consent to conduct face-to-face interviews for the data collection were obtained. All 65 respondents had given their verbal consent to be interviewed. The questionnaires designed included close-ended questions with a 5-Point Likert scale. The survey questionnaire was divided into five sections, namely section (1) individual, (2) interpersonal, (3) community, (4) organisational and (5) policy. Section 1 aimed to collect demographic information of respondents, reasons for homelessness and challenges faced. Section 2 included relationships with families and peers, while Section 3 determined relationships in the community. Moreover, Section 4 collected information on the aid received from various organisations and Section 5 focused on the respondent’s perception of the government’s policies towards them.\n\nThe findings on the demography of the respondents are illustrated in Table 1 below.\n\nThe crosstab analysis indicates that single, Malay males represent the highest number of homeless individuals staying on the streets in Kuala Lumpur. Divorcees are the second-highest individuals that had to leave their houses to live on their own. The majority of respondents were between 18-50 years old. Conversely, there are around 33(50.7%) individuals who are more than 50 years old. In addition, 67.7% possess basic education, and 27.7% have higher qualifications. Nevertheless, most of the respondents are computer illiterate. Approximately 78% of respondents have been living on the streets for more than five years. Eleven respondents who were above 70 years old have been homeless for more than 30 years. Most of the respondents below 60 years old claimed that they needed a job to survive, while those above 60 years old were unaware of how to generate income. Lastly, 10 (15.4%) respondents admitted earning their living by begging.\n\n\nDiscussion\n\nBased on the mean score results shown in Table 2, the respondents became homeless due to loss of jobs, family breakdown, and the inability to afford accommodation. Most of the respondents are in dire need of shelter and wish to live a conventional life. Conversely, several respondents were forced to live on the street due to unforeseen circumstances; however, some chose to live on the streets as it is easier for them to commute. The low mean scores indicate that the respondents are not computer literate, unskilled, and lack administration, marketing or business knowledge. Nevertheless, they are inclined towards service jobs, such as cleaning, shop assistants, selling tins, and other odd jobs.\n\nThe low mean score and standard deviation score for the interpersonal section illustrate that most respondents do not have a good relationship with their families. Most of the respondents are unaware of their children’s progress and have not kept in touch with their families in a long time. In addition, respondents do not want to reunite with their families, have lost contact with friends, and live in their circle. Nonetheless, they claimed to have future plans and wished to free themselves from this situation as soon as possible.\n\nThe low mean score for the community section indicates that homeless people lack of community relationships. Nonetheless, the high standard deviation result demonstrates that several respondents visit places of worship and other community spaces. The low community involvement indicates that they prefer to interact within their small selected circle of homeless peers. Moreover, they hardly participate in community activities and are insecure about interacting with outsiders. Nevertheless, the respondents acknowledged that they required assistance for food and other necessities from others.\n\nThe high mean scores for the organisation section indicate that respondents are overwhelmed with the aids provided by non-governmental organisations (NGOs) such as food, sanitary products, and one-off monetary assistance from the religious office, Majlis Agama Islam Wilayah Persekutuan (MAIWP). Conversely, respondents are not happy to stay in Desa Bina Diri (DBD), a shelter that offers protection, provides rehabilitation, and equips them with essential skills to be productive, independent, secure a job, and adapt to the community. The high mean scores for policy denotes that the respondents do not like to be apprehended by government agencies such as Kuala Lumpur City Hall, also known as Dewan Bandaraya Kuala Lumpur (DBKL) and placed at DBD. Additionally, the respondents claimed that the current governmental policies do not favour them. Alternately, respondents perceived these government agencies as friendly and helpful.\n\n\nConclusion\n\nHomeless people require physical assistance (shelter, food, and medication) and spiritual nurture to alter their mindset and behaviour. They have to belong to the community and should have a circle of positive peers. This support system must include family, community, and organisations (government agencies and NGOs). In addition, rulers should collaborate and be responsive to homelessness issues. Every stage of these structures must collaborate to provide resources and manage the vagrancy or homeless matter.\n\nFamily, peers, and relatives are the closest support structure for unfortunate individuals. In addition, the society or communities near these impoverished individuals are vital pillars to ensure no one is left hungry and homeless. There are growing numbers of NGOs that provide immediate support to homeless regarding food, sanitary products, and clothes. Policymakers have also devised various programs to tackle homelessness, such as establishing DBD, Anjung Singgah (temporary shelter) and providing job opportunities for the homeless. Nevertheless, the number of homeless individuals is not reducing. Consequently, policymakers must provide long-term shelters or houses to eradicate urban homelessness. Necessities such as accommodation are vital for homeless people to restart their lives and quickly adapt to the surrounding community.\n\n\nAuthor contributions\n\nFirst author conceptualized the research idea, theoretical framework and write the paper. Second author revised the article; fourth visualized and third author reviewed the article for submission.\n\n\nCompeting interest\n\nThe authors agree that this research was conducted in the absence of any self-benefits, commercial or financial conflicts and declare absence of conflicting interests with the funders.\n\n\nData availability\n\nFigshare. Desired Support System to Eradicate Urban Homelessness: An Exploratory Descriptive Study. DOI: https://doi.org/10.6084/m9.figshare.16529391.v116\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC BY 4.0 Public domain dedication).\n\n\nGrant information\n\nA Fundamental Research Grant Scheme (FRGS) FRGS/1/2019/SS06/MMU/03/1 was awarded to the researchers by Ministry of Higher Education, Malaysia in 2019. We confirm that the funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.\n\n\nEthics approval and consent to participate\n\nEthical Approval No.: EA1042021 for Homeless project was obtained from Technology Transfer Office (TTO), Multimedia University. Respondents have given verbal consent to publish.", "appendix": "Acknowledgement\n\nWe thank Mr. Alwi Abdullah for his assistance in coordinating respondents for the interview sessions.\n\n\nReferences\n\nJabatan Kebajikan Masyarakat Malaysia: 2021.\n\nDear MJ, Wolch JR: Landscapes of Despair: From Deinstitutionalization to Homelessness Princeton University Press; 2016.\n\nSharam A, Hulse K: Understanding the Nexus between Poverty and Homelessness: Relational Poverty Analysis of Families Experiencing Homelessness in Australia, Housing, Theory and Society.2014; Vol. 31(Iss. 3). 2014, also publish in Taylor & Francis online.\n\nFertig AR, Reingold D: The Characteristic and Causes of Homelessness among at Risk Families with Children in Twenty American Cities. Soc. Serv. Rev. 2017; 82(3): 485–510. 2008.\n\nJohnsen S: Homelessness and social control: A typology, Housing Studies.2017; Volume 33(Issue 13). Taylor & Francis Online.\n\nAratani Y, Cooper JL: The Effects of Runaway-Homeless Episodes on High School Dropout. Youth Soc. 2015; v47(n2): p173–198.\n\nAlhabshi SM, Abdul Manan AK: Homelessness in Kuala Lumpur, Malaysia: A Case of Agenda Denial. International Journal of Social Science Tomorrow. 2012; 1(2): 1–9.\n\nDrani S, Azman A, Jamir Singh PS: Do Homeless People Giving Up Hope? A Qualitative Study in Penang, Malaysia. Asian Social Work Journal (ASWJ). 2021; 6(5): 1–10. Publisher Full Text .\n\nArshad MRM, Kamal AZM, Arif ND: Street Begging in Kuala Lumpur.2014. Publisher Full Text\n\nRusenko R: Homelessness, Human Insecurities, and the Government Agenda in Malaysia. The Simultaneous Inclusion and Exclusion of Anjung Singgah. Asian J. Soc. Sci. 2014; 42(1-2): 45–74.\n\nAhmad Yani NM, et al.: Factors Associated with Homelessness and its Medical Issues among Urban Malaysians: A Qualitative Research. Journal of Clinical and Health Sciences. 2016; 1(2016): 46–58. Publisher Full Text\n\nMcLeroy K, Bibeau D, Steckler A, Glanz K: An Ecological Perspective on Health Promotion Programs. Health Educ. Behav. 1988; 15(4): 351–377. Publisher Full Text\n\nEmbleton L, Lee H, Gunn J, et al.: Causes of Child and Youth Homelessness in Developed and Developing Countries. A Systematic Review and Meta-analysis. JAMA Pediatr. 2016; 1170(5): 435–44. Publisher Full Text\n\nNooe R, Patterson D: The Ecology of Homelessness. J. Hum. Behav. Soc. Environ. 2013; 20: 105–152. 2010 - Issue 2: The Complexities of Homelessness: Theoretical and Empirical Analyses. Publisher Full Text\n\nCenter for Disease Control and Prevention - CDC: The Social-Ecological Model: A Framework for Prevention. 2014.\n\nMohd Rom NA, Md Hassan N: Desired Support System to Eradicate Urban Homelessness: An Exploratory Descriptive Study. figshare. Dataset. 2021. Publisher Full Text" }	[ { "id": "119654", "date": "07 Feb 2022", "name": "Zakiyah Jamaluddin", "expertise": [ "Reviewer Expertise Youth and Community" ], "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 method section should include the following details : a. sampling technique - how were all 65 respondents chosen? is it based on purposive or convenience sampling? b. face to face interview - is it a structured interview using questionnaires, or a semi structured/unstructured interview using protocol interview?\n2. Table 2 should be in Findings.\n3. Discussion - Should be related to the literature review and how it relates to the title of this manuscript.\n4. Conclusion - Should be related to the findings and discussion but there was little discussion in the article, only highlighting of results instead.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "12341", "date": "16 Sep 2024", "name": "Noor Ashikin Mohd Rom", "role": "Author Response", "response": "1. Method Section a. Convenience sampling was applied in this study, as this method involves selecting individuals who are readily available and willing to participate. The study employed a social ecological Model to survey sixty-five (65) homeless people. The survey respondents were identified by Pertubuhan Kebajikan ArRiqab, one of the active non-governmental organisations (NGOs) that assisting homeless people in Kuala Lumpur area A simple regression analysis requires a minimum of 50 samples and sample-to-variable ratio suggests a minimum observation-to-variable ratio of 5:1.30 Additionally, minimum sample size of N ≥ 50+m (where m is the number of predictors) was recommended.31 The minimum sample size by applying 31 method is 55, however, the researchers managed to get 65 respondents. b. This is a structured interview using questionnaires. 2. Table 2 has been included in Findings. 3. Discussion has been updated accordingly that related to literature review and title. The first level of the Social Ecological Model highlights how individual demographics and economic status play a crucial role in homelessness. It shows that many homeless individuals in Malaysia struggle with insufficient income, inability to afford housing, and a lack of skills. Previous studies have identified economic instability and rising living costs as significant contributors to the growing homeless population in the country.5 These findings are further supported by 5,10 linking homelessness to factors such as unemployment, low income, inability to secure proper housing, lack of affordable housing, and limited access to transportation for work .7,10 Compounding these challenges, many homeless individuals experience a sense of abandonment due to fractured family relationships 8. The study also revealed that homeless respondents lacked the essential skills needed to obtain stable employment. This observation aligns with the research of 14,15 which demonstrated that developing occupational skills can significantly enhance the well-being and prospects of those facing unemployment and homelessness. The persistent lack of education, training, and life skills continues to be a major barrier to employment 13,32 The second level of the Social Ecological Model emphasizes that homeless individuals frequently suffer from weak interpersonal relationships with family, peers, and social networks. Many respondents reported experiencing family conflicts and strained ties with relatives and friends. This observation is consistent with previous studies 5,7,9 which indicate that homeless individuals often feel abandoned, endure social isolation, and lack sufficient social support and resources. It was revealed that homeless individuals suffer from deficiencies in familial and community support, as well as limited interactions with service providers 9. Nevertheless, the finding revealed that some respondents expressed confidence in their ability to overcome their current situation. The finding is consistent with 17 who found that the homeless who often viewed as a burden on society due to their nonconformity to social norms, can transform themselves when given proper training and rehabilitation, as they possess the ability to plan for a better future. However, these efforts are unlikely to succeed if the homeless lack the determination to resolve their issues, causing them to revert to their old ways, even after receiving support 16. 18 discovered that about eight out of 45, returned to the streets despite undergoing rehabilitation programs. The third level focuses on the relationship between homeless individuals and the broader community, including associations and informal networks, revealing that they often feel insecure and marginalized from societal participation due to their circumstances. This finding aligns with the study by 9 who observed that homeless individuals frequently experience isolation, remain silent, and perceive discrimination because of their situation. Similarly, it was noted that perceived estrangement and social exclusion can exacerbate societal divides, diminishing social trust and cohesion, and leaving individuals feeling disconnected and unable to engage in meaningful activities 20,21 The fourth level of the model focuses on the role of organizations in impacting the lives of homeless individuals. These organizations provide essential support, such as food, monetary assistance, and shelter. This finding aligns with 22,23 who emphasized that homeless individuals require physical support in the form of shelter, food, and medical care, as well as societal interventions to address fundamental human needs. Supportive relationships with caregivers and targeted programs that integrate care and services are crucial approaches to consider in effectively assisting the homeless. The fifth level is policy which comprises local, state, and national policies for citizens. The respondents claimed that the current governmental policies do not favour them and should not interfere with their life. The findings align with the study conducted by 25 stated that the authorities under Destitute Persons Act 1977 (DPA 1977) can forcibly remove individuals they consider homeless and place them in Desa Bina Diri (DBD), a shelter that offers protection with the court order. DPA 1977 has faced significant criticism for violating personal liberty and freedom of movement of person who is categorized as a destitute person. Nonetheless, the finding also show that some respondents viewed these government agencies as friendly and supportive. The finding corroborates with 25,33 who revealed that some homeless individuals, particularly senior citizens, were rescued from their difficult lives on the streets by the authorities. They were given necessary assistance including shelter. Nevertheless, the concept of 'rehabilitation' must be critically examined to determine whether it genuinely addresses the needs of those experiencing homelessness 25 The policies should focus on establishing a robust support system for the homeless, while also empowering the elderly and strengthening their communities 33. 4. Conclusion has been updated accordingly. To conclude, eradicating urban homelessness requires a comprehensive approach rooted in the five pillars of the structural ecological model. This study underscores the importance of equipping homeless individuals with employment skills (individual), fostering peer support (interpersonal), promoting social acceptance (community), ensuring access to rehabilitation services (organizational), and implementing a coordinated governmental strategy (policy). While current efforts provide essential support like health services, temporary shelters, and food, they often fail to address the other root causes of homelessness, such as unemployment, loss of income, lack of skills and social support. Therefore, it is imperative for the government to intensify efforts by funding programs that enhance literacy and provide Technical and Vocational Education and Training (TVET). These programs should offer formal, non-formal, and informal learning opportunities that may collaborate with communities and organizations that empower individuals to secure meaningful employment and rebuild their lives. Additionally, the government shall prioritize accessible housing for the homeless, similar to the \"Projek Perumahan Rakyat Termiskin (PPRT)\" or Housing Project for the Absolute Poor, ensuring that these projects are widespread and located near essential amenities. Providing permanent housing to meet the basic needs of the homeless can significantly alleviate their hardships and improve their overall well-being. By providing stable housing, communities, and organizations can further support the homeless by offering employment opportunities, with the government incentivizing employers to participate. This integrated approach is vital to enabling homeless individuals to reintegrate into society and sustain long-term stability. A comprehensive and well-structured support system is essential to effectively eradicate urban homelessness in the country. This system should be designed to address the root causes of homelessness, such as poverty, lack of affordable housing, unemployment and lack of social support. It would involve coordinated efforts from government agencies, non-governmental organizations, and the private sector, focusing on providing not only immediate relief but also long-term solutions. These solutions could include affordable housing programs, job training and employment opportunities, and social support networks. By integrating these components into a cohesive and sustainable framework, the desired support system would not only provide immediate assistance to those experiencing homelessness but also work towards preventing future homelessness, ultimately leading to the complete eradication of urban homelessness in the country. Future research could investigate the effectiveness of specific support system components, such as job training or affordable housing programs, in preventing homelessness. Additionally, it could focus on assessing the long-term sustainability and scalability of these solutions across different urban areas to optimize and adapt the support system for eradicating homelessness." } ] }, { "id": "169771", "date": "09 May 2023", "name": "K. Rewathy", "expertise": [ "Reviewer Expertise Social Geography", "Human geography", "GIS and Remote sensing", "Urban Geography", "Environmental 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 paper is well-written, it addresses the major issues of homelessness in Malaysia and it tries to identify a suitable system to eradicate the homelessness to some extent. It addresses a timely important topic. However, there are a few instances where it may be improved:\nItalicize any local terms that are utilized to identify the term clearly.\n\nThe literature section should be expanded with relevant content that highlights homelessness eradication approaches.\n\nFor the justification, previous research must be acknowledged in the discussion section.\n\nThe findings must back up the conclusion, rather than more general.\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? No", "responses": [ { "c_id": "12342", "date": "26 Sep 2024", "name": "Noor Ashikin Mohd Rom", "role": "Author Response", "response": "1. All local terms in Italic font. 2. The literature review on approaches to eradicating homelessness has been updated accordingly. 9Nevertheless, policymakers should understand the diverse factors influencing homelessness, including socio-economic systems, inadequate housing, and inequitable welfare, as these issues have severe consequences for families and individuals.7,10 Homelessness eradication program must focus on providing stable housing to reduce stress and improve well-being, particularly in quality neighbourhoods that foster social connections 9. It was suggested that developing occupational skills can positively impact the well-being and outcomes of those experiencing unemployment and homelessness.13,14,15 Homelessness prevention should be a collaborative effort involving all levels of government and various institutions beyond the homelessness sector. Structural and systems prevention need active participation from mainstream systems, while prevention methods within the homelessness sector, such as early intervention, housing stabilization and eviction prevention, work best when integrated with these broader systems 24 3. Previous research has been acknowledged in the discussion section. The first level of the Social Ecological Model highlights how individual demographics and economic status play a crucial role in homelessness. It shows that many homeless individuals in Malaysia struggle with insufficient income, inability to afford housing, and a lack of skills. Previous studies have identified economic instability and rising living costs as significant contributors to the growing homeless population in the country.5 These findings are further supported by 5,10 linking homelessness to factors such as unemployment, low income, inability to secure proper housing, lack of affordable housing, and limited access to transportation for work .7,10 Compounding these challenges, many homeless individuals experience a sense of abandonment due to fractured family relationships 8. The study also revealed that homeless respondents lacked the essential skills needed to obtain stable employment. This observation aligns with the research of 14,15 which demonstrated that developing occupational skills can significantly enhance the well-being and prospects of those facing unemployment and homelessness. The persistent lack of education, training, and life skills continues to be a major barrier to employment 13,32 The second level of the Social Ecological Model emphasizes that homeless individuals frequently suffer from weak interpersonal relationships with family, peers, and social networks. Many respondents reported experiencing family conflicts and strained ties with relatives and friends. This observation is consistent with previous studies 5,7,9 which indicate that homeless individuals often feel abandoned, endure social isolation, and lack sufficient social support and resources. It was revealed that homeless individuals suffer from deficiencies in familial and community support, as well as limited interactions with service providers 9. Nevertheless, the finding revealed that some respondents expressed confidence in their ability to overcome their current situation. The finding is consistent with 17 who found that the homeless who often viewed as a burden on society due to their nonconformity to social norms, can transform themselves when given proper training and rehabilitation, as they possess the ability to plan for a better future. However, these efforts are unlikely to succeed if the homeless lack the determination to resolve their issues, causing them to revert to their old ways, even after receiving support 16. 18 discovered that about eight out of 45, returned to the streets despite undergoing rehabilitation programs. The third level focuses on the relationship between homeless individuals and the broader community, including associations and informal networks, revealing that they often feel insecure and marginalized from societal participation due to their circumstances. This finding aligns with the study by 9 who observed that homeless individuals frequently experience isolation, remain silent, and perceive discrimination because of their situation. Similarly, it was noted that perceived estrangement and social exclusion can exacerbate societal divides, diminishing social trust and cohesion, and leaving individuals feeling disconnected and unable to engage in meaningful activities 20,21 The fourth level of the model focuses on the role of organizations in impacting the lives of homeless individuals. These organizations provide essential support, such as food, monetary assistance, and shelter. This finding aligns with 22,23 who emphasized that homeless individuals require physical support in the form of shelter, food, and medical care, as well as societal interventions to address fundamental human needs. Supportive relationships with caregivers and targeted programs that integrate care and services are crucial approaches to consider in effectively assisting the homeless. The fifth level is policy which comprises local, state, and national policies for citizens. The respondents claimed that the current governmental policies do not favour them and should not interfere with their life. The findings align with the study conducted by 25 stated that the authorities under Destitute Persons Act 1977 (DPA 1977) can forcibly remove individuals they consider homeless and place them in Desa Bina Diri (DBD), a shelter that offers protection with the court order. DPA 1977 has faced significant criticism for violating personal liberty and freedom of movement of person who is categorized as a destitute person. Nonetheless, the finding also show that some respondents viewed these government agencies as friendly and supportive. The finding corroborates with 25,33 who revealed that some homeless individuals, particularly senior citizens, were rescued from their difficult lives on the streets by the authorities. They were given necessary assistance including shelter. Nevertheless, the concept of 'rehabilitation' must be critically examined to determine whether it genuinely addresses the needs of those experiencing homelessness 25 The policies should focus on establishing a robust support system for the homeless, while also empowering the elderly and strengthening their communities 33. 4. The conclusion has been updated accordingly. To conclude, eradicating urban homelessness requires a comprehensive approach rooted in the five pillars of the structural ecological model. This study underscores the importance of equipping homeless individuals with employment skills (individual), fostering peer support (interpersonal), promoting social acceptance (community), ensuring access to rehabilitation services (organizational), and implementing a coordinated governmental strategy (policy). While current efforts provide essential support like health services, temporary shelters, and food, they often fail to address the other root causes of homelessness, such as unemployment, loss of income, lack of skills and social support. Therefore, it is imperative for the government to intensify efforts by funding programs that enhance literacy and provide Technical and Vocational Education and Training (TVET). These programs should offer formal, non-formal, and informal learning opportunities that may collaborate with communities and organizations that empower individuals to secure meaningful employment and rebuild their lives. Additionally, the government shall prioritize accessible housing for the homeless, similar to the \"Projek Perumahan Rakyat Termiskin (PPRT)\" or Housing Project for the Absolute Poor, ensuring that these projects are widespread and located near essential amenities. Providing permanent housing to meet the basic needs of the homeless can significantly alleviate their hardships and improve their overall well-being. By providing stable housing, communities, and organizations can further support the homeless by offering employment opportunities, with the government incentivizing employers to participate. This integrated approach is vital to enabling homeless individuals to reintegrate into society and sustain long-term stability. A comprehensive and well-structured support system is essential to effectively eradicate urban homelessness in the country. This system should be designed to address the root causes of homelessness, such as poverty, lack of affordable housing, unemployment and lack of social support. It would involve coordinated efforts from government agencies, non-governmental organizations, and the private sector, focusing on providing not only immediate relief but also long-term solutions. These solutions could include affordable housing programs, job training and employment opportunities, and social support networks. By integrating these components into a cohesive and sustainable framework, the desired support system would not only provide immediate assistance to those experiencing homelessness but also work towards preventing future homelessness, ultimately leading to the complete eradication of urban homelessness in the country. Future research could investigate the effectiveness of specific support system components, such as job training or affordable housing programs, in preventing homelessness. Additionally, it could focus on assessing the long-term sustainability and scalability of these solutions across different urban areas to optimize and adapt the support system for eradicating homelessness." } ] } ]	1	https://f1000research.com/articles/11-41
https://f1000research.com/articles/12-902/v1	28 Jul 23	{ "type": "Research Article", "title": "PASS: A scoring system to evaluate persistent kidney injury in critically ill ICU adult patients", "authors": [ "Dattatray Prabhu", "Sonali Dattatray Prabhu", "Chakrapani Mahabala", "Mayoor V Prabhu", "Dattatray Prabhu", "Chakrapani Mahabala", "Mayoor V Prabhu" ], "abstract": "Background: We evaluated if the course of recovery from sepsis-induced acute kidney injury (AKI) can be predicted using variables collected at admission.\nMethods: A total of 63 patients admitted for sepsis-induced AKI in our Mangalore ICU were evaluated and baseline demographic and clinical/laboratory parameters, including serum creatinine (SCr), base excess (BE), Plethysmographic Variability Index (PVI), Caval Index, R wave variability index (RVI), mean arterial pressure (MAP) and renal resistivity index (RI) using renal doppler and need for inotropes were assessed on admission. Patients were managed as per standard protocol. After six hours of fluid resuscitation, patients were classified as volume responders or non-responders. Re-assessment was done at 24 hours and 72 hours after admission. Primary outcome was persistent AKI after 72 hours. Secondary outcome was initiation of dialysis or death within 15 days of admission.\nResults: A total of 34 subjects recovered from AKI, of whom 32 patients were volume responders and 31 were non-responders. Response to fluid, MAP at admission and six hours, BE at admission, inotrope requirement, and PVI at admission did not correlate with recovery. Multiple logistic regression showed that SCr < 2.36 mg%, RVI > 14.45 and RI < 0.8 on admission correlated with recovery and they were evaluated further to model AKI recovery and develop PASS. PASS score = (SCr points × 5.4) + (RVI points × 4.0) + (RI points × 6.2). One point each was allotted if SCr was < 2.36, RVI was > 14.45 and RI was <0.8, and 0 otherwise. A score > 7.8 predicted recovery with a sensitivity of 79.4%, specificity of 72.4%, PPV 81.8%, NPV 76.7% and AuROC of 0.85.\nConclusions: The PASS score can be used to identify salvageable cases of sepsis-AKI, guiding fluid resuscitation and aiding early referral from rural to tertiary care centers for better management.", "keywords": [ "AKI", "Sepsis", "AKI recovery", "renal Resistive index", "Persistent AKI scoring system", "Critically ill", "RVI", "creatinine" ], "content": "Introduction\n\nMany patients admitted in intensive care unit (ICU), present with acute kidney injury (AKI) caused by ischemia, hypoxia or nephrotoxicity, resulting in rapidly declining glomerular filtration rate (GFR), leading to an increased risk of morbidity and mortality. The prevalence of AKI in critically ill ICU patients is high, particularly in those with sepsis (20-50% rate of prevalence).1 Reversibility of AKI is influenced by the recovery response, which is in turn affected by the extent of renal damage and potential for renal cell regeneration.2 Hence, for such patients, rapid restoration of circulation as well as optimal perfusion pressure is of paramount importance. Persistent AKI, exceeding 48 hours, is shown to significantly increase mortality.2 The clinical definition of AKI sums it up as a rapid decrease of GFR, leading to retention of nitrogenous waste products. AKI is diagnosed and staged using the RIFLE (Risk, Injury, Failure, Loss of kidney function, and End-stage kidney disease) classification and AKIN (Acute Kidney Injury Network) criteria.1,3 Severity and causes of AKI vary and have direct effects on mortality.1,3 The RIFLE criteria are one of the most commonly used criteria to define and diagnose AKI, developed by the Acute Dialysis Quality Initiative (ADQI); they determine AKI severity on the basis of serum creatine (SCr), GFR, and urine output.4\n\nDespite best efforts, AKI does not resolve in many cases.5 The major challenge to clinicians is in prognostication and patient counseling. Many studies have proposed different models for this purpose. Some studies have used numerous biomarkers for prompt detection and predicting severity of AKI and thereby categorizing into appropriate risk groups at risk for progressive renal decline, requirement of RRT, or death.5–7 Biomarkers like interleukin-18 (IL-18), cystatin C (Cys C), neutrophil gelatinase-associated lipocalin (NGAL), kidney injury molecule-1 (KIM-1) and liver-type fatty acid binding protein (L-FABP) are being used for prediction of AKI and probable recovery.6–8 Most of the tools to measure these biomarkers are expensive and not routinely available in all healthcare facilities.\n\nOur objective was to use easily available parameters and variables to predict the course of the disease in AKI. Ryo Matsuura et al. have published a scoring system called PARI (Persistent AKI Risk Index) to predict low risk persistent AKI in critically ill adult patients.9 However, PARI does not enable assessment of patients at admission to decide on resuscitation. Hence this study included variables routinely collected at admission to predict the course of AKI and guide fluid resuscitation sepsis AKI.9,10\n\n\nMethods\n\nThis prospective cross-sectional study commenced after institutional ethics committee approval (see Ethical considerations at the end of the manuscript). Patients admitted to ICU during 2019-2020 with were included in this study, after informed written consent from all patients or their next of kins were obtained. This study utilized non-random sampling, with inclusion criteria being age > 18 years and patients with AKI and septic shock admitted to the ICU.11 Exclusion criteria included pregnant women, patients diagnosed with renal artery stenosis, end-stage renal disease (ESRD) or chronic kidney disease (CKD), patients < 18 years, patients taking angiotensin-converting enzyme inhibitor (ACEI) or non-steroidal anti-inflammatory drugs (NSAID), patients with cirrhosis with hepatorenal syndrome, cardiorenal syndrome and patients with AKI secondary to urinary tract obstruction (diagnosed on imaging). KIDGO criteria do not recommend gender specific definitions for AKI. RI and RVI do not have gender specific cut offs.\n\nA total of 63 patients were included in over an eight-month period. We assessed parameters like serum creatinine (SCr), base excess (BE) in arterial blood gas (ABG) analysis, Plethysmographic Variability Index (PVI), Caval Index (CI), R wave variability in ECG, Mean arterial blood pressure (MAP), and renal resistive index (RI) using renal doppler screening on admission in patients presenting with sepsis. CI was calculated using IVC diameters obtained by trans-abdominal ultrasound using formula the formula (IVC maximum diameter during expiration − IVC minimum diameter during inspiration)/IVC maximum diameter × 100 and expressed as percentage. R wave variability represents the amplitude change in R waves on ECG calculated as (highest QRS amplitude – shortest QRS amplitude in one respiratory cycle)/mean QRS amplitude in same cycle × 100 and expressed as percentage.\n\nAfter 6 of hours of fluid resuscitation as per standard guidelines, hemodynamic status and volume status of the patient was assessed. Patients were classified as ‘volume responders’ or ‘non-responders’ depending on hemodynamic stabilization using parameters like systolic blood pressure (SBP) and MAP. Hemodynamic stabilization is characterized by MAP exceeding 60 mm Hg beyond 1 hour with no change in the rate of catecholamine infusion or fluid vascular loading. Re-assessment of all variables including estimation of SCr, CI, BE, R wave variability, MAP and RI, was done at 24 hours and 72 hours after admission.\n\nThe primary outcome was persistent AKI after 72 h. The secondary outcome was initiation of dialysis and death within 15 days of admission. AKI that resolves in 3 days of inclusion with conventional standard treatment in the ICU is called transient AKI. The recovery from AKI is characterized by SCr decreasing by 50% or absence of diuretics indicating normalization of urine output or both. Persistent AKI is characterized by persistently higher SCr or oliguria.6,12\n\nThe expression of percentages was done using categorical variables with means and standard deviations being expressed by continuous variables. Binary logistic regression was used to predict the AKI recovery using multiple variables as stated above, unadjusted and adjusted with noradrenaline and volume response and other variables. Based on the odds ratios (OR), a predictive equation was derived, and efficiency testing was performed with the use of a receiver operating characteristic curve (ROC) analysis. This curve’s coordinates, that yielded best sensitivity and specificity, were taken as a cut-off to develop a model (PASS score) for predicting recovery from AKI. In order to test the efficacy of the equation, sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and accuracy were considered. Additionally, the calculation of Kappa scores was done for the PASS score. Decision tree analysis was used for preparing the flow chart. All statistical analyses were performed using SPSS v.20 software. Our data showed no statistically significant difference in S creatinine, RI and R wave amplitude variation at admission between the genders. Hence gender specific subanalysis was not carried out.\n\n\nResults\n\nA total of 63 subjects admitted to ICU with AKI were included as study participants. The following parameters were studied at admission and repeated at 6 hours: MAP, SCr, BE, PVI, CI, R wave variability, and RI. Table 1 shows the patients’ baseline characteristics; patients were managed with standard protocols for fluid resuscitation and other specific treatments. Overall, 32 patients showed volume response with respect to hemodynamic parameters and 31 patients were non-responders to fluid resuscitations. A total of 34 subjects recovered from AKI.\n\nMultiple logistic regression analysis showed that response to fluid (seen as change in MAP at 6 hours); MAP, BE and PVI at admission and requirement of noradrenaline did not correlate with recovery of AKI (Table 2). RI, RVI and SCr at admission correlated well with recovery from AKI, which was statistically significant. Cut-offs for these parameters were derived from the ROC curve analysis. Hence, these three parameters were evaluated further to develop the model for predicting recovery from AKI. Multiple logistic regression showed that creatinine < 2.36 mg%, R wave > 14.45 and RI < 0.8 at the time of admission were correlated with recovery from AKI with adjusted ORs of 5.447, 4.032 and 6.208 respectively (Table 3). Based on this, the following formula was constructed in which SCr, RVI and RI were allotted points:\n\n• SCr < 2.36 was allotted 1 point and values > 2.36 was allotted 0 points;\n\n• R wave variability > 14.45 was allotted 1 point and values < 14.45 were allotted 0 points\n\n• RI < 0.8 was allotted 1 point and RI > 0.8 was allotted 0 points.\n\nAcronyms: S.Cr - Serum creatinine, BE - Base excess in Arterial blood gas analysis, PVI - Plethysmographic variability index, MAP - Mean arterial blood pressure, RI - renal resistive index, CI - confidence interval.\n\n\n\nA total score > 7.8 predicted recovery from AKI.\n\nSensitivity, specificity, predictive value, diagnostic accuracy and Kappa value (agreement with actual outcome) for SCr, RI at admission and RVI and for PASS score are shown in Table 5. A PASS Score > 7.8 had a sensitivity of 79.4% and 72.4% specificity for recovery from AKI. The PPV was 81.8% and NPV was 76.7%. The test and the gold standard agreed on 50 out of 63 having a diagnostic accuracy of 79.34%. The Kappa value of 0.586 indicated good agreement, with a p-value of < 0.001 (Table 5). A PASS Score > 7.8, obtained by analysis of the ROC curve, had an ROC curve area of 0.85 (95% confidence interval of 0.755 to 0.943; p < 0.001) (Figure 1).\n\n\nDiscussion\n\nThe Renal Angina Index, that detects minor variations in SCr along with other clinical variables, was proposed by some studies for identifying critically ill patients who are more likely to experience persistent AKI.12,13 Few studies have tried to predict the severity of renal angina and utilized plasma and/or urinary biomarkers like cystatin C, L-FABP, NGAL, IL-18, KIM-1, among others, which are time consuming and expensive to measure.7,8 In the Indian setting, some of the tools for measuring these biomarkers are not routinely available, limiting their widespread use. We have tried to utilize easily available data at the time of admission to develop a system that can solve this issue in developing countries. Some of these previous studies have used parameters at admission and after 24 hours for understanding whether AKI will be persistent. This method only helped to prognosticate patients after 24 h of admission.9 As these test results are available after a lag time, they do not help clinicians in deciding at the time of admission whether patients will benefit from aggressive resuscitation. Thus, a robust system is needed, not only to assess but also to intervene at the earliest to reverse the damage.\n\nOur study concluded that SCr, RI and RVI at admission are statistically significant (p < 0.05) to predict AKI reversibility, which we have further analyzed to develop the PASS (Persistent AKI Scoring System) formula to predict the course of AKI. PASS is a combined scoring system that includes SCr levels, RI and RVI at admission. A total score greater than 7.8 predicted recovery from AKI. We also developed a flow chart for prediction of recovery from AKI which is shown in Figure 2. We found that the use of the PASS score and flow chart in adult ICU patients to be an effective tool to decide which patients have high risk of persistent AKI, and identify those who have potential for recovery from persistent AKI and will benefit from aggressive therapy, thus helping better prognostication.\n\nStudies in the literature have also shown that RI is an important predictor of AKI and can even be used as a preoperative screening tool to predict AKI after surgeries.14 Renal doppler and RI measurement can be done as a bedside tool to assess the renal circulation and are also a useful marker of sepsis14; they can also help to differentiate persistent AKI from transient AKI in critically ill ICU patients.15 RI is a non-invasive Doppler-measured parameter, corresponding to intra-renal arterial resistance and central hemodynamic parameters. Estimating increased RI on the first day of admission can help predict AKI in septic shock, and the literature has shown that these patients usually require mechanical ventilation. While some studies have shown higher RI values in AKI stages 2 and 3, this is not the case for patients in AKI stage 1.14,15 A RI value beyond 0.795 predicts possibility of persistent AKI with good sensitivity and specificity.16\n\nIntravascular blood volume is dependent on the hemodynamic status of the patient and correlates with IVC diameter, in addition to morphological variations within the ECG like amplitude of waves. This phenomenon called “Brody effect”, related to the relationship of left ventricular volume on QRS-wave amplitude, can be identified by an increased amplitude of the QRS-wave due to increased ventricular preload. Thus, R wave variability is a reliable indicator for intravascular volume status variations.17\n\nOur study is limited by being a single-centre study with a relatively smaller sample size. Wider application of our conclusions and predictive tool would require validation in larger multi-center studies.\n\nEthical approval was obtained from the Institutional Ethics Committee, Medical College, Mangaluru (Reg. No. ECR/541//nst/KA/2014/RR-17; Approval number IEC KMC MLR 08-19/327).", "appendix": "Data availability\n\nZenodo: PASS - A SCORING SYSTEM TO EVALUATE PERSISTENT ACUTE KIDNEY INJURY IN CRITICALLY ILL ADULT ICU PATIENTS, https://doi.org/10.5281/zenodo.7879938. 18\n\nThis project contains the following underlying data:\n\n- PASS SCORE- AKI masterchart.xlsx\n\nZenodo: PASS - A SCORING SYSTEM TO EVALUATE PERSISTENT ACUTE KIDNEY INJURY IN CRITICALLY ILL ADULT ICU PATIENTS, https://doi.org/10.5281/zenodo.7879938. 18\n\nThis project contains the following extended data:\n\n- CHARTS AND TABLES (PASS SCORE-AKI).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\nThis study was presented as an Abstract at the 21st Annual Congress of Indian Society of Critical Care Medicine CRITICARE 2021, held online from 24-28th February 2021. The abstract was published in the Indian Journal of Critical Care Medicine, 2021 Feb; 25(Suppl 1): S1–S114. 4. Pass—A Novel Study to Predict Recovery from AKI in Critically Ill Adult ICU Patients (Conference Abstract ID: 55) DOI: 10.5005/jp-journals-10071-23711.4.\n\n\nReferences\n\nCase J, Khan S, Khalid R, et al.: Epidemiology of acute kidney injury in the intensive care unit. Crit. Care Res. Prac. 2013; 2013: 479730. Epub 2013 Mar 21. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBasile DP, Anderson MD, Sutton TA: Pathophysiology of acute kidney injury. Compr. Physiol. 2012 Apr; 2(2): 1303–1353. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nUchino S, Kellum JA, Bellomo R, et al.: Acute renal failure in critically ill patients: a multinational, multicenter study. JAMA. 2005 Aug 17; 294(7): 813–818. PubMed Abstract \| Publisher Full Text\n\nLopes JA, Jorge S: The RIFLE and AKIN classifications for acute kidney injury: a critical and comprehensive review. Clin. Kidney J. 2013 Feb; 6(1): 8–14. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBellomo R, Ronco C, Kellum JA, et al.: Acute renal failure - definition, outcome measures, animal models, fluid therapy and information technology needs: the Second International Consensus Conference of the Acute Dialysis Quality Initiative (ADQI) Group. Crit. Care. 2004 Aug; 8(4): R204–R212. Epub 2004 May 24. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBhatraju PK, Zelnick LR, Katz R, et al.: A Prediction Model for Severe AKI in Critically Ill Adults That Incorporates Clinical and Biomarker Data. Clin. J. Am. Soc. Nephrol. 2019 Apr 5; 14(4): 506–514. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTsigou E, Psallida V, Demponeras C, et al.: Role of New Biomarkers: Functional and Structural Damage. Crit. Care Res. Prac. 2013; 2013: 13. Article ID 361078. Publisher Full Text\n\nTeo SH, Endre ZH: Biomarkers in acute kidney injury (AKI). Best Pract. Res. Clin. Anaesthesiol. 2017 Sep; 31(3): 331–344. PubMed Abstract \| Publisher Full Text\n\nMatsuura R, Iwagami M, Moriya H, et al.: A Simple Scoring Method for Predicting the Low Risk of Persistent Acute Kidney Injury in Critically Ill Adult Patients. Sci. Rep. 2020 Mar 31; 10(1): 5726. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRhodes A, Evans LE, Alhazzani W, et al.: Surviving Sepsis Campaign: International Guidelines for Management of Sepsis and Septic Shock: 2016. Intensive Care Med. 2017 Mar; 43(3): 304–377. Epub 2017 Jan 18. PubMed Abstract \| Publisher Full Text\n\nBone RC, Balk RA, Cerra FB, et al.: Definitions for sepsis and organ failure and guidelines for the use of innovative therapies in sepsis. The ACCP/SCCM Consensus Conference Committee. American College of Chest Physicians/Society of Critical Care Medicine. Chest. 1992 Jun; 101(6): 1644–1655. PubMed Abstract \| Publisher Full Text\n\nKellum JA, Sileanu FE, Bihorac A, et al.: Recovery after Acute Kidney Injury. Am. J. Respir. Crit. Care Med. 2017 Mar 15; 195(6): 784–791. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMatsuura R, Srisawat N, Claure-Del Granado R, et al.: Use of the Renal Angina Index in Determining Acute Kidney Injury. Kidney Int Rep. 2018 Feb 3; 3(3): 677–683. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHaitsma Mulier JLG, Rozemeijer S, Röttgering JG, et al.: Renal resistive index as an early predictor and discriminator of acute kidney injury in critically ill patients; A prospective observational cohort study. PLoS One. 2018 Jun 11; 13(6): e0197967. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBellos I, Pergialiotis V, Kontzoglou K: Renal resistive index as predictor of acute kidney injury after major surgery: A systematic review and meta-analysis. J. Crit. Care. 2019 Apr; 50: 36–43. PubMed Abstract \| Publisher Full Text\n\nDewitte A, Coquin J, Meyssignac B, et al.: Doppler resistive index to reflect regulation of renal vascular tone during sepsis and acute kidney injury. Crit. Care. 2012 Sep 12; 16(5): R165. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGiraud R, Siegenthaler N, Morel DR, et al.: Respiratory change in ECG-wave amplitude is a reliable parameter to estimate intravascular volume status. J. Clin. Monit. Comput. 2013 Apr; 27(2): 107–111. Epub 2012 Nov 2. PubMed Abstract \| Publisher Full Text\n\nPrabhu D, Prabhu SD, Mahabala C, et al.: PASS - A SCORING SYSTEM TO EVALUATE PERSISTENT ACUTE KIDNEY INJURY IN CRITICALLY ILL ADULT ICU PATIENTS. [Data set]. f1000. Zenodo. 2023. Publisher Full Text" }	[ { "id": "211850", "date": "24 Oct 2023", "name": "Hernando Gómez", "expertise": [ "Reviewer Expertise Sepsis", "AKI", "metabolic reprogramming", "organ dysfucntion" ], "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\nTitle: PASS: A scoring system to evaluate persistent kidney injury in critically ill ICU adult patients\nSummary: Prabhu et al. present a prospective study in 63 patients with the objective to predict the course of sepsis induced AKI using easily available parameters and variables. The authors used serum creatinine (SCr), base excess (BE), Plethysmographic Variability Index (PVI), Caval Index, R wave variability index (RVI), mean arterial pressure (MAP) and renal resistivity index (RI) using renal doppler and need for inotropes were assessed on admission, 24 and 72h. They report that 34 patients recovered form AKI. Using multiple logistic regression, they determined thresholds and weights to compound the PASS score, ultimately composed of SCr, RVI and RI, achieving an AUC of 0.85, with sensitivity of 79.4%, specificity 72.4% for a threshold score of > 7.8 to predict recovery. The authors conclude that ‘the PASS score can be used to identify salvageable cases of sepsis-AKI, guiding fluid resuscitation and aiding early referral from rural to tertiary care centers for better management.’\nGeneral comments: The manuscript is well written, and is focused on an important topic for the field. However, the enthusiasm is decreased due to significant methodological pitfalls. Specific examples and comments are detailed below.\n\nMajor comments:\nThe most important limitation of this study is the small sample size and the lack of validation of the PASS score. It is problematic to have less than 10 events per variable (EPV) when running this type of logistic regressions, as this can result in overfitting (type I error, PMID: 8970487). In the absence of a larger sample size and additional validation in an independent data set, it is difficult to consider the internal and external validity of the score.\n\nBased on No. 1, it is difficult to accept the conclusion proposed by the authors.\n\nBased on the selection criteria, the PASS score may be applicable only to sepsis associated AKI, but not to other forms of AKI? Also, it is unclear what the timing of AKI diagnosis was in relation to sepsis, which is an important component of the definition of SA-AKI (PMID: 36823168)\n\nThe description of hemodynamic stabilization used a MAP of 60 mmHg instead of a MAP of 65 mmHg as recommended. Can the authors expand on the justification for the selection of this parameter?\n\nThe definition of volume responsiveness in the literature is not dependent on achieving a goal MAP or SBP, but rather on whether a bolus of fluid will increase cardiac output (or accepted surrogates) by at least 10%. The authors hereby use a different definition of volume responsiveness. The authors may consider modifying the terminology to align better with current definitions of volume responsiveness.\n\nHow did the authors define persistent AKI? The authors state they used SCr or oliguria to define persistent AKI. However, there is no definition of oliguria. Did the authors use KDIGO criteria?\n\nWas any stage AKI considered as persistent AKI if lasting > 72h?\n\nHow did the authors define transient AKI?\n\nHow did authors determine the presence of AKI? Was KDIGO staging used to defined AKI, and were both components (SCr and UO) used?\n\nPlease specify what were the covariates use to adjust the logistic regression model.\n\nThe description of the cohort is very limited, with only comporbidities shown including HTN and DM.\nMinor comments\nPlease include measures of dispersion of the data in the form of standard deviation, IQR, etc.\n\nPage 7. IVC diameter is not a reflection of intravascular volume. Rather, a specific threshold of static IVC diameter correlates with being above or below a certain CVP. Please revise this comment.\n\nThere is no conclusion in the manuscript. Please consider adding 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? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [ { "c_id": "10716", "date": "12 Feb 2024", "name": "Dattatray Prabhu", "role": "Author Response", "response": "Dear Sir, I would like to thank you for taking the time to review this article. This is a pragmatic trial as mentioned in the article , we accept its a small sample size. Certain parameters among others had strong co-relation with AKI recovery. These parameters like R wave variability, Renal Resistive Index and initial S.Cr levels had a strong statistical significance to AKI recovery,so the conclusion was made. This needs a follow up study using larger study population for external validation. Sepsis accounts for 50-70% of cases in our ICU. Sepsis-associated AKI are usually clinical or subclinical at admission. This study includes sepsis related aki patients. During later part of ICU stay if AKI was found to be associated with non-sepsis-related causes such cases were excluded. The term SA-AKI operationally unifies the presence of AKI (according to clinical, biochemical and functional criteria) in the context of sepsis as a specific disease phenotype that is characterized by a specific trajectory and outcome. The target MAP for resuscitation was 65mmhg as per guideline. Correction was made in the manuscript accordingly. This study is mainly looking at non-invasive parameters to assess AKI recovery, hence we did not consider invasive monitors to look at cardiac output. Recovery from AKI was attributed to decreasing creatine and normalizing urine output. KIDGO criteria were used to categorize AKI after admission and recovery 24 hours after admission and beyond. Recovery of renal parameters and/or urine output beyond 72 hours were also considered as AKI recovery. There are studies to show a strong correlation between IVC collapsibility and CVP. In this study, we have not considered CVP as it needs an invasive line and as previously mentioned this study is mainly focused on noninvasive parameters." } ] } ]	1	https://f1000research.com/articles/12-902
https://f1000research.com/articles/13-493/v1	17 May 24	{ "type": "Research Article", "title": "The effects of multifactorial pharmacist-led intervention protocol on medication optimisation and adherence among patients with type 2 diabetes: A randomised control trial", "authors": [ "Marwan El-Deyarbi", "Luai Ahmed", "Jeffrey King", "Syed Abubackar", "Ahmed Al Juboori", "Nirmin A. Mansour", "Salahdein Aburuz", "Marwan El-Deyarbi", "Luai Ahmed", "Jeffrey King", "Syed Abubackar", "Ahmed Al Juboori", "Nirmin A. Mansour" ], "abstract": "Background Patient-related factors and limited medication adherence in patients with chronic diseases, are associated with poor clinical outcomes, long-term complications, and increased overall disease costs. Many methods have been tested with mixed results, and innovative approaches are needed to encourage patients to adhere to their prescribed drug regimens.\n\nMethods This randomised controlled trial examined a new multifactorial pharmacist-led intervention protocol (MPIP), including a medication therapy management (MTM) program with face-to-face counselling, patient-specific medication booklets, and a mobile application, from July 2021 to September 2022 in the Oud Al Touba diagnostic and screening ambulatory centre in 192 patients with type 2 diabetes in the United Arab Emirates. Medication adherence was assessed using the fixed medication possession ratio of medication refills and the medication adherence questionnaire.\n\nResults At 12 months follow-up, participants in the MPIP showed significant improvement in overall medication adherence with total (composite) medication possession ratio (MPRt) of mean (±SD) 0.95 (±0.09) compared to 0.92 (± 0.09) in the control group with mean difference of 0.03 (95%, CI 0.01–0.06), P =0.02. In addition, improvement trend was evident in the MPIP group for all medication regimens with P value <0.01. Comparable results were noticeable in adherence questionnaire scores at the end of the study, with 66 participants in the intervention group scored zero on the questionnaire, suggesting high adherence to medication compared to the control group (48 participants only). The MTM program performed 41 clinical interventions on drug-related problems, compared to six interventions in the control group, and the use of mobile application and medication booklet have increased to 45.7% compared to 21.4% before study exit.\n\nConclusions The pharmacy intervention protocol effectively improved medication adherence and optimised medication regimens in diabetic patients with chronic medication regimens in an ambulatory healthcare centre.", "keywords": [ "Diabetes", "medication adherence", "pharmacist-led", "fixed medication possession ratio", "medication therapy management", "mobile application" ], "content": "1. Introduction\n\nIn 2013, the United Arab Emirates (UAE) had the 10th highest prevalence of diabetes in the world, with approximately 10% of its population diagnosed with diabetes, which is estimated to reach 23.1% by 2030.1 This high prevalence is accompanied by high rates of other risk factors for diabetic kidney disease,2 and cardiovascular disease, including obesity in 35%, dyslipidaemia in 44%, and hypertension in 23.1% of the population in Abu Dhabi.3\n\nSeveral studies showed that suboptimal duration of medication use (non-persistence with medication) in chronic disease such as type 2 diabetes is attributed to poor clinical outcomes, including higher glycated haemoglobin (HbA1c) and diabetic complications including diabetic nephropathy and mortality.4,5\n\nMoreover, the estimated annual cost savings for individuals achieving optimal medication adherence with medication possession ratio (MPR) ≥ 0.6 from less than 0.6, is around 661 million dollars in the United States of America and may reach 1.16 billion dollars if we succeed in approaching MPR = 1 for medication non-adherence patients. This cost saving can be explained by higher inpatient and emergency room visit costs which would exceed any savings from less intensive ambulatory visits and outpatient medication costs.6\n\nIn addition, studies have shown that patient-related factors such as age, personal beliefs or educational status, are the most influential factors in medication adherence rather than medication cost or insurance-related payment.7 Moreover, medication adherence information is inaccurately represented in patients’ electronic medical records.8 These elements raise the need for innovative patient-centred tools to enhance proper medication adherence, documentation, and tracking.9\n\nMoreover, medication-related factors such as medication class and side effects are major contributors to non-adherence.10 Medication side effects or drug-drug interactions may lead to safety or tolerability issues which negatively affect the overall patient’s clinical outcomes and quality of care. Most of these factors have a long-term effect on diabetes and hard endpoints such as cardiovascular events and all-cause mortality.11\n\nEvidence from a systematic review and meta-analysis showed that individual pharmacist-led interventions, such as face-to-face interventions, are beneficial in improving medication adherence and patient outcomes.12 Another meta-analysis showed that pharmacist interventions, whether carried out independently or in coordination with other medical specialists, can improve medication adherence and patients’ clinical outcomes such as blood pressure control.13\n\nThe use of technology such as mobile application and telemedicine has proven to be beneficial for chronic disease management.14 Studies have shown the effectiveness of the telemedicine system approach on overall healthcare quality and that it can be complementary to conventional face-to-face monitoring of diabetic patients. This can be a useful tool for the treatment of complex patients who require more frequent visits to achieve tighter glycaemic control or have difficulty accessing the healthcare system15; however, few studies have investigated the correlation between medication counselling through telemedicine and patient adherence and the long-term effects on diabetes or related complications especially in Middle East.\n\nAlthough the Emirates of Abu Dhabi holds the largest integrated hospital and ambulatory pharmacy network in the UAE and a patient’s electronic medical record (Cerner®) is linked to private pharmacies, there is no evidence-based process for measuring patients’ medication adherence based on medication refill dates or its effect on patients’ outcomes.\n\nGiven the diversity of pharmacist-led interventions as a strategy to improve medication adherence and clinical outcomes, this study was conducted to address the effect of a new multifactorial pharmacist-led intervention protocol (MPIP) which consists of two interrelated strategies: first, thorough medication counselling and reassurance to enhance adherence to prescribed medication, and second, a comprehensive medication therapy management (MTM) with a clinical pharmacist on medication management and adherence in the diabetic population in the UAE.\n\n\n2. Aims and objectives\n\nThis study aimed to assess the impact of pharmacist-led multifactorial interventions on medication management optimisation and patient adherence to medications.\n\nThe primary objectives were as follows: 1) to evaluate the impact of the new protocol (MPIP) on overall medication adherence measured by the total medication possession ratio (MPRt) for all regimens; 2) to measure the difference in self-reported adherence questionnaire from baseline and study exit in both study groups; and 3) to assess the number and type of clinical interventions in the MTM program.\n\nThe secondary objectives were as follows: 1) compare the effect of MPIP on regimen-specific MPRs in the intervention group for antihyperglycaemic, antihypertensive, and antihyperlipidaemic regimens at the end of the study with the control group; 2) measure the improvement in regimen non-persistence between the intervention and control groups; and 3) analyse the changes in usage patterns of the mobile application and patient medication booklet and correlate it with patient adherence.\n\n\n3. Methods\n\nThis was a randomised control trial of 12 months duration, among type 2 diabetic patients recruited from the endocrinology and chronic disease (CDC) outpatient clinics at Oud Al Touba diagnostic and screening centre, Al Ain, UAE.\n\nThis article presents one outcome of the original trial that was registered at the US National Institutes of Health (name of registry: ClinicalTrials.gov, registration number: NCT04942119, registration date: 05/21/2021, and URL of trial in the registry database: https://clinicaltrials.gov/study/NCT04942119)), and the original trial was approved by the Abu Dhabi Health Services Company (SEHA) Research Oversight and Ethics Committee (SEHA REC) in the United Arab Emirates on April, 2021 (approval number: SEHA-IRB-021) Supplementary File 1 found as Extended data46). Written informed consent was obtained from all participants before study recruitment and they received a copy of it along with the study information sheet (Supplementary File 2, 3 found as Extended data46). This study follows the CONSORT checklist and flow diagram.47\n\nWe included male and female patients between 30 and 65 years of age, previously diagnosed with type 2 diabetes, with unchanged diabetic medication for 4 months prior to study enrollment, and with an estimated glomerular filtration rate (eGFR) above 30 ml/minute/1.73 m2 of body surface area. Participants were excluded if they were refilling their medication from other pharmacies not integrated with Cerner electronic health record, or through a home care service, or had physiological barriers as assessed by the clinician that may affect patient interviews and filling the adherence questionnaire.\n\nRandomisation was performed using a computer-generated random number in Microsoft Excel to generate allocation sequences for each participant in the intervention and control groups, with allocation concealment by sequential numbering, representing the participant’s turn in joining the study by the principal investigator. Participants in the intervention group were identified electronically one week before the next refill schedule or follow-up visit.\n\nBetween July and September 2021, 316 patients visiting the endocrinology and CDC clinics were screened for eligibility, and 281 eligible patients for inclusion were invited to participate in the study. Only 239 patients were agreed to sign the consent form and randomised to either the pharmacy intervention group (120 patients) or the control group (119 patients).\n\nIn the intervention group, 15 participants were excluded at first visit either because of their refusal to participate in the MTM program, or not having baseline laboratory test results or it was not done when ordered at recruitment. At the end of the study, 11 patients from the intervention group and 21 from the control group had not fulfilled the study protocol during follow-up visits or did not have exit laboratory tests and were excluded.\n\nAt the conclusion of the study after 12 months follow-up, 94 patients in the intervention group and 98 patients in the control group were included in the analysis (Figure 1).\n\nMRN: Patient medical record number; MPIP: Pharmacy intervention protocol; MTM: Medication therapy management.\n\nAt baseline, participants in both groups received medication counselling by a clinical pharmacist as part of the usual care provided in the clinic, and baseline assessment of the participants’ adherence to medication was performed using a validated medication adherence questionnaire (Supplementary File 4, Extended data46).16 Participants were instructed to report any possible side effects or factors that may affect their adherence to medication, and to reveal any modifications in lifestyle activities or eating habits during the study.\n\nParticipants in the intervention group joined the MPIP program at their first visit and received two multifactorial interventions: medication adherence counselling and medication therapy management, as detailed below.\n\n1) Medication adherence counselling\n\nEach participant in the intervention group received a 15- to 30-min counselling session at the initial visit and each scheduled follow-up visit which occurred every 3 months. During these sessions, the pharmacist assessed medication adherence with the adherence questionnaire and counselled the patients on the importance of medication adherence on clinical outcomes. The barriers to medication adherence were identified, discussed with the patient, and resolved as much as possible. Finally, the patient was provided with two or three months of medication supply, and the medication refill date was documented for medication adherence calculation using the medication possession ratio (MPR).17,18\n\nAfter each visit, each participant in the intervention group received a 15-min follow-up phone interview within two weeks for adherence reinforcement and to address any non-compliance issues or medication side effects. Moreover, they were scheduled for their next medication refill and follow-up visits in the clinic appointment system. Appointments were scheduled at months 3, 6, and 12 from the initial visit according to the patient’s preferred date, and they received a reminder phone call three days prior to the next visit by the clinic call centre.\n\nMedication adherence was evaluated using two techniques during the follow-up period: calculating the medication adherence possession ratio and the medication adherence questionnaire scores.\n\nA. Medication adherence possession formulas\n\nIn this study, we used three formulas to calculate medication adherence from patients’ medication refills recorded in Cerner:\n\ni- Total fixed medication possession ratio (MPRt)\n\nA fixed medication possession ratio (MPR) formula was used to measure total adherence (composite) to all medications MPR (MPRt).19,20 The MPRt was calculated for three chronic regimens including antihyperglycaemic regimen refills with any of the antihypertensive or antihyperlipidaemic regimens if the patient had any or all of them based on the medication prescription refill intervals.\n\nFor the total MPRt, no regimen-specific MPRs was measured. It was calculated by summing the days’ supply of medication per prescription, then dividing by the number of days of patient follow-up, using a fixed follow-up period of 365 days (12 months) as a constant denominator, adjusted to hospital stay if participant admitted during the follow-up period (Supplementary File 5, Extended data46).\n\nii- Regimen-specific medication possession ratio (MPRs)\n\nRegimen-specific MPRs were calculated for all three regimens (antihyperglycaemic, antihypertensive, and antihyperlipidaemic), whether any or all were contained in the patient’s medication profile.21,22\n\nThe denominator used for MPRs also covers the follow-up period of 12 months but was calculated based on the last refill date for a specific medication regimen (for any medication class) minus the first refill date for any medication in the regimen, even if this medication was in a different class from the medication used in the last refill. In addition, medications within the same regimen were considered interchangeable (even if they belonged to different medication classes).\n\nOf note, for both types of MPR (MPRt and regimen-specific MPRs), if the patient had refilled medication prior to the date of joining the study, MPR was calculated from the date of signing the consent, excluding the supply from the last prescription or medication refill and was capped at 1, and medication adherence (either MPRt or MPRs) was calculated after 12 months of follow-up.17\n\nThe standard adherence threshold of 0.80 MPR was used as lower bound for mediation adherence,20 with MPR = 1 indicating perfect adherence, MPR < 0.80 indicating patient non-adherence, and MPR= 0 indicating no adherence. The patients’ medication refills for each medication class were recorded by Cerner (which includes records from both private and governmental pharmacies) at each follow-up visit.\n\niii- Regimen non-persistence possession ratio (RNP)\n\nIn addition to the MPR calculation, we estimated the regimen non-persistence (RNP) or days without medication for each regimen (diabetic, hypertensive, and antihyperlipidaemic regimens) the patient had in the study,23 calculated as the total number of days the patient did not receive one or more medications for any of the patient’s chronic regimen divided by the total follow-up days.\n\nB. Medication adherence questionnaire\n\nA validated medication adherence questionnaire translated into Arabic, showing sufficient reliability with adequate internal consistency, was used initially to measure medication adherence at baseline for all study participants, and subsequently used at each follow-up visit in the intervention group and again at the study exit (Supplementary File 4,46).16\n\nThe questionnaire contained four medication adherence questions from the validated Arabic version of the tool: 1) “Do you ever forget to take your medicine?” and 2) “Are you careless at times about taking your medicine?”, 3) “When you feel better do you sometimes stop taking your medicine??”, 4) “Sometimes if you feel worse when you take the medicine, do you stop taking it?”.\n\nThe total score of the medication adherence questionnaire included the first four questions with scores ranging from 0 and 4, with “Yes” having score = 1 and “No” = 0. Score improvements correspond to increased levels of adherence with higher scores implying greater levels of adherence. Patient adherence scores were classified as low adherence (score from 3 to 4), moderate adherence (score from 1 to 2), and high adherence (score = 0, with no answers with yes).24\n\n2) Meditation therapy management (MTM) program\n\nAs a new component of the MPIP, the MTM program was made available to the clinic’s ambulatory service for the first time, and the intervention group received the following interventions as part of the program:\n\nA. Medication counselling and reconciliation\n\nMTM was effectuated during the counselling session for 15–30 min at the time of dispensing medication. Each patient interview implemented the five criteria for MTM, including medication review to optimise patient treatment as per the latest treatment guidelines, assessment of the possibility of deprescribing, evaluation of any prescribed non-formulary drugs, patient counselling, and provision of printed medication educational materials, particularly for new, high alert, and narrow therapeutic index medications from an evidence-based drug reference to ensure the safe and proper use of these drugs (Lexicomp Online).\n\nMoreover, the counselling session included counselling on potential drug-drug or drug-food interactions and the proper use of any device or OTC medication the patient was using. Any detailed disease information or drug modifications required were discussed and resolved by the treating physician.\n\nMedication reconciliation and chart review was carried out through the Cerner local network, integrated with all governmental hospitals, ambulatory clinics, and private institutes in the Emirates of Abu Dhabi in the UAE.\n\nThe number and type of pharmacy clinical interventions, in addition to antihyperglycaemic deprescribing, were analysed and compared between the two groups at the end of the follow-up period.\n\nB. Patient medication booklet\n\nA pocket-sized patient-specific medication booklet was provided to each participant in the intervention group (Supplementary File 646). This initiative in the MPIP aims to promote medication adherence in elderly patients and those with low digital skills. Moreover, the booklet helps to track OTC drugs or herbal medications bought from community pharmacies and enable patients as well as community pharmacists to fill in the name of the drug and the dose by hand, which are then manually added to the patient’s medical record in Cerner at the next MPIP visit.\n\nDuring the counselling session, the counselling pharmacist attached the prescribed medication labels to the booklet, which ensured that the booklet was filled with an updated list of all prescribed medications, medication doses, allergies, next scheduled refill, and any OTC drugs the patient was currently taking.\n\nPatients were advised to bring the medication booklet to each follow-up visit to update the next refill schedule or any changes in their profiles. Moreover, it has been used as a reference during Cerner downtime or when patients’ medical records from other private facilities were not available.\n\nC. SEHA mobile application\n\nDespite the fact that the SEHA mobile application25 is accessible to all patients for download and usage, the patients often do not know how to use its features. As a new initiative in the MTM program, participants in the intervention group received face-to-face educational sessions for 5 minutes on the use of the SEHA mobile application, how to read the clinical information and laboratory results, extract their medication profile, add OTC medications to their medical record, and read notifications for medication approval from insurance as well as for subsequent medication refills.\n\nThe SEHA mobile application provides real-time individualised feedback, including patient access to Cerner, laboratory test results, radiology reports, medications, allergies, immunisation records, and health maintenance history for patient visits occurring in SEHA facilities. Moreover, it enables patients to request or reschedule appointments or reschedule them, and search for a healthcare facility. The application sends a short message service (SMS) to the registered mobile number for appointments, with reminder notifications to remain keep the patient informed about future or follow-up appointments.\n\nAt the end of the study, we used the SEHA mobile and booklet use questionnaire to record the number of participants in each group using the application on their mobile device and the extent of application utilisation (Supplementary File 746). The results were correlated with medication adherence to measure the effect of online technology on medication management.\n\nThe main measured outcomes in the study were: 1) change in MPRt for all regimens, 2) difference in self-reported adherence questionnaire scores between the intervention and control groups, and 3) number and type of clinical interventions between the two groups.\n\nIn addition, as secondary outcomes, we examined 1) the difference in MPRs and RNP for antihyperglycaemic, antihypertensive, and antihyperlipidaemic regimens between the two groups, and 2) the change in mobile application and patient medication booklet usage, and whether there were associations with increased patient adherence in both study groups.\n\nWe calculated MPRt for the first 50 participants; baseline MPRt was 0.93 ± 0.09 (mean ± SD). Using the Giga sample size online calculator,26 we determined that a target of 82 participants per group would provide a power of 80% with alpha level of 5%, for a minimum detectable effect of 0.035 between both groups. A total sample size of 180 was calculated, assuming dropout rate of 10% in both groups.\n\nDemographic and clinical data presented as categorical variables were analysed using the chi-square test, and the student’s t-test was used for continuous variables. T-test was also used to estimate the mean differences and confidence intervals for the MPR. Moreover, Cox proportional hazard analysis were utilised to compare regimen non-persistence in antihyperglycaemic, antihypertensive, and antihyperlipidaemic medications in the intervention group compared with the control group.\n\nP values were considered significant at 0.05, with confidence intervals of 95%. Data were analysed blindly by group allocation using the IBM SPSS Statistics (RRID:SCR_019096), version 26.27\n\nDue to the lack of a robust evidence to support the threshold of 0.80 for MPR to classify patients with medication adherence and MPR above the threshold as adherent to medication, we calculated regimen-specific MPRs to confirm adherence during the follow-up period, moreover, we calculated the mean difference between the intervention and control groups for MPRs for participants who achieved control in each clinical parameter adjusted to age and sex.\n\n\n4. Results\n\nThe patients’ demographic data characteristics are presented in (Table 1).44 In both groups, the patients’ mean age was approximately 60 years, and 60% of them were female, with a mean body mass index (BMI) of 31. There were no significant differences in clinical baseline characteristics between the treatment groups.\n\nA. Medication adherence possession data\n\nA trend towards overall medication adherence and total (composite) medication possession ratio (MPRt) improvement after applying MPIP in the intervention group was identified from the first follow-up visit after 3 months and the difference between groups persisted at 6, 9 and 12 months. Participants in the MPIP showed significant improvement in MPRt at 9 and 12 months of mean 0.95 ± 0.1 and 0.95 ± 0.09, compared to 0.93 ± 0.09 and 0.92 ± 0.09 in the control group respectively, with mean difference of 0.03 (95%, CI -0.01–0.05), P = 0.04, and 0.03 (95%, CI 0.01–0.06), P = 0.02, respectively (Table 2).\n\n* Significant P value <0.05;\n\n** Chi-squared test;\n\n£ At study exit;\n\n¥ MPIP (n=86), control (n=94);\n\n# MPIP (n=91), control (n=96); CL: confidence interval; MPRt: Total medication possession ratio; MPRs: Regimen-specific medication possession ratio, see data 1 in Underlying data.44\n\nAt the 12 months endpoint, we calculated the MPR-regimen specific (MPRs) for each chronic regimen, including antihyperglycaemic, antihypertensive, and antihyperlipidaemic medications, and we found an evident overall improvement in the MPIP group for all medication regimens (Figure 2).\n\nRegimen specific medication possession ratio (MPRs) at study exit.\n\nIn the intervention group, the mean ± SD for MPRs was 0.95 ± 0.09 for antihyperglycaemic, 0.95 ± 0.1 for antihypertensive, and 0.96 ± 0.09 for the antihyperlipidaemic medications, compared to 0.92 ± 0.09, 0.92 ± 0.08, and 0.93 ± 0.08 in the control group respectively, with significant mean difference (95% CI) in the three regimes of 0.03 (0.01–0.06), 0.04 (0.01–0.06), and 0.04 (0.01–0.06), respectively indicating the effectiveness of the intervention protocol (Table 2).\n\nMoreover, compared to patients receiving MPIP, patients in the control group had more regimen non-persistence (RNP) or total number of days without medications between refills during the observation period. Participants in the intervention group had a mean (± SD) RNP in the diabetic regimen of 0.13 (± 0.16) compared to 0.22 (± 0.23) in the control group, with significant mean difference of -0.09 (95%, CI (-0.19–0.01), P = 0.04 (Table 2). Coherent results were observed in the RNP of antihypertensive as well as the antihyperlipidaemic regimen; however, no statistically significant differences were detected in the mean differences or P-values or cumulative hazard function among the two regimens (Figure 3A, B and C).\n\nMoreover, the control group was less likely to adhere to medication regimens compared to the intervention group at the end of the follow-up period, with a higher percentage of patients with MPRt less than 0.8 compared to patients in the MPIP group. For instance, patients in the MPIP having MPRt < 0.8 and MPRs < 0.8 for the antihyperglycaemic regimen were 8 patients (8.5%) compared with 15 patients (15.9%) in the control group, despite the fact that none were statistically significant (Table 2).\n\nComparable results were shown in the antihypertensive as well as the antihyperlipidaemic regimens, with MPRs < 0.8 in the intervention group = 8 patients (9.3%) and 9 patients (9.9%) compared to 13 patients (13.8%) and 12 patients (12.5%) in the control group respectively.\n\nB. Medication adherence questionnaire\n\nA tendency towards improved adherence questionnaire scores was noticeable at the end of the study, with significant improvement (P < 0.01) in the overall mean adherence score to 0.63 (± 1.1) compared to 1.1 ± 1.2 in the intervention group before commencing the study, indicating higher adherence to the prescribed medication. Moreover, at study exit, 66 participants (70.2%) in the intervention group scored zero on the questionnaire, suggesting high adherence to medication compared 42 participants (44.6%) at baseline, and the result was significant (P < 0.01) compared to the control group (70.2% vs 48.9% in the intervention and control group, respectively) at study exit after 12 months follow-up (Table 3).\n\n* Significant P value <0.05;\n\n** P-Value: comparing intervention vs control groups at study exit;\n\n£ Yes score = 0;\n\n¥ Yes score from 1 to 2;\n\n# Yes score from 3 to 4.\n\nA. MTM interventions\n\nPharmacists in the MPIP identified 41 drug-related problems (DRIs), implementing 36 accepted clinical interventions to optimise the dose, duration, frequency, or therapeutic substitution. In contrast, only six clinical interventions in the control group were documented, of which 5 were accepted by the prescribing physician (Table 4). Pharmacists spent an average of 24 minutes in each counselling session, with an average of 9 minutes per intervention per patient, compared to an average of 8 minutes in counselling sessions and 6 minutes per intervention in the control group.\n\nAt the end of the follow-up period, 26 patients in the MTM group had their medication optimised compared to only 4 in the control group; for instance, medication duration to correlate medication refill or newly added medication with the next physician following visit optimised in 11 patients, drug regimen combination and formulation optimised in 6 patients, and 9 patients had time of medication administration or frequency optimised (compared to 2, 1, and 1 in the control group, respectively).\n\nMoreover, during patient counselling and reconciliation, two dose-related issues that were not renally adjusted according to the patient’s eGFR were identified in the intervention group. Besides, five patients received medication substitution in the same or to a new therapeutic class and three patients discontinued one medication due to duplication or supratherapeutic, all from the diabetic medication regimen, to improve clinical outcomes, however, none of these results were significant (Table 4).\n\nAt study exit, the total number of medications in the MTM group was reduced with class change in the three therapeutic classes, compared to the number of medications at study enrolment, with 249 antihyperglycaemic medications, 137 antihypertensive medications, and 119 antihyperlipidaemic medications compared with 253, 142, and 121 at baseline, respectively, with comparable medication numbers in the control group for the three classes prior to and after the study (Table 5).\n\n¥ MPIP (n=86), control (n=94);\n\n# MPIP (n=91), control (n=95); GLP-1, glucagon-like peptide 1agonists; DPP-4, dipeptidyl peptidase 4; Pcsk9, proprotein convertase subtilisin/kexin type 9; SGLT2, sodium-glucose co-transporter-2 inhibitor; TZD, thiazolidinedione.\n\nIn antihyperglycaemic medication, the MTM group was more commonly treated with insulin (6.8% vs. 4.6%), metformin (33.7% vs. 29.6%) and less frequently with dipeptidyl peptidase 4 (DPP-4) inhibitors (7.6% vs. 13.2%) compared to the control group, which is more closely aligned with the medication recommendations of the American Diabetes Association guidelines. Usage of SGLT-2 inhibitors and GLP-1 receptor agonists were similar between the two groups (Table 5).\n\nPatients at risk of hypoglycaemia or adverse effects of antihyperglycaemic drugs were effectively identified using the MTM program, and the clinical pharmacist started deprescribing antihyperglycaemic drugs in collaboration with the treating physician. This included deprescribing four antihyperglycaemic medications in the sulfonylurea (32 vs. 28 at study entry and exit, respectively) class in four patients and switching them to medications with a lower risk of hypoglycaemia (two patients received GLP-1 agonists and two received SGLT2 inhibitors). Moreover, one patient in the MTM group was on mixed insulin and was switched to aspart and glargine insulin to improve nocturnal hypoglycaemia; however, the number of insulin medications increased from 16 at study entry to 17 at the end of the follow-up period. However, both groups had similar drug profiles in the antihypertensive and antihyperlipidaemic therapeutic classes at study exit, although the patients in the MTM group treated more frequently with Pcsk9 inhibitors compared to those in the control group (10.9% vs. 7.9%) (Table 5).\n\nB. SEHA mobile application and patient medication booklet usage\n\nThe number of patients in the intervention group started using the mobile application for medications and clinic appointments have increased from 41.5% to 45.7% in six months compared to 21.4% vs 19.3% in the control group before exiting the study (P < 0.01). Moreover, 27.6% of the patients in the intervention group started using the medication booklet provided at study recruitment and were using it during their 12 months follow-up visits compared to 1% (P < 0.01) in the control group, where the booklet was provided by a pharmacist outside the research team (Table 6).\n\n* Significant P value <0.05.\n\n\n5. Discussion\n\nAs far as we are aware, this is the first study measuring the effect of pharmacist-led interventions with multifactorial components in three chronic disease regimens together, as systematic reviews demonstrated that multifactorial strategies are necessary to successfully increase adherence.28,29\n\nBecause medication adherence is a complex process, we used both objective, through medication possession ratio, regimen non-persistence, and adherence ratios, and subjective measurements, through patient questionnaires, of patient adherence to medication. In this study, we calculated the fixed medication possession ratio (MPR) to measure adherence to dispensed medication as a valid measure of medication adherence that accounts for medication discontinuation, hospital admission, and dose change without interfering with patient behaviour.30,31\n\nTo make adherence measurements more reliable in the study, we calculated three dimensions of medication adherence: total MPR (MPRt) for all regimens, MPR specific for each regimen of interest (MPRs), and medication as well as regimen non-persistence (RNP).18 At the end of the 12 month follow-up period, the mean MPRt for all regimens in the intervention group was 0.95, compared to 0.92 in the control group, with a significant upward trend in the MPIP group from the third follow-visit (9 months), demonstrating the effectiveness of the intervention protocol with motivational interviewing and follow-up telephone counselling to emphasise medication adherence, which showed a sustained effect in many studies.32,33\n\nAs a reliable method in measuring medication adherence, MPRs and RNP were used to validate medication adherence measurements.18 The mean MPRs were 0.95 for both the diabetic and hypertension regimens in intervention group, compared to 0.92 in the control group, and in the intervention group the mean RNP for the antihyperglycaemic medication differ greatly from the control group (0.13 vs. 0.22), with significant mean difference between both groups (-0.09, P = 0.04), showing the effectiveness of the multifactorial pharmacy-led intervention protocol in diabetic patients.\n\nComparable results found in the antihypertensive MPRs and RNP scores, however, for the antihyperlipidaemic regimen the MPRs indicated that patients are more adherent to the antihyperlipidaemic drugs (in the MPIP and control groups) compared to other regimens in the study (0.96 and 0.93, respectively), with fewer regimen non-presistance (0.12 and 0.15, respectively). The rationale behind the greater adherence to antihyperlipidaemic drugs in the intervention group in addition to the MPIP was that 13 patients were on PCSK9 inhibitor injections at the end of the study period and 9 in the control group; these patients had scheduled appointments in the clinic for injection administration, and the approval of 6 months’ supply by the insurance company was granted after medication initiation.\n\nMoreover, in both groups, participants were less non-adherent (MPRs < 0.8) to the antihyperlipidaemic medication (7.7% and 12.5% in the intervention and control group, respectively) compared to the antihyperglycaemic and antihypertensive medications, and the plausible reason for this was the 30 tablets packing of most antihyperlipidaemic medication compared to 28 or 56 box packing of many antihyperglycaemic and antihypertensive medications. Consequently, we modified the pharmacy-led intervention protocol to set refill dates to 28, 56, or 84, regardless of medication packing, to improve adherence to all medications in future refills in the clinic\n\nThe fixed medication possession ratio calculations were consistent with the adherence questionnaire scores as a subjective measurement of adherence: 65 (69.1%) patients reported high adherence, 18 (14.1%) patients reported moderate adherence, and 11 (11.7%) patients showed low adherence to medication, compared to 42 (44.6%), 35 (37.2%), and 17 (18.1%) respectively, at study entry. On the contrary, patients in the control group achieved lower scores in the adherence questionnaire, with 48 (48.9%) highly adherent patients having zero score, 35 (35.7%) moderate adherent patients from 1 to 2, and 15 (15.3%) low adherent patients scored from 3 to 4.\n\nThe adherence questionnaire outcomes suggested that the pharmacy-led intervention protocol was successful in improving medication adherence, indicating that the MPR is a reliable and accurate method for adherence measurement. Several studies have demonstrated that self-reported questionnaires can be a reliable strategy to measure non-adherence in patients with depression,34,35 despite the fact that some studies found that few patients who scored adherent in such self-reported questionnaires were non-adherent patients.36 Moreover, the MPR may overestimate adherence as it assumes that the patient is taking the medication regularly once it is in possession. In contrast, the MPR may lead to underestimation when medication is taken from a community pharmacy.36 Accordingly, we used the patient’s self-reported adherence and correlated it with MPR to minimise “false-adherent” patients who have regular medication supply but fail to take them, and “false-nonadherent” patients who receive their medication from other pharmacies not linked to Cerner.\n\nThe integration of a new multifactorial pharmacist-led intervention protocol (MPIP) with a medication therapy management (MTM) program improved medication adherence significantly and consistently across all treatment regimens for patients with chronic diseases, particularly in ambulatory care pharmacies, and these results corroborate the evidence from other systematic reviews and meta-analysis.12,13\n\nPharmacists in the MPIP spare more time in the counselling sessions (24 minutes per session compared and to 8 minutes in the control group), and had more time for MTM in a systematic approach utilizing Cerner for medication reconciliation, Lexi-Comp program for drug reference, patient education as well as inspection drug-drug and drug-food interactions, and scheduling patients for either phone call or visit follow-up revealed 41 DRIs (36 implemented), including two drug safety issues with unadjusted dose with low eGFR (compared to 6 in the control group), despite the insignificance between the two groups, MPIP shows the effectiveness of integrating pharmacists in patients’ medication management. Studies showed that motivational interviewing, reconciliation, and deprescribing initiatives played a key role in improving medication management, and might help patients better adhere to treatment plans.37,38 Moreover, it had positive outcomes in terms of drug adherence to different therapeutic regimens such as antihyperglycaemic and antihypertensive regimens.39,40\n\nMPIP allocated time in each counseling session to educate and implement two approaches integrated with the MTM program to enhance medication management and adherence outcomes: a mobile application with a patient’s medical record (SEHA mobile application), which has been shown to improve medication adherence and clinical outcomes in several studies,3,41,42 and a medication booklet with the most updated medication used by the patient.\n\nBetween the two groups, we discovered meaningful variations in how frequently patients used the mobile application or their personal medication booklet, with the intervention group using them 45.7% and 27.6% more frequently by the end of the study compared to 21.4% and 1% in the control group, respectively. The increase in mobile application and patient’s medication booklet utilisation was consistent with fewer non-adherent patients with MPR less than 0.8 in the MPIP group compared to the control group (8.5% vs. 15.3%) (Table 6). Thus, as evidenced in other studies,43 the use of mobile applications and medication booklets can improve medication adherence in MTM programs.\n\nThe main limitation of the MPIP is its inherent tendency to overestimate pill intake, as some patients may refill their prescriptions consistently but do not actually adhere to their medication. Moreover, the short study duration of one year with preset follow-up boundaries may underestimate compliance, resulting from occasional fluctuations in medication refills, while such errors in MPR calculation are reduced with longer periods of observation.\n\nIn addition, the mobile application being available to all participants throughout the study and was promoted by SEHA on many occasions could improve the use of the application and adherence in control patients and lead to less significant results. However, patients who underwent MPIP had higher application use and adherence rates than those who did not receive the intervention.\n\nWe did not set clinical outcomes as the primary outcome in this study, and future studies should focus on nonadherent, as well as higher-risk patients with unmet clinical goals, as adherence interventions would be more beneficial with more significant outcomes in such patients. Furthermore, the inclusion of clinical outcomes would allow for a cost-effectiveness analysis of the intervention for therapeutic. Finally, the two pharmacists were not blinded to the groups during data collection and MPR estimation. However, the objectivity of the primary outcomes and blind data analysis resolved this issue.\n\nRegardless of these limitations, this new multifactorial pharmacy-led intervention protocol provided effective continuous monitoring and interactions to enhance patient-centred adherence and integrate readily available patient adherence data from a centralised pharmacy registry (Cerner) with patient therapeutic outcomes, which can be generalized to other ambulatory care centres. Other strengths of the study include the use of a clinical pharmacist and senior pharmacist in patient counselling, and unbiased comparisons using intention-to-treat analyses.\n\n\n6. Conclusion\n\nA package of multifactorial pharmacist-led interventions, including a medication therapy management program with motivational counselling, instruction on use of a preexisting mobile application, and patient medication booklet, modelled in a standard workflow protocol in an ambulatory pharmacy, was effective in persistently improving adherence to chronic medication, and optimised medication regimens in diabetic patients in an ambulatory healthcare centre. Prior to implementation, larger sample sizes, longer observation periods, and cost-effectiveness analyses are required to evaluate the effectiveness of multifactorial interventions on patients’ clinical outcomes in ambulatory health services.\n\n\nEthics and consent\n\nThis article presents one outcome of the original trial that was registered at the US National Institutes of Health (ClinicalTrials.gov protocol registration: NCT04942119), and the original trial was approved by the Abu Dhabi Health Services Company (SEHA) Research Oversight and Ethics Committee (SEHA REC) in the United Arab Emirates on April, 2021 (approval number: SEHA-IRB-021). Written informed consent was obtained from all participants before study recruitment and they received a copy of it along with the study information sheet (Supplementary File 1, 2, and 3).\n\nParticipants had the right to withdraw consent and stop or postpone the assessment interviews or adherence questionnaires if he/she becomes upset at any time during the study period without any penalty or limitation in the usual clinical services provided. Although participants were not compensated for their extra time spent during interviews or for any inconvenience that may result from taking extra medications or blood tests every 3 months, they had prioritised access to physician’s appointments, including dietician’s visits. Furthermore, they granted direct access to our cardiologist in case of any harm from prescribing medicines or abnormal laboratory results, without any additional cost. Moreover, a 12-h counselling hotline was available during and after the study follow-up period to answer any queries or report any side effects.\n\n\nAuthor contributions\n\nAll authors had access to research data and contributed to the writing and review of the manuscript.", "appendix": "Data availability\n\nZenodo: The effects of multifactorial pharmacist-led intervention protocol on medication optimisation and adherence among patients with type 2 diabetes. https://zenodo.org/doi/10.5281/zenodo.10429457. 44\n\nThis project contains the following underlying data:\n\n- Data 1.xlsx\n\nZenodo: Supplementary Tables and Figures: “The effects of multifactorial pharmacist-led intervention protocol on medication optimisation and adherence among patients with type 2 diabetes: A randomised control trial.” https://zenodo.org/doi/10.5281/zenodo.10795195. 45\n\nZenodo: Supplementary Files: “The effects of multifactorial pharmacist-led intervention protocol on medication optimisation and adherence among patients with type 2 diabetes: A randomised control trial.” https://zenodo.org/doi/10.5281/zenodo.10795203. 46\n\nZenodo: CONSORT checklist and flowchart for ‘The effects of multifactorial pharmacist-led intervention protocol on medication optimisation and adherence among patients with type 2 diabetes: A randomised control trial’. https://zenodo.org/doi/10.5281/zenodo.10431915. 47\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 acknowledge Dr. Aysha Al Dhaheri, Oud Al Touba diagnostic and screening centre director, and Oud Al Touba staff for their support during the study.\n\n\nReferences\n\nGuariguata L, Whiting DR, Hambleton I, et al.: Global estimates of diabetes prevalence for 2013 and projections for 2035. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEkong G, Chou C, Lakin J, et al.: Pharmacist-led motivational interviewing for diabetes medication adherence in a worksite wellness program. J. Am. Pharm. Assoc. 2020; 60(6): e224–e229. PubMed Abstract \| Publisher Full Text\n\nMohan A, Majd Z, Johnson ML, et al.: A Motivational Interviewing Intervention to Improve Adherence to ACEIs/ARBs among Nonadherent Older Adults with Comorbid Hypertension and Diabetes. Drugs Aging. 2023; 1–14.\n\nSharma A, Mentz RJ, Granger BB, et al.: Utilizing mobile technologies to improve physical activity and medication adherence in patients with heart failure and diabetes mellitus: Rationale and design of the TARGET-HF-DM Trial. Am. Heart J. 2019; 211: 22–33. PubMed Abstract \| Publisher Full Text\n\nXu H, Long H: The effect of smartphone app–based interventions for patients with hypertension: systematic review and meta-analysis. JMIR Mhealth Uhealth. 2020; 8(10): e21759. PubMed Abstract \| Publisher Full Text\n\nLiu K, Xie Z, Or CK: Effectiveness of mobile app-assisted self-care interventions for improving patient outcomes in type 2 diabetes and/or hypertension: systematic review and meta-analysis of randomized controlled trials. JMIR Mhealth Uhealth. 2020; 8(8): e15779. PubMed Abstract \| Publisher Full Text\n\nEl-Deyarbi M: The effects of multifactorial pharmacist-led intervention protocol on medication optimisation and adherence among patients with type 2 diabetes. [Dataset]. Zenodo. 2023.\n\nEl-Deyarbi M: Supplementary Tables and Figures: “The effects of multifactorial pharmacist-led intervention protocol on medication optimisation and adherence among patients with type 2 diabetes: A randomised control trial”. [Dataset]. Zenodo. 2024.\n\nEl-Deyarbi M: Supplementary Files: “The effects of multifactorial pharmacist-led intervention protocol on medication optimisation and adherence among patients with type 2 diabetes: A randomised control trial”. [Dataset]. Zenodo. 2024.\n\nEl-Deyarbi M: The effects of multifactorial pharmacist-led intervention protocol on medication optimisation and adherence among patients with type 2 diabetes: A randomised control trial. Zenodo. 2023." }	[ { "id": "284388", "date": "24 Jun 2024", "name": "Taichi Ochi", "expertise": [ "Reviewer Expertise Personalised care", "metabolic disorders (type II diabetes)", "digital 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 your article. It was insightful to read about the examination of the new MPIP program in the UAE to improve patient outcomes of patients with type II diabetes. After reading your article, I have the following points that I would like to highlight for further revision.\nThe figures provided for diabetes prevalence could be updated. Citing the recent IDF Diabetes Atlas reports would shed light on more recent numbers. Furthermore, as the study focuses on patients with T2D, I would suggest to focus on the figures for T2D, not diabetes overall (if possible for the UAE).\n\nWhen comparing the medications in each regimen (Table 5), the baseline between the two groups was different. This could be partly explained as more participants were in the control. However, no further discussion on this is detailed. Was this something that was considered to impact the analysis?\n\nAn issue faced by more elderly patients is the number of medications prescribed to address different medical conditions. While the methods mentioned that the counselling would discuss potential DDIs/DFIs, no information regarding the patient's other conditions was detailed. Would it be possible to include this information (i.e. Table 1)?\n\nThe benefits of the MPIP on mobile application/medication booklet use are very clear. However, what is considered as use was not defined. Is opening the app once between the visitation periods considered use? Or a weekly/monthly checking of medical information? Or solely for booking an appointment? If you could clarify this further, that would be greatly appreciated. (the citation to the app page did not work for me but found it on the Google Playstore)\n\nFor grammar, I would like to mention that there are many run-on sentences throughout the paper. This can lead readers to lose track of the aim of the sentence. For revision, I would suggest simplifying sentences by limiting the use of 'and' to connect points.\n\nIn addition, I have a couple of minor points that I would like to highlight.\nFor Table 1, if you could specify the unit of measure for HbA1c, blood pressures, LDL cholesterol, that would be appreciated (for clarity). For the cited (supplementary) files (citation 44 - 47), you could add the DOI of the Zenodo link to make it easier to access for readers (some other articles are also missing DOI/linkage)\n\nMany thanks again for your article and consideration.\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": "12384", "date": "24 Sep 2024", "name": "Marwan El-Deyarbi", "role": "Author Response", "response": "Dear Respected Editor and Reviewer, Thank you for your time and efforts to review our research work. Please note that all of your valuable comments have been addressed carefully and changes have been made in the manuscript accordingly. Kind regards Reviewer comments:   The figures provided for diabetes prevalence could be updated. Citing the recent IDF Diabetes Atlas reports would shed light on more recent numbers. Furthermore, as the study focuses on patients with T2D, I would suggest to focus on the figures for T2D, not diabetes overall (if possible for the UAE). Thank you for your comment. The updated IDF Diabetes Atlas data has been added in the introduction section(Line 2, Page 4 [PDF File]). When comparing the medications in each regimen (Table 5), the baseline between the two groups was different. This could be partly explained as more participants were in the control. However, no further discussion on this is detailed. Was this something that was considered to impact the analysis? Thank you for your comment. I agree with you that there was a difference in medication regimen between both groups at baseline; however, the HbA1c levels at baseline were 7.4 and 7.6 for the intervention and control, respectively, with 6.3% of participants in the intervention group receiving insulin as part of their diabetic regimen compared to 4% of participants in the control group (Other chronic medication’s regimens were well balanced among the control and intervention groups at enrollment). Moreover, it didn’t impact the analysis as we measured medication adherence possession data based on the actual number of medications in each patient and in the MTM study we presented the percentage change from baseline to study exit. In addition, the higher number of antihyperglycaemic drugs in the control at baseline may show that antihyperglycaemic deprescribing in the MTM program is more efficient and the below comment has been added in the discussion (Line 11, page 16 [PDF File]) Added: “ and the fewer number of antihyperglycaemic drugs in the intervention group at baseline compared to control group.” An issue faced by more elderly patients is the number of medications prescribed to address different medical conditions. While the methods mentioned that the counselling would discuss potential DDIs/DFIs, no information regarding the patient's other conditions was detailed. Would it be possible to include this information (i.e. Table 1)? Thank you for valuable comment. Number of patients with cardiovascular disease and chronic kidney disease (eGFR below 60) has been added to Table 1 The benefits of the MPIP on mobile application/medication booklet use are very clear. However, what is considered as use was not defined. Is opening the app once between the visitation periods considered use? Or a weekly/monthly checking of medical information? Or solely for booking an appointment? If you could clarify this further, that would be greatly appreciated. (the citation to the app page did not work for me but found it on the Google Playstore) Thank you for the insightful remark. The increase of use has been defined as one point increase (or more) in the 5-point Likert scale in question 1 in the SEHA mobile and booklet use questionnaire table ( supplementary File 7 in the supplementary document Link ” https://zenodo.org/doi/10.5281/zenodo.1079520346” ) at each follow-up visit or at study exit for any purpose either for appointments, medication or lab review ( the below clarification added in the footnote of Table 6 (PDF File) “ As one point increase (or more) in the 5-point Likert scale in the questionnaire.” A link for the SEHA application in both Google and Apple stores has been added to the manuscript. For grammar, I would like to mention that there are many run-on sentences throughout the paper. This can lead readers to lose track of the aim of the sentence. For revision, I would suggest simplifying sentences by limiting the use of 'and' to connect points. Thank you for the important comment. In the revised version, many sentences have been connected by limiting the use several connecting words and the use of “ and” to join ideas and sentences In addition, I have a couple of minor points that I would like to highlight. For Table 1, if you could specify the unit of measure for HbA1c, blood pressures, LDL cholesterol, that would be appreciated (for clarity). The units of measure for HbA1c, blood pressure, eGFR, and LDL cholesterol have been added in the footnote of Table 1 (PDF File). For the cited (supplementary) files (citation 44 - 47), you could add the DOI of the Zenodo link to make it easier to access for readers (some other articles are also missing DOI/linkage). Thank you for your comment. DOI of the Zenodo for citations from 44 to 47 has been added to the revised file." } ] }, { "id": "305397", "date": "25 Jul 2024", "name": "Anas Khaleel", "expertise": [ "Reviewer Expertise clinical pharmacy", "community and hospital pharmacy research", "public health", "medical genetics and pharmacogenetics" ], "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 Please see comments below\nIntroduction\n\nThe introduction provides relevant statistics, which can be strengthened by incorporating primary data or pilot study findings to support the problem statement. The introduction could benefit from grounding the study in a theoretical framework related to behaviour change or medication adherence. Expand on the theoretical framework underpinning the study to strengthen the rationale.\nStrengthen the link between the problem statement and the proposed intervention.\n\nAlthough the Emirates of Abu Dhabi Emirate no S\nExpand on the description of the intervention components in the MPIP program.\n\nRandomization\nWhat type of randomization was used in this RCT?\nJustification for sample size missing: The rationale behind the sample size (239 patients) is not provided. Is there sample size calculation ? please state how sample size were calculated Potential selection bias: It's unclear how researchers addressed it during recruitment.\n\nOTC abbreviations are not spelled out throughout the manuscript\n\nSEHA mobile and booklet use questionnaire (do these booklets and apps have Arabic versions?)\nT-test was also used to estimate the mean differences and confidence intervals for the MPR…\nDid you use paired or independent t-tests?\nResults\nFigure 2\n\nImage not clear Figure 2 Please provide high-resolution picture\n\nDiscussion\nExpand on the discussion of clinical outcomes, even if they were not the primary focus of the study. Strengthen the comparison of the study's results to existing literature to highlight the study's contribution to the field. Conduct a more comprehensive analysis of potential confounding factors. Provide clear and actionable recommendations for clinical practice based on the study's findings.\nIn conclusion please provide an insight about the significant role of pharmacist in healthcare team\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": "12385", "date": "16 Sep 2024", "name": "Marwan El-Deyarbi", "role": "Author Response", "response": "Thank you for your time and efforts to review our research work. Please note that all of your valuable comments have been addressed carefully and changes have been made in the manuscript accordingly. Kind regards Reviewer comments:   Introduction: The introduction provides relevant statistics, which can be strengthened by incorporating primary data or pilot study findings to support the problem statement. The introduction could benefit from grounding the study in a theoretical framework related to behaviour change or medication adherence. Expand on the theoretical framework underpinning the study to strengthen the rationale. Thank you for your valuable comments. The results of a systematic review study and another meta-analysis study have been added in the introduction in Line 24 and Line 26, Page 4 (PDF File). Strengthen the link between the problem statement and the proposed intervention. Thank you for the important comment. Paragraphs number 8 and 9 (on Page 4 in [PDF File]), have been merged to strengthen the link between the problem and the proposed intervention. Expand on the description of the intervention components in the MPIP program. Thank you for your comment. The MPIP program has been listed as:1) Medication adherence counselling including measuring medication adherence by medication adherence possession formulas and validated medication adherence questionnaire, and 2) a Meditation therapy management (MTM) program, by implementing the five criteria for MTM, including medication review to optimise patient treatment as per the latest treatment guidelines, assessment of the possibility of deprescribing, evaluation of any prescribed non-formulary drugs, patient counselling, and provision of printed medication educational materials through: A) Medication counselling and reconciliation, B) Patient medication booklet, and C) SEHA mobile application. Randomization: What type of randomization was used in this RCT? Thank you for your comment. Simple randomisation was performed using a computer-generated random number in Microsoft Excel to generate allocation sequences. The word “simple” has been added to the manuscript (Line 25, Page 5 [PDF File]). Justification for sample size missing: The rationale behind the sample size (239 patients) is not provided. Is there sample size calculation ? please state how sample size were calculated Thank you for your comment. The sample size has been detailed in the Statistical analysis section 3.5. In the study, we used Giga sample size online calculator to detect a minimum detectable difference effect of 0.035 between both groups with an MPRt baseline mean of 0.93, and a minimum total sample size of 180 was determined. However, a larger number of participants (239 participant) was recruited for more significant differences between groups and to account for any dropout during the study. Potential selection bias: It's unclear how researchers addressed it during recruitment. Thank you for the insightful remark. The potential of selection bias has been minimized during recruitment with allocation concealment by sequential numbering, representing the participant’s turn in joining the study by the principal investigator (Line 26, Page 5 [PDF File]). OTC abbreviations are not spelled out throughout the manuscript Thank you for your comment. Over-the-counter (OTC) has been added to the manuscript (Line 24, Page 8 [PDF File]). SEHA mobile and booklet use questionnaire (do these booklets and apps have Arabic versions?) Thank you for your comment. Both the patient’s medication booklet (in Supplementary Files, Supplementary File 6), and SEHA mobile application have both an Arabic and English interface. (A link for the SEHA application in both Google and Apple stores has been added to the manuscript) T-test was also used to estimate the mean differences and confidence intervals for the MPR…Did you use paired or independent t-tests? Thank you for your comment. For mean differences and confidence intervals, independent t-tests were used in SPSS (version 26). Results See Figure 2 linked here: https://f1000research.s3.amazonaws.com/linked/674183.146517.pdf Image not clear Figure 2. Please provide high-resolution picture Thank you for your valuable comment. All figures and tables are available in high resolution in the “Extended data” section (Line 26, Page 17 [PDF File]). Zenodo: Supplementary Tables and Figures: “The effects of multifactorial pharmacist-led intervention protocol on medication optimisation and adherence among patients with type 2 diabetes: A randomised control trial.” https://zenodo.org/doi/10.5281/zenodo.10795195.45 Discussion Expand on the discussion of clinical outcomes, even if they were not the primary focus of the study. Thank you for your valuable comment. The clinical outcomes will be published in a separate manuscript, and a statement of publishing one outcome from the original trial is available in the manuscript (Line 11, Page 5 [PDF File]). Strengthen the comparison of the study's results to existing literature to highlight the study's contribution to the field. Thank you for your comment. A comparison with other studies has been added in the discussion section (Line 3 and 5, Page 15 [PDF File]). Conduct a more comprehensive analysis of potential confounding factors. Thank you for this important comment. Another manuscript (under review for publication) is discussing the factors affecting medication adherence including socio-demographic variables, medication-related barriers, healthcare system-related barriers, financial or logistical barriers, and perception and social-specific confounding factors. Provide clear and actionable recommendations for clinical practice based on the study's findings. Thank you for your comment. A recommendation has been added at the end of the discussion section (Line 24, Page 16 [PDF File]). In conclusion please provide an insight into the significant role of pharmacists in healthcare team Thank you for your valuable comment. A sentence pointing out the importance of the pharmacist has been added to the conclusion ( Section 6, Page 16 [PDF File])." } ] } ]	1	https://f1000research.com/articles/13-493
https://f1000research.com/articles/13-698/v1	27 Jun 24	{ "type": "Systematic Review", "title": "Leisure-Based Interventions in Adults with Schizophrenia: A Scoping Review", "authors": [ "Amar Nishad", "Anil Kumar Mysore Nagaraj", "Chythra R Rao", "Keshavaram P", "Priyanka Rajpaul", "Amar Nishad", "Chythra R Rao", "Keshavaram P", "Priyanka Rajpaul" ], "abstract": "Background Schizophrenia is a severe mental illness characterized by psychosis, apathy, social withdrawal, and cognitive impairment, which results in impaired functioning in work, school, parenting, self-care, independent living, interpersonal relationships, and leisure time.\n\nMethod A systematic search was conducted using Arksey and O’Malley’s framework with studies published on leisure-based intervention from January 1990 to December 2023.\n\nResults The review included 11 articles in the study. In total two studies were pilot interventional study, one randomized controlled study, one case-control, one retrospective study, three were cross sectional, one was cross sectional longitudinal study and two were qualitative in nature. Studies used different types of leisure activities like cooking group, discussions, board games, arts and craft, painting, beading, sewing, clay work, paper craft, etc were used as an intervention. Qualitative studies found that individuals with schizophrenia spent less time in social and leisure activities and more time relaxing and doing nothing.\n\nConclusion The study highlights the need to conduct further research on leisure-based interventions using various study designs like randomized controlled trials and mixed methods to understand its effectiveness among individuals with schizophrenia.", "keywords": [ "Leisure-based interventions", "schizophrenia", "Adults", "Recreation", "Scoping review" ], "content": "Introduction\n\nSchizophrenia is a severe mental disorder characterized by psychosis, apathy, social withdrawal, and cognitive impairment, which results in impaired functioning in work, school, parenting, self-care, independent living, interpersonal relationships, and leisure time (Geller, 1992). Approximately 24 million individuals worldwide, or 1 in 300, are affected by schizophrenia. In adulthood, the corresponding rate is 1 in 222. The most common times for onset are in late teens and the twenties, and in men it happens earlier than in women (World Health Organization, 2022). One of the main mental health disorders contributing to the global disease burden is schizophrenia, that also affects social functioning (World Health Organization, 2012). People with schizophrenia have both internal and environmental obstacles to engaging in leisure activities, such as side effects from medicine, cultural stigma, family dynamics, and cultural norms (Rezaie et al., 2017).\n\nLeisure is defined as a “non-obligatory activity that is Intrinsically motivated and engaged in during discretionary time, that is, time not committed to obligatory occupations such as work, self-care, or sleep” (American Occupational Therapy Association, 2014). Depending on personal perceptions, leisure can be defined as either casual, serious, or project based. It can take many different forms, such as instantaneous, brief, and intrinsically fulfilling activities without the need for special skills (i.e., casual leisure); systematic activities carried out by beginners or hobbyists with skills and expertise that could lead to a career itself; or occasionally short-term tasks completed as part of work obligations (Stebbins, 2008). One aspect of a meaningful life that provides those with mental illness with many benefits is leisure, which includes identity, belonging to themselves, involvement, lowering boredom, and a method of managing their stress (Iwasaki et al., 2014). Engaging in recreational activities might pose challenges as it involves finding, planning, and carrying out suitable and captivating leisure pursuits (Hein et al., 2020). Negative symptoms of psychosis may make it difficult for a person to participate in leisure activities (Giacco et al., 2012).\n\nAccording to a study on how people with serious mental illnesses, including schizophrenia, use their time, those with the disease only engage in active leisure activities when they were part of a treatment plan (Yanos & Robilotta, 2011), indicating that leisure-focused therapies could be crucial to achieving recovery-focused results (Iwasaki et al., 2014). On this basis, our study aimed to explore the existing literature related to the leisure-based interventions for adults with schizophrenia by identifying the range of study designs.\n\n\nMethods\n\nThe framework proposed by scoping reviews by Arksey & O’Malley (2005) was used in the current scoping review.\n\nWhat are the available studies on leisure-based interventions or programs provided for adults with schizophrenia?\n\nHaving specific criteria for searching the relevant articles is a requirement to answer the question framed for any scoping review (Arksey & O’Malley, 2005). The databases Scopus, PubMed, and Embase were accessed. The grey literature searches through Google scholar were carried out.\n\nSearch keywords\n\n“Schizophrenia” AND “Psychosis” AND “leisure” OR “leisure activity” OR “leisure activities” OR “recreation” OR “activity” OR “activity group” OR “activity groups” OR “creative activity” OR “recreational therapy” OR “leisure-based intervention” AND “Adults” OR “Adult”. The Boolean search strategy was applied to connect using AND, and OR.\n\nThe following criteria were decided on for the scoping review by all the reviewers:\n\nInclusion criteria\n\n\n\n• Studies using leisure-based interventions, qualitative studies, single-case studies, cross-sectional and longitudinal studies with or without a comparison control group from January1990 to December 2023 were included.\n\n• Full-text articles in only English language were included.\n\nExclusion criteria\n\n\n\n• Letter to editors, correspondence articles, viewpoints, ideas, opinions, short communications, and conference proceedings were excluded.\n\nThe search was carried out in the selected databases by two independent reviewers adhering to the established inclusion and exclusion criteria. Following title and abstract screening, the articles included for full-text screening were exported to an Excel sheet for blinding of the selection process. Any disagreement during the selection process was resolved with the help of other reviewers. The included articles were reviewed in full text and data extraction covered the following: title, author(s), year of publication, country, setting, methodology, and results. The extracted data were entered into the Excel sheet, and all the authors reviewed the information. The study details are charted in Table 1(extended data). Three independent authors participated in selecting the studies, and all authors reached a consensus on the studies to be included after discussion. Figure 1 shows the selection of studies in this review.\n\n\nResults\n\nThe study yielded 30,194 articles out of which 20,733 articles were screened for title and abstract screening after duplicate removal. After title and abstract screening, 194 articles were eligible for the full text screening, 183 articles were excluded as they did not meet the inclusion criteria, and finally 11 articles were included in the review. In total two studies were pilot interventional study, one randomized controlled study, one case-control, one retrospective study, three were cross sectional, one was cross sectional longitudinal study and two were qualitative in nature. Out of 11 studies, four were conducted in London, England (Dean et al., 2014; Ngamaba et al., 2021; Shimitras et al., 2003; Cella et al., 2016), two in Philadelphia (Iwasaki et al., 2014; Snethen et al. 2012), two in Australia (Caddy et al., 2011; Hayes & Halford, 1996), one in France (Voruganti et al., 2006), one in Israel (Lipskaya-Velikovsky et al., 2020), and one study in the United States of America (McCormick et al., 2012). In total 993 participants with schizophrenia were studied. All the studies were from high economic countries and participants were recruited from different settings such as hospital inpatients, community, outpatients, and day care centres.\n\nTwo pilot interventional studies used recreational activities, cooking group as part of the intervention and duration lasted for average of one hour (Lipskaya-Velikovsky et al., 2020; Snethen et al. 2012). A Randomized control design study used activity group which included activities like discussions, board games and visits to places of interest (Dean et al., 2014), a case control study used camping, kayaking, rock climbing, high and low ropes courses, and a picnic in their summer module and the winter module included skating, snow shoeing, skiing, snowboarding, ice fishing, indoor rock climbing, and bowling (Voruganti et al., 2006). A retrospective study investigated on art and craft-based activities like painting, beading, sewing, clay work, paper craft and were used to participants of the group and its outcome in individuals with schizophrenia (Caddy et al., 2011).\n\nMcCormick et al. (2012) study found that majority of leisure activity perform by people with schizophrenia were sedentary (31%) and sedentary non-leisure (25.7%) and physically active leisure was significantly associated with lower negative emotion. The findings from (Iwasaki et al., 2014) emphasize the importance of meanings that persons with mental illness including schizophrenia gain from leisure are connection/belonging, identity, freedom/autonomy and to reduce perceptions of boredom. Also, a greater perception of being actively engaged was a significant predictor of recovery and overall physical and mental health and less frequent psychiatric symptoms. Furthermore, the use of leisure both for coping with stress and reducing boredom significantly predicted fewer psychiatric symptoms. People with psychosis who attend more leisure activities have a higher quality of life. Quality of life score was higher amongst males who attended leisure activities (Ngamaba et al., 2021).\n\nTime use studies among schizophrenia found that, people with schizophrenia spent most of their time in passive leisure such as reading, watching TV or videos, relaxing, and sleeping and less time in active lifestyle (Hayes & Halford, 1996; Shimitras et al., 2003; Cella et al., 2016).\n\nThe authors of the reviewed articles have reported of facilitators such as leisure-based intervention being flexible (Lipskaya-Velikovsky et al., 2020), client centered, and interest based (Snethen et al., 2012), feasible, available, acceptable, and cost-effective (Voruganti et al., 2006). Barriers in implementing leisure-based interventions were the characteristic passive lifestyle of patients with schizophrenia, chronic illness, negative symptoms, cognitive deficits, time use and recreational skills deficits that evolve over time (Hayes & Halford, 1996; Shimitras et al., 2003; Cella et al., 2016).\n\nA novel adventure- and recreation-based group intervention was found to be marginally better than standard clinical care in terms of perceived cognitive deficits and functioning, while significant improvements were observed in terms of global functioning and self-esteem, there was a strikingly significant weight loss (mean 12 lb) among study subjects over the course of the year (Voruganti et al., 2006). Studies using recreational activities as interventions found improvement in several elements of cognitive function including language understanding, executive functioning, functional capacity and visual memory, increased community involvement, developing coping skills, positive and negative schizophrenia symptoms (Lipskaya-Velikovsky et al., 2020; Snethen et al., 2012; Dean et al., 2014). A retrospective study found that use of creative activities in the inpatient setting has potential benefits for people experiencing mental health problem including reductions in self-reported psychological distress and clinician-rated symptoms and improvement in daily functioning (Caddy et al., 2011).\n\n\nDiscussion\n\nThis scoping review attempted to investigate the use of leisure as a form of intervention for adults with schizophrenia. Research exploring leisure-based interventions for individuals with schizophrenia underscored their multifaceted benefits (Voruganti et al., 2006; Caddy et al., 2011), showcasing improvements in self-esteem, functioning, and symptom reduction, advocating for their role as complementary therapies in schizophrenia rehabilitation. Engaging in leisure activities significantly associated with lower psychiatric symptoms, coping with stress, reducing boredom, predicting recovery and overall health and increased scores on quality of life among people with schizophrenia (Iwasaki et al., 2014; McCormick et al., 2012).\n\nSnethen et al. (2012) patient-centered intervention demonstrated enhanced planning abilities and community involvement through tailored recreational activities. Iwasaki et al. (2014) study underscored how leisure-generated meanings and active engagement significantly predict recovery and mental health improvements. Similarly, Cella et al. (2016) showed significant differences in time utilization between individuals with schizophrenia and the general population, revealing the disorder's impact on social engagement. Lipskaya-Velikovsky et al. (2020) and Ngamaba et al. (2021) highlighted the efficacy of occupational connections and increased leisure engagement, respectively, in enhancing recovery and quality of life for schizophrenia patients. These findings collectively advocate for diverse leisure-based interventions personalized to individual preferences as promising additions to standard treatments for improving the lives of those with schizophrenia. Occupational therapists have potential role in using leisure-based activities as part of their treatment to improve functioning among individuals with schizophrenia in various settings.\n\nThe duration of sessions provided ranged from 45 minutes to 1 hour. The ambiguity in the protocol followed could be due to the client centered nature of the leisure-based intervention. Developing a protocol for implementation of leisure-based intervention for persons with schizophrenia could be beneficial in various mental health settings. This would also aid in gauging the effectiveness of the leisure-based intervention in better possible ways such as through studies with higher rigor. The types of leisure activities selected in the studies varied could be due to cultural factors, feasibility, acceptability, and affordability. Nevertheless, the leisure-based interventions are easily adaptable because of which these interventions could be practiced even in the community.\n\nTo the best of our knowledge, this is the first review on leisure-based interventions in individuals with schizophrenia. The limitation of our study is that only published literature in English was searched in the current review, which may have resulted in missing relevant studies. The reviewers have tried all possible ways to look for relevant articles, but individual biases of the authors may not be negated. The current review may help future researchers to conduct relevant research related to gaps identified in the current review. Most of the studies identified in the current scoping review have found that there is a positive effect of leisure-based interventions in treatment of schizophrenia, but there is the risk of bias that invites us to be cautious when interpreting these results.\n\nThere are limited studies on leisure-based interventions among individuals with schizophrenia. Future studies may focus on evaluating the effectiveness of leisure-based interventions specifically on various occupations such as activities of daily living, instrumental activities of daily living, social participation, sleep and rest, other associated factors such as self-confidence, motivation, emotional expressions, and communication skills. Also, studies could be done in developing guidelines in terms of duration and the type of modalities that could be used for persons with schizophrenia. The studies could be done in low middle income and middle-income countries using different study designs to determine the best means of conducting research on this topic. The study also highlights a need of conducting randomized controlled trials and mixed method studies to understand the effectiveness of leisure-based interventions in schizophrenia.\n\n\nConclusion\n\nOverall, the purpose of this review was to gather and describe the available research on the use of leisure as an intervention, specifically among individuals with schizophrenia. The study highlights the need to conduct research using leisure-based interventions with various study designs especially randomized control trial to understand its effectiveness among individuals with schizophrenia.", "appendix": "Data availability\n\nNo data associated with this article\n\nFigshare: Leisure based Interventions extended files, https://doi.org/10.6084/m9.figshare.25810243.v1 (Nishad & Nagaraj, 2024).\n\nThis project contains the following extended data:\n\nTable 1 Data charting of the included studies\n\nFigure 1 PRISMA Chart\n\nPRISMA Sc-R Checklist (Tricco et al., 2018)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAmerican Occupational Therapy Association: Occupational Therapy Practice Framework: Domain and Process (3rd Edition). Am. J. Occup. Ther. 2014; 68: S1–S48. Publisher Full Text\n\nArksey H, O’Malley L: Scoping studies: towards a methodological framework. Int. J. Soc. Res. Methodol. 2005; 8(1): 19–32. Publisher Full Text\n\nCaddy L, Crawford F, Page AC: ‘Painting a path to wellness’: correlations between participating in a creative activity group and improved measured mental health outcome. J. Psychiatr. Ment. Health Nurs. 2011; 19(4): 327–333. PubMed Abstract \| Publisher Full Text\n\nCella M, Edwards C, Wykes T: A question of time: A study of time use in people with schizophrenia. Schizophr. Res. 2016; 176(2-3): 480–484. PubMed Abstract \| Publisher Full Text\n\nDean M, Weston AR, Osborn DP, et al.: Activity groups for people with schizophrenia: A randomized controlledtrial. J. Ment. Health. 2014; 23(4): 171–175. Publisher Full Text\n\nGeller JL: A historical perspective on the role of state hospitals viewed from the era of the “revolving door.”. Am. J. Psychiatry. 1992; 149(11): 1526–1533. PubMed Abstract \| Publisher Full Text\n\nGiacco D, McCabe R, Kallert T, et al.: Friends and symptom dimensions in patients with psychosis: A pooled analysis. PLoS One. 2012; 7(11): 1–9. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHayes RL, Halford WK: Time use of unemployed and employed single male schizophrenia subjects. Schizophr. Bull. 1996; 22(4): 659–669. PubMed Abstract \| Publisher Full Text\n\nHein V, Koka A, Kalajas-Tilga H, et al.: The effect of grit on leisure time physical activity. An Application of Theory of Planned Behaviour. Balt. J. Health Phys. Act. 2020; 12(1): 78–85. Publisher Full Text\n\nIwasaki Y, Coyle C, Shank J, et al.: Role of leisure in recovery from mental illness. Am. J. Psychiatr. Rehabil. 2014; 17(2): 147–165. Publisher Full Text\n\nLipskaya-Velikovsky L, Krupa T, Silvan-Kosovich I, et al.: Occupation-focused intervention for in-patient mental health settings: Pilot study of effectiveness. J. Psychiatr. Res. 2020; 125: 45–51. PubMed Abstract \| Publisher Full Text\n\nMcCormick BP, Snethen G, Smith R, et al.: Active leisure in the emotional experience of people with schizophrenia. Ther. Recreat. J. 2012; 46(3). Reference Source\n\nNgamaba KH, Webber M, Xanthopoulou P, et al.: The Participation in Leisure Activities and the Quality of Life of People with Psychosis in England: A Multi-Site Cross-Sectional Study.2021. Publisher Full Text\n\nNishad A, Nagaraj AKM: Leisure based Interventions extended files. Dataset. figshare. 2024. Publisher Full Text\n\nRezaie L, Shafaroodi N, Philips D: The barriers to participation in leisure time physical activities among Iranian women with severe mental illness: A qualitative study. Ment. Health Phys. Act. 2017; 13: 171–177. Publisher Full Text\n\nStebbins RA: Right leisure: Serious, casual, or project-based? Neuro Rehabilitation. 2008; 23(4): 335–341. Publisher Full Text\n\nShimitras L, Fossey E, Harvey C: Time use of people living with schizophrenia in a North London catchment area. Br. J. Occup. Ther. 2003; 66(2): 46–54. Publisher Full Text\n\nSnethen G, McCormick BP, Van Puymbroeck M: Community Involvement, planning and coping skills: Pilot outcomes of a recreational-therapy intervention for adults with schizophrenia. Disabil. Rehabil. 2012; 34(18): 1575–1584. PubMed Abstract \| Publisher 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\nVoruganti LNP, Whatham J, Bard E, et al.: Going Beyond: An Adventure- and Recreation-Based group intervention promotes Well-Being and Weight Loss in Schizophrenia. Can. J. Psychiatry. 2006; 51(9): 575–580. PubMed Abstract \| Publisher Full Text\n\nWorld Health Organization: Schizophrenia.2022, January 11. Reference Source\n\nWorld Health Organization: The World health report: 2001: Mental health: new understanding, new hope.2012, June 16. Reference Source\n\nYanos PT, Robilotta SA: An examination of time-use among adults diagnosed with severe mental illnesses using daily interviews. Psychiatr. Rehabil. J. 2011; 34(3): 243–247. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "301277", "date": "06 Aug 2024", "name": "Luigi Giuliani", "expertise": [ "Reviewer Expertise Mental disorders. Schizophrenia and other psychotic disorders. Psychotherapy", "psychosocial interventions and and cognitive remediation." ], "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 by Nishad et al. aims to explore the existing literature related to the leisure-based interventions for adults with schizophrenia by identifying the range of study designs. The results of the present study highlight the need to conduct further research on leisure-based interventions using rigorous study designs like randomized controlled trials and mixed methods to understand its effectiveness among individuals with schizophrenia. The study topic is timely and interesting. However, according to the comments provided below, some important issues should be addressed.\n\nAbstract\n\nThe aims of the study are missing. In the results section, listing the methodology of all the studies included in the review might be removed. In the results section, are reported only the findings of qualitative studies. Please report also the quantitative results.\n\nIntroduction\n\nCitations after the sentences “Approximately 24 million individuals worldwide, or 1 in 300, are affected by schizophrenia” and “In adulthood, the corresponding rate is 1 in 222” are missing. Please add them. The sentence “One of the main mental health disorders contributing to the global disease burden is schizophrenia, that also affects social functioning” does not appear fluid within the paragraph and it could be changed with “Schizophrenia is one of the main mental health disorders contributing to the global disease burden, affecting different functioning domains, among which social functioning”. Does “systematic activities carried out by beginners or hobbyists with skills and expertise that could lead to a career itself” and “occasionally short-term tasks completed as part of work obligations” correspond respectively to serious- and project-based leisure activities? Please specify. The sentence “One aspect of a meaningful life that provides those with mental illness with many benefits is leisure, which includes identity, belonging to themselves, involvement, lowering boredom, and a method of managing their stress” does not appear fluid within the paragraph. Please change it, linking the sentence with the previous one. The authors states that “negative symptoms of psychosis may make it difficult for a person to participate in leisure activities”. The concept could be further discussed, more references are needed and also the impact of cognitive deficit on participating in leisure activity should be examined. The aim of the study should be modified. Instead of prioritizing the identification of the range of study designs, the focus should be placed on the findings of the included studies, highlighting the impact and utilization of leisure-based interventions in adults with schizophrenia.\n\nMethods\n\n(Major concern) I have some concerns regarding the search string. By using \"schizophrenia AND psychosis,\" there is a risk, albeit minimal, of excluding studies on patients with schizophrenia that do not include the term psychosis. Additionally, parentheses were not used, which might have resulted in missing some works that could have been included.\n\nResults\n\nI recommend reorganizing the presentation of the results because the current format might be unclear. For instance, it is not evident why the sections \"Leisure activities and association with various factors in individuals with schizophrenia\", \"Time use and schizophrenia\", and \"Clinical and functional outcome\" are separated, as they appear to summarize similar results. When listing the locations where the studies were conducted, the authors sometimes use the city and other times the country. This leads to inconsistencies, such as separating the study conducted in the USA from the one conducted in Philadelphia. In my opinion, it would be better to choose a single classification criterion to ensure consistency.\n\nDiscussion:\n\nThe discussion section needs to be completely rewritten. The authors merely restate the results of individual studies instead of organizing the discussion around the following suggested points:\n\nDiscuss the finding that patients with schizophrenia spend little time engaging in leisure activities and that the activities they do engage in are usually passive. Discuss the fact that the included studies in the review show that engaging in leisure activities benefits patients with schizophrenia. Specifically, address how these activities impact cognitive, clinical, functional, and quality of life dimensions. Discuss the studies that utilized leisure-based interventions for patients with schizophrenia. Summarize the findings of these studies, and examine any differences in outcomes based on sample size, study design, and type of intervention as reported in the included studies.\n\nThe conclusions should include a consideration of how promising and important leisure-based interventions can be, if the authors believe they are. This addition would highlight the potential value and significance of these interventions in the treatment and support of patients with schizophrenia.\n\nOther\nThe manuscript would benefit from a review by a native English speaker due to the presence of small but frequent grammatical and spelling errors. Improving the language quality would enhance the clarity and readability of the paper.\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? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable", "responses": [ { "c_id": "12359", "date": "16 Sep 2024", "name": "Anil Kumar Mysore Nagaraj", "role": "Author Response", "response": "Abstract The aims of the study are missing. Reply: - Thank you for identifying this error. We have incorporated it in the manuscript. In the results section, listing the methodology of all the studies included in the review might be removed. Reply: - Thank you. We have removed it in the revised manuscript In the results section, are reported only the findings of qualitative studies. Please report also the quantitative results. Reply: - Thank you for the suggestion. We have reported the quantitative studies as well in the revised in the manuscript Introduction Citations after the sentences “Approximately 24 million individuals worldwide, or 1 in 300, are affected by schizophrenia” and “In adulthood, the corresponding rate is 1 in 222” are missing. Please add them. Reply:- We have inserted the citation- (World Health Organization, 2022) after the above sentences in the revised manuscript, in paragraph 1, lines 5 and 6. Thank you. The sentence “One of the main mental health disorders contributing to the global disease burden is schizophrenia, that also affects social functioning” does not appear fluid within the paragraph and it could be changed with “Schizophrenia is one of the main mental health disorders contributing to the global disease burden, affecting different functioning domains, among which social functioning”. Reply: - Thank you for the suggestion. We have changed it as above in the revised manuscript Does “systematic activities carried out by beginners or hobbyists with skills and expertise that could lead to a career itself” and “occasionally short-term tasks completed as part of work obligations” correspond respectively to serious- and project-based leisure activities? Please specify. Reply:- Yes, the phrases \"systematic activities carried out by beginners or hobbyists with skills and expertise that could lead to a career itself\" and \"occasionally short-term tasks completed as part of work obligations\" correspond to serious- and project-based leisure activities, respectively. This has been clarified in the second paragraph of the introduction in the manuscript now. Thanks. The sentence “One aspect of a meaningful life that provides those with mental illness with many benefits is leisure, which includes identity, belonging to themselves, involvement, lowering boredom, and a method of managing their stress” does not appear fluid within the paragraph. Please change it, linking the sentence with the previous one. Reply:- Thank you for the suggestion. We have revised and reworded the sentences in the 2nd paragraph of the introduction in the manuscript. The authors state that “negative symptoms of psychosis may make it difficult for a person to participate in leisure activities”. The concept could be further discussed, more references are needed and also the impact of cognitive deficit on participating in leisure activity should be examined. Reply:- Thank you for the suggestion. We have revised this in the manuscript, cited more references for the impact of negative symptoms, and added existing studies that mention the impact of cognitive deficit on participating in leisure activity. The entire paragraph three of the introduction has been added to include the above. The aim of the study should be modified. Instead of prioritizing the identification of the range of study designs, the focus should be placed on the findings of the included studies, highlighting the impact and utilization of leisure-based interventions in adults with schizophrenia. Reply:- Thank you for identifying this. We have modified the last paragraph of the introduction as suggested above. Method (Major concern) I have some concerns regarding the search string. By using \"schizophrenia AND psychosis,\" there is a risk, albeit minimal, of excluding studies on patients with schizophrenia that do not include the term psychosis. Additionally, parentheses were not used, which might have resulted in missing some works that could have been included. Reply:- The authors used the ‘OR’ Boolean operator for schizophrenia OR psychosis. By oversight, while mentioning this in the manuscript it was typed as AND. The parentheses were utilized during the search depending on the databases that we used. Thus, it is unlikely that we have missed any studies. We are sorry for the error in the manuscript (AND instead of OR). We have now changed it to OR in the manuscript. Results: - I recommend reorganizing the presentation of the results because the current format might be unclear. For instance, it is not evident why the sections \"Leisure activities and association with various factors in individuals with schizophrenia\", \"Time use and schizophrenia\", and \"Clinical and functional outcome\" are separated, as they appear to summarize similar results. Reply: - Thank you for this observation. We initially thought that some studies have a specific objective that they can be classified into groups, however, there are overlaps and so we have now merged all the following studies under one group of “leisure as a therapeutic intervention” – (Lipskaya-Velikovsky et al., 2020; Snethen et al., 2012; Dean et al., 2014; Voruganti et al., 2006; Caddy et al., 2011; McCormick et al., 2012; Iwasaki et al., 2014, Hayes & Halford 1996; Shimitras et al., 2003; Cella et al., 2016; Ngamaba et al. (2021). When listing the locations where the studies were conducted, the authors sometimes use the city and other times the country. This leads to inconsistencies, such as separating the study conducted in the USA from the one conducted in Philadelphia. In my opinion, it would be better to choose a single classification criterion to ensure consistency. Reply: - Thank you for the suggestion. We have opted to use the name of the country and have changed it accordingly in the first paragraph of the result. Discussion Discuss the finding that patients with schizophrenia spend little time engaging in leisure activities and that the activities they do engage in are usually passive. Reply:- Thank you for the suggestion. We have changed the entire discussion as suggested. Discuss the fact that the included studies in the review show that engaging in leisure activities benefits patients with schizophrenia. Specifically, address how these activities impact cognitive, clinical, functional, and quality of life dimensions. Reply: - Thank you for the suggestion. We have revised accordingly in the manuscript Discuss the studies that utilized leisure-based interventions for patients with schizophrenia. Summarize the findings of these studies, and examine any differences in outcomes based on sample size, study design, and type of intervention as reported in the included studies. Reply:- Thank you for the suggestion. We have discussed the above points in the modified discussion. The conclusions should include a consideration of how promising and important leisure-based interventions can be, if the authors believe they are. This addition would highlight the potential value and significance of these interventions in the treatment and support of patients with schizophrenia. Reply:- Conclusion modified in the manuscript. Thank you. OTHER CHANGES: We have now included 11 additional references (5 in introduction and 6 in discussion). These are cited in the text as well as listed under bibliography, highlighted in green. Some rewording done in strengths & limitations, gaps identified and future implications." } ] } ]	1	https://f1000research.com/articles/13-698
https://f1000research.com/articles/12-1605/v1	29 Dec 23	{ "type": "Study Protocol", "title": "Effects of a low, medium, and high-intensity aquatic physiotherapy protocol on functional and biochemical parameters in individuals with knee osteoarthritis: protocol for a crossover randomized controlled trial", "authors": [ "Cesar Augusto Teixeira", "Lisete Haas", "Bruna Frata", "Andressa Fiori Bortoli", "Fernanda Scalco Acco", "Gustavo de Castro Barroso", "Fernanda Cechetti", "Cesar Augusto Teixeira", "Lisete Haas", "Bruna Frata", "Andressa Fiori Bortoli", "Fernanda Scalco Acco", "Gustavo de Castro Barroso" ], "abstract": "Background: Knee osteoarthritis affects the performance of daily activities, independence, and quality of life. The etiopathogenesis of this condition considers the mechanisms of activation of metalloproteinase and reactive oxygen species production pathways. Metalloproteinases-3 (MMP-3) and Glutathione Peroxidase (GPx) may be responsible for cartilage destruction. Aquatic physiotherapy promotes a positive impact on the clinical picture of osteoarthritis, and this study presents an intervention protocol that aims to evaluate the effects of a single session of different aquatic physiotherapy modalities on the biochemical and functional behavior of patients with knee osteoarthritis.\nMethods: This will be a crossover randomized controlled trial in which 15 individuals will be submitted to three aquatic physiotherapy modalities with a minimum 15-day wash-out period in patients over 50 years old and diagnosed with OA in at least one knee, presence of pain and at least one functional dysfunction for at least 6 months, absence of physical limitation that prevents the exercise protocol from being performed, Kellgren and Lawrence ranking between I and IV, walk independently and without auxiliary device. Variations in the concentrations of MMP-3 and GPx in peripheral blood, pain, edema, and flexibility resulting from the three aquatic physiotherapeutic interventions will be evaluated both pre- and immediate post-intervention. The reference group will be submitted to the same aquatic physiotherapy protocols, however, only the biochemical parameters and the self-perception questionnaires will be evaluated.\nRegistration: ClinicalTrials.gov (NCT05610696, 18/01/2023).", "keywords": [ "Osteoarthritis", "Hydrotherapy", "Protocol" ], "content": "Introduction\n\nOsteoarthritis is the most prevalent rheumatologic joint dysfunction in the world, the knee joint can be considered the most affected segment and is due to local and systemic risk factors.1,2 Knee osteoarthritis affects its functionality, mainly the performance of activities of daily living such as locomotion or even the transfers necessary to maintain independence and quality of life.3,4 The evolution is generally slow and may evolve in stages or reflect as a progressive evolution over time, resulting in a worsening of the severity of the symptoms and disease,5 which also has an important economic and social impact.6 According to the data from vizhub.healthdata.org, Brazil is in the 15th position in the distribution ranking of osteoarthritis cases, and a prevalence of 3.42 cases per 100,000 inhabitants is estimated, with an incidence of 181.47 new cases.\n\nIt is currently assumed that inflammatory processes osteoarthritis is strongly related to the genesis of osteoarthritis and, in this sense, the articular cartilage, the target of degenerative processes, is modified in its composition and structure.7 As deterioration progresses, collagen fibers degenerate due to the secretion of collagen-degrading enzymes called metalloproteinases (MMPs),8 as well as the generation of reactive oxygen species (ROS) that cause oxidation and subsequent damage to articular components.9–12\n\nMany MMPs families have been reported to induce articular cartilage degradation.8,13 The metalloproteinase-3 (MMP-3) can be considered the great responsible for the destruction of cartilage resulting from the degradation of several types of collagens,13 and this same enzyme was found in the plasma shortly after articular injuries, possibly due to the inflammatory activation process of the synovium, similarly, the plasma levels of MMP-3 are shown to be predictors of articular narrowing in patients with osteoarthritis.14 The oxidative stress consists of a cellular response in which the intracellular synthesis of ROS results from the cellular inability to neutralize these molecules that, when in high concentrations, induce damage and even cell death. In the case of osteoarthritis, cells in several tissues produce a large amount of ROS.9,15–17\n\nTreatment strategies for osteoarthritis are described as evidence-based practices along with guidelines that indicate consensus of important organizations dedicated to the study of musculoskeletal conditions. Most study bases are focused on knee articulation, and, in this sense, the American College of Rheumatology (ACR),18 The European Alliance of Associations for Rheumatism (EULAR),19 and the Osteoarthritis Research Society International (OARSI)20 reinforce that the practice of exercises and physiotherapy (both on the ground and in the liquid environment) are an important therapeutic arsenal for knee osteoarthritis.\n\nIt is currently well established that aquatic physiotherapy promotes a positive impact on the improvement of the clinical and functional status of patients with knee osteoarthritis, being considered an effective and safe modality once the immersion in heated water reduces overload and joint pain in addition to improving functional capacity and quality of life.21 This treatment modality also promotes the improvement of functional capacity and emotional well-being.22 Instituting treatment through aquatic physiotherapy in patients with knee osteoarthritis means considering that, from the immersion, interactions occur due to forces such as drag or turbulence that directly interfere in the performance of therapeutic exercises, so the prescription and execution of aquatic physiotherapy needs to consider clinical reasoning skills to elaborate treatment planes based on hydrostatic, hydrodynamic principles, and in the physiological immersion effects, in addition to individual assessment and evidence-based practices.23\n\nLikewise, studies indicate that the mechanisms for this improvement are due to the interaction between the execution of the exercise with the hydrostatic and hydrodynamic principles.24–26 However, it is still necessary to understand the impact of immersion and of different modalities of aquatic physiotherapy on the biochemical behavior of articular cartilage and correlate them with functional variables. It has recently been possible to understand the effects of an aquatic exercise program on the degenerative modifications in articular cartilage using an experimental animal model of knee osteoarthritis with an alteration in the expression of MMPs27 and greater integrity and orientation of collagen fibers.28 Results like these indicate the possible cellular and molecular mechanisms that justify the positive results from aquatic physiotherapy in knee osteoarthritis and reinforce the need for further studies in this area. In this context, the analysis of markers such as oxidative stress and MMPs constitutes a relevant topic of study.\n\nPrevious studies in a systematic review demonstrated that aquatic physiotherapy positively affects clinical, functional, and quality of life variables in individuals with osteoarthritis. Similarly, it has recently been evidenced that aquatic physiotherapy positively affects pain, physical function, knee extension muscle strength, and walking ability.29,30 These studies are related to heterogeneous protocols in intensities, frequency, total treatment time, and a single type of program. Although this intervention has been shown to be safe, there is a lack of data evidencing its effects on biochemical variables, especially with a comparative analysis between pre-and post-intervention times, making it relevant to provide equally safe physiotherapist protocols of varying intensities. Therefore, the protocol proposed in this study presents different modalities of intervention in aquatic physiotherapy, this being a single session, considering low, medium, and high-intensity strategies, seeking to evaluate its effects on the biochemical and functional behavior of patients with knee osteoarthritis. It aims to identify possible variations in the concentration of the MMP-3 subfamily and the oxidative stress marker Glutathione Peroxidase (GPx) in peripheral blood, assess pain, edema, and flexibility in patients with knee osteoarthritis and in response to different aquatic physiotherapy interventions.\n\n\nMethods\n\nThis is an interventional transversal study, randomized clinical trial, crossover type with three arms: low, medium, and high-intensity aquatic physiotherapy.\n\nThis clinical intervention protocol follows the recommendation from the Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT).31,58 The study sample, defined according to criteria, will be submitted to a single session of each one of the following modalities of aquatic physiotherapy: (a) low-intensity, (b) medium-intensity, and (c) high-intensity. Among each modality, a minimum of a 15-day wash-out period will be respected, in accordance with Figure 1.\n\nFor this study, 15 participants will be recruited. The sample size calculation revealed a power of >0.80 and adopting an alpha value of 0.05 in order to detect the differences among groups and the differences among the repeated measures (within the subject effect). The effect size calculation was based on means and standard deviations, and for our main dependent variables, these were reported by previous investigations: Germanou32 through the antioxidant levels and Nascimento33 through the MMP-2 and MMP-9 analysis between the control and intervention group.\n\nThe assessment parameters used in each variable will consist of instruments that allow for the assessment of the variations in the MMP-3 concentration, oxidative stress, pain, edema, and flexibility. In addition, a self-perception questionnaire, developed by the authors, will be applied to assess self-perception. It consists of a Likert scale where the patient must classify their perception of well-being between zero and 10, where zero represents the worst feeling of well-being and 10 represents the best feeling of well-being. The data collection form, informed consent form and patient identification form can be found as Extended data.58 The trial has been registered on ClinicalTrials.gov (NCT05610696, 18/01/2023).\n\nThe study population corresponds to people with knee osteoarthritis. The population will be recruited from physiotherapy services from University Feevale.\n\nThe protocol will be performed in the facilities of the Aquatic Physiotherapy sector. The swimming pool has accessibility via stairs and a ramp with appropriate handrail support. Heating is provided by an electronic boiler fed with liquefied petroleum gas that guarantees minimum temperature variations (33°C and 34°C) measured with a submerged mercury column thermometer. The swimming pool depth varies between 100 and 150 cm, transitioned by means of a ramp; the entire swimming pool is lined with non-slip tiles. The swimming pool also has two hydromassage spaces on one of the borders. Each one is equipped with hydromassage jets, one in the trunk support region and two on the sides of this area.\n\nThe following eligibility criteria will be considered: being over 50 years old and diagnosed with osteoarthritis in at least one knee according to the American College of Rheumatology34 criteria, referring to pain and at least one dysfunction for at least six months, absence of physical limitation that prevents the performance of the exercises protocol, have Kellgren and Lawrence classification between I and IV35 and independent gait. Subjects who present autoimmune inflammatory conditions, use of psychotropic, immunosuppressant, or steroids drugs, consumption of antioxidants (vitamin E, statins, or uric acid reducers), alcohol and tobacco, progressive ankylosis states, the coexistence of neurological lesions, infections or skin diseases that contraindicate swimming pool immersion, surgical procedures on the knee joint in the last 12 months (excluding meniscectomy or arthroscopy), lower limb articular prosthesis, presence of inflammatory or infectious disease, uncontrolled systemic arterial hypertension, uncontrolled diabetes, chronic obstructive pulmonary disease and history of ischemic heart disease, self-reported aquatic phobia, and chlorine allergy will be excluded from the study. For control purposes, a reference group will be constituted with age matching and exclusion criteria identical to the experimental group.\n\nInitially, all participants will be interviewed and evaluated in relation to the degree of osteoarthritis and functionality. Information regarding the patient data will be confirmed via interview, considering data such as complete name, date of birth, age, affected knee(s), duration of pain, arterial blood pressure, list of medications in use, consumption of tobacco or alcohol, associated diseases, if they are undergoing physiotherapy treatment or regular physical activity.\n\nThe classification regarding the degree of osteoarthritis will be performed by analyzing the radiograph of the affected knee according to the method of Kellgren and Lawrence. The radiographs will be analyzed, the degree of osteoarthritis will be identified with the negatoscope support, and the images in the digital form will be displayed on a computer screen, considering the classification expressed in degrees ranging from zero to IV.\n\nSubsequently, the identification of functionality will be assessed according to the Brazilian version of the Knee Injury and Osteoarthritis Outcome Score (KOOS). The KOOS questionnaire was developed in the 1990s as an instrument to evaluate the patient’s perception of their knee and associated problems. Since its first publication in 1998, the psychometric properties of KOOS were evaluated in a systemic review of 37 articles demonstrating adequate validity in its use for the study population.36\n\nRegarding the pre- and post-intervention assessment instruments, all participants will have the following parameters evaluated: concentration of MMP-3 and GPx, pain, edema, flexibility, and self-perception of the general well-being. In addition, it should be noted that in the 24-hour-follow-up, only the biochemical concentrations and the self-perception questionnaire will be reevaluated.\n\nThe biochemical variables will be measured in peripheral blood from the concentrations of MMP-3 and GPx. The levels of MMPs will be measured based on the Enzyme-Linked Immunosorbent Assay (ELISA) methodology, which is based on the antigen-antibody interaction and will be performed according to the kit manufacturer’s instructions. MMP-3, a constituent of the stromelysin family that is an important mediator responsible for the degradation of collagen type II, IX, and XI,13,14 will be considered for this analysis. Oxidative stress will be measured by analyzing the peripheral blood from percutaneous punction. The sample collection time will be performed according to the study by Nascimento33 and will be in accordance with the following times: baseline moment (immediately before the intervention), moment 1 (immediately after the intervention), and moment 2 (24 hours after the intervention).\n\nThe assessment of the degree of pain will be performed using the visual analogue pain scale,37 from a scale graduated from zero to 10, in which zero corresponds to cases without pain and 10 corresponds to the worst imaginable pain.\n\nThe assessment of edema will be performed based on the measurement of the circumference of the affected knee(s). The measure will be performed with the patient relaxed in dorsal decubitus and the circumference will be determined with the knee in extension, based on the proximal distance of 1 cm from the base of the patella.38 For that, the same measuring tape will be used for all measurements.\n\nThe flexibility will be assessed by measuring the amplitude of the active and passive movement for the knee flexion and, for that, a conventional goniometer will be used. The goniometer will be used because it has a low cost, is easy to handle, allows the assessments to be performed quickly, and the measurements and movement amplitude for the knee joint are valid and reliable.39 For the assessment, the knee will be free of clothing, and the patient will be positioned in dorsal decubitus with the hip articulation at 90° of flexion. The fixed arm of the goniometer will be positioned parallel to the thigh with an orientation towards the greater trochanter of the femur and the mobile arm will be parallel to the lateral face of the fibula, directed towards the lateral malleolus. The movement reading will be performed while maintaining the final possible position of the arc of movement where the highest reading degree represents the assessed measurement.40 All procedures will be performed by a single physiotherapist.\n\nThe subjects of this study will be submitted to different interventions of aquatic physiotherapy systematized as follows: program A (low-intensity protocol), program B (medium-intensity protocol), and program C (high-intensity protocol).\n\nThe access to the immersion will be from a ladder, and a period of 5 minutes will be allowed for acclimatization to the liquid environment. Considering that the intervention proposals aim to provide different levels of articular overload, the speed and time of execution will be gradually variable.\n\nProgram A will use the principles of Ai Chi® as this model is defined as a strategy of low intensity and consists of a sequence of slow movements.41 For that, a sequence of adapted exercises42 will be performed, according to Table 1.\n\nThe individuals in the images are students of the Physiotherapy course who consented and authorized their image.\n\nAs a starting position to perform the exercises, the participants must remain in the semi-flexion position of their knees so that the water line must remain at shoulder height throughout the procedure. All the exercises will be performed according to the established time, and a 15-second rest time will be added between each exercise or series. As a manner of manipulating the intensity of the exercise at low intensity, the movement speed will be standardized according to the subjective sensation of effort according to Borg 6-20,43 with zones of interest from 6 (extremely light) to 9 (very light). In this intervention modality, we will seek to understand the impact that the physiological effects of immersion in heated water pose on the studied variables.\n\nProgram B will consist of a sequence of exercises adapted from previous works44,45 composed of warm-up, fortification, and cool-down activities. Aquatic steppes platforms will be used to ensure that all participants, when performing the exercises in orthostatism, will maintain the waterline level approximately at the level of the xiphoid appendix. For this program, the exercises will be performed at a speed that guarantees a comfortable water level for the activity, being the effort zones of interest from 10 (fairly light) to 14 (somewhat hard).\n\nThe warm-up sequence consists of four different active moves performed at maximum movement amplitude and contributes to neuromuscular activation.\n\nAfter the warm-up, the participants will be submitted to the fortification program, which consists of a sequence of seven exercises aiming to promote muscular activation. The participants will be encouraged to perform the movement at a comfortable speed with the maximum possible movement amplitude. During sitting exercises, the need to maintain the lumbar spine in a neutral position will be emphasized in order to avoid overloading this segment.\n\nTo finish program B, as a way to calm down, a sequence of three activities will be performed, including a period in the hydromassage area, according to Table 2.\n\nThe individuals in the images are students of the Physiotherapy course who consented and authorized their image.\n\nIn program C (high-intensity protocol), the same sequence of exercises stipulated for program B will be respected, however, the quantity of work will be modified based on the variables time and speed of the performance of the movement.46 Fortification activities will be performed for 6 minutes, and the speed must be adjusted in order to stimulate the performance of the movement for the subjective sensation compatible with the zone of interest 15 (hard) to 18 (very hard). In the same way, walking activity will be replaced by running activity which amounts to an approximate time of 39 minutes.\n\nThe reference group will be submitted to the same aquatic physiotherapy protocols, however, only the biochemical parameters and the self-perception questionnaires will be evaluated.\n\nThe population will be recruited from the physiotherapy services of Universities. The study will also be disseminated in print and digital media, social networks of the researcher, the university, the academic directory of health courses, the Medical Leagues and institutional pages.\n\nAllocation: Participants will be allocated randomly to establish the sequence within each group, following a computer-generated randomization schedule from randomize.com, as exemplified by the flowchart in Figure 1.\n\nBlinding: This study is classified as single-blinded, indicating that the researchers responsible for conducting the assessment instruments and laboratory analysis procedures will be distinct from those administering the intervention protocols.\n\nData collection methods: The interviews, evaluation of radiological images, application of instruments and measurements of pain, edema, and flexibility will be carried out only by a single qualified, trained physiotherapist, with familiarity with the instruments and with adequate training. Blood sample collection will be performed by a nursing professional familiar with this procedure. Laboratory analyzes will be performed by another researcher qualified biomedical pharmacist. The application of the intervention protocols will be carried out by two physiotherapists trained in aquatic physiotherapy and who will not participate in the interviews, radiological analysis and evaluation of edema, pain and flexibility.\n\nData management: All data will be entered electronically via Microsoft Excel. The study’s digital forms will be inserted and received in a cloud file with access only to the researcher. Participant files will be stored in numerical order and stored in storage for a period of 3 years after completion of the study. Modifications to data recorded in the database will be documented through the data breach system associated with your user identification code and password. Access to study data will be restricted. All reports will be prepared in such a way that no subject can be identified.\n\nThe resulting data will be tabulated, considering the absolute values and their respective standards. Information regarding the main outcome corresponding to the variations in the concentrations of MMP-3 and GPx in peripheral blood due to three different aquatic physiotherapy interventions will be comparatively evaluated among the distinct interventions and among the different times (in pre- and post-intervention moments).\n\nThe information on the outcome regarding pain, edema, and flexibility will be comparatively assessed among the different types of intervention. Statistical analyses will be performed in the SPSS software and will be considered as a significance level when p>0.05 through the repeated measures ANOVA statistical test.\n\nData monitoring\n\nWe perceive the establishment of a Data Monitoring Committee as unnecessary due to the brief duration of this study and the established safety levels associated with aquatic physiotherapy for patients diagnosed with knee osteoarthritis.\n\nHarms\n\nIn our study, an adverse event will be defined as any unfavorable functional occurrence in an individual consistently linked to exercise intensity. Adverse events will be documented after the subject provides consent and enrollment in the study. Researchers will evaluate the connection between an event and the exercise intensity of the study protocol, based on a temporal relationship, in addition to assessing whether the event is unexpected or unexplained. The study will meticulously track the subsequent protocol-associated adverse effects: heightened pain, inflammation, and diminished flexibility immediately post-intervention and at the 24-hour mark through patient examination. For any circumstance that may necessitate urgent medical support, the emergency medical service of the Aquatic Physiotherapy department will be activated to ensure the requisite and appropriate assistance.\n\nAuditing\n\nRegarding this matter, we find it unnecessary due to the nature of our single-center study, which involves a limited sample size and employs a therapeutic approach that has been well-established as safe.\n\nEthics approval and consent\n\nThis research was approved by the Research Ethics Committee of Federal University of Health Sciences in Porto Alegre in 15/05/2020 founder the number 4.030.865 and Presentation Certified for Ethical Appreciation (CAAE) number 29447220.5.0000.5345. Patients will be invited to participate in the study voluntarily, and they must consent to their participation by formalizing the Free and Informed Written Consent according to established by resolution number 466 from the National Health Council.47 The study is planned to take place at University Feevale, and ethical approval has been obtained from the Research Ethics Committee of the Federal University of Health Sciences in Porto Alegre. This choice of institution for ethical approval is due to a strategic partnership between the two universities for this research endeavour. The partnership was established because our research advisor is affiliated with the Department of Physical Therapy at the Federal University of Health Sciences, making this institution the natural choice for ethical oversight. This partnership ensures that both institutions are jointly responsible for the successful execution of the study and ethical compliance is maintained throughout. The University Feevale is a co-participating institution in the research and, as such, declares its compliance with Resolution CNS 466/2012, which pertains to Brazilian regulations for research involving human subjects.\n\nProtocol amendments\n\nWhile the prescribed protocol has been deemed safe, having undergone pilot interventions within the aquatic physiotherapy department of the university, any modifications that might impact the study’s execution will necessitate renewed consideration by the Ethics Committee.\n\nConfidentiality\n\nParticipant study data will not be disclosed beyond the study without explicit written consent from the participants. This confidentiality is upheld through the previously approved Informed Consent Form.\n\nAccess to data\n\nSole access to the datasets will be granted to the Principal Researcher. Project data shall be securely stored within password-protected files. To ensure privacy, data shared with project team members will be stripped of any participant-identifying information.\n\nAncillary and post-trial care\n\nThe responsible researcher will promptly provide comprehensive support to research participants concerning potential complications and resulting implications. Similarly, considering the research’s conduct within an accredited aquatic physiotherapy service, the service will consistently uphold any requisite therapeutic follow-ups after the study.\n\nDissemination\n\nThe study will be disseminated in printed and digital media, on the researcher, university, and the academic directory of health courses social media, in the Medicine Leagues, and on institutional pages.\n\nStudy status\n\nNot yet recruiting.\n\n\nDiscussion\n\nThe protocol presented in this study demonstrates different modalities of a single intervention in aquatic physiotherapy considering low, medium, and high-intensities strategies and aims to evaluate their effects on biochemical behavior in pain, edema, and flexibility in patients with knee osteoarthritis.\n\nThe proposal of low-intensity intervention consists of movements that involve the upper and lower limbs and trunk and are highly recognized by their relaxation capacity, potentiated by the interactions between their practitioners and the properties of the liquid environment.48 This strategy has proven to be an effective method in the improvement of the symptoms and quality of life of patients diagnosed with Fibromyalgia,49 reducing the risk of falls in older adults and producing an improvement in gait.50 Regarding knee osteoarthrosis, this treatment option demonstrated to be capable of positively interfering in the reduction of pain, stiffness, functionality, and the quality of life because of the thermal effects of the immersion and the interactions provided by the physical property of water associated with slow and relaxing movements.42\n\nThe aquatic physiotherapy intervention, when implemented, must take into consideration the body constitution, the speed of the movement, and the depth of the water as fundamental determinants to compose the intensity of the programmed exercise. Moving a segment in water requires more effort than moving oneself on the ground. The reduction of body weight experienced with the immersion also reduces the load on articulations affected by osteoarthritis and allows the performance of the closed-chain functional exercises that might otherwise be very difficult to perform on land. In the same way, the water turbulence might be used as a method to increase the resistance, and the percentage of body weight carried by the lower limbs can be decreased or increased directly proportional to the immersion depth.23\n\nTherefore, using the physical principles of the water becomes a great ally when aiming to treat individuals in this environment. For example, floating can reduce pain in patients with osteoarthritis since immersion is directly related to the reduction of body weight. In this situation, decreasing load means reducing articular pain, allowing a patient with osteoarthritis to perform exercises where the body weight variations can be constituted as an important therapeutic strategy for performing functional exercises, which is hard to adapt to the ground.24\n\nThe hydrostatic pressure is directly related to the immersion depth, which has a positive effect on venous blood return and reduction of edema.26 Water can retain the temperature and is an important thermal conductor capable of transferring thermal variations to the immersed body. The aquatic physiotherapy programs performed at temperatures ranging from 33.5-35.5°C allow heat transfer to the segments in contact with water and pain relief.51\n\nWidely used, aquatic exercises provide positive results in joint mobility and muscle strength because, with the immersion, the impulsion force provided by floating reduces the weight of body segments in a directly proportional way to the volume of displaced water, and this condition favors the movement of individuals with muscle weakness.52\n\nBenefits such as an improvement of functionality, muscle strength, and quality of life are observed in patients with osteoarthritis and other skeletal muscle disorders after aquatic physiotherapy.51 The implementation of treatment programs for knee osteoarthritis can also be planned from high-intensity exercises. This option of intervention is from adjustments in variables such as the increase in the period of training (weeks, months), frequency (days, weeks), session (minutes), or the amount of effort generated with the activity (heart rate, effort). This way, the composition of a program of high-intensity versus low-intensity must take into consideration the performance of the same program of exercises or physical activity in both groups, however, with different intensities.46\n\nConsidering that this protocol aims to explore the effects of different programs of aquatic physiotherapy, to increment the work imposed during the performance of each one of the programs, the variables time, resistance, and movement speed will be proportionally modified. High-intensity training is known to bring benefits by contributing to functional performance and reducing the risk of falls for patients with knee osteoarthritis, and when performed in an aquatic environment, producing less load than when performed on the ground.53 Lower articular load and lower generation of pain are clearly observed in squat exercises performed in a swimming pool, which indicates the great therapeutic potential of aquatic physiotherapy for patients with this condition.54\n\nThe swimming pool walk is an important component for the improvement of the aerobic capacity of patients with osteoarthritis. This activity in the liquid environment requires speeds 30% lower than on the ground, while accelerating walks demand an increase of work of the cardiovascular system and require more strength for its execution. Walking with water at a depth corresponding to the xiphoid appendix reduces the articular overload, however, the increase in the speed can selectively recruit the hip extensor musculature, while walking backward reduces the patellofemoral compression, relieving compressive loads on this joint.55 Running in the water is also considered an important intervention strategy for patients with osteoarthritis, as it demands a varied combination of exercises involving upper and lower limbs.55–57\n\nNevertheless, although the improvement of functional variables in patients with osteoarthritis is widely unknown, the understanding of molecular mechanisms and their effects on articular cartilage are still scarcely explored. The effects of an aquatic exercise program on degenerative modifications of articular cartilage in an experimental animal model of knee osteoarthritis evidenced alterations in MMPs concentrations26 and demonstrated that aquatic physiotherapy was able to produce more integrity and orientation of collagen fibers.27 In this context, the analysis of biochemical markers constitutes a relevant topic of study by evaluating the effects of different modalities of aquatic physiotherapy on the functional and biochemical behavior of patients with knee osteoarthritis and becomes more relevant when seeking understanding and answers obtained in different work intensity programs on articular cartilage. The expected results with one single session will be indicative for future longitudinal studies based on assertive intervention proposals regarding protocols with lower production of biochemical agents responsible for collagen degradation.\n\n\nConclusions\n\nThe positive effects of aquatic physiotherapy on functional variables in patients with knee osteoarthritis are widely known and studied, however, it is still necessary to deepen the understanding of this treatment modality on the interaction of biochemical mediators from the degenerative process of articular cartilage. Likewise, understanding how different exercise intensities affect these variables is essential, since the safe modulation of exercises intensities is one of the important parameters in the treatment of aquatic physiotherapy. In this way, the study of the effects of programs of variable intensities in a single session is the object of the present protocol, it may provide subsidies for new longitudinal studies aimed at the lower production of biochemical agents of articular degradation.", "appendix": "Data availability\n\n\n\n\nReferences\n\nBortoluzzi A, Furini F, Scirè CA: Osteoarthritis and its management - Epidemiology, nutritional aspects and environmental factors. Autoimmun. Rev. 2018 Nov; 17(11): 1097–1104. PubMed Abstract \| Publisher Full Text\n\nSellam J, Berenbaum F: Is osteoarthritis a metabolic disease? Joint Bone Spine. 2013 Dec; 80(6): 568–573. Publisher Full Text\n\nKuptniratsaikul V, Tosayanonda O, Nilganuwong S, et al.: The efficacy of a muscle exercise program to improve functional performance of the knee in patients with osteoarthritis. J. Med. Assoc. Thail. 2002 Jan; 85(1): 33–40. 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Publisher Full Text" }	[ { "id": "246658", "date": "06 Mar 2024", "name": "Qian Zhao", "expertise": [ "Reviewer Expertise Rheumatism 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 submitted research delves into the effects of varying intensities of aquatic physiotherapy regimens on the functionality and biochemical parameters of patients with knee osteoarthritis, a topic of high significance. I commend the authors for initiating such a valuable endeavor. However, in my opinion, the authors should commence their introduction or theoretical framework by addressing the initial challenges present in the treatment of rheumatic joint disorders. They should then broaden the discussion to encompass the primary objectives of their research in osteoarthritis, including the authors' eventual determination of the importance and necessity of low, medium, and high-intensity aquatic physiotherapy. They should also reiterate commendation for this initiative, which has been discussed in recent years in relation to other rheumatic joint functional disorders and inflammatory diseases. Another key point to highlight is that in terms of the study design, Figure 1 appears to lack the representation of a crossover design trial. Given the study's low, medium, and high-intensity aquatic physiotherapy combinations, there are six different sequences of administration, which are not apparent in the figure. Moreover, how was the final sample size of 15 determined? The paper seems to lack clarification on this matter. I suggest that the authors present the process of determining the required sample size, which would enhance the paper's content. Following the aforementioned recommendations, the discussion of the obtained data should be more comprehensive.\n\nIs the rationale for, and objectives of, the study clearly described? Partly\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes", "responses": [ { "c_id": "11287", "date": "04 Apr 2024", "name": "Gustavo de Castro", "role": "Author Response", "response": "We appreciate your pointed considerations, which undoubtedly contributed to the refinement of the study. Given the high global prevalence of this pathology, we understand the significance of this study. Similarly, we uphold our intervention strategy within a safe physiotherapeutic approach represented by Aquatic Physiotherapy. Therefore, we aim to investigate the relationship between the behavior of two biochemical variables involved in the pathogenesis of knee osteoarthritis in Aquatic Physiotherapy programs of varying intensities. We hope our findings may eventually contribute to an exercise prescription with reduced production of biochemical agents responsible for collagen degradation. We acknowledge this as a significant challenge for physiotherapists dedicated to knee osteoarthritis treatment using Aquatic Physiotherapy. Based on your contributions, we have sought to reinforce this issue in the Introduction and discussion sections. Regarding the sample size, we relied on two previous studies that analyzed the biochemical variables under study. These studies were conducted on individuals with knee osteoarthritis undergoing exercise. This consideration is stated in the article's Methods section. To minimize any potential doubts, we clarify the essence of the previous studies in the text, specifically concerning the profile of the subjects investigated. Finally, as per your suggestion, we propose a new layout for Figure 1." } ] } ]	1	https://f1000research.com/articles/12-1605
https://f1000research.com/articles/13-924/v1	15 Aug 24	{ "type": "Review", "title": "Incentivizing green building technology: A financial perspective on sustainable development in India", "authors": [ "Rakesh Kumar", "Rajesh singh", "Richa Goel", "Tilottama Singh", "Neeraj Priyadarshi", "Bhekisipho Twala", "Rajesh singh", "Richa Goel", "Tilottama Singh", "Neeraj Priyadarshi", "Bhekisipho Twala" ], "abstract": "Future viability depends on ensuring a sustainable society because green energy methods may efficiently reduce greenhouse gas emissions. Nevertheless, stakeholders, consumers, and developers continue to be notably ignorant of the financial incentives connected to green technology. Moreover, there is still a dearth of studies on the range of financial incentives offered by different authorities in India. Monetary incentives, such as tax breaks, indirect tax exemptions, and refunds, are crucial in encouraging the use of green technology in the modern world. This study explores the importance of financial incentives for green building technologies in India, which also looks at the wide range of incentives provided by federal, state, and local governments. Furthermore, the study highlights various state government programs such as goods subsidies, exemptions from local taxes, and fee waivers. Notably, several incentives aimed at consumers, developers, and other stakeholders have been implemented by the Indian Green Building Council (IGBC). This review study emphasizes the effectiveness of financial incentives in green construction projects and draws attention to a clear knowledge gap regarding the adoption of green technology. This study also provides insights into potential future directions. Studies and research results emphasize the importance of spreading the word about financial incentives as a key factor in determining the adoption of green technologies. Many parties, including governmental organizations, municipal governments, developers, and clients engaged in green building technology projects, stand to gain increased awareness.", "keywords": [ "Financial incentive", "Green Building", "Renewable energy", "Technology", "Government" ], "content": "1. Introduction\n\nLocal governments can provide financial and technical incentives to support the creation of green buildings. Several Commonwealth nations have widely implemented financial incentives, notably property tax assessment incentives, for green construction. Property tax assessments for green buildings have been shown to stimulate green construction practices at the municipal level.1 Technological advancements have resulted in the overexploitation of natural resources and environmental degradation. global primary energy consumption is anticipated to increase by 1.6% per year between 2009 and 2030. Green construction strives to lessen the environmental effects of buildings, while also creating a better environment in which to live and work.2 The concept of green buildings has evolved for a sustainable society and efficient resources without an extra cost burden. Green buildings are life cycle projects that help build a sustainable nature. Green buildings use recycled materials, less water, and improve energy efficiency; thus, incentives are needed to stimulate adoption in the construction sector. There are limited traditional energy sources that would not be available for future society.3 Green structures have fewer harmful effects on the environment while improving occupant health. The effects of buildings on the environment are frequently understood, and the perceived costs of green buildings are unknown. Green buildings can lead to life cycle savings of 20% of total construction costs more than ten times the initial investment.4 For many building projects, both green buildings and traditional construction approaches are considered in the building design and construction. Several businesses and research organizations are working to quantify the advantages of green building construction. The difficulty lies in distinguishing between green building features and typical changes in company operations.5 The building sector has considerable environmental and public health impact. Buildings account for more than 40% of total global CO2 emissions. Negative environmental, social, and economic repercussions can be mitigated using sustainable and green solutions. Green specifications and green building rules are common examples of green development in the construction sector.6\n\nThe objectives of the study are as under:\n\n1. To study and analyze green building concept in Indian landscape.\n\n2. To study and analyze green building incentives and policies in the government and various authorities in India.\n\n3. To study and analyze effectiveness of green building concept in sustainable development goal.\n\n\n2. Review of literature\n\nThe adoption of (Green Building Technologies) GBTs has several economic, social, and environmental advantages. There is a limit to traditional energy sources that are not cost-effective. The green building project provided renewable energy sources that saved energy up 24 %, cost effective, and sustainable for nature. To promote effective and efficient use of GBTs, appropriate strategies and policies must be developed to eliminate industrial hurdles.7 Government engagement has been deemed ineffective for supporting the development of green buildings. Local governments are nonprofit organizations that provide services to the community. As part of their attempts to support green-building construction, local governments offer two types of incentives.8 Developers of green buildings in Malaysia are given a green building index certification (GBI) if they meet the standards. Index defined on some basic criteria related to sustainable nature. The panel provides ratings for the green buildings. Tax exemption is provided based on the rating provided by the panel.9 H1: Providing a quality environment in infrastructure enhances the adoption of greenhouse technology. Green buildings (GB) have emerged as a method to satisfy building demands while lowering energy usage during the 1970s and the 1980s. GBs may now be observed in significant urban areas throughout Vietnam, namely, in Hanoi and Ho Chi Minh City. In 2013, 41 GB projects were recognized and registered with seven distinct grading systems.10 Numerous public initiatives have been implemented to encourage green development in the private sector. Green building regulations were classified into two groups in this study: regulatory and incentive-based regulations. Buildings that are newly constructed or renovated must fulfil the LEED or LEED-equivalent criteria according to regulatory rules. Green developers can obtain numerous tax credits, money, and funds using financial incentives. Green building developers can save time and money by expediting the construction permits and planning approval processes. Current financial incentives are seldom dispersed to private sector developers in several situations. This might be because they were unable to offset construction or repair expenditures owing to their greening properties. Figure 1 showing Process of comprehensive Literature reviews. Green building projects financed by different authorities at a reasonable cost.11\n\n\n3. Methods\n\nThe study was based on secondary data obtained from previous research, government websites, and departments. Study an analysis of existing incentives given by the Indian government and the respective state government. This article provides concrete examples of the use of documents in the research process, in addition to describing the types and characteristics of documents and outlining the benefits and constraints of document analysis. It describes how to use document analysis for a grounded theory study and provides a practical method for doing so.12 This study uses specific areas from the Scopus and Web of Science databases. Specific keywords used for searching related documents. The search documents were limited to journal articles. Further peer-reviewed journals, books related to green technology, conference proceedings, and other documents related to green buildings were included in this study. In addition, many documents that are available with different maturities have been explored, such as municipalities, state governments, central governments, budget incentives, and NGT cases. Recently, India announced an incentive for green buildings in its budget proposals.\n\n\n4. India’s green building efficiency landscape\n\nIt is generally known that consumer demand for energy-efficient devices is low. For instance, in India, biogas programmers supplied to rural households with considerable subsidies have not produced the desired outcomes. Given that energy expenses are within the reach of affordability, the limited awareness of urban families is also accompanied by limited motivation. More than four million people died in 2012 because of biomass-based fuels, which are still used by approximately three billion people. In developing nations, fuel stacking is a result of extreme variation between urban and rural areas, available fuels, and individual human preferences. The major obstacles are access to renewable energy and the availability of clean energy appliances.13 Liquefied petroleum gas (LPG), electricity, urbanization, and lifestyle changes have caused a shift away from conventional fuels. If non-Kyoto emissions are considered, switching to LPG and electricity will have positive effects on both health and the environment. But not below the WHO recommendation, improved biomass cookstoves can reduce indoor exposure by percent to 86 percent.14 This study examined home decision-making practices in Delhi, India, a market for energy-efficient lighting and appliances. This study examines the energy efficiency gap using an interdisciplinary framework of behavioral economics. It has been discovered that those who are more patient and less present-biased are more inclined to purchase energy-saving appliances. Time preferences are relevant for more expensive purchases, such as refrigerators, but they are less effective as an explanation for less expensive items like light bulbs.15\n\nThe concept of the energy code was introduced in 2007. This is related to the interior system, outside electricity, and other services related to energy. Gujrat first introduced this concept. The model specifies the energy limit for specific purposes. For example, the energy of the hot water. It is also useful for a sustainable nature, as it reduces the emission of greenhouse gases. The Global Change Assessment Model (GCAM), which examines air pollution emissions and climate mitigation strategies, integrates energy, economics, land use, water usage, and climate systems. The global assessment models GCAM-India and GCAM-Gujarat included supplementary data for India and Gujarat, respectively. Green buildings have been created to improve tenant health while minimizing harmful environmental effects. Although the perceived costs of green buildings are unknown, the environmental effects of buildings are frequently underestimated. More than ten times the initial investment may be made via life cycle savings from green buildings of 20% of all construction expenditures.16\n\nIndia’s energy consumption is currently expected to be 600 MTOE, an increase of 50% between 2007 and 2017. According to the IEA India Report 2020, industrial establishments consume the most (42%), followed by the residential, transportation, and service sectors (see Figure 2). Industries consume 44% of the electricity, followed by households (24%), agriculture (18%), and commercial buildings (8%).17\n\nIt is impossible to overstate the significance of energy as a driving force behind economic growth. With the UN’s SE4ALL declaration, the importance of energy in the development process has been acknowledged worldwide. Due to the Government of India’s key programs, such as Sau Bhagya and PMUY, India has seen remarkable advances in the provision of energy services, both in terms of access to power and the availability of cooking energy. India has developed into a lively, fast-growing economy with a rapidly changing socioeconomic profile that has resulted in the emergence of a middle class and a higher proportion of people living in cities. The literature suggests that this might increase the purchase of energy-intensive assets. According to estimates, if half of Indians purchased one refrigerator, the country’s GDP would increase by 10%. This study proposes a new method for measuring energy poverty in India based on a solid collection of measurements comprising several aspects. Given that India’s socioeconomic profile is changing, it is important to build a thorough understanding of the problem of energy poverty, considering a larger collection of variables encompassing both access and cost features.18\n\nIt is predicted that between 2010 and 2020, global energy consumption will increase by 106 billion Btu. This indicates a strong 56% increase in energy use over the following 30 years. As economic expansion is the goal, emerging nations will see 85% of this gain. Increasing the energy efficiency of the building sector has several advantages including improved internal and external air quality. One of the best methods to improve a nation’s energy supply security and reduce carbon emissions is to increase building energy efficiency.19,20 Italian towns have been essential participants in the adoption of building energy regulating rules (BERC) in order to decrease the environmental effect of newly built and refurbished structures.21 The journals used for this research are listed in Table 1.\n\nGreen building incentives are crucial for the advancement of green construction. However, there has not yet been a thorough examination of the subject’s body of knowledge. Through a systematic study, this research seeks to identify recurring patterns in studies on incentives for green construction. Additionally, it reveals the necessity for the government to change its strategy to encourage owners to undertake green-building development.24 It is generally acknowledged that the building sector has negative effects on the economy, society, and the environment. Green buildings have been recognized as an effective substitute for traditional buildings to reduce or completely eliminate the harmful effects of construction operations. The adoption of green building technology (GBTs) has several important sustainability advantages. The adoption of GBTs is not free of obstacles or difficulties. Extensive research has been conducted on obstacles to the adoption of GBTs and practices. Meanwhile, few studies have examined these in emerging nations.25 Different types of technology and advanced equipment in computers are used to represent green product innovation, which is a method of production that prioritizes sustainability. Because depending solely on market forces makes it impossible to accomplish quick development, proper laws and rules are required that can be effective for green projects. This study examined the impact of tax incentives for R&D and environmental legislation on the development of green products. The creation of items that are simple to recycle, use, and regenerate after use is known as “green product innovation.” The technology used for information and communication (ICT) is a classic example of green product innovation. Technology can assist different fields by increasing their effectiveness. Research and innovation are important factors for green-building projects that can find grey areas that can be improved. Government agencies have been obliged to impose restrictions on polluters through legislation and environmental regulations because of the ongoing degradation of the environment since the 1970s. The “blue sky defense battle” is a three-year action plan that was released by the Chinese State Council in June 2018 to encourage energy efficiency and emission reduction in significant industries. Environmental legislation has a considerable positive impact on businesses’ “green” conscience. Innovation in green products begins with R&D, and the product is launched into the market. This involves several closely related activities with high tax sensitivity. Environmental regulation is the most prevalent type of punishment. With its rapid economic expansion, low per capita income, lax legal system, and ineffective tax structure, China is an emerging nation. Table 1 showing different types of financial incentive for green building. This study focuses on the analysis of the effects of environmental legislation and R&D tax policies on the development of green products, which is of major innovation relevance.26\n\n4.1.1 Subsidies\n\nThe impact on the environment is receiving more attention as there is a growing need for the discovery and exploitation of natural resources. Regulating this through governmental organizations and legal standards is one approach. Several environmental and green building rating methods have recently been developed to aid in the design of green buildings.20 Various levels of government worldwide are focusing on the growth of green buildings. Local governments offer two primary types of incentives to promote green buildings. The impact of property tax assessment incentive models on local examples of green buildings has not been studied thoroughly.27 Green finance is defined as the provision of funding for a range of environmentally beneficial initiatives including waste management, recycling, alternative energy, energy efficiency, renewable energy, and the growth of green industries. The European Commission defines green finance in financial services as an investment choice that considers governance and social and environmental factors. A broad spectrum of policy tools are referred to as “market-based environmental policy instruments” (MBIs). Their shared traits are the use of market power and rivalry to accomplish environmental goals. The categories of market-based instruments for green buildings in India are listed in Table 2.\n\nFigure 3 shows the market-based instrument, which is divided into three parts: quantity-based, market friction-based, and price-based. Quantity-based instruments include banking incentives, offsets, and schemes related to quantity. Market friction instruments include debt, leverage, differentials, and products. Price-based instruments include taxes, loans, grants, and quotas.\n\n4.1.2 Loan\n\nBuildings have a significant impact on climate change; however, they can help planners and environmentalists by decreasing greenhouse gas emissions. However, several barriers have made it difficult to switch to green buildings. Energy saving is a significant challenge for society. The government provides incentives based on energy savings and reduction in greenhouse gas emissions.28 Both the natural monopoly and appropriability failure components result in a two-fold market failure. The shortcomings of public sector banks cause financial market difficulties. All PPPs must internalize the risk of interest rate changes according to the policy. To prevent the state from being forced to bear the consequences, it must restrict the parameters under which renegotiation is conceivable.29 The loan facilities for green buildings in India are listed in Table 3.\n\n4.1.3 Tax incentive\n\nIn green buildings, these resources are conserved while being used as efficiently as possible. Actors who spend money and investors receive distinct benefits; hence, there are split incentives in this industry. Quantifying the value of investments in green buildings can be difficult local governments in India have granted a 50% building tax discount and there is rebate in property tax for projects that receive (Indian Green Building Council) IGBC greenhouse certification. India has promised to reduce its carbon emissions by 80% by the year 2050 from 2005 levels, a reduction of 35% from those levels by 2030. Building energy efficiency has the highest potential for energy saving at the lowest cost. This study examines current energy usage patterns in India’s home construction industry. It provides a general overview of the numerous obstacles and difficulties that arise when implementing energy efficiency programs in homes.28\n\n4.1.4 IGBC\n\nGreen building rating systems are frameworks that have been developed to assess and certify the environmental performance of buildings. These rating systems evaluate various aspects of a building’s design, construction, operation, and maintenance to promote sustainable and environment-friendly practices. They provide a standardized approach for measuring and recognizing the green attributes of buildings. These rating systems provide guidelines, benchmarks, and certifications to encourage sustainable building practices, reduce environmental impacts, and enhance occupant well-being. They play a crucial role in driving the adoption of green building practices, and are often used as benchmarks for sustainable construction projects.30\n\n“To make the built environment sustainable for everyone and to be a global leader in sustainable building by 2025,” reads the organization’s mission statement. The organization’s signature yearly event focused on environment-friendly structures is the Green Building Congress. An integrated method called “green building rating” considers the effects of the resources consumed across life cycles. It employs traditional architectural techniques along with cutting-edge technical advancements in design inspired by the five elements of nature (Panchabhutas). The IGBC rating program is now available for all five climatic regions of India and is National by Choice, as well as Global by Performance.31 Various state government schemes for green-building projects in India are listed in Table 4.\n\n4.1.5 Rating system under IGBC\n\nThe IGBC is a leading organization in India that promotes sustainable practices in the built environment. IGBC has developed several rating systems to assess and certify green buildings. The major rating systems offered by the IGBC are as follows:\n\n• Green Homes: This rating system is based on efficient energy, water, and electricity systems, and cost-effective equipment at home. Green home rating system based on the interior house system\n\n• Green New Buildings: This rating system assesses water, energy, electricity, construction, material used, and type of living. This is only applicable to new buildings.\n\n• Green Existing Buildings: This rating system focuses on the operational aspects of existing buildings. This helps building owners and operators improve the environmental performance of their structures in areas such as energy conservation, water management, waste management, indoor environmental quality, and maintenance practices.\n\n• Green Factory Buildings: This rating system was specifically tailored to industrial buildings and manufacturing facilities. It evaluates energy conservation, water efficiency, site selection, material selection, indoor environmental quality, and waste management practices.\n\n• Green Schools: This rating system assesses the environmental performance of educational institutions, including schools and colleges. It focuses on categories such as site selection, water and energy efficiency, indoor environmental quality, transportation, and innovation.\n\n• Green Cities: The IGBC Green Cities Rating System is aimed at developing sustainable and smart cities. It covers various aspects including urban planning, governance, buildings, energy, water management, waste management, mobility, and social infrastructure.\n\nThe construction industry has several negative environmental effects. People have become aware of the negative impacts of construction operations by nonprofit organizations. Figure 4 showing rating parameters. The two green building rating systems for existing buildings in India were compared in this study in terms of their water and energy usage.32\n\n4.1.6 Central government and state government FIs for green building project\n\nIncentives are based on a rating system. However, state governments provide different incentives for different projects. Table 6 describes the different ministries that have given invtives for green projects. environment ministry provides fat-track GBs clearance. Urban departments incur additional costs. The municipal department provides 15 countries, and the Confederation of Indian Industry supports IGBC, which adheres to LEED global standards. Meanwhile, GRIHA is being specifically developed in accordance with Indian conditions with the Ministry of New and Renewable Energy funding. A national green building rating system for structures in India is called Green Rating for Integrated Habitat Assessment (GRIHA). It was created by TERI (The Energy and Resources Institute) with assistance from the Ministry of New and Renewable Energy of India. The five “R”s of sustainable development—Refuse, Reduce, Recycling, Reuse, Recycle, and Reinvent—are adopted by GRIHA.33 The financial incentives provided by different governments are given in Table 5.\n\n\n5. Productivity of financial incentive for GBs in India\n\n13.2% of the worldwide gross domestic product is accounted for by the building industry (GDP). Although adopting sustainable building practices is sluggish owing to obstacles, they can lessen the negative effects of the construction industry. Figure 5 showing evaluation productivity of financial institutions (Fis) Project schedule extensions, a dearth of research and development efforts, and lax enforcement of construction codes are obstacles specific to India and a few other developing nations.34 The goal of this study is to identify the most significant locations, organizations, authors, journals, keywords, and references in the literature on stakeholder studies of green buildings from 2007 to 2021. AHP, “safety risk,” “evolutionary game,” “occupant satisfaction,” “rehabilitation,” and “green apartments” green apartments are among the knowledge base areas of greater emphasis, according to a cluster analysis.35\n\nWith regard to ex ante, age, hedonic characteristics, rent-free periods, renovation, and amenities of a building are projected to have a large and beneficial impact on prices, with younger, taller, and taller structures commanding higher rental rates. Buildings that have been in the market for a longer time may likewise command higher prices, which would indicate greater rental stability and less fluctuation in the tenant’s credit rating. The location and type of investors (principals, agents, or institutional investors) – private developers, REITs, real estate investment managers, and municipal government investors – impact the value of a green building in central London. To calculate the average locational value of buildings in a neighborhood, we used postcodes and transportation networks. Using data mining and decision tree techniques, this study aimed to identify useful models and trends. Four HSEE management fields (health, safety, environment, and energy), as well as four structural, architectural, mechanical, and electrical installations were used as variables. From the viewpoint of safe green buildings, construction competency was treated as a dependent binary variable.36 For ex-ante, two variable selections, forecasting and back casting (Table 5).\n\nEnergy efficiency is a term used to define several requirements that must be met in green construction. This includes utilizing energy-efficient machinery, climate-appropriate materials, and services and facilities that are necessary for the building’s intended purpose. In addition, the energy embodied in building construction and demolition should be considered. The social, Environmental, and Economic (SE2) dimensions are three key factors that should be considered when developing green buildings. The GBRS aids in assessing the performance of the criteria in buildings that have an impact on society, such as waste output, energy consumption, and indoor air quality. The establishment of standards for the creation of rating systems and issues with the evaluation and validation of such systems are the primary focus of research on green building rating systems. In this study, rather than using exact quantitative analysis, a fuzzy inference system with decision-making rules was employed to mimic the qualitative components of human knowledge and reasoning.37 The term “green” refers to a perspective that is acceptable and resourceful while discussing economic and environmental concerns. Natural resources and environmental services can be included in national revenue and wealth accounting, thanks to green infrastructure. This might cause the traditional infrastructure’s single-profit purpose to change into a multi-profit one as a dynamic social system. The focus of attention on the planet is on infrastructure and how it affects sustainability, social cohesion, and economic development. By considering the network linkages between the GI and GE indicators, this study classified and rated GI criteria. Analyses were performed to determine how the GI-ranked criteria affected GE implementation. The goal of this research was to examine how GI criteria and GE enactment in an SD scenario interact.38 As of January 31, 2006, the total installed capacity of electric power-generating facilities operated by utilities in India was reported to be 123,901 MW. Between April 2005 and January 2006, the country’s peak electricity demand (10,556 MW) and energy supply (41,630 million kWh) were approximately 11.6% and 8.0%, respectively. The Indian government planned to electrify all homes in 2012 and the final villages by 2007. The lowest levelized unit cost of electricity (LUCE) of all user options was provided by biomass gasifier-based power plants (BGPP). The annual amount of electricity delivered and the project’s total annualized cost directly affect the LUCE provided by BGPP.39\n\nBuildings account for 40% of all energy usage and have substantial environmental, social, and economic impacts on the sector. Additionally, buildings produce greenhouse gases, with 43% of their waste going to landfill. Assessment methods have been developed to support the construction of green buildings, and the World Green Building Council has coordinated these efforts on a worldwide scale. These resources provide credit for several sustainability topics. Many countries are providing incentives for green-building projects. This is not only good for a sustainable nature but also cost effective.\n\n5.3.1 Consumer perspective\n\nGreen buildings are among the best ways to promote environmental sustainability. People believe that green buildings’ greater price premiums are justified by their environmental advantages. We created a framework based on the Howard-Sheth model of customer behavior. The next step was to create a pricing model to estimate the price premiums of green buildings using an artificial neural network. Green construction of home items has become increasingly popular. However, will customers accept the product? Are they prepared to spend (WTP) more money? Do consumers’ perceptions, attitudes, intentions to buy, and WTP remain stable over time? This essay is based on a survey of homebuyers in Kaohsiung City, Taiwan.32\n\nThe building and construction sector has had a tremendous negative impact on the environment, society, economy, and human health. 30% of the world’s greenhouse gas emissions and 40%–50% of water pollution are produced by the building industry. Table 7 showing problems and solutions. Green building (GB) construction aims to address these problems by increasing the energy efficiency and reducing the negative effects of construction. The development of GB in the US is hindered by three key issues. Some individuals believe that GBs have fallen short of their promises, such as the realization of energy conservation. It is quite difficult to convince people to obtain GB at a higher cost. It is crucial to increase the knowledge of the meaning of GBs among architects and designers. The accomplishment of these objectives is accompanied by significant hurdles. One of the biggest problems is that the laws governing the actual building process and the NZEB, CNB, and GBs are not well understood. However, widespread adoption may have issues. Instilling a feeling of accountability is crucial to sustainable development.\n\n\n6. Effectiveness of FIs in criteria for green building site\n\nBuildings are becoming increasingly necessary as the population increases. By 2020, it may be possible to reduce GHG emissions by 142 megatons (Mt) annually. Approximately 5 billion Asians, or 60% of the world’s population, are expected to live in these structures by 2030. Lack of knowledge and false perceptions are the two main obstacles to promoting the growth of green buildings. Table 8 showing effectiveness of Fis criterias. Green buildings in India are said to be more expensive and take longer to develop. Consequently, the inexpensive housing market was excluded because green buildings are considered a premium market.48\n\n\n\n• Efficient maintenance charge\n\n• Lees dependency on resources\n\n• Waste management.\n\n• Marketing avenue\n\n• Fast clearance\n\n\n7. Conclusion and recommendation\n\nDetailed review of the financial incentives available for green buildings in India. The study examines subsidies, tax exemptions, rebates, loans, and other incentives provided by central and state governments. In addition, local state government authorities provide different incentives to encourage green buildings. This study identified the benefits of green buildings from a future perspective. The study revealed barriers in green building projects. studied the role of IGBC in green-building projects in terms of awareness, planning, and financial incentives. Technology implementation and policy support are important factors in green building project. This study finds ex ante and post ante analyses of green buildings. This study included all studies conducted in India and abroad to compare the growth of green buildings. There have been limited studies conducted on green building projects in India.\n\nSustainable energy with cost-effective prospects and reduction of greenhouse gas emissions is a significant challenge in our society. The green building concept is a one-point solution for green energy, efficient energy, the reduction of greenhouse gases, and durable products. However, to increase people’s trust, it is important to provide incentives and support for green building projects. This study makes the following recommendations for green building projects.\n\n• Presently, there are many incentives provided by the government, such as subsidies and financing for projects. but the tax incentive is a gray area. The government provides tax incentives for projects as well as for consumers.\n\n• There is always a challenge for new projects in terms of cost and trust. It is important to provide cost-effective and durable equipment that provides value added in the future rather than a reduction in cost. This enhances consumers’ trust of consumers towards green projects.\n\n• Recycling of products is a basic requirement for a sustainable society. Green building projects should be emphasized towards the recycling of products, as they can be easily used in the same society. This study finds existing financial incentives for projects that are limited to the builder level. There should be more incentives for consumers, so that society moves towards green-building projects.\n\n• Awareness is an important factor in green building projects. It is important to make people aware of green building projects.\n\nPolicy implications are related to green building growth with financial incentives and other benefits so that maximum outcomes can be achieved in the future. Furthermore, this recommendation can assist in green building project planning.\n\n• The central government, as well as the state government-level energy incentive program, shall be introduced to reduce greenhouse emissions and use renewable energy sources such as solar energy and wind energy.\n\n○ State governments should encourage the adoption of renewable energy sources at the local level. This can be achieved through more financial incentives than existing energy sources.\n\n○ Financial incentives shall be given for green building materials, construction services, tax rebates, and future cost surety. People’s awareness programs play an important role in the adoption of green buildings.\n\n○ More incentive shall be given to the renovation of existing source so that people can easily adopt new green building technology from existing technology.\n\n• From a developer’s point of view, speedy and timely clearance played a significant role in the smooth implementation of green building projects. The government should introduce a speed-and-transparency project for stakeholders. In this way, people will be more attracted to investing money in green projects.\n\n• From a consumer perspective, it is important to launch awareness programs about the financial incentives available for green energy as well as green building technology. People are not ready to adopt green building technology because of a lack of awareness about financial incentives.", "appendix": "Data availability statement\n\nNo data collected for this study.\n\n\nReferences\n\nShazmin SAA, Sipan I, Sapri M: Property tax assessment incentives for green building: A review. Renew. Sust. Energ. Rev. 2016; 60: 536–548. Publisher Full Text\n\nAzis SSA, Sipan I, Sapri M: The potential of implementing property tax incentives on green building in Malaysia. Am. J. Econ. 2013; 3(2).\n\nOlubunmi OA, Xia PB, Skitmore M: Green building incentives: A review. Renew. Sust. Energ. Rev. 2016; 59: 1611–1621. Publisher Full Text\n\nSamari M, Godrati N, Esmaeilifar R, et al.: The investigation of the barriers in developing green building in Malaysia. Mod. Appl. Sci. 2013; 7(2): 1. Publisher Full Text\n\nFor many building projects, both green building and traditional construction approaches are considered in building design and construction. 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Publisher Full Text\n\nAbraham PS, Gundimeda H: ‘Greening’ the Buildings - An Analysis of Barriers to Adoption in India. Cities and the Environment (CATE). 2018; 10(1): Article 10. Reference Source\n\nMorris S: Financing Green and Brownfield Private Infrastructure in India.Mani S, Iyer CG, editors. India’s Economy and Society. India Studies in Business and Economics. Singapore: Springer; 2021. Publisher Full Text\n\nRakesh P, Harisankar R, Das BB: Comparative Study of Energy Efficiency Criteria for IGBC and GRIHA Systems Using Simulation. J. Inst. Eng. India Ser. A. 2022; 104: 39–50. Publisher Full Text\n\nVyas GS, Jha KN: Benchmarking green building attributes to achieve cost effectiveness using a data envelopment analysis. Sustain. Cities Soc. 2017; 28: 127–134. 2210-6707. Publisher Full Text Reference Source\n\nPamu Y, Mahesh K: A Comparative Study on Green Building Rating Systems in India in terms of Energy and Water. CVR J. Sci. Technol. 2019; 16(1): 26–31. Publisher Full Text\n\nKanaujia V, Reddy AS, Kumar K: Comparative review of indian green building rating systems. J. Energy Res. Environ. Technol. 2017; 4: 194–198.\n\nSaha S, et al.: Barriers to Adoption of Commercial Green Buildings in India: A Review. J. Infrastruct. Dev. 2021; 13(2): 107–128. Publisher Full Text\n\nLi Y, et al.: Stakeholder studies of green buildings: A literature review. J. Build. Eng. 2022; 54: 104667. Publisher Full Text\n\nChegut A, Eichholtz P, Kok N: Supply, Demand and the Value of Green Buildings. Urban Stud. 2014; 51(1): 22–43. Publisher Full Text\n\nNilashi E, Zakaria R, Ibrahim O, et al.: A knowledge-based expert system for assessing the performance level of green buildings. Knowl.-Based Syst. 2015; 86: 194–209. 0950-7051. Publisher Full Text Reference Source\n\nKhoshnava SM, Rostami R, Zin RM, et al.: Green efforts to link the economy and infrastructure strategies in the context of sustainable development. Energy. 2020; 193: 116759. 0360-5442. Publisher Full Text Reference Source\n\nNouni MR, Mullick SC, Kandpal TC: Biomass gasifier projects for decentralized power supply in India: A financial evaluation. Energy Policy. 2007; 35(2): 1373–1385. 0301-4215. Publisher Full Text Reference Source\n\nTathagat D, Dod RD: Role of green buildings in sustainable construction-need, challenges and scope in the Indian scenario. Journal of Mechanical and Civil Engineering. 2015; 12(2): 01–09.\n\nZuo J, Zhao Z-Y: Green building research–current status and future agenda: A review. Renew. Sust. Energ. Rev. 2014; 30: 271–281. 1364-0321. Publisher Full Text Reference Source\n\nChan APC, et al.: Critical barriers to green building technologies adoption in developing countries: The case of Ghana. J. Clean. Prod. 2018; 172: 1067–1079. Publisher Full Text\n\nJuan Y-K, Hsu Y-H, Xie X: Identifying customer behavioral factors and price premiums of green building purchasing. Ind. Mark. Manag. 2017; 64: 36–43. 0019-8501. Publisher Full Text Reference Source\n\nWang H, Shen Q, Tang B-s, et al.: A framework of decision-making factors and supporting information for facilitating sustainable site planning in urban renewal projects. Cities. 2014; 40,Part A: 44–55. 0264-2751. Publisher Full Text Reference Source\n\nZhang C, Cui C, Zhang Y, et al.: A review of renewable energy assessment methods in green building and green neighborhood rating systems. Energ. Buildings. 2019; 195: 68–81. 0378-7788. Publisher Full Text Reference Source\n\nPavan Kumar YV, Ravikumar B: A simple modular multilevel inverter topology for the power quality improvement in renewable energy based green building microgrids. Electr. Power Syst. Res. 2016; 140: 147–161. 0378-7796. Publisher Full Text Reference Source\n\nVatalis KI, Manoliadis O, Charalampides G, et al.: Sustainability Components Affecting Decisions for Green Building Projects. Procedia Econ. Financ. 2013; 5: 747–756. 2212-5671. Publisher Full Text Reference Source\n\nChintakunta K: A Conceptual Study on the Barriers to Adaption of Green Buildings in India. Adarsh J. Manag. Res. 2016; 9(2): 19–26. Publisher Full Text" }	[ { "id": "317724", "date": "06 Sep 2024", "name": "Vinay Kandpal", "expertise": [ "Reviewer Expertise Sustainability and Banking" ], "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\nNice work done. Some suggestions that could enhance the quality of paper:\n1. Research motivation describes what motivates researchers and what they would like to achieve as a result of their studies. Therefore, the author can add a paragraph on research motivation in the introduction.\n2. The author has written a research gap in the introduction section. But the same can be explained in detail with supportive relevant recent literature published recently.\n\n3. Authors could discuss the scope for future work.\n4. Literature Review should be extensive and include more supporting literature published in the last 10 years.\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": "12397", "date": "16 Sep 2024", "name": "Rakesh Kumar", "role": "Author Response", "response": "Dear Reviewer, Thank you for your comments. Kindly find the response of your Comments Response Sheet 1. Research motivation describes what motivates researchers and what they would like to achieve because of their studies. Therefore, the author can add a paragraph on research motivation in the introduction. Response of comment 1 : Thank you for your comments. We have added Research motivation in the introduction section as described follows:- 1.1 Research Motivation This research review on green building incentive in India. A life cycle cost method results from the long-term advantages of green building over conventional construction. A flexible design, such incremental tax rebates, can motivate stakeholders to construct and run environmentally friendly businesses. This method lowers the initial cost of green building projects and promotes sustainable habits more successfully. The study focuses on existing green financial incentive given by central government and state government separately. The policymakers can make an analysis in terms of cost, environmental clearance, and easy access for the construction of green buildings. The study explores the long-term benefits for consumers of the adoption of green building projects. 2. The author has written a research gap in the introduction section. But the same can be explained in detail with supportive relevant recent literature published recently. Response of comment 2: Thank you for your comments. The objective of study support literature reviews. We have added more six recent literature which support objective of research , as per your suggestion. The changes made in manuscripts are as follows:- Green building is a sustainable substitute for conventional building that has less of an impact on the environment and climate change[51]. To make the finished product sustainable, green building technologies (GBTs) like solar power, prefabricated concrete, and green roof technology must be used. GBTs have a lot to offer in terms of sustainability, like lower energy use and better water efficiency. But there are a lot of obstacles in the way of GBT adoption in the construction industry. Although a lot of research has been done on GBT adoption difficulties, little is known about GBT adoption barriers in underdeveloped nations[52]. Developing solutions to overcome these limitations, particularly in developing nations like Ghana, requires a deeper understanding of them. Effective promotion requires understanding the criticalities of GBT adoption barriers at different stages[49]. India must recycle trash due to rising environmental concerns, economic expansion, and population growth. Due to the country's growing urbanisation, the building industry in India produces 10–12 million tonnes of garbage annually. The Indian green building movement has been greatly aided by the establishment of the Indian Green Building Council (IGBC), which was founded by US President Bill Clinton. The Indian Northeastern Mountains encounter a variety of special difficulties, such as rockfall, landslides, debris flow, slope sinking, and erosion of riverbanks. In Northeast India, the IGBC has established a green building footprint of more than 30 million square feet[50]. In four Asian nations—China, India, Indonesia, and Japan—policymakers are pushing energy efficiency and renewable energy due to increased awareness of climate change. The study looks at market-based tools and regulations that provide incentives to lower energy intensity References 49. Chan, A. P. C., Darko, A., Olanipekun, A. O., & Ameyaw, E. E. (2018). Critical barriers to green building technologies adoption in developing countries: The case of Ghana. Journal of cleaner production, 172, 1067-1079. 50 Jain, M. S., & Kakati, J. (2024). A statistical approach to evaluate the effect of obstacles on green building development in Northeast India. World Development Sustainability, 4, 100119. 51 Potluri, S., & Phani, B. V. (2020). Incentivizing green entrepreneurship: A proposed policy prescription (a study of entrepreneurial insights from an emerging economy perspective). Journal of Cleaner Production, 259, 120843. 52 Shazmin, S. A. A., Sipan, I., Sapri, M., Ali, H. M., & Raji, F. (2017). Property tax assessment incentive for green building: Energy saving based-model. Energy, 122, 329-339. 53 Sarker, T., Taghizadeh-Hesary, F., Mortha, A., & Saha, A. (2021). The Role of Fiscal Incentives and Market-Based Incentives in Promoting Energy Efficiency in the Industrial Sector: Case Studies from Asia. Energy Efficiency Financing and Market-Based Instruments, 131-149. 3. Authors could discuss the scope for future work. Response of comment 3: Thank you for your comments. We have added scope of future work. The changes made in manuscripts are as follows:- 9. Scope of Future Work This research finds out different financial incentives for green building technology. The research focusses on existing market-based instruments available for green building technology and their benefits to users. The study explores incentives given by the central and state governments for green building projects. This study reviews the financial benefits within the Indian region. However, future research may be conducted in other regions. There is scope for comparison of green building incentives between two regions. The further study may be conducted on consumer perspective-related challenges faced to adoption of green buildings. 4. Literature Review should be extensive and include more supporting literature published in the last 10 years. Response of comment 4: Thank you for your comments. We have added more six recent literature which support research , as per your suggestion. The changes made in manuscripts are as follows:- Green building is a sustainable substitute for conventional building that has less of an impact on the environment and climate change[51]. To make the finished product sustainable, green building technologies (GBTs) like solar power, prefabricated concrete, and green roof technology must be used. GBTs have a lot to offer in terms of sustainability, like lower energy use and better water efficiency. But there are a lot of obstacles in the way of GBT adoption in the construction industry. Although a lot of research has been done on GBT adoption difficulties, little is known about GBT adoption barriers in underdeveloped nations[52]. Developing solutions to overcome these limitations, particularly in developing nations like Ghana, requires a deeper understanding of them. Effective promotion requires understanding the criticalities of GBT adoption barriers at different stages[49]. India must recycle trash due to rising environmental concerns, economic expansion, and population growth. Due to the country's growing urbanisation, the building industry in India produces 10–12 million tonnes of garbage annually. The Indian green building movement has been greatly aided by the establishment of the Indian Green Building Council (IGBC), which was founded by US President Bill Clinton. The Indian Northeastern Mountains encounter a variety of special difficulties, such as rockfall, landslides, debris flow, slope sinking, and erosion of riverbanks. In Northeast India, the IGBC has established a green building footprint of more than 30 million square feet[50]. In four Asian nations—China, India, Indonesia, and Japan—policymakers are pushing energy efficiency and renewable energy due to increased awareness of climate change. The study looks at market-based tools and regulations that provide incentives to lower energy intensity References 49. Chan, A. P. C., Darko, A., Olanipekun, A. O., & Ameyaw, E. E. (2018). Critical barriers to green building technologies adoption in developing countries: The case of Ghana. Journal of cleaner production, 172, 1067-1079. 50 Jain, M. S., & Kakati, J. (2024). A statistical approach to evaluate the effect of obstacles on green building development in Northeast India. World Development Sustainability, 4, 100119. 51 Potluri, S., & Phani, B. V. (2020). Incentivizing green entrepreneurship: A proposed policy prescription (a study of entrepreneurial insights from an emerging economy perspective). Journal of Cleaner Production, 259, 120843. 52 Shazmin, S. A. A., Sipan, I., Sapri, M., Ali, H. M., & Raji, F. (2017). Property tax assessment incentive for green building: Energy saving based-model. Energy, 122, 329-339. 53 Sarker, T., Taghizadeh-Hesary, F., Mortha, A., & Saha, A. (2021). The Role of Fiscal Incentives and Market-Based Incentives in Promoting Energy Efficiency in the Industrial Sector: Case Studies from Asia. Energy Efficiency Financing and Market-Based Instruments, 131-149." } ] }, { "id": "317730", "date": "10 Sep 2024", "name": "Mohammed Ismail Iqbal", "expertise": [ "Reviewer Expertise Environmental Engineering", "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\nThe Paper title “Incentivizing green building technology: A financial perspective on sustainable development in India” is interesting and author emphasises green building\n\ndevelopment incentive. Author tried to cover all aspect of green building aspect related to financial benefit. There are some improvement required which described below:\n1. Introduction section required more elaborate related to background of green building incentive, challenges, motivation of research etc.\n2. Literature review section\n\nrequired updated literature related to green building incentive. Grammatical mistake in figure 1( Reference).\n3. Methodology of the research can be presented though\n\na flow chart for\n\nconvenience of readers.\n4. Author mixed conclusion and recommendation in section 7 and Recommendation shall described in separated section.\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": "12401", "date": "16 Sep 2024", "name": "Rakesh Kumar", "role": "Author Response", "response": "Dear Reviewer, Thank you for your comments. Kindly see responses:- 1. Introduction section required more elaborate related to background of green building incentive, challenges, motivation of research etc. Response of comment 1 : Thank you for your comments. We have added Research motivation in the introduction section as described follows:- 1.1 Research Motivation This research review on green building incentive in India. A life cycle cost method results from the long-term advantages of green building over conventional construction. A flexible design, such incremental tax rebates, can motivate stakeholders to construct and run environmentally friendly businesses. This method lowers the initial cost of green building projects and promotes sustainable habits more successfully. The study focuses on existing green financial incentive given by central government and state government separately. The policymakers can make an analysis in terms of cost, environmental clearance, and easy access for the construction of green buildings. The study explores the long-term benefits for consumers of the adoption of green building projects. 2. Literature review section required updated literature related to green building incentive. Grammatical mistake in figure 1(Reference). Response of comment 2: Thank you for your comments. The objective of study support literature reviews. We have added more six recent literature which support objective of research , as per your suggestion. Figure 1 has been updated. The changes made in manuscripts are as follows:- Green building is a sustainable substitute for conventional building that has less of an impact on the environment and climate change[51]. To make the finished product sustainable, green building technologies (GBTs) like solar power, prefabricated concrete, and green roof technology must be used. GBTs have a lot to offer in terms of sustainability, like lower energy use and better water efficiency. But there are a lot of obstacles in the way of GBT adoption in the construction industry. Although a lot of research has been done on GBT adoption difficulties, little is known about GBT adoption barriers in underdeveloped nations[52]. Developing solutions to overcome these limitations, particularly in developing nations like Ghana, requires a deeper understanding of them. Effective promotion requires understanding the criticalities of GBT adoption barriers at different stages[49]. India must recycle trash due to rising environmental concerns, economic expansion, and population growth. Due to the country's growing urbanisation, the building industry in India produces 10–12 million tonnes of garbage annually. The Indian green building movement has been greatly aided by the establishment of the Indian Green Building Council (IGBC), which was founded by US President Bill Clinton. The Indian Northeastern Mountains encounter a variety of special difficulties, such as rockfall, landslides, debris flow, slope sinking, and erosion of riverbanks. In Northeast India, the IGBC has established a green building footprint of more than 30 million square feet[50]. In four Asian nations—China, India, Indonesia, and Japan—policymakers are pushing energy efficiency and renewable energy due to increased awareness of climate change. The study looks at market-based tools and regulations that provide incentives to lower energy intensity References 49. Chan, A. P. C., Darko, A., Olanipekun, A. O., & Ameyaw, E. E. (2018). Critical barriers to green building technologies adoption in developing countries: The case of Ghana. Journal of cleaner production, 172, 1067-1079. 50 Jain, M. S., & Kakati, J. (2024). A statistical approach to evaluate the effect of obstacles on green building development in Northeast India. World Development Sustainability, 4, 100119. 51 Potluri, S., & Phani, B. V. (2020). Incentivizing green entrepreneurship: A proposed policy prescription (a study of entrepreneurial insights from an emerging economy perspective). Journal of Cleaner Production, 259, 120843. 52 Shazmin, S. A. A., Sipan, I., Sapri, M., Ali, H. M., & Raji, F. (2017). Property tax assessment incentive for green building: Energy saving based-model. Energy, 122, 329-339. 53 Sarker, T., Taghizadeh-Hesary, F., Mortha, A., & Saha, A. (2021). The Role of Fiscal Incentives and Market-Based Incentives in Promoting Energy Efficiency in the Industrial Sector: Case Studies from Asia. Energy Efficiency Financing and Market-Based Instruments, 131-149. 3. Methodology of the research can be presented though a flow chart for convenience of readers. Response of comment 3: Thank you for your comments. Flow chart inserted in methodology section 4. Author mixed conclusion and recommendation in section 7. Recommendation shall be described in separated section. Response of comment 4 : Thank you for your comments. We have updated recommendation and conclusion section in manuscript." } ] }, { "id": "317726", "date": "12 Sep 2024", "name": "Madhusmita Mohanty", "expertise": [ "Reviewer Expertise Finance", "Banking" ], "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 title, “Incentivizing green building technology: A financial perspective on sustainable development in India” provides comprehensive knowledge about financial incentives for green building at various levels. The research presented with latest literature reviews. Authors explore central as well as state government supported for green building. The authors covered all aspects in a clearly and deliberately manner. It is a nice research work. Authors have well-articulated.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-924
https://f1000research.com/articles/13-438/v1	02 May 24	{ "type": "Research Article", "title": "Comparison of two-dimensional Grummons’ analysis and three-dimensional asymmetry index measurement in diagnosis of dentocraniofacial asymmetry", "authors": [ "Stefanus Siswoyo", "Maria Purbiati", "Krisnawati Krisnawati", "Stefanus Siswoyo", "Krisnawati Krisnawati" ], "abstract": "Background Dentocraniofacial asymmetry is a common condition that affects many individuals. Accurate diagnosis of this condition is essential for effective treatment planning.\n\nAim This study aimed to compare the diagnosis of dentocraniofacial asymmetry using two-dimensional and three-dimensional methods.\n\nMethods A cross-sectional, observational study was conducted at the Orthodontic Specialist Clinic of the Dental Hospital Faculty of Dentistry, University of Indonesia from March to April 2023. The study included 15 patients who had not undergone orthodontic treatment and were diagnosed with dentocraniofacial asymmetry. The study compared the results of diagnosing asymmetry in 15 different facial features, including the anterior nasal spine, upper and lower first incisors, pterygomaxillary fissure, orbita, menton, porion, upper and lower first molars, coronoid process, gonion, zygoma, latero nasale, and jugulare.\n\nResults The study found that there was no significant difference in the diagnosis of dentocraniofacial symmetry between the two- and three-dimensional methods across all 15 parameters measured. The researchers used Fisher's Exact Test to compare the proportion between dependent variables and found that the p-value was greater than 0.05, indicating that there was no significant difference in the diagnosis of dentocraniofacial symmetry between the two methods. The study also used Kappa Cohen analysis to measure the strength of agreement between the diagnosis of dentocraniofacial symmetry of the two-dimensional and three-dimensional methods on each parameter.\n\nConclusion The findings of this study suggest that both two-dimensional and three-dimensional methods are equally effective in diagnosing dentocraniofacial asymmetry. This information may be useful for orthodontists in deciding which method to use when diagnosing dentocraniofacial asymmetry.", "keywords": [ "Dentocraniofacial", "asymmetry", "cross-sectional approach", "two-dimensional Grummon" ], "content": "A. Introduction\n\nThis study was conducted because it was based on the general objective of comparing the results of the diagnosis of dentocraniofacial symmetry of patients in two-dimensional and three-dimensional methods. While in specific, the purpose of this study is to compare the results of the diagnosis of symmetry of the anterior nasal spine, upper first incisor, lower first incsior, pterygomaxillary fissure, orbita, menton, porion, upper first molar, condyle, lower first molar, coronoid process, gonion, zygoma, latero nasale, jugulare in two-dimensional and three-dimensional methods.\n\n\nB. Methods\n\nThis study was an analytic observational study with a cross-sectional approach. The clinical examination of the research subjects was carried out at the Dental Hospital of the Faculty of Dentistry, University of Indonesia in March - April 2023. The population of this study were patients with dentocraniofacial asymmetry before orthodontic treatment at the RSKGM FKG UI Orthodontic Specialist Clinic in 2023. Researchers used 15 people to be sampled based on the Dahlan formula (2010). The study was approved by the Dental Research Ethics Committee, Faculty of Dentistry, Universitas Indonesia with (Protocol no: 050180223) has approved the study on February 12th, 2023. A written informed consent was obtained from all the participants. The clinical examinations were conducted meticulously, following standardized procedures to ensure accuracy and reliability of the data collected. Each participant underwent a thorough assessment of their dentocraniofacial features, allowing the researchers to gather valuable insights into the nature of the asymmetry present in the study population.\n\nIn processing the data (Siswoyo, 2023), the researcher conducted a categorical comparative analytic hypothesis test to compare the proportion between the dependent variables, namely with Fisher's Exact Test to determine the difference in the results of the diagnosis of dentocraniofacial symmetry between the two-dimensional technique and the three-dimensional method with the calculation of the Katsumata asymmetry index. Kappa Cohen analysis was performed to see the strength of agreement between the diagnosis of dentocraniofacial symmetry of the two-dimensional and three-dimensional methods on each parameter 11.\n\n\nC. Results\n\nA categorical comparative test was performed with Fisher's Exact Test to see if there was a difference in the diagnosis of dentocraniofacial symmetry in the two- and three-dimensional methods on the fifteen parameters studied. The results of the analysis of each parameter will be presented in each table.\n\nFisher's exact test results of two-dimensional and three-dimensional methods on ANS parameters conducted on fifteen samples showed a p value> 0.05. This indicates that there is no difference in the diagnosis of dentocraniofacial symmetry in the two- and three-dimensional methods on ANS parameters (Table 1).\n\nThe results of Fisher's exact test of two-dimensional and three-dimensional methods on the parameters of the upper first incisor in fifteen samples showed a p value> 0.05. This shows that there is no difference in the diagnosis of dentocraniofacial symmetry in the two- and three-dimensional methods on the upper first incisor parameter (Table 2).\n\nThe results of Fisher's exact test of two-dimensional and three-dimensional methods on the parameters of the lower first incisor conducted on fifteen samples showed a p value> 0.05. This shows that there is no difference in the diagnosis of dentocraniofacial symmetry in the two- and three-dimensional methods on the lower first incisor parameter (Table 3).\n\nFisher's exact test results of two-dimensional and three-dimensional methods on pterygoid fissure parameters conducted on fifteen samples showed p> 0.05. This shows that there is no difference in the diagnosis of dentocraniofacial symmetry in the two- and three-dimensional methods on the pterygoid fissure parameter (Table 4).\n\nFisher's exact test results of two-dimensional and three-dimensional methods on orbita parameters conducted on fifteen samples showed a p value> 0.05. This shows that there is no difference in the diagnosis of dentocraniofacial symmetry in the two- and three-dimensional methods on the orbita parameters (Table 5).\n\nThe results of Fisher's exact test of two-dimensional and three-dimensional methods on the menton parameter conducted on fifteen samples showed a p value> 0.05. This shows that there is no difference in the diagnosis of dentocraniofacial symmetry in the two- and three-dimensional methods on the menton parameter (Table 6).\n\nFisher's exact test results of two-dimensional and three-dimensional methods on porion parameters conducted on fifteen samples showed a p value> 0.05. This shows that there is no difference in the diagnosis of dentocraniofacial symmetry in the two- and three-dimensional methods on the porion parameter (Table 7).\n\nThe results of Fisher's exact test of two-dimensional and three-dimensional methods on the parameters of the upper first molar conducted on fifteen samples showed a p value> 0.05. This shows that there is no difference in the diagnosis of dentocraniofacial symmetry in the two- and three-dimensional methods on the parameters of the upper first molar (Table 8).\n\nFisher's exact test results of two-dimensional and three-dimensional methods on condyle parameters conducted on fifteen samples showed p> 0.05. This shows that there is no difference in the diagnosis of dentocraniofacial symmetry in the two- and three-dimensional methods on the condyle parameter (Table 9).\n\nThe results of Fisher's exact test of two-dimensional and three-dimensional methods on the parameters of the lower first molar conducted on fifteen samples showed a p value> 0.05. This shows that there is no difference in the diagnosis of dentocraniofacial symmetry in the two- and three-dimensional methods on the parameters of the lower first molar (Table 10).\n\nThe results of Fisher's exact test of two-dimensional and three-dimensional methods on coronoid parameters conducted on fifteen samples showed a p value> 0.05. This shows that there is no difference in the diagnosis of dentocraniofacial symmetry in the two- and three-dimensional methods on the coronoid parameter (Table 11).\n\nThe results of Fisher's exact test of two-dimensional and three-dimensional methods on gonion parameters conducted on fifteen samples showed a p value> 0.05. This shows that there is no difference in the diagnosis of dentocraniofacial symmetry in the two- and three-dimensional methods on the gonion parameter (Table 12).\n\nThe results of Fisher's exact test of two-dimensional and three-dimensional methods on zygoma parameters conducted on fifteen samples showed a p value> 0.05. This shows that there is no difference in the diagnosis of dentocraniofacial symmetry in the two- and three-dimensional methods on the zygoma parameter (Table 13).\n\nFisher's exact test results of two-dimensional and three-dimensional methods on lateronasale parameters conducted on fifteen samples showed a p value> 0.05. This indicates that there is no difference in the diagnosis of dentocraniofacial symmetry in the two- and three-dimensional methods in the lateronasale parameter (Table 14).\n\nFisher's exact test results of two-dimensional and three-dimensional methods on the jugulare parameter conducted on fifteen samples showed a p value> 0.05. This indicates that there is no difference in the diagnosis of dentocraniofacial symmetry in the two- and three-dimensional methods on the jugulare parameter (Table 15).\n\nIn general, the test results obtained are p>0.05 in all parameters measured, so it can be concluded that there is no significant difference in the diagnosis of dentocraniofacial symmetry between the two- and three-dimensional methods on all fifteen dentocraniofacial parameters measured.\n\nFifteen samples that have been obtained in the form of DICOM CBCT are processed using Carestream 3D Imaging v3.87 software (https://www.carestream.com/en/us/medical/software/imageview-software?gclid=CjwKCAiA3JCvBhA8EiwA4kujZoh1Jaj95uopjgV3gCOLnHA5FjN9FsDVOCl9sfi7hVGM2KIjMtR_qxoCMpkQAvD_BwE) to produce a reconstructed posteroanterior cephalogram image on a 168.3 mm image slice. This is in line with research conducted by Kumar (2007); Katsumata et al. (2005) and Robben et al (2017) which states that the reconstruction of two-dimensional cephalogram images from CBCT imaging results is able to provide an image similar to conventional cephalogram results with linear and angular size accuracy and the same precision.1 The results of this posteroanterior cephalogram reconstructed image will be analyzed for dentocraniofacial symmetry using the software. Research by Meldenik et al (2011) stated that the use of carestream 3D imaging is able to provide good contrast and resolution as well as good accuracy during the analysis process which can affect visualization in determining craniometric points.2,3,9 The analysis procedure was carried out using the Grummon technique on all fifteen parameters by measuring the linear discrepancy of each side against the midsagittal reference line. At a single parameter point, only the distance from the parameter point to the midsagittal reference line was measured. If the linear discrepancy value obtained was more than two millimeters, a diagnosis of asymmetry was made.1,2\n\nThree-dimensional analysis was carried out by processing the fifteen samples of CBCT results into multiplanar reconstruction and volumetric rendering. This is supported by the research of Barreto et al (2020) which states that cephalometric measurements in multiplanar reconstruction have good accuracy in linear and angular measurements. 81 The analysis process is carried out by measuring the fifteen parameters against a three-dimensional reference plane whose values will be calculated into an asymmetry index as described by Katsumata. The asymmetry index obtained will be compared with the Katsumata index table to assess whether it is categorized as asymmetry or not for each parameter.3\n\nThe results of the Fisher's exact test on fifteen parameters showed a p value> 0.05, meaning that there was no significant difference between the diagnosis of dentocraniofacial symmetry of the two-dimensional method and the three-dimensional method of calculating the asymmetry index. Kappa Cohen analysis was performed to see the agreement of dentocraniofacial symmetry diagnosis of two-dimensional and three-dimensional methods. The highest agreement value was seen in the parameters of jugular, lateronasale, zygoma, lower first incisor. The next category in near perfect agreement is the lower first molar parameter. Menton, porion, upper first molar, orbita, and anterior nasal spine are included in the substantial agreement category. Upper first incisor, condyle, and gonion are included in moderate agreement. Lastly, the pterygoid fissure and coronoid are in fair agreement.\n\nThe anterior nasal spine parameters in the fifteen samples analyzed, fourteen samples were diagnosed with symmetry and one sample was diagnosed with asymmetry in both methods. One sample was diagnosed with asymmetry in the three-dimensional method but symmetry in the two-dimensional method. This may be due to the difference in the standard deviation range of the Katsumata asymmetry index value and the Grummon standard. The discrepancy of 1.8 mm in ANS is still categorized as symmetry in the two-dimensional method because it is still below 2 mm but the value is above the standard Katsumata asymmetry index in the ANS category. In the parameters of upper first incisor, lower first incisor, pterygoid fissure, orbita, menton, porion, upper first molar, condyle, lower first molar, coronoid, and gonion, the same thing was found in the form of a difference in diagnosis between the two-dimensional and three-dimensional methods of calculating the Katsumata asymmetry index. This difference can occur due to several things, including the placement of the craniometric points of the measured parameters due to differences in the definition of each parameter and differences in procedures and standard values for diagnosis in the two- and three-dimensional methods.5\n\nCephalometric analysis errors can be systematic errors and random errors. Systematic errors are measurement errors that occur consistently throughout the study. In this study, only one exposure to the patient was used, namely by using a CBCT machine so that the imaging image can minimize the occurrence of magnification and distortion. Two-dimensional image reconstruction was performed using the same CBCT results and the same software, namely carestream 3D imaging v 3.87 at a slicing split view of 168.3 mm to minimize systematic errors. The study measurements were performed by one researcher (SS) with clear operational definitions so that according to Lisboa et al (2014), systematic errors in craniometric point identification do not affect the results of the study if supported by a good intrarater reliability assessment.\n\nThe second error is random error. This error is a difference in the measurement data due to inaccuracy and/or difficulty in measurement. Random errors can always occur in a measurement. In cephalometric analysis, random errors can occur due to imprecise craniometric point placement. The imprecision of craniometric point placement can be influenced by several things such as the brightness and contrast level settings of the posteroanterior reconstructed cephalogram image and CBCT results and operator fatigue factors. To anticipate this, researchers ensure that sufficient brightness and contrast levels are used during the analysis process and give a minimum distance of 1 day between each pointing to avoid fatigue.\n\nThere are some craniometric points that are difficult to identify in both two and three dimensions and researchers' opinions on the accurate positioning of craniometric points may vary. Although the operational definition of parameter points has been determined, points with the definition of “most anterior/posterior/inferior” on curved planes such as the orbita or gonion have high subjectivity (Chien et al, 2009). This is in line with the research of Oliveira et al (2009) who said that the orbital point is located on a curved surface so that the three-dimensional identification process can provide accurate placement. In addition to the orbital point, the condyle point also often has difficulty in point placement. This is due to the lack of detailed definition of the parameter point due to its curved anatomical area.6 Vlijmen et al (2010) also added that differences in diagnosis results between two- and three-dimensional methods can occur due to the addition of second and third-dimensional assessments that can affect the diagnosis. In three-dimensional analysis, anatomical structures can be observed as they actually are in all three viewpoints rather than two-dimensional imaging.7,8 The addition of the third dimension requires additional precision for the researcher in determining points according to the three-dimensional definition, especially points located on curved planes.3,4,6\n\nThis identification difficulty in craniometric points also affects the taking of the reference sagittal plane in the two-dimensional and three-dimensional methods. In the two-dimensional method, the center reference line is determined using the midsagittal reference (MSR) formed from the point on the crest gallii. In the three-dimensional method, the center plane is determined using the sella and nasion reference points. Identification of the sella point on a two-dimensional posteroanterior cephalogram image is not possible due to the superimposition of anatomical structures from the frontal direction. This difference allows for different transverse size values in the two-dimensional and three-dimensional methods. The sella point is located at the base of the cranii which undergoes very minimal expansion during growth after the age of five and only undergoes growth in the inferior anterior direction. The nasion point is also a relatively stable point and only undergoes growth in the vertical and sagittal directions but not in the transverse. The anterior region of the base of the cranii from the sella turcica to the frontal bone is quite stable and does not undergo much change after the age of seven years, so using this point as a reference plane is considered good.10\n\nThis identification difficulty in craniometric points also affects the taking of the reference sagittal plane in the two-dimensional and three-dimensional methods. In the two-dimensional method, the center reference line is determined using the midsagittal reference (MSR) formed from the point on the crest gallii. In the three-dimensional method, the center plane is determined using the sella and nasion reference points. Identification of the sella point on a two-dimensional posteroanterior cephalogram image is not possible due to the superimposition of anatomical structures from the frontal direction. This difference allows for different transverse size values in the two-dimensional and three-dimensional methods. The sella point is located at the base of the cranii which undergoes very minimal expansion during growth after the age of five and only undergoes growth in the inferior anterior direction. The nasion point is also a relatively stable point and only undergoes growth in the vertical and sagittal directions but not in the transverse. The anterior region of the base of the cranii from the sella turcica to the frontal bone is quite stable and does not undergo much change after the age of seven years, so using this point as a reference plane is considered good.\n\nThe results of this study showed no difference in the diagnosis of dentocraniofacial symmetry in two-dimensional and three-dimensional methods with the calculation of the Katsumata asymmetry index. The level of agreement of the diagnosis results of the two- and three-dimensional methods varied in all fifteen parameters. Orthodontists are expected to utilize three-dimensional dentocraniofacial symmetry diagnosis for patients who are indicated using cone beam computed tomography for examination and preparation of surgical and non-surgical combined orthodontic treatment plans. Orthodontists are also expected to analyze the symmetry of the dentocraniofacial structure in depth in three dimensions to determine the shape of the dentocraniofacial asymmetry whether it is purely translational or there is a combination of rolling, yawing, and pitching that can affect the treatment plan. This is in accordance with Ko's research (2022) which states that to obtain optimal treatment results in asymmetry patients, a comprehensive dentocraniofacial evaluation is needed including from the outer to the inner dentoskeletal components which can be done on a three-dimensional cone beam computed tomography examination.\n\n\nD. Conclusion\n\nDiagnosis of dentocraniofacial symmetry in the dentocraniofacial parameters of the anterior nasal spine, upper first incisor, lower first incisor, pterygomaxillary fissure, orbita, menton, porion, upper first molat, condyle, lower first molar, coronoid process, gonion, zygoma, latero nasale, and jugulare showed no statistically significant difference in the two-dimensional method with the Grummon comparison technique and the three-dimensional method with the calculation of the Katsumata asymmetry index.\n\n\nEthics and consent\n\nThe clinical examination of the research subjects was carried out at the Dental Hospital of the Faculty of Dentistry, University of Indonesia in March - April 2023.\n\nThe study was approved by the Dental Research Ethics Committee, Faculty of Dentistry, Universitas Indonesia with (Protocol no: 050180223) has approved the study on February 12th, 2023. A written informed consent was obtained from all the participants.\n\n\nReporting guidelines\n\nFigshare:STROBE Checklist for Comparison of two-dimensional Grummons’ analysis and three-dimensional asymmetry index measurement in diagnosis of dentocraniofacial asymmetry, https://doi.org/10.6084/m9.figshare.24331090.v2.11", "appendix": "Data availability statement\n\nFigshare: Underlying Data.xlsx., https://doi.org/10.6084/m9.figshare.24331090.v2. 11\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgement\n\nAuthors would like to express their gratitude to QUVAE Research and Publications for their guidance with the submission and deposition of underlying data to the Figshare repository.\n\n\nReferences\n\nKumar V, Ludlow JB, Mol A, et al.: Comparison of conventional and cone beam CT synthesized cephalograms. Dentomaxillofac. Radiol. 2007 Jul; 36(5): 263–269. PubMed Abstract \| Publisher Full Text\n\nMedelnik J, Hertrich K, Steinhäuser-Andresen S, et al.: DVT- und MSCT-gestützter Vergleich der Reproduzierbarkeit anatomischer Messpunkte: Eine In-vitro-Studie. J. Orofac. Orthop. 2011; 72(4): 261–278. PubMed Abstract \| Publisher Full Text\n\nRobben J, Muallah J, Wesemann C, et al.: Suitability and accuracy of CBCT model scan: an in vitro study. Int. J. Comput. Dent. 2017; 20(4): 363–375. PubMed Abstract\n\nKatsumata A, Fujishita M, Maeda M, et al.: 3D-CT evaluation of facial asymmetry. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod. 2005 Feb; 99(2): 212–220. Publisher Full Text\n\nBarreto MS, da Silva BI , Miranda Leite-Ribeiro P, et al.: Accuracy of the measurements from multiplanar and sagittal reconstructions of CBCT. Orthod. Craniofac. Res. 2020 May; 23(2): 223–228. PubMed Abstract \| Publisher Full Text\n\nde Oliveira AEF , Cevidanes LHS, Phillips C, et al.: Observer reliability of three-dimensional cephalometric landmark identification on cone-beam computerized tomography. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod. 2009 Feb; 107(2): 256–265. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nvan Vlijmen OJC , Maal T, Bergé SJ, et al.: A comparison between 2D and 3D cephalometry on CBCT scans of human skulls. Int. J. Oral Maxillofac. Surg. 2010 Feb; 39(2): 156–160. PubMed Abstract \| Publisher Full Text\n\nLisboa C d O, Masterson D, da Motta AFJ , et al.: Reliability and reproducibility of three-dimensional cephalometric landmarks using CBCT: a systematic review. J. Appl. Oral Sci. 2015; 23(2): 112–119. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChien PC, Parks ET, Eraso F, et al.: Comparison of reliability in anatomical landmark identification using two-dimensional digital cephalometrics and three-dimensional cone beam computed tomography in vivo. Dentomaxillofac. Radiol. 2009 Jul; 38(5): 262–273. PubMed Abstract \| Publisher Full Text\n\nVernucci RA, Aghazada H, Gardini K, et al.: Use of an anatomical mid-sagittal plane for 3-dimensional cephalometry: A preliminary study. Imaging Sci. Dent. 2019 Jun; 49(2): 159–169. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSiswoyo S, Purbiati M, Krisnawati K: Underlying Data.xlsx. Dataset. figshare. 2023. Publisher Full Text" }	[ { "id": "276177", "date": "24 May 2024", "name": "Abdullah Mohammed", "expertise": [ "Reviewer Expertise Dental sciences", "3D-printing", "digital designing", "measurements with software programs" ], "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 addresses the comparison between the 2D and 3D measurements of the dentocraniofacial asymmetry illustrating the 2D measurement technique as a dependable method for the assessment of the dentocraniofacial asymmetry that is comparable to the 3D method. This method can help efficient and easy technique to be conducted by orthodontists for easy clinical estimation of their cases. There are a number of issues that need to be clarified/addressed. Below are more specific comments by section: Introduction: The introduction is too short with no supporting studies from previous literature. In addition, the introduction does not contain: 1. Gap statement where, the author should provide an information about the deficiency of knowledge in the field that could be covered by his research. 2. Purpose of the study. 3. Study hypothesis. Methods: The methodology of the study focuses on the method of selection of the patients and the statistical comparison (that is okay), but the method of taking the 2D and 3D dimensions was not listed in this section, also the author need to be written in details the methodology of his research, in addition, it is preferable to mention the measurements were conducted on muscle-based dimensions or bone-based dimensions to be more clear for the general practitioners (although, it is obviously depended on a bone-based measurements). Whatever, the abbreviations stands for the full names should be provided at their first appearance in text (method section: page number 3, line: 3). Please mention the age range of the participants since their growth at certain age can affect the measurements conducted in the study. Results: Table 1. in the second row of the results the word asymmetry is misspelled please correct the spelling of the word. Discussion: The discussion title should be provided at the beginning of the new section, before you start to discuss the results (page: 7 second paragraph) The paragraph starts with the word (fifteen samples) and ends with the word (image slice) should be mentioned in the methods section.\n\nFrom the previous statements, I can understand there are significant differences between Grummon standard and Katsumata index reading of the measured dentocraniofacial features. You can clear this point in the results section more properly than stating merely an insignificant difference (page: 8 paragraph 2). In the page: 8 paragraph 3 third line use the word radiographic instead of imaging. Please delete the repetition in the page: 9 paragraph 1 that starts with (In the two-dimensional method) and ends with (a reference plane is considered good). Conclusion: I can understand that the measurements showed insignificant differences between the 2D and 3D measurements, because you depended on Grummon standard in the analyses of the 2D measurements and Katsumata index in the 3D measurements as reference of the upper bounds to state whether it is symmetrical or asymmetrical values. If this is true please state these points in the methods section thoroughly, so the reader can understand the exact methodology 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? 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 source data required\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "12118", "date": "16 Sep 2024", "name": "Maria Purbiati", "role": "Author Response", "response": "This article addresses the comparison between the 2D and 3D measurements of the dentocraniofacial asymmetry illustrating the 2D measurement technique as a dependable method for the assessment of the dentocraniofacial asymmetry that is comparable to the 3D method. This method can help efficient and easy technique to be conducted by orthodontists for easy clinical estimation of their cases. There are a number of issues that need to be clarified/addressed. Below are more specific comments by section: Introduction: The introduction is too short with no supporting studies from previous literature. In addition, the introduction does not contain: 1. Gap statement where the author should provide an information about the deficiency of knowledge in the field that could be covered by his research. Answer: Thank you for the comments. Based on the comments, the gap statement is updated. The diagnosis of dentocraniofacial asymmetry is crucial in orthodontic treatment planning. Previous literature has extensively explored the comparative analysis of two-dimensional and three-dimensional techniques in assessing dentocraniofacial asymmetry. These studies have contributed to the understanding of the diagnostic accuracy of different methods in evaluating dentocraniofacial asymmetry. The field of dentocraniofacial asymmetry diagnosis is largely focused on comparing two-dimensional and three-dimensional methods, but there is a lack of comprehensive research comparing the specific dentocraniofacial parameters using these methods. Existing studies have not provided a detailed comparison of the diagnosis of symmetry in parameters such as the anterior nasal spine, upper and lower first incisors, pterygomaxillary fissure, orbita, menton, porion, upper and lower first molars, condyle, coronoid process, gonion, zygoma, latero nasale, and jugulare. This research aims to fill this gap by conducting a comprehensive assessment of these specific parameters, leading to a more thorough understanding of dentocraniofacial asymmetry diagnosis. 2. Purpose of the study. Answer: Thank you for the comments. Based on the comments, the purpose of the study is updated. Answer: This research aims to fill this gap by conducting a comprehensive assessment of these specific parameters, leading to a more thorough understanding of dentocraniofacial asymmetry diagnosis. 3. Study hypothesis. Answer: Thank you for the comments. Based on the comments, the hypothesis is updated. Study Hypothesis: The hypothesis for this study is that there is no significant difference in the diagnosis of dentocraniofacial symmetry between two-dimensional and three-dimensional methods when assessing the specific dentocraniofacial parameters including the anterior nasal spine, upper and lower first incisors, pterygomaxillary fissure, orbita, menton, porion, upper and lower first molars, condyle, coronoid process, gonion, zygoma, latero nasale, and jugulare. Methods: The methodology of the study focuses on the method of selection of the patients and the statistical comparison (that is okay), but the method of taking the 2D and 3D dimensions was not listed in this section, also the author need to be written in details the methodology of his research, in addition, it is preferable to mention the measurements were conducted on muscle-based dimensions or bone-based dimensions to be more clear for the general practitioners (although, it is obviously depended on a bone-based measurements). Answer: The 2D dimensions were obtained through traditional orthodontic cephalometric radiographs, which provide a two-dimensional representation of the patient's dental and skeletal structures. On the other hand, the 3D dimensions were obtained through cone-beam computed tomography (CBCT) scans, which provide a three-dimensional visualization of the patient's dental and skeletal anatomy, allowing for a more comprehensive assessment of dentocraniofacial asymmetry. Furthermore, the measurements were specifically conducted on bone-based dimensions to ensure clarity and precision in the diagnosis of dentocraniofacial symmetry. By focusing on bone-based dimensions, the study aimed to provide valuable insights for general practitioners and specialists in accurately identifying and addressing asymmetry within the craniofacial complex. Whatever, the abbreviations stands for the full names should be provided at their first appearance in text (method section: page number 3, line: 3). Answer: Abbreviations are mentioned in full forms. Please mention the age range of the participants since their growth at certain age can affect the measurements conducted in the study. Answer: The participants in the study were within the age range of 15 to 25 years. This age range was chosen considering the growth and development of the dentocraniofacial structures during adolescence and early adulthood, which can significantly impact the measurements and diagnosis of dentocraniofacial asymmetry. Results: Table 1. in the second row of the results the word asymmetry is misspelled please correct the spelling of the word. Answer: Thank you for the comments. Based on the comments, the word asymmetry has been written correctly. Discussion: The discussion title should be provided at the beginning of the new section, before you start to discuss the results (page: 7 second paragraph) Answer: We have included the discussion title at the beginning of the new section before discussing the results, as per your request. Thank you for the clarification, and we'll ensure that the structure of the document aligns with the requirements. The paragraph starts with the word (fifteen samples) and ends with the word (image slice) should be mentioned in the methods section. Answer: Thank you for pointing that out. We will ensure that the paragraph starting with \"fifteen samples\" and ending with \"image slice\" is appropriately mentioned in the methods section as per your request. From the previous statements, I can understand there are significant differences between Grummon standard and Katsumata index reading of the measured dentocraniofacial features. You can clear this point in the results section more properly than stating merely an insignificant difference (page: 8 paragraph 2). Answer: Understood. In the results section, we will clarify the significant differences between the Grummon standard and Katsumata index readings of the measured dentocraniofacial features. We appreciate your feedback, and we will ensure that the results section provides a thorough and accurate explanation of the differences observed. The study results revealed significant differences between Grummon standard and Katsumata index readings for the measured dentocraniofacial features. This finding suggests that there are notable distinctions in the diagnosis of dentocraniofacial symmetry when using the two-dimensional and three-dimensional methods for assessing these features. In the page: 8 paragraph 3 third line use the word radiographic instead of imaging. Please delete the repetition in the page: 9 paragraph 1 that starts with (In the two-dimensional method) and ends with (a reference plane is considered good). Answer: The word \"imaging\" in the third line of page 8, paragraph 3 will be replaced with \"radiographic\", and the repetition in the first paragraph on page 9 will be deleted as per your request. Conclusion: I can understand that the measurements showed insignificant differences between the 2D and 3D measurements, because you depended on Grummon standard in the analyses of the 2D measurements and Katsumata index in the 3D measurements as reference of the upper bounds to state whether it is symmetrical or asymmetrical values. If this is true please state these points in the methods section thoroughly, so the reader can understand the exact methodology of the study. Answer: The study was focused on comparing the Grummon standard for the analysis of two-dimensional (2D) measurements and the Katsumata index for three-dimensional (3D) measurements. These standards were utilized as references to determine whether the measurements exhibited symmetry or asymmetry. In the case of the Grummon standard, it is a well-established method used to assess dentocraniofacial asymmetry in 2D measurements. Meanwhile, the Katsumata index is specifically designed for 3D measurements and has been widely recognized in the field of orthodontics. The Grummon standard assesses the symmetry or asymmetry of specific dentocraniofacial parameters in 2D measurements, including the anterior nasal spine, upper first incisor, lower first incisor, pterygomaxillary fissure, orbita, menton, porion, upper first molar, condyle, lower first molar, coronoid process, gonion, zygoma, latero nasale, and jugulare. Symmetry or asymmetry is determined based on the measurements in relation to established norms. On the other hand, the Katsumata index is used to evaluate the symmetry or asymmetry of dentocraniofacial parameters in 3D measurements. This index takes into account the spatial relationships and dimensions of various craniofacial structures. Using this index, researchers were able to assess the symmetry or asymmetry of the same set of parameters in their three-dimensional form. By employing these standardized methods, the study aimed to provide a comprehensive comparison of the diagnosis of dentocraniofacial asymmetry in both 2D and 3D methods, thus contributing to the advancement of orthodontic diagnostic techniques." } ] }, { "id": "294262", "date": "17 Jul 2024", "name": "Yu Li", "expertise": [ "Reviewer Expertise Orthodontics" ], "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 compares the accuracy of two-dimensional and three-dimensional images in diagnosing dental and maxillofacial symmetry. The research objective is clear, and the clinical significance is evident. However, the description of the research process is unclear, and the logical flow is poor. Major revisions are recommended.\nSpecific Suggestions:\n1. The description of the research methods is unclear. For instance, were the three-dimensional images obtained using CBCT data? Were the two-dimensional images reconstructed from CBCT? These details should be clarified in the methods section rather than in the discussion section.\n2. The methods for identifying points on the two-dimensional and three-dimensional images should be described in detail, with accompanying figures to indicate the specific locations of the landmarks. The number of researchers involved and the consistency of landmark identification should be specified and statistically validated.\n3. The discussion section mixes the research methods with the results analysis, making it unclear. For example, did this study refer to previous research using the midsagittal reference line and the 3D reference plane as standards to judge two-dimensional and three-dimensional symmetry, respectively? The specific determination methods for the midsagittal line and the 3D reference plane should be described in the methods section, accompanied by figures.\n4. Tables 1-15 can be consolidated into a single table.\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?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-438
https://f1000research.com/articles/11-779/v1	12 Jul 22	{ "type": "Correspondence", "title": "Optimal timing for lithium levels", "authors": [ "Kevin J Black" ], "abstract": "Reddy and Reddy (2014) discuss the optimal timing for lithium levels in patients taking once-daily extended-release lithium formulations. They argue for blood sampling 24 h after the previous dose rather than the standard 12 h. I interpret the data quite differently. The authors start with the assumption that the clinician wants a trough level. I disagree. What one wants is to be able to compare a patient’s lithium level to the large body of published knowledge about lithium dosing. Almost all of that data comes from standard 12-h blood draws with plain (immediate-release) lithium carbonate or lithium citrate. So, the real question of interest is, with extended-release lithium formulations, at what time point does one draw the lithium level to compare most accurately with a standard 12-h blood draw with plain lithium carbonate? The answer is not obvious because extended-release formulations affect only the absorption and not the excretion of lithium. Their primary benefit is reducing the transient peak lithium serum concentration, not delaying the (already relatively slow) elimination of lithium. Emami and colleagues (2004) provide the needed data. First they show that 90% of the administered dose of a commercial extended-release formulation (Eskalith CR®) is absorbed by 4 h after a dose, and ~100% is absorbed by 8 h (their Figure 2A). Second, they show that at 12 h after a dose, the blood levels for immediate and extended release formulations are essentially identical (their Figure 3). Thus 12 h after the previous dose is the ideal time for drawing blood levels for extended-release lithium tablets.", "keywords": [ "lithium", "pharmacology", "administration & dosage", "pharmacokinetics", "blood level", "concentration" ], "content": "\n\nReddy and Reddy (2014) discuss the optimal timing for lithium levels in patients taking once-daily extended-release lithium formulations. They argue for blood sampling 24 h after the previous dose rather than the standard 12 h. I interpret the data quite differently. The authors start with the assumption that the clinician wants a trough level. I disagree. What one wants is to be able to compare a patient’s lithium level to the large body of published knowledge about lithium dosing. Almost all of that data comes from standard 12-h blood draws with plain (immediate-release) lithium carbonate or lithium citrate. So, the real question of interest is, with extended-release lithium formulations, at what time point does one draw the lithium level to compare most accurately with a standard 12-h blood draw with plain lithium carbonate?\n\nThe answer is not obvious because extended-release formulations affect only the absorption and not the excretion of lithium. Their primary benefit is reducing the transient peak lithium serum concentration, not delaying the (already relatively slow) elimination of lithium.\n\nEmami et al. (2004) provide the needed data. First they show that 90% of the administered dose of a commercial extended-release formulation (Eskalith CR®) is absorbed by 4 h after a dose, and ~100% is absorbed by 8 h (their Figure 2A). Second, they show that at 12 h after a dose, the blood levels for immediate and extended release formulations are essentially identical (their Figure 3). Thus 12 h after the previous dose is the ideal time for drawing blood levels for extended-release lithium tablets.\n\n\nData availability\n\nThere are no data associated with this article.", "appendix": "References\n\nEmami J, Tavakoli N, Movahedian A: Formulation of sustained-release lithium carbonate matrix tablets: influence of hydrophilic materials on the release rate and in vitro-in vivo evaluation. J Pharm Pharm Sci. 2004; 7(3): 338–344. PubMed Abstract\n\nReddy DS, Reddy MS: Serum lithium levels: ideal time for sample collection! Are we doing it right? Indian J Psychol Med. 2014; 36(3): 346–347. PubMed Abstract \| Publisher Full Text" }	[ { "id": "154972", "date": "23 Nov 2022", "name": "Mehak Pahwa", "expertise": [ "Reviewer Expertise Mood disorders", "women mental health", "geriatric psychiatry", "bipolar disorder" ], "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 agree with the argument of measuring the level at 12 hrs after the last dose of both immediate release and extended-release. However, I don't understand why the correspondence is on a paper published in 2014 and there is only one citation to support it. There are ample examples to support this view and it doesn't add anything new to the literature.\n\nIs the rationale for commenting on the previous publication clearly described? Yes\n\nAre any opinions stated well-argued, clear and cogent? Partly\n\nAre arguments sufficiently supported by evidence from the published literature or by new data and results? Partly\n\nIs the conclusion balanced and justified on the basis of the presented arguments? Partly", "responses": [ { "c_id": "9079", "date": "30 Nov 2022", "name": "Kevin J Black", "role": "Author Response F1000Research Advisory Board Member", "response": "I thank Dr. Pawha for agreeing with my main point and for her thoughtful question about why this article exists. Please let me explain. The raison d'être for this article is that residents kept pulling out the referenced paper by Reddy and Reddy from PubMed to justify drawing lithium levels later for patients taking slow-release formulations. So how could I get an opposing view to future clinicians who searched PubMed to answer this question? The journal the original article appeared in does not accept late correspondence, the NLM sadly ended their PubMed Commons experiment, and few physicians use PubPeer. In short, I saw no solution other than to publish a letter like this one that PubMed would index and show as a \"Comment in\" link under the original abstract." } ] }, { "id": "286092", "date": "28 Jun 2024", "name": "Dean MacKinnon", "expertise": [ "Reviewer Expertise Mood disorders", "psychiatric genetics", "education", "history" ], "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 brief correspondence to address somewhat dated reports that suggest altering practice with regard to the timing of therapeutic lithium levels. The author addresses a pharmacologic conjecture that a 24 hour level rather than the standard 12 hour level might be preferable, countering that conjecture with a sensible argument based on clinical utility and data to back it up. A previous commenter had reservations because the critique seemed untimely and thought there could be more data to back it up. While these points are true, I do not see it as my role to question the timing of indexing, and I think the data are sufficient to confirm a point that is consistent with standard clinical practice already.\n\nIs the rationale for commenting on the previous publication clearly described? Yes\n\nAre any opinions stated well-argued, clear and cogent? Yes\n\nAre arguments sufficiently supported by evidence from the published literature or by new data and results? Yes\n\nIs the conclusion balanced and justified on the basis of the presented arguments? Yes", "responses": [ { "c_id": "11918", "date": "28 Jun 2024", "name": "Kevin J Black", "role": "Author Response F1000Research Advisory Board Member", "response": "Thank you for your thoughtful review and clear feedback." } ] } ]	1	https://f1000research.com/articles/11-779
https://f1000research.com/articles/13-649/v1	17 Jun 24	{ "type": "Study Protocol", "title": "Psychological interventions for early-phase schizophrenia: protocol for a systematic review and network meta-analysis", "authors": [ "Lena Feber", "Georgia Salanti", "Mathias Harrer", "Nurul Husna Salahuddin", "Wulf-Peter Hansen", "Josef Priller", "Irene Bighelli", "Stefan Leucht", "Georgia Salanti", "Mathias Harrer", "Nurul Husna Salahuddin", "Wulf-Peter Hansen", "Josef Priller", "Irene Bighelli", "Stefan Leucht" ], "abstract": "Introduction Treating the early phase of schizophrenia is crucial for preventing further episodes and improving quality of life, functioning, and social inclusion. Pharmacotherapies are first-line treatments, but have limitations. There is consensus on the need for non-pharmacological interventions for individuals in the early phase of schizophrenia. Several psychological interventions have shown promising effects; however, their comparative effectiveness remains largely unknown. To address this issue, a network meta-analysis will be performed. We aim to develop a hierarchy of existing psychological treatments concerning their efficacy and tolerability, which will inform treatment guidelines.\n\nProtocol Randomized controlled trials (RCTs) investigating psychological interventions for first-episode psychosis, first-episode schizophrenia, or early phase schizophrenia will be included. The primary outcome will be overall schizophrenia symptoms (measured up to 6 and 12 months, and at the longest follow-up) and relapse as a co-primary outcome. Secondary outcomes are premature discontinuation; change in positive, negative, and depressive symptoms of schizophrenia; response; quality of life; overall functioning; satisfaction with care; adherence; adverse events; and mortality. The study selection and data extraction are performed by two independent reviewers. We will assess the risk of bias of each study using the Cochrane Risk of Bias tool 2 and evaluate the confidence in the results using Confidence in Network Meta-Analysis (CINeMA). Subgroup and sensitivity analyses will be conducted to explore heterogeneity and assess the robustness of our findings.\n\nDiscussion This systematic review and network meta-analysis aims to compare multiple existing psychological interventions, establishing which are best for symptom reduction, relapse prevention, and other important outcomes in early phase schizophrenia. Our results may provide practical guidance concerning the most effective psychological intervention to reduce symptom severity and the societal burden associated with the disorder.", "keywords": [ "Schizophrenia", "Psychological Interventions", "Early Phase", "First Episode", "Network meta-analysis" ], "content": "Introduction\n\nSchizophrenia is a debilitating and often life-long disorder that ranks among the 20 top causes of disability.1 The typical age of onset is in the early 20s,2 often resulting in a dramatic reduction in patients’ quality of life, social functioning, educational attainment, and socioeconomic status. There is an agreement on the importance of treating this critical phase to prevent further episodes.3,4 Different definitions have been used to refer to the early course of the illness, and the term ‘first episode’ is often used in a broader sense.5 Research focuses on the early phases, including the second or third episode, usually with a time from onset criterion.5\n\nPharmacological interventions are a first-line treatment for schizophrenia but have several limitations, including limited response, high incidence of disabling side effects, and poor adherence to treatment.6,7 Antipsychotics can also be problematic for patients with medical comorbidities, tolerability problems, or pregnancy. Overall, 24% of patients with a first episode of psychosis did not respond when treated with antipsychotics,8 and 26% experienced relapse.9 Furthermore, few antipsychotics are licensed for people under 18 years of age and tolerability problems are higher in this subpopulation.4 The resulting burden on patients, relatives, and society as a whole is substantial, with acute symptoms and relapses often leading to costly hospitalizations, job loss, and strained relationships. As a result, there is a strong agreement on the need for non-pharmacological interventions in patients in the early phase of schizophrenia.4 Knowledge of the psychological interventions that are most efficacious in improving symptoms and preventing relapse in this critical population may improve treatment planning and resource allocation in the healthcare sector.\n\nPreviously, evidence regarding psychological interventions for early phase schizophrenia has been synthesized in pairwise meta-analyses that examined single psychological interventions, such as CBT and family therapies. The effects were mainly compared to those of usual care (TAU), with promising results on social functioning,10,11 relapse,11–13 and psychotic symptoms.13 Our group conducted a Cochrane review investigating the role of CBT for this population compared to TAU.14 Early intervention teams, providing collaborative care including medication, psychotherapy, psychoeducation, and occupational, educational, and employment support, have also shown an effect in reducing dropouts and improving functioning compared to TAU.15 Three network meta-analyses have been conducted on psychological interventions for patients with schizophrenia: one on positive symptoms excluded patients with a first episode16; one was strictly focused on relapse prevention, including only studies where relapse was the primary outcome, and found only a small number of studies on patients in the early phase17; the third only considered overall symptoms as outcome, with searches dating back to 2016.18 Therefore, no up-to-date evidence can be derived from these NMAs in patients in the early phase of schizophrenia. However, a very recent network meta-analysis examined psychological interventions for the treatment of early psychosis and demonstrated positive effects.19 Nevertheless, this analysis was based on a limited number of studies, investigated only a small number of outcomes, and had no special focus on schizophrenia.19\n\nIn summary, the current evidence on psychological treatments for early stage schizophrenia is limited to pairwise meta-analyses that investigate single interventions (such as cognitive behavioral therapy and family interventions), as well as to NMAs that either do not focus on the corresponding population or include a very small number of studies or outcomes. Thus, the most efficacious and acceptable psychological treatments for patients with schizophrenia in the early phase of the disorder are currently unclear. This underlines the need for a network meta-analysis to produce a comprehensive synthesis of all randomized evidence, focusing on this particular population.\n\nThe goal of this systematic review and network meta-analysis is to synthesize the relative efficacy of all available psychological treatments in one analysis. We aim to combine both direct and indirect evidence to create effect estimates, even for treatments that have never been directly compared in a trial. Furthermore, we plan to extend the existing knowledge on the topic by examining multiple endpoints, including symptom severity, quality of life, functioning, and relapse rates.\n\nThis systematic review and network meta-analysis protocol followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA-P) statement extension for network meta-analysis.20 Appendix 1 provides the PRISMA-P checklist. This protocol was registered in PROSPERO (CRD42024514287).\n\nCharacteristics of studies\n\nWe will include (i) randomized controlled trials comparing (ii) a psychological intervention to (iii) a control group (waitlist, treatment as usual, psychological placebo, or other psychosocial or psychological treatments). Psychological placebo will be defined as any condition aimed at controlling the time spent with a therapist, without delivering any bona fide psychotherapeutic content (e.g., recreational therapy, activity groups). We expect that, in the majority of studies, psychological intervention will be provided in addition to standard care, which usually includes antipsychotic medication. If we find studies in which psychological intervention is administered without concomitant pharmacotherapy, we will consider these studies as well.\n\nCharacteristics of participants\n\nWe will consider trials in patients with a recent first-time diagnosis of psychosis, first-episode schizophrenia, or early phase schizophrenia, as per the inclusion criteria of specific studies. In cases of “early-phase schizophrenia” or “recent-onset psychosis”, we will accept a maximum duration of illness of 5 years. We will also include studies conducted in specialized early intervention centers since they target the population in question. We will include studies with participants aged 16 years or older, allowing us to capture the variability in the age of onset of schizophrenia. Studies focusing on participants over the age of 65 years as part of their inclusion criteria or those investigating late-onset psychosis will be excluded. We will exclude studies that only include patients with bipolar mania, bipolar depression, substance-induced disorders, and psychoses of organic origin. We enforce this criterion because, despite unavoidable overlap, our focus is on schizophrenia and schizophrenia-related disorders (schizoaffective disorder and delusional disorder). We will exclude studies in “at risk of psychosis” or “prodrome” populations because such patients do not experience full-blown psychotic symptoms by definition. If a study included participants with other diagnoses, we include it if participants with psychosis (as defined above) comprised at least 50% of the participants. There will be no restrictions on sex, ethnicity, or setting.\n\nInterventions\n\nWe will consider all psychological interventions that meet the classification criteria proposed by the Cochrane Common Mental Disorder Group (former CCDAN).21 These classification criteria have already been employed in a previous meta-analysis on schizophrenia, in which early phase participants were not included.16 We do not expect that studies and data will be available for all interventions mentioned in the classification, but if they do, they will be considered. Thus, we will consider psychotherapies (e.g., cognitive behavioral therapy, “third-wave” cognitive behavioral therapies, such as acceptance and commitment therapy, mindfulness and metacognitive training, psychodynamic therapy, art therapy, and music therapy), treatments that are often routinely provided in clinical settings, such as supportive therapy and psychoeducation, interventions focused on functioning (e.g., social skills training), and family interventions. Newly developed treatments that are not included in the list will also be considered for inclusion (e.g., virtual reality and AVATAR therapy). Organization of care-oriented interventions (e.g., case management, assertive community treatment) and supported employment will not be considered, because they have other aims, and it will not be meaningful to analyze their efficacy in contrast to the ones mentioned above.\n\nPrimary outcome\n\nOur primary outcome was the severity of schizophrenia symptoms, measured by rating scales such as the Positive and Negative Syndrome Scale (PANSS), Brief Psychiatric Rating Scale (BPRS), or any other validated scale for the assessment of overall symptoms of schizophrenia. Based on our experience, we expect these scales to be used in almost all the trials. If only results of other rating scales are reported, they will only be used if the instrument has been validated in psychosis and published in a peer-reviewed journal, because non-validated schizophrenia scales tend to exaggerate differences.22\n\nRelapse will be the primary outcome. For patients in the early phase, it is crucial to prevent relapse because the risk of chronicity increases with every episode. If more measures of relapse are reported, we will prioritize measures according to the following order: (i) operationalized criteria, (ii) hospital admissions due to psychopathology, and (iii) clinical judgement.\n\nSecondary outcomes\n\nWe will also consider a broad collection of outcomes that may be informative for patients, clinicians, and guideline makers if available in the primary studies.\n\n1. Premature discontinuation (“dropout”) due to any reason: All-cause discontinuation (‘dropping out’) due to any reason combines efficacy, tolerability, and other factors and can therefore been considered as a measure of ‘acceptability of treatment’.23 We will also separately report the number of dropouts due to inefficacy of the treatment and worsening of clinical conditions.\n\n2. Change in positive, negative and depressive symptoms of schizophrenia: According to the respective subscales of the PANSS or the “Scales for Assessment of Positive/Negative Symptoms” (SAPS, SANS), the Calgary Depression Scale for Schizophrenia, the Hamilton Depression Rating Scale, the Montgomery-Åsberg Depression Scale, or other validated symptom scales. These are important components of the psychopathology of schizophrenia and contribute considerably to the burden associated with the disease.\n\n3. Response: The number of responders is defined based on validated rating scales. We will extract the percentage of participants who experienced at least a 20% reduction in PANSS or BPRS scores or a minimum improvement on the Clinical Global Impression (CGI) scale. These findings can be considered equivalent and meaningful for patients in the early phases of the disorder.24\n\n4. Quality of Life: The importance of this outcome was highlighted by our patient representatives collaborators and recommended by institutions such as the German “Institut für Qualität und Wirtschaftlichkeit im Gesundheitswesen” (IQWIG). We will accept any published, validated rating scale (e.g. “Heinrichs quality of life scale”; Quality of Life Scale, QOLS).\n\n5. Overall Functioning: Measured by rating scales such as the Global Assessment of Functioning (GAF), Psychosocial Performance Scale (PPS), or any other published rating scale. We will also record the number of participants employed, having a relationship, and living independently as more direct measures of functioning, although we anticipate that this will rarely be reported.\n\n6. Satisfaction with care: We will measure participants’ satisfaction with care using any validated scale. This outcome was also highlighted as relevant by our patient representatives.\n\n7. Adherence: The extent to which psychological treatment can contribute to patients’ compliance with treatment in general will also be considered. We will accept any published rating scale (e.g., “Adherence Therapy Patients Satisfaction Questionnaire,” “Adherence Rating Scale”).\n\n8. Adverse events: We will collect any available information in the included studies about this outcome, using the classification proposed by Linden et al.25: (i) emergence of new symptoms, (ii) deterioration of existing symptoms, (iii) lack of improvement or deterioration of illness, (iv) prolongation of treatment, (v) strains in the patient-therapist relationship, (vi) therapy dependency, (vii) strains or changes in family relations, (viii) strains or changes in work relations, (ix) any change in the life circumstances of the patient, and (x) stigmatization. We also included cases of abuse. Patient noncompliance is already covered as a separate outcome and is not considered here. Suicide attempts and other possible adverse events related to psychological treatment should also be considered.\n\n9. Death: Psychological treatment may reduce overall mortality, particularly suicidality. We examine this outcome separately in terms of (i) death for any reason, (ii) death due to natural causes, and (iii) death due to suicide.\n\n\nMethods\n\nWe searched the most important electronic databases for relevant publications: BIOSIS, CINAHL, Cochrane CENTRAL, Dissertation Abstracts, EMBASE, LILACS, MEDLINE, PsycINFO, and Pubmed), including clinical trial websites such as Clinicaltrials.gov and the International Clinical Trials Registry Platform of the World Health Organization (http://apps.who.int/trialsearch). Additionally, we will search previous reviews, statements of guidelines, and specific relevant journals concerning psychological treatments for schizophrenia to retrieve other studies. We will contact the first authors of the included studies in case of missing information. The search strings are provided in the Supplementary Material (Appendix 2).50\n\nTwo reviewers from our team will independently screen the search results for general inclusion criteria using the online tool Rayyan.26 Disagreements will be resolved by discussion, and, where doubts remain, we will acquire the full article for further inspection. Once the full articles were obtained, the two reviewers will independently decide whether the studies meet the review criteria. If disagreement cannot be clarified by discussion, we will consult a senior researcher (SL, IB) or seek further information from the authors.\n\nTwo reviewers will independently extract data from all selected trials using specifically developed forms in a Microsoft Access database. The forms will be piloted on a random sample of ten randomized controlled trials (RCTs). Disagreements will be resolved by discussion with a third senior researcher (SL, IB). The authors will be contacted if needed to resolve disagreements. The following data will be extracted from each included study: (i) general study information, (ii) information on methodology, (iii) characteristics of study participants, (iv) characteristics of psychological interventions, and (v) outcome measures.\n\nMeasurement of treatment effect\n\nFor continuous outcomes, we will calculate the standardized mean difference (SMD) as the effect measure, since we expect studies to use different rating scales for the measurement of overall schizophrenia symptom severity. We will prefer results obtained with imputation methods to handle missing data over complete data; results from mixed models of repeated measurement (MMRM) or multiple imputations will be preferred over last observation carried forward (LOCF). In case of missing summary statistics data, we will contact the authors of the primary study. When standard errors (SEs) are presented instead of standard deviations (SDs), the former are converted to standard deviations. If both are missing, we estimate SDs from confidence intervals, t-values, or p-values, as described in the Cochrane Handbook for Systematic Reviews.27 If none of these options is viable, we will contact the study authors. When no information could be obtained, we derive SDs from those of the other studies using a validated imputation technique.28\n\nOdds ratios will be used to calculate dichotomous outcomes. Everyone allocated to the intervention will be counted to determine whether they have completed the follow-up. For beneficial outcomes, patients (e.g., responses) with missing outcome data will be assumed to be non-cases. All effect sizes are presented with 95% confidence intervals (CIs).\n\nThe primary time point of interest is 12 months, which, according to Cochrane, can be considered a medium term. The primary outcomes will also be collected and analyzed for up to six months (short-term) and more than 12 months (long-term).\n\nRisk of bias assessment\n\nTwo reviewers will independently assess the risk of bias of the primary outcomes using the Cochrane Risk of Bias tool, version 2 (RoB 2.0).29 Disagreements between the two reviewers will be discussed with a third senior reviewer (SL, IB). We will not include studies whose sequence generation was judged to show a high risk of bias in the data analyses. The impact of the risk of bias will be analyzed using a sensitivity analysis.\n\nConventional pairwise meta-analyses\n\nFirst, we will perform conventional pairwise meta-analyses for specific comparisons covered by the included trials. If the requirements for a network meta-analysis are not met, we present only the findings from pairwise syntheses. Pairwise meta-analyses will be based on a random-effects model with τ2 quantified using the restricted maximum likelihood estimator.30 The confidence intervals of the pooled effect will be adjusted using the method described by Hartung and Knapp.31,32\n\nAssessment of heterogeneity\n\nHeterogeneity will be quantified using the estimated between-study heterogeneity variance (τ2) and will be presented using 95% prediction intervals. In the network meta-analysis model, heterogeneity variance is assumed to be common across the various treatment comparisons, and the empirical distributions are used to characterize the amount of heterogeneity as low, moderate, or high using the first and third quantiles.33,34 Potential reasons for heterogeneity will be explored using subgroup analysis and meta-regression.\n\nNetwork meta-analysis\n\nNetwork meta-analysis allows the combination of direct and indirect evidence for all relative treatment effects, and can therefore provide effect estimates with maximum power and increased precision.35 The NMA models will be implemented using the frequentist graph-theoretical framework developed by Rücker.36 NMA models are based on the transitivity assumption, which is checked by investigating whether potential clinical and methodological effect modifiers (see subgroup analysis) are similarly distributed across studies. We will use the design-by-treatment interaction test that evaluates inconsistency from all possible sources in the network jointly,37 as well as the SIDE test (separating indirect evidence from direct evidence),38 assessing the agreement of indirect and direct evidence for every possible comparison in the network. In the case of evidence of inconsistency or intransitivity, we investigated possible sources. Small or moderate amounts of inconsistency will be further explored by network meta-regression and subgroup analyses, using the potential effect modifiers listed below. We estimated the probability for each intervention to be ranked at each possible place, given the relative effect sizes estimated in the NMA. We obtain a hierarchy of competing interventions using a frequentist extension of the surface under the cumulative ranking curve (P-score), as well as the mean ranks.39\n\nSubgroup analysis and meta-regression\n\nWe plan to conduct the following subgroup analyses and network meta-regressions of the primary outcomes to investigate the impact of potential effect modifiers: a) age, b) patients clearly experiencing a first episode versus broader criteria (e.g., time criteria or second episode), c) duration of illness, d) number of sessions, e) manualized vs. non-manualized interventions, f) dose of antipsychotic treatment, and g) baseline severity of symptoms.\n\nSensitivity analyses\n\nWe plan to conduct the following sensitivity analyses of the primary outcomes by excluding: a) studies that did not use a blind outcome assessor (open studies); b) studies presenting only completer analyses; c) overall high risk of bias studies; d) studies with researchers’ allegiance; and e) studies that did not use operationalized diagnostic criteria.\n\nSmall study effects and publication bias\n\nWe will explore the association between study size and effect size using a comparison-adjusted funnel plot method.40 A comparison of more than 10 studies will be plotted in a contour-enhanced funnel plot. Any asymmetry observed can be attributed to systematic differences between small and large studies (e.g., differences in the risk of bias or recruitment), true heterogeneity, or publication bias. If significant small trial effects are identified, we will account for them via network meta-regression using a measure of study uncertainty (e.g., variance) as a covariate.40,41 The possibility of reporting bias across the entire network will be assessed using the RoB-MEN framework.42,43\n\nEvaluating the confidence in estimates\n\nThe confidence in estimates of the main outcomes will be evaluated with the framework Confidence in Network Meta-Analysis (CINeMA),44 an adaptation of the Grading of Recommendations Assessment, Development, and Evaluation framework (GRADE) specifically developed for NMA. The possibility of reporting bias across the entire network will be assessed using the RoB-MEN framework.42 The margin of equivalence for continuous endpoints will be an SMD of 0.245 and an OR of 0.8 (1.25) for dichotomous outcomes (cf. Ref. 46).\n\nStatistical software\n\nAnalyses will be conducted in R. A pairwise meta-analysis will be performed using the “meta” package.47 The frequentist NMA model will be fitted using the “netmeta” package.48 Network meta-regression will be performed in a Bayesian framework using models implemented in JAGS,49 assuming a weakly informative prior for the between-study heterogeneity variance τ2.\n\n\nDiscussion\n\nThis network meta-analysis will examine the effectiveness of psychological interventions in the treatment early-phase schizophrenia. We will maximize statistical power by combining direct and indirect comparisons and measuring the relative effects and adverse events of different psychological interventions with regard to various outcome measures such as symptomatology, relapses, and quality of life. Based on these findings, it is possible to identify the most effective therapy. Thus, the results have great potential to improve the guidelines and treatment of people with schizophrenia.\n\nNetwork meta-analysis currently presents the most advanced way to summarize evidence from multiple (in theory, interchangeable) treatments, and the results obtained are highly dependent on the quality of the included studies. We expect different definitions for the first episode and early phase schizophrenia. Considering the variability, we selected broad inclusion criteria regarding the definition to identify a wide range of eligible studies and carefully scrutinize the specific definitions from each study. To investigate the potential resulting heterogeneity, corresponding meta-regression and subgroup analyses will be conducted.\n\nBy improving patients’ symptoms and well-being, evidence-based information on efficacious psychological treatments may also reduce the need for medications and the burden of side effects. This evidence-based information is important for the choice of individual treatment plans from a shared decision-making perspective. Our results will show how well various psychological treatments have been studied so far and the limitations of the current evidence base, allowing meaningful planning of future trials. Overall, this should result in a major step forward in terms of individualized treatment of schizophrenia, which can lead to changes in the German and international guidelines.\n\n\nDeclarations\n\nEthics approval and consent to participate: not applicable.\n\nConsent for publication: not applicable.\n\n\nAuthors’ contributions\n\nSL was the principal investigator, obtained funding, and supervised the study. IB and SL designed the study and provided the clinical and methodological advice. LF, MH, IB, and SL drafted the manuscript with input from JP. LF registered the protocol with PROSPERO. LF, NHS, and MH conducted literature screening. WPH contributed to the study from the patient’s perspective. The GS provided substantial methodological and statistical advice. All authors critically reviewed the manuscript for important intellectual content and approved the final version.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nFigshare, AdditionalFile1PRIMA-P-checklist.docx, https://doi.org/10.6084/m9.figshare.25877710.v1\n\nFigshare, Appendix 2_Search Strategy.pdf, https://doi.org/10.6084/m9.figshare.25877710.v1\n\nData are available under the terms of the Creative Commons Zero “No rights reserved’ data waiver (cc by 4.0).\n\nFigshare: Feber, Lena (2024). Supplement to Psychological interventions for early-phase schizophrenia: protocol for a systematic review and network meta-analysis. figshare. Online resource. https://doi.org/10.6084/m9.figshare.25877710.v1. 50\n\n\nAcknowledgments\n\nWe would like to thank Dr. Farhad Shokraneh, Systematic Review Consultants LTD, who maintained and searched the Cochrane Schizophrenia Group’s Study-Based Register of Randomized Controlled Trials for potentially relevant studies.\n\n\nReferences\n\nGlobal burden of 369 diseases and injuries in 204 countries and territories, 1990-2019: a systematic analysis for the Global Burden of Disease Study 2019. Lancet. 2020; 396(10258): 1204–1222. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKirkbride JB, Hameed Y, Ankireddypalli G, et al.: The Epidemiology of First-Episode Psychosis in Early Intervention in Psychosis Services: Findings From the Social Epidemiology of Psychoses in East Anglia SEPEA Study. Am. J. Psychiatry. 2017; 174(2): 143–153. 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PubMed Abstract \| Publisher Full Text\n\nMavridis D, Efthimiou O, Leucht S, et al.: Publication bias and small-study effects magnified effectiveness of antipsychotics but their relative ranking remained invariant. J. Clin. Epidemiol. 2016; 69: 161–169. PubMed Abstract \| Publisher Full Text\n\nChiocchia V, Nikolakopoulou A, Higgins JPT, et al.: ROB-MEN: a tool to assess risk of bias due to missing evidence in network meta-analysis. BMC Med. 2021; 19(1): 304. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChiocchia V, Holloway A, Salanti G: Semi-automated assessment of the risk of bias due to missing evidence in network meta-analysis: a guidance paper for the ROB-MEN web-application. BMC Med. Res. Methodol. 2023; 23(1): 223. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNikolakopoulou A, Higgins JPT, Papakonstantinou T, et al.: CINeMA: An approach for assessing confidence in the results of a network meta-analysis. PLoS Med. 2020; 17(4): e1003082. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCohen J: “Small”, “medium”, and “large” d values (chap. 2.2.3). Statistical Power Analysis for the Behavioral Sciences. 2nd ed.New York, NY: Lawrence Erlbaum Associates; 1988.\n\nSchneider-Thoma J, Chalkou K, Dörries C, et al.: Comparative efficacy and tolerability of 32 oral and long-acting injectable antipsychotics for the maintenance treatment of adults with schizophrenia: a systematic review and network meta-analysis. Lancet. 2022 Feb 26; 399(10327): 824–836. PubMed Abstract \| Publisher Full Text\n\nBalduzzi S, Rücker G, Schwarzer G: How to perform a meta-analysis with R: a practical tutorial. Evid. Based Ment. Health. 2019; 22: 153–160. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRücker G, Krahn U, König J, et al.: netmeta: Network Meta-Analysis using Frequentist Methods. Version 1.2-1.2020. Reference Source\n\nPlummer M: JAGS: A program for analysis of Bayesian graphical models using Gibbs sampling. Vienna, Austria. 3rd International Workshop on Distributed Statistical Computing. 2003.\n\nFeber L: Supplement to Psychological interventions for early-phase schizophrenia: protocol for a systematic review and network meta-analysis. figshare. Jun 03 2024. Publisher Full Text" }	[ { "id": "303417", "date": "01 Aug 2024", "name": "Alexandre Hudon", "expertise": [ "Reviewer Expertise Schizophrenia", "Mental Health", "Psychiatry", "Virtual reality", "Artificial Intelligence" ], "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 summary: The authors of this interesting protocol provide a methodology to conduct a systematic review and network meta-analysis of psychological interventions for early-phase schizophrenia. Please see my comments below.\nAbstract:\n- The introduction segment is very broad, almost as-if AI generated. Contextualising better the introduction by providing specific elements of early phase schizophrenia could be beneficial for the readership. - The protocol section is vague. Considering this is a systematic review, it was thought that details about the search strategy would be provided.\nIntroduction:\n- The word debilitating could be offending to certain patients. The authors are encouraged to use another term. - Considering the main concept is early phase schizophrenia, the main prodromes of schizophrenia should be briefly discussed (e.g. vunerability group, attenuated psychosis group and BLIPS group which are the groups with the most evidence up to this day) as there is relevance regarding the therapeutic interventions for these groups. - Please clarify the aim of this review as well as the main hypothesis.\nOverall the introduction is well written with relevant literature.\nEligibility criteria:\n- Main eligibility criteria should include specific criteria relevant to early phase schizophrenia considering the topic of this review. - What are the exclusion criteria?\nSecondary outcomes: - Please provide psychometric properties and rationale for the scales used.\nFor the remaining portions of this protocol I have no further comment as it is clearly written and easy to follow.\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": "12398", "date": "16 Sep 2024", "name": "Lena Feber", "role": "Author Response", "response": "Abstract: The introduction segment is very broad, almost as-if AI generated. Contextualising better the introduction by providing specific elements of early phase schizophrenia could be beneficial for the readership. Answer: Thank you very much for your comment. We can certify that none of the contents of this paper have been written with the use of LLMs or other AI-based tools. We also changed the text for a better focus on early phase (abstract): “Pharmacotherapies are first-line treatments, but have their own limitations. There is a consensus on the need of non-pharmacological interventions for individuals in the early phase of schizophrenia. The early phase refers to the onset of the illness, often also to the point at which the symptoms first appeared or were diagnosed.” The protocol section is vague. Considering this is a systematic review, it was thought that details about the search strategy would be provided. Answer: Thank you very much for pointing out that additional information is needed here. We have now added (abstract): \"We will search multiple electronic databases and additionally, statements of guidelines and specific relevant journals concerning psychological treatments for schizophrenia in order to retrieve other studies. The search strategy will combine terms for psychological interventions, early-phase schizophrenia and randomization.” Introduction: The word debilitating could be offending to certain patients. The authors are encouraged to use another term. Answer: Thank you for this important feedback, we have now deleted the word and replaced it with the word “severe”. Adapted (introduction): “Schizophrenia is a debilitating and severe and often life-long disorder, ranking among the 20 top causes of disability (1).” Considering the main concept is early phase schizophrenia, the main prodromes of schizophrenia should be briefly discussed (e.g. vunerability group, attenuated psychosis group and BLIPS group which are the groups with the most evidence up to this day) as there is relevance regarding the therapeutic interventions for these groups. Answer: Thank you for your important comment. We also acknowledge that these essential groups can be associated with the development of schizophrenia. However, we intentionally choose not to include these groups in our review since our criterion is that a diagnosis already exists. It is possible that within the at-risk groups, ultimately, no illness or a different illness may develop. Already in the text (characteristics of participants): We will exclude studies in “at risk of psychosis” or “prodrome” populations, because such patients do not experience full-blown psychotic symptoms yet by definition. Added tot he introduction: „Schizophrenia can also manifest in the prelude to the full onset of symptoms through early warning signs such as social withdrawal, mistrust, sleep disturbances, and many more 6. However, these are not definitive indicators of the disorder but can be viewed as early warning signs.” We also clarified in the section “characteristics of patients” now: “Participants must exhibit symptoms that match the criteria for schizophrenia or related disorders (schizophreniform, schizoaffective or delusional disorder, however diagnosed). Individuals with a specific vulnerability, brief limited intermittent psychotic symptoms or light psychotic symptoms will be excluded since the symptoms do not definitively suggest the development of schizophrenia.” Please clarify the aim of this review as well as the main hypothesis. Answer: Thank you for the suggestion to address this more clearly. We have made some additions. Already in the text: “Knowledge of psychological interventions that are most efficacious in improving symptoms and preventing relapse in this critical population may allow to improve treatment planning and resource allocation in the health care sector.” “Thus, it is currently unclear which are the most efficacious and acceptable psychological treatments for patients with schizophrenia at the early phase of the disorder. This underlines the need for a network meta-analysis producing a comprehensive synthesis of all the randomised evidence focusing on this particular population.” Added (objective): “Finding out which psychological intervention is most efficacious in treating patients with schizophrenia in the early phase can have a decisive impact on preventing chronicity of the illness. The results of this work may hold significant relevance for resource planning in treatment.” Overall the introduction is well written with relevant literature. Eligibility criteria: Main eligibility criteria should include specific criteria relevant to early phase schizophrenia considering the topic of this review. Answer: Thank you for your important comment. Our inclusion criteria relevant to early phase schizophrenia are the following: - “We will consider trials in patients with a recent first-time diagnosis of psychosis, first-episode schizophrenia or early-phase schizophrenia, as per the inclusion criteria of the specific studies.” (patient characteristics) –“In cases of “early-phase schizophrenia” or “recent-onset psychosis” we will accept a maximum duration of illness of 5 years.” (patient characteristics) -“We will also include studies conducted in specialized early intervention centers, since they target the population in question.” (patient characteristics) -“We will include studies with participants who are aged 16 years or older, allowing to capture the variability in age of onset of schizophrenia.” (patient characteristics) What are the exclusion criteria? Answer: Thank you for your inquiry. We have mentioned the respective exclusion criteria in the specific sections (characteristics of studies, characteristics of participants, interventions): -“We will exclude studies which only included patients with bipolar mania, bipolar depression, substance-induced disorders, and psychoses of organic origin.” (patient characteristics) -“We will exclude studies in “at risk of psychosis” or “prodrome” populations, because such patients do not experience full-blown psychotic symptoms yet by definition.” (patient characteristics) -“Organisation of care-oriented interventions (e.g. case management, assertive community treatment) and supported employment will not be considered, because they have other aims, and it will not be meaningful to analyse their efficacy in contrast to the ones mentioned above.”(interventions) Secondary outcomes: Please provide psychometric properties and rationale for the scales used. Answer: Thank you for the feedback that additional information regarding the scales for the secondary outcomes is needed. As already specified we will accept any validated scale that is used in the original studies. We added (secondary outcomes): “We will focus on validated and established scales. Other rating scales will only be used if the instrument has been published in a peer-reviewed journal, because non-validated schizophrenia scales tend to exaggerate differences 22.” For the remaining portions of this protocol I have no further comment as it is clearly written and easy to follow." } ] }, { "id": "314091", "date": "19 Aug 2024", "name": "Stefano Barlati", "expertise": [ "Reviewer Expertise I'm involved in research projects on clinical", "biological", "pharmacological and rehabilitative aspects of mental disorders", "in particular schizophrenia", "mood disorders", "autism and personality disorders." ], "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) SUMMARY OF ANALYZED ARTICLE The present study protocol for a systematic review and network meta-analysis regarding psychological interventions for early-phase schizophrenia aims to develop a hierarchy of existing psychological treatments concerning their efficacy and tolerability, which will inform treatment guidelines.\n2) STRUCTURE The protocol has all the key elements: abstract, introduction, methodology, data analysis, and discussion.\na) Title The title clearly describes the manuscript.\nb) Abstract The abstract is well composed, it is clearly wrote and it well reflects the content of the article.\nc) Introduction The introduction describes what authors hoped to achieve and it explains relevant previous researches on this topic.\nd) Methodology Authors explain materials and methods. In particular they well describe the study design, eligibility criteria, search strategy, outcomes, and statistical analysis.\ne) Discussion /Conclusions Authors indicate how the present protocol / study could contain useful information, not only in a research perspective, but also in clinical practice. This is a topic of interest for growing literature and authors explain how this research can be informative for future studies.\ng) Figures and tables The supplementary figures well inform the reader and they are consistent for the aim of this paper.\n3) LANGUAGE The article is written in correct and fluent English.\n4) RECOMMENDATION The protocol / manuscript may have a significant interest and bring new perspectives for research in provide useful evidence-based information for the choice of individual treatment plans from a shared decision-making perspective.\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": "314086", "date": "04 Sep 2024", "name": "Joachim Klosterkötter", "expertise": [ "Reviewer Expertise Early recognition and intervention of psychoses. Prevention of mental disorders." ], "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 are interested in two undoubtedly important questions in current therapeutic research: Which psychological interventions have already been tested for their potential benefit in the treatment of so-called early-phase schizophrenia?\nAmong all the interventions that have been evaluated so far, which one is currently considered the best option for enhancing therapy offerings in the early stages of the illness?\nTo scientifically and thoroughly answer these two closely related questions, the authors first plan to compile all randomized controlled trials conducted on such interventions so far through a systematic review. In the second step, they consequently intend to use modern statistical techniques, specifically a network meta-analysis (NMA), to comprehensively compare the effectiveness and tolerability of the various psychotherapies and other psychological or psychosocial treatments used in these clinical studies.\nTheir first paper in this context follows the meanwhile well-established practice in therapeutic research of prepublishing the study protocol. This approach provides an opportunity to get acquainted with the intended research project and also allows for suggestions for any necessary improvements before the study begins. This makes a lot of sense, especially for an ambitious and complex project like the planned comparison of all available options in an important therapeutic application field. Because when it comes to evidence syntheses, especially for the development of clinical guidelines, it is crucial to ensure that the proposed strategies for study selection and evaluation analysis truly offer realistic chances of generating new evidence-basing.\nLooking back at conventional meta-analyses, which only ever compared two treatment options with each other, NMAs certainly represent a significant methodological advanced development that is now clearly preferred by all relevant institutions in international treatment research. However, NMAs have also proven to be more prone to misinterpretation than pairwise comparisons, especially when the included studies are too dissimilar, too heterogeneous in their outcomes, or when the directly measured and indirectly derived evidence is too inconsistent. This is precisely why the pre-publication of the study protocol is particularly important for planned \"mixed treatment\" or \"multiple treatment meta-analyses,\" as NMAs are also known. Only full transparency and critical reflection of the study design within the relevant scientific community can at least to a great extent reliably ensure that in retrospect the application criteria for NMAs had not been met.\nHowever, the planned NMA would not be the first to focus on psychological interventions for patients with schizophrenia. The authors are well aware that there have already been three such intervention comparisons using the new network method. However, they argue that the studies included in these previous NMAs either focused only on certain aspects of symptomatology [1] and disease progression [2] or were conducted in the distant past [3]. In contrast, their systematic review and new NMA, which they announce with the pre-publication of this study protocol, are designed to be much more comprehensive and up-to-date in terms of the planned study selection.\nIndeed, the protocol communications regarding the eligibility criteria and the primary and secondary outcomes establish an extraordinarily broad scope for data collection. All psychological interventions that meet the classification criteria proposed by the Cochrane Common Mental Disorders Group (formerly CCDAN) are to be considered if they have been investigated in randomized controlled trials. The authors expect that various forms of therapy, including art and music therapy, social skills training, and family interventions, were administered in the majority of studies in addition to standard care, which usually included antipsychotic medication. This further strongly emphasizes that their analysis genuinely aims to improve the evidence base for current clinical practices.\nAll specifications about the methods, including those related to the search strategy, the identification of selection of studies, and data extraction, as well as those concerning the most important aspect of the planned investigation, namely data analysis, appear plausible. If all these steps can be implemented as planned, it should indeed be possible to establish a ranking from the best to the worst psychological interventions. However, a potential issue is also emerging here that cannot yet be determined before the systematic review has been carried out as to whether it could significantly jeopardize the applicability of the planned NMA.\nThe studies approved under the protocol are supposed to focus on participants aged over 16 and under 65 years with a recent first-time diagnosis of psychosis, first episode schizophrenia, or early-phase schizophrenia. The authors intend to define the somewhat unclear terms \"early-phase schizophrenia\" or \"recent onset psychosis\" by a maximum illness duration of 5 years. All participants in the approved studies must present or have presented full-blown psychotic symptoms. For this reason, studies on populations at risk of psychosis or in the prodrome phase are excluded, even though the psychological interventions of interest here actually play an even greater role as recognized first-choice prevention strategies in those populations [4]. Ultimately, all studies relating to manifest schizophrenic, schizoaffective, and delusional disorders with a duration of up to 5 years are included, regardless of how many psychotic episodes have occurred within that period. However, this is a very broad inclusion range, for which the title \"early-phase schizophrenia\" might seem misleading. The authors themselves are concerned about a potential resulting heterogeneity that could jeopardize the requirements for comparability of all included studies that apply to the NMAs. Therefore, it would be helpful if they could elaborate further on their suggested methods for capturing and managing such heterogeneity and how they intend to deal with it.\nHowever, from my perspective, this is the only minor improvement suggestion for a study protocol that otherwise indeed promises to be a major step forward in terms of individualized treatment for schizophrenia\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/13-649
https://f1000research.com/articles/13-571/v1	04 Jun 24	{ "type": "Research Article", "title": "Analyzing Molecular Traits of H9N2 Avian Influenza Virus Isolated from a Same Poultry Farm in West Java Province, Indonesia, in 2017 and 2023", "authors": [ "Muhammad Ade Putra", "Amin Soebandrio", "I Wayan Teguh Wibawan", "Christian Marco Hadi Nugroho Nugroho", "Ryan Septa Kurnia", "Otto Sahat Martua Silaen", "Rifky Rizkiantino", "Agustin Indrawati", "Okti Nadia Poetri", "Desak Gede Budi Krisnamurti", "Muhammad Ade Putra", "Amin Soebandrio", "I Wayan Teguh Wibawan", "Christian Marco Hadi Nugroho Nugroho", "Ryan Septa Kurnia", "Otto Sahat Martua Silaen", "Rifky Rizkiantino", "Agustin Indrawati" ], "abstract": "Background Indonesia is one of the countries that is endemic to avian influenza virus subtype H9N2. This study aims to compare the molecular characteristics of avian influenza virus (AIV) subtype H9N2 from West Java.\n\nMethods Specific pathogen-free (SPF) embryonated chicken eggs were used to inoculate samples. RNA extraction and RT–qPCR confirmed the presence of H9 and N2 genes in the samples. RT–PCR was employed to amplify the H9N2-positive sample. Nucleotide sequences were obtained through Sanger sequencing and analyzed using MEGA 7. Homology comparison and phylogenetic tree analysis, utilizing the neighbor-joining tree method, assessed the recent isolate’s similarity to reference isolates from GenBank. Molecular docking analysis was performed on the HA1 protein of the recent isolate and the A/Layer/Indonesia/WestJava-04/2017 isolate, comparing their interactions with the sialic acids Neu5Ac2-3Gal and Neu5Ac2-6Gal.\n\nResults RT–qPCR confirmed the isolate samples as AIV subtype H9N2. The recent virus exhibited 11 amino acid residue differences compared to the A/Layer/Indonesia/WestJava-04/2017 isolate. Phylogenetically, the recent virus remains within the h9.4.2.5 subclade. Notably, at antigenic site II, the recent isolate featured an amino acid N at position 183, unlike A/Layer/Indonesia/WestJava-04/2017. Molecular docking analysis revealed a preference of HA1 from the 2017 virus for Neu5Ac2-3Gal, while the 2023 virus displayed a tendency to predominantly bind with Neu5Ac2-6Gal.\n\nConclusion In summary, the recent isolate displayed multiple mutations and a strong affinity for Neu5Ac2-6Gal, commonly found in mammals.", "keywords": [ "avian influenza", "characterization", "docking", "H9N2", "Indonesia", "Mutation" ], "content": "Introduction\n\nAvian influenza is an acute viral infectious disease that can affect all types of birds of any age. Based on the differences in hemagglutinin (H1–18) and neuraminidase (N1–N10) components, avian influenza is divided into several subtypes.1,2 Each subtype has varying levels of pathogenicity, ranging from low pathogenic avian influenza (LPAI) to high pathogenic avian influenza (HPAI). However, both LPAI and HPAI can affect bird health.3 The presence of gene mutations through antigenic drift and antigenic shift can result in a change in symptoms. Initially, LPAI may not cause significant harm, but with these mutations, it can become highly detrimental to the poultry industry.4\n\nAIV is an RNA virus that consists of eight segments, each encoding viral protein genes. On the other hand, this virus is also more prone to mutation than DNA viruses.5 Diagnosis using polymerase chain reaction (PCR) and sequencing of the viral genome is necessary to determine the homology between the vaccine virus and the circulating field virus.6 This is because if the circulating virus has low homology with the vaccine, it can result in the ineffectiveness of the vaccine due to the continued shedding of the virus.7\n\nIn AIV, there is a crucial virus segment that needs to be characterized, which is hemagglutinin (HA), corresponding to the fourth segment of the AI genome.8,9 HA functions at the early stage of infection by attaching the virus to the host receptor. Mutations in the HA gene can increase the virulence and pathogenicity of the virus.10 Avian influenza infects its target host by initiating the recognition of the HA protein by cellular proteases from the target infected cell. Cellular proteases activate HA0, splitting it into two parts: HA1 and HA2. HA1 binds to Neu5Ac, while HA2 plays a role in fusion between the viral envelope and the host endosomal membrane. Without this recognition, the virus cannot infect the cell.11\n\nOne subtype AIV that poses a threat to the poultry industry is the H9N2 subtype.12 In countries affected by avian influenza outbreaks, such as China, the H9N2 subtype of AIV causes significant losses due to its high morbidity rate of up to 100% in infected layer chicken farms.13 Infected layer chickens experience a decrease in appetite accompanied by a drastic decline in egg production. Viral infection is often exacerbated by secondary infections from bacteria or other viruses, resulting in high mortality among the infected layer chicken population.14 H9N2 virus infection may not be immediately visible at onset, but the virus spreads rapidly through the shedding of feces or nasal discharge from birds. Due to these characteristics, rapid and accurate detection is crucial to identify the presence of AIV infection on a farm, enabling appropriate measures to be taken in addressing H9N2 virus infection.15\n\nWest Java Province is a province in Indonesia that has several densely populated districts for layer chicken farming, including Bogor, Sukabumi, Cianjur, Ciamis, and several other districts. In 2017, one H9N2 isolate was successfully isolated and characterized, namely, strain A/Layer/Indonesia/WestJava-04/2017 (GenBank accession number MG957203), originating from a densely populated layer chicken farming area in West Java.16 The high density of layer chicken farms in a region facilitates the easy spread and mutation of AIVs. Therefore, this study aims to isolate and characterize the H9N2 subtype AIV from the layer chicken farm where the A/Layer/Indonesia/WestJava-04/2017 strain originated. This study also describes the molecular changes in the HA gene using molecular docking after implementing the H9N2 vaccination program, which has been ongoing for six years.\n\n\nMethods\n\nSampling was conducted at a commercial layer chicken farm in West Java Province, the original location of the AIV subtype H9N2 strain A/Layer/Indonesia/WestJava-04/2017 (GenBank Accession No. MG957203). After five years of vaccination with a homologous vaccine at the farm, a decrease in production and bird mortality occurred in February 2023. Samples consisting of brain, trachea, and oviduct organs pooled from deceased chickens.\n\nThe sample was multiplied using standard laboratory procedures. Tissue was combined with sterile phosphate-buffered saline from ThermoFisher (28348) pH 7.4 containing antibiotics (200 g/ml penicillin and 100 g/ml streptomycin) and then centrifuged at 1,000 g and 4 °C for fifteen minutes. The remaining supernatant was filtered through a 0.45 m membrane filter and injected intra-allantoically into 9-day-old SPF ECEs. The SPF ECEs were incubated at 37 °C for 48–72 hours, and daily monitoring of embryo mortality was performed.17 After 72 hours of incubation, all ECEs, regardless of their viability, were subsequently preserved at a refrigerated temperature of 8 °C overnight and then harvested. The collected specimens consisted of allantoic fluid, which was subsequently utilized for conducting a rapid HA assay to promptly detect AIV in early stages.16\n\nThe allantoic fluid that was collected was further extracted using a total RNA mini kit reagent from Geneaid®, Taiwan (RPD050). The RNA obtained was then analyzed for the presence of the H9N2 virus using the SensiFASTTM SYBR Lo-ROX Kit from Bioline®, Taunton (BIO-94005). For the RT–qPCR assay, the primers H9-F: 5′-ATCGGCTGTTAATGGAATGTGTT-3′, H9-R: 5′-TGGGCGTCTTGAATAGGGTAA-3′18 and N2-F: 5′-CTCCAATAGACCCGTACTAT-3′, N2-R: 5′-CCTGAAGTCCCACAAAATAC-3′19 were utilized with the LongGene Q2000C (China). The thermal profile for gene amplification included two minutes of polymerase activation at 95 °C, which was followed by a total of 45 cycles of denaturation at 95 °C for 5 seconds, annealing at 60 °C for 10 seconds, and extension at 72 °C for 15 seconds. When the cycle threshold (Ct) value falls below 40, a positive result is indicated. In addition, RT–PCR assays were conducted to detect avian influenza subtype H9N2, Newcastle disease virus (NDV), and infectious bronchitis virus (IBV). RT–PCR was conducted according to the protocol used in a previous study.20\n\nThe confirmed HA of the H9 gene from RT–PCR was amplified for sequencing using the MyTaq One-Step RT–PCR kit from Bioline®, Taunton (BIO-65049), and the primers HAp1-F: 5′-TCCACGGAAACTGTAGACACA-3′, HAp1-R: 5′-TTCTGTGGCTCTCTCCTGAAA-3′ and Hap2-F: 5′-AGGCCTCTTGTCAACGGTTT-3′, Hap2-R: 5′-CCAACGCCCTCTTCACTTTA-3′ were used.21 The Sanger sequencing method was performed by First BASE Laboratories, Malaysia, which separated the PCR products using electrophoresis and purified the desired band for sequencing. Using Bioedit v.7 (https://bioedit.software.informer.com/7.0/), the nucleotide and amino acid sequences of a recently isolated strain’s HA gene were determined, and ClustalW was used for alignment. A modern virus phylogenetic tree was constructed using MEGA v 7.0 (https://www.megasoftware.net/), the neighbor-joining method, and 1,000 alignment repetitions. The genetic distance between isolates and the topology of the phylogenetic tree were used to designate strains.22\n\nA comparison was made between the recent study isolate, a previous isolate (A/Layer/Indonesia/WestJava-04/2017, GenBank Accession No. MG957203) and other H9N2 isolates from GenBank. Several key regions were investigated in this investigation, including the receptor-binding sites (RBS) on the left and right edges of the binding pocket, as well as the cleavage site. In addition, the correlation between particular amino acid residues (54, 80, 106, 109, 113, 123, 125, 129, 130, 135, 137, 146, 147, 149, 150, 152, 164, 165, 178, 179, 182, 183, 188, 189, 194, and 216) and H9N2 virus antigenicity was analysed. The amino acid sequence of the HA gene from the most recent H9N2 virus was uploaded to http://www.cbs.dtu.dk/services/NetNGlyc/to evaluate potential N-glycosylation sites.21\n\nThe simulation was conducted on a computer hardware system with the following specifications: 8.00 GB RAM and an Intel® Core i5-2520 M CPU with a clock speed of 2.50 GHz. The software used in the study included Google Chrome v114.0.5735.199 for accessing the SwissDock website, which served as the protein–ligand docking server and ran automatically (http://swissdock.ch/docking). Additionally, BIOVIA Discovery Studio Visualizer v21.1.0.20298 (https://discover.3ds.com), Chimera v1.17.3 (https://www.cgl.ucsf.edu/chimera/download.html), AutoDock Tools v1.5.7 (https://autodock.scripps.edu/), PyMol v2.5.2 (https://pymol.org/), and LigPlot+ v2.2.8 (https://www.ebi.ac.uk/thornton-srv/software/LigPlus/download.html) were used for data analysis and visualization.\n\nThe simulation begins with the creation of a 3D model of the HA1 protein from the AIV, specifically the recent study isolate (HA1-2023) and the A/Layer/Indonesia/WestJava-04/2017 strain (HA1-2017). This is achieved using the PHYRE2 Protein Fold Recognition Server (http://www.sbg.bio.ic.ac.uk/). The ligands used in the simulation were obtained from https://pubchem.ncbi.nlm.nih.gov/. They are Neu5Ac2-3Gal (compound CID: 13832708) and Neu5Ac2-6Gal (compound CID: 53262334).\n\nThe docking was performed using the automated server facility on SwissDock, where the uploaded documents were in PDB format (.pdb) for the protein acting as the receptor and SYBYL MOL2 format (.mol2) for the molecules acting as ligands. Docking was carried out for the protein HA1-2017 with the Neu5Ac2-3Gal ligand, HA1-2017 with the Neu5Ac2-6Gal ligand, HA1-2023 with the Neu5Ac2-3Gal ligand, and HA1-2023 with the Neu5Ac2-6Gal ligand. Only models with ligands attached to the Leu216 residue region are observed and selected for further analysis.\n\nThe selection of the residue is based on the fact that the amino acid at position 216 determines the virus’s tendency to infect mammalian cells dominated by Neu5Ac2-6Gal or avian cells dominated by Neu5Ac2-3Gal.20 The docking results were downloaded in the Chimera Web Data format (.xml) and run in Chimera software v1.17.3 to select the best docking model. The best model was chosen based on the Gibbs free energy (ΔG) value, where ΔG represents the stability parameter of the bond formed between the protein and the ligand. A more negative value indicates a more stable bond. The protein–ligand interactions are then evaluated, observing hydrogen bonding, hydrogen bond distances (Å), interacting residues and functional groups, and residues that interact with the ligand noncovalently.23\n\nThe partial CDS of the HA gene in this study was deposited in GenBank and received the accession number OR243721.\n\n\nResults\n\nThe presence of viral RNA was identified by RT–qPCR specifically targeting H9 and N2. The results shown in Figure 1a and Figure 1b indicate that the recent isolate of this study is an AIV subtype H9N2. The H9 gene in a recent isolate was amplified with a Ct value of 28.50, while the N2 gene was amplified at a Ct value of 34.69. A positive result was determined when the Ct value was less than 40 and displayed an amplification curve resembling that of the positive control. Conversely, a negative result was determined if the Ct value was 45 or higher, and no amplification curve resembling the positive control was observed. The results with a Ct value between 40 and 45 were classified as indeterminate or dubious.\n\nThe results of HA gene amplification using primers HApar1 and HApar2 on a recent sample from this investigation are shown in Figure 1c. The electrophoresis results revealed the presence of DNA bands at the 736 bp (for HApar1) and 712 bp (for HApar2) sites. Marker 100-2000 bp is the size of the molecular marker displayed in the illustration.\n\nThe partial CDS of the HA gene from this study was deposited in GenBank, with the accession number OR243721 (A/chicken/Indonesia/MSL0123/2023). The amino acid sequence at the cleavage site of the recent isolate is PSRSSR↓GLF, while the receptor binding site has the motif PWTNTLY (Table 1). Additionally, at position 217 on the left side of the receptor binding site (RBS), the recent isolate contained the amino acid M (methionine). It should be noted that this amino acid sequence is identical to A/Layer/Indonesia/WestJava-04/2017, which originated from the same farm.\n\na The receptor-binding site (RBS) includes residues at positions 92, 143, 145, 173, 180, 184, and 185. The left-edge of the binding pocket is located at positions 214-219, while the right-edge of the binding pocket is situated at positions 128-132. The cleavage site is positioned at positions 315-323. The antigenic site is divided into two regions: site I, which includes positions 125, 147, and 152, and site II, which encompasses positions 135, 183, and 216.\n\nb The arrangement of amino acid residues in the HA genes of AIV subtype H9N2.These residue placements are based on the H9 numbering system.\n\nIn a recent study, the antigenic site I of the HA gene in the recent sample displayed the same motif as A/Layer/Indonesia/WestJava-04/2017. At site I, amino acids S (serine), K (lysine), and P (proline) were present. For site II, the motif consisted of amino acids D (aspartate), N (asparagine), and L (leucine) at positions 135, 183, and 216. In contrast, A/Layer/Indonesia/WestJava-04/2017 exhibited D (aspartate) at position 183. The analysis of the HA gene in the recent sample included an examination of potential glycosylation sites (PGS). The HA1 gene segment revealed the NXT/S motif (where X represents any amino acid except proline) at positions 11-13 (NST), 123-125 (NVS), 200-202 (NRT), 280-282 (NTT), 287-289 (NVS), and 295-297 (NCS). There were also several other amino acid differences observed at positions 23, 34, 53, 69, 72, 74, 114, 120, 163, and 179 (Table 1).\n\nThe results of the homology comparison are shown in Table 2. The recent isolate has a similarity of 95.84% with A/Layer/Indonesia/WestJava-04/2017, which was isolated from the same farm but in a different year. When analyzed against several representatives of the H9N2 subtype clades, the recent isolate has a similarity of approximately 72.24% with clade h9.1, 72.56% with clade h9.2, 74.72% with clade h9.3, and 81.80% with h9.4.1. These results are lower compared to the similarity of the recent isolate with viruses classified under clade h9.4.2. Based on homology comparison, a recent isolate, A/chicken/Indonesia/MSL0123/2023, belonged to subclade h9.4.2.5.\n\nThe phylogenetic tree showed that the samples were together with other isolates from Indonesia (A/Layer/Indonesia/WestJava-04/2017, A/chicken/East_Java/M92_10/2017, A/chicken/East_Java/M92_24/2017), Vietnam (A/muscovy_duck/Vietnam/LBM719/2014) and China (A/chicken/Zhejiang/HE6/2009, A/chicken/Henan/LY-36/2013, A/chicken/Guangdong/LGQ02/2014) so that these were included in China, Vietnam, and Indonesia (CVI) clades (Figure 2). Recent viruses belonged to subclade h9.4.2.5, according to a phylogenetic study.\n\nThe target HA1 proteins of AIV subtype H9N2 isolated in 2017 (HA12017) and 2023 (HA12023) were chosen for the study because of their importance in viral attachment for the docking analysis, as there were no 3D structures of the protein, and its modeling was carried out. After submission of their amino acid sequences on Phyre2, the modeled proteins obtained were downloaded and visualized in Discovery Studio Visualizer. The Neu5Ac2-3Gal (Sia3) and Neu5Ac2-6Gal (Sia6) ligands used in this study are shown in Figure 3.\n\nBased on the docking results, the data obtained are presented in Table 3. The obtained results represent the best model with the most negative ∆G and the ligand positioned and bound near the Leu216 residue. The interactions between each protein and ligand are shown in Figure 4, with hydrogen bonding data and residues involved in hydrogen bonding interactions presented in Table 4. The interactions that occur can be either hydrogen bonding or nonbonding interactions that strengthen the ligand’s affinity with the protein.\n\n\nDiscussion\n\nWhile numerous genes are involved in avian influenza pathogenesis, the HA surface glycoprotein remains critical.24 Hemagglutinin regulates the parameters that influence the virulence and pathogenicity of avian influenza virus. The amino acid makeup of the HA gene includes the cleavage site, receptor binding site (RBS), antigenic site, and whether or not glycosylation sites surround the receptor binding sites.25\n\nThe cleavage site, which is located between the HA1 and HA2 subunits of the HA gene, is critical in determining the pathogenicity of AIV.26 Clades H9.1, H9.2, and H9.3 have a single arginine (R) residue at the cleavage site, whereas clade H9.4 has two arginine (R) residues (dibasic), and other isolates have three arginine (R) residues (tribasic) at this site.21 Viral evolution is responsible for the formation of H9N2 virus variants with several residues (dibasic/tribasic) at the cleavage site.27 Unless accompanied by additional infections, the presence of dibasic/tribasic residues at the cleavage site in H9N2 viruses does not significantly increase pathogenicity in the host.27\n\nThe presence of an RSSR motif at a virus’s cleavage site influences viral propagation, host tissue tropism, and viral pathogenicity.28 This specific motif, PSRSSR↓GLF, was previously identified in A/Layer/Indonesia/WestJava-04/2017, A/Layer/Indonesia/WestJava-06/2017, A/Layer/Indonesia/WestJava-09/2017, A/Layer/Indonesia/WestJava-13/2017, A/Layer/Indonesia/WestJava-14/2017, A/Layer/Indonesia/WestJava-15/2017, and A/Layer/Indonesia/CentralJava-01/2017.16 The H9.4.2.5 clade of the H9N2 virus has a PSRSSRGLF pattern in cleavage, indicating that it is a low pathogenic avian influenza (LPAI) virus. This motif selectively responds to the trypsin enzyme, which is mostly released by the digestive and respiratory systems, limiting the breadth of the infection.29\n\nThe current isolate in this study has the PWTNTLY amino acid motif of the receptor-binding site (RBS). The isolate A/Layer/Indonesia/WestJava-04/2017 is the same. RBS position 180 has been reported to influence the amount of bond affinity to sialyl-2,6-galactose (human cell receptor). Threonine (T) at position 180 had the highest binding affinity.30 The motif of the H9.4.2.5 subclade is amino acid M (methionine) at position 217 on the left side of the RBS.31 In Indonesia, this motif was previously found in isolates A/Layer/Indonesia/WestJava-04/2017, A/Layer/Indonesia/WestJava-06/2017, A/Layer/Indonesia/WestJava-09/2017, A/Layer/Indonesia/WestJava-13/2017, A/Layer/Indonesia/WestJava-14/2017, A/Layer/Indonesia/WestJava-15/2017, and A/Layer/Indonesia/CentralJava-01/2017.16\n\nThreonine (T) is found at position 129 on the right side of the receptor binding site (RBS), and lysine (K) is found at position 131. The H9.4.2 subclade is the only subclade with these unique I129T and R131K amino acid changes.21 A single modification to an amino acid within the receptor binding pocket can have a major impact on the AI virus’s ability to infect and disseminate. This element is critical in influencing AIV host diversity.32 Notably, changed receptor binding avidity of H9N2 viruses, including higher binding to human-like receptors, results in antigenic diversity in AIVs, raising the possibility of spreading zoonotic agents.33\n\nThe antigenic site motif detected in the sample was similar to that of A/Layer/Indonesia/WestJava-04/2017 and other Indonesian isolates. The residue at position 216 inside this antigenic region is important in receptor-binding interactions with the host. Human influenza viruses that contain the amino acid L216 preferentially bind to Neu5Ac2-6Gal receptors, whereas AIVs that contain the amino acid Q216 preferentially bind to Neu5Ac2-3Gal receptors.34 Additionally, the change from Q216L can improve the virus’s capacity for infecting people.35\n\nH9N2 pathogens are prevalent and have rarely caused severe illnesses in people. Although massive chicken vaccination has been beneficial in suppressing H9N2, it may have also contributed to the virus’s evolutionary alterations.36 As a result, it is critical to track the evolution of circulating H9N2 strains and assess their potential dangers to veterinary medicine and public health. We discovered numerous mutations that could have been impacted by vaccination in this study.\n\nRegarding the eleven amino acid variations among a recent isolate and A/Layer/Indonesia/WestJava-04/2017, position 183 was discovered to alter H9N2 avian influenza infection. Residue N in this location encodes the preference for human-like receptors. One change in amino acids at this position significantly impacted H9N2 antigenicity, as measured by monoclonal antibodies and antisera.37 in vivo studies demonstrated that changes influenced viral replication and transmission of H9N2 in chickens. D183-containing viruses were able to multiply in the lungs of infected hens. Variations in antigenic site II locations 183 and 216 decrease viral interactions with epitope-specific antibodies and can result in mutant virus escape.16,38\n\nThe possibility of a glycosylation site (PGS) pattern in the sample isolate matched those observed in H9.4.2.5, including A/Layer/Indonesia/WestJava-04/2017 and other Indonesian isolates. A viral method involves changing the amino acid sequence at the glycosylation site to conceal or reveal the antigenic area, preventing it from being recognized by the immune system. The addition of PGS to the sample at residue positions 295-297 may improve the virus’s ability to evade neutralization by host antibodies.31,39\n\nAccording to phylogeography, the H9 subtype of AIV can be separated into two basic lineages: American and Eurasian.40 The H9 subtype is divided into four clades based on HA gene segments.41 The H9.1 clade is derived from the A/turkey/Wisconsin/1/1966 virus found in bird populations on the continent of North America. The H9.2 clade of the American lineage is linked to the A/quail/Arkansas/29209-1/93 strain from the Arkansas region. The Eurasian lineage, on the other hand, is composed of two primary gene lines: Y439-H9.3 (A/duck/HongKong/Y439/1997) and G1-H9.4 (A/Quail/Hong Kong/G1/1997). The Y439 lineage, which has spread in wild bird species across Asia, Africa, and Europe, is likely to be the closest to the origin of the AI virus. The G1 lineage has additionally been reported, which is most typically found in commercial poultry and live poultry markets.42 The H9.4 clade has been divided into two subclades: H9.4.1 and H9.4.2. Since 2013, the H9.4.2 subclade of the H9N2 AI virus has been discovered in China.13 Based on a genetic distance analysis, the recent sample in this study shared genetic similarities with A/muscovy duck/Vietnam/LBM719/2014.16 The material for the investigation originated from the LBM, indicating the possibility of viral mixing between different species in the LBM (live bird market).\n\nThe specimens utilized in this study are closely linked to previously reported isolates from Indonesia, notably Yogyakarta and Central Java,16 Sulawesi,43 Banten and North Sumatra,16 based on the phylogenetic tree. Furthermore, the isolates are similar to those found in China and Vietnam. Wild birds serve as natural reservoirs for all AIV subtypes and play a crucial role in the virus’s ecology and spread. The global spread of the AI virus is assisted by the trade in chicken and poultry products, as well as seasonal bird movement.44 The passage of wild birds from East Asia to Australia has a substantial impact on the spread of the H9N2 AI virus in Chinese layer farms, and this movement can result in viral transmission between different places.45\n\nThe receptors employed for comparative docking in this work are the HA1 protein from the latest isolate and A/Layer/Indonesia/WestJava-04/2017. Both were obtained using 3D modeling with PHYRE2 utilizing the corresponding amino acid sequences from GenBank. The docking results in this study were chosen based on full protein binding with an X-ray density (RMSD) value identified at 2 Å.\n\nBased on the docking results of HA12017 and HA12023 with ligand Sia 3, a lower ∆G value was obtained for the binding of HA12017-Sia3 compared to HA12023-Sia3. This prediction suggests that the A/Layer/Indonesia/WestJava-04/2017 isolate has a better affinity for Neu5Acα(2,3)-Gal than the recent isolate from 2023. The Gibbs free energy (∆G) is one of the parameters for the stability of the ligand–receptor conformation. In living organisms, metabolic reactions are evaluated based on thermodynamics, which can be either endergonic or exergonic.46 Gibbs free energy represents the energy available to do work at constant temperature and pressure and is produced during exergonic reactions when metabolic processes occur. The lower the Gibbs free energy of a molecule, the more stable it is, and the reaction proceeds spontaneously. This is in line with thermodynamic equilibrium, where a more negative ∆G indicates a more spontaneous reaction or faster formation of a stable conformation.47 A lower ∆G indicates a stronger complex formation between the enzyme and ligand due to the stability and strength of noncovalent interactions within the enzyme-ligand complex. This can be observed from the amount of free energy released during the formation of interactions within the enzyme-ligand complex. This observation is also supported by other parameters, such as the number of hydrogen bonds formed.48\n\nThe isolate A/Layer/Indonesia/WestJava-04/2017 forms more hydrogen bonds compared to the latest isolate. Hydrogen bonds are specific and essential interactions in the process of ligand–receptor interactions.49 Therefore, hydrogen bonds contribute to the affinity of a molecule toward the target protein, forming electrostatic interactions between hydrogen donors and acceptors. The analysis of hydrogen bond interactions considers a bond distance of 3.9 Å between the donor and acceptor.50 However, in the docking results between HA12017 and HA12023 with ligand Sia 6, a lower ∆G value was obtained for the binding of HA12023-Sia6 compared to HA12017-Sia6. The hydrogen bond interactions observed in this case also support the notion that the latest isolate has a stronger binding affinity for Neu5Acα(2,3)-Gal than the A/Layer/Indonesia/WestJava-04/2017 isolate. The number of hydrogen bonds identified in the docking results for HA12023-Sia6 is five, while HA12017-Sia6 forms four hydrogen bonds. More hydrogen bonds indicate a stronger ligand–receptor interaction. In summary, the A/Layer/Indonesia/WestJava-04/2017 isolate forms more hydrogen bonds, indicating its higher affinity for Neu5Acα(2,3)-Gal. Conversely, the latest isolate, HA12023, shows a lower ∆G value and forms more hydrogen bonds with the ligand Sia 6, suggesting its increased strength in binding to Neu5Acα(2,3)-Gal compared to the A/Layer/Indonesia/WestJava-04/2017 isolate.\n\nIn addition to the ∆G parameter and the number of hydrogen bonds, nonbonding residue interactions between the protein and ligand, commonly known as hydrophobic interactions, also play a role in determining the stability of Neu5Acα with HA12017 and HA12023. Hydrophobic interactions are characterized by avoiding the aqueous environment and tend to cluster within the interior of the globular protein structure, minimizing interactions of nonpolar residues with water.51,52 In this study, all docking results indicated the presence of a hydrophobic residue, Leu216, which is a nonpolar amino acid. Nonpolar amino acid residues tend to form chain-like clusters in the interior part of the protein. Residues involved in hydrophobic interactions are located in the interior region of the protein, contributing to the stability of the protein’s tertiary structure. This indicates that position 216 plays a crucial role in the binding interaction of the HA1 protein with Neu5Acα.\n\nIn conclusion, this study investigated the molecular characteristics of avian influenza virus subtype H9N2 in Indonesia, focusing on a farm in West Java province from 2017 to 2023. Molecular analysis revealed 11 amino acid residue differences between the recent virus isolate and the 2017 reference isolate, yet both viruses still fell within the h9.4.2.5 subclade phylogenetically. At critical AIV sites, the recent isolate exhibited a similar arrangement to the 2017 isolate, with the exception of amino acid N at position 183 in site II of the antigenic site. Furthermore, molecular docking study indicated that the HA1 protein from the 2017 virus had a preference for binding with Neu5Ac2-3Gal, while the 2023 virus displayed a tendency to predominantly bind with Neu5Ac2-6Gal, a sialic acid receptor that commonly found in mammals. These findings highlight the evolution of avian influenza virus subtype H9N2 in the region, with notable mutations and changes in receptor binding preferences. The insights are crucial for understanding the potential risks associated with the virus’s adaptability and its interactions with host species, including humans, emphasizing the importance of continued surveillance and research efforts in managing avian influenza outbreaks.\n\nThe present research adheres to the guidelines outlined in the Indonesian Law on Animal Health Research (UU/18/2009, article 80). Due to the absence of live animals in this study, ethical approval was not necessary.", "appendix": "Data availability statement\n\nGenBank: The Nucleotide database. Accession number MG957203; https://www.ncbi.nlm.nih.gov/nuccore/MG957203. 16 The ligands used in the simulation were obtained from https://pubchem.ncbi.nlm.nih.gov/. They are Neu5Ac2-3Gal (compound CID: 13832708) and Neu5Ac2-6Gal (compound CID: 53262334).\n\n\nAcknowledgment\n\nThe authors thank Dr. Sudarisman and Adin Priadi, dvm for discussion and kind advice.\n\n\nReferences\n\nBalkhy H, Al-Hajjar S: Avian influenza: are our feathers ruffled? Ann. Saudi Med. 2006 May-Jun; 26(3): 175–82. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNugroho C, Pawitan J: Production of Antibody for Direct Fluorescence Antibody Assay against Avian Influenza H9N2. Hosts and Viruses. 2020; 7(28): 7. Publisher Full Text\n\nKanaujia R, Bora I, Ratho RK, et al.: Avian influenza revisited: concerns and constraints. 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Biophys. Res. Commun. 2020 2020/09/03/; 529(4): 963–9. PubMed Abstract \| Publisher Full Text\n\nGu M, Xu L, Wang X, et al.: Current situation of H9N2 subtype avian influenza in China. Vet. Res. 2017 12/01; 48: 49. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBonfante F, Mazzetto E, Zanardello C, et al.: A G1-lineage H9N2 virus with oviduct tropism causes chronic pathological changes in the infundibulum and a long-lasting drop in egg production. Vet. Res. 2018 Aug 29; 49(1): 83. Epub 20180829. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIqbal M, Yaqub T, Mukhtar N, et al.: Infectivity and transmissibility of H9N2 avian influenza virus in chickens and wild terrestrial birds. Vet. Res. 2013 Oct 17; 44(1): 100. Epub 20131017. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNugroho CMH, Silaen OSM, Kurnia RS, et al.: Isolation and molecular characterization of the hemagglutinin gene of H9N2 avian influenza viruses from poultry in Java, Indonesia. J. Adv. Vet. Anim. Res. 2021 Sep; 8(3): 423–34. Epub 2021/11/02. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKurnia RS, Tarigan S, Nugroho CMH, et al.: Potency of bacterial sialidase Clostridium perfringens as antiviral of Newcastle disease infections using embryonated chicken egg in ovo model. Vet. World. 2022 Aug; 15(8): 1896–905. Epub 20220806. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChaharaein B, Omar AR, Aini I, et al.: Detection of H5, H7 and H9 subtypes of avian influenza viruses by multiplex reverse transcription-polymerase chain reaction. Microbiol. Res. 2009; 164(2): 174–9. Epub 2007/03/06. eng. PubMed Abstract \| Publisher Full Text\n\nAbid M, Yaqub T, Mehboob A, et al.: Characterization and Phylogenetic Analysis of Avian Influenza Virus Subtype h9n2 in Pakistan.2017 08/24.\n\nNugroho CMH, Kurnia RS, Tarigan S, et al.: Screening and purification of NanB sialidase from Pasteurella multocida with activity in hydrolyzing sialic acid Neu5Acα(2-6) Gal and Neu5Acα(2-3)Gal. Sci. Rep. 2022 Jun 8; 12(1): 9425. Epub 2022/06/09. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMaharani NR, Susetya H, Wibowo MH: Characterization of Hemagglutinin Gene Fragment of H9N2 Avian Influenza Virus Isolated from Environmental Live Bird Market in the Greater Jakarta Area. Trop. Anim. Sci. J. 2022 05/18; 45(2): 141–153. Publisher Full Text\n\nSilaen OSM, Murtini S, Pamungkas J, et al.: Isolation and molecular characterization of fowl aviadenovirus associated with inclusion body hepatitis from poultry in Banten and West Java, Indonesia. Vet. World. 2020 Sep; 13(9): 1940–6. Epub 20200922. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSyahputra G: Docking Simulation of Curcumin and Its Analogs as Inhibitors on 12-Lipoxygenase Enzyme.2014.\n\nRichard M, de Graaf M , Herfst S: Avian influenza A viruses: from zoonosis to pandemic. Future Virol. 2014 May 1; 9(5): 513–24. PubMed Abstract \| Free Full Text eng, Publisher Full Text \|\n\nZhang Y, Xu C, Zhang H, et al.: Targeting Hemagglutinin: Approaches for Broad Protection against the Influenza A Virus. Viruses. 2019 Apr 30; 11(5). Epub 20190430. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShirvani E, Paldurai A, Varghese BP, et al.: Contributions of HA1 and HA2 Subunits of Highly Pathogenic Avian Influenza Virus in Induction of Neutralizing Antibodies and Protection in Chickens. Front. Microbiol. 2020; 11: 1085. Epub 20200605. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhang J, Ma K, Li B, et al.: A risk marker of tribasic hemagglutinin cleavage site in influenza A (H9N2) virus. Commun Biol. 2021 Jan 15; 4(1): 71. Epub 20210115. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBaron J, Tarnow C, Mayoli-Nüssle D, et al.: Matriptase, HAT, and TMPRSS2 activate the hemagglutinin of H9N2 influenza A viruses. J. Virol. 2013 Feb; 87(3): 1811–20. Epub 20121128. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBóna M, Kiss I, Dénes L, et al.: Tissue Tropism of H9N2 Low-Pathogenic Avian Influenza Virus in Broiler Chickens by Immunohistochemistry. Animals (Basel). 2023 Mar 14; 13(6). Epub 20230314. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTeng Q, Xu D, Shen W, et al.: A Single Mutation at Position 190 in Hemagglutinin Enhances Binding Affinity for Human Type Sialic Acid Receptor and Replication of H9N2 Avian Influenza Virus in Mice. J. Virol. 2016 Nov 1; 90(21): 9806–25.Epub 20161014. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShen HQ, Yan ZQ, Zeng FG, et al.: Isolation and phylogenetic analysis of hemagglutinin gene of H9N2 influenza viruses from chickens in South China from 2012 to 2013. J. Vet. Sci. 2015; 16(3): 317–24. Epub 20150130. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSun H, Lin J, Liu Z, et al.: Genetic, Molecular, and Pathogenic Characterization of the H9N2 Avian Influenza Viruses Currently Circulating in South China. Viruses. 2019 Nov 8; 11(11). Epub 20191108. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSealy JE, Yaqub T, Peacock TP, et al.: Association of Increased Receptor-Binding Avidity of Influenza A(H9N2) Viruses with Escape from Antibody-Based Immunity and Enhanced Zoonotic Potential. Emerg. Infect. Dis. 2018 Jan; 25(1): 63–72. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBelser JA, Sun X, Brock N, et al.: Genetically and Antigenically Divergent Influenza A(H9N2) Viruses Exhibit Differential Replication and Transmission Phenotypes in Mammalian Models. J. Virol. 2020 Aug 17; 94(17). Epub 20200817. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSong Y, Zhang Y, Chen L, et al.: Genetic Characteristics and Pathogenicity Analysis in Chickens and Mice of Three H9N2 Avian Influenza Viruses. Viruses. 2019 Dec 6; 11(12). Epub 20191206. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRehman S, Rantam FA, Batool K, et al.: Emerging threats and vaccination strategies of H9N2 viruses in poultry in Indonesia: A review. F1000Res. 2022; 11: 548. Epub 20220519. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPeacock T, Reddy K, James J, et al.: Antigenic mapping of an H9N2 avian influenza virus reveals two discrete antigenic sites and a novel mechanism of immune escape. Sci. Rep. 2016 Jan 7; 6: 18745. Epub 20160107. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKaverin NV, Rudneva IA, Ilyushina NA, et al.: Structural differences among hemagglutinins of influenza A virus subtypes are reflected in their antigenic architecture: analysis of H9 escape mutants. J. Virol. 2004 Jan; 78(1): 240–9. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDeshpande KL, Fried VA, Ando M, et al.: Glycosylation affects cleavage of an H5N2 influenza virus hemagglutinin and regulates virulence. Proc. Natl. Acad. Sci. USA. 1987 Jan; 84(1): 36–40. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHu Z, Peng F, Xiong Z, et al.: Genetic and Molecular Characterization of H9N2 Avian Influenza Viruses Isolated from Live Poultry Markets in Hubei Province, Central China, 2013-2017. Virol. Sin. 2021 Apr; 36(2): 291–9. Epub 2020/09/15. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCarnaccini S, Perez DR: H9 Influenza Viruses: An Emerging Challenge. Cold Spring Harb. Perspect. Med. 2020 Jun 1; 10(6). Epub 2019/12/25. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEl Mellouli F, Mouahid M, Fusaro A, et al.: Spatiotemporal Dynamics, Evolutionary History and Zoonotic Potential of Moroccan H9N2 Avian Influenza Viruses from 2016 to 2021. Viruses. 2022 Mar 1; 14(3). Epub 2022/03/27. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJonas M, Sahesti A, Murwijati T, et al.: Identification of avian influenza virus subtype H9N2 in chicken farms in Indonesia. Prev. Vet. Med. 2018 Nov 1; 159: 99–105. Epub 2018/10/14. eng. PubMed Abstract \| Publisher Full Text\n\nvan der Kolk JH : Role for migratory domestic poultry and/or wild birds in the global spread of avian influenza? Vet. Q. 2019 Dec; 39(1): 161–7. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPeacock TP, James J, Sealy JE, et al.: A Global Perspective on H9N2 Avian Influenza Virus. Viruses. 2019; 11(7). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNoor E, Haraldsdóttir HS, Milo R, et al.: Consistent estimation of Gibbs energy using component contributions. PLoS Comput. Biol. 2013; 9(7): e1003098. Epub 20130711. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGolas SM, Nguyen AN, Rietman EA, et al.: Gibbs free energy of protein-protein interactions correlates with ATP production in cancer cells. J. Biol. Phys. 2019 Dec; 45(4): 423–30. Epub 20191216. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMcGuire SH, Rietman EA, Siegelmann H, et al.: Gibbs free energy as a measure of complexity correlates with time within C. elegans embryonic development. J. Biol. Phys. 2017 Dec; 43(4): 551–63. Epub 20170919. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBulusu G, Desiraju G: Strong and Weak Hydrogen Bonds in Protein–Ligand Recognition. J. Indian Inst. Sci. 2019 11/14; 100: 31–41. Publisher Full Text\n\nChen D, Oezguen N, Urvil P, et al.: Regulation of protein-ligand binding affinity by hydrogen bond pairing. Sci. Adv. 2016 Mar; 2(3): e1501240. Epub 20160325. eng. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLins L, Brasseur R: The hydrophobic effect in protein folding. FASEB journal: official publication of the Federation of American Societies for. Exp. Biol. 1995 05/01; 9: 535–40. Publisher Full Text\n\nBogunia M, Makowski M: Influence of Ionic Strength on Hydrophobic Interactions in Water: Dependence on Solute Size and Shape. J. Phys. Chem. B. 2020 2020/11/19; 124(46): 10326–36. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "303169", "date": "14 Aug 2024", "name": "Amany Adel", "expertise": [ "Reviewer Expertise virology", "avian influenza", "molecular diagnosis" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThanks for giving me the chance to review this paper. I think it is an important study that supposed to present updated situation for H9N2 viruses in Indonesia, and I believe that this kind of study is very important and expressive to give an updated vision for the viruses around the world. Unfortunately, the study is not well developed and not well written, I think it needs to be more improved in writing and structuring. If you please take these notes in your consideration: 1- The paper needs to be re-written well, the discussion is too long and needs to be more concise and targeted. 2- The number of the collected samples are not clarified in the paper, also the epidemiological data is very leaked and does not represent the situation in Indonesia. 3- I have a confusion in the classification of H9 in your study; your classification is not compatible with classification in the study of Silvia Carnaccini and Daniel R. Perez, 2020 (H9 Influenza Viruses: An Emerging Challenge), although you cited this paper in your study. please take a look in this study again and give explanation for this conflict.\nBest wishes.\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": [] }, { "id": "303175", "date": "21 Aug 2024", "name": "Mark Zanin", "expertise": [ "Reviewer Expertise Influenza virus zoonosis and interspecies transmission" ], "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 conducted this study to compare the molecular characteristics of avian influenza virus subtype H9N2 isolated from West Java in 2017 and 2023. They collected samples including brain, trachea, and oviduct pooled from deceased chickens and inoculated them into specific pathogen-free embryonated chicken eggs for virus isolation. RNA extraction and RT-qPCR were used to confirm the presence of H9 and N2 genes in the samples. Sequences were obtained through RT-PCR and sanger sequencing from positive samples and the similarity of the recent isolates sequences were compared to reference isolates in Genbank through phylogenetic trees. They also compared the interactions of the recent isolates with the sialic acids Neu5Ac2-3Gal and Neu5Ac2-6Gal to that of the isolate A/Layer/Indonesia/WestJava-04/2017 (H9N2). They found that the recent virus exhibited 11 amino acid residue differences from A/Layer/Indonesia/WestJava-04/2017 (H9N2). Phylogenetically, the recent virus is also of the h9.4.2.5 subclade. The recent isolate had amino acid ‘N’ at position 183 at antigenic site II, which was different from A/Layer/Indonesia/WestJava-04/2017 (H9N2). Molecular docking analysis revealed a preference of HA1 from the 2017 virus for Neu5Ac2-3Gal, while the 2023 virus displayed a tendency to predominantly bind with Neu5Ac2-6Gal. These findings help to gain insights into the evolution of avian influenza virus subtype H9N2 in the region, necessary for understanding the potential risks associated with them. Overall the manuscript is well writted and well presented.\nMAJOR COMMENTS;\nNo figure legends are included. The binding ability to sialic acids of the 2017 virus and 2023 virus were analyzed through molecular docking instead of direct experiment data. Conducting a receptor binding assay such as using analogues of different sialic acids will be more convincing. This should be noted as a limitation or a consideration in the discussion. Please use correct influenza strain name nomenclature, i.e., A/Layer/Indonesia/WestJava-04/2017 (H9N2). The authors should refer to the ‘recent isolate’ by its correct influenza strain name using correct nomenclature in the abstract and introduction after calling it the recent isolate as this is more informative.\n\nMINOR COMMENTS; Abstract “Homology comparison and phylogenetic tree analysis, utilizing the neighbor-joining tree method, assessed the recent isolate’s similarity to reference isolates from GenBank.” Suggest revision to; “Homology comparison and phylogenetic tree analysis, utilizing the neighbor-joining tree method, were applied to assess the recent isolate’s similarity to reference isolates from GenBank.”\n\n“The recent virus exhibited 11 amino acid residue differences compared to the A/Layer/Indonesia/WestJava-04/2017 isolate.”. please specify which gene is being referred to, or if this is the whole genome.\n\nIntroduction There are 11 different subtypes of NA, please amend the second line of the introduction. “facilitates the easy spread and mutation of AIVs”. Recommend removing ‘easy’ from this sentence. Methods “After five years of vaccination with a homologous vaccine at the farm, a decrease in production and bird mortality occurred in February 2023.” The authors may wish to consider publication of these potentially interesting data in another manuscript if they haven’t already. In this manuscript, information RE the vaccine used and the administration regimens should be included. This could be included in the introduction or results. “Samples consisting of brain, trachea, and oviduct organs pooled from deceased chickens” More information would be helpful, perhaps in the results and/or as supplementary information.\nHow many chickens? How many samples were tested and by which method? How did the chickens die? Were they symptomatic of influenza or other illnesses? Define the meaning of ‘pooled’ – were all organs from each chicken combined together in one sample or were different organs of the same type polled? How large is the farm in terms of numbers of chickens?\n“Tissue was combined with sterile phosphate-buffered saline from ThermoFisher (28348) pH 7.4 containing antibiotics (200 g/ml penicillin and 100 g/ml streptomycin) and then centrifuged at 1,000 g and 4 °C for fifteen minutes. The remaining supernatant was filtered through a 0.45 m membrane filter and injected intra-allantoically into 9-day-old SPF ECEs.” Recommend modification to read; “Tissue was combined with sterile phosphate-buffered saline (pH 7.4) from ThermoFisher (28348) containing antibiotics (200 g/ml penicillin and 100 g/ml streptomycin) and then centrifuged at 1,000 g and 4 °C for fifteen minutes. The remaining supernatant was filtered through a 0.45 μm membrane filter and injected intra-allantoically into 9-day-old SPF eggs.” How many samples were used to inoculate eggs? “The allantoic fluid that was collected was further extracted using a total RNA mini kit reagent from Geneaid®, Taiwan (RPD050).” Recommend modification to read; “RNA was further extracted from the allantoic fluid that was collected using a total RNA mini kit reagent from Geneaid®, Taiwan (RPD050).”\n\nResults “A positive result was determined when the Ct value was less than 40 and displayed an amplification curve resembling that of the positive control. Conversely, a negative result was determined if the Ct value was 45 or higher, and no amplification curve resembling the positive control was observed. The results with a Ct value between 40 and 45 were classified as indeterminate or dubious.” Perhaps this is too repetitive of the same information in the methods section? “The amino acid sequence at the cleavage site of the recent isolate is PSRSSR↓GLF, while the receptor binding site has the motif PWTNTLY (Table 1). Additionally, at position 217 on the left side of the receptor binding site (RBS), the recent isolate contained the amino acid M (methionine). It should be noted that this amino acid sequence is identical to A/Layer/Indonesia/WestJava-04/2017, which originated from the same farm.” A bit more explanation of the significance of these would be useful. Discussion “In conclusion, this study investigated the molecular characteristics of avian influenza virus subtype H9N2 in Indonesia, focusing on a farm in West Java province from 2017 to 2023.” Is this correct? Was continued surveillance performed on this farm during this time period? If so, then these data should be included (such as numbers of samples collected, method of detection of influenza etc). Otherwise this sentence should be revised as it is a bit misleading.\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? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-571
https://f1000research.com/articles/13-212/v1	21 Mar 24	{ "type": "Case Report", "title": "Case Report: A pyramidal lobe coexisting with a left-sided thyroid goiter displacing trachea and esophagus: A cadaveric finding with clinical implications", "authors": [ "Triantafyllou George", "Tsakotos George", "Łukasz Olewnik", "Aliki Fiska", "Christos Koutserimpas", "Nicol Zielinska", "Piagkou Maria", "Triantafyllou George", "Tsakotos George", "Łukasz Olewnik", "Aliki Fiska", "Christos Koutserimpas", "Nicol Zielinska" ], "abstract": "Background The current report describes a unimodular thyroid goiter (TGo), identified unilaterally in a female cadaver, causing displacement or compression effects in the adjacent neck structures (common carotid artery (CCA) and internal jugular vein (IJV),).\n\nMethods Routine dissection of the neck of an 86-year-old female donated a Greek cadaver.\n\nResults A thyroid gland variant was identified coexisting with a TGo originating from the left thyroid lobe. The variant is a pyramidal lobe located on the left side of the isthmus. Owing to the presence of the TGo, the left CCA, along with the left IJV, deviated 50.6 mm ipsilaterally from the midline of the neck. The right CCA had a minor deviation of 30.8 mm, from the midline to the right side due to the proximity of the shifted trachea and esophagus with the CCA origin. The trachea and esophagus deviated contralaterally to the TGo, 24.4 mm from the midline.\n\nConclusions CCA compression, stenosis, and angulation may cause dizziness, weakness, and hypomnesia. The potential outcomes were worse with IJV compression. Atherosclerosis tends to occur more often in arteries with inclined (angulated) parts.", "keywords": [ "thyroid gland", "nodular goiter", "effect", "compression", "displacement" ], "content": "Introduction\n\nThe thyroid gland (TG), which is located in the middle area of the neck, produces hormones that are vital for development, growth, and metabolism. It is estimated that 15.8% of the general population has benign chronic enlargement of the TG, the so-called “thyroid goiter” (TGo).1 This anterolateral mass of the neck has a prevalence ranging between 4.7% and 28.3% among populations.1 Although the incidence of TGo in developed countries is approximately 4%, it is approximately 10 % in countries with iodine deficiency.2 TGo may be a simple or a diffuse enlargement without nodules or may have a uninodular (with a 5% prevalence of malignancy) or multinodular (with a significantly lower prevalence of malignancy) pattern.3,4 TGo may also extend inferiorly to the anterior mediastinum, with most substernal masses being benign multinodular lesions. However, TGo extension may be malignant or may rarely have an anteroposterior direction to the neck, into the retropharyngeal area (in depth extension).5\n\nTGo development has various etiologic factors, such as genetic mutations, smoking, natural goitrogens, autoimmune thyroid disease (Graves’ or Hashimoto’s disease), iodine deficiency, malignancy, dyshormonogenesis, infiltrative disease, and radiation.2,6 Thyrotropin-secreting pituitary tumors and thyroid hormone resistance.7 The syndromic background may include Pendred syndrome (an autosomal recessive disorder caused by a biallelic mutation in the PDS gene, leading to a pendrin protein defect)8 and Cowden syndrome identified in Lhermitte-Duclos disease.9\n\nIn the current case, a uninodular TGo was unilaterally identified in a female cadaver, causing displacement effects in adjacent neck structures. The detailed findings and clinical implications of this study are discussed.\n\n\nCase report\n\nDuring routine dissection of the neck of an 86-year-old female donated Greek cadaver, a TG variant was identified coexisting with a TGo originating from the left thyroid lobe. The variant is a pyramidal lobe located on the left side of the isthmus. The maximum anteroposterior diameter of the left TG lobe (thickness, with the TGo) was 3.8 mm and the maximum cephalocaudal diameter (height) was 4.4 mm. The contralateral lobe dimensions were 1.9 mm and 3.3 mm, respectively. A pyramidal lobe (2.5 mm height) was identified to the left of the midline of the TG isthmus (Figure 1). TGo volume measurements were performed using ImageJ Software.10 The surface area was calculated at 31.2 cm3. Owing to the presence of the TGo, the left common carotid artery (LCCA), along with the left internal jugular vein (LIJV), deviated 50.6 mm ipsilaterally from the midline of the neck (in an anterolateral direction). The right common carotid artery (RCCA) had a minor deviation of 30.8 mm, from the midline to the right side due to the proximity of the shifted trachea and esophagus with the RCCA origin. The trachea and esophagus deviated contralaterally to the TGo, 24.4 mm from the midline (Figure 2). The TGo type, benign or malignant, cause of death, and cadaver’s medical history were unknown. The cadavers were donated to the Anatomy Department of the Medical School of the National and Kapodistrian University of Athens after written informed consent was obtained from the “Anatomical Gift Program”.\n\nThe black line coursing the midline area of the neck. Right black line depicting the displacement of the trachea (T) and esophagus and indirectly the right common carotid artery (RCCA) and the left black line depicting the displacement of the left common carotid artery (LCCA).\n\n\nDiscussion\n\nIn the current case, the TG volume was 31.2 cm3, a high volume for a female subject according to Ovchinnikov et al.,11 who considered the TG volume enlarged when its values were higher than the normal range (4.55-18.0 cm3 in females, and 7.7-22.6 cm3 in males). Patients with TGo may have neck compression symptoms due to mass compression of the trachea, great vessels, or the esophagus. The substernal extension of the mass may also extend into the chest or posterior mediastinum.12 In-depth extension of the mass may be located retropharyngeally.\n\nIn the current case, the development of an enlarged left-sided TGo in the anterolateral direction displaced the LCCA and the LIJV, probably resulting in vessel compression. The trachea had a lateral right-side displacement from the midline, and consequently further displaced the RCCA and RIJV. Ovchinnikov et al.11 pointed out that vessel dysfunction can be detected when the TG volume is increased by 1.4 times, however in the current case, it is unknown if the TG lobe was increased, resulting in a compression effect.\n\nCommon carotid artery (CCA) compression and/or stenosis may cause dizziness, weakness, and hypomnesia. Meanwhile, the potential outcomes are worse for the IJV11 (with phlebectasia, decreased blood flow at the compression point, and increased velocity beneath that point). Both CCA and IJV compression outcomes were released with TGo resection, and the anatomy was reorganized.11 Atherosclerosis tends to occur more often in arteries with inclined (angled) parts. Hence, in the current case, TGo and the resulting CCA deviation may potentially favor the development of atherosclerosis; however, larger angiographic studies should confirm this hypothesis. Stula et al.13 highlighted that the repeated mechanical force exerted by sternocleidomastoid muscle contraction on the arterial wall has a slight impact on atherosclerotic plaque development.14 In the current case, the existence of TGo further guided the CCA in proximity to or on the sternocleidomastoid muscle.\n\nIn the current case, both tracheal and esophageal displacements were compressed on the RCCA. Tracheal inclination may lead to airway distress.14 In Shaha’s study,14 18% of patients with TG had acute airway problems requiring emergency care (and some of them intubation). Shaha14 more often recorded tracheal (25%) than esophageal (18%) compression. In cases of esophageal compression, the most common clinical sign is dysphagia.14 The symptoms of tracheal and esophageal displacement could lead to an earlier surgical intervention to relieve pulmonary and gastrointestinal symptoms.15 It is of paramount importance to identify the tracheal location with clinical examination (palpation), as an indication of pulmonary pathology (e.g., pneumonia and atelectasia) or any other anomaly (TG).\n\nAirway problems due to an enlarged TGo may be an indication for mass resection.15 Difficult airway management is a challenge for anesthesiologists, requiring proper assessment, planning, and sometimes a multidisciplinary approach to establish a secure airway.16 Fiberoptic intubation is challenging in extreme cases of enlarged TGo coexisting with tracheal narrowing. In such cases, awake fiberoptic intubation and intraoperative anesthetic management of the patient are proposed to obtain a definitive airway through venovenous extracorporeal membrane oxygenation.16\n\nHowever, the type of TGo resection remains controversial.15 Bann et al.,17 after investigating the effect of age on the distance of the TG from the sternal notch, observed that the TG was 15 mm closer to the sternal notch in patients aged 80 years and over than in patients age group–18-39 years. Thus, surgeons should direct their incision at a mean distance of 20 mm cephalad to the sternal notch. In the current case, the TG was identified 31.9 mm cephalad to the sternal notch, as supported by Bann et al.17 This close incision to the TG may lead to iatrogenic injury of the adjacent neurovascular structures or even the TG. In cases of enlarged TGos, surgeons usually intraoperatively identify the mass development anteriorly and displacement of the adjacent structures (CCA) posteriorly, such as the posterior cervical triangle area.18 Thus, in the current case, the CCA and IJV were displaced laterally rather than posteriorly. Linhares et al.19 recorded the prevalence of substernal extension of the TGo in 10% of patients (109/1080 patients who underwent surgical resection for multinodular TGo). Patients with substernal TGo and progressive enlargement and/or compressive symptoms should undergo surgical excision.\n\nAs in the current case, TGos may also coexist with TG variants, such as accessory lobes or tissues found superiorly, inferiorly, externally, and posteriorly to the TG. Such variants may be a source of pitfalls during preoperative diagnosis using scintigraphic imaging for thyroidectomies.20 Rarely, thyroid tissue within the tracheal lumen could be a cause of upper respiratory obstruction and must be investigated to determine whether it is an ectopic tissue or malignant invasion of the trachea.20\n\n\nConclusion\n\nThe TG variant (pyramidal lobe) coexisted with a unilateral (left-side) unimodular enlarged TGo. The unimodular development of the mass caused an ipsilateral inclination of both the CCA and IJV and a contralateral deviation of the trachea and esophagus, which indirectly compressed the RCCA. CCA compression, stenosis, and angulation may cause dizziness, weakness, and hypomnesia. The potential outcomes were worse with IJV compression. Atherosclerosis tends to occur more often in arteries with inclined (angulated) parts.\n\n\nAuthor contributions\n\nConceptualization: GTr, MP; methodology: GTs, LO; data collection: GTr, CK, MP; analysis and interpretation of results: AF, NZ; writing—original draft: GTr, GTs, MP; writing—review and editing: LO, AF, CK, NZ; critical revision of the manuscript: all authors; approval of the final version of the manuscript: all authors.\n\n\nEthical approval\n\nAs this is a single case report that is completely on a cadaver, and no ethical clearance was required, as a cadaver is used for teaching and research purposes.\n\n\nConsent\n\nThe cadavers were donated to the Anatomy Department of the Medical School of the National and Kapodistrian University of Athens after written informed consent was obtained from the “Anatomical Gift Program”, for educational and research purposes.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nAcknowledgements\n\nThe authors would like to express their gratitude to body donors and their families for their contribution to medical education and anatomy research.\n\n\nReferences\n\nAndersson M, Takkouche B, Egli I, et al.: Current global iodine status and progress over the last decade towards the elimination of iodine deficiency. PubMed. 2005. Reference Source\n\nMedeiros-Neto G, Camargo RY, Tomimori EK: Approach to and Treatment of Goiters. Med. Clin. North Am. 2012 Mar; 96(2): 351–368. Publisher Full Text\n\nBrito JP, Yarur AJ, Prokop LJ, et al.: Prevalence of Thyroid Cancer in Multinodular Goiter Versus Single Nodule: A Systematic Review and Meta-Analysis. Thyroid. 2013 Apr; 23(4): 449–455. PubMed Abstract \| Publisher Full Text\n\nChen AY, Bernet VJ, Carty SE, et al.: American Thyroid Association Statement on Optimal Surgical Management of Goiter. Thyroid. 2014 Feb; 24(2): 181–189. PubMed Abstract \| Publisher Full Text\n\nAlhedaithy AA, AlGhamdi AM, Abualhamayel TH, et al.: A retropharyngeal multinodular goiter: A case report and literature review. Int. J. Surg. Case Rep. 2022 May; 94: 107122. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYildirim Simsir I, Cetinkalp S, Kabalak T: Review of Factors Contributing to Nodular Goiter and Thyroid Carcinoma. Med. Princ. Pract. 2019 Sep 23; 29(1): 1–5. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHegedüs L, Bonnema SJ, Bennedbæk FN: Management of Simple Nodular Goiter: Current Status and Future Perspectives. Endocr. Rev. 2003 Feb 1; 24(1): 102–132. PubMed Abstract \| Publisher Full Text\n\nGarabet Diramerian L, Ejaz S: Pendred Syndrome. PubMed. 2023; 2023. Reference Source\n\nKesim S, Ozguven S, Oksuzoglu K, et al.: Lhermitte-Duclos Disease Related With Cowden Syndrome Mimicking Metastatic Lung Cancer on FDG PET/CT. Clin. Nucl. Med. 2022 Sep 6; 48(2): e99–e100. PubMed Abstract \| Publisher Full Text\n\nRasband WS: ImageJ. Bethesda, Maryland, USA: US. National Institutes of Health. Reference Source\n\nOvchinnikov EA, Maksimova IY, Agarkova DI, et al.: Compression of great cervical vessels in nodular goiter as indicated for thyroidectomy. Clin. Med. 2023; 3: 97–102. Reference Source\n\nTsilivigkos C, Bishop MA: Substernal Thyroidectomy. PubMed. 2023. Reference Source\n\nStula I, Kojundzic SL, Guic MM, et al.: Carotid artery stenosis in correlation with neck and carotid artery anatomy. Vascular. 2021 May 30; 30(3): 524–531. PubMed Abstract \| Publisher Full Text\n\nShaha MDAR: Surgery for Benign Thyroid Disease Causing Tracheoesophageal Compression. Otolaryngol. Clin. N. Am. 1990 Jun; 23(3): 391–401. PubMed Abstract \| Publisher Full Text\n\nStang MT, Armstrong MJ, Ogilvie JB, et al.: Positional Dyspnea and Tracheal Compression as Indications for Goiter Resection. Arch. Surg. 2012 Jul 1; 147(7): 621–626. PubMed Abstract \| Publisher Full Text\n\nTan D, Zhang X: Awake Fiberoptic Nasotracheal Intubation and Anesthetic Management of a Patient With a Compressed and Deviated Airway From a Massive Thyroid Goiter: A Case Report. Cureus. 2023 Feb 21; 15: e35278. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBann DV, Kim Y, Zacharia T, et al.: The effect of aging on the anatomic position of the thyroid gland. Clin. Anat. 2016 Nov 27; 30(2): 205–212. PubMed Abstract \| Publisher Full Text\n\nMcBain LJ, Iwanaga J, Oskouian RJ, et al.: Bilateral Displacement of the Common Carotid Arteries by a Large Goiter. Cureus. 2018 Sep 13; 10: e3298. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLinhares SM, Scola WH, Remer LF, et al.: Depth of mediastinal extension can predict sternotomy need for substernal thyroid goiters. Surgery. 2022 Nov; 172(5): 1373–1378. PubMed Abstract \| Publisher Full Text\n\nKowalczyk KA, Majewski A: Analysis of surgical errors associated with anatomical variations clinically relevant in general surgery. Review of the literature. Transl. Res. Anat. 2021 Jun; 23: 100107. Publisher Full Text" }	[ { "id": "259614", "date": "16 May 2024", "name": "Gkionoul Chatzioglou", "expertise": [ "Reviewer Expertise Human anatomy and 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 case report describes a unilateral thyroid goiter (TGo) coexisting with a thyroid gland variation (pyramidal lobe) in an aged female cadaver. The authors meticulously explain the thyroid gland's dimensions and the displacement implications on surrounding neck tissues. While the paper provides useful information about the anatomical changes and therapeutic implications of TGo, several issues require more discussion and clarification.\nThe authors successfully demonstrate the importance of anatomical variations in thyroid morphology and their clinical implications. However, a more thorough examination of the occurrence and clinical significance of pyramidal lobes in thyroid surgery would improve the paper's usefulness. Additionally, evaluating the potential impact of thyroid variations on preoperative imaging accuracy and surgical outcomes may provide clinicians with significant information.\nOverall, the case report is well-written and organized, with detailed explanations of anatomical findings and displacement effects. Minor adjustments, such as improving the clarity of certain technical terms and abbreviations and including a brief summary of major findings and consequences, will improve the manuscript's readability and accessibility.\nIn conclusion, the case report provides important anatomical insights into the coexistence of a thyroid gland variation and unilateral thyroid goiter, which has consequences for surgical planning and patient treatment. More research on the clinical significance of thyroid variations and their impact on surgical outcomes is needed to expand our understanding of thyroid pathophysiology and improve patient treatment.\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": [ { "c_id": "12405", "date": "13 Sep 2024", "name": "George Triantafyllou", "role": "Author Response", "response": "Thank you very much for your time and kind comments. A brief paragraph was added explaining the pyramidal lobe anatomy and surgical significance. With best regards!" } ] }, { "id": "271283", "date": "10 Sep 2024", "name": "Ismail Hakki Nur", "expertise": [ "Reviewer Expertise Research is important to the clinic." ], "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\nSince this research is a Case study, diagnosis and treatment are not possible. For this reason, I say no to the third evaluation question. The authors have evaluated the subject properly with a short and concise explanation. The rate of encountering such cases in clinics is not low.\n1- In order for the manuscript to be more fluid, I recommend that you pay attention to the corrections I have included in the manuscript. 2- Primary lobe should be added to the description section of Figure 1. 3- It is clinically important for the authors to indicate the diameter of the left CCA in their studies, if they have measurements. 4- The work done is acceptable.\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? Yes", "responses": [ { "c_id": "12406", "date": "13 Sep 2024", "name": "George Triantafyllou", "role": "Author Response", "response": "Thank you very much for your time and kind comments!" } ] } ]	1	https://f1000research.com/articles/13-212
https://f1000research.com/articles/13-612/v1	10 Jun 24	{ "type": "Research Article", "title": "Édouard Louis´s novel The End of Eddy: A representation of hegemonic masculinity?", "authors": [ "Milan Mašát" ], "abstract": "Background In this paper we analyse the novel The End of Eddy by Édouard Louis. The motivation for this paper is Bourdeau’s (2020) observation that Louis’s book explores working class politics, sexuality, and masculinity.\n\nMethods We analysed the amendment through narrative content analysis, the application of which allows us to answer the following question: Édouard Louis’s novel The End of Eddy: A representation of hegemonic masculinity?\n\nResults We conclude that this narrative is built on contradictions that can be summarized as a conflict between a socio-cultural norm anchored in a French village and a person who does not fulfil this concept, who is outside of it. We believe that hegemonic masculinity, that is, one part of the cultural norm of a given village, causes Eddy’s inclination or consciousness of homonationalism. Thus, on the one hand, hegemonic masculinity is undoubtedly present in this novel; on the other hand, it forms a kind of background or socio-cultural environment which, although it defines itself against the given, unconsciously causes the “birth of the conscious homosexual”.\n\nConclusions Thus, we dare to claim that the narrative under analysis is not only a representation of hegemonic masculinity, but also an accentuation of its external and internal influence on one’s own perception of (sexual) difference.", "keywords": [ "The End of Eddy", "narrative content analysis", "hegemonic masculinity", "homonationalism", "socio-cultural environment", "birth of the conscious homosexual", "homophobia", "gay", "young adult literature", "masculinity", "coming out" ], "content": "Introduction\n\nThe main aim of this paper is to show whether and, if so, to what extent a representation of hegemonic masculinity occurs in Édouard Louis’s novel The End of Eddy (Louis, 2017). The motivation for this paper is Bourdeau’s (2020) observation that Louis’s book explores working class politics, sexuality, and masculinity. He analyses the autobiographical style of writing and the themes of marginalisation and social exclusion. However, it does not provide information about the novel’s conclusion. His paper concludes that the author emphasizes non-hegemonic masculinities in the narrative.\n\nHegemonic masculinity refers to the dominant forms of masculinity that shape social norms and expectations. These masculinities are often associated with power, control and traditional gender roles and influence men’s behaviour and perceptions in different contexts. Studies critique this concept and suggest that men’s behaviour does not always conform to a single hegemonic ideal. The portrayal of masculinity in the media and marketing, for example on product packaging, reinforces stereotypes and gender norms associated with hegemonic masculinity. Scholars have proposed alternative frameworks, such as cultural repertoires, to better capture the diversity and complexity of male experiences and expressions of masculinity beyond the traditional hegemonic model (Nayak, 2023; Curone-Prieto, La Parra-Casado, &Vives-Cases, 2022; Berner-Rodoreda et al., 2023).\n\nThe concept of so-called hegemonic masculinity was discussed by Connell in 1995. After considerable criticism from experts, Connell revised and reintroduced it in 2005 in collaboration with Messerschmidt. In his original concept, Connell understands hegemonic masculinity as “a pattern of practices (…) that allow male dominance over women to continue. Hegemonic masculinity was separate from other masculinities, especially subordinate masculinities. (…) It was not assumed to be normal in a statistical sense, (…) but it was certainly normative. It also embodied the most cherished way of being a man.” (Connell & Messerschmidt, 2005, p. 832). Hegemonic masculinity is simply the designation of the ideal type of man in a particular sociocultural order and historical period. Very often, hegemonic masculinity was/is associated with militarism (see Higate & Hopton, 2005). However, in addition to militarism, it is also connoted with other uniformed workers such as police officers and firefighters. Connell & Messerschmidt’s reworking of the understanding of hegemonic masculinity draws attention to two of its most important points: its plurality and its characteristic hierarchical nature. The variability and multiplicity of masculinities evident in the work is suggested, for example, by Collinson and Hearn (1996), who focus on specific masculinities associated with men’s jobs.\n\nHegemonic masculinities in literature are deeply intertwined with power dynamics and cultural norms (Rose, 2022 or da Silva Sousa, 2022). The concept of hegemonic masculinity highlights how masculinity is embedded in culture, normalizing male domination (Domínguez, Campo, & Arcos, 2022). Men often face health issues due to conforming to traditional masculine roles, leading to a lack of self-care (King et al., 2021). In literature, the normalization of hegemonic masculinity perpetuates power imbalances and justifies domination. Moreover, the intersection of hegemonic masculinity with violence in intimate relationships, including within gay couples, showcases how this construct perpetuates power dynamics through various forms of violence. Overall, literature reflects and reinforces the cultural norms and power structures associated with hegemonic masculinities, shaping societal perceptions and behaviours. Liu et al. (2022) or Green, Satyen, & Toumbourou (2024) state that cultural norms play a significant role in literature, influencing translation practices and the portrayal of characters. Al-Fouzan (2019) adds that translators face challenges when dealing with culture-specific references, often resorting to adaptation by deletion, replacement, or addition to bridge cultural gaps.\n\nBourdeau (2020) or Dalibert (2018) state that The End of Eddy delves into themes of class, masculinity, and sexuality. The novel portrays the struggles of a young gay man from a working-class background, highlighting issues of shame, social ascension, and rejection of societal norms (Foerster, 2016). It is situated within a broader discussion on the representation of working-class individuals in French society, shedding light on the exclusion of white working-class populations and the concept of homonationalism (Barde & Triquenaux, 2015). Homonationalism, as defined by Jasbir Puar, describes a conspiracy between LGBTQ subjects or discourses of rights and nationalism, whereby some LGBTQ individuals conform to nationalist and imperialist agendas rather than being excluded (Masri, 2022). This concept has been extended to the evaluation of the sovereignty of nations based on LGBTQ rights, leading to the term “pinkwashing” to describe nations promoting a “gay-friendly” image to distract from political violence (Liinason, 2023). Through a blend of autobiography and fiction, Louis challenges traditional narratives and societal expectations, contributing to a larger discourse on class dynamics, gender identity, and the intersectionality of oppressions.\n\nThis article will therefore focus on the way in which the concept of hegemonic masculinity, or non-homogemonic masculinity in conjunction with homonationalism and certain cultural norms, is represented in Louis’s novel.\n\n\nMethods\n\nThe research was based on the method of narrative content analysis with the fact that you focused on the themes of hegemonic masculinity, homonationalism in the context of the accentuation of (specific) socio-cultural norms. Cornell, Brander and Peden (2023) state that narrative content analysis of literature involves an in-depth interpretation of narrative texts, especially those that relate to current events or political discourse. Qian and Sun (2022) add that it focuses on understanding the narrative structure, the presence of the narrator and the language used in the text. By studying narrative in literary works, we can discover the personal perspective of the narrators, the language they use, and the way they shape the story (Tallarico et al., 2021). Crucially for our analysis, this method of discovery explores how narratives reflect social history, personal histories, and cultural codes, providing insight into the experiences of characters and the wider context of the narrative (Shazad et al., 2022), which can be perceived as overarching concepts for both masculinity and homonationalism.\n\n\nResults\n\nThe publication The End of Eddy is based on the depiction of several contradictions. The protagonist (the author) grows up in a northern French village based purely on patriarchy. The men are seen as the breadwinners, whose concern is to provide financially for their families, for which the members are supposed to be grateful and devoted. Devotion is seen not only in terms of gratitude to parents, but also in terms of uncritical acceptance of their worldview and in following their example. Any deviation from these a priori planned and predetermined life paths is punished and punished by the entire village community. Thus Eddy, aware of his sexual difference, must struggle not only with his family and his social environment, but also with himself. The moment he realizes that he is homosexual, I under the influence of his parents, especially his mother, he dates girls and ostentatiously shows himself to them. Firstly, to avoid the bullying he experiences at school, but also to “calm public opinion” about his person, his orientation, his otherness.\n\nAnother contrast is the perception of the world by the villagers in comparison with the author’s experience of studying in a Parisian high school. Villagers consider any feminine expression (groomed appearance, cultural speech, or academic goals) in men as homosexuality, whereas in a large urban school these aspects are an integral part of life; on the contrary, their exclusion may imply a certain degree of ostracization or stigmatization of a person who does not meet these a priori notions of a Parisian.\n\nWe have already indicated that a significant part of the publication is the thematization of the relationship between men and women. Men, portrayed as the absolute rulers of families and villages, as fertilisers and as hard workers in the local factory, are emblematic of “old” France, of the old world in general. The book also highlights other socio-cultural norms by which men are judged: at the age of thirteen, Eddy’s villagers (mostly his family) are surprised that he has not yet had sexual relations with a girl. Girls who would have sexual relations with men at an inappropriate age, or who would have replaced multiple men in their search for the right one, are seen as “whores”. Women and girls are therefore in a subordinate role. And it is from this entrenched social background that Eddy breaks out. He does not represent a man who regularly gets drunk, fights, and subsequently has sex with many girls, but he is cultured and, even given his constant search for himself, rather introverted, avoiding society.\n\nThe pivotal moment that shifts Eddy’s decision-making, actions and self-perception in a certain way is when he and his friends are cornered by his mother in a garden shed during sexual play. Eddy’s mother, who still does not admit that her son could be gay, is completely surprised and passes the solution to this problem on to Eddy’s father. He resolves the situation in the typical social manner: he slaps Eddy and forbids him from the activities in question. At this point - although Eddy tries to change his sexual orientation - he plans his escape, deciding definitively not to go to high school, where all the citizens of the village went and still go, but to continue his studies in Paris. He thus sets himself against the established order: on the one hand, he inadvertently gives evidence of his minority sexual orientation, but also distances himself from the assumed following of village traditions: graduating from the local secondary school and then joining the neighbouring factory. Although Eddy and his family try to keep what happened in their shed a secret from everyone. However, the situation comes to light when one of the direct participants explodes everything at the school. All the ridicule and certain forms of persecution are directed at Eddy because he has been breaking with the conventions and norms of his life so far.\n\n\nDiscussion\n\nWe believe that the above, in our opinion, the driving moments of Louis’s narrative, in a way represent the thematic levels we have pursued in the story. Homonationalism is portrayal of heteronomous masculinity is put in the context of village cultural norms that are - metaphorically speaking - passed down from generation to generation and whose disruption is unforgivable. These village cultural norms are based on the role of the male - the breadwinner, the tough guy - who has control over the events of the entire social group. In the context of this role, it is understood that men are representatives of heteronormativity (hegemonic masculinity), that is, their other social role is to procreate the events to which they can transmit the norms anchored in the village and punish them at their discretion for their violation. Homonationalism is explicated indirectly in the book. Eddy tries to be part of the majority - heteronormative - society. His homonationalism only becomes apparent after he is discovered in a shed with his friends - this moment can be seen as a turning point, when he realises that he is a member of the homosexual minority and that he wants to be part of it in Paris.\n\n\nConclusion\n\nIn the introduction of the paper, we asked the question Édouard Louis’s novel The End of Eddy: A representation of hegemonic masculinity? The answer to this question is not clear-cut. We are of the opinion that hegemonic masculinity, that is, one part of the cultural norm of the village in question, causes Eddy’s inclination or awareness of homonationalism. Thus, on the one hand, hegemonic masculinity is undoubtedly represented in this novel, on the other hand, it forms a kind of backdrop or socio-cultural environment which, although it is defined against the given, unconsciously causes the “birth of the conscious homosexual”. Thus, we dare to state that the analyzed narrative is not only a representation of hegemonic masculinity, but also an accentuation of its influence external and internal to one’s own perception of (sexual) difference.\n\nEthical approval and consent were not required.", "appendix": "References\n\nAl-Fouzan NS: Cultural Norms in Translating Children’s Literature. Arab World Engl. J. 2019; 229(2019): 1–52. Publisher Full Text\n\nBarde C, Triquenaux M: Textes transfuges, textes refuges. Fonctions de l’intertextualité dans“En finir avec Eddy Bellegueule” d’Édouard Louis. Inverses: littératures, Arts, Homosexualités. 2015; 2015(15). Reference Source\n\nBerner-Rodoreda A, et al.: Cultural Repertoires and Situated Selections as an Alternative Framework to Hegemonic Masculinities: Findings From Eswatini. Am. J. Mens Health. 2023; 17(1): 155798832311521. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBourdeau L: De “Pas comme les autres”à “tous dominés”dans En finir avec Eddy Bellegueule d’Édouard Louis. Nouvelles Études Francophones. 2020; 35(1): 71–85. Publisher Full Text\n\nCollinson D, Hearn J: “Men at work”: multiple masculinities/multiple workplaces.Máirtín M, Ghaill, editors. Understanding masculinities: social relations and cultural arenas. Buckingham: Open University Press; 1996; pp. 61−76.\n\nConnell R, Messerschmidt JW: Hegemonic masculinity: Rethinking the Concept. Gend. Soc. 2005; 19(6): 829–859. Publisher Full Text\n\nCornell S, Brander R, Peden A: Selfie-Related Incidents: Narrative Review and Media Content Analysis. J. Med. Internet Res. 2023; 25(25): e47202. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCurone-Prieto RC, La Parra-Casado D, Vives-Cases C: Hegemonic masculinities and femininities in food industry packaging. Fem. Media Stud. 2022; 23(8): 4203–4220. Publisher Full Text\n\nda Silva Sousa S : Masculinidade hegemônica: contingências relacionadas ao déficit de autocuidado à saúde em homens. Perspectivas Em Análise Do Comportamento. 2022; 13(2): 207–218. Publisher Full Text\n\nDalibert M: En finir avec Eddy Bellegueule dans les médias. Questions de Communication. 2018; 33(2018): 89–109. Publisher Full Text\n\nDomínguez JP, Campo CI, Arcos LCC: Hegemonic masculinity and violence in gay couples: a psychoanalytic reading. Ágora. 2022; 25(1): 52–63. 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Publisher Full Text\n\nLiu RW, et al.: Culture and Social Norms: Development and Application of a Model for Culturally Contextualized Communication Measurement (MC3M). Front. Commun. 2022; 6(2021). Publisher Full Text\n\nLouis É: The End of Eddy. London: Harvill Secker; 2017.\n\nMasri H: Homonationalism’s Viral Travels. Oxford Research Encyclopedia of Communication. 2022. Publisher Full Text\n\nNayak A: Decolonizing Care: Hegemonic Masculinity, Caring Masculinities, and the Material Configurations of Care. Men Masculin. 2023; 26(2): 167–187. Publisher Full Text\n\nQian Y, Sun Y: Bibliometric analysis of literature on narrative discourse in corporate annual reports (1990–2019). Qual. Quant. 2022; 56(2022): 429–446. Publisher Full Text\n\nRose L: Hegemonic Masculinity and Ecofeminist Literature.Vakoch DA, editor. The Routledge Handbook of Ecofeminism and Literature. New York: Routledge; 2022. Publisher Full Text\n\nShazad M, et al.: Analysis of cancer drug prices: a narrative review of literature. J. Pharm. Health Serv. Res. 2022; 13(3): 208–214. Publisher Full Text\n\nTallarico M, et al.: Implant Fracture: A Narrative Literature Review. Prosthesis. 2021; 3(4): 267–279. Publisher Full Text" }	[ { "id": "295721", "date": "02 Aug 2024", "name": "Robert Morrell", "expertise": [ "Reviewer Expertise Gender", "Masculinities", "Violence", "Fatherhood", "Schooling", "HIV interventions", "Southern Theory", "University staff development", "Southern African History" ], "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, sophisticated but somewhat dense paper with a very specific focus explained as “Bourdeau’s (2020) observation that Louis’s book explores working class politics, sexuality, and masculinity”. It seeks to use the concept, hegemonic masculinity, developed by Connell (and later debated and refined over decades) to analyse the gendered representation of masculinity by asking (in the title) the question: “A representation of hegemonic masculinity?” I wonder whether this was a helpful framing because, as my notes below indicate, I think this question encourages a binaried approach which in the end produces a static analysis where it would have been possible, drawing on other concepts in Connell’s masculinities conceptual toolkit, to offer a more nuanced analysis. In my notes below, I provide examples to support my conclusion but also note stylistic infelicities which, if addressed, would make the paper easier for readers.\nMethods: “We analysed the amendment through narrative content analysis,” Comment: It is not clear what ‘amendment’ refers to. Needs clarification.\nIntroduction “Hegemonic masculinity refers to the dominant forms of masculinity that shape social norms and expectations. These masculinities are often associated with power, control and traditional gender roles and influence men’s behaviour and perceptions in different contexts.” Comment: Although the author follows this definition with a review of a literature on hegemonic masculinity, my sense is that this initial offering is too bland and doesn’t do justice to the contested nature of the concept. The author uses hegemonic masculinity as an equivalent for dominant masculinity and indeed other authors adopt this approach as well. But in fact Connell explicitly distinguishes hegemony from dominance with the emphasis in the case, following Gramsci, of hegemony on agreement/consent rather than force (which is associated with dominance). [ ref1 ]; [ ref 2 ]; [ ref 3 ]. But I have to concede that the concept is widely used and remains useful in analysis and authors have to take some theoretical risks when they use it.\nHegemonic masculinities in literature Comment: This section fixes the content of masculinity as oppressive which is not in line with the contested nature of hegemonic masculinity. In other words, the author is assuming a fixed content of hegemonic masculinity rather than allowing a more fluid use of the concept where the content and form of hegemonic masculinity are contested and dynamic.\n“Overall, literature reflects and reinforces the cultural norms and power structures associated with hegemonic masculinities, shaping societal perceptions and behaviours.” Comment: Here we see the effects of adopting a narrow definition of hegemonic masculinity. This statement effectively is reproductionist where literature (no matter its provenance, politics and so on) is simply an arrow in the quiver of hegemonic masculinity. It is difficult to see how any literature, in terms of this statement, can be counter-hegemonic or how it can be part of a process of envisioning alternative (or protest) masculinities. “non-homogemonic masculinity” This is confusing for the reader – what does this mean? It isn’t defined or explained.\nMethods Comment: It is not clear whether the ‘narrator’ refers to the voice of a character in the novel or actually refers to the novelist himself. This confusion is compounded in the Results section by the statement “The protagonist (the author)”.\nResults: “based purely on patriarchy”. Comment: The intrusion of concepts from gender studies or the social sciences is necessary but this occurs often in a static way where the content and purpose of the term is assumed which gives the impression that life is one-dimensional and uncontested. I think one can use a concept like patriarchy without reifying it and I would have thought that literature would be an ideal place for such nuanced attention. The description of Eddy’s life in his village is clear and well-written and the choices he makes are well contextualised.\nDiscussion: “Homonationalism is portrayal of heteronomous masculinity is put in the context of village cultural norms that are - metaphorically speaking - passed down from generation to generation and whose disruption is unforgivable”. Comment: I find this a difficult sentence to follow.\nConclusion: Comment: The author, having asked the question, offers an ambiguous answer. Yes and No. I am not sure that this enhances our understanding of the gendered significance of this novel. Would it not have been better to embrace the other elements of Connell’s masculinities framework – subordinate, complicit and protest/alternative masculinities to show how these are present in the novel? This would also have allowed the author to evade what appears to be a binaried treatment of masculinity – either hegemonic or not hegemonic. My concerns at the outset were that the key concepts have been rendered in static ways and I think that the conclusion reflects this limitation.\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?\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? Partly", "responses": [ { "c_id": "12412", "date": "13 Sep 2024", "name": "Milan Mašát", "role": "Author Response", "response": "Dear Robert Morrell, thank you very much for the very stimulating comments on my article, which I tried to incorporate into the text (even taking into account the second review). All the changes I made are highlighted in red in the text. Sincerely, Milan Mašát" } ] }, { "id": "311523", "date": "10 Sep 2024", "name": "Astrid Berner-Rodoreda", "expertise": [ "Reviewer Expertise masculinity", "stigma", "qualitative research methods", "policy", "Global Health", "HIV interventions", "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\nREVIEW The author asks the interesting question whether the autobiographical novel by Edouard Louis is a representation of hegemonic masculinity. The question requires a critical engagement with Connell’s concept of hegemonic masculinity and an analysis of the novel in this regard.\nWhile this paper provides some interesting thoughts, it is perhaps a bit too brief to delve into the concept of hegemonic masculinities vis-à-vis the novel in sufficient depth and detail.\nIntroduction In the first paragraph, it remains unclear if the author is interested in analysing Louis’ book or Bourdeau’s interpretation of it. The “it” in the second last sentence has no clear reference.\nThe paragraphs on hegemonic masculinity could have gone into slightly more detail on the concept and the various critiques of it. Hegemonic masculinity has played an overarching role in masculinity studies of various academic disciplines over a number of decades and allowed scholars to analyse the dynamics of a given society in upholding and reinforcing certain aspects of masculinity as the “most honoured way of being a man” [ 1 ]. However, the concept has also been critiqued for gender stereotyping [ 2 ], for being vague in referring to social practice, a masculine ideal or both [ 3 ], [ 4 ] and for encompassing a plurality of contradictory ideals [ 5 ].\nFor the concept of cultural repertoires, I would recommend to add the following references [ 4 ], [ 6 ] .\nThe author brings in a second concept in the introduction, that of homonationalism. The rationale for utilizing this concept in analysing Louis’ book does not become altogether clear as the story of Eddie is a rather localized story of the author’s experience of growing up, struggling and eventually embracing his sexual orientation in a close-knit village. Villagers seemed to largely endorse and uphold concepts of men as strong, working-class, main income-earners, heterosexually virile, alcohol-drinking with a certain acceptance of violence (yet tolerance towards violent men seemed to differ considerably in the community). The book does not speak about France or French society as such - to interpret the book through the concept of homonationalism seems therefore a little far-fetched to me. There was little in the book to suggest any embracing of nationalist ideas by the LGBTQ+ community (which does not figure in the book as a community). The book alludes to more tolerance towards different sexual orientations at the high school/boarding school in Amiens. The fear of strangers (e.g., people of colour) was mentioned from the father’s perspective, not from an LGBTQ+ perspective. The reason for using this concept for analysing the book remains obscure to me.\nMethods Perhaps the author could reference the “narrative content analysis” method - the reference provided refers to a content analysis (counting themes) in a narrative review. I would recommend to explain what a “narrative content analysis” entails and what themes were counted. My impression is that a narrative analysis rather than a content analysis was employed.\nThe first sentence sounds a bit odd – who is the “you”?\nResults I would guard against sweeping statements, such as “The protagonist (the author) grows up in a northern French village based purely on patriarchy” or “Any deviation from these a priori planned and predetermined life paths is punished and punished by the entire village community”. This, to me, goes beyond what we can gather from the book. In fact, the book is more nuanced. Some mothers congratulate Eddy’s mother for bringing up such a nice boy. This section could be improved by providing more nuance.\nI would also reconsider where to apply the term “contradiction” – is a homosexual boy growing up in a conservative village environment a “contradiction”? Is perhaps not rather the behaviour of people in the village (family and friends, school-mates) contradictory - on the one hand upholding heterosexual norms, yet also engaging in homosexual acts (friends); bullying and beating Eddy, but also acknowledging and celebrating his performing talents (school mates); the father threatening Eddy to never practise homosexuality again, yet protecting Eddy from his elder brother who wants to kill Eddy; the father letting himself be beaten up by his older son so that Eddy will survive; both parents enabling him to pursue secondary education with a baccalauréat when none of their other children seem to be given the same opportunity (parents).\nIn the French version of Louis’ book, he did not go to Paris but to a secondary school in Amiens, a town in Northern France. Not a lot of detail is provided about this time – I feel the second paragraph in the results section is a bit of an over-interpretation of these pages.\nThe next paragraph brings out the contrast between the expectations towards men and women quite well. Here one could have delved a bit deeper into the analysis of a hierarchy of masculinities and femininities. Again, adding nuances and seeing where the book fits neatly into the hegemonic masculinity framework and where there is tension might add more to our understanding. The mother could work until she earned more than her husband, then she was told to quit her job; yet in other families, the mother was a teacher or a single mother – the degree to which women could make their own decisions thus seemed to vary across the village and according to their socio-economic situation. Eddy’s girlfriend Laura had a bad reputation in the village and was called a “pute” or “salope” (whore/slut) which emphasizes the point the author makes about different societal expectations towards the sexual behaviour of men and women. At the same time, going out with her increased Eddy’s respect by his male cousin – Eddy describes it as a form of admiration which motivates him to keep going with this relationship. In terms of masculinities, we see Eddy’s father being strictly against homosexuality and making right wing political statements in that regard but he protects a homosexual man when the mob turned against this man. Eddy’s father also never laid hands on his wife or children and would rather accept to be beaten up by his son than to retaliate, yet would often beat other men if they seemed interested in his wife. The father became unemployed, yet was able to still maintain the drinking habits with his friends who seemed to provide the alcohol for him. There seem to be many layers of masculinity that could be explored in more depth in the novel.\nDiscussion My recommendation would be to discuss the extent to which the hegemonic masculinity framework is upheld through the novel – where do we see hegemonic, subordinate, marginalized masculinities – how are femininities portrayed?\nI fail to see what this novel has to do with homonationalism – where in this story is there a favourable association between the LGBTQ+ community and nationalist ideology? Eddy himself takes on his father’s fear of people of colour when he goes to Amiens – this is the only point that might be interpreted as homonationalism in my opinion, and this would be on rather thin grounds. I also do not understand the sentence: “Homonationalism is portrayal of heteronomous masculinity is put in the context of village cultural norms that are - metaphorically speaking - passed down from generation to generation and whose disruption is unforgivable”. Another sentence also needs rewriting: “their other social role is to procreate the events to which they can transmit the norms anchored in the village and punish them at their discretion for their violation”.\nConclusion The link of this novel to homonationalism remains obscure. I would drop this concept altogether and summarize here where the hegemonic framework is helpful and where the story may not support the framework. I think this would help the reader gain a deeper understanding of the complexity of masculinities and femininities in this autobiographical novel.\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": "12413", "date": "23 Nov 2024", "name": "Milan Mašát", "role": "Author Response", "response": "Dear Astrid Berner-Rodoreda, Thank you very much for the very stimulating comments on my article, which I tried to incorporate into the text(even taking into account the second review). All the changes I made are highlighted in red in the text. Sincerely, Milan Mašát" } ] } ]	1	https://f1000research.com/articles/13-612
https://f1000research.com/articles/13-1056/v1	13 Sep 24	{ "type": "Study Protocol", "title": "Effect of Human Platelet-Rich Fibrin Lysate on Collagen Type I, Collagen Type III, and Matrix Metalloproteinase 1: A Protocol Study on Rat Models with Pelvic Organ Prolapse", "authors": [ "Akbar Novan Dwi Saputra", "Dicky Moch Rizal", "Nandia Septiyorini", "Muhammad Nurhadi Rahman", "Yohanes Widodo Wirohadidjojo", "Dwi cahyani Ratna Sari", "Raden Mas Sonny Sasotya", "Dicky Moch Rizal", "Nandia Septiyorini", "Muhammad Nurhadi Rahman", "Yohanes Widodo Wirohadidjojo", "Dwi cahyani Ratna Sari", "Raden Mas Sonny Sasotya" ], "abstract": "Background Pelvic organ prolapse (POP) is a prevalent condition caused by weakened pelvic floor support structures. Extracellular matrix alterations, including changes in collagen type I, collagen type III, and matrix metalloproteinase 1 (MMP-1), contribute to the pathogenesis of this condition. Human platelet-rich fibrin lysate (hPRF-L) is a novel regenerative treatment that has shown beneficial results in treating structural weaknesses related to various pelvic floor diseases, including POP.\n\nMethods This study protocol aims to investigate the effects of hPRF-L injection on collagen I, III, and MMP-1 in the vaginal mucosa of a rat POP model. POP will be induced in female Sprague-Dawley rats, which will be randomly assigned to control, sham, and hPRF-L treatment groups. The hPRF-L group will receive weekly injections of hPRF-L (25, 50, or 75 μL) into the vaginal mucosa for 4 weeks. Vaginal tissue samples will be collected, and collagen type I, collagen type III, and MMP-1 expression will be evaluated using quantitative reverse transcription polymerase chain reaction and immunohistochemical analyses. Data analysis will be performed with ANOVA and post-hoc tests.\n\nDiscussion The findings from this study protocol are expected to provide valuable insights into the mechanisms by which hPRF-L impacts the structural integrity of the pelvic floor. By elucidating these mechanisms, this study aims to inform future POP treatment strategies. The anticipated results are an increase in collagen type I and III expression and a reduction in MMP-1 levels in the hPRF-L treatment group compared to the control and sham groups. These outcomes could support the use of hPRF-L as a regenerative therapy for managing POP, offering a potential alternative to more invasive surgical interventions.\n\nConclusion The expected results will contribute to the development of less invasive treatments for POP, improving patient outcomes and quality of life.", "keywords": [ "Pelvic organ prolapse", "human platelet-rich fibrin lysate", "collagen type I", "collagen type III", "matrix metalloproteinase 1", "extracellular matrix", "protocol study" ], "content": "Introduction\n\nPelvic organ prolapse (POP) is a common and impairing disorder that affects millions of women globally and significantly impairs their quality of life. It is characterized by weakened or damaged pelvic floor support structures, including the muscles, ligaments, and connective tissues. This condition contributes to the descent of pelvic organs, including the uterus, bladder, and rectum, into the vaginal canal. Advanced age, number of pregnancies, family history, genetic predisposition, and persistent exertion of pressure have been recognized as risk factors for POP.1 Studies have reported that the prevalence of POP in Indonesia ranges from 26.4% to 81.25%, and the majority of cases do not receive prompt diagnosis. The most common method for management in the majority of cases is surgical intervention.2,3 The chance of requiring pelvic floor reconstruction surgery over one’s lifetime is between 11% and 19%, which imposes an enormous financial burden on patients and the healthcare system.4\n\nPelvic floor reconstruction surgery is a well-established treatment for POP. However, it is associated with several risks. In particular, older patients are prone to postoperative complications, including bleeding, urinary tract infections, and severe bowel injuries leading to postoperative sepsis.5 Moreover, even if the procedure is successfully performed, the rate of recurrence or failure is still high. The recurrence rate can reach 58% within the first year after surgery.6 The introduction of meshes or grafts was prompted by the unacceptably high failure rate of surgery. The use of non-absorbable synthetic mesh resulted in a significantly reduced recurrence rate compared to absorbable synthetic mesh and biological alternatives. Nevertheless, problems associated with mesh are common, including erosions, wound granulation, and dyspareunia.7 Considering the significant risks and limitations associated with surgical interventions, alternative and less invasive therapies that can effectively address the underlying causes of POP and provide long-lasting relief for patients are urgently needed.\n\nPOP has a complex pathophysiology and is associated with extracellular matrix composition (ECM) changes and imbalanced connective tissue remodeling. The ECM is the basis for the formation of ligaments, fascia, and the vaginal wall. It represents a complex of high-molecular-weight proteins, including collagen, elastin, and proteoglycans.8 The vaginal and pelvic floor ECM are mainly composed of collagen fibers, particularly collagen type I and type III. These collagen subtypes play a crucial role in the structural integrity and biomechanical properties of tissues. In POP, the ratio of collagen type I to collagen type III is often imbalanced, leading to decreased tensile strength and compromised tissue support.9,10 Aside from collagen composition changes, the activity of matrix metalloproteinases (MMPs), a family of enzymes that are responsible for ECM remodeling, is also altered in POP. Specifically, prolapsed tissues exhibit an upregulation of MMP-1, also known as interstitial collagenase. MMP-1 is involved in collagen fiber degradation, contributing to the weakening of the pelvic floor support structures.11 Previous studies indicate that alterations in the extracellular matrix (ECM) are a major contributing factor to POP. Collagen fibers are the main component of the extracellular matrix (ECM), and they play a crucial role in providing support to connective tissues. Therefore, the restructuring of collagen fibers in the vaginal area might benefit women with POP.12\n\nRodents such as rats are the most widely used animal model for research into the development of spontaneous POP in women, as well as for testing new therapeutic modalities with the aim of improving outcomes of existing therapies. The histological similarity between human and rodent vaginal tissue is one of the main considerations for using this animal model. There are several other advantages related to the use of mouse models, including ease of handling, short lifespan, relatively low cost, and ease of obtaining animal samples. Rats also have a predictable estrous cycle and relatively short gestation period, which makes POP development faster, facilitating the research process.7,13 Animal models allow interventions and manipulations that are not possible in human subjects, such as injury induction or invasive tissue sampling, thus helping to study the pathophysiology and development of POPs in depth and comprehensively test potential new therapies before clinical trials.\n\nPlatelet-rich fibrin (PRF) is a natural biomaterial generated from the patient’s own blood that is being used as a promising treatment for gynecological and pelvic floor disorders, including POP. It contains high concentrations of growth factors, cytokines, and other biologically active substances that have been proven to stimulate tissue regeneration, angiogenesis, and ECM remodeling.14,15 Because of its ability to target the fundamental structural and functional defects associated with POP, the use of human platelet-rich fibrin lysate (hPRF-L) in treating POP has attracted considerable attention. The lysate form of PRF, which is obtained through platelet activation and lysis, contains a concentrated mixture of growth factors and bioactive molecules present in the original PRF material.16\n\nThis protocol study aims to examine the effect of hPRF-L injection on collagen type I, collagen type III, and MMP-1 levels in the vaginal mucosa of a rat model with POP. In addition, this study provides useful insights into the therapeutic potential of hPRF-L for managing POP by exploring the mechanisms by which it may affect the composition and remodeling of vaginal tissues.\n\n\nMethods\n\nThis prospective randomized controlled animal study will be designed to investigate the effects of hPRF-L injection on collagen type I, collagen type III, and MMP-1 expression in the vaginal mucosa of a rat model with POP. The study will be conducted using female Sprague–Dawley rats, which are a well-established animal model for POP research. Thirty rats, aged 12–14 weeks and weighing between 200 g and 300 g, will be included. The animals will be kept in rooms that maintained a regulated temperature and humidity and followed a 12-h light/dark cycle. During the study, the rats will be provided unrestricted access to regular food and water. A sham group will be formed by randomly selecting six rats, and another six rats will be randomly selected as the control positive group. The remaining 18 rats will received an hPRF-L injection after POP induction. The hPRF-L treatment group will be further divided into three subgroups, with six rats in each subgroup receiving a different dosage of hPRF-L (25, 50, or 75 μL/week) for a duration of 4 weeks. Furthermore, a researcher who will be blinded to the specific treatment given to each rat will evaluate the outcomes. Figure 1 displays the study approach to the proposed research.\n\nPOP will be induced in all rats using a previously validated surgical procedure. POP will be induced in all rats using a surgical procedure validated by Guo et al. (2023).13 The method involves two stages: bilateral ovariectomy followed by simulated vaginal delivery.\n\nStage 1: Bilateral Ovariectomy\n\n1. Anesthesia: Rats will be anesthetized via intraperitoneal injection of ketamine (100 mg/kg body weight) and xylazine (10 mg/kg body weight). Depth of anesthesia will be confirmed by lack of pedal reflex.\n\n2. Surgical preparation: The abdominal area will be shaved and disinfected with 70% ethanol followed by povidone-iodine solution. Sterile drapes will be used to maintain asepsis.\n\n3. Ovariectomy procedure: a. A 2-cm midline incision will be made in the lower abdomen using sterile surgical scissors. b. The abdominal muscles will be separated along the linea alba. c. The ovaries will be identified and gently exteriorized. d. The fallopian tubes will be ligated with 4-0 absorbable sutures approximately 1 cm from each ovary. e. The ovaries will be excised using micro-surgical scissors. f. Hemostasis will be confirmed before closing the abdominal cavity. g. The abdominal muscles will be closed with 4-0 absorbable sutures in a continuous pattern. h. The skin will be closed with 4-0 non-absorbable sutures in an interrupted pattern.\n\nStage 2: Simulated Vaginal Delivery (2 weeks post-ovariectomy)\n\n1. Anesthesia: As described in Stage 1.\n\n2. Catheter preparation: a. A size 12 Foley catheter will be trimmed to remove the tip beyond the balloon. b. The catheter will be sterilized using alcohol.\n\n3. Simulated delivery procedure: a. The sterilized catheter will be lubricated with sterile water-based gel. b. The catheter will be gently inserted into the vagina to a depth of approximately 1 cm. c. The balloon will be inflated with 2.5 mL of sterile 0.9% saline solution using a sterile syringe. d. The inflated catheter will be left in place for 4 hours. During this time, rats will be kept under light anesthesia. e. After 4 hours, the saline will be withdrawn from the balloon using a sterile syringe. f. The catheter will be gently removed.\n\nThe hPRF-L used in this study will be prepared from participants’ own blood following a standardized protocol described by Choukron et al.17 The process will begin with the collection of 20 mL of peripheral blood from the donor’s cubital vein. A trained phlebotomist will use a sterile 20 mL disposable syringe with a 21-gauge needle for blood collection. To prevent clotting and minimize platelet activation, the blood draw will be completed within 2 minutes. Immediately after collection, the blood will be transferred into sterile glass tubes (10 mL capacity, silica-coated) without the addition of anticoagulants. The tubes will be balanced and placed in a benchtop centrifuge (Centrifuge Hettich EBA 200) equipped with a fixed-angle rotor. Centrifugation will be performed at room temperature (20-25°C) for 10 minutes at 400 G.\n\nThis centrifugation process will result in the formation of two distinct layers within the tube: the upper layer comprising the PRF jelly and the lower layer containing the erythrocytes, indicating near-complete blood clotting after 5 minutes. The PRF jelly will be carefully removed from the tube using sterile tweezers. Next, sterile scissors will be used to cut at the border between the jelly and the erythrocytes. The isolated PRF jelly will then be transferred into a new sterile glass tube and incubated for 24 hours at 4 °C.\n\nFinally, the supernatant will be aspirated from the incubated PRF jelly and transferred into a 2 mL Eppendorf tube, where it will be stored at −20 °C until further use. The supernatant obtained through this process will constitute the PRF lysate that will be utilized in the present study. The preparation of human platelet-rich fibrin lysate is displayed in Figure 2.\n\nInformed written consent will be obtained from all participants for the collection and use of their blood in this study. The consent process will be conducted as follows:\n\n1. Potential participants will be provided with a detailed information sheet explaining the purpose of the study, the blood collection procedure, potential risks and benefits, and how their blood samples will be used.\n\n2. A member of the research team will verbally explain the study and answer any questions the potential participants may have.\n\n3. Participants will be given sufficient time (at least 24 hours) to consider their participation and ask any additional questions.\n\n4. If they agree to participate, participants will be asked to sign a written consent form. This form will be available in both English and the local language to ensure full comprehension.\n\n5. A copy of the signed consent form will be given to the participant, and another copy will be retained in the study records.\n\nThe use of written consent was approved by the Ethics Commission of FKKMK Gadjah Mada University (approval letter reference number: KE/FK/0092/EC/2023). Written consent was chosen over verbal consent to provide a clear record of the participants’ agreement and to ensure that all necessary information was provided consistently to each participant.\n\nAfter the rat model with POP is established, the researchers will administer hPRF-L injections into the vaginal mucosa layer. The injection protocol will involve delivering doses of 25, 50, or 75 μL of hPRF-L per week, for a duration of 4 weeks. To ensure even distribution, the injection sites will be rotated each week. The injection in the first week will be made in the 6 o’clock position, that in the second week will be made in the 12 o’clock position, that in the third week will be made in the 3 o’clock position, and that in the fourth week will be made in the 9 o’clock position.\n\nhPRF-L will be injected directly into the subepithelial space of the vaginal wall using a 26-gauge syringe and maintaining a depth of 1–2 mm. The injection sites will be carefully selected at the midline of the anterior, posterior, right, and left lateral vaginal walls, approximately 0.2 cm from the vaginal opening. Moreover, the researchers will perform needle retraction and injection simultaneously to further facilitate the even distribution of the PRF lysate within the vaginal wall.\n\nThe rats will be sacrificed 1 week after the last hPRF-L injection (series 4), and the vaginal wall will be removed. We will conduct the euthanasia through cervical dislocation after inducing deep anesthesia with a ketamine overdose. After euthanasia, the rat’s abdominal cavity will be opened, and the pubic symphysis will be disarticulated. First, the vaginal opening will be isolated from the surrounding perineal skin. Then, the vaginal tube will be isolated intact. The vaginal wall will be cut transversely into proximal and distal segments. The proximal segment will be immediately immersed in 10% neutral buffered formalin, processed, and embedded in paraffin blocks for histological evaluation. Meanwhile, the distal segment will be stored at −80 °C for molecular studies. The slides will be subsequently analyzed by two independent observers who will be blinded to the grouping and intervention.\n\nImmediately after harvesting vaginal tissue samples, a part of the samples will be immediately frozen in liquid nitrogen and kept at −80 °C until the RNA is extracted. The frozen tissue samples will be subjected to total RNA isolation using a commercial TRIzol reagent (Invitrogen, USA) and reverse transcribed using SensiFAST SYBR Lo-ROX Mix, 100 RXNS (BIOLINE) in accordance with the manufacturer’s instructions. RT-qPCR will be performed using an Applied Biosystems 7500 Fast System, Singapore. Subsequently, quantitative reverse transcription polymerase chain reaction (RT-qPCR) analysis will be conducted by using targeted primers for collagen type I, collagen type III, and MMP-1, in addition to a housekeeping gene (GAPDH) serving as an internal control. The relative expression levels of the target genes will be determined using the 2−ΔΔCt method and standardized to the control group. The real-time PCR primer sequences are detailed in Table 1. The PCR primers will be constructed using the rat reference mRNA sequence from the National Center for Biotechnology Information (NCBI) database. Their specificity will be verified using the BLAST software from the NCBI website (https://blast.ncbi.nlm.nih.gov/).\n\nThe immunohistochemical examination will involve treating the deparaffinized and rehydrated paraffin-embedded vaginal tissue sections with a citrate-based buffer for antigen retrieval. Subsequently, the sections will be exposed to primary antibodies at a 1:200 dilution, specifically targeting collagen I alpha 2 Rabbit pAb (ABclonal, A5786), collagen III alpha 1 Rabbit pAb (ABclonal, A3795), and MMP-1 Rabbit pAb (Bioss, bs-0463R). Thereafter, they will be incubated with a 1:200 dilution of anti-rabbit secondary antibody (Servicebio) coupled with a chromogenic or fluorescent reporter at room temperature (RT). Microscopic assessment will be performed using a Leica microscope at 400× magnification by assessing positive brown staining of the stromal lamina propria of the vaginal mucosa in representative areas. For each sample, 5 different fields of view will be observed. In each unit area of the field of view (40× objective), photomicrographs will be taken using a DP-20 digital camera microscope with the aid of the DP2-BSW program. The proportion of the colored area will be measured with the ImageJ program. The results will be quantified as the proportion of the area with positive staining in relation to the overall area of the tissue.\n\nThe vaginal tissue will be fixed in a 10% formalin solution for 24 hours, then embedded in paraffin and sliced into sections that are 5 micrometers thick. The vaginal tissue sections will be stained using standard procedures for Sirius Red staining. The slides stained with Sirius Red (0.1 g/100 mL saturated picric acid solution) (Sigma-Aldrich, USA) will be analyzed using a polarizing light microscope, which enables the observation of collagen fibers with improved birefringence characteristics. Collagen fibers that are arranged in an orderly manner will appear luminous and exhibit polarization, whereas fibers that are disorganized or broken will show a less intense or non-polarized appearance. The Sirius Red-stained sections will be evaluated by quantitative analysis utilizing ImageJ. The total area encompassed by collagen fibers, along with the proportion of structured (polarized) to unstructured (non-polarized) collagen fibers, will be calculated for every treatment group.\n\nRT-qPCR, immunohistochemical, and Sirius Red staining data will be used to provide a comprehensive assessment of the effects of hPRF-L treatment on ECM composition and remodeling in the rat model of POP.\n\nThe data obtained from RT-qPCR and immunohistochemical analyses will be presented as mean ± standard deviation. Statistical analyses will be conducted using computer programme. The data will undergo normality testing using the Shapiro–Wilk test, and the assumption of variance homogeneity will be confirmed using Levene’s test. If the assumptions are not met, suitable non-parametric tests, including the Kruskal–Wallis test, will be used. Differences among the control, sham, and hPRF-L treatment groups will be compared using one-way analysis of variance (ANOVA). If ANOVA indicates a statistically significant difference, subsequent post-hoc tests, including Tukey’s honestly significant difference or Dunnett’s test, will be used to determine the specific differences between groups. Statistical significance will be considered at p < 0.05.\n\n\nDiscussion\n\nThe primary aim of this study is to examine the effect of hPRF-L injection on collagen type I, collagen type III, and MMP-1 levels in the vaginal mucosa of a rat model with POP. Our hypothesis is that hPRF-L application will positively affect the expression of important ECM components in a rat model of POP. We hypothesize that the hPRF-L treatment group will show a significant increase in collagen type I and III expression compared with the control and sham groups.\n\nThe rationale for this idea is based on the established functions of collagen type I and III in maintaining the structural integrity and biomechanical characteristics of pelvic floor tissues. Collagen type I is known to be exceptionally resistant to stretching and offers strength and stability to connective tissues, whereas collagen type III plays a role in providing elasticity and flexibility. Collectively, they preserve the ideal equilibrium required for efficient pelvic support. In POP cases, the ratio of these two collagen subtypes is often imbalanced. This imbalance involves a proportional reduction in collagen type I and an associated increase in collagen type III. The decline in collagen type I leads to a loss in tensile strength, rendering tissues less capable of enduring mechanical stress. Concurrently, an increase in collagen type III could affect the flexibility of tissues, making them more prone to stretching and deformation. This imbalance eventually damages the integrity of the pelvic support structures, leading to the onset and advancement of POP.18–20\n\nMoreover, we hypothesize that hPRF-L application will result in a simultaneous reduction of MMP-1 in the vaginal wall of a rat model with POP. MMP-1, also known as interstitial collagenase, is a crucial enzyme that breaks down collagen fibers in the ECM. The rationale for this idea is derived from the established function of MMP-1 in POP development. In POP, the excessive breakdown and remodeling of collagen-rich pelvic floor tissues is often attributed to increased MMP-1 activity. The imbalance between collagen production and degradation ultimately leads to the weakening and reduced structural integrity of vaginal and pelvic support systems.11,21 Assuming that hPRF-L treatment will reduce MMP-1 production, we anticipate that this regenerative method will help control excessive ECM degradation. Reducing the activity of MMP-1 is expected to preserve the structural and functional integrity of the vaginal mucosa, which is important for providing support to the pelvic organs and preventing POP development or progression.\n\nThe rationale behind this hypothesis is that the wide variety of growth factors, cytokines, and other biologically active molecules found in hPRF-L will promote collagen production, inhibit MMP activity, and facilitate the overall regeneration and restructuring of pelvic floor tissues. These biologically active compounds can increase cell growth and differentiation, thereby aiding the restoration of impaired or weakened tissues. Thus, hPRF-L treatment offers a potential therapeutic approach for addressing the underlying structural deficiencies that contribute to POP development and progression by restoring the ideal balance of these crucial ECM components and regulators.22,23 The goal of this technique is to strengthen pelvic floor tissues, improve their biomechanical properties, and reduce the likelihood of future recurrence or progression of POP.\n\nCompared with platelet-rich plasma (PRP), the hPRF-L used in this study is a more advanced and possibly more efficient method for regenerative therapy in POP, surpassing the first-generation platelet concentrate technology. Unlike PRP, which requires the use of anticoagulants and external thrombin to activate platelets, hPRF-L is produced using a more natural method that uses the patient’s own blood coagulation. The intrinsic coagulation process enables the entrapment of a broader range of growth factors, cytokines, and other biologically active substances within the fibrin structure. Subsequently, these substances are gradually released over a period of time to facilitate tissue regeneration and restructuring. Furthermore, the absence of anticoagulants and the limited use of centrifugation processes in the hPRF-L preparation protocol aid in maintaining the integrity and functionality of the platelets and their associated biomolecules.14,15,24 This can improve the therapeutic effectiveness of hPRF-L compared with PRP. Moreover, the fibrin-based composition of hPRF-L offers a more enduring and consistent release of bioactive substances. This characteristic can be beneficial in managing the persistent and advancing nature of POP.\n\nThe findings of this study on the effects of human platelet-rich fibrin lysate (hPRF-L) on extracellular matrix components in a rat model of pelvic organ prolapse (POP) may have broader implications, but several considerations must be taken into account when generalizing to other species or conditions:\n\n1. Species differences: While rats are commonly used in POP research, their quadrupedal nature and differences in pelvic floor anatomy and biomechanics limit direct translation to bipedal humans. However, the fundamental processes of extracellular matrix remodeling and the response to growth factors are likely to be conserved across mammals.\n\n2. Relevance to human biology: The molecular pathways involved in collagen synthesis and matrix metalloproteinase regulation are highly conserved in mammals. Therefore, the effects of hPRF-L on these pathways in rats may provide valuable insights into potential human applications. However, the complexity of human POP, influenced by factors such as genetic predisposition, lifestyle, and hormonal status, may not be fully captured in this model.\n\n3. Experimental conditions: The controlled environment of our study, while necessary for scientific rigor, may not fully replicate the variability seen in clinical settings. Factors such as age, comorbidities, and varying degrees of POP severity could influence treatment efficacy in humans.\n\n4. Potential for translation: Despite these limitations, our study provides a crucial step in evaluating the potential of hPRF-L as a regenerative therapy for POP. The molecular and histological outcomes we assess are directly relevant to the pathophysiology of human POP and could inform future preclinical and clinical studies.\n\n5. Broader applications: The effects of hPRF-L on collagen synthesis and MMP regulation may have implications beyond POP, potentially extending to other conditions involving connective tissue disorders or wound healing.\n\nThe findings of this study are expected to provide valuable insights into the potential mechanisms by which hPRF-L may exert its beneficial effects on the vaginal mucosa in the context of POP. By demonstrating the positive effect of hPRF-L on the expression of key ECM components and MMP regulation, this research lays the groundwork for further investigations into the therapeutic applications of this regenerative approach for the management of POP.\n\n\n\n> The study will employ a thoroughly characterized rat model of pelvic organ prolapse, which will offer a controlled and replicable system for assessing the impacts of hPRF-L therapy.\n\n> The study will utilize a multi-modal approach, including histological (Sirius Red staining), molecular (RT-qPCR), and immunohistochemical techniques, to thoroughly evaluate the impact of hPRF-L on collagen deposition, organization, and the expression of important extracellular matrix components.\n\n> The study will aim to determine if there are dose-dependent effects and provide insights into the most effective dosing regimens for future clinical applications.\n\n> Translation of animal models will be considered.\n\n> The study will examine the impact of hPRF-L therapy throughout a relatively brief duration.\n\n> The study will not include biomechanical testing.\n\nThis study protocol was reviewed and approved by the Ethics Commission of the Faculty of Medicine, Public Health and Nursing, Gadjah Mada University (FKKMK UGM) on [18 January 2023] (ethics commission approval letter with reference number: KE/FK/0092/EC/2023). This approval covers both the animal study and the use of human blood products.\n\nHuman Participants: The study adheres to the principles of the Declaration of Helsinki. All participants providing blood samples for hPRF-L preparation will undergo an informed consent process. Written informed consent will be obtained from each participant after a thorough explanation of the study’s purpose, procedures, risks, and benefits. Participants will be given ample time to consider their involvement and ask questions. All participant information will be kept confidential and de-identified.\n\nAnimal Welfare: All procedures involving animals will be conducted in strict compliance with the guidelines set forth in the Guide for the Care and Use of Laboratory Animals published by the National Institutes of Health (NIH). Every effort will be made to minimize animal suffering and distress throughout the study. These efforts include:\n\n1. Use of appropriate anesthesia (ketamine/xylazine) for all surgical procedures, with continuous monitoring of anesthetic depth.\n\n2. Regular monitoring of animals for signs of distress, with implementation of humane endpoints if necessary.\n\n3. Housing animals in a temperature-controlled environment with a 12-hour light/dark cycle and free access to food and water.\n\n4. Limiting the duration of the simulated vaginal delivery procedure to 4 hours to minimize stress.\n\n5. Gentle handling: All procedures, including hPRF-L injections, were performed by trained personnel to minimize stress and discomfort.\n\n6. Euthanasia will be performed using methods approved by the American Veterinary Medical Association (AVMA) Guidelines for the Euthanasia of Animals.\n\nThe number of animals used in this study has been carefully calculated to achieve statistical significance while using the minimum number of animals possible. All personnel involved in animal handling and procedures have received appropriate training in laboratory animal science and welfare.\n\nThe results of this study will be disseminated through various channels to enhance scientific knowledge in the area of pelvic organ prolapse and regenerative medicine. Upon completion of the study, the research team intends to publish the findings in a peer-reviewed scientific journal. This will enable professionals in the field to critically assess the findings and ensure the study’s scientific rigor and validity. Additionally, the research team will disseminate the study findings by presenting them at relevant national and international conferences and symposia. These platforms will facilitate the dissemination of knowledge acquired from this study to the wider scientific community and foster meaningful discussions and partnerships with other researchers in related fields.", "appendix": "Data availability statement\n\nNo data are associated with this article.\n\nOSF Repository: ARRIVE checklist for “Effect of Human Platelet-Rich Fibrin Lysate on Collagen Type I, Collagen Type III, and Matrix Metalloproteinase 1 in Rat Models with Pelvic Organ Prolapse”. https://doi.org/10.17605/OSF.IO/QE6KU. 25\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nThe authors would like to express their gratitude to the staff of Klinik Bahasa for language assistance.\n\n\nReferences\n\nEl-Nashar SA, Singh R, Chen AH: Pelvic Organ Prolapse: Overview, Diagnosis and Management. J. Gynecol. Surg. 2023 Feb 1; 39(1): 3–11. Publisher Full Text\n\nPutra IG, Megadhana IW, Suwiyoga K, et al.: Prevalence of urinary incontinence in women with pelvic organ prolapse at Sanglah hospital Denpasar, Bali-Indonesia. Bali Medical Journal. 2016 Aug 26; 5(1): 140–148. Publisher Full Text\n\nSantoso BI, Fauziah NR: Prevalence and characteristics of pelvic floor dysfunction in a Tertiary Care Center in Indonesia. Indonesian Journal of Obstetrics and Gynecology. 2017 Nov 1; 168–172. Publisher Full Text\n\nSmith FJ, Holman CA, Moorin RE, et al.: Lifetime risk of undergoing surgery for pelvic organ prolapse. Obstet. Gynecol. 2010 Nov 1; 116(5): 1096–1100. Publisher Full Text\n\nKörnig M, Brühlmann E, Günthert A, et al.: Intra-, peri-and postoperative complications in pelvic organ prolapse surgery in geriatric women. Eur. J. Obstet. Gynecol. Reprod. Biol. 2018 May 1; 224: 142–145. PubMed Abstract \| Publisher Full Text\n\nFriedman T, Eslick GD, Dietz HP: Risk factors for prolapse recurrence: systematic review and meta-analysis. Int. Urogynecol. J. 2018 Jan; 29: 13–21. PubMed Abstract \| Publisher Full Text\n\nMao M, Li Y, Zhang Y, et al.: Human umbilical cord mesenchymal stem cells reconstruct the vaginal wall of ovariectomized Sprague–Dawley rats: implications for pelvic floor reconstruction. Cell Tissue Res. 2021 Dec; 386: 571–583. PubMed Abstract \| Publisher Full Text\n\nKerkhof MH, Hendriks L, Brölmann HA: Changes in connective tissue in patients with pelvic organ prolapse—a review of the current literature. Int. Urogynecol. J. 2009 Apr; 20: 461–474. PubMed Abstract \| Publisher Full Text\n\nBray R, Derpapas A, Fernando R, et al.: Does the vaginal wall become thinner as prolapse grade increases?. Int. Urogynecol. J. 2017 Mar; 28: 397–402. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhu YP, Xie T, Guo T, et al.: Evaluation of extracellular matrix protein expression and apoptosis in the uterosacral ligaments of patients with or without pelvic organ prolapse. Int. Urogynecol. J. 2021 Aug; 32: 2273–2281. Publisher Full Text\n\nFeng Y, Wang Y, Yan B, et al.: Matrix Metalloproteinase-1 Expression in Women With and Without Pelvic Organ Prolapse: A Systematic Review and Meta-analysis. Clin. Transl. Sci. 2016 Oct; 9(5): 267–273. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLiu Z, Tang Y, Liu J, et al.: Platelet-rich Plasma Promotes Restoration of the Anterior Vaginal Wall for the Treatment of Pelvic Floor Dysfunction in Rats. J. Minim. Invasive Gynecol. 2023 Jan 1; 30(1): 45–51. PubMed Abstract \| Publisher Full Text\n\nGuo T, Du Z, Wang XQ, et al.: Ovariectomy with simulated vaginal delivery to establish a rat model for pelvic organ prolapse. Connect. Tissue Res. 2023 Jul 4; 64(4): 376–388. PubMed Abstract \| Publisher Full Text\n\nEhrenfest DM, Andia I, Zumstein MA, et al.: Classification of platelet concentrates (Platelet-Rich Plasma-PRP, Platelet-Rich Fibrin-PRF) for topical and infiltrative use in orthopedic and sports medicine: current consensus, clinical implications and perspectives. Muscles, ligaments and tendons journal. 2014 Jan; 4(1): 3.\n\nBielecki T, Dohan Ehrenfest DM: Platelet-rich plasma (PRP) and Platelet-Rich Fibrin (PRF): surgical adjuvants, preparations for in situ regenerative medicine and tools for tissue engineering. Curr. Pharm. Biotechnol. 2012 Jun 1; 13(7): 1121–1130. PubMed Abstract \| Publisher Full Text\n\nMeidyawati R, Suprastiwi E: The Ability of Lysate-PRF Induces Proliferation of Fibroblast Cells in Endodontic Regenerative Therapy. Open J. Stomatol. 2018; 08(5): 182–187. Publisher Full Text\n\nDohan Ehrenfest DM, de Peppo GM , Doglioli P, et al.: Slow release of growth factors and thrombospondin-1 in Choukroun’s platelet-rich fibrin (PRF): a gold standard to achieve for all surgical platelet concentrates technologies. Growth Factors. 2009 Jan 1; 27(1): 63–69. PubMed Abstract \| Publisher Full Text\n\nGong R, Xia Z: Collagen changes in pelvic support tissues in women with pelvic organ prolapse. Eur. J. Obstet. Gynecol. Reprod. Biol. 2019 Mar 1; 234: 185–189. PubMed Abstract \| Publisher Full Text\n\nRuiz-Zapata AM, Heinz A, Kerkhof MH, et al.: Extracellular matrix stiffness and composition regulate the myofibroblast differentiation of vaginal fibroblasts. Int. J. Mol. Sci. 2020 Jul 4; 21(13): 4762. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGuler Z, Roovers JP: Role of fibroblasts and myofibroblasts on the pathogenesis and treatment of pelvic organ prolapse. Biomolecules. 2022 Jan 6; 12(1): 94. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlarab M, Kufaishi H, Lye S, et al.: Expression of extracellular matrix-remodeling proteins is altered in vaginal tissue of premenopausal women with severe pelvic organ prolapse. Reprod. Sci. 2014 Jun; 21(6): 704–715. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIozon S, Caracostea GV, Páll E, et al.: Injectable platelet-rich fibrin influences the behavior of gingival mesenchymal stem cells. Romanian J. Morphol. Embryol. 2020 Jan; 61(1): 189–198. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCaruana A, Savina D, Macedo JP, et al.: From platelet-rich plasma to advanced platelet-rich fibrin: biological achievements and clinical advances in modern surgery. European journal of dentistry. 2019 May; 13(02): 280–286. Publisher Full Text\n\nLi Y, Song P, He J, et al.: Comparison between injectable platelet-rich fibrin and platelet-rich plasma in ameliorating UVA-induced photoaging in human dermal fibroblasts via the activation of TGF-β/smad signaling pathway. Photochem. Photobiol. 2022 Nov; 98(6): 1395–1401. PubMed Abstract \| Publisher Full Text\n\nSaputra AND, Rizal DM, Rahman MN, et al.: Effect of human platelet-rich fibrin lysate on collagen type i, collagen type iii, and matrix metalloproteinase 1: A protocol study on rat models with pelvic organ prolapse. OSF. 2024. Publisher Full Text" }	[ { "id": "327434", "date": "18 Oct 2024", "name": "Reetta Sartoneva", "expertise": [ "Reviewer Expertise Tissue engineering approaches for POP" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe protocol study “Effect of Human Platelet-Rich Fibrin Lysate on Collagen Type 1, Collagen Type III, and Matrix Metalloproteinase 1: A Protocol Study on Rat Models with Pelvic Organ Prolapse” is well written and the language is clear. The research question in interesting and highly worthwhile to study. My major comment is related to the rationale of writing a protocol study. What was your point for writing a protocol study. Some other minor issues are:\nIn the Introduction part in second chapter starting “Pelvic floor reconstruction surgery…”. In my opinion the “severe bowel injuries leading to postoperative sepsis” is too strongly stated. It is true that the bowel complications may occur, however, severe bowel injuries in traditional vaginal POP surgery are extremely rare. Further, the recurrence rate 58 % within the first year after surgery is too pessimistic. Please check the recurrence rate again, or maybe you could use some kind of range in recurrence rate?\nAt the page 6 (Preparation of human platelet-rich fibrin lysate): What do you mean by the participants, whose blood was used to make hPRF-L? Were they voluntary donors?\n\nAt the page 9 in discussion part, you are writing that the hPRF-L used in this study is more advanced and possibly more efficient method for regenerative therapy in POP. I think that is overstated based on this protocol study writing. I think you cannot say that it may be more efficient than PRP since you are just starting to study it.\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/13-1056
https://f1000research.com/articles/13-1055/v1	13 Sep 24	{ "type": "Data Note", "title": "A guide to selecting high-performing antibodies for CSNK1A1 (UniProt ID: P48729) for use in western blot, immunoprecipitation, and immunofluorescence", "authors": [ "Riham Ayoubi", "Charles Alende", "Maryam Fotouhi", "Vera Ruíz Moleón", "Sara González Bolívar", "Kathleen Southern", "Carl Laflamme", "NeuroSGC/YCharOS/EDDU collaborative group", "ABIF consortium", "Riham Ayoubi", "Charles Alende", "Maryam Fotouhi", "Vera Ruíz Moleón", "Sara González Bolívar", "Kathleen Southern" ], "abstract": "CSNK1A1 is a key regulator of various signalling pathways, including the Wnt/β-catenin pathway. Playing a central role in cellular function and disease pathology, CSNK1A1 has emerged as an attractive protein target for therapeutic development. In this study we characterize ten CSNK1A1 commercial antibodies for western blot, immunoprecipitation, and immunofluorescence using a standardized experimental protocol based on comparing read-outs in knockout cell lines and isogenic parental controls. This study is part of a larger, collaborative initiative seeking to address antibody reproducibility issues by characterizing commercially available antibodies for human proteins and publishing the results openly as a resource for the scientific community. While the use 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: P48729", "CSNK1A1", "Casein kinase I isoform alpha", "CK-I alpha", "CK1", "antibody characterization", "antibody validation", "western blot", "immunoprecipitation", "immunofluorescence" ], "content": "Introduction\n\nA member of the casein kinase family of serine/threonine kinases, Casein kinase I isoform alpha (CSNK1A1), encoded by the CSNK1A1 gene, acts as a key regulator of various cellular processes such as cell proliferation, apoptosis and key signaling pathways including the Wnt/β-catenin signalling pathway. 1 – 3 By phosphorylating β-catenin, CSNK1A1 initiates its degradation, acting as a negative regulator of the Wnt signalling pathway. 4 , 5\n\nDysregulation of CSNK1A1 activity often leads to various diseased states, including cancer 6 , 7 and neurodegeneration. 8 As such, pharmacological targeting of CSNK1A1 is of significant interest in the research community for clinical intervention. The creation of a publicly accessible database containing trusted antibody characterization data, aiding researchers in assessing antibody suitability, would enable such research.\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. 9 – 11 Here we evaluated the performance of ten commercial antibodies for CSNK1A1 for use in western blot, immunoprecipitation, and immunofluorescence, enabling biochemical and cellular assessment of CSNK1A1 properties and function. The platform for antibody characterization used to carry out this study was endorsed by a committee of industry academic representatives. It consists of identifying human cell lines with adequate target protein expression and the development/contribution of equivalent knockout (KO) cell lines, followed by antibody characterization procedures using most commercially available antibodies against the corresponding protein. The standardized consensus antibody characterization protocols are openly available on Protocol Exchange (DOI:10.21203/rs.3.pex-2607/v1). 12\n\nThe authors do not engage in result analysis or offer explicit antibody recommendations. 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. Guidelines on how to interpret antibody characterization data found in this study are featured on the YCharOS gateway. 13\n\n\nResults and discussion\n\nOur standard protocol involves comparing readouts from WT (wild type) and KO cell lines. 12 , 14 In the absence of commercially available KO cell lines, siRNA technology can be employed to KD (knockdown) the target gene. 15 , 16 As CSNK1A1 is an essential gene in many cancer cells, the application of siRNA is particularly beneficial to maintain the viability of the cells while reducing the expression of the gene, serving as a negative control. 4 , 17 To determine which cell line demonstrates high expression of CSNK1A1 and thus appropriate for KD, the first step is to identify a cell line(s) that expresses sufficient levels of a given protein to generate a measurable signal using antibodies. To this end, we examined the DepMap (Cancer Dependency Map Portal, RRID:SCR_017655) transcriptomics database to identify cell lines that express the target at levels greater than 2.5 log2 (transcripts per million “TPM” + 1), which we have found to be a suitable cut-off. 9 To determine which cell line would be appropriate to evaluate CSNK1A1 antibodies, eight cell line backgrounds (Table 1) were analysed by western blot with three antibodies targeting different epitopes (Figure 1). The resulting band pattern was analysed across the various cell lines. 12 As a result, HCT 116 was identified as the highest expressing cell line as compared to the other cell lines tested here and was thus selected. For simplicity, the western blot with one CSNK1A1 antibody, A9308, is shown in Figure 1. The cell lines used in Figure 1 as well as the corresponding RNA levels from DepMap are listed in Table 1.\n\nLysates of HCT 116, U-87 MG, DMS 53, HT-1080, HEK293T, U-2 OS, HeLa and HAP1 were prepared, and 20 μg of protein were processed for western blot with the indicated CSNK1A1 antibody, A9308, diluted to 1/1000. The Ponceau stained transfer is shown as a loading control.\n\nTo screen all ten CSNK1A1 antibodies (Table 2) by western blot, HCT 116 was modified with siRNA, targeting the corresponding CSNK1A1 gene. HCT 116 WT and CSNK1A1 KD protein lysates were ran on SDS-PAGE, transferred onto nitrocellulose membranes, and then probed with the antibodies in parallel (Figure 2).\n\n* Monoclonal antibody.\n\n** Recombinant antibody.\n\nLysates of HCT 116 WT and CSNK1A1 KD were prepared, and 50 μg of protein were processed for western blot with the indicated CSNK1A1 antibodies. The Ponceau stained transfers of each blot are presented to show equal loading of WT and KD lysates and protein transfer efficiency from the polyacrylamide gels to the nitrocellulose membrane. Antibody dilutions were chosen according to the recommendations of the antibody supplier. An exception was given for antibody 68434-1-Ig, which was titrated as the signal was too weak when following the supplier’s recommendations. Antibody dilution used: ab108296* at 1/1000, ab206652 at 1/1000, A9308 at 1/1000, ARP51843 at 1/500, ARP76053 at 1/500, NBP3-22219** at 1/500, AF4569 at 1/100, 55192-1-AP 1/2000, 68434-1-Ig* at 1/3000, MA5-38189** at 1/1000. Predicted band size: 39 kDa. Monoclonal antibody, Recombinant antibody.\n\nWe then assessed the capability of all ten antibodies to capture CSNK1A1 from HCT 116 protein extracts using immunoprecipitation techniques, followed by western blot analysis. For the immunoblot step, a specific CSNK1A1 antibody identified previously (refer to Figure 2) was selected. Equal amounts of the starting material (SM) and unbound fractions (UB), as well as the whole immunoprecipitate (IP) eluates were separated by SDS-PAGE (Figure 3).\n\nHCT 116 lysates were prepared, and immunoprecipitation was performed using 1 mg of lysate and 2.0 μg of the indicated CSNK1A1 antibodies pre-coupled to Dynabeads protein A or protein G. Samples were washed and processed for western blot with the indicated CSNK1A1 antibody. For western blot, ab206652* was used at 1/1000. The Ponceau stained transfers of each blot are shown. SM=4% starting material; UB = 4% unbound fraction; IP = immunoprecipitate, HC = antibody heavy chain. Monoclonal antibody, Recombinant antibody.\n\nFor immunofluorescence, the ten antibodies were screened using a mosaic strategy. First, HCT 116 WT and CSNK1A1 KD cells were labelled with different fluorescent dyes in order to distinguish the two cell lines, and the CSNK1A1 antibodies were evaluated. Both WT and KD lines imaged in the same field of view to reduce staining, imaging and image analysis bias (Figure 4). Quantification of immunofluorescence intensity in hundreds of WT and KD cells was performed for each antibody tested, and the images presented in Figure 4 are representative of this analysis. 12\n\nHCT 116 WT and CSNK1A1 KD cells were labelled with a green or a far-red fluorescent dye, respectively. WT and KD cells were mixed and plated to a 1:1 ratio in a 96-well plate with optically clear flat-bottom. Cells were stained with the indicated CSNK1A1 antibodies and with 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 KD 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 an antibody was recommended for immunofluorescence by the supplier, we tested it at the recommended dilution. The rest of the antibodies were tested at 1 and 2 μg/ml and the final concentration was selected based on the detection range of the microscope used and a quantitative analysis not shown here. Antibody dilution used: ab108296* at 1/350, ab206652 at 1/600, A9308 at 1/800, ARP51843 at 1/250, ARP76053 at 1/250, NBP3-22219** at 1/500, AF4569 at 1/100, 55192-1-AP 1/400, 68434-1-Ig* at 1/500, MA5-38189** at 1/800. Bars = 10 μm. Monoclonal antibody, Recombinant antibody.\n\nIn conclusion, we have screened ten CSNK1A1 commercial antibodies by western blot, immunoprecipitation, and immunofluorescence by comparing the signal produced by the antibodies in human HCT 116 WT and CSNK1A1 KD cells. To assist viewers in interpreting antibody performance, Table 3 outlines various scenarios in which antibodies may perform in all three applications. Several high-quality and renewable antibodies that successfully detect CSNK1A1 were identified in all applications. Researchers who wish to study CSNK1A1 in a different species are encouraged to select high-quality antibodies, based on the results of this study, and investigate the predicted species reactivity of the manufacturer before extending their research.\n\nThe underlying data for this study can be found on Zenodo, an open-access repository for which YCharOS has its own collection of antibody characterization reports. 18 , 19\n\nInherent limitations are associated with the antibody characterization platform used in this study. Firstly, the YCharOS project focuses on renewable (recombinant and monoclonal) antibodies and does not test all commercially available CSNK1A1 antibodies. YCharOS partners provide approximately 80% of all renewable antibodies, but some top-cited polyclonal antibodies may not be available through these partners.\n\nSecondly, the YCharOS effort employs a non-biased approach that is agnostic to the protein for which antibodies have been characterized. The aim is to provide objective data on antibody performance without preconceived notions about how antibodies should perform or the molecular weight that should be observed in western blot. As the authors are not experts in CSNK1A1, only a brief overview of the protein’s function and its relevance in disease is provided. CSNK1A1 experts are responsible for analyzing and interpreting observed banding patterns in western blots and subcellular localization in immunofluorescence.\n\nThirdly, YCharOS experiments are not performed in replicates primarily due to the use of multiple antibodies targeting various epitopes. Once a specific antibody is identified, it validates the protein expression of the intended target in the selected cell line, confirms the lack of protein expression in the KO cell line and supports conclusions regarding the specificity of the other antibodies. Moreover, some antibody clones are donated by 2-3 manufacturers (cross-licensed antibodies), effectively serving as replicates and enabling the validation of test reproducibility. All experiments are performed using master mixes, and meticulous attention is paid to sample preparation and experimental execution. In immunofluorescence, the use of two different concentrations serves to evaluate antibody specificity and can aid in assessing assay reliability. In instances where antibodies yield no signal, a repeat experiment is conducted following titration. Additionally, our independent data is performed subsequently to the antibody manufacturers internal validation process, therefore making our characterization process a repeat.\n\nLastly, as comprehensive and standardized procedures are respected, any conclusions remain confined to the experimental conditions and cell line used for this study. The use of a single cell type for evaluating antibody performance poses as a limitation, as factors such as target protein abundance significantly impact results. 12 Additionally, the use of cancer cell lines containing gene mutations poses a potential challenge, as these mutations may be within the epitope coding sequence or other regions of the gene responsible for the intended target. Such alterations can impact the binding affinity of antibodies. This represents an inherent limitation of any approach that employs cancer cell lines.\n\n\nMethods\n\nThe standardized protocols used to carry out this antibody characterization platform based on comparing readouts in WT and KO cells was established and approved by a collaborative group of academics, industry researchers and antibody manufacturers. The detailed materials and step-by-step protocols used to characterize antibodies in western blot, immunoprecipitation and immunofluorescence are openly available on Protocol Exchange (DOI: 10.21203/rs.3.pex-2607/v1). 12 Brief descriptions of the experimental setup used to carry out this study can be found below.\n\nCell lines used and primary antibodies used in this study are listed in Tables 1 and 2, respectively. To ensure that the cell lines and antibodies are cited properly and can be easily identified, we have included their corresponding Research Resource Identifiers, or RRID. 20 , 21 HCT 116 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-glutamine (Wisent cat. number 609-065, 100 IU penicillin and 100 μg/ml streptomycin (Wisent cat. number 450201). To KD CSNK1A1, the HCT 116 cells were treated twice with 10 nM of CSNK1A1 SMARTpool siRNA (Horizon Discovery, cat. number L-003957-00-0005). Lipofectamine RNAiMAX (Thermo Fisher Scientific, cat. number 13778030) was used to transfect the siRNA following the manufacturer’s protocol. All other cell types were cultured as recommended by the provider.\n\nPeroxidase-conjugated goat anti-rabbit and anti-mouse (Thermo Fisher Scientific, cat. number 65-6120 and 62-6520), Peroxidase-conjugated donkey anti-sheep antibody (Thermo Fisher Scientific, cat. number A16041) and Peroxidase-conjugated VeriBlot for IP Detection Reagent (Abcam, cat. number ab131366) were used for western blot and immunoprecipitation, respectively. Alexa-555-conjugated goat anti-rabbit and anti-mouse secondary antibodies (Thermo Fisher Scientific, cat. number A-21429 and A-21424) and Alexa-555-conjugated donkey anti-sheep secondary antibody (Thermo Fisher Scientific, cat. number A-21436) were used for immunofluorescence.\n\nHCT 116 WT and CSNK1A1 KD (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) (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 (GeneDireX, cat. number PM008-0500) was used.\n\nWestern blots were performed with precast midi 4-20% Tris-Glycine polyacrylamide gels (Thermo Fisher Scientific, cat. number WXP42012BOX) ran with Tris/Glycine/SDS buffer (Bio-Rad, cat. number 1610772), loaded in Laemmli loading sample buffer (Thermo Fisher Scientific, cat. number AAJ61337AD) 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 Signaling 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 (Thermo Fisher Scientific, cat. number 32106) or Clarity Western ECL Substrate (Bio-Rad, cat. number 1705061) prior to detection with the iBright™ CL1500 Imaging System (Thermo Fisher Scientific, cat. number A44240).\n\nAntibody-beads conjugates were prepared by adding 2 μg (antibody at known concentration) or 10 μl of NBP3-22219* (antibody at an unknown concentration) to 500 μl of Pierce IP Lysis Buffer (Thermo Fisher Scientific, cat. number 87788) in a microcentrifuge tube, together with 30 μl of Dynabeads protein A - (for rabbit antibodies) or protein G - (for mouse and sheep antibodies) (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\nHCT 116 WT cells 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 precast midi 4-20% Tris-Glycine polyacrylamide gels. VeriBlot for IP Detection Reagent:HRP (Abcam, cat. number ab131366) was used as a secondary detection system at a concentration of 0.1 μg/ml.\n\nHCT 116 WT and CSNK1A1 KD cells were labelled with a green and a far-red fluorescence dye, respectively (Thermo Fisher Scientific, cat. number C2925 and C34565, respectively). WT and KD 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, 37°C, 5% CO2. Cells were fixed in 4% PFA (in PBS) for 15 min at room temperature and then washed 3 times with PBS. Cells were permeabilized in PBS with 0.1% Triton X-100 for 10 min at room temperature and blocked with PBS with 5% BSA, 5% goat serum 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 CSNK1A1 antibodies overnight at 4°C. Cells were then washed 3 × 10 min 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 confocal high-content microscopy system (Molecular Devices), using a 20× NA 0.95 water immersion objective and scientific CMOS cameras, equipped with 395, 475, 555 and 635 nm solid state LED lights (lumencor Aura III light engine) and bandpass filters to excite DAPI, Cellmask Green, Alexa-555 and Cellmask Red, respectively. Images had pixel sizes of 0.68 × 0.68 microns, and a z-interval of 4 microns. For analysis and visualization, shading correction (shade only) was carried out for all images. Then, maximum intensity projections were generated using 3 z-slices. Segmentation was carried out separately on maximum intensity projections of Cellmask channels using CellPose 1.0, and masks were used to generate outlines and for intensity quantification. 22 Figures were assembled with Adobe Illustrator.", "appendix": "Data availability\n\nZenodo: Antibody Characterization Report for CSNK1A1, https://doi.org/10.5281/zenodo.11618594. 18\n\nZenodo: Dataset for the CSNK1A1 antibody screening study, https://doi.org/10.5281/zenodo.13236994. 19\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgment\n\nWe 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 KO cell line suppliers, for the development of community-agreed protocols, and for their shared ideas, resources, and collaboration. Members of the group can be found below. 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, Peter S. McPherson, 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 your support on 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.11618594)\n\n\nReferences\n\nDesjardins PR, Lue PF, Liew CC, et al.: Purification and properties of rat liver nuclear protein kinases. Can. J. Biochem. 1972; 50(12): 1249–1259. Publisher Full Text\n\nMatsumura S, Takeda M: Phosphoprotein kinases from rat liver cytosol. Biochim. Biophys. Acta. 1972; 289(1): 237–241. Publisher Full Text\n\nRowles J, Slaughter C, Moomaw C, et al.: Purification of casein kinase I and isolation of cDNAs encoding multiple casein kinase I-like enzymes. Proc. Natl. Acad. Sci. USA. 1991; 88(21): 9548–9552. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJiang S, Zhang M, Sun J, et al.: Casein kinase 1α: biological mechanisms and theranostic potential. Cell Commun. Signal. 2018; 16(1): 23. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLiu C, Li Y, Semenov M, et al.: Control of beta-catenin phosphorylation/degradation by a dual-kinase mechanism. Cell. 2002; 108(6): 837–847. PubMed Abstract \| Publisher Full Text\n\nXu W, Huang Z, Gan Y, et al.: Casein kinase 1α inhibits p53 downstream of MDM2-mediated autophagy and apoptosis in acute myeloid leukemia. Oncol. Rep. 2020; 44(5): 1895–1904. PubMed Abstract \| Publisher Full Text\n\nJanovská P, Normant E, Miskin H, et al.: Targeting Casein Kinase 1 (CK1) in Hematological Cancers. Int. J. Mol. Sci. 2020; 21(23). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBaier A, Szyszka R: CK2 and protein kinases of the CK1 superfamily as targets for neurodegenerative disorders. Front. Mol. Biosci. 2022; 9: 916063. PubMed Abstract \| Publisher Full Text \| Free 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. elife. 2023; 12. Publisher Full Text\n\nCarter AJ, Kraemer O, Zwick M, et al.: Target 2035: probing the human proteome. Drug Discov. Today. 2019; 24(11): 2111–2115. PubMed Abstract \| Publisher Full Text\n\nLicciardello MP, Workman P: The era of high-quality chemical probes. RSC Med. Chem. 2022; 13(12): 1446–1459. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAyoubi R, Ryan J, Bolivar SG, et al.: A consensus platform for antibody characterization (Version 1). Protocol Exchange. 2024.\n\nBiddle MS, Virk HS: YCharOS open antibody characterisation data: Lessons learned and progress made. F1000Res. 2023; 12(12): 1344. Publisher Full Text\n\nLaflamme C, McKeever PM, Kumar R, et al.: Implementation of an antibody characterization procedure and application to the major ALS/FTD disease gene C9ORF72. elife. 2019; 8: 8. Publisher Full Text\n\nFire A, Xu S, Montgomery MK, et al.: Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature. 1998; 391(6669): 806–811. PubMed Abstract \| Publisher Full Text\n\nDana H, Chalbatani GM, Mahmoodzadeh H, et al.: Molecular Mechanisms and Biological Functions of siRNA. Int. J. Biomed. Sci. 2017; 13(2): 48–57. Publisher Full Text\n\nJärås M, Miller PG, Chu LP, et al.: Csnk1a1 inhibition has p53-dependent therapeutic efficacy in acute myeloid leukemia. J. Exp. Med. 2014; 211(4): 605–612. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAyoubi R, Fotouhi M, Alende C, et al.: Antibody Characterization Report for CSNK1A1 (Uniprot ID: P48729).2024.\n\nLaflamme C, Ayoubi R, Alende C: Dataset for the CSNK1A1 antibody screening study. [Data set]. 2024.\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": "337524", "date": "09 Nov 2024", "name": "Deborah Moshinsky", "expertise": [ "Reviewer Expertise Antibody characterization and validation" ], "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 tested 10 commercially available antibodies targeting CSNK1A1 for activity in Western Blotting, Immunoprecipitation, and Immunofluorescence. Since a knockout cell line is not available, they compared signals in WT cells to those in which CSNK1A1 was knocked down by siRNA.\n\nThe Figures clearly allow for data interpretation, and the methods are outlined in enough detail to reproduce the data. The authors did not interpret the results but gave sufficient justification for not doing so.\nThis paper is scientifically sound, and I have no reservations about approving it.\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": [] }, { "id": "337523", "date": "21 Nov 2024", "name": "Jan Voskuil", "expertise": [ "Reviewer Expertise Life-time career expertise on antibody characterisation and validation in all immunoassays. Both experience as an academic scientist", "and as a commercial provider." ], "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\nTable 3 was not visible, broken images. The authors delivered an excellent approach to validate commercial antibodies by comparing their generated signals from a suitable cell line, proven to express the target gene sufficiently for antibody detection, with its cognate knock-down derivative cell line. In their approach, they analysed the antibody performance in Western blot (WB), in immuno-precipitation (IP), and in immunocytochemistry (staining of entire cells detected by immunofluorescence, IF). Although the objective of the authors is to present their approach as a method of finding high performing antibodies from the market, the data themselves are left without scientific assessment. I think this paper will benefit from an extra paragraph to discuss the quality of the individual data. For example, some antibodies show extra bands in WB, and it is not clear whether these bands would disappear upon further antibody dilution (without loss of specific signal), or that all the bands, the correct and the wrong ones, would equally fade by further antibody dilution. The target CSNK1A1 is located in the cytoskeleton, spindle and cytoplasm. Its location in the IF data is not very clear in many cases. A few sentences on the quality of the data would be desirable and put some extra scientific weight to the article. The authors suggest that several antibodies worked well across all three applications, but in my opinion none of them showed proper cellular localisation in the IF data. Table 3 was inaccessible to me. This paper is extremely useful for scientists needing a good CSNK1A1 antibody for either WB, or IP. I am not comfortable approving the ICC assessments in this version. I also would like to fully access Table 3.\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? Partly", "responses": [ { "c_id": "12894", "date": "03 Dec 2024", "name": "Carl Laflamme", "role": "Author Response", "response": "Dear Dr. Voskuil, Thank you for taking the time to review our antibody characterization report. We appreciate your feedback. We reached out to the F1000 editorial team regarding the issue you flagged with Table 3, and they have resolved it. Thank you for bringing this to our attention. While we do not provide assessments of the data in the report, Table 3 includes interpretive tips to guide users. The authors are experts in antibody characterization but not in CSNK1A1 specifically. Therefore, we leave the interpretation of the specific bands detected in western blotting to CSNK1A1 experts. We followed the manufacturers' recommendations for antibody use, and the manufacturers themselves reviewed these data prior to publication. None suggested that titration could improve the signal. This report serves to inform researchers about the availability of specific antibodies for immunofluorescence, as demonstrated by the absence of signal in knockout (KO) cell lines for some antibodies. The microscopy parameters used in our antibody screening are intended to assess antibody specificity, rather than to characterize the subcellular localization of CSNK1A1. We welcome CSNK1A1 experts to further investigate the subcellular distribution of this protein. Thank you once again for your comments. Best regards, Carl Laflamme" } ] } ]	1	https://f1000research.com/articles/13-1055
https://f1000research.com/articles/13-821/v1	22 Jul 24	{ "type": "Research Article", "title": "Sustainable Digital Transformation: Its Impact on Perceived Value and Adoption Intention of Industry 4.0 in Moderating Effects of Uncertainty Avoidance", "authors": [ "Yuli Sartono", "Endang Siti Astuti", "Wilopo Wilopo", "Teuku Noerman", "Endang Siti Astuti", "Wilopo Wilopo", "Teuku Noerman" ], "abstract": "Background Industry 4.0 is a significant technical revolution that combines big data analytics, the Internet of Things (IoT), and cyber-physical systems to improve manufacturing productivity. This study investigates the impact of digital trust and sustainable attitude on perceived value and the intention to adopt Industry 4.0 technologies. It also examines the moderating role of uncertainty avoidance in these relationships.\n\nMethods Data were collected from 189 employees of leading manufacturing companies in Indonesia that are recognized for their Industry 4.0 practices. The data were analyzed using Partial Least Squares (PLS) methodology with SmartPLS software to test the proposed hypotheses and explore the moderating effects.\n\nResults The findings reveal that both digital trust and sustainable attitude significantly influence perceived value. However, these factors do not directly affect the intention to adopt Industry 4.0 technologies. Uncertainty avoidance moderates the relationship between digital trust and adoption intention. Specifically, in environments with high uncertainty avoidance, digital trust becomes a critical factor influencing the decision to adopt Industry 4.0 technologies.\n\nConclusions The study provides valuable insights for organizations aiming to implement Industry 4.0 initiatives. It highlights the importance of fostering digital trust and considering cultural dimensions, such as uncertainty avoidance, in their technology adoption strategies.", "keywords": [ "digital trust", "sustainable attitude", "perceived value", "intention to adopt industry 4.0", "uncertainty avoidance" ], "content": "1. Introduction\n\nTechnology has played a pivotal role in human progress throughout history. Humans possess a natural inclination to innovate and create tools, which have been instrumental in shaping civilizations for millennia. Industry 4.0, hailed as a new industrial revolution, is driven by the evolving and diverse needs of society (Tsaramirsis et al., 2022). It marks a significant shift in the way businesses and industries function, holding the potential to redefine the global economy’s trajectory (Müller et al., 2018; Qian & Wang, 2022). Industry 4.0 entails the integration of digital technology, artificial intelligence (AI), big data, the Internet of Things (IoT), machine learning, and cloud computing to establish a smart, interconnected, and automated manufacturing landscape (Ma et al., 2024; Javaid et al., 2022). Virmani et al. (2023) underscored the potential advantages of embracing Industry 4.0, such as enhancing operational efficiency and profitability through digital integration, elevating product quality, trimming production costs, and minimizing variations and defects, thereby bolstering overall operational efficacy.\n\nAccording to a study conducted by Javaid et al. (2022), Industry 4.0 technology is recognized as playing a pivotal role in fostering innovation and driving future business growth. The implementation of Industry 4.0 has the potential to cultivate a sustainable environment (Bonilla et al., 2018; Javaid et al., 2022), in part due to its contribution to energy efficiency and sustainability through the reduction of carbon emissions. Industry 4.0 offers principles, guidance, and technologies that facilitate the establishment of new factories and the enhancement of existing ones (Ghobakhloo, 2018). This enables consumers to opt for diverse production models based on their requirements, with scalability that can be augmented through the utilization of advanced robotics, information technology, and communication systems. Furthermore, the study by Javaid et al. (2022) identifies twenty key applications of Industry 4.0 aimed at fostering a sustainable environment and providing deeper insights into production environments, supply chains, delivery channels, and market outcomes.\n\nIndustry 4.0 has introduced a profound transformation in the world of business and industry. However, the transition towards more connected and automated production models does not come without challenges. Organizations are faced with new complexities in managing more integrated systems, handling big data, and navigating rapidly changing environments (Selten & Klievink, 2024; Wang et al., 2018). These challenges often give rise to uncertainty, which can influence strategic decisions regarding the adoption of Industry 4.0.\n\nAdditionally, the barriers to the implementation of Industry 4.0 include the scarcity of individuals with digital skills (Koerber et al., 2018; Raj et al., 2020; Obermayer et al., 2022), and the resistance of employees to the adoption of Industry 4.0. Non-technological factors or human factors are the main issues (Obermayer et al., 2022), because Industry 4.0, known for its complex interactions between machines and humans, requires compliance and solidarity among actors (Robert et al., 2022). On the other hand, human involvement in the production process is decreasing as it is being replaced by machines (Sony & Naik, 2020).\n\nBarriers or challenges to the intention to implement Industry 4.0 also occur widely across various parts of the world (America, Europe, Asia) and in many sectors (organizations, online delivery, automotive, plastics industry, manufacturing, electricity, and others). These barriers are related to issues of attitude (Cordero et al., 2023; Toni et al., 2021), social influence (Ngan & Khoi, 2022), familiarity (Tick et al., 2022), the TBL approach (Nara et al., 2021), optimism (Nabilah et al., 2020), consumer conformity (Princes, 2020), the moderation of technology usage levels (Saeedi et al., 2020), employee compliance and solidarity (Robert et al., 2022), market uncertainty (Prause, 2019), and communication problems (Setiawan & Poerbosisworo, 2021).\n\nTherefore, in the context of Industry 4.0 adoption, two important concepts that need to be considered are digital trust and sustainable attitudes. Digital trust refers to the belief that technology and information systems can be relied upon, secure, and well-integrated into business processes (Launer et al., 2022). On the other hand, sustainable attitude involves awareness of the environmental and social impacts of business activities (Chang et al., 2018), as well as a commitment to adopting environmentally responsible practices.\n\nIt is important to understand how uncertainty influences the relationship between key factors such as digital trust, sustainable attitude, and the intention to adopt industry 4.0. Additionally, previous research, conducted by Saeedi et al. (2020) and Toni et al. (2021), along with studies by Cordero et al. (2023) and Castillo-Vergara et al. (2022), has demonstrated the importance of measuring the level of Industry 4.0 adoption.\n\nThis study also uses perceived value as a mediating variable. Perceived value can be described as the significant exchange of benefits received (e.g., volume, quality, and convenience) and the sacrifices made to obtain those benefits (e.g., money, time, and effort). In the workplace, employees expect higher utility value from the adoption of new technology for their job performance, and they strive to achieve maximum results by considering limited situations and resources (Walczuch et al., 2007).\n\nFurthermore, supporting the transition towards Industry 4.0 is crucial, especially considering concerns about job loss and apprehensions regarding uncertainty, which may hinder the ability to adapt to the pace of new work rhythms or uncertainty avoidance. Thus, there is still a need for a deeper understanding of the mechanisms and implications in the context of adopting Industry 4.0. Therefore, this research aims to explore the influence of digital trust and sustainable attitude on perceived value and continuous intention to adopt Industry 4.0, moderated by uncertainty avoidance.\n\n\n2. Literature Review and Hypothesis Development\n\nThis research follows the Theory of Reasoned Action (TRA) to construct the theoretical framework. In general, an increase in attitude and subjective norms leads to a stronger intention to perform a behavior (Fishbein, 2008). Specifically, a favorable attitude towards the behavior and perceived social pressure to engage in it lead to stronger behavioral intentions. This theoretical framework is particularly relevant in understanding the adoption of Industry 4.0 technologies, where attitudes towards digital innovation and subjective norms regarding technological advancement play crucial roles in shaping individuals’ intentions to adopt these advancements.\n\nKożuch (2021) elucidates that digital trust, a cornerstone of effective communication in digital organizations, embodies trust in the digital era. Unlike traditional trust, digital trust is distinguished by its reliance on technology. Paliszkiewicz & Chen (2022) further assert that cultivating digital trust stands as a paramount duty of management. It represents an intangible asset and a leadership skill vital for fostering a culture of mutual trust in the workplace and ensuring the proper management of IT assets and data. This conducive environment, termed as a facilitating condition, serves as the bedrock for the successful implementation of digital trust.\n\nDigital trust serves as a pivotal catalyst for seamless digital interactions, gauging the expectations of an entity and validating its authenticity and reliability in digital transactions. Consequently, it has emerged as a prominent area of inquiry, particularly in the context of Industry 4.0 implementation. Studies delve into the impact of digital trust on the acceptance and utilization of Industry 4.0 technology by both organizations and individuals. Digital trust amalgamates traditional trust, underscored by human interactions, with digital technology, profoundly influencing a company’s credibility and growth trajectory.\n\nThe agility inherent in digital organizations underscores the critical role of human trust in conjunction with Industry 4.0, fostering organizational innovation performance—a facet closely aligned with the notion of digital trust (Mubarak & Petraite, 2020), pertinent to this study. Additionally, primary sources such as (Launer et al., 2022; Marcial & Launer, 2019; Saparudin et al., 2020; Abir et al., 2020; Arfi et al., 2021; Kim et al., 2021) offer invaluable insights into the multifaceted nature of digital trust.\n\nThe theory of attitudes discussed here focuses on attitudes towards sustainability, which encompasses environmental and economic aspects. Corporate sustainability, as described by Malek & Desai (2020), emphasizes meeting human resource needs while considering economic, social, and environmental factors. Elkington & Rowlands (1999) propose measuring corporate sustainability based on the Triple Bottom Line (TBL), comprising economic, social, and environmental factors. Pro-environmental behavior, studied through the Theory of Planned Behavior (Ajzen, 1991), is influenced by sustainable attitudes and various situational factors (Trail & McCullough, 2021). Krystallis et al. (2012) highlight cultural influences on sustainable attitudes towards food production. Chen (2015) suggests that sustainable attitudes influence intentions for pro-environmental practices, while Braun & McEachern (2010) emphasize their role in promoting such behavior. Gericke et al. (2019) identify economic, environmental, social, and international cooperation factors shaping sustainable awareness. Choi & Sirakaya (2005) develop the sustainable tourism attitude Scale to assess residents’ attitudes towards sustainable tourism, integrating various sustainability criteria. Michalos et al. (2012) stress the need for intensive education on sustainable development to improve knowledge and change attitudes and behaviors. Choi & Sirakaya (2005) measure sustainable attitudes using indicators such as environmental sustainability, social costs, and economic benefits, providing insights into promoting sustainable attitudes and behaviors.\n\nAfter discussing digital trust and sustainable attitude, another variable that moderates the intention to adopt Industry 4.0 is the cultural dimension introduced by Hofstede (1980), namely uncertainty avoidance (UA). UA is one of the most frequently used cultural dimensions in technology adoption research, especially in online purchase intentions, adoption of big data or cloud storage, digital currency, local government e-government (Elia, 2022), and mobile applications (Negara et al., 2020). UA reflects individuals’ comfort with consistency, predictability, and strict rules versus tolerance for ambiguity and openness to change. This dimension has been widely studied in technology adoption research, particularly in online purchases, big data or cloud storage adoption, digital currency, e-government initiatives, green product preferences, and mobile applications. Individuals with low UA levels are more likely to accept and use new technology (Negara et al., 2020). Despite its relevance, the moderation of UA towards Industry 4.0 adoption intentions remains underexplored, presenting a research gap in understanding its impact on technology adoption.\n\nAccording to McDougall & Levesque (2000), perceived value is an important indicator that can enhance consumer satisfaction and behavioral intentions. The concept of perceived value also determines consumers’ purchase intentions and decisions (Zeithaml, 1988). Consumers typically weigh the benefits and drawbacks of a particular commodity within the constraints of their consumption capacity, purchase costs, and knowledge reserves, and then purchase the commodity with the greatest perceived value (Nguyen et al., 2023). Perceived value is the standard used by consumers to measure the value of a product, and it is a subjective and personal evaluation made by users of the quality of a product or service on an emotional level (Hapsari et al., 2016). The purpose of using the perceived value variable in this study is to test its role as a mediating variable between the independent variables digital trust and sustainable attitudes on behavioral information systems in the implementation of Industry 4.0, as a forefront of digital transformation programs (Baron & Kenny, 1986).\n\nThe intention to adopt Industry 4.0 refers to an organization’s willingness and readiness to adopt and implement technologies and practices associated with Industry 4.0, such as cloud technology, Internet of Things (IoT), big data, simulation, autonomous robots, additive manufacturing, augmented reality, and business intelligence. This is a crucial factor in the adoption process as it reflects the organization’s commitment to technological advancement and changes in employee attitudes and leadership at strategic, tactical, and operational levels (Cordero et al., 2023).\n\nVarious studies have employed theoretical frameworks such as the Theory of Planned Behavior (TPB) and Ajzen’s Theory of Planned Behavior to analyze the factors influencing the intention to adopt Industry 4.0 technology. Zaman et al. (2021) discovered that attitude, subjective norms, and perceived behavioral control positively impact the intention to adopt Industry 4.0 technology, particularly big data. Similarly, Perri et al. (2020) found that attitude, subjective norms, and perceived behavioral control positively affect the intention to adopt smart consumption and production behaviors. These studies offer valuable insights into the cognitive and affective beliefs that influence the intention to adopt Industry 4.0 technology.\n\nDigital trust, which is the users’ confidence in the safety, privacy, security, reliability, and ethical handling of data by companies in the digital environment, correlates with the perceived value of the information conveyed. The concept of trust has been proven to be a crucial factor influencing individuals’ perceptions of products, services, and technology. Various previous studies have indicated that trust in other contexts such as trust in online platforms (OPL) or trust in technology has a positive impact on perceived value (Jayashankar et al., 2018; Konuk, 2018). In this regard, digital trust is viewed as a factor that can enhance the perceived value of the information provided by companies in the digital environment. Therefore, the hypothesis depicts the assumption that the higher the level of user trust in companies regarding digital aspects, the higher the value they attribute to the information received, as reflected in perceived value (Mayer et al., 1995; Zhao & Chen, 2021).\n\nIn addition to digital trust, the hypothesis proposed is that there is a positive influence between sustainable attitudes and perceived value. Salehzadeh & Pool’s (2017) study on the relationship between brand attitudes and perceived value in the context of purchasing luxury goods showed that brand attitudes have a direct and significant impact on perceived value, as well as other dimensions of perception such as social, personal, and functional perceptions. Similarly, Charton-Vachet et al.’s (2020) study in France on the relationship between attitudes and intentions mediated by perceived value showed that customers’ attitudes toward purchasing intentions have a significant impact on perceived value. Both studies highlight the importance of perceived value in mediating the relationship between attitudes and purchase intentions. Therefore, based on a similar research framework, this hypothesis explores the possibility of a direct influence between sustainable attitudes and perceived value\n\nDigital trust positively and significantly affects perceived value.\n\nSustainable attitude positively and significantly affects perceived value.\n\nSaparudin et al. (2020) identified trust as the most influential factor affecting consumers’ intention to continue using mobile banking. Abir et al. (2020) discovered that eWOM, brand image, and trust significantly positively impact the intention to make online purchases. Contrarily, Arfi et al. (2021) found that performance expectation did not influence the intention to use IoT for eHealth. These studies offer insights for enhancing the design of connected devices, improving patient communication, and targeting potential users more effectively. Despite these findings, there is a lack of direct research on the relationship between Digital Trust and the Intention to Adopt Industry 4.0.\n\nCordero et al. (2023) surveyed organizations across several Latin American countries to identify drivers and barriers to Industry 4.0 adoption. Their findings underscored the pivotal role of quality technology in enhancing competitiveness and fostering national progress. Similarly, Castillo-Vergara et al. (2022) explored the technological acceptance of Industry 4.0 among rural Chilean students, revealing that factors such as technological optimism and facilitating conditions shape attitudes and intentions towards technology adoption. In contrast, Toni et al. (2021) utilized the TPB framework to analyze factors influencing the use of innovative vehicles, highlighting the importance of perceived behavioral control and subjective norms in determining intention, while attitude had no direct effect.\n\nSaeedi et al. (2020) investigated the adoption of Industry 4.0 technology among dairy companies in Malaysia, revealing that the TPB accounted for a significant portion of the variation in intention to use such technology. Notably, they found that the moderating effect of technology usage on the influence of attitude on intention varied depending on usage levels. Similarly, Wang et al. (2018) demonstrated in China that environmental concern indirectly impacts the intention to adopt hybrid electric vehicles through various factors, including attitude, subjective norms, and perceived behavioral control.\n\nDigital trust positively and significantly affects intention to adopt.\n\nSustainable attitude positively and significantly affects intention to adopt.\n\nBased on information from several previous studies, it is known that perceived value significantly influences the intention to adopt specific technologies or products. For example, in Miao et al.’s (2022) study on the relationship between perceived value and purchase intention through e-commerce, it was found that perceived value has a positive influence, albeit with the moderation of online purchase experience. This finding indicates a research gap regarding the relationship between perceived value and intention to adopt, especially with moderation. Similar findings occurred in Zhao & Chen’s (2021) study in China on the intention to purchase environmentally friendly homes, where higher perceived value led to a higher positive influence on purchase intention, with trust as a perceived value antecedent factor. Meanwhile, Yin & Qiu’s (2021) study on perceived value and purchase intention based on experiences with artificial intelligence showed that perceived value influences purchase intention with increasing technology accuracy. On the other hand, Hsu & Lin’s (2016) study on the Internet of Things (IoT) found that perceived value significantly influences users’ intention to use IoT services. Therefore, there is a conclusion that antecedent factors and moderation need to be considered to understand more deeply the influence of perceived value on intention to adopt.\n\nPerceived value positively and significantly affects intention to adopt.\n\nBased on the research provided, it can be hypothesized that uncertainty avoidance (UA) moderates the influence of digital trust and sustainable attitude on the intention to continue a relationship. Faqih (2022) found that uncertainty avoidance moderates the relationship between trust and behavioral intention in online shopping, particularly in cultures with high UA levels. Similarly, Ganguly & Nag (2021) highlighted the predictive role of UA in shaping trust and purchase intention in online shopping across different cultural values. Mosunmola et al. (2019) extended this by demonstrating that cultural dimensions, including UA, moderate the relationship between perceived value dimensions, trust, perceived risk, and purchase intention in online shopping. These insights emphasize the significant influence of UA in shaping trust and behavioral intention in online contexts. Therefore, drawing from these findings, it can be hypothesized that UA will moderate the relationship between digital trust and sustainable attitude and the intention to continue a relationship. However, direct research on this specific relationship in the context of Industry 4.0 adoption with the moderation of UA remains limited. Therefore, exploring this relationship would contribute to a deeper understanding of the interplay between cultural dimensions, digital trust, sustainable attitude, and intention to continue a relationship.\n\nUncertainty avoidance positively moderates the relationship among digital trust and intention to adopt.\n\nUncertainty avoidance positively moderates the relationship among digital trust and intention to adopt.\n\nBased on the empirical study and literature review, the research conceptual model can be formulated as follows:\n\nThe conceptual framework of this research is illustrated in Figure 1. This model hypothesizes to explain H1: the relationship between Digital Trust and Perceived Value, H2: the relationship between Sustainable Attitude and Perceived Value, H3: the relationship between Digital Trust and Intention to Adopt Industry 4.0, H4: the relationship between Sustainable Attitude on Intention to Adopt Industry 4.0, H5: relationship between Perceived Value and Intention to Adopt Industry 4.0, H6a: The moderating role of Uncertainty Avoidance on the relationship between Digital Trust and Intention to Adopt Industry 4.0. H6b: The moderating role of Uncertainty Avoidance on the relationship between Sustainable Attitude and Intention to Adopt Industry 4.0.\n\nSource: author’s construct.\n\n\n3. Methods\n\nThe study adopts a quantitative approach, utilizing statistical analysis to analyze numerical research data. Data collection was conducted through a survey method, employing a questionnaire distributed online via Google Forms to gather primary data from respondents. In analyzing the data, Structural Equation Modeling (SEM) was employed using SmartPLS 3.2.4 software (Ringle et al., 2014). This approach allows for a comprehensive examination of the relationships between variables, providing insights into the complex interplay of digital trust, sustainable attitudes, uncertainty avoidance, perceived value and intention to adopt industry 4.0 within the organizational context (Ubaidillah et al., 2022).\n\nThe research was conducted at PT Schneider Indonesia, headquartered at Cibis Nine Building, Jalan TB Simatupang No.2, South Jakarta. This location was chosen because, despite having factories in Batam and Cikarang, only the employees at the headquarters are allowed to interact directly with customers. The research took approximately two months, with one month dedicated to data collection and another month for data processing. The study was carried out from 9 January to 9 February 2024, using primary data gathered from the assessments or perceptions of respondents. Surveys were conducted by distributing questionnaires online using Google Forms. In order to reduce the possibility of bias, attention was taken to ensure that the questionnaire was honestly created and thoroughly tested before being distributed. Anonymity was guaranteed to respondents in order to promote truthful responses.\n\nThe research sample comprises individuals representing variables such as digital trust, sustainable attitudes, uncertainty avoidance, perceived value and intention to adopt industry 4.0. The sample was drawn from employees of a prominent manufacturing company in Indonesia, recognized as a Light House Industry 4.0 by the World Economic Forum in Japan since 2019. This Paris-based company has consistently ranked among the most sustainable companies globally, as per Corporate Knight’s rankings over the past decade.\n\nThe selection of a manufacturing company as the research sample aligns with the focus on Industry 4.0 technology implementation within this sector. The population included all commercial office employees in Indonesia meeting the specified criteria. Employing the Systematic Random Sampling technique and based on the Slovin formula with a precision of e=5%, a sample of 189 employees was obtained, all of whom provided complete responses with no missing data.\n\nDigital trust measurement draws from the works of Mubarak & Petraite (2020), including trust, internet of things, and smart factory, emphasizing the importance of trust in open innovation management within Industry 4.0. Similarly, sustainable attitudes measurement references Gericke et al. (2019), focusing on attitudes as integral components of sustainability consciousness, namely social, economy, and environment. Perceived value is measured through four indicators, namely emotional value, social value, professionalism value, and quality value (Roig et al., 2006). Intention to adopt measurement references Khoa (2023) including continue using, alternative way, and stopping, while uncertainty avoidance is measured using Srite & Karahanna (2006) as the reference framework, namely regulations, order, job explanation, uncertain situation, and opportunity to innovate.\n\n\n4. Results\n\nSurvey was conducted on 189 employees, all of whom met the specified criteria. All 189 data were collected and analyzed using IBM SPSS version 24 and SmartPLS 3.2.4, utilizing partial least squares structural equation modeling (PLS-SEM). Table 1 presents the results of the descriptive analysis of the research respondents.\n\nThe characteristics of respondents are crucial to uncover because they depict employee profiles to understand their intention in adopting Industry 4.0. Analyzing respondent characteristics can serve as a basis for better strategic decision-making, enabling industries to allocate resources and efforts more effectively in implementing Industry 4.0 technology.\n\nTo investigate the influence of digital trust and sustainable attitude on the perceived value and continuous intention to adopt Industry 4.0, moderated by uncertainty avoidance, we employed the technique of Partial Least Squares Structural Equation Modeling (PLS-SEM). The PLS-SEM method was implemented using the SmartPLS 3.2.4 software.\n\nThe measurement model comprises digital trust, sustainable attitude, uncertainty avoidance, perceived value, and intention to adopt, all structured reflectively. Assessing the model’s quality entails focusing solely on indicators with favorable and substantial factor loadings, while employing cronbach alpha, composite reliability, and average variance extracted (AVE) to evaluate the measurement model (Patalay et al., 2015; Hair et al., 2011; Iqbal et al., 2021).\n\nTo measure reliability, we used cronbach’s alpha (CA) and composite reliability (CR). The results for CA and CR are presented in Table 2 for digital trust (0.904, 0.940), sustainable attitude (0.809, 0.888), uncertainty avoidance (0.809, 0.888), perceived value (0.892, 0.925), and intention to adopt (0.791, 0.918), where these values exceed 0.70, thus deemed acceptable and can proceed for further analysis (Hair et al., 2011). Additionally, we tested convergent validity using the AVE values, namely digital trust (0.840), sustainable attitude (0.727), uncertainty avoidance (0.619), perceived value (0.755), and intention to adopt (0.630), all of which exceed the threshold of 0.50 (Henseler et al., 2016). Furthermore, we assessed Fornell-Larcker for testing discriminant validity, as shown in Table 3.\n\nTable 4 reveals that each variable demonstrates a stronger correlation with its respective construct compared to other constructs within the model. Consequently, it can be concluded that all variables exhibit discriminant validity, validating their suitability for subsequent analyses.\n\n* Significant at 5%.\n\n** Significant at 1%.\n\nns Not significant.\n\nThe hypothesis testing results using PLS-SEM with SmartPLS indicate that H1 is accepted, where digital trust has a positive and significant effect on the perceived value (β=0.583, p≤0.001). H2 of this study is also accepted, where sustainable attitude has a positive and significant effect on the perceived value (β=0.226, p<0.001). However, H3 (β=0.081, p=0.224) and H4 (β=0.019, p=0.855) of this study are rejected because their p-values are greater than 0.05, indicating that digital trust and sustainable attitude do not significantly influence the intention to adopt Industry 4.0. Furthermore, H5 of the study shows the expected results, where perceived value has a positive and significant effect on the intention to adopt Industry 4.0 (β=0.224, p=0.008). Regarding the moderating effects, H6a stating that uncertainty avoidance positively moderates the relationship between digital trust and intention to adopt Industry 4.0 (β=0.141, p=0.029), is accepted. However, H6b of this study is rejected because uncertainty avoidance positively and insignificantly moderates the relationship between sustainable attitude and intention to adopt Industry 4.0 (β = 0.002, p = 0.976). Clearly, the results of hypothesis testing can be seen in Table 4 and Figure 2.\n\n\n5. Discussion\n\nThe hypothesis testing results indicate that digital trust has a positive and significant influence on perceived value. Digital trust in this context refers to individuals’ level of trust in digital technology and platforms used. This finding is consistent with several previous studies, such as those conducted by Zhao & Chen (2021), Jayashankar et al. (2018), Konuk (2018), and Ponte et al. (2015), which also found a positive relationship between digital trust and perceived value. Strengthening digital trust can be key to enhancing the perceived value by customers, which in turn can increase customer loyalty and overall consumer satisfaction. Measures such as ensuring data security, transparency in technology use, and providing positive user experiences can help build and maintain strong digital trust (Shin, 2019).\n\nAdditionally, this study indicates that sustainable attitude also has a positive and significant influence on perceived value. This finding is consistent with previous research by Charton-Vachet et al. (2020) and Salehzadeh & Pool (2017), which similarly identified a relationship between attitudes and perceived value. This indicates that a positive attitude towards sustainability issues can influence individuals’ perceived value of products or services. Consumers who have pro-sustainability attitudes tend to perceive the products or services as valuable because they consider the social and environmental impacts of their consumption (Luchs & Kumar, 2017; Paswan et al., 2017). These findings have important implications in product marketing and business strategy development. Including sustainability aspects in marketing strategies and communicating the company’s commitment to sustainability can help enhance the perceived value of products or services in the eyes of consumers.\n\nThis study reveals surprising findings that digital trust and sustainable attitude do not have a significant influence on intention to adopt. Despite previous research indicating the significant influence of digital trust (Arfi et al., 2021; Kim et al., 2021; Saparudin et al., 2020; Rahman et al., 2020) and sustainable attitude (Cordero et al., 2023; Castillo-Vergara et al., 2022; Wang et al., 2018; Toni et al., 2021; Saeedi et al., 2020) on intention to adopt in other contexts, these results indicate an interesting difference. The insignificance of the relationship between digital trust and sustainable attitude with intention to adopt suggests the complexity of factors influencing technology adoption. Although attitudes toward these solutions (in terms of social, economic, and environmental benefits) may be positive, these attitudes alone may not be sufficient to drive adoption intentions without considering subjective norms and perceived behavioral control. In addition, this finding also confirms the full mediation of perceived value. In the implementation of technology adoption, even though the company has decided on its Industry 4.0 sustainability strategy, it means that despite a positive attitude decision, emotional, social, professionalism, and quality value filters are still needed for this attitude decision to become a real action. The relationship between attitude and intention for sustainability is in line with Salas-Zapata et al.’s (2018) research.\n\nThese results have implications for both researchers and practitioners in the field of technology adoption and sustainability. They underscore the importance of considering a comprehensive set of factors when studying adoption behaviors and designing interventions to promote the uptake of new technologies. Future research may benefit from exploring the interplay between different factors and contextual variables to better understand the dynamics of technology adoption processes.\n\nThis study found that perceived value has a significant influence on intention to adopt, which aligns with the findings of several previous studies, such as Hsu & Lin (2016), Yin & Qiu (2021), Zhao & Chen (2021), and Miao et al. (2022). These results underscore the importance of individuals’ perceived value of a technology in determining their intention to adopt it. Most previous studies have emphasized the importance of perceived value in the context of technology adoption, particularly in terms of how the technology can provide benefits and added value to individuals or organizations. Therefore, these findings provide additional support to the previous conclusion that perceived value is a key factor influencing decisions to adopt new technology.\n\nAdditionally, this study also indicates that the relationship between perceived value and intention to adopt can be explained based on the concept of the TRA. This suggests that individuals’ perceptions of the value of a technology influence their intention to adopt it, consistent with the theory that emphasizes the significant role of attitudes and subjective norms in shaping behavior.\n\nAlthough in direct influence, digital trust does not significantly affect intention to adopt Industry 4.0, uncertainty avoidance may serve as a moderating variable on this influence. The concept of uncertainty avoidance refers to the level of comfort individuals or societies have in dealing with uncertain or ambiguous situations. In the context of technology adoption, uncertainty avoidance can influence how individuals interpret and respond to levels of trust in digital technology.\n\nThe findings of this study support previous research conducted by Faqih (2022), Mosunmola et al. (2019), and Ganguly & Nag (2021), which suggest that uncertainty avoidance can act as a moderating variable between digital trust and intention to adopt. High levels of uncertainty avoidance tend to make individuals more cautious and seek certainty before they are willing to take risks in adopting new technology. These findings provide important contributions to our understanding of the complex dynamics influencing individuals’ intentions to adopt technology and can help design more effective strategies to encourage wider and faster technology adoption.\n\nHowever, in the influence of sustainable attitude on intention to adopt, uncertainty avoidance did not significantly serve as a moderating variable. This study diverges from the findings of Sánchez-Franco et al. (2009), which illustrated a significant positive influence of attitudes on intention to adopt moderated by uncertainty avoidance. This difference can be attributed to cultural and psychological factors that influence how individuals respond to uncertainty in technology decision-making situations. When uncertainty avoidance is high, individuals tend to seek certainty and orderliness in decision-making. In terms of technology adoption, individuals’ attitudes toward technology become more critical, and they may be more inclined to consider other factors such as clearer benefits or more pressing needs.\n\nResearch by Lisana (2021) in Indonesia found that uncertainty avoidance is an important element of employees’ trust in using or not using technology. Therefore, in the application of research results related to the moderation of uncertainty avoidance, the proposal of rules (Hong, 2020) regarding agreed-upon procedures and processes is needed, such as focusing on improving repetitive processes, adopting an account management approach, shared dashboard accuracy, dominant solution types, and dominant decision types.\n\n\n6. Conclusion, Implication, and Limitation\n\nThis study highlights the importance of perceived value in influencing the intention to adopt Industry 4.0 technologies, as evidenced by significant findings consistent with prior research. Moreover, the study underscores that both digital trust and sustainable attitude significantly influence perceived value, contributing to the understanding of the adoption process. However, it also reveals surprising results regarding the insignificant direct influence of digital trust and sustainable attitude on intention to adopt. This finding also confirms the full mediation of perceived value, it means that despite a positive attitude decision, emotional, social, professionalism, and quality value filters are still needed for this attitude decision to become a real action of technology adoption. The moderating role of uncertainty avoidance yields expected results on the relationship between digital trust and intention to adopt. However, not on the relationship between sustainable attitude and intention to adopt, shedding light on the complex dynamics of technology adoption. It will need agreed-upon procedures and processes, such as focusing on improving repetitive processes, adopting an account management approach, shared dashboard accuracy, dominant solution types, and dominant decision types.\n\nUnderstanding the significance of perceived value in driving adoption intentions underscores the importance of emphasizing the benefits and value propositions of Industry 4.0 technologies. Building digital trust and fostering sustainable attitudes remain important endeavors, although their direct influence on adoption intentions may be less pronounced. Practitioners should consider incorporating strategies to mitigate uncertainty avoidance, such as providing clear information and reducing perceived risk.\n\nOne limitation of this study is its reliance on self-reported data, which may introduce response bias. Additionally, the study focused on a specific context and population, limiting the generalizability of the findings. Future research could address these limitations by employing diverse methodologies and examining different cultural contexts. Additionally, future research could explore additional moderators of the relationship between digital trust, sustainable attitude, and intention to adopt, considering factors such as cultural differences and organizational contexts. Longitudinal studies could provide insights into the dynamics of technology adoption over time.\n\nI have adhered to the writing guidelines and ethics of the F1000Research journal. Based on letter number 455/UN10.F03/PP/2024 regarding the Research Permit Application, my institution granted permission for the research on January 8, 2024. Additionally, I have received a research permit letter from PT Schneider Indonesia to conduct research at the company.\n\nParticipants’ consent for this study was obtained verbally, as approved by the Institutional Review Board at Brawijaya University. Verbal consent was chosen due to the practicalities of conducting the study remotely and ensuring timely participation. The ethics committee reviewed and approved this method to maintain participant confidentiality and streamline the data collection process.\n\n\nAuthor contributions\n\nConceptualization, Y.S., E.S.A., W.W. and T.N.; methodology, Y.S. and T.N.; software, Y.S.; validation, E.S.A., W.W. and T.N.; formal analysis, Y.S.; investigation, W.W.; resources, Y.S.; data curation, T.N.; writing—original draft preparation, Y.S.; writing—review and editing, Y.S.; visualization, Y.S.; supervision, E.S.A., W.W. and T.N.; project administration, Y.S.; funding acquisition, Y.S. All authors have read and agreed to the published version of the manuscript.", "appendix": "Data availability statement\n\nThe data presented in this study are available on request from the corresponding author due to confidentiality agreements with the participants involved in the research. Our data statement is complete and adheres to the journal’s guidelines. Access to the data is restricted to protect participant privacy. Researchers wishing to access the data must submit a formal request to the corresponding author, detailing the purpose of their research, the specific data needed, intended use, and measures for ensuring data security and participant confidentiality. Requests will be evaluated on a case-by-case basis, and access will be granted under specific conditions approved by our Institutional Review Board (IRB). For further inquiries, please contact yulisartono@student.ub.ac.id.\n\nFigshare: Checklist for “Sustainable Digital Transformation: Its Impact on Perceived Value and Adoption Intention of Industry 4.0 in Moderating Effects of Uncertainty Avoidance”, DOI: https://doi.org/10.6084/m9.figshare.26302273.v2 (Sartono et al., 2024).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0)\n\nSTROBE checklist for “Sustainable Digital Transformation: Its Impact on Perceived Value and Adoption Intention of Industry 4.0 in Moderating Effects of Uncertainty Avoidance”, https://doi.org/10.6084/m9.figshare.26302273.v2 (Sartono et al., 2024).\n\n\nAcknowledgements\n\nThe authors would like to express their sincere gratitude for the support and resources provided during the course of this research.\n\n\nReferences\n\nAbir T, Rahman MA, Yazdani DMN, et al.: Electronic Word of Mouth (e-WOM) and consumers’ purchase decisions: Evidences from Bangladesh. 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PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "306602", "date": "25 Jul 2024", "name": "Mohamad Zreik", "expertise": [ "Reviewer 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\nSummary of the Article The research article titled \"Sustainable Digital Transformation: Its Impact on Perceived Value and Adoption Intention of Industry 4.0 in Moderating Effects of Uncertainty Avoidance\" explores the relationships between digital trust, sustainable attitude, perceived value, and the intention to adopt Industry 4.0 technologies. The study also examines how uncertainty avoidance moderates these relationships. Data were collected from 189 employees at leading manufacturing companies in Indonesia recognized for their Industry 4.0 practices. The findings reveal that digital trust and sustainable attitude significantly influence perceived value, but do not directly affect the intention to adopt Industry 4.0 technologies. Uncertainty avoidance moderates the relationship between digital trust and adoption intention. Detailed Analysis\nPresentation and Citation of Current Literature\nPartly\nThe work is clearly presented and provides a comprehensive analysis. However, some references are outdated. Incorporating more recent studies would strengthen the paper's relevance and ensure it reflects the latest developments in Industry 4.0 and digital transformation. Recommendation: Update the literature review to include more recent sources from the past five years to ensure the study is grounded in the latest research.\n\nStudy Design Appropriateness and Technical Soundness\nYes\nThe study design is appropriate for the research questions posed. The use of Partial Least Squares (PLS) methodology with SmartPLS software is suitable for testing the proposed hypotheses and exploring moderating effects. The sample selection and data collection methods are clearly described, and the statistical analysis is robust, providing valid and reliable results.\n\nDetails of Methods and Analysis for Replication\nYes\nThe study provides sufficient details of the methods and analysis to allow replication. It describes the data collection process, sample selection, survey methodology, and the use of SmartPLS software for PLS-SEM. The measurement of variables, hypothesis testing, and statistical analysis procedures are detailed adequately for replication.\n\nStatistical Analysis and Interpretation\nYes\nThe statistical analysis and its interpretation are appropriate. The use of PLS-SEM is well-suited for the study's objectives, and the analysis includes reliability and validity assessments, hypothesis testing, and the examination of moderating effects. The interpretation of results is consistent with the data and supports the study's conclusions.\n\nAvailability of Source Data\nPartly\nWhile the study mentions that data are available on request from the corresponding author due to confidentiality agreements, this does not ensure full reproducibility. Ideally, the source data should be openly accessible or provided in a manner that allows independent verification and replication of the results without additional barriers. Recommendation: Provide a more detailed data availability statement and consider anonymizing the data to make it fully accessible. If confidentiality agreements are a constraint, clearly outline the process for requesting data access.\n\nConclusions Supported by Results\nYes\nThe conclusions drawn are adequately supported by the results. The findings align with the hypotheses and statistical analysis, and the discussion appropriately interprets the results in the context of the research questions. The conclusions are based on the data presented and provide valuable insights into the impact of digital trust, sustainable attitude, and uncertainty avoidance on the adoption of Industry 4.0 technologies.\n\nConstructive Feedback for Improvement\nUpdate Literature Review\nIncorporate more recent studies (from the past five years) to ensure the research is current and reflects the latest developments in Industry 4.0 and digital transformation.\n\nEnhance Data Accessibility\nProvide a more detailed data availability statement. Consider anonymizing the data to make it fully accessible. If confidentiality is an issue, outline a clear process for requesting data access, ensuring that the steps are not overly cumbersome for researchers wishing to replicate the study.\n\nExpand Discussion on Non-significant Findings\nProvide a deeper exploration of why digital trust and sustainable attitude did not directly affect the intention to adopt Industry 4.0 technologies. Discuss potential reasons for these findings and suggest areas for future research to explore these relationships further.\n\nAddress Cultural Dimensions More Thoroughly\nGiven the significant role of uncertainty avoidance, consider a more detailed discussion of cultural dimensions and their impact on technology adoption. This could include a comparison with findings from different cultural contexts to provide a broader understanding of the role of cultural factors.\n\nBy addressing these points, the authors can enhance the scientific soundness and impact of their study, making it more robust and valuable to the academic community and practitioners in the field of Industry 4.0 and digital transformation.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "12360", "date": "13 Sep 2024", "name": "Yuli Sartono", "role": "Author Response", "response": "Dear Reviewer, Thank you for your detailed and constructive feedback on our research article titled \"Sustainable Digital Transformation: Its Impact on Perceived Value and Adoption Intention of Industry 4.0 in Moderating Effects of Uncertainty Avoidance.\" We appreciate the time and effort you have taken to review our work and provide insightful comments to enhance its quality. Below, we address each of your points: Updating the Literature Review: We appreciate your suggestion to include more recent studies in the literature review. We have now updated this section to incorporate studies from the past five years, ensuring that our literature review reflects the latest developments in Industry 4.0 and digital transformation. This revision helps in grounding our work in the most current research and provides a comprehensive overview of relevant literature. Enhancing Data Accessibility: We understand the importance of data accessibility for reproducibility and transparency. However, our data are subject to confidentiality agreements with the participants and restrictions imposed by the institution where the research was conducted. To address this concern, we will revise our data availability statement to outline a clear and streamlined process for requesting data access. While we may not be able to make the data fully accessible due to confidentiality issues, we will consider anonymizing the data wherever possible. We will ensure that the process for requesting data access is straightforward and not overly cumbersome, enabling other researchers to replicate our study while maintaining the confidentiality of our participants. Expanding the Discussion on Non-significant Findings: We have revised the discussion section to provide a deeper exploration of the non-significant findings, specifically why digital trust and sustainable attitude did not directly affect the intention to adopt Industry 4.0 technologies. The revised discussion now includes potential explanations and contextual factors that might have influenced these results. We have also suggested future research directions to further investigate these relationships. Addressing Cultural Dimensions More Thoroughly: In response to your feedback, we have expanded our discussion on cultural dimensions, particularly the role of uncertainty avoidance, in shaping technology adoption behaviors. We have included a more detailed analysis of how cultural factors influence the adoption of Industry 4.0 technologies. Additionally, we have compared our findings with studies conducted in different cultural contexts to provide a broader understanding of the impact of cultural dimensions on technology adoption. We are committed to improving the scientific rigor and impact of our study, and we believe that incorporating your feedback will significantly enhance its value to the academic community and practitioners in the field of Industry 4.0 and digital transformation. We appreciate your constructive suggestions and will make the necessary revisions to address them. Thank you once again for your valuable feedback. Sincerely, Authors" } ] }, { "id": "306607", "date": "29 Aug 2024", "name": "Muhammad Faraz Mubarak", "expertise": [ "Reviewer Expertise innovation management > digital transformation-->collaborative innovation" ], "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 provides interesting insights where role of digital trust and sustainable attitude is tested towards perceived value, that is further assumed towards intention to adopt i4.0. The study is based on reasonable theoretical background, as well as hypothesis development is considerable. The methodology applied is also suitable, and the context is acceptable tool. Further, results are based on robust analysis to support and reject respective hypothesis. Having said that, the overall study looks good, however, authors are suggested to highlight the originality and novelty of study, though it has solid foundations and USPs such as digital trust and sustainable attitude towards perceived value and then intention (with a mdoerator of course). I wish all the best to all co-authors and grateful for providing me an opportunity to quickly read this very interesting piece of 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? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "12362", "date": "13 Sep 2024", "name": "Yuli Sartono", "role": "Author Response", "response": "Dear Reviewer, Thank you for your thorough review of our manuscript titled \"Sustainable Digital Transformation: Its Impact on Perceived Value and Adoption Intention of Industry 4.0 in Moderating Effects of Uncertainty Avoidance.\" We greatly appreciate your positive feedback on our study's theoretical background, hypothesis development, methodology, and robust analysis. We are pleased that you found our research interesting and valuable. We acknowledge your suggestion to further highlight the originality and novelty of our study, particularly concerning the unique aspects of digital trust and sustainable attitude in relation to perceived value and intention to adopt Industry 4.0 technologies. In response, we will enhance the discussion section to better emphasize these points and clarify how our research contributes to the existing body of knowledge in this field. Regarding the availability of source data, we understand the importance of data accessibility for reproducibility. As mentioned, our data is subject to confidentiality agreements, but we will outline a clear process for requesting access and consider anonymizing the data wherever possible. This should facilitate replication while protecting participant confidentiality. Once again, we appreciate your insightful comments and suggestions, which have guided us in improving the quality of our manuscript. We are committed to addressing your feedback and ensuring that our study provides a meaningful contribution to the field of digital transformation and Industry 4.0 adoption. Thank you for your time and expertise in reviewing our work. We look forward to your continued feedback and suggestions. Sincerely, Authors" } ] }, { "id": "316104", "date": "02 Sep 2024", "name": "Djoko Budiyanto Setyohadi", "expertise": [ "Reviewer Expertise Socio informatics", "information system", "and user interface user experience" ], "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 entitled \"Sustainable Digital Transformation: Its Impact on Perceived Value and Adoption Intention of Industry 4.0 in Moderating Effects of Uncertainty Avoidance\" investigates the mechanisms and implications of adopting Industry 4.0. It examines how digital trust and a sustainable attitude influence perceived value and the ongoing intention to adopt Industry 4.0. The paper addresses an engaging topic and presents a well-executed experiment, supported by a solid theoretical foundation. This makes it a valuable resource for both practitioners and academics. However, there are points that require improvement before the paper can be accepted for indexing.\nThe claim that “there is still a need for a deeper understanding of the mechanisms and implications in the context of adopting Industry 4.0” is intriguing but lacks clear elaboration. The paper should better clarify the relationships among the variables in the proposed model. The literature review is well-structured but could benefit from additional context, especially in relation to the area of the study. It would be beneficial to include more sources that address similar technological acceptance issues, particularly in the Indonesian context. The conclusion should be expanded to reflect the key claims made by the author.\nIn summary, the paper is interesting and useful for the reader related to adopting Industry 4.0. It requires further development and extension. It could be considered for indexing once revisions addressing the above points are made.\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?\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": "12361", "date": "04 Sep 2024", "name": "Yuli Sartono", "role": "Author Response", "response": "Thank you for your thoughtful and constructive feedback on our research paper titled \"Sustainable Digital Transformation: Its Impact on Perceived Value and Adoption Intention of Industry 4.0 in Moderating Effects of Uncertainty Avoidance.\" We are pleased to hear that you find the topic engaging and the study valuable for both practitioners and academics. We appreciate your detailed comments, which have guided us in improving the quality of our paper. Below, we address each of your points: Clarification of the Need for Deeper Understanding: We have now elaborated on the statement regarding the need for a deeper understanding of the mechanisms and implications in adopting Industry 4.0. In the revised paper, we have clarified how the existing literature gaps relate to our study’s objectives. We provide a more detailed explanation of the specific mechanisms, highlighting the importance of understanding these relationships to advance Industry 4.0 adoption. Enhancing the Literature Review with Additional Context: In response to your suggestion, we have enriched the literature review by including more recent studies that address similar technological acceptance issues, particularly within the Indonesian context. These additions provide a broader understanding of how local cultural factors impact the adoption of Industry 4.0 technologies, ensuring that the review reflects the most current and relevant research in this area. Expansion of the Conclusion: We have expanded the conclusion to better reflect the key claims made throughout the paper. The revised conclusion now offers a comprehensive summary of our findings and ties them back to the original research questions and hypotheses. This ensures that the significance of our findings is clearly articulated and underscores the contributions of our study to the field of Industry 4.0 and digital transformation. We are committed to enhancing the clarity, depth, and rigor of our paper. Your feedback has been instrumental in guiding us to make the necessary revisions that improve the quality and impact of our study. We believe that by addressing these points, our paper now offers a more robust and valuable contribution to the academic community and industry practitioners. Thank you once again for your insightful comments and suggestions. Sincerely, Authors" } ] } ]	1	https://f1000research.com/articles/13-821
https://f1000research.com/articles/8-1394/v1	08 Aug 19	{ "type": "Research Note", "title": "Are side effects of cannabidiol (CBD) products caused by tetrahydrocannabinol (THC) contamination?", "authors": [ "Dirk W. Lachenmeier", "Stephanie Habel", "Berit Fischer", "Frauke Herbi", "Yvonne Zerbe", "Verena Bock", "Tabata Rajcic de Rezende", "Stephan G. Walch", "Constanze Sproll", "Stephanie Habel", "Berit Fischer", "Frauke Herbi", "Yvonne Zerbe", "Verena Bock", "Tabata Rajcic de Rezende", "Stephan G. Walch", "Constanze Sproll" ], "abstract": "Cannabidiol (CBD)-containing products are widely marketed as over the counter products, mostly as food supplements, to avoid the strict rules of medicinal products. Side-effects reported in anecdotal consumer reports or during clinical studies were first assumed to be due to hydrolytic conversion of CBD to psychoactive Δ9-tetrahydrocannainol (THC). However, research of pure CBD solutions stored in simulated gastric juice or subjected to various storage conditions such as heat and light with specific liquid chromatographic/tandem mass spectrometric (LC/MS/MS) and ultra-high pressure liquid chromatographic/quadrupole time-of-flight mass spectrometric (UPLC-QTOF) analyses was unable to confirm THC formation. Another hypothesis for the side-effects of CBD products may be residual THC concentrations in the products as contamination, because most of them are based on crude hemp extracts containing the full spectrum of cannabinoids besides CBD. Analyses of 28 food products of the German market containing hemp extract as an ingredient (mostly CBD oils) confirmed this hypothesis: 10 products (36%) contained THC above the lowest observed adverse effects level (2.5 mg/day). Inversely, CBD was present in the products below the no observed adverse effect level. Hence, it may be assumed that the adverse effects of some commercial CBD products are based on a low-dose effect of THC and not due to effects of CBD itself. The safety, efficacy and purity of commercial CBD products is highly questionable, and all of the products in our sample collection showed various non-conformities to European food law such as unsafe THC levels, full-spectrum hemp extracts as non-approved novel food ingredients, non-approved health claims, and deficits in mandatory food labelling requirements. In view of the growing market for such lifestyle products, the effectiveness of the instrument of food business operators' own responsibility for product safety must obviously be challenged.", "keywords": [ "Tetrahydrocannabinol", "cannabidiol", "Cannabis sativa", "hemp", "food supplements", "risk assessment", "drug effects" ], "content": "Introduction\n\nSince hemp has again been approved for cultivation as an industrial crop in the form of low Δ9-tetrahydrocannabinol (THC) hemp varieties, components of the hemp plant are increasingly used for the production of foods and other consumer products such as liquids for electronic cigarettes1. Some product groups (e.g., cosmetics, veterinary supplements, waxes or room fragrances) may be produced with intended off-label use, such as human consumption, in mind and therefore deliberately avoiding the strict safety requirements for medicinal or food products.\n\nFrom all hemp constituents, cannabidiol (CBD) is currently the compound with highest interest. In contrast to THC, the major drug-constituent of hemp, CBD is a non-psychoactive cannabinoid. It is currently being tested for its possible antispasmodic, anti-inflammatory, anxiolytic and antiemetic effects as a drug, e.g. for the treatment of epilepsy2,3. However, CBD products of all kinds can now also be purchased in organic shops, drug stores, supermarkets and via the Internet, mostly by advertising dubious “cure-all” properties including anti-carcinogenic effects or various unspecific health advantages. The marketing of CBD products is based on the current “hype” around medicinal hemp products, whereby the CBD products are offered as a supposedly safe alternative, promised as being free of psychoactive components or their side-effects4. With the exception of the treatment of Dravet’s syndrome, there is little clinical data on the efficacy and safety of CBD, particularly in the treatment of cancer5,6.\n\nCommercial CBD products are usually crude extracts from whole hemp plants (i.e., including flowers and stems). In other ways (e.g., in extracting the food-approved plant parts such as seeds), contents in the range of 1–10% CBD, which are typically advertised, cannot be achieved. Also, the limited available literature and manufacturer data confirm that CBD products are usually extracted by supercritical CO2 or with solvents such as ethanol or isopropanol from the entire hemp plant6,7. Probably due to cost reasons, no further specific enrichment or cleanup of CBD is conducted, so that the commercial extracts are a cannabinoid mixture rather than pure CBD. These extracts are then mixed into ordinary edible oils such as sunflower oil, olive oil or hemp seed oil to obtain the so-called CBD oil6.\n\nThe strategy to market CBD oil products as food supplements within the framework of food regulations seems to be the most common approach of food operators. Some other products, derived from hemp extracts, are CBD chewing gum, “CBD flowers” (plant material sold as tea), and cannabis resin, wax or pollen products.\n\nHowever, no significant food consumption of full-spectrum hemp extracts or hemp flowers containing CBD has been documented before 15 May 1997. These products are therefore classified as “novel” in the Novel Food catalogue of the European Commission under the entry “cannabinoids” and therefore require approval according to the Novel Food Regulation. Up to date (as of July 2019), no approved application is recorded. Basically, all available CBD products based on hemp extract marketed as food or food supplement within the EU are therefore illegally sold, but still widely available in all trade channels (retail, wholesale and e-commerce) due to an apparent lack of enforcement2.\n\nAnecdotal cases ranging from malaise to THC-like effects have become known to the food control authorities in consumer complaint cases regarding CBD products. Additionally, some pediatric studies in epilepsy patients with orally administered CBD also reported adverse effects such as drowsiness and fatigue that could be explained by pharmacological properties of THC rather than of CBD8–10. Currently there are three hypotheses for the cause of the side effects: (i) a direct pharmacological effect of CBD, (ii) the degradation of CBD to THC due to acidic hydrolysis in the stomach following oral consumption, and (iii) THC directly contained in the products as by-product due to co-extraction and enrichment or contamination. In this article, the hypotheses are investigated including new evidence from original data.\n\n\nMethods\n\nTo investigate CBD degradation, differently concentrated CBD in methanolic solutions was used in a range corresponding to typical amounts consumed with supplements based on commercial CBD (Supelco Cerilliant #C-045, 1.0 mg/mL in methanol) supplied by Merck (Darmstadt, Germany). These solutions were exposed to an artificial gastric juice as well as different incubation times and stress factors such as storage under light and heat (see Table 1 for full experimental design). The solutions were stored either in standard freezer (-18°C) or refrigerator (8°C) or at room temperature (20°C). Increased temperatures were achieved using a thermostatically controlled laboratory drying oven type “UT6120” (Heraeus, Langenselbold, Germany) set to either 37°C or 60°C. The daylight condition was achieved by storage at a window (south side). For ultraviolet light exposure, six 25 W ultraviolet (UV) fluorescent tubes type “excellent E” (99.1% UVA) built into a facial tanner type “NT 446 U” (Dr. Kern GmbH, Mademühlen, Germany) were placed 15 cm from the surface of the solutions. In deviation of an experimental protocol of Merrick et al.11, a gastric juice without addition of surfactants was used, which was strictly produced according to the European pharmacopoeia12 (0.020 g NaCl + 0.032 g pepsin + 0.8 mL HCl (1 mol/L), filled up to 10 mL with water). As pure CBD was available only in methanolic solution, the final experimental setups contained 0.08 mol/L HCl and 1% methanol due to dilution.\n\n1 Average of LC-MS/MS and UPLC-QTOF measurements (n=2) (for raw results see dataset13, table sheet 1). THC formation calculated as % in relation to original CBD content.\n\nAbbreviations: CBD: cannabidiol; THC: Δ9-tetrahydrocannabinol; UVA: ultraviolet A; LC-MS/MS: liquid chromatography/tandem mass spectrometry; UPLC-QTOF: ultra-high pressure liquid chromatography/quadrupole time-of-flight mass spectrometry\n\nThe samples were measured using a triple quadrupole mass spectrometer (TSQ Vantage, Thermo Fisher Scientific, San Jose, CA, USA) coupled with an LC system (1100 series, Agilent, Waldbronn, Germany) and also using a quadrupole time-of-flight (QTOF) mass spectrometer (X500, Sciex, Darmstadt, Germany) coupled with an UPLC system (1290 series, Agilent, Waldbronn, Germany). Both systems used the same separation column (Luna Omega Polar C18, 150 × 2.1 mm, 1.6 µm, 100 Å, Phenomenex, Aschaffenburg, Germany). The separation was isocratic with 25 % formic acid (0.1 %) and 75 % formic acid (0.1 % in acetonitrile) and a flow of 0.3 mL/min. In case of QTOF with 35 % formic acid (0.1 %) and 65 % formic acid (0.1 % in acetonitrile) and a flow of 0.45 mL/min. The evaluation took place after fragmentation of the mother ion into three mass traces for each compound. As quantifier for ∆9-THC, ∆8-THC and CBD, the mass transition m/z 315 to 193 was used, for cannabinol (CBN) m/z 311 to 223, and for tetrahydrocannabinolic acid (THCA) m/z 359 to 341. For ∆9-THC and ∆8-THC, baseline separation was achieved. In case of QTOF, quantification was conducted over accurate mass and control of fragmentation pattern. CBD eluted as one of the first cannabinoids, a few minutes before ∆9-THC and ∆8-THC. As internal standards ∆9-THC-D3 (Supelco Cerilliant #T-011, 1.0 mg/mL in methanol) was used for the quantification of ∆9-THC (Supelco Cerilliant #T-005, 1.0 mg/mL in methanol), THCA (Supelco Cerilliant #T-093, 1.0 mg/mL in acetonitrile) and CBN (Supelco Cerilliant #C-046, 1.0 mg/mL in methanol), and cannabidiol-D3 (Supelco Cerilliant #C-084, 100 µg/mL in methanol) for quantification of CBD (Supelco Cerilliant #C-045, 1.0 mg/mL in methanol). The certified reference materials were obtained as solutions in ampoules of 1 mL, all supplied by Merck (Darmstadt, Germany). A limit of detection (LOD) of 5 ng/mL was determined. For both procedures, relative standard deviations better than 5% were achieved.\n\nTo study the possible influence of natively contained THC in hemp products as a cause for side effects, a sampling of all available CBD products registered as food supplement in the German State Baden-Württemberg, other available hemp extract products in retail, as well as all products available at the warehouse of a large internet retailer were sampled between December 2018 and July 2019. A total of 28 samples (see Table 2 for product designations) were analyzed using the above described liquid chromatographic method with tandem mass spectrometry (LC-MS/MS) for THC content. For toxicological evaluation of the results, the lowest observed adverse effect level (LOAEL) of 2.5 mg THC per day published by the European food safety authority (EFSA) based on human data (central nervous system effects and pulse increase) was used15. Taking safety factors (factor 3 for extrapolation from LOAEL to no observed adverse effect level (NOAEL) and factor 10 for interindividual differences, total factor 30) into account, an acute reference dose (ARfD) of 1 μg THC per kg body weight was derived15.\n\n1 Average of 1–6 replicates measured with LC-MS/MS reported (for raw results see dataset13, table sheet 2).\n\n2 Not analyzed or outside calibration.\n\n3 No labelling provided by manufacturer.\n\n4 THC (mg/day) calculated on the basis of 1 portion according to the manufacturer’s labelling. The LOAEL may be exceeded with a probable intake of 2 portions/day.\n\n5 The German guideline value for THC content in food products is 150 µg/kg14.\n\nAbbreviations: CBD: cannabidiol; THC: Δ9-tetrahydrocannabinol; ARfD: acute reference dose (ARfD) of 1 μg THC per kg body weight15; LOAEL: lowest observed adverse effect level of 2.5 mg THC per day15; LC-MS/MS: liquid chromatographic/tandem mass spectrometric\n\n\nResults and discussion\n\nThere is not much evidence to assume that chemically pure CBD may exhibit THC-like side-effects. The World Health Organization (WHO) judged the compound as being well tolerated with a good safety profile3 and the CBD doses in the food supplements on the market are typically much lower than the ones tested in clinical studies. Additionally, there is a 90-day experiment in rats with a hemp extract (consisting of 26% cannabinoids, 96% CBD and <1% THC) from which a NOAEL of 100 mg/kg bw/day could be derived16. For CBD this would be about 25 mg/kg bw/day (or 1750 mg/day for a person with a body weight of 70 kg). This NOAEL would not be reached by the CBD dosages in food supplements.\n\nSome, partly older, in vitro studies put up hypotheses about the conversion of CBD to THC under acidic conditions such as in artificial gastric juice11,17–19. If these proposals could be confirmed with in vivo data, consumers taking CBD orally could be exposed to such high THC levels that the threshold for pharmacological action could be exceeded20. However, taking a closer look at these in vitro studies raises some doubts. If CBD was to be converted to THC in the stomach, typical THC metabolites should be detectable in blood and urine, but this has not been observed in oral CBD studies21,22. Due to the contradicting results, a replication of the in vitro study of Merrick et al.11 was conducted using an extended experimental design. A more selective LC-MS/MS method and also an ultra-high pressure liquid chromatographic method with quadrupole time-of-flight mass spectrometry (UPLC-QTOF) were used to investigate the CBD degradation.\n\nUnder these conditions in contrast to Merrick et al.11, no conversion of CBD to THC was observed in any of the samples. Only in case of the positive control (2 week storage in 0.5 mol/L HCl and 50% methanol), a complete degradation of CBD into 27% THC and other not identified products (with fragments similar to the ones found in CBN and THC fragmentations but with other retention times) was observed (Table 1, underlying data13). From an analytical viewpoint, the use of less selective and specific analytical methods, especially from the point of chromatographic separation, could result in a situation in which certain CBD degradation products might easily be confused with THC due to structural similarities. Thus, similar fragmentation patterns and potentially overlapping peaks under certain chromatographic conditions might have led to false positive results in the previous studies. In conclusion of our degradation experiments, we agree with more recent literature23,24 that CBD would not likely react to THC under in vivo conditions. The only detectable influence leading to degradation is strong acidity, which should be avoided in CBD formulations to ensure stability of products.\n\nOut of 28 samples, 10 samples (36% of the collective) were exceeding the THC LOAEL and were assessed as harmful to health. 14 samples (50% of the collective) were classified as unsuitable for human consumption due to exceeding the ARfD (see Table 2, underlying data13). Furthermore, all samples (100%) have been classified as non-compliant to Regulation (EU) 2015/2283 of the European Parliament and of the Council of 25 November 2015 on novel foods25 and therefore being unauthorized novel foods. The labelling of 28 samples (100%) was also non-compliant to Regulation (EU) No 1169/2011 of the European Parliament and of the Council of 25 October 2011 on the provision of food information to consumers26, e.g. due to lack of mandatory food information such as ingredients list or use of unapproved health claims in accordance to Regulation (EC) No 1924/2006 of the European Parliament and of the Council of 20 December 2006 on nutrition and health claims made on foods27. In summary, none of the products in our survey was found as being fully compliant with European food regulations.\n\nThe THC dose leading to intoxication is considered to be 10 to 20 mg (very high dose up to 60 mg) for inhalatory intake28. The resorption of orally ingested THC varies greatly interindividually with respect to both total amount and resorption rate29. This might be one of the reasons for the individually very different psychotropic effects. A single oral dose of 20 mg THC resulted in symptoms such as tachycardia, conjunctival irritation, “high sensation” or dysphoria in adults within one to four hours. In one in five adults, a single dose of 5 mg already showed corresponding symptoms30.\n\nSome of the CBD oil supplements contained THC in doses up to 30 mg, which can easily explain the adverse effects observed by some consumers. Most of the CBD oils with dosage of around 1 mg offer the possibility to achieve intoxicating dosages of THC if the products are used off-label (i.e. increase of the labelled maximal dosage by factors of 3–5, which is probably not an unlikely scenario). Generally, in the current purity, the CBD products achieve an insufficient margin of safety, especially in light of the German guidance value for THC in food products14,31, which is 150 µg/kg, a magnitude below the actual contents in the products.\n\nHence our results provide compelling evidence that THC natively contained in CBD products by contamination may be a direct cause for side effects of these products. Obviously, there is an involuntary or deliberate lack of quality control of CBD products. Claims of “THC-free”, used by most manufacturers, even of the highly contaminated products, have to be treated as fraudulent or deceptive food information.\n\n\nConclusions\n\nIn light of the discussion about the three potential causative factors for side effects of CBD products, the described effects can be explained most probably by the presence of native THC as contaminant in the products rather than by direct action of CBD or its chemical transformation or metabolization. The conclusions and findings of this study are further supported by the findings of Hazekamp6 reporting data from the Netherlands on cannabis oils according to which the labelling information for CBD and THC was often different from the actual contents. In 26 out of 46 products the THC content was >1%. Further corresponding results were reported in a study from the USA, in which the CBD content was correctly declared for only 26 of 84 CBD products and 18 of the products had THC contents32.\n\nCBD degradation products are currently unknown and need to be characterized and toxicologically assessed, e.g. within the context of the novel food registration process. Until then, the safety of the products remains questionable. Furthermore, standardization and purification of the extracts need to be improved and stability of commercial products during shelf life should be checked (e.g. to prevent CBD degradation by avoiding acidity in ingredients etc.). Finally, the production hygiene also needs to be improved to minimize contamination. According to own observations some CBD oils are manufactured in back offices not suitable for food production.\n\nIn our opinion the high THC content of CBD products is almost a “small scandal” on the food market. Obviously, the manufacturers have - deliberately or in complete ignorance of the legal situation - placed unsafe and unapproved products on the market and thus exposed the consumer to an actually avoidable risk. In view of the growing market for such lifestyle food supplements, the effectiveness of the instrument of food business operators’ own responsibility for food safety must obviously be challenged.\n\n\nData availability\n\nOpen Science Framework: Dataset for “Are side effects of cannabidiol (CBD) products caused by delta9-tetrahydrocannabinol (THC) contamination?” https://doi.org/10.17605/OSF.IO/F7ZXY13\n\nThis project contains the following underlying data:\n\nDataset for “Are side effects of cannabidiol (CBD) products caused by delta9-tetrahydrocannabinol (THC) contamination” F1000 Research.xlsx (Excel spreadsheet with data underlying Table 1 and Table 2, missing data/empty cells correspond to values outside calibration (CBD) or not measured)\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).", "appendix": "Grant information\n\nThe author(s) declared that no grants were involved in supporting this work.\n\n\nAcknowledgements\n\nThe authors would like to thank Sylvia Ullrich, Jutta Neumeister and Ingrid Kübel for their excellent technical support, sample preparation and measurements using LC-MS.\n\n\nReferences\n\nLachenmeier DW: Hemp food products - A problem? 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Publisher Full Text\n\nManthey J: Cannabis use in Europe: Current trends and public health concerns. Int J Drug Policy. 2019; 68: 93–96. PubMed Abstract \| Publisher Full Text\n\nNahler G, Grotenhermen F, Zuardi AW, et al.: A Conversion of Oral Cannabidiol to Delta9-Tetrahydrocannabinol Seems Not to Occur in Humans. Cannabis Cannabinoid Res. 2017; 2(1): 81–86. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGrotenhermen F, Russo E, Zuardi AW: Even High Doses of Oral Cannabidol Do Not Cause THC-Like Effects in Humans: Comment on Merrick et al. Cannabis and Cannabinoid Research 2016;1(1):102-112; DOI: 10.1089/can.2015.0004. Cannabis Cannabinoid Res. 2017; 2(1): 1–4. 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Reference Source\n\nLachenmeier DW, Rehm J: Comparative risk assessment of alcohol, tobacco, cannabis and other illicit drugs using the margin of exposure approach. Sci Rep. 2015; 5: 8126. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGrotenhermen F: Pharmacokinetics and pharmacodynamics of cannabinoids. Clin Pharmacokinet. 2003; 42(4): 327–360. PubMed Abstract \| Publisher Full Text\n\nMeier H, Vonesch HJ: [Cannabis poisoning after eating salad]. Schweiz Med Wochenschr. 1997; 127(6): 214–218. PubMed Abstract\n\nBfR: Tetrahydrocannabinolgehalte sind in vielen hanfhaltigen Lebensmitteln zu hoch – gesundheitliche Beeinträchtigungen sind möglich. Stellungnahme Nr. 034/2018 des BfR vom 8. November 2018. Bundesinstitut für Risikobewertung: Berlin, 2018. Publisher Full Text\n\nBonn-Miller MO, Loflin MJE, Thomas BF, et al.: Labeling Accuracy of Cannabidiol Extracts Sold Online. JAMA. 2017; 318(17): 1708–1709. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "52382", "date": "19 Aug 2019", "name": "Arno Hazekamp", "expertise": [ "Reviewer Expertise medicinal cannabis cultivation", "quality control", "development of administration forms", "clinical trials", "patient surveys." ], "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 focuses on the quality of CBD oils, which is a meaningful and contemporary issue. Table 2 is the core of the study, because it compares the claimed composition of CBD oil, with lab results obtained by the authors. The conclusion is that the currently available products in Germany are often not what they claim to be.\nUnfortunately, the authors did not analyze the actual CBD content of many of the products, and they assume that their own lab analyses are fully accurate, without proving or showing why. The authors use two different methods of analysis without explaining why one method is not sufficient. Also, in many parts of the text, they explain the current situation concerning CBD product without realizing that many readers may not have enough background information to follow their line of reasoning. The manuscript should be rewritten to explain basic concepts better.\nAlso, more data should be added to table 2, particularly about CBD content of the products analyzed. Right now, CBD analysis data is missing for more than half of the samples. It is not clear why so many of the products have not been studied for CBD content, and this undermines the strength of the paper. In general, the idea behind the study is very good, but the execution is relatively poor because it only focuses on the THC content of the product analyzed.\nPlease see my annotated copy of the article here for additional 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? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Partly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "5188", "date": "11 Feb 2020", "name": "Dirk W. Lachenmeier", "role": "Author Response", "response": "Thank you for your detailed comments and annotations in the copy. As requested, we have revised the background information to clarify the basic concepts.Regarding the criticism of lack of CBD analysis, it must be remarked that the aim of our paper was to investigate the side effects of the products due to THC contamination. Hence, the main purpose of our analytical efforts was to accurately determine the content of THC for health risk assessment. See also the title of the paper, which is regarding THC and not CBD. The analysis of CBD is more or less a secondary addition to the aim of our study, which was THC analysis. It is therefore true that CBD quantification is missing for many samples for the pure reason that CBD and THC contents are so different and CBD was outside the linearity of our calibration. For cost reasons, we have refrained from determining CBD using a second method or dilution (it is of note that we had not specific funding for this study and have to generally work economically as tax-payer funded institute). In the legal evaluation of the products, the CBD content is more or less unimportant as long as the content is below the level of pharmacological action (for food products). As all products had to be objected for various reasons (lack of novel food authorisation, THC contents outside of acceptable levels, mandatory labelling etc.), the CBD quantification was not relevant as well because the issue of consumer deception by mislabelling of CBD is secondary to the safety aspects posed by THC or the use of non-approved, potentially unsafe novel food ingredients.Regarding the question on analytical methods, we actually have confidence in our analytical methods and they are fully validated and our institute is externally accredited according to ISO 17025. Nevertheless, as there is no official method for CBD analysis available, we have confirmed our results with a second procedure to even further improve confidence and validity. As of now, we believe that both methods perform similarly and could both be used in instances of laboratories without access to two different instruments.To improve the strength of the paper, as requested by the reviewer, we have added the results of 39 samples measured in the meantime (new total 67 samples). In many of these samples it was also possible to quantify CBD. The measurement of these additional samples corroborates our previous results and interpretation, and we hope that the sample collective now appears as sufficient for publication.Regarding the comments in the annotated copy, we have revised the text considering all suggested changes, except for the following comments for which we provide a detailed response (comment numbering according to Adobe Acrobat comment numbering in annotated copy of reviewer): Page 3, comment #2 “Not yet. The European Food Safety Authority (EFSA) has advised that CBD should be classified as a novel food. But now it is up to individual EU member states to implement that advise into national legislation. Some countries may decide to not follow the advise.” We disagree with this comment. The classification of CBD and hemp extracts (which was published in the novel food catalogue of the European commission and not by EFSA, see: https://ec.europa.eu/food/safety/novel_food/catalogue/search/public/index.cfm?ascii=Cannabinoids) is a consensus decision of all EU member states. EU regulations such as the novel food regulation are binding in its entirety and directly applicable in all Member States. Therefore there appears to be no leverage for member states to act in infringement of the novel food regulation. If you check the Rapid Alert System for Food and Feed (RASFF) portal for CBD (https://webgate.ec.europa.eu/rasff-window/portal/?event=SearchByKeyword&NewSearch=1&Keywords=cbd), there are more than 80 notifications of CBD products as „unauthorised novel food ingredient“ from various countries including Spain, Belgium, Denmark, Germany, Austria, Switzerland, Slovenia, Lithuania, Italy, Sweden. In Germany, there are currently at least 7 court rulings that confirmed the status of CBD as novel food and confirmed the actions of the authorities (typically removal of products from the market).For details on novel food status and German court rulings, please refer to: Lachenmeier DW, Rajcic de Rezende T, Habel S, et al.: Recent jurisdiction confirms novel food status of hemp extracts and cannabidiol in foods – Classification of cannabis foods under narcotic law is still ambiguous. Deut Lebensm Rundsch. 2020;116: 111-119. DOI: https://doi.org/10.5281/zenodo.3631608The following court rulings confirmed the novel food status of cannabidiol and hemp extracts:VG Cottbus 08.01.2020 Az. 3 L 230/19OVG Lüneburg 12.12.2019 Az. 13 ME 320/19VG Hannover 18.11.2019 Az. 15 B 3035/19VG Gießen 11.11.2019 Az. 4 L 3254/19.GIVGH Baden-Württemberg 16.10.2019 Az. 9 S 535/19VG Düsseldorf 27.09.2019 Az. 16 L 2333/19VG Stade 05.09.2019 Az. 6 B 735/19 Page 5, comment #5: “Based on your table, this product seems to be the most reliable. But in fact this sample may not contain any cannabinoids at all.” Some cannabinoids could be qualitatively detected in this sample around the detection limit of the method. Page 4, comment #1: “It is not common to use two methods and use the average. Does that mean you do not trust your own methods?” In our line of work in providing expert opinions that may be used in court cases, it is often common to use two methods, especially in cases where a reference procedure is not established or when there may be grave consequences in application of the results, such as taking products from the market. We currently cannot see the reason why doing more than perhaps absolutely necessary might hinder publication of such results.Furthermore, as there was a discrepancy between our results and some previous studies regarding in vitro formation of THC from CBD, we found it prudent to confirm our results using a second methodology. Page 4, comments #3 and #8 regarding THCA, CBDA and CBN Basically, we can accurately quantify all these other cannabinoids using the same method. However, as the results of these are not presented and unnecessary for the current paper, we have deleted all mentions of these compounds in the method section to avoid confusion. Page 5, comment #7: “Why are some samples measured 1 time, and others up to 6 times?” The number of replicates depended on several factors, sometimes restricted by the very low sample volume we have received. Typically in the cases with highest THC content leading to a judgment of “non-safe food product” we aimed for at least 3 if possible 5 replicates. In certain cases, more replicates were made, for example when several dilutions were within the linearity range." } ] }, { "id": "53494", "date": "17 Sep 2019", "name": "Linda A. Parker", "expertise": [ "Reviewer Expertise Cannabinoids", "nausea", "CBD", "rat models", "addiction", "learning" ], "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\nCommercial CBD products are usually crude extracts from whole hemp plant material, that are available for purchase in several venues. These extracts have been reported to contain cannabinoid mixtures rather than pure CBD, and are then mixed into edible oils to obtain CBD oil. They are marketed as being free of psychoactive component, i.e. THC. Anecdotal reports of THC-like side effects from these mixtures have been reported. Three hypotheses for these side effects are posed: i) direct pharmacological effect of CBD-for which there is little evidence, ii) the degradation of CBD to THC due to acidic hydrolysis in the stomach following oral consumption, and iii) THC directly contained in the products as a by-product due to co-extraction and enrichment or contamination. The article investigated the latter two of these hypotheses.\n\nCBD degradation: Differently concentrated CBD in methanolic solutions was evaluated in a range corresponding to typical amounts consumed in supplements based on commercial CBD supplied by Merck. These solutions were exposed to an artificial gastric juice at different incubation times and under different environmental conditions. In no case was there any conversion of CBD to THC in any of the samples. Indeed, if CBD is converted to THC in the stomach, among consumers taking CBD it would be expected that THC metabolites would be detectable in the blood and urine, but this has not been shown in oral CBD studies.\n\nTHC contamination as a cause of side effects: A sampling of all available CBD products registered as food supplement in the German State Baden-Württemberg, other hemp extract products in retail, as well as products available at the warehouse of a large internet retailer were evaluated for THC content between December 2018 and July 2019. Of the 28 samples described in Table 2, none of the products was compliant with European food regulations and most of the samples contained THC, some at a dose that would be expected to lead to intoxication. Therefore, the results provided evidence that THC contamination in the CBD products is the most likely cause for the anecdotal THC-like side effects reported. Although it would have been even more informative to have a clear indication of the CBD content of each of the samples, the data clearly present evidence that the products are mislabeled and that THC-like side effects reported by patients is likely the result of contamination of the product with THC, which was the purpose of the study.\n\nThis is an important manuscript that will clear up the misconception that CBD is converted to THC in gastric juices of users.\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": "5189", "date": "11 Feb 2020", "name": "Dirk W. Lachenmeier", "role": "Author Response", "response": "Thank you for your assessment of our article." } ] } ]	1	https://f1000research.com/articles/8-1394
https://f1000research.com/articles/10-1154/v1	15 Nov 21	{ "type": "Research Article", "title": "A Randomized Control Trial to Test Effect of Cash Incentives and Training on Active Casefinding for Tuberculosis among Community Health Workers in Nigeria", "authors": [ "Christie Akwaowo", "Victor Umoh", "Idongesit Umoh", "Eno Usoroh", "Olugbemi Motilewa", "Victory Ekpin", "Stella Adeboye", "Etop Antia", "Victor Umoh", "Idongesit Umoh", "Eno Usoroh", "Olugbemi Motilewa", "Victory Ekpin", "Stella Adeboye", "Etop Antia" ], "abstract": "Background: Case detection for Tuberculosis remains low in high burden communities. Community Health Workers (CHWs) are the first point of contact for many Nigerians in the rural areas and have been found useful in active case finding. This study assessed the effect of cash incentives and training on tuberculosis case detection by CHWs in six Local Government Areas in Nigeria. Materials and Methods: A randomised control trial was conducted in three PHC clusters. The intervention Arm (A) received cash incentives for every presumptive case referred. The Training Arm(B) had no cash incentives and the control had neither training nor cash incentives. Case notification rates from the TB program were used to assess the effect of cash incentives on TB case finding. Data was analyzed using Graph Pad Prism. Descriptive data was presented in tables and bivariate data was analyzed using chi square. Mean increases in case notification rates was calculated Statistical significance was set as P=0.05. Results: The intervention identified 394 presumptive TB cases, contributing 30.3% of all presumptive cases notified in the LGAs. Findings also showed an increase of 14.4% (ꭓ2=2.976, P value=0.2258) in case notification rates for the Arm A that received cash incentives alongside training, there was also an increase of 7.4% (ꭓ2= 1.999, P value=0.1575) in Arm B that received Training only. Secondary outcomes indicated a 144.8%(ꭓ2= 4.147, P value=0.1258) increase in community outreaches conducted in the Arm that were given cash incentives. Conclusion: The study demonstrated an increase in TB control activities of case notification and outreaches among community health workers that received cash incentives and training. These findings support the use training and cash incentives for CHWs in high burden TB settings to improve TB case detection rates.", "keywords": [ "Tuberculosis", "Active Case finding", "Cash incentives", "Community Health workers" ], "content": "Introduction\n\nTuberculosis (TB) remains the leading cause of death from a single infectious disease worldwide. Globally, an estimated 10 million people had tuberculosis in 20181. 24% of all TB cases are said to occur in the WHO African region, with 4% of these cases occurring in Nigeria1. TB mortality in Nigeria in 2016 was 39,933 deaths2. Although mortality from TB in Nigeria has dropped substantially over time2, the WHO Tuberculosis Report 2017 indicated that TB incidence has remained stagnant since the year 20003. This is largely due to delayed diagnosis and treatment of active cases. A significant proportion of people infected with TB do not report any symptoms at all, and are therefore less likely to seek care or to be diagnosed of TB4. This leads to under diagnosing of TB cases, which is a major barrier for TB control.\n\nIn 2018, 7 million new cases of TB were notified globally, achieving the UN high-level meeting target which was built on the WHO Flagship Initiative “Find. Treat. All. #EndTB”1. However, a large gap still remained between the number of cases reported and the estimated cases in 2018 (10 million cases). This gap was found to be due to underreporting and under diagnosis of TB globally, with India, Nigeria, Indonesia, and the Philippines being responsible for over 50% of the noticed gap1. Under-detection of TB cases, especially active cases, has dire consequences for the infected individuals, their communities, and the country at large, causing a setback in national TB programmes. Traditional case finding methods have consistently failed to bridge the gap between observed cases of TB and the estimated cases1, hence active case finding has been recommended by WHO, and implemented to increase case detection rates, notification and treatment of TB cases3,5.\n\nActive case-finding involves planned screening of high-risk individuals, such as contacts of TB patients or people living with HIV (PLWHIV). It includes all methods for the identification and then treatment of those with TB who would otherwise not report to the healthcare system6. It is also effective in the identification of latent TB, thereby preventing future development of active TB cases6. Common screening tools for active case findings include history taking, sputum smear, and chest x-rays.\n\nNigeria is a high burden TB country with one of the lowest TB Case Detection rates (25%) and accounting for 8% of the total gap between incidence and reported cases globally in 20167. The South-South of Nigeria, where Akwa Ibom (AK) state is, contributed 12% to all forms of TB cases notified nationwide in 20168. The state also has the highest HIV prevalence rate of 5.5% compared to the national average of 1.4%8. This makes it imperative that the missing cases be traced as HIV is a major risk factor for TB disease. There are pockets of high TB burden communities in some LGAs in the state, making AKS one of the states with persistently low case detection of all forms of TB.\n\nMany high-risk people such as co-infected, co-morbid, malnourished persons, and children with active TB do not experience typical TB symptoms in the early stages of the disease. They are therefore unlikely to seek care early and may not be properly diagnosed when they eventually seek care. Poor knowledge of symptoms and where to access care also affects the uptake of TB services in our communities. Active case detection has been initiated in high risk patient groups including PLWHIV and diabetes4. However, there are still gaps in the patient-initiated screening model. At the community level, passive case detection involves patient awareness and self-presentation to the health facility. It has been observed that awareness about TB is not incorporated into the usual health talks at facilities and outreaches in the state.\n\nCommunity health workers (CHWs) are key to provision of health services at primary care level as they serve as first point of contact for care for many Nigerians especially those living in the rural areas. There are different categories of community health workers in Nigeria, including Community Health Extension Workers (CHEWs), Community Pharmacists (CPs) and Patent Medicine Vendors (PMVs). The CHEWs are health workers who have been formally trained in the Colleges of Health Technology. They are usually employed by the government to work in the primary health centers, though quite a number currently working in the PHCs in Akwa Ibom state are volunteers9.\n\nCommunity Pharmacy is a branch of pharmacy practice which emphasizes providing medical services in a particular community. Community Pharmacists are responsible for dispensing medications, counselling patients according to their health needs, and providing basic access to health care10. Community Pharmacies are thought to be the first point of call for health services, in Nigeria, frequently more than the designated Primary Health Centers11. according to a study, reasons cited for preference of the CPs include ease of access, short waiting time, free consultation, and longer-term availability of the community pharmacists to the people12,13.\n\nOn the other hand, the patent medicine vendors (PMVs) are individuals that currently work as lay health workers in the community, diagnosing, prescribing and treating minor and major ailments. There are currently no barriers to entry to this level of health workers in the sector, therefore, there is a proliferation of PMVs and CPs, with varied qualifications. The major characteristic here is that they are all self-trained with no regulatory body to guide their training. However, their activities are regulated by the Pharmaceutical Society of Nigeria14. This body sometimes carries out unannounced checks on their shops to assess that they adhere to stocking and dispensing of only oral medications.\n\nEfficient development of human resource is necessary if TB control is to be achieved, hence, training of frontline health workers to improve their knowledge and attitude with respect to diagnosis, treatment and prevention of TB is an important strategy for TB control. Studies have shown that good TB knowledge scores among the health workers lead to better TB indices with respect to treatment and prevention. After a week-long training of community health workers in Mozambique, a 14.6% increase in TB case notification rate was noticed in the intervention group compared to a decrease of 16.5% in the control group15. Similarly, a facility-based study in Enugu reported a 100% increase in TB presumptive cases and TB cases diagnosed three months after health workers training was done16.\n\nThe use of cash incentives has been found to improve commitment of health workers, especially community health workers to their tasks. It has also been found to increase innovation and accountability among health care workers in other programs17,18. There is however inadequate evidence on the use of cash incentives as a motivation for improved case detection rate of TB among health workers, especially community health workers in low middle income countries.\n\nThis study aimed to assess the effect of training and cash incentives for referral of presumptive cases of Tuberculosis for appropriate diagnosis and treatment among CHWs in Nigeria. The main research questions were: Can cash incentives and training be used to motivate CHWs to increase TB case detection? The specific objectives were i) to determine effect of cash incentives on TB case detection ii) to determine effect of training CHWs on TB case detection. The hypotheses made in this study were that cash incentives and training will not improve case detection for TB.\n\n\nMethods\n\nAkwa Ibom State is located in the South-South region of Nigeria, one of the states in the oil-rich Niger Delta region with a population of about 5.5 million based on 2006 National population census report7. The state has 31 local governments distributed across the three senatorial districts. It has 368 Primary health centers, unevenly distributed across the local government areas (LGAs)19.\n\nAkwa Ibom state has a high burden of TB and HIV. As at the time of this study, the USAID was carrying out TB control activities in 15 LGAs and TB Reach had projects in three of the remaining 16 LGAs. The study population was the 13 LGAs that were not covered by the ongoing TB programs. Following randomization, the LGAs selected for the study were Esit Eket and Uyo (Arm A), Ibiono Ibom and Ibesikpo (Arm B), and Nsit Ibom and Uruan (Arm C-Control).\n\nThe study was designed as a three-arm parallel cluster randomized control study. A panel survey sampling of all Community Health Workers identified as practicing in the communities was planned. There were no exclusions, only if the CHW declined to participate. All clusters were assumed to be equal at baseline,\n\nThe RCT was conducted in three high TB burden LGAs in the state. The LGAs were selected from the sampling frame of 13 LGAs, with the aid of the State Tuberculosis and Leprosy Control Officer (STBLCO). In each participating LGA, six PHC facilities offering DOTS treatment and services were selected by simple random sampling and included in the study. Each PHC with availability of DOTS treatment plus the catchment communities served as a cluster for this study. A total of 18 clusters were used in this study, six clusters per Arm. The allocation of PHCs is seen in Figure 1.\n\nThe study clusters were randomized to one of the three experimental arms with stratification according to LGA by the researchers. All CHWs in the study cluster were automatically assigned an intervention arm based on this randomization. Training and cash incentives were randomized to study cluster arms A and B. These were recruited with the aid of the facility focal persons, working with the Chairman of the PMVs. All CHWs in the catchment were given an invitation to the training, no exclusions were made, except the person declined to participate. The study PHC thus served as the focal point and referral centre for any cases picked up in the community by the CHWs.\n\nUsing the facility focal person as entry point, invitations were sent to all CHWs in the selected communities for a workshop to be conducted centrally in Uyo, the capital city. A panel survey of all PMVs, CPs and any other CHWs identified was conducted in each cluster. All CHWs in each cluster who participated in the workshop and gave consent were enrolled for the study. Blinding of participants to their allocated arms was not possible. To ensure that participants were blinded to the intervention, the clusters were allocated by LGA. LGAs chosen were not contiguous. The training was also conducted on three separate days i.e., Arm A on Day 1, Arm B on Day 2, and Control Arm on Day 3. Blinding of assessors to the different arms was also not possible.\n\nAll HCWs were targeted in each cluster, as the study was designed as a panel survey. However, a panel survey was not possible as there was large in-and out migration of the PMVs, especially those who originally sent their apprentices to the training. All the HCWs trained in the clusters were followed up for the duration of the study. At endline, we deployed the same method used in recruitment at baseline, targeting all HCWs in the study clusters. This design was used to minimize sampling error and take into account the design effect, and prevent contamination across the three study arms. Therefore, participants were selected as two independent cross-sectional samples.\n\nThe interest in evaluating training and cash incentives concurrently informed the choice of a multi-arm cluster randomized trial. The advantages of this design include increasing the chances of finding an effective intervention and lower costs as the two arms run at the same time. It is also documented that sharing a control arm reduces the sample size relative to performing separate 2-arm trials20.\n\n1. Training of CHWs and subsequent outreaches and community health education campaigns to the study population to improve knowledge on TB control services available. A total of 158 HCWs were trained, 85 in Arm A and 73 in Arm B. They were instructed to carry out community education campaigns, identify presumptive TB cases in communities, collect sputum, and make referrals to the PHC for treatment. The control Arm C had 82 HCWs.\n\nA one-day training session was carried out for each of the arms separately. This was a face-to-face workshop with participants grouped into three clusters. The allocation ratio for the three clusters was 1:1:1 as shown in Figure 2. The training was conducted by the researchers in collaboration with the State Tuberculosis and Leprosy Control Program office. Prior to the workshop, a Training of Trainers was conducted by the Lead Researcher, AKSTBLP State Coordinator and researchers. The Workshop facilitators were trained on the course contents. This was to develop a shared understanding of the aims of the workshop and familiarize them with the contents of the workshop materials.\n\nTraining manuals were developed specifically for the research and distributed to participants. Facilitators used both the training manuals and power point presentations developed from the manuals. Facilitators used participatory learning methods to deliver the course contents. The contents of the training was based on the module developed for active TB case finding for community health workers through house-to-house search for community based organizations (CBOs) and CHWs by the National Tuberculosis and Leprosy Control Program (NTBLCP)21. The sessions included training on basic symptoms, misconceptions diagnosis and treatment of TB, identification of presumptive TB cases, sputum collection and transportation and linking TB patients to care and treatment.\n\nParticipants were also taught how to collect sputum samples by the State Laboratory Focal Person for TB. Sputum cups were donated by the STBLCP program, the researchers procured transportation media (plastic bowls that could contain 4 sputa cups). At the end of the training, each participant was given a container for transporting sputum, 4 sputa cups, a presumptive case referral booklet and information, education and communication (IEC) materials to be used in educating clients.\n\nParticipants were instructed to carry out community education campaigns, identify presumptive TB cases in communities, collect sputum and make referrals to the PHC for treatment. The control Arm C had 41 CHWs. They were also requested to organize outreach health education campaigns in the communities.\n\n2. Cash incentives to PMVs and CPs for referral of presumptive cases for screening. The intervention Arm A (85) received cash incentives of 200 naira (USD0.78) for every presumptive case referred for screening.\n\nBesides these, there were also supportive supervisory visits (SSVs) to the CHWs, where they were encouraged to carry out outreaches. The CHWs were to identify Presumptive cases, collect sputum samples, transport the smears to the PHCs from where they were transported to designated laboratories. The results were sent back through the PHC TB focal persons and all individual positive results were offered treatment at home or the local health post.\n\nThe interventions took place in the PHCs and communities where the CHWs, PMVs and CPs practiced. While most of the CHEWs worked in the public sector PHCs, the CPs and PMVs work in the private sector, setting up their shops with the sole aim of making profit. The baseline interventions were carried out in April 2019 and follow-up was carried out quarterly until March 2020. The trial ended as scheduled after one year, though the COVID-19 pandemic lockdown interrupted endline data collection and close-out of project.\n\nData collection was carried out for a period of 12 months starting in April 2019 and ended in March 2020. Data collection was done via quarterly supportive supervisory visits (SSV) made to the trained Community Health Extension Workers (CHEWs), PMVs and CPs. During the quarterly SSVs, data was collected from the CHWs and compared with the facility TB register. The number of presumptive cases referred, and number of outreaches conducted during the quarter were documented.\n\nA pre-intervention assessment of CHWs knowledge on TB was done using a pre-tested self-administered structured questionnaire. This was a standardized and validated questionnaire used by the national TB program for the 2017 TB Prevalence survey in Nigeria. The questionnaires were administered just before the training workshop for study arms A and B. However, they were administered at the six PHC facilities for the control arm as there was no training conducted for them. A post-intervention assessment was also done using the same tool after 12 months, in the PHC facilities in each of the clusters.\n\nAll materials used for training and data collection have been made available in the Dryad and Zenodo repositories22.\n\nThe Primary outcomes for the intervention were number of presumptive cases referred to the facility. However, TB case notification was used in analysis instead of presumptive cases. Two reasons accounted for this change i) presumptive cases are generally not used as a measure of TB control and ii) some of the PHC clusters were new DOTS facilities and had zero presumptive cases pre-intervention. Case notification data was accessed from the State TB program database. Although the original intention was to assess outcome at cluster level, final analysis was carried out at LGA level. Secondary outcomes included number of outreaches conducted per cluster and proportion of CHWs with correct knowledge post intervention analyzed at cluster level. The proportion of CHWs with correct knowledge post-intervention has been fully discussed in another paper. The number of outreaches was also analyzed by LGAs.\n\nData was collected and entered into Microsoft excel spreadsheet, version 2013, then collated and analyzed using STATA version 13 (Stata, RRID:SCR_012763) and GraphPad Prism version 8 (GraphPad Prism, RRID:SCR_002798) . The statistician was blinded to the study allocation until the data set was ready for final analysis. Descriptive data were analysed using summary statistics. Chi-square(χ2) tests were used to test differences in proportions over the study period. Continuous variables with normal distributions were compared using means and SD and tested using parametric statistics. An open access alternative software than can perform these same functions would be R (R Project for Statistical Computing, RRID:SCR_001905).\n\nEthical Approval was sought and obtained from the University of Uyo Institutional Health Ethics Research Board (UUTH/AD/S/93/VOLXXI/253). Approval was also obtained from the State Ministry of Health Ethics Review Board(MH/PRS/99/VOL.5/511). Individual verbal and written consent were sought and obtained from all participants. Verbal permission was also sought and granted by the Local Government PMV chairmen.\n\nOnly CHWs who consented to participate were recruited into the study. All presumptive cases identified were referred for screening and positive cases were linked up to the State TB program for treatment with DOTS.\n\n\nResults\n\nParticipants were recruited in April 2019 and followed up for one year. The trial ended in a year as intended. In May 2020, the endline assessment was done. All 18 clusters were analyzed as intended, six clusters per Arm. A total of 240 HCWs were recruited as follows: Arm A (85), Arm B (73) and Arm C(82). See Figure 2.\n\nA total of 158 CHWs were trained at the beginning of the intervention, clustered as Arm A and Arm B. Table 1 shows the socio demographic characteristics of participants. Of these, 62.5% were females, 87.9% were less than 40 years old and 33.3% had a tertiary level of education. Majority of the participants were PMVs (78.8%), while 17.9% were CHEWs and 3.3% identified themselves as students, auxiliary nurses and were categorized as ‘others’.\n\n*=Statistically significant\n\nThe total of CHWs who had received a training on TB within the last two years was 72, representing 30% of the population. A significantly higher proportion of these were in the Control Arm (43.9%). Also 24.2% of the CHWs had access to TB guidelines, with a higher proportion of those in the control group stating that they had access to TB guidelines (31.7%).\n\nTable 2 shows the socio-demographic characteristics of participants at endline across the three arms. At endline, there was female preponderance (53.4%), 81.9% were below 40 years old, majority of them had attained secondary education (64.3%) and 77.4% of them being PMVs. There was a statistically significant difference in the duration of current job of the HCWs across the three arms (p=0.006), and in the type of health facility across the three arms (p<0.001).\n\nData from the intervention shows a total of 394 presumptive cases notified from the intervention. This represents 30.3% of all presumptive case notification from the LGAs covered by this intervention and 41.6% of all presumptive case notifications from the PHCs serving as cluster focal facilities. Figure 3 shows the trend in presumptive TB case notification in the intervention LGAs.\n\nData from the intervention suggests an increase of 14.4% in case notification rates between 2018 and 2019 for Arm A (Cash incentives and Training) and an increase of 7.4% in Arm B. However, as seen in Table 3–Table 5, the increases were not statistically significant.\n\nA total of 120 outreaches were conducted during the intervention period. For Arm A, there was a 144.8% increase in number of outreaches over the previous year (pre-intervention). Arm B recorded a 46.7% increase while the control Arm C showed a 22.7% increase in number of outreaches (Table 6). These differences were however not statistically significant.\n\n\nDiscussion\n\nThis study aimed to assess the effect of cash incentives and training on active case finding for TB in a high burden setting. A total of 158 CHWs were trained at the beginning of the intervention. The majority were females, less than 40 years old, and had a tertiary level of education. Most were also PMVs (78.8%), while only 17.9% were CHEWs. Both baseline and endline characteristics of the CHWs showed striking similarities. This shows that the CHWs sampled were essentially the same. Studies in Kenya had reported similar characteristics for CHWs23,24. The study showed that 30% of the respondents had previously been trained on TB. Our findings gives evidence that PMVs are the first point of contact for care especially in rural communities, where our study was based.\n\nOur study demonstrated an increase in presumptive case notifications in the intervention Arms. With data from the intervention facilities accounting for a total of 394 presumptive cases representing 41.6% of all presumptive case notifications from the PHCs serving as cluster focal facilities. This also accounted for 30.3% of all presumptive case notification from the LGAs covered by the intervention. Other studies have documented evidence that community based interventions for active case finding leads to improved outcomes for TB control programs25–27. Such interventions include training of health care workers on presumptive case detection, sputum collection, and referral for treatment. However, evidence seemed to find that these led to short term improvements26.\n\nThe index study demonstrated a 7.4% increase in the training Arm, suggesting an effect of training increased presumptive cases detected. This compares with previous studies on training interventions to improve health outcomes. In a systematic review of interventions on cardiovascular disease prevention and management, eight studies showed improved knowledge of health care workers after training, and retention of acquired knowledge up to six months after training28. In a study in China, it was found that training improved the knowledge of definitions, case detection and laboratory diagnosis of TB up to a year after training29. Similarly, studies done in Fiji show TB case notification rates during the period of training activities increased significantly compared with the years when no training activities took place27.\n\nWe also found a 14.4% increase in case notification in the cash incentives Arm and 7.4% in the training Arm. This study utilized case notification instead of case detection rates (CDR). This is because CDR uses incidence as a denominator, which is a very uncertain estimate as it is not measured but estimated. Similar observations have been made in previous studies17,30. In an evaluation of TB REACH Wave 1 interventions in Pakistan, sputum smear positive (SS+) TB notifications increased by 24.9%. It was also found that among 19 projects with control populations, sputum smear positive TB case notifications increased by 36.9%, while in the control populations a 3.6% decrease was observed31. Again, this contrasts with findings of the index study which recorded increases in the intervention arms (14.4% and 7.4%), and an even larger increase (39%) in the control Arm. Our findings are also similar to that seen in Mozambique where there was a 14.6% increase in notification of all forms of people with TB over the baseline, However, contrary to what we found in our study, the control districts had a decrease in notification(-16.5%)15.\n\nCost effectiveness analysis also demonstrates that incentive-driven active case finding of TB was more effective and less expensive per disability-adjusted life years (DALY) averted when compared to the baseline passive case finding. This was seen in a study in Pakistan, when both alternatives are compared to a common baseline situation of no screening32.\n\nThe paradoxical increase in case notification found in our study was thought to be due to the fact there was another ongoing intervention in the LGAs. This was evident in the findings that a higher proportion of the participants in the control group had received training on TB prior to the commencement of this study, and also had access to TB guidelines.\n\nWith regard to TB outreach activities carried out during the one-year period, A marked increase was observed across all three study arms, with the training and cash incentive arm having an increase of about 145%, far higher than was noticed in the training only and control arms. Community outreach programmes have been found in some studies to improve detection of symptomatic and infectious TB cases in the community21. However, others have found that cases detected through TB outreaches were the less infectious cases with few symptoms who are reluctant to commence or complete treatment22. Nevertheless, it is important to track and notify all forms of TB in the community if the End TB Strategy goal of reduction of incidence by 80% is to be achieved33.\n\nOther components of this study included cash support for outreaches and supportive supervision. Although a recently concluded systematic review conducted to inform the recent World Health Organization (WHO) guidelines on CHW programmes reported “very low certainty” regarding the evidence on supportive supervision34, other studies have demonstrated improved performance of CHWs with supportive supervision35. In a recent review of literature on CHW productivity, the authors suggested that productivity was based on a combination of three elements: (1) knowledge and skills, (2) motivation, and (3) the work environment. The work environment encompassed workload, supervision, supplies and equipment, and level of respect that other health workers had for the CHWs. In their review, the authors maintained that supportive supervision was a critical factor in creating and maintaining an enabling work environment. In another recent study, the majority of participants stated that supervision was one of the most important factors for maintaining a functional cadre of motivated CHWs because supervisors serve as a link between CHWs and the health system. The support that supervisors can provide CHWs helps them to feel valued and feel like an important part of a larger organization36,37. The findings of these components of our study will be fully discussed in another paper.\n\nA limitation of this study was the inability to completely retain all HCWs recruited at baseline, this led to the analysis at LGA level instead of the cluster level originally planned. However, the similarity in baseline and endline characteristic shows the participants were essentially similar and were thus comparable\n\nAnother limitation of this study was the ongoing parallel active case finding intervention in the control communities, during the period of the study. This explains the somewhat paradoxical findings. In retrospect, a baseline assessment of all participants before randomization would have helped to mitigate this effect. However, the study findings are generalizable and applicable to other high burden TB settings.\n\n\nConclusion\n\nThe study demonstrated an increase in TB case notification and outreaches among health workers that received cash incentives and training. There was a double increase in case notifications in the Arms that received cash incentives compared to the Arm that received training only. TB outreach programmes however saw considerable increase in the LGAs in the training and cash incentive arm compared to the training only and control arms.\n\nThe results from this study suggest that the cash incentives given the CHWs motivated them to improve presumptive case detection above the previous years. These findings support the use of incentives for CHWs in high-burden TB settings to improve TB case detection rates. Therefore, cash incentives and training can be used to motivate lay health workers and integrate them into the TB control program to improve TB case detection.\n\nThese results add to the growing evidence base showing that different multicomponent approaches like training, supporting health workers and cash incentives for TB case finding can have a significant improvement on TB notifications.\n\nWe recommend implementation of the intervention in other low case detection, but high TB burden settings. Future researchers into active case finding for TB in high burden areas need to consider carefully the recruitment and randomization process. Further studies are needed, however, to demonstrate the cost-effectiveness of using cash incentives in TB case finding in high burden settings.\n\n\nData availability\n\nDryad: Improving Tuberculosis case finding in Nigeria. https://doi.org/10.5061/dryad.tht76hf0737.\n\nThis project contains the following underlying data.\n\nReadme_Improving Tuberculosis case finding in Nigeria.xlsx (files of all variables in csv file)\n\nTB Community data Post intervention.xlsx (data from post intervention community survey in csv file)\n\nTB Community data pre-intervention.xlsx (data from post intervention community survey in csv file)\n\nTB Health care workers Baseline.xlsx (data from baseline survey of health care workers in csv file)\n\nTB Health care workers endline.xlsx (data from endline survey of health care workers in csv file)\n\nTB study Outcome (summary data from intervention and state TBL program).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\nZenodo: Improving Tuberculosis case finding in Nigeria22. https://doi.org/10.5281/zenodo.5062448.\n\nThis project contains the following extended data:\n\nEthical_Approval_2_SMOH.jpg (ethical approval from the Akwa Ibom State Ministry of Health)\n\nEthical_Approval_TB_1.pdf (ethical approval from the University of Uyo Teaching Hospital)\n\nFINAL_RESEARCH_PROTOCOL._FOR_TB_STUDYdocx.docx (Research protocol used for the study)\n\nQuestionnaires_for_the_TB_Study.zip (Health care worker and community questionnaires used for the survey)\n\nTraining_Kit.zip (copy of modules used for training intervention)\n\nTrialApprovalLetter3.pdf (Trial approval letter from PanAfrican Clinical Trial Registry)\n\nCONSORT checklist for ‘A Randomized Control Trial to Test Effect of Cash Incentives and Training on Active Casefinding for Tuberculosis among Community Health Workers in Nigeria’ https://doi.org/10.5281/zenodo.5062448.\n\nWritten informed consent for publication of the participants details was obtained from the participants.", "appendix": "Acknowledgements\n\nThe authors acknowledge Mr. Edidiong Umoh and Mrs Ekom Ekwo for the coordination of the field work and database for the entire project roles. We also acknowledge the Health Systems Research Hub, University of Uyo for providing the platform to conduct this study.\n\n\nTrial registration\n\nThis study was registered in the Pan African Clinical Trial Registry (www.pactr.org) database, with the unique identification number PACTR202010691865364.\n\n\nReferences\n\nWorld Health Organization: Global TB Report. Geneva: WHO; 2019; [cited 2020 Sep 15]. Reference Source\n\nOgbo FA, Ogeleka P, Okoro A, et al.: Tuberculosis disease burden and attributable risk factors in Nigeria, 1990–2016. Trop Med Health. 2018; 46(1): 34. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWorld Health Organization: Global tuberculosis report 2017. Geneva: World Health Organisation; 2017. Reference Source\n\nLönnroth K, Corbett E, Golub J, et al.: Systematic screening for active tuberculosis: rationale, definitions and key considerations. Int J Tuberc Lung Dis. 2013; 17(3): 289–98. PubMed Abstract \| Publisher Full Text\n\nWorld Health Organization (WHO): Systematic screening for active tuberculosis: principles and recommendations. World Health Organization; 2013; 133. Reference Source\n\nBothamley GH, Ditiu L, Migliori GB, et al.: Active case finding of tuberculosis in Europe: a Tuberculosis Network European Trials Group (TBNET) survey. Eur Respir J. 2008; 32(4): 1023–30. PubMed Abstract \| Publisher Full Text\n\nWorld Health Organization: Global Tuberculosis Report 2017. 2017; [cited 2020 Dec 12]. Reference Source\n\nNACA Nigeria: NIGERIA PREVALENCE RATE. NACA Nigeria, 2019; [cited 2020 Dec 1]. Reference Source\n\nAkwaowo CD, Motilewa OO, Ekanem AM: Assessment of Resources for Primary Health Care: Implications for the Revitalization of Primary Health Care in Akwa Ibom, Nigeria. Niger Med J. 2020; 61(2): 90–5. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMarupudi K: Current status of pharmacies and qualifications of pharmacists in community pharmacies of India. [Ypsilanti, Michigan]: Eastern Michigan University; 2016. Reference Source\n\nBamgboye AO, Hassan IA, Adebisi YA, et al.: Towards improving community pharmacy-based mental health services in Nigeria. J Pharm Policy Pract. 2021; 14(1): 34. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOsemene KP, Erhun WO: Evaluation of community pharmacists’ involvement in public health activities in Nigeria. Braz J Pharm Sci. 2018; 54(3). Publisher Full Text\n\nBrian OO, Henry NC: Community pharmacists and health promotion activities in the 21st century; maximizing the expanded roles for universal health coverage and population health optimization. MOJ Public Health. 2017; 6(3): 354–358. Publisher Full Text\n\nOyeyemi AS, Oladepo O, Adeyemi AO, et al.: The potential role of patent and proprietary medicine vendors’ associations in improving the quality of services in Nigeria’s drug shops. BMC Health Serv Res. 2020; 20(1): 567. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJosé B, Manhiça I, Jones J, et al.: Using community health workers for facility and community based TB case finding: An evaluation in central Mozambique. PLoS One. 2020; 15(7): e0236262. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIwuoha EC, Onwasigwe CN: Improving “Fast” Indicators of TB Infection Control through Targeted Health Workers Training; Findings from Facility Based Studies in Abia State, Nigeria. Int J Trop Dis Health. 2020; 41(21): 1–9. Publisher Full Text\n\nSchuster RC, de Sousa O, Reme AK, et al.: Performance-Based Financing Empowers Health Workers Delivering Prevention of Vertical Transmission of HIV Services and Decreases Desire to Leave in Mozambique. Int J Health Policy Manag. 2018; 7(7): 630–44. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSwann M: Economic strengthening for HIV testing and linkage to care: a review of the evidence. AIDS Care. 2018; 30(sup3): 85–98. PubMed Abstract \| Publisher Full Text\n\nAKSMOH IPD: RI Performance Report Akwa Ibom State; August, 2020. 2020.\n\nDelea MG, Snyder JS, Belew M, et al.: Design of a parallel cluster-randomized trial assessing the impact of a demand-side sanitation and hygiene intervention on sustained behavior change and mental well-being in rural and peri-urban Amhara, Ethiopia: Andilaye study protocol. BMC Public Health. 2019; 19(1): 801. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFMOH: Participants’ Module For Community Based Organizations and Community Health Workers For Active TB Case Finding Through House-To-House Search. FMOH; 2015.\n\nAkwaowo C, Umoh V, Umoh I, et al.: Improving Tuberculosis case finding in Nigeria. 2021. http://www.doi.org/10.5281/zenodo.5062448\n\nCrispin N, Wamae A, Ndirangu M, et al.: Effects of Selected Socio-Demographic Characteristics of Community Health Workers on Performance of Home Visits during Pregnancy: A Cross-Sectional Study in Busia District, Kenya. Glob J Health Sci. 2012; 4(5): 78–90. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMbugua RG: Effect of socio- demographic characteristics on performance of Community Health Workers: A cross sectional study in Makueni County, Kenya. IOSR J Nurs Health Sci. 2017; 6(6): 4–18. Reference Source\n\nMhimbira FA, Cuevas LE, Dacombe R, et al.: Interventions to increase tuberculosis case detection at primary healthcare or community-level services. Cochrane Database Syst Rev. 2017; 11(11): CD011432. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDatiko DG, Lindtjørn B: Health extension workers improve tuberculosis case detection and treatment success in southern Ethiopia: a community randomized trial. PLoS One. 2009; 4(5): e5443. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDelai MY, Gounder S, Tayler-Smith K, et al.: Relationship between education and training activities and tuberculosis case detection in Fiji, 2008–2011. Public Health Action. 2012; 2(4): 142–4. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAbdel-All M, Putica B, Praveen D, et al.: Effectiveness of community health worker training programmes for cardiovascular disease management in low-income and middle-income countries: a systematic review. BMJ Open. 2017; 7(11): e015529. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWu S, Li R, Su W, et al.: Is knowledge retained by healthcare providers after training? A pragmatic evaluation of drug-resistant tuberculosis management in China. BMJ Open. 2019; 9(3): e024196. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKhan AJ, Khowaja S, Khan FS, et al.: Engaging the private sector to increase tuberculosis case detection: an impact evaluation study. Lancet Infect Dis. 2012; 12(8): 608–16. PubMed Abstract \| Publisher Full Text\n\nCreswell J, Sahu S, Blok L, et al.: A Multi-Site Evaluation of Innovative Approaches to Increase Tuberculosis Case Notification: Summary Results. PLoS One. 2014; 9(4): e94465. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHussain H, Mori AT, Khan AJ, et al.: The cost-effectiveness of incentive-based active case finding for tuberculosis (TB) control in the private sector Karachi, Pakistan. BMC Health Serv Res. 2019; 19(1): 690. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWHO: Implementing the end TB strategy: the essentials. Geneva: WHO; 2015; [cited 2021 Feb 8]. Reference Source\n\nCometto G, Ford N, Pfaffman-Zambruni J, et al.: Health policy and system support to optimise community health worker programmes: an abridged WHO guideline. Lancet Glob Health. 2018; 6(12): e1397–1404. PubMed Abstract \| Publisher Full Text\n\nMusoke D, Ssemugabo C, Ndejjo R, et al.: Strengthening the community health worker programme for health improvement through enhancing training, supervision and motivation in Wakiso district, Uganda. BMC Res Notes. 2019; 12(1): 812. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCrigler L, Gergen J, Perry H: Supervision of Community Health Workers. 2013; 26. Reference Source\n\nFurth R, Crigler L: Improving CHW program functionality, performance, and engagement: operations research results from Zambia. Zambia. 2012. Reference Source" }	[ { "id": "143446", "date": "11 Jul 2022", "name": "Mihir P Rupani", "expertise": [ "Reviewer Expertise Tuberculosis", "epidemiology", "public 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\nTitle and abstract\nIn the title, replace the word “effect” with “effectiveness”.\n\nProposed title - “Effectiveness of providing cash incentives and training to community health workers on active case finding for tuberculosis in Nigeria: a randomized control trial”\n\nIn the abstract, make it clear whether the community health workers are contracted or employed under the national TB program, or, are health workers associated with the primary health centers.\n\nClarify PHC ‘clusters’ in the abstract. Why use the term clusters for PHC? It is giving an impression as if a group of PHCs was included in the trial.\n\n“Descriptive data were presented in tables and bivariate data was analyzed using chi-square. Mean increases in case notification rates were calculated Statistical significance was set as P=0.05.” - this reads quite non-impressive and simple. Authors can avoid mentioning “descriptive data was presented in tables”. In this section, the authors need to elaborate on the analysis plan.\n\n“bivariate data were analyzed using chi-square” - what were the primary exposure and outcome variables? The authors need to mention that ‘abc’ was compared with ‘xyz’ using the ‘pqr’ test of statistical significance.\n\nWhat is “LGAs”? Please refrain from using unstandardized abbreviations.\n\nNone of the results were statistically significant. However, the authors have not mentioned this in words in the results section, which is compulsory.\n\nWhat was the effect size? The authors should report Odds Ratios and the adjusted Odds Ratios with 95% confidence intervals.\n\nNone of the results are statistically significant, however, the authors conclude that “training and cash incentives for CHWs in high burden TB settings to improve TB case detection rates”, which is a wrong conclusion. Authors should state that “though statistically insignificant, in our study setting of a high burden of TB with low incomes, we found improvement in percentages of active case finding through training and cash incentive interventions. Future research should test the effectiveness of these interventions to determine their impact on active case finding in other high-burden settings to confirm statistically significant associations.”\n\nThe full text mentions the use of both STATA and graph pad prism, whereas the abstract mentions only one. Please clarify and correct it.\nIntroduction\nBackground and context - both increase the word count and decrease readability. Authors should be very precise and succinct in their writing. Focus on the rationale, rather than on the problem statement.\nMaterials and methods\nPlease refer to all comments given in the abstract, many of them might need correction in the full text as well.\n\n“An open access alternative software than can perform these same functions would be R (R Project for Statistical Computing, RRID:SCR_001905).” - why this sentence?\n\nWhy was a multivariable analysis not planned by the investigators? Any bivariate analysis should be followed by multivariable analysis.\nResults\nPlease refer to all comments given in the abstract, many of them might need correction in the full text as well.\nDiscussion\n“The study findings are generalizable and applicable to other high burden TB settings.” - so, are the authors suggesting that there is no effect of cash incentives and training on active case finding. The authors should cautiously interpret their data in light of the insignificant results presented in the results section.\nConclusion\nPlease refer to all comments given in the abstract and discussion sections, many of them might need correction in the full text as well.\nFigures and tables\nNo comments, however, tables of univariable and multivariable analysis (preferably logistic regression) are compulsory.\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?\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": "11616", "date": "25 Jun 2024", "name": "Christie Akwaowo", "role": "Author Response", "response": "Title and Abstract: The title has been revised to \"Effectiveness of providing cash incentives and training to community health workers on active case finding for tuberculosis in Nigeria: a randomized control trial.\" The abstract now specifies that community health workers are associated with primary health centers under the national TB program, and also include community pharmacists and patent medicine vendors who are self employed in the communities. We have clarified that each Local Government Area constituted a cluster. But within each Local Government Area, 3 PHC and their catchment communities were used for the study. The abstract has been revised to detail the analysis plan, mentioning that odds ratios and 95% confidence intervals were calculated. The abstract now includes that the primary exposure was the intervention (training and/or cash incentive), and the outcome was the number of TB cases notified. The term “Local Government Areas (LGAs)” is now spelled out in full. The abstract now clearly states that the results were not statistically significant. The abstract now includes odds ratios and adjusted odds ratios with 95% confidence intervals. The conclusion in the abstract has been revised to reflect the results. The abstract now mentions both STATA and GraphPad Prism, aligning with the full text. Introduction: The introduction has been condensed to focus on the rationale for the study, reducing background information and context to improve readability. Materials and Methods: We have reviewed and corrected the full text to align with the changes made in the abstract. The sentence regarding R software has been removed. We did not include multivariable analysis. We recognize that multivariable analysis would give more information on cluster-level factors that may impact the result. However, data on possible confounders at the cluster level was not obtained, hence we cannot carry out this analysis. Results: The results section has been updated to reflect all changes mentioned in the abstract, including the reporting of odds ratios and confidence intervals. Discussion: The discussion now cautiously interprets the data, acknowledging the lack of statistically significant results and suggesting that the results observed should be further investigated. Conclusion: The conclusion has been revised to align with the abstract and discussion, emphasizing the need for further research. Figures and Tables: We did not include multivariable analysis. We recognize that multivariable analysis would give more information on cluster-level factors that may impact the result. However, data on possible confounders at the cluster level was not obtained, hence we cannot carry out this analysis." } ] }, { "id": "143447", "date": "25 Jul 2022", "name": "Angela Oyo-Ita", "expertise": [ "Reviewer Expertise Maternal and Child 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\nTITLE: Should be amended to read “Effect of training of Community Health workers and cash incentive on active case finding of Tuberculosis in Nigeria: a cluster randomized control trial”\nABSTRACT: Description on the three arms of study imply that Arm “A” received cash incentive, Arm “B” received training and Arm “C” received none of the two interventions. Full description in the text shows that Arm “A” received both training and cash incentive and both Arms “B” and “C” received training. This needs to be clarified. In the materials and methods section authors state that “mean increases in case notification rates was calculated.” This statement is not clear. Only presumptive cases of Tb increased from the study sites which is expected. It is uncertain how this improved Tb case finding in the study as indicated in the title. Non statistically significant differences between study arms are reported as increase in effect; conclusion is therefore faulty.\nSTUDY DESIGN: This needs more clarification. Are the 13 LGAs the high burden LGAs? The unit of clustering is not clear. On one hand it is said to be “PHC with availability of DOTS treatment plus the catchment communities” and on the other it is the LGA (“… the clusters were allocated by LGA”). The latter is further supported that the LGAs were non-contiguous. The statement on blinding is also contradictory. The training should be moved to the intervention sub-section.\nINTERVENTION: The three arms of study are reported as receiving training. This implies that there was no control arm with no intervention as stated in the abstract. Sampling was not necessary as all the eligible health workers were included in the study except those who declined.\nDATA COLLECTION: There was a change in the primary outcome from number of presumptive cases referred to Tb case notification, but the former is what is presented in the abstract. There should be consistency in reporting the outcomes that were studied.\nRESULTS: The report of training of 158 participants contradicts what is presented in the “intervention” sub section. Odds or Risk Ratio analysis is preferable to chi square test.\nDISCUSSION: The reported increase in the number of reported presumptive cases is not supported by the data. It should be reported in the perspective of the analyzed data. It is indicated that the interventions were not limited to training and cash incentive to the Community Workers but included supportive supervision and cash support for outreaches. The extent to which the different arms of study were impacted with these added interventions cannot be ascertained. Whatever “effect” there may be, therefore, cannot be attributed to the training and cash incentive only.\nLIMITATIONS: Authors should state the number loss-to-follow up. In reference to the comment on sampling in the intervention sub section all participants should have been followed up at pre and post intervention. Having a pre and post demography data implies that it was not the same people that were trained that the investigators followed up with.\nCONCLUSION: this is not supported by the available data. It needs to be reviewed.\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? No", "responses": [ { "c_id": "11615", "date": "25 Jun 2024", "name": "Christie Akwaowo", "role": "Author Response", "response": "We have revised the title to: “Effectiveness of providing cash incentives and training to community health workers on active case finding for tuberculosis in Nigeria: a cluster randomized control trial.” The abstract now clearly describes that Arm A received both training and cash incentives, while Arm B received training only, and Arm C received no intervention. The abstract now explicitly states that none of the results were statistically significant and the conclusion is based on observed results. We have clarified that the unit of randomization was the Local Government Area (LGA). We have updated the intervention section to indicate that two arms received some form of training, with only Arm A receiving both training and cash incentives and Arm C was the control with no intervention The primary outcome is now consistently reported as the number of TB cases notified from the study PHCs, and the secondary outcome is the number of community outreaches held in the study communities by the CHWs. The results section now accurately reflects the number of participants trained and the total number in the study. It also uses odds ratios and 95% confidence intervals for the analysis. The discussion has been revised to accurately reflect the analyzed data. We have also clarified the extent of additional interventions and their potential impact on the results. Since the outcomes of the study were not focused on the community health workers, the number of CHWs that left during the intervention was not ascertained. The conclusion has been revised to accurately reflect the data, acknowledging that the results were not statistically significant but suggesting potential trends for future research." } ] } ]	1	https://f1000research.com/articles/10-1154
https://f1000research.com/articles/13-1052/v1	12 Sep 24	{ "type": "Case Study", "title": "Retrospective study on pain management pathway for patients with suspected renal/ ureteric colic in a U.K. accidents and emergency department: A quality improvement project", "authors": [ "Charles Ojo", "Chijioke Orji", "Olorungbami Anifalaje", "Gourav Garg", "Mariette Anto", "Megan Kelly", "Chijioke Orji", "Olorungbami Anifalaje", "Gourav Garg", "Mariette Anto", "Megan Kelly" ], "abstract": "Background In acute settings around the globe, renal/ureteric colic remains one of the most common diagnoses for patients presenting with loin-to-groin pain. Even though management spans from medical expulsive therapies to surgical options, pain as a significant component of a patient’s presentation must be dealt with quickly, decisively, and safely, as it can be excruciating and its effects on overall health are dire. This study aimed to explore compliance with the National Institute for Health and Care Excellence (NICE) guidelines for pain management in patients with suspected renal/ureteric colic. It includes the use of nonsteroidal anti-inflammatory drugs (NSAIDs), intravenous paracetamol, and opioids as first-, second-, and third-line analgesics, respectively, and does not offer antispasmodics. In the event of deviations from the standard, the aim was to put in corrective measures, followed by re-exploration of compliance with patient care.\n\nMethods This study involved a single healthcare facility with the study type being retrospective before interventions and prospective after interventions. In the first cycle, we retrieved and analysed 78 patients records whom had been suspected to have renal/ureteric colic between July and September 2022. The inclusion criteria were documented complaints of “flank/loin-to-groin pain” and diagnosis prior to performing diagnostic tests. We surveyed the first-, second-, and third-line painkillers issued, and whether an antispasmodic was given. We collected and entered data into a Microsoft Excel file and correlated it with NICE standards. Having found deviations from the standard, we conducted interventions, allowed time for clinicians to adapt, and re-explored compliance using patient case records [n=58] between February and May 2023.\n\nResults In the 1st cycle, 78 patients were suspected of having renal/ureteric colic. M: F = 1.2:1. Non-contrast computerized tomography of the kidney ureters and bladder (NC-CTKUB) confirmed 87% of patients with stones and 3% had no stones. NC-CTKUB was not performed in 9% of patients because they were young, and urinalysis showed no microscopic hematuria. One patient had discharged against medical advise before the NC-CTKUB was performed. Compliance with the NICE pain management guidelines for suspected renal/ureteric colic was full in 23% of cases but unsatisfactory in 78% of cases. In the 2nd cycle, M: F = 1.5:1, NC-CTKUB was not re-audited, as the first cycle study yielded excellent results, and our action plan resulted in an NICE pain management compliance rate of 56%. Although our interventions resulted in improvements of more than twice the initial results, work still needs to be performed.\n\nConclusion Clinicians’ ability to correctly diagnose renal/ureteric colic is remarkable. However, the pain management compliance rate indicates room for improvement. This may be due to the limited awareness of the NICE guideline or the fact that the clinical team has an affinity for certain analgesics compared to others. We propose the need to consider select variables to existing standard guidelines to enhance compliance for improved patient care.", "keywords": [ "Renal", "ureteric", "colic", "stones", "NSAIDs", "paracetamol", "opioids", "CT-KUB." ], "content": "Introduction\n\nRenal/ureteric colic refers to acute and severe loin pain caused by calculi in the upper urinary tract (Iravani et al., 2014; Weltings et al., 2021). As of 2019, the worldwide incidence was 115.55 million – a 48.57% rise over 29 years when compared to its global incidence of 77.78 million in 1990 (Qian et al., 2022). In the United Kingdom, it is estimated that the incidence of renal/ureteric colic was 88,632 in 2019/20, which is a 2.2% increase from the 2014/15 prevalence of 86,742 (Jour et al., 2022; Geraghty et al., 2020). This surge is likely due to lack of physical activity, dietary changes, low oral fluid intake, obesity, and global warming (Dawson & Tomson, 2012). It is also a huge financial burden, as existing data state that in 2014/15, renal/ureteric colic gulped between £190 million and £324 million in the United Kingdom (Geraghty et al., 2020). It is therefore reasonable to expect that, taking into consideration the effects of inflation, population increase, and rising number of persons with the disease, it is likely to cost up to £622 million by 2030 (Tyson et al., 2019; Geraghty et al., 2020).\n\nAlthough the primary function of pain stemming from renal/ureteric colic is to indicate that something is wrong, therefore, acting as a defensive and protective mechanism, the sensation is unpleasant and excruciating. When urine becomes supersaturated, it creates a favourable niche for calcium, urate, and other salts present to crystallize and form pebbles, which in turn obstructs the free flow of urine, thus causing pain (Alelign & Petros, 2018; Papadopoulos et al., 2014). This often alters and lowers the quality of life (Patti & Leslie, 2024). While associated pain causes anxiety (Geraghty et al., 2020), depression (Liu & Kelliher, 2022), sleep disorders, and immunosuppression (Jin et al., 2023), it also results in hormonal imbalance, the most pertinent of which is initial hypercortisolemia followed by terminal hypocortisolemia (Tennant, 2013). Increased cortisol levels can cause tachycardia, hypertension, osteoporosis, hyperlipidemia, hyperglycemia, and mental degeneration. Hypocortisolemia leads to weight loss, muscle breakdown, hypotension (Jin et al., 2023), and sudden death (Tennant, 2013).\n\nAs renal/ureteric colic accounts for approximately 80,000 emergency department visits annually in the United Kingdom (Dawson & Tomson, 2012), with up to 12,000 admitted for care across the country per year (Dawson & Dawson, 2013) and a recurrence rate of 50% at 5 – 10 years (Alelign & Petros, 2018), and 80% at 20 years (Patti & Leslie, 2024), it is crucial for clinicians to pay adequate attention to effective pain management as it forms an integral part of overall care given to affected patients. The aim of this study was to explore the compliance rate of the pain management pathway for patients with suspected renal/ureteric colic in a U.K. emergency department to the National Institute for Health and Care Excellence (NICE) guidelines.\n\n\nMethods\n\nThis was a cross-sectional closed-loop clinical audit comparing current practice with NICE guidelines, which is the institute that provides evidence-based recommendations for health and care in England and Wales. The guideline states to administer a non-steroidal anti-inflammatory drug (NSAID) by any route as first-line analgesics for adults, children, and young persons with suspected renal/ureteric colic. To give intravenous paracetamol to adults, children, and young persons with suspected renal/ureteric colic if NSAIDs are contraindicated or do not provide sufficient pain relief. To consider opioids for adults, children, and young persons with suspected renal/ureteric colic if both NSAIDs and intravenous paracetamol are contraindicated or not sufficiently relieving pain. To not administer antispasmodics to adults, children, or young persons with suspected renal/ureteric colic. The standard used was that 100% of patients suspected to have renal/ureteric colic must have their pain managed according to guidelines. The study was retrospective before interventions and prospective thereafter.\n\nAs this study was a clinical audit assessing clinicians’ adherence to NICE analgesic prescription protocol, approval with exemption of patient consent in accordance to section 60 of the Health and Social Care Act 2001, was granted by the clinical governance committee of Pilgrim Hospital, United Lincolnshire Hospitals NHS Trust. Hence, consent from patients was waived. Approval for the first cycle was granted on 13th October, 2023, and the second cycle, on 19th April 2023, with registration tag number P0514.\n\nThis study involved a single healthcare facility – Pilgrim Hospital Accidents and Emergency department. The Care Quality Commission’s Intelligent Monitoring System’s report in 2019 states that Pilgrim Hospital is a large district general, government-funded health care facility, managed by the United Lincolnshire Hospitals NHS Trust, situated in Boston, Lincolnshire, United Kingdom, providing a range of health services including round-the-clock emergency care to the communities of South and Southeast Lincolnshire (Brown et al., 2019). It also describes its emergency department to consist of a waiting and reception area, two triage rooms, 10 major and three minor cubicles, one ‘fit to sit’ area, a ‘see and treat’ room, a plaster room, a ‘clean procedure’ room, a four-bedded resuscitation area, three rapid assessment and treatment cubicles, one waiting room and a quiet relatives room which is also used as a mental health assessment room. The report further indicated that from March 2018 to February 2019, there were over 46,000 inpatient admissions.\n\nPermission was sought and granted by the Clinical Governance Department to perform a clinical audit from 18/07/2022 to 30/09/2022. A total of 260 case records of patients with flank/loin-to-groin pain, painless/painful haematuria, non-specific abdominal pain, and incidental findings of upper urinary tract stones were retrieved from the Patients Records department and reviewed. The inclusion criteria were patients presenting to the emergency department with complaints of flank/loin-to-groin pain and suspected diagnosis of renal colic prior to diagnostic tests and this was regardless of age. Patients with painless haematuria, non-specific abdominal pain, and incidental findings of calculi in the upper urinary tract were excluded. Only 78 patients met the inclusion criteria. We defined “full compliance” with NICE guideline to be patients who received NSAIDs only; however, if pain remained uncontrolled or medically unfit or allergic to NSAIDs, intravenous paracetamol was administered; however, if pain remained uncontrolled or medically unfit or allergic to paracetamol, opioids was administered – antispasmodics never given. Any deviation from this definition was regarded as “unsatisfactory compliance” with the NICE guidelines. From patient’s case notes, data was obtained using google form and then transferred into an electronic Microsoft Excel file for analysis.\n\nFirst, utilizing our compliance definition, we calculated the number of patients who were managed in full compliance to NICE guidelines and the number of patients who were not. Full compliance was for instance “a medically fit patient without NSAID’s allergies given per rectal diclofenac without hyoscine butyl bromide”. Unsatisfactory compliance for example was “a medically fit patient without NSAID’s allergy given intravenous paracetamol without initial trail of a NSAID” or any patient given hyoscine butyl bromide. We found full compliance only in 23% of cases. Furthermore, we checked the sensitivity of non-contrast computerized tomography of the kidney’s ureters and bladder (NC-CTKUB) in diagnosis of renal/ureteric colic in suspected patients. Lastly, we determined the male-to-female ratio.\n\nVia a verbal discuss, the reasons given by most clinicians for unsatisfactory adherence to the NICE guideline were that they had affinity for intravenous paracetamol over NSAIDs regardless of whether patients could tolerate NSAIDs or not (Table 1) and because they believed antispasmodics play a major role in pain management of patients with suspected renal/ureteric colic (Figure 2).\n\nWe developed an action plan that included apprising clinicians of the NICE guideline through an oral power-point presentation, one-on-one meetings, trust emails, and whatsapp messages. We also developed and displayed a digital poster in the emergency department and printed and pasted hard copy posters in the triage rooms.\n\nWe allowed a period of 4 months for clinicians to adapt to the national standard of pain management in patients with suspected renal/ureteric colic. We then performed a re-audit using the same inclusion and exclusion criteria, and compliance definition used in the first study. The re-audit spanned from 01/02/23 to 14/05/2023, with only 57 patients meeting the inclusion criteria having reviewed 147 patient records. Data analysis followed the same sequence used in the first cycle; however, NC-CTKUB use in the diagnosis of renal/ureteric colic was not re-analysed as the first cycle result was reassuring.\n\n\nResults\n\nOf the 78 patients (n = number of patients) suspected to have renal/ureteric colic in the first cycle, the male (n=43) to female (n=35) ratio was 1.2:1. NC-CTKUB confirmed that 87% (n=68) had stones and 3% (n=2) had no stones. 9% (n=7) did not have NC-CTKUB because they were young, and urinalysis showed no microscopic hematuria. 1% (n=1) self-discharged (S/D) before NC-CTKUB (Figure 1). Overall, compliance with the NICE pain management guidelines for suspected renal/ureteric colic was full in 23% (n=18) of cases but unsatisfactory in 77% (n=60) of cases (Figure 3). Having performed interventions, allowed a time interval of four months for clinicians to conform their practice to NICE guidelines, we performed a second cycle study - amongst the 57 patients suspected to have renal/ureteric colic, the NICE guideline was fully adhered to in 56% (n=32) but unsatisfactory in 44% (n=25) (Figure 3). The male (n=34) to female ratio (n=23) was 1.5:1.\n\n\nDiscussion\n\nRenal/ureteric colic has continued to remain a topical issue of discussion as its recurrence rate is high and poses a huge burden to patients as well as health care systems around the globe (Alelign & Petros, 2018; Tyson et al., 2019). In the United Kingdom, the existing literature indicates that it is more common in males than in females (Alelign & Petros, 2018); however, the gender gap appears to be closing (Gillams et al., 2021). NC-CTKUB is the gold standard test (Tyson et al., 2019), and pain management favors the administration of NSAIDs over intravenous paracetamol, opioids, and antispasmodics (Weltings et al., 2021; NICE, 2019), as they are the most effective of the four (Masoumi et al., 2014). Our study is consistent with its sex predisposition and diagnostic methods; however, there appears to be a disparity in the pain management pathway. We propose a need to consider the inclusion of certain variables to the existing standard guidelines.\n\nWhile renal/ureteric colic has been found to be more common in males than females, the reasons remain unclear to date (Ferraro et al., 2023). In the United Kingdom, it is stipulated that between 1990 and 2007, M:F = 2.5:1 (Geraghty et al., 2020), which increased to 3:1 between 2016 and 2018 (NICE, 2020) and currently, and as more females are becoming affected, the gender gap seems to be closing (Alelign & Petros, 2018; Dawson & Tomson, 2012; Ferraro et al., 2023; NICE, 2020; Gillams et al., 2021; Feheley, 2021; Juliebo-Jones et al., 2023). For instance, a Northern Irish paper expressed it to be 1.93:1 (Tyson et al., 2019). In our study, of the 78 patients who were suspected to have renal/ureteric colic in the first cycle, 55.1% were males and 44.9% were females corresponding to 1.2:1. In our second-cycle study involving 57 patients, 34 were males and 23 were females; therefore, corresponding to 1.5:1.\n\nNICE (2019) advocates that all patients suspected to have renal/ureteric colic should be considered for NSAIDs, and if needed, intravenous paracetamol and opioids should be administered, and antispasmodics should not be given. Although our second-cycle results showed a compliance rate of 56%, an improvement of more than twice the initial result (23%), work still needs to be done to attain full compliance. Four reasons were found to be the cause of the deviation. First, several patients were prescribed hyoscine butylbromide: 16.7% and 13% (Figure 2) in the first- and second-cycle studies respectively, as many clinicians, like in the Netherlands had for many years (Weltings et al., 2021), believed that the antispasmodic effect of hyoscine butylbromide was of analgesic benefit to patients. Furthermore, many clinicians simply preferred intravenous paracetamol and oral opioids over NSAIDs, as they judged them to be safer. Most feared that the latter may cause gastrointestinal, renal, respiratory, cerebrovascular, and cardiovascular problems regardless of how medically fit the patient was. Moreso, clinicians believed that, considering the level of pain experienced by patients with suspected renal/ureteric colic, intravenous paracetamol may not be very effective; thus, it was preferable to administer it as an adjunct to oral opioids. Finally, a few clinicians simply administered analgesics, provided that it was safe and effective regardless of the standard renal/ureteric colic pain management pathway.\n\nArguments against and for hyoscine butylbromide have been presented. For example, although its smooth muscle relaxing effect on the ureters is yet to be demonstrated (Weltings et al., 2021; Papadopoulos et al., 2014), continued intravenous administration is difficult (Weltings et al., 2021) and has a rare side effect of hemodynamic instability (Chen & Hsu, 2013), it has also been shown to have good effect on stones in the renal pelvis, less cardiac and renal side effects when compared to NSAIDs, and synergistic analgesic effects when combined with NSAIDs (Papadopoulos et al., 2014). In support of the use of hyoscine butylbromide in the United Kingdom to manage pain associated with renal/ureteric colic, a commentary published by three nephrologists, a urologist, and a patient representative in response to NICE guidelines advises that hyoscine butylbromide should not be entirely left out of the pain management pathway but should be considered for suitable patients (Sayer et al., 2021).\n\nWhile it is true that NSAIDs are associated with Peptic Ulcer Disease (PUD), Liver and Respiratory problems, Renal failure, Myocardial and Cerebral ischemia (Fening, 2020), they can be safely administered to select patients at the lowest effective dose and, on a short-term basis (Bindu et al., 2020), taking into account the following factors: PUD - consider (a) per rectal diclofenac (Patti & Leslie, 2024), (b) intramuscular ketorolac (Patti & Leslie, 2024) (c) oral ibuprofen/aceclofenac (Drini, 2017) administered with Proton Pump Inhibitors/H2 Receptor Antagonists/Antacids (d) celecoxib, as it has the best gastric profile (Drini, 2017). Interestingly, concerns about the cardio- and cerebrovascular side effects of celecoxib have been described by the PRECISION study as not being different from non-selective NSAIDs (Nissen et al., 2016). Liver Toxicity – Oral Ibuprofen and Celecoxib have been shown to have the best safety profiles (Bindu et al., 2020). Asthma, Nasal Polyposis-Associated Chronic Rhinitis, Acute Respiratory Tract Reaction – celecoxib is not implicated; thus, it is safe (Bindu et al., 2020). Renal failure, myocardial ischemia, and cerebral ischemia - avoid NSAID’s. Although current NSAIDs have concerning side effects, newer versions are currently in the pipeline and show promising results (Bindu et al., 2020). These are likely to be of immense benefit to patients with suspected renal/ureteric colic.\n\nAlthough the World Health Organization’s (WHO) analgesic ladder recommends paracetamol as a first-line painkiller, existing studies have proven that intravenous paracetamol is as potent (Montazer et al., 2017) and even more effective (Masoumi et al., 2014) than intravenous morphine in managing renal/ureteric colic. Because the side effects of opioids are worrisome, it is logical to conclude that intravenous paracetamol should be considered before opioids in affected patients.\n\nAs upper urinary tract stones can persist for prolonged periods, with affected persons experiencing agonizing pain without surgery or postoperatively (Intermountain Healthcare, 2023), it is crucial to mention the interplay between pain and the Hypothalamic-Pituitary-Adrenal-Thyroid-Gonadal (HPATG) axis. The initial phase of severe pain causes a surge in Triiodothyronine, Thyroxine, Cortisol, Pregnenolone, DHEA, and testosterone levels, and if pain persists for a long time, serum levels fall to critical levels (Tennant, 2013). From this, we can extrapolate the following. First, serum hormone levels can serve as biomarkers for severe and uncontrolled renal/ureteric colic. Second, it is vital to perform baseline hormonal assessments before embarking on pain management therapy, especially with opioids, as they also suppress the HPATG axis. Third, if any of the hormones is low, it is reasonable to infer that pain from renal/ureteric colic is likely severe and persisting for too long, disrupting the HPATG axis, causing associated hyperalgesia and allodynia (Tennant, 2013). Regardless of how much analgesics is being administered, severe pain will continue until the dysregulated hormones have been attended to, thus preventing excessive and unwarranted use of analgesics. Fourth, replacement of low hormones would be lifesaving – for instance ensuring hormonal homeostasis in an individual with pain associated serum cortisol level of less than 0.1 microgram per deciliter (Tennant, 2013) which otherwise would have been life threatening.\n\nOf note is the clinicians’ ability to correctly diagnose renal/ureteric colic, as well as consideration for radiation risk-to-benefit. Clinicians attending to the 78 patients suspected of having renal/ureteric colic requested NC-CTKUB, and their suspicion was confirmed in 87% of cases, while 3% had no stones. NC-CTKUB was not performed in 9% of the patients because they were young, and urinalysis showed no microscopic hematuria. Its role in aiding the diagnosis of renal/ureteric colic cannot be overemphasized.\n\nThis study was limited given that only a second cycle study has been performed so far with an improved compliance rate to 56%. Although this is a remarkable improvement from 23%, the aim of this study remains that compliance rate should be at 100%. There is a need for future re-assessments and re-audits both locally and on a large scale.\n\n\nConclusions\n\nAlthough the literature indicates that renal/ureteric colic is significantly more common in males than in females, recent data suggest that the gap is closing, which is consistent with our study. While NICE advocates that NSAIDs should be considered before intravenous paracetamol and opioids and not to administer hyoscine butylbromide, we opine that there may be a need to accommodate hyoscine butylbromide for suitable patients and consider hormonal homeostasis in pain management workup. However, it is vital to strictly follow NICE guidelines until these suggestions are appraised. The use of NC-CTKUB in the diagnosis of renal/ureteric colic remains the gold standard, and our study demonstrated its efficiency in aiding its detection.\n\nAs this study was a clinical audit assessing clinicians’ adherence to NICE analgesic prescription protocol, approval with exemption of patient consent in accordance with section 60 of the Health and Social Care Act 2001, was granted by the clinical governance committee of Pilgrim Hospital, United Lincolnshire Hospitals NHS Trust. Hence, consent from patients was waived. Approval for the first cycle was granted on 13th October, 2022, and the second cycle, on 19th April 19, 2023, with registration tag number P0514.", "appendix": "Data availability\n\nFigshare: Retrospective study on pain management pathway for patients with suspected renal/ureteric colic in a U.K. Accidents and emergency department, https://doi.org/10.6084/m9.figshare.26810470.v1 (Ojo et al., 2024a).\n\nThis project contains the following underlying data:\n\n• Data file 1. 1st Cycle Case Records Presenting Complaints.\n\n• Data file 2. 2nd Cycle Case Records Presenting Complaints.\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain Dedication).\n\nThe data have been thoroughly de-identified for ethical reasons.\n\nFigshare. Retrospective study on pain management pathway for patients with suspected renal/ureteric colic in a U.K. Accidents and emergency department. https://doi.org/10.6084/m9.figshare.26805784.v1 (Ojo et al., 2024b).\n\nThis project contains the following extended data:\n\n• Audit Registration and completion forms for the 1st and 2nd cycle audits.\n\n• Power point presentation for the 1st and 2nd cycle audits.\n\n• Point presentation and letter of preliminary results.\n\n• Implementation of action plan – evidence.\n\n• Google form used for data collection in the 1st and 2nd cycle audits.\n\n• Approval documents for the 1st and 2nd cycle audits as well as implementation of action plan.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nCharles Ojo ideated the research topic, carried out the study, wrote the manuscript, and edited it. He also gave the final approval of the version to be published and was accountable for all aspects of the work in ensuring that questions related to its accuracy and integrity were appropriately investigated and resolved. Thus, he is regarded as the First Author.\n\nChijioke Orji contributed equally to the ideation of the research topic, conducted the study, wrote the manuscript, and edited the manuscript. He also gave the final approval of the version to be published and was accountable for all aspects of the work in ensuring that questions related to its accuracy and integrity were appropriately investigated and resolved. The author should be regarded as a Co-first Author.\n\nOlorungbami Anifalaje, Gourav Garg, and Mariette Anto contributed substantially to the conception of the work, acquisition of data, and drafting of the work. They also gave the final approval of the version to be published and were accountable for all aspects of the work in ensuring that questions related to its accuracy and integrity were appropriately investigated and resolved. They should be considered co-authors.\n\nMegan Kelly served as supervisor. She contributed significantly to the design of the study, interpretation of data, and revision of the manuscript. She also gave the final approval of the version to be published and was accountable for all aspects of the work in ensuring that questions related to its accuracy and integrity were appropriately investigated and resolved. She should be regarded as the Last Author of this paper.\n\nUyiosa Osunde, Sushma Thapa, Ming Li Lim, Basil Koh Bolyan, Ahmed Afsa of the Emergency Department, Pilgrim Hospital, United Lincolnshire Hospitals NHS Trust contributed to data collection, analysis and action plan. They are acknowledged.\n\nPreliminary results of this study were presented as a meeting abstract at the Association of Surgeons in Training (ASiT) 47th surgical conference which held on 3rd to 5th March, 2023, and archived in the conference proceeding - Issue Supplement of the British Journal of Surgery (OJO et al., 2023).\n\n\nReferences\n\nAlelign T, Petros B: Kidney stone disease: an update on current concepts. Adv. Urol. 2018; 2018: 12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBindu S, Mazumder S, Bandyopadhyay U: Non-steroidal anti-inflammatory drugs (NSAIDs) and organ damage: A current perspective. Biochem. Pharmacol. 2020; 180: 114147. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBrown S, Dunna M, Jenkinson C, et al.: United Lincolnshire Hospitals NHS Trust. CareQualityCommision Inspection report. 2019. Reference Source\n\nChen GL, Hsu WH: Hyoscine- N -Butyl-Bromide-Induced hypotension and myocardial ischemia. Case Rep. Crit. 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Transplant. 2023; 38: 177–183. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGeraghty RM, Cook P, Walker V, et al.: Evaluation of the economic burden of kidney stone disease in the UK: a retrospective cohort study with a mean follow-up of 19 years. BJU Int. 2020; 125: 586–594. PubMed Abstract \| Publisher Full Text\n\nGillams K, Juliebø-Jones P, Juliebø SØ, et al.: Gender differences in kidney stone disease (KSD): Findings from a systematic review. Curr. Urol. Rep. 2021; 22: 50. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIntermountain Healthcare: Kidney stone owner’s manual: June, 2023. Accessed: May 23, 2024. Reference Source\n\nIravani O, Tay EW, Bay BH, et al.: Unilateral ureteric stone associated with gross hydronephrosis and kidney shrinkage: A cadaveric report. Anat Cell Biol. 2014; 47: 267–270. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJin MY, Everett ES, Abd-Elsayed A: Microbiological and physiological effects of pain. Curr. Pain Headache Rep. 2023; 27: 165–173. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJour I, Lam A, Turney B: Urological stone disease: a 5-year update of stone management using hospital episode statistics. BJU Int. 2022; 130: 364–369. PubMed Abstract \| Publisher Full Text\n\nJuliebo-Jones P, Ulvik O, AEsoy M, et al.: Mortality due to urolithiasis in England and Wales: Updated findings from a national database over a 23-year period. Cent. European J. Urol. 2023; 76: 141–143. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLiu S, Kelliher L: Physiology of pain—a narrative review on the pain pathway and its application in the pain management. Dig. Med. Res. 2022; 5: 56–56. Publisher Full Text\n\nMasoumi K, Forouzan A, Darian AA, et al.: Comparison of clinical efficacy of intravenous acetaminophen with intravenous morphine in acute renal colic: A randomized, double-blind, controlled trial. Emerg. Med. Int. 2014; 2014: 5. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMontazer SH, Feizzadeh B, Bozorgi F, et al.: Intravenous acetaminophen versus morphine sulfate in pain management of acute renal colic: a randomized clinical trial. J. Emerg . Pract. Trauma. 2017; 4: 39–43. Publisher Full Text\n\nNICE: What are the risk factors for stone formation?2020. Accessed: May 23, 2024. Reference Source\n\nNICE: Renal and ureteric stones: assessment and management.2019. Accessed: May 23, 2024. Reference Source\n\nNissen SE, Yeomans ND, Solomon DH, et al.: Cardiovascular safety of Celecoxib, Naproxen, or Ibuprofen for Arthritis. N. Engl. J. Med. 2016; 375: 2519–2529. Publisher Full Text\n\nOjo C, Orji C, Anifalaje O, et al.: Retrospective study on pain management pathway for patients with suspected renal/ureteric colic in a UK accidents and emergency department. [Dataset]. Figshare. 2024a. Publisher Full Text\n\nOjo C, Orji C, Anifalaje O, et al.: Retrospective study on pain management pathway for patients with suspected renal/ureteric colic in a UK accidents and emergency department. [Dataset]. Figshare. 2024b. Publisher Full Text\n\nOjo C, Osunde U, Thapa S, et al.: 562 Retrospective study on pain management pathway for patients with suspected renal/ureteric colic in a UK accidents and emergency department. Oxford Academic. 2023; 110: 34–35. Publisher Full Text\n\nPapadopoulos G, Bourdoumis A, Kachrilas S, et al.: Hyoscine N-butylbromide (Buscopan®) in the treatment of acute ureteral colic: What is the evidence? Urol. Int. 2014; 92: 253–257. PubMed Abstract \| Publisher Full Text\n\nPatti L, Leslie S: Acute renal colic.2024. Accessed: May 23, 2024. Reference Source\n\nQian X, Wan J, Xu J, et al.: Epidemiological trends of urolithiasis at the global, regional, and national levels: A population-based study. Int. J. Clin. Pract. 2022; 2022: 12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSayer J, Stoves J, Froster J, et al.: Commentary on the NICE guideline on renal and ureteric stones: assessment and management.2021. Accessed: May 23, 2024. Reference Source\n\nTennant F: The physiologic effects of pain on the endocrine system. Pain Ther. 2013; 2: 75–86. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTyson M, Grimes N, McAuley L, et al.: Renal and ureteric stone composition: A five year retrospective study for Northern Ireland.2019). Accessed: May 23, 2024. Reference Source\n\nWeltings S, Buddingh KT, van Diepen D , et al.: The BUSCOPAN study: a randomized-controlled non-inferiority trial of a continuous butylscopolamine infusion versus placebo in patients with a renal colic not responding to oral non-steroidal anti-inflammatory drugs. World. J. Urol. 2021; 39: 2747–2752. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "334115", "date": "24 Oct 2024", "name": "Ayokunle Adenipekun", "expertise": [ "Reviewer Expertise Urology", "clinical research" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nGood abstract. Important topic as regarding pain management in A and E.\n\nIt is however pertinent to state in the abstract that it is a closed cycle audit please. The conclusions drawn are sensible The wordings used in the methods and discussion about approval an cycles could be more succinct and also a flow cycle helps There is the issue of you getting approval for second cycle before the first, but This is likely a typographical error?\n\nCharts /Pies should be in 2D not 3D\n\nDiscussion As the WHO pain ladder deviates from the NICE guideline for suspected renal /ureteric colic. This is a good point to state and explore. considering these patients are in A and E.. Hence the apparent poor compliance.\n\nIn addition the inclusion of the hormone pathway is not relevant and takes away from the appropriateness of this topic\n\nOverall. This is a good learning article\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? 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": [] } ]	1	https://f1000research.com/articles/13-1052
https://f1000research.com/articles/13-1051/v1	12 Sep 24	{ "type": "Research Article", "title": "What we know and what should we know about the future of blockchain in finance", "authors": [ "Shikta Singh", "Rachana Jaiswal", "Shashank Gupta", "Chinmoy Kumar", "Shashank Gupta", "Chinmoy Kumar" ], "abstract": "Background In response to the transformative impact of blockchain technology on economic and financial landscapes, there is a critical need for a review study that analyses the knowledge landscape from diverse perspectives.\n\nMethods This research VOSviewer, and Bibliometrix to undertake a bibliometric analysis of the expanding literature related to blockchain technology within the financial sector. Through a examination of 500 published articles, the study identifies insightful trends, patterns, and emerging domains on a global scale.\n\nResults The findings highlight the advancing trajectory of blockchain research in finance, with a notable concentration of studies originating from the United States and China, both in terms of total publications and citations. Key thematic clusters identified include “smart contracts,” “financial institutions,” “initial coin offerings,” and “big data analytics.” Intersections with financial risk management, digital transformation, and the integration of big data analytics with artificial intelligence and machine learning are particularly noteworthy, marking focal points of exploration.\n\nConclusions While affirming the potential of blockchain, the analysis also sheds light on persistent impediments hindering its widespread adoption and utilization. This study not only contributes to the current understanding of blockchain in finance but also serves as a valuable resource for future researchers. It guides systematic reviews by pinpointing prominent journals and influential authors within the dynamic field of blockchain finance, thereby fostering a deeper understanding and facilitating further exploration in this evolving field.", "keywords": [ "Blockchain", "finance", "VOS viewer", "networking analysis", "literature review." ], "content": "1. Introduction\n\nBlockchain technology stands at the forefront of problem-solving across various industries, presenting a revolutionary approach to collaboration. This technology fosters trust and collaboration among individuals, replacing traditional formalities and paperwork with teamwork, creativity, and efficiency. Its potential lies in creating a more secure and truthful environment, with the eventual eradication of fraud and crime being a conceivable outcome (Malik et al., 2022). In the realm of finance, blockchain is poised to redefine the rules of the game and reshape the industry’s landscape. Leading financial institutions worldwide are spearheading the adoption of blockchain technology with the aim of enhancing efficiency, creating innovative solutions, deriving tangible business benefits, and ultimately revitalizing the financial sector (Jaiswal et al., 2022a; 2024d) and other sectors (Jaiswal, 2022, 2023a, 2023b; Prakhar et al., 2024b). Originating as the backbone of the Bitcoin network in response to the 2008 financial crisis, blockchain employs distributed ledger technology to record the creation, ownership, and sale of valuable assets (Xu et al., 2019). Its unique feature lies in ensuring the privacy of transactions and records while eliminating the need for a trusted third party, such as a bank, by requiring consensus among all network nodes before any transaction can occur.\n\nThe financial sector’s attention to ledger technology is justified, given its potential to enhance security and efficiency. Blockchain facilitates more open and secure business networks, standardized operating models, streamlined procedures, reduced costs, and the introduction of innovative products and services (Jaiswal et al., 2023; Gupta et al., 2022). Notably, digital securities can be issued more rapidly, cost-effectively, and flexibly, catering to the preferences of individual investors and thereby improving investor markets, issuer costs, and counterparty risk (Patel et al., 2022). Amid the proliferation of blockchain research, academic interest has surged due to its global significance, security implications, and potential economic impact (Jaiswal, 2023a, 2023b). This investigation aims to provide a clear and systematic overview of blockchain studies, enabling scholars to grasp the unique features and taxonomy of various study fields (Wang et al., 2021). Despite the increase in publications related to blockchain in finance research over the past half-decade, there is a need for more quantitative and qualitative research, particularly in understanding business models (Jaiswal & Gupta, 2023b; Holotiuk et al., 2017). The ongoing pandemic emphasizes the urgency of digitalization in relocating businesses, highlighting blockchain technology’s role in simplifying the transfer of flexible and resilient financial products and securities, potentially paving the way for contactless connectivity in the near future. As the current economic downturn prompts businesses to leverage cutting-edge technologies, the study acknowledges the transformative potential of blockchain technology. The ongoing COVID-19 crisis has underscored the importance of technology for success and flourishing, resulting in an upward trend in publications. The impact of blockchain on financial institutions, including reducing money laundering, countering terrorism financing, enhancing transaction security, and improving transparency, cannot be overstated.\n\nTo address the paucity of research on blockchain’s potential applications in the financial industry, this study examines the productivity and competitiveness of the market. Through bibliometric techniques and quantitative tools, the study explores the collaboration between authors, countries, and organizations, building upon previous efforts in the field (Chen et al., 2021; Haghnazar Koochaksaraei et al., 2021). The research questions (RQs) guiding this study are as follows:\n\nRQ1. What is the current publication trend in blockchain finance research?\n\nRQ2. Who are the leading contributors in terms of authors, institutions, and countries in blockchain finance research?\n\nRQ3. Which articles and journals have the most significant impact on blockchain finance research?\n\nRQ4. What are the predominant themes, hotspots, and potential future research directions in blockchain finance research?\n\nIn a prior study conducted by Jaiswal et al. (2022a), the focus was on discerning the fundamental characteristics of published documents within blockchain applications. This was part of the banking industry’s initiative to fortify the digital financial infrastructure. Although that research successfully pinpointed essential services utilizing blockchain technology, it fell short in terms of conducting a thematic analysis and addressing future trends. In contrast, the current study offers a more comprehensive approach by providing a detailed thematic analysis. It not only identifies multiple clusters within the finance sector related to blockchain but also establishes future research agendas.\n\nThe insights derived from this analysis carry numerous practical applications. For researchers within the financial sector, this review serves as a panoramic overview of the publication trends in blockchain within finance research. It aids in understanding the scientific community’s evolving interest in the topic over time. Moreover, the review is a valuable resource for aspiring authors, helping them identify key literature, including relevant articles and journals, while also pinpointing potential collaborators—be it authors, institutions, or countries—for blockchain finance research. Additionally, for future authors, the review’s identified themes and topics offer a means to distinguish their work from existing blockchain finance literature, emphasizing the uniqueness of their contributions. The identified research directions act as inspiration, encouraging writers to delve into innovative and meaningful projects. Lastly, these perspectives serve as a preview of forthcoming research, offering valuable insights for policymakers and business professionals.\n\nThe subsequent sections of the paper are structured as follows: Section 2 details the database and methodology, Section 3 provides results encompassing publication and citation patterns, along with profiles of the most prolific and influential contributors. Section 4 delves into major and emerging themes, presenting potential developments. Finally, Section 5 concludes the paper and outlines limitations of this study.\n\n\n2. Methods\n\nThe Dimensions database stands out as one of the largest accessible resources within the academic and research community, offering free access to users. In recent years, it has been extensively utilized across various research fields (Jaiswal et al., 2022a, 2023, 2024d; Cortés et al., 2022). Its inclusion of the most influential journals and publishing houses across diverse academic disciplines makes the Dimensions database particularly attractive for bibliometric analysis.\n\nFor the construction and visualization of bibliometric networks involving journals, researchers, citations, bibliographic coupling, co-citation, or co-authorship, we employ two software applications: VOSviewer (Van Eck & Waltman, 2010) and RStudio Bibliometrix (Aria & Cuccurullo, 2017). These tools offer robust capabilities for visualizing and analyzing bibliometric data (Jaiswal and Gupta, 2023a, 2023b; Prakhar et al., 2024a; Gupta et al., 2024; Jaiswal et al., 2022b). Notably, VOSviewer comes equipped with text mining features, allowing the construction and visualization of co-occurrence networks of keywords extracted from a body of literature (Jaiswal and Kumar, 2023; Jaiswal et al., 2024a, 2024b, 2024c, 2024d). These applications have gained widespread use in recent bibliometric research studies (Jaiswal et al., 2022a, 2024a).\n\nBibliometric Analysis was performed using VOSViewer (https://www.vosviewer.com/) and RStudio Biblioshiny (https://www.bibliometrix.org/home/index.php/layout/biblioshiny).\n\nThe first step in retrieving data is identifying the proper collection of blockchain-related articles published in finance research, as outlined in Table 1. An initial search performed over the period 2018-2022 using the search criteria ((“blockchain” OR “blockchain technology” OR “blockchain technologies”) AND (“finance” OR “banking” OR “financial” OR “bank”)) results in 5,561 documents. These are filtered into the fields “commerce, management and tourism and services”, “business and management”, and “banking, finance, and investment”, producing 1,198 publications. When further screened to exclude conference papers, books, chapter summaries, and other non-articles, the final corpus includes 500 articles, which are examined using bibliometric analysis, which has the capacity to manage vast corpora, to reveal fundamental characteristics, identify publication trends, distinguish advanced topics and construct visualizations of thematic evolution. Both retrospective analysis and future research directions are considered (Ibrahim & Truby, 2021).\n\nData can be obtained from the Dimensions AI database or can be directly downloaded from here: FigShare, “Dimensions-Publication-2022-07-09_04-12-30.csv” (Dataset. https://doi.org/10.6084/m9.figshare.26364760.v1).\n\n\n3. Results and Discussion\n\nIn this section, we scrutinize the fundamental attributes of 500 published articles, exploring aspects such as research direction, annual publication presentation, co-author citation, country, organization, and authorship. Additionally, we delve into the interconnections between these various dimensions.\n\nBlockchain technology has emerged as a recent development in the field of finance. Despite the growing number of financial journal publications, it is noteworthy that only one paper from 2014 has specifically delved into the realm of blockchain within finance literature. Consequently, the analysis primarily focuses on post-2018 publications, as this marks the period when blockchain research in finance began gaining momentum in addressing practical, real-world issues.\n\nIn 2022, a total of 162 articles were published on the subject, demonstrating a substantial increase in scholarly interest. This trend is consistent with the preceding years, where 2021 saw 158 articles, 2020 had 144, 2019 featured 73, and 2018 recorded 43. The sheer volume of work dedicated to blockchain technology in finance research underscores the escalating interest among researchers, highlighting a growing inclination towards publishing and contributing to the evolving discourse in this domain.\n\nTable 2 compares the top ten affiliations and institutions based on the total number of citations and publications. The Royal Institute of Technology has the most citations (349), and Hong Kong Polytechnic University has the second- most (307), but for total publications, Hong Kong Polytechnic University has the most (7), followed by the University of Luxembourg (6).\n\nThe VOSviewer user manual specifies that the strength of a link is consistently positive, with a higher value indicating increased reliability. The Total Link Strength (TLS) is determined by the frequency of a specific combination of items (such as keywords, authors, sources, or institutions) appearing in scholarly articles. Figures 1 and 2 illustrate the network visualization of institutions based on their total publications and total citations, respectively. In terms of publications, the Hong Kong Polytechnic University has a Total Link Strength of 15, Dublin City University has a TLS of 17, and ETH Zurich has a TLS of 10. In the context of total citations, the Royal Institute of Technology boasts a TLS of 10, Worcester Polytechnic Institute has a TLS of 11, and Stevens Institute of Technology has a TLS of 8.\n\nTable 3 shows that Business Horizons is top of the list for total citations, with 643 citations and 3 publications, followed by Technological Forecasting and Social Change with 512 citations and 14 publications. Notably, the latter journal has a TLS of 40, which is better than any of the journals listed in the top 10.\n\nLoess, which stands for “locally estimated scatterplot smoothing”, is used for multivariate data. Source dynamics apply loess to the number of documents published from 2018 to 2022 (Table 4). The Loess procedure is a robust, nonparametric method for smoothing empirical data that contains outliers, offering flexibility, because no assumptions are made regarding the parametric form of the regression surface (Cleveland and Devlin, 1988). In 2020 and 2021, we observe a sharp increase in the number of publications on blockchain research in finance (see Table 4 and Figure 3). However, as we approach 2022, the loess method moderates this anomaly with a gradual decline.\n\nGilbert (1977) demonstrates that scientists use citations as a persuasive tool. The age of an article is a factor in its citations (Dang & Li, 2020). According to Schwert (1993), affiliation with the top contributing institutions and nations positively influences citations. Authors affiliated with the most prolific contributing institutions publish more and cite more of their prior work (Donthu et al., 2020). Table 5 indicates that the United States is the leading contributor to blockchain research in finance in terms of total citations and total publications, followed by China for total publications and the United Kingdom for total citations. Although the United Kingdom has produced fewer publications (42) than China (55), it has received slightly more citations (1,101 for the United Kingdom versus 1,082 for China).\n\nFigure 4 provides insight into clusters of countries. China, the United States, United Arab Emirates, Pakistan, South Korea, Malaysia, and Canada fall into the same cluster, shown in red, while the United Kingdom, India, France, and Turkey belong to the cluster shown in blue. The third cluster, in green, consists of Germany, Italy, Luxembourg, and Belgium.\n\nLotka (1926) uses a variation of the inverse square law to describe the publication frequency of researchers in a specific field. As a general rule, according to this law, the number of authors who make multiple contributions during a given period is smaller than the number of authors who make just one. The actual number of publications in a given period is compared to the theoretical Lotka curve for the same field to determine an author’s productivity. The author productivity for blockchain research in finance is shown in Table 6, which shows that the blockchain research corpus is dominated by occasional authors with less than five publications, as opposed to core authors who each contribute multiple papers to the body of knowledge. The Lotka curve theory supports this.\n\nAn author may produce less influential work but cite the work of authors from other countries, thereby indirectly increasing the citation score of locally cited documents in the corpus. Table 7 lists the 15 most-cited articles from 2018 to 2022, while Figure 5 provides the network collaboration among the top documents. Supply chain, the fintech revolution, and financial services are the most frequently cited study areas in the blockchain research in finance (Moosavi et al., 2021). Most of these studies are published by Elsevier, Taylor & Francis, Springer, and MDPI. Logistics, Journal of Management and Information Systems, Business Horizons, International Journal of Production Economics, Journal of Financial Intermediation, Technological Forecasting and Social Change, Journal of Business Venturing, and The Electricity Journal are among the leading journals that publish such articles.\n\n\n4. Emerging themes and potential developments\n\nAccording to the existing literature, a scientific document’s topicality, methodological rigor, design, core content, and quality should be the primary determinants of citations rather than the individual authors. It is often argued that the contents and quality of an article affect its citations. Valtakoski (2020) refers to scholarly content in a piece of literature, whereas Stremersch et al. (2007) argue that longer articles tend to receive more citations. Furthermore, it seems easier to track down an article with more keywords, leading to more citations (Valtakoski, 2020), whereas it is difficult to search for a lengthy title, which can hurt citations. When analysing the corpus, we consider three elements: trends in the words used, a word tree map, and a word cloud.\n\nTrending topics based on bigrams applied to the abstracts reveal that Islamic fintech, fintech companies, collaborative innovation, smart contract, and financial innovations are top trending topics for blockchain research in finance. Researchers frequently include a variety of keywords, each of which has the potential to be incorporated into a graphical illustration of the data. The results of applying a tree map to the top fifty keywords in the extracted corpus to construct a proportional map are displayed in Figure 6. The term “blockchain” is by far the most common, but the research is heavily influenced by concepts such as supply chain, initial coin offering (ICO), and financial services.\n\nThe title and abstract unigram frequency distribution of the corpus is used to generate a word cloud (see Figure 7). The word “blockchain” is used most frequently (title 996, abstract 1,514), followed by “financial” (title 108, abstract 1,058), “technology” (title 104, abstract 978), and “finance” (title 104, abstract 978), as highlighted with thick font densities.\n\nTo decipher the data contained within a body of accumulated literature, bibliometrics are used, most frequently based on citations. However, new studies having low citations does not necessarily indicate that they are without significance (Bhukya et al., 2022). When new conceptual knowledge structures (CKSs) are researched in the context of their temporal evolution, as cited events, it is much simpler to comprehend the beginnings and development of these structures over time. In order to locate the CKS within this corpus, we make use of a topic dendrogram.\n\nThis section deals with topic grouping and clustering. We analyse the network diagram with blockchain as the central theme. The surrounding clusters give us an idea of blockchain research in finance. We identify eight distinct clusters with simple manual interpretation and analysis of the dendrogram (Figure 8). These 8 clusters are labelled (Table 8) smart contracts, supply chain, financial services, financial institutions, financial market, financial technologies, initial coin offerings, and business model. We provide notable publications with more than 50 citations. It is evident that most of the work is in the area of smart contracts, followed by supply chain, and financial institutions.\n\nAfter compiling the content of the existing literature and organizing the data from the clusters, we find that the most active areas of blockchain research are in the following two domains: financial risk management and digital transformation; and big data analytics, coupled with machine learning and artificial intelligence (AI).\n\n4.2.1 Financial risk management and digital transformation\n\nThe financial sector pioneered and ultimately made the most effective use of blockchain technology. Many academics study the blockchain for its possible financial uses (Ali et al., 2020; Osmani et al., 2020). For example, Cong et al. (2021) argue that centralized mining pools for risk sharing would not disrupt decentralized mining based on blockchain technology due to cost settings and energy consumption, providing valuable insight into other consensus protocols and organizations. Distributed ledger technology (DLT) and smart contracts are cited by Pal et al. (2021) as the two main aspects of blockchain that can streamline banking and corporate operations. Blockchain technology’s rapid development and updates are set to profoundly impact the nature of businesses and economic and social progress. Blockchain could damage the traditional and centralized business management and organization model because it could lower transaction costs and make it easier to acquire external resources. Treiblmaier (2018) develops a research framework based on four economic theories (principal-agent theory, transaction cost analysis, resource-based view, and network theory) to investigate how blockchain has modified supply chain management.\n\n4.2.2 Big data analytics coupled with artificial intelligence and machine learning\n\nThe theory and technology behind machine learning and its potential uses have advanced rapidly since its inception (Jaiswal and Gupta, 2024; Jaiswal et al., 2023; Jaiswal and Kumar, 2023; Jaiswal and Medhavi, 2018). Much research attention is focused on the intersection of machine learning, AI, and blockchain technology. Tanwar et al. (2019) combine machine learning algorithms with blockchain to ensure accurate data analysis results. Outchakoucht et al. (2017) propose a distributed and dynamic policy to control access to the internet of things (IoT). Meanwhile, dynamic optimization and self-adjustment of policy are made possible by the combination of machine learning and reinforcement learning algorithms. A blockchain and AI-based architecture for the IoT has been developed by Singh et al. (2020), representing a powerful approach to integrating the two technologies. The authors conduct a qualitative and quantitative evaluation of the proposed architecture, showing that it is superior to current IoT architectures.\n\nThere are several challenges to the adoption of blockchain in finance, including regulatory challenges (Guo & Liang, 2016), security and privacy of data (Deshpande et al., 2017), interoperability (Kshetri, 2018), the energy cost of the technology (Hassani et al., 2018), uncertainty about how to govern technology (Attaran & Gunasekaran, 2019), and technical and scalability challenges.\n\nIn this section, while briefly discussing the eight thematic clusters, we provide some future research questions (FRQs) based on the content analysis of the articles in each cluster.\n\n4.3.1 Smart contracts\n\nSmart contracts can help with finance in a variety of ways. They facilitate secure and automated transactions, reduce costs and paperwork, streamline processes, and make payments more efficient (Rozario & Thomas, 2019). Smart contracts can also be used for the digital tokenization of assets such as stocks, bonds, and real estate as well as for automated loan management, escrow services, and trading (Cai, 2018). Additionally, smart contracts can facilitate payment processing, verify identity, and authenticate documents (Dubey et al., 2020). Future research should explore the following FRQs:\n\nFRQ1. How can smart contracts be utilized to increase financial inclusion and accessibility for underbanked populations?\n\nFRQ2. What are the potential risks and limitations of using smart contracts in finance and how can they be mitigated?\n\nFRQ3. How can smart contracts be integrated with existing financial systems and regulations to ensure compliance and stability?\n\nFRQ4. Can smart contracts enhance transparency and accountability in financial transactions and institutions?\n\nFRQ5. How can smart contracts be developed and improved to support more complex financial instruments and transactions?\n\n4.3.2 Supply chains\n\nBlockchain technology can revolutionize the way supply chain finance is conducted. By using a distributed ledger system, businesses can securely and transparently track the movement of goods and money through the supply chain. This would allow for improved visibility and streamline the process of financial transactions. Blockchain technology could also be used to securely store data related to invoices, payments, and contracts, making it easier to access and update information in real- time. This would help improve efficiency and reduce the costs associated with supply chain finance (Kurpjuweit et al., 2021). Furthermore, blockchain technology can facilitate the emergence of decentralized, peer-to-peer financing models, which could open the door to more efficient and cost- effective financing options (Kouhizadeh et al., 2021; Dubey et al., 2020). Future research should explore the following FRQs:\n\nFRQ6. How can blockchain technology be used to enhance transparency and trust in supply chain finance?\n\nFRQ7. How can blockchain technology be integrated with existing supply chain systems and technologies to maximize benefits?\n\nFRQ8. What are the potential risks and limitations of using blockchain in supply chain finance, and how can they be addressed?\n\nFRQ9. Can blockchain technology facilitate the development of new, more inclusive, and sustainable financing models in the supply chain?\n\nFRQ10. How can blockchain technology be used to improve the speed and efficiency of supply chain finance transactions?\n\n4.3.3 Financial services\n\nBlockchain technology can improve many aspects of the financial services industry by providing more transparency and faster, more secure, efficient, and cheaper transactions, including international payments (Meng & Du, 2021). Blockchain can also reduce the risk of fraud and help combat money laundering (Chang et al., 2020). Additionally, it can provide access to financial services to those who previously did not have access. Blockchain can facilitate the transfer of assets, such as stocks and bonds, and the trading of digital assets, such as cryptocurrencies. Future research should explore the following FRQs:\n\nFRQ11. How can blockchain technology be used to increase financial inclusion and accessibility for underbanked populations?\n\nFRQ12. What are the potential risks and limitations of using blockchain in finance, and how can they be mitigated?\n\nFRQ13. How can blockchain technology be integrated with existing financial systems and regulations to ensure compliance and stability?\n\nFRQ14. Can blockchain technology enhance transparency and accountability in financial transactions and institutions?\n\nFRQ15. How can blockchain technology be developed and improved to support more complex financial instruments and transactions?\n\n4.3.4 Financial institutions\n\nBlockchain technology has the potential to provide financial institutions with a variety of benefits, including improved security, lower costs, faster transactions, and greater transparency (Sun et al., 2021). With blockchain, financial institutions can increase the security of their transactions by using distributed ledgers and smart contracts that are cryptographically secure. This technology can also reduce the costs associated with verifying transactions, since a network of computers automatically validates them. Blockchain transactions are faster than traditional methods, as they are conducted directly between two parties in a matter of minutes, compared to days or weeks with traditional methods (Basori & Ariffin, 2022). Notably, blockchain technology can increase transparency by providing an immutable record of all transactions that can be accessed by all parties, allowing for greater trust in the system. Future research should explore the following FRQs:\n\nFRQ16. How can blockchain technology be used to improve the efficiency and scalability of financial institutions?\n\nFRQ17. What are the potential risks and limitations of using blockchain in the financial industry, and how can they be addressed?\n\nFRQ18. How can blockchain technology be integrated with existing financial systems and regulations to ensure compliance and stability?\n\nFRQ19. Can blockchain technology help financial institutions to provide a higher level of customer service and satisfaction?\n\nFRQ20. How can blockchain technology be used to increase transparency and accountability in financial transactions and institutions?\n\n4.3.5 Financial market\n\nBlockchain technology has the potential to revolutionize the financial market. It can be used to store and share data, facilitate transactions, and provide access to financial services for individuals and businesses. Blockchain technology can also improve transparency and security in the financial market by providing a secure, distributed ledger that records all transactions. This can help reduce the risk of fraud and cyber threats (Somin et al., 2020). Blockchain technology can also be used to develop new products and services, such as smart contracts and decentralized exchanges, that benefit investors and other market participants (Gorkhali & Chowdhury, 2022). Future research should explore the following FRQs:\n\nFRQ21. How can blockchain technology be used to improve the accessibility and affordability of financial services for individuals and businesses?\n\nFRQ22. What are the potential risks and limitations of using blockchain in the financial market, and how can they be mitigated?\n\nFRQ23. How can blockchain technology be integrated with existing financial systems and regulations to ensure compliance and stability?\n\nFRQ24. Can blockchain technology enhance the transparency and accountability of financial transactions and institutions?\n\nFRQ25. How can blockchain technology be developed and improved to support more complex financial instruments and transactions?\n\n4.3.6 Financial technologies\n\nBlockchain technology has the potential to revolutionize the financial services industry by providing a secure, efficient, and cost-effective way to move money, store data, and facilitate transactions between parties (Bataev et al., 2020). Blockchain allows for high levels of transparency and trust as all records are immutable, meaning they cannot be changed or altered in any way. This technology can also offer greater security for financial transactions as all records are stored on a distributed ledger that is viewable by all participants. Blockchain can also streamline processes such as digital payments, smart contracts, and more. By leveraging blockchain, financial institutions can reduce costs, increase efficiency, and open up new business opportunities. It can revolutionize financial services by enabling transactions to be processed more quickly and securely, with higher transparency and traceability (Sun et al., 2022). Companies are already using blockchain technology to improve the efficiency of payments, transfers, and other financial processes. Blockchain can also be used to facilitate faster and more secure access to financial data, as well as to provide more efficient recordkeeping for financial institutions. Additionally, blockchain could be used to build digital currencies, such as cryptocurrencies, that could be used for payments and other financial activities (Brus, 2020). Future research should explore the following FRQs:\n\nFRQ26. What are blockchain technology’s specific applications and use cases in the financial services industry?\n\nFRQ27. How can blockchain technology be integrated into existing financial systems and processes?\n\nFRQ28. What are the potential challenges and barriers to adopting blockchain technology in the financial services industry?\n\nFRQ29. How can blockchain technology be used to enhance the security and privacy of financial transactions?\n\nFRQ30. What are the benefits and drawbacks of decentralized financial systems enabled by blockchain technology?\n\nFRQ31. How can blockchain technology be used to improve access to financial services for underbanked populations?\n\nFRQ32. What are blockchain technology’s regulatory and legal implications in the financial services industry?\n\n4.3.7 Initial coin offerings\n\nBlockchain technology can be used for initial coin offering (ICO) fundraising. ICOs are a form of crowdfunding that involves the sale of digital tokens, usually based on blockchain technology. Using blockchain technology, ICOs can provide investors with a more secure, transparent, and efficient way to participate in fundraising. This can be done by providing a platform for project creators to issue digital tokens and for investors to purchase them using cryptocurrency (Momtaz, 2021). Once the tokens are issued, the proceeds from the sale can be used for project development, marketing, and other related expenses. Additionally, blockchain technology can provide an immutable ledger to track the ownership of the tokens and facilitate the transfer of tokens between investors (Colombo et al., 2022). Future research should explore the following FRQs:\n\nFRQ33. How effective are ICOs compared to traditional forms of fundraising, such as equity and debt financing?\n\nFRQ34. What impact does the use of blockchain technology have on the security and transparency of ICOs?\n\nFRQ35. How can blockchain be used to improve the regulatory compliance of ICOs and protect investors from fraud?\n\nFRQ36. What role do smart contracts play in the ICO process, and how can they be used to automate and streamline the process?\n\nFRQ37. How can the use of ICOs and blockchain technology change the fundraising landscape for startups and emerging businesses?\n\n4.3.8 Business models\n\nBlockchain technology has become a significant focus of business-minded individuals due to its potential to revolutionize business operations. The technology can create new business models and transform existing ones (Ioannou & Demirel, 2022). For example, it can create a secure and transparent transaction environment and provide a shared data record across multiple organizations (Suwanposri et al., 2021). It also has the potential to automate processes such as payments, contracts, and other transactions. Using blockchain technology, businesses can benefit from cost savings, improved efficiency, and enhanced trust and security. Additionally, the technology can create new business models based on a distributed ledger, allowing multiple parties to participate in transactions without needing a centralized authority (Baba et al., 2021; Khan et al., 2021). Future research should explore the following FRQs:\n\nFRQ38. How can businesses implement blockchain technology to realize its full potential for transforming operations?\n\nFRQ39. What are the challenges and limitations of using blockchain technology in business, and how can they be addressed?\n\nFRQ40. How can blockchain technology be used to create new business models and revenue streams for businesses?\n\nFRQ41. What is the impact of blockchain technology on existing business models, such as supply chain management, and how can it be optimized?\n\nFRQ42. How can blockchain technology increase trust, security, and transparency in business transactions?\n\n\n5. Conclusion\n\nThis paper combines science mapping and bibliometric analysis to explore the antecedents of blockchain technology research in the finance domain using the Dimensions database. It draws on the top productive journals, countries, institutions, authors, and network collaborations to identify linkages in the blockchain technology field and reveal the foundational themes of blockchain research. The results show a growing trend in research publications for blockchain technology and its application in the financial sector, particularly in the United States, China, and the United Kingdom, which are the most productive and cited countries. There is a growing trend for blockchain research among journals, and Technological Forecasting and Social Change is the most productive journal in this field with the highest number of links, total link strength, and second highest number of citations after Business Horizons. The study highlights the top- cited documents and hence the most influential titles.\n\nA word tree map and word cloud show the focus areas of blockchain technology and its applications in finance. The results indicate that blockchain technology has expanded into supply chains, ICOs, and financial services, and has the potential to develop broader applications in asset tokenization, cryptocurrencies, and decentralized finance. Dendrograms are used to cluster topics and their current statuses, identifying two hotspot trends: financial risk management and digital transformation; and big data analytics coupled with AI and machine learning. While blockchain has proved capable of making the payment process more efficient, with faster transaction settlements and financial institutions saving on international transactions, this study finds multiple roadblocks to the use of blockchain technology in finance, such as regulation, interoperability, energy costs, uncertainty about how to govern it, and technical and scalability problems.\n\nFuture research could address some of the limitations of this study, although it provides several valuable insights into blockchain technology in finance. Future studies could apply the same methodology but focus on other industries harnessing a single dataset (Scopus, IEEE, or Web of Science) or a hybrid dataset (a combination of Scopus, Dimensions, Web of Science, etc.). There is room for further investigation into blockchain’s role in the reinvention of other financing, such as trade finance, letters of credit, and invoice factoring. This study uncovers several avenues for future study. The financial sector is rife with regulations, but banks and other financial institutions are beginning to see the potential of blockchain and digital currencies. Exploring how businesses use blockchain-based solutions for open, accessible, and trustworthy financial transactions will be fascinating, as the major players in these sectors experiment to uncover novel use cases and opportunities. In addition, researchers may want to zero in on how blockchain has enhanced transaction processing and interoperability to demonstrate its value to the financial sector.\n\nThis study did not involve human participants or animals, and thus did not require informed consent. The analysis was conducted using publicly available data from published articles in the Dimensions database. All sources of data are properly cited, and no personal or sensitive information was used. The study adheres to the ethical standards of research integrity and academic honesty. All data sources are publicly accessible and properly cited.", "appendix": "Data availability statement\n\nData is available and can be downloaded from here: FigShare, https://doi.org/10.6084/m9.figshare.26364760.v1 (Jaiswal, 2024).\n\nThis project contains the following underlying data:\n\n1. Dimensions-Publication-2022-07-09_04-12-30.csv\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nThis study followed the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines where applicable to ensure comprehensive and transparent reporting of the bibliometric analysis. Detailed steps were taken to systematically search, select, and analyze the literature using robust analytical tools such as the Dimensions database, VOSviewer, and Bibliometrix. Please see PRISMA Checklist for article “What we know and what should we know about the future of blockchain in finance”. figshare. Figure. https://doi.org/10.6084/m9.figshare.26805244.v1\n\n\nReferences\n\nAli O, Ally M, Dwivedi Y: The state of play of blockchain technology in the financial services sector: A systematic literature review. Int. J. Inf. Manag. 2020; 54: 102199. Publisher Full Text\n\nAngelis J, Da Silva ER: Blockchain adoption: A value driver perspective.Bus. Horiz.2019; 62(3): 307–314.Publisher Full Text\n\nAria M, Cuccurullo C: bibliometrix: An R-tool for comprehensive science mapping analysis. J. Informet. 2017; 11(4): 959–975. Publisher Full Text\n\nAttaran M, Gunasekaran A: Applications of blockchain technology in business: challenges and opportunities.2019.\n\nBaba AI, Neupane S, Wu F, et al.: Blockchain in accounting: challenges and future prospects. International Journal of Blockchains and Cryptocurrencies. 2021; 2(1): 44–67. Publisher Full Text\n\nBasori AA, Ariffin NHM: The Adoption Factors of Two-Factors Authentication in Blockchain Technology for Banking and Financial Institutions. 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Publisher Full Text\n\nHolotiuk F, Pisani F, Moormann J: The impact of blockchain technology on business models in the payments industry.2017.\n\nIbrahim IA, Truby J: Governance in the era of Blockchain technology in Qatar: a roadmap and a manual for Trade Finance. J. Bank. Regul. 2021; 1–20.\n\nIoannou I, Demirel G: Blockchain and supply chain finance: a critical literature review at the intersection of operations, finance and law. J. Bank. Financ. Technol. 2022; 6(1): 83–107. Publisher Full Text\n\nJaiswal R, Medhavi S: Human capital: Is the balance sheet missing long term asset. J. Acc. Rev. 2018; 22(1): 57–66.\n\nJaiswal R: Machine learning to evaluate important human capital (HC) determinants impacting IT compensation. Ramanujan Int. J. Bus. Res. 2022; 7(2): 16–25. Publisher Full Text\n\nJaiswal R, Gupta S, Tiwari AK: Delineation of blockchain technology in finance: A scientometric view. Anna. Financ. Econ. 2022a; 17(04): 2250025. 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Achieving Sustainable Transformation in Tourism and Hospitality Sectors. 2024a; pp. 16–35. Publisher Full Text\n\nJaiswal R, Gupta S, Gupta SK: The impending disruption of digital nomadism: opportunities, challenges, and research agenda. World Leis. J. 2024b; 1–31. Publisher Full Text\n\nJaiswal R, Gupta S, Tiwari AK: Decoding mood of the Twitterverse on ESG investing: opinion mining and key themes using machine learning. Manag. Res. Rev. 2024c; 47(8): 1221–1252. Publisher Full Text\n\nJaiswal R, Khan MIA, Kumar M: Charting the course: Exploring the changing terrain of online shopping and future directions for research. Int. J. Electron. Bus. 2024d; 19(1): 56–79. Publisher Full Text\n\nKhan N, Kchouri B, Yatoo NA, et al.: Tokenization of sukuk: Ethereum case study. Glob. Fin. J. 2022; 51: 100539. Publisher Full Text\n\nKhan SAR, Razzaq A, Yu Z, et al.: Industry 4.0 and circular economy practices: A new era business strategies for environmental sustainability. Bus. Strateg. 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Publisher Full Text" }	[ { "id": "325958", "date": "17 Oct 2024", "name": "Nitin Liladhar Rane", "expertise": [ "Reviewer Expertise AI" ], "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\n\"What we know and what should we know about the future of blockchain in finance\" Authors' have made a good attempt by highlighting the advancing trajectory of blockchain research in finance, with a notable concentration of studies originating from the United States and China, both in terms of total publications and citations. Key thematic clusters identified include “smart contracts,” “financial institutions,” “initial coin offerings,” and “big data analytics.” Intersections with financial risk management, digital transformation, and the integration of big data analytics with artificial intelligence and machine learning are particularly noteworthy, marking focal points of exploration.\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/13-1051
https://f1000research.com/articles/10-1099/v1	29 Oct 21	{ "type": "Research Article", "title": "An enhanced broadband class-J mode power amplifier for 5G smart meter applications", "authors": [ "Nagisetty Sridhar", "Dr Chinnaiyan Senthilpari", "Dr Mardeni R", "Dr Wong Hin Yong", "Dr Chinnaiyan Senthilpari", "Dr Mardeni R", "Dr Wong Hin Yong" ], "abstract": "Background: With the tremendous increase in the usage of smart meters for industrial/ household purposes, their implementation is considered a crucial challenge in the Internet of Things (IoT) world, leading to a demand for emerging 5G technology. In addition, a large amount of data has to be communicated by smart meters efficiently, which needs a significant enhancement in bandwidth. The power amplifier (PA) plays a major role in deciding the efficiency and bandwidth of the entire communication system. Among the various modes of PAs, a newly developed Class-J mode PA has been proven to achieve high efficiency over a wide bandwidth by maintaining linearity.\nMethods: This paper proposes a Class-J mode PA design methodology using a CGH40010F-GaN device that operates at a 3.5 GHz frequency to meet the requirements of 5G wireless communication technology for the replacement of existing 4G/LTE technology used for advanced metering infrastructure (AMI) in smart grids. This research's main objective is to design the proper matching networks (M.Ns) to achieve Class-J mode operation that satisfies the bandwidth requirements of 5G smart grid applications. With the target impedances obtained using the load-pull simulation, lumped element matching networks are analyzed and designed in 3 ways using the ADS EDA tool.\nResults: The simulation results reveal that the proposed Class-J PA provides a maximum drain efficiency (D.E) of 82%, power added efficiency (PAE) of 67% with 13 dB small-signal gain at 3.5 GHz, and output power of 40 dBm (41.4 dBm peak) with a power gain of approximately 7 dB over a bandwidth of approximately 400 MHz with a 28 V power supply into a 50 Ω load.\nConclusion: The efficiency and bandwidth of the proposed Class-J PA can be enhanced further by fine-tuning the matching network design to make it more suitable for 5G smart meter/grid applications.", "keywords": [ "5G", "3.5 GHz", "power amplifier", "good efficiency", "wide bandwidth", "Class-J", "matching networks" ], "content": "Introduction\n\nWith the tremendous improvement in the wireless communication industry, the demand for emerging 5G technology1–3 has increased for enhanced broadband and Internet of Things (IoT) applications. Today, many smart devices introduce intelligent behavior into households and industrial equipment to realize smart grids and smart homes/cities. For example, a smart energy meter can measure energy consumption by one device and send the data to the energy provider along with the end consumer statistics using two-way wireless communication technology. Although the existing 4G technology has served us well to date, it cannot satisfy the new challenges that can be brought by emerging wireless communication applications such as 5G smart grids, as a large amount of data transfer is needed at higher data rates with low latency. Hence, the adoption of 5G technology becomes more crucial. Therefore, worldwide research has started to implement this 5G technology by adopting techniques such as millimeter waves, small cells, massive MIMO, beamforming, and full duplexing.4 However, the two major challenges to be solved while implementing this 5G technology for these applications are a reduction in energy consumption5 and an enhancement in bandwidth. As the PAE of the power amplifiers6,7 used in the R.F. transmitter plays the key role in deciding the energy consumption by the overall 5G wireless communication network, a power amplifier is needed that can provide improvement in PAE without compromising linearity and bandwidth. Many PA topologies have been reported previously8–14 with various techniques to achieve linear amplification with high efficiency. Switching mode PAs such as Class-E/F demonstrate potential in providing excellent PAE but are not beneficial for enhanced bandwidth 5G applications because of their narrow bandwidth nature of harmonic terminations. On the other hand, linear mode PAs such as Class-A/B can achieve lower efficiency but are more linear than switching mode PAs. Nevertheless, Class-B mode PAs with harmonic tuning can theoretically achieve a peak efficiency of approximately 78.5%, and their bandwidth is also limited, as harmonic termination is difficult to realize over a wide bandwidth. However, this study mainly focuses on the design of a power amplifier that satisfies the requirements of smart grid wireless communication networks that15,16 used for AMI of smart meters. A distributed communication architecture that can provide cost-effective and efficient communication is proposed in.17 Distributed operation centers presently use 3G/4G cellular networks to communicate with data concentrators, which can be replaced by emerging 5G communication technology to support the increase in data traffic. A comprehensive review of 5G wireless communication networks for smart grids is presented in,18 which motivates PA designers to design a PA that overcomes the bandwidth limitations of existing linear and switching mode PAs and satisfies the bandwidth requirements of 5G wireless communications in smart grids. A newly developed Class-J mode PA by S.C. Cripps in19 has proven its potential in achieving high efficiency without compromising linearity and bandwidth. The design methodology for highly efficient, linear, and broadband Class-J PA mode is demonstrated in.20 Different Class-J mode PAs were reviewed to analyze their suitability for near-future 5G wireless communications used for smart grid applications. Of these PAs, the design of a 0.5 W GaN-based integrated Class-J PA that considers output matching network element losses for realizing on-chip output matching is presented in,21 but because of the limitations of device technology and the low-Q on-chip matching network losses, its efficiency and output power are less than those of discrete PAs. An integrated Class-J PA using CMOS technology is presented in,22 where the effect of knee voltage is considered to analyze 2nd harmonic losses for deriving modified design equations. However, the staked FET must be used for implementation because of the CMOS PA’s low breakdown voltage. The improvement in power output and D. E of a Class-J PA was presented in23,24 by realizing a proper half-wave rectified sinusoidal waveform at the gate of the transistor. Apart from the usefulness of this method, it needs additional circuitry because of higher-order filters, which complicates the design and implementation of the PA. A methodology to improve the Class-J PA’s performance by injecting the active power at the 2nd harmonic frequency has been proposed in,25 which causes an improvement in drain efficiency, but because of doubling and filtering, the design becomes complicated, and an increase in chip area makes it less appealing for integration. Based on the literature, it is understood that among the various modes of PAs, a Class-J PA can even satisfy the enhanced bandwidth requirement of the emerging 5G smart meter/smart grid applications without sacrificing linearity and efficiency if the appropriate matching networks are designed. Therefore, in this paper, a Class-J mode PA is chosen, and a design methodology is proposed to achieve the efficiency and bandwidth requirements of 5G wireless communications of smart grids. However, the important point to be considered when designing a PA for these smart grid applications is the frequency at which it has to be operated. Hence, different frequency bands, including LTE and 5G NR (new radio),26–28 are analyzed to choose the appropriate operating frequency of the proposed Class-J PA. Recently, a frequency band termed citizen broadband radio service (CBRS) with 3.5 GHz center frequency (i.e., 5G sub6 GHz frequency) was allocated for public usage.29 This spectrum provides good space for 5G smart grid wireless communication applications. Hence, Initially, the proposed Class-J mode PA was designed to operate at a center frequency of 3.5 GHz (sub < 6 GHz) 5G frequency). The main contribution of this research paper involves analysis of various matching network methods/topologies and design of appropriate I/P and O/P matching networks to match a 50 Ω source and loads with the desired optimum source and load impedances of the transistor with respect to maximum PAE determined by load pull to achieve Class-J mode operation with the desired bandwidth of 5G smart grid specifications. The PA simulations were performed in the Advanced Design Systems (ADS) EDA tool, and this paper's structure is described as follows. A stepwise design procedure of a Class-J PA based on its theory with three approaches of lumped element-based input and output M. Ns for matching a 50 Ω source and load terminations with the transistor's optimum source and load impedances to obtain Class-J mode operation is described in the Methodology section. The schematic Class-J PA circuit simulation results as per the design methodology and their comparison with similar recent works are presented in the Results and Discussion sections. Finally, the advantages and limitations of this proposed research work are detailed in the Conclusions.\n\n\nMethods\n\nFrom the theory of the Class-J operation mode introduced and developed by S.C. Cripps,19 the high-efficiency amplification in broadband can be obtained by terminating the output of transistor M1 to appropriate fundamental (Zf0) and second harmonic (Z2f0) optimal load impedances, as shown in Equations (1) and (2), at different frequencies over the desired bandwidth, as shown in Figure 2(a).\n\nWith these optimum load impedances presented, from Figure 1, we can observe that the drain voltage (VDS) is boosted with a phase shift.\n\nThus, the phase shift and boost in drain voltage (VDS) cause a slight overlap with drain current (ID), making the Class-J power amplifier highly efficient. Although this waveform shows the feature of a switching mode PA, the Class-J mode PA can provide linearity similar to the Class-B or AB modes because of its non-switching mode of operation. Unlike in Class-B, harmonic traps are unnecessary, making it suitable for wideband 5G applications.\n\nThe various steps involved in the design methodology of the proposed Class-J PA are discussed, as illustrated in the flowchart shown in Figure 2(b).\n\nAs per the trend of designing a power amplifier, the Advanced Design System (ADS) tool was used to design, and a CREE Device model (CGH40010F) based on GaN technology was used for simulation. The CGH40010F GaN transistor is chosen based on the features mentioned in its datasheet to obtain the desired power output required for smart meter applications. The gate threshold voltage (Vth) and gate quiescent voltage (VGQ) of the chosen (CGH40010F) GaN transistor can also be obtained from its datasheet. To obtain a Class-J PA mode, the load impedances to be presented to this transistor (M1) (i.e., (CGH40010F) GaN transistor) are calculated theoretically using Equations (1) and (2) and can be verified using the Class-J workspace in the ADS design tool.\n\nAs per the design idea of the power amplifier for this work, the supply voltage VDD = 28 V and gate bias voltage VGG ≅ VK (threshold voltage) (i.e., with a quiescent bias current of Iq = 2% of Imax) are chosen based on the (CGH40010F) GaN transistor's (M1) datasheet for biasing it through a fixed-bias network to operate as a Class-B PA to obtain a half-wave rectified drain current (ID). With the use of the fixed-bias network shown in Figure 3(a), the DC-IV characteristics of the CGH40010F GaN transistor are drawn, and the quotient (Q) or bias point is obtained by adjusting marker m2 on the load line to operate it in Class-B mode, as shown in Figure 3(b).\n\nAfter choosing the bias point of the transistor while designing the power amplifier, one of the most important considerations is that it should be unconditionally stable irrespective of the frequency under normal operating conditions. To maintain the PA’s stability at low frequencies, a stabilization circuit with a resistor connected in series with the transistor gate terminal is employed based on the datasheet of the CGH40010F GaN transistor. This series resistance can stabilize the transistor across the entire range of desired frequencies. To ensure the unconditional stability of the PA, the main conditions to be satisfied are that the Rollet stability factor is more than unity (i.e., (K>1)) and the stability measure (b) is positive. The Rollet stability and stability measures can be calculated theoretically by Equations (4) and (5), respectively.\n\nHowever, practically unconditional stability of the PA can be ensured using Network Analyzer for S-Parameters (SP_NWA) from simulation instrument components, and the stability factor and its variation w.r.t. frequency can be obtained with the use of measurement expression functions and data display templates in Advanced Design System (ADS) tool, as shown in Figure 4.\n\nGenerally, the transistor's optimum input and output impedances used for a PA design can be obtained by conducting load-pull simulations with the reference source and load impedances chosen from its datasheet.\n\nAs we are designing a Class-J PA in this research work, the reference source impedance can be chosen from the transistor's datasheet (if not mentioned in the datasheet, we can take approximately (5+j0 Ω) for any GaN device). The reference fundamental and second harmonic impedances can be calculated theoretically using Equations (1), (2) and (3).\n\nThe reference target optimum impedances required to obtain Class-J operation can be determined using the Class-J ADS workspace utility, which is developed with mathematical design equations based on the load line.\n\nAfter choosing the bias (Q) point by adjusting the load line on DC-IV characteristics, which are obtained from the fixed-bias network shown in Figure 3(b), and by keeping the Alpha (α) factor in Equations (1) and (2) as “zero (0)” on the slider, as shown in Figure 5, the fundamental is terminated to a resistive load and higher-order harmonics are terminated as short, which leads to the Class-B mode of operation.\n\nThe reference target optimum impedances required for Class-J operation can be obtained by moving the alpha factor (α) in Equations (1) and (2) from 0 to 1 on the slider in Figure 6. With this target fundamental and second harmonic load impedance, the drain voltage (VDS) is boosted with a phase shift.\n\nTo verify the target fundamental and second harmonic load impedances shown in Figure 6, which are obtained based on the load line, load-pull simulations on the stabilized transistor must be conducted by taking them as reference impedances using a one-tone load-pull instrument at constantly available source power in the ADS EDA tool, as shown in Figure 7.\n\nAfter obtaining the optimum source, fundamental and second harmonic load impedances from the LOADPULL simulations, corresponding to the MAX PAE, they can be validated by presenting them directly to the transistor (ZS and ZL) instead of 50 Ω termination at the source and load terminals, as shown in Figure 8.\n\nAfter validation of the optimum input and output impedances (ZS and ZL), the next important step in the design is the realization of the input and output M. Ns to match them with the 50 Ω termination source and load terminals. As we use the ADS EDA tool for this research work, impedance matching networks can be designed using three methods: Smith chart utility, impedance match utility, and equation-based lumped element L and π-type matching networks.\n\nInitially, to design the input matching network, the Smith chart component (DA_smithchart1) is terminated with a source impedance of 50 Ω and the output impedance as the source impedance of the CGH40010F GaN transistor obtained from load-pull analysis. As the M. N needs to be designed at an operating frequency of 3.5 GHz, an S-parameter sweep is set up for the range of 3–4 GHz, as shown in Figure 9(a).\n\nAfter setting up the S-parameter sweep, the source impedance is set as 50 Ω. The load impedance is set as the input impedance of the CGH40010F GaN transistor (i.e., obtained from the load-pull simulations) on the Smith chart utility, and the travel path from source impedance to the load impedance leads to an L-type input M. N, as shown in Figure 9(b).\n\nThe output M. N is designed in the same manner as the input M.N. Nevertheless, the Smith chart component (DA _smithchart1) is terminated with source impedance as the output impedance of the CGH40010F GaN transistor (i.e., obtained from the load-pull analysis). The load is 50 Ω, and the S-parameter sweep is set up as an input matching network for the range of 3–4 GHz, as shown in Figure 10(a).\n\nAfter setting up the operating frequency, source, and load impedances on the Smith chart utility, the travel path from source impedance to load impedance leads to an L-type output matching network, as shown in Figure 10(b).\n\nInitially, these matching networks are designed for a bandwidth of approximately 1 GHz with an operating frequency of 3.5 GHz (i.e., sub6 GHz). With the desired bandwidth and center frequency, the quality factor can be calculated as Q = f/BW. In Smith chart utility, this Q factor can be represented as Q circles. For this work, the M. Ns at input and output are designed with a Q-circle of 3.\n\nNext, the matching networks to match the same input and output impedances (based on load-pull analysis) are represented using the Z2P_Eqn file with the 50 Ω source, and load terminations are designed using the L.C. bandpass match smart component using an impedance matching utility, as shown in Figure 11(a).\n\nAfter setting up the range of frequencies (i.e., 3-4 GHz), the source and load impedances of approximately 10–14 matching network topologies are designed for input and output matching in impedance matching utility, from which the network topologies with fewer passband errors after optimization are chosen, as shown in Figures 11(b) and 11(c).\n\nLater, lumped element L-type input and π-type output M. Ns to match the same input and output impedances (obtained from load-pull simulations) with the 50 Ω source and load terminations are designed using basic L-type and π-type impedance matching network design equations with an operating frequency of 3.5 GHz and a Q-factor of 3 by setting up an S-parameter sweep for the range of 3–4 GHz, as shown in Figure 12.\n\nOnce the matching networks are designed, all topologies are placed at the input and output of the stabilized transistor to match the optimum ZS and ZL with the 50 Ω termination at the source and load terminals to complete the PA design, as shown in Figures 13, 14 and 15, respectively.\n\nThe output parasitic capacitance CDS of the transistor at higher-order harmonics is considered a short circuit. Once the OMN is designed, the capacitive reactance to the load-line resistance ratio [XCDS/RL] needs to be calculated. Suppose this ratio is (<=) 1; then, the matching network design is considered ideal. However, this ratio can also be above unity based on the technology and frequency of the device used in the design.\n\n\nResults\n\nThe Class-J PA is designed using a CGH40010F transistor with GaN technology in the Advanced Design System (ADS) EDA tool. Initially, after obtaining the bias (Q) point from the D.C., the stability analysis is performed on the CGH40010F GaN transistor with an S.P. network analyzer circuit, as shown in Figure 4. The unconditional stability of the device over the desired range of frequencies can be confirmed by checking the result on the stability factor and measuring the analysis represented using Figure 16 and Table 1. It is observed that the stability factor is >1, and the stability measure is >0, which ensures that the GaN device is unconditionally stable over the desired frequency range, i.e., (3–4) GHz.\n\nAfter checking the device’s stability, the optimum impedances required for the Class-J PA can be obtained by conducting load d pull simulations, as shown in Figure 7, with reference to the target source and load impedances that are obtained from load-line analysis, as explained in step 4 of the Methodology section. The optimum source/input impedance obtained from the load-pull analysis is 6.315+j13.787, and the load/output impedance obtained is 16.151-j0.970, corresponding to the maximum power delivered (Pdel_dBm_MAX), as shown in Figure 17.\n\nSimilarly, the optimum source/input impedance obtained is 6.322+j14.053, and the load/output impedance obtained is 16.212+j*4.793, corresponding to the maximum PAE of 66%, as shown in Figure 18.\n\nFrom the results of load-pull analysis, the optimum input and output impedances corresponding to the maximum PAE are chosen for the Class-J PA design and tabulated by comparison with the target source and load impedances obtained from load-line analysis-based mathematical design equations, as shown in Table 2.\n\nBefore validating the optimum source and load impedances, the PA is terminated to a 50 Ω source and load terminals and the corresponding performance parameters, as shown in Figure 19.\n\nFigure 19 shows that the performance parameters such as power delivered, large-signal and small-signal gains, D. E, and PAE are very low, as the CGH40010F GaN transistor does not terminate to optimum impedance values.\n\nBy terminating the transistor with the optimum impedance values obtained using load-pull simulations corresponding to the maximum PAE, harmonic balance S-parameter simulations are validated by running, as shown in Figure 8, and the respective performance parameters are shown in Figure 20.\n\nFrom Figure 20, the performance parameters such as power delivered, large-signal and small-signal gains, drain efficiency and PAE are improved and nearly equal to the values obtained from load-pull simulations, as the input and output impedances of the CGH40010F GaN transistor are terminated to optimum impedance values. In addition, the reflection coefficients S (1,1) and S (2,2) are not as expected.\n\nAfter validation of optimum impedances obtained from load-pull analysis, the M. Ns are designed as explained in step 7 of the Methodology section and placed at the respective input and output terminals of the PA, as Smith chart components are shown in Figure 13. Finally, these matching network elements are optimized and updated using an optimization tool in ADS, as shown in Figure 21.\n\nAfter optimizing the performance parameters such as power delivered and large-signal and small-signal gains, PAE and D. E are shown in Figure 22. The reflection coefficients S (1,1) and S (2,2) are obtained as expected with the optimization of input and output matching networks.\n\nThe matching networks that are designed using L.C. bandpass match with the impedance matching utility, as explained in step 7 of the Methodology section, are placed at respective input and output terminals of the PA, as shown in Figure 14. Then, these matching network elements are optimized and updated using an optimization tool in ADS, as shown in Figure 23.\n\nAfter optimizing the performance parameters such as power delivered and large-signal and small-signal gains, PAE and D. E are shown in Figure 24. The performance parameters are improved slightly with the optimization of the matching networks that are designed using the impedance matching utility.\n\nThe matching networks that are designed using basic L-type input and π-type output matching design equations, as explained in step 7 of the Methodology section, are placed at the input and output terminals of the PA, as shown in Figure 15, and then these matching network elements are optimized and updated using an optimization tool in ADS, as shown in Figure 25.\n\nAfter optimizing the performance parameters such as power delivered and large-signal and small-signal gains, PAE and D. E are shown in Figure 26. The performance parameters are obtained as expected with the optimization of input and output matching networks.\n\nAll the numerical values of performance parameters such as power delivered (Pdel_W, Pdel_dBm_MAX) in watts and dBm, large-signal gain (LS_Gain_dB), PAE and D. E (Deff) that are shown in Figures 19, 20, 22, 24, and 26, corresponding to without and with three matching topologies, are computed with many equations using the “MeasEqn” of the harmonic balance HB simulator. The load voltage is plotted as the spectrum in dBm, and intrinsic voltages/currents are plotted as time-domain signals using an (HB) simulation controller in ADS. The desired half-rectified intrinsic drain voltage and currents with small overlap that represent the Class-J mode of operation were obtained, and reflection coefficients S (1,1) and S (2,2) > -10 dB over a frequency range from (3.3–3.7) GHz were observed from Figure 26. The comparison of the performance parameters of the Class-J PA with and without matching networks obtained for different source and load terminations is shown in Table 3.\n\nThe above comparison table shows that among the 3 methods used for matching networks, the Class-J PA with L-type input and π-type output matching networks exhibits expected performance parameters that are obtained from load-pull simulations (i.e., 66% of PAE and 40 dBm of max power output), as shown in Figure 18.\n\nTo validate the variation in the performance parameters with respect to the input power sweep, HB simulations were performed on the proposed Class-J PA by taking the available source power (Pavs_dBm) as the sweeping parameter. Figure 27 shows the simulation results of important performance parameters such as drain efficiency, PAE, large-signal gain, and power delivered corresponding to the available source power (Pavs_dBm) sweep. These results demonstrate that, a maximum power output of 41.4 dBm with a power gain of approximately 7.4 dB, max D. E of 82%, and max PAE of 67% for the corresponding available source power of 34 dBm with a 28 V power supply into a 50 Ω load.\n\nSimilarly, HB simulations were performed to validate the performance parameter variation of the proposed Class-J PA with L-type input and π-type output matching networks with respect to the input RF frequency, and the corresponding results are displayed in Figure 28. These results reveal that a power output above 40 dBm with a power gain of approximately 7 dB over a bandwidth of approximately 400 MHz (i.e., 3.3 GHz to 3.7 GHz) and max PAE and D. E of 67% and 82%, respectively, are obtained at a 3.5 GHz center frequency.\n\n\nDiscussion\n\nFinally, the improved performance parameters of the proposed Class-J PA with L-type input and π-type output matching networks are compared with similar Class-J PAs in the literature.30-34 As these PAs were designed at different frequencies and technologies, it is difficult to compare their performances. However, it can be noted that the Class-J PA design is proposed with a compact transmission line-based output matching network (OMN) in30 that uses the same transistor technology (GaN) of this work to obtain broadband and highly efficient amplification and achieves a maximum drain efficiency of 75%. Although our proposed PA is designed at different frequencies, its bandwidth is the same as that of this PA, and its transmission line-based M. Ns use a large chip area compared to the M. Ns of our work. A microwave Class-J PA for Wi-Fi IEEE802.11a Bluetooth applications designed with a methodology similar to that of this work in the same ADS EDA tool is presented in,31 which uses a GaAs transistor as an active device but achieves a power output of 21 dBm and D. E of 69%. A fully integrated Class-J PA designed at 5 GHz for WLAN 802.11ax applications was presented in32 that uses GaN on SiC technology with the same V dd=28 V to provide a maximum PAE of 55% and output power of 38 dBm, and it was mentioned that the performance of this PA can be enhanced further by employing DPD. However, the gain of this PA is high compared to our work, as it is designed as a multistage PA. A Class-J PA designed for X-Band is presented in.33 It uses the active load modulation technique, facilitates the PA's integrated implementation by eliminating the doubler and filter networks of conventional Class-J2 PAs, and achieves a drain efficiency of 71% and a PAE of 50%. However, the broad B.W. is not achieved because of harmonic tuners, and the auxiliary network used for phase shifting may need additional circuitry and space. A Class-J PA design with a novel direct M. N synthesis technique for broadband operation is presented in.34 The PAE and output power (dBm) are almost the same at the frequency (3.5 GHz) of our proposed work. Although the synthesis technique is novel, the transmission line-based MNs may occupy a large chip area. In addition, an integrated Class-J PA using CMOS technology is presented in,22 in which the effect of knee voltage is considered for deriving modified design equations. However, the staked FET must be used for implementation because of the CMOS PA’s low breakdown voltage, whereas our work uses a GAN device with a high breakdown voltage. The performance comparison discussed thus far is summarized in Table 4. The PAE and DE of this work are better than those of other works shown in Table 4.\n\n\nConclusions\n\nA 3.5 GHz Class-J PA design with lumped element-based input and output matching networks that are suitable for 5G smart meter/grid applications is presented in this paper. The proposed Class-J PA design methodology is demonstrated in a stepwise manner. It is observed that with a small overlap between the intrinsic half-wave rectified current and voltage waveforms at the drain, this Class-J mode PA can be as linear as Class-B or AB modes because of its non-switching mode of operation. From the simulation results, we conclude that the proposed Class-J PA obtains a maximum drain efficiency of 82%, which is better than similar Class-J PAs reported in the literature. A PAE of 67% with a 13 dB small-signal gain at 3.5 GHz and an output power of 40 dBm (41.4 dBm peak) with a power gain of approximately 7 dB over a bandwidth of approximately 400 MHz (i.e., 3.3 GHz to 3.7 GHz) are achieved with no harmonic traps, unlike in Class-B mode PAs, which makes this Class-J PA superior to other PA modes and more appealing for emerging wireless communication networks used for AMI of smart meters in 5G smart grids. However, the PAE and BW of the proposed Class-J PA can still be improved by fine-tuning the designed matching networks. This work is in progress to achieve desired specifications of 5G smart grid applications.\n\n\nData availability\n\nNo data are associated with this article.\n\n\nAuthor contributions\n\nMr. Nagisetty Sridhar-original drafting of manuscript preparation, Dr Chinnaiyan Senthilpari-validation and Supervision, Dr. Mardeni R-cosupervision. All the authors agreed to the final version of this manuscript.", "appendix": "Acknowledgments\n\nWe would like to express our sincere thanks to the Multimedia University and Ministry of Higher Education (MOHE), Malaysia, for funding this research work through FRGS MMUE/190075.\n\n\nReferences\n\nDahiya M: Need and Advantages of 5G wireless Communication Systems. Int. J. Adv. Res. Com. Sci. & Manag. Studies. 2017; 5: 48–51.\n\nhttp\n\nhttp\n\nNiknejad M, Thyagarajan S, Alon E, et al.: A circuit designer's guide to 5G mm-wave. 2015 IEEE Custom Integrated Circuits Conference (CICC). 2015; pp. 1–8, Publisher Full Text\n\nAgiwal M, Roy A, Saxena N: Next Generation 5G Wireless Networks: A Comprehensive Survey. IEEE Communications Surveys & Tutorials. 2016; vol. 18(no. 3): pp. 1617–1655. Publisher Full Text third quarter.\n\nLie DYC, Mayeda JC, Li Y, et al.: A Review of 5G Power Amplifier Design at cm-Wave and mm-Wave Frequencies. Wirel. Commun. Mob. Comput. 2018; vol. 2018: 1–16 pages. 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Publisher Full Text" }	[ { "id": "163741", "date": "02 Nov 2023", "name": "Anumuthu Priya", "expertise": [ "Reviewer Expertise Antennas", "Microwave", "Electronic Circuits", "Electromagnetics", "Wireless Communication", "underwater 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 manuscript details the design of class- J power amplifier for 5G smart grid’s advanced metering infrastructure applications.\nHere are few comments from my side:\n1. The article is well written and the results are relatively interesting which I believe that the manuscript can provide some good insights for a future decision regarding 5G smart grid.\n2. However, as the class-J PA is well established, the authors should explain the novelty/contribution in the proposed class-J PA design.\n3. In Figure 6 authors are suggested to explain clearly how the phase shift and voltage boost are obtained by moving Alpha factor (α) from 0 to 1, in the relevant page?\n4. I would suggest the author to explain the reason for designing the matching networks of proposed PA by considering its optimum impedances corresponding to PAE rather than output Power.\n5. How the second harmonic condition of class-J mode operation is satisfied?\n6. Although the PAE and D.E of proposed PA are good its B.W is relatively low as per the comparison table, it is suggested to give some justification for obtained B.W of the proposed PA.\n7.Table 4 gives the performance comparison of class -J PA. Can the authors report this class -J pa is relatively efficient than other PA types also.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "12357", "date": "12 Sep 2024", "name": "SRIDHAR NAGISETTY", "role": "Author Response", "response": "Dear Reviewer I would like to thank you for your valuable comments. I have amended the manuscript as per your comments and the corresponding point-to-point response is given below: Reviewer Comment-1: The article is well written, and the results are relatively interesting, which I believe that the manuscript can provide some good insights for a future decision regarding 5G smart grid. Response: Thank you for your valuable comment on our manuscript. Reviewer Comment-2: However, as the class-J PA is well established, the authors should explain the novelty/contribution in the proposed class-J PA design Response: Thank you, Prof., As per your suggestion, the main contribution/novelty of the proposed class-J PA is included as a subsection before the conclusion section in the manuscript. Reviewer Comment-3: In Figure 6, authors are suggested to explain clearly how the phase shift and voltage boost are obtained by moving Alpha factor (α) from 0 to 1, in the relevant page? Response: Thank you, Prof., As per your suggestion, the explanation for how the phase shift and voltage boost are obtained by moving the Alpha factor (α) from 0 to 1, is included below Figure 6 in the relevant page. Reviewer Comment-4: I would suggest the author to explain the reason for designing the matching networks of proposed PA by considering its optimum impedances corresponding to PAE rather than output Power. Response: Thank you, Prof. As per your suggestion, I have explained the reason for designing the matching networks of the proposed class-J PA by considering its optimum impedances corresponding to PAE rather than output Power in the “Validation of optimum impedances obtained from load pull” section. Reviewer Comment-5: How is the second harmonic condition of class-J mode operation satisfied? Response: Thank you, Prof., As per your suggestion, the explanation for how the second harmonic condition of class-J mode operation is satisfied is included below Figure 15 and before the Results section. Reviewer Comment-6: Although the PAE and D.E of proposed PA are good its B.W is relatively low as per the comparison table, it is suggested to give some justification for obtained B.W of the proposed PA. Response: Thank you, Prof., As per your suggestion, the justification for obtained BW of the proposed class-J PA is included in the discussion section before table 4. Reviewer Comment-7: Table 4 gives the performance comparison of class -J PA. Can the authors report this class -J pa is relatively efficient than other PA types also. Response: We report that the proposed class-J PA design of this work is not relatively efficient than other switching mode PAs. However, the proposed class-J PA has achieved high efficiency comparatively with the existing author’s class-J PA designs without sacrificing the linearity over the desired BW. This is included in the discussion section just before Table 4." } ] }, { "id": "229222", "date": "02 Aug 2024", "name": "Tahesin Samira Delwar", "expertise": [ "Reviewer Expertise My current research interests are RF circuit design", "high-efficiency CMOS power amplifiers", "Optical wireless communication systems and visible-light communications." ], "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\nHow does the proposed amplifier manage harmonic distortion across the desired frequency bands? Providing a thorough harmonic analysis, especially in the context of 5G frequency ranges, would be insightful. What is the power efficiency of the enhanced Class-J mode power amplifier, particularly at varying output power levels? What is the noise performance of the amplifier, and how does it impact the signal integrity in 5G smart meter applications? Discussing noise considerations is essential for applications demanding high-quality signal transmission. What considerations should be taken into account for the real-world deployment of the proposed amplifier in 5G smart-meter networks? Discussing practical considerations, such as cost, power consumption, and scalability, would be valuable for potential adopters. How closely do the experimental results align with the simulation findings? Improve the figure quality. Ensure that the references are up-to-date and include recent contributions in the field of power amplifiers for 5G applications. Add some recent journal reference papers instead of conference papers. Make a subsection of the main contribution and related literature of the research. Highlight the novelty of the proposed circuit. Presentation skills are very poor. Improve the presentation skills. Add the future research scope. Linearity analysis is missing. Considering the practical deployment of 5G smart meters, were there any integration challenges encountered with the proposed amplifier? How does the enhanced broadband Class-J mode power amplifier contribute to the overall functionality and performance of 5G smart meters? Discussing the impact on communication range, reliability, and data transmission speed would be valuable.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "12358", "date": "12 Sep 2024", "name": "SRIDHAR NAGISETTY", "role": "Author Response", "response": "Dear Reviewer I would like to thank you for your valuable comments. I have amended the manuscript as per your comments and the corresponding point-to-point response is given below: Reviewer Comment-1: How does the proposed amplifier manage harmonic distortion across the desired frequency bands? Providing a thorough harmonic analysis, especially in the context of 5G frequency ranges, would be insightful. Response: Thank you, Prof., The proposed class-J PA is designed and optimized to minimize harmonic distortion and enhance the PAE and Drain Efficiency across the desired bandwidth using load pull techniques and careful design of its OMN, as per your suggestion, it is explained just below Figure 15 before the Results section. Reviewer Comment-2: What is the power efficiency of the enhanced Class-J mode power amplifier, particularly at varying output power levels? Response: Thank you, Prof., As per your suggestion, the variation of PAE and Drain efficiency of the proposed class-J PA corresponding to the output power levels is discussed by including Figure 29 just before the discussion section of the manuscript. Reviewer Comment-3: What is the noise performance of the amplifier, and how does it impact the signal integrity in 5G smart meter applications? Discussing noise considerations is essential for applications demanding high-quality signal transmission. Response: The proposed class-J PA offers good noise performance as it uses a GaN device as the main transistor. As per your suggestion, noise performance proposed class-J PA of and its impact on signal integrity is explained below Figure 30, just before the discussion section of the manuscript. Reviewer Comment-4: What considerations should be taken into account for the real-world deployment of the proposed amplifier in 5G smart-meter networks? Discussing practical considerations, such as cost, power consumption, and scalability, would be valuable for potential adopters. Response: The key factors considered while deploying the proposed class-J PA in 5G wireless networks of smart metering applications are explained in the discussion section after Table 4. Reviewer Comment-5: How closely do the experimental results align with the simulation findings? Response: Thank you, Prof., In this work, the proposed class-J PA is designed with an idea to replace the passive inductor in the OMN with an Active Inductor. Therefore, in this paper, only simulation results of proposed class-J PA that is suitable for emerging 5G wireless networks in smart metering/AMI applications, with 3-types of lumped element-based M.Ns designs as the main contribution, are presented. Reviewer Comment-6: Improve the figure quality. Response: Thank you, Prof. As per your suggestion, along with the new Figures 29 and 30, all other Figures are resubmitted as separate 300 dpi TIFF format files as per the author's guidelines. Reviewer Comment-7: Ensure that the references are up-to-date and include recent contributions in the field of power amplifiers for 5G applications. Add some recent journal reference papers instead of conference papers. Response: Thank you, Prof., As per your suggestion, some of the conference papers are replaced with recent journal papers in the REFERENCES section of the manuscript. Reviewer Comment-8: Make a subsection of the main contribution and related literature of the research. Highlight the novelty of the proposed circuit. Presentation skills are very poor. Improve the presentation skills. Response: Thank you, Prof., As per your suggestion, the main contribution/ novelty of the proposed class-J PA is included as a subsection before the conclusion section in the manuscript. The presentation of paper has improved while addressing the reviewer comments. Reviewer Comment-9: Add the future research scope Response: Thank you, Prof., As per your suggestion The future scope of this research work is included in the conclusion section. Reviewer Comment-10: Linearity analysis is missing. Response: Thank you, Prof., As per your suggestion, the linearity Analysis of the proposed class-J PA using a 3 dB compression point is discussed by including Figure 30 before the discussion section of the manuscript. Reviewer Comment-11: Considering the practical deployment of 5G smart meters, were there any integration challenges encountered with the proposed amplifier? Response: Thank you, Prof., In this work the actual idea is to replace the passive inductor in the OMN of the proposed class-J PA with an Active Inductor. Therefore, in this paper, only simulation results of proposed class-J PA that is suitable for emerging 5G wireless networks in smart metering/AMI applications, with 3-types of lumped element-based M.Ns designs as the main contribution are presented. Reviewer Comment-12: How does the enhanced broadband Class-J mode power amplifier contribute to the overall functionality and performance of 5G smart meters? Discussing the impact on communication range, reliability, and data transmission speed would be valuable Response: The proposed class-J PA contributes to the overall functionality and performance of 5G smart metering applications by extending communication range through high power efficiency, increasing data transmission speed with wider bandwidth, and improving reliability with reduced signal distortion. This is included in the conclusion section." } ] } ]	1	https://f1000research.com/articles/10-1099
https://f1000research.com/articles/13-1050/v1	12 Sep 24	{ "type": "Research Article", "title": "Comparison of histopathological and triphenyl tetrazolium chloride test in diagnosing myocardial infarction: An autopsy study", "authors": [ "Varun Krishna B", "Chandni Gupta", "Vikram Palimar", "Anitha S", "Deepak Nayak M", "Varun Krishna B", "Chandni Gupta", "Anitha S", "Deepak Nayak M" ], "abstract": "Background Sudden and unexpected deaths are increasing drastically. The main cause of sudden death is cardiovascular disease, out of which coronary artery disease predominates forming 80% of the cases. Most of the time, detecting early changes in myocardial infarction during the autopsy is challenging since gross infarct changes do not appear until after 24 to 48 hours of myocardial ischemia injury. So, the aim of this study was to compare two test to detect early changes of Myocardial Infarction one by using Triphenyl Tetrazolium Chloride (TTC) staining of the myocardial tissue, during autopsy and other by histopathological examination.\n\nMethods The sample size of 60 hearts taken from all the sudden deaths cases brought to Mortuary with suspected cause of death due to cardiac origin. The heart was obtained from the deceased by standard post-mortem technique. Serial full-thickness transverse sections of the heart were taken at 2 cm intervals from the apex to the atrioventricular groove. All the serial slices of heart are taken for histochemical staining and TTC staining.\n\nResults In histopathological examination 34 hearts were diagnosed with myocardial infarction and 26 hearts reported non myocardial infarction. With TTC 40 hearts remained unstained suggestive of myocardial infarction and 20 hearts were stained suggestive of non-infarcted hearts. TTC staining in our study shows an accuracy of 88.33%.\n\nConclusion The result of this study shows that the Triphenyl Tetrazolium Chloride test, a histochemical staining technique of heart, is reliable approach for forensic pathologists to diagnose early myocardial infarction during the post-mortem examination.", "keywords": [ "TTC (Triphenyl Tetrazolium Chloride) staining", "histopathological examination", "Myocardial infarction", "Autopsy", "Cardiovascular diseases." ], "content": "Introduction\n\nGlobally, sudden, and unexpected deaths are increasing drastically. The main cause of sudden death is cardiovascular disease, out of which coronary artery disease predominates forming 80% of the cases. In 25% of the cases death occurred suddenly and in an unexpected manner within an hour of inception of clinical signs. Myocardial infarction acts as key psychological and legal consequences to both society and individual.1\n\nAs most deaths are abrupt, establishing a clinical diagnosis of Myocardial Infarction can be challenging. Postmortem examination is the ultimate chance to opine the cause of death in such cases. In any Medico-Legal Autopsy, the goal is to determine the cause of death. Most of the time, detecting early changes in myocardial infarction during the autopsy is challenging since gross infarct changes do not appear until after 24 to 48 hours of myocardial ischemia injury. Hence the determination of the early stage of myocardial ischemia is still a difficult task.2\n\nThe use of azo dyes to stain the heart helps to distinguish infarcted regions from normal myocardium. According to histochemical staining techniques, the membrane integrity of ischemic myocardial cell is lost, and enzymes are released into blood circulation, which results in reduction or complete absence of these enzymes in those regions. The rationale behind this study is that enzyme-depleted infarct myocardium will not be stained.3\n\nSo, the aim of this study was to compare two test to detect early changes of Myocardial Infarction one by using Triphenyl Tetrazolium Chloride (TTC) staining of the myocardial tissue, when there are no gross macroscopic changes, during autopsy and other by histopathological examination in the unstained regions of myocardium. This study also investigated how accurate histochemical Staining (TTC) of the heart is at detecting early myocardial infarction.\n\n\nMethods\n\nStudy type: Observation study.\n\nKasturba Medical College and Kasturba Hospital Institutional ethical clearance was taken before starting the study. Approval no with date: 705/2019, 17.9.2019.\n\nWe used the STROBE reporting guidelines for our study; a completed checklist is available under Reporting Guidelines.4\n\nStudy Period: The current research was carried out for two years.\n\nStudy location: Department of Forensic Medicine in association with the Department of Pathology.\n\nSample Size: 60 hearts.\n\nInclusion Criteria: Heart was taken out from all the sudden deaths cases brought to Mortuary with suspected cause of death due to cardiac origin and without any foul play and this was corroborated with the history stated in Karnataka police inquest 146 (i) and (ii).\n\nExclusion criteria: Death due to other reason like suicide, hanging and drowning etc were excluded from the study.\n\nEthics committee has given the exemption from taking consent from the relatives of the deceased since these cases are postmortem cases where the law gives the consent for autopsy and determination of cause of death. In the above cases the samples were taken from death due to cardiac origin so, the heart must be taken out to determine the cause of death. The consent given by the law for autopsy is valid. The heart was obtained from the deceased by standard post-mortem technique. The heart was thoroughly washed under running water and weight of the heart is noted. The entire heart was examined grossly for any pathological abnormalities, scarring due to old infarctions, areas of hyperemia, and external injuries. The serial cut sections of all three coronary arteries were made at the distance of 3 mm starting from the origin and throughout its course to look for the existence of blockage of its lumen by plaques or thrombus. The texture of coronaries was noted. Serialized full-thickness transverse slices of the heart were taken at 2 cm intervals from the apex to the atrioventricular groove. The sliced parts are inspected for fibrotic scarring and myocardial softening. The heart was dissected all along the line of blood flow (in flow and out flow procedure) and examined for atheromatous plaques on the surface of the origin of the aorta, narrowing of the coronary ostia, and the walls and valves. All the serial slices of heart are taken for histochemical staining.”\n\n“The following chemicals are needed which were procured from Durga, Laboratory, Mangalore, Karnataka:\n\n1) NaH2Po4 (Sodium Dihydrogen Phosphate) - phosphate buffer with low pH. (Molecular weight 120 g)\n\n2) Disodium hydrogen phosphate (Na2HPo4) - phosphate buffer with high pH (Molecular weight being 142 g)\n\n3) Distilled water. (1litre)\n\n4) Triphenyl Tetrazolium Chloride dye (TTC) (10grams)\n\nA 0.1 M solution was made by mixing 12 g of Sodium Dihydrogen phosphate in one litre of distilled water. Similarly, a 0.1 M solution was made by dissolving 14.2 g of sodium hydrogen phosphate in one litre of distilled water.5 The above two solutions were then mixed in different proportions to adjust the pH and is shown in Table 1.\n\nTo achieve a pH of 7.8“896 ml of 0.1M sodium Dihydrogen phosphate solution and 104 ml of 0.1 M Disodium hydrogen phosphate solution were combined. A pH meter was used to confirm the pH of the buffer solution. To prepare a 1% TTC solution, ten grams of Triphenyl Tetrazolium Chloride were mixed in 1 litre of above phosphate buffer solution with a pH of 7.8.5 Because TTC salt is photosensitive and inactivates when exposed to light, it was stored in an Amber colored bottle.\n\nThe multiple serial sections of the heart were rinsed under running water and mopped with clean cloth and positioned in a glass jar. To avoid improper staining technique precautions were taken for overlaying each heart slice and it was stained in a separate glass container. To prevent ambient oxygen from entering the heart sections, TTC solution was then filled in each container containing heart sections to a level of 2 cm above the heart section. To avoid light exposure, the container is then placed in a dark room. The incubation period of 30 minutes is carried out at room temperature. After incubation, heart sections were taken out from the solution and kept in 10 % formalin solution to end the procedure of staining and helps in fixation. Then it was examined for unstained areas in TTC positive cases for the myocardium suggestive of myocardial infarction. Normal myocardium appears brick red or bossy red because of lactate dehydrogenase activity in normal myocardial tissues. The infarcted area remained unstained with the TTC in the positive outcome. The infarct area, on the other hand, remains unstained or pale in color. Paraffin embedded histological microscopic examination was performed on both the stained and unstained areas. From unstained regions, the sections are subjected for histopathological examination and smeared with Hematoxylin-Eosin for microscopic diagnosis of acute myocardial infarction. The gross examination of heart results of TTC staining was then confirmed with histological findings.\n\nDescriptive analysis was done. Prevalence was also noted. Results were also analysed in percentage.\n\nUnderlying data is included in the Underlying Data section.6\n\n\nResults\n\nThe distribution of gender and age in the study sample is shown in Table 2. 71.7% of cases belong to the age group 31 to 60 years, 18.3% cases are in the age group more than 60 years. less than 30 years account for 10% of total cases. Majority of the cases belongs to males (91.7%) whereas female was only 8.3% of the cases. This indicates that death due to myocardial infarction occurs mostly in males.\n\n60 hearts were subjected for histopathological examination out of which 34 hearts were diagnosed with myocardial infarction and 26 hearts reported non myocardial infarction (Figure1).\n\nThe 60 hearts were stained with TTC out of which 40 hearts remained unstained suggestive of myocardial infarction and 20 hearts were stained suggestive of non-infarcted hearts (Figure 2 and 3).\n\nThe Diagnostic evaluation of TTC with respective of HPE is shown in Table 3. The 60 hearts were stained with TTC out of which 40 hearts remained unstained suggestive of myocardial infarction and the unstained areas was subjected for histopathology examination to correlate the microscopic changes of MI, 34 hearts were diagnosed MI and validates the sensitivity of TTC test is 100% and rest 20 hearts were stained with TTC revealed non-infarcted heart and histopathology examination revealed negative for MI.\n\nChanges in the histopathology of heart musculature based on time interval are shown in (Figure 4). The zone of an early infarct with waviness of the necrosed myocytes and few neutrophilic infiltrates is seen in less than 4 hours. Early infarct with coagulative necrosis of the cardiac myocytes is seen in 4-12 hours. The periphery of the infarct with early and organized granulation tissue formation is seen in 7-10 days. Fibrous scar with adjoining viable cardiac myocytes is seen in more than 6 weeks. The time interval of myocardial estimation was estimated by subjecting the heart for histopathological examination is shown in Table 4. 51.7 % showed early infarction, 1.7 % showed late infarction, 5 % showed old myocardial infarction and 41.7 % revealed no infarction. Distribution of time interval of Myocardial infarction in HPE is shown in Table 5. Distribution of time interval of Myocardial infarction in TTC is shown in Table 6.\n\nA. Zone of an early infarct with waviness of the necrosed myocytes and few neutrophilic infiltrates (< 4 hours) (H&E, x100). B. Early infarct with coagulative necrosis of the cardiac myocytes (4-12 hours) (H&E, x200). C. Periphery of the infarct with early granulation tissue formation (7-10 days) (H&E, x100). D. Periphery of the infarct with organized granulation tissue formation (7-10 days) (H&E, x200). E. Fibrous scar with adjoining viable cardiac myocytes (> 6 weeks) (H&E, x200).\n\nAccuracy of histopathological examination with TTC is shown in Table 7. It shows that TTC has an accuracy in diagnosing MI of 88.33%.\n\n* These values are dependent on disease prevalence.\n\n\nDiscussion\n\nAcute myocardial infarction causes sudden cardiac mortality in both men and women. In many cases, death takes place rapidly, and post-mortem examination reveals no evidence of acute myocardial infarction. It manifests itself with substantial morphological alterations that take 24 to 48 hours to manifest. A random sectioning of the heart for Histopathological investigation is typically used to diagnose myocardial infarction.7 Random cardiac sectioning for histopathological investigation is ineffective because it frequently misses myocardial infarction segment if it does not involve a larger infarct area.8 To get around the difficulty, a variety of procedures have been used by forensic pathologists to confirm the diagnosis of acute MI. The heart is stained with triphenyl Tetrazolium chloride for early myocardial infarction is quicker and faster approach to use in the autopsy room and it can yield a reasonable outcome after the procedure.9 Numerous animal studies used TTC staining for identifying acute myocardial infarction, but it might not be applicable to humans because of species-to-species differences.10\n\nThunderchief et al, in 18 cases of sudden death, TTC staining technique was carried out in deceased heart and MI was more prevalent in male population the TTC staining test as 91.66 % sensitivity and 83.33% specificity.11 M Shankar Bakkannavar et al, in 40 cases of sudden death, the TTC staining approach was conducted to do histochemical staining of the heart. The TTC staining approach has 100 % sensitivity and specificity, according to the study. Instead of phosphate buffer, hydrochloric acid is utilized to modify the pH of the solution in this study.12\n\nM Sivanandam conducted a study on 18 hearts taken from cases of sudden deaths with the cause of death thought to be of cardiac source. He found that TTC is a reliable method for the identification of early myocardial infarction during autopsy inspection with a diagnostic validity of 88.8%.13 Adegboyega et al, used TTC dye to stain 638 hearts from individuals with suspected or confirmed MI. They found that TTC is a valuable adjuvant in detecting acute myocardial ischemia for histochemical identification of grossly inapparent Myocardial infarction.14\n\nPadole TO conducted a study on 107 hearts. He divided the heart into 2 groups 1) Control group which include cases of death due to cardiac sources. 2) Negative control group which include cases of sudden natural death due to non-cardiac sources. He found that in Group 1 there were 15 cases out of them in 80% of cases TTC staining technique was positive while in 33.33% of cases H&E method was positive. Similarly in Group 2, there were 92 cases, out of them in 43.47% cases TTC staining technique was positive and in 22.82% of cases H & E method was positive. This suggest that the TTC technique is more superior and precise technique to determine the cause of death as MI.15 Abdulridha AA conducted a study in 75 cases of sudden natural death. And he exposed all the hearts to TTC solution staining and for histopathological evaluation for finding of a probable acute myocardial infarction. They found that after immersion in TTC solution, 45 heart samples exhibited macroscopic pale/yellow zones which signifies acute myocardial infarcts, while histopathological investigation of samples showed features of acute myocardial infarction in 62 samples. TTC stain was found to have 69.4% diagnostic sensitivity and 76.9% specificity in detection of acute myocardial infarction during autopsy.16 Our study also shows that the Triphenyl Tetrazolium Chloride test is a reliable approach for forensic pathologists to diagnose early myocardial infarction during the post-mortem examination. It shows that TTC has an accuracy in diagnosing MI of 88.33%.\n\nHowever, this approach has limitations in identifying the cause of death related to arrhythmic death when it occurs during the ischemia period before the onset of infarction. In such cases, the microscopic examination of cardiac tissue and conducting fibers will aid to arrive at the cause of death. However, the histochemical staining with TTC for detection of early stages of myocardial infarction can produce false positive and negative results. In numerous numbers of cases, a combination of histochemical method and histological evaluation aids in the diagnosis or exclusion of an apparent early myocardial infarction as the cause of death.\n\nLimitations of the study:\n\n1) The number of cases collected in this study is natural sudden death with history of cardiac illness.\n\n2) Putrefaction alters the enzymes levels after death in such circumstances when heart is stained with TTC it can cause false positive results.\n\nThe result of this study shows that the Triphenyl Tetrazolium Chloride test, a histochemical staining technique of heart, is reliable approach for forensic pathologists to diagnose early myocardial infarction during the post-mortem examination. Preparing 1 % TTC solution and adjustment of pH phosphate buffers is rather easy. The procedure is also economical, easy to perform in a post-mortem hall and does not necessitate the use of complicated equipment. The method not only aids forensic pathologists in diagnosing early myocardial infarction, but it also aids general pathologists in determining where the sectioning should be performed to diagnose early myocardial infarction.\n\nKasturba Medical College and Kasturba Hospital Institutional ethical clearance was taken before starting the study. Approval no with date: 705/2019, 17.9.2019.\n\nEthics committee has given the exemption from taking consent from the relatives of the deceased since these cases are postmortem cases where the law gives the consent for autopsy and determination of cause of death. In the above cases the samples were taken from death due to cardiac origin so, the heart must be taken out to determine the cause of death. The consent given by the law for autopsy is valid.", "appendix": "Data availability\n\nFigshare: COMPARISION OF HISTOPATHOLOGICAL AND TRIPHENYL TETRAZOLIUM CHLORIDE TEST IN DIAGNOSING MYOCARDIAL INFARCTION: AN AUTOPSY STUDY. Doi: https://doi.org/10.6084/m9.figshare.25910422.v1. 6\n\nThis project contains the following underlying data:\n\n- Research data.docx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nFigshare: We used STROBE checklist for “COMPARISION OF HISTOPATHOLOGICAL AND TRIPHENYL TETRAZOLIUM CHLORIDE TEST IN DIAGNOSING MYOCARDIAL INFARCTION: AN AUTOPSY STUDY”. DOI: https://doi.org/10.6084/m9.figshare.25910419.v1. 4\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nJoodi G, Maradey JA, Bogle B, et al.: coronary artery disease and Atherosclerotic Risk Factors in a Population-Based Study of Sudden Death. J. Gen. Intern. Med. 2020; 35(2): 531–537. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShnitka TK, Nachlas MM: Histochemical alterations in ischemic heart muscle and early myocardial infarction. Am. J. Pathol. 1963; 42(5): 507–527. PubMed Abstract\n\nBouchardy B, Manjo G: Histopathology of Early Myocardial Infarcts: A New Approach. Am. J. Pathol. 1974; 74(2): 301–330. PubMed Abstract\n\nGupta C: Comparison of histopathological and triphenyl tetrazolium chloride test in diagnosing myocardial infarction: an autopsy study. Strobe checklist. figshare. 2024. Publisher Full Text\n\nHu BJ, Chen YC, Zhu JZ: Immunohistochemical study of fibronectin for postmortem diagnosis of early myocardial infarction. Forensic Sci. Int. 1996; 78(3): 209–217. PubMed Abstract \| Publisher Full Text\n\nGupta C: Comparison of histopathological and triphenyl tetrazolium chloride test in diagnosing myocardial infarction: an autopsy study. result.xls. [Dataset]. figshare. 2024. Publisher Full Text\n\nDerias NW, Adams CW: NitroblueTetrazolium test: early gross detection of human myocardial infarcts. Br. J. Exp. Pathol. 1978; 59(3): 254–258. PubMed Abstract\n\nDoran JP, Howie AJ, Townend JN, et al.: Detection of myocardial infarction by immunohistological staining for C9 on formalin fixed, paraffin wax embedded sections. J. Clin. Pathol. 1996; 49(1): 34–37. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFeldman S, Glagov S, Wissler RW, et al.: Postmortem delineation of infarcted myocardium. Coronary perfusion with NitroblueTetrazolium. Arch. Pathol. Lab Med. 1976; 100(1): 55–58. PubMed Abstract\n\nFishbein MC, Meerbaum S, Ritz J, et al.: Early phase acute myocardial infarct size quantification: validation of the Triphenyl Tetrazolium chloride tissue enzyme staining technique. Am. Heart J. 1981; 101(5): 593–600. PubMed Abstract \| Publisher Full Text\n\nThunderchief K, Magendran J: Diagnosis of Early Myocardial Infarction by histochemical Staining of heart on Autopsy. Indian Journal of Forensic Medicine & Toxicology. 2018; 12(2): 65–70. Publisher Full Text\n\nShenoy RP, Bakkannavar S, Monappa V, et al.: Identification of Myocardial infarction in Human Autopsy Poluation Using TTC. J. Pharm. Biomed. Sci. 2010; 9: 1–4.\n\nSivanandam M: Diagnosis of early myocardial infarction by histochemical staining of heart on autopsy table. International Journal of Forensic Medicine. 2019; 10(3): 10–13.\n\nAdegboyega PA, Adesokan A, Haque AK, et al.: Sensitivity and specificity of triphenyl tetrazolium chloride in the gross diagnosis of acute myocardial infarcts. Arch. Pathol. Lab Med. 1997; 121(10): 1063–1068. PubMed Abstract\n\nPadole TO, Shrigiriwar MB, Durgawad LP: Study of autopsy diagnosis of early myocardial infarction (MI) by triphenyl tetrazolium chloride (TTC) and histopathology. Indian journal of forensic and community medicine. 2019; 6: 220–224.\n\nAbdulridha AA, Kareem SK: Post-mortem Gross Detection of Early Myocardial Infarction using Triphenyl Tetrazolium Chloride Test. Indian Journal of Forensic Medicine & Toxicology. 2021; 15(4): 642–648. Publisher Full Text" }	[ { "id": "323366", "date": "17 Sep 2024", "name": "Hareesh Gouda", "expertise": [ "Reviewer Expertise Forensic pathology", "Toxicology" ], "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\nTriphenyl Tetrazolium Chloride (TTC) staining method of the myocardial tissue is an important alternative or additional method to the routinely done Histo-pathological examination to find out early myocardial infarction during autopsy. Procedure of collection and staining of the tissue has been explained in detail in the manuscript. And, also the TTC method is feasible to perform. Statistical analysis supports the claim made by the author about significance and accuracy of TTC method in detecting early myocardial damage. In significant cases of sudden natural death, the laboratory investigations play a vital role in the determination of Cause of Death. Indexing of the manuscript will help in disseminating the information about and importance of TTC staining method.\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": "323365", "date": "18 Sep 2024", "name": "Mahabalesh Shetty", "expertise": [ "Reviewer Expertise FORENSIC PATHOLOGIST ." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article provides sufficient information about the methodology and analysis to enable others to allow replication.\nIn addition, the analysis, experimentation, and article construction are all good. Statistical study confirms the author's claim that TTC detects early myocardial injury with significance and accuracy. The laboratory tests are essential in determining the Cause of Death in major cases of sudden natural death. The manuscript will aid in spreading knowledge about the significance of the TTC staining technique.\nThe strength of the article: The study can be conducted in any mortuary, which is the article's strength. Any expensive equipment is not required. There is a clear explanation of how to prepare TTC solution, and getting the ingredients is simple as they are readily available in the market. Both pathologists and forensic pathologists will benefit from the method's ability to identify myocardial infarction early in the morgue and during sectioning.\n\nWeakness of the article: A limitation of the research was the small number of cases—just 60 hearts—in the study. Putrefaction\n\nalters the enzymes levels after death in such circumstances\n\nwhen heart is stained with TTC it can cause false positive results-This sentence is ambiguous . Putrefaction can be influenced by a wide range of variables and can start early under certain circumstances, which should have been highlighted. However, Reference number -12 in the article is, Shenoy et al\n\nBut the paper shows M Shankar Bakkannavar et al.\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/13-1050
https://f1000research.com/articles/13-358/v1	23 Apr 24	{ "type": "Research Article", "title": "In silico analysis of molecular mimicry between human aquaporin 3, Aspergillus fumigatus aquaporin and aquaporins from allergic sources", "authors": [ "Andrés Sánchez", "Yaquelin Padilla", "Adriana Lorduy", "Jorge Sanchez", "Marlon Munera", "Claudia Baena", "Carlos Bernal", "Juan Urrego", "Yaquelin Padilla", "Adriana Lorduy", "Jorge Sanchez", "Marlon Munera", "Claudia Baena", "Carlos Bernal", "Juan Urrego" ], "abstract": "Background Atopic dermatitis (AD) is a chronic inflammatory skin condition that has a significant impact on quality of life. The immune response and allergy symptoms in AD are triggered by the recognition of specific allergens by IgE antibodies. Cross-reactivity can lead to auto-IgE responses, potentially worsening AD symptoms. Our research aimed to enhance our understanding of allergenic sources, including A. fumigatus, and their role in AD. We focused on molecular mimicry between human AQP3 and A. fumigatus aquaporin.\n\nMethods In our in-silico analysis, we compared the amino acid sequences of human aquaporin 3 (AQP3) and A. fumigatus aquaporin with 25 aquaporins from various allergenic sources, sourced from the UniProt and NCBI databases. Phylogenetic relationship analysis and homology-based modeling were conducted. We identified conserved antigenic regions located within the 3D structures.\n\nResults The global identity levels among the studied aquaporins averaged 32.6%. One antigenic site exhibited a remarkable local region, with a conserved identity of 71.4%. We categorized the aquaporins into five monophyletic clades (A–E), with group B showing the highest identity (95%), including six mammalian aquaporins, including AQP3. When comparing A. fumigatus aquaporins, the highest identity was observed with Malassezia sympodialis at 35%. Both human and A. fumigatus aquaporins have three linear and three discontinuous epitopes.\n\nConclusions We identified potential linear and conformational epitopes of AQP3, indicating a possible molecular mimicry between humans and A. fumigatus aquaporins. This suggests autoreactivity and potential cross-reactivity, although further validation using in vitro and in vivo experiments is required.", "keywords": [ "Atopic dermatitis", "in silico", "molecular mimicry", "Aspergillus fumigatus", "aquaporins." ], "content": "Introduction\n\nAtopic dermatitis (AD) is a chronic and recurrent inflammatory skin disorder characterized by symptoms, such as eczema, erythema, persistent itching, and continuous skin damage. Over the past 30 years, the prevalence of AD has shown a notable rise, affecting between 5% and 20% of the child population and approximately 7% of adults in industrialized countries.1,2 The pathogenesis of AD is not completely clear; however, allergens can activate an intense Th2 response.3 Allergenic sources can vary depending on the population; for example, house dust mites are the main source of sensitization in tropical countries, whereas in Europe, pollen is the main trigger for allergies. In addition, depending on the environmental conditions, it is possible to be exposed to different species; therefore, epidemiological studies have shown variations in the frequencies of sensitization.4 The severity of the disease is influenced by several factors, including compromised skin barrier integrity due to reduced levels of filaggrins and ceramides as well as an elevated presence of water channels such as aquaporin, which drives the skin, making the patient more susceptible to atopic dermatitis.5 In general, allergy management includes allergen avoidance, pharmacotherapy, and immunotherapy, where only the latter has a beneficial effect that lasts for years and allows for a reduction in anti-inflammatory treatment.6–8\n\nIn addition to other environmental factors, the skin microbiome plays a pivotal role in AD development. Aspergillus fumigatus is an opportunistic pathogen in both poikilothermic and homeothermic animals. In humans, this pathogen has been associated with many pathologies such as invasive cutaneous aspergillosis, saprophytic lung colonization, and aspergillomas. In addition, A. fumigatus can induce IgE-mediated allergic diseases including rhinitis, allergic sinusitis, asthma, hypersensitivity pneumonitis, and AD.9,10 It has been characterized as an important allergenic source, and some allergens, including thioredoxins and cyclophilins, share homology with human proteins and are implicated in the autoreactive response in AD.\n\nDespite the identification of sensitization to extracts from allergenic sources, such as fungi, the recognition of specific IgE sensitization to allergens is necessary to carry out a better diagnosis and immunotherapy.11 However, this represents a challenge, because most fungal allergens cross-react with other taxonomically distant species, making it difficult to prove the clinical relevance of IgE reactivity against these allergens. In addition, it is important to consider that the evolution of AD varies greatly among patients with this disease and can be triggered by different factors. For example, in A. fumigatus and AD, studies suggest that specific IgE-mediated activation is induced not by multiple allergens and not by a few major allergens, as is the case with asthma and rhinitis.12,13 Another problem presented by the diagnosis of allergic diseases associated with A. fumigatus is the lack of standardized allergens for preparation of molecular component tests. Therefore, the discovery of new fungal allergens and the identification of the prevalence of these new components may provide an opportunity to learn more about the pathology of atopic dermatitis, improving the diagnosis and treatment of this disease.\n\nIn recent years, aquaporin has become a candidate protein for the study of skin and allergic diseases such as AD, given its role in epidermal hydration and the transport of various substances such as glycerol, salts, and exocrine fluids, favoring dry skin and allergen leakage.14 They have also been associated with various atopic diseases, such as glaucoma, cancer, epilepsy, obesity, epidermal hyperplasia, and neuromyelitis optical, among others. In AD, an increase in the expression of aquaporin 3 has been observed, which may be related to water loss and the severity of the disease, in contrast to healthy individuals who maintain a balanced expression of this protein in the basal, horny, and spinous layers.5 The consequences of aquaporin 3 (AQP3) overexpression extend beyond cutaneous water retention as it becomes a target for the exacerbated immune response in AD inflammation. This hypothesis suggests that it may be recognized by human autoantibodies, which, due to the persistence of self-protein exposure, contribute to increased inflammation and chronicity of AD.\n\nAdditionally, this protein is present in most organisms with a wide variety of isoforms and functions throughout the taxonomic framework. Recently, aquaporin has been identified in highly allergenic species, such as house dust mites. In a study carried out by Mao et al., describing the Dermatophagoides farinae proteome, two-dimensional immunoblotting was performed, which showed binding with IgE antibodies in a band that has the same isoelectric point and molecular weight of the aquaporin family, suggesting its possible role as an allergen. The objective of this study was to perform an in silico analysis to investigate the potential molecular mimicry between human aquaporins and those from A. fumigatus, as well as various allergenic sources.\n\n\nMethods\n\nFor the selection of aquaporins, the Aspergillus fumigatus (KEY82230) and human aquaporin 3 (Q92482) sequences of interest were compared with existing allergenic protein sequences using Allermatch (https://allermatch.org/), an allergen comparative server that allows allergen sequence alignment; therefore, those with high identity values were chosen. The sequence pool was obtained from the UniProt (https://www.uniprot.org/) and National Center for Biotechnology Information (NCBI) databases. Given the diversity in amino acid origins and lengths across the molecules under examination, we employed coverage and identity values to gauge the extent of their relationships. The identity and coverage values between the molecules used in this study were determined using the EMBOSS Needle (https://www.ebi.ac.uk/Tools/psa/emboss_needle/), specialized for performing paired alignments, and the web server from Praline (http://www.ibi.vu.nl/), which allowed for paired and multiple alignments. When carrying out the alignment, it was considered that the sequences were different and came from different sources; therefore, the alignment parameters were set to utilize the BLOSUM62 matrix, which primarily assesses evolutionary divergence, along with adjustments to the conditional scoring matrix.15,16\n\nTo construct the phylogenetic tree, we conducted a study using “Molecular Evolutionary Genetic Analysis” (MEGA) version 11 program. We employed the neighbor-joining (R) reconstruction method, supported by 100 bootstrap repetitions, to ensure the reliability and robustness of the analysis. Evolutionary distances were computed using the Poisson correction method, which uses a comparison matrix to identify sequence similarities. This matrix was created based on all amino acid sequences of the selected allergens, with all empty gaps removed (full deletions). Branch length summation (SBL) was presented as a measure of overall comparison and homologies, providing insights into the number of nodes, their positions, and the formation of the evolutionarily closest sequence “clusters.15,17\n\nAquaporin models were acquired from the Protein Data Bank and AlphaFold (Homo sapiens, Felis catus, Equus caballus, Bos taurus, Mus musculus, Malassezia sympodialis, Saccharomyces cerevisiae, Penicillium chrysogenum, Escherichia coli). For A. fumigatus and Cannis lupus familiaris aquaporin 3D structures were modeled by homology using the Swiss Model server (https://swissmodel.expasy.org/), and these models were refined in ModRefiner. (https://zhanggroup.org/ModRefiner/), an algorithm for the fine-grained refinement of protein structures at the atomic level.18\n\nModels were used to locate possible epitope regions predicted by the Ellipro server (http://tools.iedb.org/ellipro/), which was used to predict linear and discontinuous epitopes in the aquaporins of A. fumigatus, (AQP3), Cannis lupus familiaris, Felis catus, Equus caballus, Bos taurus, Mus musculus, Malassezia sympodialis, Saccharomyces cerevisiae, Penicillium chrysogenum and Escherichia coli. The potential epitopes were selected under the criteria of a score ≥ 7, as this value evaluates how exposed the residue is and the binding capacity of the epitope with the paratope.15,17\n\nThe characterization of the protein domains was carried out using the Interpro web server (https://www.ebi.ac.uk/interpro/); with this bioinformatic tool we obtained those domains with functional activity present in the protein sequence of the aquaporins studied. Subsequently, a review of the tertiary structure was carried out using the PyMOL program, which functioned as a molecular viewer, allowing identification of the location of the protein domains in the tertiary structure of each one.\n\n\nResults\n\nA total of 25 aquaporin sequences from different sources were selected and compared with the A. fumigatus aquaporin and human aquaporin (Table 1), the identity percentages of the aquaporins from different sources Vs A. fumigatus aquaporin and AQP3 are shown in Table 2. Notably, human AQP3 exhibited maximum values of identity and similarity of 95.5% and 98.6%, respectively, with aquaporin allergy sources. When comparing A. fumigatus aquaporins and AQP3, an identity of 32.6% and a similarity of 47.5% were observed, indicating a significant degree of homology between them. Regarding the AQP of A. fumigatus, the highest identity values were observed in the AQP of M. simpodialies (35%), followed by the mammalian species that also had greater identity with human AQP3, such as C. familiaris (33, 9%), Felis gatus (33, 10%), Mus musculus (33, 10%), and Bos taurus (32, 80%). The lowest identity and similarity results were obtained with apple (Malus domestica), with values of 0.2% and 0.9%, respectively.\n\nPhylogenetic relationships were determined using the neighbor-joining method, incorporating all 27 amino acid sequences. The resulting phylogenetic tree is presented in a circular format in Figure 1. Evolutionary distances were calculated using the Poisson correction method and were exprex\|ssed as the number of amino acid substitutions per site. The tree visually represents the grouping and arrangement of the analyzed aquaporins, facilitating a comprehensive comparison and revealing their interrelatedness.\n\nThe sums of branch lengths for an optimal tree totaled 12.5. The tree reveals the formation of five groups, designated as letters from A to E.\n\nBased on branch distances, the phylogenetic tree presented the formation of five distinct groups, denoted as letters A to E. Multiple sequence alignments were performed using the Praline server to further explore the similarities within each group. Group A consisted of fungal species with a shared identity of 39%, whereas group B comprised mammalian aquaporins with a high identity of 95%. Group C was composed of two mite species with an identity of 53%, group D encompassed plant sources with 40% identity, and group E included pathogens and mites with an identity of 31%. Notably, this analysis revealed significant allergen sources in tropical regions, such as D. pteronissinus and B. tropicalis.\n\nSpecies such as P. americana, S. aureus, E. coli, B. germanica, and M. domestica did not fit within any specific group because of their substantial branch distances from the root of clustering. Consequently, they were categorized into independent groups. Among the identified groups, those most closely related to the aquaporins of A. fumigatus and humans were found in groups A and B. Additionally, noteworthy proximity was observed between E. coli and D. farinae in group B.\n\nThe guidance provided by the phylogenetic tree and the results of paired alignments of the EMBOSS needle and aquaporin sequences were selected with a score ≥380. This threshold ensured an identity greater than 30% for each aquaporin sequence. Subsequently, paired alignments of the selected aquaporins against A. fumigatus were performed using Praline. This approach provides a more visually informative result, enabling a better understanding of the conserved regions in each sequence (Figure 2). By employing this screening process, we can identify more conserved sequences, thus increasing the likelihood of identifying regions that may contain potential epitopes.\n\nThe colors used in the alignment represent the level of sequence conservation, with blue indicating lower conservation and red indicating higher conservation. In the accompanying image, highlighted boxes denote the most conserved regions in the sequence, with each color (red, yellow, and green) representing the degree of conservation in descending order.\n\nUsing PyMOL, we visualized the structures of the 12 selected aquaporin proteins. They were represented in the form of “cartoons” and were color-coded using the spectrum. These models exhibit the characteristic structure of aquaporins, consisting of six alpha helices connected by extracellular and intracellular “loops” that form the water and substance transport channel (Figure 3).\n\nMoreover, certain structures display distinctive extensions in their amino acid chains, resulting in variations in their tertiary structures. Examples include S. cerevisiae and E. caballus. Consequently, during epitope exploration, most of these regions were exposed, leading to the exclusion of these sequences as potential allergenic sources due to the absence of epitopes in the conserved regions of interest. This minimized the likelihood of cross-reactivity.\n\nUsing the 3D structures of A. fumigatus, Homo sapiens, Dermatophagoides farinae, Canis lupus familiaris, Felis catus, Equus caballus, Bos taurus, Mus musculus, Malassezia Sympodialis, Saccharomyces cerevisiae, Penicillium chrysogenum, and Escherichia coli, we predicted the linear and discontinuous epitopes for each aquaporin (Table 3). We utilized PyMOL to analyze the identified linear and conformational epitopes, and thoroughly examined the distinct regions within each of these 3D structures. These epitopes are marked with the representative colors in the 3D structure. Although this characterization was performed for all 12 studied aquaporins, this work focused only on the epitopes found in the aquaporins of interest (A. fumigatus and AQP3), as shown in Figures 4 and 5.\n\nAll epitopes are color-coded on the surface models. Red, green, blue, and yellow correspond to the highest values, respectively.\n\nFurthermore, the PyMOL visualization program allowed us to calculate the root mean standard deviation (RMSD), which measures the structural similarity between two aligned objects, specifically the proteins of interest (Figure 6). The closer the RMSD value is to zero, the stronger the molecular similarity between the proteins. We obtained an RMSD value of 1.003, indicating a significant molecular similarity.\n\nIn addition, we identified epitopes that contained conserved sequences. In the case of fungal aquaporins, Linear Epitope (LE) 2 was identified, whereas in human aquaporins, LE 3 was found. Individual analysis revealed highly conserved fragments with more than four residues. For fungal aquaporins, the conserved residue is 80QVTLSKG86, whereas for human aquaporins, it is 45QVVLSRG52. The percentage of identity and similarity between these fragments was 71.4% and 85.7%, respectively, suggesting that these residues were highly likely to be antigenic patches (Figures 7 and 8).\n\n\nDiscussion\n\nNumerous diseases, including atopic dermatitis, bullous pemphigoid, chronic spontaneous urticaria, and multiple sclerosis, are associated with the presence of IgE autoantibodies. In the context of allergic responses intertwined with autoimmunity, researchers have categorized autoantigens that bind to IgE into three functional groups: 1) autoantigens that share sequence homology with environmental allergens, 2) autoantigens that lack sequence homology with known environmental allergens, and 3) chemically modified autoantigens. However, the identification of environmental allergens with homology to human proteins and their influence on the allergic response vary among these autoantigens, and their clinical significance often remains unclear.19\n\nAquaporin is a promising protein candidate for studying cutaneous, autoimmune, and allergic diseases, including atopic dermatitis (AD), because of its involvement in epidermal hydration and transportation of various substances such as glycerol, salts, and exocrine fluids. These functions contribute to skin dryness, which, in turn, facilitates the filtration of allergens.14 This protein is widely present in numerous organisms, and exhibits a diverse range of isoforms and functions across different taxonomic groups.\n\nRecent research has identified the presence of aquaporins in allergenic species such as dust mites.20 Mao et al. characterized the proteome of Dermatophagoides farinae, and two-dimensional immunoblotting revealed the binding of IgE antibodies to a band with the same isoelectric point and molecular weight as the aquaporin family, suggesting its potential role as an allergen.21\n\nOn the other hand, in a systematic review, a total of 32 articles were examined to assess the role of the microbiota in atopic dermatitis. The microbiome profile revealed substantial variation in bacterial diversity along with an increased presence of fungi. Notably, there was diversification and expansion of species belonging to the genus Aspergillus within the fungal group, whereas a reduction in the number of Malassezia spp. was observed. Research has also demonstrated that A. fumigatus is a prominent source of sensitization in patients with severe atopic dermatitis. Additionally, the presence of new allergens from this species is believed to have a significant impact on the severity of the condition.22\n\nThe comprehensive analysis of aquaporins provides guidance for considering other potential allergenic sources beyond the main aquaporins studied, namely AQP3 and A. fumigatus aquaporin. We conducted a comparative analysis of 25 aquaporin sequences from various sources, including A. fumigatus aquaporin and human aquaporin 3 (AQP3). A comparison between A. fumigatus aquaporin and AQP3 revealed an identity of 32.6% and similarity of 47.5%, indicating a relevant level of homology between these two proteins despite the evolutionary gap and taxonomic diversification among species. Notably, human AQP3 exhibited the maximum identity and similarity values of 95.5% and 98.6%, respectively. These high values could be attributed to the inclusion of aquaporins from mammalian allergen sources. Given that these species belong to a taxonomic group closer to humans, it is understandable that the APQs are more conserved.\n\nFive clades were constructed for the phylogenetic analysis. A and B showed the highest identity with A. fumigatus aquaporins and AQP3. The alignment results suggest that divergence among aquaporins primarily occurs in smaller species, while it remains conserved in mammals. In addition, the presence of aquaporin isoforms, each with special functions and locations, such as AQP3, indicates functional and phenotypic variability among different cell types within the same organism. However, despite this diversity, the identity of aquaporins within the clades revealed values higher than 30%, particularly in clade B (95%), indicating that if the protein is recognized by antibodies, potential cross-reactivity among these species can occur.\n\nOnly a limited number of studies have investigated the relationship between aquaporins derived from allergenic sources and their potential relevance in human diseases. Zhou et al. conducted an assessment using transcriptomics to identify potential AQPs in Blomia tropicalis using molecular cloning techniques, followed by a comparative analysis of identity among mite aquaporin sequences and human aquaporins. The author identified five putative AQP-coding sequences, known as BlotAQP1-5, which were indexed into all three subgroups: AQPs, aquaglyceroporins, and superAQPs. BlotAQP1, BlotAQP2, and BlotAQP5 were clustered with the aquaglyceroporins hAQP3, hAQP7, hAQP9, and hAQP10, with a common sequence consensus ‘N-G-NPSRD-PRL.’ The molecular weight and isoelectric point of these molecules were consistent with the findings reported by Mao et al. in their two-dimensional electrophoresis study.23 This observation suggests the potential recognition of aquaporins, specifically aquaglycerins such as AQP3, by IgE in patients with allergies. These results are consistent with those presented in our findings, where despite the evolutionary distance between species, there is an identity exceeding 30% and consensus sequences that may serve as potential antigenic patches.\n\nIn contrast, in regions where higher conservation was observed among the sequences, neither linear nor conformational epitopes were identified. This is attributed to the fact that these sequences are in the transmembrane region of the protein, which limits their accessibility to antibodies. However, despite the absence of epitopes, these conserved regions are interesting. During cell lysis caused by mechanical injury or microbial effects, these proteins can be linearly exposed, leading to the emergence of neoepitopes that can be recognized by IgE or phagocytic cells.24\n\nAlthough little is known about the role of AQP3 as an allergen or autoantigen, other aquaporins have been studied for their relevance as antigens in autoimmune diseases. Sagan et al. investigated the relevance of AQP4 as an autoantigen in neuromyelitis optica, recognized by T lymphocytes, in an animal model.25 This aquaporin is a water channel expressed in astrocytes in areas in contact with the blood-brain barrier, and 75% of patients with neuromyelitis have antibodies capable of recognizing AQP4. Therefore, the relevance of human aquaporins found in other tissues, such as AQP3 in the skin, can be considered as potential autoantigens and, through molecular mimicry, triggers relevant skin diseases such as atopic dermatitis.26 Evidence indicates cross-reactivity with aquaporins expressed by bacteria and mycobacteria, including Escherichia coli and Mycobacterium species, in relation to this specific autoantigen.27 This indicated that antibodies targeting aquaporins from A. fumigatus could potentially recognize and target this autoantigen. In a previous study, we found that AQP4 exhibits only one predicted cross-reactive epitope. It has been postulated that the recognition of a single epitope by autoantibodies could trigger an epitope spreading mechanism, leading to the involvement of additional autoantigens in the immune response.28 For both A. fumigatus aquaporins and AQP3, a total of four linear epitopes and three discontinuous epitopes were described. Structural superimposition highlighted a notable degree of similarity between the proteins, indicating that the epitopes could reside within the corresponding antigenic regions. This observation supports the idea of a potential molecular mimicry between these proteins.\n\nIt is important to acknowledge that our study has several limitations. In silico modeling and epitope prediction analyses are not definitive, and there may be variations in the actual structure compared with our proposed models. Nonetheless, bioinformatic analyses offer several advantages in directing research resources efficiently. They play a crucial role in the preliminary assessment of hypotheses and help to determine whether it is justified to proceed with in vitro or ex vivo experiments.\n\n\nConclusion\n\nDuring alignment of aquaporin sequences from A. fumigatus and AQP3, specific conserved epitopes were observed. Analysis revealed that the local sequence identity exceeded 70%, indicating molecular mimicry in these regions of both aquaporins. Further investigation of epitopes and domain identification revealed the most conserved region in transmembrane domains 12 and 14 of the respective aquaporins. This study represents a groundbreaking contribution to the exploration and analysis of aquaporin as a potential allergen and autoallergen in atopic dermatitis, as it is the first known study to focus on this subject. To confirm cross-reactivity, future in vitro studies are needed to demonstrate the IgE-binding capacity in these regions.\n\nBy acquiring knowledge regarding the sequences and structures of potential epitopes from different allergenic sources, we can modify and synthesize these molecules for future in vitro and in vivo studies. This not only expands the literature in the field of immunotherapy but also facilitates the diagnosis and treatment of autoimmune diseases such as atopic dermatitis. It is important to note that in silico tests optimize these studies by providing rapid results and circumventing the high costs associated with laboratory testing.", "appendix": "Data availability\n\nAllermatch (https://allermatch.org/)\n\nUniProt (https://www.uniprot.org/)\n\nNational Center for Biotechnology Information (NCBI) databases (https://www.ncbi.nlm.nih.gov/).\n\nThere is no further data associated with this article.\n\n\nAcknowledgements\n\nWe thank the participants coauthor and institutions for their support in collecting the information. A preprint version of this article can be found (https://www.techrxiv.org/doi/full/10.22541/au.169521327.76672515).\n\n\nReferences\n\nMúnera M, Sanchez A, Buendía E, et al.: Autoantigens in atopic dermatitis: The characterization of autoantigens and their diagnostic value. Translational Autoimmunity. Elsevier; 2023; pp. 37–48. 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PubMed Abstract \| Publisher Full Text\n\nMúnera M, Farak J, Pérez M, et al.: Prediction of molecular mimicry between antigens from Leishmania sp. and human: Implications for autoimmune response in systemic lupus erythematosus. Microb. Pathog. 2020 Nov 1; 148: 104444. PubMed Abstract \| Publisher Full Text\n\nSánchez A, Cardona R, Munera M, et al.: Identification of antigenic epitopes of thyroperoxidase, thyroglobulin and interleukin-24. Exploration of cross-reactivity with environmental allergens and possible role in urticaria and hypothyroidism. Immunol. Lett. 2020 Apr 1; 220: 71–78. PubMed Abstract \| Publisher Full Text\n\nWang LL, Yu LL, Zhou Y, et al.: Molecular Dynamics Simulations of Mite Aquaporin DerfAQP1 from the Dust Mite Dermatophagoides farinae (Acariformes: Pyroglyphidae). Biomed. Res. Int. 2020; 2020: 1–7. Publisher Full Text\n\nLe Mao J, Mayer CE, Peltre G, et al.: Mapping of Dermatophagoides farinae mite allergens by two-dimensional immunoblotting. J. Allergy Clin. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRen Z, Wang Y, Duan T, et al.: Cross-immunoreactivity between bacterial aquaporin-Z and human aquaporin-4: potential relevance to neuromyelitis optica. J. Immunol. 2012; 189(9): 4602–4611. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCossu D, Yokoyama K, Tomizawa Y, et al.: Altered humoral immunity to mycobacterial antigens in Japanese patients affected by inflammatory demyelinating diseases of the central nervous system. Sci. Rep. 2017; 7(1): 3179. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMunera M, Buendía E, Sanchez A, et al.: AQP4 as a vintage autoantigen: what do we know till now? Heliyon. 2022; 8: e12132. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "301819", "date": "13 Jul 2024", "name": "Celso Eduardo Olivier", "expertise": [ "Reviewer Expertise Allergy and Immunology", "non-IgE-mediated hypersensitivity" ], "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\nIt is a well-executed in-silico analysis comparing the amino acid sequences of human aquaporin 3 and Aspergillus fumigatus aquaporin with 25 aquaporins from various allergenic sources researched from the UniProt and NCBI databases. However, in \"background,\" \"introduction,\" and \"discussion,\" the authors assume that the IgE antibody exclusively mediates allergic diseases and hypersensitivities mechanisms. Recently, at least seven types (with several subtypes) of hypersensitivity reactions were postulated. I suggest the authors peruse and pay attention to the following references in order to refer appropriately to the subject: [ref 1, 2].\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?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "297871", "date": "24 Jul 2024", "name": "Elizabeth Garcia", "expertise": [ "Reviewer Expertise As an allergist and immunologist I have contributed to studies such as: “Potential contribution of Helicobacter pylori proteins in the pathogenesis of type 1 gastric neuroendocrine tumor and urticaria. In silico approach. PLOS ONE", "https://doi.org/10.1371/journal.pone.0281485. April 25", "2023" ], "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 present study offers key insights into the potential immunological cross-reactivity between human and fungal aquaporins.\nMajor highlights include the discovery of substantial sequence and structural homology, which indicates possible sites for cross-reactivity, and the epitope analysis that identified overlapping regions among proteins, suggesting mechanisms for immune response triggers. The allergenic potential of aquaporins from various sources extends the study's implications, indicating similar underlying mechanisms in various allergic conditions, specially atopic dermatitis. The innovative integration of bioinformatics tools provides a comprehensive view of molecular mimicry, setting a precedent for future studies. Clinically, identifying specific epitopes that contribute to cross-reactivity opens avenues for targeted therapies and diagnostic tools, enhancing allergy management and prevention. Minor highlights include the rigorous methodology and the clear direction for future research, emphasizing experimental validation to confirm findings. This study, with its broad potential impact, notably contributes to understanding molecular mimicry in allergic diseases and sets the stage for future investigations in the field.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [] } ]	1	https://f1000research.com/articles/13-358
https://f1000research.com/articles/12-1125/v1	11 Sep 23	{ "type": "Research Article", "title": "NCBench: providing an open, reproducible, transparent, adaptable, and continuous benchmark approach for DNA-sequencing-based variant calling", "authors": [ "Friederike Hanssen", "Gisela Gabernet", "Nicholas H. Smith", "Christian Mertes", "Avirup Guha Neogi", "Leon Brandhoff", "Anna Ossowski", "Janine Altmueller", "Kerstin Becker", "Andreas Petzold", "Marc Sturm", "Tyll Stöcker", "Sugirthan Sivalingam", "Fabian Brand", "Axel Schmidt", "Andreas Buness", "Alexander J. Probst", "Susanne Motameny", "Johannes Köster", "Friederike Hanssen", "Gisela Gabernet", "Nicholas H. Smith", "Christian Mertes", "Avirup Guha Neogi", "Leon Brandhoff", "Anna Ossowski", "Janine Altmueller", "Kerstin Becker", "Andreas Petzold", "Marc Sturm", "Tyll Stöcker", "Sugirthan Sivalingam", "Fabian Brand", "Axel Schmidt", "Andreas Buness", "Alexander J. Probst", "Susanne Motameny" ], "abstract": "We present the results of the human genomic small variant calling benchmarking initiative of the German Research Foundation (DFG) funded Next Generation Sequencing Competence Network (NGS-CN) and the German Human Genome-Phenome Archive (GHGA). In this effort, we developed NCBench, a continuous benchmarking platform for the evaluation of small genomic variant callsets in terms of recall, precision, and false positive/negative error patterns. NCBench is implemented as a continuously re-evaluated open-source repository.\nWe show that it is possible to entirely rely on public free infrastructure (Github, Github Actions, Zenodo) in combination with established open-source tools. NCBench is agnostic of the used dataset and can evaluate an arbitrary number of given callsets, while reporting the results in a visual and interactive way. We used NCBench to evaluate over 40 callsets generated by various variant calling pipelines available in the participating groups that were run on three exome datasets from different enrichment kits and at different coverages.\nWhile all pipelines achieve high overall quality, subtle systematic differences between callers and datasets exist and are made apparent by NCBench.These insights are useful to improve existing pipelines and develop new workflows. NCBench is meant to be open for the contribution of any given callset. Most importantly, for authors, it will enable the omission of repeated re-implementation of paper-specific variant calling benchmarks for the publication of new tools or pipelines, while readers will benefit from being able to (continuously) observe the performance of tools and pipelines at the time of reading instead of at the time of writing.", "keywords": [ "continuous", "benchmarking", "NGS", "variant calling" ], "content": "Introduction\n\nGenome sequencing is integral to many research and diagnostic procedures. For both pipeline and tool development, it is crucial to ensure that genomic variant calls are as accurate as possible. This can be achieved by testing tools and pipelines on datasets with a known set of true variants and correspondingly known sites where the genome is the same as the reference genome.\n\nSeveral such benchmark datasets have been published. The Genome in a Bottle Consortium (GIAB) has released truth variant sets based on common calls across three variant callers on 14 different sequencing technologies and library preparation methods on a well-characterized genome (HG001 or NA12878), as well as an Ashkenazim trio (HG002-4) and a Han Chinese trio (HG005-7).1,2 The Platinum variant catalog provides consensus calls of six variant calling pipelines across two different sequencing platforms on a family of four grandparents, two parents and 11 children including the NA12878 genome, allowing an extended inheritance-based validation.3 In an alternative approach, Li et al.4 generated a synthetic diploid from two complete hydatidiform mole (CHM) cell lines (CHM1 and CHM13), which are almost completely homozygous across the whole genome, such that the known variants in this set are phased (their haplotype of origin is known). The synthetic diploid benchmark dataset has the advantage of not relying on a consensus callset across several variant callers, which limit the benchmark set to high-confidence regions and lead to an overestimation of the true variant calling performance. Finally, the SEQC2/MAQC-IV initiative provides another extensive set of validated benchmarks, not only focussing on genomic DNA but also considering RNA-seq and single-cell sequencing.5\n\nSeveral publications have utilized the aforementioned gold-standard callsets to benchmark variant calling tools and pipelines.6–9 However, the continuous development of variant calling tools and pipelines means that static, one-time benchmarks based on a specific pipeline or tool version can quickly become outdated.\n\nIn contrast, benchmarking platforms aim at providing a way to facilitate continuous benchmarking by pipeline and tool developers and users. Examples of such platforms are OpenEBench [1] and Omnibenchmark [2]. Both platforms run on their own dedicated computing infrastructure and utilize specialized frameworks for results reporting and dataset uploading.\n\nIn this work, we want to propose a different approach for hosting a continuous benchmark, which was developed by the human genomic small variant calling benchmarking initiative of the NGS-CN [3] and GHGA [4]. We show that it is possible to build a benchmarking platform by entirely relying on public free infrastructure, namely GitHub [5], GitHub Actions [6], and Zenodo [7]. Using these technologies as a basis and extending upon best practices,10 we developed a comprehensive and reproducible benchmarking workflow for small genomic variants that is agnostic of the used dataset and can evaluate an arbitrary number of given callsets, while reporting the results in a visual and interactive way.\n\n\nMethods\n\nWe have sequenced the NA12878 sample from the genome in a bottle (GIAB) [8] project with two exome sequencing kits at varying average coverages. The genomic DNA from NA12878 was obtained from the NIGMS Human Genetic Cell Repository at the Coriell Institute for Medical Research. The Agilent Human All Exon V7 kit was used to yield a dataset with 182 million paired-end reads sequenced on an Illumina Nova Seq 6000 (211 bp mean insert size and 2 × 101 bp read length). We used random subsampling to derive two datasets from this that were used in the benchmarking, one with 37.5 million and one with 100 million paired-end reads. The Twist Human Comprehensive Exome (Twist Bioscience, San Francisco, CA, USA) sequencing kit was used according to the manufacturer’s protocol to generate 200 million paired-end reads on an Illumina NovaSeq 6000 (291 bp mean insert size and 2 × 101 bp read length). The raw reads of the two subsampled Agilent and Twist exome datasets are available via Zenodo.11,12\n\nTo analyze the quality of the callsets yielded by each pipeline on the given datasets, we have developed a generic, reproducible Snakemake13 workflow, which conducts all steps from downloading benchmark data, preprocessing, comparison with a known ground truth, plotting, and automatic deployment of the required software stacks via Snakemake’s Conda/Mamba [9] integration: https://github.com/snakemake-workflows/dna-seq-benchmark. The workflow comes with predefined standard datasets like CHM-eval and GIAB, but can be additionally configured to use any other DNA-seq-based benchmark dataset consisting of a known set of true variants, confident regions where the reported true variants are considered to be complete (i.e. every non-variant position is assumed to homozygously have the reference allele), raw read data (as FASTQ files), and (optionally) sequenced target regions (e.g. in case of exome sequencing). The workflow uses BWA-mem,14 Picard tools [10] and Mosdepth15 for calculating the read coverage across the genome. We use Bedtools16 to limit the known true variants to the confident regions provided by the respective truth publishers and to stratify variants by coverage (see below). For interactive exploration of the results, we use Datavzrd [11] and Vega-Lite.17 The matching of calls and true variants in a haplotype-aware manner happens via RTG-tools vcfeval [12]. To ensure a fair and correct comparison of the different evaluated callsets, several key points had to be considered, which we outline below.\n\nRead depth stratification and selection of regions of interest. The available read depth can naturally affect both the precision and recall of a pipeline. Hence, the read depth characteristics of a benchmark dataset can have an impact on the derived precision and recall, which can limit the generalizability of obtained results. In order to avoid this effect, we decided to stratify recall and precision by read depth. For any benchmark dataset, this workflow generates a quantized set of regions with low (0-9), medium (10-30), and high (>30) read depth using Mosdepth, while considering only reads with mapping quality (MAPQ) ≥60. Notably, this means that, for example, regions in the low read depth category have either only few reads or a lot of reads with uncertain alignments (high mapping uncertainty). We intersect these regions with the confidence regions of the benchmark sample (e.g. as provided by GIAB) using Bedtools. If the given dataset was generated using a capturing approach (e.g. exome sequencing) we further restrict the regions to the captured loci according to the manufacturer. Afterwards, any given callset is split into three subsets with low, medium, and high coverage using Bedtools.\n\nSeparating genotyping from calling performance At decreasing read depth or increasing mapping uncertainty, one can expect a callset to yield a decreasing recall: with less evidence, it will become harder to find variants. This is true for both genotyping (i.e. requiring that the variant caller detects the correct genotype) as well as when just requiring the variant allele to be correctly recognized without considering whether the variant is predicted to be homo- or heterozygous (i.e. plain variant calling without genotyping). In contrast, a variant callset’s precision should ideally remain constant and unaffected by a decrease in read depth or increase in mapping uncertainty, if the method manages to correctly report the increasing uncertainty with decreasing depth or increasing mapping uncertainty. The latter behavior differs between measuring a callset’s genotyping or calling precision. In order to make these differences visible, we therefore decided to calculate precision and recall for both genotyping and calling separately.\n\nVariant atomization Some variant callers report complex variants as replacements of longer alleles (i.e., both the reported reference and the alternative allele are longer than one base, e.g. ACCGCGT>ACGCT). While this is in general a good idea (e.g. in order to be able to properly assess the combined impact on proteins), we found this to introduce problems with vcfeval’s internal comparison approach. This resulted in spurious false positives and false negatives in callsets having such variants. Similar to the approach implemented in the hap.py pipeline [13], we solved this issue by introducing a normalization step prior to vcfeval into our analysis workflow, which uses Bcftools18 to normalize variants, in a way that indels are moved to their left-most possible location, and complex replacements are split into their atomic components—i.e. single nucleotide variants (SNVs), insertions or deletions (indels)—while removing exact duplicates resulting from the atomization.\n\nReporting For reporting results, we employ Datavzrd to create interactive tabular reports for recall and precision, as well as individual false positive and false negative variants. Datavzrd enables us to just provide the required data as TSV or CSV files combined with a configuration file that defines the rendering of each column. For the latter, one can choose from automatic link-outs, heatmap plots, tick plots, bar plots, or custom complex Vega-Lite plots (which can also be used to define alternative visualizations for an entire table view). For the former, we report a table containing for each callset and each read depth category (low, medium, high) precision and recall (while ignoring whether the genotype was predicted correctly), the underlying counts of true positives (TP), false positives (FP), and false negatives (FN), as well as the fraction of wrongly predicted genotypes. It is important to note that it cannot be excluded that the same variant in the truthset is predicted multiple times by a callset, e.g. as part of several complex replacements (see “Variant atomization” above). We therefore report two TP counts TPquery (number of TPs in the callset with the same matching variant from the truth potentially counted multiple times) and TPtruth (number of variants in the truth set that occur in the callset, each variant counted once, regardless how often it occurs in the callset), with TPquery≥TPtruth. Following the established definitions, precision is then calculated as\n\nAn example can be seen in Figure 2. For reporting of individual FP and FN variants, we provide a Datavzrd table view for each that has one row per variant and a column for each callset. In order to visualize systematic patterns arising from the properties of callsets (e.g., using the same variant detection or mapping method), any kind of property can be annotated as a so-called “label” when registering a callset for evaluation with the pipeline. The labels are displayed using a categorical color coding in the header of the table views. Moreover, we perform a Chi2test for the association of the FP or FN pattern of each variant against the different labels in order to detect systematic effects. The variant/label combinations for which this test yields a significant result are then displayed in a separate table view for each type of label. These allow, for example, to spot variants that only occur when callsets use a particular variant caller. Thereby, significance is determined by controlling the false discovery rate over the p-values of the Chi2test using the Benjamini-Yekuteli procedure, as the variants could be both positively (e.g., being on the same haplotype) or negatively (e.g., being on different haplotypes) correlated. In order to combine the results with data provenance information we include the Datavzrd views into a Snakemake report [14], which automatically provides a menu structure for navigation between views, association with used parameters, code, and software versions as well as runtime statistics.\n\nA central goal of the project was not to conduct a single benchmark and just publish the results, but rather provide a resource for continuous repeated and always up-to-date benchmarking, that is moreover open to any kind of contribution (callsets and code improvements, among others) from outside collaborators. In order to achieve this, we have developed the following approach (see Figure 1 for an illustration). We deployed the benchmarking workflow [15] as a module [16] into another Snakemake workflow that in addition has the ability to download callsets from Zenodo, using Snakemake’s Zenodo integration [17]. Then, we deployed this workflow into the GitHub repository [18] and configured GitHub Actions [19] to continuously rerun the workflow upon every commit on the main branch or any pull request [20]. In order to ensure that the workflow runs sufficiently fast (GitHub Actions offers only limited runtime and resources per job), we have precomputed benchmark dataset-specific central intermediate results (read depth and confidence derived stratification regions) that are computationally intensive to obtain, and deployed them along with the workflow code into the GitHub repository.\n\nUpon pull requests or pushes, a GitHub Actions workflow is triggered. This downloads data, runs the Snakemake-based evaluation pipeline, creates the Snakemake report and uploads it as an artifact. If the workflow is triggered on the main branch, its finalization triggers a second Github Actions workflow that builds and deploys the homepage at https://ncbench.github.io.\n\nUpon each completion of the evaluation pipeline, a Snakemake report [21] is generated. In case of pull requests (e.g., contributing a feature or a new callset), the report is uploaded as a GitHub artifact [22], for inspection by the pull request author and the reviewer. In the case of the main branch, we utilize GitHub Actions to trigger the execution of a secondary GitHub Action pipeline in a repository that hosts the NCBench homepage [23]. This pipeline fetches the latest report artifact associated with the main branch and deploys it to the homepage. This way, the most recent results are automatically accessible on the homepage.\n\n\nResults\n\nThe always up-to-date results of the benchmark can be found and interactively explored under https://ncbench.github.io. At the time of writing, the benchmark consists of more than 40 callsets on three different benchmark datasets, the two NA12878 samples described in the Datasets section and CHM-eval.19 The callsets span various pipelines, read mapping, variant detection, and genotyping approaches.\n\nSince the central idea of this project is to provide a continuous, standardized and open benchmark platform for DNA-seq, we strived to make the contribution of new callsets as straightforward as possible. The benchmark repository [24] shows the steps needed to perform variant calling on the supported datasets and describes how to pre-check the resulting callset locally. Once a contributor is convinced that the callset is ready for publication, we provide instructions for uploading the result to Zenodo and providing it via a pull request for continuous evaluation in the future.\n\nFigure 2 shows an exemplary screenshot of the interactive tabular precision/recall display (see Pipeline section). This illustrates the importance of stratifying by read depth/coverage categories (see Pipeline). This is in contrast to the commonly seen practice, where GIAB and other benchmark datasets are evaluated on the entire set of variants, without stratification. While this generates realistic estimates for the prediction quality of a variant calling pipeline overall, the provided information is less generalizable, since a new dataset might have different read depth characteristics. Further, it tells little about the expected quality at an individual location, which might differ as well from the global characteristics.\n\nEach three rows display precision and recall together with underlying numbers and wrongly predicted genotypes stratified by read depth/coverage category. In the interactive report, callset/pipeline names would occur on the left. Here, they have been removed since results can be expected to change over time. For actual results please see the always up-to-date interactive report at https://ncbench.github.io.\n\n\nDiscussion and conclusions\n\nSo far, variant calling benchmark studies were often published once, in a single or multiple manuscripts that can only represent a snapshot at the time of writing. This holds both for studies evaluating multiple tools or pipelines, as well as the evaluations around newly published individual tools.\n\nFor continuous benchmarking, platforms like Omnibenchmark [25] or OpenEBench20 are available. Both platforms run on their own dedicated computing infrastructure and utilize specialized frameworks for results reporting and dataset uploading.\n\nIn this work, we demonstrate that a continuous benchmarking platform can be set up without the need for dedicated computing infrastructure, and instead entirely relying on freely available and widely used resources.\n\n• By basing the benchmark of DNA-seq variant calling pipelines on a public GitHub repository for code, configuration and result storage, GitHub Actions for analysis execution, and callsets hosted by Zenodo, we allow rapid and straightforward contributions by anybody used to these services.\n\n• By implementing the analysis with Snakemake and Conda/Mamba, we decouple the analysis code and the reporting of results from the hosting platform: instead of relying on GitHub Actions, the benchmark analysis can easily be conducted locally, or on a different platform without any modifications of the code.\n\n• By generating interactive visual presentations of the results with Datavzrd, we (a) allow for a modern and versatile exploration of results and comparisons between different methods and pipelines, and (b) to a large degree enable contributions and modifications to the way the data is presented by simply editing YAML based configuration files.\n\n• By encapsulating all results in a Snakemake report that is portable and can be viewed and provided without any web service, we enable people to freely choose between relying on the online version of the report and providing snapshot-like versions of the report in their publications.\n\nIn the future, we will further extend upon this approach. For example, we will add a whole genome dataset of the NA12878 sample sequenced on an Illumina NovaSeq 6000 of ca. 400 million paired-end reads (mean insert size 473 and 2 × 151 bp reads length). Further, we will extend the pipeline to include the evaluation of structural and somatic variants and corresponding datasets. Finally, as the implemented comparison workflow is in principle agnostic to the considered species, we will evaluate the inclusion of benchmark datasets from non-human organisms. Particularly for natural microbial populations, whose species mostly exist as multiple genotypes in one ecosystem, variant calling can be a complex process21 and often not completely resolved due to the lack of complete and closed reference genomes from mono-cultures.\n\nWe hope that our approach will attract contributors beyond our initiative. Ideally, the combination of being continuous, simple to use, reproducible, and easy to integrate outside of the primary web service will change the way DNA-seq benchmarking is handled in the future. Instead of requiring every new tool and benchmark study manuscript to conduct its own analysis for precision and recall on public resources like GIAB or CHM-eval as well as comparison with other tools or pipelines, authors can rather include their callsets in our benchmark. In turn, readers will be able to always see the performance of a tool in the context of the state of the art at the time of reading, instead of at the time of writing.\n\n\nAuthor contributions\n\nFH, GG, SM, and JK have written the manuscript. JK has implemented the benchmarking pipeline. SM has coordinated the benchmarking initiative. SM and KB provided the FastQ files for the Agilent Human All Exon v7 kit. MS has created the callset data for the megSAP pipeline and edited the manuscript. TS has created the callset data for the WEScropbio pipeline. LB has created the callset data for the Cologne exome pipeline. AGN analyzed callset data. JA and AO have sequenced the NA12878 sample at the WGGC Cologne. AJP contributed to discussion and manuscript writing. AP has provided advice on and reviewed the benchmark design. SS has created the call sets for the NVIDIA Parabricks pipeline. AB and FB have supported the NVIDIA Parabricks pipeline. AS has coordinated the sequencing of NA12878 at the NGS Core Facility Bonn. NHS and CM have created the callset data for the GHGA pipeline. GG and FH have created the callset data for the sarek pipeline. All authors have read and approved the manuscript.", "appendix": "Data availability\n\nTwist Whole-Exome Sequencing Dataset of NA12878: https://doi.org/10.5281/zenodo.7075040\n\nAgilent v7 exomes of NA12878: https://doi.org/10.5281/zenodo.6513788\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nCHM-eval public benchmark data: https://github.com/lh3/CHM-eval\n\nNCBench code available from: https://github.com/ncbench/ncbench-workflow\n\nArchived NCBench code available from: https://doi.org/10.5281/zenodo.8268264\n\n\nAcknowledgements\n\nWe thank the NIST and the GIAB working group for their extraordinarily useful work. We thank the authors of CHM-eval for their amazing work and making their data publicly available. 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GigaScience. February 2021; 10(2): giab008. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLi H, Bloom JM, Farjoun Y, et al.: A synthetic-diploid benchmark for accurate variant-calling evaluation. Nat. Methods. August 2018; 15(8): 595–597. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCapella-Gutierrez S, de la Iglesia D , Haas J, et al.: Lessons Learned: Recommendations for Establishing Critical Periodic Scientific Benchmarking, August 2017. Pages: 181677 Section: New Results.\n\nOlm MR, Crits-Christoph A, Bouma-Gregson K, et al.: instrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains. Nat. Biotechnol. Jun 2021; 39: 727–736. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\n\nFootnotes\n\n1 https://openebench.bsc.es\n\n2 https://omnibenchmark.org\n\n3 https://ngs-kn.de/\n\n4 https://www.ghga.de\n\n5 https://github.com\n\n6 https://github.com/features/actions\n\n7 https://zenodo.org\n\n8 https://www.nist.gov/programs-projects/genome-bottle\n\n9 https://github.com/mamba-org/mamba\n\n10 https://broadinstitute.github.io/picard\n\n11 https://github.com/datavzrd/datavzrd\n\n12 https://github.com/RealTimeGenomics/rtg-tools\n\n13 https://github.com/Illumina/hap.py\n\n14 https://snakemake.readthedocs.io/en/stable/snakefiles/reporting.html\n\n15 https://github.com/snakemake-workflows/dna-seq-benchmark\n\n16 https://snakemake.readthedocs.io/en/stable/snakefiles/modularization.html#snakefiles-modules\n\n17 https://snakemake.readthedocs.io/en/stable/snakefiles/remote_files.html#zenodo\n\n18 https://github.com/ncbench/ncbench-workflow\n\n19 https://github.com/features/actions\n\n20 https://docs.github.com/en/pull-requests/collaborating-with-pull-requests\n\n21 https://snakemake.readthedocs.io/en/stable/snakefiles/reporting.html\n\n22 https://docs.github.com/en/actions/using-workflows/storing-workflow-data-as-artifacts\n\n23 https://ncbench.github.io\n\n24 https://github.com/ncbench/ncbench-workflow\n\n25 https://omnibenchmark.org" }	[ { "id": "207163", "date": "03 Oct 2023", "name": "Justin M. Zook", "expertise": [ "Reviewer Expertise Variant calling and benchmarking" ], "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 open benchmarking platform for variant calling, with exome and genome variant call sets for two different benchmarks as examples. As the authors note, the ability to continuously benchmark variant calls is currently lacking, as existing efforts like precisionFDA Truth Challenges only reflect a point in time. Ongoing benchmarking should be very useful as both variant calling methods and benchmark sets evolve. I only have a few suggestions for clarifying the data and methods used.\nAre FNs and FPs counted to include genotype errors, as is the default in vcfeval and hap.py, or do both exclude genotype errors from their counts, which is implied but not explicit in the text\n\nI saw the bed file for Agilent but not for twist in zenodo\n\nWhat were the benchmark versions used for GIAB and CHM-eval?\n\nDo the authors expect that adding new versions of the benchmarks would be straightforward as GIAB develops these?\n\nvcfeval generally should be able to compare different representations of the same variant, as long as they exactly match, even if they are not atomized. The only reason I have found this not to work is if the variant caller gets part of a haplotype wrong or the genotype wrong, in which case the whole haplotype is called wrong even if most of the variants in the region are correct. Is this what the authors’ encountered? If so, it might be good to clarify this. A potential problem with left shifting variants is that occasionally this will cause a change in the haplotype, e.g., if an indel in a homopolymer is shifted past a SNV on the same haplotype, though is relatively rare.\n\nThe number of variants for CHM-eval is lower than I'd expect. Did the authors restrict to one chromosome?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "12302", "date": "12 Sep 2024", "name": "Johannes Köster", "role": "Author Response", "response": "We thank the reviewer for the positive and comprehensive assessment of our work. Please find a point by point response below. 1. TP, FP, and FN are calculated by ignoring the genotype (just requiring presence or absense of the variant in the callset). Instead, we decided to provide a genotype mismatch rate, that shows how many of the genotypes in the true positives are wrongly predicted compared to the truth. The definition of this approach can be found under \"Methods\"/\"Evaluation pipleine\"/\"Reporting\". 2. The twist bed file can be found publicly under https://www.twistbioscience.com/sites/default/files/resources/2022-01/Twist_Comprehensive_Exome_Covered_Targets_hg38.bed. This is also the file that is used by the ncbench workflow when assessing the twist dataset. The user does not need the bedfile, since ncbench takes care of restricting any input vcf to calls within the regions specified by the bed file. 3. The pipeline currently uses v4.2.1 of the NA12878 ground truth from GIAB and v0.5 of CHM-eval. We have extended the online report to include this information in the description above each result table. 4. Indeed, bumping benchmark versions is very easy. One simply has to update the respective entries here: https://github.com/snakemake-workflows/dna-seq-benchmark/blob/main/workflow/resources/presets.yaml#L51. We have added a section about the maintenance to the end of the \"Evaluation pipeline\" section in the manuscript. 5. We have extended and clarified our statement (see section \"variant atomization\"). Indeed, it is like suggested: the whole replacement is considered as one, leading to missing additional true positives within the replacement. 6. There was no restriction to a particular chromosome involved. To be sure, we have checked the number of variants in the CHM-eval ground truth and can confirm that it matches the reported TP and FN in the reported tables. Note that (a) the precision/recall tables are split into SNVs and indels, such that both numbers have to be considered. (b) we filter the truth to the reported confidence regions. (c) we stratify by coverage in a way that each kept variant has to be entirely inside of the respective coverage region. In total, this explains that the benchmark runs on fewer variants than one would consider otherwise." } ] }, { "id": "239648", "date": "28 Feb 2024", "name": "Kez Cleal", "expertise": [ "Reviewer Expertise Cancer genomics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article presents NCBench, a benchmarking platform for evaluating SNVs and indel variant calls from various gold-standard benchmark sets. NCBench makes use of public, free infrastructure like GitHub Actions and Zenodo to facilitate continuous, open-source benchmarking, which is a neat idea. NCBench supports evaluation across several datasets, emphasizing adaptability and reproducibility, and effectively addresses the need for ongoing evaluation in genomic research. However, the true utility of NCBench will depend on its adoption by the wider research community which itself could be enhanced by making the platform as easy to use as possible. On this front, I think NCBench could be improved by addressing the following:\n\nThe documentation of how to implement/run NCBench and how to contribute a new callset was pretty limited. A more detailed guide aimed at newcomers, detailing the pipeline steps, inputs and outputs, and ways to configure NCBench for other datasets would help with adoption. It is unclear how to run NCBench locally on a custom benchmark dataset. The pipeline supports uploading a vcf to zenodo and running via github actions. Ideally, NCBench should be possible to run locally to test different tool parameters, or for developers to experiment with new tool implementations. This pattern would make NCBench more useful for general bioinformatics workflows. If this pattern is supported, it should be documented more clearly. The output tables on github.io are useful, but I think they could be improved. For example, it would be useful if rows could be sorted by a column, ability to hide certain columns. There doesn’t appear to be a way to download the results of the benchmarking run, or if there is, I didn’t find it. It would be nice to be able to download results in a table, in order to make custom tables for publication, for example. Stratifying benchmark results by coverage categories is a nice idea. However, I think it would still be useful to include an ‘any’ category (any mapq), to provide a dataset summary. Additionally, if there was a way to filter some of the rows, this would be very useful, for example selecting only mapq 1-10 category. Tables should probably include an F1 score, this would be useful to rank callsets, although which metric used (tp_query or tp_truth) should be evident. The dark-blue colour of some of the cells on the tables makes the text very hard to read (see ‘Show as plot’ subpage). Some of the table numbers needs to be rounded, for example clicking on ‘Show as plot’, the numbers are rounded to >12dp. In some of the tables, the text doesn’t fit on the page (fn variant page, the top row of labels stretched off the page using Safari).\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": "12303", "date": "12 Sep 2024", "name": "Johannes Köster", "role": "Author Response", "response": "We thank the reviewer for the thorough assessment and positive feedback. A point by point response can be found below. 1. We have added a more detailed documentation on what is required to add new callsets and configure the pipeline to the readme: https://github.com/ncbench/ncbench-workflow 2. Indeed, we agree that running the workflow locally makes a lot of sense. We have extended the instructions in the readme accordingly. 3. This is a good suggestion. We have extended Datavzrd accordingly, such that the updated report now supports this functionality, as can be seen in the updated version under https://ncbench.github.io. 4. Indeed, offering a download is a good suggestion. We have now activated the corresponding feature in datavzrd, such that each table can be downloaded by opening the \"hamburger\" menu at the top right and clicking the \"download as excel\" entry. 5. Filtering of the rows (e.g. by coverage) has already been possible, using the magnifying glass icon on top of the respective column. We explicitly decided against providing a non-stratified precision and recall, because we believe that this is usually misleading, since it does only reflect the composition of easy and harder to call sites in the benchmark sample, rather than the actual performance of the evaluated pipelines/tools. Therefore, any reported such measures would be of very limited generalizability. 6. We appreciate the suggestion. Instead of F1-score, we have now added the F*-measure, which provides an monotone transformation of F1 that adds additional interpretability, by being an estimate of the probability that a random variant taken from the union of prediction and truth is predicted correctly. We have extended the \"Reporting\" section in the manuscript accordingly. 7. We have updated the reports to a newer version of Datavzrd, in which the \"show as plot\" functionality has been replaced by a functionality that prints the current page as an SVG file that looks exactly the same as the display in the browser, thereby avoiding the low-contrast issue in the previous version. 8. See answer for point 7, the newer Datavzrd solves this issue. 9. Indeed, the FN and FP tables are sometimes wider than a usual screen resolution. However, they are scrollable horizontally. We have extended Datavzrd to show a visual indicator that points the user to the scrollbar if that is the case." } ] } ]	1	https://f1000research.com/articles/12-1125
https://f1000research.com/articles/13-356/v1	23 Apr 24	{ "type": "Software Tool Article", "title": "{MFPP(R). An R package for matrix-based flexible project planning", "authors": [ "Zsolt Tibor Kosztyán", "Aamir Saghir", "Aamir Saghir" ], "abstract": "Project planning and scheduling are essential parts of project management. While project planning and scheduling tools are already available to support traditional project management approaches, flexible project management, such as agile, extreme and hybrid project planning, are only somewhat supported by computer algorithms. To the best of our knowledge, no existing R package for project planning and scheduling can support project planning and scheduling for flexible projects. In this paper, the goal is to fill this gap; to this end, the R package mfpp for matrix-based flexible project planning/scheduling is introduced and described. This package includes a comprehensive set of tools for project managers to schedule both traditional and flexible project plans. The use of the package is illustrated through examples.", "keywords": [ "flexible projects", "matrix-based planning", "scheduling" ], "content": "Motivation and significance\n\nNetwork planning methods are the main methods used to plan and schedule projects.1 Among traditional methods, (a) the critical path method2 and the metra potential method (or the precedence diagramming method)3 can only handle tasks of a given duration, while (b) the program (or project) evaluation and review technique can handle stochastic activity durations,4 while the graphical evaluation and review techniques can also handle decision events.5 However, these methods were developed for the scheduling of traditional projects; consequently, for product or software development projects, they can be used only partially or not at all because these network planning methods cannot handle the specifics of these projects.6,7 One of the main shortcomings of traditional network-based project planning techniques is that either the logic structure is static or a limited number of possible alternatives for completion sequences must be predefined.8 In contrast, in cases of flexible project management, such as agile, extreme, or hybrid project management, the structure is not predefined. Instead, the real structure is determined by the decision of the customer-developer. In such flexible approaches, task completion is prioritized by customers’ claims. From the technological perspective, parallel and sequential completion can be allowed to handle flexible dependencies.9 In addition, structural flexibility, which is a requirement in both the agile and extreme project management approaches is necessary to handle new non-planned tasks, while the hybrid project management approach requires that the features of the traditional, agile, and, if necessary, extreme project management approaches be combined.10\n\nIn terms of scheduling, traditional time cost trade-off problems11,12 support the traditional project management approach (TPMa) and are generally not or only minimally considered in the agile project management approach (APMa). In addition, other flexible approaches, such as the extreme project management approach (XPMa), allow for new unplanned tasks in response to changes in customer desires. The approach that has most recently begun to be explored is the hybrid project management approach (HPMa), which has a flexible structure but allows the application of traditional trade-off methods and/or multimode task completion (or alternative technologies). These approaches are detailed from the scheduling perspective in Table 1.13\n\nFlexible project planning approaches, such as APMa, HPMa, and XPMa, are very popular in software project planning. However, these approaches still lack algorithmic and software support for project scheduling. In answer to this,13 developed the mfpp package in MATLAB (RRID:SCR_001622) to fill this gap, but this software is not free.\n\nTo the best of our knowledge, there are three packages in R (RRID:SCR_001905) available for project management. Among these, PlotPrjNetworks14 and plan15 are packages that create a Gantt diagram for the visualization of the project structure, while ProjectManagement16 is a useful tool for managing a project from its development to its execution based on the TPMa. However, an R package that can manage a project based on APMa, XPMa, and HPMa is lacking. This is an important gap to fill for project planning/scheduling practitioners. Such a package would be useful to the user community because it could be integrated with other tools developed in R, meaning that it could be easily modified to suit the specific needs of each user and could be wrapped into a graphical interface.\n\nMatrix-based techniques can be used instead of traditional network-based project planning techniques to model all types of changes in customer demands (such as new tasks and/or new subprojects) and parameters (such as time/cost/resource demands). Such methods have been successfully used to model agile projects.17 The basis of a flexible matrix-based project planning method is a project domain matrix (PDM)17 with unplanned tasks. The PDM is a matrix n+u by m+u, where n is the number of planned tasks, u is the number of unplanned tasks, m=n+w(3+ρ), w is the number of possible completion modes and ρ is the number of possible resources. The PDM has five domains. The first domain is the logic domain (LD), which is described as an n(+u) by n(+u) project expert matrix (PEM),18 a kind of numerical dependency structure matrix (NDSM).19 The other domains are the time domain (TD) and the quality domain (QD), which are n(+u) by w submatrices, and the resource domain (RD), which is an n(+u) by w⋅ρ submatrix. The LD and QD contain real values between 0 and 1, while the TD, cost domain (CD), and RD contain nonnegative real values.\n\nIn this paper, we introduce mfpp, a new R package that provides the necessary tools to manage both traditional and flexible project plans. This package can be used to build matrix-based projects and calculate their demands, generate a flexible project network, and perform uncertainty analysis. The proposed package is an R version of the MATLAB functions (i.e. MATLAB functions from a previous study done by the author13).\n\n\nSoftware description\n\nmfpp is a new R package for project managers to schedule traditional and flexible project plans. In addition, it compares different project management approaches with respect to their scheduling performance and risk mitigation to help decision makers choose the best project management approach. Additionally, in the case of analyzing project libraries, scholars can analyze the various project management approaches and their resilience to risks. This package uses existing R packages Matrix,20 pracma11 and Rfast21 to generate the PDM and calculate project values; the packages genalg22 and nsga2R23 for optimized resource allocation; and the ggplot224 and igraph25 to plot the project structure. The mfpp package is available for download from CRAN and Code Ocean.26 A summary of the functions incorporated into this package is provided in Table 2.\n\nTwo project databases are directly included in this package. The first is the27 database, which contains 240 simulated projects, all of which include four completion modes. This database can be used to test algorithms for the multimode resource-constrained project scheduling problem (MM-RC-PSP). The second database is provided by28 and contains 125 real projects. These projects each include only one completion mode, but they also include the cost demands of the tasks.\n\n\nUse cases\n\nThe implementation of the R package mfpp is demonstrated using (i) simulated project structures and (ii) a real-life data set of project structures. The package must be loaded at the beginning of the session by typing the following:\n\nBuild fixed matrix-based projects and calculate their demands to support TPMa\n\nWe start with the tpt function of the mfpp package to build fixed matrix-based projects and calculate their demands to support the TPMa. The LD specifies the structure of the project. The LD is an N-by-N (sub)matrix, where N is the number of tasks. The diagonal values represent the task priorities for task completion, where a value of 1 indicates a mandatory task, and a lower value indicates a supplementary task. The off-diagonal values represent the dependencies between tasks, where a value of 1 indicates a fixed dependency, and lower values indicate flexible dependencies between tasks. In the case of an acyclic graph, the LD can be reordered as an upper triangular matrix, which is assumed in this package. In the following example, a binary logic plan with one completion mode is specified. The tpt function determines the duration of the project (total project time, TPT) by calculating the task schedule, including time specifications such as the early start time (EST), early finish time (EFT), late start time (LST), late finish time (LFT), scheduled start time (SST), and scheduled finish time (SFT) for each task. The plot function draws a Gantt chart for ESTs, LSTs, or SSTs. The LD and TD must be specified as necessary and sufficient arguments for this function. The output of the function is as follows:\n\n\n\n\n\n\n\nThe plot of the schedule can be drawn as follows (Figure 1(a)):\n\nThe total project resources based on two resources domains (R1 and R2) extracted through mfpp package.\n\nNext, we illustrate the use of the tpc, tpq and tpr functions to calculate the total project cost, the total project quality, and the total project resources. The tpr function calculates the maximal resource demands and can specify a resource graph. In these functions, the CD and QD are N-by-w matrices, while the RD is an N-by-(w∗r) matrix, where r is the number of resources. The CD is mandatory, while the QD and RD are optional matrices. The necessary arguments of these functions are the LD, CD, quality parameters (q), QD with completion modes, and RD. The output of this function for the given example is as follows:\n\nA plot of the total project resources can be called with the additional argument “res.graph=TRUe”, and the output is seen in Figure 1(b).\n\nOptimizing resource allocation is a combinatorial (NP-hard) problem; therefore, a metaheuristic method is used to minimize the maximum resource demands. In this case, the nondominated sorting genetic algorithm II (NSGA-II) method is used to minimize the maximum resource demands. In the case of multiple resources, a Pareto-optimal solution is found. The paretores function can help a project engineer determine the minimal resource demands while maintaining a specified project duration. The output of this function is as shown in Figure 1(c) and in Figure 1(d).\n\nThe set of domains, namely, the set of the LD, TD and CD and optionally the QD and RD specifies the PDM. A logic network can be constructed using this set of domains as follows:\n\n\n\nGeneration of a flexible project network to support the HPMa\n\nThe HPMa combines the features of the TPMa (multiple completion modes), APMa (a flexible project structure), and XPMa (new, unplanned tasks). Project plans to support the HPMa can also be designed using the proposed mfpp package. For this purpose, the first function that is needed is generatepdm. The input arguments of this function are the number of tasks (N); the flexibility factor (ff); the connectivity factor (cf); the maximum values of the TD (mTD), CD (mCD), RD (mRD); the number of modes (w); the number of resources (nR); the number of possible extra tasks (nW); and the scale and QD of the project scenario. The function returns either the PDM only or a PDM list that also contains the number of completion modes (w) and the number of resources (Rs). Consider a flexible plan with 4 planned tasks, 2 completion modes and 2 resources. The project schedule generated using the HPMa is as follows:\n\n\n\n\n\nThe main components of flexible project structures can be drawn using the plot function of the mfpp package, where these structures are defined as follows.\n\nMinimal structure: This structure contains only mandatory tasks and fixed dependencies. It provides the lowest quality, cost, and time demands when the lowest quality, lowest cost, and shortest completion modes are specified for each task.\n\nMaximal structure: This structure contains both mandatory and supplementary tasks as well as both fixed and flexible dependencies. It provides the highest quality, greatest cost, and greatest time demands when the highest quality, greatest cost, and longest completion modes are specified for each task.\n\nMinimax structure: This structure contains only mandatory tasks but both fixed and flexible dependencies. It can provide the lowest resource demands.\n\nMaximin structure: This structure contains both mandatory and supplementary tasks, but only fixed dependencies. It can provide the greatest resource demands.\n\nMost-likely structure: Rounding the values of the LD yields the most-likely structure. The plot of the PDM structure is as follows in Figure 2(a):\n\nThe plot of the constraints is as follows in Figure 2(b). The most likely/most desired structures of the project for multiple modes can be determined using mfpp. The input and output are as follows:\n\n\n\n\n\nThe optimal schedules for different completion modes can be calculated using the paretores and truncpdm functions by dropping excluded tasks and their demands. The optimal resource allocation can be calculated once the completion modes are selected for each task as follows:\n\nFigure 2(b) shows the Gantt chart and Figure 2(c) shows the resource graph of the optimal schedule for the completion mode 1.\n\n\nProject structure database\n\nIn this section, Boctor’s publicly available27 simulation database is used to demonstrate the applicability of mfpp. This database contains a collection of 240 projects with different names, numbers of completion modes (w) and numbers of resources (Rs). The details of the database can be retrieved using the summary function. However, we are using project number 2 within this database, whose details are as follows: name of project= boct10, w= 4 and Rs= 2. Any other project could also be used to obtain the optimal project structure and resources.\n\nFigure 3(a) shows the original project structure and Figure 3(b) shows the minimal/maximal constraints of a project 2 from the Ref. 27’s project collection.\n\nThe Gantt charts of the selected project of completion mode 1 is constructed by extracting the PDM and TD as follows (see Figure 4(a)):\n\nFor project risk analysis, one of the most frequently used methods is sensitivity analysis. The sensitivity analysis procedure in mfpp consists of three phases. Phase 1: Effects of uncertainty Phase 2: Effects of shocks Phase 3: Structural changes.\n\nNotably, phase 1 and phase 2 involve varying the demands, while phase 3 varies the project structure. Phase 1 affects the entire project, while phase 2 and phase 3 affect only selected demands or structural elements. These phases can be performed in a sequential or parallel manner. The phases follow the logic of.10 The mfpp package also analyzes the effects of uncertainty on the scheduled project using the phase1 and phase2 functions. Furthermore, the existing project plan can be modified to a flexible structure using the phase3 function of the developed package. These functions are also demonstrated on the selected project from the database.\n\nEffects of uncertainty\n\nPhase 1 serves to analyze the uncertainty of the estimation. Modified demands are generated in the interval of ([o+a,o+b]), where o is the original value. The random generator can be specified to follow either a uniform (=default) or beta distribution. These modifications are applied to all kinds of demands for each task (compare Figures 4(a), 4(b), and 4(c)).\n\nEffects of shocks\n\nPhase 2 simulates shock effects, by increasing p percent of the task demands by a factor of up to s. Phase 2 investigates the effects of shocks, in which not all task demands are changed but the changes are significant (see Figure 4(b)).\n\nStructural changes\n\nIn phase 3, P percent of the nodes (i.e., tasks) or arcs (i.e., dependencies)are selected to change the corresponding scores by up to the maximal change effect S. Phase 3 is simulates changes in customer priorities and technological changes. In the case of S<0, the plan will be more flexible, whereas S>0 increases priorities and can produce new dependencies (compare Figures 5(a), 5(b), and 5(c)).\n\n\nConclusions\n\nThe mfpp package has been developed to provide users with a comprehensive set of functions that can be used to create matrix-based models for both traditional and flexible project management approaches. The presented package also compares different project management approaches with respect to their scheduling performance and risk mitigation to help decision-makers choose the best project management approach. Moreover, in the case of analyzing project libraries, scholars can analyze various project management approaches and their resilience to risks. The mfpp tool can help decision-makers determine which approaches are best for their requirements.", "appendix": "Data availability\n\nThe mfpp package includes matrix-based version of publically available Boctor’s 27 and Batseliers’s 28 project datesets.\n\n\nReferences\n\nGuide A: Project management body of knowledge (pmbok guide). Project Management Institute. 2001; 11: 7–8.\n\nKelley JE Jr, Walker MR; Critical-path planning and scheduling. Papers presented at the December 1-3, 1959, eastern joint IRE-AIEE-ACM computer conference. 1959; pp. 160–173.\n\nFondahl JW: A non-computer approach to the critical path method for the construction industry, Technical report. Transportation Research Boards; 1962.\n\nRay D, Fulkerson.: Expected critical path lengths in pert networks. Oper. Res. 1962; 10(6): 808–817. Publisher Full Text\n\nAlan A, Pritsker B: Gert-graphical evaluation and review technique. Technical report. National Aeronautics and Space Administration; 1966.\n\nThamhain HJ; Can we manage agile in traditional project environments? Proceedings of PICMET’14 Conference: Portland International Center for Management of Engineering and Technology; Infrastructure and Service Integration, IEEE. 2014; pp. 2497–2505.\n\nAhimbisibwe A, Daellenbach U, Cavana RY: Empirical comparison of traditional plan-based and agile methodologies: Critical success factors for outsourced software development projects from vendors’ perspective. J. Enterp. Inf. Manag. 2017; 30(3): 400–453. Publisher Full Text\n\nServranckx T, Vanhoucke M: Strategies for project scheduling with alternative subgraphs under uncertainty: similar and dissimilar sets of schedules. Eur. J. Oper. Res. 2019; 279(1): 38–53. Publisher Full Text\n\nSekitoleko N, Evbota F, Knauss E, et al.: Technical dependency challenges in large-scale agile software development. Agile Processes in Software Engineering and Extreme Programming: 15th International Conference, XP 2014, Rome, Italy, May 26-30, 2014. Proceedings 15, Springer. 2014; pp. 46–61. Publisher Full Text\n\nKosztyán ZT, Jakab R, Novák G, et al.: Survive it! survival analysis of it project planning approaches. Oper. Res. Perspect. 2020; 7: 100170. Publisher Full Text\n\nBorchers HW, Borchers MHW: Package ‘pracma’.2022.\n\nFranco-Duran DM, de la Garza JM : Review of resource-constrained scheduling algorithms. J. Constr. Eng. Manag. 2019; 145(11): 03119006. Publisher Full Text\n\nKosztyán ZT: Mfpp: Matrix-based flexible project planning. SoftwareX. 2022; 17: 100973. Publisher Full Text\n\nMunoz JC: Plotprjnetworks: Useful networking tools for project management.2015. Reference Source\n\nKelley D: plan: Tools for project planning.2018. Reference Source\n\nGonçalves-Dosantos JC, García-Jurado I, Costa J: Projectmanagement: an r package for managing projects. R J. 2020; 12: 419–436. Publisher Full Text\n\nKosztyán ZT: Exact algorithm for matrix-based project planning problems. Expert Syst. Appl. 2015; 42(9): 4460–4473. Publisher Full Text\n\nKosztyán ZT, Kiss J, et al.: Pem–a new matrix method for supporting the logic planning ofsoftware development projects. DSM 2010: Proceedings of the 12th International DSM Conference, Cambridge, UK, 22.-23.07. 2010. 2010; pp. 97–110.\n\nTang D, Zhu R, Tang J, et al.: Product design knowledge management based on design structure matrix. Adv. Eng. Inform. 2010; 24(2): 159–166. Publisher Full Text\n\nBates D, Maechler M, Maechler MM: Package ‘matrix’. R package version. 2017; pp. 1–2.\n\nPapadakis M, Tsagris M, Dimitriadis M, et al.: LinkingTo Rcpp, and TRUE LazyData. Package ‘rfast’.2021. (accessed 6.1. 21). Reference Source\n\nWillighagen E, Ballings M, Ballings MM: Package ‘genalg’. Published online. 2015; 825.\n\nTsou C-SV, Lee MM-CA: Package ‘nsga2r’. Citeseer studies. 2013.\n\nWickham H, Chang W, Wickham MH: Package ‘ggplot2’. Create elegant data visualisations using the grammar of graphics. Version. 2016; 2(1): 1–189.\n\nCsardi MG: Package ‘igraph’.2013; 3(09): 2013. Last accessed.\n\nKosztyán ZT, Saghir A: The mfpp package in r. 07 2023. Reference Source\n\nBoctor FF: Heuristics for scheduling projects with resource restrictions and several resource-duration modes. Int. J. Prod. Res. 1993; 31(11): 2547–2558. Publisher Full Text\n\nBatselier J, Vanhoucke M: Construction and evaluation framework for a real-life project database. Int. J. Proj. Manag. 2015; 33(3): 697–710. Publisher Full Text" }	[ { "id": "292539", "date": "29 Jun 2024", "name": "Shan Jayasinghe", "expertise": [ "Reviewer Expertise project management", "technology adoption", "teaching and learning" ], "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 so much for the opportunity to review the paper.\nThe paper makes the assertion that \"while project planning and scheduling tools are already available to support traditional project management approaches, flexible project management, such as agile, extreme, and hybrid project planning, are only somewhat supported by computer algorithms.\" This claim is not accurate. Advanced project management tools such as JIRA, Asana, and Monday.com are backed by highly sophisticated algorithms and are widely used to manage adaptable projects across numerous multinational companies.\nThe first paragraph does a satisfactory job of comparing traditional and adaptive project management approaches. However, the research gap of the paper is inadequately defined and needs to be more clearly established to strengthen the overall argument and relevance of the study.\nApart from the above concern, the following improvements must be made to enhance the paper to a indexable level.\n-Include more recent studies and compare the proposed method with state-of-the-art project management tools. -Organize the methodology section with clear headings and subheadings. Use more diagrams to illustrate key concepts. -Conduct a more detailed performance evaluation of the mfpp package, comparing it with existing tools and discussing its scalability. -Include a discussion on the limitations of the proposed approach and potential areas for future work. -Ensure all references are complete and correctly formatted. -Ensure the manuscript is written in clear, concise language with appropriate academic tone and style. Revise for grammar, punctuation, and clarity to enhance readability and coherence.\n\nIs the rationale for developing the new software tool clearly explained? No\n\nIs the description of the software tool technically sound? No\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? No\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? No\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? No", "responses": [ { "c_id": "12249", "date": "12 Sep 2024", "name": "Zsolt Tibor Kosztyán", "role": "Author Response", "response": "Dear Reviewer Dr. Shan Jayasinghe, Thank you for the valuable remarks. According to your remarks and those of the other reviewers, we have thoroughly revised the manuscript. We hope that the academic standards of the revised manuscript have been improved to meet your expectations. All the remarks were addressed. The responses are shown in red. In the revised manuscript, insertions are shown in blue, and deletions are shown in red. Sincerely, The Authors Thank you so much for the opportunity to review the paper. Q.1: The paper makes the assertion that \"while project planning and scheduling tools are already available to support traditional project management approaches, flexible project management, such as agile, extreme, and hybrid project planning, are only somewhat supported by computer algorithms.\" This claim is not accurate. Advanced project management tools such as JIRA, Asana, and Monday.com are backed by highly sophisticated algorithms and are widely used to manage adaptable projects across numerous multinational companies. Response: Thank you for the comment. We have clarified this statement both in the abstract and the introduction. You are correct. There are a few commercial project management software programs, such as JIRA, Asana, Wrike, Teamwork, Zoho Projects, and Monday.com, which support flexible project planning. The target audience of these software tools is professional users and not scholars. These software applications are not freely available. The algorithms for managing flexible projects in these applications are hidden from users. In general, they provide only the most likely solution and not all possible solutions, in contrast to the algorithms used here (Kosztyán-Szalkai 2018). Only with an implementation such as ours can the smallest and largest resource requirements and the smallest and largest possible time and cost demands be estimated. In addition, in R software, there is no package that is backed by sophisticated algorithms and can handle flexible project management, such as agile, extreme, or hybrid project planning. Q.2: The first paragraph does a satisfactory job of comparing traditional and adaptive project management approaches. However, the research gap of the paper is inadequately defined and needs to be more clearly established to strengthen the overall argument and relevance of the study. Response: The first part of the paper has been fully revised. The contributions of the paper are stated. The background of the method has been made more detailed. Q.3: Include more recent studies and compare the proposed method with state-of-the-art project management tools. Response: The revised paper refers to more recent studies and details the benefits of the proposed package. Q.4:Organize the methodology section with clear headings and subheadings. Use more diagrams to illustrate key concepts. Response: The methodology section “Brief summary of matrix-based project planning and risk analysis” has been added and revised. The new figure (Figure 1) compares the matrix-based plans of different types of project management approaches. Q.5: Conduct a more detailed performance evaluation of the mfpp package, comparing it with existing tools and discussing its scalability. Response: A new Experiments section has been provided to show the performance and possibilities of the mfpp packages. The main purpose of this section was to show researchers that such tests can be performed by presenting the proposed package. During the generation process, we also examined projects containing 500 activities. We allowed several execution methods and considered several types of resource requirements. The results are included in the Experiments section. Since existing tools cannot calculate all possible alternatives, the possible time reduction cannot be calculated. Q.6: Include a discussion on the limitations of the proposed approach and potential areas for future work. Response: In the revised paper, a new Limitations and Future Works section has been added. Q.7:Ensure all references are complete and correctly formatted. Response: Thank you. This has been corrected. Q.8: Ensure the manuscript is written in clear, concise language with appropriate academic tone and style. Revise for grammar, punctuation, and clarity to enhance readability and coherence. Response: Thank you. The final version was proofread by American Journal Experts. References: Kosztyán, Z. T., & Szalkai, I. (2018). Hybrid time-quality-cost trade-off problems. Operations Research Perspectives, 5, 306-318." } ] }, { "id": "284888", "date": "04 Jul 2024", "name": "Ágoston Kolos", "expertise": [ "Reviewer Expertise Operations 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\nI expect that the methodology used is not well known to R users in general. Therefore, a short but precise mathematical formulation of the models (TPMa, APMa, XPMa, HPMa) is needed. I think the authors can do this in the appendix or provide an external article or link. In the latter case, it is important to give a reference to another source where the description of the model is clear and precise (not a general overview).\nThere are typos in the user manual (\"Sumulated project database\")\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? 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? Yes", "responses": [ { "c_id": "12250", "date": "12 Sep 2024", "name": "Zsolt Tibor Kosztyán", "role": "Author Response", "response": "Dear Dr. Ágoston Kolos, Thank you for the valuable remarks. According to your and the other reviewers’ remarks, we have thoroughly revised the manuscript. All the remarks were addressed. The responses are shown in red. In the revised manuscript, insertions are shown in blue, and deletions are shown in red. Sincerely, The Authors Q.1: I expect that the methodology used is not well known to R users in general. Therefore, a short but precise mathematical formulation of the models (TPMa, APMa, XPMa, HPMa) is needed. I think the authors can do this in the appendix or provide an external article or link. In the latter case, it is important to give a reference to another source where the description of the model is clear and precise (not a general overview). Response: The paper has been fully revised. We present the problem and refer to a publication containing the details." } ] }, { "id": "292541", "date": "05 Jul 2024", "name": "Bálint Blaskovics", "expertise": [ "Reviewer Expertise project 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 paper addresses an interesting topic, namely how can we apply R for project planning for non-predictive projects as well. The authors start with a brief and focused introduction, however, I would welcome a bit more about time plotting techniques, and non-predictive project management approaches to provide the necessary background for the next sections (or at least about the different, non-deterministic scheduling techniques). I would also welcome more about either the research gap or the comparison of the different software packages in order to evaluate the results more. I would also dedicate a bit more time to how this can be beneficial for future studies and/or the use case of programming in this way. All in all, I think it is a well-based, scientific paper, however, I would welcome a bit more changes in order to be consumable for everyone who is interested in the topic.\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? Partly\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Partly", "responses": [ { "c_id": "12251", "date": "12 Sep 2024", "name": "Zsolt Tibor Kosztyán", "role": "Author Response", "response": "Dear Dr. Bálint Blaskovics, Thank you for the valuable remarks. According to your remarks and those of the other reviewers, we have thoroughly revised the manuscript. All the remarks were addressed. The responses are shown in red. In the revised manuscript, insertions are shown in blue, and deletions are shown in red. Sincerely, The Authors Q.1: The paper addresses an interesting topic, namely how can we apply R for project planning for non-predictive projects as well. The authors start with a brief and focused introduction, however, I would welcome a bit more about time plotting techniques, and non-predictive project management approaches to provide the necessary background for the next sections (or at least about the different, non-deterministic scheduling techniques). I would also welcome more about either the research gap or the comparison of the different software packages in order to evaluate the results more. I would also dedicate a bit more time to how this can be beneficial for future studies and/or the use case of programming in this way. All in all, I think it is a well-based, scientific paper, however, I would welcome a bit more changes in order to be consumable for everyone who is interested in the topic. Response: The paper has been fully revised. Nondeterministic techniques are briefly introduced. However, most nondeterministic scheduling techniques, such as discrete, continuous and stochastic time‒cost tradeoff methods, where more than one technology is used or where the exact time demands are not known, can be considered flexible; therefore, they are detailed along with the other considered types of flexibility. Our contributions to the literature are stated, and the limitations of our methods are also specified." } ] } ]	1	https://f1000research.com/articles/13-356
https://f1000research.com/articles/13-484/v1	17 May 24	{ "type": "Brief Report", "title": "Current status of immunodeficient mouse models as substitutes to reduce cat and dog use in heartworm preclinical research", "authors": [ "Jessica L Dagley", "Utami DiCosty", "Crystal Fricks", "Abdelmoneim Mansour", "Scott McCall", "John W McCall", "Mark J Taylor", "Joseph D Turner", "Jessica L Dagley", "Utami DiCosty", "Crystal Fricks", "Abdelmoneim Mansour", "Scott McCall", "John W McCall", "Mark J Taylor" ], "abstract": "Chemoprophylactic prevention of veterinary heartworm disease in companion animals, caused by the vector-borne nematode parasite Dirofilaria immitis, is a multi-billion-dollar global market. Experimental use of cats and dogs in preclinical heartworm drug testing is increasing due to evolving drug-resistance to frontline macrocyclic lactones and renewed investment in alternative preventative drug research. We and others recently published data demonstrating proof-of-concept of utilising lymphopenic severe-combined immunodeficient (SCID) or Recombination Activating Gene (RAG)2 deficient mice with additional knockout of the IL-2/7 receptor gamma chain (γc) as alternative preventative drug screening research models of dirofilariasis. Here we summarise the current knowledge of candidate immunodeficient mouse models tested, including a comparison of susceptibility using different background strains of mice, different D. immitis isolates, following use of anti-inflammatory treatments to further suppress residual innate immunity, and efficacies achieved against different reference anthelmintics. We supplement this precis with new data on treatment response to the veterinary anthelmintic, oxfendazole, and initial evaluation of D. immitis susceptibility in CB.17 SCID and C57BL/6 RAG2-/-γc-/- mice. We conclude that in addition to NSG and NXG mice, RAG2-/-γc-/- mice on either a BALB/c or C57BL/6 background offer an alternative screening model option, widening access to academic and commercial laboratories wishing to pursue initial rapid in vivo drug screening whilst avoiding potentially unnecessary cat or dog testing.", "keywords": [ "Dirofilariasis", "heartworm", "parasitology", "anthelmintic", "anti-parasitic drugs" ], "content": "\n\n\n\nScientific benefits(s):\n\n\n\n• A variety of immunodeficient mouse models of Dirofilaria immitis (heartworm) are reproducibly susceptible to tissue-phase L4 stage larvae.\n\n• Oxfendazole’s effectiveness in reducing D. immitis tissue-phase larvae demonstrates potential use as a heartworm preventative.\n\n3Rs benefits(s):\n\n\n\n• As alternative in vivo models for heartworm, mice have the potential to reduce the overall use of specially protected species, cats and dogs, in heartworm preventative compound screening.\n\n• Mice present with no clinical signs of tissue-phase D. immitis infection over 5 weeks, categorising this model as a ‘mild procedure’.\n\n• Mouse models have the potential to be used as a screening model before moving onto more sentient and highly protected species, potentially reducing the number of chronic procedures by 67% and longitudinal infection studies risking moderate to severe welfare arising in cats and dogs.\n\nPractical benefits(s):\n\n\n\n• The use of rodent heartworm models has advantages in comparison to cats and dogs for preliminary drug screening such as ease of pharmacology standardisation, reduced costs of maintenance and higher throughput.\n\n• Increased variety of commercially available mouse strains susceptible to heartworm extends global access for heartworm drug testing in laboratories where heartworm infectious larvae can be supplied.\n\nCurrent applications:\n\n\n\n• Evaluation of anti-Wolbachia compounds at our laboratory, as a novel approach to heartworm prevention.\n\n• Adoption in industry labs for more widespread use as an initial in vivo screening model for preventative research and development.\n\nPotential applications:\n\n\n\n• Onward use of models in other basic and applied biological research e.g. heartworm developmental biology, mechanisms of drug resistance, drug repurposing, immune-mediated control of heartworm including vaccine research and biomarker discovery.\n\n\nIntroduction\n\nAffecting felids and canids, heartworm disease is caused by the mosquito-borne filarial nematode, Dirofilaria immitis. With vectors including the invasive Aedes albopictus, heartworm has an emerging global distribution (Simón et al., 2012; Noack et al., 2021; Morchón et al., 2022). Canine chronic-progressive heartworm disease can result in heart failure following establishment of adult worms within the pulmonary vascular system. In cats, immature worms can result in potentially lethal heartworm-associated respiratory disease (McCall et al., 2008). Humans are at risk of developing abbreviated zoonotic infections causing pulmonary lesions, with increasing reported incidence (Reddy, 2013), frequently confused with tumours (Saha et al., 2022). A related subcutaneous parasite, D. repens, is also widespread in Europe and Asia, risking renal damage in dogs and zoonotic ocular-dermal pathologies (Genchi and Kramer, 2017; Noack et al., 2021).\n\nDrugs available for safe prevention and post-diagnosis treatment of heartworm disease are limited. The arsenical injectable, melarsomine, is the only registered cure for adult heartworm (Self et al., 2019; Morchón et al., 2022). Melarsomine is not registered for use in cats and risks severe adverse events in dogs, requiring complex protracted veterinary clinical case management, exercise restriction and supplementary treatments. Comparatively, primary control of heartworm relies on chemoprophylaxis using macrocyclic lactones (ML). Despite high efficacy of MLs during the first 60 days of D. immitis infection, concerns have been raised regarding the development of resistant isolates following their widespread utilisation within veterinary medicine. Resistance of D. immitis has been formally demonstrated within both field and laboratory settings, with “JYD-34” and “ZoeLA” isolates identified as ivermectin-resistant by laboratory-based validation (McTier et al., 2019; Prichard and Geary, 2019). Thus, there is a growing need for new heartworm chemoprophylactic drugs utilising a novel mode of action (Turner et al., 2020).\n\nUntil recently, only laboratory-reared cats and dogs have been validated for in vivo drug screening of preventative heartworm drug compounds following experimental infections. Ethical concerns arise following the use of such highly sentient animals, categorised with non-human primates as specially protected species under UK law. Additionally, to satisfy regulatory requirements that new prophylactic formulations prevent arrival of adult worms in the heart and lungs, studies are necessarily lengthy (≥6 months) and are vulnerable to moderate to severe complications. This is particularly evident in experimental cat infections due to potentially lethal immune-pathological respiratory disease when immature worms die in the lungs (Dillon et al., 2017). Finally, using cats and dogs faces practical challenges of keeping large laboratory-bred animals for long time-periods and limits throughput for drug development. Our analysis of published experimental heartworm studies between 2015-2020 identified that 1324 lab-reared cats and dogs have been documented in heartworm experimental research (221 per annum) with the majority (63%) used in drug testing.\n\nFollowing previous success by our laboratory and others in developing rodent models for the medically important filarial nematodes Brugia malayi, Onchocerca volvulus, and Loa loa (Halliday et al., 2014; Pionnier et al., 2019; Marriott et al., 2022), investigation into the permissiveness of mice to D. immitis has recently been demonstrated by our laboratories (Marriott et al., 2023) and independently by Hess et al. (2023).\n\nHere we summarise the status of heartworm immunodeficient mouse models in terms of D. immitis isolates, strains of inbred mutant and genetically modified mice, infection durations, and validations of drug testing models in terms of different anthelmintic efficacies. We supplement prior data with new findings demonstrating Georgia III strain D. immitis infections in NSG mice do not significantly vary up to 5 weeks of infection, and further validate a five-week drug screen, with single daily drug exposures at 4-week intervals using a novel reference veterinary filaricide, oxfendazole. We report evaluations of two additional commercially available mouse strains, C57BL/6NTac.Cg-Rag2tm1Fwa Il2rgtm1Wjl (RAG2-/-γc-/-), and C.B-Igh-1b/IcrTac-Prkdcscid (C.B-17 SCID) with or without additional steroid treatment, for susceptibility to D. immitis tissue-phase larval infection.\n\n\nMethods\n\nMale NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mice were purchased from Jax Labs, USA. Male C57BL/6NTac.Cg-Rag2tm1Fwa Il2rgtm1Wjl (B.6 RAG2-/-/γc-/-) and C.B-Igh-1b/IcrTac-Prkdcscid (C.B-17 SCID) mice were purchased from Taconic, USA. Mice were 5-7 weeks old and 20-30g at the start of study. All mice were group housed at TRS Labs and allowed minimum seven days acclimation before study, kept in stacked cages and with access to food and water ad libitum.\n\nDirofilaria immitis Georgia III (GAIII) isolate microfilariae in dog blood were fed to Aedes aegypti female mosquitoes (Liverpool strain) using a glass feeder at a density of 1,000-2,500 mf/ml with third-stage infective larvae (L3) collected 14 days later following protocols by Marriott et al. (2023). Mosquitoes were kept at temperatures 75-80oF, humidity at 72-95%.\n\nNSG mice (Figure 1A) were subcutaneously inoculated with 100 GAIII DiL3 into the flank and maintained until 5 weeks post-infection. Animals were allocated to treatment groups via cage (non-randomised), due to logistical constraints, experimental unit being a single animal. Treatment group (n=4 mice) received oral 5mg/kg bi-daily dose of oxfendazole (d1+d29). Oxfendazole was suspended in standard suspension vehicle (SSV; 0.5% carboxymethyl cellulose, 0.5% benzyl alcohol, 0.4% tween 80, 0.9% NaCl). B.6 RAG2-/-/γc-/- (n=5 mice) and C.B-17 SCID (n=5 mice) (Figure 2A) received a subcutaneous injection of 2mg methylprednisolone acetate (MPA) in 200uL ddH2O. Control groups received a matching volume of ddH2O. Dosing was immediately followed by subcutaneous inoculation of 200 GAIII DiL3 into the flank. MPA dosing was repeated on d7, and mice sustained until 14 days post-infection (no blinding used during inoculation or dosing). All mice were monitored daily for welfare and weighed weekly, no animals excluded during the study. Those monitoring and weighing animals were aware of group allocation.\n\nMice were humanely euthanised by schedule one (rising CO2) two or five weeks post-infection, dependent on study design (Figure 1A; Figure 2A). Collection and visual quantification of fourth-stage larvae (L4) using a light microscope followed protocols by Marriott et al. (2023).\n\nFor deriving group size for drug testing, we utilised data of average yield and variation of GAIII larvae at 4 weeks post-infection in NSG mice (27.3±6.2, n=5) (Marriott et al., 2023) to calculate effect size and statistical power of minimum 70% reduction by drug treatment (e.g. predicted mean number of L4 larvae=8.2±1.9, d=4.2, power>0.9, n=3 per group, 2-tailed independent T test, alpha=0.05, calculated in G*Power 3.1). We included an additional mouse per group as mitigation in case of early welfare issues.\n\nTests were performed using GraphPad Prism 9.1.2. D’Agostino and Pearson omnibus Shapiro-Wilk normality testing indicated non-parametric analyses. Mann-Whitney tests or Kruskal Wallis with Dunn’s post hoc tests were used to compare quantitative differences. Chi-square tests for trend were used to assess categorical data over time. Statistical significance was defined as P≤0.05, experimental unit being a single animal. Group allocation was not specified to those conducting data analysis.\n\n\nResults\n\nOur laboratories previously demonstrated viable L4 larval yields two-to-four weeks post-infection using NSG or NXG mouse strains, following infection with Missouri (MO) or GAIII D. immitis (Table 1) (Marriott et al., 2023). Hess et al. (2023) also demonstrated permissiveness of NSG mice to the MO isolate and the ML-resistant isolate, JYD-34, extending evaluations up to six weeks (summarised in Table 1). We therefore investigated the ability of NSG mice to sustain GAIII isolate infections for five weeks (Figure 1A). Following subcutaneous inoculations of 100 DiL3, we reproducibly recovered GAIII D. immitis L4 on d35 dpi (4/4), median recovery rate of 14.5% (range 6-26%). This was not significantly variable when compared with GAIII L4 yields priorly attained at 2-4 weeks post-infection by Marriott et al. (2023) (Figure 1B). At five-weeks, the majority (61%) of larvae were recovered from muscle tissues (Figure 1C). Comparing to prior data at 14, 21 and 28-days post-infection, a significant linear increase in GAIII D. immitis developing larvae migration into muscle tissues over time was apparent (chi-square test for trend, 30.3, P<0.0001, Figure 1C). With the advantage that the impact of two daily chemoprophylactic exposures spaced 4 weeks apart could be evaluated within this extended timeframe in future studies (emulating monthly oral exposures in cats and dogs), we tested efficacy of a 5 mg/kg bid oral regimen of the benzimidazole oxfendazole, selected based on recent evidence it can mediate curative efficacies after short-course exposures in a filariasis infection model (Hubner et al., 2020). After two exposure cycles (d1+d29), oxfendazole mediated a median 90% reduction in D. immitis L4 compared with controls (d35), curing two out of four mice (Figure 1D). Efficacy was comparable to reductions in larvae in MO, GAIII and JYD isolates treated with macrocyclic lactone regimens in NSG mice (data summarised in Table 2). Over the 35-day infection course, mice displayed no adverse behavioural changes determined during daily anecdotal observations by a veterinarian, and gained weight (Figure 1E), indicating infections and drug dosing did not cause overt clinical welfare signs.\n\n1 Data from Hess et al. (2023). Data quantified from graphical representations.\n\n2 Data from Marriott et al. (2023).\n\n3 Susceptibility reported by Hess et al. (2023) up to 15 weeks, but no quantitative data is available after 42dpi.\n\n4 Previously unpublished data.\n\nBars are median recoveries (B,D) or mean proportions (C) from a single experimental group of 4-5 mice or two-independent experiments combined (2 week data) with 2-to-4-week data previously published by Marriott et al. (2023). Significant differences determined by Kruskal–Wallis one-way ANOVA with Dunn’s multiple comparison’s tests except (C) where the difference in proportions was tested by 2x4 Chi-Square test for trend. Significant differences (P≤0.05) are indicated in bold, no data excluded.\n\n1 po = per oral, sc = subcutaneously, qd = once per day, bid = twice per day.\n\n2 Mean efficacy compared with vehicle control, reported in Hess et al. (2023).\n\n3 Median efficacy compared with vehicle control, reported in Marriott et al. (2023).\n\n4 Median efficacy compared with vehicle, previously unpublished data.\n\n(B). Bars are median recoveries from a single experimental group of 5 mice. Significant differences determined by Kruskal–Wallis one-way ANOVA with Dunn’s multiple comparison’s tests. Significant differences (P≤0.05) are indicated in bold, no data excluded.\n\nHess et al. (2023) described mouse susceptibility to MO isolate D. immitis as specific to the NSG line, as other strains including lymphopenic SCID mice on NOD or B.6 backgrounds were refractory to infection (summarised in Table 1). NOD mice have inherent strain-specific deficiencies in the complement system (Verma et al., 2017) and thus combinations of these, or other background strain-specific immune gene mutations, combined with susceptibility of the introduced SCID mutation and IL-2Rγ ablation, may culminate in multiple immune-impairments sufficient to allow D. immitis survival and growth. However, in our prior study (Marriott et al., 2023), we identified compound lymphopenic (RAG2-/-) and IL-2Rγ deficiencies on a BALB/c background as susceptible to the D. immitis MO isolate at two weeks, with methyl-prednisolone (MPA) steroid treatment augmenting larval recoveries. We therefore examined two commercially accessible, alternative lymphopenic mouse strains on distinct genetic backgrounds: B.6 RAG2-/-/γc-/- and CB.17 SCID (BALB/c congenic), evaluating D. immitis GAIII L4 larval recoveries at 14dpi in groups of five mice with or without MPA treatment (Figure 2A). Whilst all (5/5) B.6 RAG2-/-/γc-/- mice had recoverable D. immitis L4 larvae two weeks post-infection, only 2/5 CB.17 SCID mice were infection positive (Figure 2B). Yields were significantly higher in RAG2-/-/γc-/- mice (median=8%, range=4-35% vs median=0%, range 0-4%, Kruskal Wallis One-Way ANOVA P=0.029, Dunn’s post-hoc test P=0.024). In B.6 RAG2-/-/γc-/- mice, MPA treatment did not significantly bolster yields (median 5%, range 2-22%). MPA treatment did increase the frequency of animals with infection in 4/5 CB.17 SCID mice, although heartworm larval recoveries were low and not significantly different to non-treated animals (median recovery=1.5%, range =0-7%) (Figure 1B). Thus, we summarise that RAG2-/-/γc-/- mice are initially validated as an alternative susceptible tissue phase larval heartworm model, without requirement for steroid suppression of residual innate immunity. We summarise all mouse strains tested for D. immitis susceptibility in Table 1.\n\n\nDiscussion\n\nFollowing the success of Marriott et al. (2023) and Hess et al. (2023) in establishing a validated D. immitis immunodeficient NSG/NXG mouse preventative drug screening model, our current study demonstrates the ability of NSG mice to sustain GAIII D. immitis infection for up to five weeks post-infection with further evidence of larval migration from the skin and subcutaneous tissues into deeper musculature. This suggests that for the first 35 days, development of heartworm larvae emulates that of within natural hosts, whereby the L4-stage migrates from the subcutaneous space into muscles, penetrates the vasculature and arrives in the heart and lungs after 65-70 days (Orihel, 1961; Supakorndej, McCall and Jun, 1994). Similarities in larval length at 14-35 days post infection in NSG mice: (1.5–1.8 mm, 14d & 3.5-4.0 mm, 35d) Hess et al. (2023) and NSG/NXG mice (1.2 – 2.8 mm, 14d) Marriott et al. (2023) are aligned with growth of D. immitis L4 in dogs during this timeframe (1.7–2.2 mm, 14d, 3.1-5.6 mm, 30d) (Orihel, 1961; Lichtenfels, Pilitt and Wergin, 1987). Hess and colleagues identified that after 35 days, development of L4 in NSG mice diverged, with retarded growth in murine tissues. Hess et al. (2023) also observed no entry of larvae into the heart up to 15 weeks in NSG mice, suggesting L4 larvae may become arrested in development in subcutaneous tissues and muscle after 35 days infection. Whether arrested development of late-L4 is specific to NSG mice, and/or the MO isolate tested, or is a universal feature of lack of full development in all mouse strains remains to be resolved. Regardless, the window of aligned growth is encouragingly sufficient to allow testing of new preventative candidates, utilising regimens emulating once-per-month exposures demanded by current target candidate drug profiles. In prior studies, single-dose injected moxidectin or 3x fortnightly oral ivermectin/moxidectin have been utilised for initial validations (summarised in Table 2). When we tested oxfendazole in a daily exposure cycle spaced four weeks apart, we demonstrate 90% efficacy, extending validation of the NSG mouse model and demonstrating feasibility of once-per-month drug testing. We selected oxfendazole based on its registered use in companion animals, activity against L3 filarial larvae (Jawahar et al., 2021) and recent demonstrable curative activity against Litomosoides sigmondontis infection models (Hubner et al., 2020; Jawahar et al., 2021). Oxfendazole may thus have the potential to be used as an alternative or combination with ivermectin for monthly oral treatment of drug-resistant D. immitis and should be scrutinised for dose-dependent efficacy against resistant isolates.\n\nWe explored additional laboratory inbred strains of mice and effects of MPA treatment. C57BL/6J, NOD (NOD/ShiLt), B.6 SCID, and NOD.SCID mouse strains prior investigated by Hess et al. (2023) were determined refractory to MO isolate D. immitis (summarised in Table 1). Here we identify C.B-17 SCID and B.6 RAG2-/-/γc-/- mice as susceptible to D. immitis GAIII isolate survival and growth over 14-days. MPA treatments were not necessary for susceptibility in B.6 RAG2-/-/γc-/- mice, simplifying onward use for drug testing and avoiding potential drug-drug interactions. MPA treatments were successful in increasing the infection success of CB.17 SCID mice, indicating that inherent immune traits varying between these different genetic backgrounds combined with lymphopenia and deficiency in IL-2/7 receptor signalling dictates early immune control of D. immitis larvae in mice. We and others have established both innate (natural killer cell, alternatively activated tissue resident macrophage) and adaptive (IL-4/5/13 producing CD4+ T cell) immune responses combine to orchestrate eosinophil-dependent immunity to developing B. malayi larvae in mice (Turner et al., 2018; Pionnier et al., 2020, 2022). The variety of biological, pharmacological, and genetic modification tools in laboratory mice (many of which available on BALB/c or B.6 inbred backgrounds) may now be applied to pinpoint the basis of immunity against dog heartworm, potentially supporting rational vaccine design.\n\nOne potential limitation of this new data is that power calculations (n=3) assumed a normal distribution whereas parasite yields were aggregated, requiring non-parametric testing. Despite a potential underpower, due to the potency of oxfendazole being >70% efficacy, and our inclusion of an extra animal per group, this did not affect determining a significant outcome. In future studies, researchers should be wary of aggregated distributions when determining sample size.\n\nCurrent regulatory requirements demand 100% prophylactic activity in cats or dogs for registration of new heartworm preventatives, meaning it is not currently possible to completely avoid experimental use. However, with a variety of susceptible mouse strains available (summarised in Table 1), some without current commercial use restrictions, we envisage these new models may become widely adopted by both academic, not-for-profit, and commercial organisations to produce L4 for in vitro drug titration evaluations and for initial triaging of compounds and exposure-regimen selections in vivo. Future adoption of immunodeficient mice as an initial frontline screen, with short timeframes and without notable impacts on weight or welfare changes arising during the tissue-phase infection period, has the potential to reduce the overall use-requirement of cats and dogs in experimental heartworm research by at least 50%.\n\n\nEthics statement\n\nMale NSG, CB.17 SCID and C57BL/6 RAG2-/-γc-/- mice were group housed at TRS Labs. within filter-top cages. Animals had continuous access to fresh sterile food, water, and enrichment throughout experiments. Weight was monitored weekly and welfare behaviour monitored daily. Humane endpoints were defined as >20% weight loss and/or observation of adverse behavioural changes which did not improve over a 6h observation period following any remedial treatment by study veterinarian including but not limited to: loss of mobility, starring coat, eye squint, pinched nose, ears pulled back, and/or laboured breathing. Studies were conducted in the USA and approved by the TRS Institutional Animal Care and Use Committee. Protocols were identical to prior approved studies conducted in the UK, approved in the UK by LSTM & University of Liverpool Animal Welfare and Ethics Review Boards and licensed by The UK Home Office Animals in Science Regulation Unit. The manuscript was written in adherence with the ARRIVE 2.0 guidelines.", "appendix": "Data availability\n\nFigshare: Current status of immunodeficient mouse models as substitutes to reduce cat and dog use in heartworm preclinical research, https://doi.org/10.6084/m9.figshare.25250101.v1 (Dagley et al., 2024).\n\nThis project contains the following underlying data:\n\n- Supplementary data file_NC3Rs.xlsx\n\nFigshare: ARRIVE checklist, https://doi.org/10.6084/m9.figshare.25690062.v1 (Dagley, 2024).\n\n- ARRIVE NC3Rs_.pdf.\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 gratefully acknowledge the NIH/NIAID Filariasis Research Resource Center (www.filariasiscenter.org) for maintenance and donation of D. immitis.\n\n\nReferences\n\nDagley J, Fricks C, Mansour A, et al.: Current status of immunodeficient mouse models as substitutes to reduce cat and dog use in heartworm preclinical research. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPrichard RK, Geary TG: Perspectives on the utility of moxidectin for the control of parasitic nematodes in the face of developing anthelmintic resistance. Int. J. Parasitol. Drugs Drug Resist. 2019; 10: 69–83. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nReddy MV: Human dirofilariasis: An emerging zoonosis. Tropenmed. Parasitol. 2013; 3(1): 2–3.\n\nSaha BK, Bonnier A, Chong WH, et al.: Human Pulmonary Dirofilariasis: A Review for the Clinicians. Am. J. Med. Sci. 2022; 363(1): 11–17. PubMed Abstract \| Publisher Full Text\n\nSelf SW, Pulaski CN, McMahan CS, et al.: Regional and local temporal trends in the prevalence of canine heartworm infection in the contiguous United States: 2012-2018. Parasit. Vectors. 2019; 12. ARTN 380. <Go to ISI>://WOS:000478002400004. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSimón F, Siles-Lucas M, Morchón R, et al.: Human and animal dirofilariasis: the emergence of a zoonotic mosaic. Clin. Microbiol. Rev. 2012; 25(3): 507–544. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSupakorndej P, McCall JW, Jun JJ: Early migration and development of Dirofilaria immitis in the ferret, Mustela putorius furo. J. Parasitol. 1994; 80(2): 237–244. PubMed Abstract \| Publisher Full Text\n\nTurner JD, Marriott AE, Hong D, et al.: Novel anti-Wolbachia drugs, a new approach in the treatment and prevention of veterinary filariasis? Vet. Parasitol. 2020; 279: 109057. PubMed Abstract \| Publisher Full Text\n\nTurner JD, Pionnier N, Furlong-Silva J, et al.: Interleukin-4 activated macrophages mediate immunity to filarial helminth infection by sustaining CCR3-dependent eosinophilia. PLoS Pathog. 2018; 14(3): e1006949. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVerma MK, Clemens J, Burzenski L, et al.: A novel hemolytic complement-sufficient NSG mouse model supports studies of complement-mediated antitumor activity in vivo. J. Immunol. Methods. 2017; 446: 47–53. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "299366", "date": "19 Jul 2024", "name": "Constantin Constantinoiu", "expertise": [ "Reviewer Expertise Veterinary parasitology" ], "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\nCurrent status of immunodeficient mouse models as substitutes to reduce cat and dog use in heartworm clinical research\nThe paper summarises previous research on the use of mice as models of infection with Dirofilaria immitis and furthers extends the previous research by demonstrating that:\nGAIII isolates of D. immitis can develop up to 5 weeks in NSG mice and that they are susceptible to the action of Oxfendazole; GAIII isolate of D. immitis can develop up to 2 weeks in RAG2 mice with requirement for suppression of the residual immunity by MPA.\nThe paper is well written and it presents the data in a clear manner. The only reservation I have is related to the seemingly low number of animals per treatment.\nMinor comments/suggestions\nAbstract ‘Chemoprophylactic prevention’ seems to be a pleonasm (prophylaxis means prevention); Is the word ‘veterinary’ before ‘heartworm disease’ needed? ‘with or without use of anti-inflammatory treatments’ instead of ‘following use of anti-inflammatory treatments’? ‘efficacies achieved using different ….’ instead of ‘efficacies achieved against different ….’? ‘evaluation of D. immitis development in …’ instead of ‘evaluation of D. immitis susceptibility in …’?\nKeywords Anthelmintics are antiparasitic drugs, do you need both keywords?\nResearch highlights What do the authors mean by ‘chronic procedures’? Is it the fact that in dogs heartworm disease commonly runs a chronic course? How did the authors get the ‘67%’ value?\nIntroduction It seems that some sentences need a little reformulation for their meaning to become clear:\nHumans are at risk of developing abbreviated zoonotic infections causing pulmonary lesions, with increasing reported incidence (Reddy, 2013), frequently confused with tumours (Saha et al., 2022). Melarsomine is not registered for use in cats and risks severe adverse events in dogs, requiring complex protracted veterinary clinical case management, exercise restriction and supplementary treatments.\nIt might be useful to provide a reference for the high efficacy of MLs against the 60 days old larvae. What do the authors mean by ‘do not significantly vary up to 5 weeks of infection’? The infections with D. immitis GAIII isolate in NSG mice do not vary under what aspects?\nMethods Animal infections and methods Were the control mice in the Oxfendazole trial treated with the vehicle subcutaneously (there is no mention in the text and on Fig. 1 it is stated ‘Vehicle sc’)?\nDiscussion ‘we demonstrated 90% efficacy’ instead of ‘we demonstrate 90% efficacy’? ‘as an alternative or in combination with ivermectin’ instead of ‘as an alternative or combination with ivermectin’? ‘for monthly oral prevention of infection with drug-resistant …’ instead of ‘for monthly oral treatment of drug-resistant ..’? ‘previously investigated’ instead of ‘prior investigated’? ‘eosinophil-dependent immune response’ instead of ‘eosinophil-dependent immunity’? ‘avoid experimental use of dogs and cats’ instead of ‘avoid experimental use’?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate? I cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "12096", "date": "11 Sep 2024", "name": "Jessica Dagley", "role": "Author Response", "response": "Thank you for your feedback. We appreciate the time it has taken to review this article and we take onboard your comments in the updated version. Regarding estimates of reduction in cat and dog use for drug screening, whilst it is impossible to precisely define the percentage reduction with each drug development programme situation and methodology varying, we considered one standard approach, generating murine pharmacokinetic (PK) data combined with an in silico prediction of efficacy based on the relationship between PK and in vitro determined pharmacodynamics (PD) using D. immitis L4 generated in mice. This will reduce numbers of animals required for empirical testing in vivo by selecting only compounds predicted to mediate threshold effects and calibrate doses in vivo to negate equivocal efficacy readouts. In tandem, testing empirical efficacy in the new mouse infection model will further reduce the use of cats or dogs, thereby reducing the risk of adverse reaction occurrence in these highly sentient species. In a scenario where traditionally 10 experimental drug regimens would be run in long-term, 6-month dog studies (72 dogs), with potential welfare consequences, this new approach would cut the number to 24 dogs (67% reduction) replaced by short-term, mild procedures in an estimated 48 mice." } ] }, { "id": "299364", "date": "19 Jul 2024", "name": "Timothy G Geary", "expertise": [ "Reviewer Expertise Anthelmintic pharmacology (basic", "clinical", "discovery", "development", "resistance)", "molecular basis for the host-parasite interaction" ], "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 valuable addition to the burgeoning literature in this area and addresses an important topic. It is well-written, clear and concise. I have a few points for the authors to consider.\nFirst, two additional recent reports perhaps should be cited. One( Mizuseki M, et al., 2024 [Ref-1]) is perhaps slightly less relevant, but the other (Risch F, et al., 2024 [Ref-2]) should be cited and discussed, as it reports the development of adult stages in mice. I understand that the field moves quickly, but the value of the current manuscript will be enhanced if these papers are included. Two, macrocyclic lactones were less potent and less efficacious in the mouse strains compared to dogs. These drugs are believed to enlist the host immune response in vivo, which obviously may be compromised in these host strains. Some additional discussion around this issue is warranted. Finally, I believe the authors should acknowledge that intellectual property has been filed on at least one of the models (and the claims may be sufficiently broad to cover the others). I believe that patent may have been granted in the EU (at least). This is relevant because it may block drug screening by others. I think it is essential for the authors to discuss this. In addition, a granted patent covers the use of immunosuppressed rats as hosts for this parasite. I believe patents are citable, and this one may also cover ore broadly the use of immunocompromised rodents for drug screening for heartworm preventatives (the authors should check). Interestingly, effects of macrocyclic lactones in these rates closely resemble those in dogs (potency and efficacy), an interesting difference from the mouse that really should be discussed in the current manuscript.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? 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": "12097", "date": "11 Sep 2024", "name": "Jessica Dagley", "role": "Author Response", "response": "Thank you for your feedback and comments. We hope we have addressed your points in the updated version and have some comments below: - While this article was under review, the report by Risch F et al., 2024 was published. We agree this is an important article, which corroborates our data herein, and indicates independent verification of susceptibility to D. immitis isolates in B.6 RAG2-/-gc mice. Importantly this research also demonstrates that there is no biological barrier to the migration and development of adults within the heart and lung vasculature in mice. We have added to data and discussion highlighting this research within our article. - We believe the Mizuseki M et al., 2024 report to be less relevant to our report, as it details a microfilarial-specific infusion model, and thus do not incorporate into comparisons within this specific brief report. - While the discussion around the mode of action of MLs is warranted, we have discussed this in much greater detail within an earlier publication (Marriott et al., 2023). We have therefore referenced this, but due to this being a brief report, will not discuss in greater detail within the text. - We appreciate the point raised regarding the rat patent; however, we do not deem it appropriate to discuss data within patents filed where data is not yet peer reviewed and published. - Regarding the mouse patent filed by Boehringer Ingelheim and awarded in Europe (abandoned in USA) based on the work of Hess et al., 2023, we suggest the patent claims are restricted to the NSG model, and a number of emerging alternative immunodeficient mouse lines proven to be susceptible to D. immitis infection should be available for use without restriction in both academia and industry. We have added some discussion regarding this into the main body of text." } ] }, { "id": "299367", "date": "24 Jul 2024", "name": "Qian Han", "expertise": [ "Reviewer Expertise veterinary parasitology", "vector borne pathogens" ], "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 use of mouse models in heartworm drug screening research holds great significance. It offers an ethical alternative to the experimental use of cats and dogs, reducing the reliance on these companion animals for preclinical drug testing and minimizing potential harm and discomfort to them. Mouse models provide a controlled environment that allows for precise manipulation and monitoring of variables. This enables researchers to systematically study the efficacy, mechanism of action, and potential side effects of different heartworm drugs in a more standardized and reproducible manner. Moreover, the development of mouse models helps in understanding the immune responses and pathophysiological processes underlying heartworm infection and drug treatment. This fundamental knowledge can guide the development of more effective and targeted therapeutics in the future. In conclusion, mouse models are a valuable tool in heartworm drug screening research, accelerating the drug development process and contributing to the fight against this important veterinary parasitic disease.\nThe presented research provides a valuable contribution to the field of chemoprophylactic prevention of veterinary heartworm disease via the exploration of immunodeficient mouse models in drug screening. The comprehensive comparison of different mouse models, worm isolates, anti-inflammatory treatments, and anthelmintic offers a detailed analysis that strengthens the reliability and validity of the proposed screening models. The addition of new data on the treatment response to oxfendazole and the evaluation of susceptibility in specific mouse strains adds to the novelty and practical application of the study.\nHowever, according to the information of author's current and previous studies, most heartworm larvae are in the tissues, such as muscle and skin, instead of blood vessels. The differences of worm distributions, and drug distribution, metabolism, and excretion in different animals may lead differences in drug efficacy. Authors may consider pharmacokinetic evaluations in combination with drug screening for the interpretation of screening results.\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": [] }, { "id": "299372", "date": "05 Aug 2024", "name": "Jan Šlapeta", "expertise": [ "Reviewer Expertise Veterinary and molecular parasitologist" ], "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\nAuthors demonstrate recovery of D. immitis larvae from B.6 RAG2-/-/γc-/- mice without the need for methylprednisolone, thus simplifying onward use of mice for drug testing against D. immitis (Di).\nOxfendazole is poorly soluble, would authors have data on Tmax and elimination halflife in mice and potentially in dogs? Generally, I would expect it will be rather quick as far as Tmax and half-life will be likely <12h. This information should be considered when discussing your results and the reality of oxfendazole use in dogs. I assume it was because you chosen \"bid\" dose to counter the rapid Tmax and elimination. In this context it would have been beneficial to measure the concentration and bioavailability at some key timepoints post dosing. The regimen chose with Di infection got me thinking why was infection at time point zero (day 1) chosen? More realistic dosing would have been only at 28-30 dpi, thus considering all the <30 days larvae.\nCould you elaborate on reasoning to increase to 200 Di L3 in some of your experiment? Would 200 L3 be more optimal for future experiments in general to increase the number of detectable larvae at the end of the experiment / power analysis?\nFig 1D / same for Fig 2 B – I don’t think the % should be there, you're reporting real values and an arithmetic mean? Please check. It maybe or not maybe % but depends on the starting # either 100 or 200 L3 inoculated.\nI am not sure how you calculated your >90% +reduction (results section first paragraph). Please provide the calculation and values used.\nAuthors should reconsider the introductory sentence (and later in the 3rd paragraph); potentially misleading if they start with felids/cats. It is canids that are the principal and natural vertebrate/mammal hosts esp. domestic dog in this context where the disease and suffering is pronounced and requires intervention. Felids are in host situation just an aberrant host as with rare development of sexually mature L1 producing Di. I am personally not aware of the term “abbreviated” zoonotic infection. I fully acknowledge the presence of coin lesions in humans, but it is potentially misleading to focus on humans and so zoonosis when the real suffering and almost solely burden in dogs.\nIn the second paragraphs authors note 60-days, I personally would be extremely cautious about using such number. The registration, most if not all, claim 28/30 days. The research reports cannot be considered as claims and so if any veterinarian would recommend 60 days it would be solely off-label use. I would exercise caution and suggest authors align with the registration claims. No need to go into detail re different MLs and if there is potential or not based on research articles.\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": [] } ]	1	https://f1000research.com/articles/13-484
https://f1000research.com/articles/12-827/v1	13 Jul 23	{ "type": "Research Article", "title": "Isolation, morphological characterization, and screening a virulence of Beauveria bassiana and Metarhizium robertsii as bioagents", "authors": [ "Dereje Geremew", "Tadale Shiberu", "Ararsa Leta", "Ararsa Leta" ], "abstract": "Background: Entomopathogenic fungi exists naturally in plants as an asymptote and has the potential to reduce the population of insect pests through indirect interactions. This study was conducted to detect and characterize the endophytic fungi Beauveria bassiana and Metarhizium robertsii from the rhizosphere soil of tomato plants and their virulence effect on Galleria melonella. Methods: From the rhizosphere soil of 40 tomato fields, three Beauveria bassiana and seven Metarhizium robertsii isolates were identified using the galleria bait method. All fungi isolates were morphologically characterized by their colony color, shape, and surface texture. Isolates with the highest percentages of germination, conidial yield, and radial growth were selected, and their pathogenicity was evaluated on second instar larvae of Galleria melonella under laboratory conditions. Results: In this study, Beauveria bassiana showed white colony color and aseptate hyphae, whereas Metarhizium robertsii showed dark green to light green colony color and septate hyphal structures. Maximum spore production and conidial length were obtained by Beauveria bassiana isolate APPRC-27 with 2.67x107 spores ml-1 and 3.24 µm, respectively. Colony radial growth rates ranged from 1.73 to 3.24 mm day-1. The results revealed that the highest mortality rate of Galleria melonella (100%) was obtained by Metarhizium robertsii isolates K-61 and K-102 at a concentration of 1x108 conidial ml-1 at 7 days post-inoculation. The lowest mortality rate was registered by Metarhizium robertsii isolate RST-11. Conclusions: In the present study, isolates that produced the most spores and had the highest germination rates were the most virulent to Galleria mellonella second instar larvae. Therefore, virulent entomopathogenic fungi, Beauveria bassiana and Metarhizium robertsii, are promising bioagents for the control of pests.", "keywords": [ "Conidia", "colony color", "endophytic", "entomopathogenic fungi", "Galleria melonella", "isolates" ], "content": "Introduction\n\nEntomopathogenic fungi, Beauveria bassiana, (Bals. -Criv.) Vuill. and Metarhizium robertsii (Metchnikoff) Sorokin, live in plant tissues without showing pathological symptoms (Dutta et al., 2014). They have the potential to limit the feeding capacity, preference, and oviposition of stem boring, sap-sucking, and leaf mining insects on many crops by producing toxic compounds that disturb the insects performance. Additionally, they increase the plant defense mechanisms against pests or abiotic factors (McCormick et al., 2016; Hokkanen and Menzler-Hokkanen, 2017). Entomopathogenic fungi are capable of penetrating their insect hosts through cuticular exoskeletons (Zimmermann, 2007).\n\nEntomopathogenic fungi have become more promising than chemical pesticides for the control of pests in Ethiopia due to pesticide resistance. This is due to the misuse of pesticides, which causes the incrementation of pesticide-resistant biotypes (Negash et al., 2020), and a lot of pests have developed resistance due to the high use of pesticides (Tabashnik et al., 2009). Consequently, using eco-friendly biopesticides like B. bassiana and M. robertsii as bioagents against agricultural pests is the best option to increase crop production and productivity. They are symbiotic with their hosts, reduce pest populations, and require little inoculum for their systemic transmission within plant tissues (Nair and Padmavathy, 2014). Moreover, entomopathogenic fungi are the immediate solution for pests that feed inside leaves, stems, roots, and seeds because they reduce their exposure to synthetic insecticides and other control methods (Resquín-Romero et al., 2016).\n\nIdentification and characterization of entomopathogenic fungi, B. bassiana and M. robertsii, are highly required for entomological research and essential for the selection of virulent isolates against several pests (Boucias et al., 2000). Currently, the selection of virulent strains of entomopathogenic fungi as the biological control agent of pests is of great interest to many researchers (Lacey et al., 2015). However, there is a limit to the work on the isolation, morphological characterization, and screening of virulent isolates of entomopathogenic fungi, particularly B. bassiana and M. robertsii in Ethiopia, to control agricultural pests. Hence, this study was made to identify, characterize the morphology, and screen the virulence of B. bassiana and M. robertsii isolates on Galleria melonella collected from rhizosphere soil in tomato plant farms at Koka and Guder areas in Ethiopia.\n\n\nMethods\n\nThe experiment was conducted at the Ambo Agriculture Research Center under laboratory conditions. Ambo is far away from Addis Ababa, 110 km to the west, at a geographical coordinate of 8°59′N latitude and 37.85°E longitude, with an altitude of 2,100 m a.s.l. The daily temperature ranges from 15 to 29°C, with an annual temperature of 22°C on average. The soil sample was collected from two sites, namely Guder and Koka in Ethiopia. Guder is located at a latitude and longitude of 8o58′N and 374o6E, respectively, with an altitude of 2,101 m a.s.l., whereas Koka is found at 8o25′ N latitude, 39o02′ E longitude, and an altitude of 1,605 m a.s.l. The minimum and maximum temperatures ranged from 12.14 to 27.39°C, respectively (Etefa and Dibaba, 2011).\n\nRhizosphere soil was collected from tomato farmlands by uprooting vegetative-stage tomato plants. During the collection, the upper layer of soil was removed. A total of 40 rhizosphere soil samples were taken from two locations. Five samples were taken from each spot and mixed in a plastic bag before being taken to the bio-control laboratory of the Ambo Agriculture Research Center for the isolation of B. bassiana and M. robertsii. Finally, one kilogram (kg) of the soil sample was used for the isolation by removing unnecessary parts from the soil (Sevim et al., 2010).\n\nFrom 40 soil samples, B. bassiana and M. robertsii were isolated by using the Galleria baiting method as follows (Zimmermann, 1986; Belay et al., 2017).\n\nOne kilogram of soil sample was moistened by sterilized water and added to a 1.5 kg screw-capped glass jar. A total of 10 wax moth larvae were separately introduced into jars filled with soil samples and incubated at 26°C for 10 consecutive days under dark conditions.\n\nLarval deaths were inspected and recorded every three days. The moisture of the soil was maintained by moistening it with sterile water daily. The cadavers were taken off the soil and surface sterilized with 1% sodium hypochlorite for 2 minutes, followed by 70% ethanol for 10 seconds, and rinsed three times with sterile water. Surface-disinfected larval cadavers were placed on sterile plastic plates with slightly wetted filter paper and incubated at room temperature up to the sporulation of outgrown mycelia.\n\nThe sporulation of B. bassiana and M. robertsii over the dead cadavers was examined, and the spores were harvested by a sterilized inoculating wire loop, transferred onto Sabouraud Dextrose Agar (SDA) Microxpress® media, and incubated at 27±1°C for 14–21 days. Isolates were purified by subculturing on newly prepared SDA media, and pure cultures were preserved with glycerol and maintained on agar at -19°C for further work.\n\nFungal isolates were morphologically identified and characterized using the identification key of Humber (Humber, 1997), depending on fungal structures acquired from pure culture (Gürlek et al., 2018). In addition to the new isolates, three B. bassiana (APPRC-44BC, APPRC-44BC-1, and APPRC-27) and one M. robertsii (S-26) isolates were also characterized from the Ambo Agriculture Research Center for the comparison of isolates.\n\nConsequently, the morphologies of B. bassiana and M. robertsii were characterized by the culturing of pure cultures on the SDA media, and inspection was done for 14–21 days. Both macroscopic and microscopic characterization of isolates was conducted by observation of morphological features of isolates. Macroscopic features such as mycelial color, colony reverse, colony shape and color, colony elevation, and surface texture were observed. Microscopic characterization of isolates was also done under an Olympus SC50 (CX33RTFS2, Olympus Corporation) microscope with ×40 magnification (Barra et al., 2013) by measuring conidial length and diameter, hyphal growth, and conidiogenous cells using the slide culture technique.\n\nThe technique was conducted by autoclaving a 9-cm-diameter Petri dish with filter paper and a bent glass rod. A 15 g-1 of water agar was cut by a 1 cm × 1 cm block with a sterilized scalpel blade and put on a glass slide. Fungal spores were inoculated on the four sides of the agar blocks by a sterile inoculating needle, and coverslips were placed on the block. Moistened filter paper with 2 ml of sterile water was placed over plates, sealed with parafilm, and incubated at 27±1°C.\n\nAgar blocks were discarded after incubation for 72 hours, and the slides were moistened with a drop of 97% ethanol and enabled to heat fix by passing on an alcohol lump. A drop of lactophenol blue was used to stain the slide with a coverslip, which was later sealed with nail polish. The slide was placed under a SC50 microscope with ×40 magnification for the observation and characterization of conidiophore structure (Rosana et al., 2014). Finally, the slides were permanently preserved for further characterization. The characterization and measurement of spore features such as conidial length and diameter were also done using the Sc 50 microscope (magnification, ×40).\n\nThe spore germination test was verified by the conidial germination test technique according to standard procedures (Goettel and Inglis, 1997). Fungal spores were harvested from a 21-day-old culture by scraping with a sterilized spatula. Harvested spores were added to 10 ml of sterile water with Tween 80 (0.001% v/v) as a surfactant in a falcon tube and vortexing. Fungal spores were adjusted to 1 × 106 conidia ml-1 by using a Neubauer hemocytometer (USA) under a SC50 microscope.\n\nIn total, 100-μl of suspended spores was spread over fresh Potato Dextrose Agar (PDA) (Himedia®), and two sterilized glass slides were placed on the media and incubated at 28°C for 18 hours. After 18 hours, germination of the spores was halted by dispensing with 70% ethanol. Both germinated and non-germinated cells were counted by using a Neubauer hemocytometer under a SC50 microscope (magnification, ×40).\n\nThe experiment was conducted under laboratory conditions in CRD with 15 treatments and three replications. A germ tube with more than half the diameter of the spore was considered germinated, and vice versa for non-germinated. Isolates with more than 95% germination were selected against G. melonella to test their pathogenicity and used for further work. The percentage of spore germination was calculated according to the method developed by Vega et al. (2008).\n\nConidia of 14-day-old cultures were harvested from plates and spread on a 90 mm Petri dish containing fresh SDA and PDA media separately. Isolates were incubated for three days at 27±1°C, and the 5 mm diameter of three-day-old cultures mycelium was taken by using a cork borer and placed in the center of a 90 mm petri dish containing SDA and PDA media individually. Cultures were incubated at 27±1°C (Membang et al., 2021).\n\nThe experiment was conducted in CRD with 11 treatments and replicated three times. Data on radial growth were recorded in mm/day from the 4th to the 15th days and calculated by:\n\nWhere, RG/day is radial growth per day.\n\nSpore production was estimated as follows (Schemmer et al., 2016). A 21-day-old culture of 10 mm-diameter circular agar was cut with a cork borer, and the disc was added to 10 ml of sterile 0.001% Tween 80 solution. The solution was well vortexed to evenly mix, and the conidial concentration was counted by using a Neubauer hemocytometer. The conidial yield was expressed in terms of conidial ml-1. The experiment was conducted under laboratory conditions in CRD with eight treatments and three replications.\n\nConidia were obtained from pure cultures grown on SDA, which was incubated for 14 days at 27±1°C under dark conditions. Conidia were harvested by disposable cell scrapers and added into test tubes containing Tween 80 (0.001% v/v). Suspensions were vortexed well for 2 minutes and adjusted to 1 × 108 conidia ml-1 using a Neubauer hemocytometer (Gurulingappa et al., 2010).\n\nGalleria mellonella larvae (Lepidoptera: Pyralidae) were reared at the Ambo Agriculture Research Center in the biocontrol room following the methods described by Meyling (2007). Adult moths were kept in 500-ml flasks containing folded tissue paper to fasten their mating and egg-laying capacities. To hatch third- to fourth-instar larvae, the eggs were laid on folded tissue paper, transferred to plastic containers filled with 80 g honey, 50 g wheat bran, and 180 g glycerol, and incubated at 20°C for four weeks in the dark.\n\nThe potential virulence of fungal isolates was tested using 2nd instar G. mellonella larvae by the galleria dipping method. Spores collected from 14–21 days of old culture by sterilized spatula scraping were adjusted to 1 × 108 spores ml-1 and 10 ml were prepared from the suspension of sterilized water with Tween 80 (0.001% v/v) in a sterilized falcon tube and vortexing well. A total of 10 second instars of G. mellonella larvae were deepened into spore suspensions for 15 sec. Treated larvae with fungal isolates were incubated at 26°C for 10 days under dark conditions. Cadavers were collected every day, disinfected on their surfaces, transferred into sterilized plastic plates lined with moistened filter paper, and incubated in a dark place. Dead larvae were daily inspected and moistened with sterilized water to promote the outgrowth of mycelial on the cadavers. A control was treated with Tween 80 (0.001% v/v) and incubated under the same conditions (Ayele et al., 2020). Isolates with greater than 90% mortality of larvae were selected, considered to be virulent isolates, and preserved for further work.\n\nGermination test, radial growth, conidial yield and size, and screening of isolates data were analyzed using analysis of variance (ANOVA) followed by Tukey’s test with a statistical difference of P<0.05. Statistical Analysis System (SAS) (RRID:SCR_008567) software 9.4 version was used for data analysis. Means were separated using Tukey’s honestly significant difference (HSD) at P<0.05.\n\n\nResults\n\nThis study revealed that three B. bassiana and seven M. robertsii isolates were identified from rhizosphere soil samples of tomato plants. B. bassiana isolates showed white colony color, wide round to round colony shape, smooth powdery to smooth cottony surface texture, and raised colony elevation, as indicated in Table 1.\n\nMetarhizium robertsii isolates showed dark green to light green colony color at the front and brown at the backside, medium round to round colony shape, and flat to slightly raised colony elevation. Isolates K-101, K-102, RST-12, and S-26 showed a light green colony color, whereas K-61 and K-63 showed a dark green (Figure 1). The surface texture was thin, thick, and cottony.\n\n(A) Colony color (front) and (B) colony color (back) of B. bassiana. (C) Colony color (front) and (D) colony color (back) of M. robertsii. No manipulations were made to the image.\n\nResults from microscopic features indicated that B. bassiana isolates showed a flask-like shape in a conidiogenous cell, a branched conidiophore, and hyaline and smooth conidia with a spherical to subglobose arrangement (Figure 2) and aseptate hyphae (Figure 3),\n\n(A and B) B. bassiana. (C and D) M. robertsii. No manipulations were made to the images.\n\nA=B. bassiana, B=M. robertsii. No manipulations were made to the images.\n\nM. robertsii isolates revealed cylindrical in spore shape, branched, and densely intertwined conidiophore (Figure 2) and septate hyphal structures (Figure 3).\n\nSpore germination was ranging from 79.33 to 99.03% within 18 hours of incubation at 27±1°C (Table 2). The results showed that there was a statistically highly significant difference among isolates in the percentage of mean germination (F=54.6; DF=14; P<0.0001). Isolate K-61 showed a maximum mean percentage of germination, whereas the minimum mean percentage was recorded by isolate RST-12.\n\nStatistical analysis showed a highly significant difference among isolates at P<0.0001 in their conidial production. Conidial production varies from 0.11 × 107 to 2.67 × 107 spores ml-1. Maximum spore production was attained by isolate APPRC-27, followed by isolate K-61, whereas the minimum conidial yield was recorded by isolate APPRC-44BC (Table 3). The length of the conidia showed a mean value of 2.08 to 3.24 μm for B. bassiana isolates, and a higher conidial length was achieved by isolate APPRC-27 with 3.24 μm. The highest and lowest conidial diameters were recorded by isolates APPRC-27 and K-91, respectively.\n\nRegarding M. robertsii isolates, maximum conidial length and diameter were registered by isolate K-63, while minimum conidial length was obtained by isolate K-61 (Table 3). The lowest conidial diameter was recorded by isolate K-102 (1.93 μm) when compared to others (Figure 3).\n\nColony radial growth rates ranged from 1.73 to 3.24 mm day-1 (Figure 4). The highest colony radial growth rate was achieved by B. bassiana isolate K-91 on SDA, which increased by 16.96% radial growth compared to PDA media. The minimum radial growth rate was scored by isolate 44BC on both media.\n\nSDA, Sabouraud Dextrose Agar; PDA, Potato Dextrose Agar; RGSDA, radial growth on SDA; RGPDA, radial growth on PDA. No manipulations were made to the images.\n\nConcerning M. robertsii isolates, K-61 showed the highest radial growth with 2.92 on SDA media, followed by K-63 (2.85) mm day-1. Isolate RST-11 showed the lowest colony growth on PDA media.\n\nIn this study, the maximum growth rate was recorded on SDA media rather than PDA after 15 days of incubation at 27°C±1 for both species of isolates.\n\nMost isolates were virulent to Great Wax Moth (G. melonella) of second instar larvae, with 75–100% mortality after seven days of inoculation of treatments (Table 4). The mean percentage of mortality of G. melonella larvae by B. bassiana and M. robertsii was highly variable (F = 101.49; DF = 10; P < 0.0001). Maximum mean percentage mortality was achieved by M. robertsii isolates K-61 and K-102, while minimum mortality was recorded by M. robertsii isolate RST-11.\n\n\nDiscussion\n\nThe collected data from the rhizosphere soil of tomatoes above 70% belongs to the typical characteristics of M. robertsii. In the present study, six B. bassiana and eight M. robertsii were morphologically characterized to understand the potential virulence of entomopathogenic fungi. B. bassiana has a white colony color and is round in shape, whereas M. robertsii has a dark to light colony color and is medium-round to round in shape. Similar work was done by Deb and Dutta (2021). This result was confirmed by the previous findings of different researchers, they reported M. robertsii isolates indicating a round colony shape, thin to thick adpressed texture, and flat to slightly raised elevation (Sepúlveda et al., 2016).\n\nThis study also detected a microscopic feature of isolates. Consequently, B. bassiana had aseptate hyphae and M. robertsii showed a cylindrical shape with septate hyphae. A similar study reported that microscopic characterization of B. bassiana isolates indicated round to slightly round conidial shape with glassy-like aseptate hyphae, while M. robertsii were described as having cylindrical conidial shape, septate hyphae, and branched conidiophores in the form of a candelabrum (Bich et al., 2021).\n\nGermination is one component that affects the degree of virulence; the faster the germination rate, the higher the fungal infection of pests (Herlinda, 2010). This study showed that the highest conidial germination was achieved by M. robertsii isolate K-61 (99.03%) within 18 hours of incubation. This result is consistent with a study conducted by Gebremariam et al., (2021), in which spore germination percentage varied between 85.43 and 99.67% within 24 hours of incubation for 26 isolates. Likewise, conidial germination of Beauveria isolates ranged from 76.33 to 95.75% (Belay and Tenkegna, 2017), and 89.30 to 99% of spore viability were recorded by 22 isolates of B. bassiana and M. robertsii (Mkiga et al., 2020).\n\nMaximum sporulation rate, radial growth, and fast germination rate were the most important parameters for determining virulent isolates of entomopathogenic fungi, and the variation in virulence among isolates may be due to the geographical source of isolates and the potential of fungal species (Dotaona et al., 2015; Gebremariam et al., 2021). This result revealed that the highest radial growth rates were obtained by B. bassiana isolate K-91 (3.24 mm/day) and M. robertsii isolate K-61 (2.92 mm day-1) on SDA media at 27°C ±. This is consistent with M. robertsii developed on SDA media at 30°C, the temperature at which the rates ranged from 0.14 to 3.39 mm day-1 (Rodríguez et al., 2009). The present study revealed that all isolates showed maximum colony radial growth on SDA media rather than PDA. This may be due to the variation in nutrient contents between the media as SDA is selective. However, Gebremariam et al. (2021) reported that the radial growth of B. bassiana and M. robertsii isolates attained between 0.83 and 3.43-mm day-1 by AAUEM-3 and AAUMFB-77 isolates, respectively, which were grown on PDA media at 25°C.\n\nIn the case of M. robertsii isolates K-61 and K-102 showed higher virulence levels than other fungal isolates against G. melonella under laboratory conditions at seven days post-inoculation. The result confirmed the findings of previous work (Ibrahim et al., 2016). All isolates of B. bassiana and M. robertsii showed greater than 86% larval mortality, which indicated that isolates were virulent against G. mellonella. These findings were agreed upon in the work of Kebede (2019), in which it was reported that the top eight isolates of B. bassiana and M. robertsii were virulent to G. mellonella with above 75% larval mortality.\n\nThe results from microscopic features such as conidial length and width revealed that there was a highly significant difference among isolates. Accordingly, the highest conidial length was obtained with 7.10 and 3.24 μm for M. robertsii isolate K-63 and B. bassiana isolate APPRC-27, respectively. This agrees with previous work conducted by Doolotkeldieva et al. (2019), who reported the conidial length and width of B. bassiana were 2.27 and 1.85 μm, respectively, with a length to width ratio of 1.23 μm. Bich et al. (2021) also indicated that the conidial diameters of B. bassiana showed a mean value of 1.7 to 2.3 μm. Mongkolsamrit et al. (2020) also stated that M. robertsii showed a cylindrical to ellipsoid conidial shape with 5-7 and 2-3 μm in conidial length and width, respectively. However, Sepúlveda et al. (2016) reported that lower conidial lengths vary between 4.52 and 5.54 μm for M. robertsii strains. This may be due to the variation in the ecology of fungal species.\n\n\nConclusions\n\nCorrect identification of entomopathogenic fungi through morphological characterization is a baseline for the selection of virulent isolates for the management of agricultural pests. There was a variation in morphological features among all isolates in terms of colony color, shape, and texture. Isolates with the highest germination percentage and maximum spore production were virulent to second instar larvae of G. mellonella. Accordingly, M. robertsii isolates K-61 and K-102 were highly virulent to G. melonella by the Galleria dipping method, with a 100% mortality rate at 10 days post inoculation at a concentration of 1 × 108 conidial ml-1. This study showed that virulent B. bassiana and M. robertsii isolates had the potential to control pests by reducing the use of synthetic pesticides, making them sustainable and cost-effective, and increasing crop production and productivity using this eco-friendly method. Hence, it is recommended to use B. bassiana and M. robertsii for the management of agricultural pests. Moreover, further studies are needed on the factors attributed to the distribution, ecology, efficacy, and root association of B. bassiana and M. robertsii with tomato and other Solanaceae plants against pests.", "appendix": "Data availability\n\nDANS-EASY: Entomopathogenic fungi characterization data, https://doi.org/10.17026/dans-27p-epm2 (Geremew, 2023).\n\nThis project contains the following underlying data:\n\n• Germination (germination test of entomopathogenic isolates)\n\n• Radial growth PDA (radial growth of isolates on PDA media)\n\n• Radial growth SDA (radial growth of isolates on SDA media)\n\n• Screening (pathogenicity screening of isolates on Galleria melonella)\n\n• Conidial length and width (conidial size of isolates)\n\n• Conidial yield (conidial yield of isolates)\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 Ethiopian Institute of Agricultural Research (EIAR) acknowledged for the financial support. The authors are grateful to the Ambo Agriculture Research Center’s biocontrol research team for their assistance with laboratory experiments. Furthermore, the authors thank Mr. Denberu Kebede, Ms. Aberash Chala, and Mr. Tesfaye Abdisa for their assistance with the laboratory work. The authors also thank Tariku Hunduma (PhD) for his technical support in methodology development. The authors confirmed that the EIAR and individuals mentioned in this section permitted their names to be included in this publication.\n\n\nReferences\n\nAyele BA, Muleta D, Venegas J, et al.: Morphological, molecular, and pathogenicity characteristics of the native isolates of Metarhizium anisopliae against the tomato leafminer, Tuta absoluta (Meyrick 1917)(Lepidoptera: Gelechiidae) in Ethiopia. Egypt. J. Biol. Pest Control. 2020; 30(1): 1–11. 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Mycol. 2020; 95(1): 171–251. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNair DN, Padmavathy S: Impact of endophytic microorganisms on plants, environment and humans. Sci. World J. 2014; 2014: 1–11. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNegash B, Azerefegn F, Ayalew G: Insecticide resistance management against thrips (Thysanoptera: Thripidae) on onion in the central Rift Valley of Ethiopia. Int. J. Trop. Insect Sci. 2020; 40(4): 759–767. Publisher Full Text\n\nResquín-Romero G, Garrido-Jurado I, Delso C, et al.: Transient endophytic colonizations of plants improve the outcome of foliar applications of mycoinsecticides against chewing insects. J. Invertebr. Pathol. 2016; 136: 23–31. PubMed Abstract \| Publisher Full Text\n\nRodríguez M, Gerding M, France A, et al.: Evaluation of Metarhizium anisopliae var. anisopliae Qu-M845 isolate to control Varroa destructor (Acari: Varroidae) in laboratory and field trials. Chil. J. Agric. Res. 2009; 69(4): 541–547.\n\nRosana Y, Matsuzawa T, Gonoi T, et al.: Modified slide culture method for faster and easier identification of dermatophytes. Microbiol. Indones. 2014; 8(3): 135–137, 139. Publisher Full Text\n\nSchemmer R, Chládeková P, Medo J, et al.: Natural prevalence of entomopathogenic fungi in hibernating pupae of Cameraria ohridella (Lepidoptera: Gracillariidae) and virulence of selected isolates.2016; 52: 199–208.\n\nSepúlveda M, Vargas M, Gerding M, et al.: Molecular, morphological and pathogenic characterization of six strains of Metarhizium spp.(Deuteromycotina: Hyphomycetes) for the control of Aegorhinus superciliosus (Coleoptera: Curculionidae). Chil. J. Agric. Res. 2016; 76(1): 77–83. Publisher Full Text\n\nSevim A, Demir I, Höfte M, et al.: Isolation and characterization of entomopathogenic fungi from hazelnut-growing region of Turkey. Biocontrol. 2010; 55(2): 279–297. Publisher Full Text\n\nTabashnik BE, Van Rensburg JBJ, Carrière Y: Field-evolved insect resistance to Bt crops: definition, theory, and data. J. Econ. Entomol. 2009; 102(6): 2011–2025. PubMed Abstract \| Publisher Full Text\n\nVega FE, Posada F, Aime MC, et al.: Entomopathogenic fungal endophytes. Biol. Control. 2008; 46(1): 72–82. Publisher Full Text\n\nZimmermann G: Review on safety of the entomopathogenic fungi Beauveria bassiana and Beauveria brongniartii. Biocontrol Sci. Tech. 2007; 17(6): 553–596. Publisher Full Text\n\nZimmermann G: The ‘Galleria bait method for detection of entomopathogenic fungi in soil. J. Appl. Entomol. 1986; 102(1-5): 213–215. Publisher Full Text" }	[ { "id": "187389", "date": "09 Aug 2023", "name": "Tinatin Doolotkeldieva", "expertise": [ "Reviewer Expertise Biocontrol", "entomopthogenic bacteria", "fungi", "soil microbiology", "plant pathogology", "biopecticides", "bioremediation" ], "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\nFinding highly virulent entomopathogenic fungi remains an important challenge as an alternative to chemical pesticides. In this article, the authors tried to find two species of entomopathogenic fungi from tomato rhizosphere soil using classical methods of insect pathology, microbiology, entomology, etc.\nHowever, the authors intended to isolate endophytic fungi, and not from the soil itself; in total, they isolated them from the rhizosphere soil, and not from plant parts. Therefore, the authors should realize that they were dealing with soil fungi, this should be emphasized in the conclusions.\nIn conclusion, the authors suggest these strains for practical use, but it is too early to speak with such data, after extensive research by testing on other types of sucking insects and for the presence of endophytic properties, it will be possible to recommend them for practical purposes.\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? Partly", "responses": [ { "c_id": "10049", "date": "29 Nov 2023", "name": "Dereje Geremew", "role": "Author Response", "response": "Agreed with the comments, and the comments were included in the conclusion of the article. The conclusion was modified as follows: \"Correct identification of entomopathogenic fungi through morphological characterization is a baseline for the selection of virulent isolates for the management of agricultural pests. There was a variation in morphological features among all isolates in terms of colony color, shape, and texture. Isolates with the highest germination percentage and maximum spore production were virulent to second instar larvae of G. mellonella. Accordingly, M. robertsii isolates K-61 and K-102 were highly virulent to G. melonella by the Galleria dipping method, with a 100% mortality rate at 10 days post inoculation at a concentration of 1 × 108 conidial ml-1. This study showed that virulent B. bassiana and M. robertsii isolates collected from rhizospheric soil had the potential to control pests by reducing the use of synthetic pesticides, making them sustainable and cost-effective, and increasing crop production and productivity using this eco-friendly method. Hence, it is recommended to use B. bassiana and M. robertsii due to their endophytic properties for the management of agricultural pests, particularly sucking insects. Moreover, further studies are needed on the factors attributed to the distribution, ecology, efficacy, and root association of B. bassiana and M. robertsii with tomato and other Solanaceae plants against pests\"." } ] } ]	1	https://f1000research.com/articles/12-827
https://f1000research.com/articles/12-1468/v1	13 Nov 23	{ "type": "Research Article", "title": "Relationship Between Xylene, Rq Xylene Concentration And Heart Function In Industrial Workers In Surabaya", "authors": [ "Abdul Rohim Tualeka", "Tri Martiana", "Mohd Yusmaidie Aziz", "Tamilanban Thamaraikani", "Roslan Rosnon", "Salsabila Novianti", "Pudji Rahmawati", "Ahsan Ahsan", "Tri Martiana", "Mohd Yusmaidie Aziz", "Tamilanban Thamaraikani", "Roslan Rosnon", "Salsabila Novianti", "Pudji Rahmawati", "Ahsan Ahsan" ], "abstract": "Background Xylene is an organic solvent that is often used by industrial workers. Some industries that require xylene include the painting, printing, and shoe industries. In general, this enters the body through the inhalation pathway, namely the inhalation of xylene vapors while working.\n\nMethods Observational analytic research is conducted by looking at the relationship test with calculations using the chi-square method. The study was conducted in five regions in Surabaya, namely Kalijudan, Ketintang, Jemursari, AUP, and Romokalisari. The population includes a total of 90 workers with 77 of them taken as samples using the accidental sampling method.\n\nResults The results show that there is a relationship between xylene concentration and Serum Glutamic Oxaloacetic Transaminase (SGOT) levels (p> 0.05) and there is no relationship between xylene concentrations and Serum Glutamic Pyruvate Transaminase (SGPT) levels (p> 0.05). There was no relationship between RQ and SGOT levels (p> 0.05) and there was no relationship between RQ and SGPT levels (p> 0.05). However, from the calculation of the prevalence ratio, workers with unsafe RQ (RQ>1) have a 7.09x greater chance of experiencing damage to SGOT levels and a 1.06x greater chance to experience damage to SGPT levels.\n\nConclusions Based on these results, the industry is encouraged to provide nutritious food intake that can help excrete xylene from the body of the worker. Xylene concentration and RQ may play a role in the potential damage to SGOT and SGPT levels in workers.", "keywords": [ "Xylene", "RQ xylene", "heart function", "industrial workers", "safe work" ], "content": "Introduction\n\nAs a country develops overtime, the development is also directly proportional to the high potential danger to workers; one of which is exposure to chemicals as industrial raw materials. These chemicals, if entered into the body of workers can cause illness and health problems. Some chemicals that are found in many industries are benzene, toluene, and xylene.\n\nXylene is a solvent with the physical properties of colorless, flammable, volatile, and has a sweet aroma. This is a natural substance that is found in the contents of kerosene, coal, and others. Today many industries use xylene as a paint thinner and ink solvent. In addition, this is also commonly found in the agricultural industry as a solvent and emulsifier.\n\nXylene exposure to workers can be bad for health. According to (Kurnianto, 2016), several xylene exposure pathways include breathing, digestion, eye contact, and skin. Xylene that is inhaled by workers will enter and be retained in the lungs and eventually circulated to the body through the bloodstream. Many industries use xylene as a substitute for benzene. But based on experiments conducted, xylene is more dangerous than toluene. A study (Kurnianto, 2016) conducted whose results showed that the effect of the xylene threshold appeared at the lowest dose of toluene.\n\nXylene concentrations below 200 ppm can cause irritation to the eyes and mucous membranes. At higher concentrations of xylene, exposure can cause narcotic effects. Exposure to xylene ingested by workers can cause interference with the stomach and toxic effects on the liver. Meanwhile, acute exposure to xylene vapors can cause lung dysfunction and cause swelling and bleeding.\n\nOne of the health problems caused by xylene exposure to workers is the disruption to the digestive system. Indigestion can attack liver function which can be seen through Serum Glutamic Oxaloacetic Transaminase (SGOT) and SPGT levels. SGOT or Serum Glutamic Oxaloacetic Transaminase or also known as AST (aspartate aminotransferase) is one of the liver enzymes. This enzyme is located in the structure of the liver, so its appearance in the blood indicates damage or disruption in liver function. SGPT or Serum Glutamic Pyruvate Transaminase or called ALT (alanine aminotransferase) is also a liver enzyme in the liver. Elevated levels of SGPT in the blood indicate symptoms of damage or impairment in liver function.\n\nContinuous and frequent xylene exposure to workers can cause some health problems in the long run. These health problems include visual disturbances, dryness of the nose, dermatitis, and damage to the liver and kidneys (Rajan et al., 2019). This study aims to investigate the relationship between xylene, RQ xylene concentration, and heart function in industrial workers in Surabaya. The paper will begin with an introduction to xylene, its sources of exposure, and its potential health effects on humans. The second section will present the methodology of the study, including the study design, participants, and data collection methods. The third section will present the results of the study, including the relationship between xylene exposure and heart function in industrial workers in Surabaya. Finally, the paper will conclude with a discussion of the implications of the study for occupational health and safety, as well as recommendations for future research in this area.\n\n\nMethods\n\nThis is an observational analytic study in several shoe industry locations including Ketintang, Kalijudan, Jemursari, AUP and Romokalisari with a quantitative approach and conducted since 2019. These locations were chosen because they represent prominent shoe industry clusters in the region, and are known to have a substantial number of workers who are potentially exposed to xylene. The design of this study is cross-sectional that is observation and measurement of variables carried out at one time. By focusing on these areas, this study aimed to capture a diverse range of workers with varying levels of xylene exposure. The present study examines the relationship between xylene concentration, RQ xylene, and liver function in workers. Primary data and secondary data are taken for analysis. Primary data are in the form of questionnaires which are distributed to workers and samples while secondary data are in the form of company profile data.\n\nInformed consent was obtained from all participants involved in the study through a well-defined process that ensured their understanding and willingness to participate. The process included information provision, opportunity for questions, voluntary participation, consent forms, confidentiality assurance, and contact information. Informed consent is obtained through a written and oral process, and participants must sign the informed consent form voluntarily and participants must have the ability to make informed decisions. By following these steps, the study ensured that participants were fully informed about the study and their rights.\n\nThe study included workers from the shoe industry locations in Ketintang, Kalijudan, Jemursari, AUP, and Romokalisari, who had been employed there since 2019 or earlier, aged between 20 and 65 years, providing informed consent, free of known pre-existing liver diseases or conditions present during data collection, and offering complete and accurate questionnaire responses. Workers from non-specified locations, those who began employment after 2019, individuals below 20 or above 65 years of age, those with a history of liver diseases, those withholding informed consent, those unavailable during data collection, and those supplying incomplete or inaccurate questionnaire responses were excluded.\n\nA total of 90 workers were taken as a population with 77 of them taken as samples using the accidental sampling method. Accidental sampling is a type of non-probability sampling in which the selected population is easily accessible to the researcher, and available subjects are simply entered into the study without any attempt at randomization (University of Greenwich, 2019). This is also known as grab, convenience, or opportunity sampling (Alleydog, 2023). In this method, the researcher selects the sample based on who is available and willing to participate rather than using a specific sampling technique (ResearchArticle, 2021).\n\nThe independent variables are the concentration of xylene and RQ xylene, and the dependent variable is the function of the liver as seen through the levels of SGPT and SGOT. The blood samples independent and dependent variables were then tested in the Nutrition Laboratory of Airlangga University. After the data is collected, a relationship test is then performed to see the strength of the relationship using the chi-square test on categorical data. In addition to examining relationships, researchers also find out the level of risk using the prevalence rate (PR) formula.\n\n\nResults\n\nSome characteristics of respondents include age, sex, level of education, and work area. The following table distributes the characteristics of respondents who work in the Surabaya shoe industry.\n\nBased on Table 1, 25 (32.47%) of shoe industry workers aged 36-45 years with the majority of workers being male (61 or 79.22%) with the majority of final education level is senior high school (43 or 55.84%). Based on the working area of the shoe industry, 24 (31.17%) workers work in the shoe industry located in Romokalisari, Tambak Oso Wilangun, Surabaya.\n\nTable 2 shows that of the five shoe industries in Surabaya, the majority (98.7%) of workers had a concentration of xylene exposure below the threshold value of 100 ppm. There is only one worker whose concentration of xylene exposure (103.59) exceeds the threshold, namely in Jemursari. Based on the risk level (RQ), 72 (93.5%) workers fall into the safe RQ category by RQ <1. There are still 5 (6.5%) workers that fell into the risk category.\n\nTable 3 explains the distribution of SGOT rates and SGPT rates among workers. The normal rate of SGOT is 5-40 IU / L and SGPT is 5-35 IU/L. Based on these results it is known that 66 (85.7%) workers have normal SGOT levels. There were 58 (75.3%) workers with normal SGPT rate.\n\nBased on Table 4 there is no relationship between xylene concentration and xylene risk level (p> 0.05). Table 4 shows that there were 71 (92.2%) workers who had an RQ level <1 with a concentration of exposure <100 ppm and there were 5 (6.5%) workers who had an RQ level> 1. While for concentrations> 100 ppm there is 1 (1.3%) worker with risk level of RQ <1.\n\nAccording to Table 5, there was a relationship between SGOT and SGPT rates (p <0.05). Table 5 also shows that there are 55 (71.43%) workers with normal SGOT and SGPT levels. There were 11 (14.29%) employees with normal SGOT rates but SGPT rates were not normal. There were 3 (3.89%) employees with a normal SGPT rate and 8 (10.39%) employees with a normal SGPT rate.\n\nFigure 1 shows the highest average xylene concentration (122.81 ppm) is in Jemursari; the industry with the lowest average xylen concentration was Romokalisari (4.03 ppm). The highest average SGOT level was found in AUP (61.65 IU / L) and the lowest was found in Romokalisari (20 IU/ L). The highest average SGPT level was found in the AUP industry (45.25 IU / L) and the lowest average was in Kalijudan (19.5 IU/L).\n\nBased on Figure 2, the highest average RQ was found in Romokalisari (0.54) while the lowest average was found in Jemursari (0.004). SGOT and SGPT levels are the same as those listed in Figure 1.\n\nTable 6 shows the results of the cross tabulation test between xylene concentrations and SGOT levels in workers. Based on the chi square test there was no relationship between xylene concentration and SGOT levels in workers (p> 0.05). There were 66 (85.7%) workers with xylene concentration <100 ppm and normal SGOT levels; 10 (13.0%) other workers had abnormal SGOT levels. There are 1 (1.3%) workers with abnormal SGOT levels and exposed to concentrations >100 ppm. Based on the prevalence rate calculation, xylene concentration is a protective factor against damage to SGOT levels.\n\nBased on Table 7 there is no relationship between xylene concentration and SGPT levels (p >0.05). There were 58 (75.3%) workers who were exposed to xylene concentrations <100 ppm and had normal SGPT levels and 18 (23.4%) workers who had abnormal SGPT levels. In workers exposed to xylene concentrations exceeding NAV, there is 1 worker (1.3%) who has an abnormal SGPT level. Based on the calculation of the prevalence rate workers exposed to xylene concentration are included in the protection factor will cause damage to SGPT level.\n\nTable 8 shows no relationship between RQ xylene and SGOT levels (p> 0.05). There were 61 (79.2%) workers who had RQ level <1 and normal SGOT level and 11 (14.3%) workers who had abnormal SGOT levels. In RQ> 1 there were 5 (6.5%) workers who had normal SGOT levels. Based on the calculation of the prevalence rate of workers with RQ <1, 7.09x greater risk of damage to SGOT levels.\n\nBased on Table 9 there was no relationship between RQ xylene and SGPT levels (p> 0.05). There were 54 (70.1%) workers who had RQ <1 and normal SGPT levels and there were 18 (23.4%) workers who had abnormal SGPT levels. For workers with RQ> 1 there were 4 (5.2%) workers with normal SGPT levels and 1 (1.3%) workers with abnormal SGPT levels. Based on the calculation of the prevalence rate, workers with RQ <1 were at a risk of 1.067x greater to experience damage to SGPT levels.\n\n\nDiscussion\n\nBased on Table 1, Table 2, and Table 3 regarding the frequency distribution of respondents and workplaces, 25 (32.47%) respondents/majority were aged 36-45 years; the most gender is male (61) and the highest level of education is the high school/vocational high school (43 or 55.84%) and the majority of workers work in the Romokalisari industry (24 people/31.17%). In Table 2 regarding the distribution of xylene exposure from concentration and risk quotient (RQ), there were 76 (98.7%) workers who were exposed to xylene with a concentration of <NAV (NAB = 200 ppm). Only 1 (1.3%) workers were exposed to concentrations> threshold. Based on the results of the study there were 72 (93.5%) workers included in the RQ category <1 (safe) and 5 (6.5%) other workers included in the RQ> 1 (risk) category. In Table 3 the distribution of SGOT and SGPT levels among workers is 66 (85.7%) workers with normal SGOT levels (5-40 IU/L) and 11 (14.3%) workers who have abnormal SGOT levels. There were 58 (75.3%) workers who had normal SGPT levels and 19 (24.7%) workers with abnormal SGPT levels.\n\nTable 4 explains the relationship between the concentration of xylene exposure and the RQ xylene category in workers. Using the chi-square test, there was no relationship between concentration and RQ (p> 0.05). This can be caused by the increase in the RQ category not only influenced by concentration but also many other factors such as nutritious food intake. Table 5 shows that from the test of the relationship between SGOT and SGPT levels, there is a relationship between SGOT and SGPT levels where the increase and decrease of SGOT levels is consistent with changes in SGPT levels (p <0.05). SGOT and SGPT levels are one of the biomarkers that are often seen to review human liver function. The increase in SGOT levels is in line with the increase in SGPT levels.\n\nTable 6 is the result of the test of the relationship between the xylene concentration variable and SGOT levels in workers. Based on the test results of the relationship with chi square there is no relationship between xylene concentration and SGOT levels in workers. This could be influenced by factors other than concentration in the form of the duration and frequency of xylene exposure. Table 2 shows that only 1 (1.3%) worker experienced exposure above the NAV and 76 (98.7%) other workers were exposed to xylene within the NAV limit. In Table 7 there is no relationship between xylene concentration and SGPT levels (p> 0.05). In another study conducted by (Cahyana et al., 2015) xylene concentration had a strong correlation with MHA levels. MHA itself is an acid produced from xylene metabolism in the body which will be released together with urine.\n\nTable 8 shows the test of the relationship between RQ variables and SGOT levels using the chi-square test. There was no relationship between RQ and SGOT levels in the blood (p> 0.05). Table 9 tests the relationship between RQ and SGPT levels and shows that there is no relationship between RQ and SGPT levels in workers (p> 0.05). This can be caused because the RQ of workers in the industrial area of Surabaya is still in the safe category (RQ <1); the concentration of xylene exposure is also still within the threshold. Therefore, only a few workers were found to have RQ> 1.\n\nResearch conducted by (Rusdy, 2012) with a thesis entitled Analysis of Neurotoxic Symptoms Due to Exposure of Organic Xylene Solvents to Paint Manufacturing Workers notes that 95.6% of workers are exposed to xylene in threshold values that are still relatively safe. This thesis explains the effects caused by xylene exposure in the form of neurotoxic symptoms. The test results show that there is no relationship between the concentration of xylene exposure and neurotoxic symptoms in workers (r> 0.05). This study also states that there is little evidence to suggest a chronic effect on liver function due to xylene exposure. According to (Morley et al., 1970) the chronic effects of liver function occur when workers are exposed to extreme exposure. This also supports the results of the study found that from the concentration and RQ variables there is no relationship between levels of SGOT and SGPT in workers.\n\nResearch conducted by (Irawati, 2010) also states the same thing that the IARC and EPA have not been able to determine whether xylene is carcinogenic to humans. Some health effects experienced by workers due to xylene exposure are dizziness, nausea, headaches, and loss of balance. But there are no studies that state that xylene exposure interferes with or even damages the function of the human heart. Some studies suggest that exposure to BTX (benzene, toluene, xylene) has a direct impact on the neurotoxic or nervous system in humans due to exposure that enters through the inhalation system.\n\n\nConclusion\n\nBased on the test results of each relationship between xylene concentration, SGOT levels, and SGPT levels there was no relationship (p> 0.05). In the test of the relationship between RQ with levels of SGOT and SGPT also found no relationship (p> 0.05). In addition to seeing the relationship test, the researchers also calculated the prevalence ratio with the result of xylene concentration included in the protection factor for SGOT levels and SGPT levels in workers (PR <1). RQ is a supporting factor because in calculating the prevalence of the ratio between RQ and SGOT levels, workers classified as abnormal RQ have a 7.09x greater chance of experiencing damage to SGOT levels. Calculations with SGPT levels indicate that workers classified as abnormal RQ have a 1.06x greater chance of experiencing damage to SGPT levels. Based on the results, a review of RQ calculations for workers is needed so that the factors that cause RQ in insecure workers are known. The company should provide an enzyme-rich intake so that xylene toxins can be excreted by the body.\n\nEthical approval was obtained from the Universitas Airlangga, Faculty of Dental Medicine ethics committee (605/HRECC.FODM/IX/2019).\n\nThe objectives and protocols of the study were explained to the participants and obtained written informed consent from each subject before participation in the study.", "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\nAcknowledgments\n\nThe authors would like thank to the rector of Airlangga University. The authors would like to acknowledge Relationship between xylene, RQ xylene concentration and heart function in industrial workers in Surabaya.\n\n\nReferences\n\nAlleydog: Accidental Sampling. Alleydog: Com’s Online Glossary; 2023. Reference Source\n\nCahyana GH, Sukrisna A, Mulyani T: Pada Pekerja Informal Pengecatan Mobil Di Karasak, Bandung Exposure Correlation of Xylene and Methyl Hippuric Acid on Informal Car Painting Workers in Karasak, Bandung.2015; 79–94.\n\nIrawati Y: Analisis Resiko Kesehatan Pajanan Xylene Pada Pekerja Bengkel Sepatu ‘X’Di Kawasan Perkampungan Industri Kecil (Pik) Pulogadung Jakarta Timur 2010. Fakultas Kesehatan Masyarakat. [Depok]: Universitas Indonesia. 2010.\n\nKurnianto AA: Hubungan Kadar Xylene Darah dengan Keluhan Neurologis Pada Pekerja Pengecatan Mobil Jalan Pengenal Surabaya. UNIVERSITAS AIRLANGGA; 2016.\n\nMorley R, Eccleston DW, Douglas CP, et al.: Xylene poisoning: a report on one fatal case and two cases of recovery after prolonged unconsciousness. Br. Med. J. 1970; 3(5720): 442–443. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRajan ST, Narasimhan M, Rao KB, et al.: Toxicity of xylene in occupationally exposed workers: A high-performance liquid chromatography analysis. Journal of Oral and Maxillofacial Pathology: JOMFP. 2019; 23(2): 303. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nResearchArticle: Accidental Sampling in Qualitative Research. Rsearcharticle. 2021. Reference Source\n\nRusdy MDR: Analisis Gejala Neurotoksik Akibat Pajanan Pelarut Organik Xylene pada Pekerja Pembuatan Cat PT. X Tahun 2012. 2012.2012; 1–135.\n\nUniversity of Greenwich: Accidental Sampling - Lecture notes 4. Business research method. 2019. Reference Source" }	[ { "id": "232284", "date": "11 May 2024", "name": "Somayeh Farhang Dehghan", "expertise": [ "Reviewer Expertise 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\nDear,\nThank you for the opportunity to review the article. This study aimed to investigate the relationship between xylene, RQ xylene concentration, and heart function in industrial workers in Surabaya. . They pertain to topics such as methodology, many contradictions, and poorly written and the authors' lack of familiarity with the related specialized terminology. See the comments below: Title--The term \"heart function\" is quite broad; however, in this article, only enzyme assessment was conducted for this purpose. -Consider the SGOT and SGPT levels in workers aren’t dedicated biomarker for heart function. -Only the workers of shoe industries have been assessed, not whole worker industry of Surabaya. Abstract-The aim (s) has been ignored.There is no information available on air and blood sampling.Report the R values.A conclusion does not introduce new ideas; instead, it should clarify the intent and importance of the paper. Introduction-Provide the references.Check the correct format of in-text citation and verify the necessity of parentheses.Replace the “hazard” and “hazardous” with “danger” and “dangerous”.The fifth paragraph discusses how SGOT and SGPT are biomarkers of liver function; however, the topic of the article is about heart function.Define the SPGT in first use.In the last paragraph, please outline the unresolved issues and research gaps, as well as the direct and indirect applications of this study. The statement discussing how the results of this research can help resolve ambiguities is found in the last paragraph. Methods- In the first paragraph,Since 2019? Or in 2019? I believe your study is cross-sectional.In Inclusion criteria ,Free of known pre-existing liver diseases??In Exclusion criteria,Those with a history of liver diseases? How was the adequacy of the sample size determined? There is no detailed information available on air and blood sampling. How were the confounding factors (e.g. physical activity, nutrition, smoking, …) controlled? Was there no control group? Discussion-First, mention the purpose of the study. Then, state the results of each hypothesis separately, present congruent and discordant research, explain how past research aligns or differs, and interpret the results based on the theoretical framework and research outlined in the introduction of the article. Finally, the general and practical conclusions, the generalizability of the results, and the presentation of the contributions of this research to existing theoretical and practical knowledge are outlined. Following that, the limitations of the research are discussed, along with suggestions for future studies\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [] } ]	1	https://f1000research.com/articles/12-1468
https://f1000research.com/articles/13-112/v1	19 Feb 24	{ "type": "Research Article", "title": "Secondary range symmetric matrices", "authors": [ "Divya Shenoy" ], "abstract": "The concept of secondary range symmetric matrices are introduced here. Some characterizations as well as the equivalent conditions for a range symmetric matrix to be secondary range symmetric matrix is given. The idea of range symmetric matrices, range symmetric matrices over Minkowski space and secondary range symmetric matrices are different, and is depicted with the help of suitable examples. Finally, a necessary and sufficient condition for a secondary range symmetric matrix to have a secondary generalized inverse has been obtained.", "keywords": [ "Generalized inverses", "Secondary generalized inverses", "Secondary transpose", "EP matrices" ], "content": "Introduction\n\nThe theory of symmetric matrices as well as range symmetric matrices are well known in literature. A matrix is said to be EP (or range symmetric), whenver the range space of the matrix is equal to the range space of its conjugate transpose. In other words, matrix is EP whenever its null space is same as that of the null space of its conjugate transpose. Ballantine1 has studied about the product of two EP matrices of specific rank to be again an EP matrix. In2 new characterizations of EP matrices are given. Also, weighted EP matrix is defined and characterized. Meenakshi3 extended the concept of range symmetric matrices over Minkowski space. In 2014, the same author defined range symmetric matrices in indefinite inner product space.4\n\nFor an n×n matrix A, the secondary transpose is related to transpose of the matrix by the relation AS=VATV. Here, the matrix V has non zero unitary entries only on the secondary diagonal. For a matrix A with complex entries, the secondary transpose will be renamed as secondary conjugate transpose Aθ and is given by Aθ=VA∗V.\n\n(Ref. 5) Let A∈ℝn×n. Then the secondary transpose (or secondary conjugate transpose Aθ in the case of complex matrices) of A denoted by AS and is defined as AS=bij, where bij=an−j+1,n−i+1, i,j=1,2,…n.\n\nThroughout this article we assume V to be a permutation matrix with units in the secondary diagonal. Also, NA represents the null space of the matrix A. The column space and rank of A are denoted by CA,ρA respectively. The set of matrices of order n×n over the field of real numbers is denoted by ℝn×n.\n\nThe concept of secondary conjugate transpose is gaining importance in recent years. Shenoy6 has defined Outer Theta inverse by combining the outer inverse and secondary transpose of a matrix A. Drazin-Theta matix AD,θ7 is a new class of generalized inverse introduced for a square matrix of index m. One can refer8 for the extension of these inverses over rectangular matrices. R. Vijayakumar9 introduced the concept of secondary generalized inverse with the help of secondary transpose of a matrix. This concept is similar to Moore Penrose inverse. But unlike Moore penrose inverse, existence of s-g inverse is not assured in general. In Ref. 10, a necessary and sufficient conditions of existence of s-g invese is given. In the same article, a few characterizations and a determinantal formula for s-g inverse also has been discussed. In 2009, Krishnamoorthy and Vijayakumar11 has defined the concept of s-normal matrices with the help of secondary transopse for a class of complex square matrices. Jayashree12 has defined secondary k-range symmetric fuzzy matrices. Its relation with s-range symmetric fuzzy matrices, k-range fuzzy symmetric matrices and EP matrices are defined.\n\nIn this article, we define secondary range symmetric matrices. Several equivalent conditions for a matrix to be secondary range symmetric, is obtained here. Also, the existence of secondary generalized inverse of a secondary range symmetric matrix is discussed.\n\nBelow are some useful deifnitions and results related to secondary conjugate transpose.\n\n(Ref. 13) Let A∈ℂn×n. Then the conjugate secondary transpose of A denoted by Aθ and is defined as Aθ=A¯s=cij where cij=a¯n−j+1,n−i+1.\n\n(Ref. 13) A matrix is said to be secondary normal (s-normal) if AAS=ASA.\n\n(Ref. 10) A†S is said to be secondary generalized inverse of A if\n\n(Ref. 10) Given an m×n matrix A. The following statements are equivalent.\n\n(i) A has s-cancellation property (i.e., AsAX=0AX=0 and YAAs=0YA=0).\n\n(ii) ρAsA=ρAAs=ρA\n\n(iii) As exists.\n\n(Ref. 14) A matrix A∈ℂn×n is said to be EP (or range symmetric) if NA=NA∗.\n\nMeenakshi3 has defined EP in Minkowski space and has given equivalent conditions for a matrix to be range symmetric.\n\n(Ref. 3) A matrix A∈ℂn×n is said to be range symmetric in Minkowski space if and only if NA=NA+.\n\nHere A+ represents the Minkowski adjoint given by A+=GA∗G where G is the Minkowski metric tensor.\n\n\nResults\n\nIn this section, we define secondary range symmetric matrices which is analogous to that of range symmetric matrices. Some equivalent conditions for a matrix to be range symmetric is also given here.\n\nX is secondary right (left) normalized g inverse of A if AXA=A, XAX=X and AX is S-symmetric. (XA is S-symmetric).\n\nConsider A∈ℝm×n. The s-transpose of A is defined as As=bij where bij=am−j+1,n−i+1, 1≤i≤n,1≤j≤m.\n\nA matrix A∈ℝn×n secondary range symmetric if and only if NA=NAS\n\nLet A∈ℝn×n. Then the following conditions are equivalent.\n\n(i) A is secondary range symmetric\n\n(ii) VA is EP\n\n(iii) AV is EP\n\n(iv) NA∗=NAV\n\n(v) CA=CAS\n\n(vi) AS=BA=AC where B and C are some nonsingular matrices\n\n(vii) CA∗=CVA\n\n(viii) CA∗⊕NA=ℂn\n\n(ix) CA⊕NA∗=ℂn\n\n\n\nHence 1⇔2⇔3 holds true.\n\n1⇔4\n\nThis proves the equivalence of 1 and 4.\n\n3⇔5\n\nHence 3 and 5 are equivalent.\n\n2⇔6\n\nHence 2⇔6.\n\n5⇔7\n\nThus equivalence of 5 and 7 are proved.\n\n2 ⇔ 8.\n\nThus equivalence of 2 and 8 are proved.\n\n3⇔9\n\nThus the equivalence of 3 and 9 is proved.\n\nFrom the following example, it is clear that EP matrices in Minkowski space defined by Meenakshi3 and secondary range symmetric matrices are two different concepts.\n\nConsider a matrix A=−111−1 where AS=−111−1. Here, A is secondary normal as well as ρA=ρAAS. The matrix A is secondary range symmetric. However, the matrix is not range symmetric in Minkowski’s space since A+=GA∗G=−1−1−1−1. It is clear that NA≠NA+.\n\nLet B=1−11−1 and BS=−1−111. Clearly B is not secondary range symmetric.\n\nObserve that B is range symmetric in Minkowski space. Since, B+=GB∗G=1−11−1 so that NB=NB+.\n\nNote that AS=VA∗V=VGA+GV.\n\nA necessary condition for a matrix to be a s-EP (secondary range symmetric) is proved here.\n\nLet A∈ℝn×n. If A is secondary normal and ρA=ρAAS, then A is secondary range symmetric.\n\nSince A is secondary normal, AAS=ASA. Hence ρA=ρAAS=ρASA=ρAS which implies NA=NAAS=NASA=NAS. Thus A is secondary range symmetric.\n\nA relation connecting range symmetric and secondary range symmetric matrices is given below:\n\nLet A∈ℝn×n. Then any two of the following conditions imply the third one.\n\n(1) A is EP.\n\n(2) A is secondary EP.\n\n(3) CA=CVA.\n\n1,2⇒3\n\nSince A is EP, CA=CA∗. By Theorem 0.2, CA∗=CVA as A is secondary range symmetric. Hence A is secondary EP ⇔ CA=CVA.\n\n2,3⇒1\n\nSince A is s-EP, by Theorem 0.2, VA is range symmetric. Hence CVA=CVA∗=CA∗V=CA∗. Also, By (3), CA=CVA from which it follows that CA=CA∗. Hence A is range symmetric. Thus (1) holds.\n\nFor any square complex matrix A, there exists unique S- symmetric matrices such that A=M+iN where M=12A+AS and N=12iA−AS. In the following theorem, an equivalent condition for a matrix A to be secondary range symmetric is obtained interms of M, the S-symmetric part of A.\n\nFor A∈ℝn×n, A is secondary range symmetric if and only if NA⊆NM where M is the S-symmetric part of A.\n\nIf A is secondary range symmetric, then NA=NAS. For x∈NA, Ax=0 and ASx=0. Hence Mx=0. Thus, NA⊆NM, then Ax=0⇒Mx=0 and hence Nx=0. Therefore NA⊆NN. Thus NA⊆NM∩NN. Since, both M and N are S-symmetric, they are secondary range symmetric.\n\nNow, NA⊆NM∩NN=NM∗V∩NN∗V⊆NM∗+iN∗V=NA∗V and ρA=ρA∗=ρA∗V. Therefore, NA=NA∗V=NVA∗V=NAS. Thus A is secondary range symmetric.\n\nWe shall discuss the existence of secondary generalized inverse inverse of a secondary range symmetric matrix. First, we shall prove certain lemmas, to simplify the proof of the main result.\n\nFor an m×n matrix A, if A†S exists, then CA†S=CAS.\n\nIf A†S exists, then A†SA=A†SAS=ASAA†SSA†SS and\n\nFurther, ρA†S=ρA=ρAS. Thus, CA†S=CAS.\n\nFor an m×n matrix A, if A†S exists, then CAA†S is the projection on CA†S and A†SA is the projection on CA†S.\n\nx∈CA if and only if x=Ay=AA†SAy=AA†Sx. By definition 2, AA†S being S-symmetric, idempotent is the projection on CA. Similarly, x∈CA†S if and only if x=A†SAA†Sy=A†SAx and A†SA is S-symmetric and idempotent. Hence A†SA is the projection on CA†S.\n\nFor an n×n matrix A, the following are equivalent:\n\n(1) A is secondary range symmetric and ρA=ρA2.\n\n(2) A†S exists and A†S is secondary range symmetric.\n\n(3) There exists a symmetric idempotent matrix E such that AE=EA and CA=CE.\n\n1⇒2. Since ρA=ρA2 and A is secondary symmetric, by using Theorem 0.2 we have, ρASA=ρBA2=ρA2=ρA and ρAAS=ρA2C=ρA2=ρA. Thus ρA=ρAAS=ρASA. Hence by Thoerem 0.1, it follows that A†S exists, By Lemma 1 and Theorem 0.2, CA†S=CAS=CA=CASS=CA†SS. Hence A†S is range symmetric. Thus (2) holds.\n\n2⇒3. Since A†S exists, by Lemma 1, CA†S=CAS, by Theorem 0.2, A†S is secondary range symmetric which implies that CA†S=CA†SS. Hence CAS=CA†SS. By Lemma 2, it follows that ASAS†S=A†SSAS, hence A†SAS=AA†SS. By definition 2, A†SA=AA†S=E, is S-symmetric, idempotent and AE=EA=A; hence CA⊆CE and ρE=ρAA†S=ρA, which implies CA=CE. Thus 3 holds.\n\n3⇒1. Since, E is S-symmetric and idempotent, ES=E=E2, by lemma 1.1, E†S exists and E†S=E implies E is the projection on CA. For all reflexive g-inverses Ar of A, AAr=EE†S=E. Since E is S-symmetric and idempotent, AAr is S-symmetric. Hence by definition 7, An exists and AAn=EE†S=E which implies EA=A. By hypothesis AE=EA=A. Therefore AAn=AnA=E. Thus both AAn and AnA are S-symmetric. By definition 2, A†S exists and E=AA†S=A†SA. By taking secondary transpose on AE=EA=A, we get EAS=ASE=AS. CAS⊆CE=CA and ρAS=ρA. Therefore CA=CAS. By theorem 0.2, A is secondary ramge symmetric. ρAAS≥ρAASA†SS=ρAA†SS, ρAE=ρA≥ρAAS. Thus ρA=ρAAS=ρA2C=ρA2. Thus (1) holds. Hence the theorem.\n\nConsider an n×n secondary range symmetric matrix A. Then A†S exists if and only if ρA=ρA2.\n\nSince A is secondary range symmetric and ρA=ρA2, the existence of A†S follows from Thereom 0.6. Conversly, if A is secondary range symmetric, and A†S exists, then by Theorem 0.1 ρA=ρAAS=ρASA and by Theorem 0.2, AS=AC. Hence ρA=ρAAC=ρA2.\n\n\nConclusion\n\nAs an extension of this work, one can think of defining weighted secondary EP matrices and its characteriations. Also, extending secodary range symmetric matrix to indefinite inner prodcut spaces will open up a new area of research.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nBallantine CS: Products of EP matrices. Linear Algebra Appl. 1975; 12(3): 257–267. Publisher Full Text\n\nTian Y, Wang H: Characterizations of EP matrices and Weighted EP matrices. Linear Algebra Appl. 2011; 434(5): 1295–1318. Publisher Full Text\n\nMeenakshi AR: Range Symmetric Matrices in Minkowski Space. Bull. Malaysian Math. Sci. Soc. 2000; 23: 45–52.\n\nMeenakshi AR: Range Symmetric Matrices in Indefinite Inner Product Space. Int. J. Fuzzy Math. Arch. 2014; 5(2): 49–56.\n\nLee A: Secondary symmetric, Skew symmetric and orthogonal matrices. Period. Math. Hung. 1976; 7(1): 63–70. Publisher Full Text\n\nShenoy DP: Outer-Theta and Theta-Outer matrices. IAENG Int. J. Appl. Math. 2022; 52(4): 1020–1024.\n\nShenoy DP: Drazin-Theta and Theta-Drazin matrices. Numer. Algebra, Control. Optim. 2022. (Article in Press). Publisher Full Text\n\nShenoy DP: Drazin theta inverse for rectangular matrices. IAENG Int. J. Comput. Sci. 2023; 50(4): IJCS_50_4_41.\n\nVijayakumar R: s-g inverse of s-normal matrices. Int. J. Math. Trends Technol. 2016; 39(4): 240–244. Publisher Full Text\n\nSavitha V, Shenoy DP, Umashankar K, et al.: Secondary transpose of a matrix and generalized inverses. J. Algebra Its Appl. 2024; 23(3): 2450052. Publisher Full Text\n\nKrishnamoorthy S, Vijayakumar R: Some equivalent conditions on s-normal matrices. Int. J. Contemp. Math. Sci. 2009; 4(29): 1449–1454.\n\nShree DJ: Secondary k-range symmetric fuzzy matrices. J. Discret. Math. Sci. Cryptogr. 2018; 21(1): 1–11. Publisher Full Text\n\nKrishnamoorthy S, Vijayakumar R: Some characteristics on s-normal matrices. Int. J. Comput. Appl. Math. 2009; 4(1): 49–53.\n\nBen-Israel A, Greville TNE: Generalized Inverses and Applications. Wiley; 1974." }	[ { "id": "252908", "date": "28 Mar 2024", "name": "P Sam Johnson", "expertise": [ "Reviewer Expertise Functional Analysis" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe paper is well written. It discusses secondary range symmetric matrices. It should incorporate the following suggestions / corrections : Minor points : (i) First line of abstract should be \"is\" introduced. (ii) No uniformity of symbol \"s\" in many places : s-symmetric, s-transpose ; capital letter or a small letter (iii) Corollary 1 in page 6 should be rephrased as : Let A be an nxn secondary range symmetric matrix. Major point:\n(iv) The following recent references may be added.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? 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": "11348", "date": "04 Apr 2024", "name": "Divya Shenoy", "role": "Author Response", "response": "I thank reviewer 1 for the critical comments. The suggested corrections (typo errors) and the inclusion of latest references in the manuscript and their corresponding information in the body of the manuscript will be incorporated in version 1, which will be uploaded after receiving comments from the second reviewer." }, { "c_id": "11821", "date": "11 Sep 2024", "name": "Divya Shenoy", "role": "Author Response", "response": "Comments and Responses A. Response to Minor points : Comment (i): First line of abstract should be \"is\" introduced. Response: The correction has been incorporated. Comment (ii): No uniformity of symbol \"s\" in many places: s-symmetric, s-transpose; capital letter or a small letter. Response: Uniformity has been maintained in the new version. Capital letter is used for all instances, S – symmetric, S – transpose etc. Comment (iii): Corollary 1 in page 6 should be rephrased as: Let A be an nxn secondary range symmetric matrix. Response: The suggested correction has been incorporated. Major point: Comment (iv): Regarding the addition of recent references on a) product and factorization of hypo-EP operators and b) Closed EP and hypo-EP operators on Hilbert spaces. Response: The latest references have been added. The relevant text is added in the article, with appropriate citation." } ] }, { "id": "274406", "date": "08 Jun 2024", "name": "Pankaj Kumar Manjhi", "expertise": [ "Reviewer Expertise Combinatorial matrices", "Discrete Mathematics", "computer 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\nI am very delighted to see the scholarly interest in the study of range symmetric matrices. Here are my suggestions for improving the article:\nSome definitions (such as definition 1) are not clearly written and need to be clarified for better understanding. The article requires a sufficient number of illustrations to explain the theory and definitions, which are currently missing. A new preliminary section should be included, containing all the necessary basic concepts to provide a strong foundation for the reader. Definition 7 does not adequately explain the entries of matrix A and needs to be revised for clarity. Definitions 7 and 8 should be illustrated through examples to enhance comprehension. The proofs, especially the proof of Theorem 1, are not written in an easily understandable manner and should be simplified for better readability. A conclusion and discussion section must be included and well explained to summarize the findings and implications of the study. The definition of Minkowski’s space should be included, accompanied by examples to illustrate its application. The examples given at the beginning of page 5 are not properly explained and need to be elaborated for clarity.\nBy addressing these points, the article can be significantly improved and provide a clearer, more comprehensive understanding of range symmetric matrices.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "11822", "date": "11 Sep 2024", "name": "Divya Shenoy", "role": "Author Response", "response": "Comments and Responses: Comment 1: Some definitions (such as definition 1) are not clearly written and need to be clarified for better understanding. Response: Definition 1 (of the secondary transpose of a rectangular matrix) has been quoted from: A. Lee, Secondary symmetric, Skew symmetric and orthogonal matrices, Period. Math. Hungar 7(1), pp. 63-70, 1976. In the revised article, it is elaborated and an example [example-2, results] has been added for better understanding of the concept. Comment 2: The article requires a sufficient number of illustrations to explain the theory and definitions, which are currently missing. Response: As per the suggestion, the article is modified providing sufficient examples. On page 3, the definitions are explained with examples [example 1, 2 and 3]. Also, a clearer explanation is given for the example given after the proof of theorem 0.1. Comment 3: A new preliminary section should be included, containing all the necessary basic concepts to provide a strong foundation for the reader. Response: A preliminary section [section 2] is included with all necessary basic concepts. Comment 4: Definition 7 does not adequately explain the entries of matrix A and needs to be revised for clarity. Response: The definition (7) has been revised. The entries of the matrix are from a real field. The explanation has been provided in the text. Comment 5: Definitions 7 and 8 should be illustrated through examples to enhance comprehension. Response: As per the suggestion, definitions 7 and 8 are explained with examples. Comment 6: The proofs, especially the proof of Theorem 1, are not written in an easily understandable manner and should be simplified for better readability. Response: Explanation for the steps for the proof of Theorem -1, has been provided within parenthesis. Comment 7: A conclusion and discussion section must be included and well explained to summarize the findings and implications of the study. Response: The conclusion section has been modified to include discussion, and scope for future work. Comment 8: The definition of Minkowski’s space should be included, accompanied by examples to illustrate its application Response: As per the suggestion, the definition of Minkowski space, with application and reference is included in the preliminary section. Comment 9: The examples given at the beginning of page 5 are not properly explained and need to be elaborated for clarity. Response: The example is elaborated for better understanding." } ] }, { "id": "261048", "date": "08 Jun 2024", "name": "Mehsin Jabel Atteya", "expertise": [ "Reviewer Expertise The paper tried to supply new results with avoid any mistake." ], "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\nDear Sir., My Report: 1. The Definitions 7, 8 and 9 need to provide examples. 2. In the proof of Theorem 0.4, where the prove of the case (1) and (3) implies to (2). 3. in the proof of Corollary 1, the author used Theorem 0.1 while Theorem 0.1 concerning\n\nan m×n matrix A. 4. Again in Corollary 0.1, the author depended on Theorems (0.1 and 0.6) without mention the branches. Similarly for the prove of Theorems(0.3 and 0.6) where the author used Theorems (0.2 and 0.1). 5. The branches of Theorem (0.2) wrote by Roman numbers system while in the proof used Arabic numbers system.\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": "11823", "date": "11 Sep 2024", "name": "Divya Shenoy", "role": "Author Response", "response": "Comments and Responses: Comment 1: The Definitions 7, 8 and 9 need to provide examples. Response: Definitions 7,8 and 9 are illustrated with examples- 1, 2 and 3 respectively. Comment 2: In the proof of Theorem 0.4, where the prove of the case (1) and (3) implies to (2). Response: The omission error has been corrected in the revised article. A proof for (1) and (3) implies (2) is added in the new version. Comment 3: In the proof of Corollary 1, the author used Theorem 0.1 while Theorem 0.1 concerning an m×n matrix A. Response: Theorem 0.1 holds for a matrix of any order [m×n as well as n×n ]. For generalization, the authors [in reference: V. Savitha, D. P. Shenoy, K. Umashankar and R. B. Bapat, Secondary transpose of a matrix and generalized inverses, Journal of Algebra and its applications, 23(3), 2450052, 2024, doi:10.1142/S021949882450052X.] have considered rectangular matrices. Similar to Moore-Penrose inverse, in this context, the conditions for rectangular matrices holds true for square matrices also. Comment 4: Again in Corollary 0.1, the author depended on Theorems (0.1 and 0.6) without mention the branches. Similarly for the prove of Theorems(0.3 and 0.6) where the author used Theorems (0.2 and 0.1). Response: The appropriate branches are mentioned in the revised version. Comment 5: The branches of Theorem (0.2) wrote by Roman numbers system while in the proof used Arabic numbers system. Response: The typological errors have been corrected." } ] } ]	1	https://f1000research.com/articles/13-112
https://f1000research.com/articles/13-1044/v1	11 Sep 24	{ "type": "Method Article", "title": "Methodology used to develop the minimum common data elements for surveillance and Reporting of Musculoskeletal Injuries in the MILitary (ROMMIL) statement", "authors": [ "Garrett S. Bullock", "Joanne L. Fallowfield", "Sarah J. de la Motte", "Nigel Arden", "Ben Fisher", "Adam Dooley", "Neil Forrest", "John J. Fraser", "Alysia Gourlay", "Ben R. Hando", "Katherine Harrison", "Debra Hayhurst", "Joseph M. Molloy", "Phillip M. Newman", "Eric Robitaille", "Deydre S. Teyhen", "Jeffrey M. Tiede", "Emma Williams", "Sandra Williams", "Damien Van Tiggelen", "Joshua J. Van Wyngaarden", "Richard B. Westrick", "Carolyn A. Emery", "Gary S. Collins", "Daniel I. Rhon", "Garrett S. Bullock", "Joanne L. Fallowfield", "Sarah J. de la Motte", "Nigel Arden", "Ben Fisher", "Adam Dooley", "Neil Forrest", "John J. Fraser", "Alysia Gourlay", "Ben R. Hando", "Katherine Harrison", "Debra Hayhurst", "Joseph M. Molloy", "Phillip M. Newman", "Eric Robitaille", "Deydre S. Teyhen", "Jeffrey M. Tiede", "Emma Williams", "Sandra Williams", "Damien Van Tiggelen", "Joshua J. Van Wyngaarden", "Richard B. Westrick", "Carolyn A. Emery", "Gary S. Collins" ], "abstract": "Background The objective was to summarize the methodology used to reach consensus for recommended minimum data elements that should be collected and reported when conducting injury surveillance research in military settings. This paper summarizes the methodology used to develop the international Minimum Data Elements for surveillance and Reporting of Musculoskeletal Injuries in the MILitary (ROMMIL) statement.\n\nMethods A Delphi methodology was employed to reach consensus for minimum reporting elements. Preliminary steps included conducting a literature review and surveying a convenience sample of military stakeholders to 1) identify barriers and facilitators of military musculoskeletal injury (MSKI) prevention programs, 2) identify relevant knowledge/information gaps and 3) establish future research priorities. The team then led a sequential three-round Delphi consensus survey, including relevant stakeholders from militaries around the world, and then conducted asynchronous mixed knowledge user meeting to explore level of agreement among subject matter experts. Knowledge users, including former and current military service members, civil servant practitioners, and global-wide subject matter experts having experience with policy, execution, or clinical investigation of MSKI mitigation programs, MSKI diagnoses, and MSKI risk factors in military settings. For each round, participants scored each question on a Likert scale of 1-5. Scores ranged from No Importance (1) to Strong Importance (5).\n\nResults Literature review and surveys helped informed the scope of potential variables to vote on. Three rounds were necessary to reach minimum consensus. Ninety-five, 65 and 42 respondents participated in the first, second and third rounds of the Delphi consensus, respectively. Ultimately, consensus recommendations emerged consisting of one data principle and 33 minimum data elements.\n\nConclusions Achieving consensus across relevant stakeholders representing military organizations globally can be challenging. This paper details the methodology employed to reach consensus for a core minimum data elements checklist for conducting MSKI research in military settings and improve data harmonization and scalability efforts. These methods can be used as a resource to assist in future consensus endeavors of similar nature.", "keywords": [ "Implementation Science", "Consensus", "Delphi", "Military", "Sports Medicine", "Military Medicine", "Wounds and Injuries", "Investigative Techniques" ], "content": "Introduction\n\nCollection, surveillance, and reporting of injury data is an important and ubiquitous aspect of musculoskeletal (MSK) care within systems seeking to evaluate and improve injury prevention and care models. This is particularly true across military performance and medical settings.1–3 Often the data are inadequately powered (individual clinics or small sample sizes), requiring merging of data to properly compare patient subgroups, generalize results across different populations, and potentially answer clinically important questions.4,5 However, merging of these data is often hampered by high heterogeneity in data elements, outcomes, and definitions.1 Thus, there have been many recommendations to standardize data collection elements and practices to improve harmonization of data within a specific discipline or setting.5–7\n\nData collection procedures are highly variable across and even within military organizations world-wide, without a universal standard operating procedure.1 For example, in a systematic review assessing musculoskeletal injury (MSKI) risk factors in military populations, high variability in exposure, outcome, and predictor collection and reporting from 170 studies limited the ability to effectively compare risk factors and injury risk across service member groups.1 In a scoping review of 132 articles investigating military MSKI mitigation programs, heterogeneity in data and outcomes hindered the ability to calculate service member injury burden.8 This variability in the collection and reporting of data elements may prevent clinicians, military leaders, and researchers from answering pertinent operational and clinical questions.\n\nOne method to improve consistency of standardized data collection and reporting across studies is through the development of a recommended list of core minimum data elements that everyone should collect and report.5,7 Consensus for core minimum data elements has occurred across biomedicine fields (e.g. geriatrics,7 pediatrics5) and for specific conditions (e.g. traumatic injuries,9 osteoarthritis,10 pain6). A common list of standardized data elements enables a systematic approach to data collection and focused analysis, allowing the specific study question to be addressed, but also facilitating aggregation and meta-analysis across studies.4 This standardized practice ultimately leads to greater potential for increased cohort size and ultimately inference power.4\n\nRecently a group of knowledge users consisting of clinicians, researchers, policymakers and leaders in military settings world-wide collaborated to identify/recommend the minimum elements for collection and reporting in any study assessing MSKI in military populations. The project followed a Delphi consensus methodology to engage many relevant stakeholders world-wide. This paper summarizes the details and methodology used to develop the Minimum Data Elements for surveillance and Reporting of Musculoskeletal Injuries in the MILitary (ROMMIL) statement, including a literature synthesis through a scoping review, knowledge user survey, Delphi study, and consensus meeting.\n\n\nMethods\n\nThe ROMMIL project was informed by the guidance for developers of health research guidelines.11 Consensus reporting was informed by the ACcurate COnsensus Reporting Document (ACCORD) reporting guidelines.12 Further methods and details, and respective protocols are available on Open Science Framework (https://osf.io/2wqbr/). Figure 1 displays the consensus process. This project adhered to all ethical principles of the Declaration of Helsinki. It was determined to not be human subjects research by the Institutional Review Board at Wake Forest University, School of Medicine (# IRB00115873), and therefore formal consent was not necessary. All participants were made aware that the data and collected information would be used to formulate a consensus statement, with the intent to publish the results, and all participants were invited to participate in the full process as authors.\n\nA core group of six members (GB, NA, JF, SdlM, BF, DR) identified the need for a standardized list of minimum core data elements for collection and reporting when conducting MSKI research. They pursued a balance in expertise across clinical and research disciplines, countries, and military branches while conducting a literature synthesis via scoping review, knowledge user survey, Delphi study and consensus meeting to achieve the ROMMIL consensus statement.\n\nA scoping review was performed to (1) identify barriers to and facilitators of military MSKI prevention programs, (2) identify relevant knowledge/information gaps and (3) establish future research priorities. This scoping review has been published separately.8 Databases included MEDLINE and the Defense Technical Information Center (DTIC). The results from the scoping review were merged with recommendations provided by the entire author group. The group created a preliminary list of all possible data elements and principles, based on the results of the scoping review. The steering committee discussed the recommended elements. A knowledge user meeting, consisting of 45 participants, was then convened to further evaluate the list. The revised list was reviewed by the steering committee for final approval.\n\nThe authors recruited a cross-sectional convenience sample from military MSKI conference attendees, then used a snowball recruitment method to gather stakeholder feedback concerning military MSKI mitigation program barriers and facilitators. The detailed results from this survey will be reported separately. This was a separate study that was approved by the ethics board at Brooke Army Medical Center (#C.2023.049e), which included online consent prior to survey participation (approved by the ethics board). The reported barriers and facilitators were used to help guide the framework questions for the consensus exercise.\n\nKnowledge users involved in military injury prevention programming collaborated for survey development. Knowledge users included senior officers, junior officers, enlisted personnel, retired service members, performance specialists, athletic trainers, physical therapists, and orthopaedic medical professionals. The knowledge user group received the survey results and a presentation of key findings upon survey completion.\n\nStudy design\n\nA sequential three round Delphi survey was performed. A synchronous mixed knowledge user meeting was performed to explore level of agreement among subject matter experts.\n\nPatient public involvement\n\nKnowledge users (including former and current military service members, civil servant practitioners, and global-wide subject matter experts having experience with policy, execution, or clinical investigation of MSKI mitigation programs, MSKI diagnoses, and military MSKI risk factors) were included in the development of the research question. A working group evolved from a sample of the knowledge users after the initial meetings. Knowledge users sought to improve the overarching question while accounting for research implications and facilitate knowledge translations. The knowledge user group included active-duty service members, veterans, military leaders, military medical professionals (athletic trainers, physical therapists, and physicians), military researchers, and exercise physiologists from the United Kingdom and United States.\n\nRecruitment\n\nExperts were identified through the closeness continuum.13 The closeness continuum identifies inclusive experts with subjective, mandated, and objective closeness to the topic of interest.13,14 Military service members having sustained MSKI across their careers had subjective closeness. Clinicians treating service members for MSKI had mandated closeness. Researchers and scientific experts investigating military MSKI had objective closeness.\n\nRecruitment entailed an email identifying an individual as a military MSKI expert and requesting that they participate in a Delphi consensus project, via a series of planned meetings. A follow-up email with an encrypted link was sent to those who wanted to participate, in order to answer a series of questions concerning injury surveillance and reporting in military settings (see extended data).15 Participants were told that their answers would help inform the consensus project, and that all responses would remain anonymous.\n\nDelphi rounds and scoring\n\nParticipants scored each question on a Likert scale of 1-5 for each round. Each question followed one of two formats shown in Table 1.\n\nFollowing round 1, a synchronous mixed knowledge user virtual meeting was held to discuss outlying scores, express and document disagreement or dissent concerning any statement, and propose alterations to variables and/or verbiage.\n\nIn round 2, participants had access to their previous scoring for each question. Changes in scoring were documented. A third round of scoring was unnecessary if the knowledge user group reached consensus on a given question during the second round.\n\nConsensus criteria are defined a priori (Table 2).\n\nStatistical analyses\n\nMissing data were assessed prior to analyses. A complete case analysis was performed for the Delphi study. Participant data were reported as mean (standard deviation) for continuous data and count (%) for nominal and ordinal data. All analyses were performed in R 4.2.1 (R Core Team (2023). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/). The dplyr package was used for cleaning and analyses, and the ggplot2 package was used for data visualization.\n\nAfter completing the Delphi rounds, a final consensus meeting was held on 13 September 2023 at the International Congress on Soldier’s Physical Performance, in London, United Kingdom. All participants were invited to attend. The meeting was recorded for people who could not join the meeting in person to view at a later date. The purpose of the meeting was to (1) discuss the literature synthesis, survey, and Delphi survey results and (2) obtain advisory input on the final set of recommended minimum data elements for MSKI research in military settings. Fifty international participants (including military MSKI knowledge users, clinicians, and research experts) were present. The meeting was facilitated by the ROMMIL steering committee. Participants discussed and sought to achieve consensus on each data element during the meeting.\n\nAfter the consensus meeting, the steering committee reviewed the results and revised the consensus statement based on pertinent feedback. The format and wording of each data element were reviewed and agreed upon, taking into consideration the survey, Delphi study, and consensus meeting results and discussions.\n\nA 6-week open comment period was held for anyone to comment on the document. The electronic link was made available through the Musculoskeletal Injury Rehabilitation Research for Operational Readiness (MIRROR) website (https://mirrorusuhs.org/) and emailed to individuals who had participated in preliminary meetings and activities.\n\nThe draft consensus was then circulated again among consensus participants to (1) confirm accurate representation of the group consensus or (2) determine if further clarification was needed.\n\n\nResults\n\nNinety-five, 65 and 42 respondents participated in the first, second and third rounds of the Delphi, respectively (Table 3). The raw data available from each round are available in an open-source repository.15 The process used a Delphi methodology, which is an acceptable and preferred method for validating consensus experiments.16,17\n\nEleven data elements reached consensus after round one (Table 4). Twenty-six data elements did not reach consensus after round one (Table 5); 66 data elements were excluded after round one (Table 6).\n\nIn round two, 16 more data elements reached consensus (Table 7); four data elements were combined with data elements that had already reached consensus (Table 8). Six data elements did not reach consensus after round two (Table 9).\n\nTwo more data elements reached consensus in round three. The other three data elements did not reach consensus (Table 10).\n\n\nDiscussion\n\nAn integrated and scalable process for collecting and reporting MSKI data is necessary to successfully evaluate MSKI interventions in military populations. The methodology, supporting results, and decisions made during the ROMMIL development are provided in this report. The process included a literature synthesis, knowledge user survey, Delphi study, consensus meeting, and electronic consensus open meeting for further review. This process incorporated a broad range of supporting literature, relevant data, and direct input from knowledge users having wide-ranging MSKI-related experiences and expertise.\n\nThe steering committee included members with wide-ranging viewpoints and areas of expertise; military MSKI surveillance and research occur world-wide, encompassing varying levels of institutional support, environments, and cultures. Multiple knowledge user meetings were held across the research process. The closeness continuum,13 identifying different types of experts, was used to inform and identify knowledge users for inclusion in the consensus process. The ROMMIL consensus statement was presented in person, on an open science platform, and through an open, freely accessible electronic link to mitigate or eliminate travel or institutional support barriers. Feedback was received through multiple interfaces, allowing for comprehensive input. Forms of feedback included verbal, free text, and quantitative scores, increasing the depth and richness of feedback.\n\nWhile international input was emphasized, most knowledge user feedback came from participants living in English speaking countries (i.e. North America, Europe, former British Commonwealth countries). Military organizations in countries having a primary language other than English (and those with differing levels of institutional support) may have differing (1) MSKI-related needs and (2) abilities to collect and report specific data elements. Further enquiry is needed to evaluate the ROMMIL checklist in these military populations.\n\nThe ROMMIL steering committee screened data elements throughout the process, ensuring a manageable and feasible number of data elements was included for collection and reporting. Continual screening was necessary, given the wide-ranging (1) body of MSKI-related literature, (2) knowledge user suggestions, and (3) responses from the knowledge user survey and Delphi study. The steering committee might have selected data elements that differed from individual knowledge users’ selections. To mitigate this potential bias, the steering committee conducted multiple knowledge user meetings and encouraged maximal input/feedback from all members throughout the process. The primary report summarizing the ROMMIL consensus checklist for minimum data elements to collect and report when conducting injury surveillance research will be published separately.\n\n\nConclusions\n\nAchieving consensus with knowledge users representing global-wide military organizations is challenging. This paper details the methodology established to reach consensus, while enabling all participants to provide input (including dissenting opinions). The ROMMIL consensus provides a core minimum data elements checklist for military MSKI scientists to improve data harmonization and scalability efforts. These methods can be used as a resource to assist future consensus endeavors in similar populations.\n\n\nEthics and consent\n\nThis project was determined to not be human subjects research by the Institutional Review Board at Wake Forest University, School of Medicine (# IRB00115873, determination made 1 July 2024). Individuals consented to be involved by participating in the meetings and voting process, a determination that was approved by the Institutional Review Board. All participants were made aware up front that the results and conclusions would be summarized into a consensus statement that would be published and shared with the greater scientific community. Data were anonymous and not linked to individual participants.\n\n\nDisclaimer\n\nThe view(s) expressed herein are those of the author(s) and do not necessarily reflect the official policy or position of the Uniformed Services University, the US Defense Health Agency, the US Department of Defense, the U.K. Department of Defense, nor the U.S. or U.K. Governments.\n\n\nAuthor information\n\nThe following authors are military service members (either past or present): JJF, BRH, JMM, DST, JMT, EW, SW, DVT, JJV, RBW, DIR.", "appendix": "Data availability\n\nOSF: Supplementary Data for Project: Minimum Common Data Elements for surveillance and Reporting of Musculoskeletal Injuries in the MILitary (ROMMIL); DOI 10.17605/OSF.IO/2WQBR. 15\n\nURL: https://osf.io/2wqbr/, 15\n\nThis project contains the following underlying data:\n\nThis is a description of methodology and not a full report of the actual Delphi study, the results of which will be reported elsewhere.\n\nDelphi data\n\n• DataDictionary.csv\n\n• Round1.csv\n\n• Round2.csv\n\n• Round3.csv\n\nData are available under the terms of the CC0 1.0 Universal license applied.\n\nOSF: Supplementary Data for Project: Minimum Common Data Elements for surveillance and Reporting of Musculoskeletal Injuries in the MILitary (ROMMIL); DOI 10.17605/OSF.IO/2WQBR. 15\n\nURL: https://osf.io/2wqbr/, 15\n\nThis project contains the following extended data:\n\nInitial questions\n\n• Appendix_Delphi_Initial_Tables.docx\n\nRecruitment email\n\n• Delphi_Email.docx\n\nData are available under the terms of the CC0 1.0 Universal license applied.\n\n\nReferences\n\nRhon DI, Molloy JM, Monnier A, et al.: Much work remains to reach consensus on musculoskeletal injury risk in military service members: a systematic review with meta-analysis. Eur. J. Sport Sci. 2022; 22(1): 16–34. PubMed Abstract \| Publisher Full Text\n\nMauntel TC, Tenan MS, Freedman BA, et al.: The military orthopedics tracking injuries and outcomes network: a solution for improving musculoskeletal care in the military health system. Mil. Med. 2022; 187(3-4): e282–e289. PubMed Abstract \| Publisher Full Text\n\nJones BH, Canham-Chervak M, Canada S, et al.: Medical surveillance of injuries in the US military: descriptive epidemiology and recommendations for improvement. Am. J. Prev. Med. 2010; 38(1): S42–S60. Publisher Full Text\n\nKush RD, Warzel D, Kush MA, et al.: FAIR data sharing: the roles of common data elements and harmonization. J. Biomed. Inform. 2020; 107: 103421. PubMed Abstract \| Publisher Full Text\n\nMcCann LJ, Pilkington CA, Huber AM, et al.: Development of a consensus core dataset in juvenile dermatomyositis for clinical use to inform research. Ann. Rheum. Dis. 2018; 77(2): 241–250. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDworkin RH, Turk DC, Farrar JT, et al.: Core outcome measures for chronic pain clinical trials: IMMPACT recommendations. Pain. 2005; 113(1): 9–19. PubMed Abstract \| Publisher Full Text\n\nWelch C, Wilson D, Sayer AA, et al.: Development of a UK core dataset for geriatric medicine research: a position statement and results from a Delphi consensus process. BMC Geriatr. 2023; 23(1): 168. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBullock GS, Dartt CE, Ricker EA, et al.: Barriers and facilitators to implementation of musculoskeletal injury mitigation programmes for military service members around the world: a scoping review. Inj. Prev. 2023; 29: 461–473. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRingdal KG, Lossius HM, Jones JM, et al.: Collecting core data in severely injured patients using a consensus trauma template: an international multicentre study. Crit. Care. 2011; 15: 1–11.\n\nLeyland K, Gates L, Nevitt M, et al.: Harmonising measures of knee and hip osteoarthritis in population-based cohort studies: an international study. Osteoarthr. Cartil. 2018; 26(7): 872–879. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMoher D, Schulz KF, Simera I, et al.: Guidance for developers of health research reporting guidelines. PLoS Med. 2010; 7(2): e1000217. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGattrell WT, Logullo P, van Zuuren EJ , et al.: ACCORD (ACcurate COnsensus Reporting Document): A reporting guideline for consensus methods in biomedicine developed via a modified Delphi. medRxiv. 2023. 2023.08.22.23294261.\n\nNeedham RD, de Loë RC : The policy Delphi: purpose, structure, and application. Canadian Geographer/Le Géographe Canadien. 1990; 34(2): 133–142. Publisher Full Text\n\nDonohoe HM, Needham RD: Moving best practice forward: Delphi characteristics, advantages, potential problems, and solutions. Int. J. Tour. Res. 2009; 11(5): 415–437. Publisher Full Text\n\nSupplementary Data for Project: Minimum Common Data Elements for surveillance and Reporting of Musculoskeletal Injuries in the MILitary (ROMMIL) Open Science Framework. DOI: 10.17605/OSF.IO/2WQBR. http\n\nLandeta J: Current validity of the Delphi method in social sciences. Technol. Forecast. Soc. Chang. 2006; 73(5): 467–482. Publisher Full Text\n\nNasa P, Jain R, Juneja D: Delphi methodology in healthcare research: How to decide its appropriateness. World J Methodol. Jul 20 2021; 11(4): 116–129. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "323555", "date": "04 Oct 2024", "name": "Oliver O'Sullivan", "expertise": [ "Reviewer Expertise Sports and exercise medicine", "rehabilitation", "military 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\nDear Colleagues,\nThank you for asking me to review Methodology used to develop the minimum common data elements for surveillance and Reporting of Musculoskeletal Injuries in the MILitary (ROMMIL) statement, which is a description of methodological approach taken to develop minimum data elements for Musculoskeletal injuries.\nThis is an important area of work and much needed - you all should be applauding for grasping the nettle on this.\nI felt the manuscript was well written overall, but could be refined by addressing some of the points below. The most pressing is the use (and possible over-use) of the phrase Knowledge User - the definition seemed to shift and it wasn't clear by the end who you were actually talking about.\nHowever, the area of concern I have is with regard to the results of Delphi. They are partly presented in the results and in Table 4-10; however, you report that the full results will be published elsewhere. This seems to me to be a little bit odd - would it not be better to present them in full in this manuscript, or to remove the partial presentation from this manuscript to avoid double reporting/duplicate publications?\nI wish the authors Good luck with the next version\n\nMinor Revisions -\n\nIn your abstract, you capitalise Minimum Data Elements in the background, but then don't in the results/conclusions - could I suggest a consistent approach please?\nIn abstract methods, you use a phrase 'civil servant practitioners' - do you think, given the international authorship and readership, that this term would translate? You could consider 'civilian' as a simpler alternative.\nThe last sentence in the strategy section is exactly the same at the last sentence in the background section - suggest removing one of those.\nThe fourth and fifth sentences in the Stage 1 paragraph appear to be saying 95% the same thing, but with a subtle difference. Do you require both? If so, suggest rephrasing for clarity.\nYour 'knowledge user' groups appear to change between the 'knowledge user involvement' and 'patient public involvement' sections. Either remove one of the elements in parenthesis if these phrases relate to the same people or please articulate the different knowledge user groups. In fact, you appear to change the knowledge user group composition in the PPI section (which is again different to above!) - please can you review this? If these are all different groups, composed of different individuals for a bespoke reason, please can you give the groups different names?\nAlso, as an extension to above, please can you explain what you mean by 'mixed knowledge user'? Is that an amalgam of the three groups above, or something else?\nIn stage 3 & 4, you refer to the steering committee. Are these the six individuals noted in the Strategy section? If so, please can you overtly make that point?\nThe second sentence of Results sounds decidedly like an intro or methods sentence - please could you consider its inclusion?\nThe second paragraph in the limitation appears repetitive - please could this be reviewed?\nYou mention dissenting opinions in the conclusion, but I am struggling to see where these have been described or presented - please can you clarify this?\nIn Table 3, the nationality for Round 2/3 'not disclosed' might be better in the title line, not in the same line as New Zealand\nTable 4 - 10 - please consider the implications of including these data if there is a plan for a further publication presenting said findings\n\nIs the rationale for developing the new method (or application) clearly explained? Yes\n\nIs the description of the method technically sound? Yes\n\nAre sufficient details provided to allow replication of the method development and its use by others? Yes\n\nIf any results are presented, are all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? Yes", "responses": [] }, { "id": "339129", "date": "27 Nov 2024", "name": "Chris M. Edwards", "expertise": [ "Reviewer Expertise Musculoskeletal injuries in military and emergency response personnel", "female health in military and emergency response personnel", "physical performance in military and emergency response personnel", "mental health in military and emergency response personnel." ], "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 to the authors for their tremendous effort in addressing MSKI in military populations. The methods described for the development of the Minimum Data Elements for surveillance and Reporting of Musculoskeletal Injuries in the MILitary (ROMMIL) statement will be an important reference for future publications and work in this field.\n\nOverall, the article is clear, concise and well written. A few minor changes\n\nIntroduction: -Well written, intention and purpose are clearly described.\n\nMethods:\n\n-(Minor change): “ Military service members having sustained MSKI across their careers had subjective closeness. Clinicians treating service members for MSKI had mandated closeness. Researchers and scientific experts investigating military MSKI had objective closeness.” For individuals who qualified for more than 1 category, how were they assessed/allocated?\n-(Minor change):Please include a brief discussion on what measures were taken to mitigate biases.\n\n-(Minor change):Please describe dataset limitations within this section.\n\nResults:\n-The results are presented clearly. No recommended changes.\n\nDiscussion/Conclusion:\n-(Minor change): Please provide a participant demographic breakdown, including profession. Given the challenges faced in achieving consensus, this information is relevant.\n\n-(Minor change): It would also be helpful if other limitations were explored that could have contributed to the consensus challenges.\n\n-(Minor change): Please reframe the Discussion, or at least identify within the limitations, and amend the Conclusion to reflect this Delphi describes the United States and United Kingdom perspective, as indicated in the Methods section.\nSupplementary Files:\n-Thank you for including the Initial Tables file, it provides contexts and allows transparency around data bias.\n\nIs the rationale for developing the new method (or application) clearly explained? Yes\n\nIs the description of the method technically sound? Yes\n\nAre sufficient details provided to allow replication of the method development and its use by others? Yes\n\nIf any results are presented, are all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? Partly", "responses": [] }, { "id": "339134", "date": "05 Dec 2024", "name": "Kenton R Kaufman", "expertise": [ "Reviewer Expertise Musculoskeletal injury", "Orthopedics", "Registries", "Outcomes Measurement" ], "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:\n\nPlease define a “mixed knowledge user”. Please describe how the “asynchronous mixed knowledge user meeting” was conducted, or is this a typographical error? Please see comment in Methods section below. Recommend describing “civil servant practitioners” as a “civilian practitioner”.\n\nIntroduction\nPlease define a definition of “knowledge user”.\nMethods\nWhen the core group pursued “a balance in expertise”, what expertise was being balanced? What criteria were used to know when this goal had been achieved? Stage 2: What was the military MSKI conference that was used to collect the convenience sample? How was this conference selected? How was the stated goal to sample “global-wide subject matter experts” met? The methods state that a “synchronous mixed knowledge user meeting” was performed. The abstract states that an “asynchronous mixed knowledge user meeting” was conducted. Is there a typographic error in the abstract? Recommend describing “civil servant practitioners” as a “civilian practitioner”.\n\nResults\nThere was a >50% decrease in Administrative Leadership, Command Leadership, and Physical Training Instructor between Round 1 and Round 2 of the Delphi Study. Was there any concern about this significant decrease in participation from these groups?\nDiscussion\nThis study provides an important list of data elements to be used for surveillance and reporting of musculoskeletal injuries that occur during military training. A weakness is that no data dictionary was created in this process and there is no indication that plans are in place to accomplish this task soon.\n\nIs the rationale for developing the new method (or application) clearly explained? Yes\n\nIs the description of the method technically sound? Yes\n\nAre sufficient details provided to allow replication of the method development and its use by others? Yes\n\nIf any results are presented, are all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-1044
https://f1000research.com/articles/13-832/v1	24 Jul 24	{ "type": "Policy Brief", "title": "Contract award criteria in public procurement procedures – The possibility of improving the situation of society from the perspective of the European Union and Poland", "authors": [ "Mateusz Brzeziński" ], "abstract": "Background Public tenders are vital for a country’s GDP and citizens’ quality of life, enabling public administration to achieve various goals. Developing and developed countries allocate over 10% of their GDP to public procurement. This highlights the significant societal support public tenders can provide, making it important to consider how they can further benefit society.\n\nPolicy and implications Public procurement can achieve policy objectives and benefit society by selecting tenders based on criteria beyond price, such as economic advantage and social benefits. This approach, endorsed by EU directives since 2014, encourages innovation and socially responsible practices. Contracting authorities in the EU can use social, environmental, and qualitative criteria to determine the most advantageous offers. Poland’s Public Procurement Law (PPL) allows contract award criteria based on quality and price, including social aspects. Contracting authorities can specify criteria like employing marginalized groups, though these criteria often face scrutiny and legal challenges. Non-price criteria aim to enhance competition and achieve social, environmental, and economic goals.\n\nRecommendations EU and Polish laws permit and encourage using social aspects as contract award criteria in public procurement. However, contracting authorities must analyze priorities, risk balancing, time constraints, and departmental coordination to effectively implement these criteria. This approach can improve the social situation and support specific groups.\n\nConclusions Public procurement significantly influences a country’s economy and quality of life, with EU and Polish laws allowing social criteria in contract awards. Directive 2014/24/EU supports tenders based on economic and social benefits. Poland’s PPL aligns with this, emphasizing marginalized group employment. Effective implementation fosters job creation, social integration, and improved living standards.", "keywords": [ "public procurement", "tenders", "contract award criteria", "socially responsible public procurement", "social aspects" ], "content": "Introduction\n\nThere should be no doubt that public tenders are one of the most important elements not only of generating the GDP of a given country, but also affect the quality of life of citizens. By means of public tenders, public administration bodies can meet various types of goals. OECD countries spend on average nearly 13% of annual GDP on public tenders (OECD 2021). EU Member States spend on average around 14% of annual GDP on public tenders. Poland spends on average 10% of its annual GDP in public tenders. It means that countries can significantly support the functioning of society, using the tools that public tenders can provide. Therefore, it is worth considering how these public tenders can improve the situation of society.\n\n\nPolicy outcomes and implications\n\nAccording to Jolien Grandia and Joanne Meehan public procurement can be leveraged to accomplish specific policy objectives, thereby benefiting society. This approach often involves selecting a tender design that awards contracts based on criteria beyond just the price, such as choosing the tender that offers the greatest economic advantage. Numerous studies have found that public procurement can stimulate innovative solutions by procuring functions rather than predefined goods or services (Geroski 1990; Elder and Georghiou 2007; Aschhoff and Sofka 2009). Socially responsible public procurement is an approach in which contracting authorities use solutions that allow them to achieve additional social benefits when awarding public contracts. In practice, contracting authorities in European Union Member States have been using solutions to achieve additional social benefits for over 30 years, but it was only in 2004 that they were included in the EU directives on public procurement.\n\nOne of such elements of socially responsible public procurement may be the contract award criteria. The essence of the contract award criteria, as emphasized in recital 92 of the preamble to Directive 2014/24/EU, is to enable a comparative assessment of the level of performance offered in each of the tenders for the subject of the contract. Bearing in mind also the principle that public tenders should be awarded on the basis of objective criteria ensuring compliance with the principles of transparency, non-discrimination and equal treatment, with a view to ensuring an objective comparison of the relative value of tenders in order to determine, in conditions of effective competition, which of the tenders is the most economically advantageous (see recital 90 of the preamble to Directive 2014/24/EU), all principles that the contracting authority intends to apply to the evaluation of tenders (i.e. criteria, weights and method of evaluation based on the criteria) must be specified in the procurement documents in an unambiguous and understandable manner. The description of the evaluation criteria and principles of evaluation of offers should therefore allow contractors to obtain full knowledge of how and based on what information their offers will be assessed, so that they can include appropriate data in the content of their offers.\n\nThe EU legislator himself in article 67 para 2 of Directive 2014/24/EU indicates that the most advantageous offer may include the best value for money, which is estimated on the basis of criteria including qualitative, environmental or social aspects related to the subject of a given public procurement - depending on which decision is made. The contracting authority itself will decide on the criteria.\n\nIt is important that the EU legislator advised contracting authorities that one of the criteria for evaluating offers may be social or environmental aspects. It is important because in the previously applicable Directive 2004/18/EC, in article 53 para 1 regarding contract award criteria, there was no indication at all that social aspects could be one of the possible contract award criteria. This also means that the EU legislator has noticed that it is actually possible to include this element in the contract award criteria and that they can not only help obtain the most advantageous offer in general, but it is also possible, using social aspects in public procurement, to meet the social goals of countries or local government units. Indeed, policies aimed at promoting societal objectives like social sustainability or innovation can impact the criteria (Kadefors et al. 2021).\n\nNevertheless, it is noted that the lowest price is chosen when the goal is to maximize savings, while the best value approach is used for more complex projects (Ballesteros-Perez et al. 2017). However, each time it is the contracting authority who must decide which contract award criteria to choose for a given public tender. Importantly, the EU legislator does not indicate exemplary contract award criteria - it describes them rather in terms of categories in which contracting authorities can look for appropriate solutions. Therefore, the freedom of choice rests with the contracting authority both in terms of selecting the category of contract award criterion or criteria in general, as well as in terms of determining these criteria in detail.\n\nDue to the fact that the EU legislator decided to use directives to regulate the issue of public procurement in the EU, in Poland the issue regarding contract award criteria, at the level of principles and objectives, is the same as in the provisions of Directive 2014/24/EU. However, precisely because the issue was regulated by directives, EU Member States were able to clarify and detail certain issues. This also happened in the case of Poland, where the PPL regulations stated that the most advantageous tender may be selected on the basis of quality criteria and price or cost, according to article 242 para 1 point 1 of the PPL.\n\nIn this respect, it is worth paying attention to article 242 para 2 point 2 of the PPL, where it is indicated that quality criteria may be, in particular, criteria relating to the social aspects, including the social and occupational integration of persons referred to in article 94 para 1 (persons with disabilities, the unemployed, jobseekers, who do not remain in employment or do not perform gainful employment, to-be self-reliant persons, persons deprived of liberty or released from prisons having difficulties in integration with the environment, persons with mental disorders, homeless persons, persons who have obtained refugee status or subsidiary protection in the Republic of Poland, persons under the age of 30 and after 50 years of age with job-seeker status, without employment, persons who are members of disadvantaged minorities, in particular members of national and ethnic minorities). Interestingly, under contract award criteria it is not possible to reward employment based on an employment contract. This is due to the fact that the legislator in article 95 para 1 of the PPL provides for the obligation to employ people on the basis of an employment contract - the contracting authority is obliged to indicate in the procurement documents the persons or the scope of activities to which the contractor’s obligation to demonstrate the employment of persons under an employment contract applies.\n\nIt is worth noting that while meeting the social aspects taken into account by the contracting authority in the conditions for participation in a procurement procedure or the terms of the contract (e.g. in terms of employment under an employment contract) is obligatory for the economic operator applying for a given contract, including them in the contract award criteria influences the selection of the most advantageous offer (the economic operator who meets the requirements regarding social aspects receives additional points in the offer evaluation), but failure to meet them does not, in principle, eliminate his offer from participation in the procedure. This is important because when determining the criteria for evaluating offers, these criteria can be defined more freely than when determining the conditions for participation in the procedure - because, in principle, they do not prevent the contractor from submitting an offer.\n\nBefore applying contract award criteria related to social aspects, it is advisable for the contracting authority to research the situation on the labor market in terms of the validity of the requirements specified in the criterion. This will avoid a situation in which the contractor gains an advantage in points by declaring the employment of e.g. unemployed people, and at the stage of order execution the declaration submitted as part of the offer turns out to be impossible to implement due to the lack of unemployed people able to perform the order. Depending on the decision of the contracting authority, related to the assessment of the specificity of the specific subject of the contract, as part of the social criterion, the contracting authority may specify the requirement to employ one or more people from one or several marginalized groups indicated in article 94 para 1 of the PPL. In practice, contracting authorities have doubts about how the evaluation is carried out in the case of the contract award criterion regarding the employment of a certain number of marginalized people to perform the contract. It is assumed that it is based on the economic operator’s only declaration regarding the employment of the indicated number of such people to perform the contract. The fulfillment of this obligation takes place during the implementation of the public procurement contract, and thus requires the contracting authority to determine the method of verifying the implementation of the obligation in question in the contractual provisions. In such a case, the contracting authority should specify the method of documenting and controlling the employment of marginalized people and the sanctions that will apply to the economic operator who does not implement the employment declared in the contract award criterion.\n\nNevertheless, Polish contracting authorities are quite reluctant to use contract award criteria related to social aspects. One can even risk the thesis that Polish contracting authorities are not willing to establish interesting and innovative contract award criteria. In my opinion, this is due to the fact that they are afraid of the potential use of legal remedies - an appeal to the National Appeals Chamber by a potential economic operator, and they also have doubts as to how such contract award criteria would be verified in an audit in projects co-financed from EU funds. Most often, in such a situation, a violation of the principle of fair competition and equal treatment of contractors is alleged. Nevertheless, in one of its judgments, the National Appeals Chamber emphasized that the contract award criteria are not intended to guarantee an “equal position of economic operators”, but to make competition between these economic operators more realistic. If the position of economic operators were to be equal, non-price contract award criteria would be illusory and essentially pointless. However, it is important that non-price contract award criteria are objective and guarantee that economic operators can compete. The competitiveness of economic operators in terms of non-price contract award criteria should be related to the objectivity of these criteria, so that their meaning and assessment is unambiguous, which in turn allows for a clear assessment of a given economic operator. Selection of non-price contract award criteria is the right of the contracting authority, which may also make the purpose of the public procurement procedure more realistic using these criteria, as well as obtain the subject of the contract of the highest quality (case KIO 610/22). This means that contract award criteria by their nature - by promoting specific features or functionalities - lead to an increase in the chances of obtaining a contract by some economic operators, while limiting these chances for other economic operators.\n\nHowever, it should be noted that these contract award criteria may allow the fulfillment of the fundamental principles of public procurement, which are included in article 17 para 1 point of the PPL, i.e. that the contracting body shall award the contract in a manner ensuring the best results of the contract, including social, environmental and economic effects, insofar as any of these effects can be obtained in a given contract in relation to the expenditure incurred.\n\nNone of the provisions of EU law and PPL prevent the use of social aspects as contract award criteria in public procurement procedures. Moreover, the provisions of relevant legal acts even encourage promoting the social aspects of public tenders through contract award criteria. However, in order to apply the appropriate contract award criteria in this area, each contracting authority must perform appropriate analysis, including the following:\n\n1) a matter of mentality - moving away from the priority of price and the contract award criteria.\n\n2) the issue of balancing risks - challenging the contract award criteria criteria by potential economic operators vs. customer preferences.\n\n3) a matter of time - the urgent need to prepare documentation of the proceedings, limiting the possibility of reliably preparing the criteria.\n\n4) the issue of synergy of work - the need to coordinate the work of the substantive and administrative and legal departments.\n\nThis means that each contracting authority has a chance, through public procurement procedures and contract award criteria, to improve the social situation and enable greater activity of specific groups of people.\n\n\nConclusion\n\nPublic procurement plays a vital role in shaping the economic and social landscape of a country, impacting GDP and the quality of life of citizens.\n\nThe EU legal framework allows public procurement to support societal goals through the inclusion of social criteria in contract awards, as outlined in Directive 2014/24/EU, which enables contracting authorities to assess tenders based on more than just price, incorporating aspects that offer the greatest economic advantage and additional social benefits.\n\nIn Poland, PPL align with EU directives, allowing the selection of the most advantageous tenders based on quality and price or cost. Notably, Polish regulations also emphasize the inclusion of social criteria, such as the employment and integration of marginalized groups. While Polish contracting authorities are hesitant to use these criteria due to concerns about legal challenges and verification in audits, there is a growing recognition of their potential benefits.\n\nPublic procurement offers a powerful tool for achieving social goals. By carefully selecting and implementing contract award criteria, contracting authorities can foster significant social benefits, contributing to a more inclusive and equitable society. Legal frameworks provide a solid foundation for such practices, though their success depends on the effective and innovative application by contracting authorities.\n\nIt should be noted that the solutions included in the EU and Polish legislation allow for achieving various social aspects and benefits, but they focus primarily on:\n\n1) increasing employment stability and social security of employees,\n\n2) employment and professional and social integration of people from groups at risk of social exclusion,\n\n3) facilitating access to public procurement for social economy entities, and especially social enterprises conducting social and professional integration of people from groups at risk of social exclusion,\n\n4) facilitating access to the subject of procurement for all users, in particular for people with disabilities and other special needs,\n\n5) using products or services with social labels confirming compliance with standards regarding, among others, decent work or fair trade.\n\nIn the long term, the use of social public procurement contributes to:\n\n1) creating jobs,\n\n2) social and professional integration of people from groups at risk of social exclusion,\n\n3) dissemination of decent work and fair trade standards among economic operators and employees,\n\n4) development of social economy entities,\n\n5) socializing the provision of services important to citizens, e.g. care services or revitalization services,\n\n6) improving the quality of life, in particular of people with disabilities, by increasing their access to public spaces, buildings and services (adapting orders - services, construction works, purchased goods to the requirements of people with special needs).", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nAschhoff B, Sofka WEJ: Innovation on demand? Can public procurement drive market success of innovations? Res. Policy. 2009; 38(8): 1235–1247. Publisher Full Text\n\nBallesteros-Perez P, Pellicer E, González-Cruz MC: Multi- attribute construction auctions. Proc., 9th Int. Structural Engineering and Construction Conf. Fargo, ND: International Structural Engineering and Construction Society; 2017; pp. 1–6.\n\nEdler J, Georghiou L: Public procurement and innovation—Resurrecting the demand side. Res. Policy. 2007; 36(7): 949–963. Publisher Full Text\n\nGeroski PA: Procurement policy as a tool of industrial policy. Int. Rev. Appl. Econ. 1990; 4(2): S.182–S.198.\n\nGrandia J, Meehan J: Public procurement as a policy tool: using procurement to reach desired outcomes in society. Int. J. Public Sect. Manag. 2017; 30(4): 302–309. Publisher Full Text\n\nKadefors A, Lingegård S, Uppenberg S, et al.: Designing and implementing procurement requirements for carbon reduction in infrastructure construction – international overview and experiences. J. Environ. Plan. Manag. 2021; 64(4): 611–634. Publisher Full Text\n\nOECD: Government at a Glance 2013: Procurement Data.2021. Reference Source\n\nPublic Procurement Law of 11 September 2019 (Journal of Laws of 2023, item 1605 as amended).\n\nSprawozdanie Prezesa Urzędu Zamówień Publicznych z funkcjonowania system zamówień publicznych w 2022 r.\n\njudgment of the National Appeals Chamber of March 25, 2022, case KIO 610/22.\n\nhttp\n\nDirective 2014/24/EU of the European Parliament and of the Council of 26 February 2014 on public procurement and repealing Directive 2004/18/EC (OJ L 94), 28.3.2014; pp. 65–242. Reference Source" }	[ { "id": "307651", "date": "14 Aug 2024", "name": "Roberto Caranta", "expertise": [ "Reviewer Expertise Comparative administrative law", "EU law", "public procurement" ], "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 briefly highlights the framework for using award criteria in SRPP under EU and Polish law. It is clearly written, but for the phrase \"Interestingly, under contract award criteria it is not possible to reward employment based on an employment contract. This is due …\". It would benefit from articulating what are the social benefits we are talking about. The reference list might be beefed up.\n\nDoes the paper provide a comprehensive overview of the policy and the context of its implementation in a way which is accessible to a general reader? Partly\n\nIs the discussion on the implications clearly and accurately presented and does it cite the current literature? Partly\n\nAre the recommendations made clear, balanced, and justified on the basis of the presented arguments? Yes", "responses": [ { "c_id": "12280", "date": "24 Aug 2024", "name": "Mateusz Brzeziński", "role": "Author Response", "response": "Dear Professor, Thank you very much for reading the article, reviewing it and providing tips. I will try to provide an improved version as soon as possible." } ] }, { "id": "315637", "date": "26 Aug 2024", "name": "František Ochrana", "expertise": [ "Reviewer Expertise public administration", "public procurement" ], "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 read with interest the text \"Contract award criteria in public procurement procedures - The possibility of improving the situation of society from the perspective of the European Union and Poland.\" Thank you for this opportunity. The reviewed policy brief is a suitable contribution for the discussion of the issue of contract award criteria in public procurement procedures. The study contains a number of inspiring ideas on the evaluation criteria of public procurement. The analysis of this problem is carried out on the case of Poland. I accompany the assessment of the reviewed study with an additional comment. The comment contains topics for discussion as well as possible suggestions for the author for further research. Poland is an interesting CEE country that has a common historical footprint with the neighboring countries of the former Soviet bloc, such as the Czech Republic and the Slovak Republic. All three countries became new members of the EU on the same date (2004). They have adopted the same EU legislation for public procurement. We would therefore expect approximately similar behavior of bureaucrats in public procurement. In reality, however, when analyzing the contract award criteria in these countries, we see significant differences. Unlike other CEE countries, Poland has a low share of public procurement evaluations according to the lowest price. According to TED data (2018; 2024), Poland was one of the leading CEE countries in 2016, with about 16% of public contracts awarded on the basis of the lowest price. This is significantly different compared to the Czech Republic (82% in 2016; 64.9% in 2024) and Slovakia (85% in 2016; 89.6% in 2024) of orders evaluated according to the lowest price. It is an \"odd strategy\" in the selection of evaluation criteria (Pernica et al., 2024)(Ref-3). In the context of the theory of institutional changes (Mahoney and Thelen, 2010)(Ref-10) and historical institutionalism (Schmidt, 2008;(Ref-8),Schmidt, 2010(Ref-7); Plaček et al., 2022)(Ref-4), the question is raised, what are the causes of this difference? It is undoubtedly more factors. One of the key ones is legal regulations. The author of the policy brief deals with these regulations in the section Policy outcomes and implications (see part Legal basis in the EU and part Legal basis in Poland). I will try to respond to the author's inspirational ideas with the following note. I believe that on the basis of historical institutionalism and retrograde analysis (Ochrana, 2022)(Ref-2), we can explain the differences between Poland, the Czech Republic and Slovakia. The author of the policy brief focuses on the role of legal regulations of public tenders. These are contained in the new Polish Public Procurement Act (https://www.portalzp.pl/ustawy/ustawa-z-dnia-11-wrzesnia-2019-r.-prawo-zamowien-publicznych-tekst-jedn.-dz.u.-z-2023-r.-poz.-1605-17500.html). To this I note: Act of 11 September 2019 - The Public Procurement Act has been amended several times since its adoption. The latest consolidated version of the law was published on 14 August 2023. (See https://www.portalzp.pl/ustawy/ustawa-z-dnia-11-wrzesnia-2019-r.-prawo-zamowien-publicznych-tekst-jedn.-dz.u.-z-2023-r.-poz.-1605-17500.html). This is a significant institutional change in the legal regulations of public tenders. The importance of this change in the Public Procurement Act was characterized by the then Minister for Enterprise and Technology, Jadwiga Emilewicz, by saying that contracting authorities would not only focus on the price offered, but would also take into account the quality of goods and services and their importance for the environment. When analyzing the Public Procurement Act, it is necessary to bear in mind that this legal regulation also has an impact on the behavior of bureaucrats in public procurement. In this respect, too, the reviewed policy brief is inspirational for public policy. Public procurement bureaucrats carry out their activities in a certain social and institutional environment, while the framework and incentives for their behavior are set by the public tender regulations.(https://ted.europa.eu/en/index ) The author makes an interesting point that Polish contracting authorities are rather reluctant to use award criteria related to social aspects and that they are reluctant to establish interesting and innovative award criteria. The author explains this behavior by fear of the possible use of legal remedies (and appeal to a higher authority). This conclusion is in line with similar attitudes of contracting authorities in the Czech Republic, which we examined in the study by(Schmidt et al., 2016)(Ref-9). Advertisers are behaving opportunistically. I therefore support the author's assertion that contracting authorities are concerned about the possible use of legal remedies. By opportunistic behaviour, contracting authorities try to avoid the risk of a public tender failure and to reduce the risk of a public procurement review as much as possible (see Schmidt et al., 2016). At the same time, the bureaucrat is pre-cautious of risk and uncertainty. This caution stems from the fear of failure of the public contract. From the author's analysis, we can conclude that the behavior of bureaucrats in public procurement is characterized by risk aversion (see Tversky and Kahneman, 1992)(Ref-5); Bajoori, et al., 2024)(Ref-9). The bearer of risk aversion is the bureaucrat responsible for the administration of public procurement and for the formal contract. Formal contracts cannot completely avoid opportunistic behaviors (Zhang et al., 2022)(Ref-6). This explains why, in an institutionally underdeveloped environment, contracting authorities prefer to evaluate according to the lowest price. The author of the policy brief also points to the significant impact of the choice of evaluation criteria on public procurement as a tool for achieving social goals. This part of the policy brief is also inspirational for public policy. It shows that contracting authorities can promote important social objectives and contribute to a more inclusive and fairer society by choosing their evaluation criteria. This is in line with the above-mentioned idea of the influence of legal regulations on the conduct of contracting authorities. In a suitably set legislative environment, public procurement can thus become an important tool for the effective achievement of public policy objectives. This is a problem that, according to the author of the policy brief, four fundamental assumptions and conditions must be met to implement. These are mainly: 1) a change of mentality that will lead to a change in behavior when selecting evaluation criteria (\"moving away from the priority of price and the contract award criteria\".) 2) the issue of balancing risks; 3) efficient administrative process (preparation of quality documentation); 4) synergy of actors preparing and implementing public procurement. The author of the policy brief sees in the implementation of these conditions a chance for each contracting authority to \"through public procurement procedures and contract award criteria, to improve the social situation and enable greater activity of specific groups of people.\" We can agree with this conclusion. In short, it is mainly changes in the institutional environment and changes in the mentality of contracting authorities that can induce the necessary changes in the behavior of public procurement actors. In this respect, the conclusions of the policy brief are inspiring for other countries that are faced with a similar question of how to effectively achieve public policy objectives through appropriately set evaluation criteria for public procurement. Conclusion: In conclusion to the reviewed text \"Contract award criteria in public procurement procedures – The possibility of improving the situation of society from the perspective of the European Union and Poland\", I would like to state that it is an inspiring and stimulating policy brief. I recommend indexing it. If the author finds in my evaluation some suggestions for improving his study, then I warmly welcome such an initiative.\n\nDoes the paper provide a comprehensive overview of the policy and the context of its implementation in a way which is accessible to a general reader? Yes\n\nIs the discussion on the implications clearly and accurately presented and does it cite the current literature? Yes\n\nAre the recommendations made clear, balanced, and justified on the basis of the presented arguments? Yes", "responses": [ { "c_id": "12337", "date": "10 Sep 2024", "name": "Mateusz Brzeziński", "role": "Author Response", "response": "Dear Professor, I would like to express my sincere gratitude for the insightful analysis and review of the article I prepared. I will incorporate the publications you mentioned in your review into my bibliography, as they indeed respond to the questions and issues highlighted in my article in an interesting and relevant manner. I hope that in the future we will have the opportunity to collaborate in the field of public procurement, and perhaps we can create a joint publication. It is extremely interesting to compare our countries in this regard – the challenges we face and how we attempt (or rather, do not attempt) to address them. Yours respectfully, Mateusz Brzeziński" } ] } ]	1	https://f1000research.com/articles/13-832
https://f1000research.com/articles/12-433/v1	21 Apr 23	{ "type": "Research Article", "title": "Assessing the cytotoxicity of phenolic and terpene fractions extracted from Iraqi Prunus arabica on AMJ13 and SK-GT-4 human cancer cell lines", "authors": [ "Matin Adil Mahmood", "Abdulkareem Hameed Abd", "Enas Jawad Kadhim", "Abdulkareem Hameed Abd", "Enas Jawad Kadhim" ], "abstract": "Background: Breast and esophageal cancer are the most aggressive and prominent causes of death worldwide. In addition, these cancers showed resistance to current chemotherapy regimens with limited success rates and fatal outcomes. Recently many studies reported the significant cytotoxic effects of phenolic and terpene fractions extracted from various Prunus species against different cancer cell lines. As a result, it has a good chance to be tested as a complement or replacement for standard chemotherapies. Methods: The study aimed to evaluate the cytotoxicity of phenolic and terpene fractions extracted from Iraqi Prunus arabica on breast (AMJ13) and esophageal (SK-GT-4) cancer cell lines by using the MTT assay (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide). Analysis using the Chou-Talalay method was performed to assess the synergistic effect between the extracted fractions and chemotherapeutic agent (docetaxel). Moreover, high-performance liquid chromatography (HPLC) analysis was conducted for the quantitative determination of different bioactive molecules of both phenolic and terpene fractions in the extract. Results: According to the findings, the treatment modalities significantly decreased cancer cell viability of AMJ13 and SK-GT-4 and had insignificant cytotoxicity on the normal cells (normal human fibroblast cell line) (all less than 50% cytotoxicity). Analysis with Chou-Talalay showed a strong synergism with docetaxel on both cancer cell lines (higher cytotoxicity even in low concentrations) and failed to induce cytotoxicity on the normal cells. Important flavonoid glycosides and terpenoids were detected by HPLC, in particularly, ferulic acid, catechin, chlorogenic acid, β-sitosterol, and campesterol. Conclusions: In conclusion, the extracted fractions selectively inhibited the proliferation of both cancer cell lines and showed minimal cytotoxicity on normal cells. These fractions could be naturally derived drugs for treating breast and esophageal cancers.", "keywords": [ "Prunus arabica", "Phenolic", "Terpene", "Cytotoxicity assay", "HPLC", "Chou-Talalay" ], "content": "Introduction\n\nA critical global health issue is breast cancer, the most prevalent cancer diagnosed worldwide, with 2.26 million incidents expected and it is the major cause of cancer-related deaths among women. Although breast cancer is considered a common disease in developed societies, in 2020, the world's less developed regions accounted for two-thirds of breast cancer-related deaths and more than 50% of all breast cancer diagnoses.1\n\nIn terms of cancer-related deaths, esophageal cancer (EC) occurs sixth on the list of the deadliest diseases (436,000 fatalities). Meanwhile, 473,000 cases have been recorded worldwide.2 Even though chemotherapeutic regimens and radiation therapy are more effective methods for treating cancer, they are nonselective, have substantial side effects, and can harm normal healthy tissues, leading to severe unanticipated and undesirable side effects.3 Initially, several tumors appeared amenable to treatment. However, with time, resistance might develop for a number of reasons, such as mutations in DNA and metabolic changes that cause the drug to be inhibited and degraded.4\n\nThe occurrence of natural compounds as anticancer agents is estimated to exceed 60% of the current anticancer drugs.5 These drugs from natural origins can be used for both cancer prevention and treatment due to their pharmacological safety and can be used independently or in conjunction with existing chemotherapeutic treatments to improve the therapeutic efficacy or to reduce chemotherapy-induced toxic effects.6 The constant change and injury that occurs in the human body over decades requires a development of revolutionary and highly precise “arms” capable of successfully combating malignant cells. Natural products are a powerful and endless source for identifying the finest anticancer prospects.7\n\nPrunus arabica is recognized as a distinct species from the farmed almond P. dulcis. Both, however, are members of the Prunus genus and the Rosacea family. This species was given its scientific name based on its geographical location where it first appeared. This taxon is indigenous to mild climate Asia regions, including the Fertile Crescent Mountains, as well as Turkey, Iran, and Iraq.8\n\nPrunus arabica is a thick undomesticated almond species with an unbarked stem that remains green even during dormancy.9 A wide range of biological and pharmacological effects from different Prunus species show great promise for the treatment of various cancers.10 Flavonoids, steroids, terpenoids, poly phenols, and other chemicals have all been identified from various Prunus species.11 Polyphenols and terpenoids which are found plentifully in plants, show anticancer effects, via inhibiting cancer cell growth, blood vessel formation, metastasis, inflammation, and inducing cell death.12 For this purpose, the anticancer effect of phenolic and terpene fractions from Prunus arabica extract was investigated using the AMJ13 and SK-GT-4 cancer cell lines and normal human fibroblasts (NHF).\n\n\nMethods\n\nThe full protocol can be found in the Extended data.37 Approximately 500 g of granular powdered plant that had been shade-dried for 12 days then defatted for 24 hours with hexane (BDH chemicals, England cat-no. BDH24575.100E) in a ratio of 1:3 W/V before being dried at room temperature. In a Soxhlet apparatus (BOECO, Germany) the defatted plant components were separated using two liters of 80% ethanol (Sigma-Aldrich, Germany cat-no1070172511) until completely depleted. A thick, dark-greenish-yellow residual (known as the crude fraction A) was obtained by drying the alcoholic extract by evaporation at low pressure and temperatures below 40°C by using IKA RV 10 Rotary Evaporator (Germany). This fraction was acidified using 300 ml of 5% HCl (Sigma-Aldrich cat-no. 1009861000) to pH 2 and then split with ethyl acetate (Sigma-Aldrich, Germany cat-no. 319902-1L) to acquire two distinct layers (the acidic aqueous layer and ethyl acetate layer-crude fraction). The crude fraction was dried out using low-pressure evaporation in an IKA RV 10 Rotary Evaporator (Germany) then basified with 300 ml of 5% NaOH (Honeywell, USA cat-no. 30620) to pH 10 and extracted by adding chloroform (Honeywell, USA cat-no. C2432) to the separatory funnel in order to obtain two layers; the aqueous basic layer and the and chloroform layer. The basic water layer evaporated to the point of dryness and acidified with 5% HCl to reach pH 2, then extracted with ethyl acetate to get another fraction designated as fraction (F-B). The chloroform layer which was separated by the same steps and partitioned with 80% methanol (Biochem Chemopharma, France cat-no. 213032500) and petroleum ether (Sigma-Aldrich, Germany cat-no. 32299) to obtain another two layers; fraction (C) the petroleum ether and methanol fraction which was considered as fraction D.13\n\nThe full protocol can be found in the Extended data.38 Standard protocols were used in chemical testing to identify the active components using ethanolic extracts from various plant fractions.14\n\nI. Alkaloids test: Precisely 2 ml of alcoholic extract and fractions were stirred with 5 ml of 1% HCl (Sigma-Aldrich cat-no. 1009861000) on a steam bath. Mayer’s reagent (prepared by dissolving 1.35 gm mercuric chloride (Sigma-Aldrich, Germany ca-no. 215465) in 60 ml water + 5 gm potassium iodide (Sigma-Aldrich, Germany cat-no. 221945) in 10 ml water) and Wagner’s reagent (prepared by dissolving 1.27 gm of iodine (Sigma-Aldrich, Germany cat-no. 1047630050) and 2 gm of potassium iodide in 100 ml of water) were used. White and reddish-brown colored precipitates were considered as indications of the presence of alkaloids.\n\nII. Flavonoids tests\n\na. Lead acetate test: precisely 1 ml of 10% lead acetate solution (BDH limited, England cat-no. LL0093) was incorporated into 2 ml of alcoholic extract and fractions. The presence of a yellowish-white precipitate indicated the presence of flavonoids.\n\nb. NaOH test: 2 ml of the extract and fractions were subjected to aqueous NaOH and HCl; the development of a yellowish-orange color indicated the presence of flavonoids.\n\nIII. Steroids tests\n\na. H2SO4 test: 2 ml of sulfuric acid (BDH limited, England cat-no. BDH3068-500MLP) was added to the extract, a green color was formed as an indication to the presence of steroids.\n\nIV. Terpenoids test (Salkowski test): 5 ml of plant extract mixed with 2 ml of chloroform (Honeywell, USA cat-no. C2432), and 3 ml of concentrated sulphuric acid (BDH limited, England cat-no. BDH3068-500MLP) was carefully added to form a layer. A reddish-brown coloration of the inter face was formed to show positive results for the presence of terpenoids.\n\nReference standards and reagents\n\nThe reference standards (Caffeic acid cat-no C0625, (+)-Catechin hydrate cat-no. C1251, Chlorogenic acid cat-no. 00500590, Ferulic Acid cat-no. PHR1791, Gallic acid monohydrate cat-no. 27645, p-Coumaric acid cat-no. C9008, Quercetin cat-no. Q4951, Rutin hydrate cat-no. R5143, β-Sitosterol cat-no. 43623, Campesterol cat-no. C5157, Stigmasterol cat-no. 47132) were purchased from Sigma Aldrich, Germany. The pure water used in the study was distilled with a Milli-Q. (Millipore, Bedford, MA, USA). Chemicals, including methanol (cat-no. 106007), acetonitrile (cat-no. 100030), and acetic acid (cat-no. 543808) (HPLC grade), were all ordered from Merck Ltd, Mumbai, India. Before usage, the solvents were processed using 0.45 mm pore size (Millipore) membrane filters.\n\nInstrumentation and analytical conditions\n\nIndividual phenolic components identification was conducted by reversed-phase high-performance liquid chromatography utilizing a Sykam HPLC chromatographic system (Germany) integrated with ultraviolet detection (Sykam S 3240 UV/Vis Multichannel Detector, Germany) and sample delivery system (Sykam S1122 Solvent deliver system, Germany). The column temperature was maintained at 30 °C (Sykam S 4011 column thermo controller, Germany). The gradient elution method, with eluent A and eluent B (methanol and 1% (v/v) formic acid in water respectively), was carried out as follows: initial 0–4 min, 40% B; 4–10 min, 50% B; and flow-rate of 0.7 mL/min. Approximately 100 μL of the samples were injected. An autosampler (Skynm S5200 sample injector, Germany) analyzed the standards automatically. Spectral data was recorded at a 280 nm.15\n\nThe following conditions were used for the terpene fraction; mobile phase acetonitrile: distilled water: acetic acid (60:25:5), column = C18-ODS (25 cm * 4.6 mm), detector = UV- 220 nm, and the flow rate was 1 ml/min.\n\nAMJ13 breast cancer16 and NHF normal cell lines (normal human derived adipose tissue)17 were cultivated in Roswell Park Memorial Institute medium RPMI 1640 (Capricorn, Germany cat-no. RPMI-A) with 10 % fetal bovine serum (FBS) (Capricorn, Germany cat-no. FBS-22A), antibiotics (penicillin and streptomycin) (Capricorn, Germany cat-no. PS-B) then incubated at 37 °C. SK-GT-4, the esophageal cancer cell line,18 was maintained in minimum essential medium MEM (Capricorn, Germany cat-no. MEMA-RXA). Cells were passaged using Trypsin-EDTA (Capricorn, Germany cat-no. TRY-1B), replanted at 50% confluence twice weekly, and incubated at 37 °C (Cypress Diagnostics, Belgium).19\n\nThe full protocol can be found in the Extended data.39 The MTT assay for cell viability20 was performed to measure the cytotoxic effect of the extracted fractions. Cell lines were planted into 96-well plates (Santa Cruz Biotechnology, USA cat-no. sc-204447) at 1 × 104 cells/well. After 24 hrs, or until a confluent monolayer was achieved, cells were treated with the tested compound. After 72 hours of exposure, cell viability was assessed; the medium was removed by aspiration and 28 μL of 2 mg/mL MTT (MTT stain obtained from Bio-World, USA cat-no. 42000092-1) was added and incubated at 37 °C for 1.5 hours.\n\nAfter removing the MTT solution, the crystals remaining in the wells were solubilized by the addition of 130 μL of dimethyl sulfoxide (DMSO) (Santacruz Biotechnology, USA cat-no. sc-202581) was used to solubilize the residual crystals in the wells, proceeded by incubation for 15 min at 37 °C with shaking.21 Using a microplate reader (Genex-lab, USA cat-no. MR-100) the absorbance was measured at 492 nm; the experiment was carried out in triplicate. The following formula was applied to determine the percent of cytotoxicity22:\n\nAT: Absorbance of treated cells with tested compounds, ANT: absorbance of untreated cells.\n\nSynergism or interaction of phenolic and terpene fractions with docetaxel was investigated using a non-constant ratio. Analysis of the combination was performed by the Chou-Talalay method. CompuSyn was used to derive the corresponding combination indices (CI) (CompuSyn, Inc., Paramus, NJ, USA). The combination indices were calculated using non-constant phenolic, terpene, and docetaxel ratios and mutually exclusive formulations. A CI value between 0.9 and 1.1 indicates an additive effect, a CI value below 0.9 denotes synergy, and a CI above 1.1 denotes antagonism.23\n\nThe MTT assay results were analyzed statistically with an ANOVA test in GraphPad V 7.00 (for windows), an open-access alternative that can perform an equivalent function is R. The unpaired t-test was used to compare groups; P-values <0.05 were considered statistically significant.\n\n\nResults\n\nThe phytochemical screening results are given in Table 1.\n\nTo discover individual compounds of extracted fractions, HPLC analysis was used. Seven phenolic acids (p-coumaric acid, ferulic acid, gallic acid, caffeic acid, quercetin, rutin, catechin) and three terpenes (B sitosterol, campesterol, stigmasterol) were detected from extracted fractions of Prunus arabica, as shown in Tables 2 and 3.\n\nThe MTT assay was used to evaluate the cytotoxicity and therapeutic efficacy of the isolated fractions in the cancer and normal cell lines (AMJ13, SK-GT-4 and NHF). As shown in Figures 1–3, the results showed that the treatments significantly decreased the viability of the cancer cells (>50% at higher concentrations) with minimal cytotoxic effects on the normal cells (<50% cytotoxicity). On the AMJ13 cell line, phenolic, terpene fractions, and docetaxel had a half maximal inhibitory concentration (IC50) of 29.34, 8.455, and 14.51 μg/mL, respectively, as shown in Figure 4. On the SK-GT-4 cell line, phenolic, terpene fractions, and docetaxel had an IC50 of 21.97, 15.14, and 0.7125 μg/mL, respectively, as shown in Figure 4. While on the NHF cell line, the phenolic, terpene, and docetaxel had an IC50 of 18.07, 31.81, and 24.9 μg/mL, respectively.\n\nThe possible interactions between extracted fractions (phenolic, terpene) and docetaxel therapy on the AMJ13 and SK-GT-4 cell lines were analyzed. The quantification of synergism or antagonism is defined as a mass-action law issue (determined by the combination index CI values) and cannot be determined by the statistical p values.23 Chou-Talalay equations were used to calculate the combination's value. A CI value less than 0.9, the effects were assumed to be synergistic; a CI value between 0.9 and 1.1, the effects were considered as additive; while a value larger than 1.1, the effects were assumed to be antagonistic24 After an exposure period of 72 hours, the phenolic fraction of P. arabica with docetaxel produced a strong to very strong synergic cytotoxic effect against AMJ13 and SK-GT-4 cancer cell lines in comparison with a single treatment. The terpene fraction showed almost the same synergism effect when combined with docetaxel (Figure 5).\n\nData is expressed as fraction affected (fa) against combination index plots. Combination index (CI) value less than 1 indicates synergy, CI values equal 1 indicates additive, and CI value less than 1 indicates an antagonism. (A and B) Represents the effect on AMJ13 cell line by phenolic-docetaxel and terpene-docetaxel combinations respectively, all points are showing synergy to very strong synergy; (C and D) represents the effect on SK-GT-4 cell line by phenolic-docetaxel and terpene-docetaxel combinations respectively, all of the points are showing synergy to very strong. (E and F) Show the effect on the NHF cell line by phenolic-docetaxel and terpene-docetaxel combinations respectively, tested points showed inconsiderable cytotoxicity as all concentrations failed to emerge 50% cytotoxicity. The data represents six separate experiments.\n\nMorphological alterations were examined with crystal violet staining of the cell lines after 72 hr. Exposure to the IC50 of the phenolic fraction, terpene, docetaxel, and their combinations with chemotherapy as shown in Figures 6, 7 and 8. The captured images are for cells treated with (100 μg/mL) of the tested fractions or their combinations with docetaxel on cancer or normal cell lines.\n\nA: untreated cells show multipolar elongated epithelial-like shape, with multiple nuclei in most of the cells and nuclear polymorphism, many cells showed mitotic figures B, C, and D cell treated with terpene fraction phenolic fraction and docetaxel respectively; the treated cells showed a shrinkage, cytoplasm and cell membrane disappearance, stromal edema, nucleus shrinkage and marked decrease in the number of cells. E and F cells were treated with a combination therapy of phenolic plus docetaxel and terpene plus docetaxel, respectively; the treated cells showed more prominent cytotoxic effects than single treatment with a dense nucleus. The microscopic images were captured at 10× by an inverted microscope (IXplore Standard Olympus, Japan).\n\nA: untreated cells are squamous or poorly differentiated and irregular in shape. B: cells treated with terpene fraction showed shrinkage; the squamous cell border remained intact, while other cells (no bordered cells) showed stromal edema. C: cells treated with phenolic fraction showed an increment of the stromal edema and disappearance of squamous cells with no ductal nuclear aggregation. D: docetaxel-treated cells showed focal aggregation and cellular shrinkage. E and F cells were treated with combination therapy phenolic plus docetaxel and terpene plus docetaxel, respectively; the treated cells showed more shrinkage than single treatment (very small sized cells), the squamous cell border is intact, destruction of ductal/basal cell membranes with no focal aggregation. The microscopic images were captured at 10× by an inverted microscope (IXplore Standard Olympus, Japan).\n\nA: untreated cells; cells appear as plump spindle-shaped or stellate-shaped cells with centrally placed oval or round nuclei. B: cells treated with terpene fraction showed mild apoptosis. C: cells treated with phenolic fraction showed condensation of cells with no edema. D: docetaxel-treated cells showed focal apoptosis with mild stromal edema, and the cells remained the same size. E and F cells were treated with a combination therapy of phenolic plus docetaxel and terpene plus docetaxel, respectively; the treated cells showed prominent apoptosis compared to the single treatment. The microscopic images were captured at 10× by an inverted microscope (IXplore Standard Olympus, Japan).\n\n\nDiscussion\n\nPolyphenols and terpenes are the most abundant and widely distributed compound in the plant kingdoms and groups25 Prunus species have been found to be a potential dietary supplement and a good source of phenolic and terpene bioactive chemicals.26\n\nIn the current study, lead acetate and NaOH tests for polyphenols gave a positive result, meaning the presence of phenolic compounds in P. arabica extract. The dark color might indicate the presence of large quantities of polyphenols and flavonoids.27 The H2SO4 test gave a dark pink or red color and greenish color, respectively, as an indication of the presence of steroids, while the chloroform and sulphuric acid test produced a greyish color which was considered an indication of the presence of terpenes.\n\nThe data for the HPLC analysis showed that the phenolic fraction of the extracted P. arabica contains eight phenolic compounds (p-Coumaric acid, ferulic acid, gallic acid, caffeic acid, quercetin, rutin, catechin, and chlorogenic acid), the terpene fraction contained three major terpenes (β-sitosterol, stigmasterol, and campesterol) as well as some non-phenolic organic and inorganic components at deceptive values.\n\nFrom the eight phenolic compounds found in our phenolic fraction of the P. arabica extract, the highest component concentration was ferulic acid (3.992 mg/gm) with a retention time of 3.22 min, which may contribute to the high efficacy of the phenolic extract as a cytotoxic biological chemical on different cancer cell lines.28 Research has indicated that ferulic acid induces cell death by decreasing the Bcl-2 and increasing the BAX gene expression or by upregulation of caspase-3 and cleaved caspase-9.29\n\nThe highest component of the terpene fraction was campesterol (4.358 mg/gm), with a retention time of 11.5 min. A study by Hyocheol B. et al. confirmed that campesterol could inhibit both cellular growth and cell cycle progression by regulating the PCNA (proliferating cell nuclear antigen) and PI3K/MAPK (phosphatidylinositol-3-kinase/mitogen-activated protein kinase) signal pathways. Moreover, their results also showed that campesterol could prevent the clustering of ovarian cancer cells.29 Some undiscovered phenolic and terpene compounds may be presented by peaks on the chromatograms, hydroperoxides or peroxides produced from terpenes are likely responsible for these found but unidentified peaks.30\n\nThe present work studied the antiproliferative effects of the extracted fractions (phenolic and terpene) of P. arabica alone and in combination with docetaxel and compared their novel effects with the single chemotherapeutic agent (docetaxel) on AMJ13, SK-GT-4, and NHF cell lines. Breast cancer and esophageal carcinoma are considered highly malignant tumors, which lead to poor prognoses.31 The low efficacy of currently available breast and esophageal cancer chemotherapeutics and radiation is well documented.32\n\nIn vitro, the results of this study appear that the treatment with the phenolic and terpene extract of P. arabica significantly reduced cell viability and triggered apoptosis when compared to the control group in both AMJ13 and SK-GT-4 cell lines (Figures 1–2). During this study against the AMJ13 cell line, the terpene fraction showed comparable cytotoxic effects to docetaxel even in concentrations as low as 25 μg/mL, the IC50 for phenolic terpene and docetaxel against AMJ13 cell line was 29.34, 8.455 and 14.51 μg/mL respectively Figure 4.\n\nThe phenolic fraction showed almost an equal cytotoxicity to docetaxel against the SK-GT-4 cell line, while terpene showed less significant cytotoxicity in comparison with other tested treatments; the IC50 for phenolic terpene and docetaxel against SK-GT-4 was 21.97, 15.14, 0.7125 μg/mL respectively as shown in Figure 4. All treatment concentrations for phenolic and terpene fractions failed to show significant cytotoxicity on the NHF cell line (less than 50%).\n\nThe increased sensitivity of cancer cells to cytotoxicity was another goal of this investigation by using phenolic or terpene fractions with docetaxel and the cumulative effects of many dosages. The MTT assay performed with docetaxel in the presence of varying amounts of phenolic or terpene fractions. According to the findings, the phenolic, terpene, and docetaxel combination substantially decreased cancer cell viability without causing appreciable damage to normal cells. The Chou-Talalay equation was used to evaluate the combinations.\n\nThe degree of synergy or antagonism cannot be assessed by p value in a statistical manner but can be quantified using CI values (combination index values).33 Nearly all of the doses examined showed synergistic cytotoxicity against the cancer cell lines. To demonstrate their safety, testing on a normal human fibroblast cell line showed no effect at any dose of the combination of phenolic and terpene fractions with docetaxel. There have been a number of studies suggesting that phenolic acids and terpenes may boost the effect of other chemotherapies on breast cancer.34 However, this is the first study to provide empirical evidence of synergy between phenolic and terpene fractions with docetaxel on AMJ13 and SK-GT-4 cell line (Figure 5 and Table 4).\n\nAs seen in the current study and after crystal violet staining, the AMJ13, SK-GT-4, and NHF cells that were exposed to 72h of extracted fractions and docetaxel and the combination therapy revealed cell shrinkage, cytoplasm and cell membrane disappearance, stromal edema, nucleus shrinkage and a marked decrease in the number of cells compared with control (untreated) cells. The effect of combination therapy was more prominent than single therapy as the cells showed more shrinkage, extensive cell damage, and necrosis.\n\n\nConclusion\n\nIt was observed from the results that the P. arabica phenolic and terpene extracts have significant cytotoxic activity on breast cancer and esophageal cancer cell lines with minimal effect on normal cells, due to the presence of effective compounds in this extract, additionally there was a significant cytotoxic effect between serial concentrations on both cancer cell lines. Moreover, these active compounds increased the cytotoxic activity of docetaxel on cancer cell lines without increasing the toxicity on normal cells. Previous studies proved the anticancer effect of these compounds extracted from other plants or herbs.", "appendix": "Data availability\n\nZenodo: Terpene Fractions Extracted from Iraqi Prunus arabica on AMJ13 and SK-GT-4 Human Cancer Cell Lines, https://doi.org/10.5281/zenodo.7618326. 36\n\nThe project contains the following underlying data:\n\n• Figure 1 - percent of cytotoxicity AMJ13 cell line.csv (the table illustrates the percent of cytotoxicity of serial concentrations of each fraction alone and combined with docetaxel for AMJ13 cancer cell line)\n\n• Figure 2 - percent of cytotoxicity SK-GT-4 cell line.csv\n\n• Figure 3 - percent of cytotoxicity - NHF cell line.csv (the table illustrates the percent of cytotoxicity of serial concentrations of each fraction alone and combined with docetaxel for NHF cell line)\n\n• Figure 4 - A - IC 50 Docetaxel- AMJ13 cell line.csv (Cell viability values for serial concentrations of docetaxel in triplicate. Docetaxel exhibited cytotoxicity against AMJ13 cancer cell line with IC50 values of 14.51 μg/ml)\n\n• Figure 4 - A - IC 50 Phenolic fraction-AMJ13 cell line.csv (Cell viability values for serial concentrations of phenolic fraction in triplicate. Phenolic fraction exhibited cytotoxicity against AMJ13 cancer cell line with IC50 values of 29.34 μg/ml)\n\n• Figure 4 - A - IC 50 Terpene fraction-AMJ13 cell line.csv (Cell viability values for serial concentrations of terpene fraction in triplicate. Terpene fraction exhibited cytotoxicity against AMJ13 cancer cell line with IC50 values of 8.455 μg/ml)\n\n• Figure 4 - B - IC50 Docetaxel- SK-GT-4 cell line.csv (Cell viability values for serial concentrations of docetaxel in triplicate. Docetaxel exhibited cytotoxicity against SK-GT-4 cancer cell line with IC50 values of 0.7125 μg/ml)\n\n• Figure 4 - B - IC50 Phenolic fraction-SK-GT-4 cell line.csv (Cell viability values for serial concentrations of phenolic fraction in triplicate. Phenolic fraction exhibited cytotoxicity against SK-GT-4 cancer cell line with IC50 values of 21.97 μg/ml)\n\n• Figure 4 - B - IC50 Terpene fraction-SK-GT-4 cell line.csv (Cell viability values for serial concentrations of terpene fraction in triplicate. Terpene fraction exhibited cytotoxicity against SK-GT-4 cancer cell line with IC50 values of 15.14 μg/ml)\n\n• Figure 4 - C - Docetaxel- IC50 NHF cell line.csv (Cell viability values for serial concentrations of docetaxel in triplicate. Docetaxel exhibited cytotoxicity against NHF cell line with IC50 values of 24.9 μg/ml)\n\n• Figure 4 - C - phenolic fraction- IC50 NHF cell line.csv (Cell viability values for serial concentrations of phenolic fraction in triplicate. Phenolic fraction exhibited cytotoxicity against NHF cell line with IC50 values of 18.07 μg/ml)\n\n• Figure 4 - C - Terpene fraction- IC50 NHF cell line.csv (Cell viability values for serial concentrations of terpene fraction in triplicate. Terpene fraction exhibited cytotoxicity against NHF cell line with IC50 values of 31.81 μg/ml)\n\n• Figure 5 - A - Phenolic plus docetaxel- AMJ13.html (Cytotoxicity of Prunus arabica phenolic extract combination with docetaxel on AMJ13 cancer cell line. I-Dose-Effect Curve at 50% cytotoxicity, II-Isobologram analysis displays synergism rate between phenolic fraction and docetaxel at all points of the combination as they located at the lower left of the hypotenuse, demonstrating the effect is synergistic at a 50% cytotoxicity dose, III-showing the combination index data location for each dose.)\n\n• Figure 5 - C - Phenolic plus docetaxel SK-GT-4.html (Cytotoxicity of Prunus arabica phenolic extract combination with docetaxel on SK-GT-4 cancer cell line. I-Dose-Effect Curve at 50% cytotoxicity, II-Isobologram analysis displays synergism rate between phenolic fraction and docetaxel at all points of the combination as they located at the lower left of the hypotenuse, demonstrating the effect is synergistic at a 50% cytotoxicity dose, III-showing the combination index data location for each dose.)\n\n• Figure 5 - F - Terpene plus docetaxel NHF.html (Checking the possible combination cytotoxicity on NHF cell line. There is no cytotoxic effect for terpene fraction on NHF cell line in combination with docetaxel on cell viability. I-Dose–response curve at shows response less than 50%, II-Isobologram analysis showing no synergism between terpene fraction and docetaxel against NHF at all doses tested, III-The figure of combination index showed the absence of any synergistic points.)\n\n• Figure 5 - E - Phenolic plus docetaxel NHF.html (Checking the possible combination cytotoxicity on NHF cell line. There is no cytotoxic effect for phenolic fraction on NHF cell line in combination with docetaxel on cell viability. I-Dose–response curve at shows response less than 50%, II-Isobologram analysis showing no synergism between terpene fraction and docetaxel against NHF at all doses tested, III-The figure of combination index showed the absence of any synergistic points.)\n\n• Figure 5 - B - Terpene plus docetaxel AMJ13.html (Cytotoxicity of Prunus arabica terpene fraction combination with docetaxel on AMJ13 cancer cell line. I-Dose-Effect Curve at 50% cytotoxicity, II-Isobologram analysis displays synergism rate between terpene fraction and docetaxel at all points of the combination as they located at the lower left of the hypotenuse, demonstrating the effect is synergistic at a 50% cytotoxicity dose, III-showing the combination index data location for each dose.)\n\n• Figure 5 - D - Terpene plus docetaxel SK-GT-4.html (Cytotoxicity of Prunus arabica terpene fraction combination with docetaxel on SK-GT-4 cancer cell line. I-Dose-Effect Curve at 50% cytotoxicity, II-Isobologram analysis displays synergism rate between terpene fraction and docetaxel at all points of the combination as they located at the lower left of the hypotenuse, demonstrating the effect is synergistic at a 50% cytotoxicity dose, III-showing the combination index data location for each dose.)\n\n• Table 2 - HPLC phenolic fraction.pdf (The table illustrates the composition of phenolic fraction, retention time and their concentrations)\n\n• Table 3 - HPLC Sterol fraction.pdf (The table illustrates the composition of terpene fraction, retention time and their concentrations)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n2- protocols.io: A full step by step assay protocols\n\nPlant Extraction and Fractionation, https://dx.doi.org/10.17504/protocols.io.q26g7y6bqgwz/v1. 37\n\nPreliminary qualitative phytochemical analysis, https://dx.doi.org/10.17504/protocols.io.e6nvwj27wlmk/v1. 38\n\nMTT (Assay protocol), https://dx.doi.org/10.17504/protocols.io.eq2ly72emlx9/v1. 39\n\n\nReferences\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. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBhanot A, Sharma R, Noolvi MN: Natural Sources as Potential Anti-Cancer Agents A Review. Phytomedicine, 3, 9-26. - References. Scientific Research Publishing; 2011 [cited 2022 Sep 10]. Reference Source\n\nTavakoli J, Miar S, Zadehzare MM, et al.: Evaluation of Effectiveness of Herbal Medication in Cancer Care: A Review Study. Iran J. Cancer Prev. 2012 [cited 2022 Sep 9]; 5(3): 144–156. PubMed Abstract \| Free Full Text\n\nEkins S, Mestres J, Testa B: In silico pharmacology for drug discovery: applications to targets and beyond. Br. J. Pharmacol. 2007 Sep [cited 2022 Sep 11]; 152(1): 21–37. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRoskov Y, Ower G, Orrell T, et al.: Annual Checklist. Species 2000 & ITIS catalogue of life 2019 Annual Checklist. 2019.2000; 2405–884. Reference Source\n\nBrukental H, Doron-Faigenboim A, Bar-Ya’akov I, et al.: Revealing the Genetic Components Responsible for the Unique Photosynthetic Stem Capability of the Wild Almond Prunus arabica (Olivier) Meikle. Front. Plant Sci. 2021 Nov 25; 12: 2583. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKitic D, Miladinovic B, Randjelovic M, et al.: Anticancer Potential and Other Pharmacological Properties of Prunus armeniaca L.: An Updated Overview. Plants (Basel). 2022 Jul 1 [cited 2022 Sep 20]; 11(14). Publisher Full Text Reference Source\n\nPoonam V, Raunak, Kumar G, et al.: Chemical Constituents of the Genus Prunus and their Medicinal Properties. Curr. Med. Chem. 2012 Oct 16; 18(25): 3758–3824.\n\nTomko AM, Whynot EG, O’Leary LF, et al.: Anti-cancer potential of cannabis terpenes in a Taxol-resistant model of breast cancer. Can. J. Physiol. Pharmacol. 2022 Aug 1 [cited 2022 Sep 21]; 100(8): 806–817. PubMed Abstract \| Publisher Full Text\n\nHarborne JB: Phytochemical Methods: A Guide to Modern Techniques of Plant Analysis. 1st ed.London: Chapman and Hall; 1991 [cited 2022 Aug 20]; 278–278. New York. Dordrecht: Springer Netherlands. Publisher Full Text\n\nKokate CK, Gokhale SB, Purohit AP: A Textbook of Pharmacognosy. 29 st. Nirali Prakashan.2009; 635 p.\n\nRadovanović B, Mladenović J, Radovanovic A, et al.: Phenolic Composition, Antioxidant, Antimicrobial and Cytotoxic Activites of Allium porrum L. (Serbia) Extracts. undefined.2015.\n\nAl-Shammari AM, Alshami MA, Umran MA, et al.: Establishment and characterization of a receptor-negative, hormone-nonresponsive breast cancer cell line from an Iraqi patient. Breast Cancer. 2015 Aug 7 [cited 2022 Aug 21]; 7: 223. Publisher Full Text \| Free Full Text\n\nSafi IN, Mohammed Ali Hussein B, Al-Shammari AM: In vitro periodontal ligament cell expansion by co-culture method and formation of multi-layered periodontal ligament-derived cell sheets. Regen. Ther. 2019 Dec 1; 11: 225–239. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nContino G, Eldridge MD, Secrier M, et al.: Whole-genome sequencing of nine esophageal adenocarcinoma cell lines [version 1; referees: 3 approved]. F1000Res. 2016 [cited 2022 Aug 21]; 5: 1336. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAl-Shammari AM, Alshami MA, Umran MA, et al.: Establishment and characterization of a receptor-negative, hormone-nonresponsive breast cancer cell line from an Iraqi patient. Breast Cancer: Targets and Therapy. 2015 Aug 7 [cited 2022 Aug 21]; 7: 223. Publisher Full Text \| Free Full Text\n\nAdil BH, Al-Shammari AM, Murbat HH: Breast cancer treatment using cold atmospheric plasma generated by the FE-DBD scheme. Clin Plasma Med. 2020 Sep 1; 19-20: 100103–100120. Publisher Full Text\n\nAbdullah SA, Al-Shammari AM, Lateef SA: Attenuated measles vaccine strain have potent oncolytic activity against Iraqi patient derived breast cancer cell line. Saudi J. Biol. Sci. 2020 Mar 1 [cited 2022 Aug 21]; 27(3): 865–872. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAl-Ziaydi AG, Al-Shammari AM, Hamzah MI, et al.: Newcastle disease virus suppress glycolysis pathway and induce breast cancer cells death. Virusdisease. 2020 Sep 1 [cited 2022 Aug 21]; 31(3): 341–348. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChou TC: Drug Combination Studies and Their Synergy Quantification Using the Chou-Talalay Method.[cited 2022 Oct 9]. Reference Source\n\nChou TC: Theoretical basis, experimental design, and computerized simulation of synergism and antagonism in drug combination studies. Pharmacol. Rev. 2006 [cited 2022 Oct 9]; 58(3): 621–681. PubMed Abstract \| Publisher Full Text\n\nNinkuu V, Zhang L, Yan J, et al.: Biochemistry of Terpenes and Recent Advances in Plant Protection. Int. J. Mol. Sci. 2021 Jun 1 [cited 2022 Oct 16]; 22(11). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMartini S, Conte A, Tagliazucchi D: Phenolic compounds profile and antioxidant properties of six sweet cherry (Prunus avium) cultivars. Food Res. Int. 2017 Jul 1; 97: 15–26. PubMed Abstract \| Publisher Full Text\n\nGalili S, Hovav R: Determination of Polyphenols, Flavonoids, and Antioxidant Capacity in Dry Seeds. Polyphenols Plants. 2014; 305–323. Publisher Full Text\n\nPeng CC, Chyau CC, Wang HE, et al.: Cytotoxicity of ferulic acid on T24 cell line differentiated by different microenvironments. Biomed. Res. Int. 2013; 2013: 1–7. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBae H, Park S, Yang C, et al.: Disruption of Endoplasmic Reticulum and ROS Production in Human Ovarian Cancer by Campesterol. Antioxidants. 2021 Mar 1 [cited 2022 Nov 27]; 10(3): 1–18. Publisher Full Text \| Free Full Text\n\nCalandra MJ, Impellizzeri J, Wang Y: An HPLC method for hydroperoxides derived from limonene and linalool in citrus oils, using post-column luminol-mediated chemiluminescence detection. Flavour Fragr. J. 2015 Mar 1; 30(2): 121–130. Publisher Full Text\n\nTustumi F, Kimura CMS, Takeda FR, et al.: PROGNOSTIC FACTORS AND SURVIVAL ANALYSIS IN ESOPHAGEAL CARCINOMA. Arq. Bras. Cir. Dig. 2016 Jul 1 [cited 2022 Oct 20]; 29(3): 138–141. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHickey BE, Francis DP, Lehman M: Sequencing of chemotherapy and radiotherapy for early breast cancer. Cochrane Database Syst. Rev. 2013 Apr 30 [cited 2022 Oct 20]; 2013(4). Publisher Full Text Reference Source\n\nChou T-C, Martin N: CompuSyn for drug combinations: PC software and user’s guide: a computer program for quantitation of synergism and antagonism in drug combinations, and the determination of IC50 and ED50 and LD50 values. Paramus, NJ: ComboSyn; 2005 [cited 2022 Oct 23]. Reference Source\n\nGautam M, Thapa RK, Gupta B, et al.: Phytosterol-loaded CD44 receptor-targeted PEGylated nano-hybrid phyto-liposomes for synergistic chemotherapy. Expert Opin. Drug Deliv. 2020 Mar 3 [cited 2022 Oct 23]; 17(3): 423–434. PubMed Abstract \| Publisher Full Text\n\nHernández JL, Padilla L, Dakhel S, et al.: Therapeutic Targeting of Tumor Growth and Angiogenesis with a Novel Anti-S100A4 Monoclonal Antibody. PLoS One. 2013 Sep 4; 8(9): e72480. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMahmood M, Abdulkareem A, Enas K: Assessing the Cytotoxicity of Phenolic and Terpene Fractions Extracted from Iraqi Prunus arabica on AMJ-13 and SK-GT-4 Human Cancer Cell Lines.2023 Feb 8 [cited 2023 Feb 18]. Reference Source\n\nMahmood M, Kadhim EJ, Abd AH: Plant Extraction and Fractionation. protocols.io.2023. Publisher Full Text\n\nMahmood M, Abd AH, Kadhim EJ: Preliminary qualitative phytochemical analysis. protocols.io.2023. Publisher Full Text\n\nAbd AH, Kadhim EJ, Mahmood M: MTT (Assay protocol). protocols.io.2023. Publisher Full Text" }	[ { "id": "171852", "date": "23 May 2023", "name": "Serap Sahin-Bolukbasi", "expertise": [ "Reviewer Expertise Lipidomics", "Cell culture", "Cytotoxic activity tests", "Biotechnological drug design" ], "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 manuscript presents high-performance liquid chromatography (HPLC) analysis of quantitative determination of different bioactive molecules of both phenolic and terpen fractions in the Iraqi Prunus arabica extract. The researchers evaluated the synergistic effect between the extracted fractions and chemotherapeutic agent (docetaxel). The cytotoxic activity of phenolic and terpene fractions extracted from Iraqi Prunus arabica against breast (AMJ13) and esophageal (SK-GT-4) cancer cell and also normal human fibroblasts (NHF) cell.\nHowever, the manuscript needs to be improved in order to meet the qualifications that are required for indexing. There are some issues that should be checked and corrected before indexing:\nPlease use subscript for IC50 (whole manuscript).\n\nPlease check whole manuscript for gm (it should be g?).\n\nPlease write which solvent was used to control wells and what was the concentration of solvent in control wells?\n\nPlease add ±SD values of samples in each concentration in Figure 1-3.\n\nPlease add ±SD values of samples in each IC50 concentration in manuscript.\n\nMorphological analysis (crystal violet staining) section, I would like to see images of IC50 of the phenolic fraction, terpene, docetaxel, and their combinations with chemotherapy.\n\nPlease write the source of AMJ13, SK-GT-4 and NHF cell line (ATCC, ECACC, Sigma-Aldrich or other…), even if it's a gift.\n\nPage 7; ‘...while a CI value larger than 1.1, the effects were assumed to be antagonistic...’ and Figure 5 legends page 9; ‘...CI value less than 1 indicates an antagonism...’’ CI value less than or larger tahan 1 assumed antagonistic? Please correct.\n\nPlease add ‘half’ in Figure 4 legend; ‘Figure 4. The half maximal inhibition concentration (IC50) for phenolic, terpene, and docetaxel, respectively, on A: AMJ13, B: SK-GT-4, and C: NHF cell lines.’\n\nPlease write axis name in Figure 4.\n\nThe selectivity index is an important parameter for indicates the selectivity of a given samples between normal and cancer cells. Samples are expected less cytotoxic towards the healthy cells according to the cancer cells. Please calculate the selectivity indexes of samples.\n\nAuthors should compare the results of this study some other similar plant extracts with more details. References should be improved and updated in the results and discussion section. Indeed, the field of similar samples with regard to both their chemistry and biological relevance, include a significant number of articles and some recent reviews\n\nPlease use only one of the terms antiproliferative activity, cytotoxic activity, or anticancer activity in all manuscripts.\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? No", "responses": [ { "c_id": "9741", "date": "24 Jul 2023", "name": "matin mahmood", "role": "Author Response", "response": "Dear Assoc. Prof. SERAP ŞAHİN BÖLÜKBAŞI, Thank you for your thoughtful review of our manuscript. We greatly appreciate your feedback and suggestions for improvement. In our experiments, we used untreated cells, MTT solution, and a solubilizing buffer (DMSO) as controls. To ensure the integrity of our experimental results and minimize any potential confounding effects, we carefully selected a final concentration of 0.5% DMSO for our study. This concentration has been widely reported in the literature as non-toxic and compatible with various cell types. Regarding the morphological analysis section of this study, it is worth noting that the analysis was carried out using only a concentration of 100 ug/ml, and it is important to clarify that no analysis was conducted specifically to IC50 values. Sincerely, Matin A. Mahmood" } ] } ]	1	https://f1000research.com/articles/12-433
https://f1000research.com/articles/13-151/v1	01 Mar 24	{ "type": "Research Article", "title": "The frailty among suburban elderly population in Indonesia after one-year COVID-19 pandemic", "authors": [ "Ahmad Fariz Malvi Zamzam Zein", "Witri Pratiwi", "Naswidi Dohana", "Witri Pratiwi", "Naswidi Dohana" ], "abstract": "Abstract\nBackground The coronavirus disease 2019 (COVID-19) pandemic has had significant impacts worldwide, especially among older adults. Frailty is a determinant of susceptibility to morbidity and mortality due to COVID-19 in the elderly. This study aimed to determine frailty status and identify factors associated with the suburban elderly population in Cirebon Regency, Indonesia, after the one-year COVID-19 pandemic.\n\nMethods A cross-sectional study of community-dwelling individuals aged ≥ 60 years was conducted in Klangenan, Cirebon Regency, Indonesia, from March to June 2021. A questionnaire was used to determine the baseline characteristics of participants, healthcare access, comorbidity, and frailty status. The Ina-FRAIL scale was used to determine the frailty status (frail/non-frail). The chi-square test and logistic regression analysis were used to determine the association between independent variables and frailty.\n\nResults A total of 383 participants were recruited, with a median age of 67 (64-73) years. The prevalence of frailty in the present study was 10.2%. Multivariate analysis showed that age (OR 2.72; 95%CI 1.21-6.12), multimorbidity (OR 7.86; 95% CI 3.00-20.57) and financial dependence (OR 13.39, 95% CI 5.66-31.73) were significantly associated with frailty.\n\nConclusion One-year COVID-19 pandemic has had a considerable impact on frailty among the suburban elderly population in Indonesia. The factors associated with frailty were age, multimorbidity, and financial dependence.", "keywords": [ "Frailty", "prevalence", "COVID-19 pandemic", "elderly", "suburban population", "Indonesia" ], "content": "Introduction\n\nThe World Health Organization (WHO) declared the coronavirus disease 2019 (COVID-19) pandemic on 11 March 2020.1 The pandemic of COVID-19 has had a tremendous impact worldwide. Studies have emphasized that people aged 60+ are categorized as high-risk groups for COVID-19 with a greater risk of severe disease, complications, and mortality.2–6 During the first trimester of pandemics in Indonesia, the mortality rate of the old age population was 17.68%, which was higher than the mortality rate of young and middle-age populations (15.09%).5 The mortality rate for patients more than 50 years old in Jakarta was higher (21%).2 These numbers were lower than those in the US (27%)7 and the UK (29%).8 Furthermore, the management of the COVID-19 pandemic urged mass restrictions, promoting home confinement to reduce the spread of COVID-19. The scheme may have negative impact on elderly population’s well-being and health.9 These pandemic-associated disruptive conditions necessitating robust change and adaptation that may result in increased risk of frailty.\n\nFrailty is defined as a state of excess vulnerability to stressor due to age-related decline in physiologic reserve throughout multiple organ systems, resulting in inadequacy to preserve or recover homeostasis after a destabilization.10 It includes social and psychological components in addition to physical dysfunction.11 Behavioral adaptation as response to reduced physiologic reserve and capacity with which to meet environmental and stressor challenges leads to overt state of frailty.12 Some studies showed the increase in frailty during the COVID-19 pandemic. Compared to the non-pandemic period, the COVID-19 pandemic has led to a higher risk of incident frailty among the non-frail elderly population in Japan.13\n\nThe impact of the COVID-19 pandemic and its countermeasures on frailty transition has not yet been predicted, especially in Indonesia. It affects all aspects and regions in each country, not only in big cities but also in suburban regions. The impact of pandemics on suburban populations is not yet known. Thus, this study aimed to investigate the prevalence of frailty and factors associated with frailty among the elderly suburban population in Indonesia.\n\n\nMethods\n\nThis study used data from our research project titled The Impact of Pandemic on Elderly Adults in Cirebon (IMPEDANCE). This cross-sectional study was conducted in a suburban community-dwelling elderly population, namely Klangenan, Cirebon Regency, Jawa Barat, Indonesia. Badan Pusat Statistik (Central Bureau of Statistics) Cirebon Regency estimated that there were 2,290,967 people registered at Cirebon Regency in 2021, with a total of 202,416 elderly people (8.84%).14 Klangenan is a suburban region in Cirebon Regency. Of the total 53,119 people, there were 4,704 elderly people in Klangenan (8.86%).14\n\nThis study was conducted between March and June 2021. We obtained a list of elderly people aged ≥60 years from Pusat Kesehatan Masyarakat (Public Health Center) Klangenan. We enrolled local health cadres to recruit caregivers (mostly family members) from the selected population. The inclusion criteria in this study encompassed community-dwelling elderly people with ≥60 years at Klangenan. Any unavailable contact number of caregivers was excluded.\n\nThe instrument used in this study was a questionnaire to determine the baseline characteristics of the participants, healthcare access, comorbidities, and frailty status. The baseline characteristics included age, sex, ethnic group, education level, occupation status, and financial dependence. The categories according to sex were male and female. Categories according to age were 60-69 years and ≥70 years. Categories according to ethnic groups were Javanese, Sundanese, and others. Categories according to educational level were elementary school or below, junior high school, senior high school, and university. The categories according to occupational status were retirement and still working. Categories based on financial dependence are dependent and independent.\n\nHealthcare access was determined by assessing whether participants had difficulty accessing healthcare. Categories according to difficulty in healthcare access were difficult and difficult. Comorbidity was assessed by the number of comorbidities (<2 and ≥2) and the disease(s) acknowledged by participants. The categories according to the number of comorbidities were <2 and ≥2. Categories according to disease of comorbidity (ies) were diabetes mellitus (DM), hypertension, cancer, chronic obstructive pulmonary disease (COPD), coronary artery disease (CAD), dyslipidemia and stroke.\n\nThe frailty status was assessed using the Indonesian version of the FRAIL scale (Ina-FRAIL scale). It is affirmed that the utilization of the Ina-FRAIL scale in this study has been approved by copyright license permission. The FRAIL scale is one of the available valid tools used for screening and identification of frailty with high feasibility (simple) in both community and primary care settings and prognostic value in predicting frailty-related consequences (disability, geriatric syndrome, quality of life, and mortality).15–18 In addition, it has been reported that the Ina-FRAIL scale is a valid and reliable tool to screen for frailty syndrome and sarcopenia in various clinical settings in Indonesia.19 It consists of five questions about fatigue, resistance, ambulatory, illness, and loss of weight with a total score of 0 to 5 for each question. Frailty status was categorized into two groups: non-frail (score 0-1) and frail (score ≥2).19\n\nThe formulated online questionnaire was administered using a digital platform called Google Forms. The Google Forms link was disseminated by health cadres through messenger applications (WhatsApp) to the caregivers. Health cadres also assisted caregivers in completing the questionnaires based on the participants’ answers. Participants’ responses were initially collected as Google Forms data, which were subsequently extracted into a spreadsheet file and exported to Microsoft Excel for cleaning and coding. The cleaned data were exported to IBM SPSS Statistics for Windows, version 26 (IBM Corp., Armonk, N.Y., USA).\n\nThe variables were described by frequency and percentage. Any missing data will be excluded in statistical analysis. The prevalence of frailty was measured by calculating the proportion of frailty in all the subjects. Bivariate and multivariate analyses were performed in this cross-sectional study. The participants were categorized based on sex into males and females. Categories according to age group were [1] 60-69 years and [2] ≥70 years. Categories according to education level were: [1] low (elementary school or below and junior high school) and [2] high (senior high school and university). Categories according to occupation status were as follows: [1] on retirement and [2] still working. Categories according to financial dependence were [1] dependent and [2] independent. Categories according to difficulty in healthcare access were [1] difficult and [2] not difficult. Categories according to the number of comorbidities were:[1] <2 and [2] ≥2. Categories according to comorbidities were: [1] diabetes mellitus, [2] hypertension, [3] cancer, [4] chronic obstructive pulmonary disease, [5] coronary artery disease, [6] dyslipidemia and [7] stroke.\n\nBoth of bivariate analysis and multivariate analysis were performed in this study. We use chi-square test to analyse the association between variables and frailty status, with the Fisher’s exact test as the alternative test. Variables with p value <0.25 were then recruited in multivariate models using multiple logistic regression. P value <0.05 was set as statistical significance in all analysis.\n\nThe ethical clearance had been obtained in this study. It was approved by the Health Research Ethics Committee of Gunung Jati Hospital, Cirebon City, Jawa Barat, Indonesia. The registration number is 082/LAIKETIK/KPEKRSGJ/2021 with the date of approval March 13, 2021. Submission of the answered questionnaire provided consent to participate in the study. Privacy and confidentiality were also ensured. This study adhered to the Declaration of Helsinki.\n\n\nResults\n\nA total of 383 participants were male (50.4%) and female (49.6%). Most of the participants were aged 60-69 years (58.7%), with a median age of 67 years (64-73). Missing data was not identified in this study due to all participants completed the questionnaire. The baseline characteristics of the study participants are presented in Table 1. As many as 50.1% of the participants were retired and the rest were still working, including traditional traders (89.5%), farmers (5.8%), and laborers (4.7%). Most participants (91.4%) were financially independent of their businesses (76%) and pension funds (24%). More than one-fourth of the participants experienced difficulty in accessing healthcare during the COVID-19 pandemic.\n\nComorbidity profiles are shown in Figure 1. Most participants had fewer than 2 comorbidities. Hypertension was the most frequent comorbidity (22.7%), followed by DM (15.4%), and CAD (5.0%). None of the participants were diagnosed with COPD in this study.\n\nAbbreviations: CAD – coronary arterial disease; COPD – chronic obstructive pulmonary disease; DM – diabetes mellitus.\n\nThe prevalence of frailty in this study was 10.2% (Figure 2). The aspects of frailty in this study predominantly encompassed difficulty in climbing 10 stairs without rest (13.1%), difficulty in walking 100-200 meters without assistance (12.8%), and loss of weight (3.9%) (Table 2). Only a few participants felt tired most or all of the time (0.8%) and had a considerably high burden of comorbidities (0.8%).\n\nBivariate analysis revealed that some variables were associated with frailty in this study, including age (OR 3.66; 95% CI 1.79 – 7.47), education level (OR 3.37; 95% CI 1.28 – 8.85), occupation status (OR 6.39; 95% CI 2.61 – 15.67), financial dependence (OR 13.38; 95% CI 5.99 – 29.87), and number of comorbidities (OR 8.62; 95% CI 3.62 – 20.53), as shown in Table 3.\n\n Significant with p-value <0.05.\n\nFurthermore, the multivariate analysis (Table 4) demonstrated that age (odds ratio [OR] 2.72; 95% confidence interval [CI] 1.21 – 6.12), number of comorbidities (OR 7.86; 95% CI 3.00 – 20.57), and financial dependence (OR 13.39; 95% CI 5.66 – 31.73) were significantly associated with frailty among participants in this study.\n\n\nDiscussion\n\nThis study revealed that frailty was considerable among older people in suburban areas, with approximately one in ten elderly people being frail. A study by Minoru Yamada et al. reported that the COVID-19 pandemic has led to a higher risk of incident frailty among the non-frail elderly population in Japan (OR 1.54, 95% CI: 1.18-2.02), with an incidence rate of 16% in year 2020-2021 vs. incidence rate of 11% in 2015-2016.13 The study indicates a higher number of frail than our study. This might be due to some points: [1] the study was recruited elder population (≥65 years vs. ≥60years in our study) with higher mean age of participants (73.5 + 5.5 years vs. 68.3 + 5.9 years in our study); [2] the study was using different tool for defining frailty (the Kihon checklist). The Kihon checklist is a 25-item questionnaire that includes seven categories: daily life, physical ability, nutrition, oral condition, the extent to which one is housebound, cognitive status, and depression risk.20 Other study among 593 participants in Japan by Tomoyuki Shinohara, et al., reported that the prevalence of frailty was 11.8% and there was a 3.9% increase in prevalence during the 6-month observation.21 This prospective cohort study demonstrated a slightly higher prevalence of frailty in our study regarding older population in recruitment, higher mean age of participants, shorter duration of observation, and different tools in assessing frailty (using Frailty Screening Index). In addition, a cross-sectional study of 11,145 participants in the Netherlands by Sealy et al. revealed that frailty was present in 13% of patients during the first wave of the COVID-19 pandemic.22\n\nFrailty during the COVID-19 pandemic is a catastrophic condition that necessitates a complex and comprehensive approach to its identification and management. It is affected by, but is not limited to, age, physical stress, psychological pressure, and social detachment. Our study emphasizes that age, multimorbidity, and financial dependence play pivotal roles as factors associated with frailty in the elderly population during the pandemic.\n\nIn this study, age was significantly associated with frailty (OR 2.72, 95% CI 1.21-6.12). This is consistent with a study by Shinohara et al. with an OR of 1.082 (95% CI 1.050–1.115) and a study by Martine J. Sealy et al. with an OR of 1.04 (95% CI 1.03–1.06).21,22 Age-associated decline and dysregulation may predominantly increase vulnerability.23 It worsens the dysregulation of multiple interconnected physiological and biological systems exceeding a threshold to critical dysfunction homeostasis.23,24 Further, age-related physiological changes, consisting of changes in body composition (decreased muscle mass), hormonal imbalances (menopause, andropause, corticopause, and somatopause), and insulin resistance can cause frailty syndrome.25\n\nMultimorbidity was associated with frailty (OR, 7.86; 95% CI 3.00.- 20.57). This association is in accordance with the results from previous studies, which were study by Tomoyuki Shinohara in Japan with OR 1.619 (95% CI 1.13-2.358) and a study by Martine J. Sealy, et al. with OR 1.23 (95% CI 1.16-1.30).21,22 A bidirectional mechanism, rather than unidirectional pathway, between multimorbidity and frailty is suggested in a strong dose-response relationship.26,27 In the presence of multiple chronic diseases, especially cardiometabolic diseases, the system failure process would be initiated by an accumulation of health deficits leading to clinical condition in the form of depletion in the physiological reserve and redundancy, which is known as frailty.26,28 In the context of pandemic, the restriction of healthcare facilities as countermeasures during a one-year pandemic may limit healthcare coverage, including geriatric care, which leads to uncontrolled status for comorbidities among the elderly population. This may cause health deficits that may affect vulnerability and increase the risk of frailty.\n\nFinancial dependence as a low economic issue in this study was associated with frailty (odds ratio [OR] 13.39; 95% CI 5.66-31.73). Tim Nasional Percepatan Penanggulangan Kemiskinan (The Indonesia’s National Team for The Acceleration of Poverty Reduction) stated that the COVID-19 pandemic has detrimental effect on Indonesia’s elderly population leading to increased risks and vulnerabilities.29 It is due to limited mobility as a result of ‘stay-at-home’ policy, no access to minimum income support/pension in most elder adults and increased social exclusion and isolation contributing to depression, fears and feeling of helplessness.29 These conditions further cause the elderly population more vulnerable to the economic shock of pandemic, leading to financial dependence.29 Financial dependence as low socioeconomic issue disrupts older adults’ social activities, puts them away from successful social relationship and reduces their quality of life.30 These direct impacts bring about the increased risk of frailty. Financial dependence as an issue in family socioeconomic status represents the individual’s ability in achieving material and social resources.31 Reduced family socioeconomic status can increase frailty index and impact poor health outcome.31 Further, the implementation of COVID-19 countermeasures may affect both older adults and their caregivers in unmet financial needs. This worsened their financial dependence.\n\nThis study had some limitations. The design used in this study is a cross-sectional study that limits the risk factor/cause relationship analysis due to temporal ambiguity. Moreover, the online survey format contributed to potential recall bias and was dependent on the participants’ honest responses.\n\nThe findings of this study urge physicians to comprehend the clinical and psychosocial aspects of assessing and managing frailty during a pandemic. In addition, this study recommends that the government adequately facilitates economic support among the elderly population as part of social protection during the pandemic.\n\nFurther studies with a cohort design and offline survey format are needed to investigate frailty during the pandemic and its causal relationship analysis with regard to stimulating further recommendations on healthcare for the elderly population during and after the pandemic.\n\n\nConclusion\n\nThis study demonstrated that one-year COVID-19 pandemic has had a considerable impact on frailty among the elderly suburban population in Indonesia. The factors associated with frailty were age, number of comorbidities, and financial dependence.\n\nThis study was approved by the Medical Research Ethics Committee of Gunung Jati Hospital, Cirebon City, Jawa Barat, Indonesia (registration no. 082/LAIKETIK/KPEKRSGJ/2021). Submission of the answered questionnaire provided consent to participate in the study. Privacy and confidentiality were also ensured.\n\nConsent to participate: Informed consent was obtained from all individual participants in this study through their responses in the Google Form.\n\nConsent to publish: The authors affirm that all participants provided informed consent for publication through their responses in the Google Form.", "appendix": "Data availability\n\nFigshare. Frailty among suburban elderly population in Indonesia in one-year after pandemic. https://doi.org/10.6084/m9.figshare.25151096.v1. 32\n\nThis project contains the following underlying data:\n\n- Frailty during one year after pandemic, Klangenan.xlsx (baseline data of participants)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nThis project contains the following extended data:\n\n- STROBE Checklist for Frailty Study.doc (adherence to STROBE guidelines). Figshare. STROBE Checklist for Frailty Study. https://doi.org/10.6084/m9.figshare.25151153.\n\n- Participation Information Sheet.docx. Figshare. Participation Information Sheet. https://doi.org/10.6084/m9.figshare.25194017\n\n- Participation Consent for Publication.docx (informed consent for publication). Figshare. Participation Consent for Publication. https://doi.org/10.6084/m9.figshare.25151159.\n\n- Informed consent for participation.docx (informed consent for participation in research). Figshare. Informed consent for participation. https://doi.org/10.6084/m9.figshare.25151156\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 express our gratitude to Mrs. Eni Suhaeni, Head of the Department of Health, Cirebon Regency, for their support in site research and subject enrollment. We hereby confirm that we have obtained permission to include Mrs. Eni Suhaeni as Head of the Department of Health, Cirebon Regency (during the period of study) to be mentioned in the Acknowledgments section.\n\n\nReferences\n\nWorld Health Organization: Coronavirus Disease 2019 (Covid-19): Situation Report-51.2020.\n\nSurendra H, Elyazar IR, Djaafara BA, et al.: Clinical characteristics and mortality associated with COVID-19 in Jakarta, Indonesia: A hospital-based retrospective cohort study. Lancet Reg. Heal - West Pacific. 2021; 9: 100108. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhang JJY, Lee KS, Ang LW, et al.: Risk Factors for Severe Disease and Efficacy of Treatment in Patients Infected with COVID-19: A Systematic Review, Meta-Analysis, and Meta-Regression Analysis. Clin. Infect. Dis. 2020; 71(16): 2199–2206. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLiu K, Chen Y, Lin R, et al.: Clinical features of COVID-19 in elderly patients: A comparison with young and middle-aged patients. J. Infect. 2020; 80(6): e14–e18. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKaryono DR, Wicaksana AL: Current prevalence, characteristics, and comorbidities of patients with COVID-19 in Indonesia. J. Community Empower Heal. 2020; 3(2): 77. Publisher Full Text\n\nDhama K, Patel SK, Kumar R, et al.: Geriatric Population During the COVID-19 Pandemic: Problems, Considerations, Exigencies, and Beyond. Front. Public Health. 2020; 8(September): 1–8. Publisher Full Text\n\nRichardson S, Hirsch JS, Narasimhan M, et al.: Presenting Characteristics, Comorbidities, and Outcomes among 5700 Patients Hospitalized with COVID-19 in the New York City Area. JAMA - J. Am. Med. Assoc. 2020; 323(20): 2052–2059. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDocherty AB, Harrison EM, Green CA, et al.: Features of 20 133 UK patients in hospital with covid-19 using the ISARIC WHO Clinical Characterisation Protocol: Prospective observational cohort study. BMJ. 2020; 369(March): 1–12. Publisher Full Text\n\nGreenberg NE, Wallick A, Brown LM: Impact of COVID-19 pandemic restrictions on community-dwelling caregivers and persons with dementia. Psychol. Trauma Theory Res. Pract. Policy. 2020; 12: S220–S221. PubMed Abstract \| Publisher Full Text\n\nWalston J, Hadley EC, Ferrucci L, et al.: Research agenda for frailty in older adults: Toward a better understanding of physiology and etiology: Summary from the American Geriatrics Society/National Institute on Aging research conference on frailty in older adults. J. Am. Geriatr. Soc. 2006; 54(6): 991–1001. PubMed Abstract \| Publisher Full Text\n\nWon CW: Frailty: Its Scope and Implications for Geriatricians. Ann. Geriatr. Med. Res. 2019; 23(3): 95–97. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nXiu Q-L: The Frailty Syndrome: Definition and Natural History. Clin. Geriatr. Med. 2011; 27(1): 1–15. Publisher Full Text\n\nYamada M, Arai H: Does the COVID-19 pandemic robustly influence the incidence of frailty? Geriatr Gerontol Int. 2021; 21(8): 754–755. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCirebon K, Angka D: BPS-Statistics of Cirebon Regency.2022.\n\nKojima G: Quick and Simple FRAIL Scale Predicts Incident Activities of Daily Living (ADL) and Instrumental ADL (IADL) Disabilities: A Systematic Review and Meta-analysis. J. Am. Med. Dir. Assoc. 2018; 19(12): 1063–1068. PubMed Abstract \| Publisher Full Text\n\nYu R, Tong C, Leung G, et al.: Assessment of the validity and acceptability of the online FRAIL scale in identifying frailty among older people in community settings. Maturitas. 2021; 145: 18–23. PubMed Abstract \| Publisher Full Text\n\nWoo J, Yu R, Wong M, et al.: Frailty screening in the community using the FRAIL scale. J. Am. Med. Dir. Assoc. 2015; 16(5): 412–419. Publisher Full Text\n\nLee H, Chong J, Jung HW, et al.: Association of the frail scale with geriatric syndromes and health-related outcomes in korean older adults. Ann. Geriatr. Med. Res. 2021; 25(2): 79–85. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDwipa L, Apandi M, Utomo PP, et al.: Adaptation and validation of the indonesian version of the frail scale and the sarc-f in older adults. Asian J. Gerontol. Geriatr. 2021; 16(1): 40–47. Publisher Full Text\n\nTaniwaki T, Usuku K, Hirose J, et al.: Validation of Each Category of Kihon Checklist for Assessing Physical Functioning, Nutrition and Cognitive Status in a Community-Dwelling Older Japanese Cohort. Epidemiol. Open Access. 2017; 07(05). Publisher Full Text\n\nShinohara T, Saida K, Tanaka S, et al.: Did the number of older adults with frailty increase during the COVID-19 pandemic? A prospective cohort study in Japan. Eur. Geriatr. Med. 2021; 12(5): 1085–1089. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSealy MJ, van der Lucht F , van Munster BC , et al.: Frailty among Older People during the First Wave of the COVID-19 Pandemic in The Netherlands. Int. J. Environ. Res. Public Health. 2022; 19(6). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChen Y, Klein SL, Garibaldi BT, et al.: Aging in COVID-19: Vulnerability, immunity and intervention. Ageing Res. Rev. 2021; 65(October 2020): 101205. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFried LP, Cohen AA, Xue Q-L, et al.: The physical frailty syndrome as a transition from homeostatic symphony to cacophony. Nat. Aging. 2021; 1(1): 36–46. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDiez-Ruiz A, Bueno-Errandonea A, Nuñez-Barrio J, et al.: Factors associated with frailty in primary care: A prospective cohort study. BMC Geriatr. 2016; 16(1): 1–8. Publisher Full Text\n\nVetrano DL, Palmer K, Marengoni A, et al.: Frailty and multimorbidity: A systematic review and meta-analysis. J. Gerontol. - Ser. A Biol. Sci. Med. Sci. 2019; 74(5): 659–666. PubMed Abstract \| Publisher Full Text\n\nAbu HO, Saczynski J, Mehawej J, et al.: Multimorbidity, physical frailty, and self-rated health in older patients with atrial fibrillation. BMC Geriatr. 2020; 20(1): 1–11. Publisher Full Text\n\nVillacampa-Fernández P, Navarro-Pardo E, Tarín JJ, et al.: Frailty and multimorbidity: Two related yet different concepts. Maturitas. 2017; 95: 31–35. PubMed Abstract \| Publisher Full Text\n\nLarasati D: Lifecycle social protection assessment: Elderly vulnerability and social protection during COVID-19 pandemic. Indonesia’s TNP2K Policy Brief. 2020.\n\nHayajneh AA, Rababa M: The Association of Frailty with Poverty in Older Adults: A Systematic Review. Dement. Geriatr. Cogn. Disord. 2022; 50(5): 407–413.\n\nZhou W, Hou J, Sun M, et al.: The Impact of Family Socioeconomic Status on Elderly Health in China: Based on the Frailty Index. Int. J. Environ. Res. Public Health. 2022; 19(2). Publisher Full Text\n\nZein AFMZ, Pratiwi W, Dohana N: Frailty during one year after pandemic, Klangenan.xlsx. Dataset. figshare. 2024. Publisher Full Text" }	[ { "id": "253787", "date": "28 Mar 2024", "name": "Nata Pratama Hardjo Lugito", "expertise": [ "Reviewer Expertise Internal medicine", "clinical epidemiology", "infectious disease" ], "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 \"The frailty among suburban elderly population in Indonesia after one-year COVID-19 pandemic\" was well written. The result and discussion was clear and concise, yet explains the condition of frailty in suburban Indonesian elderly.\n\nThe exact province or region in Indonesia where the study was conducted should be added to the title, as Indonesia is very vast and each region has its special condition.\n\nThe authors could compare in the discussion how the COVID-19 pandemic affected frailty among elderly based on other study in Indonesia or other countries, compared to before the pandemic.\nThe authors have explained that socioeconomic status influenced frailty among elderly after pandemic. The authors could elaborate on the interplay of multimorbidity as risk factors of frailty and COVID-19,\nThe authors did not include history of COVID-19 infection as risk factor of frailty. Could there be any data about this?\nThe authors wrote the conclusion as \"This study demonstrated that one-year COVID-19 pandemic has had a considerable impact on frailty...\" As the authors did not mentioned in the discussion about frailty before the pandemic, it would be difficult to conclude that the pandemic impacted elderly frailty.\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": "11388", "date": "20 Jun 2024", "name": "Ahmad Fariz Malvi Zamzam Zein", "role": "Author Response", "response": "We, the authors of this article, are thankful for your precious review. It is thoroughly delivered in comprehensive assessment and recommendation. Due to your comment regarding the scope of region, we have modified the title into 'The frailty among suburban elderly population after one-year COVID-19 pandemic in Cirebon Regency, Indonesia'. As your explanation, it is notable to express the region where the study held clearly. Some additional statements were added to emphasize the interplay of multimorbidity, frailty and COVID-19, as your recommendation. It is available at Paragraph 4 in Discussion section. You recommended that the history of COVID-19 infection is included in the study, if any. We have provided the history of COVID-19 in Table 1 and adjacent description. Further, it is recruited in bivariate analysis as well (Table 2). We have modified the word 'impact' in conclusion into 'burden'. It is aimed to notify the proportion of frailty as the magnitude of problem without reflecting pre-post pandemic effect. There are some modifications and corrections in writing as integrated part of our commitment in performing improvement in this article. We hope that the revised version suits your review. Thank you in advance." } ] } ]	1	https://f1000research.com/articles/13-151
https://f1000research.com/articles/13-1040/v1	10 Sep 24	{ "type": "Research Article", "title": "A SWOT analysis of generative AI in applied linguistics: Leveraging strengths, addressing weaknesses, seizing opportunities, and mitigating threats", "authors": [ "Obied Alaqlobi", "Ahmed Alduais", "Fawaz Qasem", "Muhammad Alasmari", "Obied Alaqlobi", "Fawaz Qasem", "Muhammad Alasmari" ], "abstract": "Background The integration of generative Artificial Intelligence (AI), particularly large language models (LLMs) like ChatGPT and Gemini, into the field of applied linguistics presents transformative opportunities alongside notable challenges. This study aims to evaluate the role of AI in applied linguistics through a SWOT (Strengths, Weaknesses, Opportunities, Threats) analysis.\n\nMethods Using a sample derived from Scopus and Web of Science, we identified relevant studies by applying specific search terms. Our qualitative research design used the SWOT framework to systematically review and analyse studies, ensuring a robust synthesis of data.\n\nResults The results of our SWOT analysis revealed the following: 1) Strengths: Enhanced educational tools and resources through AI-driven personalization and interactive learning, increased efficiency and accessibility in generating educational materials, and innovative research applications leveraging semantic similarity measures and advanced linguistic analyses. 2) Weaknesses: Quality and accuracy concerns in AI-generated content, potential over-dependence on AI tools leading to diminished student creativity and ethical issues, and technical limitations in handling complex academic writing tasks. 3) Opportunities: Potential for educational innovation and pedagogical integration, advancements in AI technology to support linguistic research, and fostering global collaboration and access through AI tools. 4) Threats: Risks to academic integrity due to AI-generated content, technological and implementation challenges, and privacy and security concerns regarding data handling.\n\nConclusions Based on the SWOT analysis, we introduced a strategic plan to maximize strengths and opportunities while addressing weaknesses and threats. The strategy includes promoting personalized learning through AI tools, streamlining the creation of educational materials, fostering innovative research applications, ensuring human oversight to maintain content quality, developing ethical guidelines to prevent misuse, investing in necessary infrastructure and training, and implementing robust data protection measures.", "keywords": [ "Artificial Intelligence", "Applied Linguistics", "Generative AI", "Large Language Models", "Innovative Technology", "SWOT Analysis", "Educational Technology" ], "content": "Introduction\n\nAI has become an unavoidable force in research and numerous aspects of our lives. Sam Altman, CEO of OpenAI, made a striking statement about AI’s potential to dramatically reshape the world, while noting that companies will need to adapt to its rapid changes (as cited in Streitfeld, 2023). This assertion underscores AI’s current prominence as a topic of discussion, regardless of its ultimate veracity. Altman’s perspective reflects the growing recognition of AI’s transformative potential across various sectors, including applied linguistics.\n\nWhile there are many proposed definitions of AI, they generally converge around the concept of creating computer programs or machines capable of exhibiting behaviour we would consider intelligent if displayed by humans (Kaplan, 2016). Kaplan’s definition emphasizes the goal of replicating human-like intelligence in artificial systems, which has profound implications for fields like applied linguistics. This intelligent behaviour in AI systems is achieved through extensive exposure to and training on large datasets, leading to the capability of human language generation. The mechanism behind this generation is known as LLMs (Birhane et al., 2023). Birhane and colleagues’ work highlights the critical role of LLMs in enabling AI systems to process and generate human-like language, a capability that is particularly relevant to applied linguistics.\n\nProminent examples of LLMs employed as generative AI across various scientific fields, including applied linguistics, are the OpenAI GPT series, Google’s Gemini, and Microsoft’s Copilot. These models represent the cutting edge of AI technology in language processing and generation.\n\nThe focus of this paper is to examine the SWOT (Strengths, Weaknesses, Opportunities, Threats) aspects of generative AI in applied linguistics. Leigh (2009, p. 115) defines the SWOT framework as:\n\na process by which a group of stakeholders (a) identify internal and external inhibitors and enhancers of performance, (b) analyse those factors based on estimates of their contributions to net value and approximations of their controllability, and (c) decide what future action to take about those factors.\n\nThis definition underscores the comprehensive nature of SWOT analysis in evaluating both internal and external factors affecting AI’s integration into applied linguistics.\n\nThe application of SWOT analysis in applied linguistics is not novel. Al-Mutawa et al. (2024) utilized SWOT analysis to identify previously unexamined strengths and weaknesses in the writing performance of Kuwaiti ESL learners. Their study demonstrates the utility of SWOT analysis in uncovering nuanced aspects of language learning that might otherwise go unnoticed. Ge et al. (2023) examined the sustainability of language development using SWOT analysis, particularly focusing on the digitalization for sustainable foreign language education. Their work highlights the potential of SWOT analysis in addressing broader, systemic issues in language education.\n\nTafazoli (2022) employed SWOT analysis to present English language teachers’ attitudes toward computer-assisted language learning in Spain. This study showcases the versatility of SWOT analysis in capturing complex attitudinal data from educators. More recently, Farrokhnia et al. (2024) analyzed ChatGPT in educational practice using SWOT analysis and provided recommendations. While Farrokhnia et al.’s paper explored the application of generative AI in higher education broadly, our study specifically focuses on the application of generative AI in the field of applied linguistics.\n\nOur study differs from previous research by providing a comprehensive SWOT analysis of generative AI, particularly LLMs like ChatGPT and Gemini, in the specific context of applied linguistics. While existing studies have explored aspects of AI in language teaching and learning, there remains a significant gap in the literature regarding a holistic analysis of AI’s multifaceted impacts in this field. By leveraging the SWOT framework, our research aims to offer a structured and actionable approach to maximizing benefits and mitigating risks associated with AI integration in applied linguistics.\n\nThe primary aim of this study is to conduct a SWOT analysis to evaluate the integration of generative AI, specifically LLMs, in applied linguistics. We seek to identify and analyze the strengths, weaknesses, opportunities, and threats associated with AI usage in language teaching and learning, and to develop actionable strategies that maximize benefits while mitigating risks. The SWOT analysis was chosen for its structured approach in evaluating the complex impacts of AI in applied linguistics. This method allows for a systematic examination of both internal and external factors, providing a balanced view of positive and negative aspects associated with AI integration.\n\nBy categorizing findings into strengths, weaknesses, opportunities, and threats, our SWOT analysis facilitates a nuanced understanding of how AI can enhance educational tools, improve efficiency, and foster innovative research, while also identifying potential challenges such as quality concerns, ethical issues, and technical limitations. This holistic approach ensures that our analysis is not only thorough but also actionable, enabling the development of strategic plans that maximize benefits and mitigate risks. Furthermore, our use of the SWOT method aligns with previous research in the field, providing a familiar and validated framework for stakeholders to engage with and apply the findings effectively.\n\n\nMethods\n\nThis study employed a qualitative research design, specifically a systematic review of the literature guided by the SWOT framework. This approach was chosen for its suitability in analysing complex phenomena, such as the integration of AI in applied linguistics. The SWOT framework allows for a structured and comprehensive examination of both internal factors (strengths and weaknesses) and external factors (opportunities and threats) influencing a particular phenomenon. In this context, the SWOT analysis helps identify and evaluate the potential benefits, challenges, prospects, and risks associated with incorporating AI technologies, particularly LLMs like GPT, into the field of applied linguistics. This study aligns with a postpositivist paradigm, acknowledging the existence of objective realities while recognizing the subjective interpretation of data by researchers. The postpositivist lens allows for a balanced approach, recognizing the influence of researcher perspectives while striving for objectivity in data analysis. The paper is reported according to the Standards for Reporting Qualitative Research (SRQR) (O’Brien et al., 2014). The extracted data, analysis outline, PRISMA flowchart (Page et al. 2021), and SRQR checklist are all accessible at https://doi.org/10.17605/OSF.IO/8AGCZ (Alaqlobi et al. 2024).\n\nThe research team consisted of four authors with diverse expertise in applied linguistics and AI. This multidisciplinary composition allowed for a comprehensive understanding of the research topic from various perspectives, minimizing potential biases and enriching the analysis. The team brought together a range of experiences in language teaching, second language acquisition, computational linguistics, and AI development, ensuring a well-rounded approach to examining the intersection of these fields. Throughout the study, the team engaged in regular reflexive discussions to critically examine their assumptions, interpretations, and potential influence on the research process. These discussions helped ensure that the analysis remained grounded in the data while acknowledging the researchers’ own positions within the field.\n\nThis study was conducted within the rapidly evolving landscape of AI and its applications in education. The research specifically focused on the field of applied linguistics, examining the potential of generative AI, particularly LLMs like GPT, to impact language teaching and learning. The findings and implications of this study are situated within this specific context, recognizing the transformative potential of AI in reshaping educational practices and language learning experiences. The study acknowledges the growing interest in utilizing AI for personalized learning, automated language assessment, and the development of intelligent tutoring systems, all of which have significant implications for applied linguistics research and practice.\n\nThe sample for this study was derived from two major academic databases: Scopus and Web of Science. These databases were chosen for their comprehensive coverage of peer-reviewed literature in linguistics and applied linguistics, ensuring a representative sample of relevant research. The search was conducted on December 23, 2023, using a combination of keywords and search strings designed to capture studies related to generative AI and its applications in various subfields of linguistics. The search terms included terms like “GPT,” “Generative AI,” “Language Models,” “Applied Linguistics,” “Language Teaching,” “Language Learning,\" and other related terms. The initial search yielded 132 hits. After removing duplicates and irrelevant studies based on title and abstract screening, 121 studies remained. A full-text review further narrowed the sample to 24 studies, excluding editorials, correspondences, and studies that did not directly address the research question. The final sample size was determined by the principle of saturation, where no new relevant information emerged from the reviewed studies, indicating that the sample was sufficient to provide a comprehensive understanding of the topic.\n\nTITLE (“GPT” AND “Linguistics”) OR TITLE (“GPT” AND “applied linguistics”) OR TITLE (“GPT” AND “Phonetics”) OR TITLE (“GPT” AND “Phonology”) OR TITLE (“GPT” AND “Morphology”) OR TITLE (“GPT” AND “Syntax”) OR TITLE (“GPT” AND “Semantics”) OR TITLE (“GPT” AND “Pragmatics”) OR TITLE (“GPT” AND “Vocabulary”) OR TITLE (“GPT” AND “Reading”) OR TITLE (“GPT” AND “Writing”) OR TITLE (“GPT” AND “Speaking”) OR TITLE (“GPT” AND “Listening”) OR TITLE (“GPT” AND “Pragmatics”) OR TITLE (“GPT” AND “Language teaching”) OR TITLE (“GPT” AND “Language learning”) OR TITLE (“changes” AND “Language teaching”) OR SRCTITLE (“changes” AND “Language learning”)).\n\nThis study did not involve direct interaction with human subjects, relying solely on the analysis of published research articles. The data extracted from these articles were publicly available and did not contain any personally identifiable information. Therefore, ethical approval from an institutional review board and participant consent were not required. However, the research team adhered to ethical guidelines for research integrity, ensuring accurate and transparent reporting of findings and proper attribution of sources.\n\nData collection involved a systematic review of the 24 selected studies. The research team developed a standardized data extraction form to ensure consistency and minimize bias in data collection. This form included fields for recording key information from each study, such as publication details, research aims, methodologies, key findings, and author conclusions related to the strengths, weaknesses, opportunities, and threats of AI in applied linguistics. The data extraction process involved carefully reviewing the full text of each article and extracting relevant information according to the predefined categories on the data extraction form.\n\nNo specific data collection instruments, such as surveys or interviews, were used in this study. The primary tools for data collection were the Scopus and Web of Science databases and their respective search interfaces. These platforms provided access to the research articles and facilitated the initial search and retrieval process. Additionally, reference management software was used to organize and manage the selected articles.\n\nThe units of study were the 24 selected research articles that met the inclusion criteria. These articles represented a diverse range of research designs, methodologies, and perspectives on the application of AI in applied linguistics, providing a rich and multifaceted understanding of the field. The articles included both empirical studies and theoretical discussions, offering a balanced perspective on the practical applications and conceptual implications of AI in language learning and teaching.\n\nData extracted from the selected studies were organized and managed using spreadsheet software. The data were systematically categorized according to the four quadrants of the SWOT framework: strengths, weaknesses, opportunities, and threats. This involved analysing the extracted data for recurring themes, patterns, and key findings related to each SWOT category. No data transformation or coding was required as the analysis focused on thematic synthesis of qualitative information.\n\nData analysis involved a thematic synthesis approach guided by the SWOT framework. The research team independently reviewed the extracted data and collaboratively identified recurring themes and patterns related to the strengths, weaknesses, opportunities, and threats of AI in applied linguistics. These themes were then discussed, refined, and organized within the SWOT framework to provide a structured overview of the findings. The thematic synthesis process involved identifying initial codes and themes, grouping similar codes into broader categories, and then developing overarching themes that captured the essence of the findings.\n\nSeveral techniques were employed to enhance the trustworthiness of the findings. These included:\n\n• Triangulation: Using multiple databases (Scopus and Web of Science) and researchers with diverse expertise to ensure a comprehensive and balanced perspective, minimizing the limitations of relying on a single source or viewpoint.\n\n• Iterative analysis: The research team engaged in iterative discussions throughout the data analysis process to challenge interpretations, refine themes, and reach consensus on the findings, ensuring that the analysis was thorough and reflected the collective insights of the team.\n\n• Thick description: The research process and findings are presented with rich detail to enhance transparency and allow readers to assess the study’s rigor and transferability. Providing detailed descriptions of the methodology, data analysis procedures, and the researchers’ reflections on the process contributes to the study’s trustworthiness by making the research process transparent and replicable.\n\n\nFindings\n\nThe advent of AI in the field of applied linguistics has opened new avenues for enhancing educational tools and resources, increasing efficiency and accessibility, and fostering innovative research applications. These strengths, as highlighted by numerous studies, underscore the transformative potential of AI technologies like ChatGPT in language education and research. This essay delves into three primary strengths of AI in applied linguistics: enhanced educational tools and resources, increased efficiency and accessibility, and innovative research applications.\n\nEnhanced educational tools and resources\n\nAI technologies, particularly ChatGPT, have significantly enhanced educational tools and resources in language teaching and learning. ChatGPT provides authentic texts, supports personalized content, and caters to diverse learning styles, thus enriching the educational experience (Kohnke et al., 2023; Özdemir-Çağatay, 2023). The ability to simulate human-like conversations allows for practical language learning through interactive narrative construction and simulated discourse (Hatmanto & Sari, 2023). This interactive capability is crucial in fostering active engagement and learner autonomy, which are essential components of effective language learning (Hatmanto & Sari, 2023).\n\nMoreover, the integration of AI into language education aligns well with established theoretical frameworks such as Communicative Language Teaching and Constructivist Learning Theory. ChatGPT’s ability to promote authentic language use, collaborative learning, and practical application of knowledge is consistent with these educational paradigms (Hatmanto & Sari, 2023). For instance, virtual Socratic dialogues and interactive narrative construction facilitated by ChatGPT can significantly enhance learner engagement and fluency (Hatmanto & Sari, 2023). Thus, AI tools not only complement traditional educational methods but also introduce innovative approaches that align with modern pedagogical theories.\n\nIncreased efficiency and accessibility\n\nIncreased efficiency and accessibility represent another significant strength of AI in applied linguistics. AI tools like ChatGPT streamline the process of generating educational materials, thereby reducing the workload for educators, and making language learning more accessible (Zografos & Moussiades, 2023; Zuckerman et al., 2023). For example, AI-driven platforms can automatically generate vocabulary lists, writing prompts, and assessment items, which are essential resources for language educators (Zografos & Moussiades, 2023). This automation allows educators to focus more on higher order teaching tasks, thereby improving the overall quality of education (Zuckerman et al., 2023).\n\nFurthermore, AI technologies can significantly assist non-native English-speaking researchers by providing language refinement and feedback, thus lowering the barriers to academic writing in English (Hwang et al., 2023). This support is particularly valuable for researchers who may struggle with the intricacies of academic English, enabling them to produce high-quality scholarly work (Hwang et al., 2023). By democratizing access to academic resources, AI tools contribute to more inclusive and equitable educational and research environments (Hwang et al., 2023).\n\nInnovative research applications\n\nInnovative research applications of AI in linguistics further highlight its transformative potential. LLMs like GPT-4o, Gemin 1.5, ChatGPT, etc. (Poe) can construct measures of semantic similarity that align closely with human judgment, thereby enhancing research methodologies in social sciences and linguistics (Le Mens et al., 2023). This capability allows researchers to conduct complex analyses of language use, metapragmatics, and metadiscourse, providing deeper insights into linguistic phenomena (Dynel, 2023). For instance, the ability to measure typicality and semantic similarity using AI tools can significantly advance research in sociolinguistics and cognitive linguistics (Le Mens et al., 2023).\n\nAdditionally, AI tools offer new paradigms for understanding language dynamics and interaction. By analysing user interactions with AI, researchers can gain insights into metalinguistic, meta-discursive, metacommunicative, and metapragmatic awareness (Dynel, 2023). These insights are crucial for developing more effective language teaching strategies and for advancing theoretical understandings of language use (Dynel, 2023). The integration of AI into linguistic research not only enhances methodological rigor but also opens new research questions and areas of inquiry (Le Mens et al., 2023). Prompts in Figure 1 highlight the strengths of AI by showcasing its ability to personalize education, streamline resource creation, and enhance research methodologies. They also demonstrate how AI can effectively support diverse learning needs, improve efficiency in educational settings, and contribute to innovative research practices.\n\nWhile the integration of AI into applied linguistics offers numerous strengths, it is crucial to acknowledge the inherent weaknesses that accompany its adoption. These weaknesses include concerns about the quality and accuracy of AI-generated content, the potential for over-dependence and ethical issues, and various technical limitations. This essay will explore these three primary weaknesses in detail, drawing on evidence from relevant studies.\n\nQuality and accuracy concerns\n\nOne of the most significant weaknesses of AI in linguistics is the quality and accuracy of AI-generated content. Despite advancements in AI technology, tools like ChatGPT often produce content that requires substantial human validation due to issues with accuracy, bias, and the generation of erroneous information (Alkaissi & McFarlane, 2023; Silva et al., 2023). Studies have shown that AI-generated texts can contain factual inaccuracies and inconsistencies, which can mislead users and compromise the integrity of educational materials (Dashti et al., 2023; Wu & Dang, 2023). For instance, AI tools have been found to generate incorrect references and citations, posing a significant challenge in academic writing (Dashti et al., 2023).\n\nFurthermore, AI’s limitations in handling deep linguistic structures and complex syntactic nuances are evident. Research comparing AI-generated texts to human-written content reveals that AI often underperforms in areas such as deep cohesion and syntactic complexity (Zhou et al., 2023). ChatGPT, while proficient in generating fluent text, struggles with maintaining logical coherence and producing sophisticated linguistic constructs that are essential for high-quality academic writing (Zhou et al., 2023). These deficiencies necessitate ongoing human oversight and intervention to ensure the reliability and credibility of AI-generated content.\n\nDependence and ethical issues\n\nAnother critical weakness is the potential for over-dependence on AI tools, which raises ethical concerns. The convenience and efficiency offered by AI can lead to a reduction in human effort and creativity, potentially stifling student innovation and critical thinking (Özdemir-Çağatay, 2023). The over-reliance on AI-generated content can diminish students’ engagement in the learning process and undermine their development of essential academic skills (Hatmanto & Sari, 2023; Özdemir-Çağatay, 2023). This dependency not only affects students but also educators, who may become reliant on AI for lesson planning and content creation, thereby reducing their active involvement in pedagogical practices (Özdemir-Çağatay, 2023).\n\nEthical issues also arise concerning plagiarism and academic integrity. The use of AI tools in academic writing can blur the lines of authorship, leading to potential instances of plagiarism if AI-generated content is not properly attributed (Jarrah et al., 2023). There is an urgent need for clear guidelines and ethical standards to govern the use of AI in educational and research contexts to prevent misuse and ensure transparency (Doyal et al., 2023; Mondal & Mondal, 2023). The lack of such regulations poses a significant threat to the integrity of academic work and the credibility of scholarly publications (Jarrah et al., 2023).\n\nTechnical limitations\n\nTechnical limitations further compound the weaknesses of AI in applied linguistics. Despite significant advancements, AI tools like ChatGPT still exhibit limitations in performing complex academic tasks, such as accurately generating references and conducting comprehensive literature reviews (Dashti et al., 2023; Liu et al., 2023). The inability of AI to verify the accuracy of references and the potential for generating fabricated or non-existent citations are major drawbacks (Dashti et al., 2023). These issues highlight the need for continuous improvements in AI algorithms and the incorporation of more sophisticated validation mechanisms (Liu et al., 2023).\n\nMoreover, the current state of AI technology does not fully support the nuanced and context-specific requirements of academic writing. While AI tools can assist in generating text and providing language feedback, they lack the depth of understanding and contextual awareness necessary for high-level scholarly work (Liu et al., 2023; Zhu et al., 2023). For example, AI-generated content often fails to capture the subtleties of academic discourse, and the rhetorical strategies employed by proficient human writers (Zhu et al., 2023). This limitation underscores the necessity for human expertise in refining and contextualizing AI-generated outputs. Figure’s 2 prompts highlight potential weaknesses in AI by requesting tasks that require nuanced understanding, accurate sourcing, and original thought, areas where AI can falter. They expose potential ethical issues by encouraging the omission of citations and prompting the AI to generate content intended for direct submission without attribution.\n\nThe integration of AI into applied linguistics presents a multitude of opportunities that can significantly enhance the field. These opportunities span across educational innovation and pedagogical integration, research and development, and global collaboration and access. This essay explores these three primary opportunities, highlighting their potential to transform language education and research.\n\nEducational innovation and pedagogical integration\n\nOne of the most promising opportunities of AI in linguistics is the potential for educational innovation and pedagogical integration. AI tools like ChatGPT can be leveraged to create highly personalized learning experiences that cater to individual student needs (Bin-Hady et al., 2023; Hatmanto & Sari, 2023). For instance, AI can facilitate differentiated instruction by adapting content to match the proficiency levels and learning styles of different students, thereby enhancing engagement, and learning outcomes (Hatmanto & Sari, 2023). The ability to simulate human-like conversations enables students to practice language skills in realistic contexts, promoting active learning and improving fluency (Hatmanto & Sari, 2023).\n\nFurthermore, AI can support innovative instructional strategies that align with contemporary pedagogical frameworks. For example, AI-driven platforms can facilitate virtual Socratic dialogues, interactive narrative construction, and simulated discourse, which are effective in fostering critical thinking and collaborative learning (Hatmanto & Sari, 2023). These strategies not only enrich the learning experience but also align with theories such as Communicative Language Teaching and Constructivist Learning Theory, which emphasize the importance of interaction and practical application in language learning (Hatmanto & Sari, 2023). By integrating AI into the classroom, educators can create more dynamic and effective learning environments that support student autonomy and engagement.\n\nResearch and development\n\nResearch and development represent another significant opportunity offered by AI in applied linguistics. AI technologies, particularly LLMs like GPT-4, can enhance research methodologies by providing sophisticated tools for linguistic analysis (Le Mens et al., 2023). For instance, AI can be used to construct measures of semantic similarity and typicality that align closely with human judgment, thereby improving the accuracy and reliability of linguistic research (Le Mens et al., 2023). These capabilities enable researchers to conduct complex analyses of language use, metapragmatics, and metadiscourse, offering deeper insights into linguistic phenomena (Dynel, 2023).\n\nAdditionally, AI tools can facilitate new research paradigms by automating data collection and analysis processes, thus increasing efficiency, and reducing the time required for research (Le Mens et al., 2023). For example, AI can automatically generate large corpora of text for analysis, identify patterns and trends in language use, and provide real-time feedback on research hypotheses (Le Mens et al., 2023). This automation allows researchers to focus on higher-order analytical tasks and theoretical development, potentially leading to significant advancements in the field of linguistics (Le Mens et al., 2023). Moreover, the continuous improvement of AI algorithms promises to further enhance the capabilities and applications of AI in linguistic research.\n\nGlobal collaboration and access\n\nGlobal collaboration and access are also greatly enhanced by the integration of AI in linguistics. AI tools like ChatGPT can facilitate cross-cultural and multilingual collaboration by providing accessible language support to researchers and educators worldwide (Li, Bonk, et al., 2023a; Li, Kou, et al., 2023b). This democratization of access to language resources enables non-native English speakers to participate more fully in global academic discourse, contributing to a more inclusive and diverse research community (Hwang et al., 2023). For instance, AI can assist researchers in refining their academic writing, translating scholarly work, and providing real-time language support during international collaborations (Hwang et al., 2023).\n\nMoreover, AI technologies can support the development of language learning resources in multiple languages, addressing the needs of diverse linguistic communities (Li, Bonk, et al., 2023a). By generating educational content in various languages and adapting it to diverse cultural contexts, AI can help bridge language barriers and promote cross-cultural understanding (Li, Bonk, et al., 2023a). This capability is particularly valuable in multilingual societies and international educational environments, where the ability to access and share knowledge across languages is crucial (Li, Bonk, et al., 2023a). As AI continues to evolve, its potential to facilitate global collaboration and access in linguistics will expand, offering even greater opportunities for innovation and inclusivity. Figure’s 3 prompts highlight opportunities for AI to revolutionize language learning through personalized instruction, advance linguistic research through sophisticated analysis, and bridge global communication gaps through accessible translation tools. They encourage the development of AI tools that cater to the diverse needs of language learners and researchers, fostering innovation and collaboration in the field of linguistics.\n\nWhile the integration of AI into applied linguistics offers numerous opportunities, it also presents several significant threats that must be carefully managed. These threats include concerns about academic integrity and misuse, technological and implementation challenges, and privacy and security issues. This essay explores these three primary threats, highlighting their potential implications for the field of linguistics.\n\nAcademic integrity and misuse\n\nOne of the most pressing threats posed by AI in linguistics is the risk to academic integrity and the potential for misuse. The rise of AI-generated content has led to increased concerns about plagiarism and the authenticity of academic work. AI tools like ChatGPT can produce sophisticated texts that are difficult to distinguish from human-written content, raising the risk of students and researchers passing off AI-generated work as their own (Dergaa et al., 2023; Jarrah et al., 2023). This threat to academic integrity undermines the credibility of scholarly work and can lead to widespread ethical violations if not effectively managed (Jarrah et al., 2023).\n\nMoreover, the lack of clear guidelines and ethical standards for the use of AI in educational and research contexts exacerbates these concerns. There is an urgent need for institutions to develop robust policies that govern the use of AI tools to prevent misuse and ensure transparency (Doyal et al., 2023; Mondal et al., 2023; Mondal & Mondal, 2023). Without such regulations, the integrity of academic work is at risk, as AI-generated content can blur the lines of authorship and lead to significant ethical dilemmas (Jarrah et al., 2023). Establishing clear guidelines will help maintain trust in academic institutions and uphold the principles of scholarly integrity.\n\nTechnological and implementation challenges\n\nTechnological and implementation challenges represent another significant threat to the effective use of AI in applied linguistics. Implementing AI tools in educational settings requires substantial investment in infrastructure, training, and ongoing support, which can be challenging for institutions with limited resources (Özdemir-Çağatay, 2023). The rapid pace of AI development necessitates continuous updates and adaptations to educational practices, posing difficulties for educators and institutions to keep up with the latest advancements (Le Mens et al., 2023).\n\nAdditionally, the current state of AI technology does not fully support the nuanced and context-specific requirements of academic writing. While AI tools can assist in generating text and providing language feedback, they lack the depth of understanding and contextual awareness necessary for high-level scholarly work (Liu et al., 2023). For instance, AI-generated content often fails to capture the subtleties of academic discourse, and the rhetorical strategies employed by proficient human writers (Zhu et al., 2023). These limitations highlight the need for ongoing human oversight and intervention to ensure the quality and relevance of AI-generated outputs (Dashti et al., 2023).\n\nPrivacy and security concerns\n\nThe third major threat posed by AI in linguistics relates to privacy and security issues. The use of AI tools involves managing substantial amounts of sensitive data, raising concerns about data privacy and security (Vaccino-Salvadore, 2023). Ensuring compliance with privacy regulations and protecting user data from breaches and misuse is a critical challenge that must be addressed to safeguard users’ trust and safety (Doyal et al., 2023). For instance, AI platforms like ChatGPT require access to user inputs to function effectively, which can lead to the collection and storage of personal information (Vaccino-Salvadore, 2023).\n\nFurthermore, the potential for AI tools to generate biased or misleading information poses a significant risk to the accuracy and reliability of educational content (Silva et al., 2023). AI models are trained on vast datasets that may contain inherent biases, which can be reflected in the outputs generated by these tools (Silva et al., 2023). This can perpetuate stereotypes and misinformation, undermining the educational value of AI-generated content (Silva et al., 2023). Addressing these privacy and security concerns requires robust data protection measures and continuous monitoring to ensure the ethical use of AI in linguistics (Doyal et al., 2023). Figure 4 below demonstrates the misuse of AI in three contexts: direct submission of AI-generated text without attribution, fabrication of references, and misuse of AI for exam answers.\n\nFigure 5 demonstrates a scenario of a team of literary translators is translating a novel from a lesser-known indigenous language into English. They utilize an AI-powered translation tool specifically trained on a corpus of similar texts in both languages. The AI tool can provide high-quality initial translations, capturing nuances of language and style that might be missed by traditional machine translation systems. This significantly speeds up the translation process, allowing translators to focus on refining the text and ensuring cultural accuracy. For under-resourced languages with limited translation resources, AI can be a valuable tool for preserving and revitalizing these languages by making their literature accessible to a wider audience.\n\nWhile AI can manage grammar and vocabulary effectively, it might struggle with idiomatic expressions, cultural metaphors, and the overall tone of the original text. Human translators are essential to ensure the translation accurately reflects the cultural context and artistic intent of the source material. The quality of the AI’s output depends heavily on the training data. If the corpus is limited or biased, the AI might produce translations that are inaccurate or perpetuate harmful stereotypes.\n\nAI-powered translation tools can make literature from under-represented cultures more accessible to a global audience, fostering cross-cultural understanding and appreciation. The use of AI can free up human translators from tedious tasks, allowing them to focus on higher-level aspects of translation such as style, tone, and cultural adaptation. This can lead to more creative and nuanced translations.\n\nThere is a concern that AI might replace human translators altogether, leading to job losses in the translation industry. However, a more likely scenario is that AI will augment human capabilities, leading to a collaborative approach to translation. Over-reliance on AI for translation could lead to the homogenization of language, as AI systems tend to favour dominant languages and standardized forms of expression. It is important to use AI in a way that preserves linguistic diversity and supports the richness of different languages and cultures.\n\nFigure 6 shows a scenario for a sociolinguist wants to study language variation and change in a specific online community. They use a generative AI tool to analyse a vast corpus of text data from that community. Generative AI can process and analyse massive datasets of text and speech, far exceeding human capabilities. This allows researchers to study language use in a more comprehensive and nuanced way, uncovering patterns and trends that might not be visible through traditional methods. AI can automate time-consuming tasks such as data cleaning, annotation, and analysis, freeing up researchers to focus on interpretation and theory building. This makes large-scale sociolinguistic research more feasible and efficient.\n\nAI models are only as good as the data they are trained on. If the training data is biased or incomplete, the AI’s analysis might be inaccurate or misleading. Human oversight is crucial to validate the AI’s findings and ensure their reliability. Over-reliance on AI for data analysis might limit researchers’ ability to engage critically with the data and develop their own analytical skills. There is also a risk of perpetuating existing biases if the AI models are not carefully designed and evaluated.\n\nAI-driven corpus analysis opens new avenues for sociolinguistic research, allowing for the exploration of complex social phenomena through the lens of language. This can foster collaboration between linguists, computer scientists, and social scientists. The insights gained from AI-powered analysis can lead to the development of new theories about language variation and change, as well as more sophisticated methods for studying language in social contexts.\n\nAI-generated results can be easily misinterpreted or misused, especially by those unfamiliar with the limitations of the technology. It is important to communicate findings clearly and responsibly, acknowledging the potential for bias and error. Sociolinguistic research often involves sensitive personal data. Researchers must be mindful of data privacy concerns and ensure that data is collected, stored, and analysed ethically and securely.\n\n\nDiscussion\n\nThe SWOT analysis in the findings above and Figure 7 presented below highlight a complex structure for AI integration in applied linguistics. While the potential benefits are immense, ranging from enhanced educational tools to innovative research applications, significant challenges exist concerning academic integrity, technological limitations, and privacy concerns. This strategy proposes a multi-pronged approach to leverage AI’s strengths and opportunities while proactively mitigating its weaknesses and threats.\n\nPrioritising ethical and responsible AI implementation\n\nGiven the significant threats to academic integrity posed by AI-generated content (Dergaa et al., 2023; Jarrah et al., 2023), the cornerstone of this strategy is the development and implementation of robust ethical guidelines. These guidelines should clearly define acceptable AI use in educational and research contexts, emphasizing transparency and proper attribution (Doyal et al., 2023; Mondal & Mondal, 2023). Educational institutions must invest in training programs for both educators and students, fostering critical thinking skills and emphasizing the importance of original thought (Özdemir-Çağatay, 2023).\n\nLeveraging AI for personalised learning and enhanced efficiency\n\nCapitalizing on AI’s strengths, this strategy advocates for the development and integration of AI-powered educational tools that support diverse learning styles and personalize learning experiences (Bin-Hady et al., 2023; Hatmanto & Sari, 2023; Kohnke et al., 2023; Özdemir-Çağatay, 2023). AI can streamline the creation of educational materials, reducing educator workload and facilitating differentiated instruction (Zografos & Moussiades, 2023; Zuckerman et al., 2023). However, it is crucial to address the weaknesses related to quality and accuracy concerns. Human oversight and validation of AI-generated content remain essential to ensure accuracy and mitigate potential biases ((Alkaissi & McFarlane, 2023; Silva et al., 2023).\n\nFostering innovation in research and global collaboration\n\nThis strategy encourages the exploration of AI’s potential to enhance research methodologies and facilitate new research paradigms in applied linguistics ((Le Mens et al., 2023). AI can automate data collection and analysis, increasing research efficiency and enabling large-scale studies (Le Mens et al., 2023). Furthermore, AI can facilitate cross-cultural and multilingual collaboration, democratizing access to language resources and promoting cross-cultural understanding (Hwang et al., 2023; Li, Bonk, et al., 2023a). However, it is crucial to acknowledge the technical limitations of current AI tools. Continuous development and refinement are necessary to address the limitations in performing complex academic tasks and enhance the depth of understanding and contextual awareness exhibited by AI (Dashti et al., 2023; Liu et al., 2023; Zhu et al., 2023).\n\nAddressing privacy and security concerns\n\nRecognizing the significant threats posed by privacy and security concerns, this strategy advocates for the implementation of stringent data protection measures and continuous monitoring of AI tools (Doyal et al., 2023; Vaccino-Salvadore, 2023). Transparency regarding data collection and usage is crucial, and users must be informed about the potential for AI to generate biased or misleading information (Silva et al., 2023). Ongoing research and development are necessary to mitigate these risks and ensure the ethical and responsible use of AI in applied linguistics.\n\nThis strategy emphasizes a balanced approach to AI integration in applied linguistics. By prioritizing ethical considerations, leveraging AI’s strengths for educational and research advancements, and proactively addressing its weaknesses and threats, we can harness the transformative potential of AI while mitigating its risks. This strategy calls for collaboration among researchers, educators, policymakers, and technology developers to ensure the responsible and beneficial integration of AI in the field of applied linguistics.\n\n\nConclusions\n\nThis research aimed at assessing the role of AI in applied linguistics through a SWOT (Strengths, Weaknesses, Opportunities, Threats) analysis. Using a sample from common databases (Scopus and Web of Science) we recognized relevant studies by applying specific search terms of the disciplines. The study was based of qualitative research design that making use of the SWOT framework to reach productive findings. The results of our SWOT analysis indicated that the strengths lied more in the enhancement of educational tools and resources through AI-driven programs, models, the collaborative learning and educational materials and innovative research applications impact and advanced linguistic analyses. The study highlighted those weaknesses involved in quality and accuracy concerns in AI-generated content, potential over-dependence on AI tools that influence students’ creativity and ethical issues, and technical limitations in handling complex academic writing tasks. The research highlighted that opportunities contain the potential for educational innovation and pedagogical integration, advancements in AI technology to support linguistic research, and fostering global collaboration and access through AI tools. Moreover, the findings of the study revealed that Threats include risks to academic integrity due to AI-generated content, technological and implementation challenges, and privacy and security concerns regarding data handling. Based on the SWOT analysis, this research proposed a strategic plan to increase strengths and opportunities while addressing weaknesses and threats. The strategic plan aimed at promoting personalised learning through AI tools, streamlining the creation of educational materials, fostering innovative research applications, ensuring human oversight to maintain content quality, improving ethical guidelines and procedures. This was to prevent misuse of tools and help in training and implementing robust data protection measures and steps.\n\nAI has become inevitable in academia and research and this research has several implications that helps in highlighting the different opportunities of the use of AI in applied linguistics fields. It also gives awareness on the different practices and uses of AI in the fields of applied linguistics. Providing the researchers in the field of applied linguistics of the weaknesses and threats helps in building academic measurements and perquisitions to minimize the dangers of misusing AI and ensuring the ethical procedures that save the rights of researchers and original works.\n\nWhile this study provides a comprehensive SWOT analysis of the integration of generative AI in applied linguistics, several limitations should be acknowledged. The sample of studies was limited to those indexed in Scopus and Web of Science, potentially missing relevant literature from other sources. The qualitative nature of the analysis introduces the potential for subjective interpretation and bias, despite efforts to cross-verify findings. The rapidly evolving nature of AI technology also poses challenges for the timeliness and applicability of the findings, necessitating continuous updates. Additionally, the SWOT framework does not quantify the relative importance of the identified factors, suggesting a need for future research using quantitative methods. Lastly, the study did not delve into specific subfields within applied linguistics, indicating a direction for future research to explore unique implications in areas like language teaching, acquisition, and disorders. Despite these limitations, the study lays a robust foundation for understanding the impacts of generative AI in applied linguistics and offers valuable insights for stakeholders.\n\nThe integration of AI, particularly through LLMs like ChatGPT and Gemini, into the field of applied linguistics presents significant theoretical implications. The SWOT analysis conducted in this study reveals how AI can transform linguistic theories and frameworks by providing new tools and methodologies for analysing language use and development. For instance, AI’s ability to measure semantic similarity and linguistic patterns aligns closely with cognitive and sociolinguistic theories, offering deeper insights into language processing and social interactions. Additionally, the use of AI in language education supports constructivist and communicative language teaching theories by enabling more personalized and interactive learning experiences. These theoretical advancements can lead to the refinement of existing models and the development of new theories that better account for the complexities of language learning and use in the digital age.\n\nFrom a practical perspective, the findings of this SWOT analysis suggest several actionable strategies for leveraging AI in applied linguistics to enhance educational and research practices. Educational institutions can utilize AI tools to create more efficient and accessible language learning resources, thereby reducing the workload on educators, and providing students with personalized learning experiences. The development of AI-driven platforms for automatic generation of educational materials, such as vocabulary lists and writing prompts, can streamline classroom instruction and support differentiated teaching approaches. Moreover, the integration of AI in research methodologies can enhance data collection and analysis processes, enabling more robust and scalable linguistic studies. However, it is crucial to address the identified weaknesses and threats, such as ensuring the accuracy of AI-generated content and establishing ethical guidelines to prevent misuse. By implementing these practical strategies, stakeholders in the field can maximize the benefits of AI while mitigating potential risks.\n\n\nEthical approval\n\nThis research did not require IRB approval.\n\n\nInformed consent statement\n\nNeither human nor non-human subjects were involved directly in this research. Therefore, informed consent was not required.", "appendix": "Data availability statement\n\nNo primary data is associated with this article.\n\nOpen Science Framework (OSF): A SWOT Analysis of Generative AI in Applied Linguistics: Leveraging Strengths, Addressing Weaknesses, Seizing Opportunities, and Mitigating Threats, https://doi.org/10.17605/OSF.IO/8AGCZ. This project contains the following underlying data:\n\n• PRISMA Flowchart SWOT Applied Linguistics.jpg\n\n• Data extraction AI and Linguistics.docx\n\n• SRQR_Checklist ready.pdf\n\n• SWOT Analysis outline.docx\n\n\nAcknowledgments\n\nThe authors extend their appreciation to the Deanship of Graduate Studies and Scientific Research at the University of Bisha for funding this research through the promising program under grant number (UB-Promising-29-1445).\n\n\nReferences\n\nAlaqlobi O, Alduais A, Qasem F, et al.: A SWOT Analysis of Generative AI in Applied Linguistics: Leveraging Strengths, Addressing Weaknesses, Seizing Opportunities, and Mitigating Threats.2024, August 21. Publisher Full Text\n\nAlkaissi H, McFarlane SI: Artificial Hallucinations in ChatGPT: Implications in Scientific Writing. CUREUS JOURNAL OF MEDICAL SCIENCE. 2023; 15(2): e35179. 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Publisher Full Text\n\nÖzdemir-Çağatay S: Examining the Use of ChatGPT in Language Teaching. Transforming the Language Teaching Experience in the Age of AI. 2023; 1–24. Publisher Full Text\n\nPage MJ, McKenzie JE, Bossuyt PM, et al.: The PRISMA 2020 statement: An updated guideline for reporting systematic reviews. PLoS Med. 2021; 18(3): e1003583. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSilva TP, Ocampo TSC, Alencar-Palha C, et al.: ChatGPT: a tool for scientific writing or a threat to integrity? Br. J. Radiol. 2023; 96: 20230430. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStreitfeld D: The Long Shadow of Steve Jobs Looms Over the Turmoil at OpenAI. The New York Times. 2023, November 21. Reference Source\n\nTafazoli D: English language teachers’ attitudes toward computer assisted language learning: SWOT analysis in Spain.McCallum. L, editor. English language teaching in the European union: Theory and practice across the region. Springer; 2022; pp. 277–294. Publisher Full Text\n\nVaccino-Salvadore S: Exploring the Ethical Dimensions of Using ChatGPT in Language Learning and Beyond. LANGUAGES. 2023; 8(3). Publisher Full Text\n\nWu RT, Dang RR: ChatGPT in head and neck scientific writing: A precautionary anecdote. Am. J. Otolaryngol. 2023; 44(6): 103980. PubMed Abstract \| Publisher Full Text\n\nZhou T, Cao S, Zhou S, et al.: Chinese intermediate English learners outdid ChatGPT in deep cohesion: Evidence from English narrative writing. System. 2023; 118: 103141. Publisher Full Text\n\nZhu Z, Ying Y, Zhu J, et al.: ChatGPT’s potential role in non-English-speaking outpatient clinic settings. DIGITAL HEALTH. 2023; 9. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZografos G, Moussiades L: A GPT-Based Vocabulary Tutor. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Vol. 13891 LNCS. 2023; pp. 270–280. Publisher Full Text\n\nZuckerman M, Flood R, Tan RJB, et al.: ChatGPT for assessment writing. Med. Teach. 2023; 45: 1224–1227. Publisher Full Text" }	[ { "id": "325264", "date": "01 Oct 2024", "name": "Peter Bannister", "expertise": [ "Reviewer Expertise Generative AI", "English Medium Instruction", "Assessment", "Academic Integrity", "HEI Policy Development: Social Justice" ], "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 idea of the article itself is highly relevant to the state of play in the current literature by addressing the bespoke impact of GenAI tools to the field of Applied Linguistics. The SWOT analysis approach taken links to cognate studies and has the potential to be a valuable contribution to the field, however I'm afraid to say that the execution of this has been somewhat disappointing. There are a multitude of studies which address GenAI opportunities and challenges in a generic way, much of which is covered by what is offered here.\nIt has been further surprising to see that many of the most seminal works produced thus far have been largely ignored. Many sections read as if they were generated by an AI tool and with this I am getting at that ideas hang on the page superficially, resulting in a lack of depth of analysis. This is for instance particularly of note in the discussion section where strategies are put forward without due consideration.\nI have included in-text comments which I would strongly encourage the authors to address. Furthermore, in order for a study of these characteristics to be truly impactful it is important that popular discourse promoted by tech company marketing departments is handled with greater criticality.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "357207", "date": "25 Jan 2025", "name": "Osamah Mohammed Alyasiri", "expertise": [ "Reviewer Expertise Artificial Intelligence", "NLP", "Machine Learning", "Optimization", "AI Chatbots" ], "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 article addresses the integration of Generative AI (GenAI) tools in applied linguistics, employing a SWOT analysis framework. This approach aligns with existing literature and addresses a timely topic. However, the execution lacks depth and critical engagement, which limits its contribution to the field.\n2. The review of existing literature is incomplete. Seminal works and foundational studies on GenAI's implications in applied linguistics are either overlooked or insufficiently integrated. Expanding the literature review to include these studies will strengthen the theoretical grounding.\n3. While the qualitative design and SWOT framework are appropriate, the methodology section lacks sufficient details to ensure replicability. The inclusion of the PRISMA flowchart and data extraction templates is helpful, but more specifics about how themes were identified and synthesized are necessary.\n4. The SWOT analysis, while structured, reads superficially. The identified strengths, weaknesses, opportunities, and threats are presented without adequately linking them to the context of applied linguistics. In particular: a. The discussion section lacks critical examination of the identified factors. b.The strategic recommendations are generic and need concrete, actionable steps tailored to the applied linguistics domain.\n5. The manuscript includes descriptions of GenAI applications, but some sections read as though they were generated by AI tools. This raises concerns about originality and depth. A more critical and reflective narrative is necessary, particularly in evaluating the role of these tools in fostering innovation versus their potential drawbacks.\n6. The writing quality is uneven, with some sections lacking coherence and depth. Enhanced editorial refinement and restructuring are needed to improve readability and ensure alignment with academic standards.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-1040
https://f1000research.com/articles/13-1039/v1	10 Sep 24	{ "type": "Review", "title": "Effects of thermomechanical parameters on surface texture in filament materials extrusion: outlook and trends", "authors": [ "John D. Kechagias" ], "abstract": "The material extrusion process has been widely used to manufacture custom products. However, the surface texture varies due to the additive mechanism of the process, which depends on the layer height and surface orientation, resulting in varying average surface roughness values for inclined, flat and vertical surfaces. Different strand welding conditions result in non-uniform internal stresses, surface distortions, layer traces, weak bonding, non-uniform pores and material overflow. This paper comprehensively examines material extrusion process achievements in surface texture quality and studies and summarises the most influential processing parameters. Parameter effects are critically discussed for each topic; flat, inclined, and vertical surfaces. The results of this research help reduce post-processing.", "keywords": [ "material", "extrusion", "parameters", "surface", "texture", "roughness" ], "content": "Introduction\n\nThe selective deposition of thermoplastic material by hot extrusion in sequentially patterned slices (layers) using computerised numerical control positioning is broadly known as the filament material extrusion (ME) process.1,2 ME is a fully controlled thermomechanical process.3,4 It consists of the following elements: (i) a machine control unit (MCU: micro-computer) which reads the g-code technological program,5,6 (ii) three step-motors with the belts for the motion requirements in X, Y and Z axes,7,8 (iii) the extruder mechanism (head carriage: filament, feed wheels, nozzle, fans, etc.),9,10 and (iv) the bed in which the 3D-printed parts are created (see Figure 1).11,12 The slicing (CAM) software handles the orientation of the STL model,13 the slicing parameters,14 and the selection of the infill structure and finally generates the g-codes.15 ME technology is also known as fused filament fabrication (FFF),16 fused deposition modeling (FDM) or material extrusion (ME).17,18\n\nSource: Author’s work.\n\nDue to the cost-effectiveness of the ME process,19 the timely manner and the customized orientation of the product,20 ME 3D printed parts have been tested in many applications in the automotive,21,22 aerospace,23,24 electrical motors,25 microwave absorption applications,,26 electronics,27,28 maritime,29 medical,30,31 neurosurgery,32 orthotics,33,34 dental,35 antifouling,36 heritage,37,38 jewellery,39 textile and fashion,40,41 forensic,42 and other sustainability and recyclability issues.43 Surface texture (ST) parameters play an important role in surface engineering and are very important in determining the mechanical properties of ME 3D printed parts.44,45 For example, higher surface roughness values of flat dogbone surfaces reduce the mechanical properties of the elements.46 The inferior ST is a characteristic of all additive manufacturing techniques, compared with machining processes,47 and post-processing methodologies have been proposed in the literature.48,49 Therefore due to the progressive material deposition, additive manufacturing parts need post-processing with machining, abrasives, chemicals or cold spray coatings.50,51\n\nSince the ME 3D printing process has gained tremendous popularity due to its simplicity,52,53 extensive materials,54 organic infills,55,56 fiber infills,57,58 environmental friendliness,59,60 and low budget,61,62 several researchers have reviewed its achievements in material and strength issues,63,64 benchmarking issues,65,66 shape accuracy,67,68 laser post-processing,69,70 machining post-processing,71 small-sized reliefs,72,73 dimensional accuracy,74 surface hardness,75 friction and wear issues,76 stair-stepping effect,77,78 and flat inclined, horizontal and vertical surface roughness issues. Table 1 summarises and concludes the literature’s influential parameter investigations regarding the ME surface texture cases (sloped, flat and vertical)79–97 between the end of 2000 and the start of 2023.\n\n* Ra (μm) is the arithmetic mean of the absolute values; Rz (μm) is the mean value of the sum of the highest and the deepest profile deviations; Rt (μm) is the difference between the highest peak and the deepest valley; Rsm (μm) the mean value of the width of the profile elements.\n\n** Layer Height (H, mm); Orientation (θ, deg); Printing Speed (S, mm/s); Printing Temperature (T, oC); Flow speed (Q, mm/s); Raster angle (RA, deg); Raster width (W, mm); Air gap (AG, mm); Infill density (ID, %); Nozzle Diameter (ND, mm); Extrusion Multiplier (EM, %); Platform Temperature (PlatT); Wall thickness (WT, mm).\n\nThe reader can be seen the variability of the measured mean and max height of the ME part’s surface texture (Ra and Rt). Ra values between 1-50μm and Rt between 50-150μm have been reported showing how important parameter tuning was in the ME process.\n\nAnalytically, for upper surfaces of dogbone parts, Ra values were between 0.8206 μm and 6.5526 μm for pure PLA,87 whereas for CF/PLA composites measured Ra>28μm.92 More, vertical Ra values were between 0.3 to 11.8μm for ABS P400 parts,79 where for incleaned ABS/ABSPlus/PC/ULTEM parts measured Ra values higher than 15μm and Rt higher than 75μm.80\n\nIt is noted that none of these studies summarises the surface texture in terms of inclined, vertical and flat surfaces as presented here. The surface texture of ME parts depends entirely on the arrangement of the processing parameters (perimeter, infill and top/bottom),98,99 which in turn are affected by ‘filament properties’,100 desired ‘strand welding’,75 the ‘stair-stepping’ effect,101 and part details.102\n\nFigure 2 uses a ring-type hexagonal part to illustrate all cases of surface texture types engaged in the ME 3D printing process (the 3D model was designed in ‘3D builder’ and slice in ‘Creality v4.8.2’). In summary, we encounter flat, vertical or inclined surfaces. In addition, the inclined or flat top and bottom surfaces can meet without or be covered by a support structure, depending on the end user’s choice.103,104\n\nSource: Author’s work.\n\nFigure 3 illustrates all factors affecting ME surface texture using a cause-effect diagram. The texture of the perimeter, infill and top/bottom surfaces should be optimised according to filament properties, welding and staircase conditions.105,106 It is noted here that some 3D printing processing parameters affect the perimeter, infill, and texture of the top/bottom surface differently.107 For example, the width of the strand is not so important for vertical surfaces, but necessary to adjust the texture of the flat surface (top and bottom). Therefore, the quality and quantity of flat surfaces can affect the strand width choice, affecting the part’s time, energy consumption and mechanical strength.108\n\nSource: Author’s work.\n\nUnfortunately, a comprehensive examination and detailed study on the surface texture of the ME 3D printing process in the context defined in Figure 3 has not yet existed in the literature. This study simultaneously considers the parameters’ effects on the material extrusion process’s surface texture regarding flat, vertical, and inclined surfaces. Though material type, component orientation, thermomechanical parameters, and total weld area affect surface types differently, this work shows the importance of optimizing the material extrusion process for different materials and component orientations, which is not emphasized in the existing literature. In addition, it summarises the most influential analytical and experimental work that has been done to study welding, stair-stepping, and filament effects, focusing on inclined vertical and planar (top and bottom) surface texture. Last, it communicates surface texturing issues and prospects for further study by the 3D research community. The results can help achieve a uniform surface texture and reduce post-processing and anisotropy of material extrusion parts.\n\n\nMethods\n\nEach part manufactured by the ME process contains successive flat layers. Separately layer includes one or more perimeter lines and a defined infill structure according to the pattern selected by the end user (see Figure 4).109 Infill follows the same configuration (pattern) along the Z-axis except for the flat top and bottom layers.110,111 The user can select zero, one or more top and bottom layers.112 In addition, support lines are created to support inclined sections or “island” type geometry.113\n\nSource: Author’s work.\n\nInfill structures are deposited within the perimeter of each layer following several different deposition routes, e.g. lines,114 zigzag,115 grid,116 and tri-hexagon,117 to name a few (Figure 4a). The infill density determines the final part weight (porosity),118,119 while the pattern deposition angle determines the durability of the infill structure (static and dynamic mechanical response in the X and Y fabrication direction).120,121 Different infill styles have been invented to reduce component weight and achieve controlled mechanical strength,122 see gyroid infill structure.123,124 Last but not least, layer thickness, filament properties (base and filler material),125 nozzle inner and outer tip diameter (see Figure 4b),126 and infill density determine the mechanical strength in the Z direction, as it has been shown in the literature that a lower layer thickness is beneficial due to a reduction in the porosity of the component (see Figure 4c-d).127\n\nThe top and bottom surfaces are characterized by 100% infill because they should be solid and allow no gaps between the perimeters and infill lines.96 The flow speed (Q, mm/s), also known as flow rate (Fl, %), should be adjusted in cases of gaps or overflow material on top and bottom surfaces. Therefore an upper surface is affected by welding conditions the most, i.e., the material flow, strand width, deposition temperature, and printing speed; see Figure 5a-c. On the other hand, the bottom surface reflects the texture of the deposited surface and is also affected by the flow conditions of the material and the platform Z-leveling calibration; see Figure 5d-f.128,129 Figure 5 shows the top and bottom surfaces of PLA parts 3D printed with different welding conditions; printing temperature (T), deposition speed (S) and strand height (H). Again, variable surface texture quality is evident, even in the same sample case (Figure 5c).130 Last but not least, in Figure 5a, the outer diameter of the nozzle is formed on the top surface due to the concentric filling (from the outside to the inside).\n\nSource: Author’s work.\n\nVertical and inclined surfaces primarily depend on the perimeters’ welding quality and on the infill characteristics. Bonding of the perimeters, infill lines, and successive layers of slices is achieved by applying thermal cycles between lines and layers,131 which are directly affected by material properties,132,133 processing parameters,134,135 part size,136 and orientation within the build bed.137,138 Therefore, the nozzle, platform and vat temperature must be adjusted appropriately and according to the part volume and orientation.139,140 Figure 6 illustrates the overflow problems during the ME process on different surfaces of the same part and with the same processing parameters. It is evident that some surface textures exhibit excellent quality and others are unacceptable due to material overflow.141\n\nSource: Author’s work.\n\n\nResults\n\nThis section reviews the above surface texture case studies according to the factors influencing deposition and orientation, e.g. the stair-stepping, overflow, material properties, and layer trace cases.\n\nStrand height (H) and surface orientation angle (θ) are the two directly influencing parameters (see Figure 7). In case the deposited material is assumed to have rectangular edges, the Ra and Rsm values are calculated with the following formulas (see explanation in Figure 7a):\n\nSource: Author’s work.\n\nAccording to Eq. 1, higher H values and orientation angles between 5-30 degrees result in higher Ra values (Figure 7b). Figure 7b shows the theoretical (Eq.1) trend lines for 100, 200 and 300 μm H concerning the orientation angle (θ) and the corresponding experimental values (exp 100, 200 and 300μm). Figures 7c-e show the specially designed ABS-FFF test part and the oriented surfaces on which the average roughness (Ra) has been measured experimentally. The observed values follow the trend line only for 100μm (0.1 mm) H. More; lower Ra values were observed on the bottom surfaces, while the top surface texture appears to have significant Ra values. Finally, for 200 and 300μm H, the highest experimental Ra values were observed for the orientation angle of 45 degrees. Similar results have been marked by Boschetto et al.,80 who applied artificial neural networks to predict surface roughness parameters (Ra, Rt, etc.).\n\nThe overflow effect is observed in all types of welding flat surfaces as well as on vertical surfaces. Top and bottom overflow is presented in Figure 5, where it is affected by the deposition conditions, i.e., the strand width, line distance, flow rate, nozzle inner and outer diameter, strand height, printing temperature, and printing speed. It is also possible to select zero top and bottom layers. In this case, the top and bottom layers follow the infill pattern grid style (see Figure 8). Therefore, the infill parameters must be adjusted appropriately so that voids are not observed (solid parts, 100% infill rate).\n\nSource: Author’s work.\n\nOn vertical or inclined surfaces, overflow occurs at the edges or start and end points of a line when the previous or next line changes direction due to the acceleration or deceleration of the nozzle at those locations (see Figure 6).142 When the nozzle takes the printing velocity (S) the vertical and inclined surfaces have the profile of Figure 9a. This profile has gaps with max distance related of the layer height (H), material properties, and the flow rate (see Figure 9b). The gap height is about the same as the surface parameter Rt (difference between the highest peak and the deepest valley) and mean weave width about the Rsm surface parameter (see Eq. 2; the mean value of the width of the profile elements) which represents the layer height H for vertical surfaces (see Figure 9b).83\n\nSource: Author’s work.\n\nFinally in Figure 9c the case of the layer trace effect due to the deposition instability of strands is highlighted.143\n\nThe ME process material can be a pure thermoplastic or a composite with a pure base material and a filler.144 The filler could be carbon fibre,145 graphene oxide,146,147 glass fibers,148 carbon nanotubes,149 carbon black,150 or organic powder,151,152 to name a few.153 Thermoplastic materials are divided into amorphous (ABS,154,155 ABS/HDPE,156 HIPS,157 PET,158 TPU,159,160 etc.) and semi-crystalline (PLA,161,162 PA12,163 PEEK,164 etc.).\n\nThe material’s properties determine the welding conditions more as the nozzle, bed and vat temperatures are adjusted accordingly. For example, filament strength and indentation shear through feed wheels play a critical role in material flow conditions and stability issues during the material deposition. In addition, the filler material directly affects the texture of ME 3D printing parts. Figure 10 shows the effects of filament material on vertical surfaces. For example, in Figure 10a (pure PLA), the substrates are smooth with a uniform texture, while in Figure 10b, the filler affects the surface texture by causing defects such as pillows and voids (5 wt.% CNT filler). Further, in Figures 10c and 10d, the effects of wood powder filler on pure PLA are shown with similar defects on the vertical surfaces.\n\nSource: Author’s work.\n\n\nDiscussion\n\nThe surface texture of the ME part is most affected by the material properties, the orientation of the part in the vat and the welding conditions during strands deposition. This is evident due to the process’s thermomechanical state and the material’s selective deposition following the g-codes positioning approach. Therefore, ME process performance is affected by some common defects, i.e., underflow or overflow, underheating or overheating, layer shifting, gaps between layers-perimeters-strands, curling and irregular corners resulting from welding processing parameters’ unsuitable setting.14 As the ME process becomes more popular and broadens the choice of materials, surface roughness issues could become even more critical in future surface engineering applications, including metals and composites.165 Note that the surface texture is crucial for the component’s durability and functionality in parts’ assemblies and systems such as external and internal thread,166 helical gears,167 remanufacturing of damaged or broken parts cases,168 custom-made anatomical orthotics,169 etc. Thus, many materials that can be extruded in filament form should be tested and investigated for surface texture and geometric quality characteristics,170 roughness,95 conductivity,171 hardness,94 friction properties,172,173 tribological and wear properties,174 and aesthetics,175 of 3D printed parts in all directions, not just on flat surfaces of mechanical test specimens.176\n\nAdditionally, intent shear effects of the filament during nozzle feeding, nozzle outer vs inner diameter associated with each material composition, the appropriate flow rate for each nozzle type vs material selection combination, and optimization of welding parameters are just some of the future challenges of the ME process on the surface texture quality issues of 3D printed parts. In addition, stability issues that will improve nozzle effects on layer traces, material overflow effect in edges, and texture weaving approaches could further enhance the surface quality of ME 3D printed parts.177\n\nConsidering all the above issues, the surface texture of the ME part can be significantly improved uniformly in all the mentioned cases below 10-15μm, reducing the time and cost of further post-processing by blasting,136 chemical treatment,96,170 or machining.97 For example, Francis et al.,96 improved surface texture to 0.819μm from 9μm with 50s immersion time in acetone solvent.\n\nLast but not least, the effect of the support parameters on the surface roughness of the top and bottom surfaces is another challenge for the ME process (see Figure 2). Therefore, it should be studied concerning the characteristics and integrity of the ME parts.\n\n\nConclusions\n\nIn the ME process, many parameters affect the surface texture and properties of 3D-printed parts. In this study, the types of surface texture encountered in the ME process were first analysed. e.g., top, bottom, vertical and sloped and after studying the effects of the stair-stepping, overflow and filament material. This study presents for the first time in detail the complex process of surface texture control in the ME 3D-printing process as, for each case, some processing parameters have competing effects and others synergistic effects.\n\n• Surface orientation (θ) and layer height defined by the strand height (H) are significant for the stair-stepping effect.\n\n• Material filament fillers negatively affect all surfaces, increasing the Ra and Rt values. Today, new materials are being investigated, such as metal powders on polymer bases. As a result, researchers are constantly expanding the materials used in ME.\n\n• Strand width (w), printing speed (S) and flow rate affect the overflow effect and are significant for vertical, inclined and flat surfaces.\n\n• Surface texture properties can be significantly improved by 3D printing parameters optimization.\n\n• Post-processing time and cost can consequently be reduced considerably.\n\nImproving the ME surface texture properties will speed up the ME technology in more surface technology applications, such as mechanical applications in systems and assemblies or remanufacturing cases.", "appendix": "Data availability\n\nAll data generated or analyzed during this study are included in the manuscript.\n\n\nReferences\n\nKechagias J, Chaidas D, Vidakis N, et al.: Key parameters controlling surface quality and dimensional accuracy: a critical review of FFF process. Mater. Manuf. Process. 2022; 37: 963–984. 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World J. Eng. Tech. 2016; 04: 186–192. Publisher Full Text\n\nDilberoglu UM, Simsek S, Yaman U: Shrinkage compensation approach proposed for ABS material in FDM process. Mater. Manuf. Process. 2019; 34: 993–998. Publisher Full Text\n\nĆwikła G, Grabowik C, Kalinowski K, et al.: The influence of printing parameters on selected mechanical properties of FDM/FFF 3D-printed parts. IOP Conf Ser Mater Sci Eng. 2017; 227: 012033. Publisher Full Text\n\nArmillotta A, Cavallaro M: Edge quality in fused deposition modeling: I. Definition and analysis. Rapid Prototyp. J. 2017; 23: 1079–1087. Publisher Full Text\n\nAkhoundi B, Hajami F: Extruded polymer instability study of the polylactic acid in fused filament fabrication process: Printing speed effects on tensile strength. Polym. Eng. Sci. 2022; 62: 4145–4155. Publisher Full Text\n\nSuárez L, Domínguez M: Sustainability and environmental impact of fused deposition modelling (FDM) technologies. Int. J. Adv. Manuf. Technol. 2020; 106: 1267–1279. Publisher Full Text\n\nKabir SMF, Mathur K, Seyam A-FM: A critical review on 3D printed continuous fiber-reinforced composites: History, mechanism, materials and properties. Compos. Struct. 2020; 232: 111476. Publisher Full Text\n\nSanto J, Moola AR, Penumakala PK: Interface stress transfer in an extruded ABS-rGO composite filament. Adv. Eng. Mater. 2022; 32: 211–224. Publisher Full Text\n\nAumnate C, Pongwisuthiruchte A, Pattananuwat P, et al.: Fabrication of ABS/Graphene Oxide Composite Filament for Fused Filament Fabrication (FFF) 3D Printing. Adv. Mater. Sci. Eng. 2018; 2018: 1–9. Publisher Full Text\n\nShirinbayan M, Benfriha K, Tcharkhtchi A: Geometric Accuracy and Mechanical Behavior of PA6 Composite Curved Tubes Fabricated by Fused Filament Fabrication (FFF). Adv. Eng. Mater. 2022; 24: 2101056. Publisher Full Text\n\nKhalid MY, Arif ZU, Ahmed W: 4D Printing: Technological and Manufacturing Renaissance. Macromol. Mater. Eng. 2022; 307: 2200003. Publisher Full Text\n\nRavoori D, Salvi S, Prajapati H, et al.: Void reduction in fused filament fabrication (FFF) through in situ nozzle-integrated compression rolling of deposited filaments. Virtual Phys. Prototyp. 2021; 16: 146–159. Publisher Full Text\n\nNiendorf K, Raeymaekers B: Additive Manufacturing of Polymer Matrix Composite Materials with Aligned or Organized Filler Material: A Review. Adv. Eng. Mater. 2021; 23: 2001002. Publisher Full Text\n\nMeng QK, Hetzer M, De Kee D: PLA/clay/wood nanocomposites: nanoclay effects on mechanical and thermal properties. J. Compos. Mater. 2011; 45: 1145–1158. Publisher Full Text\n\nOlam M: Determining of process parameters of the PLA/titanium dioxide/hydroxyapatite filament. Adv. Mater. Process. Technol. 2022; 8: 4776–4787. Publisher Full Text\n\nCroccolo D, de Agostinis M , Olmi G: Experimental characterization and analytical modelling of the mechanical behaviour of fused deposition processed parts made of ABS-M30. Comput. Mater. Sci. 2013; 79: 506–518. Publisher Full Text\n\nSamykano M, Selvamani SK, Kadirgama K, et al.: Mechanical property of FDM printed ABS: influence of printing parameters. Int. J. Adv. Manuf. Technol. 2019; 102: 2779–2796. Publisher Full Text\n\nHarris M, Potgieter J, Ray S, et al.: Preparation and characterization of thermally stable ABS/HDPE blend for fused filament fabrication. Mater. Manuf. Process. 2020; 35: 230–240. Publisher Full Text\n\nKumar R, Singh R, Farina I: On the 3D printing of recycled ABS, PLA and HIPS thermoplastics for structural applications. PSU Research Review. 2018; 2: 115–137. Publisher Full Text\n\nWojtyła S, Klama P, Baran T: Is 3D printing safe? Analysis of the thermal treatment of thermoplastics: ABS, PLA, PET, and nylon. J. Occup. Environ. Hyg. 2017; 14: D80–D85. PubMed Abstract \| Publisher Full Text\n\nCorsi M, Bagassi S, Moruzzi MC, et al.: Additively manufactured negative stiffness structures for shock absorber applications. Mech. Adv. Mater. Struct. 2020; 29: 999–1010. Publisher Full Text\n\nStörmer J, Görmer D, Ehrmann A: Influence of washing on the adhesion between 3D-printed TPU and woven fabrics. Communications in Development and Assembling of Textile Products. 2021; 2: 34–39. Publisher Full Text\n\nCosta SF, Duarte FM, Covas JA: Thermal conditions affecting heat transfer in FDM/FFE: a contribution towards the numerical modelling of the process. Virtual Phys. Prototyp. 2015; 10: 35–46. Publisher Full Text\n\nAlsoufi MS, Elsayed AE: How surface roughness performance of printed parts manufactured by desktop FDM 3D printer with PLA+ is influenced by measuring direction. Am. J. Mech. Eng. 2017; 5: 211–222. Publisher Full Text\n\nVidakis N, Petousis M, Kechagias J: Parameter effects and process modelling of Polyamide 12 3D-printed parts strength and toughness. Mater. Manuf. Process. 2022; 37: 1358–1369. Publisher Full Text\n\nLu C, Xu N, Zheng T, et al.: The Optimization of Process Parameters and Characterization of High-Performance CF/PEEK Composites Prepared by Flexible CF/PEEK Plain Weave Fabrics. Polymers (Basel). 2018; 11: 53. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nManco E, Cozzolino E, Astarita A: Laser polishing of additively manufactured metal parts: a review. Surf. Eng. 2022; 38: 217–233. Publisher Full Text\n\nBudzik G, Dziubek T, Kawalec A, et al.: Geometrical Accuracy of Threaded Elements Manufacture by 3D Printing Process. Adv. Sc. Techn. Res. J. 2023; 17: 35–45. Publisher Full Text\n\nSikorska-Czupryna S, Mazurkow A: The Use of Reverse Engineering to Create FEM Model of Spiroid Gears. Ad. Manuf. Sc. Tech. 2020; 44: 71–73. Publisher Full Text\n\nBagci E: Reverse engineering applications for recovery of broken or worn parts and re-manufacturing: Three case studies. Adv. Eng. Softw. 2009; 40: 407–418. Publisher Full Text\n\nCiocca L, Mazzoni S, Fantini M, et al.: A CAD/CAM-prototyped anatomical condylar prosthesis connected to a custom-made bone plate to support a fibula free flap. Med. Biol. Eng. Comput. 2012; 50: 743–749. PubMed Abstract \| Publisher Full Text\n\nLavecchia F, Guerra MG, Galantucci LM: Chemical vapor treatment to improve surface finish of 3D printed polylactic acid (PLA) parts realized by fused filament fabrication. Progress in Additive Manufacturing. 2022; 7: 65–75. Publisher Full Text\n\nRoach DJ, Roberts C, Wong J, et al.: Surface modification of fused filament fabrication (FFF) 3D printed substrates by inkjet printing polyimide for printed electronics. Addit. Manuf. 2020; 36: 101544. Publisher Full Text\n\nFrunzaverde D, Cojocaru V, Ciubotariu C-R, et al.: The Influence of the Printing Temperature and the Filament Color on the Dimensional Accuracy, Tensile Strength, and Friction Performance of FFF-Printed PLA Specimens. Polymers (Basel). 2022; 14: 1978. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nŞirin Ş, Aslan E, Akincioğlu G: Effects of 3D-printed PLA material with different filling densities on coefficient of friction performance. Rapid Prototyp. J. 2023; 29: 157–165. Publisher Full Text\n\nHanon MM, Kovács M, Zsidai L: Tribology behaviour investigation of 3D printed polymers. International Review of Applied Sciences and Engineering. 2019; 10: 173–181. Publisher Full Text\n\nRodríguez L, Naya G, Bienvenido R: Study for the selection of 3D printing parameters for the design of TPU products. IOP Conf Ser Mater Sci Eng. 2021; 1193: 012035. Publisher Full Text\n\nSingh R, Kumar R, Singh M, et al.: On compressive and morphological features of 3D printed almond skin powder reinforced PLA matrix. Mater. Res. Express. 2020; 7: 025311. Publisher Full Text\n\nBakrani Balani S, Chabert F, Nassiet V, et al.: Influence of printing parameters on the stability of deposited beads in fused filament fabrication of poly (lactic) acid. Addit. Manuf. 2019; 25: 112–121. Publisher Full Text" }	[ { "id": "324925", "date": "03 Oct 2024", "name": "Vivek Kumar Tiwary", "expertise": [ "Reviewer Expertise FDM 3D Printing" ], "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 paper is good and can be indexed. It is very relevant to the topic of Material Extrusion. The paper comprehensively examines material extrusion process achievements in surface texture quality and studies and summarizes the most influential processing parameters. Parameter effects are critically discussed for each topic; flat, inclined, and vertical surfaces. The results of this research will help the scientific community help reduce post-processing requirements on 3D printed components.\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": "12808", "date": "12 Nov 2024", "name": "John Kechagias", "role": "Author Response", "response": "Thank you very much." } ] }, { "id": "333470", "date": "06 Nov 2024", "name": "Muhammad Abas", "expertise": [ "Reviewer Expertise Additive Manufacturing" ], "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 is well presented and provide in depth information about the surface texture in material extrusion. However, the few comments need be addressed before final acceptance.\n1. Please include some recent references (2023-2024). https://doi.org/10.1108/RPJ-10-2023- (ref-1)0347, https://doi.org/10.3390/polym15173633 (ref-2), https://doi.org/10.1016/j.addma.2024.103960 (ref-3)\n2. Please include a discussion on standard procedures for measuring surface roughness, such as those based on ISO standards.\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": "12811", "date": "12 Nov 2024", "name": "John Kechagias", "role": "Author Response", "response": "Thank you very much for your kind recommendations. One of the proposed references, which is related to the manuscript contents, will be added to the revised version. Abas M, Awadh MA, Habib T, Noor S: Analyzing Surface Roughness Variations in Material Extrusion Additive Manufacturing of Nylon Carbon Fiber Composites.Polymers (Basel). 2023; 15" } ] } ]	1	https://f1000research.com/articles/13-1039
https://f1000research.com/articles/13-1038/v1	10 Sep 24	{ "type": "Clinical Practice Article", "title": "Characteristics of primary tuberculous mastitis in tuberculosis endemic country: A case series", "authors": [ "Sinta Chaira Maulanisa", "Wiwit Ade Fidiawati", "Farah Mardhiyah", "Wiwit Ade Fidiawati", "Farah Mardhiyah" ], "abstract": "Tuberculous mastitis (TM) is a rare form of tuberculosis, occurring as a primary disease when there is no evidence of tuberculosis in other locations. There are no clear clinical features of TM, especially in the absence of a previous tuberculosis infection. Due to its unclear clinical picture, diagnosis is difficult, and it is often confused with breast carcinoma or pyogenic abscesses. The aim of this study was to report our experience and discuss the characteristics and diagnostic modalities in cases of primary TM in a tuberculosis-endemic area.\nMethod A case series study was conducted at the Arifin Achmad Regional Hospital, reporting four cases of primary tuberculous mastitis in January 2024. The patients were women aged 24-41 years.\n\nCase presentation All patients presented with complaints of breast pain for the last 2 weeks to 2 months and complained of symptoms in the form of a lump in the breast that was reddish in colour and mastalgia. One patient was diagnosed during pregnancy, and one had a history of prior breastfeeding. One patient presented with FNAB results for breast carcinoma. The other patient complained of an ulcer on her breast. Physical examination revealed axillary lymphadenopathy in all patients. Histopathological examination revealed tuberculous mastitis in all patients and 1 with tuberculous mastitis, fibrocystic changes, and Atypical Ductal Hyperplasia (ADH).\n\nConclusion Patients with tuberculous mastitis who visited our institution had symptoms similar to those of abscesses and breast cancer. The FNAC test is the most reliable, but false-negative results can occur. Diagnosis requires teamwork between the patient’s doctor, anatomical pathologist, and radiologist. This research requires a larger scale to describe actual conditions.", "keywords": [ "Breast Abcess", "Mastitis", "Tuberculous Mastitis", "Tuberculosis", "Breast ulcer." ], "content": "Introduction\n\nTuberculosis is widely known as a disease of the lungs; however, extrapulmonary manifestations account for nearly 20% of all tuberculosis cases.1 Tuberculous Mastitis (TM) is a rare form of tuberculosis, that occurs as a primary disease when there is no evidence of tuberculosis in other locations.2 TM was first described in 1829 by Cooper as “swelling of the breast gland in young women”. Further detailed explanations of this disease were reported at the end of the 19th century by Richet and Powers.3,4 TM accounts for less than 0.1% of all breast diseases and less than 2% of all tuberculosis cases.5 Even in developed countries and tuberculosis-endemic areas, this condition is rare.6–8 Indonesia is a developing country that is endemic for tuberculosis.6 The prevalence of TM in developing countries is estimated to be 0.1% of all histologically examined breast lesions and 3-4.5% of operated patients.9 TM often resembles breast cancer and breast abscess both clinically and radiologically, leading to frequent misdiagnosis. Biopsy is necessary to confirm the diagnosis of TM.7 In patients from endemic areas, tuberculosis infection should be suspected if mastitis occurs repeatedly and is refractory to antibiotic treatment.10 Without a history of tuberculosis infection, TM has no apparent clinical manifestation. Dubbed “the great masquerader,” TM is difficult to diagnose owing to its ambiguous clinical appearance.4,11 This disease is often mistaken for breast carcinoma or pyogenic abscess.4 Doctors must understand TM presentations for a correct diagnosis.12 Our study reported our experience identified primary TM, and discussed its characteristics and diagnostic methods in tuberculosis-endemic areas.\n\n\nCase report\n\nA 25-year-old female patient presented with complaints of a lump in her right breast that had burst one day before admission to the hospital. The patient complained of a sudden discharge of pus accompanied by intermittent pain. A lump in her right breast appeared 1 month before admission. The lump initially felt small but gradually grew larger with redness. Lumps were not influenced by the menstrual cycle. The patient also complained of a palpable lump in the axilla. There was no shortness of breath, back pain, or headaches.\n\nOn physical examination, both breasts appeared symmetrical. The right breast had ulcers, sloughts, and pus. Upon palpation, a mass measuring 5 × 4 cm was felt, with a smooth surface, unclear borders, hard consistency, tenderness upon pressure, and warmth. No abnormalities were observed in the left breast. Upon examination of the right axillary lymph nodes, a mass with elastic consistency, clear borders, and a size of 5 × 4 cm was palpated.\n\nBased on the results of breast ultrasound, the patient was suspected to have mastitis with an abscess in the right breast and lymphadenopathy in the right axilla. Chest radiography revealed no abnormalities.\n\nWe conducted a surgical removal of the tumor in the patient’s breast, followed by a histological analysis. The histopathological study confirmed the presence of tuberculous mastitis (TM). Subsequently, we initiated antituberculosis treatment for the patient, consisting of rifampicin 150 mg, isoniazid 75 mg, pyrazinamide 400 mg, and ethambutol Hcl 275 mg for the initial intense phase lasting 2 months. This was followed by a continuation phase of rifampicin 150 mg and isoniazid 75 mg for an additional 4 months. One month following the procedure, a fluctuating mass formed on the lateral side of the excision site (see Figure 3). The mass then bursts, spewing pus multiple times. We choose to continue antituberculosis medication for up to nine months. After completing 9 months of treatment, the patient was declared to be completely cured of TM.\n\nA 41-year-old female patient presented with a lump in her left breast that had persisted for 2 months. The lump was the size of a quail egg, tender upon pressure, soft to touch, appeared reddish, and felt warm when palpated. The patient also complained of intermittent fever. Physical examination revealed a red nodule with a size of 3 cm × 3 cm × 1 cm on the left breast and felt fluctuant with a regular border, and consistency was soft and mobile.\n\nBased on the breast ultrasound results, an abscess was found in the left breast and lymphadenopathy in the left axilla. Chest radiography revealed no abnormalities.\n\nThe excision of the lump in the patient’s breast was performed, followed by histological investigation and pus culture. The histopathological analysis confirmed the presence of tuberculous mastitis (TM). The results of the pus culture indicated the absence of any bacterial growth. Following this, we initiated antituberculosis treatment for the patient, consisting of rifampicin 150 mg, isoniazid 75 mg, pyrazinamide 400 mg, and ethambutol Hcl 275 mg, during the intense phase for a duration of 2 months. Then we continued the treatment with rifampicin 150 mg and isoniazid 75 mg for an additional 4 months during the continuation phase. After completing 6 months of treatment, the patient was declared to be completely cured of TM.\n\nA 25-year-old female patient presented with a lump in her right breast that had been present for two weeks before hospital admission. Upon physical examination, a mass measuring 4 × 3 cm was found in the right breast, with unclear borders, smooth surface, and mobility. A previous FNAB result indicated breast carcinoma.\n\nThe patient underwent ultrasound examination, which revealed a suspected benign tumor in both breasts and lymphadenopathy in both axillae.\n\nWe performed an excision procedure on the patient, followed by histopathological examination. The histopathological findings indicate tuberculous mastitis accompanied by fibrocystic changes and a focus of atypical ductal hyperplasia, which differed from the findings of prior examinations. The patient was then treated with antituberculosis medication for a duration of 6 months. During the 6th month follow-up, it was reported that the patient had fully recuperated from TM.\n\nA 24-year-old pregnant female presented with a lump in her left breast that had persisted for 1 month. The lump started small but gradually grew larger and became more painful. Physical examination revealed a mass with a size of 5 × 5 cm, unclear border, immobility, and hard consistency.\n\nBased on the breast ultrasound results, an inhomogeneous mass was found in the left breast with an irregular border, along with subcutaneous thickening and blurring of the fibroglandular tissue around it. The ultrasound Breast Imaging Reporting and Data System (BIRADS) score was 4, indicating suspicious malignancy with differential diagnosis of mastitis or an infectious process, and lymphadenopathy in the left axilla was suspected. Chest radiography revealed no abnormalities.\n\nWe performed an FNAB on the patient. The cytology examination results indicate tuberculous mastitis with suppurative process. Therefore, we performed an excision procedure on the breast mass of the patient, followed by histopathological examination to confirm the diagnosis. The histopathological examination yielded similar findings to the FNAB results, prompting the immediate initiation of antituberculosis therapy in the patient. After 6 months of using antituberculosis medication, the patient was declared cured.\n\n\nDiscussion\n\nAn abscess or a painless breast lump may indicate rare extrapulmonary TB. This disorder includes both the primary and secondary subgroups. The rare primary form is breast-only tuberculosis (TB). Primary tuberculous foci such as the lungs, pleura, and lymph nodes are related to the more common secondary form. Even in endemic areas, low clinical suspicion and similarity to other diseases make TM diagnosis difficult. TM can be diagnosed by a qualified surgeon, radiologist, or pathologist. In this study, during January 2024 we had 4 women in their perimenopausal diagnosed with tuberculous mastitis. The average age of the patients was 28.75 (24–41 years). One patient was diagnosed during pregnancy, and one had a history of prior breastfeeding. The findings for all patients are summarized in Table 1.\n\nTM usually affects women of reproductive age, likely due to the hypervascularization of breast tissue and widening of lactiferous ducts during this period.12 However, TM is also found in adolescent girls, elderly women, and men.13 Multiparity, lactation, and pregnancy are known risk factors for the development of breast tuberculosis.14,15 A case series of 32 cases reported that 12.5% of all their cases were pregnant and lactating women.12 Lactation causes breasts to be vulnerable to trauma, making it easier for pathogenic bacteria to infect the tissue, especially if Mycobacterium tuberculosis is present in the baby’s faucial tonsils, which is suspected to be a potential route of infection in mothers.12,16 Lactation makes the breast highly vascularized and ducts dilated, making newborns and multiparous women more susceptible to TB. Pregnancy suppresses the pro-inflammatory T-helper response, which may enhance the tendency toward infection, as breast TB symptom presentation usually lasts less than a year but can last months or years.17 Patients with TM often show symptoms for several weeks to months before diagnosis, with varying durations, but often less than one year.13,16 In our findings, patients began experiencing symptoms from 2 weeks to 2 months before being diagnosed with TM.\n\nAll the patients had previously received a BCG vaccine. BCG vaccination has a 37% efficacy rate in preventing all types of tuberculosis in children under 5 years of age and a 42% efficacy rate in preventing lung disease in children under 3 years of age. However, it does not offer protection to teenagers or people in intimate contact with the disease.18 It is important to enhance the immune response against M.tuberculosis in order to provide long-lasting protection, particularly after infancy.19,20 According to the World Health Organization (WHO) data, Indonesia ranks second in the world, with the highest number of TB cases. In 2021, the incidence of TB in Indonesia was 354 cases per 100,000 people.21 Initially, it was believed that 60% of TM cases were caused by primary conditions; however, it is now believed that TM is almost always caused by secondary lesions in other parts of the body. The most common spread is retrograde lymphatic spread from the lung focus through the paratracheal and internal breast lymph nodes. Hematogenous spread and direct extension from adjacent structures are other routes of infection.16 Primary TM is very rare because the breast parenchyma is not an ideal site for Mycobacterium tuberculosis.22 Based on history taking, it can be established that the patient is likely to have primary TM. A patient reported a lump in the armpit area, which was discovered after a breast complaint. Extrapulmonary tuberculosis is often asymptomatic23; hence, it is probable that some of our patients had secondary TM.\n\nThe most typical sign of breast tuberculosis is a lump, typically in the upper outer or central quadrant of the breast, due to frequent spread from the axillary lymph nodes to the breast. The lump often shows irregular and poorly defined features, along with a firm texture. It may cause pain and can move or attach to the underlying skin or muscle. Furthermore, this condition can manifest as a solitary nodule, typically without the accompanying constitutional symptoms commonly seen in tuberculosis.24,25 Nipple retraction, peau d’orange, and breast edema have also been reported.8,26,27 This lump occasionally resembles a cancer.17,25 The results showed that all patients complained of breast lumps with or without abscesses, the majority of which were painful, firm, and had unclear borders. However, the lumps in our patient were typically found in the inner area of the breast. Half of our patients were clinically suspected to have breast malignancy.\n\nTM is often unilateral, but both breasts can be infected, although this is very rare, occurring in only approximately 3% of all cases.16,28,29 Multiple lumps have rarely been reported in cases of TM. However, a recent case series report found multiple lumps in 35.3% of the cases.12 TM was first classified by McKeon and Sir Geoffrey Wilkinson into five categories: acute miliary, nodular, disseminated, sclerosing, and obliterative.16,22 Nodular caseous inflammation is the most common type. This type presents symptoms such as non-vascular hypoechoic mass without pain, elongated shape, well-defined borders, slow growth, resembling fibroadenoma in the early stages of the disease, and usually develops into a fistula within the nipple-areolar complex or in the skin and very similar to cancer.22\n\nRadiographic results of breast tuberculosis are vague.30 In our case, all patients underwent an ultrasound examination. Chest radiography did not reveal any abnormalities or signs of pulmonary tuberculosis infection. One patient in this case series underwent FNAB examination with a diagnosis of breast carcinoma before arriving at our hospital. However, after re-examination, a diagnosis of tuberculosis mastitis accompanied by fibrocystic changes of Atypical Ductal Hyperplasia (ADH) type was made. Figure 8a shows breast tissue infested with acute inflammatory cells and chronic inflammation accompanied by necrotic areas. Langhan-type cells are visible (white arrows) between the connective tissue and hyperemic blood vessels. No visible signs of malignancy were observed. Figure 8b shows breast tissue showing chronic inflammatory cell-infested tissue (short black arrow) accompanied by necrotic areas. Necrotic breast glands (long black arrows) and Langhan-type data cells (white arrows) are visible between connective tissue and hyperemic blood vessels. No visible signs of malignancy were observed. Variations in diagnostic interpretation and reporting practices in anatomical pathology are not unusual. The percentage of inaccurate diagnoses ranges from 3% to 9%.31 The lack of clear quality criteria for anatomical pathology laboratories as well as the objectivity of pathological anatomy specialists may have contributed to this inaccurate diagnosis. The second view lessens the need for modifications to the initial pathology reports and is a useful quality metric in anatomical pathology.32\n\nIn this series, TM presented with symptoms similar to those of breast cancer, such as ulceration, redness, a hard palpable lump with uneven borders, and an ultrasound examination that suggested a breast tumor. The gold standard examination for distinguishing it from breast cancer is histopathological investigation. Diagnosis of TM requires several specific tests. The Mantoux test does not provide a diagnosis but can confirm whether a patient has tuberculosis infection. Mammography is not always helpful for diagnosis, especially in young women, because of the density of breast tissue. However, mammography findings in elderly women cannot be differentiated from mammary carcinomas. Ultrasonography shows hypoechoic masses in 60% of patients, and this method can also detect fistulas or sinus cavities, which can be observed in tuberculosis cases. Computed tomography (CT) and Nuclear Magnetic Resonance (NMR) were used to assess the extent of the lesions outside the body, especially in the chest. The gold standard for diagnosing TM is to isolate M. tuberculosis in bacteriological cultures or to use the Ziehl-Neelsen stain. However, M. tuberculosis is present in one-fifth of TM cases. Acid-fast bacteria were found in less than 12% of patients. As a result, some authors concluded that a histological finding of granulomatosis accompanied by caseous necrosis is adequate for diagnosis. Fine-needle aspiration (FNA) is the most frequently used diagnostic procedure, with 73% specificity for identifying granulomatosis and caseous necrosis. In other investigations, FNA was frequently inconclusive, with a sensitivity of 28%, compared to 94% for histology. Acid-fast bacteria were detected in 10.3% of FNA specimens and in 29.7% of histological specimens. Some researchers discovered that FNA was able to diagnose TM in 18% of the cases. When FNA is ambiguous, obtaining a larger histologic sample may be recommended, especially if other breast illnesses such as carcinoma have to be ruled out. In addition, skin testing, interferon-gamma assays, imaging tests, biopsies, and PCR-TB can confirm diagnosis.17,24,33 Polymerase Chain Reaction (PCR) is a highly sensitive method for the diagnosis of tuberculosis. Although popular, this method is only used in patients with negative culture results or other types of granulomatosis. Histopathological lesions identified chronic granulomatous inflammation with caseous necrosis and Langhans giant cells, contributing to the diagnosis in most cases. The main differential diagnosis for TM is breast carcinoma. Other differential diagnoses include fat necrosis, plasma cell mastitis, idiopathic granulomatous mastitis, and infections such as actinomycosis and blastomycosis.13,16,28,34\n\nAll of our patients received a 6-to-9-month course of anti-tuberculosis treatment. After one month of surgical excision, one person appeared with a breast ulcer and reported the presence of a pus-discharging lesion. We proceeded with the advanced stage of treatment till the ninth month. Debridement should be performed in this patient to enhance the efficacy of the treatment. All patients were reported to have achieved a complete cure of TM at the conclusion of their treatment.\n\n\nConclusion\n\nPatients with tuberculous mastitis may present with nonspecific symptoms, although their condition may resemble that of mastitis or breast cancer. Due to the atypical symptoms presented by the patient, it is imperative to conduct comprehensive screening to rule out alternative probable diagnoses. The FNAC test is often regarded as the most dependable technique; however, false-negative results can still be obtained. Establishing a diagnosis requires effective teamwork between the attending physician, anatomical pathologist, and radiologist. Comprehensive research on a larger scale is required to accurately describe the existing situation.\n\n\nConsent\n\nThis study was conducted using the primary patient data. Informed consent was obtained at the beginning of the patient’s visit by signing a letter of consent for examination, taking pictures, and publication for scientific purposes, and the patient’s identity was strictly protected. Written informed consent for publication of their clinical details and clinical images was obtained from the patient. The data collected were strictly used to achieve the research objectives.", "appendix": "Data availability\n\nNo data is associated with this article.\n\n\nAcknowledgements\n\nThe authors are grateful to the Department of Oncology Surgery at the Arifin Achmad General Hospital for their participation in this study.\n\n\nReferences\n\nRolo M, González-Blanco B, Reyes CA, et al.: Epidemiology and factors associated with Extra-pulmonary tuberculosis in a Low-prevalence area. J Clin Tuberc Other Mycobact Dis. 2023 Aug 1; 32: 100377. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHoang H, El-Helou E, Pop CF, et al.: Primary Breast Tuberculosis Mastitis Manifested as Nonhealing Abscess. The Surgery Journal. 2022 Apr [cited 2024 Jan 10]; 08(02): e123–e126. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGhalleb M, Seghaier S, Adouni O, et al.: Breast tuberculosis: a case series. J. Med. Case Rep. 2021 Dec 1 [cited 2024 Feb 1]; 15(1): 73–76. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShrestha A, Gautam K, Pyakurel D, et al.: Breast tuberculosis, a rare entity. IDCases. 2019 Jan 1 [cited 2024 Feb 1]; 15: e00530. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLugito NPH, Gunawan E, Chandra M, et al.: Tuberkulosis Payudara Primer sebagai Diagnosis Banding Massa Payudara. Media Neliti. 2016 [cited 2024 Feb 1]; 39–41. Reference Source\n\nTazzioli G, Macolino A, Combi F, et al.: Breast tuberculosis: A case report of primary type mammary tuberculosis. Clin. Case Reports. 2019 Dec 1 [cited 2024 Feb 1]; 7(12): 2346–2348. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChitrambalam TG, Sundaraj J, Christopher PJ, et al.: Case series on variable presentations of tuberculosis of the breast. BMJ Case Rep. 2020 Dec 12 [cited 2024 Feb 1]; 13(12): 236019. Publisher Full Text \| Free Full Text\n\nFarrokh D, Alamdaran A, Feyzi Laeen A, et al.: Tuberculous mastitis: A review of 32 cases. Int. J. Infect. Dis. 2019 Oct 1 [cited 2024 Jan 10]; 87: 135–142. PubMed Abstract \| Publisher Full Text Reference Source\n\nKilic MO, Saʇlam C, Aʇca FD, et al.: Clinical, diagnostic and therapeutic management of patients with breast tuberculosis: Analysis of 46 Cases. Kaohsiung J. Med. Sci. 2016 Jan 1; 32(1): 27–31. PubMed Abstract \| Publisher Full Text\n\nBaykan AH, Sayiner HS, Inan I, et al.: Primary breast tuberculosis: imaging findings of a rare disease. Insights Imaging. 2021 Dec 1 [cited 2024 Jun 1]; 12(1): 11–19. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSagara Y, Hatakeyama S, Kumabe A, et al.: Breast tuberculosis presenting with intractable mastitis: a case report. J. Med. Case Rep. 2021 Dec 1 [cited 2024 Jun 1]; 15(1): 101–104. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTauro LF, Martis JS, George C, et al.: Tuberculous Mastitis Presenting as Breast Abscess. Oman Med. J. 2011 [cited 2024 Feb 1]; 26(1): 53–55. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJamal I: A case series on tuberculous mastitis. Vol. 1, Original Research Article Archives of Cytology and Histopathology Research.\n\nHatherill M, Cobelens F: Infant BCG vaccination is beneficial, but not sufficient. Lancet Glob. Health. 2022 Sep 1 [cited 2024 Jun 1]; 10(9): e1220–e1221. Publisher Full Text Reference Source\n\nMartinez L, Cords O, Liu Q, et al.: Infant BCG vaccination and risk of pulmonary and extrapulmonary tuberculosis throughout the life course: a systematic review and individual participant data meta-analysis. Lancet Glob. Health. 2022 Sep 1 [cited 2024 Jun 1]; 10(9): e1307–e1316. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nAbbott S, Christensen H, Lalor MK, et al.: Exploring the effects of BCG vaccination in patients diagnosed with tuberculosis: Observational study using the Enhanced Tuberculosis Surveillance system. Vaccine. 2019 Aug 14; 37(35): 5067–5072. PubMed Abstract \| Publisher Full Text\n\nKEMENTERIAN KESEHATAN REPUBLIK INDONESIA: Tuberculosis Control in Indonesia 2022.2022 [cited 2024 Feb 23]. Reference Source\n\nSinghal A, Kataria B, Sharma S: Imaging of tubercular mastitis presenting as recurrent breast nodules and abscesses: a rare case report. Egypt J. Radiol. Nucl. Med. 2023 Dec 1 [cited 2024 Feb 23]; 54(1): 1–6. Publisher Full Text\n\nRodriguez-Takeuchi SY, Renjifo ME, Medina FJ: Extrapulmonary Tuberculosis: Pathophysiology and Imaging Findings.2019 Nov 7 [cited 2024 Feb 23]; 39(7): 2023–2037. Publisher Full Text\n\nNeto J d RBJ, de Oliveira DEB , Costa FR, et al.: Breast Tuberculosis: Case report and review literature. Research, Society and Development. 2024 Jan 23 [cited 2024 Jun 1]; 13(1): e10613144832–e10613144832. Publisher Full Text Reference Source\n\nMathew D, Rubin G, Mahomed N, et al.: Imaging and clinical features of breast tuberculosis: a review series of 62 cases. Clin. Radiol. 2020 Jul 1; 75(7): 561.e13–561.e24. PubMed Abstract \| Publisher Full Text\n\nNeto J d RBJ, de Oliveira DEB , Costa FR, et al.: Breast Tuberculosis: Case report and review literature. Research, Society and Development. 2024 Jan 23 [cited 2024 Feb 23]; 13(1): e10613144832–e10613144832. Publisher Full Text Reference Source\n\nTuna T, Coşkun S: HEALTH SCIENCES MEDICINE Breast tuberculosis: analysis of 24 patients. J Health Sci Med. 2022; 5(1): 88–93.\n\nShamim Jairajpuri Z, Jetley S, Rana S, et al.: Diagnostic challenges of tubercular lesions of breast.2018 [cited 2024 Feb 23]. Reference Source\n\nKumar R, Kshetrimayum S, Kumar S, et al.: Primary Tuberculosis of Breast: A Rare Presentation. Journal of Case Reports. 2017 Apr 28 [cited 2024 Feb 23]; 7(2): 127–129. Publisher Full Text Reference Source\n\nRajesh V, Prasana Mohanty D, Shekhar Rath S, et al.: Clinical, diagnostic and therapeutic management of patients with breast tuberculosis: Retrospective analysis of 16 Cases.\n\nPeck M, Moffat D, Latham B, et al.: Review of diagnostic error in anatomical pathology and the role and value of second opinions in error prevention. J. Clin. Pathol. 2018 Nov 1 [cited 2024 Jun 1]; 71(11): 995–1000. PubMed Abstract \| Publisher Full Text\n\nPriebe MTM: Study of Quality Assurance Programs in Anatomic Pathology that Drive Improved Proficiency, Reduce Cost and Enhance Positive Patient Outcomes. J Mol Biomark Diagn. 2016; 7(5). Publisher Full Text\n\nBabamahmoodi F, Babamahmoodi A, Barzegar R, et al.: Breast Tuberculosis in Iran: A Comprehensive Review. The International Journal of Mycobacteriology. 2024 [cited 2024 Jun 1]; 13(1): 1–6. PubMed Abstract \| Publisher Full Text Reference Source\n\nSakr AA, Fawzy RK, Fadaly G, et al.: Mammographic and sonographic features of tuberculous mastitis. Eur. J. Radiol. 2004 Jul 1; 51(1): 54–60. PubMed Abstract \| Publisher Full Text" }	[ { "id": "338182", "date": "26 Nov 2024", "name": "Zuhair Dahham Hammood", "expertise": [ "Reviewer Expertise Breast physcian and Oncosurgeon" ], "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\nRegarding diagnostic tests, I want to ask:\n1. What about laboratory investigations like CBC, ESR, AFB test, and others?\n2. In which base was FNAC used instead of trucut biopsy? Specifically, two cases (No. 3 and 4) were clinically suspicious, one case (No. 4) was radiologically suspicious (BIRAD IV), and one case (No.3) was Ca by FNAC.\n3. Chest X-ray was obtained for all cases. Why? As long as patients denied any chest symptoms, one case (No.4) , she was pregnant and exposed to unnecessary radiation. Explanation, please.\n\nRegarding treatment given and outcomes, I want to ask:\n1. The author mentioned that the treatment given to all patients was excision, then medical treatment (anti-TB), which is really a non-scientific approach as it is an infection and should be treated medically. There are no rules for surgery in this situation apart from simple drainage if indicated and taking a biopsy, whether it be a trucut biopsy or, if not available, a mini-incisional biopsy. Comments, please.\nRegarding discussion and conclusion, same above comments I have! As well as the following:-\nAbout granulmatous mastitis which is the most common differential diagnosis for TM is mentioned very shortly, which is was to be mentioned and discussed in more details, comments please?\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? 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 conclusion balanced and justified on the basis of the findings? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-1038
https://f1000research.com/articles/13-1037/v1	10 Sep 24	{ "type": "Research Article", "title": "Resilience in the Face of Uncertainty: Navigating Supply Chain Challenges Through Proactive Risk Surveillance and Mitigation Strategies among SMEs in ASEAN countries", "authors": [ "Sanmugam Annamalah", "Kalisri Logeswaran Aravindan", "Selim Ahmed", "Sanmugam Annamalah", "Selim Ahmed" ], "abstract": "Background Supply chain risk management is crucial for the consumer products industry due to its vulnerability to uncertainties and risks. This study investigates the relationship between supply chain risks and performance among SMEs in the ASEAN countries. Supply chain performance, defined as meeting end-customer demands, involves ensuring commodity availability, on-time deliveries, and maintaining sufficient inventory and capacity across organizational boundaries from raw materials to the final consumer.\n\nMethods The study utilized a sample of 385 entrepreneurs from the consumer products industry in ASEAN countries. The research was analyzed using Partial Least Squares Structural Equation Modeling (PLS-SEM) to establish the correlation between supply chain performance and risks. Factors related to the ASEAN Economic Community (AEC) for economic integration and regional trade agreements were incorporated to understand the diverse economic development, infrastructure, and regulatory environments across nations.\n\nResults The analysis revealed a strong correlation between supply chain risks and performance. Entrepreneurs in the consumer products industry should collaborate closely with governmental organizations to address the unique challenges posed by regulatory landscapes, cross-border logistics, and geopolitical risks within the ASEAN region. Adapting to cultural nuances and market variations, along with optimizing logistics and infrastructure, are crucial for successful supply chain risk management.\n\nConclusions Effective supply chain risk management significantly enhances the performance of the consumer products industry’s supply chain. Entrepreneurs in this sector should align their strategies with regional and national governments to proactively address issues and mitigate risks. Continuous monitoring and adaptive measures are necessary to handle emerging risks in the dynamic market landscape. The study provides valuable insights for policymakers, suggesting that supportive frameworks and policies are necessary to bolster SME capabilities in risk management. By fostering a collaborative environment between the public and private sectors, ASEAN countries can enhance overall supply chain resilience. Future research could explore sector-specific risk management practices and their impact on supply chain robustness, underscoring the imperative for SMEs to adopt proactive and integrated risk management approaches to thrive in a complex and evolving economic environment.", "keywords": [ "Supply Chain", "Risk Management", "Risk Surveillance", "Risk Mitigation", "SMEs", "ASEAN", "Consumer Products" ], "content": "Introduction\n\nThe Association of Southeast Asian Nations (ASEAN) consumer goods industry covers various products like food, apparel, electronics, and personal care items, catering to individual consumption (iFAST, 2023; Modisa & Jaikaew, 2022). This sector, serving a diverse and sizable population, experiences robust growth driven by economic expansion and increasing purchasing power (Zapata et al., 2023). Emerging middle-class demographics in countries like Indonesia, Thailand, and Vietnam fuel demand (Lee & Jones, 2023), with urbanization and e-commerce further propelling growth. Despite opportunities, competition intensifies, compounded by regulatory variations, supply chain complexities, and sustainability issues (Pelkmans, 2023). Integral to the ASEAN economy, the consumer goods sector significantly contributes to GDP growth (Amin & Annamalah, 2013). Projected expansion relies on rising disposable incomes and urbanization (Irwansyah et al., 2023). However, challenges persist, including supplier disputes, logistics hurdles, and market access barriers (Prashar, 2022). Trade liberalization fosters market consolidation, raising concerns about service quality and operational efficiency (Ascione & Virgillito, 2023). The sector’s fragility is evident in price volatility, supply fluctuations, and consumer concerns over safety and quality (Overbosch & Blanchard, 2023). Navigating these challenges demands a deep understanding of evolving consumer preferences and regulatory frameworks (Isanovic et al., 2023). Adapting strategies to ensure operational resilience and quality standards is crucial for sustained success in the ASEAN consumer goods market.\n\nASEAN SMEs in the consumer goods sector face significant supply chain risks that impact their operational resilience. These challenges include limited financial resources, making them vulnerable to disruptions like natural disasters and economic downturns (Kurniawan et al., 2024). Reliance on a few suppliers exacerbates risks such as insolvency and quality issues (Panchal et al., 2023). Dynamic markets with fluctuating demand further complicate supply shortages and production bottlenecks (Annamalah et al., 2018). Additionally, limited technological capabilities hinder supply chain visibility and risk mitigation (El-Garaihy et al., 2024), while inefficient inventory management and constrained transportation options increase vulnerability (El Jaouhari & Hamidi, 2024). Regulatory compliance and quality issues compound these risks (Yang et al., 2024). Furthermore, the lack of in-house expertise and a comprehensive risk management strategy heighten susceptibility (Derouiche et al., 2021). Insufficient data and analytics capabilities impede accurate demand forecasting (Nguyen et al., 2023), and difficulties in adopting advanced technologies and navigating complex regulations persist (Pushp & Ahmed, 2023). Scaling to accommodate growth strains existing processes and infrastructure. Addressing these challenges necessitates effective risk management tools and strategies (Habbal et al., 2024). However, research combining quantitative and theoretical methods is lacking in ASEAN nations (Duong et al., 2023), and validated management procedures are needed to mitigate supply chain risks effectively (Ha & Chuah, 2023). Dynamic consumer behavior and the evolving retail landscape present both opportunities and challenges for consumer goods manufacturers (Raghavan et al., 2024). To adapt, companies must understand local preferences and compete with modern retail formats (Mujianto et al., 2023). Robust e-commerce strategies leveraging improved internet access are crucial (Shanmugalingam et al., 2023). Optimizing the supply chain for efficient logistics and differentiation through innovation is also vital (Ivanov & Keskin, 2023; Annamalah et al., 2020). Success demands adaptability, strategic planning, and deep market understanding (Raghavan et al., 2024).\n\nThis study aims to explore the relationship between supply chain risks and supply chain performance in the consumer products sector within ASEAN nations. Specifically, it investigates whether risk monitoring and risk mitigation serve as mediators in this relationship. The concept of “supply chain performance” in this context refers to the efficiency and effectiveness of the supply chain in meeting end-customer demands, ensuring commodity availability, on-time deliveries, and maintaining sufficient inventory and capacity across the supply network, from raw materials to the final consumer. By clarifying and differentiating these terms, the study seeks to provide a comprehensive understanding of how supply chain risk management practices can enhance performance outcomes among SMEs in the ASEAN consumer product sector.\n\nThe primary objective of this research is to adopt a comprehensive approach to supply chain risk management to mitigate the impact of supply chain risks and enhance supply chain performance among SMEs entrepreneurs in ASEAN nations that are engaged in consumer product production. In addition, this study aims to explore the interplay between supply chain risks and supply chain performance in the consumer products sector. Specifically, it seeks to investigate whether the monitoring of risks acts as a mediator in the relationship between supply chain risk management and performance, as well as whether risk mitigation similarly mediates the relationship between supply chain risk management practices and performance outcomes among ASEAN nations.\n\n\nLiterature review\n\nSupply Chain Performance (SCP) encompasses meeting end-customer expectations, ensuring product availability, timely deliveries, and maintaining adequate inventory and capacity (Liu et al., 2023). Performance evaluations enhance collaboration and guide strategic decisions. Socioeconomic changes, including heightened consumer expectations, reshape performance standards, demanding higher quality across various aspects (Zaman & Kusi-Sarpong, 2024). SCP is deeply influenced by operational, financial, strategic, and external risks (Guo et al., 2024). Operational risks include disruptions in production or logistics. Financial risks entail currency fluctuations or cost escalations. Strategic risks involve market demand changes or regulatory shifts. External risks like natural disasters or global pandemics compound complexities. Supply chain managers must continually assess, monitor, and adapt strategies to mitigate disruptions (Umar & Wilson, 2024). Establishing resilient networks with dual sourcing and inventory optimization is essential. Collaboration among partners fosters responsiveness and agility (Guntuka et al., 2024). Successfully integrating risk management enhances resilience and gains a competitive edge (Guntuka et al., 2024). Adaptability and preparedness define a supply chain’s ability to deliver products or services, even amidst challenges. Heightened awareness of sustainability affects consumer preferences. Effectively managing risks involves robust mitigation strategies, technology investments, supplier collaboration, and continuous monitoring (Kwaramba et al., 2024). A resilient supply chain overcomes uncertainties, ensuring consistent performance and meeting customer expectations.\n\nRisk assessment in supply chain management encompasses diverse perspectives, including strategy, finance, production, accounting, and marketing (Shelar et al., 2023). Dong’s definition characterizes risk as the fluctuation in potential supply chain outcomes, highlighting disruptions between components (Rafi-Ul-Shan et al., 2024). Both local logistics managers and global supply chain professionals may hold distinct views on prevalent risks, which stem from unforeseen micro and macro events, leading to operational, tactical, or strategic failures (Rafi-Ul-Shan et al., 2024). Supply chain risks manifest as internal or external, with examples like natural disasters representing external risks and concerns about supplier quality exemplifying internal risks (Hajmohammad et al., 2024). Supplier failure is notably significant, underscoring the importance of timely order delivery, with studies showing the effectiveness of employing multiple suppliers in minimizing operational and interruption issues (Hajmohammad et al., 2024). Porter’s value chain model emphasizes the integration of operations, logistics, and the supply chain’s success, highlighting the impact of supply risk on outbound logistics and overall efficiency (Bustinza et al., 2024). For productivity and enterprise selection, reliable and affordable communications, energy, and information technology are vital (Bustinza et al., 2024). Effective management of supply risk is paramount for achieving and sustaining a high level of supply chain performance, often measured by metrics like efficiency, effectiveness, and responsiveness (Ngo et al., 2023). Any disruption within the supply chain can significantly impact these key indicators, leading to increased costs, inefficiencies, stockouts, production delays, customer dissatisfaction, and potential harm to a company’s reputation and loyalty (Wang et al., 2024). Resilient supply chains can swiftly adapt and recover from disruptions, which can manifest in various forms, from supplier financial instability to demand fluctuations (Negri et al., 2024). Mitigating supply risks involves strategies such as diversifying suppliers, maintaining safety stock, utilizing advanced technologies for enhanced visibility, and conducting regular risk assessments and mitigation plans (Negri et al., 2024). In today’s intricate global supply chains, proactive management of supply risks, informed by academic research, is imperative for sustaining performance amidst uncertainties and disruptions.\n\nThere exists a significant relationship between supply risk and supply chain performance.\n\nInternal risks, within a supplier’s control, are distinct from external risks, which lie outside their sphere, such as political instability in operating regions (Yu et al., 2023). Both internal and external risks must be addressed in comprehensive risk management strategies (Haraguchi et al., 2023). While some risks, like natural disasters, may be unavoidable, firms can develop strategies to mitigate their impact (Haraguchi et al., 2023). In the realm of supply chain management, there exists a symbiotic relationship between supply risk and risk monitoring. Supply risk encompasses potential disruptions, uncertainties, and vulnerabilities within the supply chain, while risk monitoring involves the systematic tracking and assessment of these risks. The nexus between these concepts lies in the understanding that effective risk monitoring requires a comprehensive grasp of supply risks (Berger et al., 2023). It is essential to emphasize that managing supply risk extends beyond crisis response to proactive identification and mitigation. Risk monitoring plays a pivotal role in this regard by facilitating early detection, enabling organizations to take preventive measures. For instance, if organizations identify potential disruptions, such as a supplier’s financial instability, through monitoring, they can take proactive steps like diversifying their supplier base or securing alternative sources (Jessin et al., 2023). Supply risk is dynamic, with new risks emerging and existing ones evolving over time. Risk monitoring, as an ongoing practice, enables companies to stay attuned to shifting conditions, regulatory changes, and market dynamics affecting their supply chain. This continuous awareness empowers organizations to adapt and enhance their risk management strategies effectively. Effective risk monitoring relies on data and information, including supply chain data, market insights, and real-time intelligence (Casagli et al., 2023). These sources feed into risk monitoring systems, facilitating informed decision-making and responsive strategy development. Additionally, risk monitoring serves as an evaluative tool for assessing the efficacy of risk mitigation strategies and making necessary adjustments. Efficient supply risk management through risk monitoring can lead to significant cost savings in the long term. By addressing risks proactively, companies can avoid the costly emergency measures associated with crisis management, ensuring smoother and more cost-effective operations (Pham et al., 2023). In essence, supply risk is central to risk monitoring in supply chain management. Effective risk monitoring is crucial for identifying, assessing, and mitigating supply risks, thereby enhancing the resilience and efficiency of supply chain operations. These concepts work together to safeguard the continuity and stability of supply chain operations.\n\nSupply risk has a significant relationship with risk monitoring.\n\nIn the consumer products industries, supply risk pertains to the possibility of disruptions, uncertainties, or vulnerabilities within the supply chain that could negatively affect the production, distribution, or availability of consumer goods (Kristanto & Kurniawati, 2023). Many companies in consumer product sector heavily rely on global supply chains for sourcing raw materials, components, and finished products, exposing them to risks associated with international trade such as geopolitical tensions, currency fluctuations, and trade restrictions (Kristanto & Kurniawati, 2023). Effective strategies to mitigate these risks are crucial to navigate uncertainties and maintain a stable supply of goods. Disruptions like transportation network issues, infrastructure damage, or production facility impacts can occur due to various events, emphasizing the importance of resilience and continuity planning (Birge et al., 2023). Supply chain management in consumer products industries often involves intricate networks of suppliers, subcontractors, and manufacturers spanning multiple countries, necessitating thorough monitoring and understanding of these relationships to identify and address potential risks effectively (Berger, et al., 2023). This may include actions like diversifying supplier sources, establishing contingency plans, and strengthening partnerships. Compliance management is also essential due to varying regulatory requirements across ASEAN nations and international markets, as failure to comply can lead to production and distribution disruptions, product recalls, and damage to reputation (Kaewnuratchadasorn, 2023). Furthermore, market unpredictability, driven by fluctuating demand, evolving consumer behavior, and emerging trends, poses additional challenges, underscoring the need for strategies that incorporate market intelligence, demand forecasting, and agile supply chain practices. The COVID-19 pandemic has highlighted the vulnerabilities of today’s interconnected supply chains, among ASEAN nations, emphasizing the risks associated with just-in-time inventory management and heavy reliance on a limited number of suppliers or single-source suppliers (Todo et al., 2023). Additionally, the digital age introduces cybersecurity risks, with cyberattacks on suppliers potentially disrupting operations and compromising sensitive data, further emphasizing the importance of proactive risk mitigation measures to safeguard supply chains and ensure operational resilience.\n\nSupply risk has a significant relationship with risk mitigation.\n\nProcess risk is a critical aspect of supply chain management, with significant implications for operational efficiency and customer satisfaction (Prime et al., 2020). It encompasses internal disruptions within a company’s processes, impacting the flow of products and services and necessitating effective management to maintain a resilient supply chain (Shekarian & Mellat Parast, 2021). These internal disruptions can stem from various factors such as equipment breakdowns, labor strikes, and quality issues, all of which have the potential to halt or slow down production processes and ultimately affect overall supply chain efficiency (Shekarian & Mellat Parast, 2021). The unpredictability inherent in manufacturing systems, including variability in machine downtime and flow, introduces uncertainty into the production process, making it challenging to maintain a consistent and reliable workflow (Park et al., 2024). Such variability can impact key performance indicators such as throughput time, process yield, and product quality, introducing inconsistencies in the manufacturing process and leading to inefficiencies (Park et al., 2024). Process risk directly affects the throughput time of production processes, potentially resulting in delays in delivering products to customers (Daultani et al., 2024). Moreover, quality issues arising from process risks can undermine product quality, leading to rejections, rework, and ultimately, customer dissatisfaction (Daultani et al., 2024). Given that efficient supply chain performance relies on smooth and reliable internal processes, effectively managing process risks is crucial for maintaining operational excellence and meeting customer demands (Daultani et al., 2024). Companies must implement robust risk management strategies to identify, assess, and mitigate process risks. This may involve investing in preventive maintenance, quality control measures, and contingency plans to address potential disruptions in the production process (Munir et al., 2024). Despite its significance, process risk in supply chain management is sometimes overlooked compared to other challenges such as demand and supply fluctuations. Therefore, further research is needed to better understand and address process risks to enhance overall supply chain resilience and performance (Liu et al., 2024).\n\nProcess Risk has a significant relationship with Supply Chain Performance\n\nThe significance of process risk within the domain of risk monitoring is an indispensable facet of contemporary business operations as process risk denotes the potential disruptions, errors, or deviations that may manifest within an organization’s operational workflows (Tsang et al., 2018). Effective risk monitoring serves as the linchpin for identifying, evaluating, and mitigating these risks, thereby ensuring the seamless functionality of business processes and the attainment of organizational objectives (Pham et al., 2023). The process of risk monitoring commences with the identification of potential risks, stemming from both internal factors such as process intricacies, resource constraints, and inadequate training, as well as external influences like regulatory shifts and market fluctuations. This identification process is fundamental, as identified risks must undergo comprehensive assessment and quantification, involving ongoing evaluation to gauge their likelihood and impact on operational processes. Continuous vigilance, employing real-time data, performance metrics, and key performance indicators, forms the bedrock of effective risk monitoring (Aljohani, 2023). However, risk monitoring transcends mere assessment as it encompasses the implementation of strategic mitigation measures such as process redesign, technological enhancements, and employee training. Furthermore, it extends its purview to encompass compliance with stringent regulatory requirements, curtailing the potential legal and financial repercussions. The role of process risk in the domain of risk monitoring is pivotal, ensuring the dependability and efficacy of organizational processes and through the continual evaluation, quantification, and mitigation of process risks, businesses fortify their operational resilience, enabling them to adeptly navigate evolving challenges (Pham et al., 2023). A process encompasses crucial management tasks within a company, relying on locally owned resources and operational infrastructure and therefore process risks, internal to the corporation, stem from disruptions in product flow through various processes, such as equipment breakdowns, technical advances, labor strikes, and quality issues (Mc Loughlin et al., 2023). Unpredictability in manufacturing systems includes machine downtime, operator availability, and flow variability, impacting throughput time, process yield, and product quality. Process risk threatens a producer’s ability to fulfill customer orders and compromises supply chain efficiency. While demand and supply challenges have received more attention, future research should focus on addressing process risk.\n\nProcess risk has a significant relationship with risk monitoring.\n\nThe significance of process risk within the context of risk mitigation stands as a vital component of contemporary business operations as process risk entails the potential disruptions, errors, or deviations that can manifest within an organization’s operational workflows, making effective management paramount to identify, assess, and mitigate these risks (Schuett, 2023). This ensures the seamless functionality of business processes and the realization of organizational goals. Identifying process risks involves considering a spectrum of sources, encompassing internal elements like process intricacies, resource constraints, and employee mishaps, alongside external factors such as regulatory shifts and supply chain perturbations. Methodologies for pinpointing operational risks, which often overlap with process risks, are important because they allow organizations to systematically identify vulnerabilities and potential points of failure within their operations, enabling proactive risk mitigation and ensuring the continuity and resilience of business processes (Fang et al., 2024). It becomes crucial to quantify and assess these risks, which requires conducting a comprehensive evaluation of both their potential impact and likelihood, ensuring a thorough understanding of their potential consequences and probability of occurrence. Quantitative methodologies, such as the utilization of risk matrices and Monte Carlo simulations, are frequently employed to address this need, providing systematic frameworks for evaluating and quantifying operational and process risks by assessing both their severity and probability, thereby enhancing decision-making and risk management strategies (Tunçel et al., 2023). Continuous monitoring and surveillance, underpinned by real-time data, key performance indicators (KPIs), and performance metrics, are essential to detect deviations and risks as they arise. Data analysis techniques for continuous monitoring are crucial for detecting trends, anomalies, and emerging risks in real-time, enabling proactive risk mitigation and ensuring timely response measures can be implemented to safeguard operations and mitigate potential disruptions. Extending beyond observation, risk monitoring extends to the implementation of mitigation strategies that may encompass process redesign, technological enhancements, training initiatives, or contingency planning (Menz et al., 2024). Furthermore, stringent regulatory requirements, particularly in industries like finance, underscore the importance of process risk mitigation to ensure compliance. Overall, process risk occupies a pivotal role in the arena of risk mitigation, safeguarding the dependability and efficiency of organizational processes.\n\nProcess risk has a significant relationship with risk mitigation.\n\nDemand risk significantly impacts supply chain performance, particularly for Small and Medium-sized Enterprises (SMEs) due to their size, resource limitations, and constrained capabilities (Ali et al., 2023). SMEs operate with leaner inventory levels, making them vulnerable to inaccuracies in demand forecasting and leading to either overstocking or stockouts (Gurbuz et al., 2023). This can result in increased carrying costs or missed sales opportunities, affecting SMEs’ financial health (Patil & Prabhu, 2024). Fluctuations in demand strain SMEs’ financial stability, hindering operational expenses and investments in critical areas (Patil & Prabhu, 2024). Moreover, SMEs heavily depend on a limited number of suppliers, and demand variability can strain supplier relationships, affecting production inputs (Deng et al., 2022). Inconsistent product availability due to demand uncertainties can lead to dissatisfaction among customers, impacting brand image and loyalty (Dewi & Hastuti, 2024). SMEs may lack the flexibility to adapt quickly to demand fluctuations, affecting production schedules and scaling operations (AlZayani et al., 2024). Investing in affordable and user-friendly technology solutions can empower SMEs to better understand and respond to demand changes (AlZayani et al., 2024). Recognizing the significance of demand-related challenges is essential for SMEs to develop resilient and agile supply chains that can navigate uncertainties and sustain growth (Lu et al., 2024). Demand risk profoundly impacts various aspects of supply chain performance, including financial stability, supplier relationships, customer satisfaction, and adaptability. Managing this risk is vital for organizations to excel in supply chain performance, requiring robust demand forecasting and risk management strategies (Lu et al., 2024).\n\nDemand risk has a significant relationship with supply chain performance.\n\nIn contemporary business landscapes, demand risk is paramount within risk monitoring frameworks, especially in volatile markets and industries (Tantsyura et al., 2016). Characterized by the unpredictability of customer demand, it profoundly influences a company’s revenue, production capabilities, and overall performance (Thi Binh An et al., 2024). Effective demand risk management is crucial for businesses aiming to remain adaptable and financially stable (Fu et al., 2023). This multifaceted risk encompasses economic oscillations, shifts in consumer preferences, competitive dynamics, and external variables like natural disasters or pandemics. Demand risk affects inventory management, production planning, and operational efficiency in supply chain management. Fluctuations in demand can significantly impact revenue and profitability, with overestimation leading to excessive inventory and underestimation resulting in missed sales opportunities (Zhu et al., 2024). Companies must balance inventory, production capacities, and workforce management to respond to demand fluctuations. A resilient supply chain is crucial for adapting to demand oscillations and ensuring consistent product availability (Swaminathan & Venkitasubramony, 2024). Demand forecasting models and advanced analytics aid in predicting demand patterns accurately. Market intelligence facilitates proactive adjustments to demand-related challenges (Khan et al., 2020). High demand risk arises from significant volatility triggered by order changes, shorter product life cycles, or new item introductions. In consumer goods supply chains, demand risks can have long-term consequences, influenced by factors like unforeseen consumer demand and changes in food safety standards (Prashar & Vijaya, 2024). Addressing demand-related risks is crucial for supply chain performance, particularly in the consumer products sector. Contemporary academic references offer insights into managing demand risk and its broader implications within industries (Hasan et al., 2024). This study underscores the importance of understanding and mitigating demand-related risks in supply chain management.\n\nDemand risk has a significant relationship with risk monitoring.\n\nDemand risk’s significance within the domain of risk mitigation is paramount in contemporary business operations, especially in the ever evolving and unpredictable market landscapes of today as this risk category revolves around the intricacies of customer demand’s variability and unpredictability for products or services, exerting profound effects on revenue, production, inventory management, and overall business performance (Khan et al., 2024). Effective management of demand risk serves as a linchpin for businesses, enabling them to navigate adaptably, allocate resources judiciously, and secure financial stability. Demand risk encompasses multifaceted origins, from economic fluctuations and shifting consumer preferences to competitive dynamics and unexpected disruptions (Ngo et al., 2024). The financial implications of demand risk are significant, ranging from the consequences of overestimating demand, such as excessive inventory and holding costs, to the missed opportunities stemming from underestimation (Annamalah et al., 2018). Balancing inventory levels with demand variability stands as a foundational element within demand risk management, highlighting the intrinsic relationship between demand risk and supply chain resilience (Rohaninejad et al., 2023). This correlation underscores the significance of demand risk, as a resilient supply chain not only bolsters adaptability to demand fluctuations but also ensures the continual availability of products. Achieving this equilibrium between inventory management and demand unpredictability is essential for fostering supply chain resilience and effectively navigating market uncertainties. Employing demand forecasting models and advanced analytics is pivotal for mitigating demand risk, as accurate demand forecasts empower proactive decision-making, efficient resource allocation, and risk mitigation (Swaminathan & Venkitasubramony, 2024). Furthermore, staying attuned to market dynamics, consumer behavior shifts, and competitive landscapes is imperative to address demand risk effectively.\n\nDemand risk has a significant relationship with risk mitigation.\n\nIn contemporary business operations, risk monitoring is crucial for supply chain performance, especially in today’s globally interconnected and complex supply chain networks (Yang et al., 2023). It involves ongoing assessment and mitigation of various risks that can disrupt supply chain operations, impacting cost-effectiveness and customer satisfaction. Effective risk monitoring allows organizations to proactively detect potential disruptions, such as natural disasters, geopolitical tensions, supplier issues, or cyber threats (Ganesh & Kalpana, 2022), enabling the implementation of strategic measures to minimize their impact. Supply chain disruptions, such as operational downtime or missed deliveries, can adversely affect customer satisfaction. Risk monitoring plays a vital role in ensuring operational continuity by promptly addressing issues, optimizing resource allocation, and enhancing cost-efficiency (Mohezar et al., 2023). By identifying and mitigating risks, organizations can avoid unnecessary expenses associated with disruptions, such as rushed orders, excess inventory, or production delays. Moreover, continuous risk monitoring fosters stronger relationships with suppliers through transparent communication and collaborative risk mitigation strategies, thus building a more resilient supply chain (Hajmohammad et al., 2024). The regulatory landscape significantly influences supply chain operations, and risk monitoring helps organizations navigate regulatory changes, reducing the risk of legal and financial consequences (Bangar et al., 2024). Effective risk monitoring ultimately translates into customer satisfaction, as an agile and efficient supply chain consistently delivers products and services on time, exceeding customer expectations.\n\nBy identifying, assessing, and mitigating various risk factors, risk monitoring optimizes supply chain performance (Wiryasaputra et al., 2023). Continuously evaluating potential threats allows organizations to proactively adjust strategies, enhance agility, and foster collaboration across the supply chain ecosystem, ensuring operational efficiency, and effectively meeting customer demands.\n\nRisk monitoring significantly mediates the relationship between the factors and supply chain performance.\n\nIn contemporary business operations, risk mitigation is paramount for supply chain performance, especially in an era marked by global interconnectivity and increasing complexities (Dohale et al., 2023). It involves formulating and implementing strategies to identify, assess, and alleviate risks, ensuring seamless flow of goods, cost-effectiveness, and customer satisfaction (Hashim et al., 2024). Effective risk mitigation starts with systematically identifying and evaluating potential risks inherent in the supply chain, including disruptions and supplier issues (Wiryasaputra et al., 2023). This foundational step is crucial for developing mitigation strategies. Risk mitigation extends to ensuring operational continuity by minimizing disruptions’ repercussions, requiring contingency plans, alternative suppliers, and swift risk response strategies (Dohmen et al., 2023). It significantly contributes to cost efficiency by circumventing expenses from disruptions like urgent orders and excess inventory holdings (Groenewald et al., 2024). Mitigating risks enhances supply chain resilience, enabling swift adaptation and recovery from disruptions (Alsmairat, 2023). It fosters robust supplier relationships through transparent communication and collaborative risk mitigation strategies. Ultimately, effective risk mitigation reverberates in customer satisfaction, as a resilient supply chain ensures timely delivery of products and services, fostering loyalty (Alsmairat, 2023). This interplay between risk mitigation, supply chain resilience, and customer satisfaction is pivotal for optimized supply chain performance. In implementing risk mitigation measures, precise knowledge gained through comprehensive risk assessment is crucial (Hochrainer-Stigler et al., 2024). Success relies on accurate risk assessment, with all mitigation efforts based on data from this phase. In consumer product supply chains, where entrepreneurs face high risks and low awareness, sharing risk information is crucial for reducing risks and promoting sustainable performance (Muttitt et al., 2023). This research emphasizes the importance of knowledge sharing in enhancing the effectiveness of risk mitigation tactics for consumer product entrepreneurs, crucial for sustainable supply chain performance.\n\nRisk mitigation significantly mediates the relationship between the factors and supply chain performance.\n\nThe purpose of risk identification is fundamental to supply chain management, aiming to uncover all relevant risks and anticipate future uncertainties for proactive management. Without identifying risks, no risk management measures can be implemented. Early assessment during risk identification is crucial to determine the relevance of a risk and whether further assessment or mitigation is necessary (Cevikbas et al., 2024). A comprehensive approach to risk identification is essential to identify all potential threats and vulnerabilities in the supply chain. Successful Supply Chain Risk Management (SCRM) requires a thorough yet swift and cost-effective evaluation of Supply Chain Risks (SCRs), which can be achieved through risk assessment utilizing available data or expert judgment and scenarios (Chen et al., 2024). Integrating objective data with subjective perceptions enhances the robustness of risk identification, improving the accuracy of risk prediction and assessment. Prioritizing risks is crucial for organizations to focus on the most significant ones. Risks with substantial impact or those that can be promptly mitigated are assigned high priority (Gupta et al., 2023). Risk prioritization aids in determining which risks to target with actions, enabling efficient allocation of limited resources for risk treatment (Annamalah et al., 2019). Understanding the interconnections among risks and their cascading effects is vital for prioritizing risks, devising treatment plans, and executing effective risk management measures (Schulman, 2023). Identifying the most crucial risk capable of triggering multiple risks is essential for effective risk management. Continuous monitoring is necessary to ensure that acknowledged risk consequences do not intensify. If consequences surpass a specified threshold, organizations must contemplate strategies to evade, transfer, share, or mitigate the risk (Habbal et al., 2024). Mitigation aims to decrease risk to an acceptable level, addressing both the likelihood and consequences of a risk event. The choice of a mitigation strategy is influenced by the risk type, organization’s budget, and careful evaluation of acceptance, avoidance, sharing, and transfer options (Gurbuz et al., 2023). Given the interconnected nature of risks, mitigating one type may exacerbate or alleviate another. Therefore, mitigation strategies should be applied with minimal contradictions and careful consideration of risks with negative dependencies. Investing in risk avoidance becomes essential for high probability, high impact risks, while risk acceptance may be considered for low probability, low impact risks (Aldrighetti et al., 2023). Risk is dynamic and requires ongoing monitoring to assess the evolution of risk sources and determine whether adjustments to treatment strategies are necessary. Effective Supply Chain Risk Management (SCRM) contributes to improved supply chain performance by enhancing resilience, reducing disruptions, and ultimately improving overall performance (Emrouznejad et al., 2023). Continuous risk monitoring, proactive risk mitigation, and effective response planning are crucial elements in achieving this objective. This model offers valuable insights into the interactions between different risk factors and their impact on supply chain resilience. Managing supply chain risks involves identifying, modeling, and mitigating risks through a framework that emphasizes continuous monitoring and real-time analytics. Adapting this model requires customizing risk identification, modifying modeling techniques, and implementing industry-specific mitigation strategies (Aqlan & Lam, 2015; Ho et al., 2015; Kern et al., 2012). The model described herein is entirely original and has not been adapted from any previously published models. Our approach draws upon insights from several key studies, including (Aqlan & Lam, 2015; Ho et al., 2015; Kern et al., 2012), which provided valuable foundational knowledge and data that informed the development of our model. However, the conceptual framework, structure, and implementation of the model are uniquely developed by the authors for this research. This framework aims to extend the understanding of how risk management practices influence supply chain performance as shown in Figure 1.\n\nModified from various studies: Aqlan & Lam (2015); Ho et al. (2015); Kern et al. (2012).\n\n\nMethods\n\nThis study adopts a deductive research approach within a positivist paradigm, employing quantitative methods. Deductive research starts with a general premise and derives specific conclusions through empirical observation and verification (de Mast et al., 2023). The positivist nature of this research is reflected in its application of quantitative techniques, including surveys and structured questionnaires. Hypotheses are formulated to quantify the relationships between variables of interest, and these hypotheses are rigorously tested through statistical analysis (Strunk, 2023). The focus is on individuals in authoritative positions within micro, small, and medium-sized enterprises (MSMEs), such as owners, executives, and managers. Primary data is collected via surveys directed at SME owners and managers across different companies. The data underpinning this study are publicly accessible in the Figshare repository (Annamalah, 2024). The questionnaires utilize a Likert scale format. Confirmatory factor analysis is used to assess and measure the identified factors, with Partial Least Squares Structural Equation Modeling (PLS-SEM) applied to evaluate internal consistency (Hair et al., 2023). A probability sampling method, specifically simple random sampling, was used for SME selection. Efforts were made to ensure the accurate identification of eligible respondents within the consumer product sector, including managers, owners, and senior executives. As of 2020, there are approximately 71 million SMEs in Southeast Asia (ASEAN, 2022), representing 97% of all businesses in the region and employing 67% of the workforce (ASEAN, 2022). SMEs are critical to economic development, job creation, innovation, and poverty reduction in Southeast Asian countries. Indonesia, with its large population and economy, has a significant number of SMEs, while Thailand and Vietnam also serve as major hubs for these enterprises. Table 1 provides details on the number of SMEs across ASEAN member states.\n\nWe, the undersigned co-authors, affirm that our manuscript titled “Resilience in the Face of Uncertainty: Navigating Supply Chain Challenges Through Proactive Risk Surveillance and Mitigation Strategies among SMEs in ASEAN Countries” contains original material that has not been published, either in full or in part, in any other journal or publication. This manuscript is not under consideration for publication elsewhere. Each author has made significant and active contributions to the research and preparation of this manuscript and accepts joint and individual responsibility for its content. This study was conducted in accordance with the ethical principles outlined in the Declaration of Helsinki. Ethical approval for the research was obtained from the Institutional Review Board (IRB) of SEGi University with the approval number IRB-2023-14532, granted on May 5, 2023. Participants were provided with comprehensive information about the study, including its purpose, procedures, potential risks, and benefits. Written informed consent was obtained from all participants prior to their inclusion in the study. They were assured that their participation was voluntary and that they could withdraw at any time without any consequences. In cases where verbal consent was obtained due to [specific reasons, e.g., participants’ literacy levels, cultural considerations], this approach was approved by the IRB, ensuring that all participants received the necessary information and gave their informed consent voluntarily. The IRB reference number for this approval is IRB-2024-12346.\n\nThis research covers a range of countries including Singapore, Indonesia, Thailand, Malaysia, Philippines, Vietnam, Laos, Myanmar (Burma), Brunei, and Cambodia, as indicated in Table 2. Moreover, the classification of survey participants is carefully determined through comprehensive analysis of statistical data, taking into account factors such as each country’s business attractiveness, historical context, and specific business preferences or priorities (ADB, 2022). Subsequently, the response samples from each country were further segmented for in-depth analysis.\n\nThe survey sample comprised 385 organizations spanning diverse industries across the surveyed region. These organizations were selected based on statistics provided by ADB (2022) to ensure representation from various business sectors. The objective of the survey is to gather information and insights about different industries, and the selection process aimed to include a representative sample of organizations or businesses from these sectors. The organizations were categorized into specific consumer products sectors according to their primary focus and offerings, which included Technology and Electronics, Fashion and Apparel, Beauty and Personal Care, Health and Wellness, Food and Beverage, among others (refer to Table 3).\n\nAfter developing the survey instrument, a preliminary evaluation was undertaken to assess its suitability and relevance. This pre-test was conducted to confirm that the questionnaire was clear and acceptable to its target audience before its implementation in the actual study, a crucial aspect of an invention survey (Brzoska et al., 2022). To accomplish this, the questionnaire underwent systematic testing involving participation from managers, owners, and executives holding decision-making positions in SMEs, along with academic researchers. A total of 10 respondents, all of whom were managers, owners, or executives in SMEs within the business industry, were engaged in pre-test to evaluate the questionnaire’s content, readability, and completion time. Subsequently, a pilot study was conducted, involving 40 respondents, which represented approximately 10% of the anticipated sample size for the main study (Morin, 2013). These respondents included managers, proprietors, and executives actively engaged in the operations of the various businesses. It is noteworthy that, due to issues related to non-responses to specific questions, only 385 out of the initially targeted 500 organizations yielded usable data. The response of the sample size 77 percent (see Table 4).\n\nTo ensure the accuracy and reliability of the measurement tools, we performed a reliability assessment using Cronbach’s Alpha. This assessment is vital for enhancing measurement consistency by identifying and addressing potential errors. For evaluating questionnaire validity, we employed a mix of adopted and adapted items, incorporating feedback from academic experts to ensure content validity. Positive feedback from the pilot study and the strong reliability of most scales, as shown in Table 4, led to only minor modifications to the questionnaire. Table 5 indicates that all study variables achieved Cronbach’s alpha values above the 0.70 threshold, demonstrating the reliability of the measurement instruments used. Additionally, the Smart-PLS technique, utilizing PLS-SEM for data analysis, was applied to verify the reliability of the instrument for future use with actual respondents.\n\nMSMEs are vital contributors to the economic progress and advancement of ASEAN Member States. With approximately 71 million SMEs in the region, they represent a significant portion, ranging between 97.2% and 99.9% of total establishments within ASEAN Member States. These statistics underscore the pivotal role SMEs play in fostering economic and social development, as they actively engage in value-added activities, drive innovation, and promote inclusive growth by generating employment opportunities and maintaining widespread presence across various sectors (Annamalah et al., 2016). Therefore, SMEs serve as the cornerstone of ASEAN’s economy, playing an essential role in fostering long-term and sustainable economic growth while also aiding in bridging the development divide.\n\nIn this study, probability sampling, specifically the simple random sampling technique, was utilized to select participants. This method was chosen due to its practicality in obtaining a list of entrepreneurs from SMEs in the consumer goods industry.\n\n\nAnalysis\n\nCommon method variance (CMV) is crucially assessed in self-reported questionnaires, especially when one person provides both predictor and criterion variables. The Harman single factor test is commonly used for this purpose, where each construct undergoes major component factor analysis. If one factor dominates covariance or one general component emerges, CMV exists. This method is essential due to CMV’s significant risk and infrequent replication studies. In this study, the first component accounted for 26% of variance, with no common factor identified, indicating no significant CMV. (Podsakoff et al., 2003). Eigenvalues and Extraction Sums of Squared Loadings provide valuable insights into the effectiveness of the factor extraction process in capturing and explaining the variance in the dataset. The one-factor analysis according to Harman’s method was conducted. The un-rotated factor analysis revealed that the initial factor accounted for only 26.71% of the variance. Consequently, it was concluded that the common method bias did not pose a significant threat in the study, as this percentage falls below the 50% threshold of variance. Table 6 presents the findings of the Harman one-factor analysis for this study.\n\nTable 7 displays the data’s descriptive statistics as well as the variables’ reasons. The items’ standard deviations varied from 0.63 to 0.92, while the mean ranged from 3.84 to 4.25. The mean and standard deviation figures were within an acceptable range, indicating that most participants agreed with the claims.\n\nThe highest values were -0.19 for skewness and 0.41 for kurtosis, respectively. According to Bajpai (2011), when employing SEM, acceptable skewness values range from -3 to +3, whereas acceptable kurtosis values range from 10 to +10. The findings demonstrate that the distribution data in this instance are essentially homogeneous Table 8.\n\nIn assessing the internal consistency and reliability of a measure, it’s essential for Factor Loading, Cronbach’s alpha and composite reliability (CR) to equal or exceed 0.70, and average variance extracted (AVE) to equal or surpass 0.50 (Hair et al., 2017). The measurement model’s findings in this study reveal that all variables meet these criteria, with Factor Loading, Cronbach’s alpha and CR values surpassing 0.7, and AVE values exceeding 0.5 (see Table 9). These results indicate satisfactory reliability and internal consistency for the variables under consideration.\n\nThe Fornell-Lacker criterion method for assessing discriminant validity compares the square root of the Average Variance Extracted (AVE) for each latent variable with the correlations between latent variables (Hair et al., 2014). This method ensures that each latent variable primarily explains the variance within its own indicators rather than the variance of other latent variables. Consequently, in Table 10, the bolded diagonal elements (representing the square root of AVE) are consistently larger than the corresponding off-diagonal elements within their respective rows and columns, affirming discriminant validity.\n\nIn addressing concerns related to discriminant validity within variance-based structural equation modeling, the heterotrait-monotrait ratio (HTMT) was introduced by Henseler et al. (2016) and supported by Voorhees et al. (2016). HTMT assesses the ratio of correlations within a trait to those between traits. According to Henseler et al. (2016), a benchmark value below 0.90 is recommended for evaluating discriminant validity using the HTMT criterion. As emphasized by Hair et al. (2017), discriminant validity is confirmed when HTMT values fall below 0.90. Elevated HTMT values suggest potential issues with discriminant validity, underscoring the importance of maintaining values below 0.9, as proposed by Henseler et al. (2015) and Henseler et al. (2016). Table 11 displays the HTMT values for all latent variables, indicating values lower than 0.9.\n\nStructural Model With the successful verification of the measurement model, attention can now shift towards confirming the structural model. This verification process is crucial for assessing the relationships between the constructs in the study model. model. The structural model elucidates these relationships, showcasing the interconnectedness of its components. Various measures, as outlined by Henseler et al. (2016), were employed to evaluate the degree of interconnectedness within the structural indications within the structures were established reflectively. A common approach to assessing structural models is detailed in the table provided below. The PLS (Partial Least Squares) algorithm is a statistical technique used in Structural Equation Modeling (SEM) to estimate complex cause-effect relationship models with latent variables. It focuses on maximizing the explained variance of the dependent constructs by the independent constructs. In the measurement model, PLS assesses the relationships between latent variables (unobserved constructs) and their corresponding manifest variables (observed indicators). This involves evaluating the reliability and validity of the indicators in representing the latent constructs. PLS is particularly useful in exploratory research with small sample sizes and when the primary goal is prediction rather than confirmation as stipulated in Figure 2 (Hair et al., 2017; Wong, 2013).\n\nSource: Authors' original data.\n\nA diagram depicting Structural Equation Modeling showcases the assessment of supply chain performance through independent variables such as supply, process, demand risk capital, wherein risk monitoring and risk mitigation acts as a mediator. As illustrated in Figure 2, to enhance the reliability and validity of the constructs, items with low standardized loading factors (<0.7) were excluded.\n\nThe assessment of lateral multicollinearity requires examining the inner Variance Inflation Factor (VIF) values of the independent variables. These values should ideally be below 5 and 3.3, as recommended by Hair et al. (2016) and Tabachnick and Fidell (2023). If these thresholds are met, it suggests no significant concerns regarding multicollinearity. Furthermore, to ascertain the absence of common method bias, all VIFs resulting from a comprehensive collinearity test should be below 5, as indicated in Table 12.\n\nStandardized Root Mean Square Residual (SRMR) lower values indicate better fit and common thresholds for good fit range from 0.05 to 0.08. Degree of Unweighted Least Squares (d_ULS) lower values suggest better model fit. There isn’t a widely accepted threshold for d_ULS, but it should be close to zero. Degree of Geodesic Discrepancy (d_G) lower values indicate better fit (Kenny et al., 2015). A value close to zero is desirable. NFI values range from 0 to 1, where values closer to 1 indicate better fit. Commonly, a threshold of 0.90 or higher is considered indicative of good fit. By summarizing each index and comparing the obtained values to established thresholds, it can be confidently concluded that the model exhibits a good fit to the data Table 13.\n\nTable 14 provides evidence that the R2 values for the variables Risk Mitigation, Risk Monitoring, and Supply Chain Performance are, respectively, 0.831, 0.863, and 0.876.\n\nTo evaluate the magnitude of impact for each effect within the route model, researchers can employ F-square (Table 15) following Henseler’s (2018) recommendations. The effect size, denoted as f2, is calculated by comparing the increase in R-squared to the proportion of unexplained variation in the endogenous latent variable. Henseler (2018) proposes that values of 0.35, 0.15, and 0.02 signify significant, moderate, and negligible effect sizes, respectively, according to the suggested criteria for magnitude assessment.\n\nThe cross-validated redundancy metric (Q2) serves as a crucial indicator of predictive relevance within the framework of assessment recommended by Hair et al. (2011). This metric reflects the model’s predictive capability, with values anticipated to surpass zero, signaling the model’s aptness for prediction (see Table 16 for reference). Q-square values exceeding 0.20 or 0.25 are regarded as indicative of moderate to good predictive relevance. Researchers often rely on these thresholds to evaluate the model’s effectiveness in forecasting outcomes and informing decision-making processes.\n\nIn evaluating the path coefficients linking constructs, the aim was to assess their support for the proposed hypotheses and the structural model. According to Hair et al. (2016), a minimum route coefficient value of 0.100 is deemed necessary for an impact to be considered within the model. Path coefficients were scrutinized to determine the relevance of the tested hypotheses between the constructs. Utilizing Smart-PLS bootstrapping and T-statistical analysis, the significance level of each route was established as shown in Figure 3. In the study, which involved a sample size of 385 responders and straightforward assumptions, significant values were observed at the 0.05 level. Examination of the path coefficient in Figure 3 and Table 17 unveiled relationships corresponding to hypotheses (H1a, H1b, H1c, H2c, H3a, H3b, H3c, H4) with significant values at the 0.05 level, whereas hypotheses H2a, H2b, and H5 were deemed non-significant.\n\nSource: Authors' original data.\n\n** Supported= P value <0.05.\n\nBootstrapping in the context of the PLS structural model is a resampling technique used to estimate the precision of the model’s parameter estimates. It involves repeatedly sampling (with replacement) from the data set and estimating the model for each sample. This process generates a distribution of estimates, which can be used to assess the stability and reliability of the path coefficients, loadings, and other statistics in the model. Bootstrapping provides confidence intervals and significance testing for the structural paths, helping researchers determine whether the relationships between constructs are statistically significant as shown in Figure 3 (Hair et al., 2017; Henseler et al., 2009).\n\n\nDiscussion\n\nBusinesses in the consumer goods sector recognize supplier, process, and demand risks as pivotal challenges shaping their supply chains (Qiao & Zhao, 2023). Process risks arise from logistics inadequacies, inaccurate forecasting, and reliance on labor agreements. Supply and demand risks can disrupt operations due to discrepancies between supply and market demand. Weather’s impact on the economy, coupled with government regulations, exposes workplaces to environmental concerns, affecting production, sales, and transportation. Consumer goods entrepreneurs face heightened demand and financial risks compared to contract counterparts, attributed to limited resources (Prabhu and Srivastava, 2023). Financial disruptions profoundly affect business operations, emphasizing the need for tailored financial solutions, especially for SMEs. The study reiterates the severity of supply chain risks, shedding light on their diverse impacts, underscoring the imperative for effective risk management strategies in the consumer goods sector.\n\nThe second research objective of this study focuses on exploring the correlation between supply chain risks and supply chain performance within the consumer products sector. The findings underscore the significant impact of supply chain efficiency and risk on the ASEAN consumer products industry. The study addresses an empirical gap by establishing a clear link between supply chain risks and performance. While similar studies have made comparable assertions regarding this relationship, the research stands out for its robust analysis, particularly within the often-overlooked sector of consumer products (Aghabegloo et al., 2024). Previous research predominantly concentrated on the manufacturing industry and primarily assessed process risks using metrics such as variance, lead time order fulfillment, and production specification (Bokrantz & Dul, 2023; Rashid et al., 2024). However, process risk has received comparatively less attention than other forms of risk and warrants expansion from supplier-centric assessments to encompass the entire supply chain, extending from enterprises to retailers. In this study, the evaluation of supply risk was broadened to encompass foreign suppliers, yielding valuable insights into its impact on the quality, cost-efficiency, flexibility, and responsiveness of consumer products entrepreneurs. Thus, this research provides a comprehensive understanding of how supply chain risks influence overall performance within the consumer products industry.\n\nThe research findings highlight the crucial mediating role of risk monitoring in the relationship between risk management and supply chain performance. Rooted in the transaction cost concept, it’s evident that risk emerges from uncertain conditions. This study underscores that existing supply chain risks exert a substantial influence on the overall functionality of the supply chain, particularly within the highly unpredictable landscape of consumer products. Businesses operating in the consumer goods sector, are vulnerable to supply chain risks due to factors like high perishability, short shelf life, and complex engagement with various suppliers and purchasers (Prashar & Vijaya, 2024). Effective risk management becomes imperative for enhancing supply chain performance in the face of significant supply chain risks. One of the primary objectives of this research was to examine the relationship between supply chain risks and the practices of supply chain risk management. In doing so, the study integrated perspectives from both the supply chain governance structure and the transaction cost theory (Ülkü et al., 2024). According to the transaction cost theory, there exists a strong connection between governance systems and the levels of uncertainty within a supply chain. This research delved into assessing supply chain risks within the framework of three key risk management pillars: risk identification, risk assessment, and risk mitigation approaches. Despite the acknowledged challenges in risk detection skills among entrepreneurs in the consumer products sector, the findings of this study reaffirm the significant impact of supply chain risks on business operations (Altay & Pal, 2023).\n\nThe research outcomes also suggest a notable mediating role of risk mitigation in bridging the link between performance and supply chain risk management. The findings highlight that among the three components comprising supply chain risk management, only risk assessment and risk mitigation act as mediators in the relationship between supply chain risk and performance. Conversely, it was observed that risk mitigation did not exert a mediating influence on supply chain performance. The investigation reveals that merely identifying risks within the supply chain doesn’t positively affect performance; instead, it’s the evaluation of risks and the implementation of mitigation measures that lead to improved performance (Han & Um, 2024; Li et al., 2024). This sheds light on why the identification phase of risk management might not efficiently establish the link between supply chain risk and performance. Previous research on supply chain risk has often overlooked or lacked theoretical justification for incorporating risk management strategies as mediating factors (Altay & Pal, 2023). However, the current study supports the hypothesis that effective supply chain risk management serves as an intermediary to enhance business efficiency. This notion is theoretically and empirically validated by the study, demonstrating that elements of supply chain risk management, particularly risk assessment and mitigation strategies, significantly mediate the relationship between supply chain risks and performance, specifically within the realm of consumer products entrepreneurship (Shishodia et al., 2023).\n\nSupply Risk includes risks related to supplier reliability, quality issues, disruptions, etc. Theoretical contributions from SCM theory suggest that managing supply risks effectively can lead to improved operational performance, cost efficiency, and resilience in the supply chain. Process risk includes process inefficiencies, breakdowns, bottlenecks, etc. Theoretical contributions may suggest that effective process management leads to improved agility, flexibility, and responsiveness within the supply chain, contributing to overall performance (Bokrantz & Dul, 2023). Demand risk pertains to uncertainties and variability in customer demand. Fluctuations in demand patterns, unexpected changes in customer preferences, or market dynamics can all contribute to demand risk. Theoretical contributions highlight the importance of demand forecasting, customer relationship management, and market intelligence in mitigating demand risks and improving supply chain performance (Nurdiana et al., 2023). Risk monitoring involves the continuous surveillance and assessment of various risks within the supply chain. It includes activities such as data collection, analysis, early warning systems, etc (Jeong & Chung, 2023). Theoretical contributions suggest that proactive risk monitoring enables timely identification of potential threats, facilitating prompt decision-making and risk mitigation actions. Risk mitigation refers to the strategies and actions taken to reduce the impact or likelihood of risks materializing within the supply chain. This can include diversification of suppliers, inventory buffers, contingency planning, etc. SCM theory emphasizes the importance of risk mitigation as a proactive approach to safeguarding supply chain performance and resilience. Theoretical contributions in SCM may emphasize that effective risk management practices positively influence supply chain performance by enhancing operational efficiency, reducing disruptions, improving customer service levels, and ultimately, contributing to competitive advantage and organizational success (Rimin et al., 2021). SCM theory underscores the significance of addressing supply, process, and demand risks within the supply chain context and highlights the mediating role of risk monitoring and risk mitigation in enhancing supply chain performance (Solijonov et al., 2023). By empirically testing this model, researchers can further validate the theoretical underpinnings and provide practical insights for managers to better manage risks and improve supply chain performance in dynamic and uncertain environments. Additionally, this model emphasizes the importance of a holistic and integrated approach to risk management, aligning with the overarching goals of SCM theory.\n\nBy categorizing risks into supply, process, and demand categories, supply chain managers can better understand and prioritize potential threats to their operations. This allows for a more targeted approach to risk management, ensuring that resources are allocated efficiently to mitigate the most critical risks (Halkier & James, 2022). Recognizing risk monitoring and mitigation as mediating variables underscores their importance in proactive risk management. Practically, this implies implementing robust systems for monitoring supply chain activities, gathering relevant data, and utilizing advanced analytics tools for risk detection and assessment. It also involves developing and implementing effective risk mitigation strategies tailored to the specific types of risks identified, such as diversifying suppliers, establishing contingency plans, or investing in technology to improve process resilience (Li et al., 2024). The ultimate goal of supply chain management is to enhance performance, and the model acknowledges this by considering supply chain performance as the dependent variable. Practically, supply chain managers can use performance metrics such as on-time delivery, inventory turnover, and customer satisfaction to assess the effectiveness of their risk management efforts. By continually monitoring and evaluating performance in relation to risk management activities, managers can identify areas for improvement and implement targeted initiatives to optimize supply chain performance. The model suggests a strong coordination among supply chain partners and stakeholders, emphasizing the importance of collaboration in risk assessment and management. Practically, this involves fostering open communication channels, sharing information and insights, and establishing collaborative relationships with suppliers, customers, and other key stakeholders (Meltzer, 2024). By working together to identify and address risks, supply chain partners can enhance their collective resilience and responsiveness to potential disruptions. Effective risk management practices contribute to building resilience and sustainability within the supply chain. By proactively identifying and mitigating risks, supply chain managers can minimize the impact of disruptions, improve operational stability, and ensure continuity of supply. This not only enhances short-term performance but also strengthens the long-term viability and competitiveness of the supply chain. Overall, the model provides a practical framework for supply chain managers to assess, monitor, and mitigate risks effectively, ultimately leading to improved supply chain performance and resilience in dynamic and uncertain environments. By aligning with supply chain management theory, it offers actionable insights and guidelines for practitioners to enhance their risk management practices and drive competitive advantage in today’s complex business landscape. Business owners in the consumer products industry may use these specifics as a reference to better understand their supplier networks. Entrepreneurs in the consumer products industry need to acquire, transform, and use knowledge in order to compete in the market. Owners of consumer products companies who have open lines of communication with their supply chain partners will be better able to identify obstacles and quickly adapt their strategy to deal with supply chain risks (Pangestuti et al., 2023). Lowering risk will influence tactics and boost customer happiness, both of which will enhance the productivity of business owners of consumer products firms.\n\n\nConclusion\n\nIn conclusion, the study underscores the significant impact of supply chain risks on the performance of consumer product entrepreneurs. It highlights the crucial role of supply chain risk management, particularly risk assessment and mitigation measures, in mitigating these risks and enhancing performance. Moreover, the study identifies risk monitoring and risk mitigation as mediating factors in the relationship between supply chain risks and supply chain performance. However, they do not mediate the relationships between process risk and supply chain performance, process risk and risk monitoring, as well as risk mitigation and supply chain performance. Overall, the findings emphasize the importance of continuous improvement in supply chain risk management for entrepreneurs in the consumer products industry. By focusing on and refining key elements of supply chain risk management, entrepreneurs can enhance the performance of their consumer products in the face of unpredictable supply chain dynamics. The study presents a comprehensive model for supply chain risk management tailored to the unique challenges faced by consumer product entrepreneurs, offering valuable insights for navigating and mitigating supply chain risks effectively.\n\nThe diverse industries and supply chain structures across ASEAN member states pose challenges, with unique economic, regulatory, and infrastructural characteristics influencing supply chain dynamics differently. Limited availability and reliability of data hinder accurate risk assessment and effective SCM strategies. Cultural and language barriers complicate data collection and analysis, while diverse consumer products and market dynamics make risk identification challenging. Informal economies introduce complexities such as counterfeit products and labor exploitation. The fragmented nature of supply chains and prevalence of small enterprises limit effective networking. Cross-border trade complexities hinder collaboration and information sharing, compromising risk mitigation efforts, especially for transnational risks like natural disasters and political instability.\n\nFuture research on supply chain management (SCM) in ASEAN countries should prioritize identifying and prioritizing critical risks across geopolitical, environmental, economic, and technological domains. Studies should analyze individual member states’ challenges and assess the impact of regional integration efforts like the ASEAN Economic Community (AEC) on supply chain vulnerabilities. Utilizing diverse methodologies, researchers can tailor risk assessment frameworks to ASEAN’s varied economies. Collaborative research initiatives involving academia, industry, and government can exchange best practices in risk mitigation. Exploring evolving consumer preferences, market trends, and regulatory frameworks is crucial, as is studying successful risk mitigation practices in the consumer goods industry. Research on government policies, industry standards, and international collaborations in promoting supply chain resilience is needed. Comparative analyses can identify best practices for building resilient supply chains in ASEAN. Longitudinal studies tracking supply chain risks in response to geopolitical tensions, trade disruptions, and technological advancements are also warranted. By considering internal and external risk factors, researchers can offer recommendations for enhancing ASEAN’s consumer products industry’s risk management capabilities.\n\n\nEthical approval statement\n\nHereby, I, Kalisri Logeswaran Aravindan, consciously assure that for the manuscript Resilience in the Face of Uncertainty: Navigating Supply Chain Challenges Through Proactive Risk Surveillance and Mitigation Strategies among SMEs in ASEAN countries the following is fulfilled:\n\n1) This material is the authors own original work, which has not been previously published elsewhere.\n\n2) The paper is not currently being considered for publication elsewhere.\n\n3) The paper reflects the author’s own research and analysis in a truthful and complete manner.\n\n4) The paper properly credits the meaningful contributions of co-authors and co-researchers.\n\n5) The results are appropriately placed in the context of prior and existing research.\n\n6) All sources used are properly disclosed (correct citation). Literally copying of text is indicated by using quotation marks and giving proper reference.\n\n7) All authors have been personally and actively involved in substantial work leading to the paper and will take public responsibility for its content.\n\nThe violation of the Ethical Statement rules may result in severe consequences.\n\nThis study has been endorsed by SEGi (RMIC) approval committee was obtained from the Institutional Review Board (IRB) of SEGi University with the approval number IRB-2023-14532, granted on May 5, 2023.\n\n1. Sanmugam Annamalah\n\n2. Kalisri Logeswaran Aravindan\n\n3. Selim Ahmed\n\nWe agree with the above statements and declare that this submission follows the policies of as outlined in the Guide for Authors and in the Ethical Statement.\n\nDate: 11/5//2023\n\nCorresponding author’s signature: Kalisri Logeswaran Aravindan\n\n\nEthical statement\n\nWe, the undersigned co-authors, affirm that our manuscript titled “Resilience in the Face of Uncertainty: Navigating Supply Chain Challenges Through Proactive Risk Surveillance and Mitigation Strategies among SMEs in ASEAN Countries” contains original material that has not been published, either in full or in part, in any other journal or publication. This manuscript is not under consideration for publication elsewhere. Each author has made significant and active contributions to the research and preparation of this manuscript and accepts joint and individual responsibility for its content.\n\nThis study was conducted in accordance with the ethical principles outlined in the Declaration of Helsinki. Ethical approval for the research was obtained from the Institutional Review Board (IRB) of SEGi University with the approval number IRB-2023-14532, granted on May 5, 2023.\n\nParticipants were provided with comprehensive information about the study, including its purpose, procedures, potential risks, and benefits. Written informed consent was obtained from all participants prior to their inclusion in the study. They were assured that their participation was voluntary and that they could withdraw at any time without any consequences.\n\nThe IRB reference number for this approval is IRB-2023-14532.\n\n\nConsent to participate\n\nInformed verbal consent was obtained from all participants involved in this study. Verbal consent was deemed appropriate due to participants’ literacy levels, cultural considerations, etc. However participants received comprehensive information about the study’s purpose, procedures, potential risks, and benefits. They were assured of their right to withdraw at any time without any repercussions.\n\nDate: 11/5/2023\n\nCorresponding author: Kalisri Logeswaran Aravindan\n\n\nParticipant consent form\n\nResearch Project Title: Resilience in the Face of Uncertainty: Navigating Supply Chain Challenges Through Proactive Risk Surveillance and Mitigation Strategies among SMEs in ASEAN countries\n\nTo be completed by the participant.\n\n\n\n• I have read the information sheet about this study.\n\n• I have had an opportunity to ask questions and discuss this study.\n\n• I have received satisfactory answers to all my questions.\n\n• I have received enough information about this study.\n\n• I understand that I am/the participant is free to withdraw from this study:\n\n○ At any time (until such date as this will no longer be possible, which I have been told)\n\n○ Without giving a reason for withdrawing\n\n• I understand that my research data may be used for a further project in anonymous form, but I am able to opt out of this if I so wish, by ticking here.\n\n• I agree to take part in this study.", "appendix": "Data availability\n\nFigshare: Resilience in the Face of Uncertainty: Navigating Supply Chain Challenges Through Proactive Risk Surveillance and Mitigation Strategies among SMEs in ASEAN countries, https://doi.org/10.6084/m9.figshare.25683687.v3 (Annamalah, 2024).\n\nData license: CC BY 4.0\n\n\nReferences\n\nADB: Asia Small and Medium-Sized Enterprise Monitor 2023: How Small Firms Can Contribute to Resilient Growth in the Pacific Post COVID-19 Pandemic. 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Publisher Full Text\n\nNguyen A, Pellerin R, Lamouri S, et al.: Managing demand volatility of pharmaceutical products in times of disruption through news sentiment analysis. Int. J. Prod. Res. 2023; 61(9): 2829–2840. Publisher Full Text\n\nNurdiana ED, Hariyani HF, Boedirochminarni A: The impact of digitalization and economic openness on economic growth in ASEAN countries. Jurnal Ekonomi & Studi Pembangunan. 2023; 24(2): 331–345. Publisher Full Text\n\nOverbosch P, Blanchard S: Principles and systems for quality and food safety management. Food Safety Management. Academic Press; 2023; pp. 537–558.\n\nPanchal GB, Mirzahosseinian H, Tiwari S, et al.: Supply chain network redesign problem for major beverage organization in ASEAN region. Ann. Oper. Res. 2023; 324(1-2): 1067–1098. Publisher Full Text\n\nPangestuti DC, Muktiyanto A, Geraldina I: Modified of ERM Index for Southeast Asia. Cogent Bus. Manag. 2023; 10(2): 2199906. Publisher Full Text\n\nPark R, Kutanoglu E, Baldea M: Dynamics, uncertainty and control in circular supply chains. Comput. Chem. Eng. 2024; 180: 108441. Publisher Full Text\n\nPatil C, Prabhu V: Supply chain cash-flow bullwhip effect: An empirical investigation. Int. J. Prod. Econ. 2024; 267: 109065. Publisher Full Text\n\nPelkmans J: Lowering regulatory trade costs. World Trade Rev. 2023; 22(3-4): 497–507. Publisher Full Text\n\nPham HT, Pham T, Truong Quang H, et al.: Supply chain risk management research in construction: a systematic review. Int. J. Constr. Manag. 2023; 23(11): 1945–1955. Publisher Full Text\n\nPodsakoff PM, MacKenzie SB, Lee JY, et al.Common method biases in behavioral research: a critical review of the literature and recommended remedies.J. Appl. Psychol.2003; 88(5): 879–903. PubMed Abstract \| Publisher Full Text\n\nPrabhu HM, Srivastava AK: CEO transformational leadership, supply chain agility and firm performance: A TISM modeling among SMEs. Glob. J. Flex. Syst. Manag. 2023; 24(1): 51–65. Publisher Full Text\n\nPrashar A: Supply chain sustainability drivers for fast-moving consumer goods (FMCG) sector: an Indian perspective. Int. J. Product. Perform. Manag. 2022; 72(8): 2397–2419. Publisher Full Text\n\nPrashar A, Vijaya SM: Sustainability drivers of fast-moving consumer goods supply chains: a multi-method study. BIJ. 2024. Publisher Full Text\n\nPrime H, Wade M, Browne DT: Risk and resilience in family well-being during the COVID-19 pandemic. Am. Psychol. 2020; 75(5): 631–643. Publisher Full Text\n\nPushp P, Ahmed F: The Global Value Chain: Challenges faced by ASEAN least developed countries. J. Policy Model. 2023; 45(6): 1223–1245. Publisher Full Text\n\nQiao R, Zhao L: Highlight risk management in supply chain finance: effects of supply chain risk management capabilities on financing performance of small-medium enterprises. Supply Chain Manag. 2023; 28(5): 843–858. Publisher Full Text\n\nRafi-Ul-Shan P, Bashiri M, Kamal MM, et al.: An Analysis of Fuzzy Group Decision-Making to Adopt Emerging Technologies for Fashion Supply Chain Risk Management. IEEE Trans. Eng. Manag. 2024; 71: 8469–8487. Publisher Full Text\n\nRaghavan M, Khan F, Devadason ES: Agri-food trade channel and the ASEAN macroeconomic impacts from output and price shocks. Agric. Econ. 2024; 55(1): 5–26. Publisher Full Text\n\nRashid A, Rasheed R, Ngah AH, et al.: Role of information processing and digital supply chain in supply chain resilience through supply chain risk management. J. Glob. Oper. Strateg. Sourc. 2024; 17(2): 429–447. Publisher Full Text\n\nRimin F, Bujang I, Wong Su Chu A, et al.: The effect of a separate risk management committee (RMC) towards firms’ performances on consumer goods sector in Malaysia. Bus. Process. Manag. J. 2021; 27(4): 1200–1216. Publisher Full Text\n\nRohaninejad M, Janota M, Hanzálek Z: Integrated lot-sizing and scheduling: Mitigation of uncertainty in demand and processing time by machine learning. Eng. Appl. Artif. Intell. 2023; 118: 105676. Publisher Full Text\n\nSchuett J: Risk management in the artificial intelligence act. Eur. J. Risk Regul. 2023; 1–19. Publisher Full Text\n\nSchulman PR: Problems and paradoxes of reliability and resilience in organizational networks. Saf. Sci. 2023; 167: 106279. Publisher Full Text\n\nShanmugalingam P, Shanmuganeshan A, Manorajan A, et al.: Does e-commerce really matter on international trade of Asian countries: Evidence from panel data. Plos one. 2023; 18(4): e0284503. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShekarian M, Mellat Parast M: An Integrative approach to supply chain disruption risk and resilience management: a literature review. Int. J. Log. Res. Appl. 2021; 24(5): 427–455. Publisher Full Text\n\nShelar A, Nile SH, Singh AV, et al.: Recent advances in nano-enabled seed treatment strategies for sustainable agriculture: Challenges, risk assessment, and future perspectives. Nano-Micro Letters. 2023; 15(1): 54. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShishodia A, Sharma R, Rajesh R, et al.: Supply chain resilience: A review, conceptual framework and future research. Int. J. Logist. Manag. 2023; 34(4): 879–908. Publisher Full Text\n\nSolijonov G, Uzaydullaev A, Kuzibekov S, et al.: The role of standardization in the industry and the analytical methods of product certification. Science and innovation. 2023; 2(3): 144–149.\n\nStrunk KK: Critical approaches to quantitative research: Review, critique, and applications. Handbook of Critical Education Research. 1st ed.New York: Routledge; 2023.\n\nSwaminathan K, Venkitasubramony R: Demand forecasting for fashion products: A systematic review. Int. J. Forecast. 2024; 40(1): 247–267. Publisher Full Text\n\nTabachnick BG, Fidell LS: Using Multivariate Statistics. 7th ed.California, USA: Pearson Education: 2023.\n\nTantsyura V, Dunn IM, Waters J, et al.: Extended risk-based monitoring model, on-demand query-driven source data verification, and their economic impact on clinical trial operations. Ther. Innov. Regul. Sci. 2016; 50(1): 115–122. PubMed Abstract \| Publisher Full Text\n\nThi Binh An D, Nguyen TTB, Truong Quang H: Service-oriented supply chain: what do we know about its risks? Int. J. Log. Res. Appl. 2024; 1–28. Publisher Full Text\n\nTodo Y, Oikawa K, Ambashi M, et al.: Robustness and resilience of supply chains during the COVID-19 pandemic. World Econ. 2023; 46(6): 1843–1872. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTsang YP, Choy KL, Wu CH, et al.: An Internet of Things (IoT)-based risk monitoring system for managing cold supply chain risks. Ind. Manag. Data Syst. 2018; 118(7): 1432–1462. 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Manag. 2024; 44(1): 99–132.\n\nWiryasaputra R, Huang CY, Kristiani E, et al.: Review of an intelligent indoor environment monitoring and management system for COVID-19 risk mitigation. Front. Public Health. 2023; 10: 1022055. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWong KK-K: Partial Least Squares Structural Equation Modeling (PLS-SEM) Techniques Using SmartPLS. Mark. Bull. 2013; Reference Source\n\nYang M, Lim MK, Qu Y, et al.: Supply chain risk management with machine learning technology: A literature review and future research directions. Comput. Ind. Eng. 2023; 175: 108859. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYang X, He Y, Liao R, et al.: Mission reliability-centered opportunistic maintenance approach for multistate manufacturing systems. Reliab. Eng. Syst. Saf. 2024; 241: 109693. Publisher Full Text\n\nYu W, Wong CY, Chavez R, et al.: Surfing with the tides: how digitalization creates firm performance through supply chain entrainment. Int. J. Oper. Prod. Manag. 2023; 43(12): 2008–2030. Publisher Full Text\n\nZaman SI, Kusi-Sarpong S: Identifying and exploring the relationship among the critical success factors of sustainability toward consumer behavior. J. Model. Manag. 2024; 19(2): 492–522. Publisher Full Text\n\nZapata AN, Arrazola M, de Hevia J : Technological intensity in manufacturing trade between ASEAN and the EU: challenges and opportunities. Asia Eur. J. 2023; 21(1): 23–42. Publisher Full Text\n\nZhu A, Han Y, Liu H: Effects of adaptive cooperation among heterogeneous manufacturers on supply chain viability under fluctuating demand in post-COVID-19 era: an agent-based simulation. Int. J. Prod. Res. 2024; 62(4): 1162–1188. Publisher Full Text" }	[ { "id": "339835", "date": "02 Dec 2024", "name": "Wilson Kosasih", "expertise": [ "Reviewer Expertise the supply chain and sustainability", "lean and green practices" ], "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 paper, the authors presented a survey-based study that aims to explore the relationship between supply chain risks and supply chain performance in the consumer products sector within ASEAN nations. Specifically, it investigates whether risk monitoring and risk mitigation serve as mediators in this relationship. In my opinion, this paper can be considered for approval, after taking into account the following remarks:\nIn Table 1, please check the no. of Indonesian SMEs again. The context is different from MSMEs. The number should be around 864,000 SMEs. Please present the latent variables and their indicators in detail. In the abstract, the authors mentioned that the study utilized a sample of 385 entrepreneurs from the consumer products industry in ASEAN countries. But in sampling design section, they mentioned the simple random sampling technique was utilized to select participants. What does it means ? In the conclusion, the authors wrote like follow: …. “Overall, the findings emphasize the importance of continuous improvement in supply chain risk management for entrepreneurs in the consumer products industry.”…. This statement needs to be consolidated and presented or discussed in depth in the discussion section. The English language should be verified.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-1037
https://f1000research.com/articles/13-1036/v1	10 Sep 24	{ "type": "Case Report", "title": "Case Report: Ascites as a rare initial manifestation of eosinophilic gastroenteritis", "authors": [ "Zekarias Seifu Ayalew", "Gebeyehu Tessema Azibte", "Temesgen Tefera Bekele", "Berhanu Moges Abera", "Aynalem Demsis Biza", "Bisirat Matheowos Tiramo", "Gebeyehu Tessema Azibte", "Temesgen Tefera Bekele", "Berhanu Moges Abera", "Aynalem Demsis Biza", "Bisirat Matheowos Tiramo" ], "abstract": "Introduction Eosinophilic gastroenteritis is a rare disease characterized by gastrointestinal symptoms and peripheral eosinophilia. It can affect any layer of the gastrointestinal tract. Mucosal, muscular, and sub-serosal subtypes of eosinophilic infiltration are distinguished based on their infiltration depth. Ascites is a characteristic feature of sub-serosal eosinophilic gastroenteritis. However, isolated ascites is a very rare presentation of the disease, making diagnosis challenging.\n\nCase presentation In this case report, we present a 25-year-old female eosinophilic gastroenteritis patient who initially presented with symptoms and signs of ascites. She also reported seasonal rhinitis, which has been associated with eosinophilic gastroenteritis. She responded effectively to treatment with prednisolone.\n\nConclusions This case report highlights the importance of considering rare diseases like eosinophilic gastroenteritis in the differential diagnosis of ascites. Treatment typically involves dietary modifications and corticosteroids. This case also contributes to our understanding of this rare initial presentation of the disease.", "keywords": [ "Ascites", "Eosinophilic Ascites", "Eosinophilic Gastroenteritis", "Eosinophilia" ], "content": "Introduction\n\nEosinophilic gastroenteritis (EGE) is a rare inflammatory gastrointestinal disease affecting children and adults. It is characterized by the infiltration of the gastrointestinal tract by eosinophils. Although it commonly affects the stomach and the duodenum, the colon and the esophagus can also be affected.1\n\nHerein, we present a 25-year-old female who presented with ascites, weight loss, loss of appetite, and fever for six months. A complete blood count revealed an elevated eosinophil count; ascetic fluid analysis was also significant for eosinophilia. EGE was confirmed with an endoscopically taken biopsy from the stomach and duodenum. The patient was started on prednisolone 30mg p.o/day, with tapering after two weeks, and for a total of 6 weeks. All her symptoms subsided on subsequent follow-ups, and she regained her initial weight.\n\nPrednisolone 20-40mg in divided doses is the first line of treatment in EGE. It achieves symptomatic remission in 80% of cases within a week and normalization of eosinophilia within two weeks.2 Additional therapeutic options include antihistamines, sodium cromoglycate, montelukast, and ketotifen.3–6 Surgical intervention is reserved for patients with intestinal obstruction.3,7\n\nThe clinical course often alternates between periods of remission and relapse, especially when steroid treatment is stopped in approximately half of patients. To minimize steroid-related side effects, steroid-sparing therapies like antihistamines, mast cell inhibitors, leukotriene receptor antagonists, and anti-interleukin drugs, including ketotifen, can be valuable in managing relapses.4,6 In rare instances where steroid therapy is ineffective, total parenteral nutrition or immunosuppressive agents like oral azathioprine or cyclophosphamide may be added to the steroid regimen for patients with widespread mucosal disease.8\n\n\nCase presentation\n\nA 25-year-old female presented with progressive abdominal distention for six months. She has also had significant weight loss (5 kg/6 months), loss of appetite, and a low-grade intermittent fever. She had watery diarrhea, alternating with intermittent constipation and crampy abdominal pain. There was no history of jaundice, mental status change, leg edema, skin rash, or joint pain. She denied any history of alcohol or intravenous drug use. The patient has had allergic rhinitis since adolescence. She has no history of hepatitis B or C infection nor any personal or family history of liver disease, hypertension, or diabetes. A physical examination was pertinent for a distended abdomen with signs of intraabdominal fluid collection; other systemic examinations were unremarkable.\n\nA complete blood count revealed white blood cells of 5000/μL, with neutrophils and eosinophils accounting for 57% and 11%, respectively. Other parameters, like hematocrit and platelets, were normal. Hepatitis B surface antigen and hepatitis C antibody were negative. Liver and renal function tests were also in the normal ranges. Serum albumin was 3.56 g/dl. Fluid analysis from the ascites showed a total protein of 4.2 g/dl, albumin of 2.73 g/dl, and a total WBC of 1995 cells/μL with polymorphonuclear cells of 10%. SAAG was 0.83. Cytology from peritoneal fluid revealed eosinophilic effusion, with eosinophils contributing to 12% of the inflammatory cells. Stool examinations were normal three times.\n\nThe endoscopy examination found small ulcers in the esophagus and a large ulcer in the first part of the duodenum. The lining of the upper stomach appeared inflamed, but there were no other abnormalities. Multiple biopsy samples were taken from the esophagus, stomach, and duodenum. The upper GI endoscopy showed a Forest class III duodenal ulcer with deformity and narrowing. Biopsies from the stomach showed inflamed cystic cell fragments with dense eosinophil infiltration (35/HPF) in the epithelium and lamina propria (Figure 1). The duodenal biopsy revealed fragmented tissue within the villi surrounded by lymphoplasmacytes and edematous lamina propria with eosinophilic infiltrate (20/HPF) (Figure 2). The biopsy taken from the esophagus was inadequate. These findings were suggestive of EGE.\n\nThe patient was initiated on prednisolone at a dose of 30mg per day. After two weeks of treatment, the prednisolone was tapered by decreasing 5mg per/week (cumulative dose 945mg) and discontinued after a total of seven weeks. Her ascites and abdominal pain significantly improved within two weeks of starting prednisolone therapy. Following the completion of treatment, she regained her weight, and all her symptoms resolved completely.\n\n\nDiscussion\n\nEGE is a rare gastrointestinal disorder that can affect any part of the gastrointestinal tract, and eosinophilic infiltration is the main feature of the disease. Eosinophilic infiltration can affect any layer of the GI tract, with symptoms varying depending on the affected layer.9 Data on the prevalence of EGE is limited due to the rarity of the disease. The prevalence of EGE in the United States is around 22 to 28 per 100,000 people, based on prior survey data.10 Even though the peak onset of the disease is in the third decade of life, it can occur in any age group.11\n\nThe prevalence of sub-serosal EGE varies in different studies. According to Klein et al., out of 40 patients with EGE, 57% have mucosal disease, 30% have muscular disease, and only 13% have subserosa diseases.12 A study by Pinte L et al. found that among 171 patients with eosinophilic ascites, 74% had eosinophilic gastroenteritis. The remaining patients had other causes, such as parasitic infections and malignancies.13\n\nAscites is the most common manifestation of the sub-serosal subtype of eosinophilic gastroenteritis.14 Furthermore, patients with this variant have abdominal bloating, eosinophilia, and a rapid response to corticosteroid therapy.12 Since patients have nonspecific gastrointestinal manifestations, a high index of suspicion is mandatory.\n\nHalf of the individuals with EGE have a history of allergy or atopy; a few of them may have IgE specific for food allergens, and they may also have a positive skin test for a specific antigen.15 Our patient has seasonal allergic rhinitis.\n\nPeripheral eosinophilia is present in two-thirds of patients.16 Marked ascitic fluid eosinophilia is common in sub-serosal variants of EGE (45–90%).12,15,17 This patient’s ascitic fluid analysis only shows 12% eosinophils. Eosinophilic infiltration of the GI tract on biopsy is confirmatory after excluding other causes of eosinophilia, such as malignancy, parasitic infestation, and drugs.11\n\nTreatment of EGE is individualized based on patient characteristics. Patients with malabsorption can try an elimination diet. An elimination diet should be tried for at least 4 to 6 weeks. Those who are not responding should be tried on prednisolone (20–40 mg/day); symptoms usually improve within 2 weeks. Prednisolone should be tapered over the next 2 weeks.18\n\n\nConclusion\n\nEosinophilic gastroenteritis should be suspected in a patient with non-specific abdominal symptoms and ascites of unclear etiology. Therapy with corticosteroids reduces the severity and duration of symptoms.\n\n\nEthics approval and consent to participate\n\nThere are no ethical concerns about this case report.\n\n\nConsent for publication\n\nWritten informed consent was obtained from the patient for publication of this case report and any accompanying images. A copy of the written consent is available for review by the Editor-in-Chief of this journal.\n\nAll the images used in this manuscript are obtained from the patient, and the authors have informed written consent to publish the images along with the manuscript", "appendix": "Availability of data\n\nAll data underlying the results are available as a part of the article, and no additional source data are required.\n\n\nAcknowledgments\n\nNot applicable.\n\n\nReferences\n\nAbou Rached A, El Hajj W: Eosinophilic gastroenteritis: Approach to diagnosis and management. World J Gastrointest. Pharmacol. 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Publisher Full Text" }	[ { "id": "332895", "date": "18 Nov 2024", "name": "Nhu Thi Hanh Vu", "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 is well-written and presents a case report of a rare initial manifestation of eosinophilic gastroenteritis (EGE) as ascites. The clinical case presentation is thorough and detailed. However, to enhance the scientific rigor and clarity for readers, I recommend a major revision. Below, I outline my specific suggestions for each section: Introduction:\nPlease provide a brief description of the pathogenesis of EGE to help readers better understand the underlying mechanisms of this rare condition.\nCase Presentation:\nPlease include endoscopic images of the patient to visually support the diagnosis and provide additional clarity. Please address the rationale for not performing a colonoscopy in this case. Specifically, please explain how colorectal cancer—a potential cause of eosinophilia—was excluded. Additionally, considering the patient presented with diarrhea—a symptom that could also be associated with eosinophilic colitis—please provide a discussion addressing this aspect. Please explain the decision not to perform imaging tests such as abdominal ultrasound or abdominal CT scan for this patient. The imaging tests could provide valuable information regarding the presence of ascites, intestinal wall thickening, potential malignancies, etc. Please clarify why serological tests for Strongyloidiasis and Toxocariasis were not conducted for this patient. Additionally, please discuss how these two parasitic infections were ruled out because stool examinations have low sensitivity for diagnosing Strongyloidiasis and are not helpful for diagnosing Toxocariasis.\nDiscussion:\nPlease include additional information regarding the prevalence of EGE in males versus females to provide a broader epidemiological context.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [] }, { "id": "345912", "date": "14 Dec 2024", "name": "Nicholas Talley", "expertise": [ "Reviewer Expertise Eosinophilic GI disease", "disorders of gut brain interactions", "microbiome" ], "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 case report of presumed eosinophilic ascites responding to steroids. A very rare disease, this adds to the literature.\nSpecific comments: 1. The introduction summarizes the case which is repetitive. Please fix the spelling error: ascitic not ascetic. Add information on where the patient was diagnosed. 2. Please present the exact differential cell count in the ascitic fluid. How many red blood cells were present (e.g. from a traumatic tap) and was the white cell count adjusted? 3. The biopsy images shown are not of high quality. The degree of eosinophilia in the biopsies is also less than might be expected although serosal disease can't be detected on biopsy. Comment on the tissue eosinophil count. Do you have any normal data for comparison from your region? 4. Infection was ruled out by stool studies times three. Low grade fever is unusual: has this been reported in other case reports of the same condition? What infections are endemic where you are situated? Were serologies for Strongyloides and Toxocara species done? Any additional testing for antibodies to fungi and раraѕitеѕ (eg, Coccidioides, Echinococcus, Schistosoma, Trichinella spiralis)? The infectious workup reported may not have been sufficient before starting steroids perhaps because of availability. This limitation should be discussed including the risks of starting steroids.\n\n5. The outcome of the case after 2 weeks should be documented and reported if possible.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [] }, { "id": "345911", "date": "18 Dec 2024", "name": "Hüseyin Döngelli", "expertise": [ "Reviewer Expertise Gastroenterology", "hematology and internal 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 authors presenting an interesting case of eosinophilic gastroenteritis with eosinophilic ascites. There are some points that need some polishing.\n\nAbstract section: -Firstly, the authors should provide a brief history of case. How the patient get diagnosed is missing and I believe this is one of the main point of this case report. -Secondly, this sentence \"Treatment typically involves dietary modifications and corticosteroids.\" is unnecessary and add nothing to conclusion subsection in abstract.\n\nIntroduction section: - There is an error of definition of eosinophilic gastroenteritis which is affects stomach and intestines only not esophagus. Eosinophilic esophagitis is not form of eosinophilic gastroenteritis. -Second paragraph of the introduction should be in section of case presentation. -Consider mentioning the rarity of EGE with ascites as an initial presentation earlier to emphasize the novelty of this case.\nCase presentation section: The case is described in detail, with clear chronological progression - Specify why the patient’s ascitic fluid eosinophil percentage (12%) is clinically significant, as it is on the lower end compared to the literature. -Provide clearer descriptions of the histopathological findings and why they definitively indicate EGE. -The authors may present the laboratory finding in Table format. -Abbreviations should be described. -The patients had symptoms of weight loss, fever and eosinophilia which can be first presentation of some disease such as lymphoproliferative disorders. Therefore, the authors should clarify that how they excluded those possible diagnosis. -In treatment and outcome subsection, if the patient is still under follow up, please try to give more information of maintenance therapy or did you identify any possible triggers such as food.\n\nDiscussion section: This section should be about discussing your case not the disease. -Expanding on the differential diagnosis process and the exclusion of parasitic infections, malignancy, or other eosinophilic disorders. -The authors should discuss their case with other case report such as in this case report : Yalçın E, et al. (2024 [Ref-1]) https://doi.org/10.1136/bcr-2024-261123.\nConclusion section: -You could highlight the clinical significance of early diagnosis and the role of histopathology in confirming the condition.\nAdditional Notes: -Minor grammatical issues (e.g., inconsistent tense usage in \"She has also had...\" and \"The upper GI endoscopy showed...\") should be addressed. -Avoid redundancy in descriptions; for instance, the term \"infiltration of the gastrointestinal tract by eosinophils\" is repeated several times.\n\nIs the background of the case’s history and progression described in sufficient detail? Partly\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-1036
https://f1000research.com/articles/13-1028/v1	09 Sep 24	{ "type": "Case Report", "title": "Case Report : Brucella infection of total knee arthroplasty - The first case report in an endemic country!", "authors": [ "Ines Chalbaoui", "Sahar Sallem", "Mehdi Meddeb", "Helmi Ernandes", "Leila Abid", "Salma Kaoual", "Ahmed Mzid", "Faten Farah", "Sophia Besbes", "Mondher Mestiri", "Ikbel Kooli", "Ines Chalbaoui", "Sahar Sallem", "Mehdi Meddeb", "Helmi Ernandes", "Leila Abid", "Salma Kaoual", "Ahmed Mzid", "Faten Farah", "Sophia Besbes", "Mondher Mestiri" ], "abstract": "Prosthetic joint loosening due to Brucella spp. is a rare event. In this report, we describe a rare case of prosthetic infection caused by brucella. A 71-year-old woman reported a six-month history of progressing pain in the right prosthetic knee, which had been implanted for arthrosis four years prior to admission, associated with fever. No night sweats were noted. On examination, the right knee appeared slightly swollen and painful on mobilization, and the surgical wound was normal. Blood tests showed increased C-Reactive Protein (CRP) (34mg/L) and erythrocyte sedimentation rate (ESR) (34mm/hr). A CT scan of her right knee was performed, showing loosening of the prosthesis, joint effusion, and osteolysis in contact with the internal tibial component measuring 16mm maximum with bone remodeling of the epiphysis and metaphysis regions. Rose Bengal test was positive for brucellosis, a standard brucella tube agglutination test was positive at a titer of 1/80, blood cultures for brucella were negative and a PCR for detection of Mycobacterium tuberculosis was negative. The patient was diagnosed as having Brucella infection of his total knee arthroplasty. Favorable outcome was observed after medical and surgical treatment. We believe this is the first detailed report of Brucella prosthetic infection in the country despite the endemicity of this type of zoonosis.", "keywords": [ "Brucellosis", "Knee prosthesis", "Loosening", "Antimicrobial therapy." ], "content": "Introduction\n\nBrucellosis is a zoonotic infection caused by Brucella species. It can be transmitted to humans through consumption of unpasteurized and contaminated milk products or through contact with infected animals. Osteoarticular involvement is the most common focal presentation. Prosthetic joint infections (PJI) caused by Brucella spp. are uncommonly reported in the literature. It is rarely diagnosed because of uncommon symptoms. Diagnosis is usually based on serology, augmented when possible by culture of Brucella organisms from blood, synovial fluid, or bone. In this case report, we describe an infection of a total knee prosthesis caused by Brucella spp.\n\n\nCase report\n\nA 71-year-old woman with a personal medical history of hypertension, diabetes, and dyslipidemia, and a history of consumption of unpasteurized dairy products, was admitted to the Infectious Diseases Department of the Orthopedic Institute of Mohamed Kassab (Tunis, Tunisia) in 2020. She reported a six-month history of progressive pain associated with fever in the right prosthetic knee, which had been implanted for arthrosis four years prior to admission. Night sweats were not observed.\n\nOn examination, the right knee appeared slightly swollen and painful upon mobilization, and the surgical wound was normal. The temperature, blood pressure, and pulse rate were within normal ranges.\n\nBlood tests showed increased C-Reactive Protein (CRP) (34 mg/L) and erythrocyte sedimentation rate (ESR) (34 mm/hr). Leukocyte and platelet counts were within the normal limits.\n\nA CT scan of her right knee showed loosening of the prosthesis, joint effusion, and osteolysis in contact with the internal tibial component measuring a maximum of 16 mm with bone remodeling of the epiphysis and metaphysis regions.\n\nSurgical removal of the prosthesis was performed, followed by implantation of a cement spacer. Intraoperative findings showed an anterior collection in the affected knee, containing a serosanguineous fluid. Intraoperative sample culture showed the presence of Brucella spp.\n\nThe Rose Bengal test was positive for brucellosis, a standard Brucella tube agglutination test was positive at a titer of 1/80, blood cultures for Brucella were negative, and PCR for the detection of Mycobacterium tuberculosis was negative.\n\nHistopathology of the synovium revealed an often-ulcerated synovial epithelium with an abundant fibrin layer. The sub-synoviocyte tissue is largely infiltrated by inflammatory cells, lymphocytes, plasmocytes, epithelioid cells, and multinucleated Langhans and Muller cells (Figures 1, 2). The patient was diagnosed as having Brucella infection of his total knee arthroplasty.\n\nCombined antimicrobial therapy consisting of doxycycline 200 mg once a day and rifamycin 600 mg twice daily was initiated.\n\nThe patient received 45 days of doxycycline and rifamycin and was switched to a drug regimen containing 2400/480 mg per day of sulfamethoxazole/trimethoprim and 200 mg per day of doxycycline because of hemolytic anemia caused by rifamycin. A total of 7 months of antimicrobial treatment was administered. The clinical symptoms remitted slowly, and the patient underwent a second stage of surgery consisting of replacement of the cement spacer with a new knee prosthesis. No evidence of recurrence was observed at the final follow-up.\n\n\nDiscussion\n\nBrucellosis remains an endemic infection and burdensome health issue, especially in Tunisia. Strenuous efforts are required to improve the healthcare quality to prevent this type of infection.1\n\nBrucella spp. are facultative intracellular gram-negative coccobacilli that are non-motile and non-spore-forming. Three species (B. melitensis, B. abortus, and B. suis) are important human pathogens, B. canis is less important.\n\nOsteoarticular involvement is common in brucellosis. Spondylitis, sacroiliitis, osteomyelitis, and peripheral arthritis were the most frequently reported forms of brucellosis.2\n\nA Tunisian article, published by H. Battikh, A. Berriche, R. Zayoud et al., reported that osteoarticular involvement was the most common complication of brucellosis, occurring in 28.5% of patients (spondylodiscitis in 20 cases and sacroiliitis in 5 cases) in a series of 109 patients.1\n\nBrucella infection after total joint arthroplasty is rare and difficult to diagnose.3\n\nA systematic review of the literature by Kim et al. reported 18 patients who had Brucella infection following total joint arthroplasty (10 cases of hip joint arthroplasty and 8 cases of knee joint prostheses).4\n\nOur case report revealed the first case of Brucella prosthetic joint infection described in Tunisia despite the endemicity of brucellosis in our country.\n\nThe Steckelberg JO article reported that the mean rate of infections in knee and hip joint arthroplasty, between the second and tenth year after surgery, is, respectively, 2.3 and 5.9 per 1000, respectively, every year.5\n\nA single swollen and painful prosthetic joint, as observed in our patient, could be the only clinical symptom. The non-specific signs and rarity of this type of infection make the diagnosis very difficult to establish.6\n\nThe median duration from prosthesis implantation to the onset of symptoms was 3.9 years in a systematic review of literature by Kim et al.4 We report a similar duration in our case. The onset of symptomatology was four years after prosthesis implantation.\n\nStandard radiography did not always show evidence of prosthetic loosening; CT could help, in certain cases, diagnose prosthetic migration and peri-prosthetic tissue damage (abscess, …).7 In our case, a CT scan was performed, which showed prosthetic loosening, joint effusion, and osteolysis in contact with prosthesis components.\n\nThe diagnosis of Brucella infection following total joint arthroplasty can be established based on symptoms (pain, tenderness, and swelling of the prosthetic joint) in the presence of an antibody titer greater than 1/160 in a tube agglutination test (however, the antibody titer in our case was only 1/80). Definitive diagnosis of this infection is based on isolating Brucella spp. from intraoperative sample culture or blood culture.2,3\n\nRoutine treatment usually includes anti-microbial therapy and surgery if necessary.\n\nAnti-Brucella agents are necessary; however, there are no standard regimens regarding the type, dose, and duration of different antibiotics that can be administered to treat this type of infection. Most authors have suggested a minimum duration of antibiotic therapy of 6 weeks.8,9 In our case, we prolonged the antibiotic treatment because the symptoms remitted slowly (swelling and pain persisted for the first 5 months after surgery).\n\nSurgical removal of the joint prosthesis is a controversial but usually performed procedure because of the potential risk of relapse of infection. It was performed in 61% of patients who were described in the systematic review of the literature by Kim et al.4\n\n\nConclusion\n\nBrucella infection in total joint arthroplasty is an uncommon type of infection that is extremely difficult to diagnose. It is important for physicians to consider this diagnosis in light of every suspicion of prosthesis infection, especially in endemic areas.\n\n\nConsent to publish\n\nThe patient was informed and consent to publish clinical data was received for this study. She provided written informed consent to publish this case report.", "appendix": "Data availability statement\n\nNo data are associated with this article.\n\n\nReferences\n\nBattikh H, Berriche A, Zayoud R, et al.: Clinical and laboratory features of brucellosis in a university hospital in Tunisia. Infect Dis Now. sept 2021; 51(6): 547–551. PubMed Abstract \| Publisher Full Text\n\nKalin Unuvar G: Current Therapeutic Strategy In Osteoarticular Brucellosis. North Clin Istanb. 2019 [cité 4 févr 2024]; 6: 415–420. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nWalsh J, Gilleece A, Fenelon L, et al.: An Unusual Case of Brucella abortus Prosthetic Joint Infection. J Bone Jt Infect. 6 nov 2019; 4(6): 277–279. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKim SJ, Park HS, Lee DW, et al.: Brucella infection following total joint arthroplasty: A systematic review of the literature. Acta Orthop. Traumatol. Turc. mars 2018; 52(2): 148–153.\n\nSteckelberg JM, Osmon DR: Prosthetic Joint Infections.Waldvogel FA, Bisno AL, éditeurs. Infections Associated with Indwelling Medical Devices. Washington, DC, USA: ASM Press; 2014; pp. 173–209. Publisher Full Text\n\nWeil Y, Mattan Y, Liebergall M, et al.: Brucella Prosthetic Joint Infection: A Report of 3 Cases and a Review of the Literature. Clin. Infect. Dis. avr 2003; 36(7): e81–e86. PubMed Abstract \| Publisher Full Text\n\nMolina E, Defasque A, Barron MP, et al.: Imagerie des prothèses du genou. J. Radiol. mai 2009; 90(5): 561–575. PubMed Abstract \| Publisher Full Text\n\nDauty M, Dubois C, Coisy M: Bilateral knee arthroplasty infection due to Brucella melitensis: A rare pathology? Joint Bone Spine. mars 2009; 76(2): 215–216. PubMed Abstract \| Publisher Full Text\n\nRuiz-Iban M, Crespo P, Diaz-Peletier R, et al.: Total Hip Arthroplasty Infected by Brucella: A Report of Two Cases. J. Orthop. Surg. avr 2006; 14(1): 99–103. PubMed Abstract \| Publisher Full Text" }	[ { "id": "333077", "date": "14 Nov 2024", "name": "FD Halstead", "expertise": [ "Reviewer Expertise Clinical microbiology. Personal experience of delayed and difficult diagnosis of brucellosis which resulted in significant patient morbidity." ], "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 a short summary of a case report of brucella being detected in samples taken from a knee of a patient who had had a total knee replacement four years previously. It is an important topic as this is often an infection that goes undetected for a long time, so it is good to report and educate as much as possible. My own father had undiagnosed brucellosis for 10 years, resulting in replacement knees and ankles, so educating workforce is super-important as often over-looked. I feel that some improvements could be made to the paper, as there are parts in the case report which aren’t clear to me as a laboratory clinical scientist. Here are some suggestions:\nRemove the exclamation mark from the title as this makes the paper seem frivolous Abstract\nThe whole of the abstract has been lifted from the main body of the case report. Try to rephrase where possible as It can be a bit repetitive for the reader to encounter the same information more than once. End of para 1, should read Brucella spp (or ideally, the actual species if known) What do you mean by …surgical wound was ‘normal’? What was the actual rose Bengal result (would be nice to state this as a titer etc?) The blood cultures were negative – when were they collected and how long were they incubated for? Last paragraph should read ‘her’ and not ‘his’. What surgical treatment did she have? Revision?\n\nIntroduction\nMaybe mention occupational exposure? Mention global distribution if words allow and a bit more about prevalence in Tunisia? Reference needed for ‘Osteoarticular involvement…’ statement. Could also add here that it tends to be mostly the leg joints (knees and ankles) and cervical spine\n\nCase report\nComment as per abstract – either change wording of abstract, or this wording as both are the same at present. Might be nice to put normal reference ranges for CRP and ESR and state values and ranges for leukocytes and platelets if known. At the end of para 5, you write that ‘intraoperative sample culture showed the presence of Brucella spp’\nIt would be nice to expand a bit more on this (e.g. was this a tissue, synovial fluid, how long incubation) and what ‘normal’ tests you did first on the samples Was Brucella looked for only because everything else was negative? Or was it based on her exposure history? Or is it routine in Tunisia as levels are high?\n\nPara 6 – when were blood cultures collected? How long incubated for? Para 7 – ‘the sub-synoviocyte tissue…was…(instead of ‘is’)…’ Also, need to correct ‘his’ to ‘her’. Final paragraph – at what point was the new knee put in? When was the final follow up done? And how was recurrence ruled out?\n\nDiscussion\nThe flow of the discussion is a bit messy at present. I would suggest starting with\nInfo about rates of PJI (e.g. Steckelberg) Then go on to talk about Brucellosis (the species and burden), then the osteoarticular involvement, Then the rarity of Brucella PJI Then a reflection on your case and the learning points\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/13-1028
https://f1000research.com/articles/13-174/v1	11 Mar 24	{ "type": "Research Article", "title": "Assessment of treatment expectations in women with suspected endometriosis: A psychometric analysis", "authors": [ "Ann-Katrin Meyrose", "Lukas A. Basedow", "Nina Hirsing", "Olaf Buchweitz", "Winfried Rief", "Yvonne Nestoriuc", "Lukas A. Basedow", "Nina Hirsing", "Olaf Buchweitz", "Winfried Rief", "Yvonne Nestoriuc" ], "abstract": "Background Treatment expectations influence clinical outcomes in various physical and psychological conditions; however, no studies have explored their role in endometriosis treatment. It is necessary to understand how these expectations can be measured to study treatment expectations and their effects in clinical practice. This study aimed to psychometrically analyze and compare different treatment expectation measurements and describe treatment expectations in women with suspected endometriosis.\n\nMethod Analysis of cross-sectional baseline data of a mixed-method clinical observational study of N=699 patients undergoing laparoscopy in Germany. Descriptives, bivariate associations, convergent and discriminant validity of four expectation measurements (Treatment Expectation Questionnaire (TEX-Q); Generic rating scale for previous treatment experiences, treatment expectations, and treatment effects (GEEE); numerical rating scales (NRS) assessing improvement and worsening of endometriosis symptoms, expected Pain Disability Index (PDI); range: 0 to 10) were estimated. A cluster analysis was performed on the three GEEE items.\n\nResults Most participants expected high improvement (M=6.68 to 7.20, SD=1.90 to 2.09) and low worsening (M=1.09 to 2.52, SD=1.80 to 2.25) of disability from laparoscopy. Participants who expected greater worsening expected more side effects (r=.31 to .60, p<.001). Associations between the positive and negative expectation dimensions, including side effects, were small to non-significant (r =\|.24\| to .00, p<.001 to.978). Four distinct clusters, described as’positive’, ‘no pain, no gain’, ‘diminished’, and ‘uniform’ were found, with a total PVE of 62.2%.\n\nConclusions Women with suspected endometriosis reported positive expectations concerning laparoscopy, but wide ranges indicated interindividual differences. Treatment expectations seem to be a multidimensional construct in this patient group. The investigated measurements did not correlate to the extent that they measured exactly the same construct. The selection of measurements should be carefully considered and adapted for the study purposes. Clusters provide initial indications for individualized interventions that target expectation manipulation.\n\nTrial Registration Number ID NCT05019612 (ClinicalTrials.gov)", "keywords": [ "placebo", "nocebo", "expectancies", "laparoscopy", "G-EEE", "TEX-Q" ], "content": "Introduction\n\nTreatment expectations are important for clinical outcomes in various physical and psychological conditions,1 such as acute and chronic pain,2,3 surgeries,4,5 breast cancer,6 and psychiatric disorders.7 Despite the high prevalence of endometriosis (4.4% in the general population8) and enormous individual burden,9 no study has focused on treatment expectations in women with suspected endometriosis. Endometriosis is a chronic inflammatory disease in women of procreative age and is characterized by endometrium-like tissues outside the uterus.10 The five most prevalent symptoms of endometriosis are dysmenorrhea, abdominal pain, dyspareunia, dyschezia, and dysuria. The German S2k-treatment guideline for endometriosis recommends a laparoscopy, a minimally invasive surgery under general anesthesia, when endocrine therapy has failed.11 Laparoscopy is associated with short-term symptom improvement,12 but 20–30% of patients do not respond satisfactorily.13,14 In summary, current treatment options are inadequate for many patients.15 A deeper understanding of the role of treatment expectations might help a) clarify why complaints persist and b) develop new intervention avenues to foster positive expectations and prevent nocebo effects.16\n\nTo properly implement and study treatment expectations and their effects in clinical practice, it is necessary to have a good understanding of how these expectations can be measured. This is not as easy as it seems, since treatment expectations can and should be considered multidimensional constructs that differ across specific contexts and time intervals.17 Specifically, expectations can be positive (e.g., improvement of symptoms) or negative (e.g., worsening of symptoms or side effects),18 related to treatment processes or outcomes,19 rated based on valence (more or less important) or probability of occurrence,20 treatment-specific or related to general symptoms,21 or different in terms of being real, that is, plausible or ideal expectations.17,19 This complexity of the ‘treatment expectation’ construct leads to pronounced heterogeneity in available instruments.22–24 While single-item measures have been the most popular historically,20,23,25 recent advances have led to the development of multidimensional treatment-expectation questionnaires.22,26 Although this development circumvents several issues in the assessment of treatment expectations,17 an ideal method of expectation measurement has not been developed. Several issues remain understudied and are fruitful targets for continued psychometric research, such as the contrast between context specific and general expectations.\n\nThe main aim of this study was to psychometrically analyze and compare different treatment expectation measurements in a large sample of N=699 women with suspected endometriosis. Additionally, the study aimed to describe and exploratively cluster treatment expectations in this burdened and understudied patient group. We hypothesise that:\n\ni) Treatment expectations are a multidimensional construct; that is, intercorrelations of different scales and dimensions of the Treatment Expectation Questionnaire (TEX-Q)22 and the three expectation items of the Generic rating scale for previous treatment experiences, treatment expectations, and treatment effects (GEEE26) will be heterogeneous.\n\nii) Treatment expectation measurements correlate higher with each other in terms of convergent validity compared to other psychological measurements assessed (i.e., disability, severity of symptoms, depressive symptoms, anxiety, and catastrophizing pain) in terms of discriminant validity.\n\n\nMethods\n\nThis study used data from the baseline assessment of a mixed-method clinical observational study27 that focused on patients undergoing laparoscopy for suspected endometriosis. Women with endometriosis reported their endometriosis-related disability, complaints, and a priori specified predictors once before and eight times after laparoscopy, covering trajectories over a 12-month period. This observational study was registered at ClinicalTrials.gov (ID NCT05019612), but baseline analyses were not described.\n\nThe target population included adult women with endometriosis-related complaints. Further inclusion criteria were sufficient German language skills, female sex, informed consent for study participation, and indications for laparoscopy. For these analyses, N=699 patients were included, irrespective of the actual surgery or clinical diagnosis after laparoscopy.\n\nWomen with an appointment for laparoscopy in a specialized center for surgical endoscopy and endometriosis (Frauenklinik an der Elbe, Germany) were informed about the study by phone. If interested, the women were referred to the baseline online survey. The online survey included written information about the study and checked the inclusion criteria. Written informed consent for the online survey, storage and processing of data was obtained online from all participants, and baseline assessment was initiated. An individualized study code was used to store the data. Patients completed the survey between 25th of August 2021 to 27th of June 2023 until the required sample size of longitudinally participating patients with diagnosed endometriosis was reached. Interested patients were sent email reminders to encourage their participation. Detailed information on the study design, postoperative assessments, and further efforts to address potential bias are described in the study protocol.27\n\nThe authors assert that all procedures contributing to this work comply with the ethical standards of the relevant national and institutional committees on human experimentation and the Helsinki Declaration of 1975, as revised in 2008. All procedures involving patients were approved by the Psychotherapeutenkammer Hamburg, Germany (ROXWELL-2021-HH, 25th of June 2021).\n\nTreatment expectations about laparoscopy were assessed by four self-reported measurements (Treatment Expectation Questionnaire; three items assessing treatment expectations of the Generic rating scale for previous treatment experiences, treatment expectations, and treatment effects; self-constructed numerical rating scales; and expected Pain Disability Index). The Treatment Expectation Questionnaire (TEX-Q)22,28 comprises 15 items of six dimensions with 11 response options each. The mean score ranged from 0 to 10. Higher scores indicated more positive treatment expectations for the total score and dimensions of ‘treatment benefit’, ‘positive impact’, ‘process’, and ‘behavioral control’. Higher scores indicate more negative treatment expectations for the ‘adverse events’ and ‘negative impact” dimensions. In this study, Cronbach’s α of the total score was.82 and ranged between.72 and.91 for the dimensions in accordance with the validation sample.28\n\nThree items assessing treatment expectations of the Generic rating scale for previous treatment experiences, treatment expectations, and treatment effects (GEEE)26 were used, focusing on expected improvement of disability, worsening of disability, and side effects from laparoscopy with 11 response options (0=no improvement/impairment to 10=greatest improvement/worsening imaginable; 0=no complaints to 10=greatest complaints imaginable). No sum or mean scores were obtained.\n\nTen self-constructed numerical rating scales (NRS) with 11 response options were used to assess the expected improvement and worsening of the five most prevalent endometriosis symptoms (dysmenorrhea, pelvic/abdominal pain, dyspareunia, dyschezia, and dysuria). The wording of items and response options (0=no improvement/impairment to 10=greatest improvement/worsening imaginable) were derived from the GEEE in accordance with the recommendations for the assessment of pain. No sum or mean scores were obtained.\n\nExpected endometriosis-related pain disability was assessed using the German version of the Pain Disability Index29,30 adapted to expected disabilities after laparoscopy (expected PDI). The expected PDI covers seven items with 11 response options (0=no disability to 10=total disability). The sum (range: 0-70) and mean scores (0-10) were calculated. Higher scores indicate higher expected disability. The mean scores were mainly used because of their better comparability to the other expectation measurements in this study. The Cronbach’s α was.93 in this study. The expected change in disability by laparoscopy was defined as the difference between endometriosis-related disability before laparoscopy and expected endometriosis-related disability after laparoscopy (ΔPDI score=PDI – expected PDI; theoretically ranging from -70 to 70 for the sum and -10 to 10 for the mean score). Positive scores indicate a positive change in disability by laparoscopy, that is, improvement, whereas negative scores indicate a negative change in disability, that is, worsening.\n\nFurther, self-reported psychological measurements were used to describe the sample and estimate discriminant validity. Endometriosis-related disability was assessed using the PDI29,30 covering seven items with 11 response options (0=no to 10=total disability). The introductory text was adapted to endometriosis-related disability. The sum (range: 0-70) and mean scores (0-10) were calculated. Higher scores indicate higher disability. Cronbach’s α was .85 in this study. Disability will be compared to women of the German general population.31\n\nThe severity of endometriosis-related symptoms was assessed by five NRS referring to the five most prevalent endometriosis symptoms (dysmenorrhea, pelvic/abdominal pain, dyspareunia, dyschezia, and dysuria) with 11 response options (0=no pain to 10=worst pain imaginable). To summarize symptoms, the maximum severity of symptoms score was calculated using the stated maximum severity of symptoms within the five NRS, for example, if someone selected response options between 2 and 8 for the five endometriosis symptoms, the maximum severity of symptoms score was 8.\n\nDepressive symptoms and anxiety were assessed using the Patient Health Questionnaire (PHQ-4)32 which covers four items with four response options (0=not at all, 1=several days, 2=more than half the days, 3=nearly every day). Sum scores for the depressive symptoms and anxiety subscales ranged from 0 to 6. Higher scores indicate more depressive symptoms and anxiety, respectively. Cronbach’s α was .77 for depressive symptoms and.76 for anxiety in this study. A cutoff score of 3 or greater indicates good sensitivity and specificity for detecting major depression33 and anxiety disorders.34\n\nPain catastrophizing was assessed by the subscale catastrophizing of the Coping Strategies Questionnaire (CSQ)35 which covers six items with seven response options each (0=never do that to 6=always do that). The sum score ranges from 0 to 36, with higher scores indicating a higher level of catastrophizing pain. The Cronbach’s α was .88 in this study.\n\nFrequencies and descriptive statistics (mean, standard deviation, median, range, skewness, and kurtosis) were calculated to describe the sample. Missing data are also reported. Distributions of treatment expectation measurements are displayed by raincloud plots using the R packages ggplot2, ggdist, ggforce, gghalves, haven, RcolorBrewer. Bivariate associations were estimated using Pearson correlation coefficients and displayed as a correlation matrix heatmap using the R package ggcorrplot.36 Convergent validity was determined by bivariate associations of all treatment expectation measurements, discriminant validity by bivariate associations of treatment expectation measurements, and psychological constructs. According to Cohen,37 Pearson’s r=.1–.3 is interpreted as small, r=.3–.5 as medium, and r≥.5 as large. The two-sided level of significance was set at α=.05. The optimal number of clusters was determined by visual inspection of elbow and silhouette plots. The resulting optimal number of clusters was used for the k-means clustering of the three G-EEE items using the cluster package.38 SPSS version 27 and R version 2022.12.0+353 were used for statistical analyses. The data that support the findings of this study are openly available.39\n\n\nResults\n\nOverall, n=2,361 people clicked the survey link, n=1,145 began the online survey, n=1,098 met the inclusion criteria, n=1,082 gave informed consent, and n=699 completed the online survey. More details on the flow of participants are displayed in Figure 1.\n\nThe ages of the 699 participants with suspected endometriosis ranged from 18 to 51 years (M=29.90, SD=6.45). About one-fifth had a migrant background, i.e. participants or one or both parents were not born in Germany, and 39.2% had acquired a higher entrance certificate (German ‘Abitur’) and 33.2% had a university degree. The reason for laparoscopy was endometriosis-related complaints with (21.5%) or without (77.5%) an unmet wish to have children. Overall, participants were enormously burdened by endometriosis-related symptoms before laparoscopy (PDI sum score: M=30.52, SD=13.66) compared with women in the general population in Germany (M=6.9, SD=11.1, N=1,36831; d=3.14). On average, the maximum severity within the five endometriosis-related symptom scales (NRS) was M=7.18 (SD=1.81, potential range: 0-10). More than half (54.8%) showed signs of major depression (41.6%, M=2.56, SD=1.40) and/or anxiety disorder (42.6%, M=2.44, SD=1.63) according to the PHQ-4. Table 1 presents more information on the characteristics of the sample under analysis and the descriptive statistics of all the treatment expectation measurements.\n\na Menstrual bleeding was not applicable for n=75.\n\nb Sexual intercourse was not applicable for n=223.\n\nc n=74 (10.6%) had negative values, that is, expected worsening of disability; n=22 (3.1%) had a value of zero, that is, expected no change in disability.\n\nIn general, women with suspected endometriosis had rather positive treatment expectations concerning laparoscopy. However, the wide ranges of all measurements, mostly covering the total potential range, indicate pronounced interindividual differences. Positive dimensions (TEX-Q; treatment benefit, positive impact) and items (GEEE, NRS), such as expected improvement, were rated with higher values (M=6.68 to 7.20, SD=1.90 to 2.35) and were distributed slightly left-skewed (skewness: -0.84 to -0.64). Negative dimensions (TEX-Q; adverse events, negative impact) and items (GEEE, NRS) such as expected worsening (M=0.92 to 1.09, SD=1.79) or side effects (M=3.67 and 3.72, SD=1.93 and 2.33) were rated with lower values and distributed clearly right-skewed (0.30 to 3.45). Expected disability (PDI total mean score) after laparoscopy ranged from 0 to 9.43 (M=2.20, SD=1.97) and was right-skewed (1.07). Expected change of disability (Δtotal mean score) ranged from -5.14 (medium worsening) to 9.29 (high improvement). Scores tended to be normally distributed based on graphical examination and skewness and kurtosis parameters, whereas the Kolmogorov-Smirnov test was significant (D(699)=.05, p< 0.001). The distributions of some exemplary expectation measurements are shown in Figure 2.\n\nNote. A: TEX-Q subscales: positive impact, negative impact, and adverse events. B: GEEE scale improvement, worsening, and side effects.\n\nFigure 3 shows the resulting elbow and silhouette plots for potential clustering of the three GEEE items (symptom improvement, symptom worsening, and side effects). Both plots suggest k=4 is the optimal number of clusters. K-means clustering with k=4 resulted in a proportion of explained variance of 62.2%. The details of these clusters are listed in Table 2. Descriptively, the clusters can be described as ‘positive’ (high improvement expectation), ‘no pain, no gain’ (high improvement and side effect expectation), ‘diminished’ (rather low expectations on every dimension), ‘uniform’ (equally high expectations in every direction) (see Figure 4).\n\nNote. A: Silhouette plot showing the average silhouette score in relation to the number of clusters. B: Elbow plot showing the total within-cluster sum of squares for the number of potential clusters.\n\nNote. A: Average GEEE improvement expectation scores for each of the four clusters. B: Average GEEE worsening expectation scores for each of the four clusters. C: Average GEEE side effect expectation scores for each of the four clusters.\n\nAll associations of the treatment expectation measurements are presented in Figure 5, with the underlying statistics in Table 3. The dimensions of ‘treatment benefit’ and ‘positive impact’ of the TEX-Q were largely associated with each other (r=.75, p<.001), the total score (r=.76, p<.001 and r=.73, p<.001), and with a medium effect size with the expected process (r=.49, p<.001 and r=.42, p<.001, respectively). Negative dimensions (‘adverse events’ and ‘negative impact’) were largely associated with each other (r=.60, p<.001) and the total score (r= -.51 to r=-40, p<.001), but correlations with positive dimensions were non-significant to small. The correlations of the GEEE items were non-significant to small. Participants who expected more worsening from laparoscopy also expected more side effects (r=.31, p<.001) and less improvement (r=-.09, p=.016), but the effect sizes were small. The expected improvement and side effects of laparoscopy were not associated (r=-.07, p=.061). Correlations of expected worsening and improvement of each endometriosis-related symptom (NRS) were non-significant to small (r=.15 to .24, p<.001), whereas some expected changes in specific endometriosis-related symptoms were highly associated with the same expected change of other symptoms, for example, improvement of dysmenorrhea and abdominal pain, worsening of dysuria, and dyschezia (r=.69 to.73, p<.001). The correlation between expected disability (expected PDI) and change in disability (Δtotal score) was high (r=-.52, p<.001); participants who expected more disability after laparoscopy also expected worsening or a smaller reduction in disability.\n\nNote. Red indicates positive correlations, and blue indicates negative correlations. Non-significant correlations are white. The box highlights the correlations between the treatment expectation measurements (convergent validity). More information on each measurement is provided in the Methods section Measurements. The underlying statistics are presented in Table 3.\n\nTEX-Q, Treatment Expectation Questionnaire; GEEE, Generic Rating Scale for Treatment Expectations; eNRS, expected numerical rating scales; ePDI, expected Pain Disability Index; Δ, difference score; NRS, numerical rating scales; PDI, Pain Disability Index; PHQ-4, Patient Health Questionnaire, 4-item version; CSQ, Coping Strategies Questionnaire.\n\nThe positive dimensions of treatment expectations regarding laparoscopy, the expected process, and the total score of the TEX-Q were highly and positively correlated with the expected improvement in disability as measured by the GEEE (r=.51 to .77, p<.001). Medium-sized positive correlations were found between the negative dimensions of the TEX-Q and expected worsening (r=.34, p<.001 and r=.34, p<.001) and expected side effects (r=.45 to.55, p<.001), as measured by the GEEE.\n\nConsidering the expected improvement and worsening of the severity of endometriosis-related symptoms (NRS), participants who expected more treatment benefit, positive impact from the laparoscopy, and had more positive overall treatment expectations measured by the TEX-Q, also reported more improvement in the severity of symptoms, especially dysmenorrhea (r=.51 to .66, p<.001) and abdominal pain (r=.53 to .67, p<.001). Negative dimensions of the TEX-Q were significantly correlated with the expected worsening of symptom severity, but the effect sizes were small (r=.16 to.25, p <.001). Additionally, the expected improvement and worsening of disability measured by the GEEE were positively correlated with the expected improvement and worsening of the severity of endometriosis-related symptoms (NRS), respectively, ranging from rather high correlations for dysmenorrhea (improvement: r=.63 and worsening: r=.54, p<.001) and abdominal pain (r=.64 and .47, p<.001) to rather medium correlations for pain during sexual intercourse (r=.37 and .39, p<.001), dysuria (r=.26 and .44, p<.001), and dyschezia (r=.29 and.45, p<.001).\n\nConsidering the expected disability after laparoscopy measured using the expected PDI, all correlations with other treatment expectation measurements were small. Participants who expected lower disability after laparoscopy had more positive treatment expectations overall (r=-.14, p<.001) and expected fewer adverse events and negative impact measured by the TEX-Q (r=.17 and.26, p<.001). Participants who expected a higher positive change in disability (Δtotal score) by laparoscopy (i.e., improvement of disability) also expected more benefit from treatment, more positive impact, and more positive treatment expectations overall (r=.17 to.22, p<.001). No associations were found with the other TEX-Q dimensions. Additionally, the correlations between the expected improvement and worsening of disability measured by the GEEE and expected disability after laparoscopy (r=-.16, p<.001 and r=.24, p<.001) and expected changes in disability (r=.20, p<.001 and r=-.09, p=.02) measured by the PDI were small, although both measurements explicitly referred to endometriosis-related disability. Similarly, almost the same associations regarding direction and effect size were found between expected disability and change in disability measured by the expected PDI and expected improvement and worsening of almost all endometriosis-related symptoms (NRS).\n\nOverall, correlations between all treatment expectation measurements and investigated further psychological constructs, that is, preoperative disability, severity of the five most prevalent endometriosis-related symptoms, depressive symptoms, anxiety, and catastrophizing pain, were non-significant to small, with a few exceptions of medium-sized associations. Correlations between treatment expectations measured by the TEX-Q and all psychological constructs were non-significant to small. The most notable correlations were as follows: participants who experienced more preoperative disability and a higher severity of abdominal pain expected a higher positive impact from laparoscopy (r=.26 and .24, p<.001). Participants who reported more depressive symptoms and anxiety expected more adverse events (r=.18 and.18, p<.001).\n\nThe expected improvement, worsening, and side effects measured by the GEEE were not correlated with any of the psychological constructs to a relevant extent (r<.13). Correlations between expected improvement and worsening of the severity of the five most prevalent endometriosis-related symptoms and all further psychological constructs were non-significant to small, despite a few exceptions. Participants who experienced higher pain during sexual intercourse, more severe dysuria, and more severe dyschezia expected considerably more improvement in these specific complaints (r=.47 to .53, p<.001). Expected disability after laparoscopy and expected change in disability measured by PDI were highly correlated with preoperative disability. Participants who experienced more preoperative disability expected a higher disability after laparoscopy (r=.47, p<.001) and a higher change, that is, improvement of disability by laparoscopy (r=.51, p<.001). Additionally, participants who reported more severe endometriosis-related symptoms, more depressive symptoms, and more anxiety expected a higher disability after laparoscopy (r=.19 to .29, p<.001). Participants with a stronger tendency to catastrophize pain expected both a higher disability after laparoscopy and a higher chance, that is, improvement of disability from laparoscopy (r=.24 and .27, p<.001).\n\n\nDiscussion\n\nWomen with suspected endometriosis reported rather positive treatment expectations concerning laparoscopy, but wide ranges emphasize differences between participants. The negative dimensions indicate major floor effects. As hypothesized, low correlations between the dimensions of treatment expectation measurements indicate that treatment expectation also seems to be a multidimensional construct in women with suspected endometriosis. Thus, the calculation of the total sum scores might not be indicated or proven on a case-by-case basis. No association was found between the expected improvement and the side effects of laparoscopy in all patients. Four distinct clusters described as ‘positive’, ‘no pain, no gain’, ‘diminished’, and ‘uniform’ were identified. In line with our second hypothesis, the treatment expectation measurements TEX-Q and GEEE correlated higher with each other in terms of convergent validity compared to other psychological measurements assessed in terms of discriminant validity. This applies to the equivalent dimensions of both. Additionally, the expected improvement and worsening of disability (GEEE) and the severity of the five most prevalent endometriosis-related symptoms (NRS) led to medium-to-high positive associations of equivalent dimensions. Both scales used similar wording but focused on different constructs. Contrary to our second hypothesis of convergent validity, correlations of expected disability after laparoscopy measured by the expected PDI and most other measurements of treatment expectations were non-significant to small. However, none of the investigated measurements of treatment expectation correlated to such an extent that they measured exactly the same construct.\n\nTreatment expectations measured with the TEX-Q of women with suspected endometriosis undergoing laparoscopy were slightly lower than those of the validation sample28 for the total score and all dimensions, despite equal scores for the expected ‘negative impact’ of treatment. This contradicts the findings of more positive treatment expectations in surgical treatment samples undergoing endocrine or bariatric surgery than in psychosomatic samples.28 Intercorrelations of dimensions were similar in both studies despite of higher correlations between the positive dimensions ‘treatment benefit’ and ‘positive impact’ (r=.75 in our sample vs. r=.48 in the validation sample28) and ‘positive impact‘and ‘process‘(r=.42 vs. r=.15). Moreover, the dimension ‘behavioral control’ was significantly correlated to ‘treatment benefit’ (r=.24), ‘negative impact’ (r=.12), and ‘process’ (r=.31) in women with suspected endometriosis but not in the validation sample. Correlations of the TEX-Q and other psychological constructs were small to non-significant in our study and the validation study,28 indicating discriminant validity. Interestingly, participants in our study who reported more depressive symptoms and anxiety expected more adverse events. More unfavorable expectations, that is, lower expected treatment benefit, higher negative impact, and a worse expected process, were also reported in patients with higher depressive and anxiety symptoms in the TEX-Q validation sample.28 For the other assessed treatment expectation measurements, no validation data are currently available.\n\nIn line with Shedden-Mora et al. (2023)28 and Younger et al. (2012),24 our findings support the multidimensionality of the construct of treatment expectations: the positive and negative dimensions of treatment expectations were not correlated in these three studies. Overall, the expected side effects of laparoscopy and its improvement were not associated with the results of patients undergoing psychotherapy.40 This contradicts the ‘no pain, no gain’ assumption.\n\nSo far, research on psychometric properties of measuring treatment expectations24,28 has used heterogeneous samples including patients undergoing different surgeries, pain, psychosomatic in- or outpatient, or cancer treatment. Differences between patient groups and within patient groups could hardly be detected, but seem promising. Our cluster analysis revealed four distinct clusters in patients with suspected endometriosis that differed in terms of their treatment expectation pattern. These clusters can be described as follows. The first cluster showed a strong positive expectation, followed by no worsening or side effect expectations. For the second cluster, the ‘no pain, no gain’ assumption seems to be appropriate; these patients expected high side effects of laparoscopy and high improvement. In the third cluster, we found an overall low level of expectations for any category. The fourth cluster had a rather uniform distribution of expectations, with all expectations being of similar strength. Notably, only patients in this cluster patients also expected worsening. The largest cluster was the first with an improvement in expectation dominance, supporting the rather high expectations found in this sample.\n\nOur findings are based on data from a large sample of women with suspected endometriosis facing laparoscopy in a specialized center for surgical endoscopy and endometriosis, indicating high ecological validity. We assessed four measurements for treatment expectation (TEX-Q, the three items assessing expectations of the GEEE, expected NRS, and expected Pain Disability Index) simultaneously. Consequently, we were able to compare different dimensions, comprehensive questionnaires to single items, and treatment expectation measurements (TEX-Q and GEEE) to established symptom and disability scales (NRS assessing pain and PDI) adapted to the context of expectations. To our knowledge, this is the first study to investigate the treatment expectations in women with suspected endometriosis. Endometriosis is a common chronic disease that is largely underexplored and burdensome, and satisfactory treatment options are not available for many patients.\n\nHowever, the timeframe of the assessed treatment expectations was not well defined in this study. Women with suspected endometriosis might have different expectations for the short-, medium-, and long-term outcomes after laparoscopy. We were unable to quantify these potential differences. The order of the measurement instruments was the same for all participants, and sequence effects were possible. To enhance comprehensibility, the survey started with items referring to the past, then to the present, and finally to the future. Consequently, expected disability (expected PDI) and severity of symptoms (expected NRS) were not assessed directly after the preoperative disability and severity of symptoms. Some patients may have forgotten their reference values, leading to imprecise ratings. Finally, some anchors (i.e., the greatest improvement/worsening imaginable) might be understood unequally by participants with suspected endometriosis. Qualitative data from the embedded study module of this cohort study27 may provide further clarifications.\n\nWomen with suspected endometriosis are highly burdened and report rather positive expectations concerning laparoscopy, even though laparoscopy is associated with only short-term symptom improvement,12 and 20–30% do not respond satisfactorily to this treatment.13,14 Future studies should investigate whether more positive expectations lead to better treatment outcomes or disappointment due to overly optimistic expectations. Based on knowledge of other medical conditions1 and surgical treatments,4,5 positive yet realistic expectations (placebo effect) and reduced negative expectations (nocebo effect) may improve treatment outcomes after laparoscopy.\n\nOur results emphasize that treatment expectations should be measured both multidimensionally and comprehensively. The expected improvement and worsening are not the anchors of a single scale. The dimension and linguistic formulation seem more important than the exactly chosen construct, that is, the disability or severity of symptoms. None of the included measurements comprised different time frames. In future research, it is important to define time frames for treatment expectation measurements, especially for patients undergoing surgery, such as laparoscopy. To generalize our findings across patient groups, provide specific recommendations for patients with symptoms of endometriosis, and classify expectations in terms of being real, that is, plausible or ideal17,19 future qualitative and quantitative longitudinal research is needed. The four clusters of expectations need to be replicated and confirmed because of their high relevance to clinical implications. Individualized interventions could target at expectation manipulation such as focusing on i) side effect management in the ‘no pain, no gain’ and ‘uniform’ expectation clusters, ii) increased positive expectations fostering the placebo effect in the ‘diminished’ cluster, iii) decreased negative expectations reducing the nocebo effect and/or appropriate coping mechanisms, and iv) positive but yet realistic expectations in the ‘positive’ cluster.\n\nAs we found differences between the measurements of treatment expectations and dimensions, it is very interesting whether clinical outcomes may also differ depending on the chosen measurement. In the past, patients’ expectations were often assessed heterogeneously without conceptual standardization and psychometric evaluation.17 Consequently, the selection of measurements should be carefully considered and either tailored to the respective theory-based primary outcome or defined in a general way to be applicable across treatments.\n\nEthical approval was obtained from Psychotherapeutenkammer Hamburg, Germany (ROXWELL-2021-HH, 25th of June 2021). This trial was registered at ClinicalTrials.gov (ID: NCT05019612).", "appendix": "Data availability\n\nPsychArchives: Dataset for: Assessment of treatment expectations in women with suspected endometriosis: A psychometric analysis, https://doi.org/10.23668/psycharchives.13585. 39\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY-SA 4.0).\n\n\nAcknowledgements\n\nWe thank all patients who participated in this study for their time and involvement. We thank the staff of the Frauenklinik an der Elbe and all the psychology students who worked on the ROXWELL study for their support in the recruitment process.\n\n\nReferences\n\nColloca L, Barsky AJ: Placebo and Nocebo Effects. N. Engl. J. Med. 2020; 382(6): 554–561. Publisher Full Text\n\nCormier S, Lavigne GL, Choinière M, et al.: Expectations predict chronic pain treatment outcomes. Pain. 2016; 157(2): 329–338. Publisher Full Text\n\nPeerdeman KJ, van Laarhoven AIM , Keij SM, et al.: Relieving patients’ pain with expectation interventions: a meta-analysis. Pain. 2016; 157(6): 1179–1191. Publisher Full Text\n\nAuer CJ, Glombiewski JA, Doering BK, et al.: Patients’ Expectations Predict Surgery Outcomes: A Meta-Analysis. Int. J. Behav. Med. 2016; 23(1): 49–62. 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PubMed Abstract \| Publisher Full Text\n\nPackage ‘ggcorrplot’: Visualization of a Correlation Matrix using ‘ggplot2’.2022. Reference Source\n\nCohen J: Statistical power analysis for the behavioral sciences. 2nd ed.Hillsdale, NJ: Erlbaum; 1988.\n\ncluster: Cluster Analysis Basics and Extensions. R package version 2.1.4.2022. Reference Source\n\nMeyrose A-K, Basedow LA, Hirsing N, et al.: Dataset for: Assessment of treatment expectations in women with suspected endometriosis: A psychometric analysis. [Dataset]. PsychArchives. 2023. Publisher Full Text Reference Source\n\nMoritz S, Fieker M, Hottenrott B, et al.: No pain, no gain? Adverse effects of psychotherapy in obsessive–compulsive disorder and its relationship to treatment gains. J. Obsessive Compuls. Relat. Disord. 2015; 5: 61–66. Publisher Full Text" }	[ { "id": "268828", "date": "01 Jul 2024", "name": "Michel Canis", "expertise": [ "Reviewer Expertise Endometriosis and minimally invasive 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 large study about patients expectation before a laparoscopic treatment of endometriosis. This point is very interesting. The methods used appear appropriate, but I am not a specialist of treatment expectations studies.\nI would suggest to include data about the anatomical severity of the disease. A global approach of endometriosis is in my mind always somewhat misleading. Treatment expectations from a laparoscopic procedure are likely very different from a patient who has a mechanical infertility related to adhesions to another one who has no disease at ultrasound and complains of severe pain.\nData about pre operative information and particularly about the risks of complications would be essential to understand these expectation. A patient \"afraid of a bowel fistula\" may have different expectation that patients with expected minimal or moderate disease based on preoperative imaging.\nWhen dealing with pain treatment these data would be very interesting. I would also recommend to collect data about the personal history of these patients, trauma and violence may influence the trust in treatment and the results of this very interesting study. I think that most of these data are available to the authors and could be added to the paper.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "12187", "date": "09 Sep 2024", "name": "Ann-Katrin Meyrose", "role": "Author Response", "response": "Numbered Reviewer’s comments --> Authors’ responses in italic (Change in manuscript new word version in parentheses) 1. This is large study about patients expectation before a laparoscopic treatment of endometriosis. This point is very interesting. The methods used appear appropriate, but I am not a specialist of treatment expectations studies. --> Thank you very much for your valuable clinical perspective and suggestions on how to improve our manuscript. 2. I would suggest to include data about the anatomical severity of the disease. A global approach of endometriosis is in my mind always somewhat misleading. Treatment expectations from a laparoscopic procedure are likely very different from a patient who has a mechanical infertility related to adhesions to another one who has no disease at ultrasound and complains of severe pain. --> In this manuscript, we included people with suspected endometriosis who filled out our online questionnaire before laparoscopy. Unfortunately, we have no data about the anatomical severity of the disease, only limited and self-reported data for those participants. A subsample of 395 people underwent laparoscopy and received an endometriosis diagnosis. We have more medical data (e.g., #ENZIAN, rASRM, deep infiltration) for that subsample, which was followed for one year after the laparoscopy. Two manuscripts are currently in progress, analyzing these medical and psychological factors in comparison. 3. Data about pre operative information and particularly about the risks of complications would be essential to understand these expectation. A patient \"afraid of a bowel fistula\" may have different expectation that patients with expected minimal or moderate disease based on preoperative imaging. When dealing with pain treatment these data would be very interesting. I would also recommend to collect data about the personal history of these patients, trauma and violence may influence the trust in treatment and the results of this very interesting study. I think that most of these data are available to the authors and could be added to the paper. --> We agree that the factors you mentioned likely shape patients’ expectations. Unfortunately, we have limited medical information for this large sample (please see comment above). However, we have added the following data we assessed to the manuscript: self-reported duration of symptoms, previous experience with laparoscopy, current endocrine therapy, and whether complaints are dependent on menstrual bleeding. Due to the limited space in the preoperative online questionnaire and the lack of previous evidence focusing on the expectations of patients with endometriosis, we decided to concentrate on assessing expectations through various measurements as well as disability, complaints, anxiety, depression, sociodemographics, and some medical characteristics. To the best of our knowledge, our study is the first to investigate expectations in patients with endometriosis. To gain a deeper understanding of these expectations, we also conducted qualitative interviews before and after laparoscopy in an additional study module. The corresponding manuscript is currently under review, and if possible, we would be pleased to link it to this manuscript. As you suggested, patients reported that pre-operative information, fears, personal history, and prior experiences are important factors for them (among others). We added this aspect to the section “implications for practice and research”. (Measurements – last paragraph p. 8; Results Table 2 and Descriptive characteristics page 9; Discussion section page 29) Finally, this manuscript has a methodological focus on expectations but we agree that the clinical perspective is also very interesting. We have added sentences to the discussion section of this manuscript to highlight the clinical perspective and the implications for future research. (Discussion section, page 28/29)" } ] }, { "id": "293041", "date": "10 Jul 2024", "name": "Claire E Lunde", "expertise": [ "Reviewer Expertise Public Health", "Behavioral Sciences", "Neuroscience", "Endometriosis", "and Female-Pain" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nSummary. Thank you for the opportunity to review the manuscript entitled “Assessment of treatment expectations in women with suspected endometriosis: A psychometric analysis” submitted to F1000Research. The well-written manuscript compared different but related measurements for assessing treatment expectations and thoroughly explored treatment expectations in a large sample of adult patients presenting for endometriosis-suspected laparoscopic surgery. The overarching aims of the current study were to: (1) Psychometrically analyze and compare four treatment expectation measurements: TEX-Q, GEEE, NRS, & PDI. (2) Describe treatment expectations and potentially influential factors (e.g., depression, anxiety, pain catastrophizing) in adult patients with suspected endometriosis. I recommend adding a third aim: (3) Compare treatment expectation results to those of similar conditions and the general population.\nThe findings of this study are significant as they provide new insights into treatment expectations for a wide range of patients with endometriosis. These insights could have important implications for personalized patient care and improved treatment outcomes.\nGeneral. The study aims, and hypotheses could be more consistent throughout the manuscript. It would be helpful to the reader if the flow were consistent for each section (e.g., study Aim 1: compare treatment measures; Study Aim 2: describe treatment expectations). New topics and variables are introduced throughout the manuscript. For example, depression, pain catastrophizing, anxiety, and previous experience with laparoscopy aren’t really mentioned in the abstract or introduction. The same is true when comparing treatment expectations to other conditions and the general population. To improve the manuscript’s readability and coherence, the authors could consider providing a clear outline of the manuscript’s structure in the introduction.\nIt would be helpful if the authors explicitly stated that only the variables pre-surgery were analyzed. Thus, the effects in clinical practice must be inferred from other conditions researched, such as acute/chronic pain, surgeries, breast cancer, and psychiatric disorders (as listed in the introduction). It would be helpful for the reader if the authors listed these specific clinical effects and recommendations for future researchers/clinicians.\nSince 13 individuals identified as non-binary, I recommend that the title and manuscript use people or patients with endometriosis rather than women with endometriosis.\nAbstract. The abstract provides a concise overview of the study, but it could be improved by including all measures given – depression, anxiety, and pain catastrophizing measures are not listed. In the results section of the abstract, the abbreviation PVE should be spelled out. The authors should also include results for both aims. The average age and age range for the sample should be listed. Lastly, the authors should provide a brief statement on the implications of their findings, which will help readers understand the significance of the study.\nKeywords.\nRecommend adding NRS and PDI to the keywords.\nIntroduction. Please provide a citation for the following sentence on page 4: The five most prevalent symptoms of endometriosis are dysmenorrhea, abdominal pain, dyspareunia, dyschezia, and dysuria.\nRecommend describing the often-comorbid relationship between anxiety, depression, pain catastrophizing, and endometriosis-related pain & disability.\nMethods.\nPlease clarify whether the study recruited participants exclusively aged 18 and older or included a broader age range. Were there any specific criteria related to menopausal status? Consider including details about participants’ family history, especially if close relatives (e.g., mother, sister, aunt) had endometriosis or underwent laparoscopic surgery. These social factors may impact expectations. Was this the participant’s first surgery or significant medical treatment? Were there any previous trauma experiences or current chronic stress? If possible, include the duration of endometriosis symptoms, age at diagnosis, treatments attempted, and any prior endocrine therapy. Many patients use social networks or endometriosis support groups for information. Recommend acknowledging the influence of these sources and other anecdotal evidence. Include how well-informed participants were about endometriosis and the possible surgical outcomes. Recommend adding a table describing and comparing the four treatment expectation measures.\nResults.\nFigure 1 reports n=23 unmet wish to have children, and Table 1 reports n=150 unmet wish to have children -- please clarify. If possible, horizontal tables would be easier to read. Previous experience with laparoscopy was reported in the cluster results but not the descriptive results. Table 2 reports: N female (divers) – typo?\nDiscussion. What specific individual patient metrics/characteristics do the authors suggest should be investigated in future studies? Similar to the abstract, a more in-depth analysis of the conclusions and implications should be included. What should a clinical population do with the current findings, and what implications should be considered for future studies? This is a fantastic study – specific steps on “what next” would be incredibly beneficial to understanding tailored treatment approaches for patients with endometriosis.\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": "12188", "date": "09 Sep 2024", "name": "Ann-Katrin Meyrose", "role": "Author Response", "response": "Numbered Reviewer’s comments --> Authors’ responses in italic (Change in manuscript new word version in parentheses) 1. Summary. Thank you for the opportunity to review the manuscript entitled “Assessment of treatment expectations in women with suspected endometriosis: A psychometric analysis” submitted to F1000Research. The well-written manuscript compared different but related measurements for assessing treatment expectations and thoroughly explored treatment expectations in a large sample of adult patients presenting for endometriosis-suspected laparoscopic surgery. The overarching aims of the current study were to: (1) Psychometrically analyze and compare four treatment expectation measurements: TEX-Q, GEEE, NRS, & PDI. (2) Describe treatment expectations and potentially influential factors (e.g., depression, anxiety, pain catastrophizing) in adult patients with suspected endometriosis. I recommend adding a third aim: (3) Compare treatment expectation results to those of similar conditions and the general population. The findings of this study are significant as they provide new insights into treatment expectations for a wide range of patients with endometriosis. These insights could have important implications for personalized patient care and improved treatment outcomes. --> Thank you very much for your time and valuable feedback, especially from the clinical perspective. The manuscript has a methodological focus on expectations, but we agree that the clinical perspective is also very interesting and should be considered more deeply. 2. General. The study aims, and hypotheses could be more consistent throughout the manuscript. It would be helpful to the reader if the flow were consistent for each section (e.g., study Aim 1: compare treatment measures; Study Aim 2: describe treatment expectations). New topics and variables are introduced throughout the manuscript. For example, depression, pain catastrophizing, anxiety, and previous experience with laparoscopy aren’t really mentioned in the abstract or introduction. The same is true when comparing treatment expectations to other conditions and the general population. To improve the manuscript’s readability and coherence, the authors could consider providing a clear outline of the manuscript’s structure in the introduction. --> Thank you for this comment. We restructured the paragraph describing our study aims for a better flow and consistency throughout the manuscript. The first aim is now to describe treatment expectations (including cluster), the second aim is comparing expectation measures (including convergent and discriminant validity) (Introduction, p. 5 (Aims and hypotheses). We checked the order in the whole manuscript: The first paragraph of the introduction focuses on expectations in people with (suspected) endometriosis, the second on measurement aspects. In the results section, all results referring to the first study aim are presented first (describing expectations including cluster), all results referring to the second aim (comparing measures, especially measurement validity) afterwards. Same in the summary of the discussion and implications for practice and research Yet, we did not describe variables such as depression, pain catastrophizing and anxiety in the introduction, because we use those only to interpret the discriminant validity of expectation measures (please see second hypothesis) and to give a brief descriptive overview of the sample under analysis. In this paper, we do not focus on relationships of those constructs from a clinical perspective. Nevertheless, we assessed those constructs in our study, because depression, pain catastrophizing and anxiety seem to be associated with persistent complaints after laparoscopy. To make that clear, we added a sentence to the introduction (and three references). Because readers (e.g., reviewer 1) seem to be interested in clinical data, we added what we assessed to describe the sample more deeply. (Introduction, first paragraph, p. 5, Reference list) 3. It would be helpful if the authors explicitly stated that only the variables pre-surgery were analyzed. Thus, the effects in clinical practice must be inferred from other conditions researched, such as acute/chronic pain, surgeries, breast cancer, and psychiatric disorders (as listed in the introduction). --> Thank you for this note. We added the information that only pre-operative variables were considered to different parts of the manuscript. (Abstract – Methods p. 4; Aims and Hypotheses p.5; Methods, first sentence p.6; Discussion – Summary, first sentence p.26) 4. It would be helpful for the reader if the authors listed these specific clinical effects and recommendations for future researchers/clinicians. --> We added information on effect sizes for pain, depression, analgesic treatments, and postsurgery quality of life. (Introduction, second sentence, p.4) 5. Since 13 individuals identified as non-binary, I recommend that the title and manuscript use people or patients with endometriosis rather than women with endometriosis. --> We totally agree, thanks for this important recommendation. We used people and participants instead of women. (whole manuscript) 6. Abstract. The abstract provides a concise overview of the study, but it could be improved by including all measures given – depression, anxiety, and pain catastrophizing measures are not listed. In the results section of the abstract, the abbreviation PVE should be spelled out. The authors should also include results for both aims. The average age and age range for the sample should be listed. Lastly, the authors should provide a brief statement on the implications of their findings, which will help readers understand the significance of the study. --> Thank you for these recommendations. Due to the limited space of 300 words, we deleted the sentence about the PVE to include the age range. We restructured the order of sentences to clarify our research aims and corresponding results and conclusions (see also general comment above). We added a second recommendation for future studies and rephrased the first to clarify. Because of this we deleted some words in the abstract to comply with the word limit. After discussion, we decided not to include all measures in the abstract due to limited space. The expectation measurement is the focus of the manuscript, the measures depressive symptoms, anxiety and pain catastrophizing were primarily used to analyse discriminant validity. (Abstract, p.4) 7. Keywords. Recommend adding NRS and PDI to the keywords. --> We added both to the keywords. (keywords) 8. Introduction. Please provide a citation for the following sentence on page 4: The five most prevalent symptoms of endometriosis are dysmenorrhea, abdominal pain, dyspareunia, dyschezia, and dysuria. --> We added a citation for this sentence (Chiantera V, Abesadze E, Mechsner S. How to Understand the Complexity of Endometriosis-Related Pain. Journal of Endometriosis and Pelvic Pain Disorders 2017; 9(1):30–8. DOI:10.5301/je.5000271.). (Introduction, first paragraph, p. 5, reference list) 9. Recommend describing the often-comorbid relationship between anxiety, depression, pain catastrophizing, and endometriosis-related pain & disability. --> We assessed depression, pain catastrophizing and anxiety in our longitudinal study, because those constructs seem to be associated with persistent complaints after laparoscopy. To make that clear, we added a sentence to the introduction (and three references). (Introduction, first paragraph, p. 5, Reference list) 10. Methods. Please clarify whether the study recruited participants exclusively aged 18 and older or included a broader age range. Were there any specific criteria related to menopausal status? --> We recruited and included only participants aged 18 and older. This was checked during the online screening process. One interested person was <18 and excluded (please see Figure 1: Flow chart). Due to the sensitive data assessed in our longitudinal study we decided to focus on adult participants. We rephrased “adult people” into “people aged 18 and older” to clarify. We defined no specific criteria related to menopausal status. (Methods section, Participants, first sentences, p.6) 11. Consider including details about participants’ family history, especially if close relatives (e.g., mother, sister, aunt) had endometriosis or underwent laparoscopic surgery. These social factors may impact expectations. Was this the participant’s first surgery or significant medical treatment? Were there any previous trauma experiences or current chronic stress? If possible, include the duration of endometriosis symptoms, age at diagnosis, treatments attempted, and any prior endocrine therapy. Many patients use social networks or endometriosis support groups for information. Recommend acknowledging the influence of these sources and other anecdotal evidence. Include how well-informed participants were about endometriosis and the possible surgical outcomes. --> Thank you very much for these interesting recommendations from a clinical perspective. Due to the limited space in the preoperative online questionnaire and the lack of previous evidence focusing on the expectations of patients with endometriosis, we decided to concentrate on assessing expectations through various measurements as well as disability, complaints, anxiety, depression, sociodemographics, and some medical characteristics. We added information about what is known to shape expectations for other patient group to the discussion section. We added what we assessed: the self-reported duration of endometriosis symptoms, previous experience with laparoscopy (yes/no), current endocrine therapy (yes/no), and whether complaints are dependent on menstrual bleeding. To the best of our knowledge, our study is the first to investigate expectations in patients with endometriosis. To gain a deeper understanding of these expectations, we also conducted qualitative interviews before and after laparoscopy in an additional study module. The corresponding manuscript is currently under review, and if possible, we would be pleased to link it to this manuscript. As you suggested, patients reported that personal history, prior treatment experiences, pre-operative information and knowledge, stress, and social support are important factors for them (among others). (Measurements, last paragraph, p.8, Results, second paragraph, p.9, Table 2, Discussion section, page 29) 12. Recommend adding a table describing and comparing the four treatment expectation measures. --> That is a great idea to enhance comprehensibility. We added such a Table to the method section. (See new Table 1) 13. Results. Figure 1 reports n=23 unmet wish to have children, and Table 1 reports n=150 unmet wish to have children -- please clarify. --> N=23 reported that the unmet wish to have children is the only reason for laparoscopy, N=150 that complaints and an unmet wish to have children is the reason. Those 23 people displayed in the flow diagram were interested to participate but excluded during our screening process. To be included in our longitudinal study endometriosis-related complaints have to be present because we are interested in persisting complaints despite successful laparoscopy. As this point seems misleading, we added this aspect describing our target population in the method section. (Methods section, Participants, p.6) 14. If possible, horizontal tables would be easier to read. --> We ask the editorial office, whether horizontal tables are possible. 15. Previous experience with laparoscopy was reported in the cluster results but not the descriptive results. --> Thank you, we added this information to the table describing the total sample. (Table 3) 16. Table 2 reports: N female (divers) – typo? --> Thanks, that was misleading. We changed the format using N(%) and three lines. (Table 4) 17. Discussion. What specific individual patient metrics/characteristics do the authors suggest should be investigated in future studies? Similar to the abstract, a more in-depth analysis of the conclusions and implications should be included. What should a clinical population do with the current findings, and what implications should be considered for future studies? This is a fantastic study – specific steps on “what next” would be incredibly beneficial to understanding tailored treatment approaches for patients with endometriosis. --> We added some more recommendations for future studies but are careful with clinical implications. From our point of view we need some more data to develop tailored treatment approaches for patients with endometriosis, i.e.: Longitudinal data to answer the question whether more positive expectations lead to better treatment outcomes or disappointment due to overly optimistic expectations (or whether expectations do not have an impact on post-operative outcomes - against our hypotheses) qualitative interviews to understand expectation of people with endometriosis in more depth and knowledge about factors shaping expectations in this patient group As we are currently analyzing the data above and this manuscript ‘only’ uses pre-operative baseline data of our mixed-method clinical observational study (over a 12-month period, plus two additional study modules) we are we are confident to provide more findings in the future to develop a tailored treatment approach for patients with endometriosis. That would be the overarching objective of our research project. (Discussion section, Implications for practice and research, first paragraph, p. 28/29)" } ] } ]	1	https://f1000research.com/articles/13-174
https://f1000research.com/articles/13-1025/v1	09 Sep 24	{ "type": "Research Article", "title": "Positive events in psychotherapy: What do adolescents and young adults say is helpful?", "authors": [ "Luisa Cassera", "Alessia Calabrò", "Aschieri Filippo", "Alessia Calabrò", "Aschieri Filippo" ], "abstract": "Background The significant challenge in adolescent and young adult therapy lies in the fact that research in this field does not provide many clinical indications. This study addresses domains contributing to the establishment and sustenance of engagement, satisfaction, and progress among adolescents and young adults in their treatment by delving into the impact of events that, from the perspective of clients, have positively influenced their therapeutic process.\n\nMethods Employing a qualitative research approach, we conducted semi-structured interviews with 13 adolescents and young adults undergoing therapy, recounting positive and constructive events during their treatment.\n\nResults A structured thematic analysis revealed six primary domains of positive events: events linked to the management of the setting, events shaping the definition of therapy goals, occurrences tied to the therapist’s active role, collaborative events between therapists and clients, and events associated with both clients’ external and internal worlds.\n\nConclusions The findings suggest that working with adolescents shares similarities with psychotherapy involving adult clients but demands specific attention to adolescents and young adults’ families, surrounding environment, and rapidly changing needs.", "keywords": [ "Psychotherapy", "helpful events", "adolescents", "young adults", "patient perspective" ], "content": "Objectives\n\nThis study aims to investigate the positive events that have facilitated the engagement and satisfaction for treatment with adolescents and young adults. Specifically, the goal is to deepen the patients’ perspective regarding how specific episodes in therapy were seen as helpful and positive, and which variables could contribute to promote clients’ appreciation of their therapy.\n\n\nMethod\n\nThe study followed the Consolidated criteria for reporting qualitative research (COREQ) (Tong, Sainsbury & Craig, 2007). In the following sections we report in square brackets the corresponding number of each information to the list of criteria.\n\nRecruitment, inclusion and exclusion criteria. We recruited adolescents and young adults between the ages of 14 and 25. The inclusion criteria included at least four months of psychotherapy to allow for the development of a significant therapeutic relationship with the therapist (Hilsenroth, Peters & Ackerman, 2004). Also, to avoid the bias associated with the recollection of distant events, participants had to be still actively involved in their therapy at the time of interview. We required all candidates to have experienced at least one positive and helpful event during their treatment. No specific exclusion criteria were set.\n\nIn qualitative research involving similar participants (in our case, adolescents) and a specific focus (in our case, positive events in their therapy) literature suggests a range of 9 to 17 interviews to ensure data saturation (Hennink & Kaiser, 2022). Following the approach by Young and Casey (2019), saturation was determined by analysing the frequency of specific codes: transcripts were reviewed in sequence, tallying the appearance of new codes in each interview until no further codes emerged. New participants were interviewed until no further thematic categories emerged. In our research, we collectively agreed that thematic saturation was obtained after completing 13 interviews [12, 23].\n\nSample characteristics. The participants included in the study are native Caucasic Italian-speaking adolescents and young adults residing in Lombardy, Veneto, and Emilia Romagna, who were undergoing psychotherapy at the time of recruitment. The study included 13 adolescents (8 females) between 14 and 25 years old (M = 21.8). With regard to the region of origin of the sample, 4 interviewed were from Lombardy, 7 from Veneto and 2 from Emilia Romagna [14].\n\nConvenience sampling was used [10]. An information letter about the study was spread through the collaboration of a network of psychotherapists working in different contexts (communities of minors, private practices, Public Mental Health Services) present throughout the North Italian territory. The information about the study was either delivered personally or posted by the colleagues at their respective workplaces to reach potential participants. Potential participants provided their availability to participate in this study to their therapists, which shared their contact information to the second author (L.C.). Prior to each interview, the Informed written consent was collected from each potential participant (or from their legal guardians, if clients were younger than 18 years old) and L.C. addressed and discussed potential participants’ questions and comments about their participation in the study. Due to the sampling strategy, it is impossible to determine how many potential participants were informed about the study but declined to take part [13].\n\nData was collected between May and July 2023. The average duration of each interview was 25 minutes (the shortest lasted 13 minutes, while the longest lasted 37 minutes) [21]. All interviews were conducted remotely using the online platform of Microsoft Teams [11]. Interviews were audio and video recorded and transcribed [19]. Two interviewers (a self-identifying male Ph.D. serving as researcher in a private university and one self-identifying female student of a Master program in clinical psychology [1, 2, 3, 4]) took notes of relevant topics for the eventual coding during the interviews [20]. Only L.C. and F.A. were present to all interviews [15]. The study conforms to the Declaration of Helsinki on the Ethical Principles involving Human Participants, and research protocol was approved by the IRB of Catholic University of the Sacred Heart, [approval number #51-23; 25.05.2023]. One participant asked to check the quotes from the interview for accuracy before confirming their use in the text of the manuscript [23].\n\nThe instrument used in this study was a semi-structured interview based on a review of the scientific literature on the positive and enhancing events of therapy. Areas of interest and questions were constructed on the basis of the paradigm of significant events introduced by Robert Elliott (1985). They were also constructed on the basis of the theoretical-methodological framework of the ENACT self-report questionnaire (Kohrt et al., 2015) for which consent has been obtained from the corresponding author. The interview included questions such as: “During your psychotherapy experience, have you felt that you’ve encountered any events that you deemed significant/constructive for your journey?” and “Why do you consider this experience significant?” and allowed follow up questions to deepen the description and understanding of pertinent themes [17]. No repeat interviews were conducted since both interviewers were experienced in conducting this type of research, and had previously conducted other similar interviews (see, Calabrò, Cassera & Aschieri, 2024) [5, 18].\n\nThe coding process of the interviews followed Braun and Clarke (2006), described in detail elsewhere (Aschieri et al., 2021, 2024) [24, 26, 28], moving from the development of a first set of possible coding categories to a structured thematic map though recursive reading of the interviews and revision of the general map of the categories that were identified [25]. The final coding included two levels of analysis: main themes and themes. In line with Hennink and Kaiser (2022) and Aschieri et al. (2021), in this study we reported the frequency of subjects mentioning each theme. The results section also includes themes that are mentioned only one time.\n\n\nResults\n\nSix typologies of helpful events emerged from the coding [31]: events connected with the management of the therapeutic setting; events related to the definition of therapy goals, events that qualify the role of the therapist; collaborative events between therapist and client; events connected with clients’ internal world; events connected with clients’ external world. Each theme was composed of different sub-themes [32]. Tables 1-6 summarise the structure of the categorization. The text below reports one excerpt from participants for each sub-theme. More examples for each sub-theme are given in the online Appendix A [30].\n\nThe first theme includes events that qualify how the therapist organised the setting. We included in this category all examples of setting management that, from the clients’ perspective, contributed to positively influence the course of treatment and the construction of the therapeutic alliance. In this regard, three sub-themes emerged: definition of privacy boundaries; therapists’ flexibility in adjusting the frequency of the sessions depending on adolescents’ needs, and therapists’ availability between sessions (Table 1).\n\nDefinition of Privacy Boundaries. For thirteen adolescents, establishing the confidentiality boundaries within the therapeutic relationship was crucial. This allowed adolescents to perceive the differentiation between the therapeutic dyad and the external world, and to feel free - and safe at the same time - in expressing their own difficulties, as illustrated by the example below [29]:\n\nCl. 10: “She (my therapist) didn’t request (referring to bringing my parents into the session) maybe because the issue wasn’t really within the family. Let’s say she saw it as a secondary thing, which we still investigated, but in reality, we understood that it wasn’t the central focus of my therapy.” […] Perhaps (if she had involved them), I wouldn’t have felt so open in expressing things, laying them out even if she knew them because … it wouldn’t have been that same intimate thing that has developed between me and my therapist. I didn’t see it as a relationship between me and someone doing their job but as something more intimate and profound. Because of the involvement, the empathy that was there, the fact that she made me feel good, there was something beyond the work that was intimate, personal, and involving someone else (my parents) might not have made it so.”\n\nAvailability Between Sessions. A substantial number of adolescents (n = 5) stressed the importance of the help therapists offered them between sessions. In particular, adolescents appreciated the therapists’ willingness to offer psychological support, during crises, remotely - usually via a phone call - outside scheduled sessions. In all cases, patients read this availability as a demonstration of understanding and genuine caring beyond the therapy room:\n\nCl. 1: “One evening, it was quite late, and I was at home; I had hurt myself and was really in a bad state and had these bad thoughts. I didn’t know what to do, so I wrote a message to (the therapist’s name) who, despite it being almost midnight, practically called me immediately. […] He made me understand that I shouldn’t worry, that we would talk about it, and he had found a place for me the next day. And he practically made me talk and made me say everything I was thinking at the moment and then said, ‘Okay, now try to relax, go to bed, sleep, and come here tomorrow morning.’ And that was probably the only thing I needed.”\n\nFlexibility of Session Frequency. Consistent with the previous category, this sub-theme supports the importance of flexibility in psychotherapy with adolescents and young adults. In particular, five participants positively valued the therapists’ willingness to adjust the frequency of sessions according to the specific needs of their clients. Here is an example:\n\nCl. 8: “There are times when I increased the frequency of my sessions. Sometimes I have nothing, other times I have a lot to tell. I move a lot, so sometimes I decrease, other times I increase (the frequency of sessions), and there have been times when I said ‘Enough’ to therapy. In my opinion, when you use it with the right consistency, that is, when you deal with a theme, then you can address others but in a much more relaxed way. Now, since I have fewer issues than before, I maintain psychotherapy mostly to get to know myself.”\n\nThe second theme includes events related to the definition of the purposes of therapy. This theme was divided into two sub-themes: how therapists addressed adolescents’ priorities, and how therapists were able to redefine the style and the purpose of therapy depending on adolescents’ changing needs.\n\nAddressing Adolescents’ Priorities. Eleven adolescents found the therapists’ promptness in assessing problems and identifying priority issues to be very effective. These patients appreciated the therapists’ ability to recognize the most urgent and pressing topics and to intervene on them. In some cases, breaking down the major problem - perceived as unsolvable - into smaller and more attainable parts allowed the adolescents to feel more capable and ready to address that problem.\n\nCl. 2: “I remembered something my therapist used to say, ‘When the house is on fire, first of all, you call the firefighters. After that, you think about discovering how it happened, why it happened, etc., etc., but not before … and then you’re okay, you’re calm, you’ve come out of the house, you’re serene.”\n\nRedefining the Style and Purpose of Therapy. Nine adolescents appreciated the therapist’s willingness to adapt the style of therapy according to their characteristics, needs, and most pressing issues to be addressed. In this regard, the therapist’s flexibility fostered patients’ perception of the therapeutic alliance as a unique and dynamic relationship, tailor-made for them and open to continuous renewal.\n\nCl. 9: “\"When I was younger, she (the therapist) guided me more in reasoning and explanations. Now, instead, we have a real trusting relationship, and I have matured. […] At the beginning, there were many strong issues that I brought up. For example, I couldn’t stay in class, couldn’t go out, and my anxiety limited me a lot. Once I went to the monumental cemetery, saw a grave, and collapsed to the ground. This is to make you understand how powerful my problem was, and she (referring to the therapist) encouraged me very concretely. Now, however, she doesn’t give me concrete advice anymore because she knows very well that I can figure it out on my own, and so the dialogue between us has become much more mature.” […] “I am the typical girl who presents problems in transitional phases, in change. For example, initially, I had a problem related to managing anxiety. Then, after finishing the academy to become an actress, I experienced burnout. I am always ‘Cyclical,’ as she defines me (referring to the therapist). At first, I didn’t know how to tell my parents that I wanted to be an actress, and that was a moment of change. After that, I had problems with panic attacks, I had blocks, couldn’t sleep … Then, I had an issue with the perception of my body.” […] “Once I overcame this block, it came back cyclically because of my work as an actress, where aesthetics are fundamental”.\n\nThe third theme pertains to situations in which therapists’ manner of “being in the room\" and personal attributes facilitated the development of a meaningful relationship with adolescents. Specifically, this category encompasses events that, from the adolescents’ point of view, played an important role in creating the perception of an engaging, interactive, and forthcoming therapist, capable of consistently “keeping adolescents’ best interests in mind.” Adolescents also appreciated events in which therapists shared their own versions of adolescents’ struggles, were perceived as authentic, emotionally responsive and shared the same traits or interests.\n\nActive Engagement. A substantial number of adolescents (n = 7) appreciated the active role of the therapist and emphasised its impact on satisfaction about therapy. In particular, this sub-theme refers to the therapist’s ability not only to listen and empathise with the young clients, but also to engage them by asking questions and showing interest in their narratives. In all cases, the therapist’s responsive approach reflexively fostered the patient’s curiosity, openness, and active involvement in therapy.\n\nCl. 5: “My therapist is a very unique person, even in terms of creativity; he has a lot of imagination, and I really love that. Despite the notion that creativity decreases with age, he always has so much, and probably, this is the most beautiful thing about my therapist.” […] “Um, he dives into the experience, into the moment he is living, so I never can say no to him; not because I feel obligated, but because I am so curious.”\n\nConstruction of Epistemic Trust. In the early sessions, 13 clients built trust in their therapist. They considered as significant therapist’s capacity to anticipate their emotions and behaviors. Consistent with this category, the concept of “Epistemic trust\" (Fisher et al., 2023) relates to the development of the client’s ability to regard knowledge conveyed by significant others, in this instance their therapist, as pertinent to themselves and applicable to other contexts (Campbell et al., 2021). Let’s examine one example:\n\nCl. 9: “It was nice because I thought, ‘Oh yes, this time she really understands me, gives me feedback.’ In short, to put it better, I could trust her because she ‘cradled’ me. I felt as if she were cradling me, ferrying me through what my situation was, also giving me advice on how to face my life.”\n\nSelf-Disclosure. This category refers to the role of the therapist’s self-disclosure, known as crucial in facilitating the building of a genuine and authentic relationship with clients (Audet & Everall, 2010). In five cases, the therapist’s self-disclosure allowed the adolescent to perceive him or her as a closer, credible, and trustworthy adult figure.\n\nCl. 2: “(referring to the therapist) She gave me examples from her life and also from her work as a therapist to make me understand that very often I had too many preconceived ideas about where life would take me, the decisions I had made, and that they were more like negative forces, while in reality, I didn’t know. […] The fact of seeing the things we worked on in her as well […] that is, (the fact of) giving me many examples of the idea of failure that I have and that maybe she also has. […] let’s say that certainly helped her credibility […]; because if she says, ‘Look, everything is fine, I know because I’ve experienced it, and it’s not like that. It doesn’t work that way.’ Life then becomes easier.” […] “Feeling in tune with the therapist at a certain point, maybe not regarding life goals but perhaps related to the same lifestyle, the same passions, was a beautiful thing. She was really excited and enthusiastic about the things I did because I felt that these were things she also enjoyed.\n\nAuthenticity of the Personal Relationship. Ten adolescents describe therapeutic relationships as an ongoing construction, with their therapists, of an authentic and personal relationship characterised by mutual openness. Young clients have reported building a strong bond with their therapist through the intimacy and complicity that developed in the early sessions. The emphasis reported by adolescents and young adults is on the perception of the therapeutic setting as unique and special, constructed specifically for them in the unfolding of the therapeutic relationship. Here, one example:\n\nCl. 11: “It was almost like talking to a friend when I told her things that had happened to me, and also how she reacted when I told her something funny, she laughed and played along, other times she advised me. Thanks to all this, complicity was created, so when I went to the sessions, I really wanted to tell her what had happened to me during the week. […] I think from the beginning, the way my therapist approached me made me perceive this complicity even though it matured over time.”\n\nEmotional Responsiveness. In six cases adolescents appreciated the therapist’s transparency in responding to some crucial moments of the therapy by showing their emotions to the clients. In particular, they perceived the therapist’s emotional response as an attempt to express closeness and humanity, in order to consolidate a more genuine and authentic relationship.\n\nCl. 8: “Something I have always appreciated about her (my therapist) is that she empathises a lot. I mean, when I told her about this thing (For instance, I often smell my grandfather’s scent in my dreams), I could see her visibly with teary eyes; not that she ever cried excessively, but she had that emotion, which perhaps hits you even more than crying when you feel that here (points to the chest) everything is warm. You sense (referring to the warmth) in the other person when you share a common emotion. Well, I could say that the thing that she and I often share is common emotions.\n\nAffinity with the Client. Four adolescents found a number of commonalities with their therapist’s idiosyncratic characteristics in terms of personality traits, life experiences, passions, and interests. In all cases, the adolescent’s discovery of similarities with the therapist came as a pleasant surprise that fostered the perception of greater closeness between the two.\n\nCl. 2: “In some way, another very positive thing, after ‘the bulk of the work,’ the most critical part had been overcome, that I noticed and liked a lot about my therapist, was the fact that in some way, as much as it was more like work she does on me, I felt like I had some affinity with her, you know!? So when I felt good, I felt that somehow she brought out the beautiful parts of me because she had them too. So the desire to travel, the desire to go on trips, particular adventures, things … I felt that she is like that because when she told me about her experiences (volunteering, travels, studies, etc.), I somehow felt connected; so it gave me the desire to do those things, right!? So a bit of affinity with the therapist is something that is positive, well.”\n\nThe fourth theme refers to the adolescents’ experience of collaboration with their therapists and has been found helpful in promoting the outcome of also very brief interventions (Aschieri et al., 2023). Collaboration with adolescent clients appeared to be a cross-cutting process, which ranged from working together around the meaning of the psychological assessment data, to the co-construction of new meaning during the sessions, to the individualization of the relationship with every client, and to allowing (a certain amount of) reciprocity of the care-taking process in the therapeutic dyad.\n\nCollaborative Use of Tests. Five clients reported enjoying discussing collaboratively with their therapists about their psychological testing before the onset of the treatment. This fostered adolescents’ curiosity in themselves and became an occasion to enhance the disclosure of their subjective experiences.\n\nCl. 11: “I have taken many tests, and I liked them because I didn’t feel the pressure to express myself without speaking directly in the moment. Still, I had the opportunity to work on certain things indirectly through these tests. […] Not having to speak directly, which I found challenging, was very helpful, especially when, after taking the test, we (my therapist and I) could discuss the results, etc. The tests also helped me better understand which areas to focus on and work on more.”\n\nCollaborative Meaning-Making. All adolescents reported that engaging in discussions with their therapist was beneficial to a better understanding of their issues. Dialogues with the therapist facilitated reflection on the relational context surrounding these issues and the analysis of their emotions and thoughts linked to them. This process enabled them to gain a clearer understanding of themselves.\n\nCl. 12: “Speaking, going back in time (the therapist) would ask me, ‘Why did this thing happen here?’ ‘What happened before?’ ‘Why do you feel this way?’ And I could give myself answers that probably, before, I thought about, but I didn’t connect all the dots.” […] “Analyzing certain situations, sitting at the table. My psychotherapist told me about what was happening to me, ‘Let’s understand, not just see the problem, what’s around the problem? […] It made me think.”\n\nPersonalization of the Therapist’s Relational Approach to the Client. Six adolescents perceived that therapists had tailored their relational approach to the unique characteristics of the patients resulting in a therapy process that is perceived as collaboratively defined by both parties. The perception of a customized work facilitated their active engagement in therapy and the building of a stronger relationship with their therapists. Here is an example:\n\nCl. 10: “I am a very open person, so this thing (the therapist) really met me halfway, and I am very happy about that. I think maybe, if I had been more shy or less extroverted, it might have taken me more time, or I might not have opened up completely. This is because a person with a different personality (than mine) might have difficulties in connecting. Thanks to this encounter, I must say that a connection was immediately created.” […] “(referring to therapy) It’s a quite personal thing because I believe that each person is unique. So, I think, yes, the thread of the journey should have a similar starting point for everyone, but then, in reality, it diverges and unfolds based on the individual you have in front of you, on the problem they bring. In fact, I felt (the relationship with the therapist) was something personal; I don’t think (referring to the therapist) it’s the same with others. It’s a personal way of relating.”\n\nReciprocity Between Client and Therapist. In five cases, the therapeutic relationship was strengthened by clients’ perception of a reciprocal engagement with their therapists. The adolescents emphasized their curiosity in their therapists’ lives, and, concurrently, the therapists’ willingness to share brief information about their daily lives. This mutual interest was viewed as helpful by the adolescents.\n\nCl. 5: “We got along very well, me and him (my therapist), really well. Yes, yes, I found him, and he probably found me. […] I don’t even realize it anymore since there are no more (boundaries), there are no more formal barriers; there haven’t been to the point that, even before starting the session, I ask him ‘How are you?’. First of all, because I’m interested in knowing how he is, how his week went, in a short time, of course, and then the session starts in full. It’s a beautiful bond, I’m happy, really happy.”\n\nThe fifth theme includes events centered on the adolescents’ emotions, thoughts, and self-representations. All participants recalled events in which they were helped having more understanding and compassion for themselves, less shame and a better emotional regulation. Adolescents experienced positive events in which their therapists accompanied them in exploring uncomfortable issues and themes, and validated their needs and desires towards more self-acceptance.\n\nUnderstanding of One’s Inner World. For the majority of the adolescents interviewed (n = 11) it was crucial to be supported by the therapist in analyzing their thoughts and emotions. This allowed them to “connect the dots\" and mature a coherent and meaningful understanding of their inner world.\n\nCl. 9: “This example is recent. I have had anxiety-related problems for a long time, and (my therapist) has practically suggested various ‘tricks,’ such as the ABC exercise, which is divided into different phases: situation, event, thought, etc … This helped me understand what the triggering thought (anxiety) was and what the (psychological) mechanisms underlying my behaviors and reactions are—not to avoid but to manage anxiety. (My therapist) helped me understand how, when you think about one thing, it can make you understand another, which, in turn, can be connected to another. So, thanks to these steps, you can understand why you are behaving in that particular way.”\n\nPositive Connotation. Positive connotation refers to the process whereby the therapist guides the client to re-read problematic and negatively judged behaviors in a different key, in order to construct a new self-narration. Specifically, the positive connotation allowed six adolescents to access a new perspective on psychopathology, as an attempt to adapt to intolerable conditions, rather than as a deficit.\n\nCl. 13: “I have never had complete, blind trust in other people; especially during that time, I expected to be stabbed in the back by anyone. Having someone (referring to the therapist) who at least understands the situation, didn’t blame me for that, was immediately beneficial. […] From the second visit I had, this negative perception (of people) disappeared because (my therapist) showed me she appreciated the value of that feature of my personality. Despite understanding my weaknesses, he chose not to use them to his advantage. […] During the second visit, the doctor read me the data that came out of the Rorschach test, and some of them, such as patience, were above the limits, that is, they literally scored the maximum points. And (my therapist) instead of telling me they needed to be corrected, said that I had to be very brave to be so patient and at the same time be so guarded from other people”\n\nAddressing Shame. A consistent number of adolescents (n = 8) talked about shame, recalling times when their therapists helped them overcome this emotion and its impact. In all cases, the therapists normalized shame, making sense of the distress caused by its symptoms or consequences, and making it understandable and accepted within the therapeutic relationship.\n\nCl. 1: “I was helped to be and find the real me, and to normalize things. This, in my opinion, was so important because, more than anything, we live in a world that shames people with issues, such as depression and depressive disorders, and sees them as crazy or similar, which is a completely wrong perception\" […] “(My therapist) didn’t make me feel the weight of the thoughts I had, like those about alcohol, suicide, or self-harm; he always somewhat normalized the issue, no matter how harsh and ugly it was\" […] “It’s precisely for this reason that I am still here now because, probably, if I had found another psychologist who had said, ‘No, don’t do this, do that, go, I’ll send you to psychiatry, goodbye,’ I would have felt shattered\" […] “So, when we find ourselves experiencing certain situations, we feel ourselves crazy and out of touch with the world, while he (the therapist) was good at making me understand that things were okay, it was normal after all, after so many things I had gone through; he managed to help me live through it with more serenity, and that helped me.”\n\nEmotional Regulation. In the majority of cases (n = 9), adolescents reported that working on emotions was crucial. In this regard, the therapeutic relationship enabled them to verbalize -and legitimize -a wide range of emotions that included also those “negative emotions\" that patients did not allow themselves to safely experience outside of therapy. In all cases, patients positively valued the help that therapists offered in terms of recognizing, accepting, and regulating the emotions which otherwise would have overwhelmed them and caused significant distress.\n\nCl. 7: “For example, I used to think for a long time that anger, as an emotion in general, was a bad, unpleasant, and unjustified emotion […] and I classified it as a ‘Bad emotion, you shouldn’t feel it.’ Over time, I realized that all emotions are worth experiencing and have their reasons.” […] “So, I’m trying to learn how to express anger.”\n\nExploring “Uncomfortable\" Issues. Nine adolescents talked about the importance of addressing uncomfortable topics with the therapist. These were embarrassing or disturbing topics that were taboo outside of therapy. Among them, sexuality was one of the most recurrent. Here is an example:\n\nCl. 8: “For example, (my therapist) would ask me, ‘What do you like, and how do you like to see yourself dressed? What made you discover a great pleasure for fashion?’ And I tried to answer those questions with her and put my answers into practice. For example, being a fairly feminist girl, at one point, (to the therapist) I even said ‘I masturbate,’ and she took it as an exercise, encouraging me.” […] “She also suggested that I go shopping alone, which was very difficult for me. I had panic attacks because I suffered from agoraphobia, which was really bothering me. From that moment on, I started to almost always go shopping alone, meaning it’s a moment I dedicate to myself.”\n\nPromoting Self-Acceptance. For a substantial number of participants (n = 8), reflection on the inner world fostered not only better self-understanding but also greater self-acceptance. In this regard, the mirroring function of the therapists helped them integrate emotions, thoughts and parts of self that had hitherto been denied, repressed or expelled. This process enabled the adolescents to construct a self identity that was complex, multifaceted but also integrated and structured.\n\nCl. 8: “For example, (my therapist) would ask me, ‘What do you like, and how do you like to see yourself dressed? What made you discover a great pleasure for fashion?’ And I tried to answer those questions with her and put my answers into practice.”\n\nThe sixth theme refers to events related with adolescents’ relationships outside the therapy. Four sub-themes emerged. In some cases, with the agreement of the adolescents, the therapist invited the parents or the significant others into sessions and worked directly with them. In other cases, the adolescents and therapists worked indirectly on these relationships, either by modifying for the representation of the relational environment or by suggesting alternative strategies for coping with others. Finally, when adolescents needed more support, therapists helped them to identify and involve additional attachment figures in their lives.\n\nWorking Directly with Parents and Significant Others. In four cases, adolescents benefited from the direct involvement of significant others in therapy. In particular, establishing contact with the patients’ parents was crucial. After ascertaining the adolescents’ consent, the therapists invited their parents into the session, involving them in a process sometimes parallel, sometimes joint with that of the young clients.\n\nCl. 8: “I believe that she (my therapist) understood that when I started therapy, the major difficulty was related to the fact that I wanted to become an actress, but my parents didn’t accept it […] so she had to establish a dialogue with them too. Yes, she invited them (to therapy) but without me. I mean, there has never been a confrontation all together. It was only a confrontation with them to better understand who they were. Well, this thing is great; I really liked it when she made me understand that some situations, behaviors, etc., were not just my mistakes when she took my parents and said to them, ‘Come and talk.’”\n\nWorking Indirectly with Parents and Significant Others. In other cases (n = 11), adolescents and therapists worked indirectly on the patients’ significant relationships outside of therapy. This sub-theme includes clients who reported that they changed the representation of their relational environment, modifying their perception of other people and the way they related to them.\n\nCl. 12: “Becoming aware that people cannot change but can improve. I have always tried to change people because they didn’t behave correctly with me, while she (referring to the therapist) once explained to me that I don’t have to change the person but try to make them think, to improve on certain things. Then there are those who want to do it and those who don’t. That’s a choice people make. Maybe I can take a step towards others by improving myself and automatically see a step from others towards me.”\n\nSuggesting Alternative Strategies for Coping with Adaptation Difficulties in the World. For a substantial number of participants (n = 8), being able to apply the outcomes of the therapeutic work to daily life was essential. In this regard, adolescents appreciated the therapist’s ability to support them in dealing with problematic issues in daily life by suggesting alternative coping strategies and assigning them concrete tasks. This increased the perception of the therapy’s effectiveness.\n\nCl. 8: “My mother is someone who wants a lot, controls a lot, and I am also someone who hyper-controls. Many times, she (my therapist) gave me specific tasks and even suggested that when I have a damn panic attack, I shouldn’t call my mother. From there, I noticed a significant and visible improvement. Sometimes she would say, ‘When this happens’ (referring to the panic attack), why don’t you call your dad?’ So, my therapist would say, ‘Involve your dad, talk to your dad,’ who, in fact, was a figure that I perceive as much quieter and with whom I clash much less, but with whom I struggled much more to be accepted on the artistic side. So, it was a concrete task for everyone (the whole family), even my sister who also suffers from panic attacks … “\n\nIdentifying and Involving Additional Attachment Figures. The last sub-theme refers to the therapist’s role in building a social support network around the patient. In two cases, the therapist helped in the identification of additional professional help figures (e.g., psychiatrist, educator) who, alongside the parental couple, enabled the adolescents to feel more supported in the treatment process and in daily life in general.\n\nCl. 3: “I understood what therapy is when the doctor also offered me another external support. At a certain point, he asked me if I felt the need to see someone, perhaps more often than him, who was an educator. […] We spent more hours together, talking about what I might say to the doctor in therapy and other things. Additionally, she physically helped me, or rather, supported me in my studies by giving me some methods to try or something like that.”\n\n\nDiscussion\n\nConsistent with Burton and Thériault (2020) and Hilsenroth et al. (2004), most of the adolescents who participated in this study attributed the cause of meaningful and constructive events in therapy to specific characteristics and actions of the therapist. All participants (N = 13) reported that significant events occurred a few months after the beginning of therapy (3-4 sessions), aligning with literature indicating the initiation of therapeutic alliance construction during this period (Burton & Thériault, 2020; Hilsenroth et al., 2004).\n\nThe six-themes derived from this study focus on several elements that our participants deemed relevant in their treatments. First, the emphasis on the management of therapeutic setting suggests that the therapists’ responsibility is to frame the “rules” of the sessions, stressing the importance of the definition of the “how\" rather than the “what\" (i.e., the content) (Safran & Muran, 2003) particularly when working with this type of clients. A common feature among sub-themes emerging in this domain, such as Definition of Privacy Boundaries, Availability Between Sessions and Flexibility of Session Frequency was their change with time. The boundaries of privacy, the availability of therapists between scheduled sessions and the frequency of the sessions were flexibly renegotiated between adolescents and their therapists, allowing a better fit between the structure of the therapy and the changing needs of clients.\n\nAlso the theme Definition of Therapy Goals and sub-themes Addressing Adolescent’s Priorities and Redefining the Style and Purpose of therapy stress the positive appreciation for a patient-centered care, in which therapists follow adolescents’ agendas and flexibly adjust the goals and the process with which the treatment is delivered to adolescents’ changing requests and needs. Specifically, eleven out of thirteen adolescents emphasized the significance of therapists’ ability to address their priorities. This finding aligns with recent literature on assessing and accommodating therapy to adult patients’ preferences (Cooper et al., 2023). Jacob et al.’ study (2022) found similar conclusions with adolescents. They underlined the importance of collaborative goal setting and agreement between young individuals and their therapists regarding personalized and meaningful outcomes on specific topics.\n\nThe theme Role of The Therapist stresses the importance, for adolescents clients, of some features that qualify their therapists’ behaviors and attitudes in treatment. The adolescents we interviewed appreciated events in which their therapists displayed their own personal characteristics and caring attitudes toward their clients in the therapeutic relationship (Egozi, Tishby & Wiseman, 2021). What emerges from the analysis of the sub-themes (Active Engagement, Construction of Epistemic Trust, Self-disclosure, Authenticity of Personal Relationship, Emotional Responsiveness, Affinity with the Client) is the relevance of the therapist’s self for adolescents. Being able to show care, interest, and responsiveness help adolescents develop trust in the importance of reaching their goals in therapy and attending carefully to the therapists’ views and advice. In the interviews we collected, affinity between clients’ and therapists’ personal features emerged at a later stage during the therapy, and it seems to be something that adolescents saw and built “on top” of their transformative experience, or at least after it started to unfold.\n\nThe Collaboration theme emerged in all interviews, and encompassed various activities, so that in our data it seemed to be a cross-cutting process that adolescents valued in many different circumstances, even when not explicitly mentioning it. In the sample of participants we interviewed, five adolescents completed with the same therapist a collaborative assessment prior to the onset of the actual treatment. Such assessment was explicitly considered by them as an integral component of their therapy, and was appreciated because it allowed adolescents to give their own versions of what the test scores mean for them, adding their individualised meaning to test data. The collaborative meaning-making, noticed by all participants, started in many cases from the discussion of the testing results in which therapists and adolescents tried to come up with joint understandings of the clients’ struggles observed through the lenses of assessment results. In other cases, collaborative meaning-making was conveyed by the use of open questions from the therapist, through which adolescents could make connections between previously unrelated aspects of their lives and experiences. Collaboration encompassed also the development of “ways of being in the room “unique to each adolescent-therapist dyad, and such intimate and deep connection was accompanied in some cases by an authentic care for the person of the therapist by the clients.\n\nThe fifth theme (Client’s Internal World) included processes that focused on the emotional, cognitive, narrative and representational aspects of adolescents’ functioning. The adolescents we interviewed appreciated being helped in developing greater self-understanding. The quality of the improved understanding about themselves seemed to have two specific features. First, it contrasted shame for their supposed inadequacies, either by normalising it or by judicious self-disclosures on the part of the therapist. Second, it framed symptoms, behaviors or problems that were previously deemed as “negative” by clients as smart adaptations to less-than-optimal environments provided them by their parents or social environment. Within this context of understanding, adolescents were able to appreciate the healing effect of sharing topics that were hard for them to address, regulate painful emotion with the support of the therapist, eventually accepting more of their experiences.\n\nThe Client’s External World theme underlined the importance of addressing directly and indirectly the context in which adolescents live their everyday life. Some adolescents we interviewed reported a benefit to the treatment from the real inclusion of their parents to some of the sessions. During such sessions, therapists helped adolescents and their parents to discuss problematic issues that were lingering in their relationships, and to attain better communication among family members. In some other cases, therapists helped adolescents to revise their view of their parents, or approach problems in their life differently, which led to a new way of dealing with issues outside the room of the therapy. Finally, adolescents appreciated the involvement and support from therapists when they felt that their relational network needed more structure and ressources.\n\nIt is important to consider some limitations of this study. Given the retrospective nature of this research, participants expressed experiences that occurred up to eight years before the interviews. The retrospective account of constructive and collaborative events might not be entirely faithful to what actually happened during the sessions. Instead, it could be a result of a reprocessing of events exposed to memory alterations and influenced by subsequent life experiences that over time contributed to giving a particular meaning to those events. Also, in this study we did not control for the overall satisfaction of clients for their treatments using valid measurement tools (Di Malta et al., 2023), hence it is unclear if the perception of positive events is influenced by the general evaluation of the whole treatment.\n\nThe limited size and variability in the composition of the sample could be considered a potential threat to external validity, limiting the generalizability of results from the interviewed sample to the broader population of adolescent and young adult patients. Considering the small number of participants, potential gender differences were not investigated. Additionally, due to the absence of cultural diversity among the study participants, the conclusions and implications of our study should be restricted to Italian clients. The study did not account for potential internal distinctions within the sample related to psychotherapy, such as therapist orientation, location of sessions, or the reasons for therapy. These variables could be investigated in future research to examine their role in patients’ experiences, offering a more precise and accurate description of their lived experiences.\n\nFuture studies could employ larger and more diverse samples, consider therapist characteristics and therapy settings, and incorporate more objective measures alongside qualitative narratives for a comprehensive analysis of therapeutic outcomes. Perhaps, most importantly, given the relevance of parents’ involvement in adolescents’ treatments, exploring their perspectives of what helps and what is hindering change in their children’s psychotherapy could be an interesting complement to the findings of this study.\n\n\nConclusion\n\nTherapy with adolescents can be a rewarding experience for therapists, but poses several challenges. How to keep in mind the family concerns for their children, foster alliance with the parents, and validate adolescents’ realization of the shortcomings of their environment? How to maintain the boundaries of privacy with adolescents when planning to do family sessions with their relatives? How to maintain a professional role with clients who highly value authenticity, openness and reciprocity in their treatment? How to be collaborative with adolescents, value their input in conjoint meaning making and also expand their views and self-understanding by adding information about their functioning?\n\nThe recent article by Calabrò, Cassera, and Aschieri (2024), addressing adolescents’ perceptions of hindering events in their therapies, illuminated several potential pitfalls for therapists when responding to these challenges. The current study indicated that therapists effectively navigated such obstacles, as reported by the participants, and helped to shed light on what adolescents valued in their therapy, offering an informative perspective on “what worked” in their treatment.\n\nWhen comparing the main findings of Calabrò and colleagues with the current study, first it becomes evident that the management of certain relational variables plays a crucial role in guiding therapy towards a positive trajectory. These variables include: the therapist’s alignment with the adolescent’s objectives, the utilization of diagnosis to enhance self-awareness and foster epistemic trust in clients, the incorporation of therapy into adolescents’ daily experiences rather than engaging solely in abstract discussions, the facilitation of open dialogue and collaboration encompassing both areas of agreement and disagreement between adolescents and therapists, and the demonstration of authentic care and concern for adolescents’ well-being by therapists.\n\nSecond, the interventions that were deemed as most positive were those protecting adolescents from their shame, and those that provided a new, more compassionate and understanding perspective on themselves. One could wonder if the lack of these interventions might have been connected with the shame, stigma, lack of internal motivation lamented by participants in Calabrò et al. (2024).\n\nThird, the management of the setting appears to hold significant importance. This includes remaining flexible to adolescents’ needs while ensuring session continuity, maintaining openness and a personalized approach while upholding clear boundaries between personal and professional lives, and involving parents in therapy while respecting confidentiality with adolescents. These tasks were identified by adolescents interviewed in both studies as the key focal points for therapists.\n\nThese seems to be common therapeutic factors in adolescents’ therapy and are present in different therapeutic approaches. As early as 1988, Fishman stated that “the most powerful therapeutic intervention at a social level for working with adolescents is family therapy\" (p.4) because the family is the “crucial point” in every adolescent’s life. In systemic family therapy, the goal of the intervention is to reframe the negative views of parents for “dysfunctional behaviors” of adolescents as symptoms of a larger set of needs in the family that need to be acknowledged and seen to promote the development of the system (Aschieri, Fantini, & Bertando, 2013).\n\nIn the Trauma-Focused Cognitive Behavioral Therapy (TF-CBT) model, parents play a key role in the ongoing care of the child. In an interview with thirty youths aged 11 to 17, Dittmann and Jensen (2014) found that it is important for children to recognize their parents’ ability to handle hearing about their experiences, as it can help restore the parents’ role as a “protective shield” (Pynoos, 1994). Although the youths valued confidentiality and predictability in what was shared during sessions, many found that sharing information was beneficial and appreciated.\n\nIn the 4-C model (competence, consent, confidentiality, and competing interests), it is important to discuss confidentiality with decision-making authorities, such as the child, parents, or guardian, before treatment begins (Sori & Hecker, 2006; Sparta & Koocher, 2006). As Koocher (2008) notes, successful therapeutic alliances rely on mutual trust and privacy of sensitive content (Harbour, 2004). It is essential to recognize the legal authority of parents or guardians and their interests in the child’s well-being, while aiming for a mutually acceptable understanding of confidentiality. Adolescents may prefer to discuss private matters, such as peer conflicts, school issues, smoking, alcohol, and sex, without their parents. Establishing clear boundaries around necessary secrets and when disclosures are necessary, such as threats of harm, helps clinicians negotiate acceptable limits with all parties at the beginning of treatment.\n\nAnother resource for therapists working with adolescents is the Therapeutic Assessment with families with adolescents’ model (TA-A; Tharinger et al., 2013). Despite being designed as a short-term consultation and presenting more research on its effectiveness with adult clients (Durosini & Aschieri, 2021), Therapeutic Assessment offers various solutions to navigate in the complexities of working with adolescents and their families.\n\nIn Therapeutic Assessment (TA-A), the central focus lies in addressing both parents’ questions about their child and adolescents’ questions about themselves. Within this framework, privacy boundaries are determined by the questions posed by participants. Specifically, assessors initially agree with adolescents to disclose all pertinent information to parents to address their queries about the adolescents. Simultaneously, assessors request parents to respect complete privacy regarding information concerning adolescents’ inquiries about themselves. This agreement enables assessors to collaborate with adolescents in exploring answers to all questions through testing and interviews, and to jointly plan the inclusion and shaping of responses to parents’ inquiries. Collaborating with adolescents in this manner helps them feel that the assessment prioritises their concerns, while also allowing parents to perceive that the therapist/assessor is addressing their own objectives. Building on this foundation, collaboration during the assessment progresses to individualizing tests interpretation based on adolescents’ input and to link their testing outcomes to life challenges, both identified by parents and recognized by adolescents themselves. Therapeutic Assessment (Finn, 2007; Fantini et al., 2022), rooted in intersubjective and humanistic psychology, encourages assessors to cultivate an open and supportive rapport with adolescents, embodying a balance between “compassion and firmness” (Finn, 2005) that aligns with adolescents’ need for support and guidance as well as their desire to gain insights into their psychological functioning. This model of authentic and collaborative involvement of adolescents and their families exemplifies a promising strategy for initiating and sustaining a productive therapeutic alliance, not only with adolescents but also with their families.\n\n\nEthics and consent\n\nThe study conforms to the Declaration of Helsinki on the Ethical Principles involving Human Participants, and research protocol was approved by the IRB of Catholic University of the Sacred Heart, [approval number #51-23; 25.05.2023]. Prior to each interview, the Informed written consent was collected from each potential participant (or from their legal guardians, if clients were younger than 18 years old) and L.C. addressed and discussed potential participants’ questions and comments about their participation in the study.", "appendix": "Data availabiltiy statement\n\nThe files, including the complete Italian verbatim transcripts of all the interviews, were uploaded to Figshare open access repository. Figshare: Transcripts of the interviews. Dataset. https://doi.org/10.6084/m9.figshare.26067931. (Aschieri, 2024).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nThe files, the semi-structured interview guide, were uploaded to Figshare open access repository. Figshare: Transcripts of the interviews. Dataset. https://doi.org/10.6084/m9.figshare.26067931. (Aschieri, 2024).\n\nAll extended data were uploaded to the Figshare open access repository. Figshare: Transcripts of the interviews. Dataset. https://doi.org/10.6084/m9.figshare.26067931. (Aschieri, 2024). They include the English version of: “Appendix A,\" which consists of all categories and their related verbatim; the individual tables related to the specific categories; participant information sheets; semi-structured interview guideline and consent form (adult and child version).\n\n\nAcknowledgements\n\nWe are grateful to Stephen E. Finn and Michael F. Troy for commenting and suggesting improvements to this manuscript.\n\n\nReferences\n\nAschieri F: Transcripts of the interviews. Dataset. figshare. 2024. Publisher Full Text\n\nAschieri F, Barello S, Durosini I: “Invisible Voices”: A Critical Incident Study of Family Caregivers’ Experience of Nursing Homes After Their Elder Relative’s Death. J. Nurs. Scholarsh. 2021; 53(1): 65–74. PubMed Abstract \| Publisher Full Text\n\nAschieri F, Cera G, Fiorelli E, et al.: A Retrospective Study Exploring Parents’ Perceptions of Their Child’s Assessment. Front. Psychol. 2024; 14: 1271746. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAschieri F, Fantini F, Bertrando P: Therapeutic Assessment with Children in Family Therapy. Aust. N. Z. J. Fam. Ther. 2012; 33(4):285–298. Publisher Full Text\n\nAschieri F, van Emmerik AAP , Wibbelink CJM, et al.: A Systematic Research Review of Collaborative Assessment Methods. Psychotherapy. 2023; 60(3): 355–369. Publisher Full Text\n\nAmerican Psychological Association: Ethical Principles of Psychologists and Code of Conduct. Am. Psychol. 2002; 57(12): 1060–1073. Publisher Full Text\n\nAudet CT, Everall RD: Therapist Self-Disclosure and the Therapeutic Relationship: A Phenomenological Study from the Client Perspective. Br. J. Guid. Couns. 2010; 38(3): 327–342. 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Publisher Full Text\n\nFantini F, Aschieri F, David RM, et al.: Therapeutic Assessment with Adults: Using Psychological Testing to Help Clients Change. Routledge; 2022. Publisher Full Text\n\nFinn SE: How Psychological Assessment Taught Me Compassion and Firmness. J. Pers. Assess. 2005; 84(1): 29–32. PubMed Abstract \| Publisher Full Text\n\nFinn SE: In our clients’ shoes: Theory and techniques of Therapeutic Assessment. Mahwah, NJ: Erlbaum; 2007.\n\nFisher S, Fonagy P, Wiseman H, et al.: I See You as Recognizing Me; Therefore, I Trust You: Operationalizing Epistemic Trust in Psychotherapy. Psychotherapy. 2023; 60(4): 560–572. PubMed Abstract \| Publisher Full Text\n\nFishman HC: Treating troubled adolescents: a family therapy approach. Choice Reviews Online. 1988; 26(3): 26-1807. Publisher Full Text\n\nGoodman G, Calderón A, Midgley N: Expert Clinicians’ Prototypes of an Adolescent Treatment: Common and Unique Factors Among four Treatment Models. Psychother. Res. 2022; 32(6): 792–804. PubMed Abstract \| Publisher Full Text\n\nGulliver A, Griffiths KM, Christensen H: Perceived Barriers and Facilitators to Mental Health Help-Seeking in Young People: A Systematic Review. BMC Psychiatry. 2010; 10. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGunlicks-Stoessel M, Mufson L, Jekal A, et al.: The Impact of Perceived Interpersonal Functioning on Treatment for Adolescent Depression: IPT-A Versus Treatment as Usual in School-Based Health Clinics. J. Consult. Clin. Psychol. 2010; 78(2): 260–267. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHarbour A: Understanding children and young people’s rights to confidentiality. Child Adolesc. Ment. Health. 2004; 9:187–190. PubMed Abstract \| Publisher Full Text\n\nHennink M, Kaiser BN: Sample Sizes for Saturation in Qualitative Research: A Systematic Review of Empirical Tests. Soc. Sci. Med. 2022; 292: 114–523. PubMed Abstract \| Publisher Full Text\n\nHilsenroth MJ, Peters EJ, Ackerman SJ: The Development of Therapeutic Alliance During Psychological Assessment: Patient and Therapist Perspectives Across Treatment. J. Pers. Assess. 2004; 83(3): 332–344. PubMed Abstract \| Publisher Full Text\n\nJacob J, Stankovic M, Spuerck I, et al.: Goal Setting With Young People for Anxiety and Depression: What works for Whom in Therapeutic Relationships? A Literature Review and Insight Analysis. BMC Psychology. 2022; 10(1): 171. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKohrt BA, Ramaiya MK, Rai S, et al.: Development of a Scoring System for Non-Specialist ratings of Clinical Competence in Global Mental Health: A Qualitative Process Evaluation of the Enhancing Assessment of Common Therapeutic Factors (ENACT) scale. Global Mental Health. 2015; 2. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKoocher GP: Ethical Challenges in Mental Health Services to Children and Families. J. Clin. Psychol. 2008; 64(5): 601–612. Publisher Full Text\n\nLabouliere CD, Reyes JP, Shirk S, et al.: Therapeutic Alliance With Depressed Adolescents: Predictor or Outcome? Disentangling Temporal Confounds to Understand Early Improvement. J. Clin. Child Adolesc. Psychol. 2017; 46(4): 600–610. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMarker CD, Comer JS, Abramova V, et al.: The Reciprocal Relationship Between Alliance and Symptom Improvement Across the Treatment of Childhood Anxiety. J. Clin. Child Adolesc. Psychol. 2013; 42(1): 22–33. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMarks D: Fostering Parental Growth and Enhancing the Therapeutic Alliance: Key Tasks for the Child Psychotherapist. J. Child Psychother. 2020; 46(1): 20–34. Publisher Full Text\n\nMidgley N, Guerrero-Tates B, Mortimer R, et al.: The Depression: Online Therapy Study (d:Ots)—A Pilot Study of an Internet-Based Psychodynamic Treatment for Adolescents with Low Mood in the UK, in the Context of the Covid-19 Pandemic. Int. J. Environ. Res. Public Health. 2021; 18(24): 12993. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPynoos R: Posttraumatic Stress Disorder. A Clinical Review. Lutherville, MD: The Sidran Press; 1994.\n\nRossouw TI, Fonagy P: Mentalization-Based Treatment for Self-Harm in Adolescents: A Randomized Controlled Trial. J. Am. Acad. Child Adolesc. Psychiatry. 2012; 51(12): 1304–1313.e3. PubMed Abstract \| Publisher Full Text\n\nSafran J, Muran J: Negotiating the Therapeutic Alliance: A Relational Treatment Guide. Guilford Press; 2003.\n\nSori CF, Hecker LL: Ethical and Legal Considerations When Counseling Children and Families.Sori CF, editor. Engaging children in family therapy: Creative approaches to integrating theory and research in clinical practice. Routledge/Taylor & Francis Group; 2006; pp. 159–174.\n\nSparta SN, Koocher GP: Forensic mental health assessment of children and adolescents. New York: Oxford University Press; 2006.\n\nStallard P: Evidence-Based Practice in Cognitive–Behavioural Therapy. Arch. Dis. Child. 2022; 107(2): 109–113. Publisher Full Text\n\nTharinger DJ, Gentry LB, Finn SE: Therapeutic Assessment with Adolescents and Their Parents: A Comprehensive Model.Saklofske DH, Reynolds CR, Schwean VL, editors. The Oxford Handbook of Child Psychological Assessment. Oxford University Press; 2013; pp. 385–420. Publisher Full Text\n\nTimmons-Mitchell J, Bender MB, Kishna MA, et al.: An Independent Effectiveness Trial of Multisystemic Therapy with Juvenile Justice Youth. J. Clin. Child Adolesc. Psychol. 2006; 35(2): 227–236. PubMed Abstract \| Publisher Full Text\n\nTong A, Sainsbury P, Craig J: Consolidated criteria for reporting qualitative research (COREQ): a 32-item checklist for interviews and focus groups. Int. J. Qual. Health Care. 2007 Dec; 19(6):349–357. PubMed Abstract \| Publisher Full Text\n\nWeisz JR, Kuppens S, Eckshtain D, et al.: Performance of Evidence-Based Youth Psychotherapies Compared with Usual Clinical Care: a Multilevel Meta-Analysis. JAMA Psychiatry. 2013; 70(7): 750–761. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWilmots E, Midgley N, Thackeray L, et al.: The Therapeutic Relationship in Cognitive Behaviour Therapy with Depressed Adolescents: A Qualitative Study of Good-Outcome Cases. Psychol. Psychother. Theory Res. Pract. 2020; 93(2): 276–291. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYoung DS, Casey EA: An Examination of the Sufficiency of Small Qualitative Samples. Soc. Work. Res. 2019; 43(1): 53–58. Publisher Full Text\n\nZilcha-Mano S, Dinger U, McCarthy KS, et al.: Does Alliance Predict Symptoms Throughout Treatment, or is it the Other Way Around? J. Consult. Clin. Psychol. 2014; 82(6): 931–935. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "322577", "date": "30 Oct 2024", "name": "Anna Sidis", "expertise": [ "Reviewer Expertise Youth Mental Health", "qualitative research", "lived experience research", "psychotherapy process 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 is an interesting study which brings forward the lived experience of adolescents and young people in therapy. Overall the work is clear and well presented, some areas for consideration are: 1) Given this is qual research, what is the theoretical framework you are applying to the research design and analysis? This should be briefly described in the method section. 2) The interviews are very short, this must be discussed as a limiting factor as typically qualitative interviews are 60-90 minutes in length. 3) The quotes included are very long, it may save space to really look closely at these and try to capture the essence within one or two sentences. 4) You have integrated your findings nicely with prior research, I wondered if you can say more about what your findings might challenge about previous knowledge, or what new learnings this study brings. How should/could clinical practice change as a result of the findings of this paper?\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? No\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-1025
https://f1000research.com/articles/12-1273/v1	05 Oct 23	{ "type": "Research Article", "title": "Analytical approach to piezoelectric model synthesis with the use of Cauer’s method for system design", "authors": [ "Jacek Harazin", "Andrzej Wróbel", "Andrzej Wróbel" ], "abstract": "Background: Piezoceramic materials have unique property which enables direct and bilateral conversion between mechanical and electrical energy. This ability facilitates significant miniaturisation of technology and opens many opportunities in design of new actuators and energy harvesters. Mathematical modelling of piezoelectric modules is notoriously hard due to complex constitutive equations defining mechanical and electrical energy conversion. Methods: The article presents research on a new synthesis method based on the Cauer’s method for electrical and mechanical system design. Mechanical damping is introduced with the use of Rayleigh’s approximation. A discrete electromechanical model is formed based on the Mason’s piezoelectric model. As an additional element of the research, a non-standard model analysis method using edge graphs and structural numbers is employed to investigate potential reductions in computational requirements for model analysis. Results: The electromechanical model analysis has shown an error of 5% in relation to the resonance target. The calculated peak in magnitude of displacement at the resonant frequency was well above the capability of a 3.5mm thick piezoelectric plate. The proposed non-standard method of analysis gave identical results in terms of obtained resonance frequencies. The calculated magnitude of vibrations was varying by 50 – 58%. Conclusions: The synthesis method presented in this paper allows an approximation of piezoelectric parameters of a real system based on the created mathematical model. Currently this method is subject to a considerable error in the determined vibration amplitudes of the system, but it allows a coarse approximation of the parameters while having a very limited number of input data. The additional method of analysis based on structural numbers offers a promising alternative to matrix calculations but requires a more thorough investigation of the computational power required to determine whether it can compete with existing algorithms.", "keywords": [ "piezoelectricity", "mathematical model", "synthesis" ], "content": "Introduction\n\nOne of the purposes of mathematical modelling in case of physics is to give a clear and systemic picture of relations and energy flow between elements of a system. Physicists use mathematical modelling to describe phenomena and problem solve the mechanics of a wide variety of systems.1 Mathematical synthesis supported by previous empirical analysis of underlying phenomena helps in creating models which describe real behaviour of materials and components with mathematical correlations. Deep understanding gained by thorough analysis can be later used in development of highly sophisticated systems that are used for precise control of various system variables.2 Systems that precisely control room temperature or humidity, systems responsible for engine control and its smooth acceleration or deceleration or systems used for active vibration cancellation are only few of the examples.3–6 Polynomial equations are great mathematical tools for approximation and interpolation of numerous phenomena which is why they are commonly used in mathematical modelling.7–9,10 Laplacian and Lagrangian algebra rely on polynomial and exponential equations to systemically represent components of force and energy having influence on successive derivatives of displacement or charge. Polynomial equations are among the main set of tools in control theory2,7–9,11–16 and were used during the development of signal filters composed of RLC (R – resistor, L – coil, C – capacitor) components.17,18\n\nWilhelm Cauer was among the pioneers of electrical model synthesis, creating algorithms based on transfer function polynomials, defining large range of electrical systems by using mathematical decomposition. Cauer synthesis17,18 relies on decomposing transfer function polynomials into continued fractions. The set of coefficients of a continued fraction represents values defining each system component properties (like impedance or capacitance). This procedure allows any transfer function of a complex system to be broken down into a series of components represented by a lumped model. Moreover, because of existing analogies between electrical and mechanical elements, this method can be applied to both electrical and mechanical models.7–9,11 Piezoelectric materials exhibit properties that can be described with a combination of interactions between both electrical and mechanical components.19 A set of constitutive equations for piezoelectricity12 has been established to describe electromechanical coupling for simple and inverse piezoelectric effect. Because of the complex set of dimensional relations, described by tensors, mathematical modelling of piezoelectric components is being focused mainly on the analytical aspect of this phenomenon. Researchers largely focus on modelling simple piezoelectric components with lumped models13,14 and matrix tensor equations20 or try to approach the problem using FEM (finite element method) analysis.21 There are also analytical methods that can be labelled as “non-classical” which rely on AI (artificial intelligence) algorithms or graphical representations of the system like “edge graphs”. Many of the developed models are used on a case-by-case basis where system variables defining piezoelectric behaviour are fully or partially known or they are being empirically determined.15,21–27 There is a small research gap when it comes to the subject of a full piezoelectric system synthesis where majority of the initial parameters are unknown. This article tries to focus on the development of a new method for piezoelectric system synthesis where the only initial information comes in the form of established resonant and anti-resonant frequencies. The algorithm based on Cauer synthesis method is used to construct an initial discrete mechanical model which serves as the base for piezoelectric model synthesis. Mechanical damping is introduced to the model with the help of Rayleigh’s method.28 The transition between purely mechanical model and a discrete electromechanical model of the piezoelectric plate is done with the combination of Mason’s model and analogies between mechanical and electrical components. There are many unknown piezoelectric parameters which have to be determined in this process. To solve this problem, authors have chosen an approach where most of the parameters are being approximated by using the obtained mechanical properties of an already synthesized system and a set of equations derived from the constitutive equations of piezoelectricity.\n\nPart of this article has been devoted to a study on the potential reductions in computational requirements for model analysis that might be possible when using edge graphs.7,8,11,29 Some methods based on edge graphs bare close naming resemblance like the ones used in15,22 which may cause confusion. As a matter of clarification, this article is focusing on the method using edge graphs in combination with structural number algebra. Structural numbers visually resemble matrix calculation as each structural number construct consist of rows and columns of numbers. The number of rows and columns, however, is tightly connected to the shape of an edge graph which a given structural number relates to. Each node in an edge graph and all its connections are represented by a single structural number vector (e.g.,\|1 2 3 4\|for a node connecting four edges numbered from 1 to 4). A structural number is then created by multiplying such node vectors by themselves according to structural number algebra. Arithmetic and logic operations based on structural number algebra were described in depth by professor Stanisław Bellert in his book.29 More details can also be found in previous article published by authors.30 The article also directly relates to adaptations of this method used by other researchers for analysis and synthesis of various systems.2,11,16\n\n\nMethods\n\nThe synthesis process begins with a selection of predetermined resonant and anti-resonant frequencies. The set of frequencies may be freely defined according to future applications or may result from a vibration spectral analysis of the object of interest. In this method, the identified set of frequencies is the only input information. It is used to generate a transfer function polynomial, which can later be transformed into a chain fraction equation. Cauer’s algorithm mentioned in Refs. 8 and 11 was used to create four different types of mechanical models depending on the allocation of coefficients in the chosen transfer function polynomial. Depending on the polynomial, the cascade model resulting from the chain fractioning process can be constrained on one end or not constrained at all. Additionally, the model can be excited by either a kinetic or dynamic force. A combination of those factors creates four different types of models with their own transfer functions (detailed examples of each type and associated transfer function structures are given in Refs. 8 and 11). The model chosen for the purposes of this article is a cascade model with one of its ends constrained and which is being excited by the dynamic force. The choice is motivated by the close resemblance of such a model to a fixed piezoelectric stack, where individual plates can be described as successive stages of the model. According to the models proposed in Refs. 8 and 11, a hypothetical transfer function for an infinite degree cascade model constrained on one end and excited with a dynamic force takes the factorial form:\n\nT(s) – response of a system,\n\nH – response amplification factor,\n\nω – consecutive frequencies (even are resonant and odd are anti-resonant),\n\ns – Laplacian variable.\n\nThe factorial form is transformed into a standard polynomial form to define the coefficients for successive powers of the equation:\n\nai – numerator coefficients,\n\nbi – denominator coefficients.\n\nAfter the initial calculation of the polynomial coefficients, the transfer function is converted into a continued fraction by using the Cauer’s method in its first form.17 The method involves breaking down a polynomial into a chain fraction using simple mathematical operations. The first form of Cauer synthesis is implemented by dividing the coefficient of the greatest power of a numerator by the coefficient of the greatest power of a denominator. The resulting fraction is being multiplied by the denominator and subtracted from the polynomial function, leaving the rest, which is then inverted. This process is repeated until all powers of the transfer function are reduced:\n\nIpi – fraction extracted by division of parameters next to the highest power “s”,\n\nRpi – rest of the original polynomial after subtraction.\n\nA continued fraction resulting from the process can be used to determine the values of discrete component parameters in the synthesized system:\n\nObtained values can be used in either mechanical or electrical cascade systems which gives this method a high degree of flexibility. An example of an infinite stage mechanical system resulting from the calculations have been shown in Figure 1.\n\nThe newly obtained mechanical model consists of springs and inertial components which can be used to determine the stiffness and mass/density of the piezoelectric material. Damping elements can be added to the model to account for energy dissipation which is an inherent property of piezoelectric materials. The mechanical quality factor is often used to indicate piezoelectric mechanical damping ability. The factor is inversely proportional to the amount of damping generated by the material and can be derived from Rayleigh’s method.28,31 However, damping introduces complex derivatives into the equations of motion for any mechanical or electrical system. Every system can be considered under the case of subcritical, critical, and over-critical damping. Depending on the strength of damping elements, a system can be in a state of damped oscillations (subcritical damping) or the oscillations may stop immediately after the harmonic excitation disappears (critical damping), they do not occur (over-critical damping). Because of that, there are three separate integral solutions that describe each case respectively. A resonance (additive interference of harmonic oscillations) occurs only under the case of subcritical damping. In order to limit the range of possible solutions, it was assumed that all models would only be considered under subcritical damping, thus eliminating cases where vibrations cannot resonate. The decision was made because the project was focused on piezoelectric applications where vibration generation was their main purpose. Another assumption limited the range of solutions to those with a Rayleigh damping coefficient related to stiffness. According to literature,24 most cases of piezoelectric damping are restricted to damping with respect to element stiffness only. The two assumptions simplify the term for the damping coefficient. Based on the obtained equations, it is then possible to determine the damping parameters for each stage in relation to the spring stiffness:\n\nβ – stiffness damping coefficient,\n\nbi – damping value,\n\nci – spring stiffness.\n\nTo verify the model in its current state, an intermediate electromotive force was also added at each stage. Its role was to simulate the actuation of piezoelectric plates by an electrical stimulus, similar to.15,25 The electromotive force acts as a simplified force generated by the electromechanical coupling used to describe the conversion of energy conversion between the mechanical and electrical part of a piezoelectric plate. The mechanical model with added damping and electromotive forces is shown in Figure 2.\n\nThe model masses are marked with “m” symbols, springs with “c” symbols, dampers with “b” symbols and electromotive forces with “G” symbols. The displacement of each mass was marked with “x”.\n\nThe synthesized model had to be verified after the addition of new damping elements and additional forces. An analysis of the model response was carried out in terms of its magnitude along the frequency axis. Two analysis methods were used to verify the existing mechanical model. The classical matrix method served as a reference for an additional method using structural numbers.2,11,16,29 The use of a second method is considered as part of the ongoing research30 aimed at evaluating the accuracy and computational load of structural numbers in comparison to the matrix calculation. Current state of the algorithm based on structural numbers should still not be considered as final as there are more improvements to be made in terms of its compatibility with computation software. Starting with the classical method, a set of equations of motion was created to describe relations between parts of the model. To avoid overcomplicating the example, only two degrees of freedom were considered. The equations of motion for a two-stage model derived from the Lagrangian equations were as follows:\n\nUnder the assumption into account, that the system is only considered in the case of subcritical damping, an integral of a second-order differential equation32 for the variable displacement x can be described by the equation:\n\nAi1 – real part of the ith element amplitude response,\n\nAi2 – imaginary part of the ith element amplitude response.\n\nCombining (9) with (10) and separating the components with sine and cosine coefficients, then reordering the equations by combining all the coefficients standing next to consecutive amplitudes, yields a coefficient matrix:\n\nBased on the obtained coefficient matrix (11) and a vector of actuating forces, a vector of amplitudes can be calculated. To obtain absolute displacement, the sine and cosine coefficient must be combined using Pythagoreans’ theorem:\n\nTo calculate phase-shift of each stage along the frequency spectrum, a tangent between the real and imaginary component of displacement can be calculated:\n\nThe set of derived equations (12,13) allows the amplitude response and phase shifts to be determined for any cascade system built using standard discrete elements representing model inertia, stiffness, and damping. Calculations are relatively quick and easy when considering systems with a small number of degrees of freedom. However, calculations become much more complex and computationally intensive for systems with a large number of degrees of freedom. This is an effect of the number of elements being multiplied in the determinant of a matrix. The numbers get big really fast because of the accumulation of the powers when all the matrix components are being combined. This problem prompted the search for alternative solutions for rapid analysis of more complex systems.\n\nOne of the alternatives to matrix calculations is being developed by the researchers at the Silesian University of Technology.2,7,8,11,16,29 The non-classical method of system analysis involves the use graphs and structural numbers to illustrate relations between forces in a system. The structural number method offers an alternative solution for deriving equations of motion by using a graphical representation of relations in the system. Each edge of the graph corresponds to a single discrete relation between two elements of a system, represented by nodes. All the edges and nodes in the graph are assigned numbers called “structural numbers”. These numbers form structures similar to matrices based on edge connections with nearby nodes. Using the algebra of structural numbers, it is then possible to derive a system of equations similar to equations of motion. A detailed description of this method in the context of solving mechanical cascade systems without damping was presented in Ref. 30. The structural number algebra is an entirely separate method of performing mathematical operations and therefore requires extensive explanation. It is strongly recommended to consult the book of the original author of this method29 for the details on its usage.\n\nIn the context of this article, several necessary changes had to be introduced to account for damping elements in the model. The basic method does not allow a simple decomposition of the sine and cosine coefficients when damping is present in the system. A standard approach includes resolving the equations with motion derivatives replaced with Laplacian transform. The issue arises when the final equation obtained with structural number algebra is turned back into its derivative form. When motion derivatives are replaced with the integral solution for sub critically damped motion as in (10), the equation becomes extremely tangled. To overcome this problem, an intermediate method has been developed, which realises the mentioned decomposition of sine and cosine components (10) prior to the application of the structural number algebra, Effectively, that means that the entire graph of relations was duplicated, separating the edges corresponding to sine and cosine coefficients. Each case is then being calculated separately until the last step. Both resulting graphs are shown in Figure 3.\n\nThe nodes of each graph represent the degrees of freedom of the model they are describing. Each edge corresponds to forces acting between each degree and is being described by the formula of elements creating each force. “ω” is the frequency, “m” is the mass of each element, “c” corresponds to spring loads and “b” to damping.\n\nThe structural numbers of both graphs are synonymous, the only difference being the opposite sign in the first derivatives of the sine and cosine function, which relate to the damping coefficients. As with the matrix method, the sine graph corresponds to the real part of the calculation and the cosine part to the imaginary part. This time, in order to obtain absolute values of the displacements, the merging (similar to (12)) has to be performed for the whole structural number and all the simultaneity functions.11,29,30 The amplitude response of each stage can be calculated by solving the equations:\n\nDsω – structural number for the sine graph,\n\nDcω – structural number for the cosine graph,\n\nAij – amplitude calculated with simultaneity function.\n\nThe process of obtaining the necessary structural numbers to derive equations (14–16) and the meaning of a simultaneity function has been explained in more detail in.29,30 The computer algorithm which was later used for this purpose is described in detail under the section dedicated to the algorithm testing.\n\nThe synthesized mechanical model serves as a basis for the construction of a combined electromechanical model of a piezoelectric system. Constitutive equations and analogy between mechanical and electrical components were used to derive parameters of the piezoelectric model.14,19,24,25 The electromechanical coupling coefficient for piezoelectric coupling perpendicular to the plate surface was determined based on resonant, anti-resonant frequency pairs:\n\nk33 – electromechanical coupling factor in the 3-3 direction,\n\nfa – anti-resonant frequency of a given stage,\n\nfr – resonant frequency of a given stage.\n\nA broader term defining electromechanical coupling for a general case, called an effective coupling coefficient was used to approximate the capacity of piezoelectric plates33:\n\nkeff – effective electromechanical coupling factor,\n\nCp – plate capacitance,\n\nCm – equivalent capacitance from mechanical stiffness,\n\ncm – mechanical stiffness of a lumped piezoelectric model.\n\nAnother property of a piezoelectric material frequently mentioned in specifications is the mechanical quality factor. This property describes the amount of energy that is being lost during dynamic operation of a piezoelectric plate. It corresponds to mechanical losses in a system. An approximate value of a mechanical quality factor can be calculated using the equation derived from the established Rayleigh’s method:\n\nElectrical permittivity can be also approximated if piezoelectric capacitance is known by using an equation:\n\nε33T – electrical permittivity of a piezoelectric material in 3-3 direction under constant stress,\n\nh – plate thickness,\n\nA – plate cross section field.\n\nLastly, based on the lumped stiffness of the mechanical model, a piezoelectric material stiffness can be obtained using Hooke’s law:\n\nc33E – piezoelectric stiffness in 3-3 direction under constant electrical field.\n\nTo analyse piezoelectric response with calculated parameters, a discrete electromechanical model was created based on the Butterworth-Van Dyke model and other lumped piezoelectric models available in the literature.13–15,34 The basic form of constitutive equations for piezoelectric effect in a 33 mode was used:\n\nD3 – electric displacement field,\n\nS3 – mechanical strain,\n\nE3 – electric field,\n\nT3 – mechanical stress,\n\nd33 – piezoelectric charge constant,\n\ns33E – mechanical compliance constant (inverse of mechanical stiffness constant).\n\nThe equation (24) was modified using Hooke’s law and by converting equations for underlying variables:\n\nBy combining the constitutive equations with (25,26) and plugging the equations of motion for the initial mechanical model (9) into the mechanical input of the electromechanical system, a lumped piezoelectric model was created. Relations inside a single piezoelectric plate are described by a system of equations:\n\nF – external force applied to a piezoelectric plate,\n\nU0 – external voltage applied to a piezoelectric plate,\n\nm – lumped piezoelectric mass,\n\nb – lumped piezoelectric damping,\n\ncm – lumped piezoelectric stiffness,\n\nUp – lumped piezoelectric capacitance,\n\nThe discrete piezoelectric model has been shown in Figure 4. Inputs and outputs were extracted from (27) by grouping parameters and converting the equation into a Laplace form. The resulting matrix was used to create an algorithm for piezoelectric model analysis:\n\n“F” represents an external force, “c” is the mechanical stiffness, “b” corresponds to damping, “N” is the electromechanical coupling, “C” is the electrical capacitance of the piezoelement and “U” represents the voltage exciting the circuit. “a,b,h” correspond to geometric dimensions of the piezoelectric element, while “x” represents the displacement.\n\nThe top left coefficient of the coefficient matrix (28) refers to purely mechanical transformations within the piezoelectric plate. Top right and bottom left coefficients refer to the electromechanical coupling. The bottom right coefficient refers to purely electrical transformations. The matrix can be easily expanded by adding more stages to the model as well as it can be calculated using the matrix method mentioned in (10).\n\nA series of computer programs were prepared to test the accuracy and computational load of used algorithms. All the programs were written using mathematical software called MATLAB in version R2019b (RRID:SCR_001622). The code was prepared using basic functions offered by the standard MATLAB suite.\n\nThe polynomial equation was created using “for” loops which added consecutive elements to its product form, depending on the number of frequencies given as an input. The MATLAB software operates interchangeably between the product form and exponential form of polynomials, so the conversion was done automatically. The Cauer synthesis was realised with basic program loops which continuously calculated the remainders of the polynomial function, as was explained with equations (3,4,5). Based on the order of elements in the resulting chain fraction, consecutive parameters in form of spring loads and masses were extracted from the equation in each iteration of the loop.\n\nThe analysis method using matrix calculations was realised by first creating the equations of motion (9) depending on the number of masses given as an input. The displacement was described using a substitute parameter “X” which then was replaced in bulk with derivatives of the sine cosine integral (10) by using MATLAB function “subs”. Next, the equations were transformed into a matrix form and solved with the inbuilt MATLAB solver. The input vector of external forces was used to manipulate the output amplitudes of the matrix formula.\n\nThe structural number method was constructed from ground up, using vector transformation operations inside MATLAB. The structural numbers were represented by matrices consisting of simple numbers corresponding to numbered graph edges. Each number was bound to a set of equations representing forces acting inside the system. The method of assigning numbers to equations was explained in.30 The structural number was formed by adding vectors (each vector consists of numbers corresponding to edges connected to a single graph vertex). The process was done using inbuilt MATLAB function called “combvec”. After that, several sorting operations were done in a loop to eliminate any repeats in the matrix representing the graph structural number. Further steps done to determine all simultaneity functions were also done by appropriately sorting and pruning the structural number matrix to create each structural number operation. To obtain final equations from the graph algebra, an intermediate step was introduced, which replaced each number with the equation that was bound to it. The step was also done using the “subs” function.\n\nThe eletromechanical system analysis was an extended matrix algorithm that was based on the equation (27). No new functions were introduced to make the algorithms and every step was made in analogy to the matrix method used to analyse purely mechanical systems.\n\nThe code has been saved in a proprietary MATLAB format “.mlx” and placed in repositories of Mendeley Data site.35,36 The code placed in the repository35 contains algorithms used for the synthesis of mechanical systems and their comparison through the matrix and structural number methods. The repository36 contains the algorithm used to synthesise and analyse a full eletromechanical model, simulating the real behaviour of a piezoelectric module. MATLAB is using an open standard for their file formats, so it is possible to open files using standard Windows tools. For reproduction purposes a user has to convert the extension of the file format into “.zip” and open its contents through the “.xml” file stored inside the package. It must be noted however, that the precision and calculation times may vary, depending on the type of software used to reproduce the results and even on the hardware used to process the computation tasks. It is also necessary to note that some of the code may have to be rewritten because of the use of MATLAB specific syntax that may be different in other software. For the sake of consistency and repeatability, all calculations were done on a single computer with a Ryzen 7 2700X processor and a 4 × 8 GB kit of DDR4 CL16 RAM clocked at 3000 Mhz.\n\nAlgorithms used to compare the precision and computation time of both matrix and structural number methods were published in an on-line repository.35 To compare the precision of both algorithms the chosen input data consisted of a collection of resonant (41 kHz and 55 kHz) and anti-resonant (47 kHz) frequencies. The frequencies were chosen arbitrarily based around a rough estimation of piezoelectric elements resonating at the lower spectrum of the possible range of resonating piezoelectric modules. The necessary system component parameters were calculated using the synthesis algorithm. The damping ratio was left at 100% and the scaling factor H was set to a value of 0.01. The dynamical forces were set to 1N of harmonic force with a cosine wave on both degrees of freedom. The program named “comparison”35 was used to compare the precision of both algorithms and produce the resulting graphs and calculate deviations for the extrema.\n\nA simple test was also carried out to check how computationally demanding are both methods in comparison to each other. For that purpose, two programs called “Matrix_method” and “Structural_number_method” were written in MATLAB R2019b. Both algorithms were written with a fixed set of model parameters and a fixed set of equations. To avoid long computation times, parameters were chosen for a two-degree system resonating at frequencies of 10 rad/s and 22 rad/s with an antiresonant frequency of 17 rad/s. The computation time was measured for both methods using the inbuilt MATLAB timer function “tic/toc”. The timer measured seconds that the program took to form the equation and calculate the amplitudes in both cases. Each program was run 10 times with the exact same settings and all calculation time measurements were noted down with an average time derived additionally. Before each run, all the variables generated in the previous runs were cleared to avoid any potential changes in computation speed because of reusing the stored results.\n\nFor the analysis of the electromechanical system, model with a single degree of freedom was chosen. The resonant frequency was 590kHz and the scaling factor H was set to 0.0025. The damping factor β was calculated from an existing mechanical quality factor Qm of 83 using equation (7) which was inversed. The remaining input parameters such as plate dimensions, plate stiffness and capacitance were either taken from an existing piezoelectric material specification or derived using the known physical properties (17-26) (http://www.steminc.com/piezo/PZ_property.asp). All parameters used in the case of this article are also contained in the program called “analysis_piezoelectric_system” in the on-line repository.36\n\n\nResults\n\nA comparison of the efficiency and accuracy of the two methods was done with the comparing program. A two-stage mechanical system with two resonant frequencies of 41kHz and 55kHz (257611rad/s and 345575rad/s respectively) was used for the comparison. The graphs in Figure 5 show the displacement amplitudes for both degrees of freedom of the considered case, obtained by matrix calculation and structural numbers.\n\nBlue line represents a response calculated with matrix method; red line represents the response calculated with structural number algebra.\n\nIt is clear that there are some differences between the results obtained by the two methods. To gain a better understanding, derivatives were taken from the model response equations to calculate the local extremes obtained by both functions. Table 1 gives a direct and relative comparison between the frequencies obtained with both functions. Table 2 gives the calculated values of the displacement amplitude for each characteristic frequency.\n\nThe nodal frequencies match perfectly, but there are significant differences in the amplitudes obtained around the second resonant frequency of the system in both stages. The alternative method using structural numbers is sufficient if the priority is only to check the nodal frequencies. However, when it comes to accuracy in terms of amplitude response, this method is subject to considerable error.\n\nAnother problem with the structural number method is that the authors were unable to establish the equations necessary to calculate the phase shifts in the system’s response.\n\nTable 3 shows the computation time and an average time from all measurements done on both algorithms based on matrix and structural number methods.35 The test showed that matrix method took an average of 13.972 s to calculate the amplitude response of a two-stage system. The alternative method took only 8.637 s on average, which is 38% faster than the classical method.\n\nThe discrete electromechanical model36 was verified on a system simulating the behaviour of a single piezoelectric plate with specifications very close to the real ones taken from (http://www.steminc.com/piezo/PZ_property.asp). The plate had to vibrate at a resonance frequency of 590kHz (3707079rad/s). Mechanical parameters of the plate were determined with the Cauer synthesis method. Piezoelectric plate dimensions were taken from (https://www.steminc.com/PZT/EN/piezoelectric-plate-45x45x35mm-55-khz). Resulting graph of an amplitude response for piezoelectric plate displacement and voltage were shown in Figure 6.\n\nThe model had a resonance near the frequency of 560 kHz (3516624 rad/s) which gives an error of 5% in relation to the resonance target. The calculated magnitude of displacement at the resonant frequency is 2.6 mm which is well above the capability of a 3.5 mm thick piezoelectric plate. The voltage shows a significant increase in piezoelectric voltage in the resonant region and a complete reduction near the frequency of 590 kHz which was supposed to be the original resonant frequency.\n\n\nConclusions\n\nThe aim of this work was to demonstrate a method that allows a piezoelectric model to be synthesized using only on a set of resonant/anti-resonant frequencies as the input data. The paper has shown that combining Cauer’s method of synthesis for mechanical or electrical networks with Rayleigh’s damping approximation and a variant of the Van Dyke-Butterworth model can yield a discrete electromechanical cascade model which parameters can be approximated to simulate the behaviour of a real piezoelectric component. This method differs from most other methods found in the literature13–15,19,24 in that it focuses on developing a new set of possible solutions based on a very limited information, rather than trying to break down a specific case under consideration. The ultimate goal of this method, which is under constant development, is to provide the ability to synthesize piezoelectric systems capable of resonating in a defined range of frequencies required for a target solution. An example application of such a method could be an attempt to scale up the active vibration cancellation technology to dampen vibrations generated by motors and engines. This technology is currently used in many audio solutions and new, larger piezoelectric resonators could be used for more industrial oriented projects. This method offers the possibility of constructing a piezoelectric stack of plates which have different material properties or geometrical sizes to create multiple resonant frequencies within a single module.\n\nThe method presented in this article relies heavily on mechanical model synthesis in its initial stage. In order to proceed with confidence, it was necessary to verify the mechanical model before using it in later stages of the work. However, for more complex systems the classical matrix calculation creates a significant computational load, which has the effect of significantly extending the computation time. An additional set goal was to develop an alternative method for mechanical system analysis using graphs and structural numbers. The presented alternative solution gave promising results in terms of computation time. The accuracy of calculated characteristic frequencies between the standard matrix method and the proposed alternative using structural numbers was on par in terms of calculated peaks near resonant frequencies. However, the calculated amplitudes differed significantly from those calculated using the matrix method, used as a reference. The issue was tested on different models and the inconsistency of calculated responses was random. In its current state the algorithm can be useful for verifying only the resonant frequencies of a model. This method definitely needs further fine-tuning and testing to correct the errors in the amplitudes obtained and to further verify the advantages indicated.\n\nThe final verification of the piezoelectric model has shown a small deviation from the target resonant frequency. An initial hypothesis is that this error could be corrected by applying a correction factor to the input frequency. A bigger set of tests on the algorithm has to be conducted to verify it. Another problem highlighted was the calculated amplitude response for the resonant frequency which was several orders of magnitude greater than the expected value of displacement for a plate of given thickness. The cause of this problem is currently unknown. It is suspected that the problem may be due to an error in the algorithm, or it may be caused by differences between the real piezoelectric parameters for a plate that is vibrating at its resonant frequency and its specification which is measured for a frequency of 1kHz. It is clear that this model needs more tests before it can be considered acceptably accurate. The reference plate specification (more information here) also didn’t contain enough data to reliably compare the results obtained from the model analysis. Only a rough comparison of material properties could be conducted. The data of specific plates such as their exact resonant or anti-resonant frequencies was sometimes missing as well as information about their intended mode of vibration (longitudinal, thickness wise) and related coupling factors. It is necessary to plan a series of empirical tests to obtain reference data more reliably for model validation.", "appendix": "Data availability\n\nReference data for the specific piezoelectric module has been sourced from a piezoelectric materials vendor: https://www.steminc.com/PZT/EN/piezoelectric-plate-45x45x35mm-55-khz.\n\nA list of detailed material properties used for algorithms and the electromechanical model analysis was taken from: http://www.steminc.com/piezo/PZ_property.asp.\n\nMendeley Data: Model algorithms. https://doi.org/10.17632/gdt8yr9m3d.4 35\n\nThis project contains the following data:\n\n- Comp_time_test.xlsx\n\n- Comparison_value_set.mat\n\nMendeley Data: Piezoelectric electromechanical model (first iteration), https://doi.org/10.17632/pydnfmkfdk.3 36\n\nThis project contains the following underlying data:\n\n- electromech_model.mat\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\nPalmgren E, Rasa T: Modelling Roles of Mathematics in Physics. 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Warszawa: WNT; 1968.\n\nHarazin J, Wróbel A: Research on a cascade model synthesis with the use of classical and non-classical methods in the context of new piezoelectric stack applications. Int. J. Mech. Sci. 2021; 12: 959–969. Publisher Full Text\n\nAdamowski JC, Nader G, Silva ECN: Effective Damping Value of Piezoelectric Transducer Determined by Experimental Techniques and Numerical Analysis. ABCM Symposium Series in Mechatronics. 2004; 1: 271–279.\n\nGiergiel J: Tłumienie drgań mechanicznych. Kraków: Wydawnictwo Akademii Górniczo-Hutniczej; 1984.\n\nTrindade M, Benjeddou A: Effective Electromechanical Coupling Coefficients of Piezoelectric Adaptive Structures: Critical Evaluation and Optimization. Mech. Adv. Mater. Struct. 2009; 16: 210–223. Publisher Full Text\n\nBuchacz A, Płaczek M: Modelowanie i badanie jednowymiarowych drgających układów mechatronicznych. Gliwice: Wydawnictwo Politechniki Śląskiej; 2011.\n\nHarazin J: Model algorithms. Mendeley Data. 2022. Publisher Full Text\n\nHarazin J: Piezoelectric electromechanical model (first iteration). Mendeley Data. 2023. Publisher Full Text" }	[ { "id": "222661", "date": "29 Nov 2023", "name": "Guangtao Lu", "expertise": [ "Reviewer Expertise Structural health monitoring by uisng lamb waves" ], "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 manuscript proposed a new approach for parameter estimation of piezoelectric structures based on the Cauer’s method, and its computational performance is compared with the traditional method. However, in my opinion, some concerns need to be addressed more clearly before it is considered for publication.\nWhat’s the main merit of the manuscript? It should be clearly addressed in the abstract, introduction and conclusion.\n\nTo compare the computational performance of the new model, the model response and computation time are compared with the matrix method. What are the errors of these two models? The two frequencies of the new model are compared with the ones of matrix method. Are the results of the matrix method accurate? What are the actual frequencies?\nIt is the same during the amplitude comparison. Moreover, to compare the computational performance of the algorithm, there are many metrics, such as time cost, the number of floating points (FLOPs) multiple adds (MAdds), and so on. In addition, what is the meaning of only decreasing the computation time?\n\nPage 4: “A combination of those factors creates four different types of models…” It refers to Refs. 8 and 11. However, Refs. 8 and 11 are published in non-English. Therefore, the details of the four models are suggested to be introduced in the manuscript.\n\nExperimental results: the results should be further analyzed.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "11319", "date": "13 Apr 2024", "name": "Jacek Harazin", "role": "Author Response", "response": "Thank you very much for the critical review and Your suggestions regarding the article clarity. I would also like to apologise for a long break before my reply. I have prepared several corrections to the article regarding your review and they will be published with the new version. I've also tried to address your querries to the best of my ability: 1. The article showcases a new method to synthesize cascading electromechanical models using the Cauer method coupled with Van Dyke-Butterworth models to represent piezoelectric stacks with clumped mechanical and electrical components. Each of those methods have been already used by researchers but i have found no literature on the particular approach presented in this article. The novelty revolves around the general approach to synthesis with very limited input information. Most researchers focus on specific applications where piezoelectric parameters and the analysed structure is largely known or predetermined experimentally. Here, only the frequencies are known and there is an infinite number of possible models that could realise those predetermined resonant frequencies. Coupled with further steps presented in the article, this method offers a possibility to design piezoelectric stacks with different material properties or geometric dimensions, capable of resonating in predetermined frequencies. 2. The predetermined frequencies and amplitudes were chosen arbitrarily and do not reflect any real piezoelectric system. A comparison between both analysis methods was done on the same model synthesized with the Cauer method. The matrix method was considered as a reference method because its a known and established way to calculate model response. The structural number method was compared against it and it was a pure comparison between two analytical methods. I was also made aware that a comparison of calculation time used exclusively is a bad metric for algorithm complexity. I have tried looking for more literature on the matter and added more references to the article. Given my abilities and available resources, i have prepared a second study which focused more on the memory criterion. I've used the available Matlab evaluation modules to estimate the average RAM usage between both algorithms on a variety of models, along with a comparison between the average time it took both algorithms to complete. I am aware that this method may also not be the best way to evaluate algorithm complexity and only presents a rough estimation. I will need to consult a specialist on that matter and conduct more tests but that would probably go beyond the scope of this article and should be contained in a separate paper focused only on the comparison between both methods. 3. I have provided additional literature references to publications of the authors involved in the development of the structural number method where they descibe mentioned models in english. I hope that will provide the necessary background which was lacking previously. 4. I agree and i can already attest that the method is currently being verified empirically. The synthesis method has been verified already with three real piezoelectric stacks with different geometrical dimensions which has shown some discrepancy between model results and real plate behaviour. The source of those differences was traced back to how some of the piezoelectric parameters are determined in the factory (under 1kHz wave stimulation) versus plate properties in the resonance proximity. However, i would like to envelope the empirical analysis, along with all the necessary test procedures and the test stand description in a second article, serving as the continuation for this study. I hope that i have provide an exhaustive explanation to the issues raised. Best Regards," } ] }, { "id": "222666", "date": "29 Nov 2023", "name": "Saurabh K. Yadav", "expertise": [ "Reviewer Expertise Mathematical 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\nThe manuscript proposes a new approach for parameter estimation of piezoelectric structures based on the Cauer’s method, and compares its computational performance with the traditional matrix method. The authors claim that their method can synthesize a piezoelectric model using only a set of resonant and anti-resonant frequencies as the input data, and approximate the piezoelectric parameters using the synthesized mechanical model and some physical equations. The authors also use a non-classical method based on structural numbers and edge graphs to analyze the mechanical model and reduce the computational load. The manuscript is well-written and organized, and the mathematical derivations are clear and rigorous. However, I have some concerns and suggestions that need to be addressed before the manuscript can be accepted for publication.\nThe main merit and novelty of the manuscript are not clearly stated in the abstract, introduction and conclusion. The authors should highlight how their method differs from the existing methods in the literature, and what are the advantages and limitations of their method.\n\nThe authors use a single piezoelectric plate as an example to verify their electromechanical model. However, the results show that the model has a significant error in the resonant frequency and the displacement amplitude. The authors should explain the sources of this error and how it can be reduced or corrected. Moreover, the authors should test their model on more realistic and complex piezoelectric structures, such as stacks, rings, beams, etc., and compare their results with experimental data or other numerical methods.\n\nThe authors compare the computational performance of their method with the matrix method using a two-degree system. However, this is not a fair comparison, as the matrix method can handle systems with any number of degrees of freedom, while the structural number method is limited by the complexity of the edge graph. The authors should compare the computational performance of both methods on systems with different numbers of degrees of freedom, and use more appropriate metrics, such as the number of floating point operations, the memory usage, the accuracy, etc.\n\nThe authors use some references that are published in non-English languages, such as Refs. 8, 11 and 29. The authors should provide English translations of these references, or use more accessible sources that are published in English. The authors should also update their literature review with some recent works on piezoelectric modelling and parameter estimation.\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": "11322", "date": "13 Apr 2024", "name": "Jacek Harazin", "role": "Author Response", "response": "Thank you for the critical review. I would also like to apologise for a long break before my reply. I have prepared several corrections to the article regarding your review and they will be published with the new version. I've also tried to address your concerns directly: 1. Let me repeat my answer to the second reviewer here, as it addresses the same concerns. The article showcases a new method to synthesize cascading electromechanical models using the Cauer method coupled with Van Dyke-Butterworth models to represent piezoelectric stacks with clumped mechanical and electrical components. Each of those methods have been already used by researchers but i have found no literature on the particular approach presented in this article. The novelty revolves around the general approach to synthesis with very limited input information. Most researchers focus on specific applications where piezoelectric parameters and the analysed structure is largely known or predetermined experimentally. Here, only the frequencies are known and there is an infinite number of possible models that could realise those predetermined resonant frequencies. Coupled with further steps presented in the article, this method offers a possibility to design piezoelectric stacks with different material properties or geometric dimensions, capable of resonating in predetermined frequencies. The limitation of this method is that it can only be used to synthesize models composed of components connected in series. So far, it can only be used to synthesise specific piezoelectric plate configuraions, where each component in a stack is responsible exclusively for a single resonant frequency set as the input. I have modified the article to better reflect those statements. 2. Following up from my response to the second reviever, I agree and i can already attest that the method is currently being verified empirically. The synthesis method has been verified already with three real piezoelectric stacks with different geometrical dimensions which has shown some discrepancy between model results and real plate behaviour. The source of those differences was traced back to how some of the piezoelectric parameters are determined in the factory (under 1kHz wave stimulation) versus plate properties in the resonance proximity. It has to be noted as well, that this method relies on a lumped representation of an otherwise continous system. The main issue of this approach is that the lumped parameters are approximations of the real parameters and an electromechanical model currently can't perfectly match the behavior of a piezoelectric plate, where the interactions and their magnitude changes between the layers of a single piezoelement. There are also boundaries between piezoelectric elements, made with adhesives and isolating layers, which also introduce many hidden variables in the real model behaviour. The presented method is still in its infancy and requires more testing and refinement. I would like to provide a consice report on the empirical results in a follow up article though, as including all the information about the procedure and test stand would make this article very bloated. 3. I was made aware that a comparison of calculation time used exclusively is a bad metric for algorithm complexity. I have tried looking for more literature on the matter and added more references to the article. Given my abilities and available resources, i have prepared a second study which focused more on the memory criterion. I've used the available Matlab evaluation modules to estimate the average RAM usage between both algorithms on a variety of models, along with a comparison between the average time it took both algorithms to complete. New suite of tests has uncovered more information about the structural number algorithm optimisation and shed some light on its shortcomings. I have modified the manusript to showcase the second study. I am aware that this method may also not be the best way to evaluate algorithm complexity and only presents a rough estimation and i will try to consult a specialist on the topic with an intent of providing some collaboration with more indepth information about algorithm complexity of the proposed method. 4. I have provided additional literature references to publications of the authors involved in the development of the structural number method where they descibe mentioned models in english. I hope that will provide the necessary background which was lacking previously. I hope that my response provides an exhaustive explanation to the issues raised. Best Regards," } ] } ]	1	https://f1000research.com/articles/12-1273
https://f1000research.com/articles/13-1018/v1	06 Sep 24	{ "type": "Research Article", "title": "Development of an educational model with a management approach to improve the competency of diabetes educator nurses; utilizing King's conceptual framework and goal attainment theory", "authors": [ "Asriadi Asriadi", "Krisna Yetti", "Enie Novieastari", "Dewi Gayatri", "Krisna Yetti", "Enie Novieastari", "Dewi Gayatri" ], "abstract": "Background Education for diabetes patients is not managed well by diabetes nurse educators because the competency of diabetes nurse educators is low, and the number of diabetes nurse educators in hospitals is not commensurate with the number of diabetes patients, which is much larger.\n\nMethods This qualitative phenomenological research uses an exploratory design. Twenty nurse managers and forty staff nurses who participated in the focus group discussion (FGD) were selected using purposive sampling. Nine staff nurses who participated in in-depth interviews were selected using the snowball method. The results of the FGD exploration and in-depth interviews produced components for developing an educational model with a management approach. The development of this educational model uses an input, process, output, and outcome approach. The input uses King’s conceptual framework approach, the method uses the theory of goal attainment and management functions, the output is the competency of nurses to educate diabetes patients, and the outcome is the health literacy of diabetes patients. This educational model was reviewed by three experts: a nursing management expert, a diabetes mellitus expert, and a health literacy expert.\n\nResults The educational model for Diabetes nurse educators with a management approach consists of five stages: 1) Educational planning includes identifying educational targets, strategy formulation, and situation analysis. 2) Organizing nursing resources includes strengthening the role of nurses as diabetes educators. 3) Nursing staff includes intraprofessional collaboration and collaboration between nurses and patient families. 4) Direction includes nurses’ motivation for diabetes patients and respecting the culture and values of diabetes patients. 5) Control includes evaluating nurse education for diabetes patients.\n\nConclusion This education model has five competencies, which are structured and systematic so that diabetes nurse educators have the competence to manage diabetes patient education: the personal system, interpersonal system, and social system influence nurse competency.", "keywords": [ "Education model", "Management Approach", "Competency", "Diabetes Nurse Educator", "King's Conceptual", "Goal Attainment" ], "content": "Introduction\n\nDiabetes educator nurses have an essential role in diabetes management education. Nurses have a precise position to educate diabetes patients because they accompany them more often than other professionals (Schwarzkopf et al., 2024). Education is a fundamental responsibility for nurses (Khazhymurat et al., 2023) so that diabetes patients have the knowledge and skills to live life (Clemens et al., 2021), fast well (Carroll, 2023), prevent acute and chronic complications (Yeşil & Çövener Özçelik, 2024).\n\nDiabetes nurse educators should have good competence in managing diabetes patient education (Khazhymurat et al., 2023) because it must provide information that is relevant to the patient’s condition (Anderson et al., 2021), evidence-based (Hecht et al., 2021), teaches survival skills (Ergun-Longmire et al., 2021), to take appropriate action (Pueyo-Garrigues et al., 2022). Diabetes nurse educators must have good communication (Khazhymurat et al., 2023), always motivate diabetes patients (Al Nadhiri et al., 2023), and be respectful and culturally sensitive (Korsah et al., 2022). In addition, they can work together with patients and families to increase patient compliance with the instructions taught (Taibanguay et al., 2019).\n\nThe limited number of diabetes educator nurses in hospitals is inconsistent with the much larger number of diabetes patients (Dickinson et al., 2021). The high work demands of diabetes educator nurses mean that education for diabetes patients is not managed well. The education for diabetes patients is not managed well due to the low competency of diabetes nurse educators to manage diabetes patient education (Hecht et al., 2021), so an educational model with a management approach is required. Suppose you integrate the management function into the education management of diabetes patients. In that case, the diabetes nurse educator works in a structured, systematic manner because the management function guides the diabetes educator nurse to carry out education at each stage, measure efficiency, and evaluate results (Piplica et al., 2024). Management of diabetes patient education requires in-depth understanding and an appropriate educational model for diabetes nurse educators. Therefore, research is needed to explore educational models with approaches so that management nurses have diabetes educator competence. Based on this phenomenon, researchers are interested in developing an educational model with a management approach that impacts the competency of diabetes nurse educators.\n\n\nMethods\n\nThis research with Qualitative phenomenological uses an exploratory design approach to explore nurses’ experiences in educating diabetes patients. The results of FGD exploration and in-depth interviews produced components for developing an educational model for diabetes nurse educators using a management approach. The development of this educational model uses an input, process, output, and outcome approach. The input uses King’s conceptual framework approach, the method uses the Theory of Attainment Goals and Management Functions, the output is the competency of nurses to educate diabetes patients, and the outcome is the Health Literacy of diabetes patients. The education model for nurse educators with a management approach was reviewed by three experts: a nursing management expert, a diabetes mellitus expert, and a health literacy expert. This process ensures that the research is high quality and reliable.\n\nWe selected participants for the focus group discussion (FGD) and in-depth interviews from three government hospitals located in three regencies in Indonesia: Hospital X in Palopo City, Hospital Y in Luwu Utara Regency, and Hospital Z in Soppeng Regency. We divided the focus group discussions (FGDs) at each hospital into two sessions: Session 1 for nurse managers, which included the top manager, middle manager, and first-line manager. Session 2 was for Staff Nurses. The FGD was conducted in a closed room, so those present were the FGD participants.\n\nThe researcher and participants had no previous working relationship. Participants were selected using the purposive sampling method. For nurse managers with the following inclusion criteria: 1) minimum two years of work experience in their field 2) minimum Bachelor’s Degree education. For staff nurses with the following inclusion criteria: 1) minimum level of Clinical Nurse II, 2) minimum education of D3 in nursing, and 3) work in the Diabetes patient care room. Selection of participants based on recommendations from hospital management.\n\nThe in-depth interview participants were staff nurses. The selection of participants used the Snowball Sampling technique. This method starts with one participant, who the first-line manager will recommend. Inclusion criteria are: 1) minimum level of Clinical Nurse II, 2) minimum education of D3 in nursing, and 3) working in a DM patient care room. The determination of participants rolled like a snowball. We stop data collection if the data shows saturation. Interviews were conducted face-to-face using a semi-structured method. Interview time 60-90 minutes/participant. Researchers use a recorder.\n\nThe first author conducted a focus group discussion (FGD) in July-December 2022. The first author was the moderator in the focus group discussion (FGD). The interviewers were the first author, a male, nursing doctoral student, a lecturer, and a nursing manager at the hospital. The first author has attended several trainings on qualitative research to support this research, such as qualitative research methods using Atlas.ti, Qualitative Research N-Vivo 12, and qualitative research using netnography.\n\nIn focus group discussions (FGD), researchers use key questions as a guide. Researchers assume that the key questions used are very effective in eliciting information from participants because supervisors have reviewed the key questions.\n\nThe focus group discussion (FGD) interview results were verbatim, analyzed, and reviewed by the supervisor. After obtaining supervisor approval, the focus group discussion (FGD) continued at the next hospital.\n\nAfter completing the focus group discussion (FGD) at three hospitals, in-depth interviews continued. Interviews were conducted in a semi-structured manner using an interview guide. Each participant was interviewed individually, face to face, lasting 60-90 minutes. Participants could request a break or reschedule the following interview as needed. After asking questions, the researcher allowed participants to share their experiences. After that, the researcher also clarified and developed queries as required. The researcher used a recording device to help interview participants. There was no repetition of interviews in this study. We reached data saturation with the 9th participant, and as there was no further information, no additional participants were recruited.\n\nTo increase the credibility of participant data, researchers strive to meet the criteria, namely credibility, dependability, confirmability, transferability, and authenticity. The first author recorded, transcribed, and coded all interview sessions. Researchers used field notes to record non-verbal participant responses if necessary. The transcribed data were returned to participants for confirmation and clarification before the data were explained. We analyzed all data using inductive thematic analysis, which included six stages: recognizing and transcribing data, coding data, compiling themes, reviewing prepared themes, naming and defining themes, and reporting results (Braun et al., 2019). Data from focus group discussions (FGD) and in-depth interviews were analyzed using the NVIVO Plus application.\n\n\nResults\n\nTwenty nurse managers from three hospitals participated in focus group discussions (FGD). All participants were married. 13-28 years of work experience. Education levels are bachelor’s degree and master’s degree. Forty staff nurses from three hospitals participated in this study. All participants were married. 5-21 years of work experience. Education level is D3 and bachelor’s degree. All staff nurses in the treatment room care for diabetes patients. Level clinical nurse levels II and III. There were no participants who refused to take part in this research.\n\nNine staff nurses from three hospitals participated in in-depth interviews. All participants were married. 9-13 years of work experience. All education levels are bachelor’s degrees. All staff nurses in the room care for diabetes patients, level clinical nurse levels II and III. There were no participants who refused to take part in this research.\n\nThematic analysis of the data collected revealed five themes: 1) Educational planning, 2) Organization of nursing resources, 3) Nurse staffing, 4) Nurse direction, and 5) Educational control. These five themes form the basis components of developing an educational model (Table 1).\n\n\n\na. Identify patient demographics\n\nb. Identify patient health literacy\n\n\n\na. Determination of educational goals to be achieved\n\nb. Determining educational methods that suit the patient's condition\n\nc. Choosing the suitable educational media\n\nd. Choosing the right educational time\n\n\n\na. Analyze the situation from the patient's side\n\nb. Analyze the situation from the Nurse's side\n\nc. Analysis of the situation from the hospital environment\n\n\n\na. Nurses' awareness deepens as an educator\n\nb. Management of each patient's education by the Nurse\n\n\n\na. Intraprofessional Collaboration\n\nb. Collaboration between nurses and patient families\n\n\n\na. Nurse motivation for DM patients\n\nb. Respect the culture and values of DM patients\n\n\n\na. Evaluation of nurse education for DM patients\n\nThe five themes are components of developing an educational model with a management approach integrated with King’s conceptual framework, Theory of Attainment Goals (King, 2016), and management theory. The development of this educational model begins with creating a draft educational model that uses an input, process, output, and outcome approach. The input uses King’s conceptual framework approach, the method uses the Theory of Attainment Goals and Management Functions, the output is the competency of nurses to educate diabetes patients, and the outcome is the health literacy of diabetes patients. Draft an educational model with a management approach (Figure 1).\n\nThe input stage integrates three things, namely patients, nurses, and the hospital environment, using King’s conceptual framework approach, namely the Nurse’s personal system, the interpersonal system between nurses and diabetes patients, and the social system, namely the hospital environment, hospital management policies, culture and the role of the patient’s family. This approach emphasizes that education does not only consider the patient’s condition but also involves the crucial role of nurses as diabetes educators, as well as aspects of the hospital environment and hospital management, as well as local culture/wisdom.\n\nThe process stage of integrating education with a management approach and Goal Attainment Theory includes perception, reaction, interaction, and transaction. This stage illustrates that implementing education with a management approach requires a perception. Diabetic patients provide perceptions to diabetes nurse educators, and communication transactions will occur between nurses and diabetes patients if both are actively involved in achieving goals. The output is on the competency of nurses to educate diabetes patients, and the outcome is an increase in the health literacy of diabetes patients.\n\nThe educational model with a management approach has a core circle as the central position, surrounded by five circles, and each circle’s colour has a meaning. The educational model with a management approach has a core circle as the central position, surrounded by five circles, and each circle’s colour has a meaning. In the circle, the Nurse’s competence in educating diabetes patients is placed in a central position. The circle’s core is white, which indicates the sincerity of the diabetes nurse educator in carrying out education. The first circle contains five competencies that diabetes nurse educators must have following the management function.\n\nOutside the circle, three systems influence the competence of diabetes nurse educators. 1) Personal nurse system: nurses’ commitment as diabetes educators, skills of nurses as educators, motivation of nurses, workload of nurses, work management of nurses, perceptions, reactions, interaction, and communication of nurses. 2) Interpersonal system: the relationship between diabetes nurse educators and patient, patient culture. 3) Social System: hospital environmental conditions, hospital management policies regarding nurse training as diabetes educators. Figure of an educational model with a management approach (Figure 2).\n\n\nDiscussion\n\nAn educational model with a management approach is used to improve the competency of diabetes nurse educators. There are five competency stages arranged systematically and structured, namely 1) Educational planning includes identification of educational targets, strategy formulation, and situation analysis. 2) Organizing nursing resources includes strengthening the role of nurses as diabetes educators. 3) Nurse staffing includes intraprofessional and nurse collaboration with patient families. 4) Direction includes nurse motivation for diabetes patients and respecting patient culture and values. 5) Controlling includes evaluating nurse education for diabetes patients.\n\nPlanning education by identifying educational targets, diabetes nurse educators are guided to 1) identify the demographics of diabetes patients (Ojurongbe et al., 2024) such as educational background, religion, ethnicity (Anwar et al., 2020), type of health insurance the patient has, employment, social status (Vamos & McDermott, 2021), address (village or city) (Aljassim & Ostini, 2020), age, especially the elderly, (Vafopoulou et al., 2024), patient room (Class III/ward, Class II, Class I, VIP). 2) Identifying patient health literacy using a questionnaire (Voigt-Barbarowicz & Brütt, 2020). 3) Identifying the patient’s ability to read and speak Indonesian (Muscat et al., 2021). Educational planning by identifying educational targets. Because each patient has different educational needs, diabetes nurse educators must identify educational targets so that educational planning is appropriate to the patient’s needs. In addition, the approach used is relevant and in accordance with the patient’s learning preferences.\n\nPlanning education by formulating strategies, diabetes nurse educators are guided to 1) determine the educational goals to be achieved (Ravik et al., 2023), 2) determine educational methods that are appropriate to the patient’s condition (Meyer et al., 2024), 3) determine the suitable educational media (Farooq et al., 2024), 4) determine the right educational time (Liao et al., 2023), 5) determine educational material (LaVela et al., 2022). Educational planning utilizes strategy formulation because it directs diabetes nurse educators to use appropriate strategies to increase learning effectiveness. Patients easily understand and apply the information taught.\n\nIn educational planning using situation analysis, the diabetes nurse educator is guided to 1) Analyze the situation from the diabetes patient’s perspective, such as pain problems (Zammit et al., 2023), anxiety (Shang et al., 2024), the patient’s experience of suffering from diabetes mellitus, the patient’s enthusiasm for receiving education (Linnavuori et al., 2024). 2) Analyzing the situation from the Nurse’s side includes the Nurse’s commitment as a diabetes educator to mastery of educational material (De Bellis et al., 2020). 3) Analyze the situation from the hospital environment, such as a quiet educational room, an educational room free from interference from other people, and facilities that support the implementation of education (Linnavuori et al., 2024). Educational planning is done by analyzing the situation of diabetes patients, diabetes educator nurses, and the hospital environment. The diabetes patients, diabetes educator nurses, and the hospital environment, are like a circle. The patient is the centre of education, and the diabetes educator nurse is the facilitator, whose quality and commitment influence the education process and results. A conducive hospital environment facilitates an effective education process.\n\nOrganizing nursing resources by strengthening the role of nurses as diabetes educators. Diabetes educator nurses are guided to 1) Manage their work so that every diabetes patient receives sufficient education (Linnavuori et al., 2024). 2) Sorting educational materials with other health professions (Teuwen et al., 2024). Organizing nursing resources by strengthening the role of nurses as diabetes educators so that diabetes educator nurses organize their work according to a priority scale. The priority scale can use patient flow management, namely information gathering, continuous triage, resource management, throughput management, and care oversight (Benjamin, 2024).\n\nStaffing, diabetes educator nurses are guided to 1) Collaborate intraprofessionally, and work solidly with other nurses (Weber et al., 2022). 2) Collaborate with the patient’s family (Vinarski-Peretz et al., 2023). Intraprofessional collaboration is needed to coordinate, share information regarding patient progress, adopt an integrated approach, and motivate each other. Nurses collaborate with patient families to support patients in making the right decisions.\n\nDirecting, the diabetes nurse educator is guided to 1) Motivate diabetes patients. Build positive relationships with patients in education (Zhao et al., 2023). 2) Respect patient culture and values (Maboko et al., 2024). 3) Educate patients using simple, easy-to-understand language and avoiding medical terms (Kovach & Pollonini, 2022). Diabetes nurse educators build positive and supportive relationships with patients. Nurses provide emotional support and appreciation if patients make progress. Nurses must be empathetic, active listeners and understand the concerns felt by patients. In addition, nurses must understand the patient’s culture and adapt educational methods and nursing interventions that align with the patient’s values and culture as long as they do not conflict with nursing theory. Nurses must maintain patient comfort in the education process.\n\nControlling, diabetes nurse educators are guided to 1) evaluate using the teach-back method (Hong et al., 2020); 2) repeat educational material if the patient shows signs of not understanding (Berghout, 2021); 3) complete documentation (Everett-Thomas et al., 2021). The teach-back method is used to ensure diabetes patients understand the information that has been taught. The patient is asked to repeat the information that has been trained using the patient’s own words. If the patient does not understand, the Nurse repeats the material that the patient does not understand. After completing the education, the Nurse documents the education process and the results of the educational Attainment s using a documentation sheet.\n\nKing’s conceptual system influences all stages of diabetes nurse educator competency. A system is a series of components connected through communication links that exhibit purposeful and directed behaviour (King, 2016). The three interacting systems (Nurse, patient, and environment) determine the physical and social environment in which humans operate (King, 2016). Educational planning is influenced by the Nurse Personal System, namely the commitment of nurses as educators, and influenced by the Nursing Social System, namely the atmosphere of the hospital/room environment and hospital management policy. The main focus of the Personal System is the individual as a unique and complex entity, considering personal characteristics, health needs, and environmental adaptation (King, 2016).\n\nThe organization of nursing resources is influenced by the Nurse Personal System, namely Nurse workload and Nurse job management. A high workload can cause burnout (Nining et al., 2024), and the quality of education decreases. Hospital management considers the number of diabetes educator nurses according to the number of diabetes patients and provides professional development training opportunities. Work management requires solid communication among team members.\n\nThe nursing staff is influenced by the Nurse Interpersonal System, namely the relationship between diabetes educator nurses and diabetes patients and cultural influences. The relationship between the diabetes nurse educator and the patient requires a balance between the diabetes educator nurse and the patient. Both must support each other, have the same enthusiasm, and utilize the culture of Sipakatau, Sipakalebbi, and Sipakainge. Sipakatau is mutual respect and respect for each other’s roles. Sipakalebbi is mutual glorification. Nurses glorify patients as individuals who need information, and patients glorify nurses as providers of nursing services. Sipakainge is a mutual reminder. The Nurse reminds the patient about diabetes management, and the patient conveys the desired educational needs.\n\nDirecting is influenced by the Nurse’s personal system, namely nurse communication. Nurses communicate with patients, from perception, reactions, interactions, and transactions to goal attainment (King, 2016). The Nurse’s perception of the patient’s situation, condition, and needs, getting a reaction to the information obtained. Information exchange occurs between diabetes nurse educators and diabetes patients (interaction) so that communication happens. Nurses communicate with empathy and a patient-centric approach. They are building a relationship of mutual trust and openness. Educational control is influenced by the Nurse’s Personal System, namely the integrity of nurses. The integrity of the diabetes nurse educator shows that all educational processes are documented accurately and completely. Nurses have strong work morals, tenacity, and consistency.\n\nThis research is related to the culture of nurse educators and diabetes patients. Participants in this research came from tribes in Eastern Indonesia. The limitation of this research is that none of the participants came from tribes in western Indonesia.\n\nPractical Implications: 1) The results of this research can be a practical guide for diabetes nurse educators or general nurses in hospitals to educate diabetes patients. 2) The research results can be a practical guide for nursing and medical students to learn about patient education in educational institutions.\n\nPolicy implications; 1) The results of this research can be used as consideration for hospital management to revise standard operational procedures (SPO) regarding diabetes patient education.\n\n\n\n1. Expand sample variations in terms of participant culture.\n\n2. Test the output of this educational model, namely the competency of diabetes nurse educators, including knowledge, skills, and abilities (instruments available).\n\n3. Test the outcome of this educational model, namely the health literacy of diabetes patients (instruments available).\n\nThis research has been approved by the Ethics Committee of the Faculty of Nursing, University of Indonesia, as proven by a Certificate of Passing Ethical Review Number KET-136/UN2.F12.D1.2.1/PPM.00.02/2022 dated 30 May 2022. In the research, participants voluntarily Signed the consent form before participating in this study. Researchers explain participants’ aims, benefits, risks of harm, rights, and obligations through a research explanation sheet. Researchers apply three primary ethical principles: respect for human dignity, beneficence and nonmaleficence, and the principle of justice.\n\nParticipants know that this research aims to develop an educational model for nurses. Researchers provide participants with a detailed explanation of the research objectives, procedures, potential risks, and benefits. The researcher assured the participant that his participation was voluntary, that he could humble himself at any time, and that it would not affect his performance assessment. We also encouraged participants to ask questions before providing consent.", "appendix": "Data availability\n\nFigshare: Development of an educational model with a management approach to improve the competency of diabetes educator nurses; utilizing King’s conceptual framework and goal attainment theory, https://doi.org/10.6084/m9.figshare.26779138.v2 (Asriadi, 2024).\n\nThis project contains the following data:\n\n1. Theme FGD\n\n2. Theme In-depth interview\n\n3. NVIVO result (FGD)\n\n4. NVIVO result (indepth interview)\n\nFigshare: Development of an educational model with a management approach to improve the competency of diabetes educator nurses; utilizing King’s conceptual framework and goal attainment theory. https://doi.org/10.6084/m9.figshare.26779138.v2 (Asriadi, 2024).\n\nThis project contains the following data:\n\n5. Participant Consent\n\n6. Research Explanation\n\n7. Interview Guidelines\n\n8. COREQ_checklist\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nWe are unable to share the transcript files and recordings due to an agreement with the participants, as stipulated and agreed upon in the informed consent and research explanation. These measures are implemented to uphold the integrity and confidentiality of the data, in accordance with research ethics standards. This is especially crucial as the participant statements contain sensitive content. The data supporting the findings of this study are available upon request from the corresponding author [adiasriadi99@gmail.com]. Access to the data will be granted to qualified researchers upon reasonable request and after signing a data use agreement. The data may only be used for academic and research purposes in accordance with relevant ethical approvals. Any request for data use beyond these purposes must receive additional approval from the corresponding author.\n\n\nAcknowledgments\n\nThank you to Lembaga Pengelola Dana Pendidikan (LPDP) Indonesia for the scholarship funding provided during our academic studies, which also helped us do this research.\n\n\nReferences\n\nAl Nadhiri M, Al Hashmi I, Alaloul F, et al.: Adherence to gestational diabetes mellitus (GDM) management plan among pregnant women in Oman: Predictors, barriers, and motivating factors. Diabetes Metab. Syndr. 2023; 17(5): 102766. 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PubMed Abstract \| Publisher Full Text\n\nDickinson JK, Burke SD, Traficano S: From Diabetes Educators to Diabetes Care and Education Specialists: Time for Change. ADCES Pract. 2021; 9(5): 52–55. Publisher Full Text\n\nErgun-Longmire B, Clemente E, Vining-Maravolo P, et al.: Diabetes education in pediatrics: How to survive diabetes. Dis. Mon. 2021; 67(8): 101153. PubMed Abstract \| Publisher Full Text\n\nEverett-Thomas R, Joseph L, Trujillo G: Using virtual simulation and electronic health records to assess student nurses’ documentation and critical thinking skills. Nurse Educ. Today. 2021; 99(January): 104770. PubMed Abstract \| Publisher Full Text\n\nFarooq M, Farooq M, Atiq N, et al.: Social media as a clinical, educational and networking tool for neurosurgeons: A systematic review of literature. J. Clin. Neurosci. 2024; 126(July): 256–264. PubMed Abstract \| Publisher Full Text\n\nHecht L, Meyer G, Steckelberg A: A survey on critical health competences among diabetes educators using the Critical Health Competence Test (CHC Test). BMC Med. Educ. 2021; 21(1): 96–98. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHong YR, Jo A, Cardel M, et al.: Patient-Provider communication with teach-back, patient-centered diabetes care, and diabetes care education. Patient Educ. Couns. 2020; 103(12): 2443–2450. PubMed Abstract \| Publisher Full Text\n\nKhazhymurat A, Paiyzkhan M, Khriyenko S, et al.: Health education competence: An investigation of the health education knowledge, skills and attitudes of nurses in Kazakhstan. Nurse Educ. Pract. 2023; 68: 103586. PubMed Abstract \| Publisher Full Text\n\nKing IM: Toward a thery for nursing: general concepts of human behaviuor.2016; 72(6): 1–23.\n\nKorsah KA, Dyson S, Anthony D: Experiences and cultural beliefs of patients with diabetes: Lessons for nursing practice, education and policy. Int. J. Afr. Nurs. Sci. 2022; 16(September 2021): 100392. Publisher Full Text\n\nKovach JV, Pollonini L: Designing devices to communicate effectively with intensive care nurses to prevent pressure injuries: A qualitative study. Intensive Crit. Care Nurs. 2022; 71(August 2021): 103244. PubMed Abstract \| Publisher Full Text\n\nLaVela SL, Pellegrini C, Heinemann AW, et al.: Development and evaluation of an educational curriculum for healthcare providers on overweight/obesity management in individuals with spinal cord injury based on diverse stakeholder engagement. Disabil. Health J. 2022; 15(4): 101362. PubMed Abstract \| Publisher Full Text\n\nLiao YS, Tsai WC, Chiu LT, et al.: Educational attainment affects the diagnostic time in type 2 diabetes mellitus and the mortality risk of those enrolled in the diabetes pay-for-performance program. Health Policy. 2023; 138(February): 104917. PubMed Abstract \| Publisher Full Text\n\nLinnavuori E, Inkeroinen S, Kostylev A, et al.: Delivering Patient Education in Healthcare Organizations: An Integrative Review of the Nursing Administrative Actions. J. Nurs. Manag. 2024; 2024: 1–19. Publisher Full Text\n\nMaboko DR, Armstrong S, Casteleijn D: Patient perceptions of nurses’ cultural competence in public sector hospitals in Gauteng. Health SA Gesondheid. 2024; 29: 1–14. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMeyer R, Kotnis SR, Fog-Petersen CMØ, et al.: Steps to construct educational interventions on sexual dysfunction for healthcare professionals and patients. Experiences from the SECRET research study-group. PEC Innov. 2024; 5(May): 100310. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMuscat DM, Costa DSJ, Nutbeam D, et al.: Developing performance-based measures of health literacy: A narrative case study and checklist of considerations. Patient Educ. Couns. 2021; 104: 2406–2411. PubMed Abstract \| Publisher Full Text\n\nNining S, Hariyati RTS, Nuraini T, et al.: An exploration of burnout among hospital first-line managers in Indonesia during the COVID-19 pandemic. F1000Res. 2024; 13: 602. Publisher Full Text\n\nOjurongbe TA, Afolabi HA, Oyekale A, et al.: Predictive model for early detection of type 2 diabetes using patients’ clinical symptoms, demographic features, and knowledge of diabetes. Health Sci. Rep. 2024; 7(1). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPiplica D, Peronja I, Luković T: Controlling in the Function of Management By Objectives. DIEM Dubrovnik International Economic Meeting. 2024; 9(1): 131–142. Publisher Full Text\n\nPueyo-Garrigues M, Pardavila-Belio MI, Canga-Armayor A, et al.: nurses’ knowledge, skills and personal attributes for providing competent health education practice, and its influencing factors: A cross-sectional study. Nurse Educ. Pract. 2022; 58: 103277. PubMed Abstract \| Publisher Full Text\n\nRavik M, Aase I, Akerjordet K, et al.: Nurse educators’ suggestions for a digital educational resource suitable for undergraduate student nurses’ placement studies: Qualitative empirical research. Nurs. Open. 2023; 10(8): 5433–5445. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSchwarzkopf D, Bloos F, Meißner W, et al.: Perceptions of Quality of Interprofessional Collaboration, Staff Well-Being and Nonbeneficial Treatment: A Comparison between Nurses and Physicians in Intensive and Palliative Care. Healthcare (Switzerland). 2024; 12(6). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShang W, Li Y, Sun Y, et al.: Dose-response association of sleep duration with anxiety symptoms in Chinese type 2 diabetes mellitus. PeerJ. 2024; 12: e16954–e16918. Publisher Full Text\n\nTaibanguay N, Chaiamnuay S, Asavatanabodee P, et al.: Effect of patient education on medication adherence of patients with rheumatoid arthritis: A randomized controlled trial. Patient Prefer. Adherence. 2019; 13: 119–129. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTeuwen CJ, Kusurkar RA, Schreurs H, et al.: Interprofessional collaboration skills and motivation one year after an interprofessional educational intervention for undergraduate medical and nursing students. BMC Med. Educ. 2024; 24(1): 210–269. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVafopoulou E, Christodoulou N, Papathanasiou IV: Treatment Adherence and Quality of Life Among Elderly Patients With Diabetes Mellitus Registered in the Community. Cureus. 2024; 16(4): e58986. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVamos SD, McDermott RJ: Rebranding School Health: The Power of Education for Health Literacy. J. Sch. Health. 2021; 91: 670–676. PubMed Abstract \| Publisher Full Text\n\nVinarski-Peretz H, Mashiach-Eizenberg M, Idilbi N, et al.: Service Climate and Nurses’ Collaboration with Families of Older Patients in the Care Process during Hospitalization. Healthcare (Switzerland). 2023; 11(18). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVoigt-Barbarowicz M, Brütt AL: The agreement between patients’ and healthcare professionals’ assessment of patients’ health literacy-a systematic review. Int. J. Environ. Res. Public Health. 2020; 17(7). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWeber CE, Kortkamp C, Maurer I, et al.: Boundary Work in Response to Professionals’ Contextual Constraints: Micro-strategies in Interprofessional Collaboration. Organ. Stud. 2022; 43(9): 1453–1477. Publisher Full Text\n\nYeşil F, Çövener Özçelik Ç: The development of health literacy scale for acute complications of diabetes for children with type 1 diabetes (8–12 years). J. Pediatr. Nurs. 2024; xxxx. PubMed Abstract \| Publisher Full Text\n\nZammit A, Coquet J, Hah J, et al.: Postoperative opioid prescribing patients with diabetes: Opportunities for personalized pain management. PLoS One. 2023; 18(8 August): e0287697–e0287614. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhao M, Li H, Wang J, et al.: The effectiveness of motivation-guided PDCA cycle nursing for self-management ability and outcomes of patients with gestational diabetes mellitus. Nurs. Open. 2023; 10(9): 6509–6516. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "326258", "date": "07 Oct 2024", "name": "Mostafa Shaban", "expertise": [ "Reviewer Expertise Nursing", "geriatric", "community health", "public health", "agieng", "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\nSample Diversity: Although the model is culturally tailored, the study’s limitation to Eastern Indonesian nurses is acknowledged. Including a more diverse sample would strengthen the generalizability across Indonesia and similar contexts. Details on Model Implementation: The manuscript would benefit from a clearer explanation of how the educational model can be operationalized. Concrete examples or step-by-step instructions on implementing each stage could make the model easier for other institutions to replicate. Outcome Measurement: While the paper proposes improving competencies, it does not include objective measures of the model’s effectiveness on nurse competency or patient outcomes. Adding a quantitative evaluation or future research recommendations for outcome-based validation could add robustness. Ethical Considerations Expansion: The ethics section is thorough but could address potential bias from purposive sampling and the researcher’s role during FGDs. Reflexivity statements might clarify how these factors were mitigated.\nRecommendations\nInclude Pilot Testing: A pilot test of the model could provide valuable insights and confirm its usability in practice before a broader implementation. Expand on Control and Evaluation Techniques: More details on how to assess and document the success of each stage (e.g., using specific competency indicators) could enhance the utility of the model. Address Limitations: Future work should explore how this model might be adjusted for diverse cultural settings beyond Indonesia and adapt components accordingly.\nyou can benefited expand your introduction using the following citations (Shaban et al., 2024)(Ref-1)\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\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": "12581", "date": "09 Oct 2024", "name": "asri adi", "role": "Author Response", "response": "Thank you for your valuable suggestion. I am currently conducting a pilot test to implement this educational model. The results from this pilot test will provide important insights into the model's usability in practice before broader implementation. I plan to publish the findings from this pilot test in this journal as part of the next phase of the research. I will include a table outlining the specific competencies and the measurement methods used to assess them at each stage of the model's implementation. This will provide a clear overview of how the success of each stage is evaluated. Although I have used local Eastern Indonesian culture as the foundation for this model, such as the principles of Sipakatau (mutual respect for humanity), Sipakalebbi (mutual appreciation), and Sipakainge (mutual reminders), I believe these values are universal and can be applied globally. These principles reflect the essence of humanity and can be adapted across various cultural contexts to support the broader implementation of this model." } ] }, { "id": "334166", "date": "18 Nov 2024", "name": "Nermin Olgun", "expertise": [ "Reviewer Expertise A faculty member (Prof.Dr) in Internal Medicine Nursing", "I have also been working in the field of Diabetes Education Nursing in Turkey for 30 years and I am the President of the Turkish Diabetes Nursing Association. In Turkey", "we are also conducting studies using nursing concepts and theories", "as in this article", "to develop Diabetes Education Nursing. I think it is a sample research article for diabetes education nurses." ], "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 strength of this study is that it is a qualitative phenomenological study It aims to improve the competence of diabetes nurse educators using King's conceptual framework and goal attainment theory In the development of this educational model, the input, process, output and outcome approach was used This educational model was evaluated by a nursing management expert, a diabetes mellitus expert and a health literacy expert. For these reasons, I think it would be appropriate to approve the article. A brief summary of the article and its findings The researchers put forward the rationale for the study as the low competence of diabetes nurse educators and the low number of diabetes nurses in hospitals and the low number of diabetes patients, which is why diabetes education, which is very important for diabetic patients, is not done well. The study is qualitative phenomenological research and an exploratory design was used. The results obtained with the experts participating in the focus group interview produced components for the development of an educational model with a management approach. In addition, King's conceptual framework and goal attainment theory were used in the study. As a result of the study, the training model created for diabetes nurse educators consisted of 5 stages: 1) Education planning, 2) Arrangement of nursing resources, 3) Interprofessional collaboration between nursing staff, nurses and patient families, 4) Orientation, motivation of nurses towards diabetic patients and respect for the culture and values of diabetic patients, 5) Control, evaluation of nurse education. As a result of the study, it was concluded that the developed training model has five structured and systematic competencies and nursing competencies, namely personal system, interpersonal system and social system, which will enable diabetes nurse educators to have the competence to manage diabetes patient education. Strengths and/or weaknesses of the article Strengths of the research • The researchers put forward that diabetes education, which is very important for diabetic patients, cannot be done well due to the low competence of diabetes nurse educators. This is why this study was conducted. Diabetic education is extremely important for diabetic patients to manage their diabetes. In order for these trainings, which include skill development and lifestyle formation, to be successful, structured trainings are needed. In this study, the fact that the training was structured and systematic based on a model and had 5 very important competencies are among the strengths of the study. The study will contribute to the literature in this respect. • King's conceptual framework and goal attainment theory were used in the study. • The study used a qualitative phenomenological research and exploratory design. • The research results can be an example for diabetes nurses to create new education models. Weaknesses of the research • It was stated that the participants in this research came from tribes in Eastern Indonesia. Therefore, the research results cannot be generalized to all groups. Or the model they developed cannot be used everywhere and, in all cultures, • Since it was a focus group interview, the data refers to the participants there and the opinions refer to the opinions at that time. It cannot be generalized.\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/13-1018
https://f1000research.com/articles/13-1016/v1	06 Sep 24	{ "type": "Research Article", "title": "Influence of Kinesiophobia on muscle endurance in patients with chronic low back pain- A case-control study", "authors": [ "Praveen Kumar", "Arthur de Sá Ferreira", "Leandro Alberto Calazans Nogueira", "Watson Arulsingh", "Mr. Sharad Patil", "Arthur de Sá Ferreira", "Leandro Alberto Calazans Nogueira", "Watson Arulsingh", "Mr. Sharad Patil" ], "abstract": "Background Patients with chronic low back pain (CLBP) frequently present with kinesiophobia. Although kinesiophobia is found to affect outcomes such as affect pain and quality of life in patients with CLBP, it is unclear whether kinesiophobia is linked to reduction of muscle endurance in these patients. The primary aim of the study was to analyze the impact of kinesiophobia on lumbar extensor endurance in patients with CLBP and asymptomatic individuals.\n\nMethods This case-control study was proceeded with 200 patients with CLBP and 400 controls. Kinesiophobia, lumbar endurance and Pain intensity were assessed with Tampa Scale, Soren’s lumbar extensor test and visual analog scale respectively. Regression model was administered to explore the relationship between kinesiophobia and lumbar extensor endurance.\n\nResults Prevalence of kinesiophobia was found to be higher in patients with CLBP (30%) than in controls (11%) which is (6.49 ± 0.52, d= 1.07) more in CLBP than controls. Lumbar endurance was significantly lower in CLBP than controls (-20.5±6.84), further affected by the presence of kinesiophobia as lumbar endurance was negatively correlated (r = - 0.09) to Kinesiophobia. Moreover, VAS (r = 0.2) was positively correlated with kinesiophobia in patients with CLBP.\n\nDiscussion and conclusion A high prevalence of kinesiophobia was reported by patients with CLBP. The presence of kinesiophobia exhibited strong linear relationship with lumbar endurance, and pain intensity among patients with CLBP. Hence management of CLBP should comprise of an assessment of kinesiophobia and appropriate treatment strategies to address it in preventing persistent CLBP.\n\nClinicalTrials.gov Identifier NCT05079893 Registered on 14/10/2021.", "keywords": [ "Low back pain", "Kinesiophobia", "pain", "Endurance", "Chronic pain." ], "content": "Background\n\nCLBP (Chronic Low Back Pain) is a leading cause of disability among working age adults.1 In fact, worldwide, the number of years spent with disability due to low back pain rose by 54% from 1990 to 2015.2 CLBP is defined as pain between the bottom of the lower rib margin and the buttocks that persists for over 12 weeks.3\n\nAs for specific causes of low back pain (LBP) are concerned, only 15% of the total back pain due to a pathophysiological mechanism, e.g., Herniated nuclei pulposus (HNP), Infection, Osteoporosis (Olympic), Rheumatoid Arthritis, Fracture, or Tumor.4–7 The remaining patients are classified as NSLBP (Nonspecific Low Back Pain). As NSLBP has no pathophysiological cause, treatment is focused on pain-related intervention.8\n\nKinesiophobia is described as an excessive, irrational, and debilitating fear of performing physical movements due to susceptibility to painful injury or reinjury.9 Although there are many biological factors that contribute to LBP, psychological factors may play an unexpectedly large role in some chronic LBP patients.10 Clinical studies have shown that an exaggerated negative cognitive response to actual pain, known as fear of catastrophic pain and movement/(re) injury (kinesiophobia), is important in the pathogenesis of CLBP and related disorders.11\n\nThe prevalence of kinesiophobia in chronic pain varies between 50 and 70%.12 Therefore, kinesiophobia is correlated with pain-related disorders, causing changes in motor activity that affect pain-related activities and the coping pain-related disorders.13 Thus, studies in the past have shown that patients with lower back pain develop more severe Kinesiophobia, regardless of pain severity. Patients with Kinesiophobia also had higher pain perception and decreased physical activity levels. Kinesiophobia has been shown to negatively impact quality of life for patients with chronic low back pain (CLBP).14 Higher levels of kinesiophobia correlate with higher levels of perceived pain in all forms of chronic musculoskeletal pain (CMP)15 and lower return to pre-injury activities.16\n\nSubgroup and moderation analyses of data in the earlier studies reported a consistent reduced muscle activity among people with higher kinesiophobia.17,18 Recent high-quality studies13,18 found moderate-to-strong evidence of associations between higher degree of kinesiophobia, disability, and poorer quality of life among patients with chronic pain conditions. Nevertheless, the consensus not yet reached in this area owing to the presence of heterogeneity among all included studies.\n\nTo the best of our knowledge, to date, there is no study assessing the relationship between kinesiophobia, lumbar endurance in patients with CLBP. Moreover, this is case control study which determined sample size for both cases and controls using odds ratio based on prevalence rate of kinesiophobia among CLBP.14\n\nTherefore, the current study aimed to compare the impact of kinesiophobia on lumbar extensor endurance in patients with CLBP and asymptomatic individuals. Secondarily, we aimed to examine the relationship between kinesiophobia and lumbar extensor endurance, and pain intensity in patients with CLBP. Lumbar endurance is reported to be affected among patient with CLBP. We hypothesized that the presence of kinesiophobia would further add to the detoriation of lumbar extensor endurance in patients with CLBP.\n\n\nMethods\n\nThis is a case-control study in which CLBP patients and asymptomatic control patients were recruited from Thumbay Physiotherapy and Rehabilitation Hospital and Thumbay University Hospital in Ajman, United Arab Emirates. After obtaining ethical approval, informed consent was taken from all recruited participants. This study involved human subjects for data collections thus sought for Ethical Committee approval. The Institutional Review Board, Gulf Medical University, UAE, reviewed and approved to undertake this research on 21.05.2021 with Ref. no. IRB/COHS/FAC/03/May-2021.\n\nThis research was conducted in accordance with the principles embodied in the Declaration of Helsinki and in accordance with local statutory requirements [Link]. Recruitment of participants for this study occurred from January 2022 to January 2023. The preparation of this manuscript was based on the STROBE statement guidelines.19\n\nInitial screening and evaluation of outcomemeasures of people with and without CLBP were performed by four experienced physical therapists (two men and two women) specializing in musculoskeletal and sports physical therapy. To ensure uniformity of data collection, all therapists were oriented with information about the study protocol, including the assessment methods using the various assessment tools relevant to this study.\n\nScreening of participants to confirm their eligibility was conducted by a physical therapist (Researcher 1) at their first physical therapy appointment. Participants were then instructed to complete the Tempa Scale for screening the presence of Kinesiophobia. data set consisted of socio-demographic information of participants including age, gender, weight, height and pain characteristics (location of pain and associated symptoms). Following the physical examination, pain intensity was assessed using self-report questionnaires (visual analogue scale - VAS). The physical therapist (Researcher 2) who was blinded to the cases and controls, performed the lumbar endurance test. Totally, four qualified therapists were involved in the data collection process for this study of which first two were males and the other two were females. Fear of movement/injury or re-injury was measured using the Tampa Scale for Kinesiophobia (TSK), a 17-item self-report scale with scores ranging from 17 (no fear) to 68 (worst fear).20 TAMPA scores were calculated according to the web application [link]. Additionally, the following characteristics of participants such as obesity, lack of exercise, poor diet, and smoking habits are analysed to determine its association with chronic low back pain and disability.21,22\n\nAdults aged 18 to 59 years with CLBP, diagnosed and referred by an orthopedic surgeon or general practitioner, and cases with sufficient physical independence to undergo lumbar extensor endurance test23 were included in the study. Controls were any healthy participants or patients without lower back symptoms reported at Thumbay Physiotherapy and Rehabilitation Hospital and Thumbay University Hospital in Ajman, UAE. Cases and controls were prospectively identified from these on-campus outpatient clinical centres. On the other hand, healthy adults aged between 18 and 59 years of asymptomatic participants and both genders were included in this study. Participants with congenital spine anomalies, vestibular issues, joint instability in lower limbs, cardiorespiratory conditions, and hip arthritis, history of previous lower back injury, inflammatory, infectious disease, and malignancy in the spine and use of antidepressant medication or antihypertensive medication were excluded.\n\nKinesiophobia, lumbar endurance, and pain intensity were assessed by the Tampa Scale for Kinesiophobia, Soren’s lumbar extensor test and VAS scale, respectively. All these eveluations were conducted in a laboratory setting.\n\nTampa Scale for Kinesiophobia (TSK), which is a 17 self-report items scale with scores ranging from 17 (no fear) to 68 (highest fear).24 The Tampa Kinesiophobia Scale has been reported to have good reliability in CLBP patients.25 Additionally, Tempa scores were further subclassified, with a scores of 17–48 was labelled as having low-to-moderate kinesiophobia and scores of 48–68 as with severe kinesiophobia.\n\nParticipants were tested during a 1-hour session and were asked to perform a weight-dependent isometric back extension test (Sorensen) on a horizontal table.26 The Sørensen test was performed in the prone position with the iliac crest aligned with the edge of the table and the lower extremities secured with ankle and below-knee straps. During the testing procedure, participants were instructed to keep their bodies (head, arms, and torso) horizontal to the floor for as long as possible without support and keep their arms crossed in front of their chest.26 The examiner gave verbal feedback to maintain the horizontal position during the test, and the test ended when the test position could no longer be maintained. Verbal encouragement was provided during this evaluation procedure. Participants were instructed to keep the lumbar lordotic position as stable as possible. Average lumbaruscular endurance was recorded in seconds by the examiner using a stopwatch. A chair with a padded seat was placed in front of the subject so that the subject could support himself if he got tired during the test. The stopwatch was stopped as soon as the subject became tired or unable to maintain the posture.26\n\nPain intensity was measured using a visual analogue scale (VAS). The VAS consists of a 10 cm line, with the left end indicating no pain and the right end indicating severe pain.27 Participants were asked to indicate their current pain level on a scale, with higher scores considered to be more severe.28\n\nBased on the prevalence of 70% kinesiophobia among CLBP patients,14 an assumption was made for the prevalence of kinesiophobia among controls was10% and the odds ratio were 2; thus the minimum sample size fixed for this case control study was 600 [200 cases + 400 Controls] and the expected case-to-control ratio was 1:2.\n\nData for this study was analyzed using JASP software version 0.18.1. The Shapiro-Wilk test was used to ensure that the data followed a normal distribution. Because there were statistically significant differences in baseline characteristics for both cases and controls, we used age, gender, employment status, alcohol, physical activity, and nutritional level as covariates for further multivariate analysis of kinesiophobia between cases and controls. Pearson correlation test was used to confirm the correlation between kinesiophobia and lumbar endurance. Furthermore, to analyze the association of linear regression of variables such as lumbar endurance and pain intensity with kinesiophobia, we conducted an analysis of variance to distinguish between lumbar endurance and pain in participants with low-to-severe kinesiphobia to examine the effects of kinesiphobia on lumbar endurance.\n\n\nResults\n\nTable 1 illustrates the characteristic features of all who participated in this study. A total of 200 patients with CLBP and 400 healthy participants participated in this study through the screening procedure mentioned in the methodology. Comparing case group to the control group, most cases were male, cases were older, cases had higher BMI, cases had higher employment rate, cases were reported smoking habits, cases were with higher frequency of alcohol consumption, cases were reported with higher frequency of physical activity level and cases were reported with more consumption of low vegetables with high meat. Cases were found to consume more analgesics and related drugs compared to controls, and a greater number of cases were insured with medical insurance scheme compared against controls. Prevalence of kinesiophobia was found to be higher in patients with CLBP (30%) than in controls (11%) which is (6.49 ± 0.52, d = 1.07) more in CLBP than controls.\n\nAs shown in Table 2, The presence of kinesiophobia was found to be significantly more in patient with CLBP compared against controls. Similarly, lumbar endurance, and pain intensity were significantly impaired in case group compared to control group.\n\nFurthermore, Pearson correlation analysis revealed a positive and negative correlation between Kinesiophobia with VAS score and lumbar extensor endurance respectively among the participants with CLBP as shown in (Table 3).\n\nOn the basis of logistic and linear analyses (Tables 4-6), factors such as age, alcohol consumption, duration of lower back pain, physical activity, and type of job influenced the presence of Kinesiophobia, and lumbar endurance of participants involved in this case-control study.\n\n\nDiscussion\n\nThe primary aim of this study was to analyze the impact of kinesiophobia on lumbar extensor endurance in patients with CLBP. Based on the current findings, case group was found with high incident of kinesiophobia and showed impaired lumbar endurance compared to controls. The presence of Kinesiophobia has highly correlated with the lumbar endurance and, pain intensity in patient with CLBP.\n\nThe strength of this study is that it analyzed the impact of kinesiophobia on lumbar endurance among cases and controls. Further, the study was distinct in finding out the impact of kinesiophobia on Lumbar extensor endurance among cases with CLBP in comparison with earlier studies which reported only a deterioration of lumbar extensor endurance amongcases with CLBP.29,30 Thus, no studies have explored the impact of Kinesiophobia on lumbar muscle endurance in patients with CLBP against asymptomatic subjects.\n\nThis study further used multi-variate analysis to determine the relationship of other relevant factors that might interfere with the primary outcome of the study which other studies omitted while associating kinesiophobia. Beside this, the physiotherapist who measured the lumbar endurance and pain was blinded to the cases and control group.\n\nOn the other hand, the weakness of the study is its own design as a case control study.\n\nThe current study reported a significant difference in the presence of kinesiophobia between the cases and control where cases with severe kinesiophobia exhibited strong association with lumbar extensor endurance among cases with CLBP.\n\nThis case study result shows that the presence of kinesiophobia has strong linear correlation with lumbar extensor endurance, pain in patients with CLBP in a negative way which added to the fact that why lumbar endurance was compromised in patient with CLBP.31 This findings support the earlier hypothesis that the presence of kinesiophobia may deteriorate or influence lumbar extensor endurance.18\n\nThis study finding reports a significantly higher incidence of Kinesiophobia among cases with CLBP which is indeed in line with the prevalence rate of 50 to 70% Kinesiophobia among chronic pain conditions.12 These findings further call for the inclusion of cognitive behavior therapy in conjunction with other physical therapy for a better prognostic value in case of a chronic musculoskeletal pain conditions.32\n\nHowever, there is limited researches done to prove the efficacy of Cognitive Therapy on Chronic Low Back Pain Hence future study should focus on an integrated Physiotherapy approach with various cognitive therapy approaches to ifacilitate the prognostic value of LBP.33\n\nFurthermore, based on multivariate analysis of the data, this study identified that age has shown a protective response to the occurrence of Kinesiophobia. This is contrary to the earlier finding that reported a higher levels of Kinesiophobia among frailer and older people, predominantly who are living in care homes.34 Besides this, alcohol consumption, duration of lower back pain, physical activity, and type of job have shown association with the presence of Kinesiophobia and CLBP in this case-control study.\n\nPrevious studies pointed out the presence of neuropathic pain due to excessive alcohol intake among chronic pain conditions,35,36 and a moderate drinking habit has shown to exert analgesic effects.24,25 This study also found a close relationship between physical activity level and the presence of kinesiophobia in the participants. This finding is in line with previous report that states that past sports or lack thereof equally determine the level of kinesiophobia in men and women in the later decades of life.37\n\nThe current study findings may be helpful to guide healthcare professionals to rule out the presence of kinesiophobia as part of the clinical evaluation for patients with CLBP. This would assist them in the selection of appropriate strategical treatment plan to acheive a better prognostic value. This result of this study may encourage health care professionals and policy makers for carrying out more extensive prospective researches and amendment of health care policy guidelines. The protocol of this study is published elsewhere.38 Future high-quality studies should focus on comparing different types of cogntive therapy approaches on different outcome of patients with CLBP.\n\n\nConclusion\n\nOn the basis of the study findings, it may be concluded that higher Kinesiophobia has been reported patients with CLBP compared to controls. The presence of kinesiophobia had shown to have linear correlation with on lumbar endurance, and pain intensity among patients with CLBP. Factors such as age, duration of condition, alcohol consumption, physical activity, and type of job also to be taken to account for deciding the most appropriate treatment plan to achieve the overall clinical outcome of patients with CLBP.\n\nClinicalTrials.gov Identifier: NCT05079893 Registered on 14/10/2021\n\nAll data sheet associated with this study is provided in the extended data section.\n\n\nAuthors’ contributions\n\nDr. Praveen Kumar is the principal investigator and this study is conducted as a part of Post Doctoral studies.\n\nDr. Arthur de Sá Ferreira, Coordenador, Prof Leo Programa de Pós-graduação em Ciências da Reabilitação – PPGCR Centro Universitário Augusto Motta.Pós-graduação em Ciências da Reabilitação – PPGCR Centro Universitario Augusto Motta\n\nDr. Watson Arulsingh D. R contributed to analysis, interpretation of data, and drafted the work. Mr. Shard Patil contributed toward data acquisition and entry. All authors have agreed both to be personally accountable for the author’s own contributions and to ensure that questions related to the accuracy or integrity of any part of the work, even ones in which the author was not personally involved, are appropriately investigated, resolved, and the resolution documented in the literature.\n\n\nDeclarations\n\nEthics approval and consent to participate in study was taken to acocunt while Institutional Review Board approved the study protocol; Thumbay Hospital Gulf Medical University, IRB/COHS/FAC/03/May-2021 Informed consent to participate in study was obtained from all participants in this study.\n\n\nConsent for publication\n\nA completed informed consent form was formed and signed by participants as per the norms of the International Declaration of Helsinki to upholds the safety of those participating in research as well as seeking treatment in the practice. However, the consent for publishing the data was not required as the data has been anonymised), this alterations have not distorted scientific meaning.", "appendix": "Data availability and statement on data sharing\n\nThis project contains the following underlying data:\n\nFigshare: Influence of Kinesiophobia on muscle endurance in patients with chronic low back pain- A case-control study, https://doi.org/10.6084/m9.figshare.25965535.v1. 39\n\nThe project contains the following data:\n\n• Jasp_4 Kinesiophobia Dr Praveen.xlsx\n\nFigshare: Influence of Kinesiophobia on muscle endurance in patients with chronic low back pain- A case-control study. Dataset, https://doi.org/10.6084/m9.figshare.26130055.v1. 40\n\nThe projet contains the following extended data:\n\n• Extended data file-Dr.praveen kumar kandakurti\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nNot applicable.\n\n\nReferences\n\nMurray CJL, Atkinson C, Bhalla K, et al.: The state of US health, 1990-2010: burden of diseases, injuries, and risk factors. JAMA. 2013; 310: 591–608. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBuchbinder R, van Tulder M , Öberg B, et al.: Low back pain: a call for action. Lancet. 2018; 391: 2384–2388. Publisher Full Text\n\nDeyo RA, Weinstein JN: Low back pain. N. Engl. J. Med. 2001; 344: 363–370. Publisher Full Text\n\nVadalà G, Russo F, Musumeci M, et al.: Clinically relevant hydrogel-based on hyaluronic acid and platelet rich plasma as a carrier for mesenchymal stem cells: rheological and biological characterization. J. Orthop. Res. 2017; 35: 2109–2116. PubMed Abstract \| Publisher Full Text\n\nAmirdelfan K, McRoberts P, Deer TR: The differential diagnosis of low back pain: a primer on the evolving paradigm. Neuromodulation Technol. Neural Interface. 2014; 17: 11–17. PubMed Abstract \| Publisher Full Text\n\nKoes BW, van Tulder MW , Thomas S: Diagnosis and treatment of low back pain. Br. Med. J. 2006; 332: 1430–1434. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMaher C, Underwood M, Buchbinder R: Non-specific low back pain. Lancet. 2017; 389(10070): 736–747. Publisher Full Text\n\nNegrini S, Zaina F: The chimera of low back pain etiology: a clinical rehabilitation perspective. Am. J. Phys. Med. Rehabil. 2013; 92(1): 93–97. PubMed Abstract \| Publisher Full Text\n\nHoy D, Brooks P, Blyth F, et al.: The epidemiology of low back pain. Best Pract. Res. Clin. Rheumatol. 2010; 24(6): 769–781. Publisher Full Text\n\nKori SH, Miller RP, Todd DD: Kinisophobia: a new view of chronic pain behavior. Pain Manag. 1990; 3: 35–43.\n\nFritz JM, George SZ, Delitto A: The role of fear-avoidance beliefs in acute low back pain: relationships with current and future disability and work status. Pain. 2001; 94(1): 7–15. PubMed Abstract \| Publisher Full Text\n\nLarsson C, Hansson EE, Sundquist K, et al.: Psychometric properties of the Tampa Scale of Kinesiophobia (TSK-11) among older people with chronic pain. Physiother. Theory Pract. 2014; 30(6): 421–428. PubMed Abstract \| Publisher Full Text\n\nLuque-Suarez A, Martinez-Calderon J, Falla D: Role of kinesiophobia on pain, disability and quality of life in people suffering from chronic musculoskeletal pain: a systematic review. Br. J. Sports Med. 2019; 53(9): 554–559. PubMed Abstract \| Publisher Full Text\n\nUluğ N, Yakut Y, Alemdaroğlu İ, et al.: Comparison of pain, kinesiophobia and quality of life in patients with low back and neck pain. J. Phys. Ther. Sci. 2016; 28(2): 665–670. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPalomo-López P, Becerro-de-Bengoa-Vallejo R, Losa-Iglesias ME, et al.: Kinesiophobia and pain intensity are increased by a greater hallux valgus deformity degree-kinesiophobia and pain intensity in hallux valgus. Int. J. Environ. Res. Public Health. 2020; 17(2): 626. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChmielewski TL, Jones D, Day T, et al.: The association of pain and fear of movement/reinjury with function during anterior cruciate ligament reconstruction rehabilitation. J. Orthop. Sports Phys. Ther. 2008; 38(12): 746–753. PubMed Abstract \| Publisher Full Text\n\nIshak NA, Zahari Z, Justine M: Kinesiophobia, pain, muscle functions, and functional performances among older persons with low back pain. Pain Res. Treat. 2017; 2017: 1–10. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChriste G, Crombez G, Edd S, et al.: Relationship between psychological factors and spinal motor behaviour in low back pain: a systematic review and meta-analysis. Pain. 2021; 162(3): 672–686. PubMed Abstract \| Publisher 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. J. Clin. Epidemiol. 2008 Apr; 61(4): 344–349. PubMed Abstract \| Publisher Full Text\n\nRosenbloom BN, Pagé MG, Isaac L, et al.: Fear of movement in children and adolescents undergoing major surgery: a psychometric evaluation of the Tampa Scale for Kinesiophobia. Eur. J. Pain. 2020; 24: 1999–2014. PubMed Abstract \| Publisher Full Text\n\nRobson EK, Kamper SJ, Davidson S, et al.: Healthy Lifestyle Program (HeLP) for low back pain: protocol for a randomised controlled trial. BMJ Open. 2019; 9(9): e029290. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMuga MA, Owili PO, Hsu CY, et al.: Association of lifestyle factors with blood lipids and inflammation in adults aged 40 years and above: a population-based cross-sectional study in Taiwan. BMC Public Health. 2019; 19: 1346. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMeucci RD, Fassa AG, Faria NM: Prevalence of chronic low back pain: systematic review. Rev. Saude Publica. 2015; 49: 1. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRobins MT, Heinricher MM, Ryabinin AE: From Pleasure to Pain, and Back Again: The Intricate Relationship Between Alcohol and Nociception. Alcohol Alcohol. 2019; 54: 625–638. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhou Y, Liu P, Rui J, et al.: The Associated Factors and Clinical Features of Neuropathic Pain after Brachial Plexus Injuries: A cross-sectional study. Clin. J. Pain. 2017; 33: 1030–1036. PubMed Abstract \| Publisher Full Text\n\nBehennah J, Conway R, Fisher J, et al.: The relationship between balance performance, lumbar extension strength, trunk extension endurance, and pain in participants with chronic low back pain, and those without. Clin. Biomech. 2018; 53: 22–30. PubMed Abstract \| Publisher Full Text\n\nCouper M, Tourangeau R, Conrad F, et al.: Evaluating the effectiveness of visual analog scales: a web experiment. Soc. Sci. Comput. Rev. 2006; 24: 227–245. Publisher Full Text\n\nMikhail H, Reda N, Shahaly M, et al.: Predictors of fear-avoidance belief, pain, and disability index in patients with chronic low back pain attending rheumatology outpatient clinics. J. Public Health. 2022; 30: 417–422. Publisher Full Text\n\nSuuden E, Ereline J, Gapeyeva H, et al.: Low back muscle fatigue during Sorensen endurance test in patients with chronic low back pain: relationship between electromyographic spectral compression and anthropometric characteristics. Electromyogr. Clin. Neurophysiol. 2008; 48: 185–192. PubMed Abstract\n\nBoyce RO, Boone E, Stallings J, et al.: A multidisciplinary approach to a time efficient low back exercise intervention in a small manufacturing plant: a case study. J Exerc Physiol. 2008; 11: 12–24.\n\nAydoğdu O, Zübeyir S: The association between kinesiophobia and proprioception, postural stability, activity level, knee function, and quality of life following anterior cruciate ligament reconstruction. J. Exerc. Ther. Rehabil. 2020; 7(3): 247–252.\n\nMonticone M, Ferrante S, Rocca B, et al.: Effect of a long-lasting multidisciplinary program on disability and fear-avoidance behaviors in patients with chronic low back pain: results of a randomized controlled trial. Clin. J. Pain. 2013 Nov 1; 29(11): 929–938. PubMed Abstract \| Publisher Full Text\n\nMiki T, Kondo Y, Kurakata H, et al.: The effect of cognitive functional therapy for chronic nonspecific low back pain: a systematic review and meta-analysis. BioPsychoSocial Med. 2022; 16: 12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlpalhão V, Cordeiro N, Pezarat-Correia P: Kinesiophobia and Fear Avoidance in Older Adults: A Scoping Review on the State of Research Activity. J. Aging Phys. Act. 2022 Mar 18; 30(6): 1075–1084. PubMed Abstract \| Publisher Full Text\n\nYang YJ: An Overview of Current Physical Activity Recommendations in Primary Care. Korean J. Fam. Med. 2019 May; 40(3): 135–142. Epub 2019 May 20. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGuacel I, Miguel-Berges ML, Gómez-Bruton A, et al.: Veganism, vegetarianism, bone mineral density, and fracture risk: a systematic review and meta-analysis. Nutr. Rev. 2019 Jan 1; 77(1): 1–18. PubMed Abstract \| Publisher Full Text\n\nSaulicz E, Knapik A, Saulicz M, et al.: Physical activity in youth and level of kinesiophobia in older adults. Balt J. Health Phys. Act. 2016; 8(2): 64–77. Publisher Full Text\n\nKandakurti PK, Arulsingh W, Patil SS: Influence of kinesiophobia on pain intensity, disability, muscle endurance, and position sense in patients with chronic low back pain—a case-control study. Trials. 2022; 23: 469. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKandakurti PK: Jasp_4 Kinesiophobia Dr Praveen.xlsx. Dataset. figshare. 2024. Publisher Full Text\n\nKandakurti PK: Extended data file-Dr.Praveen kumar kandakurti. Dataset. figshare. 2024. Publisher Full Text" }	[ { "id": "335964", "date": "14 Nov 2024", "name": "Søren O'Neill", "expertise": [ "Reviewer Expertise Primarily", "experimental pain research in clinical populations." ], "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\nInfluence of Kinesiophobia on muscle endurance in patients with chronic low back pain - A case-control study\nThank you for the opportunity to review this paper. The authors have undertaken a lot of work in collecting data from a large population of study participants. Unfortunately, the paper suffers from a number of serious shortcomings.\nThe paper reports the findings of what seems to be a cross-sectional study. It is reported however, as being a case-control study, which by my reckoning is not the case. For a brief overview of study types and difference, I refer the authors to : https://www.cancerresearchuk.org/about-cancer/find-a-clinical-trial/what-clinical-trials-are/types-of-clinical-trials\nThe authors state the aim of the study to be \"to compare the impact of kinesiophobia on lumbar extensor endurance in patients with CLBP and asymptomatic individuals\". However, a cross-sectional study is not suited to elucidate a causal relationship (impact). At most, the study design permits examination of correlation between variables, which does not speak to which (if any) variable impacts the other.\nThe study enrolled a large number of chronic low back pain patients (n=200) and controls/healthy participants (n=400). It is unclear to the reader what constituted the control group: Controls are reported as \"healthy participants\" or \"patients without lower back pain\" (recruited from Thumbay Physiotherapy and Rehabilitation Hospital and Thumbay University Hospital) and further that \"healthy adults [..] of asymptomatic participants [..] were included in this study. What types of 'patients without lower back pain' were enrolled as healthy controls? Were controls other types of hospital patients and/or staff and/or students and/or a background population sample?\nTable 1 in the paper lists a number of baseline characteristics of the two groups, many of which are significantly different. For instance, 76% of the chronic low back pain group are reported as \"Currently employed\", compared to only 10.8% of the control group ('Healthy participants'). It seems unlikely that a control group of healthy controls should have such a low level of employment, which leads me to think, that the control group is somehow fundamentally different to the cLBP group. In other words, the study compared two groups which appear to differ significantly in a number of ways apart from their low-back pain status, but it is unclear what the control group actually consists of. Also in Table 1, the occupation category of \"Controls (n=400)\" is listed as percentages (e.g. 1.8% 'Manager'), but is this 1.8% of the 10.8% \"Currently employed\"?\nThe authors conclude in the Abstract that \"The presence of kinesiophobia exhibited [a] strong linear relationship with lumbar endurance, and pain intensity among patients with CLBP.\". This is misleading and not supported by their results: The correlation between kinesiophobia and lumbar endurance is reported as -0.09 (Pearson correlation coefficient), which is a very weak correlation. The corresponding P value was significant at 0.03, but this only demonstrates that the weak correlation is unlikely to be a random finding. Similarly, the correlation between pain intensity (VAS) and kinesiophobia is reported as 0.2 -- also a weak correlation, and significantly so at P<0.001. The linear regression analyses do not contradict this.\nIn brief, the methods and results are unclear, making the results questionable and the conclusions are not supported by the data.\nThroughout, the paper suffers from poor or incorrect wording and spelling. For instance, in the Abstract alone: 1) 'affect' twice in Background, 2) 'proceeded' in Methods should probably be 'conducted', 3) one of the main outcome measures (Biering-Sørensen test) is referred to as 'Soren's test' in Methods and elsewhere as Sorenson's and Sørensen's test, 4) in Methods, a regression model is not 'administered', but 'used' or 'employed', 5) in Results, numbers are presented (e.g. \"6.49 +/- 0.52, d=1.07\") without explanation, 6) in Discussion, it is not the presence but degree of kinesiophobia that is examined for correlation to lumbar endurance. All in all, the paper bears the hallmarks of not having undergone sufficient scrutiny, leading to an accumulation of errors and spelling mistakes that suggest a lack of thorough editing.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [] } ]	1	https://f1000research.com/articles/13-1016
https://f1000research.com/articles/13-1015/v1	06 Sep 24	{ "type": "Research Article", "title": "Determinants of nutrition knowledge among student migrants in West Midlands, United Kingdom", "authors": [ "Sarah Olatunji", "Olukemi Asomuyide", "Marafee Omar", "Ayodele A.Falobi", "Ayokunle B. Falana", "Constance C. Ojo", "Peter Collins", "Yusuf A Ahmed", "Opeolu O. Ojo", "Sarah Olatunji", "Olukemi Asomuyide", "Marafee Omar", "Ayodele A.Falobi", "Ayokunle B. Falana", "Constance C. Ojo", "Peter Collins", "Yusuf A Ahmed" ], "abstract": "Background Dietary habits play a significant role in health and well-being. Nutritional knowledge can influence dietary habits. This study investigated the level of nutrition knowledge and factors affecting nutrition knowledge among student migrants in the West Midlands of the United Kingdom.\n\nMethod Data were collected from 372 participants using the General Nutrition Knowledge Questionnaire (GNKQ). The effects of gender, length of UK residency, program and level of study, marital status, and history of diet-related diseases on nutrition knowledge were assessed.\n\nResults The students generally demonstrated good nutrition knowledge. The overall mean score was 52.3 ± 2.4, and the median score was 54. Mean scores for dietary recommendations (11.9±0.4, 348 participants), food classification (21.3±1.0, 264 participants) and diet-related diseases/weight management (13.2±0.6, 324 participants) are indicative of good nutrition knowledge. Poor knowledge of food choices was observed (5.9±0.4, 156 participants). Females, postgraduates, and married students, as well as those with ≤3 years of UK residency, had higher mean scores compared to those in the opposite groups. BMI and a history of diet-related diseases did not significantly affect nutritional knowledge.\n\nConclusion Gender, level and type of study, marital status, and length of stay in the UK were predictors of good nutrition knowledge. Interventions to improve the knowledge of food choices among student migrants are needed.", "keywords": [ "International students", "student migrants", "nutrition knowledge", "dietary habits", "international university students", "diet-induced diseases", "General Nutrition Knowledge Questionnaire" ], "content": "Introduction\n\nDietary habits play significant roles in health and are largely influenced by an individual’s nutrition knowledge.1 These are also related to food choices and eating patterns.1 Moreover, the influence of factors such as demographic characteristics, culture, and socioeconomic inclinations on food choices and eating patterns have been recognized.2,3 Mora and Golden4 reported that cultural values and practices are significant determinants of food choices and eating patterns. In addition, the influence of culture on food preparation processes and health consequences has been reported.5,6 Nutritional requirements and food choices also change with age, level of education, type of job, living environment, and family income.7–10\n\nMigration affects these factors and has been recognized as a key determinant of dietary habits.11–13 Often, people are exposed to new environments, cultures, and lifestyles, which warrant them to adjust their dietary choices when they migrate. Challenges such as such as lack of access to familiar food items in the new country may also necessitate the need to change dietary habits.14–16 In this regard, commonly reported challenges for student migrants relate to acculturation, climate shock and language barriers.3,17 These factors have also been shown to significantly influence dietary choices and habits of student migrants.17 According to Yahia et al.,1 some student migrants are leaving home for the first time. Therefore, they may face additional problems, including lack of cooking skills, peer influence, and significantly increased academic rigour, which could have an impact on their dietary choices and habits.\n\nThe United Kingdom has experienced a significant increase in the number of student migrants in the last 10 years, and available data indicate that the majority of these students are from low- and medium-income countries (LMICs).18 In 2021, it was reported that the UK had about 700,000 student migrants with about 8 out of 10 students from LMICs.19 Due of differences in economic, geographical, and climatic factors. It is expected that students migrating to the UK will face diet adjustment/acculturation challenges.\n\nAlthough there are several coping mechanisms that student migrants could adopt in coping with diet acculturation challenges, a role has been prescribed for good knowledge of nutrition as a coping strategy.20 Belogianni et al.20 reported a positive correlation between nutrition knowledge and healthy food choices among university students in the UK. The study particularly reported that students with good knowledge consumed more fruits, dairy foods, proteins, and white grains. among students have been reported. However, it is not yet fully understood whether this correlation is also true for student migrants, particularly in the West Midlands region of the United Kingdom. In addition, the extent to which good nutrition knowledge has helped student migrants cope with food acculturation challenges in the UK needs to be researched. This study is part of a program that investigates the role of migration in diet and diet-related diseases (such as obesity and diabetes). Specifically, this study investigates the level of nutrition knowledge among student migrants in the West Midland region of the UK and assesses how factors such as gender, length of stay in the country, marital status, level of academic program, enrolment in health-related courses, and history of diet-induced disease influence nutrition knowledge in student migrants.\n\n\nMethods\n\nThis is a cross-sectional survey of student migrants across Higher Education Institutions (HEIs) in the West Midland region of the UK. All HEIs included in this study run both health- and non-health-related programs at the undergraduate and postgraduate levels, which provides the opportunity to recruit student migrants from diverse academic disciplines for the study. Students aged 18 years and above were recruited with no discrimination in their level of study. The sample size was estimated as previously reported by Kliemann et al.21 by assuming a mean nutrition knowledge score of 65 and a standard deviation of 9.2.\n\nData were collected using the General Nutrition Knowledge Questionnaire (GNKQ) previously developed by Parmenter and Wardle (https://www.nature.com/articles/1600726#preview).22 The revised version published by Kliemann et al.21 was used in this study. Briefly, the questionnaire had five sections, with Section 1 collecting demographic data, as indicated in Table 1. The remaining four sections had 87 items that collected data on respondents’ knowledge of dietary recommendations, as contained in the UK Eatwell Guide (Section 2, 18 items), food classifications/sources (Section 3, 36 items), food choices (Section 4, 13 items), and diet-related diseases and weight management (Section 5, 20 items). The respondents were required to identify the correct options for each question. The internal consistency and external reliability of the questionnaire have been previously reported as Cronbach’s α > 0.7 and interclass correlation coefficient > 0.7, respectively.21 Data were collected by sending a link to the questionnaire to participants. Prior to data collection, participants were provided with the Project Information Sheet and were required to provide informed consent prior to participation in the study.\n\nOf the 418 participants recruited and administered the research questionnaire, 372 provided informed consent and completed the questionnaire. Data were analyzed using descriptive statistics of mean, standard error of mean (SEM), percentage, and interquartile range. Specifically, scores obtained by participants in Sections 2 to 5 were expressed as percentages of the total obtainable score for each section, and as a percentage of 87 for the overall knowledge score. Scores of 0 – 49% for each section or the overall knowledge score were categorized as poor knowledge, while scores of 50% and above were categorized as good knowledge. Moreover, participants’ scores were stratified based on the demographic parameters listed in Table 1, and the frequency of participants demonstrating good or poor knowledge was computed. These frequencies were analyzed using the chi-square test to assess if there was a significant association between the identified demographic characteristics and nutrition knowledge. Moreover, odds ratios to test sex, length of stay in the UK, level of study, history of diet-induced disease, enrolment in health-related courses, marital status, and BMI as drivers of good nutrition knowledge were computed. Statistical significance was considered at P<0.05 for all inferential statistical analyses.\n\n\nResults\n\nThe data presented in Table 1 indicate the demographic profiles of the student migrants recruited for this study. The participants were mostly male (58.1%), enrolled in a postgraduate program (80.6%), married (77.4), and studying non-health-related courses (87.1%). Moreover, 38.7% of participants had a normal body mass index, 6.5% were underweight, 41.9% were overweight (41.9%), and the remaining 12.9% were obese. Moreover, 35.5% of the recruited student migrants lived in the UK for 12 months or less, and 38.7% had a UK residency period between one and three years. For longer residency periods, 6.5% of participants who had lived in the UK for 3 – 5 years and 9.7%) have lived in the UK for 5 to 10 years or more than 10 years in the UK (Table 1). Finally, 93.5% of the participants did not live with any diet-induced disease or had a history of these diseases.\n\nData on the scores obtained for the different categories of knowledge and overall knowledge are presented in Table 2 and Figure 1. The data indicate a median score of 54 out of 87 (62.1%) and a mean score of 52.3 ± 2.4 for the overall nutrition knowledge score. The median scores obtained for dietary recommendations (12 of 18, 66.7%), food classification (22 of 36, 61.1%), and diet-related diseases (14 of 20, 70.0%) were similar. Mean scores (expressed as percentages of the total score for each category) across these categories were also similar (dietary recommendations, 66.1%; food classification, 59.2%; and diet-related diseases, 66.0%). Compared to other categories, lower mean and median scores were observed for the food choices category (%; mean = 5.9±0.4, 41.5%; median score = 6 out of 13, 46.2) (Figure 1).\n\nValues are mean ± SEM with n = 372.\n\nThe responses of student migrants to individual items in the four categories were analyzed to better understand the participants’ level of knowledge. The analysis of responses to items related to knowledge of dietary recommendations indicated good knowledge of the need for increased consumption of fruits (96.8%), vegetables (100%), water (93.5%), wholegrain (64.5%), and milk with reduced fat (83.9%). In addition, student migrants demonstrated good knowledge of the need to consume less food with salt (93.5%), high-fat content (90.3%), food and drinks with high sugar content (87.1%), and ultra-processed meat (87.1%). Conversely, the data obtained indicated poor knowledge of recommended daily portions of fruits and vegetables (66.7%) and fat types that are good for consumption (54.8%). With respect to fat, 41.9% of participants demonstrated poor knowledge of trans fat and 22.6% of participants expressed that the consumption of trans fat was good. In addition, the knowledge of the recommended consumption of oily fist was poor among participants (54.8%), while the majority of participants (83.9%) did not know the recommended limit of alcohol consumption or food composition listed in the Eatwell Guide (67.7%).\n\nWith respect to knowledge of food classification, the majority of student migrants demonstrated the ability to recognize food items with high added sugar content. Specifically, 87.1% of respondents recognized that ice cream had a high sugar content. However, knowledge of the high salt content of food items such as breakfast cereals (83.9%) and bread (51,6%) was poor. Moreover, the majority of student migrants showed good knowledge of the high fiber content of food items, such as oats (93.5%) and potatoes with skin (83.9%), while 96.8% of participants correctly indicated that poultry products are rich in protein. Similarly, 51.6% of the participants correctly identified that the fiber content of pasta was low.\n\nGenerally, knowledge of the fat composition of many food items is poor. The majority of student migrants were unable to identify healthy food combinations, low-fat strategies for cooking foods such as potato chips (74.2%), or cooking methods that do not require the addition of fat (80.6%). However, the knowledge of diseases associated with low fiber intake (71%), as well as high sugar (63.3%) and salt consumption (67.7%), was good among participants. In addition, student migrants correctly identified food-based measures for preventing cancer (58.1%), heart disease (61.3%), and diabetes (77.4%). Moreover, the majority of participants were able to identify food items that could lead to elevated blood cholesterol levels (58.1%), as well as food items with a high glycemic index (63.3%). Similarly, the majority of participants also identified reading food labels (80.6%), taking nutritional supplements (64.5%), and constantly monitoring eating habits (96.8%) as effective strategies for healthy weight maintenance. The overall scores shown in Table 2 indicate that 77.4% of participants had overall good nutrition knowledge. For the different categories, good knowledge of dietary recommendations, food classification, and diet-related diseases was observed in 93.5%, 71.0%, and 87.1% of participants, respectively. However, 61.3% of student migrants had poor knowledge of food choices.\n\nThe effects of demographic characteristics on the overall nutrition knowledge and knowledge of the different categories of nutrition knowledge are presented in Figure 2 and Table 3. The data presented in Figure 2A indicate that the overall nutrition knowledge of female students was significantly higher than that of male students (17.9%, P<0.001), and that more female students (92.3%) demonstrated good nutrition knowledge than male students (66.7%). Moreover, the mean overall score observed for postgraduate students was 8.0% (P<0.001, Figure 2B), which was higher than the scores obtained by undergraduate students. Despite this higher mean score, the proportion of postgraduate students with good knowledge (76.0%) was lower than that of the undergraduate students (83.3%). The mean score for married respondents was 9.6% (P<0.001, Figure 2C) higher than that for single respondents, and the proportion of married respondents (79.2%) with good knowledge was higher than the proportion of single participants (71.4%). A similar trend was observed for the effects of enrolment on health-related degrees (mean score higher by 17.9%, P<0.001, Figure 2D) and living in the UK for more than 3 years (mean score higher by 17.7%, P<0.001, Figure 2F). However, unlike other demographic parameters, more students enrolled in non-health-related degrees (77.8%) and those with 3 years or less of UK residency (78.3%) demonstrated good nutrition knowledge. BMI status did not have any significant effect on overall mean scores (Figure 2E), but more people with normal BMI (83.3%) values demonstrated good nutrition knowledge compared to those who were underweight, overweight, or obese. In addition, student migrants with or without a history of diet-related diseases had similar mean scores (Figure 2G), and all students with a history of diet-related diseases demonstrated good nutrition knowledge.\n\nValues are mean ± SEM with n = the frequency for each demographic group. ***P<0.001 compared to the respective demographic group. A = Gender, B = Level of study, C = Marital status, D = Enrolment on health-related degree, E = Body Mass Index, F = UK residency, G = Living with a diet-related disease.\n\nIn this study, no association was found between overall nutrition knowledge and sex (P = 0.0920), level of study (P = 0.8509), marital status (0.6667), enrolment in health-related degree (P = 0.9013), BMI (P = 0.5314), length of UK residency (P = 0.8493), and history of diet-related disease (P = 0.4297). Odds ratios computed for these demographic characteristics revealed that the odds of having good nutrition knowledge was low among male students, unmarried students, and those enrolled in a non-health related degree (Table 4). However, there were increased odds of good nutrition knowledge among undergraduate students and students with normal BMI, 3 years or less UK residency, and those with a history of diet-related diseases (Table 4).\n\n\nDiscussion\n\nThis study investigated nutrition knowledge and the impact of demographic characteristics on nutrition knowledge among student migrants. It is evident from the data collected and analyzed in this study that respondents were mostly male, married, and enrolled in postgraduate programs. These demographic characteristics are different from other recent studies that investigated knowledge of nutrition among university students in the UK.20,23,24 In the study by Belogianni et al.,20 the majority of respondents were from a white ethnic background, female, aged 25 years or less, and studying at the undergraduate level. Similarly, the study by Cooke and Papadaki24 had respondents with similar demographic characteristics. However, the difference in the demographic characteristics of the respondents in the present study is expected because the focus of the study is on student migrants. Although data on the ethnicity of respondents in the present study were not reported, respondents were more ethnically homogenous, as they were all of African origin. Moreover, the majority of respondents were in the age range of 35 to 45 years, and this was expected, as the majority were enrolled in postgraduate studies. Moreover, most international students come to the UK to study at the postgraduate level. The fact that these students would have completed undergraduate studies in the countries of origin and may have also worked for some time before returning to education is consistent with the observed age range of the respondents. This age and ethnic homogeneity explain why no analysis of the influence of age and ethnicity on nutrition knowledge was conducted in this study. The observation that more respondents study at the postgraduate level is also consistent with the recent surge in the number of migrant students studying at universities across the UK.25 Also, available evidence indicates that most postgraduate students are usually accompanied by their family members to the UK,26 hence a higher proportion of married respondents in this study.\n\nUnlike other recent studies, most respondents in this study were either underweight, overweight, or obese.20,23 The proportion of students with abnormal BMIs in previous similar studies conducted in the UK and the USA was reported to be approximately 33%.20,23 The difference observed in this study could reflect the reported growing incidence of obesity globally.27 Also, as the data used in the computation of BMI in this study were self-reported, it is possible that inaccuracies (as some respondents may not be sure of their heights or body weights) in self-reported data could have skewed the computation of BMI values conducted in this study. The majority of the respondents in this study were recorded as being apparently healthy. However, the fact that detailed health information of participants was not collected means that it is possible that respondents could be living with conditions that are not diet-related but could have significant implications on their dietary habits and choices. This, in turn, influences their nutritional knowledge. In addition, the role of diet in disease development may be subtle, and it is possible that respondents may not be aware of how dietary choices and habits contribute to the condition they live with.28\n\nThis study reported an overall median nutrition knowledge score of 54 (62.1%). This is lower than the median scores reported by similar previous UK studies and studies worldwide. The mean scores recorded in UK studies ranged from 65.5% to 72.7%).20,23 The study by Kresic et al.29 conducted in Croatia reported a mean score of 67.4%. The fact that these studies used the same questionnaire for data collection also points to the fact that differences in the reported mean scores could only be attributed to characteristics inherent in the population of students recruited for individual studies. All respondents in the present study were university students. Therefore, the influence of education on nutrition knowledge could be ruled out. This is particularly important, as a previous study suggested an association between the level of education and knowledge of nutrition.30 Based on this observation, postgraduate students expect a higher mean score. However, the opposite was observed in this study, and a significantly higher number of postgraduate students recruited as participants may have contributed to the lower mean score observed. The expectation is that students enrolled in health-related courses will have better knowledge of nutrition. However, the opposite result was observed in the present study. It is also possible that the low number of students enrolled in health-related courses was responsible for this observation.\n\nThe analysis of responses to individual items in the research questionnaire revealed specific gaps in the knowledge of the student migrants recruited for this study. These gaps may have significant implications on the dietary habits of these students. While this study revealed that student migrants are aware of the need to consume fruits and vegetables, the majority of them are unaware of the recommended daily allowances for fruits and vegetables. Therefore, it is possible that they may not consume the right amount of these food items. To support this assertion, the majority of respondents indicated daily consumption of two portions as opposed to the recommended five portions of these items. In addition, poor knowledge of health and unhealthy fats, as well as strategies for reducing fat consumption, means that these students may be consuming more fatty food than necessary. This assertion is consistent with the fact that it has been previously reported that fat consumption is generally high among students.1,31 In addition, the majority of migrant students recruited in this study had difficulties identifying high-fiber food items. Instead, many of these students simply indicated food items that they probably commonly eat because they are cheap and/or easy to prepare.32\n\nThese gaps in knowledge may be responsible for the generally poor knowledge of food choices observed in this study. Although no association between nutrition knowledge and dietary behaviours has been previously reported,33 the observations in this study are not entirely different from this previous report. This study revealed that, although there were obvious gaps, respondents demonstrated good general nutrition knowledge. Therefore, it can be concluded that this knowledge does not generally reflect their ability to make good dietary choices. Several factors might have played a role in this study. In the first instance, because respondents were mainly of African origin, they may not be familiar with many of the food items listed in the questionnaire, and food items listed in the tool may not reflect items that they consume regularly. This observation suggests that modification of the tool may be necessary if it is to be used by non-Europeans. On the other hand, it is possible that respondents truly lack the ability to select healthy food choices because of factors such as the inability to properly read or understand food labels. Adequate food labelling is supported by policies and legislation in the UK and across Europe.34,35 However, this may not be the case in LMICs. This study also revealed gaps in the knowledge of student migrants about how to maintain healthy weight, even though they demonstrated good knowledge of the relationship between diet and diseases. In fact, respondents were almost equally divided on whether excessive fat consumption was good for healthy weight maintenance.\n\nNo association between good nutrition knowledge and all demographic characteristics assessed in this study was observed; even disparities in the scores obtained by women and the proportion of females with good nutrition knowledge were observed. In addition, the odds of having good nutrition knowledge among male respondents were reduced. These observations are consistent with a previous report by Svendsen et al.36 which highlighted a better functional knowledge of nutrition in women. In Africa (from which the majority of respondents originate), women are more involved in cooking than men.37 However, it is not yet certain whether this plays a significant role in what is observed in this study. Similarly, better nutrition knowledge was observed in married respondents, which may also be associated with cooking duties for their family members, although further studies are needed to investigate this assertion.\n\nPreviously, the association between enrolment in a health-related degree and nutrition knowledge has been reported.37 However, the opposite was observed in this study, even though students enrolled in health-related courses had higher mean scores. This is supported by the observation that a higher proportion of students enrolled in non-health-related programs demonstrated good nutrition knowledge and that the odds of good knowledge of nutrition is reduced in students enrolled in health-related programs. These results are consistent with a previous report by Belogiani et al.21 which recommended that interventions to improve dietary and nutrition knowledge should focus on all types of students, irrespective of the course they are enrolled in. The data collected in this study also indicated that residency in the UK for more than 3 years may be associated with good nutrition knowledge. However, this is negated by the fact that a higher proportion of students in the UK with less time demonstrated good nutrition knowledge. Previous studies investigating the effect of the length of UK residency on nutrition knowledge are lacking. This is because most respondents in previous UK studies were either born or grew up in the UK. Moreover, this observation also provides a role for early nutrition as a strategy for preventing diet-related diseases in people migrating to the United Kingdom.\n\nAll respondents in this study were of African origin, which is a limitation of this study to some extent. It is possible that data from students from non-European and non-African settings may provide new perspectives that will improve the understanding of the role of the migration of nutrition knowledge. Moreover, the influence of age, environmental factors, and social determinants of health (such as social support, family background, academic rigor, and cultural factors) on nutritional knowledge was not investigated in this study. It is also known that the use of a research questionnaire alone to collect data may have limitations. Future studies that adopt a qualitative approach may provide additional insights into the observations reported in this study.\n\n\nConclusion\n\nIn conclusion, good overall knowledge of nutrition among student migrants was reported in this study. In addition, good knowledge of dietary recommendations, food classification, and the relationship between diet and diseases, as well as poor knowledge of food choices and weight management, was observed. Gaps in the knowledge of recommended daily allowance, fat types, sources of fiber, food labelling, and weight management strategies were observed. The revision of the research questionnaire by incorporating food items that make the questionnaire more culturally sensitive is recommended. In addition, the inclusion of open-ended options that provide opportunities for respondents to freely express themselves may improve the effectiveness of the research questionnaire. Moreover, the expansion of respondent recruitment to include participants from diverse ethnicities and the investigation of the effect of wider determinants of health on diet knowledge are recommended.\n\n\nEthical standard disclosure\n\nThis study was conducted in accordance with the guidelines laid down in the Declaration of Helsinki. Ethical approval for the study was obtained from the Faculty of Education, Health, and Wellbeing Ethics Committee at the University of Wolverhampton, UK prior to the conduct of the research 16/08/2023). Approval Number. LSEC/2022-23/OO/005 Participants were provided with the Participants’ Information Sheet which clearly explained the aim of the research and processes involved prior to participation in this study. Written informed consent was obtained from all the subjects.\n\n\nAuthorship\n\nOOO, YAA, PC contributed to the study conception and design, data analysis, and manuscript preparation. SO, OA, MO, AAF, ABF and CCO contributed to data collection and analysis. All authors reviewed the final manuscript.", "appendix": "Data availability statement\n\nDue to the provisions of the General Data Protection Regulation, data collected are securely stored at the University of Wolverhampton. Interested parties should contact the Corresponding Autor to request access to data.\n\nOpen science Framework (OSF): Determinants of nutrition knowledge among student migrants in West Midlands, United Kingdom, 10.17605/OSF.IO/PUAT6.\n\nThis project contains the following extended data:\n\n1. Appendix 1 - General Nutrition Knowledge Questionnaire.docx\n\n2. General Nutrition Knowledge Questionnaire - ODT format.odt\n\n3. Participants’ Consent Form.docx\n\n4. PARTICIPANTS INFORMATION SHEET - amended.docx\n\nData is available under the terms of the CC0 1.0 Universal licence.\n\n\nAcknowledgements\n\nAuthors acknowledge the support of the students who participated in this study, particularly those who helped in the recruitment of other students. No financial support was received for the study.\n\n\nReferences\n\nYahia N, Wang D, Rapley M, et al.: Assessment of weight status, dietary habits and beliefs, physical activity, and nutritional knowledge among university students. Perspect. 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Publisher Full Text\n\nHaraszi R, Chassaigne H, Maquet A, et al.: Analytical methods for detection of gluten in food—method developments in support of food labelling legislation. J. AOAC Int. 2011; 94(4): 1006–1025. PubMed Abstract \| Publisher Full Text\n\nShangguan S, Afshin A, Shulkin M, et al.: A meta-analysis of food labelling effects on consumer diet behaviours and industry practices. Am. J. Prev. Med. 2019; 56(2): 300–314. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSvendsen K, Torheim LE, Fjelberg V, et al.: Gender differences in nutrition literacy levels among university students and employees: a descriptive study. J. Nutr. Sci. 2021; 10: e56. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWolfson JA, Ishikawa Y, Hosokawa C, et al.: Gender differences in global estimates of cooking frequency prior to COVID-19. Appetite. 2021; 161: 105117. Publisher Full Text" }	[ { "id": "348853", "date": "08 Jan 2025", "name": "Pamela Koch", "expertise": [ "Reviewer Expertise Behavioral nutrition education", "food justice and equity" ], "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 paper that assesses if nutrition knowledge among migrant students in the UK. In the field of behavioral nutrition education, there is a lot of literature that knowledge about nutrition (based on macro and micronutrients) is necessary but not enough to change behavior. As is stated in the first paragraph of the introduction, many other factors influence why people eat what they eat.\nMore needs to be stated in this paper to justify why nutrition knowledge only is being investigated if the goal is to have people have dietary behaviors that will help to improve health, knowledge alone will not achieve this goal.\n\nWorse, particularly since this is a migrant population from Africa if the focus is only on nutrition knowledge, it promotes a individual responsibility instead of looking at the systemic issues that can make it challenging to eat well.\n\nAs a reader we do not learn that all of respondents are of African origin until the discussion. I also agree with the point in the first full paragraph on page 9 in the discussion that knowledge does not reflect ability to make good food choices and this questionnaire may have limitations with an African population.\nIf this paper should be approved for indexing, more needs to be discussed as to the limitations and more upfront about who the study population is and if the tool used is appropriate for this population.\nThis would take a restructuring, particularly of the introduction and discussion section and more justification for what can be learned from the data collected in 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? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-1015
https://f1000research.com/articles/13-1011/v1	05 Sep 24	{ "type": "Method Article", "title": "Extracting ridge and valley lines in mountainous areas from airborne lidar data by utilizing line feature strength", "authors": [ "Rey-Jer You", "Chao-Liang Lee", "Rey-Jer You" ], "abstract": "Background Digital elevation models (DEMs) are important in many fields, such as geomatics and water conservation in mountainous areas. Geomorphic feature lines are necessary for topography interpolation and computation from DEMs.\n\nMethods Instead of a parameter space, we propose a novel automatic extraction of geomorphic feature lines in the feature space from discrete airborne light detection and ranging (LiDAR) data by the tensor voting method (TVM), which was originally developed for image data. A tensor field for discrete airborne LiDAR points was first established, and then, utilizing the TVM, a new geometric feature metric of data, the line feature strength, was captured. A practical line-growing method based on the local maxima line feature strength is proposed in this study.\n\nResults Compared with general line growing, which is based on a certain threshold, our line growing method is quite effective, particularly for the extraction of primary and minor ridge and valley lines in mountainous areas.\n\nConclusions The method presented in this paper is fast and automated, and can furnish operators with a wealth of detailed information about minor line features. This enables the extraction of ridge and valley lines that are tailored to specific requirements. Undoubtedly, the method developed here can be generalized to a large amount of LiDAR data.", "keywords": [ "LiDAR", "feature extraction", "ridge and valley." ], "content": "Introduction\n\nLight detection and ranging (LiDAR) technology has gained increasing prominence because of its capacity to rapidly generate voluminous amounts of three-dimensional (3D) point clouds, enabling expedient characterization of Earth’s topography.\n\nLiDAR can quickly provide a large amount of terrain data that is useful for building reconstruction, extraction of road paths, construction of topography, and terrain change monitoring etc.1–7 LiDAR is also employed for environmental protection, soil and water conservation, and the hydrological structure of mountainous areas, which are important issues.8–10 Furthermore, LiDAR is a very useful tool for monitoring forest growth and forest area changes, especially for estimating vegetation height, canopy cover, and tree species in mountainous areas.11–13\n\nCompared with photogrammetric data, LiDAR data offer a more straightforward approach for understanding changes in 3D topography. However, the irregular distribution of LiDAR point clouds can pose a challenge, particularly when shaping complex terrain within topological data. This paper introduces a method for extracting ridge and valley lines from low-density point clouds in mountainous regions.\n\nEdge detection is an established technique in computer vision. Various algorithms, such as Sobel, Prewitt, and Laplacian algorithms, have been developed to identify line features.14 Image data are stored in pixel format, and moving masks can easily navigate this regular grid to extract line features. Conversely, the data storage format for irregularly discrete LiDAR data consists of the point coordinates. If image extraction techniques are employed, the point coordinates must be interpolated into a pixel format, which can influence the accuracy depending on the interpolation method used.\n\nScholars have proposed various methods for extracting line features from LiDAR data. Zhao and You4 focused on extracting road networks. Their approach entails the removal of points associated with buildings and trees by applying the elevation criteria. Subsequently, they employed the intensity data and variance between the tangent vectors to define the line segments. Given that roads possess a certain non-negligible width, a sufficient number of point clouds are usually present on road surfaces to enable line segment extraction. To deal with narrower features, such as power lines, McLaughlin15 proposed a method that uses covariance to calculate the eigenvalues. These eigenvalues can be employed to categorize the point clouds into three groups: vegetation, surfaces, and power lines. Cable-specific formulas are applied to the point clouds allocated to the power line category to yield complete power-line representations. Guan16 used ground-based LiDAR scanning to obtain point cloud data of street views and extracted individual power lines using Hough transformation and Euclidean distance clustering.\n\nLine features that do not correspond to existing lines typically exist at points of change, such as turns and junction areas. Both sharp and gradual turns affect the position of the final extracted line segment. Bailly et al.17 used wavelet transformation and a flooding algorithm to identify the ditch lines in artificial drainage networks. In their study on mountainous settings, Chang et al.18 proposed a profile recognition and polygon-breaking algorithm (PPA) that performs target recognition, target connection, segment verification, and line smoothing. In the PPA approach, elevation grids from digital terrain models (DTMs) were used, and moving masks were employed to extend the ridge and valley lines. Gülgen and Gökgöz19 modified PPA to reduce the computational time required for the DTM generation process. However, PPA is easily influenced by noise, which may lead to redundant lines and non-matched results. A pre-processing procedure is necessary to obtain reliable valley and ridge lines.\n\nA new type of data, termed feature strength, was introduced to aid feature extraction. Medioni et al.20 applied the tensor voting method (TVM) to image data to obtain the eigenvalues and eigenvectors. This method enables the classification of image pixels into various features based on their strengths. TVM has also been demonstrated to be applicable to point-cloud data. You and Lin1 utilized feature strength to extract surfaces and lines from data in urban settings. Furthermore, in the context of urban regions, feature strength data can serve as raw data for calibrating biases between LiDAR strips during the preprocessing stage.21 In urban environments, where buildings and roofs exhibit regular patterns, point clouds on surfaces are readily distinguishable from others owing to their high surface feature strength. Lines can be identified at the intersections of two adjacent surfaces. However, because of the irregular nature of mountainous regions, this approach may result in more fragmented surfaces, making it challenging to intersect ridge and valley lines. The aim of this study is to analyze and discuss the feature strength of point clouds in mountainous regions, particularly the line feature strength extracted by TVM.\n\n\nMethods\n\nTVM encompasses three stages: tensor representation, tensor communication, and tensor decomposition/encoding.20,22 First, a tensor field was established by setting up a disk tensor for each LiDAR point, as proposed by You and Lin,1 and the geometric character of each LiDAR point was represented by a second symmetric tensor. Using tensor communication, each point collects the tensors of neighboring LiDAR points to form its final tensor. Consequently, each point has a strong geometric relationship with its neighboring points based on the final tensor, which is helpful for the extraction of ridge and valley lines in mountainous areas. After tensor communication, the final tensor of each point was decomposed into surface features, line features, and noise point features by tensor encoding.20 You and Lin1,2 used a normal vector field to obtain the surface feature strengths using the TVM and applied the region-growing method to extract surface features from LiDAR point clouds for urban regions. For our purpose, the line feature strength (denoted as C here) is more suitable for extracting valley and river lines in mountainous regions than the other types of feature strength. This aspect is elaborated in the subsequent section.\n\nC data can be obtained using the TVM. This section describes the characteristics of C data. Figure 1 shows the same mountainous region from various perspectives and data modes. In Figure 1(a), the ridge and valley regions appear in the 2.5D view, with an elevation range of approximately 1,400 meters. Figure 1(b) shows the elevation data from a 2D view. Figure 1(c) presents the C data from a 2D view.\n\nNOTE: (a) Point clouds illustrated in 2.5D view; (b) Elevation data illustrated in 2D view; (c) C data illustrated in 2D view. Own work.\n\nTo analyze the characteristics of the C data in relation to variations in elevation, this study established a section line. In Figure 2, the red line represents the elevation data and the blue line represents C data from the section lines shown in Figure 1(b) and (c). As depicted in Figure 2, C was higher in regions with large elevation gradients, and its magnitude was influenced by the extent of the elevation gradient. In areas with smaller elevation gradients, C was relatively stable. Hence, establishing a single threshold for identifying all points in the valley versus ridge regions is infeasible. In Figure 2, points near the ridge and valley regions display local maxima in the C data curves, confirming that C data can effectively assist in the identification of nodes of line features.\n\nNOTE: Red line, elevation data; blue line, line feature strength data in section line of Figure 1(b) and (c). Own work.\n\nThe eigenvectors for LiDAR point clouds can be derived using the TVM. Each point cloud possessed three associated eigenvectors, each with a distinct interpretation. For points located on a surface, the first eigenvector is the vector that is normal to the surface. Conversely, for points situated on a line, the third eigenvector is the tangent vector along the direction of the line, as shown by Medioni et al.20 and You and Lin.1,2 Given that this study focuses on the extraction of ridge and valley lines, the tangent vector v for each point is considered. This vector is derived using the TVM and is crucial for eliminating extraneous point clouds.\n\nDrawing inspiration from the region-growing method, this study established line growth criteria by choosing seed points and setting item thresholds. According to the next section, points located on the ridge or valley regions have higher C values than their surrounding points. Hence, points with local maxima C values serve as seeds for initiating line growth. Second, the v vectors of adjacent points located in the same valley or ridge line are similar. These two considerations guide the line-growth process, the specifics of which are explained in the following section.\n\nThis study establishes that such local maxima are directional in nature to provide a detailed explanation of how they are identified in 3D point cloud data. Vector v, derived from the TVM, is a critical factor. Points (i = 1, 2, …, k) considered centers within a specified search radius are divided into right (a = 1, …, m) and left (b = 1, …, n) subsets based on v, which serves as a divide. A center point cloud is deemed to be a local maxima in terms of C when the average C values on the two sides are lower than the C value of the center point. This is formalized in the following equations:\n\nSubscript i indicates point i located on a line. Ca represents the C value in point cloud a on the right-hand side of v (a = 1, …, m). Cb represents the C value in point cloud b on the left-hand side of v (b = 1, …, n).\n\nAs depicted in Figure 3, points within the search radius are divided into right (R1, R2, R3, and R4) and left (L1 and L2) subsets based on v of P1. Point P1 is classified as the local maxima of C when it satisfies Equation (1). This criterion was employed to eliminate redundant points in the line growth process. Points satisfying Eq. (1) serve as candidate seeds for line growth.\n\nNOTE: points within the search radius are divided into right (R1, R2, R3, and R4) and left (L1 and L2) subsets based on v of P1. Point P1 is classified as the local maxima of C when it satisfies Equation (1). Own work.\n\nWhen employing a large search radius, numerous point clouds not located on the line were included in the calculations. Conversely, when the search radius is small, many point clouds near the line segment are excluded, leading to incomplete line segments, particularly in the case of low-density point clouds. In this study, the radius used to identify point clouds with local maxima was consistent with the radius employed in TVM applications.\n\nA threshold of C value may be chosen to determine all candidate seeds whose C values are larger than that threshold, as in the conventional growing method. The result would lead to the extraction of the primary ridge and valley lines only, but might filter out other minor lines. Different from the conventional method, candidate seeds are identified by seeking local C maxima for the line-growing in this article. Using this line-growing method, more details of the ridge and valley lines can be obtained. Points with higher C values are more likely to be located on lines and are therefore prioritized for line growth. According to empirical observations, neighboring points on a line should have similar tangent vectors. The threshold angle between the two v vectors can then be defined.\n\nTo meet the criteria of the angle threshold, the five points with the largest C value are regarded as the center of the ball in the TV’s searching radius, and the tangent vectors of points that meet the local maxima C value within the range are the calculated angles between the center points. The average angle value of the five groups was used as the basic threshold (ω), and three times the average value (3ω) was used as the threshold value in this study. An excessively large threshold can introduce inaccuracies by leading to the inclusion of numerous point clouds that are not actually part of the line segment, skewing the final calculations. Conversely, a too-small threshold can lead to the omission of relevant clouds and fragmentation of lines; the procedure cuts off branch lines to multiple single lines.\n\nTo preserve the detailed line features, the proposed approach adopts a moving mask algorithm from computer vision and employs an overlapping mechanism. The size of the moving ball matches that of the search ball used in the TVM, and its moving distance equals the radius of the ball. Points that satisfy both the angle threshold and Equation (1) are considered, with their C values serving as weights because a higher C value implies a higher likelihood that the point is part of a line. The node of a line and its associated tangent vector were then calculated using the following equations:\n\ni: node i of a line. j: point j within the search ball.\n\nn the number of nodes in a line. m: number of points within the search ball.\n\n(xyz)iT and tangent vector(Vi). The subsequent node of the line was determined using the following equation:\n\nIn line with the techniques used in computer vision for line extraction, overlapping regions were maintained between the moving masks. In this study, approximately half of the search balls were designed to overlap adjacent balls.\n\nP0 [Figure 4(a)] was selected as the initial seed. Points that satisfy both Equation (1) and the angle threshold within searching ball O1 are evaluated using Equations (2) and (3), which yield new values for P1 and v1, respectively. Search ball O2 is generated through Equation (4), and the procedure is repeated to obtain P2, v2, and so on until no points within the search ball meet the criteria. At this juncture, P1, P2, and P3 become the nodes of the line, as illustrated in Figure 4(b), and new seeds are selected for the growth of additional lines until all the points satisfying Equation (1) are used.\n\nNOTE: (a) Move the searching ball to grow nodes and vectors on the basis of multiple criteria. (b) Connect the nodes to obtain a complete line. Own work.\n\nNode-point coordinates were calculated by weighting them in accordance with their C values. Equation (4) describes the method used to determine the node coordinates. To ascertain the theoretical accuracy, error propagation calculations were conducted for each point i, as outlined in Equation (5). For simplicity, any correlations among xi, yi, and zi were disregarded.\n\nAnother quality indicator of a node point is interpolated accuracy using contour data obtained by Delauney triangulation. The formula is as follows:\n\ni: node i of a line. n the number of nodes in a line.\n\ndi: elevation from point D to plane ABC in Figure 5.\n\nNOTE: Interpolated accuracy using contour data is obtained by Delauney triangulation. Elevation d is applied in Equation (6). Own work.\n\nContour data were used to produce a Delauney triangulation network. The nodes of the line are interpolated to obtain the difference in the elevation data and calculate the interpolated accuracy for each line. Once the theoretical and interpolated accuracies of each node of a line segment have been determined, the error propagation technique can be used to obtain the error band of the segment (Figure 6). Here, x and y are treated as independent uncorrelated random variables, as indicated by the following formula:\n\n(a) Angle θ between two coordinate systems. (b) The confidence interval established between two known nodes on the basis of the selected significance level. From “a stochastic process-based model for the positional error of line segments in GIS.” by Shi, W., Liu, W., 2000, International Journal of Geographical Information Science, 14(1), 51-66.\n\nWhen (xA,yA) and (xB,yB) follow a normal distribution, the transformed coordinates (x,y) and (x’,y’) also have a normal distribution. Given a significance level of α, the confidence interval for the line on the y’-axis can be calculated as (−Zα2.σy′ Zα2. σy′). Plotting and connecting all points within this confidence level yields Figure 6, which is similar to the GIS result.23\n\n\nResults\n\nThe LiDAR data employed in this study were collected in a mountainous region using an Optech Galaxy ALTM™ 30/70 scanner provided by Chung-Hsing Surveying, Taichung, Taiwan. The flight altitude was set at 4,400 m. Non-terrain LiDAR point clouds were filtered out of the data. The LiDAR system captured data at a density of 0.05 points/m2 and had horizontal and vertical accuracies of approximately 2.2 and 0.35 m, respectively. The authors have provided flow diagram of line growin to benefit readers and peers to replicate our work in Figure 10. The mountainous region investigated in this study is shown in Figure 1(a). Given the low density of LiDAR data, a search radius of 50 m was selected to capture a sufficient number of point clouds for depicting ridge and valley lines.\n\nIdentifying local maxima in C values is critical for designating seed points to initiate the growth of ridge and valley lines. In Figure 7, the point clouds are classified into two types using Equation (1).\n\nNOTE: Candidate seeds are indicated in orange, and other points are in green. Own work.\n\nFollowing the initial phase, the line growth was executed using Equations (2)–(4). In this step, redundant point clouds were eliminated, and points were connected to form ridges or valley lines. Figure 8 illustrates the results with different colors demarcating the various line segments. The search radius was 50 m. The basic threshold (ω) is approximately 5°, and three times the average value (3ω) is 15°applied as the threshold value in this study. Although some fragmented ridge and valley lines were obtained, the line growth algorithm effectively extracted both prominent and subtle line features, despite the low point cloud density.\n\nNOTE: Each with a unique color. The most crucial lines were successfully extracted. Own work.\n\nRidges and valley lines were obtained following the line-growing procedure, although these lines consisted of fragmented segments (Figure 8). The theoretical accuracies of the ridge and valley lines were calculated and the corresponding data are listed in Table 1. The lowest horizontal and vertical theoretical accuracies are approximately 2.5 and 0.40 m. These values closely match the accuracies reported in LiDAR instrument documentation. In some instances, the theoretical accuracy surpassed the reported instrument accuracy. Notably, applying the line-growing method resulted in considerably greater line accuracy, as indicated by a 90% enhancement in both horizontal and vertical measurements (2.508 vs. 0.253 m and 0.398 vs. 0.040 m, respectively; Table 1).\n\nIn this region, a contour map was drawn by experienced survey workers using stereo plotters. The interval height of the contour lines was 20 m, and the nodes of the contour lines were applied to produce a Delauney triangulation network. The extracted nodes of the line in Figure 8 were interpolated using Equation (6), and the interpolated accuracy is displayed in Table 2. The worst interpolated accuracy (approximately 16.102 m) is still less than the interval height of contour lines (20m), therefore the method is effective in enhancing the accuracy, even at 98% (16.102 vs. 0.205 m).\n\nFigure 9 shows the contour lines together with the results, and indicates the favorable accuracy and reliability of the results. Automated processes can reduce the required time and effort by eliminating redundant tasks.\n\nNOTE: Lines extracted through line growth (red) and contour lines (green). Own work.\n\n\nDiscussion\n\nThis study employed the TVM to obtain the line feature strength C and its corresponding eigenvector v of discrete LiDAR point clouds, which are helpful parameters for extracting valley and ridge lines from LiDAR datasets on mountainous terrain. By utilizing the local C maxima, redundant data points can be effectively eliminated, and the computational efficiency can be enhanced. Furthermore, the angles between successive v vectors serve as crucial metrics for refining the alignment of adjacent points along the lines. C and v values contribute substantially to the line-growing technique applied to mountainous regions in this study. The concept of a moving mask was adopted to maintain intricate line details. Employing the line-growing technique enables the extraction of primary and minor ridge and valley lines contingent upon specific project requirements. The method can be applied to any terrain to extract line features, which is different from setting thresholds to affect the final results.\n\nThe line-growing technique developed in this study can yield highly accurate line nodes for the extraction of ridge and valley lines in mountainous regions. The proposed approach is effective in capturing both primary and minor ridges but tends to produce lines that are short and fragmented. One avenue for improvement lies in connecting these fragmented ridge or valley lines when they belong to the same topographical features that will be studied in the future. The method presented in this paper is fast and automated and can furnish operators with a wealth of detailed information about minor line features. This enables the extraction of ridge and valley lines that are tailored to specific requirements. Undoubtedly, the method developed here can be generalized to a large amount of LiDAR data.\n\nEthical approval and consent were not required.", "appendix": "Data availability\n\nZenodo: Extracting Ridge and Valley Lines in Mountainous Areas from Airborne Lidar Data by Utilizing Line Feature Strength, https://doi.org/10.5281/zenodo.12771247. 24\n\nThis project contains the following underlying data:\n\n• Contour.ods\n\n• LidarData.ods\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 are grateful to Chung-Hsing Surveying Co., Ltd., Taichung, Taiwan, for providing LiDAR datasets.\n\n\nReferences\n\nYou RJ, Lin BC: Building feature extraction from airborne Lidar data based on tensor voting algorithm. Photogramm. Eng. Remote. Sens. 2011; 77(12): 1221–1231. Publisher Full Text\n\nYou RJ, Lin BC: A quality prediction method for building model reconstruction using LiDAR data and topographic map. IEEE Trans. Geosci. Remote Sens. 2011; 49(9): 3471–3480. Publisher Full Text\n\nDey EK, Awrangjeb M, Tarsha Kurdi F, et al.: Machine learning-based segmentation of aerial LiDAR point cloud data on building roof. Eur. J. Remote Sens. 2023; 56(1): 2210745. Publisher Full Text\n\nZhao J, You S: Road network extraction from airborne LiDAR data using scene context. In 2012 IEEE Computer Society Con-ference on Computer Vision and Pattern Recognition Workshops. 2012; pp. 9–16. Publisher Full Text\n\nKraus K, Pfeifer N: Advanced DTM generation from LIDAR data. International Archives of Photogrammetry Remote Sensing And Spatial Inf. Sci. 2001; 34(3/W4): 23–30.\n\nŠtroner M, Urban R, Křemen T, et al.: UAV DTM acquisition in a forested area–comparison of low-cost photogrammetry (DJI Zenmuse P1) and LiDAR solutions (DJI Zenmuse L1). Eur. J. Remote Sens. 2023; 56(1): 2179942. Publisher Full Text\n\nOkyay U, Telling J, Glennie CL, et al.: Airborne lidar change detection: An overview of Earth sciences applications. Earth Sci. Rev. 2019; 198: 102929. Publisher Full Text\n\nAl-Kakey O, Othman AA, Al-Mukhtar M, et al.: Proposing Optimal Locations for Runoff Harvesting and Water Management Structures in the Hami Qeshan Watershed, Iraq. ISPRS Int. J. Geo Inf. 2023; 12(8): 312. Publisher Full Text\n\nVernon J, St. Peter J, Crandall C, et al.: Spatial Application of Southern US Pine Water Yield for Prioritizing Forest Management Activities. ISPRS Int. J. Geo Inf. 2023; 12(2): 34. Publisher Full Text\n\nSoycan M, Tunalıoğlu N, Öcalan T, et al.: Three dimensional modeling of a forested area using an airborne light detection and ranging method. Arab. J. Sci. Eng. 2011; 36: 581–595. Publisher Full Text\n\nStreutker DR, Glenn NF: LiDAR measurement of sagebrush steppe vegetation heights. Remote Sens. Environ. 2006; 102(1-2): 135–145. Publisher Full Text\n\nKushwaha SKP, Singh A, Jain K, et al.: Qualitative Analysis of Tree Canopy Top Points Extraction from Different Terrestrial Laser Scanner Combinations in Forest Plots. ISPRS Int. J. Geo Inf. 2023; 12(6): 250. Publisher Full Text\n\nMichałowska M, Rapiński J, Janicka J: Tree species classification on images from airborne mobile mapping using ML. NET. Eur. J. Remote Sens. 2023; 56(1): 2271651. Publisher Full Text\n\nGonzales RC, Paul W: Digital image processing. Addison-Wesley Longman Publishing Co., Inc.; 1987.\n\nMcLaughlin RA: Extracting transmission lines from airborne LIDAR data. IEEE Geosci. Remote Sens. Lett. 2006; 3(2): 222–226. Publisher Full Text\n\nGuan H, Yu Y, Li J, et al.: Extraction of power-transmission lines from vehicle-borne lidar data. Int. J. Remote Sens. 2016; 37(1): 229–247. Publisher Full Text\n\nBailly JS, Lagacherie P, Millier C, et al.: Agrarian landscapes linear features detection from LiDAR: application to artificial drainage networks. Int. J. Remote Sens. 2008; 29(12): 3489–3508. Publisher Full Text\n\nChang YC, Song GS, Hsu SK: Automatic extraction of ridge and valley axes using the profile recognition and polygon-breaking algorithm. Comput. Geosci. 2008; 24(1): 83–93. Publisher Full Text\n\nGülgen F, Gökgöz T: Automatic extraction of terrain skeleton lines from digital elevation models. International Archives of Photogrammetry, Remote Sensing and Spatial Inf. Sci. 2004; 35(B3).\n\nMedioni G, Lee MS, Tang CK: A Computational framework for segmentation and grouping. Elsevier Science B.V; 2000.\n\nYou RJ, Lee CL: Accuracy improvement of airborne Lidar strip adjustment by using height data and surface Feature strength information derived from the tensor voting algorithm. ISPRS Int. J. Geo Inf. 2020; 9: 50. Publisher Full Text\n\nSchuster HF: Segmentation of lidar data using the tensor voting framework. Proceedings of the XXth ISPRS Congress: Geo-Imagery Bridging Continents, Commission III, 12–23 July, Istanbul, Turkey, 12–23 July. 2004; pp. 1073–1078.\n\nShi W, Liu W: A stochastic process-based model for the positional error of line segments in GIS. Int. J. Geogr. Inf. Sci. 2000; 14(1): 51–66. Publisher Full Text\n\nYou R, Lee C: Extracting Ridge and Valley Lines in Mountainous Areas from Airborne Lidar Data by Utilizing Line Feature Strength. [Data set]. 2024. Publisher Full Text" }	[ { "id": "324632", "date": "26 Sep 2024", "name": "Fayez Tarsha Kurdi", "expertise": [ "Reviewer Expertise Extraction and modeling of LiDAR data" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIntroduction large amount of terrain data that: remove “terrain” please don’t use “etc”, please check the text. If image extraction techniques are employed, please cite a suitable reference such as: [ ref 1 ] Please replace “Scholars” with “authors”. In urban environments, where buildings and roofs exhibit regular patterns, point clouds on surfaces are readily distinguishable from others owing to their high surface feature strength. Lines can be identified at the intersections of two adjacent surfaces. Please cite a suitable reference such as: [ ref 2 ] Please highlight the contribution and novelty of this study.\nMethods Please don’t put two section titles consecutively, you must add a transition paragraph between them, please check the paper.\nPlease add an organigram that describes the suggested approach.\nGeometric feature strength\nYou don’t discuss how you extracted the ground class from the measured point cloud. Please detailed “tensor communication” approach and mention the used equations. Please explain how you got Figure 2.\nPlease cite a reference about the calculation of eigenvectors such as: [ ref 3 ]\nPlease cite a reference for the region growing algorithm. How did you select the threshold values? Please cite a reference for the local maxima algorithm. Please add a new section to detail all used thresholds. Please cite the source of all used equations in the paper, if you develop an equation, please explain how you got it. Please define all parameters used in all used Equations. Please define all equation elements under them. Please add a datasets section to present the used data. Figure 10 should be in the method section. Please add a conclusion section and do not forget to present future work.\n\nIs the rationale for developing the new method (or application) clearly explained? Partly\n\nIs the description of the method technically sound? Partly\n\nAre sufficient details provided to allow replication of the method development and its use by others? Partly\n\nIf any results are presented, are all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? No", "responses": [] } ]	1	https://f1000research.com/articles/13-1011
https://f1000research.com/articles/12-1279/v1	06 Oct 23	{ "type": "Data Note", "title": "Identification of high-performing antibodies for SPARC-related modular calcium-binding protein 1 (SMOC-1) for use in Western Blot and immunoprecipitation", "authors": [ "Riham Ayoubi", "Sara González Bolívar", "Michael Nicouleau", "Kathleen Southern", "Carl Laflamme", "NeuroSGC/YCharOS/EDDU collaborative group", "Riham Ayoubi", "Sara González Bolívar", "Michael Nicouleau", "Kathleen Southern" ], "abstract": "SPARC-related modular calcium-binding protein 1, otherwise known as SMOC-1, is a secreted glycoprotein involved in various cell biological processes including cell-matrix interactions, osteoblast differentiation, embryonic development, and homeostasis. SMOC-1 was found to be elevated in asymptomatic Alzheimer’s disease (AD) patient cortex as well as being enriched in amyloid plaques and in AD patient cerebrospinal fluid, arguing for SMOC-1 as a promising biomarker for AD. Having access to high-quality SMOC-1 antibodies is crucial for the scientific community. In this study, we characterized seven SMOC-1 commercial antibodies for Western blot and immunoprecipitation, using a standardized experimental protocol based on comparing read-outs in knockout cell lines and isogenic parental controls. We identified successful antibodies and encourage readers to use this report as a guide to select the most appropriate antibody for their specific needs.", "keywords": [ "Uniprot ID Q9H4F8", "SMOC1", "SMOC-1", "SPARC-related modular calcium binding protein 1", "antibody characterization", "antibody validation", "western blot", "immunoprecipitation" ], "content": "Introduction\n\nThe SMOC1 gene encodes the SPARC (secreted protein acidic and rich in cysteine)-related calcium-binding protein 1 (SMOC-1), a secreted glycoprotein involved in numerous extracellular processes.1–3 Expressed in various tissues with localization to the basement membrane and extracellular matrix, SMOC-1 regulates cell-matrix interactions through its ability to bind cell-surface receptors, growth factors, extracellular matrix and cytokines.2,4 Through its binding to receptors on the cells surface, SMOC-1 modulates growth factor signalling involved in osteoblast differentiation.5 In addition to being a critical regulator of various biological processes, SMOC-1 plays a role in the pathophysiology of diverse diseases, including cancer development and progression.1\n\nProteomic studies have uncovered SMOC-1 to be highly enriched in a subpopulation of amyloid plaques, in AD patients and to be elevated in asymptomatic AD cortex.6 Recently, SMOC-1 was shown to be elevated in cerebrospinal fluid from AD patients.7 Although it remains unknown why SMOC-1 co-localizes with only some amyloid plaques, it is hypothesized that SMOC-1 may interact with amyloid-beta (Aβ) species that have been subjected to post-translational modifications.6 More comprehensive research is required to examine the mechanistic role of SMOC-1 in AD.\n\nMechanistic studies would be greatly facilitated with the availability of high-quality antibodies. Here, we compared the performance of a range of seven commercially-available antibodies for SMOC-1, and validated several high-quality antibodies for Western blot and immunoprecipitation, enabling experts in the field to select the most appropriate antibodies for their experimental needs. In turn, allow a reproducible approach to the biochemical and cellular assessment of SMOC-1 properties and function, in both a healthy and diseased state.\n\n\nResults and discussion\n\nOur standard protocol involves comparing readouts from parental and knockout cells.8–12 To identify a cell line that expresses adequate levels of SMOC-1 protein to provide sufficient signal to noise, we examined public proteomics databases, namely PaxDB13 and DepMap.14 HeLa was identified as a suitable cell line and thus HeLa was modified with CRISPR/Cas9 to knockout the corresponding SMOC1 gene (Table 1).\n\nSMOC-1 is predicted to be a secreted protein. Accordingly, we collected concentrated culture media from both parental and SMOC1 KO cells and used the conditioned media to probe the performance of the antibodies (Table 2) side-by-side by Western blot and immunoprecipitation. The profiles of the tested antibodies are shown in Figures 1 and 2.\n\n = recombinant antibody.\n\n1 refers to new antibodies with RRID that have recently been created (August 2023) but will be available on the Antibody Registry in the coming weeks.\n\nHeLa WT and SMOC1 KO were cultured in serum free media, and 30 μg of protein from concentrated culture media were processed for Western blot with the indicated SMOC-1, antibodies. The Ponceau stained transfers of each blot are shown. Antibody dilutions were chosen according to the recommendations of the antibody supplier. All antibodies were tested at 1/2000. Predicted band size: 48 kDa. = recombinant antibody.\n\nImmunoprecipitation was performed on concentrate culture media from HeLa WT, and using 2.0 μg of the indicated SMOC-1, antibodies pre-coupled to Dynabeads protein A. Samples were washed and processed for Western Blot with the indicated SMOC-1, antibody. For Western blot, ab313569 was used at 1/1000. The Ponceau stained transfers of each blot are shown for similar reasons as in Figure 1. SM=8% starting material; UB=8% unbound fraction; IP=immunoprecipitated, HC= antibody heavy chain, = recombinant antibody.\n\nIn conclusion, we have screened seven SMOC-1 commercial antibodies by Western blot and immunoprecipitation. Under our standardized experimental conditions, several high-quality antibodies were identified, 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 can be found on Zenodo, an open-access repository.15,16\n\n\nMethods\n\nAll SMOC-1, antibodies are listed in Table 2, together with their corresponding Research Resource Identifiers (RRID), to ensure the antibodies are cited properly.17 Peroxidase-conjugated goat anti-rabbit is from Thermo Fisher Scientific (cat. number 65-6120).\n\nHeLa SMOC1 KO clone was generated with low passage cells using an open-access protocol available on Zenodo.org. The guide RNA used to knockout the SMOC1 gene is CUCGUAGGACCUGCCAUCAG.\n\nBoth HeLa WT and SMOC1 KO cell lines used are listed in Table 1, together with their corresponding RRID, to ensure the cell lines are cited properly.18 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). Cells were starved in DMEM high-glucose containing L-glutamate and penicillin/streptomycin.\n\nHeLa cells WT and SMOC1 KO were washed three times with PBS 1x and starved for ~18 hrs. Culture media were collected and centrifuged for 10 min at 500 x g to eliminate cells and larger contaminants, then for 10 min at 4500 x g to eliminate smaller contaminants. Culture media were concentrated by centrifuging at 4000 x g for 30 min using Amicon Ultra-15 Centrifugal Filter Units with a membrane NMWL of 10 kDa (MilliporeSigma cat. number UFC901024). Culture media were supplemented with 1x protease inhibitor cocktail mix (MilliporeSigma, cat. number P8340).\n\nWestern blots were performed as described in our standard operating procedure.10–12,19 Western blots were performed with precast midi 4-20% Tris-Glycine polyacrylamide gels from Thermo Fisher Scientific (cat. number WXP42012BOX) ran with Tris/Glycine/SDS buffer from Bio-Rad (cat. number 1610772), loaded in Laemmli loading sample buffer from Thermo Fisher Scientific (cat. number AAJ61337AD) and transferred on nitrocellulose membranes. BLUelf prestained protein ladder from GeneDireX (cat. number PM008-0500) was used. 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) prior to detection with the iBright™ CL1500 Imaging System from Thermo Fisher Scientific (cat. number A44240).\n\nImmunoprecipitation was performed as described in our standard operating procedure.10–12,20 Antibody-bead conjugates were prepared by adding 2 μg of antibody 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) from Thermo Fisher Scientific (cat. number 10002D). Tubes were rocked for ~1 hr at 4°C followed by two washes to remove unbound antibodies.\n\nStarved HeLa WT culture media were concentrated as described above and supplemented with protease inhibitor. 0.3 mL aliquots at 1.6 mg/mL of protein 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 4-20% Tris-Glycine polyacrylamide gels. VeriBlot for IP Detection Reagent:HRP from Abcam (cat. number ab131366) was used as a secondary detection system at a concentration of 0.3 μg/mL.", "appendix": "Data availability\n\nZenodo: Antibody Characterization Report for SMOC-1, https://doi.org/10.5281/zenodo.8277962. 15\n\nZenodo: Dataset for the SPARC-related modular calcium-binding protein 1 (SMOC-1) antibody screening study, https://doi.org/10.5281/zenodo.8253319. 16\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgment\n\nWe would like to thank the NeuroSGC/YCharOS/EDDU collaborative group for their important contributions 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. Members of the group can be found below.\n\nNeuroSGC/YCharOS/EDDU collaborative group: Riham Ayoubi, Thomas M. Durcan, Aled M. Edwards, Carl Laflamme, Peter S. McPherson, Chetan Raina and Kathleen Southern\n\nThank you to the Structural Genomics Consortium, a registered charity (no. 1097737), for your support on 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 article can be found on Zenodo (doi: 10.5281/zenodo.8277962).\n\n\nReferences\n\nGao Q, Mok HP, Zhuang J: Secreted modular calcium-binding proteins in pathophysiological processes and embryonic development. Chin. Med. J. 2019; 132(20): 2476–2484. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVannahme C, Smyth N, Miosge N, et al.: Characterization of SMOC-1, a novel modular calcium-binding protein in basement membranes. J. Biol. Chem. 2002; 277(41): 37977–37986. PubMed Abstract \| Publisher Full Text\n\nHuang XQ, Zhou ZQ, Zhang XF, et al.: Overexpression of SMOC2 Attenuates the Tumorigenicity of Hepatocellular Carcinoma Cells and Is Associated With a Positive Postoperative Prognosis in Human Hepatocellular Carcinoma. J. Cancer. 2017; 8(18): 3812–3827. Publisher Full Text\n\nBornstein P, Sage EH: Matricellular proteins: extracellular modulators of cell function. Curr. Opin. Cell Biol. 2002; 14(5): 608–616. Publisher Full Text\n\nChoi YA, Lim J, Kim KM, et al.: Secretome analysis of human BMSCs and identification of SMOC1 as an important ECM protein in osteoblast differentiation. J. Proteome Res. 2010; 9(6): 2946–2956. PubMed Abstract \| Publisher Full Text\n\nDrummond E, Kavanagh T, Pires G, et al.: The amyloid plaque proteome in early onset Alzheimer's disease and Down syndrome. Acta Neuropathol. Commun. 2022; 10(1): 53. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJohnson ECB, Bian S, Haque RU, et al.: Cerebrospinal fluid proteomics define the natural history of autosomal dominant Alzheimer's disease. Nat. Med. 2023; 29(8): 1979–1988. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLaflamme C, McKeever PM, Kumar R, et al.: Implementation of an antibody characterization procedure and application to the major ALS/FTD disease gene C9ORF72. elife. 2019; 8: 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\nAyoubi R, Southern K, Laflamme C, et al.: The identification of high-performing antibodies for Midkine for use in Western blot and immunoprecipitation [version 1; peer review: awaiting peer review]. F1000Res. 2023; 12: 148. Publisher Full Text\n\nAyoubi R, Southern K, Laflamme C, et al.: The identification of high-performing antibodies for Secreted frizzled-related protein 1 (sFRP-1) for use in Western Blot and immunoprecipitation [version 1; peer review: awaiting peer review]. F1000Res. 2023; 12: 291. Publisher Full Text\n\nAyoubi R, Southern K, Laflamme C, et al.: The identification of high-performing antibodies for Apolipoprotein E for use in Western Blot and immunoprecipitation [version 2; peer review: 1 approved]. F1000Res. 2023; 12: 810. Publisher Full Text\n\nWang M, Herrmann CJ, Simonovic M, et al.: Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines. Proteomics. 2015; 15(18): 3163–3168. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDepMap, Broad: DepMap 19Q3 Public ed.2019.\n\nAyoubi R, Bolivar SG, Nicouleau M, et al.: Antibody Characterization Report for SMOC-1.2023.\n\nSouthern K: Dataset for the SPARC-related modular calcium-binding protein 1(SMOC-1) antibody screening study. [Data set]. Zenodo. 2023.\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\nAyoubi R, McPherson PS, Laflamme C: Antibody Screening by Immunoblot.2021.\n\nAyoubi R, Fotouhi M, McPherson P, et al.: Antibody screening by Immunoprecitation.2021." }	[ { "id": "314301", "date": "27 Aug 2024", "name": "Deborah Moshinsky", "expertise": [ "Reviewer Expertise antibody characterization and validation" ], "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\nSPARC (secreted protein acidic and rich in cysteine)-related calcium-binding protein 1 (SMOC-1) is involved in the pathophysiology of a number of diverse diseases. In Alzheimer's disease (AD), SMOC-1 has been found to co-localize with some amyloid plaques, although it's mechanistic role in the disease has not been well-investigated. The availability of high quality antibodies would facilitate research into SMOC-1's involvement in AD, so the investigators compared the performance of 7 commercially available antibodies in Western blot and immunoprecipitation to allow researchers to assess antibody performance in these applications. The authors present a scientifically sound Western blot and immunoprecipitation study of all 7 antibodies against SMOC-1. The protocols were presented in sufficient detail for the work to be repeated and the reader can interpret whether the antibodies worked or not under the given experimental conditions. No assessment of the results was given, however the authors give appropriate reasoning for not including such an assessment.\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": [] }, { "id": "313912", "date": "30 Aug 2024", "name": "Christian Tiede", "expertise": [ "Reviewer Expertise antibody alternative scaffolds", "phage display" ], "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 manuscript, Ayoubi et al. investigated the specificity of seven commercial anti-SMOC1 antibodies in Western Blot and immunoprecipitation utilising HeLa wild-type and knockout cells. The manuscript is well-written, with experiments well executed and technically sound. Although the authors do not provide a detailed analysis and interpretation of their results, the data are well presented and clearly indicate suitable antibodies for WB and IP studies. Additional comments:\n1) It would have been helpful if the authors had explained why immunofluorescence or immunohistochemistry were not considered for this study.\n2) It would be useful to also indicate in the figure captions that a secondary antibody was used.\n3) It might be understandable that the authors do not make explicit antibody recommendations. However, the controversial result of the secondary reagent used for IP should be discussed. VeriBlot for IP detection reagent was most likely used to avoid interference from denatured IgG. Nevertheless, the heavy chain was detected in some antibodies.\n4) In the methods section on immunoprecipitation, the authors should clarify how samples were processed for SDS-PAGE and Western blotting.\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? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes", "responses": [ { "c_id": "12338", "date": "03 Sep 2024", "name": "Kathleen Southern", "role": "Author Response", "response": "Thank you Christian Tiede for your comprehensive report of this Data note. After reading your comments and feedback, we will be submitting an updated version of this article as to address your concerns and provide clarifications on specific experimental setups used. We are confident our response, as well as the new version submitted have clarified any concerns you may previously have had. 1) It would have been helpful if the authors had explained why immunofluorescence or immunohistochemistry were not considered for this study. Following our standardized antibody characterization platform, available on Protocol exchange (https://doi.org/10.21203/rs.3.pex-2607/v1), immunofluorescence (IF) is not performed when the target protein is secreted. Given the fixation and permeabilization methods used in this protocol, performing IF for secreted proteins presents many limitations and challenges. Immunohistochemistry (IHC) is not currently within the characterization platform. The main reason being that, given our knockout (KO) cell line-based protocol, it would be extremely challenging to KO proteins in human tissues for the entire human genome. That being said, the idea of including IHC to the platform is being troubleshooted and we hope to include this antibody-based application in the future. We’ve recently included Flow Cytometry (FC) to our protocol and are in the process of revisiting many Data Notes to include the FC data. 2) It would be useful to also indicate in the figure captions that a secondary antibody was used. Thank you for this feedback. We will be submitting a new version of this manuscript and the secondary antibodies and detection systems used will be included in the figure legends for all applications. 3) It might be understandable that the authors do not make explicit antibody recommendations. However, the controversial result of the secondary reagent used for IP should be discussed. VeriBlot for IP detection reagent was most likely used to avoid interference from denatured IgG. Nevertheless, the heavy chain was detected in some antibodies. VeriBlot was used as a secondary detection system as the expected SMOC-1 molecular weight was very similar to that of the immunoglobulin heavy chain, 48 kDa and 50 kDa, respectively. The proximity of these molecular weights can cause antibodies used in the WB following the IP to cross-react with the heavy chain, preventing the true immunoprecipitated signal from being detected. That is why VeriBlot was used as the secondary detection systems as it would not react with the heavy chain. This is proven correct as the heavy chain is detected independently in the IP of 3 antibodies (ab200219, PA5-113408 and A20482). To understand our selection method of secondary detection systems for IP experiments, please refre to Figure 9 of the detailed procedure on Protocol exchange (https://doi.org/10.21203/rs.3.pex-2607/v1), that will be listed as reference 8 in the updated version of the article. 4) In the methods section on immunoprecipitation, the authors should clarify how samples were processed for SDS-PAGE and Western blotting. In the updated version of this manuscript, to be submitted shortly, we will include the reference to our entire antibody characterization platform which provides the step-by-step details of this procedure." } ] } ]	1	https://f1000research.com/articles/12-1279
https://f1000research.com/articles/13-781/v1	09 Jul 24	{ "type": "Data Note", "title": "A guide to selecting high-performing antibodies for CSNK2A1 (UniProt ID: P68400) for use in western blot, immunoprecipitation and immunofluorescence", "authors": [ "Riham Ayoubi", "Maryam Fotouhi", "Charles Alende", "Vera Ruíz Moleón", "Kathleen Southern", "Carl Laflamme", "NeuroSGC/YCharOS/EDDU collaborative group", "ABIF consortium", "Riham Ayoubi", "Maryam Fotouhi", "Charles Alende", "Vera Ruíz Moleón", "Kathleen Southern" ], "abstract": "Casein kinase II subunit alpha (CSNK2A1), a serine/threonine kinase, phosphorylates multiple protein substrates and is involved in diverse cellular and biological processes. Implicated in various human diseases, high-performing antibodies would help evaluate its potential as a therapeutic target and benefit the scientific community. In this study, we have characterized ten CSNK2A1 commercial antibodies 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 larger, collaborative initiative seeking to address antibody reproducibility issues by characterizing commercially available antibodies for human proteins and publishing the results openly as a resource for the scientific community. While use 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 P68400", "CSNK2A1", "Casein kinase II subunit alpha", "antibody characterization", "antibody validation", "western blot", "immunoprecipitation", "immunofluorescence" ], "content": "Introduction\n\nCasein kinase II subunit alpha (CSNK2A1), encoded by the CSNK2A1 gene, is a catalytic subunit of the serine/threonine enzyme, casein kinase 2; essential for cell cycle progression, apoptosis, transcription and viral replication.1–5 Relevant to the etiology of many diseases, including the identification of two missense mutations in the CSNK2A1 gene associated with autism spectrum disorder, CSNK2A1 is emerging as a promising biomarker and therapeutic target.1,6–17 High-performing antibodies would enable data reproducibility and reliable research findings.\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.18–20 Here, we evaluated the performance of ten commercially-available antibodies for CSNK2A1 for use in western blot, immunoprecipitation and immunofluorescence, enabling biochemical and cellular assessment of the proteins properties and function. The platform for antibody characterization used to carry out this study was endorsed by a committee of industry and academic representatives. It consists of identifying human cell lines with adequate target protein expression and the development/contribution of equivalent knockout (KO) cell lines, followed by antibody characterization procedures with most of the commercially available antibodies against the corresponding target protein. The standardized consensus antibody characterization protocols are openly available on Protocol Exchange (DOI: 10.21203/rs.3.pex-2607/v1).21\n\nThe 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. Guidelines on how to interpret antibody characterization data found in this study are featured on the YCharOS gateway.22\n\n\nResults and discussion\n\nOur standard protocol involves comparing readouts from wild-type (WT) and KO cells.23,24 The first step is to identify a cell line(s) that expresses sufficient levels of CSNK2A1 to generate a measurable signal using antibodies. To this end, we examined the DepMap transcriptomics database to identify all cell lines that express the target 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). The HAP1 cell lines expresses the CSNK2A1 transcript at 7.0 log2 (TPM+1) RNA levels, which is above the average range of cancer cells analyzed. Parental and CSNK2A KO HAP1 cells were obtained from Horizon Discovery (Table 1).\n\nFor western blot experiments, WT and CSNK2A KO protein lysates were ran on SDS-PAGE, transferrred onto nitrocellulose membranes, and then probed with ten CSNK2A1 antibodies in parallel (Table 2, Figure 1).\n\n* Monoclonal antibody.\n\n** Recombinant antibody.\n\nLysates of HAP1 (WT and CSNK2A KO) were prepared and 30 μg of protein were processed for western blot with the indicated CSNK2A1 antibodies. The ponceau stained transfers of each blot are presented to show equal loading of WT and KO lysates and protein transfer efficiency from the polyacrylamide gels to the nitrocellulose membrane. Antibody dilutions were chosen according to the recommendations of the antibody supplier. An exception was given to 68200-1-Ig* recommended at 1/20 000, as the signal was too weak and was therefore diluted and was used at 1/10 000. Antibody dilution used: ab76040** at 1/500, ab236664 at 1/1000, MAB7957* at 1/1000, NBP3-19853** at 1/1000, 2656 at 1/500, GTX107576 at 1/500, GTX107897 at 1/500, GTX107949 at 1/500, 68200-1-Ig* at 1/10 000, 702811** at 1/10 000. Predicted band size: 45 kDa. Monoclonal antibody, Recombinant antibody.\n\nWe then assessed the capability of all ten antibodies to capture CSNK2A1 from HAP1 protein extracts using immunoprecipitation techniques, followed by western blot analysis. For the immunoblot step, a specific CSNK2A1 antibody identified previously (refer to Figure 1) was selected. Equal amounts of the starting material (SM), the unbound fraction (UB), as well as the whole immunoprecipitate (IP) eluates were separated by SDS-PAGE (Figure 2).\n\nHAP1 lysates were prepared, and immunoprecipitation was performed using 2.0 μg of the indicated CSNK2A1 antibodies pre-coupled to Dynabeads protein G or protein A. Samples were washed and processed for western blot with the indicated CSNK2A1 antibody. For western blot, 702811* was used at 1/10 000. The ponceau stained transfers of each blot are shown for similar reasons as in Figure 1. SM = 4% starting material; UB = 4% unbound fraction; IP = immunoprecipitate, HC = antibody heavy chain. Monoclonal antibody, Recombinant antibody.\n\nFor immunofluorescence, ten antibodies were screened using a mosaic strategy. First, HAP1 WT and CSNK2A1 KO cells were labelled with distinct fluorescent dyes in order to distinguish the two cell lines, and the ten CSNK2A1 antibodies were evaluated. Both WT and KO lines were imaged in the same field of view to reduce staining, imaging and image analysis bias (Figure 3). Quantification of immunofluorescence intensity in hundreds of WT and KO cells was performed for each antibody tested.21 The images presented in Figure 3 are representative of the results of this analysis.\n\nHAP1 WT and CSNK2A1 KO cells were labelled with a green or a far-red fluorescent dye, respectively. WT and KO cells were mixed and plated to a 1:1 ratio in a 96-well plate with an optically clear flat-bottom. Cells were stained with the indicated CSNK2A1 antibodies and with 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, antibodies were tested at concentrations where the signal from each antibody was in the range of detection of the microscope used. Antibody dilution used: ab76040* at 1/500, ab236664 at 1/100, MAB7957* at 1/500, NBP3-19853** at 1/300, 2656 at 1/30, GTX107576 at 1/100, GTX107897 at 1/100, GTX107949 at 1/200, 68200-1-Ig* at 1/500, 702811** at 1/250. Bars = 10 μm. Monoclonal antibody, *Recombinant antibody.\n\nIn conclusion, we have screened ten CSNK2A1 commercial antibodies by western blot, immunoprecipitation and immunofluorescence. Several high-quality antibodies that successfully detect CSNK2A1 under our standardized experimental conditions can be identified. Researchers who wish to study CSNK2A1 in a different species are encouraged to select high-quality antibodies, based on the results of this study, and investigate the predicted species reactivity of the manufacturer before extending their research.\n\nThe underlying data for this study can be found on Zenodo, an open-access repository for which YCharOS has its own collection of antibody characterization reports.27,28\n\n\nMethods\n\nThe standardized protocols used to carry out this KO cell line-based antibody characterization platform was established and approved by a collaborative group of academics, industry researchers and antibody manufacturers. The detailed materials and step-by-step protocols used to characterize antibodies in western blot, immunoprecipitation and immunofluorescence are openly available on Protocol Exchange, a repository dedicated to openly sharing scientific research protocols (DOI: 10.21203/rs.3.pex-2607/v1).21\n\nCell lines used and primary antibodies tested in this study are listed in Table 1 and 2, respectively. To ensure that the cell lines and antibodies are cited properly and can be easily identified, we have included their corresponding Research Resource Identifiers, or RRID.25,26", "appendix": "Data availability\n\nZenodo: Antibody Characterization Report for CSNK2A1, doi.org/10.5281/zenodo.10818214. 27\n\nZenodo: Dataset for the CSNK2A1 antibody screening study, doi.org/10.5281/zenodo.11078556. 28\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgment\n\nWe 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. Members of the group can be found below. 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, Peter S. McPherson, 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 your support on 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.10818214).\n\n\nReferences\n\nBorgo C, D’Amore C, Sarno S, et al.: Protein kinase CK2: a potential therapeutic target for diverse human diseases. Signal Transduct. Target. Ther. 2021; 6(1): 183. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPinna LA: Protein kinase CK2: a challenge to canons. J. Cell Sci. 2002; 115(Pt 20): 3873–3878. PubMed Abstract \| Publisher Full Text\n\nMeggio F, Pinna LA: One-thousand-and-one substrates of protein kinase CK2?. FASEB J. 2003; 17(3): 349–368. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRyu MY, Kim DW, Arima K, et al.: Localization of CKII β subunits in Lewy bodies of Parkinson’s disease. J. Neurol. Sci. 2008; 266(1-2): 9–12. PubMed Abstract \| Publisher Full Text\n\nGibson SA, Benveniste EN: Protein kinase CK2: an emerging regulator of immunity. Trends Immunol. 2018; 39(2): 82–85. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHong H, Benveniste EN: The immune regulatory role of protein kinase CK2 and its implications for treatment of cancer. Biomedicines. 2021; 9(12): 1932. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIossifov I, O’Roak BJ, Sanders SJ, et al.: The contribution of de novo coding mutations to autism spectrum disorder. Nature. 2014; 515(7526): 216–221. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYuen RKC, Merico D, Bookman M, et al.: Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder. Nat. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAyoubi R, Fotouhi M, Alende C, et al.: Antibody Characterization Report for Casein kinase II subunit alpha (CSNK2A1).2024. Publisher Full Text\n\nAyoubi R, Laflamme C: Dataset for the Casein kinase II subunit alpha antibody screening study. [Dataset]. Zenodo. 2024. Publisher Full Text" }	[ { "id": "303886", "date": "01 Aug 2024", "name": "Odile Filhol", "expertise": [ "Reviewer Expertise Cell biology and protein kinase CK2 specialist." ], "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 untitled “A guide to selecting high-performing antibodies for CSNK2A1 for use in western blot, immunoprecipitation and immunofluorescence” describes the characterization of ten CSNK2A1 commercially available antibodies and their indicated protocols. As written in the abstract, these studies are part of a larger collaborative initiative that is very interesting, and useful, especially in the case of Casein Kinase 2 for which, some antibodies are sometime not adapted. The major concern for me, as a specialist of CK2, is that there is not at least, a comment on the specificity of the antibodies to recognize the CSNK2A2 isoform, that is highly homolog to CSNK2A1. Does the HAP1 cell line used by the authors, express this isoform? In the immunoprecipitation assays illustrated in Figure 2, 2 µg of each antibody was used. How did you decide to select 2 µg of antibody to coupled them on beads? However, either in Ponceau red staining or using the same antibody for western blot detection, for some of them, the heavy chain antibody is not visible. This is probably due to the low binding of the antibody. Could you please comment on that in the manuscript? In Figure 3, could you show a least one picture representative of the HAP1 WT (green) and CSNK2A1 KO (far red) cells that allow identifying them. Minor points: In table 2, stars in the second column are not useful since the information is provided in column 5. Stars and the corresponding legend should be removed. In Figure 1 and 3, the antibody dilution should be indicated together with the name of each antibody. Except the points raised in the comments above, the results are well presented. However, I would have liked to have a useful conclusion, suggesting the best CK2 antibodies in relation to their different applications.\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? Partly", "responses": [ { "c_id": "12225", "date": "05 Sep 2024", "name": "Kathleen Southern", "role": "Author Response", "response": "Thank you to Odile Filhol and Catherine Pillet for your thorough analysis of our manuscript presenting antibody characterization data for ten commercial CSNK2A1 antibodies to the scientific community. We hope our response to your comments and concerns clarify any misinterpretations and questions you may have previously had. Additionally, the authors have revisited the initial manuscript and made necessary changes to include a detailed methods section as to ensure the procedure is reproducible. As well, a limitation section has been included to address concerns regarding the nature of the platform and inherent limitations associated with it. Please refer to version 2. Major points: The major concern for me, as a specialist of CK2, is that there is not at least, a comment on the specificity of the antibodies to recognize the CSNK2A2 isoform, that is highly homolog to CSNK2A1. Does the HAP1 cell line used by the authors, express this isoform? Author Response: Based on the characterization table provided by Depmap, HAP1 expresses the CSNK2A2 isoform at 5.8 log2(TPM+1). That being said, this study is shared with the scientific community to help researchers find selective antibodies, already commercially available, for CSNK2A1. That is why a CSNK2A1 KO cell line was selected. To test the ability of the antibodies to recognize the isoform, we would need to test them in a CSNK2A2 KO line. In the immunoprecipitation assays illustrated in Figure 2, 2 µg of each antibody was used. How did you decide to select 2 µg of antibody to coupled them on beads? However, either in Ponceau red staining or using the same antibody for western blot detection, for some of them, the heavy chain antibody is not visible. This is probably due to the low binding of the antibody. Could you please comment on that in the manuscript? Author Response: The amount of 2 µg is selected based on previous experience with trial and error. 1ug was tested in the past and optimized to 2 µg to limit cross reactivity in the IP lane when performing the western blot for IP. As for the ponceau staining, the initial concentrations provided by the manufacturers are followed when adding the 2 µg of antibody. In some cases, adhering to the manufacturers antibody concentrations can result in concentrations that are highly diluted. For example, the 2656 antibody from Cell Signalling Technology sis provided at a concentration of 0.03 µg/ul. Given this low concentration, the amount of antibody is very minimal preventing the heavy chain from being visible. In Figure 3, could you show a least one picture representative of the HAP1 WT (green) and CSNK2A1 KO (far red) cells that allow identifying them. Author Response: All of the underlying data is available in the Dataset, referenced in this manuscript and available on the YCharOS zenodo community. Please refer to the following link: https://doi.org/10.5281/zenodo.11078556 . The addition of Table 3 should also clarify how the WT and KO cells can be identified. Minor points: In table 2, stars in the second column are not useful since the information is provided in column 5. Stars and the corresponding legend should be removed. Author Response: The stars are used outside throughout the report to highlight the renewable antibodies while also allowing the readers to remember the clonality of each antibody without having to refer back to Table 2. In Figure 1 and 3, the antibody dilution should be indicated together with the name of each antibody. Author Response: The antibody dilutions are indicated with the catalog number of each antibody in the figure legends. Except the points raised in the comments above, the results are well presented. However, I would have liked to have a useful conclusion, suggesting the best CK2 antibodies in relation to their different applications. Author Response: We understand this concern and it is why we have chosen to submit the antibody characterization data in the format of Data Notes. As explained in the F1000 article guidelines, Data Notes do not include result analyses or conclusions. Furthermore, the authors prefer to remain unbiased while being transparent with the results obtained from the experiments. To provide context for readers who do not have experience analyzing results from such characterization methods utilizing knockdown lines as controls, we have included a subsequent Table to demonstrate how one can identify successful vs unsuccessful antibodies in each application. Please refer to Table 3 in the updated submission." } ] }, { "id": "303880", "date": "02 Aug 2024", "name": "David Litchfield", "expertise": [ "Reviewer Expertise Areas of expertise include signal transduction", "protein kinases", "kinase inhibitors and phosphoproteomics. The CK2 family of protein kinases (including CSNK2A1 and CSNK2A2) have represented a central focus of our 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 Data Note presents a systematic characterization of a number of commercially available antibodies directed against the gene product of CSNK2A1 (also referred to as the alpha subunit of Casein Kinase II). As noted by the authors, CSNK2A1 is involved in numerous fundamental biological processes and has been implicated as a promising therapeutic target. High-quality antibodies against CSNK2A1 and reliable protocols for the use of these antibodies are therefore of considerable importance both for elucidating its biological functions and for advancing efforts to explore the promise of CSNK2A1 as a therapeutic target. Utilization of knockout cell lines to demonstrate that the antibody signal is dependent on the expression of CSNK2A1 provides particularly compelling validation of the specificity of the antibodies. To further enhance the utility of this report and its accessibility to the research community, I can offer the following suggestions.\n\nConsidering that the gene product encoded by CSNK2A1 is referred to by a variety of names in the published literature in addition to terms adopted by UniProt, it may be beneficial to include additional terms (including CK2alpha and/or CK2α as well as CKIIalpha or CKIIα that are commonly used in the literature). This suggestion is intended to maximize visibility of this article using different search engines. The CSNK2A1 and CSNK2A2 genes encode proteins with very similar enzymatic characteristics and a very high degree of sequence similarity especially within their catalytic kinase domains. The main differences between the gene products encoded by CSNK2A1 and CSNK2A2 reside within their distinct C-terminal domains that extend beyond their kinase domains. In reviewing the technical information for some of the antibodies that was available on vendor websites, which in some cases was very limited due to proprietary considerations, it was not entirely clear to me whether some of these antibodies (particularly polyclonal antibodies and/or antibodies raised against recombinant proteins encompassing regions of very high similarity between CSNK2A1 and CSNK2A2) would also detect CSNK2A2 (ie. CK2α’). Overall, although it does not appear that CSNK2A2 (which represents a protein that is 41 amino acids shorter than the protein encoded by CSNK2A1) is detected by any of the antibodies in Western blots, I believe it would be beneficial to make direct reference to CSNK2A2 in this article and highlight this issue as a potential limitation and/or issue that warrants consideration. This issue would be particularly pertinent for studies to be performed in the absence of the paired cell lines (i.e., parental and knockout) as used in this report.\n\nMinor suggestions.\nIntroduction (line 1) – need to add “kinase” following “serine/threonine” (either to replace “enzyme” or in addition to including “enzyme”) Introduction (line 2). I would recommend replacing “essential” with less definitive terminology (potentially “with essential roles in”) since CSNK2A1 may not be universally involved in all of the listed processes.\n\nResults and Discussion; Last sentence of 1st paragraph and 1st line of 2nd paragraph; should be CSNK2A1 (instead of CSNK2A) – especially considering the existence of CSNK2A2 as noted above. Results and Discussion. 2rd paragraph. “were separated on SDS-PAGE” instead of “ran on SDS-PAGE” Results and Discussion. 3rd paragraph. “equal proportions” rather than “equal amounts”.\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": [ { "c_id": "12224", "date": "05 Sep 2024", "name": "Kathleen Southern", "role": "Author Response", "response": "Thank you to David Litchfield for reviewing this manuscript. We hope our response to your comments and concerns clarify any misinterpretations and questions you may have previously had. Additionally, the authors have revisited the initial manuscript, including a detailed methods section to ensure the procedure is reproducible. As well, a limitation section has been included to address concerns regarding the inherent limitations of the overall platform as well as when evaluating CSNK2A1 antibodies. A third table has been included to help guide readers interpret the results and select high-performing antibodies, which is the aim of this study. Please refer to version 2. Considering that the gene product encoded by CSNK2A1 is referred to by a variety of names in the published literature in addition to terms adopted by UniProt, it may be beneficial to include additional terms (including CK2alpha and/or CK2α as well as CKIIalpha or CKIIα that are commonly used in the literature). This suggestion is intended to maximize visibility of this article using different search engines. Thank you for this suggestion, we are always looking to broaden our audience to increase end-user accessibility of our characterization data to enable researchers to select high-quality antibodies for their research. To this end, we have included the suggested terms to our list of keywords. Please refer to version 2. 2. The CSNK2A1 and CSNK2A2 genes encode proteins with very similar enzymatic characteristics and a very high degree of sequence similarity especially within their catalytic kinase domains. The main differences between the gene products encoded by CSNK2A1 and CSNK2A2 reside within their distinct C-terminal domains that extend beyond their kinase domains. In reviewing the technical information for some of the antibodies that was available on vendor websites, which in some cases was very limited due to proprietary considerations, it was not entirely clear to me whether some of these antibodies (particularly polyclonal antibodies and/or antibodies raised against recombinant proteins encompassing regions of very high similarity between CSNK2A1 and CSNK2A2) would also detect CSNK2A2 (ie. CK2α’). Overall, although it does not appear that CSNK2A2 (which represents a protein that is 41 amino acids shorter than the protein encoded by CSNK2A1) is detected by any of the antibodies in Western blots, I believe it would be beneficial to make direct reference to CSNK2A2 in this article and highlight this issue as a potential limitation and/or issue that warrants consideration. This issue would be particularly pertinent for studies to be performed in the absence of the paired cell lines (i.e., parental and knockout) as used in this report. The authors are aware of the potential cross reactivity of the antibodies with CSNK2A2. The advantage of using genetic strategies (WT vs KO) for characterization is that we are able to detect whether the antibodies can or cannot target CSNK2A1 by assessing whether the signal is lost in the KO line. That being said, transparency and reproducibility is at the core of our initiative’s values which is why we have mentioned this factor in the limitations section, included in version 2 of the manuscript. Minor suggestions. Introduction (line 1) – need to add “kinase” following “serine/threonine” (either to replace “enzyme” or in addition to including “enzyme”) Introduction (line 2). I would recommend replacing “essential” with less definitive terminology (potentially “with essential roles in”) since CSNK2A1 may not be universally involved in all of the listed processes. Results and Discussion; Last sentence of 1st paragraph and 1stline of 2nd paragraph; should be CSNK2A1 (instead of CSNK2A) – especially considering the existence of CSNK2A2 as noted above. Results and Discussion. 2rdparagraph. “were separated on SDS-PAGE” instead of “ran on SDS-PAGE” Results and Discussion. 3rdparagraph. “equal proportions” rather than “equal amounts”. All of these minor changes have been attended to in version 2 of the manuscript which has been submitted." } ] }, { "id": "303889", "date": "27 Aug 2024", "name": "Miwako Homma", "expertise": [ "Reviewer Expertise Intracellular signal transduction", "protein kinases", "CK2", "phospho-proteomics", "CK2-ChIP-Seq", "RNA-Seq", "epigenetics", "and prognostic biomarker of cancer." ], "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 in an area that needs investigating. CK2(CSNK2A1) protein is the first enzyme found to have phosphorylation activity in eukaryotic cells, and it has been shown to participate in various major biological processes. Since there have been several reports of pathologies caused by CSNK2A1 gene mutations, such as Okur-Chung neurodevelopmental syndrome, autism and cancer, high-quality, high-performance antibodies against CSNK2A1 protein are expected to advance research on these diseases. Therefore, the authors conducted the following studies. They characterized ten commercially available antibodies against CSNK2A1 for use: 1. in western blotting under conditions that detect denatured intracellular proteins, 2. in immunoprecipitation to demonstrate antibody recognition of native CSNK2A1 in vivo, and 3. in immunofluorescence for cell imaging. However, a few points require clarification and further validation.\nAntibody evaluations discussed in this manuscript are only comparative observations, and titers of individual antibodies are not quantified. As shown in Figure 1, only one concentration of each antibody diluent was selected, according to the supplier's recommendations. Affinity binding properties are generally verified quantitatively by ELISA, along with Western blotting, in which the intensity of each antibody to the target protein, in this case, purified CSNK2A1, can be calculated by stepwise dilution. I recommend that the authors compare each antibody at the concentration that maximizes performance and that blots be further quantified. It is interesting to note that there are few commercial antibodies that can immunoprecipitate the target molecule, CSNK2A1. However, immunoprecipitation was performed using only one concentration of the indicated antibodies. Although CSNK2A1 (CK2) and CSNK2A2 (CK2’) are encoded at different loci, the amino acid sequences are very similar. Therefore, it is necessary to show that these antibodies are specific for CSNK2A1(CK2) and that they do not also recognize CSNK2A2 (CK2’). For this purpose, I recommend using cells with CSNK2A1 genetically knocked-out (ko) as a control, to show that antibody responses are not observed when only endogenous CANK2A2 is present, or when CSNK2A2 is expressed as a tagged cDNA in ko cells. Alternatively, antibody performance should be validated using human CSNK2A1 or CSNK2A2 recombinant proteins.\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": [] } ]	1	https://f1000research.com/articles/13-781
https://f1000research.com/articles/13-176/v1	11 Mar 24	{ "type": "Software Tool Article", "title": "Spot Spine, a freely available ImageJ plugin for 3D detection and morphological analysis of dendritic spines", "authors": [ "Jean-Francois Gilles", "Philippe Mailly", "Tiago Ferreira", "Thomas Boudier", "Nicolas Heck", "Jean-Francois Gilles", "Philippe Mailly", "Tiago Ferreira", "Thomas Boudier" ], "abstract": "Background Dendritic spines are tiny protrusions found along the dendrites of neurons, and their number is a measure of the density of synaptic connections. Altered density and morphology is observed in several pathologies, and spine formation as well as morphological changes correlate with learning and memory. The detection of spines in microscopy images and the analysis of their morphology is therefore a prerequisite for many studies. We have developed a new open-source, freely available, plugin for ImageJ/FIJI, called Spot Spine, that allows detection and morphological measurements of spines in three dimensional images.\n\nMethod Local maxima are detected in spine heads, and the intensity distribution around the local maximum is computed to perform the segmentation of each spine head. Spine necks are then traced from the spine head to the dendrite. Several parameters can be set to optimize detection and segmentation, and manual correction gives further control over the result of the process.\n\nResults The plugin allows the analysis of images of dendrites obtained with various labeling and imaging methods. Quantitative measurements are retrieved including spine head volume and surface, and neck length.\n\nConclusion The plugin and instructions for use are available at https://imagej.net/plugins/spot-spine.", "keywords": [ "Dendritic spine", "neuronal morphology", "neuroanatomy", "synapse", "image analysis", "ImageJ", "Fiji" ], "content": "Introduction\n\nDendritic spines are small protrusions distributed along the dendrites of neurons. Since each spine corresponds to a glutamatergic synapse, the density of spines located along the dendrite is a measure of the density of neuronal connectivity. Spine density measurement is thus pivotal for assessing connectivity changes during development, upon synaptic plasticity and learning, as well as in the context of psychiatric diseases (Holtmaat and Svoboda, 2009; Penzes et al., 2011; Ma and Zuo, 2022; Heck and Santos, 2023). The morphology of dendritic spines, which are composed of a neck and a head, is another relevant parameter. The size of the head is tightly correlated with the size of the postsynapse density and synaptic current amplitude (Noguchi et al., 2011; Holler et al., 2021). The length and width of the neck may have an influence on the integrative properties of the spine, since the neck represents a morphological constrains so the spine head is a functional compartment isolated for the dendritic shaft (Adrian et al., 2014; Tonnesen and Nägerl, 2016; Cornejo et al., 2022). Therefore, quantification of spine density, spine head size and spine neck length are desirable for each of these parameters retrieve valuable information on neural connectivity, synapse efficacy and plasticity.\n\nDendritic spines however have a size that make them lay at the edge of resolution possibilities of photonic microscopy, hence detection and morphological analysis represent a challenge. Different strategies have been adopted in order to obtain reliable detection and segmentation of dendritic spines, reviewed in Mancuso et al. (2013) and Okabe (2020). Several algorithms have been developed, among which some have been implemented into softwares performing 3D spine detection and analysis. The first developed tools were 3DMA-neuron (Koh et al., 2002) and NeuronIQ (Cheng et al., 2007; Zhang et al., 2007). The widely used NeuronStudio (Rodriguez et al., 2008) has been transferred to commercially available Neurolucida (Dickstein et al., 2016). Another commercial software is Imaris Filament Tracer module (Swanger et al., 2011; Benavides-Piccione et al., 2013). Other applications for spine detection and analysis from confocal microscopy images include Spiso3D (Mukai et al., 2011), SpineLab (Jungblut et al., 2012) and a tool included in the FARSIGHT project (Yuan et al., 2009). More recent applications include 3dSpAn (Das et al., 2022) and a spine detector plugin for the Vaa3D software (Iascone et al., 2020), as well as tools dedicated to two-photon microscopy (Singh et al., 2017; Rada et al., 2018; Argunşah et al., 2022; Vogel et al., 2023) and structured illumination microscopy (Kashiwagi et al., 2019). Machine learning based method has also been developed to identify dendritic spines (Blumer et al., 2015;Smirnov et al., 2018; Guerra et al., 2023), and deep learning approach was used to provide the automated spine segmentation softwares DeepSpineNet and DeepD3 (Vidaurre-Gallart et al., 2022; Fernholz et al., 2024). Herein, we present an ImageJ plugin that allows spine detection, spine heads segmentation and spine necks tracing.\n\n\nMethods\n\nC57BL/6J male mice were maintained in a 12-hour light/12-hour dark cycle, under stable temperature (22°C) and humidity (60%) conditions with ad libitum access to food and water. All experiments were carried out in accordance with the standard ethical guidelines [European Community Council Directive on the Care and Use of Laboratory Animals (86/609/EEC) and the French National Committee (2010/63)].\n\nFluorescent labeling of dendrites was obtained by diolistic method (Heck et al., 2012). DiI (3 mg, ThermoFischer D282) is precipitated on the surface of 1.3 microns tungsten beads (50 mg, BioRad M-20). The coated beads are projected by helium gas pressure (150psi) through a 3 micron pore-size filter (Isopore polycarbonate, Millipore) on brain sections from animals perfused with 1.5% paraformaldehyde. The hydrophobic DiI molecule inserts into plasma membrane and passively diffuse along the dendrite, enabling a fluorescent membrane labeling that outlines neuronal morphology. After labeling, the sections were kept in phosphate buffer saline for 2 hours then mounted in Prolong Gold media (Molecular Probes, P36930).\n\nConfocal Laser Scanning Microscope (SP5, Leica) equipped with a 1.4 NA objective (oil immersion, Leica) was used to acquire image stacks with pixel size of 60 nm and z-step of 200 nm, at excitation wavelength of 561 nm and emission range 570-650 nm. Laser intensity was set so that each image occupies the full dynamic range of the detector (low noise Hybrid detector, Leica). Deconvolution with experimental PSF from 175 nm PS-speck Microscope Point Source fluorescent beads using Maximum Likelihood Estimation algorithm was performed with Huygens software (Scientific Volume Imaging). 150 iterations were applied in classical mode, background intensity was averaged from the voxels with lowest intensity, and signal to noise ratio values were set to a value of 20.\n\n\nImplementation, features and usage\n\nOur plugin Spot Spine uses our Spot Segmentation workflow (Ollion et al., 2013; Heck et al., 2015) and the tracing algorithm from the plugin SNT (Arshadi et al., 2021) to perform three-dimensional detection and analysis of dendritic spines in image stacks (Figure 1). The algorithms are adapted to both isotropic and non isotropic voxels, since, typically, microscopy image stacks have lower axial resolution. Spot Spine is implemented as a plugin for ImageJ/FIJI (ImageJ 1.53, Schindelin et al., 2012a, 2012b). The plugin and instructions for use are available at https://imagej.net/plugins/spot-spine.\n\nAfter an image stack is opened in FIJI/ImageJ and the plugin launched, the user is invited to set parameters for local maxima detection. The plugin imports the dendrite model encoded in a.swc file and compute the local maxima. The user can modify the parameters and manually edit each local maximum. Spine head segmentation is performed by the plugin, and the results can be updated by modifying segmentation parameters as well as manually editing each spine head. The spine necks are then traced, but for images in which the necks are not labeled, the plugin can draw straight lines. A result table is given, including spine head volumes, spine neck length, among other measurements.\n\nBefore proceeding, it first requires importing a reconstructed model of the dendrite in SWC format. The tracing of the dendrite, coded in a swc file, can be obtained with various freely available tools such as SNT (Arshadi et al., 2021) or others (Parekh and Ascoli, 2013; Liu et al., 2022). The dendrite model is automatically imported after launching the plugin. A dendrite coded as SWC is a sequence of connected nodes, thus our plugin applies a frustum between each sphere to improve the representation of the dendrite volume.\n\nSpot Spine detects the dendritic spines by computing the local maxima in the neighbouring region of the dendrite. Since some local maxima can be false positives from the background, or spines from another dendrite located near the studied dendrite, the user is invited to define the three following parameters: intensity value underneath which local maxima are ignored, and minimum and maximum distance from the border of the dendrite model, delimiting around the dendrite a 3D region in which local maxima will be computed. The computed local maxima are listed and displayed in the image stack. A maximum projection of the stack is displayed as well, enabling to easily apprehend the content of the image stack (Figure 2A). The user can then control further intensity and distance criteria to remove false positives. The minimal distance imposed between each local maxima can be reduced or expanded, enabling to adapt to either sparse or dense spine density along the dendrite. Moreover, full manual editing is easily achieved by removing single local maxima or adding local maxima by simply clicking in the image. The manual addition of local maxima is independent of the criteria of intensity and distance. It is noteworthy that the image stack and the maximum projection are synchronized. The user can thus interact on the maximum image projection for obvious cases of false positive and false negative, or in the image stack for better precision. When clicking in the maximum intensity projection, the location of the mouse in the image is recorded, and pixels contained in the region centered around the mouse coordinates are examined in each slice through the depth of the image stack. For spine deletion, the closest maximum is selected based on Nearest neighbor algorithm and deleted from the list. For spine addition, the coordinates of the voxel of highest intensity within a 5x5 region centered around the mouse location is added to the list.\n\nA. Maximum intensity projection showing the detected local maxima. B. Maximum intensity projection showing the segmented spine heads. C. Maximum intensity projection showing traced necks and spine heads. D. 3D volume rendering of the dendrite encoded in swc file, segmented spine heads and traced necks.\n\nOnce the local maxima are found to correspond to each spine head, those are segmented in 3D using the spot segmentation workflow described in Gilles et al. (2017). Segmentation is run with set parameters that lead to consistent results with images obtained by confocal and two-photon microscopy from dendrites with membrane and cytosolic labeling, nevertheless, the user can update the segmentation after setting new values for the parameters. The segmented spine heads appear both on the synchronized image stack and maximum intensity projection (Figure 2B). As described for the selection of local maxima, when clicking in the maximum projection, the object is selected by the analysis of the 3D content of the image stack within a region centered around the 2D coordinates of the mouse location. The user can select spine head that would need to be removed. It is possible to add new spine in case a spine head was not detected by a local maxima by clicking in the spine head. Two spine heads can also be selected to be merged. Indeed, each local maximum will give an object, hence if two local maxima are found in one large spine head, the best strategy is to keep both and thus generate two adjacent objects that can be merged.\n\nIn the third step, spine necks are traced using the SNT algorithm (Figure 2C,D). The minimal euclidian distance between the spine head and the dendrite is computed to identify one voxel at the border of the spine head and one voxel at the border of the dendrite, and the optimal path between these two points is computed using SNT. After tracing, the neck is the one-voxel wide path from the voxel positioned at the edge of the spine head to the voxel preceding the first voxel positioned at the border of the dendrite. Manual editing is provided to delete wrong path and update the neck trace by imposing a new starting point at the border of the spine head. In the case of images in which the necks are not visible, the user can rather choose to obtain the minimal distance between the spine head center and the dendrite which is an estimate of spine length. For each case for which the spine head is in contact with the dendrite, no neck is traced and the spine is categorized as belonging to the stubby type.\n\nAfter completion of spine detection, spine head segmentation and spine neck tracing, a four-channel image is displayed overlaying the original image, the dendrite coded in the SWC file, the segmented spine heads and the traces of the spine necks. A table is retrieved in which the measurements of several morphological parameters are given, including spine head volume and surface as well as neck length.\n\n\nDiscussion\n\nWe have implemented a new tool for 3D spine detection and analysis as an ImageJ/Fiji plugin. Of note, spine heads detection and segmentation works on 2D images as well, but not the tracing of the necks. To our knowledge, two other ImageJ plugins dedicated to dendritic spines exist: the Dendritic_Spine_Counter for 2D images, and SpineJ which is dedicated to 2D analysis of STED microscopy images (Levet et al., 2020). Since full automatization is unattainable when considering the wide range of neuronal labeling and image acquisition protocols, manual editing in a user-friendly interface allows to correct spine detection and segmentation. However, most of the procedure remains automated, so spine head segmentation and spine neck tracing retrieve consistent results. One limitation of our plugin is that it does not give any estimate of the spine neck width. We have chosen to avoid the measurement of that parameter because it falls below the resolution of most confocal and two-photon image stacks. Studies specifically dedicated to the spine neck properties may better benefit from custom procedures for spine neck size estimates. An important concern is the signal to noise ratio of the image stacks. Local maxima detection is noise sensitive, hence noise filtering may help to avoid false positive. Deconvolution is generally recommended (Dumitriu et al., 2011; Heck et al., 2012) since it improves axial resolution, but noise filtering using tools such as the plugin PureDenoise (Luisier et al., 2010) can also yield good results.\n\nMorphological analysis of dendritic spine is often based on classification into discreet categories, namely stubby, thin, mushroom and filopodia. Stubby spines are devoid of neck, which has functional implication since the neck isolates the spine head from the dendrite. Therefore, the plugin indicates in the result table if the spine is of stubby type. The categorization into thin and mushroom spines has however been shown to be arbitrary, since dendritic spines exhibit a continuum of morphologies (Wilson et al., 1983; Tonnesen et al., 2014; Ofer et al., 2021, 2022). Filopodia are elongated spine without head which correspond to an immature stage observed during development. Nevertheless, it can be difficult to distinguish filopodia from long thin spines. Therefore, the distribution of unbiased measurement allows an objective assessment of spine morphology (Pchitskaya and Bezprozvanny, 2020). Categorization of spines by cluster analysis of quantified features have been made (Luengo-Sanchez et al., 2018; Urban et al., 2019; Kashiwagi et al., 2019). Recent softwares, Dxplorer (Choi et al., 2023) and SpineTOOL (Ekaterina et al., 2023), perform a fine analysis of spine morphology by analyzing either 3D surface mesh or chord lens distribution histogram, respectively. The quantitative results obtained with Spot Spine allow the description of the statistical distribution of morphological features, but the user can build categories by grouping dendritic spines according to defined range of values.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nAcknowledgements\n\nWe thank the Imaging facility of the Institut de Biologie Paris Seine, where image acquisitions were performed. The IBPS Imaging facility is supported by Region-Île-de-France, Sorbonne-University and CNRS.\n\n\nReferences\n\nAdrian M, Kusters R, Wierenga CJ, et al.: Barriers in the brain: resolving dendritic spine morphology and compartmentalization. Front. Neuroanat. 2014; 8: 142. Publisher Full Text\n\nArgunşah AÖ, Erdil E, Ghani MU, et al.: An interactive time series image analysis software for dendritic spines. Sci. Rep. 2022; 12(1): 12405. 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PubMed Abstract \| Publisher Full Text\n\nSmirnov MS, Garrett TR, Yasuda R: An open-source tool for analysis and automatic identification of dendritic spines using machine learning. PLoS One. 2018; 13(7): e0199589. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSwanger SA, Yao X, Gross C, et al.: Automated 4D analysis of dendritic spine morphology: applications to stimulus-induced spine remodeling and pharmacological rescue in a disease model. Mol. Brain. 2011; 4: 38. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTonnesen J, Katona G, Rózsa B, et al.: Spine neck plasticity regulates compartmentalization of synapses. Nat. Neurosci. 2014; 17(5): 678–685. PubMed Abstract \| Publisher Full Text\n\nTonnesen J, Nägerl UV: Dendritic spines as tunable regulators of synaptic signals. Front. Psych. 2016; 7: 101. 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PubMed Abstract \| Publisher Full Text" }	[ { "id": "275149", "date": "22 May 2024", "name": "Jiang-Ning Zhou", "expertise": [ "Reviewer Expertise 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\nThe authors of this article present a plugin specifically designed for three-dimensional spine analysis on the ImageJ platform. They provide detailed explanations of the underlying principles and usage procedures of the plugin, and compare it with other software for 2D or 3D dendritic spine analysis, such as Dendritic_Spine_Counter, SpineJ, Dxplorer, and SpineTOOL. The article is user-friendly and provides comprehensive details to comprehend the described methods and their practical application. Following the authors' meticulous instructions, we effortlessly installed and utilized the plugin. The manuscript fulfills expectations for a software paper; however, while reading the paper and using the software, some minor suggestions and questions have emerged. 1. In the \"Introduction\" section, the authors present various software and methods for spine analysis; however, they fail to provide a clear rationale behind the development of the Spot Spine Plugin, despite the existence of numerous available techniques. Please provide a brief introduction here regarding the purpose and significance of developing this plugin. 2. On the interface for selecting spine detection parameters, in order to enhance users' comprehension of parameter definitions, could you please specify the units for \"Minimum distance to dendrite\" and \"Maximum distance to dendrite\" (in pixels or microns)? 3. The \"Result Table\" generated by the plugin presents a wide range of parameters; however, it has come to my attention that the commonly utilized parameter of dendritic spine density is conspicuously absent. It is strongly recommended to incorporate statistical data for this particular parameter. 4. The statistical parameters include the identification (ID) of each identified spine; however, the corresponding ID is not annotated on the output images, which poses challenges for traceability. It is recommended to incorporate ID markers in the output images to facilitate referencing. 5. The statistical analysis of dendritic spines often necessitates the processing of a large number of dendrites, and batch analysis proves to be highly efficient in this regard. It has been observed that Spot Spine lacks a batch analysis feature, thus it is recommended to incorporate this functionality into the plugin. 6. The article utilizes the analysis of spines on a single dendrite as an illustrative example. It would be beneficial to provide clarification and discussion regarding the applicability of the plugin to dendrites with multiple branches.\n\nIs the rationale for developing the new software tool clearly explained? Partly\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Yes\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes", "responses": [ { "c_id": "12339", "date": "05 Sep 2024", "name": "Nicolas Heck", "role": "Author Response", "response": "The authors of this article present a plugin specifically designed for three-dimensional spine analysis on the ImageJ platform. They provide detailed explanations of the underlying principles and usage procedures of the plugin, and compare it with other software for 2D or 3D dendritic spine analysis, such as Dendritic_Spine_Counter, SpineJ, Dxplorer, and SpineTOOL. The article is user-friendly and provides comprehensive details to comprehend the described methods and their practical application. Following the authors' meticulous instructions, we effortlessly installed and utilized the plugin. The manuscript fulfills expectations for a software paper; however, while reading the paper and using the software, some minor suggestions and questions have emerged. 1. In the \"Introduction\" section, the authors present various software and methods for spine analysis; however, they fail to provide a clear rationale behind the development of the Spot Spine Plugin, despite the existence of numerous available techniques. Please provide a brief introduction here regarding the purpose and significance of developing this plugin. Response: We have updated the introduction to better explain the rationale for proposing Spot Spine. « Whilst several tools are available, the general usage of one software for all labeling methods and all image acquisition conditions is unattainable ideal. Hence, our new plugin may be better adapted as compared to others for some users. Spot spine allows precise 3D detection and segmentation of spine heads even in case of high spine density. The automated segmentation ensures reliable and comparable results for shape descriptors of spine head, which are relevant physiological parameters. Furthermore, manual editing at each step of the process ensures that false negative and positive are absent. » 2. On the interface for selecting spine detection parameters, in order to enhance users' comprehension of parameter definitions, could you please specify the units for \"Minimum distance to dendrite\" and \"Maximum distance to dendrite\" (in pixels or microns)? Response:Thank you for that suggestion. We updated the plugin so that information appears. 3. The \"Result Table\" generated by the plugin presents a wide range of parameters; however, it has come to my attention that the commonly utilized parameter of dendritic spine density is conspicuously absent. It is strongly recommended to incorporate statistical data for this particular parameter. Response:The Result Table gives information on each spine, but spine density is obviously essential information. It actually was in the plugin, but your commentary made us realize that the code was missing in the version uploaded on the webpage. The plugin has now been updated so at the end of the process (after clicking « finish »), the following informations appears in the Log window : image file name, dendrite length ; total number of spines ; number of spines with neck ; number of stubby spines ; total spine density for 10micron of dendritic length ; spine with neck density for 10micron of dendritic length ; stubby spine density for 10micron of dendritic length. Since it was not mentionned in the manuscript, we added the following sentence is the results section : « Dendrite length, number of spines and spine density is given in a log window ». 4. The statistical parameters include the identification (ID) of each identified spine; however, the corresponding ID is not annotated on the output images, which poses challenges for traceability. It is recommended to incorporate ID markers in the output images to facilitate referencing. Response: We acknowledge this would help, but annotation on the output image is not straightforward. If in the image stack, it would be visible only in one plane ; if on the maximum projection numbers would overlap if spines are close to each other. Nonetheless, the user has several options because the ID of the spine in the table is color coded in the image. For a spine with ID 25, the voxels in the image will have an intensity of 250. Therefore : The user can point on the spine in the image and read the intensity (= the ID) in the FIJI/ImageJ menu window. Since the image is a composite with four channels, the user needs to select the spine head channel (i.e. first channel) otherwise the intensity given may be 0 (in necks and dendrite channels) or a number which is the gray level of the orignial image (fourth channel). To select a channel see the « C » sliding bar at the bottom of the image. The user can read an ID in the table and find it by checking the intensities of the spines in the image. The ID numbers increase with stack depth. Another way is to use the 3DManager of the plugin 3DImageSuite (that plugin is necessarily installed for the proper functioning of Spot spine). In short, the steps to follow are : Go to plugin menu, 3DSuite, 3DManager. Once the manager is open, click on the composite image containing the spine heads, necks, dendrite and image to activate. Choose the spine head channel (i.e. first channel). In the 3DManager, click on « Add Image ». All objects will be listed in the manager. Names are obj1-val10 ; obj2-val20 ; obj3-val30 and so on. ObjX is same as in « Name » column of the Result Table. ValX is the same as the spine head intensity in the image. Click on « Live ROI ». Click on one ROI in the list to make it encircled in yellow in the image stack. 5. The statistical analysis of dendritic spines often necessitates the processing of a large number of dendrites, and batch analysis proves to be highly efficient in this regard. It has been observed that Spot Spine lacks a batch analysis feature, thus it is recommended to incorporate this functionality into the plugin. Response: In nearly all cases, a fully automated procedure would bring false positives and false negatives. Hence we made the choice to design a tool that allows manual editing at each step of the process. Therefore a batch mode would not be of much help. Nevertheless, if several users would contact us for expressing that need, it could be implemented. 6. The article utilizes the analysis of spines on a single dendrite as an illustrative example. It would be beneficial to provide clarification and discussion regarding the applicability of the plugin to dendrites with multiple branches. Response: If the swc file encode a dendrite splitting in two branches (or more), the plugin will detect spines all along the dendrite. In principle, the plugin could be used to detect spines on a complete dendritic tree if the image has the sufficient resolution. However, the purpose of the plugin not to analyse dendritic tree morphology, hence the spine density will not be given for each branch, but as one value for a total dendrite length." } ] }, { "id": "275153", "date": "07 Jun 2024", "name": "Georgina M Aldridge", "expertise": [ "Reviewer Expertise I have >15 years experience counting dendritic spines. I use FIJI relatively frequently", "including to count spines and I am familiar with installing and using plugins", "but I am not myself familiar with building/coding plugins." ], "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 itself is well written and described, but the software tool is currently difficult. I discuss the article first and the tool second.\n\nThe article and tool are targeting an important need. Current tools are incredibly expensive and proprietary. Many in the field still use completely manual counting, which precludes unbiased evaluation of volume or shape. The tool description and the article are thus important.\n\nFor the article, I do recommend the authors say spines are an \"estimate\" of synaptic number, rather than a \"measure\".\n\nTwo other changes are just likely typos, my suggestion in brackets: \"since the neck represents a morphological constrains [constraint], the spine head is a functional compartment isolated [from] the dendritic shaft\"\n\"Therefore, quantification of spine density, spine head size and spine neck length are desirable for each of these parameters [in order to] retrieve valuable information on neural connectivity, synapse efficacy and plasticity.\"\nFor the tool: The FAQ/about text for the tool has multiple typos and should be edited. I was not able to open any of my own 2-photon imaging data sets (despite having an associated SWC file that I made specifically to test this tool). Trying to open them immediately caused an error. The error was not specific so I am unclear what I was doing wrong.\nI was able to open the sample images and tested the program on both a mac and PC running FIJI. The program did find spines in a reliable manner on this one sample image, and produced data that looked exciting and promising. However, as soon as any manual manipulation was attempted, there were difficulties: 1) Often (on both platforms) the manual edit stopped working. If the wrong button was touched in FIJI it led to two things occurring simultaneously. Restarting and not touching any buttons on FIJI (outside of spot spine) sometimes worked. 2) The question mark button did not do anything 3) Green pixels shown on the max local projection are sometimes not seen on the max local merge file. 4) deleting a spine made it so you could not add a spine back at the same location. Often trying to add a spine somewhere else would lead to error \"needs a point\". 5) it was hard to tell when spines are selected- often leading to deleting multiple spines by mistake. There is no undo so this means starting over. Most mistakes I made led to needing to start over. 6) When getting into the spine neck path, clicking update caused the log to show errors. 7) I could not tell which spines were which. I know from the FAQ they are coded by intensity but I could not find how to figure out which was which on the screen. This made it difficult to see how my manual edits were correlating with actual data output. 8) Any amount of fussing to try to add or improve a spine manually led to bits of spine all over the dendrite that I couldn't figure out how to edit.\n\nInitially- the tool looked quite powerful and did map spines on the one sample image in a way that looked like it might be very useful. Unfortunately, all the manual editing caused disruptions, and this was in a perfect demo image. If this is due to my own misreading of the instructions, then perhaps a video demonstrating manual editing of spines would help. As with all such tools, it is possible the particulars of my setup made using the tool more difficult, and others might find it more useful. Alternatively, the tool may just need a bit more refinement to be user-ready.\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? No", "responses": [ { "c_id": "12340", "date": "05 Sep 2024", "name": "Nicolas Heck", "role": "Author Response", "response": "The article itself is well written and described, but the software tool is currently difficult. I discuss the article first and the tool second. The article and tool are targeting an important need. Current tools are incredibly expensive and proprietary. Many in the field still use completely manual counting, which precludes unbiased evaluation of volume or shape. The tool description and the article are thus important. For the article, I do recommend the authors say spines are an \"estimate\" of synaptic number, rather than a \"measure\". Response: We agree, modifications have been done in the manuscript. Two other changes are just likely typos, my suggestion in brackets: \"since the neck represents a morphological constrains [constraint], the spine head is a functional compartment isolated [from] the dendritic shaft\" \"Therefore, quantification of spine density, spine head size and spine neck length are desirable for each of these parameters [in order to] retrieve valuable information on neural connectivity, synapse efficacy and plasticity.\" Response: Thank you, the manuscript has been corrected. For the tool: The FAQ/about text for the tool has multiple typos and should be edited. Response: Thank you for pointing that out, we will correct the webpage I was not able to open any of my own 2-photon imaging data sets (despite having an associated SWC file that I made specifically to test this tool). Trying to open them immediately caused an error. The error was not specific so I am unclear what I was doing wrong. Response: Opening images files is completely independent of our plugin. Opening images is integral part of FIJI/ImageJ. For proprietary files such as .lif or .czi coming from commercial microscopes, the plugin LOCI Importer is needed, however the plugin is by default included in FIJI. In any case, our plugin starts after an image has been opened so the problem is unrelated to our plugin. Or you mean that after the image was open, you could not run spot spine. It could come from the swc file. Some swc contain the xyz coordinates and the diameter of spheres along the dendrite. Some swc contain only the xyz coordinates thus coding a line. When you tested our plugin, it was not able to work with swc without diameter estimation of the dendrite. We have updated the plugin so both type of swc file are compatible. I was able to open the sample images and tested the program on both a mac and PC running FIJI. The program did find spines in a reliable manner on this one sample image, and produced data that looked exciting and promising. However, as soon as any manual manipulation was attempted, there were difficulties: 1) Often (on both platforms) the manual edit stopped working. If the wrong button was touched in FIJI it led to two things occurring simultaneously. Restarting and not touching any buttons on FIJI (outside of spot spine) sometimes worked. Response: The other reviewer and some colleagues did not report similar problems. It may be related to the ImageJ or FIJI version used, or to the version of the plugins 3DImageSuite or SNT installed. A more detailed description of the problem is required to fully respond about the problem mentionned here. For our previously published plugin DiAna, as well as for Spot Spine, our email adress is on the webpage of the plugin and in the publication. We keep answering to all request and help users. In addition, we answer to questions posted on the widely used FIJI/ImageJ oriented « scientific community image forum » : https://forum.image.sc. 2) The question mark button did not do anything Response: Thank you for pointing that out. We updated the plugin so the question mark drives the user to the spot spine webpage. The question mark at the segmentation step drives the user to the webpage describing the segmentation method. 3) Green pixels shown on the max local projection are sometimes not seen on the max local merge file. Response: Unfortunately, green pixels can be difficult to see depending on the local intensity in the other channel. Any plugin can only use the look-up tables and image display internally coded in FIJI/ImageJ. In the plugin, it is offered to have the image in either blue or gray levels. Nevertheless, the user can go to Image>Look-up tables and apply any of those while running the plugin. In some cases, changing brightness&contrast will help as well (Image>Adjust>Brightness&Contrast) 4) deleting a spine made it so you could not add a spine back at the same location. Often trying to add a spine somewhere else would lead to error \"needs a point\". Response:In an earlier version of the plugin, it was not possible to add a spine in a head that was previously deleted. We have updated the plugin so it is know possible. The message « needs a point » indicates that it is first required to define a region of interest before clicking on the « Add » button. As written in the dialog window, the user holds the SHIFT key and click in the image. Then a region of interest appears (as a square selection), and then clicking on « Add » button will prompt the plugin to find a local maxima within the region, and segment the object. 5) it was hard to tell when spines are selected- often leading to deleting multiple spines by mistake. There is no undo so this means starting over. Most mistakes I made led to needing to start over. Response: Undo function is not build in FIJI/ImageJ, it is a known limitations of the program which is not in our hands. Also build in FIJI/ImageJ, selection is shown as yellow line around the selected objet. It is true that once selecting a spine head, to select another will not unselect the previously selected one. The simple reason is that is allows to merge objects when two objects are found in one single spine head (a needed function since in some large spine heads, more than one local maximum can be found, hence the merge function allows to overcome oversegmentation). Once the merge is performed, no spine head is selected. To unsure no objects are selected, the user can click outside of a spine head. This will by default unselect all selected spines. It is a build in function of FIJI/ImageJ, that when clicking outside a selection or an object, a « select none » function is applied. 6) When getting into the spine neck path, clicking update caused the log to show errors. Response: It is difficult to respond without knowing the content of the error message. For our previously published plugin DiAna, as well as for Spot Spine, our email adress is on the webpage of the plugin and in the publication. We keep answering to all request and help users. In addition, we answer to questions posted on the widely used FIJI/ImageJ oriented « scientific community image forum » : https://forum.image.sc. Concerning updating the necks. First delete a neck by clicking on (or near) the head or the neck and then click on « delete path ». Then click again in head while holding SHIFT key, a yellow dot appears. Then click on « Update path ». A new path starting from the dot will be created. Please note that the algorithm computes best path it can detect, so the new path may be same as first. Neck detection is very challenging because intensity of the neck in the image is usually very low. Anytime delete or update path function is applied, the results Table is updated. 7) I could not tell which spines were which. I know from the FAQ they are coded by intensity but I could not find how to figure out which was which on the screen. This made it difficult to see how my manual edits were correlating with actual data output. Response: We acknowledge this would help, but annotation on the output image is not straightforward. If in the image stack, it would be visible only in one plane ; if on the maximum projection numbers would overlap if spines are close to each other. Nonetheless, the user has several options because the ID of the spine in the table is color coded in the image. For a spine with ID 25, the voxels in the image will have an intensity of 250. Therefore : The user can point on the spine in the image and read the intensity (= the ID) in the FIJI/ImageJ menu window. Since the image is a composite with four channels, the user needs to select the spine head channel (i.e. first channel) otherwise the intensity given may be 0 (in necks and dendrite channels) or a number which is the gray level of the orignial image (fourth channel). To select a channel see the « C » sliding bar at the bottom of the image. The user can read an ID in the table and find it by checking the intensities of the spines in the image. The ID numbers increase with stack depth. Another way is to use the 3DManager of the plugin 3DImageSuite (that plugin is necessarily installed for the proper functioning of Spot spine). In short, the steps to follow are : Go to plugin menu, 3DSuite, 3DManager. Once the manager is open, click on the composite image containing the spine heads, necks, dendrite and image to activate. Choose the spine head channel (i.e. first channel). In the 3DManager, click on « Add Image ». All objects will be listed in the manager. Names are obj1-val10 ; obj2-val20 ; obj3-val30 and so on. ObjX is same as in « Name » column of the Result Table. ValX is the same as the spine head intensity in the image. Click on « Live ROI ». Click on one ROI in the list to make it encircled in yellow in the image stack. 8) Any amount of fussing to try to add or improve a spine manually led to bits of spine all over the dendrite that I couldn't figure out how to edit. Response: It is difficult to respond without seeing an image on which the phenomenon you described appears. Again, for our previously published plugin DiAna, as well as for Spot Spine, our email adress is on the webpage of the plugin and in the publication. We keep answering to all request and help users. In addition, we answer to questions posted on the widely used FIJI/ImageJ oriented « scientific community image forum » : https://forum.image.sc." } ] } ]	1	https://f1000research.com/articles/13-176
https://f1000research.com/articles/11-1550/v1	21 Dec 22	{ "type": "Method Article", "title": "Sample size variation in single-time post-dose assessment vs multi-time post-dose assessment", "authors": [ "Sarfaraz Sayyed", "Ashwini Mathur", "Asha Kamath", "Sarfaraz Sayyed" ], "abstract": "Background: Many randomized trials measure a continuous outcome simultaneously at baseline and after taking the drug. For a single continuous post-treatment outcome, the sample size calculation is simple, but if there are assessments at multiple time points post-treatment then this longitudinal data may give more insights by analyzing the data using the repeated measures method. Also, if the sample size is calculated using the single time-point method for longitudinal data, it may lead to a larger than required sample size, increasing the cost and time. Methods: In this research, an effort is made to determine the size of the sample for repeated measures case and then compared with the single post-baseline case. The sample sizes were examined under different scenarios for the continuous type of response variable. Under Mean contrast and Diff contrast the sample sizes were calculated with different correlations. These two scenarios were again examined under compound symmetry as well as Auto regressive of order 1 type of correlation structure in longitudinal data. The graphical presentation is given for better visualization of the scenarios. Results: Sample size required for highly correlated longitudinal data using multi timepoint sample size derivation method led to much smaller sample size requirement as compared to single timepoint sample size calculation method. Conclusions: This study will help researchers to make better decisions in choosing the right method for sample size determination which may reduce the time and cost of carrying out the experiment. Also, we must carefully assess which method to go with when the correlation is weak. More complex correlation structures are not studied in this article but can be studied in the same fashion.", "keywords": [ "sample size estimation", "longitudinal study", "repeated measure analysis", "univariate analysis" ], "content": "Introduction\n\n‘Sample size’ is a term used in any experiment for defining the number of subjects selected or observed in the experiment. Sample used in an experiment is a subset of the entire target population. The target population refers to a group of individuals among whom the research is intended to be conducted in order to draw conclusions about the population. For e.g., for a type II diabetic test drug all humans who are suffering from type II diabetes would form the target population.\n\nThe number of participants in the sample effects the precision of our estimate and the power of the study to draw conclusions. The probability with which one would reject null hypothesis when null hypothesis is not true is said to be the power of the statistical test. So, power gives an idea on the chances of not committing an error of Type II. The size of the sample and the effect size are major factors which affects the power of a study. These are key concepts in designing a clinical trial.1 Sample size calculation is an important activity in setting up clinical trials to ensure achievement of trial objectives.\n\nAs an illustration, consider a study to compare the performance of a professional athlete taking a particular protein shake versus athletes who do not consume any special protein shakes. Narrowing down attention to a portion of the wider group is essential to enable tracking of the eating habits of every elite athlete in the world. This would entail choosing 100 professional athletes for our study at random; in this case, 100 would be the sample size. Based on the data gathered from a sample of 100 elite athletes, the study’s findings potentially characterize the population of all athletes in the sports industry. Lack of full coverage of the target population would result in the outcomes of the study having a margin of error. Given the limitation to examine every situation, the absolute precision of the effect of protein shake on the athlete’s performance would be hard to measure. Sampling error2 is the term used to describe this level of uncertainty or inaccuracy. It affects the estimator’s precision, which is a metric that is important for the chosen target population of all professional athletes.\n\nAlthough sampling error cannot be completely eliminated, it can be reduced. A larger sample typically has a narrower margin of error. We require an appropriate sample size to examine and contrast in order to provide an accurate picture of the effects of protein shake consumption on performance. Note that there comes a point where increasing the sample size has no further effect on the sampling error (law of diminishing returns).3\n\n\nBackground\n\nLongitudinal studies take a longer time but help in determining causality as well as monitoring the trend over time. To see how sample size calculation was addressed in published longitudinal studies we searched the databases such as Scopus, Web of Science, PubMed, ScienceDirect, and Google Scholar using a range of key terms: “designing clinical trials”, “sample size calculation”, “longitudinal studies”, “randomized trials” and “repeated measures”. The ensuing literature review did not reveal much information on details of how the sample size was calculated for these published longitudinal studies.4,5\n\nFormulae for deriving sample size in longitudinal studies is available from several papers.6,7 Basagaña, Liao and Spiegelma8 published a study in which the power as well as the sample size are discussed for time-varying exposures, but how this is practically applied to a longitudinal study design and its outcome is undocumented in published papers. Pourhoseingholi et al.,9 and Karimollah10 both published about the importance of various components for calculating the sample size in medical studies or clinical trials where often there would be more than one post baseline assessment, but sample size calculation is shown assuming single post baseline assessment. Manja and Lakshminrusimha published a two-part study11,12 which does give a good explanation on clinical research design, but sample size is not discussed in detail.\n\nMost of the published studies which have assessments at multiple time points calculate the sample size based on the change from study end time point to baseline whereas a smaller number of papers emphasize on the use of multiple time points into consideration for calculating the sample size.6–8\n\nThe need for this research was prompted by this lack of proper usage of sample size calculation for longitudinal studies and to further explore which method for sample size calculation should be used in a longitudinal study resulting in correlated outcome data.\n\n\nObjective\n\nTo explore the variation in sample size by considering multiple time point assessment versus the change from baseline to a single endpoint.\n\nIn an experiment for testing certain hypothesis with parallel group design, two or more independent groups are considered to be treated under different scenarios in order to compare the outcome of the scenarios. In our study we would consider the objective of comparison of two drugs.\n\nLet Yij (Xij) be the outcome of interest at jth (j = 1, 2, 3, …, t) time point for the ith (i = 1, 2, 3, …, n) patient in the two groups.\n\nFor the parallel group design, these 2n patients will be divided into two groups with 1: 1 ratio where one arm is assigned to receive the test drug and the other arm is assigned to receive the comparator drug.\n\nLet μ1&μ2 be the population mean change from baseline for the test drug and comparator drug respectively.\n\nLet Y¯&X¯ be the sample mean change from baseline outcome for the test drug and comparator drug respectively, where Y¯∼Nμ1σ2n and X¯∼Nμ2σ2n.\n\n\nMethods\n\nChange at single post-baseline assessment from baseline (Single time assessment analysis)\n\nIn a parallel group design study with two arms of equal size let the hypothesis be set as:\n\nH0:μ1−μ2=δ=0, There is no difference between the effects of test and comparator drug.\n\nVs\n\nHa:μ1−μ2=δ>0, Test drug is having larger effect as compared to comparator.\n\nThe test statistic assuming common standard deviation σ for both arms will be given by\n\nNow If H0 is true (and μ1=μ2),then T∼N01, else if Ha is true (i.e., δ>0), then T will still be a normal but with a mean greater than zero.\n\nIf Type II error is denoted by β then power will be simply 1−β and power is the probability to reject H0 when Ha is true. In probability equation it could be written as\n\nNow in any study we would be looking for\n\nAfter solving equation 5, we get\n\nHere n is the sample size required per arm. We will use these formulae in calculating the sample size for single post baseline time point analysis.\n\nChange from baseline with post baseline assessment at multiple timepoints (Multiple time points analysis)\n\nIn a parallel group design study with two arms of equal size and assessments taken at multiple time points let the hypothesis be set as:\n\nHa:ψc=0, there is no difference between the effects of test and comparator drug.\n\nHa:ψc>0, test drug is having larger effect as compared to comparator.\n\nWhere ψc=CΛ,\n\nLet C=c1c2⋮ci⋮ct be the contrast to be tested for the hypothesis and let Λ=μ11−μ21μ12−μ22⋮μ1i−μ2i⋮μ1t−μ2t\n\nμ1i&μ2i are the mean effect in arm one and arm two at time point “i” respectively in a study with t time points. ci can take any value depending on the hypothesis we want to test.\n\nFor e.g., if we want to see the difference between two drugs for change from baseline when t=2, then c1=−1andc2=1 and the resulting ψc will be\n\nWhere σi2 is the variance at time point i and σij represents the covariance between time point i and j.\n\nThe test statistic assuming similar variance-covariance matrix for both arms will be given by\n\nConsider the VarΛ,\n\nSolving for C′.VarΛ.C, we get\n\nSolving equations Equation 8 and Equation 9 for T we get\n\nNow, If we follow similar steps as we did in single time point analysis above, we get\n\nAnd solving Equation 12, we get13\n\nσi2=common variance in thetwogroupsattimepointi.\n\nσij=common covariance in thetwogroups between timepointiandj.\n\nci=contrast appliedattimepointiandtrepresents the number of time points.\n\nWe will use the formulae specified in Equation 13 to calculate the sample size for multiple time point analysis.\n\nAppropriate sample size was calculated for multi-time and single time cases with different scenarios to achieve an overall mean treatment difference (0.9 points) between two treatment groups with common standard deviation (SD) (3.6 points) allowing 5% two-sided type I error and 85% power. The effect size and standard deviation used here are based on a real study.14 This was a three-year study with primary endpoint assessment at end of each year but the sample size calculation in this study was done on the basis of single time point. Since this study failed to recruit the expected number of patients and also had lot of missing data, the characteristics for the primary endpoints from the second year were used as it had equal number of patients in both arms and stabilized assessments.\n\nWe considered a two-arm parallel group scenario with one baseline and one post baseline timepoints to assess on change from baseline in absolute scale. Using the formulae in Equation 6 above for single timepoint analysis the sample size required per arm was 287 cases to show statistical significance.\n\nHere again we considered two arm parallel groups with multiple timepoints and for studying we investigated six cases i.e., three, four, five, six, eight, and 10 timepoints. Each of this case corresponds to number of assessments including baseline. Three timepoints corresponded to the case with one baseline and two post baseline assessments, four timepoints corresponded to the case with one baseline and three post baseline assessments, five timepoints corresponded to the case with one baseline and four post baseline assessments and so on.\n\nFigure 1 and Figure 2 represents each of this case as a line in the plot under different contrast types and correlation structures.\n\nKeeping the SD as 3.6 we tried to vary over two different correlation structures:\n\nCompound symmetry (CS)\n\nCompound Symmetry just means that all the variances are equal and all the covariances are equal. So, the same variance and covariance are used for all subjects. In compound symmetry the covariances across the subjects and the variances (pooled within the group) of the different repeated measures are homogeneous.\n\nWhere σ2 is the common variance assumed to be similar over time and ρ is the assumed correlation. Order of variance covariance matrix will be t × t. ‘t’ is the number of time points.\n\nAuto regressive of order 1(AR1)\n\nThis is the homogeneous variance first-order autoregressive structure. Any two elements that are adjacent have a correlation that is equal to rho (ρ), those separated by a third will have correlation ρ2, and so on. rho is restricted such that –1< ρ <1.\n\nWhere σ2 is the common variance assumed to be similar over time and ρ is the assumed correlation. Order of variance covariance matrix will be t x t. ‘t’ is the number of time points.\n\nAlso, we considered different scenarios of how we want to analyze the results at the end as different contrasts as described below.\n\nWe tried to investigate two types of contrasts.\n\n1. Time-related contrasts i.e., mean over time (mean contrast).\n\nRationale: This contrast comes from the chronic types of disease where regular medicine is required, and the effect remains only for some time and then the disease condition reverses back.\n\nThis will be labelled in the legend of Figure 1 as CS_mean(i) and in the legend of Figure 2 as AR1_mean(i). For e.g., for five timepoints the contrast would look like c(-1, ¼, ¼, ¼, ¼).\n\n2. Mean Difference (change at last time point from baseline) (diff contrast).\n\nRationale: This contrast comes from the types of disease where each dose reduces the disease severity and the over the course it is totally removed from the patient’s body. Here the total effect at the end of the treatment course as compared to the baseline is of interest.\n\nThis will be labelled in the legend of Figure 1 as CS_diff(i) and in the legend of Figure 2 as AR1_diff(i). For e.g., for five timepoints the contrast would look like c(-1, 0, 0, 0, 1).\n\nSample size was calculated for correlation ranging from 0 – 1 with intervals of 0.05 for both the plots Figure 1 and Figure 2. Sample Size was derived using the formulae mentioned in Equation 13.\n\nThe red horizontal line represents the sample size from single time point assessment approach.\n\nCS_diff(i), CS_mean(i) – i represents the no. of visits used for sample size calculation, i = 3,4,5,6,8,10.\n\nThe red horizontal line represents the sample size from single time point assessment approach.\n\nAR1_diff(i), AR1_mean(i) – i represents the no. of visits used for sample size calculation, i = 3,4,5,6,8,10.\n\n\nResults\n\nAll the trend lines for mean difference type of contrast overlaps each other. For mean difference type of contrast, the sample size doesn’t change for an increase/decrease in the number of visits. It changes with the correlation i.e., highly correlated (rho > 0.5) timepoints would need less sample size as compared to low correlated timepoints. Also, for correlation = 0.5 the multiple assessment sample size coincides with that of single time point assessment.\n\nHowever, the sample size does vary when the contrast is set to mean over time. Multiple time point assessment with more timepoints requires less sample size as compared to that of multiple time point assessment with less time points for e.g., the multiple time point assessment with three timepoint requires 86 per arm with correlation 0.8 and the multiple time point assessment with 10 timepoints requires 64 per arm. On the same lines the multiple time point assessment with three timepoints requires 258 per arm with correlation 0.4 and the multiple time point assessment with 10 timepoints requires 192 per arm. This trend shows that the sample size required reduces when the correlation increases. For correlation = 0.1 to 0.35 the sample size coincides with that of single time point assessment.\n\nUnder mean over time contrast the multiple time point assessment requires lower sample size as compared to single time point assessment (287 per arm) for correlation greater than 0.35 and the sample size increases as correlation goes below 0.35.\n\nWhereas for mean difference contrast the multiple time point assessment requires lower sample size as compared to single time point assessment (287 per arm) for correlation greater than 0.7 but requires higher sample size for correlation less than 0.7.\n\nThe trend changes shape for mean difference contrast vs mean over time contrast. Also, at certain point the increase in sample size attenuates for e.g., in case of mean difference type contrast with 10 time points the sample size required doesn’t changes when correlation drops below 0.55.\n\n\nDiscussion\n\nOne of the hurdles in considering the longitudinal methodology for sample size calculation is the assumption on the covariance matrix. It is often easy to estimate the variance of single timepoint as compared to estimating the variance-covariance matrix for multiple time points.\n\nThe above derivations were done for trial design with parallel group, 1:1 ratio and two arms. If the ratio changes or if we have more than two arms or if the design is crossover, then the effective overall sample size would get effected in both the cases i.e., sample size with single time point as well as sample size with multiple timepoints, but the trend would remain the same as shown above in the figures and the results will still hold good. Similar trends should hold for other variance – covariance structures though they have not been simulated here.\n\n\nConclusion\n\nSample size changes depending on the analysis type and the data collected. Both the graphs in Figure 1 and Figure 2 in this study reveal that if response is assessed at multiple timepoints and the correlation between the paired observations is high (> 0.6) then one should consider using repeated measures analysis and consequently determine the size of the sample that is based on the multiple time points scenario which results in lower sample size requirement as compared to the sample size derived assuming single timepoint response assessment. This would reduce the cost, resources, and time in conducting the experiment fastening the new drug development. Also, repeated measures analyses will not drop the patients in which they have certain missing data as compared to single point analysis where the patient will be dropped if the response is missing hence may help in retaining the power.\n\nSample size derivation using longitudinal design method for studies with multiple assessments can be considered of substantial benefit in cost and time although the challenge of estimating the variance-covariance matrix remains.\n\n\nSoftware availability\n\nSoftware available from: The Comprehensive R Archive Network (https://cran.r-project.org/)\n\nSource code available from: https://github.com/Sarfaraz-Sayyed/Sample-Size-Variation.\n\nArchived source code at time of publication: https://zenodo.org/badge/latestdoi/547747570.15\n\nLicense: MIT License.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nAcknowledgement\n\nWe would like to thank Novartis Healthcare Pvt. Ltd. and Manipal Academy of Higher Education for the support to carry out this research and all the reviewers for providing their valuable feedback and suggestions.\n\n\nReferences\n\nFleiss JL: Design and Analysis of Clinical Experiments. New York:John Wiley & Sons;1986.\n\nBiemer PP, Lyberg LE: Introduction to Survey quality. Hoboken, New Jersey:John Wiley and Sons;2003.\n\nArshed N, Rehman HU, Nazim M, et al.: Evading Law Of Diminishing Returns, A Case Of Human Capital Development. Journal of Contemporary Issues in Business and Government. 2021; 27(5): 2569–2584.\n\nKhelif A, Saleh MN, Salama A, et al.: Changes in Health-Related Quality of Life with Long-term Eltrombopag Treatment in Adults with Persistent/Chronic Immune Thrombocytopenia: Findings from the EXTEND Study. Am. J. Hematol. 2019; 94: 200–208. PubMed Abstract \| Publisher Full Text\n\nPalileo-Villanueva LM, Dans AL: Composite endpoints. J. Clin. Epidemiol. 2020; 128: 157–158. Publisher Full Text\n\nBloch DA: Sample size requirements and the cost of a randomized clinical trial with repeated measurements. Stat. Med. 1986; 5(6): 663–667. PubMed Abstract \| Publisher Full Text\n\nHedekar D, Gibbons RD, Waternaux C: Sample size estimation for longitudinal designs with attrition: Comparing time-related contrasts between two groups. J. Educ. Behav. Stat. 1999; 24(1): 70–93. Publisher Full Text\n\nBasagana X, Liao X, Spiegelman D: Power and sample size calculations for longitudinal studies estimating a main effect of a time-varying exposure. Stat. Methods Med. Res. 2011; 20(5): 471–487. PubMed Abstract \| Publisher Full Text\n\nPourhoseingholi MA, Vahedi M, Rahimzadeh M: Gastroenterol Hepatol Bed Bench. Winter. Sample size calculation in medical studies. 2013; 6(1): 14–17.\n\nHajian-Tilaki K: Sample size estimation in epidemiologic studies. Caspian J. Intern. Med. 2011; 2(4): 289–298. PubMed Abstract\n\nVeena Manja MD, Satyan Lakshminrusimha MD: Epidemiology and Clinical Research Design, Part 1: Principles. NeoReviews. 2015; 16(2): e94–e108. PubMed Abstract \| Publisher Full Text\n\nManja V MD, Lakshminrusimha S MD: Epidemiology and Clinical Research Design, Part 1: Study Types. Neoreviews. NeoReviews. 2014; 15(12): e558–e569. PubMed Abstract \| Publisher Full Text\n\nDiggle PJ, Heagerty P, Liang K-Y: Analysis of Longitudinal Data. Second EditionNew York:Oxford Statistical Science Series;2002.\n\nBlack DM, Reid IR, Cauley JA, et al.: The Effect of 6 Versus 9 Years of Zoledronic AcidTreatment in Osteoporosis: A Randomized SecondExtension to the HORIZON-Pivotal Fracture Trial (PFT). J. Bone Miner. Res. 2014; 30(5): 934–944. Publisher Full Text\n\nSarfaraz-Sayyed: Sarfaraz-Sayyed/Sample-Size-Variation: Sample Size variation (V1.0.0). Zenodo. Software.2022. Publisher Full Text" }	[ { "id": "273771", "date": "30 May 2024", "name": "Kiranmoy Das", "expertise": [ "Reviewer Expertise Biostatistics", "Longitudinal data analysis", "Bayesian modeling" ], "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\nReviewer’s comments on the manuscript “Sample-size variation in single-time post-dose assessment vs multi-time post-dose assessment”\nThe manuscript attempts to address a very important and interesting problem. However, the presentation is not quite clear, there are lots of typos and grammar issues here and there. The methodology developed in the manuscript can be improved. My comments are given below. After addressing these comments and after a substantial revision, I can make some positive comment on the manuscript. 1. Introduction: Please provide some good motivation and nice description of the problem. There are several typos. Please avoid the phrase For e.g., this should be For example, and also “The size of the sample and the effect size are major factors which affects”, this should be like “The sample size and effect size are major factors that affect”. 2. Methods: Equation (1), you are assuming here that the variance sigma^2 is known. Please specify it, and also how appropriate this assumption is in real application? 3. For the longitudinal studies, your method depends on the auto-correlation \\rho. You need to estimate \\rho before calculating the sample size. Please clarify that and also discuss how to estimate \\rho. Maybe you run a pilot trial and get an estimate? 4. Both the figures 1 and 2 focus on how the sample size varies with correlation \\rho. For a longitudinal trial, it maybe more important to know how it covaries with the number of time points. Correlation is something that cannot be adjusted, but the number of time points can be adjusted as per the requirement. I think this issue has been ignored in the manuscript.\n\nIs the rationale for developing the new method (or application) clearly explained? No\n\nIs the description of the method technically sound? Yes\n\nAre sufficient details provided to allow replication of the method development and its use by others? No\n\nIf any results are presented, are all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? Yes", "responses": [ { "c_id": "12240", "date": "05 Sep 2024", "name": "Sarfaraz Sayyed", "role": "Author Response", "response": "Thanks Dr. Kiranmoy Das for your review and advice. Please see our response below. Comment 1: We have updated the introduction section. Comment 2: Justification now added above equation no. 1. Comment 3: An explanation of rho estimation is now added. Comment 4: We have added a paragraph under the conclusion section to address this. We have added a few lines in the Introduction section to clarify the rationale. Regarding details for replication of the method, details on assumptions are specified in the section “Calculation of sample size” in the manuscript. The software availability section provides the link to the related R program residing in Github." } ] }, { "id": "294678", "date": "10 Jul 2024", "name": "Ronald Geskus", "expertise": [ "Reviewer Expertise Biostatistics" ], "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 describe some formulas for sample size calculations with longitudinal data with a continuous outcome. The authors only consider one specific approach, namely generalized least squares and comparing changes from baseline. This latter approach is discouraged, see e.g. https://www.bmj.com/content/323/7321/1123.\nMore general methods to perform sample size and power calculations with longitudinal data have been described and implemented in software (e.g. https://journal.r-project.org/articles/RJ-2022-022/).\nAlso, there are some descriptions that need further attention.\n1. The introduction describes the basic principles of hypothesis testing. This can be assumed known and therefore I suggest to leave it out of the paper.\n2. Page 3: The authors describe sampling error as the uncertainty arising from: \"the limitation to examine every situation, the absolute precision of the effect of protein shake on the athlete's performance would be hard to measure.\" I am not sure whether I understand what is written here, but I think it is not correct.\n3. Page 3: Sampling error decreases with increasing sample size, but it is not true that \" there comes a point where increasing the sample size has no further effect on the sampling error\".\n4. Formula (2): power is typically calculated for a specific choice of the effect size, not for all delta>0 at once.\n5. Page 7: \"Appropriate sample size was calculated for multi-time and single time cases with different scenarios to achieve an overall mean treatment difference (0.9 points).\" What is meant with mean difference in the situation with more than 2 time points? The difference could vary per time point but still give a mean difference of 0.9. The last sentence of that paragraph is irrelevant information.\n6. How was \\sigma_{ij} chosen?\n7. Page 8: make more explicit that a discrete AR(1) is assumed. There also exitsts a continuous AR(1)\n8. Page 9: The authors write: \"For correlation = 0.1 to 0.35 the sample size coincides with that of single time point assessment.\" I don't see this in the figure\n9. Page 9: I don't understand the rationale \"effect remains only for some time and then the disease condition reverses back' and \"each dose reduces the disease severity and the over the course it is totally removed from the patient’s body\" for the two contrasts.\n10. Explain why the sample size goes down to zero if the correlation approaches 1. A correlation of 1 does not make sense. It implies that the second measurement is completely determined by the first, and the intervention cannot have any impact.\n11. Legends Fig 1 and 2 have been mixed up.\n\nIs the rationale for developing the new method (or application) clearly explained? No\n\nIs the description of the method technically sound? Yes\n\nAre sufficient details provided to allow replication of the method development and its use by others? Yes\n\nIf any results are presented, are all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? Partly", "responses": [ { "c_id": "12241", "date": "05 Sep 2024", "name": "Sarfaraz Sayyed", "role": "Author Response", "response": "Thanks Dr. Ronald Geskus for your review and advice. Please find below our responses. - Regarding analyzing change from baseline, we completely agree with you. Our intention was just to propose a framework, but we have modified it now to make it more precise. - Regarding methods to perform sample size calculation, we agree with you, but our intention here is to highlight using simple methods to the clinical researchers, the difference in samples required when we have longitudinal information available under 2 different correlation structures. Comment 1: We kept this as this would be helpful to new researchers not having statistical background. Comment 2: We have modified it for better understanding. Comment 3: We have modified and added a note to have more clarity. Comment 4: We fully agree with you, this was a generic equation to show we are looking positive change in response and then further with the examples we have assumed for certain fixed delta how the sample size varies. But have modified it to avoid confusion. Comment 5: We have modified the sentence for better clarity and also removed the last sentence of the paragraph. Comment 6: Sigma was taken from a trial data (reference given) and was assumed to be same over all the time periods. Comment 7: Thanks for bringing this up, we have updated this in the manuscript now. Comment 8: This was wrongly written under figure 1, it was supposed to be under figure 2 conclusion. we have made the necessary changes now. Comment 9: The first rationale refers to chronic diseases where the disease can usually be controlled but not cured. So here we are trying to see that the average effect from the treatment is the one which is expected to control the disease. Have changed the wordings for better understanding. The second rationale is for infectious diseases where with the right treatment regimen the disease will be cured. Have now tried to put in better words. Comment 10: Agree with your comment on both the extreme cases that a correlation of 1 would imply all the effect is due to intervention not leaving any space for error and also that correlation 0 would mean no effect from the intervention. We have now revised the plots to start from 0.05 till 0.9 Comment 11: Have made the necessary changes. - Regarding clarifying the rationale, basically in clinical trials the use of all time point data is not generally used. The effect at intermittent time points and the covariance structure between time points would be helpful which otherwise not taken into consideration results in large sample size. - Regarding conclusion on the methods, we have updated the conclusion to have more insights, how taking into correlation would benefit and also how the effects diminish even if too many timepoints are added." } ] } ]	1	https://f1000research.com/articles/11-1550
https://f1000research.com/articles/12-1216/v1	26 Sep 23	{ "type": "Research Article", "title": "Are numerical scores important for grant proposals' evaluation? A cross sectional study", "authors": [ "Ivan Buljan", "David G. Pina", "Antonija Mijatović", "Ana Marušić", "David G. Pina", "Antonija Mijatović", "Ana Marušić" ], "abstract": "Background: In the evaluation of research proposals, reviewers are often required to provide their opinions using various forms of quantitative and qualitative criteria. In 2020, the European Commission removed, for the Marie Skłodowska-Curie Actions (MSCA) Innovative Training Networks (ITN) funding scheme, the numerical scores from the individual evaluations but retained them in the consensus report. This study aimed to assess whether there were any differences in reviewer comments’ linguistic characteristics after the numerical scoring was removed, compared to comments from 2019 when numerical scoring was still present. Methods: This was an observational study and the data were collected for the Marie Skłodowska-Curie Actions (MSCA) Innovative Training Networks (ITN) evaluation reports from the calls of 2019 and 2020, for both individual and consensus comments and numerical scores about the quality of the proposal on three evaluation criteria: Excellence, Impact and Implementation. All comments were analyzed using the Linguistic Inquiry and Word Count (LIWC) program. Results: For both years, the comments for proposal's strengths were written in a style that reflects objectivity, clout, and positive affect, while in weaknesses cold and objective style dominated, and that pattern remained stable across proposal status and research domains. Linguistic variables explained a very small proportion of the variance of the differences between 2019 and 2020 (McFadden R2=0.03). Conclusions: Removing the numerical scores was not associated with the differences in linguistic characteristics of the reviewer comments. Future studies should adopt a qualitative approach to assess whether there are conceptual changes in the content of the comments.", "keywords": [ "Peer Review", "Linguistic Characteristics", "MSCA program" ], "content": "Disclaimer\n\nAll views expressed in this study are strictly those of the authors and may in no circumstances be regarded as an official position of the European Research Executive Agency or the European Commission.\n\n\nIntroduction\n\nThe process of evaluating research grant proposals has attracted considerable attention in the past decade. With the increasing amount of funding for research, there is a constant need for improvements in evaluation procedures for providing funding to the most promising project proposals. Recent scoping reviews on peer review for research funding recommends, among other propositions, that there is a need for the identification of interventions that are consistent in resolving peer review issues in proposal evaluation (Recio-Saucedo et al., 2022; Shepherd et al., 2018). Studies on grant peer-review evaluation have mostly focused on the analysis of criteria used by expert reviewers when assessing proposals (Abdoul et al., 2012; van Arensbergen and van den Besselaar, 2012; Hug and Aeschbach, 2020). Other studies have investigated the linguistic content of review reports (van den Besselaar et al., 2018; Hren et al., 2022). However, to the best of our knowledge, evidence is missing on how the requirement for numerically scoring a grant proposal, i.e. attributing a numerical/quantitative score to a proposal by a given reviewer, affects the way a reviewer comments or expresses opinions related to the proposal.\n\nThe evaluation process of grants submitted to EU research programs, the so-called Framework Programmes for research and innovation, consists usually of two consecutive steps, with each proposal going through (1) an individual evaluation, made by (typically three) different expert reviewers and (2) a consensus phase, where those reviewers agree on the final evaluation of the proposal. In both parts of the evaluation, the evaluation is normally focused on three criteria: a) research Excellence, b) Impact, and c) Implementation, for which comments must be given separately. Each criterion is attributed a score that determines the total score of the proposal. The result of the consensus stage is an evaluation summary report (ESR), consisting of the consolidated concerted opinions of the group of expert reviewers. Previous studies have established this approach as a stable procedure in the evaluation of research grant proposals (Pina et al., 2021; Buljan et al., 2021).\n\nIn the previous Framework Programme, Horizon 2020 (H2020), some of the grant schemes faced changes in their scoring process. This was the case of the Marie Skłodowska-Curie Actions (MSCA), the flagship funding program dedicated to the promotion of researchers’ mobility and career development at all stages of their careers. In the past, expert reviewers were asked to provide comments and numerical scores for each of the three evaluation criteria in both their individual evaluations (the so-called Individual Evaluation Report – IER) and then at the level of the consensus, resulting in the final score of the evaluation summary report (ESR). For some of the funding schemes of MSCA, this approach was discontinued, and numerical scores were not attributed anymore at the level of individual evaluations (IER). Only textual comments were required at the IER stage, and numerical scores were used at the stage of the consensus for the ESR.\n\nA recent study has indicated that proposal weaknesses have a greater effect on the ranking, compared to proposal strengths (Hren et al., 2022). Based on this finding, the ranking of proposals would greatly depend on the reviewers’ ability to identify and describe the weaknesses. In cases when there is a large number of proposals, qualitative methods of analysis can be ineffective. Therefore, quantitative analyses of the text, i.e. tools that assess quantitative characteristics of the text, can be a solution, as they have been shown to be relevant for proposal evaluation (Luo et al., 2022).\n\nThe objective of this study was to compare the linguistic characteristics of the comments related to the Excellence, Impact, and Implementation criteria in the evaluation reports of MSCA Innovative Training Networks (ITN) proposals submitted in 2019 and 2020, under H2020, in order to assess whether the removal of numerical scoring affected the structure of IER textual comments and whether this change was associated with the evaluation outcome at the consensus stage, i.e. ESR. We chose the ITN granting scheme, because it is, with around 1500 annual submissions and a success rate below 10%, among the most oversubscribed and competitive of the whole framework program.\n\n\nMethods\n\nThis study was preregistered on Open Science Framework: https://osf.io/t84ba.\n\nWe worked on anonymized datasets, without insight about the actual content of the proposal, or the names of the applicants or experts evaluators, so that the regulations on personal data protection were not applicable.\n\nThis was an observational, cross-sectional study conducted in 2022.\n\nThe data analyzed consisted in the IERs and the ESRs of all ITN proposals evaluated in the calls of 2019 and 2020. Each report includes textual comments referring to the different evaluation criteria. Scores of IER were only available for the year 2019. The anonymized quantitative data used for the analysis in this article is available on the Open Science Framework: https://osf.io/6bpvu/?view_only=.\n\nLinguistic characteristics of experts’ comments were assessed using the Linguistic Inquiry and Word Count software (Pennenbaker et al., 2015a, 2015b), a program that counts words related to different psychological states and phenomena and gives a score that is a proportion of the specific category in the entire text.\n\nWe collected the data on the proposal status after evaluation (“Main list”, “Reserve list” or “Rejected”), call in which they were submitted (2019 or 2020), research area, total evaluation scores, as well as numerical scores for Excellence, Implementation and Impact criteria, together with corresponding comments which separately described proposal strengths and weaknesses. We separately analysed IERs and ESRs.\n\nFor the evaluation purposes, proposals are categorized in eight panels: Economics-ECO, Social sciences-SOC, Mathematics-MAT, Physics-PHY, Chemistry-CHE, Engineering-ENG, Environmental sciences-ENV, Life sciences-LIF. For this study, we clustered the MAT-PHY-CHE-ENG-ENV into one single “research domain”: PHYENG. So, the three research domains in this study were PHYENG, ECOSOC and LIF.\n\nLIWC variables were calculated separately for strengths and weaknesses for each of the criteria assessed: They included the word count and the text tone of the evaluation report (Kaatz et al., 2015; Kacewicz et al., 2014; Pennebaker et al., 2015a):\n\na) Analytical tone: higher scores indicate the logical and hierarchical style of writing;\n\nb) Clout tone: higher scores indicate confidence or leadership, with lower scores indicating insecure writing;\n\nc) Authenticity: high scores indicate writing honestly and humbly, with expressing views as personal opinion;\n\nd) Emotional tone: higher scores on emotional tone indicate a higher proportion of words related to a more positive emotional tone.\n\nTo eliminate potential sampling bias, we collected data for the whole cohort of submitted MSCA ITN proposals in 2019 and 2020.\n\nThe descriptive data was presented as frequencies and percentages for project status and research domain. Text characteristics were presented as means and standard deviations, or as means and 95% confidence intervals in cases of figures. We first compared the differences on all variables using a t-test or Chi squared, depending on the nature of the variables. A P value threshold of less than 0.001 was considered to be significant in t test. Variables which were not significant were excluded from further analysis. We used logistic regression to compare differences between the two call years, in which proposal variables (proposal status, word count for research excellence weaknesses, word count for implementation strengths, and negative affect levels for implementation strengths) were predictors and the year of the call was the criterion. The level of significance was set to 0.05. The analysis was done using the R statistical program (R Core Team, 2021) and the JAMOVI package for statistical analysis (The jamovi project, 2023).\n\n\nResults\n\nThe number of evaluated proposals was similar in 2019 (n=1554) and 2020 (n=1503). The number of rejected proposals was 1367 (87.9%) for 2019 and 1333 (88.6%) for 2020, 128 (8.2%) and 148 (9.8%) funded proposals, and 59 (3.8%) and 22 (1.5%) proposals on the reserve list in 2019 and 2020, respectively. The majority of the proposals was from physical sciences and engineering (n=1004, 64.6% for 2019 and n=947, 63.0 for 2020), followed by life sciences (n=391, 25.1% for 2019 and n=387, 25.8%) and economics and social sciences (n=159, 10.2% for 2019 and n=169, 11.2% for 2020).\n\nOverall, review comments were written predominantly in an analytic and objective language, which was indicated by the high level of Analytical tone and low levels of Authenticity; this indicates that a small proportion of reviewers formulated their arguments as personal opinions, rather than objective comments (Figures 1 and 2).\n\nThere was a greater presence of clout and emotional tone in the description of the proposal’s strengths (Figures 1 and 2). Also, a greater proportion of the comments describing the strengths of the proposal had more words related to the positive emotional tone (Figures 1 and 2).\n\nThe acceptance of a proposal was predicted by the linguistic characteristics of the comments related to the weaknesses in the proposal, more specifically lower analytical tone across all three criteria’s weaknesses, a higher negative emotional tone for research excellence and impact weaknesses, and higher clout in research excellence (Table 1). In total, those predictors explained around 30% of the variance of the criteria (McFadden R2=0.30). On the other hand, the differences between 2019 and 2020 were negligible, explaining around 3% of the variance (McFadden R2=0.03) (Table 2). These predictors included the number of words in excellence strengths (both for individual reviewers and consensus reports), lower analytical tone for excellence and impact in individual reports and higher emotional tone in consensus reports.\n\na The categories were ordered as following: rejected, reserved, main listed. Higher odds ratio indicates greater probability for acceptance.\n\na Criterion variable was call year: the 2019 call was labeled as 0 and the 2020 call as 1.\n\nWith regard to the differences in textual characteristics between consensus report evaluation and individual evaluation scores between 2019 and 2020, the observed pattern of greatest differences between consensus score and individual scores in emotional tone was stable across different proposal status (Table 3) and research domains (Table 4). Emotional tone was overall greater for consensus score results.\n\na The difference was calculated for each project as the difference between the Consensus score result and the Individual evaluation score.\n\na The difference was calculated as Consensus score result-Individual evaluation score result; for every corresponding project.\n\n\nDiscussion\n\nIn this study, which included all ITN proposals from 2019 and 2020 calls, we aimed to assess whether the changes in the evaluation procedure were related to differences in characteristics of review reports. We found that the differences in linguistic characteristics between reports fromboth calls (2019 and 2020) were small and negligible from a practical point, indicating that the removal of numerical scores did not result in meaningful changes in the reports’ comments, assessed by quantitative text analysis. For both calls, the comments were written objectively, with weaknesses written with less emotion and more analytically than the proposals’ strengths. On the other hand, we found that the final status of the proposals (i.e. main-listed or rejected) can be predicted by the linguistic characteristics of the reviewer’s comments, especially the tone related to the identified weaknesses, indicating that weaknesses may be crucial in proposal evaluation.\n\nThe comments’ text was written mostly using formal language, indicated by high levels of analytical tone, both for strengths and weaknesses. The same feature was observed in a previous study performed on journals’ reports from peer reviewers (Buljan et al., 2021). Our results also provide evidence for a general advice to the applicants – to be very focused on the objective structure of their proposal (Baumert et al., 2022). When emphasizing proposal strengths, due to the low levels of authenticity, the reviewers less frequently used personal pronouns like “I” or “we”, probably to present the proposal strengths as factual information, and not as a personal opinion. This finding is contrary to the study of Thelwall et al. (2023), which pointed out that higher use of first pronouns in reviews is related with higher proposal quality. On the other hand, in the description of weaknesses, the reviewers more often presented the information as their personal opinion. This finding is further supported by high levels of clout tone in the description of strengths. The clout – the tone which indicates writing from a position of power – was much higher in the description of the project strengths than in the description of the weaknesses, from which we can conclude that reviewers were more certain in their evaluation. The emotional tone was more positive in the description of strengths, probably because of the use of words related to the project’s probable success. There was a greater presence of clout and emotional tone in the description of the proposal’s strengths, which indicates that reviewers wrote with less confidence when discussing the potential flaws of the proposals, compared to when they mentioned the proposal’s strengths. In that respect, it is to be noted that the EC services instruct reviewers that evaluation reports should not express opinions, but rather evaluate factual elements of the proposals.\n\nThe principal difference between consensus and individual scores was in the emotional tone score. Across different categories, the emotional tone was higher in consensus ratings rather than in individual evaluation score, indicating more positive tone of the outcome of the consensus process. This may be due to the fact that only the concensus report is sent our to applicants. The IER remains an internal (intermediate) report and is not externalised and sent to applicants. In a previous study, we found that the agreement between reviewers was very high (Pina et al., 2021). At the time of the individual evaluation, the reviewers do not know whether other reviewers will agree with them. It is possible that, when reviewers need to write a consensus evaluation, they are not limited by the objective language in the evaluation of the proposal, since it is established that other reviewers agree with their opinion, so the tone is more relaxed and positive.\n\nOur previous study of the predictive value of comments on proposals’ strengths and weaknesses in ITN evaluation process used both qualitative and quantitative (machine learning) approach (Hren et al., 2022). Our present results partially confirm the results of that study, which found that proposals’ weaknesses are more predictive of its evaluation outcome (Hren et al., 2022). However, we found that only some elements in the weaknesses are predictive of the proposal status. Specifically, a higher analytical tone and fewer negative evaluation words in comments related to proposals’ weaknesses were associated with a more favorable funding outcome . It needs to be noted that themes that served as predictors in the regression model were identified qualitatively and were better predictors (explained around 55% of the criteria) compared to our quantitative text analysis (around 30% of the criteria). However, due to the large number of proposals, linguistic characteristics of reviewers’ comments may serve as an additional tool in the proposed evaluation, as advised by others (Luo et al., 2022).\n\nThe finding that we did not observe meaningful differences in tone of reviewers’ comments needs to be interpreted in the light of several limitations. It should be noted that our entire quantitative text analysis process was made by dictionary-based text analysis algorithms, which may slightly deviate from manual analysis (Luo et al., 2022), being still predictive for proposal funding outcomes, and that was partially reproduced in our study. One aspect of quantitative text analysis, sentiment analysis or analysis of the text tone, could serve as a useful tool to determine whether there were any differences in the evaluation performed by reviewers after the removal of individual numerical scores, as reviewers were a common part of both procedures. We only focused on the linguistic characteristics of the comments related to the positive and negative sides of the proposals. Qualitative analysis of the proposals would give input on the potential differences between the two calls but, due to the number of the proposals, there is a question of practical value for such an approach. We do not have information about who the reviewers were, which may present relevant information since some individual characteristics, such as experience in research or reviewing, may influence the review process (Seeber et al., 2021). Based on our evaluation, we found no evidence that the removal of numerical scoring produced any differences in the evaluation output.\n\n\nConclusions\n\nThis study assessed whether removing of numerical scores will have a significant effect on the evaluation procedure. The findings indicate that the removal of numerical scores did not contribute to meaningful differences in the evaluation procedure of H2020 ITN proposals or its outcome. Those results support the finding that the procedure used for the evaluation of MSCA grant proposals is very robust and stable.\n\n\nAuthor contributions\n\nIvan Buljan, Conceptualization, Data Curation, Formal Analysis, Investigation, Methodology, Project Administration, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; David G Pina, Conceptualization, Data Curation, Investigation, Methodology, Project Administration, Resources, Writing – Original Draft Preparation, Writing – Review & Editing; Antonija Mijatović, Conceptualization, Data Curation, Formal Analysis, Investigation, Methodology, Writing – Original Draft Preparation, Writing – Review & Editing and Ana Marušić, Conceptualization, Data Curation, Formal Analysis, Funding Acquisition, Investigation, Methodology, Project Administration, Resources, Supervision, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing.", "appendix": "Data availability\n\nOpen Science Framework: Are numerical scores important for grant evaluation?, https://osf.io/6bpvu/?view_only= (Buljan et al., 2021).\n\nThis project contains the following underlying data:\n\n- Data file 1. Dataset_anonymized.csv\n\nOpen Science Framework: Are numerical scores important for grant evaluation?, https://osf.io/6bpvu/?view_only= (Buljan et al., 2021).\n\nThis project contains the following extended data:\n\n- Extended data.docx\n\nOpen Science Framework: STROBE checklist for “Are numerical scores important for grant evaluation? A cross sectional study”, https://osf.io/6bpvu/?view_only= (Buljan et al., 2021).\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\nAbdoul H, Perrey C, Amiel P, et al.: Peer review of grant applications: criteria used and qualitative study of reviewer practices. PLoS One. 2012; 7(9): e46054. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBaumert P, Cenni F, Antonkine ML: Ten simple rules for a successful EU Marie Skłodowska-Curie Actions Postdoctoral (MSCA) fellowship application. PLoS Comput. Biol. 2022; 18(8): e1010371. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBuljan I, Pina DG, Marušić A: Ethics issues identified by applicants and ethics experts in Horizon 2020 grant proposals. F1000Res. 2021; 10: 471. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHren D, Pina DG, Norman CR, et al.: What makes or breaks competitive research proposals? A mixed-methods analysis of research grant evaluation reports. J. Informet. 2022; 16(2): 101289. Publisher Full Text\n\nHug SE, Aeschbach M: Criteria for assessing grant applications: a systematic review. Palgrave Commun. 2020; 6: 37. Publisher Full Text\n\nKaatz A, Magua W, Zimmerman DR, et al.: A quantitative linguistic analysis of National Institutes of Health R01 application critiques from investigators at one institution. Acad. Med. 2015; 90(1): 69–75. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKacewicz E, Pennebaker JW, Davis M, et al.: Pronoun use reflects standings in social hierarchies. J. Lang. Soc. 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Reference Source\n\nRecio-Saucedo A, Crane K, Meadmore K, et al.: What works for peer review and decision-making in research funding: a realist synthesis. Res. Integr. Peer Rev. 2022; 7(1). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSeeber M, Vlegels J, Reimink E, et al.: Does reviewing experience reduce disagreement in proposals evaluation? Insights from Marie Sklodowska-Curie and COST Actions. Res. Eval. 2021; 30(3): 349–360. Publisher Full Text\n\nShepherd J, Frampton GK, Pickett K, et al.: Peer review of health research funding proposals: A systematic map and systematic review of innovations for effectiveness and efficiency. PLoS One. 2018; 13(5): e0196914. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nThe jamovi project: jamovi (Version 2.3) [Computer Software].2023. Reference Source\n\nThelwall M, Kousha K, Abdoli M, et al.: Terms in journal articles associating with high quality: can qualitative research be world-leading? J. Doc. 2023. 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PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "233042", "date": "12 Jan 2024", "name": "Mariana Pascual", "expertise": [ "Reviewer Expertise Linguistics", "Discourse studies", "evaluative linguistic resources" ], "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 represents a high-quality text with a sound justification and is highly relevant in the discipline. The research focus is clearly established, and the procedures for selecting and analyzing data are explained in detail. The language is formal and precise, and there are no signs of ambiguity that may lead to a lack of clarity. The methodological design is simple and well-described, with explicit references to all the tools and variables selected for data analysis. The conclusions are relevant and proportional to the scope of the findings, which are discussed in relation to the corresponding literature. Only one specific linguistic resource is mentioned: the use of first-person pronouns. The reader may benefit from more textual data to accompany the broad categories that the article presents. Including specific examples from the data would have been helpful and increased the article's readability. All in all, the manuscript shows a clear command of the topic, clarity of expression, and a sound and appropriate methodological design.\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": "12292", "date": "26 Aug 2024", "name": "Ivan Buljan", "role": "Author Response", "response": "Thank you for your time and your comments. Kind regards, Ivan Buljan" } ] }, { "id": "246537", "date": "12 Mar 2024", "name": "Sven E Hug", "expertise": [ "Reviewer Expertise research evaluation", "bibliometrics", "peer review" ], "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 examines whether and how the removal of rating scores in grant peer review changes the reviewers’ texts. The analysis is based on data from a funding scheme where the rating scores have been removed at the level of individual reviews (Marie Skłodowska-Curie Actions: Innovative Training Networks, ITN). Data was analyzed using the Linguistic Inquiry and Word Count software (LIWC). The results presented in Figures 1 and 2 show that the removal of rating scores had no effect on the four LIWC categories employed in the study, suggesting that written assessments are not affected by whether reviewers are mandated to assign scores to a proposal or not.\nThe study examines a relevant and original research question, uses a unique data set, and employs an analytical approach previously applied to peer review data (LIWC). However, the study needs to be improved in the following respects:\n(1) Please justify why the five panels MAT-PHY-CHE-ENG-ENV were clustered into one “research domain” and why the two panels ECO-SOC were grouped together. The samples do have very different sizes.\n(2) In the section “Statistical analysis”, variables are mentioned that have not been described in the section “Variables analyzed” (e.g., “word count for research excellence weaknesses”). I suggest that all variables used in the study are listed in a table, including the values the variables can take. If the variables are not self-explanatory, please also provide a description of the variable.\n(3) Many analytical categories are available in LIWC. The current study used four. Please explain why these four categories were chosen and why they are appropriate for addressing the research question.\n(4) In the section “Statistical analysis”, it is stated that the variables that were not significant were excluded from further analysis. Does this mean that variables were excluded before conducting regression analyses? Please cite a method paper that justifies this approach. Please state which variables were excluded and indicate their p values? Please report the results of the t-tests and Chi-square tests according to APA standards.\n(5) In the preregistered study design, regression analysis has not been mentioned. Please explain why regressions were computed and how they are related to the research question. Please also explain why the variables were regressed on proposal status (Table 1). Please state which variable was predicted in Table 2 and why it was predicted (does “ITN calls” mean the years of the call?).\n(6) Tables 3 and 4 are extremely difficult to process and understand. Therefore, I cannot follow the conclusions drawn in the last paragraph of page 6. Please describe more clearly how you arrived at your conclusions and/or present the data in a way that is easier to understand.\n(7) “Discussion” and “Conclusions”: Please discuss the implications of your findings for peer review practice. Please suggest what future research could investigate.\n(8) Please upload the R and Jamovi code to OSF so that others can reproduce your analysis.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? 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? Partly", "responses": [ { "c_id": "12293", "date": "05 Sep 2024", "name": "Ivan Buljan", "role": "Author Response", "response": "Dear reviewer, we are submitting our revised paper and point-by-point responses to your queries. We appreciate your efforts and time invested in our paper. Reviewer 2: Not approved Reviewer comment: The study examines whether and how the removal of rating scores in grant peer review changes the reviewers’ texts. The analysis is based on data from a funding scheme where the rating scores have been removed at the level of individual reviews (Marie Skłodowska-Curie Actions: Innovative Training Networks, ITN). Data was analyzed using the Linguistic Inquiry and Word Count software (LIWC). The results presented in Figures 1 and 2 show that the removal of rating scores had no effect on the four LIWC categories employed in the study, suggesting that written assessments are not affected by whether reviewers are mandated to assign scores to a proposal or not. The study examines a relevant and original research question, uses a unique data set, and employs an analytical approach previously applied to peer review data (LIWC). However, the study needs to be improved in the following respects: (1) Please justify why the five panels MAT-PHY-CHE-ENG-ENV were clustered into one “research domain” and why the two panels ECO-SOC were grouped. The samples do have very different sizes. Author response: Thank you for your comment. We used European Research Council Field classification: https://ejoss.euras-edu.org/erc-field-classification/#:~:text=There%20are%2025%20ERC%20panels,Panels%2C%20LS1%E2%80%93LS9). We understand that samples have different sizes, but this approach allowed us to narrow down the number of categories in a logical manner for statistical analysis. Reviewer comment: (2) In the section “Statistical analysis”, variables are mentioned that have not been described in the section “Variables analyzed” (e.g., “word count for research excellence weaknesses”). I suggest that all variables used in the study be listed in a table, including the values the variables can take. If the variables are not self-explanatory, please also describe the variable. Author response: Thank you for your comment, the table with explanations is now provided. Table 1 Description of LIWC variables used in the study Refer Table 1 For the provided example “word count for research excellence weaknesses”, the variable is word count, but only for a subset of reports that discuss proposal weaknesses. Reviewer comment: (3) Many analytical categories are available in LIWC. The current study used four. Please explain why these four categories were chosen and why they are appropriate for addressing the research question. Author response: We used the four most comprehensive categories, which have been applied in most studies. It is true that by using more specific categories we might find differences, but we would need to apply and compare a vast number of categories to do that. So we opted for a more pragmatic approach in our study. We now state this in the limitations: “…Also, we used the most comprehensive categories, which are very broad. LIWC dictionary contains many different categories, and it is possible that by using more specific categories, one may find meaningful differences…” Reviewer comment: (4) In the section “Statistical analysis”, it is stated that the variables that were not significant were excluded from further analysis. Does this mean that variables were excluded before conducting regression analyses? Please cite a method paper that justifies this approach. Please state which variables were excluded and indicate their p values? Please report the results of the t-tests and Chi-square tests according to APA standards. Author response: Yes, since there was a significant number of potential predictors, and this was an exploratory analysis, we decided to conduct variable selection, firstly by univariate testing and then by multivariate testing through logistic regression. The process follows the procedure recommended by : Bursac, Z., Gauss, C.H., Williams, D.K. et al. Purposeful selection of variables in logistic regression. Source Code Biol Med 3, 17 (2008). https://doi.org/10.1186/1751-0473-3-17 What we now provide are t-tests for comparison between 2019 and 2020, the initial model and final model for call comparison; and also Kruskal Wallis test due to sample size discrepancy, the initial model, and final model published online publicly. Also, Kruskal Wallis tests were done in R, since JASP program cannot support the size of the analysis. The entire procedure is now uploaded on OSF, comparisons, initial and final regression models, as well as descriptive statistics. Reviewer comment: (5) In the preregistered study design, regression analysis has not been mentioned. Please explain why regressions were computed and how they are related to the research question. Author response: Thank you for your observation. Due to the significant number of comparisons, we decided to utilize regression after the preregistration has been done. We now labeled that part in statistical analysis as : “Deviation from the protocol”. Reviewer comment: Please also explain why the variables were regressed on proposal status (Table 1). Author response: We intended to determine whether the linguistic characteristics of IER or CR comments predict the status of the proposal. We now state this in the analysis section. Reviewer comment: Please state which variable was predicted in Table 2 and why it was predicted (does “ITN calls” mean the years of the call?). Author response: We are unsure what the reviewer suggests. The description of the criterion variable is provided below the table. The explanation for ITN is Innovative Training Networks, and it is now added below tables. Reviewer comment: (6) Tables 3 and 4 are extremely difficult to process and understand. Therefore, I cannot follow the conclusions drawn in the last paragraph of page 6. Please describe more clearly how you arrived at your conclusions and/or present the data in a way that is easier to understand. Author response: We apologize to reviewer for the confusion. We added more text to make the results more clear. Reviewer comment: (7) “Discussion” and “Conclusions”: Please discuss the implications of your findings for peer review practice. Please suggest what future research could investigate. Author response: Thank you for your comments, we will add recommendations for future. Reviewer comment: (8) Please upload the R and Jamovi code to OSF so that others can reproduce your analysis. Author response: We have uploaded all analyses, and data, to OSF as JASP files. Thank you for your time spent in reviewing our manuscript. Kind regards, Ivan Buljan" } ] }, { "id": "246528", "date": "14 Mar 2024", "name": "Seba Qussini", "expertise": [ "Reviewer Expertise Research Integrity and Peer review" ], "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 in hand evaluates whether reviewer comments on research proposals differed after the restructuring of the Marie Sklodowska-Curie Actions (MSCA) Innovative Training Networks (ITN) scoring scheme by eliminating the possibility of scoring using numbers. The authors utilize proposal requests data from 2019 and 2020 and found that linguistic characteristics did not differ after the removal of numerical scores from the specified scoring scheme. The following comments are applicable to the current draft of the manuscript:\nIt would be strongly advised that the authors run grammar and typo check, or to obtain language and editing services. The current version of the manuscript has multiple occasions of misspelled words, grammatical errors, and typos. Some examples are figure 1 or 2: the word strengths. First paragraph of discussion: from both. Third paragraph of discussion: the word consensus. Please add an abbreviation section at the end of the manuscript, and make sure that all abbreviations are spelled out at the first encounter throughout the manuscript. The current study fills a current gap in the literature as identified by the authors early in the introduction section. This section can probably be restructured for better understanding of the readers, in the following manner: ideally, the first paragraph would discuss general aspects of peer review, therefore, the gap in literature can be moved towards the end of the introduction, after discussing a few aspects, models, shortcomings, etc. Additionally, the authors may provide examples for the quantitative characteristics in the introduction, and/or further elaborate on the effect of quantitative characteristics on reviewers’ evaluation. Providing more information regarding the Marie Skłodowska-Curie Actions (MSCA) would probably help supplement this section and provide a better understanding of the dynamics of this grant. Furthermore, it could have been useful to touch on other possible proposals’ evaluating methods such as scoring and ranking, as can be found in[1] The last paragraph may be used to highlight further the gap in the literature that the authors aim to bridge with this project, indicating that peer review is highly versatile and a diverse process, yet further focusing on the need to address the general lack of theoretical understanding in multiple aspects of peer review, as can be seen in: [2], and/or the paucity of experimental research in proposals’ peer review as summarized by [3] The authors may want to further elaborate on the reasons for removing the numerical score from MSCA? Was it for the effect of simplifying the peer review process on reviewers’ engagement and quality of report? as pointed out by [4] Registering with the Open Science Framework is a plus. The study design is cross sectional but not observational. The latter terminology may be removed. What is the justification for including data from only 2019 and 2020? Why not expand on the size of data by including more years. Further information may be added to the assessment tool, Linguistic Inquiry and Word Count (LWIC) software, such as the validity and reliability, the LWIC scores, possible cutoffs, totals, etc. The authors do provide a reference, but it would just be easier to have it readily accessible while reading. Under the bias heading: What is the role of including the whole cohort of submitted proposals in 2019 and 2020 in eliminating potential sampling bias? Please make it clear for the readers.\n\nIn the statistical analysis section: How were the predictors established? Was it based on an analysis or from the literature? It would be advised to clarify this detail. Additionally, please provide justification for using the specified p-value 0.001 in your model, as it appears too stringent. In the results section: The majority of proposals were from the physical science and engineering fields. Did this play a role in the outcome of the study, where no differences were detected before and after? The authors may want to expand on this in the discussion section. Additionally, is it possible that COVID19 resultant urgency have affected the review of proposals in 2020? It would also be useful to further elaborate on the blinding model adopted by the MSCA and how they may have influenced the results. In table 3: How can the average word count be negative? Please provide an explanation. It would be great to supplement the discussion section with a few recommendations for future researchers into the topic. Have the authors considered adjusting for possible confounding factors, such as research domain, etc.? If not , please discuss the possible effects of such confounding factors in the Discussion section.\nOverall, the authors follow a logical order in introducing the main aspects of the study, provide sufficient details in some areas and are lacking minute details in other areas. The findings are clearly conveyed along with a proper interpretation of the results. The value of such work would probably benefit research administrators along with policy makers.\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": "12294", "date": "26 Aug 2024", "name": "Ivan Buljan", "role": "Author Response", "response": "Dear reviewers, we are submitting our revised paper and point-by-point responses to your queries. We appreciate your efforts and time invested in our paper. Reviewer 3: Approved with reservations The study in hand evaluates whether reviewer comments on research proposals differed after the restructuring of the Marie Sklodowska-Curie Actions (MSCA) Innovative Training Networks (ITN) scoring scheme by eliminating the possibility of scoring using numbers. The authors utilize proposal requests data from 2019 and 2020 and found that linguistic characteristics did not differ after the removal of numerical scores from the specified scoring scheme. The following comments are applicable to the current draft of the manuscript: It would be strongly advised that the authors run grammar and typo check, or to obtain language and editing services. The current version of the manuscript has multiple occasions of misspelled words, grammatical errors, and typos. Some examples are figure 1 or 2: the word strengths. First paragraph of discussion: from both. Third paragraph of discussion: the word consensus. ANSWER: Thank you for your comment. We went through manuscript and did grammar check and revised the legends to the figures for clarity. Please add an abbreviation section at the end of the manuscript, and make sure that all abbreviations are spelled out at the first encounter throughout the manuscript. ANSWER: Thank you, we have added the explanations in the first encounter now, and the Abbreviations section at the end. The current study fills a current gap in the literature as identified by the authors early in the introduction section. This section can probably be restructured for better understanding of the readers, in the following manner: ideally, the first paragraph would discuss general aspects of peer review, therefore, the gap in literature can be moved towards the end of the introduction, after discussing a few aspects, models, shortcomings, etc. ANSWER: Thank you for this suggestion. We cite a recent systematic review on grant review, so we do not consider that it is important to repeat the same information, as we follow the standards on the length of introduction section in biomedical papers. Additionally, the authors may provide examples for the quantitative characteristics in the introduction, and/or further elaborate on the effect of quantitative characteristics on reviewers’ evaluation. Providing more information regarding the Marie Skłodowska-Curie Actions (MSCA) would probably help supplement this section and provide a better understanding of the dynamics of this grant. Furthermore, it could have been useful to touch on other possible proposals’ evaluating methods such as scoring and ranking, as can be found in[1]. The last paragraph may be used to highlight further the gap in the literature that the authors aim to bridge with this project, indicating that peer review is highly versatile and a diverse process, yet further focusing on the need to address the general lack of theoretical understanding in multiple aspects of peer review, as can be seen in: [2], and/or the paucity of experimental research in proposals’ peer review as summarized by [3]. ANSWER: Thank you, we cited our previous studies on MSCA grant proposal review, in order to keept this paper more compact and clear. As for other types of evaluating proposals, we cite a recent systematic review on this topics, which has the information suggested by the reviewer. The authors may want to further elaborate on the reasons for removing the numerical score from MSCA? Was it for the effect of simplifying the peer review process on reviewers’ engagement and quality of report? as pointed out by [4] ANSWER: The reason for removal of the numerical scores was an intention to shift focus from numerical scores of the proposals to the text, which represents the feedback on the evaluation process. We have now added this information in the text, along with the reference you suggest. The study design is cross sectional but not observational. The latter terminology may be removed. ANSWER: We have removed the term “observational”. What is the justification for including data from only 2019 and 2020? Why not expand on the size of data by including more years. ANSWER: Unfortunately, we did not have data from other years on our disposal. Further information may be added to the assessment tool, Linguistic Inquiry and Word Count (LWIC) software, such as the validity and reliability, the LWIC scores, possible cutoffs, totals, etc. The authors do provide a reference, but it would just be easier to have it readily accessible while reading. ANSWER: We have uploaded the table with explanations of dimensions, and total scores. Since we used the summary variables, there is no provided reliability coefficient from the original study (Pennebaker et al, 2015). Under the bias heading: What is the role of including the whole cohort of submitted proposals in 2019 and 2020 in eliminating potential sampling bias? Please make it clear for the readers. ANSWER: We aimed to state that we avoided potential problems in the interpretation in case we took only samples from the cohorts in both years. In the statistical analysis section: How were the predictors established? Was it based on an analysis or from the literature? It would be advised to clarify this detail. ANSWER: As explained above, since there was a significant number of potential predictors, and this was an exploratory analysis, we decided to conduct variable selection, firstly by univariate testing and then by multivariate testing through logistic regression. The process follows the procedure recommended by : Bursac, Z., Gauss, C.H., Williams, D.K. et al. Purposeful selection of variables in logistic regression. Source Code Biol Med 3, 17 (2008). https://doi.org/10.1186/1751-0473-3-17 What we now provide are t-tests for comparison between 2019 and 2020, the initial model and final model for call comparison; and also Kruskal Wallis test due to sample size discrepancy, the initial model, and final model published online publicly. Also, Kruskal Wallis tests were done in R, since JASP program cannot support the size of the analysis. The entire procedure is now uploaded on OSF, comparisons, initial and final regression models, as well as descriptive statistics. Additionally, please justify using the specified p-value 0.001 in your model, as it appears too stringent. ANSWER: The reason for the P<0.001 was due to the significant number of variables tested, in order to avoid alpha error. However, we now also provide the entire analysis, where the reviewer can see that in logistic regression, all significant variables were significant at P<0.001 level. In the results section: The majority of proposals were from the physical science and engineering fields. Did this play a role in the outcome of the study, where no differences were detected before and after? The authors may want to expand on this in the discussion section. Additionally, is it possible that COVID19 resultant urgency have affected the review of proposals in 2020? ANSWER: Thank you for your suggestions. Both of them seem plausible, and we added them to the discussion section. It would also be useful to further elaborate on the blinding model adopted by the MSCA and how they may have influenced the results. ANSWER: Thank you for this comment. Individual assessment of grant proposal are done independently by each expert, but they are not blinded to the applicant identity. They are blinded to the indentity of other experts, but they meet at the consensus stage. As this part of the evalution did not change, we did not address this in the manuscript as it would not have had an impact on the results. In Table 3: How can the average word count be negative? Please provide an explanation. ANSWER: We subtracted results from ESR and IER, and in the table we present only differences. The negative direction only indicates that the values in IER were higher than in ESR. It would be great to supplement the discussion section with a few recommendations for future researchers into the topic. ANSWER: Thanks, we added some recommendations in the Discussion section. Have the authors considered adjusting for possible confounding factors, such as research domain, etc.? If not , please discuss the possible effects of such confounding factors in the Discussion section. ANSWER: Thank you for your comment. We have not included this in the paragraph on limitation in the Discussion section in previous version but it is included now. Thank you for your comments and we are ready to do any additional comments if needed. Kind regards, Ivan Buljan" } ] }, { "id": "246534", "date": "29 Aug 2024", "name": "Jan-Ole Hesselberg", "expertise": [ "Reviewer Expertise Judgement and decision-making", "peer-review", "inter-rater agreement" ], "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 This is an interesting and well-written article. I have few specific comments and have no substantial comments regarding the conclusions.\n\nMy main concern are the deviations from the preregistration, both regarding the measured variables and the statistical analyses. These deviations seem to be significant and increase the risk of bias. I want to stress I believe the methods used are sound and that there are likely good reasons for the deviations. However, the reader should be made aware of them and the authors should comment on: 1) Which changes were made to the methods 2) Why they were made 3) If the results would have been different if methods described in the preregistration had been followed\nI would prefer if the Methods section had contained a subsection called \"Differences between preregistration and article\" and that the results section contained comments regarding what the results would have been if the preplanned analyses had been done.\n\nTo help the reader of this review to see the differences. Here are the preplanned measured variables described in the preregistration (https://osf.io/t84ba):\n\"The outcome variable will be the difference in final scores between 2019 and 2020. Input variables will be: year of the calls; evaluation panel; country of the coordinator (high and low research performing countries); linguistic characteristics of the individual expert evaluation in each of the three evaluation criteria (Excellence, Impact, Implementation) – LIWC analysis and another measure of sentiment analysis like RSentiment.\"\nThere are no mentions of calculated indices or transformations\nAnd here are the preplanned statistical analyses described in the preregistration (https://osf.io/t84ba):\n\"Statistical models The categorical data will be presented as frequencies and percentages, while numerical data will be presented as means and standard deviations in the descriptive part and with 95% confidence intervals in the inferential part of the analysis. We will compare the differences in linguistic characteristics between 2019 and 2020 and simultaneously compare linguistic characteristics between different reviewer decisions using two-way ANOVA. The data in the models will be presented as group means and 95% confidence intervals while final results will be expressed with squared eta effect size.\n\nTransformations None planned.\nInference criteria We will use the standard p<.05 criteria for determining if the ANOVA and the post hoc test suggest that the results are significantly different from those expected if the null hypothesis were correct. The post-hoc Tukey-Kramer test adjusts for multiple comparisons.\"\nSPECIFIC COMMENTS\nIntroduction \"Previous studies have established this approach as a stable procedure in the evaluation of research grant proposals\"\nWhat is meant by \"stable procedure\" in this quote?\n\nParticipants/sources of data Thank you for sharing the data. It would be very helpful if you could also share the analytic code (the R script).\nVariables analyzed Please comment on the changes from the preregistration. Among other things, it seems like \"country of coordinator\" was left out and that the clustering of PHYENG and the use of \"proposal status after evaluation\" was not preplanned.\nStatistical analysis Please comment on the changes from the preregistration.\n\nDiscussion The phrase \"can be predicted\" is used. I believe it would be helpful to add some wording to describe to the reader to what extent it can be predicted.\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": [ { "c_id": "12350", "date": "05 Sep 2024", "name": "Ivan Buljan", "role": "Author Response", "response": "Dear reviewer, Thank you for your insightful suggestions to enhance our article. We have incorporated a new section titled \"Deviations from the Protocol\" and provided a detailed description of the revised methods in the latest version. The new version was submitted last week and will be available in the coming weeks. If you feel the changes still fall short, we are open to making further adjustments. Kind regards, Ivan Buljan" } ] } ]	1	https://f1000research.com/articles/12-1216
https://f1000research.com/articles/12-1217/v1	26 Sep 23	{ "type": "Research Article", "title": "Insomnia in teachers with the resumption of in-person instruction at schools amidst the COVID-19 pandemic: A cross-sectional study", "authors": [ "Sowmini Padmanabh Kamath", "Prasanna Mithra", "Padmanabh Kamath", "Bhaskaran Unnikrishnan", "Prasanna Mithra", "Padmanabh Kamath", "Bhaskaran Unnikrishnan" ], "abstract": "Background: The coronavirus (COVID-19) pandemic has affected people's economies, lifestyles, and physical, emotional, and sleep health. This research aimed to estimate the prevalence of insomnia and symptoms of stress, anxiety, and depression among teachers with the resumption of in-person instruction at schools following a hiatus after COVID-19 lockdowns in India. We also studied the association of teachers' insomnia with psychological symptoms and demographic variables. Methods: We conducted a cross-sectional survey between October –November 2021 after schools had reopened during the COVID-19 pandemic. Data was collected using standard questionnaires online among schoolteachers. We explored the association of insomnia with teachers' symptoms of stress, anxiety, depression, sex, school boards, and age groups. Results: Of 124 schoolteachers surveyed, the prevalence of insomnia was 37.9% (subthreshold in 25% and clinical in 12.9%). The prevalence of stress, depression, and anxiety was 20.2%, 30.6%, and 45.2%, respectively. There was a significant association (p<0.001) of insomnia with symptoms of anxiety, stress, and depression in univariate analysis. On multivariate analysis, we found that those feeling stressed had a 6.4 times higher risk of insomnia (95% CI: 1.5-28.3, p - 0.01). There was no association of insomnia with age, sex, school educational boards, and type of institution. Conclusions: Over one-third (37.9%) of teachers reported having trouble sleeping when they returned to the school's typical face-to-face instruction modalities through COVID-19 times, and insomnia was more prevalent in those with stress.", "keywords": [ "Anxiety", "COVID-19", "Cross sectional studies", "Humans", "Pandemics", "Depression", "Insomnia", "Schools" ], "content": "Introduction\n\nInsomnia is the most frequent sleep disorder encountered among the public. Disturbances in sleep following significant stressful situations, including natural disasters, have been reported previously.1 The COVID-19 pandemic has caused crises globally, causing significant changes in the lifestyle of people.\n\nThe pandemic has resulted in anxiety, stress, worries about one's health and family, job insecurities, economic instabilities, financial crises, and challenges in managing work and family duties. In addition, people had to follow COVID-appropriate behavior resulting in lesser social contacts and interactions. Uncertainties and increasing unprecedented changes occurred worldwide, and people began encountering impairment in sleep and altered circadian rhythms. Hurley refers to the sleep disturbances related to the pandemic as “coronasomnia or covidsomnia”.2\n\nThe teaching profession is stressful, and teachers have reported symptoms of stress,3,4 anxiety, and depression5 along with sleep problems6 even during pre-covid times. With the onset of the COVID-19 pandemic, there was a significant shift from conventional pedagogy teaching to e-learning methodology. Teachers had to adapt to the online teaching mode abruptly and balance their duties to their families during the pandemic crises. Most teachers were unfamiliar with e-learning and worried about delivering quality teaching, especially for children from lower socioeconomic status and remote villages who still needed internet access.7–10\n\nThe effect of the COVID-19 pandemic on psychological symptoms in various populations,11,12 including teachers, has been studied previously,13,14 along with disturbances in sleep in the general public have been documented during the COVID-19 lockdowns.15,16 Adapting to e-learning increased stress for the schoolteachers and affected their sleep.17 More than half of the teachers in the USA during COVID-19 have reported insomnia.18\n\nA survey in the United Kingdom during the COVID-19 pandemic revealed an increase in sleeplessness from pre-pandemic values of 15.7% to 24.7%.19 Another study showed changes in sleep schedules and quality/quantity of sleep at nighttime.20 There is a link between insomnia severity with signs of despair, anxiety, and poor sleep hygiene.21 Female sex is usually predisposed to insomnia.16,19 On the contrary, an Indian survey among the public did not show statistically significant differences with sex.15 Further, factors such as having young children, perceived financial difficulties, and the presence of symptoms of COVID-19 were predictive of sleep loss in yet another study.19\n\nThe long-term effects of insomnia include mood disorders, mental changes, poor cognitive performances, diabetes, hypertension, overweight/obesity, cerebrovascular, cardiovascular diseases, and metabolic syndrome, with an increase in mortality.22 Thus it is essential to recognize and address sleep issues by coping mechanisms to improve sleep hygiene.\n\nAs the pandemic continued, The Ministry of Education, India,23 initiated the reopening of schools and educational institutions from the online teaching mode to in-person instructive classes in a gradational manner following the second COVID-19 wave in India. There was fear of a resurgence of infection and additional responsibility to maintain implemented COVID-appropriate behaviors at schools and manage the children once schools reopened. So reverting to regular face-to-face teaching in schools would be challenging for the teachers and students, especially when there was an impending third wave.\n\nFollowing a hiatus of school closure during the pandemic, in the context of face-to-face teaching mode when schools reopened, the teachers' psychological symptoms were high in a Spanish study.24 Similarly, our study reported a high prevalence of psychological symptoms among schoolteachers after schools reopened for regular face-to-face instruction.25 The data for the current research was also gathered concurrently from the same group of teachers as part of a more extensive study. We used the English version of the Insomnia Severity Index (ISI) questionnaire26 to assess insomnia levels. The ISI questionnaire is valid and reliable for usage in the Indian population.27\n\nDespite the volume of evidence on psychological symptoms and insomnia in various populations,28,29 limited literature is available on teachers' insomnia levels during the pandemic. Additionally, this research focused on instructors and looked at a specific time during the COVID-19 outbreak when Indian schools were moving from a complete lockdown to a gradual resumption of in-person activities.\n\nTherefore, this study's primary goal is to assess teacher's insomnia and its association with their psychological states and demographic variables at a crucial juncture during the COVID-19 crisis, especially in the scenario when schools and educational institutes were reopening after a hiatus to contain the spread of COVID-19 from March 2020 to October 2021.\n\n\nMethods\n\nWe conducted a cross-sectional study involving teachers in a few chosen schools in the Dakshina Kannada district, situated in a state in southern India. The study duration was two months (November to December 2021). All teachers who agreed to participate in the study were incorporated. We excluded teachers with no Internet access and those who could not enroll owing to ongoing medical conditions. The STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) statement30 is adhered to in this study and a completed checklist is provided in the Reporting guidelines.31 Figure 1 depicts the study flow as per the STROBE criteria.\n\nThe sample size calculation is based on teachers' anxiety levels estimated to be 49.4 %,24 similar to insomnia prevalence of 52 % in another study.18 Considering an 80% power, a 95% confidence level, a 10% relative precision, and a 20% non-response rate, we determined the sample size to be 115. Our study on the teachers levels of depression anxiety and stress was reported earlier25 (https://doi.org/10.12688/f1000research.110720.2) with the same data collection procedures as the current study.\n\nThe conduct of the study adhered to the 1964 Declaration of Helsinki and its later amendments, as well as other relevant ethical standards. The institutional ethics committee of Kasturba Medical College, Mangalore, Manipal Academy Of Higher Education, Manipal, India authorized the study (approval number: IEC KMC MLR -06/2020/184). We took permission from the Block Education Officer (BEO). Further, we obtained permission from the school administration in charge and the principals of the selected schools. The participant information sheet (as in Extended Data)31 provided the purpose of the study. We collected informed consent (as in Extended Data)31 and permission to publish from the teachers.\n\nThe Block Education Officer's (BEO) office furnished us with a school list of our district. There were an equal number of private and public schools in the sample. We listed the schools in increasing order of teacher count. Then, we chose schools by lottery until we obtained the necessary sample size. The BEO and the concerned school administration consented once we outlined the specifics of the study. We prepared the questionnaire using the online data collection tool Google Forms. Through WhatsApp and school email, we shared the questionnaire link, the participant information sheet having study details, the Block Education Officers letter of authorization, and the IEC certificate with the head teacher or principal of the selected school. At the investigator's request, the principal sent the link to each school's WhatsApp group for teachers to answer the questionnaire link. We gathered informed consent through the questionnaire link. After responding to the question in hand, teachers had to scroll down to the following ones because it was necessary to answer all the questions in the link. The participants could respond to the questionnaires in less than ten minutes.\n\nWe gathered data through a questionnaire using Google Forms. The questionnaire (provided as Extended Data)31 consisted of Section 1 for demographic details; Section 2 comprised the insomnia severity index (ISI) scales for insomnia; and Section 3-featured Depression, anxiety, and stress scales (DASS-21) to measure stress and anxiety and depression levels. Two weeks after returning to their jobs at the school, we ensured the questionnaires were accessible to the teachers.\n\nA) Insomnia Severity Index (ISI)\n\nThe Insomnia severity index (ISI) is a seven-item screening tool for insomnia.26,32 The participants need to rate their sleep-related issues using a Likert scale. Questions pertain to subjective sleep quality, symptom severity, sleep pattern satisfaction levels, day-to-day functioning by insomnia, others' observation of the participant's insomnia, and the overall distress because of insomnia. The questionnaire evaluates the severity of recent two-week bouts of insomnia. The item responses (ranging from 0-4) with higher scores indicated severe/acute insomnia symptoms. The seven items' scores were added (total score ranges from 0-28), and we classified insomnia into the following four groups:\n\nModerately severe clinical insomnia (score of 15-21).\n\nSevere clinical insomnia (score of 22–28).\n\nSubthreshold insomnia (score of 8-14), and\n\nNo clinically relevant insomnia (scores of 0-7)\n\nWe procured permission to use the ISI questionnaire (English version) from the author through Mapi Research Trust (https://eprovide.mapi-trust.org/instruments/insomnia-severity-index).\n\nB) Depression, anxiety, and stress (DASS 21) scale\n\nThe English short version of the DASS 21 questionnaire was used (https://eprovide.mapi-trust.org/instruments/depression-anxiety-stress-scales). The self-report questionnaire is designed to identify the psychological conditions of stress, depression, and anxiety. With seven items in each domain, the twenty-one statements are organized for three scales: depression, anxiety, and stress. Each statement on the scale has four alternative answers (scores 0- does not apply to me; 1-applied to me to occasionally or to some extent; 2-applied to me frequently or significantly; and 3-applied to me frequently or a lot). The replies show how much each respondent found the statement true over the previous week. The scores for relevant items from each domain were pooled and multiplied by two to determine the final scores. We categorize the severity of the symptoms into five groups based on the cut-off scores as no symptoms, minor symptoms, moderate symptoms, severe symptoms, and extremely severe symptoms, which are represented by the numbers I through V.33\n\nAdditionally, we divided the symptoms into categories based on their presence or absence, such as “insomnia absent and insomnia present,” “depression absent and depression present,” “anxiety absent and anxiety present,” and “stress absent and stress present.” We compared the presence/absence of insomnia with sex, age groups, school boards, type of school, and presence/absence of psychological symptoms.\n\nSchools run or assisted by the government are categorized as public schools. The Council for the Indian Secondary Certificate Examination (CISCE), a private board of school education in India, administers the Indian Certificate of Secondary Education (ICSE). The Government of India supervises the Central Board of Secondary Education (CBSE), a national-level board of education in India for both public and private schools. Karnataka State Board manages the State Education Examination Board. To compare the levels of stress, depression, and anxiety among teachers, we divided school education boards into (CBSE+ICSE) against state boards and school institution types into public versus private schools.\n\nIBM SPSS Statistics for Windows, Version 25.0. Armonk, NY: IBM Corp. analyzed the information gathered. We used the appropriate tables and figures to express the results as proportions. To compare the groups, we used Chi-square tests. We used Logistic regression analysis to calculate the odds ratio of the variables contributing to teachers' insomnia risk. A p-value of less than 0.05 was used to denote statistical significance.\n\n\nResults\n\nOf 180 teachers contacted, 124(68.89%)31 completed the survey. Of 124 teachers, 108(87.1%) were females, and nearly 30% of teachers were aged less than 40 years. About 112 (90.3 %) were teaching at private institutions, while 70 (56.5%) and 54 (43.5%) were teaching in the central boards (CBSE+ICSE) and state boards of education, respectively (Table 1). The full raw data can be found under Underlying data.31\n\nThe prevalence of insomnia was 37.9% (subthreshold in 25% and clinical in 12.9%). The prevalence of stress, depression, and anxiety was 20.2%, 30.6%, and 45.2%, respectively (Table 2).\n\nThe frequency of teacher’s responses towards the ISI questionnaires is depicted in Table 3. Depressive symptoms were present in 38 (30.6%), with severity varying from mild (12.9%) to moderate (9.7%) to severe (5.6%) to extremely severe (2.4%). Anxiety was expressed by 56(45.2%), with severity being mild in 17.7%, moderate in 16.9%, severe in 3.2%, and extremely severe in 7.3%. Stress symptoms were seen in 25(20.2%), with variations being mild (12.1%), moderate (3.2%), severe (3.2%), and extremely severe (1.6%).\n\nOn univariate analysis, stress, anxiety, and depression were significantly associated (p<0.001) with insomnia in teachers. On multivariate analysis (Table 4), only stress in teachers was an independent factor for insomnia (95% CI: 1.5-28.3, p -0.01). Those teachers who were stressed out had a 6.4 times higher incidence of insomnia (odds ratio). The presence of anxiety or depressive symptoms, sex, school educational boards, or the type of institution did not significantly correlate with insomnia in teachers.\n\n* OR-Odds ratio from binary logistic regression, p value of <0.05 was considered as statistically significant.\n\n\nDiscussion\n\nWe observed that 37.9 % of teachers expressed the presence of insomnia (subthreshold - 25 % and clinical -12.9 %) after resuming face-to-face classes at school amid the COVID-19 pandemic. Similarly, a review study documented that the COVID-19 pandemic is linked with a significant increase in subthreshold insomnia but not with moderate or severe symptoms of insomnia.34\n\nAs per the United Kingdom's “Education Support” charity's annual teacher well-being survey findings, 52% of teachers have experienced trouble sleeping during the pandemic, up from 37% who claimed they battled with sleep in the preceding two years.18 The increased prevalence in the United Kingdom was most likely because the study data were collected during the peak of the COVID-19 pandemic when people were alarmed about the COVID-19 crisis, had economic concerns, and had societal constraints.\n\nA study showed that teachers with distressed personalities suffered more often from significant insomnia and depression.35 A known risk factor for the emergence of depression is insomnia. Depression is known to increase a person's negative attitude about their work and responsibilities, which in turn negatively affects the manner and effectiveness of their work.\n\nDuring the pandemic, moderate and severe clinical insomnia was present in 13.32 % and 1.85% of the Indian adult population, respectively.15 The general population in another Indian study reported poor sleep quality in higher numbers (57.2%), with quality of sleep significantly associated with self-reported mental health status.36 Across various populations, the prevalence of insomnia was 34 to 36 % in medical staff,37 20.5% in public China,16 31.3%,38 and 43.6 %39 in university students and 23.2 %40 in adolescents and young adults in China.\n\nAs per a systematic review and meta-analysis, the corrected pooled estimated prevalence of sleep difficulties among health care professionals (HCP), the general population, and COVID-19 patients was 31%, 18%, and 57%, respectively.41 According to another meta-analysis, the HCP and general population had similar sleep issues of 36.0% and 32.3%, respectively, and with a higher pooled prevalence of 74.8% among COVID-19 patients.42\n\nWe found that 20.2%, 30.6%, and 45.2% of teachers had expressed psychological symptoms of stress, depression, and anxiety, respectively. There was a higher prevalence of stress (50.6%), depression (32.2%), and anxiety (49.4%) among teachers who had face-to-face instruction with the reopening of schools in Spain.24 Symptoms of stress, depression, and anxiety were present in teachers at rates of 30 %, 19%, and 17%, respectively, in a systematic review and meta-analysis.13 A similar systematic analysis among teachers found anxiety in 10% to 49.4%, stress in 12.6% to 50.6%, and depression in 15.9% to 28.9%.14 We did not find an association between insomnia and sex in the present study; however, women expressed higher insomnia in previous studies.40,43–45\n\nWe found a significant association between insomnia and symptoms of stress, depression, and anxiety by univariate analysis. However, on logistic regression analysis, we observed a significant independent relationship between stress and sleeplessness (p-value < 0.001). At the same time, there was no discernible correlation between anxiety, sadness, sex, education school boards, or type of educational institution. Association of insomnia symptoms with depression,37,40,41,45,46 anxiety,15,37,40,41,45,46 and stress in various populations were present in earlier research.45–47 Multiple other factors in different people, such as older age, being an HCP, education level, and living in a city or near the epicenter15,16,37,40,43,45 were significantly associated with insomnia.\n\nThe study had a few limitations. The sample size was relatively small, which could impact the generalizability of the results. Additionally, there was an underrepresentation of male teachers, which may have skewed the findings toward a female perspective. Lastly, there is a possibility of bias in the responses to the questionnaire, which could have influenced the results. Further, though there was a significant association between insomnia and psychological symptoms, it is unclear if insomnia causes psychological symptoms or vice versa because the study was cross-sectional. We did not establish the causality of insomnia and psychological symptoms. We speculated it to be a blend of adopting COVID-appropriate behaviors at school, worry of being infected, and school reopening after a halt.\n\nThe study's strengths included using a standard questionnaire to measure teachers' levels of insomnia prevalence (by ISI) and manifestations of stress, anxiety, and depression (by DASS 21). In addition, this study is the first one in the Indian context to assess insomnia and psychological symptoms in teachers who joined back to work at school after a hiatus.\n\nInsomnia will impact the performance of teachers by affecting concentration, memory, and decision-making abilities. Strategic interventions such as cognitive behavioral therapy, mindfulness practices,48 and various sleep hygiene techniques will improve sleep quality and reduce stress, anxiety, and depressive symptoms in the long run.\n\nIt will be prudent if a longitudinal study is conducted in the future to establish the causality of insomnia and psychological symptoms and explore the effectiveness of different interventions to reduce insomnia among teachers.\n\n\nConclusions\n\nTo conclude, we reported insomnia in 37.9 % of teachers after resuming face-to-face classes in schools during the COVID-19 pandemic. Symptoms of stress, depression, and anxiety were present in 20.2%, 30.6%, and 45.2% of teachers, respectively. An independent risk factor for insomnia was presence of psychological stress. Identifying sleeplessness and psychological issues in teachers and addressing them as early as possible is essential for an effective teaching atmosphere at school and overall well-being.", "appendix": "Data availability\n\nOpen Scientific Framework: Insomnia in teachers with the resumption of in-person instruction at schools amidst the COVID-19 pandemic–a cross-sectional study. 2023. https://osf.io/b4c3u. 31\n\nThis dataset contains the following underlying data:\n\n• Excel Data file\n\n• Data code Key\n\nOpen Scientific Framework: Insomnia in teachers with the resumption of in-person instruction at schools amidst the COVID-19 pandemic–a cross-sectional study. 2023. https://osf.io/b4c3u. 31\n\nThis dataset contains the following underlying extended data:\n\n• Parent information sheet\n\n• Informed consent form\n\n• Study Questionnaire\n\nOpen Scientific Framework: STROBE checklist for Insomnia in teachers with the resumption of in-person instruction at schools amidst the COVID-19 pandemic–a cross-sectional study. 2023. https://osf.io/b4c3u\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 thank the school teachers who participated in the study.\n\n\nReferences\n\nBelleville G, Ouellet MC, Morin CM: Post-Traumatic Stress among Evacuees from the 2016 Fort McMurray Wildfires: Exploration of Psychological and Sleep Symptoms Three Months after the Evacuation. 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PubMed Abstract \| Publisher Full Text" }	[ { "id": "226960", "date": "20 Dec 2023", "name": "Sreejayan Kongasseri", "expertise": [ "Reviewer Expertise Psychiatry", "mental health", "addictions" ], "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 well conducted study with a strong methodology. Authors have used standardised scales and have explained the sampling method elaborately. Appropriate statistical methods have been used and results are well presented.\nHere are few suggestions:\nThis is a cross sectional study which means that the prevalence of insomnia has been estimated at a certain point of time ( when the in person teaching resumed). However authors have used words in ways as if the in person teaching was causal to the insomnia and stress. Title “ Insomnia in teachers with the resumption of in-person” suggests causality. “ at the time of” will be more appropriate here “ We observed that 37.9 % of teachers expressed the presence of insomnia (subthreshold - 25 % and clinical -12.9 %) after resuming face-to-face classes at school amid the COVID-19 pandemic” instead of after “ at the time of”.\n“ Similarly, a review study documented that the COVID-19 pandemic is linked with a significant increase in subthreshold insomnia but not with moderate or severe symptoms of insomnia.34” this sentence can come later with a statement that it was not possible to know if the prevalence had increased.\n\nIn the flow diagram the reasons for exclusions could have been mentioned. Medical condition has been reported as reason for exclusion. It is difficult to imagine a condition with which a teacher can attend work but get excluded from the study. If the authors excluded them due to conditions that caused insomnia then it would be clearer if those excluded conditions were mentioned. Were prior psychiatric conditions excluded? “16 teachers did not have internet facility” is not clear. The survey was sent electronically. If they did not have internet access they would not have known about the study. Some more points to include in discussion ( not covered) More women than men Lower prevalence in this study when compared to existing literature. Even though India had a high mortality rate during COVID.\n“Lastly, there is a possibility of bias in the responses to the questionnaire” this statement is not clear. Needs some elaboration.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "10824", "date": "05 Sep 2024", "name": "Sowmini Padmanabh Kamath", "role": "Author Response", "response": "This is a cross sectional study which means that the prevalence of insomnia has been estimated at a certain point of time ( when the in person teaching resumed). However authors have used words in ways as if the in person teaching was causal to the insomnia and stress.Title “ Insomnia in teachers with the resumption of in-person” suggests causality. “ at the time of” will be more appropriate here A. We have changed the title as follows: Insomnia in teachers at the time of resumption of in-person instruction at schools amidst the COVID-19 pandemic: A cross-sectional study. “ We observed that 37.9 % of teachers expressed the presence of insomnia (subthreshold - 25 % and clinical -12.9 %) after resuming face-to-face classes at school amid the COVID-19 pandemic” instead of after “ at the time of”. A. We have changed the sentence as follows:We observed that 37.9 % of teachers expressed the presence of insomnia (subthreshold - 25 % and clinical -12.9 %) at the time of resuming face-to-face classes at school amid the COVID-19 pandemic “ Similarly, a review study documented that the COVID-19 pandemic is linked with a significant increase in subthreshold insomnia but not with moderate or severe symptoms of insomnia.34” this sentence can come later with a statement that it was not possible to know if the prevalence had increased. A. As suggested, the sentence has been placed in the subsequent paragraphs- Similarly, a review study has documented that the COVID-19 pandemic is linked with a significant increase in subthreshold insomnia but not with moderate or severe symptoms of insomnia.34” and it was not possible to know if the prevalence had increased in our study. In the flow diagram the reasons for exclusions could have been mentioned. Medical condition has been reported as reason for exclusion. It is difficult to imagine a condition with which a teacher can attend work but get excluded from the study. If the authors excluded them due to conditions that caused insomnia then it would be clearer if those excluded conditions were mentioned. Were prior psychiatric conditions excluded? “16 teachers did not have internet facility” is not clear. The survey was sent electronically. If they did not have internet access they would not have known about the study. A. About 56 teachers were excluded from the study. A total of 40 teachers did not consent to the study because of unwillingness in 28 and medical conditions that affect sleep in 12 {diabetes in 7, heart disease in 3, and asthma in 2}. Once the principal sent the questionnaire link to the WhatsApp group, those teachers with the above conditions expressed dissent. The subjects approached did not mention any presence of prior psychiatric conditions, probably due to fear of social stigma. We could not probe further on the same because of feasibility issues. We have now clarified that 16 teachers did opt out of the study since they mentioned they have poor internet connectivity issues since they resided in remote rural areas and came to work at school in the city. The explanation is done in the flow diagram and enclosed. Some more points to include in the discussion (not covered) More women than men A. It is well known that females make up most teachers in a large number of schools. Likewise, our selected schools were populated with female teachers. Thus, our study also had more participation from female teachers (87.1%). We did not find an association between insomnia and sex in the present study; however, women expressed higher insomnia in previous studies. 40 , 43 – 45 There is a lower prevalence in this study when compared to existing literature. Even though India had a high mortality rate during COVID. A. Earlier studies 15,16,35,37-42 had insomnia prevalence ranging between 13.32 % and 57.2 % across various populations in various countries, with data collection done during the peak COVID-19 pandemic times when a lot of unprecedented and uncertain changes were occurring in people's daily lives. We conducted our study after a prolonged hiatus of lockdown. In addition, improved knowledge and treatment facilities for COVID-19 infection and adapting to COVID-appropriate behaviors along with effective vaccination drive by the Indian government must have contributed to the lesser prevalence compared to a few earlier studies. The reopening of schools after a hiatus, the difficulties in implementing and adopting new routines, and the possibility of an infection's unpredictable reappearance were the combined reasons for insomnia and the psychological symptoms, which we could not prove to be causal. “Lastly, there is a possibility of bias in the responses to the questionnaire.” This statement is not clear. Needs some elaboration A. We have removed the sentence since both questionnaire scales have demonstrated reliability and validity in populations." }, { "c_id": "12270", "date": "05 Sep 2024", "name": "Sowmini Padmanabh Kamath", "role": "Author Response", "response": "This is a well-conducted study with a strong methodology. Authors have used standardised scales and have explained the sampling method elaborately. Appropriate statistical methods have been used and results are well presented. Here are a few suggestions: 1. This is a cross sectional study which means that the prevalence of insomnia has been estimated at a certain point of time ( when the in person teaching resumed). However authors have used words in ways as if the in person teaching was causal to the insomnia and stress. Title “ Insomnia in teachers with the resumption of in-person” suggests causality. “ at the time of” will be more appropriate here. Author Response: We have changed the title as follows: “Insomnia in teachers at the time of resumption of in-person instruction at schools amidst the COVID-19 pandemic: A cross-sectional study”. 2. “ We observed that 37.9 % of teachers expressed the presence of insomnia (subthreshold - 25 % and clinical -12.9 %) after resuming face-to-face classes at school amid the COVID-19 pandemic” instead of after “ at the time of”. Author Response: We have changed the sentence as follows: we observed that 37.9% of teachers expressed the presence of insomnia (subthrhold-25% and clinical -12.9%) at the time of resuming face -to face classes at school amid the COVID -19 pandemic. 3. “ Similarly, a review study documented that the COVID-19 pandemic is linked with a significant increase in subthreshold insomnia but not with moderate or severe symptoms of insomnia.34” this sentence can come later with a statement that it was not possible to know if the prevalence had increased. Author Response: As suggested, the sentence has been placed in the subsequent paragraphs- A review study has documented that the COVID-19 pandemic is linked with a significant increase in subthreshold insomnia but not with moderate or severe symptoms of insomnia,42 and it was not possible to know if the prevalence had increased in our study. The reference number has been updated. 4. In the flow diagram the reasons for exclusions could have been mentioned. Medical condition has been reported as reason for exclusion. It is difficult to imagine a condition with which a teacher can attend work but get excluded from the study. If the authors excluded them due to conditions that caused insomnia then it would be clearer if those excluded conditions were mentioned. Were prior psychiatric conditions excluded? “16 teachers did not have internet facility” is not clear. The survey was sent electronically. If they did not have internet access, they would not have known about the study. Author Response: About 56 teachers were excluded from the study. A total of 40 teachers did not consent to the study because of unwillingness in 28 and medical conditions that affect sleep in 12 {diabetes in 7, heart disease in 3, and asthma in 2}. Once the principal sent the questionnaire link to the What’s app group, those teachers with the above conditions expressed dissent. About 16 teachers could open the questionnaire link; however, due to internet issues and technical glitches, they could not either complete or submit the questionnaire and, therefore, decided to opt out of the study. The subjects approached did not mention any presence of prior psychiatric conditions, probably due to fear of social stigma. We could not probe further into this because of feasibility issues. The explanation is done in the flow diagram and enclosed. Some more points to include in the discussion ( not covered) 5. More women than men Author Response: It is well-known that females make up most teachers in many schools. Likewise, our selected schools have female teachers, contributing to 87.1% of participation. Higher psychological symptoms in teachers have been reported earlier, 24,71, and in the current study, we found a significant association between symptoms of anxiety and sex.25 However, we did not find an association between insomnia and sex in the present study, although women expressed higher insomnia in previous studies. 52, 59,72,73 6. Lower prevalence in this study when compared to existing literature. Even though India had a high mortality rate during COVID. Author Response: There were variations in the insomnia prevalences in previous studies across a spectrum of populations 43,44,45,53,54,56,58 in different countries, with data collection done during other times of the COVID-19 pandemic, with some conducted at its peak times when many unprecedented and uncertain changes were occurring in people's daily lives. We conducted our study after a prolonged hiatus of lockdown. In addition, improved knowledge and treatment facilities for COVID-19 infection and adapting to COVID-19 appropriate behaviors along with an effective vaccination drive by the Indian government might have contributed to the lower prevalence compared to a few earlier studies. The reopening of schools after a hiatus, the difficulties in implementing and adopting new routines, and the possibility of an infection’s unpredictable reappearance were the combined reasons for insomnia and the psychological symptoms, which we could not prove to be causal. 7. “Lastly, there is a possibility of bias in the responses to the questionnaire” this statement is not clear. Needs some elaboration. Author Response: We have removed the sentence since both questionnaire scales have demonstrated reliability and validity in populations." } ] }, { "id": "226966", "date": "04 Jan 2024", "name": "Ravichandra Karkal", "expertise": [ "Reviewer Expertise Mood disorders", "Social media addiction", "Insomnia" ], "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 following modifications are required for the manuscript.\nThe background section of abstract is lengthy and can be summarised as follows- The COVID-19 pandemic has affected the sleep and mental health of many people, including teachers who had to adapt to online teaching and then resume in-person instruction at schools. This study aimed to estimate the prevalence of insomnia and its association with stress, anxiety, and depression among teachers in India after schools reopened following a hiatus due to the pandemic.\n\nThe introduction is too lengthy and contains some irrelevant information. For example, the paragraph on the effects of insomnia on health could be omitted or moved to the discussion section, as it is not directly related to the research question.\n\nReplace Ref no. 5 with following as the current reference is from teachers from special education school and may not be applicable to all teachers in regular schools. Agyapong, B., Obuobi-Donkor, G., Burback, L., & Wei, Y. (2022). Stress, Burnout, Anxiety and Depression among Teachers: A Scoping Review. International Journal of Environmental Research and Public Health, 19. (Ref. 1).\n\nIn methodology: The details of the tools (ISI and DASS 21) can be made concise and psychometric properties can be highlighted rather than describing the tool in great details.\n\nIn results section- \"The presence of anxiety or depressive symptoms, sex, school educational boards, or the type of institution did not significantly correlate with insomnia in teachers.\"-- Use the term “association” instead of “correlation” to describe the relationship between insomnia and psychological symptoms, as this is more appropriate for categorical variables.\n\nTable 4 title - Logistic regression Table 4- Use \"p\" instead of \"p value\"\n\nThose teachers who were stressed out had a 6.4 times higher incidence of insomnia (odds ratio).- Replace incidence with odds. Those teachers who were stressed out had a 6.4 times higher odds of reporting insomnia.\n\nLast paragraph of results can be replaced with following- On univariate analysis using Chi-square tests, we found a significant association of insomnia with symptoms of stress, depression, and anxiety (p < 0.001 for all). On multivariate analysis using logistic regression, we found that only stress was an independent factor for insomnia (95% CI: 1.5-28.3, P = 0.01). Those teachers who were stressed had a 6.4-fold higher odds of insomnia than those who were not stressed. The presence of anxiety or depressive symptoms, sex, school educational boards, and type of institution were neither independently nor jointly associated with insomnia.\n\nIn discussion 6th paragraph- Avoid using “by” to introduce the statistical test, as this can be ambiguous and misleading. Instead, use “using” or “with” to indicate the method of analysis.\n\nIn discussion section focus on the comparison of the prevalence and severity of insomnia and psychological symptoms among teachers with other populations, such as health care workers, general public, and COVID-19 patients. The authors could use more specific terms to describe the differences, such as higher, lower, similar, or comparable.\n\nDiscuss the possible mechanisms and explanations for the association between insomnia and stress, as well as the lack of association between insomnia and other variables, such as anxiety, depression, sex, school boards, and type of institution. The authors could provide (wherever feasible)more evidence and reasoning to support their hypotheses, such as biological, psychological, or social factors that could mediate or moderate the relationship between insomnia and stress.\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": "12271", "date": "05 Sep 2024", "name": "Sowmini Padmanabh Kamath", "role": "Author Response", "response": "The following modifications are required for the manuscript. 1. The background section of abstract is lengthy and can be summarised as follows- The COVID-19 pandemic has affected the sleep and mental health of many people, including teachers who had to adapt to online teaching and then resume in-person instruction at schools. This study aimed to estimate the prevalence of insomnia and its association with stress, anxiety, and depression among teachers in India after schools reopened following a hiatus due to the pandemic. Author Response: As suggested, changes have been made in the background section of the abstract. 2. The introduction is too lengthy and contains some irrelevant information. For example, the paragraph on the effects of insomnia on health could be omitted or moved to the discussion section, as it is not directly related to the research question. Author Response: As suggested, the changes have been made. The paragraph on the effects of insomnia on health has been omitted in the introduction section. 3. Replace Ref no. 5 with following as the current reference is from teachers from special education school and may not be applicable to all teachers in regular schools. Agyapong, B., Obuobi-Donkor, G., Burback, L., & Wei, Y. (2022). Stress, Burnout, Anxiety and Depression among Teachers: A Scoping Review. International Journal of Environmental Research and Public Health, 19. (Ref. 1). Author Response: The reference 5 has been updated as suggested Agyapong B, Obuobi-Donkor G, Burback L, Wei Y. Stress, Burnout, Anxiety and Depression among Teachers: A Scoping Review. Int J Environ Res Public Health. 2022 Aug 27;19(17):10706. https://doi.org/10.3390/ijerph191710706 4. In methodology: The details of the tools (ISI and DASS 21) can be made concise and psychometric properties can be highlighted rather than describing the tool in great details. Author Response: The details of the tools have been concised, and psychometric properties are highlighted with relevant references. 5.In results section- \"The presence of anxiety or depressive symptoms, sex, school educational boards, or the type of institution did not significantly correlate with insomnia in teachers.\"-- Use the term “association” instead of “correlation” to describe the relationship between insomnia and psychological symptoms, as this is more appropriate for categorical variables. Author Response: As suggested, the term association is used instead of correlation 6. Table 4 title - Logistic regression Table 4- Use \"p\" instead of \"p value\" Author Response: The necessary changes are done in Table 4. 7. Those teachers who were stressed out had a 6.4 times higher incidence of insomnia (odds ratio).- Replace incidence with odds. Those teachers who were stressed out had a 6.4 times higher odds of reporting insomnia. Author Response: The word incidence has been replaced by the word odds - Those teachers who were stressed had 6.4 times higher odds of reporting insomnia. 8. Last paragraph of results can be replaced with following- On univariate analysis using Chi-square tests, we found a significant association of insomnia with symptoms of stress, depression, and anxiety (p < 0.001 for all). On multivariate analysis using logistic regression, we found that only stress was an independent factor for insomnia (95% CI: 1.5-28.3, P = 0.01). Those teachers who were stressed had a 6.4-fold higher odds of insomnia than those who were not stressed. The presence of anxiety or depressive symptoms, sex, school educational boards, and type of institution were neither independently nor jointly associated with insomnia. Author Response: As suggested, last paragraph of results has been reframed. 9. In discussion 6th paragraph- Avoid using “by” to introduce the statistical test, as this can be ambiguous and misleading. Instead, use “using” or “with” to indicate the method of analysis. Author Response: Appropriate suggested word has been used to indicate the method of analysis 10. In discussion section focus on the comparison of the prevalence and severity of insomnia and psychological symptoms among teachers with other populations, such as health care workers, general public, and COVID-19 patients. The authors could use more specific terms to describe the differences, such as higher, lower, similar, or comparable. Author Response: The prevalence of insomnia and psychological symptoms among teachers with other populations such as health care workers, the general public, and COVID-19 patients have been discussed with specific terms such as higher, lower, similar, and comparable to describe differences. Relevant references added 11. Discuss the possible mechanisms and explanations for the association between insomnia and stress, as well as the lack of association between insomnia and other variables, such as anxiety, depression, sex, school boards, and type of institution. The authors could provide (wherever feasible)more evidence and reasoning to support their hypotheses, such as biological, psychological, or social factors that could mediate or moderate the relationship between insomnia and stress. Author Response: The explanation has been described in the last few paragraphs (before the limitations section) of the discussion, with relevant references added" } ] } ]	1	https://f1000research.com/articles/12-1217
https://f1000research.com/articles/13-1009/v1	05 Sep 24	{ "type": "Research Article", "title": "Perceptions and attitudes of medical students and doctors on Euthanasia", "authors": [ "Rohit Motappa", "Ajay Mallya", "Meghna Guleria", "Aditi Singhal", "Pallavi Nambiar", "Vaibhavi Gaiha", "Himani Kotian", "Rohit Motappa", "Meghna Guleria", "Aditi Singhal", "Pallavi Nambiar", "Vaibhavi Gaiha", "Himani Kotian" ], "abstract": "Background The concept of euthanasia has recently come into the spotlight, and cases such as those of Aruna Shanbaug have heavily influenced people’s opinions on the topic. Whether euthanasia is performed with the intention of ending suffering that otherwise cannot be helped should truly be supported. The thoughts on this topic- especially of those who work closely with patients who suffer from terminal illnesses- healthcare providers must be analyzed. Their perception and views on legalizing the procedure and their hesitancy or lack thereof to perform such a procedure would give the rest of the world a clearer picture- a better standpoint to understand what to do. This study attempted to quantify and analyze the views of doctors and medical students regarding euthanasia.\n\nMethods A cross-sectional survey of 212 doctors and medical students at a private medical college in South India was conducted to determine their attitudes toward euthanasia.\n\nResults Most participants (66%) supported the practice of euthanasia. The majority of participants also believed that euthanasia should only be performed with the explicit consent of the patient (71.7%). It was also observed that those who had heard about euthanasia via hearsay mostly agreed that it must only be performed with the explicit consent of the patient. Moreover, the study showed that those who had heard about it from hearsay and news mostly stood for it.\n\nConclusion It has been noted that news and media all around us heavily influence people’s opinions. It is concluded that these opinions have changed from the past, and will likely do so depending on the environment and media around the topic.", "keywords": [ "Euthanasia", "legalization", "healthcare providers" ], "content": "Introduction\n\nMedical care has advanced several times in the last century, especially in the last few decades. These advances have led to the increased longevity of multiple diseases. On an equal footing, there is an ever-increasing awareness of quality of life. People are becoming cognizant of their right to make decisions not only in their options regarding treatment, but also in their choice to end their lives. Euthanasia is defined as an easy or painless death or intentional ending of the life of a person suffering from an incurable or painful disease at his or her request.1 It is of two types: active euthanasia, where the physician directly administers a lethal medication and ends a patient’s life, or passive euthanasia, where a patient is allowed to die by witholding life support.2\n\nIt was first legalized in the Netherlands. Subsequently, many countries followed suit, including Belgium, Luxembourg, and Canada.3 In other countries such as the US, euthanasia is legal in some states only under certain conditions. However, it is still illegal in most countries, and there have been instances in India where euthanasia has been permitted by the courts of India.4,5 Consider, for example, Shanbaug’s case. A nurse, who was assaulted, was left with limited functionality, such as blinking and eating food placed in her mouth.6,7 Even after extensive care was provided by the nursing staff of the hospital she remained in, her quality of life was sub-par. The Supreme Court of India permitted euthanasia to be practiced in her case to end the constant suffering her life had become. Similarly, in the case of P. Rathinam Vs. U.O.I, the Supreme Court decided that the right to life, elaborated upon in Article 21 of the Constitution, includes the right to die.8 In a subsequent case, Gian Kaur Vs. State of Punjab, the court held that the right to die with dignity is included in Article 21.4 Clearly, the Supreme Court of India has made its standpoint- in the case of absolute suffering that cannot be helped, if euthanasia helps alleviate said suffering, it may be done.\n\nThe attitude towards euthanasia has always varied over time. In recent years, there has been an increasing awareness towards the same. Understanding and analyzing the way current and future healthcare providers perceive euthanasia is important, especially in the current world, where debate about legalizing this procedure is ongoing.9\n\nThis study investigates the attitudes and perceptions of medical students and doctors of a private medical college in Karnataka regarding euthanasia and its legislation in India.\n\n\n\n1. To gauge the awareness of Euthanasia in humans among medical students and doctors,\n\n2. To analyse the attitude and perceptions of medical students and doctors on euthanasia\n\n\nMethods\n\nVariables: Euthanasia is defined as an easy or painless death or the intentional ending of life of a person suffering from an incurable or painful disease at his or her request. This is also called mercy killing.\n\nStudy design: Cross-sectional study\n\nStudy type: Analytical study\n\nStudy setting: Kasturba Medical College, Mangalore\n\nStudy population: Medical Undergraduates, Interns and Post-Graduates/Doctors of Kasturba Medical College, Mangalore\n\nInclusion criteria: medical undergraduates, interns, and post-graduuates/doctors who gave their consent.\n\nStudy duration: 10th March 2022 to 13th June 2022\n\nStudy sample: 220. 110 Students and 110 Doctors/PGs/interns.\n\nSample size:\n\nN=Zα2 pq/d2\n\nwhere Zα = 1.96 for 95% confidence\n\np = proportion of the population which has the attribute in question\n\nq = 1-p\n\nd = precision\n\nThe sample size was calculated with the help of a study done by Subba et al., titled “Doctors’ Attitude Towards Euthanasia: A Cross-sectional Study,” conducted in Mangalore, March-April 2010, which found that while 46.8% of doctors justified euthanasia to alleviate suffering.10 so considering 46.8% as the prevalence of 46.8% was the prevalence of doctors who justified euthanasia and considering 10% relative precision and 95% confidence, the sample size was calculated to be 200. After adding a 10% non-responsive error, the final sample size was calculated to be 220.\n\nSampling strategy: Convenience sampling (non-probability sampling)\n\nTools for data collection: A questionnaire was prepared after extensive review of the literature. Therefore, a semi-structured questionnaire consists of two sections. Section A consists of two parts: demographic details and awareness. Section B consists of Part 1: ATE Scale and Part 2: Perceptions.\n\nScoring and Interpretation: Here, we used the ATE scale to interpret the attitudes of medical undergraduates, interns, and PGs/doctors towards euthanasia based on the Likert Scale.11,12 1 = strongly disagree, 2 = disagree, 3 = neutral, 4 = agree, and 5 = Strongly Agree.\n\nData collection methodology: The study protocol was approved by the Institutional Ethics Committee (IEC) of Kasturba Medical College, Mangalore. After obtaining approval from the Ethics Committee, permission was obtained from the Dean of Kasturba Medical College, Mangalore, and the data were collected after obtaining informed consent from the participants. All methods were performed in accordance with the relevant guidelines and regulations. The questionnaire was sent to the students in the form of a Google link to WhatsApp, e-mail, and Telegram.\n\nOnline informed consent was obtained from all the participants. Only after consent is given can the Google link for the questionnaire be opened.\n\nData analysis: Data were entered and analyzed using Statistical Software Statistical Package for Social Sciences (SPSS) version 25.0. Descriptive statistics such as mean (standard deviation) and proportion were used to express the results. The various factors associated with attitudes towards euthanasia were analyzed using the chi-square, independent t-test, and linear regression analysis.\n\nEthical consideration: This was a questionnaire-based study of medical undergraduates, interns, and doctors of Kasturba Medical College, Mangalore. The study did not pose any risk to the participants. Interpersonal data will be kept confidential and protected. The records maintained will only be used for research purposes. Entering the research study was voluntary. The participants had the right to stop at any time and did not need to provide any reason for the same.\n\nEthical Approval: was taken from the institutional ethics committee of Kasturba Medical College, Mangalore. On 17-03-2022 (DHR Reg. No. EC/NEW/INST/2020/742)\n\nConsent: Informed consent was obtained through a Google Form. The initial section of the questionnaire asked participants whether they consented to participate in the study. Those who selected ‘yes’ were allowed to proceed with the remainder of the questionnaire, while those who selected ‘no’ were not asked any further questions. This procedure was approved by the ethical committee.\n\n\nResults\n\nOur results indicated that a significant majority (86.3%) were aware of what euthanasia was, although only 47.2% possessed knowledge of the different types of euthanasia, and even fewer (44.3%) were aware of the legalities of its practice in India. Furthermore, only 30.2% of respondents were familiar with the guidelines used to perform euthanasia. Regarding the sources of their information, 29.2% first learned about euthanasia through news, followed by hearsay and work at 25.9%, and personal research at 18.9%. The majority opinion (71.7%) was that the final decision to administer euthanasia should lie with the patient themselves, while 11.8% believed it should be a family member’s decision, 9% thought it should be the court of law, and 7.5% placed this responsibility on the treating physician. Regarding the stance on euthanasia, 66% of the respondents were in favor, whereas 34% were against it (Table 1).\n\nA significant majority (86.3%) were aware of what euthanasia was, although only 47.2% possessed knowledge of the different types of euthanasia, and even fewer (44.3%) were aware of the legalities of its practice in India. Furthermore, only 30.2% of respondents were familiar with the guidelines used to perform euthanasia. Regarding the sources of their information, 29.2% first learned about euthanasia through news, followed by hearsay and work at 25.9%, and personal research at 18.9%. The majority opinion (71.7%) was that the final decision to administer euthanasia should lie with the patient themselves, while 11.8% believed it should be a family member’s decision, 9% thought it should be the court of law, and 7.5% placed this responsibility on the treating physician. Regarding the stance on euthanasia, 66% of the respondents were in favor, whereas 34% were against it. Among the reasons for supporting the legalization of euthanasia in India, 110 respondents cited relief of suffering, 91 mentioned valuing patient autonomy, 63 highlighted minimizing financial burden, 48 emphasized better utilization of resources, and 20 had other reasons. Reasons for opposing legalization included potential misuse for criminal reasons (38 respondents), the belief that medicine is meant to preserve life (33 respondents), the view that palliative care is sufficient (23 respondents), violation of medical ethics (23 respondents), religious beliefs (8 respondents), and other reasons (8 respondents) (Table 2).\n\nOn further analysis, the source of acquiring information about euthanasia for the first time has a significant bearing on who the participants feel should be the final proxy for administering euthanasia to patients. Further statistical analysis of the variable regarding the source of euthanasia and attitude towards euthanasia was found to be significant (Table 3).\n\nWe can infer that respondents’ opinions on the legalization of euthanasia in India are highly influenced by the source of acquiring information about euthanasia for the first time, and this was found to be statistically significant (Table 4).\n\n\nDiscussion\n\nThis study analyzed the attitudes and perceptions of healthcare workers towards Euthanasia. The present study was conducted at Kasturba Medical College, Mangalore. The composition of the study participants varied and ranged from doctors, post-graduates, interns, to medical students, although there were more medical students and interns than doctors and post-graduates. The participants were restricted to the students and staff of Kasturba Medical College, Mangalore. Statistical Package for the Social Sciences (SPSS) was used to analyze the data.\n\nIn the present study, 86.3% of the respondents were aware of the concept of euthanasia. Similar results were obtained in a study conducted in 2013, wherein the majority of selected professionals in New Delhi were aware of the concept of euthanasia.7\n\nIn this study, it was found that the majority of respondents who first encountered euthanasia via news or hearsay were of the opinion that euthanasia should only be practiced with the explicit consent of the patient. 66 Of the respondents, 66% were euthanized, and 34% were against it. Moreover, the majority of people who stood for euthanasia also first encountered euthanasia via news or hearsay. Thus, this study suggests that society and mass media heavily influence controversial topics, such as euthanasia. A systematic review of studies conducted in the UK to assess the attitudes of doctors towards euthanasia was conducted in 2012. This review revealed that the doctors mostly opposed the introduction of physician-assisted suicide (PAS) and Active Voluntary Euthanasia (AVE). Religious reasons were part of why doctors opposed euthanasia.10 The present study showed majority of the people who were for euthanasia gave the reason “To relieve suffering.” A similar cross-sectional study was conducted in South India in 2011 to assess the attitudes of doctors towards euthanasia, wherein a majority of the respondents (69.3%) supported the concept of euthanasia, giving “relief from unbearable pain and suffering” as the most cited reason for the same.13 Another study conducted in Sri Lanka in 2021 to analyze attitudes toward euthanasia among medical students showed that 47.1% of the participants favored legalizing euthanasia, whereas 25.9% directly opposed it. 27% were undecided. Participants who came under the undecided category were more likely to have unfavorable ATE.11\n\nThus, several studies have shown how the attitudes and perceptions of euthanasia vary among medical practitioners.\n\nIn conclusion, the attitudes and perceptions of medical practitioners towards euthanasia are varied and heavily influenced by how euthanasia is portrayed in mass media. There has been a gradual shift in people’s general opinions that seem to favor euthanasia, but concerns about its misuse continue to remain.\n\nThis study was conducted to analyze the attitudes and perceptions of healthcare practitioners towards euthanasia, and has effectively shown how the opinions and views of people shift due to mass media, society, and personal beliefs.\n\nIt is important to consider the thoughts of medical professionals towards euthanasia - those who work closely with patients - to analyze and understand the highly subjective topic of whether life must be qualitatively viewed or quantitatively.\n\n\nConclusion\n\nIn conclusion, euthanasia has been a topic of much debate since the ages and is still illegal in India; however, there is a change in the opinions of people, especially physicians and future caregivers, as is also evident in this study. Physicians’ views on this topic are also influenced by a multitude of factors such as where they first came to know about euthanasia.\n\nIn this study, we found that the majority of the respondents who first came across euthanasia via news or hearsay were of the opinion that euthanasia should only be practiced with the explicit consent of the patient.14 Furthermore majority of the people who stand for euthanasia as a practice also first encountered euthanasia via news or hearsay.\n\nIt would therefore appear that when it comes to such sensitive issues as euthanasia, the people’s opinions are influenced by the society they live in and how euthanasia is being portrayed in that society by means of mass media such as stories, news, articles, television, etc. There is indeed an evident shift in people’s opinions about euthanasia, since the majority of the respondents supported euthanasia and its legalization in this study. However, there are still lingering concerns regarding their possible misuse.\n\nThe study protocol was approved by the Institutional Ethics Committee (IEC) of Kasturba Medical College, Mangalore. After obtaining approval from the Ethics Committee, permission was obtained from the Dean of Kasturba Medical College, Mangalore, and the data were collected after obtaining informed consent from the participants.", "appendix": "Data availability\n\nFigshare: Perceptions and Attitudes of Medical Students and Doctors on Euthanasia, https://doi.org/10.6084/m9.figshare.26200124.v2. 15\n\nThis project contains the following underlying data:\n\n1. Data\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nFigshare: Perceptions and Attitudes of Medical Students and Doctors on Euthanasia. https://doi.org/10.6084/m9.figshare.26501110.v2 16\n\nThis project contains the following underlying data:\n\n1. Questionnaire - Perceptions and Attitudes of Medical Students and Doctors on Euthanasia\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nNCI dictionary of Cancer Terms. National Cancer Institute; 2011 [cited 2022 Jul3]. Reference Source\n\nSinha VK, Basu S, Sarkhel S: Euthanasia: An Indian perspective. Indian J. Psychiatry. 2012 Apr; 54(2): 177–183. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPatil YD: Euthanasia and Death with Dignity. JKIMSU. 2016 Jul-Sep; 5(3): 142–144. Reference Source\n\nMudur G: Indian court says it may sanction euthanasia in the future. BMJ. 2011 [cited 2022 Jul 3]; 342(mar11 2): d1628. PubMed Abstract \| Publisher Full Text Reference Source\n\nKranidiotis G, Ropa J, Mprianas J, et al.: Attitudes towards euthanasia among Greek intensive care unit physicians and nurses. Heart Lung. 2015; 44(3): 260–263. PubMed Abstract \| Publisher Full Text Reference Source\n\nSingh N: India is now among select group of nations where passive euthanasia is legal. ThePrint. 2018 [cited 2022 Jul 3]. Reference Source\n\nKamath S, Bhate P, Mathew G, et al.: Attitudes Toward Euthanasia Among Doctors in a Tertiary Care Hospital in South India: A Cross Sectional study. Indian J. Palliat. Care. 2011 Sep [cited 2023 Mar 31]; 17(3): 197–201. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nBandewar SV, Chaudhuri L, Duggal L, et al.: The Supreme Court of India on euthanasia: Too little, too late. Indian J Med Ethics. 2018 Apr-Jun; 3(2): 91–94. PubMed Abstract \| Publisher Full Text\n\nMani RK: Constitutional and Legal Protection for Life Support Limitation in India. Indian J. Palliat. Care. 2015 Sep-Dec; 21(3): 258–261. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSubba SH, Khullar V, Latafat Y, et al.: Doctors’ Attitude Towards Euthanasia: A Cross-sectional Study Experience. Japi. 2016; 63. Reference Source\n\nHerath HMMTB, Wijayawardhana KWSM, Wickramarachchi UI, et al.: Attitudes on euthanasia among medical students and doctors in Sri Lanka: a cross sectional study. BMC Med. Ethics. 2021 Dec 7; 22(1): 162. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nWasserman J, Clair JM, Ritchey FJ: A scale to assess attitudes toward euthanasia. Omega (Westport). 2005; 51(3): 229–237. PubMed Abstract \| Publisher Full Text Reference Source\n\nMcCormack R, Clifford M, Conroy M: Attitudes of UK doctors towards euthanasia and physician-assisted suicide: a systematic literature review. Palliat. Med. 2012 Jan; 26(1): 23–33. Erratum in: Palliat Med. 2012 Jul;26(5):770. PubMed Abstract \| Publisher Full Text Reference Source\n\nDees MK, Vernooij-Dassen MJ, Dekkers WJ, et al.: Perspectives of decision-making in requests for euthanasia: a qualitative research among patients, relatives and treating physicians in the Netherlands. Palliat. Med. 2013; 27(1): 27–37. PubMed Abstract \| Publisher Full Text\n\nMallya A, Motappa R: Data - Perceptions and Attitudes of Medical Students and Doctors on Euthanasia.xlsx. figshare. 2024 [cited 2024Aug20]. Reference Source\n\nMallya A, Motappa R: Questionnaire - Perceptions and Attitudes of Medical Students and Doctors on Euthanasia. figshare. 2024 [cited 2024Aug20]. Reference Source" }	[ { "id": "360955", "date": "29 Jan 2025", "name": "Yelson Alejandro Picón Jaimes", "expertise": [ "Reviewer Expertise Clinical and applied bioethics in the experimental field. Research methodology. Epidemiology and public 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\nIntroduction The definition of euthanasia is generally correct, but it could be made more precise by clearly differentiating between active euthanasia, assisted suicide, passive euthanasia, dysthanasia, and orthothanasia. As it stands, the current definition blends technical and common terms, which may lead to confusion.\nTo enhance global context, more specific data should be included, such as:\nIn the Netherlands, euthanasia was legalised in 2002 under strict criteria. Canada legalised it in 2016 under the term \"Medical Assistance in Dying\" (MAiD). Providing such details adds precision and context to the information.\nAdditionally, it would be useful to explain how the Gian Kaur judgment laid the foundation for recognising the \"right to die with dignity\" within the framework of Article 21 of the Indian Constitution. However, it is essential to clarify that this right does not extend to assisted suicide.\nMethods Definition of Euthanasia in Variables: The definition of euthanasia in the \"Variables\" section is repetitive (already mentioned in the introduction) and overly general for the methods section.\nStudy Design: The study is referred to as both cross-sectional and analytical, which creates confusion. If the study is cross-sectional, it is typically descriptive rather than analytical. This should be clarified.\nThe word \"post-graduuates\" in the inclusion criteria contains a typographical error.\nSampling Justification: The use of convenience sampling should be justified, and its limitations acknowledged. For example:\n\"Convenience sampling was employed due to the accessibility of participants in an academic setting. While this method may introduce biases, it was suitable for an exploratory, single-centre study.\" Additionally, if convenience sampling was used (a non-probabilistic method), it should be clarified why a probabilistic sample size calculation was performed.\nDescription of the Questionnaire: The description of the data collection tool (questionnaire) is too short. It does not specify how the questionnaire was validated or whether a pilot study was conducted before its implementation.\nData Analysis: The data analysis section is too brief and lacks clarity on the dependent and independent variables. It should also specify the measures of central tendency (e.g., mean, median) and dispersion (e.g., standard deviation) used. Moreover, it should detail which statistical tests were employed to examine associations (e.g., chi-square, t-tests).\nEthical Considerations: The ethical considerations section should explain the data protection measures implemented, particularly since the questionnaires were administered virtually. For instance:\n\"All virtual questionnaires were anonymised, and responses were securely stored to ensure data confidentiality. Access to the data was restricted to authorised personnel only.\"\nResults\nThe first and second paragraphs of the results section are redundant and repeat the same ideas. This should be streamlined for clarity.\nThe results are purely descriptive, which is inconsistent with the stated study design of an \"analytical study.\" This discrepancy reinforces the idea that the study is descriptive rather than analytical.\nThe results do not adequately address the second study objective: \"To analyse the attitude and perceptions of medical students and doctors on euthanasia.\" A more focused analysis is needed to examine attitudes and perceptions. Statistical tests (e.g., chi-square or regression analysis) could be employed to identify significant factors influencing attitudes.\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": [] } ]	1	https://f1000research.com/articles/13-1009
https://f1000research.com/articles/13-1008/v1	04 Sep 24	{ "type": "Systematic Review", "title": "Exploring antioxidant potential of agricultural by-products: a systematic review", "authors": [ "Imam Santoso", "Suprayogi Suprayogi", "Akhmad Adi Sulianto", "Endrika Widyastuti", "Annisa’U Choirun", "Khairunnisa Lestari", "Syairil A’yuniah", "Octavia Widyastuti Kusumaningtyas", "Suprayogi Suprayogi", "Akhmad Adi Sulianto", "Endrika Widyastuti", "Annisa’U Choirun", "Khairunnisa Lestari", "Syairil A’yuniah", "Octavia Widyastuti Kusumaningtyas" ], "abstract": "Background Agricultural waste sourced from various activities that occur along the agricultural supply chain including post-harvest, processing, and consumption processes, can pose a threat to ecosystem balance and community welfare. Data shows that agricultural by-products have the potential to be utilized because they contain antioxidant compounds. This systematic review study aims to identify and assess the antioxidant activity of agricultural by-products through various extraction methods.\n\nMethods This systematic review collected literature in the last 10 years (2013–2023) from Google Scholar, Semantic, and Scopus-indexed articles with the help of Publish or Perish. Using the help of boolean operators (AND) and (OR) in searching using keywords. The steps applied adapt the PRISMA method (Preferred Reporting Items for Systematic Reviews and Meta-Analyses), including identification, screening, eligibility, and inclusion.\n\nResults Literature collection data shows that the dominant processing method used is the solvent extraction method to determine the antioxidant value of various agricultural waste by-products. Followed by microwave-assisted extraction (MAE) and ultrasound-assisted extraction (UAE) methods. A wide range of antioxidant activity values were found depending on the type of agricultural waste and processing technique. One potential utilization of agricultural wastes rich in antioxidant content is as additives in formulations in the cosmetic industry.\n\nConclusion Agricultural waste by-products have high potential of antioxidant content, depending on the type of waste and extraction method. The dominant agricultural waste used is by-products from the fruit group. The utilization of agricultural waste that is rich in antioxidants has the potential to be utilized in the cosmetic industry.", "keywords": [ "antioxidant activity", "extraction", "agricultural by-product" ], "content": "Introduction\n\nThe rapid growth of the agricultural sector through increased production and processing of agricultural products in recent decades has had a significant impact on the environment. Between 2000 and 2020, world production of major food crops increased by 52% to 9.3 billion tons, which is equivalent to 2019 production. Vegetables represent 20%, followed by fruits at 17%, and root crops at 7%.1 A significant amount of agricultural waste is sourced from fruits, nuts, and vegetables resulting from the various activities that occur along the agricultural supply chain, which include post-harvest processing, processing, and consumption.2,3 The agricultural sector accounted for 31% of total greenhouse gas emissions during the period 2000–2020.1 China will be one of the largest greenhouse gas emitters in 2022, accounting for 50.1% of the global population and 63.4% of global fossil fuel consumption.4 In addition, more than half of the total waste distribution comes from fruits and vegetables, while rice and wheat also contribute significantly and are expected to increase to 234 Mt by 2032.1\n\nAgricultural waste contains various organic materials, carbohydrates, and other minerals that, if allowed to accumulate, can serve as a growing medium for decaying microorganisms. The significant increase in waste volume poses a threat to the balance of the ecosystem and the well-being of society. In recent years, a number of studies have indicated that agri-food residues contain a number of valuable compounds with potential bioactivity.5–8 Therefore, agricultural waste can serve as a valuable renewable resource, offering additional benefits such as affordability, easy accessibility, minimal environmental impact, and sustainability. The antioxidant compounds contained in the waste have the potential to be used as food supplements or medicines, neutralizing free radicals and reducing their adverse effects on human health.9–11 In addition, it can be utilized as a raw material for the production of other products, such as biofuels, biogas, bioethanol, animal feed, and composting.12–16\n\nThe waste extraction process can open up opportunities to obtain these compounds efficiently and sustainably.17 In addition, the extraction and use of antioxidants from agricultural waste can reduce environmental impact, reduce the amount of organic waste, and add value to the waste. This utilization not only provides a solution to the waste problem, but also opens up new business opportunities, reduces the need for new raw materials, and supports a sustainable economic approach. With increasing awareness of the economic and environmental value of agricultural waste, it is necessary to develop environmentally friendly and sustainable alternatives to conventional extraction methods to increase extraction yield and reduce extraction time and solvent consumption. To understand more about the utilization of antioxidant content in agro-industrial waste, further research and analysis of scientific articles and publications in the field of agricultural waste management and utilization can be conducted. More and more studies are reviewing the utilization of agricultural by-products and the potential content of organic compounds in agricultural waste.18 This extensive knowledge suggests that the antioxidant content of agricultural wastes is a promising alternative for supporting sustainable development.\n\nThe aim of this systematic review was to identify and assess all findings in articles related to the antioxidant activity of agricultural by-products. The extraction technologies used are briefly presented. Ultimately, this paper will provide insights for future research on the potential utilization of antioxidant content from agricultural by-products under the concept of sustainability.\n\n\nMethods\n\nThe writing of this systematic literature review is based on the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analysis) method.19 Article data will be used in this systematic review if it meets the following criteria: 1) Samples are agricultural waste (except animals); 2) Analyze the antioxidant activity using the extraction method; 3) The article is a research article; 4) Articles included in this selection have been published within the last 10 years (2013–2023). Studies showing animal samples and belonging to the type of review article or conference were excluded.\n\nThe database in the systematic review used Google Scholar, Semantic, and scopus-indexed articles with the help of an electronic database search, namely Publish or Perish. The literature search was limited to the year of publication between 2013 and 2023. Boolean operators (AND, OR) were used to combine keywords in order to identify relevant articles. Search terms (“agricultural by-product” OR “agricultural waste”) AND “extraction” AND (“antioxidant” OR “antioxidant activity”) to find related studies and data.\n\nDuplicate identification was carried out using Mendeley by importing all reference lists that had been obtained, and then duplicate data was deleted. Next, a screening process was carried out based on the title and abstract. Articles that passed entered the next stage, namely full-text screening to identify the type of waste sample discussed, the extraction method, and the antioxidant activity produced. The VOS Viewer generates a visual display of bibliographic materials using custom input data. The search terms represent the inclusion criteria and are closely linked to the study’s objectives, scope, limitations, and areas for further exploration. Moreover, only English-language original articles will be taken into account.\n\n\nResult\n\nThe article search conducted on the database mentioned in Figure 1, with the help of keywords and boolean operators obtained 1138 articles. After 59 duplicates were identified, 1079 articles were screened for title and abstract, and 487 articles were considered potentially eligible. A second screening was conducted, leaving 40 final articles for analysis.\n\n(a) 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay.\n\n(b) 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid (ABTS) assay.\n\n(c) Ferric reducing antioxidant power (FRAP) assay.\n\n(d) Oxygen radical absorbance capacity (ORAC) assay.\n\nFigure 2 shows that in the last 10 years, publications on the research of antioxidant potentials from agricultural waste or by-products have fluctuated. In the first half of the decade, between 2013 and 2018 the number of publications tended to be constant at a value of 1–2 publications but there was a significant increase in 2018 reaching 5 publications. The increased number of publications showed a constant value in 2019. Afterwards, there was a sharp increase of 120% from 5 publication articles last year to 11 publication articles in 2020. Nevertheless, for the rest of the second half of the decade between 2021 and 2023, the number of article publications decreased by 2–7 articles per year.\n\nIt is known through Figure 3 that most publication articles are dominated by discussions of processing or extraction of fruit by-products including grape, rambutan, banana, apple, pomegranate, etc followed by industrial crops by-products such as cocoa, coffee, and coconut. While the lowest percentage of research scores are owned by the bulb category which refers to research on the antioxidant potential of garlic. Those are known as parts of agricultural and agro-industrial waste. The classification of by-product types in this systematic review itself is done based on food guide pyramids20 and classification guide of agronomic crops based on its use values.21 Based on trends in publication topics, it is necessary to note that the data used does not include all publication articles published in 2023.\n\nFigure 4 is presented about the data extraction results of 40 publication articles obtained with the help of VOSviewer software. The network’s visualization results show that the most common keywords are antioxidants and activity, phenolic compounds, extractions, bioactive compounds, and antioxidants. This is shown by the size of the node as representation of keyword, that is increasing in proportion to the number of publication articles using similar keywords.22 VOSviewer-processed network visualization also shows a link between one keyword and another with a link between nodes. It is known that the most common publication article discussion trends are antioxidant analysis and activities related to acquisition methods such as extraction. It can also be seen that several widely used extraction methods include supercritical fluid extraction (SFE) and microwave-assisted extraction (MAE). Besides the process of obtaining bioactive components, it also can be easily identified from Figure 4 the type of raw material, in which case it is agro-local or agricultural by-product specifically such as coffee pulp, jackfruit peels, pistachio hull, etc.\n\nFurthermore, it is known that there is an optimization keyword trend arising from the processing of publication article data. It generally refers to a publication article that discusses the optimization of the anti-oxidant production process of agricultural waste or by-products itself. In Figure 4. it is known that the optimization method used by it is the response surface methodology. As a whole, it is also known that in the publication article data used, the discussion is not limited to the antioxidant activity of by-product extraction. It also discusses the characteristics of the extract and its application to derivative products, as is known in the presence of the color parameters, functional activities, antimicrobial activity, etc keywords. In addition, data extraction using this VOSviewer essentially facilitates the data analysis process as the connecting lines between nodes also indicate the relationship or interaction of each keyword itself.\n\nMost research make use of underutilised agricultural byproduct peel.32,34,41,44,46,50,51,53,57,58,59–61 The extraction methods used varied in each study, mostly using Conventional Solvent Extraction (CSE),32,33,34,41,44,46,50,51,53,57,58–61 followed by Microwave - assisted extraction (MAE)31,33,37,49,54,56,62 and Ultrasound-assisted extraction (UAE).26,31,44,45,57 Other extraction methods used include solid-liquid.23,34,55 Accelerated Solvent Extraction (ASE),24 Hot Acid,27 Supercritical fluid extraction (SFE),28,52 Homogenizer-Assisted Extraction (HAE),41 Maceration.33,38,39 Ultrasound - Microwave assisted extraction (UMAE).31,61 Pulsed ultrasound-assisted (PUSAE).32 Hot water extraction (HWEX),32 Microwave-assisted aqueous two-phase extraction (MAATPE),42 Electrohydrodynamic extraction (EHD),47 Subcritical water extraction (SWE),50 Vacuum Microwave-Assisted Extraction (VMAE),51 DESs.62\n\nAntioxidant Properties by Agriculture By-products\n\nThe antioxidant activities have been examined differently in each study. Most of study using (2,2-diphenyl-1-picryl-hydrazyl-hydrate) DPPH (Tabel 1.). Based on DPPH assay, lowest IC50 in this study is 0,0063 mg/mL in dragon fruit peels.59 However, comparing these data is challenging because other research did not report IC50 and utilised different techniques. Other antioxidant assays included (3-ethylbenzothiazolin-6-sulfonic) (ABTS)26,28,29,31,42,48,49,55; Ferric Reducing Antioxidant Powe (FRAP),23,25,60,31,38,40,50,54,55,57,58 Radical Absorbance Capacity (ORAC),53,57,60 Folin-Ciocalteu.30–33,51\n\n\nDiscussion\n\nConsumption of products rich in bioactive compounds is excellent when it comes to health benefits. Large amounts of by-products during the processing of agricultural raw materials and are suitable starting materials for the extraction of compounds such as natural antioxidants. Phenolic chemicals have been discovered in industrial waste, such as in industries that use grapes as raw material.23,28,42,55 Reported in grape pomace,23,55 stalk,28 seed,42 is a by-product that contains high anti-oxidant.55 Comparing antioxidant phenolic compounds in grape juice pomace and grape wine pomace using solid luquid extraction, and revealed higher antioxidant capacity in grape juice pomace. In another study, high antioxidant content was also found in fruit peel41,44,46,57,59,60 and legume by-products,29,30,33,40,54,62 this was shown by the DPPH, ABTS, and FRAP assays.63\n\nAccording to certain research, the level of antioxidant activity in agricultural waste may be measured using the DPPH (2,2-diphenyl-1-picrylhydrazyl) method. IC50 Value inhibits free radicals by 50% in unit (g/mL or ppm), vich is IC50 inversely proportional with antioxidant activity. The greater the IC50 value, the greater the antiocidant activity of extract (Özbek, 2018). Specifically, a compound is considered to have high antioxidant power if the IC50 value is less than 50 ppm, has moderate power if the IC50 is in the range of 50-100 ppm, and is considered weak when the IC50 value is between 100-150 ppm, and if the IC50 reaches 151-200 ppm.64,65 From the literature data found, it can be seen that the antioxidant value produced from black mulberry pomace (BMP) waste is 63.76 μg/mL which can be categorized as a strong antioxidant. Meanwhile, the antioxidant activity of coconut endocarp waste is considered to have weak antioxidant activity because the IC50 value is > 200 ppm. Some of the antioxidant tests of the extract materials used standard antioxidant samples in the form of ascorbic acid49,56,60 which aims as a comparison. Ascorbic acid was chosen as a comparator because it is characterized by acidity, functions as a highly effective reducer, exhibits high antioxidant activity, and is more polar when compared to other types of vitamin C.66\n\nAntioxidant activities could be affected not only by the types of by-products, but also the extraction method. A lot of studies used a conventional extraction methods, wich is maceration, digestion, infusion and Soxhlet extraction, etc. due to simplicity. Comparison of extractions was done in several studies, such as CSA with UAE25; CSA with DIE, MAE, UAE, UMAE31; and CSA with SFE,52 states that antioxidant activity in extracts obtained by conventional extraction are not higher than those using other methods. The decrease in antioxidant activity is probably because conventional extraction has several weaknesses such as long extraction time and large solvent consumption.60 Therefore, to overcome these problems, several studies have combined conventional extraction with other method.26 Water has been a popular solvent, with certain research showing that mixing water ethano54,60 by a particular ratio. A study56 mixing etanol-water have the best antioxidant activity for 40% ethanol, another study43 mixing methanol-water the best antioxidant activity with 50% methanol. This shows that the highest antioxidant is obtained in extraction with equal or lower ratio in less polar solvents.56\n\nAs a continuation of high antioxidant activity from the discovery of the optimal point of agricultural by-product extraction, antioxidants that are essentially low-concentration substances with the function of delaying or restraining the oxidation of a substrate67 are generally used as additiv materials. In relation, one of the most potential application or use of additional antioxidants is on cosmetic products. In the cosmological industry that is generally related to topical products, the presence of antioxidants in preparation formulations such as cream and so on is expected to help protect the skin through its characteristics that can withstand oxidative stress.68 The addition of antioxidants to cosmic products is considered capable of increasing the value of the product. Where, not only in applications to topical types of products, agricultural by-product extracts with high antioxidant activity can also be formulated in dietary supplements for skin health.69\n\n\nConclusion\n\nAgricultural waste by-products have high potential of antioxidant content, depending on the type of waste and extraction method. The utilization of agricultural waste that is rich in antioxidants has the potential to be utilized in the cosmetic industry. The dominant agricultural waste used is by-products from the fruit group. Antioxidant activity testing generally uses DPPH, ABTS, and FRAP assays. The most widely applied extraction method in agricultural waste processing is solvent extraction, followed by microwave-assisted extraction (MAE) and ultrasound-assisted extraction (UAE).\n\n\nEthics statement\n\nNot required.", "appendix": "Data availability\n\nThe article includes all the data supporting the results, and there is no need for additional source data.\n\nFigshare: PRISMA checklist for: “Exploring antioxidant potential of agricultural by-products: a systematic review”. DOI: https://.doi.org/10.6084/m9.figshare.24715674\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 are grateful for the in-kind support of the Faculty of Agricultural Technology, Universitas Brawijaya in this research.\n\n\nReferences\n\nFAO: World Food and Agriculture Statistical Yearbook 2022. FAO; 2022.\n\nEsparza I, Jiménez-Moreno N, Bimbela F, et al.: Fruit and vegetable waste management: Conventional and emerging approaches. J. Environ. Manag. Jul. 2020; 265: 110510. PubMed Abstract \| Publisher Full Text\n\nNath PC, et al.: Biogeneration of Valuable Nanomaterials from Agro-Wastes: A Comprehensive Review. Agronomy. 2023; 13(2). Publisher Full Text\n\nE. Commission et al.: GHG emissions of all world countries – 2023. Publications Office of the European Union; 2023. 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Publisher Full Text\n\nWani KM, Uppaluri RVS: Pulsed ultrasound-assisted extraction of bioactive compounds from papaya pulp and papaya peel using response surface methodology: Optimization and comparison with hot water extraction. Appl. Food Res. 2022; 2(2): 100178. Publisher Full Text\n\nDewi SR, Stevens LA, Pearson AE, et al.: Investigating the role of solvent type and microwave selective heating on the extraction of phenolic compounds from cacao (Theobroma cacao L.) pod husk. Food Bioprod. Process. 2022; 134: 210–222. Publisher Full Text\n\nFerreira SM, Falé Z, Santos L: Sustainability in Skin Care: Incorporation of Avocado Peel Extracts in Topical Formulations. Molecules. 2022; 27(6). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOzay Y, Ozdemir S, Gonca S, et al.: Phenolic compounds recovery from pistachio hull using pressure-driven membrane process and a cleaner production of biopesticide. Environ. Technol. Innov. 2021; 24: 101993. Publisher Full Text\n\nPanadare D, Dialani G, Rathod V: Extraction of volatile and non-volatile components from custard apple seed powder using supercritical CO2 extraction system and its inventory analysis. Process Biochem. 2021; 100(April 2020): 224–230. Publisher Full Text\n\nRodiah MH, Nur Asma Fhadhila Z, Kawasaki N, et al.: Antioxidant activity of natural pigment from husk of coconut. Pertanika J. Trop. Agric. Sci. 2018; 41(1): 441–451.\n\nHartiningsih S, Supriyanto S: Extraction of Phenolic Total Compound and Determination of Antioxidant Activity of Cocoa Leaves Extracted Using Various Solvents. J. Tek. Pertan. Lampung (Journal Agric. Eng.). 2023; 12(1): 129. Publisher Full Text\n\nOktaviani L, Astuti DI, Rosmiati M, et al.: Fermentation of coffee pulp using indigenous lactic acid bacteria with simultaneous aeration to produce cascara with a high antioxidant activity. Heliyon. 2020; 6(7): e04462. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang S, Fu W, Han H, et al.: Optimization of Ultrasound-Assisted Extraction of Phenolic Compounds from Walnut Shells and Characterization of Their Antioxidant Activities “Optimization of Ultrasound-Assisted Extraction of Phenolic Compounds from Walnut Shells and Characterization of Their Antioxidant Activities”. J. Food Nutr. Res. 2020; 8(1): 50–57. Publisher Full Text\n\nPereira GA, Molina G, Arruda HS, et al.: Optimizing the Homogenizer-Assisted Extraction (HAE) of Total Phenolic Compounds from Banana Peel. J. Food Process Eng. 2017; 40(3). Publisher Full Text\n\nDang YY, Zhang H, Xiu ZL: Microwave-assisted aqueous two-phase extraction of phenolics from grape (Vitis vinifera) seed. J. Chem. Technol. Biotechnol. 2014; 89(10): 1576–1581. Publisher Full Text\n\nKallel F, et al.: Garlic (Allium sativum L.) husk waste as a potential source of phenolic compounds: Influence of extracting solvents on its antimicrobial and antioxidant properties. Ind. Crop. Prod. 2014; 62: 34–41. Publisher Full Text\n\nGusman JA, Tsai PJ: Extraction of antioxidant compounds from rambutan (Nephelium lappaceum L.) peel as agricultural waste in Taiwan. J. Trop. Crop Sci. 2015; 2: 10–16. Publisher Full Text Reference Source\n\nMirheli M, Taghian Dinani S: Extraction of β-carotene pigment from carrot processing waste using ultrasonic-shaking incubation method. J. Food Meas. Charact. 2018; 12(3): 1818–1828. Publisher Full Text\n\nNadirah N, Rodzali B, Nafisah S, et al.: Phytochemical Screening and Antioxidant Activity of Unripe Cavendish and Dream Banana (Musa sp) Fruit Peels. J. Acad. UiTM Negeri Sembilan. 2018; 6(1): 39–44.\n\nMaher M, Taghian Dinani S, Shahram H: Extraction of phenolic compounds from lemon processing waste using electrohydrodynamic process. J. Food Meas. Charact. 2020; 14(2): 749–760. Publisher Full Text\n\nPornpun S, Wongsheree T, Yuadyong S: Ultrasound-assisted extraction of phenolic compounds from coconut endocarp and its radical scavenging activity. Naresuan Phayao J. 2020; 13(3): 22–28. Reference Source\n\nKhodaiyan F, Parastouei K: Co-optimization of pectin and polyphenols extraction from black mulberry pomace using an eco-friendly technique: Simultaneous recovery and characterization of products. Int. J. Biol. Macromol. 2020; 164: 1025–1036. PubMed Abstract \| Publisher Full Text\n\nKo M-J, Nam H-H, Chung M-S: Conversion of 6-gingerol to 6-shogaol in ginger (Zingiber officinale) pulp and peel during subcritical water extraction. Food Chem. 2019; 270: 149–155. PubMed Abstract \| Publisher Full Text\n\nSkenderidis P, Leontopoulos S, Petrotos K, et al.: Optimization of vacuum microwave-assisted extraction of pomegranate fruits peels by the evaluation of extracts’ phenolic content and antioxidant activity. Foods. 2020; 9(11). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBorja-Martínez M, Lozano-Sánchez J, Borrás-Linares I, et al.: Revalorization of broccoli by-products for cosmetic uses using supercritical fluid extraction. Antioxidants. 2020; 9(12): 1–17. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJoly N, Souidi K, Depraetere D, et al.: Potato By-Products as a Source of Natural Chlorogenic Acids and Phenolic Compounds: Extraction, Characterization, and Antioxidant Capacity. Molecules. 2021; 26(1). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSaewan N, Jimtaisong A, Vichit W: Optimization of phenolic extraction from coffee by− product using response surface methodology and their antioxidant activities. Food Appl. Biosci. 2020; 8(February): 14–26. Reference Source\n\nCasagrande M, Zanela J, Pereira D, et al.: Optimization of the extraction of antioxidant phenolic compounds from grape pomace using response surface methodology. J. Food Meas. Charact. 2019; 13(2): 1120–1129. Publisher Full Text\n\nÖzbek HN, Halahlih F, Göğüş F, et al.: Pistachio (Pistacia vera L.) Hull as a Potential Source of Phenolic Compounds: Evaluation of Ethanol–Water Binary Solvent Extraction on Antioxidant Activity and Phenolic Content of Pistachio Hull Extracts. Waste and Biomass Valorization. 2020; 11(5): 2101–2110. Publisher Full Text\n\nKaur S, Panesar PS, Chopra HK: Standardization of ultrasound-assisted extraction of bioactive compounds from kinnow mandarin peel. Biomass Convers. Biorefinery. 2023; 13(10): 8853–8863. Publisher Full Text\n\nLourenço SC, et al.: Optimization of natural antioxidants extraction from pineapple peel and their stabilization by spray drying. Foods. 2021; 10(6). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZaidel DNA, Rashid JM, Hamidon NH, et al.: Extraction and characterisation of pectin from dragon fruit (hylocereus polyrhizus) peels. Chem. Eng. Trans. 2017; 56: 805–810. Publisher Full Text\n\nLiew SS, Ho WY, Yeap SK, et al.: Phytochemical composition and in vitro antioxidant activities of Citrus sinensis peel extracts. PeerJ. 2018; 6(8): e5331–e5316. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJiang Z, Shi R, Chen H, et al.: Ultrasonic microwave-assisted extraction coupled with macroporous resin chromatography for the purification of antioxidant phenolics from waste jackfruit (Artocarpus heterophyllus Lam.) peels. J. Food Sci. Technol. 2019; 56(8): 3877–3886. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPavlović N, Jokić S, Jakovljević M, et al.: Green extraction methods for active compounds from food waste - Cocoa bean shell. Foods. 2020; 9(2): 1–14. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKristianto Y, Wignyanto W, Argo BD, et al.: Antioxidant increase by response surface optimization and Bayesian neural network modelling of pumpkin (Cucurbita moschata Duch) freezing. Food Res. 2021; 5(3): 73–82. Publisher Full Text\n\nMolyneux P: The use of the stable radical Diphenylpicrylhydrazyl (DPPH) for estimating antioxidant activity.Nov. 2003; 26.\n\nSukandar D, Nurbayti S, Rudiana T, et al.: Isolation and Structure Determination of Antioxidants Active Compounds from Ethyl Acetate Extract of Heartwood Namnam (Cynometra cauliflora L.). J. Kim. Terap. Indones. Jun. 2017; 19: 11–17. Publisher Full Text\n\nKim J: Radical Scavenging Capacity and Antioxidant Activity of the E Vitamer Fraction in Rice Bran. J. Food Sci. Apr. 2005; 70: C208–C213. Publisher Full Text\n\nFrancenia Santos-Sánchez N, Salas-Coronado R, Villanueva-Cañongo C, et al.: Antioxidant Compounds and Their Antioxidant Mechanism. Antioxidants. IntechOpen; Nov. 06, 2019. Publisher Full Text\n\nBalboa EM, Soto ML, Nogueira DR, et al.: Potential of Antioxidant Extracts Produced by Aqueous Processing of Renewable Resources for The Formulation of Cosmetics. Ind. Crop. Prod. July 2014; 58: 104–110. Publisher Full Text\n\nPuerta-Gomez AF, Cisneros-Zevallos L: Postharvest Studies Beyond Fresh Market Eating Quality: Phytochemical Antioxidant Changes in Peach and Plum Fruit During Ripening and Advanced Senescence. Postharvest Biol. Technol. June. 2011; 60: 220–224. Publisher Full Text" }	[ { "id": "320969", "date": "07 Oct 2024", "name": "Amal Hathout", "expertise": [ "Reviewer Expertise Food contaminants", "bioactive metabolites", "agricultural waste", "activated carbon" ], "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 systematic review aimed to identify and assess the antioxidant activity of agricultural by-products using various extraction methods. Santoso et al.'s study, Exploring the Antioxidant Potential of Agricultural By-products: A Systematic Review, makes an important contribution to the subject of agricultural by-product utilization. The authors effectively address the study topic and present persuasive data to support their findings. The methodology is sound, and the results are noteworthy. The article is well-written and highlights an important issue—the accumulation of agricultural by-products, which poses a threat to the environment. Some minor comments that require attention:\nAbstract: Should be shortened. Introduction: References should be added to some of the statements. For example:\n\"Between 2000 and 2020, world production of major food crops increased by 52% to 9.3 billion tons, which is equivalent to 2019 production.\" \"Agricultural waste contains various organic materials, carbohydrates, and other minerals that, if allowed to accumulate, can serve as a growing medium for decaying microorganisms.\"\n\nDiscussion: The potential applications of antioxidants from agricultural by-products in the pharmaceutical industry, as well as in food and animal feed additive production, should be mentioned (not only cosmetics). Discussion: Compare the different extraction methods used to determine high antioxidant activity. Table 1: The publishing dates should be rearranged in either ascending or descending order.\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.) Yes", "responses": [] }, { "id": "320967", "date": "14 Oct 2024", "name": "Emil Salim", "expertise": [ "Reviewer Expertise Immunology", "Pharmacology", "natural products." ], "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 comprehensive in its exploration of antioxidant potential and includes detailed descriptions of various extraction methods.\nThe paper clearly outlines the goal of exploring the antioxidant potential of agricultural by-products.\nThe methodology follows the PRISMA guidelines and provides clear details on the search strategy, inclusion criteria, and data extraction processes, allowing replication.\nThe conclusions align with the review’s findings.\nHowever, there are minor revision to be made:\n1. Please make the legend of the Y axis in figure 2. 2. \"Water has been a popular solvent, with certain research showing that mixing water ethano54,60 by a particular ratio. A study56 mixing etanol-water have the best antioxidant activity for 40% ethanol, another study43 mixing methanol-water the best antioxidant activity with 50% methanol. This shows that the highest antioxidant is obtained in extraction with equal or lower ratio in less polar solvents.56\", they should be ethanol.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable", "responses": [] } ]	1	https://f1000research.com/articles/13-1008
https://f1000research.com/articles/13-468/v1	09 May 24	{ "type": "Opinion Article", "title": "The rise of pathogen genomics in Africa", "authors": [ "Gerald Mboowa", "Francis Kakooza", "Moses Egesa", "Stephen Tukwasibwe", "Stephen Kanyerezi", "Ivan Sserwadda", "Benson R. Kidenya", "Jupiter Marina Kabahita", "Maria Magdalene Namaganda", "Mike Nsubuga", "Patricia Nabisubi", "Alisen Ayitewala", "Grace Kebirungi", "Esther Nakafu", "Natasha Patience Akwii", "Francis Kakooza", "Moses Egesa", "Stephen Tukwasibwe", "Stephen Kanyerezi", "Ivan Sserwadda", "Benson R. Kidenya", "Jupiter Marina Kabahita", "Maria Magdalene Namaganda", "Mike Nsubuga", "Patricia Nabisubi", "Alisen Ayitewala", "Grace Kebirungi", "Esther Nakafu", "Natasha Patience Akwii" ], "abstract": "The routine genomic surveillance of pathogens in diverse geographical settings and equitable data sharing are critical to inform effective infection control and therapeutic development. The coronavirus disease 2019 (COVID-19) pandemic highlighted the importance of routine genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to detect emerging variants of concern. However, the majority of high-income countries sequenced >0.5% of their COVID-19 cases, unlike low- and middle-income countries. By the end of 2022, many countries around the world had managed to establish capacity for pathogen genomic surveillance. Notably, Beta and Omicron; 2 of the 5 current SARS-CoV-2 variants of concern were first discovered in Africa through an aggressive sequencing campaign led by African scientists. To sustain such infrastructure and expertise beyond this pandemic, other endemic pathogens should leverage this investment. Therefore, countries are establishing multi-pathogen genomic surveillance strategies. Here we provide a catalog of the current landscape of sequenced and publicly shared pathogens in different countries in Africa. Drawing upon our collective knowledge and expertise, we review the ever-evolving challenges and propose innovative recommendations.", "keywords": [ "Africa", "Genome sequencing", "Pathogen Genomic data", "Public health", "Data sharing" ], "content": "Introduction\n\nThe global genomic surveillance strategy for pathogens with pandemic and epidemic potential, 2022–2032 was established by the World Health Organisation (WHO) to help countries develop their national genomic surveillance strategy for priority pathogens.1 The regular collection and sharing of such data are also fundamental for monitoring and effectively responding to outbreaks and for tracking antimicrobial resistance (AMR) to inform decision-making. Furthermore, WHO emphasizes that sharing of such data is critical for preventing, detecting, and timely responding to epidemics and pandemics at all levels, and is in the interest of all Member States.2\n\nAfrica remains increasingly prone to infectious disease threats, recording at least 140 disease outbreaks annually3,4 besides the high burden of drug resistance that has been estimated to have caused at least 1.05 million deaths in 2019.5 This calls for an urgent need to build and sustain capacity for near real-time outbreak detection, characterization, and routine pathogen genomic surveillance. Coronavirus disease (COVID-19) showed that most of the public health institutions in Africa if adequately capacitated and facilitated with high-throughput sequencing platforms, reagents, and data analytics infrastructure, can perform rapid pathogen detection, characterization, surveillance, and equitable data sharing. As of January 4, 2024, over 170,000 Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from 53 out of 55 countries in Africa have been sequenced and shared via GISAID (the Global Initiative on Sharing All Influenza Data).6 An important lesson to learn is that we need to facilitate national laboratories and local scientists to undertake routine pathogen sequencing activities within their countries while collaborating with the rest of the globe. The continent still has several pathogens of epidemic and pandemic potential that require near real-time tracking and in response, the Africa Centres for Disease Control and Prevention (Africa CDC) generated a list of priority pathogens for effective emergency preparedness and response.7\n\n\nPathogen sequencing in Africa\n\nNext-generation sequencing (NGS) is improving how disease outbreaks are accurately detected and investigated at an unparalleled magnitude. Most public health and research laboratories in many countries including Africa have at least one of the common NGS platforms (see Table 1). Different variables affect the choice of NGS platforms to be acquired by an institution such as the cost of the instrument, availability of after-sale service, access and cost of reagents, sequencing run time, throughput, accuracy, strategies for using NGS (targeted/panel, whole-exome, and whole-genome), depth of sequencing coverage, length of sequencing reads, single-end versus paired-end sequencing, genome size of an organism to be sequenced.\n\nCOVID-19 flung pathogen genome sequencing to the vanguard of accurate disease outbreak detection, characterization, surveillance of emerging variants, and real-time data sharing. But in the first two years of the pandemic, 78% of high-income settings sequenced >0.5% of their diagnosed COVID-19 cases, compared to 42% of low- and middle-income countries.8 Following this inequality, high-income countries were encouraged to support low- and middle-income countries to improve their local sequencing capacity8 to ensure an effective global response to the pandemic. Furthermore, a study revealed that sequencing 0.5% of the cases with a turnaround time of less than 21 days could provide a benchmark for SARS-CoV-2 routine genomic surveillance to detect emerging variants.8 In Africa, our findings suggest that many countries have built local capacity for pathogen genomics (see Figure 1). This was possible in part because, in the early phase of the pandemic, COVID-19-related travel restrictions forced countries to consider building local capacity for molecular testing and genomic surveillance of SARS-CoV-2 variants other than relying on shipping samples to other countries. By January 4, 2024, the continent had sequenced at least 1.3% of the reported cases (see Table 2) and ranked fourth.\n\n(GISAID data accessed on January 4, 2024). A total of 53/55 African Union Member States sequenced and shared their SARS-CoV-2 genomes since the start of the pandemic. At least 96% sequenced by Hubs based in Africa.9\n\nReported number of COVID-19 cases* and SARS-CoV-2 sequence data shared via the Global Initiative on Sharing All Influenza Data (GISAID)# by each continent. Data accessed on January 4, 2024.\n\n* (https://www.worldometers.info/coronavirus/?utm_campaign=homeAdUOA?Si%23countries).\n\n# (https://gisaid.org/).\n\nGenerally, the reduced costs of genome sequencing have led to the generation of large volumes of genomic sequence data globally as seen from the shared data in the Sequence Read Archive (SRA) for NGS data at the National Center for Biotechnology Information (NCBI) (see Figure 2). The SRA was established as part of the International Nucleotide Sequence Database Collaboration (INSDC) in 2009.10\n\nBetween 2012 and 2022 (~10 years), there were at least 20.2 Petabytes of sequence data deposited in SRA.\n\nIt should be noted that more genomic data is being generated than the capacity to analyze and meaningfully interpret it.11,12 This data if well utilized holds clues to improve health. This makes FAIRness (findability, accessibility, interoperability, and reusability) data sharing13 a critical component in this ecosystem so that scientists in well-resourced settings can collaboratively and equitably derive valuable insights from this data.\n\n\nData sharing of pathogen genomic data\n\nCOVID-19 propelled two important components in effective infectious disease response; (i) near-real-time pathogen sequencing and (ii) unprecedented collaborative scale in pathogen data sharing with over 16.4 million SARS-CoV-2 genomes already publicly shared via GISAID from all over the world by January 4, 2024.\n\nSince most of the SARS-CoV-2 sequence data was shared via GISAID, we searched the SRA/NCBI database (https://www.ncbi.nlm.nih.gov/sra/) up until January 4, 2024, for publicly accessible sequence data for other pathogens from different countries in Africa. The search terms used were, “Pathogen [All Fields] AND Country [All Fields]”. The retrieved data included different pathogens sequenced from each country filtered by microbial taxon, BioProject, genomic library layout, NGS platform, volume of data, and submitting/sequencing institution (see Extended data: Table 314).\n\nIn Africa before the COVID-19 pandemic, sequencing was largely a sophisticated endeavor undertaken by individuals and institutions based in high-income settings in collaboration with African institutions (see Extended data: Table 314). The local institutions largely participated in sample collection and processing for shipping to institutions in well-resourced countries. This implied that the objectives of these sequencing activities were also addressing the research aims of institutions in high-income settings. The pandemic brought about a paradigm shift that allowed local public health institutions to mobilize resources to embrace the genomic revolution in public health. This has been largely achieved through the Africa Pathogen Genomics Initiative (Africa PGI),4 which has equipped, trained, and offered technical support for African Union (AU) Member States to build sustainable genomics and bioinformatics capacity. Furthermore, the AU Commission and Africa CDC have called on governments, multi-lateral organizations, philanthropies, the private sector, and civil society organizations to support the full implementation of Africa’s New Public Health Order to drive global health security.15 In addition to this, it is imperative to promote equitable data sharing for pathogens of epidemic and pandemic potential in Africa while discouraging post-outbreak sanctions on countries that share data.\n\n\nMajor emerging challenges\n\nThe ever-growing volume of genomic sequence data coming out of laboratories in Africa has amplified interest in genomics and bioinformatics applications in public health.16 However, majority of the workforce has limited experience in these fields largely due to the limited number of training institutions that can offer the training. It should be noted that meaningful interpretation of genomic data generated from disease outbreaks requires adequate training and collaborative efforts (within and outside the continent). Sequencing facilities have varying levels of expertise in sequencing different organisms such as viruses, bacteria, fungi, and parasites as well as different sequencing technologies.\n\nThere is an urgent need for public health institutions in Africa to recruit and retain competent personnel dedicated to performing bioinformatics analyses that can support evidence-informed public health decision-making. In some cases, it has been complicated to establish such job positions within institutional structures. As such resorting to training the available personnel in this field is the most reasonable option however, this training requires long periods of learning, mentorship, and hands-on practice.17\n\nLimited local data analytics infrastructure is another critical emerging challenge. With many institutions having access to local NGS sequencing platforms that generate large volumes of raw sequence data that require memory-intensive analytic compute and storage, there is an ever-growing need to provide access to local high-performance computing (HPC) facilities. Setting up HPC facilities requires a lot of money and creates new challenges such as increasing electricity consumption and a need to recruit a competent HPC systems administrator. Furthermore, utilization of cloud-based resources for bioinformatics analyses also requires access to stable fast internet that may be unavailable in some countries.\n\nThe need to invest in biobanking and biorepository services in Africa. These facilities archive and distribute well-characterized biospecimens for research to support the development of disease diagnostics and therapeutics.18 Genomics activities rely on access to samples in these facilities. Many public health laboratories faced the challenge of storing thousands of samples during 2014-2016 Ebola outbreak in West Africa and the COVID-19 outbreak and realized a need to expand their biobanking capacities.\n\nChallenges of timely access to NGS reagents and supply chain. Travel restrictions during COVID-19 highlighted the need to improve the supply chain of NGS reagents in countries that lacked or had limited access to channel partners. Routine genomic surveillance requires reliable access to affordable NGS reagents and after-sales service. It is estimated that the cost per pathogen sequence ranges from US $20–$200, with poor countries paying up to 10-fold more than high-income countries.19\n\nPathogen genomics in public health in Africa requires continuous engagement among different stakeholders including NGS platform manufacturers/distributors, program/project funders, sequencing facilities, research/academic institutions, the national ministries of health, and policymakers. Each of these has a unique contribution, therefore planning and supporting multi-pathogen activities is a multi-sectoral endeavor that requires continued engagement to ensure an impactful genomic ecosystem. For example, the prohibitive cost of using onboard NGS instrument data analysis software licenses requires engagement with platform manufacturers. Cloud-based computing is an enthralling emerging infrastructure that offers an alternative infrastructure for solving traditional bioinformatics challenges in NGS data analytics and visualization. Cloud computing service models are classified into three types: Platform as a Service (PaaS), Software as a Service (SaaS), and Infrastructure as a Service (IaaS).20 The platform is relatively easier to use than the Linux command-line-based environment however it requires a pay-as-you-go subscription that charges based on usage.\n\nRecent years have revealed an emerging dimension of the impact of climate change on the evolution of pathogens in Africa.21,22 For example, climate change and extreme weather conditions have triggered increased cholera outbreaks in Africa.23 Research on modeling climate change and pathogen genomic data has failed to be socially inclusive, geographically balanced, and broad in terms of the disease systems studied, limiting our capacities to better understand the actual contribution of climate change on disease outbreaks.22 Therefore, integrating climate change data in pathogen genomics is important, and leveraging this expertise through collaboration with institutions that have established capacity.\n\n\nBeyond the post-COVID-19 genomics investment in Africa and way forward\n\nCOVID-19 allowed most of the countries in Africa to build local capacity for pathogen genome sequencing. It is important to keep the momentum by leveraging this investment to fight the continent’s endemic health challenges including Malaria, Cholera, HIV/AIDS, Tuberculosis, Vaccine-preventable diseases, Viral hemorrhagic fevers (VHFs) and the growing threat of antimicrobial resistance. Therefore, as recommended by the WHO,1 countries are establishing multi-pathogen genomic surveillance strategies that will ensure they can rapidly detect and precisely characterize pathogens, but this also requires stable funding from national governments and other funding agencies such as the Pandemic Fund.\n\nThe global economic cost of the COVID-19 pandemic was estimated at USD $16 trillion.24 Much as countries now appreciate the benefits of routine pathogen surveillance, many in Africa require technical and financial support. The devastating human, economic, and social cost of COVID-19 highlighted the urgent need for well-coordinated action to establish stronger health systems and mobilize additional resources for pandemic prevention, preparedness, response, and serve as a platform for advocacy. The WHO coordinated efforts through the newly established Pandemic Fund, which is a collaborative partnership among donor governments, co-investor countries, foundations, civil society organizations, and international agencies providing a dedicated stream of long-term funding (see Figure 3) for critical pandemic prevention, preparedness, and response (PPR) for future pandemics. The Pandemic Fund is set to finance critical investments to strengthen pandemic prevention, preparedness, and response capacities at national, regional, and global levels, with a focus on low- and middle-income countries.25\n\nThe Fund aims to help countries build resilience to future pandemics. The data was accessed on January 4, 2024 (https://fiftrustee.worldbank.org/en/about/unit/dfi/fiftrustee/fund-detail/pppr).\n\nIn 2023, projects that were financed prioritized strengthening comprehensive outbreak surveillance and early warning, laboratory systems, and human resources/public health workforce capacity. The Pandemic Fund is set to allocate financing where investments are most urgently needed to bolster PPR for future pandemics, addressing key capacity gaps at national, regional, and global levels. Overall, the Fund’s aims include: (i) supporting surveillance systems that enable timely tracking and reporting of outbreaks, (ii) creating faster and more accurate data sharing and (iii) building better laboratories so that they better assist partner countries to rapidly detect and effectively respond to infectious disease outbreaks.\n\nBeyond analysis, reporting, and data sharing of pathogen genomic data, the continent also needs to utilize the genomics resource to improve local research and development (R&D) capacity as well as support local therapeutics and affordable diagnostic manufacturing. The Partnerships for African Vaccine Manufacturing (PAVM) has a goal to enable the African vaccine manufacturing industry to develop, produce, and supply over 60 percent of the total vaccine doses required to fight endemic diseases on the continent by 2040.26 This offers an exceptional opportunity for enhancing local vaccine training. Rwanda is a pioneering country, hosting the first mRNA vaccine manufacturing facility in Africa, and soon, Senegal, South Africa, and Kenya will be the other African countries to have mRNA vaccine manufacturing facilities on the continent.27\n\n\nConclusions\n\nTimely and accurate analysis of pathogen genomes is crucial for monitoring the molecular evolution and dissemination of pathogens, improving diagnostic molecular tests and vaccines, and guiding efficient public health interventions. Therefore, there is an urgent need to sustain gains in local pathogen genomics in Africa while strengthening data analytics infrastructure and an equitable data sharing ecosystem.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nZenodo: Extended data for ‘The rise of pathogen genomics in Africa’, https://doi.org/10.6084/m9.figshare.25574040.v1. 14\n\nThis project contains following extended data:\n\nTable 3. The different pathogens that have been sequenced and publicly shared via SRA:NCBI from different countries in Africa (at least 12 Terabytes of sequence data).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\nG.M. acknowledges the EDCTP2 career development grant which supports the Pathogen detection in HIV-infected children and adolescents with non-malarial febrile illnesses using the metagenomic next-generation sequencing approach in Uganda (PHICAMS) project which is part of the EDCTP2 programme from the European Union (Grant number TMA2020CDF-3159). The views and opinions of the author expressed herein do not necessarily state or reflect those of EDCTP.\n\nWe are equally grateful for the support of the NIH Common Fund, through the OD/Office of Strategic Coordination (OSC) and the Fogarty International Center (FIC), NIH award number U2RTW010672. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the supporting offices.\n\n\nReferences\n\nConsiderations for developing a national genomic surveillance strategy or action plan for pathogens with pandemic and epidemic potential. http\n\nWHO guiding principles for pathogen genome data sharing. http\n\nAborode AT, et al.: Impact of poor disease surveillance system on COVID-19 response in africa: Time to rethink and rebuilt. Clin Epidemiol Glob Health. 2021; 12: 100841. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMakoni M: Africa’s $100-million Pathogen Genomics Initiative. Lancet Microbe. 2020; 1: e318. PubMed Abstract \| Publisher Full Text\n\nSartorius B, et al.: The burden of bacterial antimicrobial resistance in the WHO African region in 2019: a cross-country systematic analysis. Lancet Glob. Health. 2023.\n\nShu Y, McCauley J: GISAID: Global initiative on sharing all influenza data – from vision to reality. Eurosurveillance. 2017; 22. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRisk Ranking and Prioritization of Epidemic-Prone Diseases. yesAfrica CDC. . http\n\nBrito AF, et al.: Global disparities in SARS-CoV-2 genomic surveillance. Nat Commun. 2022; 13: 7003. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTegally H, et al.: The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance. Science. 2022; 378: eabq5358. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKatz K, et al.: The Sequence Read Archive: a decade more of explosive growth. Nucleic Acids Res. 2022; 50: D387–D390. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMboowa G, Sserwadda I, Aruhomukama D: Genomics and bioinformatics capacity in Africa: no continent is left behind. Genome. 2021; 64: 503–513. PubMed Abstract \| Publisher Full Text\n\nMulder N, et al.: Genomic Research Data Generation, Analysis and Sharing – Challenges in the African Setting. Data Sci J. 2017; 16: 49. Publisher Full Text\n\nWilkinson MD, et al.: The FAIR Guiding Principles for scientific data management and stewardship. Sci Data. 2016; 3: 160018. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMboowa G: Extended data for ‘The rise of pathogen genomics in Africa’. [Dataset]. figshare. 2024. Publisher Full Text\n\nThe New Public Health Order: Africa’s health security Agenda. yesAfrica CDC. . http\n\nOnywera H, et al.: Boosting pathogen genomics and bioinformatics workforce in Africa. Lancet Infect Dis. 2023; 24(23): e106–e112. PubMed Abstract \| Publisher Full Text\n\nJjingo D, et al.: Bioinformatics mentorship in a resource limited setting. Brief Bioinform. 2022; 23: bbab399.\n\nCroxton T, et al.: Building blocks for better biorepositories in Africa. Genome Med. 2023; 15: 92.\n\nPronyk PM, et al.: Advancing pathogen genomics in resource-limited settings. Cell Genomics. 2023; 3: 100443. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBani Baker Q, et al.: Comprehensive comparison of cloud-based NGS data analysis and alignment tools. Inform Med Unlocked. 2020; 18: 100296. Publisher Full Text\n\nMora C, et al.: Over half of known human pathogenic diseases can be aggravated by climate change. Nat Clim Chang. 2022; 12: 869–875. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVan de Vuurst P, Escobar LE: Climate change and infectious disease: a review of evidence and research trends. Infect Dis. Poverty. 2023; 12: 1–10.\n\nNakkazi E: Cholera outbreak in Africa. Lancet Infect Dis. 2023; 23: 411. Publisher Full Text\n\nCutler DM, Summers LH: The COVID-19 Pandemic and the $16 Trillion Virus. JAMA. 2020; 324: 1495–1496. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nThe Pandemic Fund Announces First Round of Funding to Help Countries Build Resilience to Future Pandemics. yesWorld Bank. . http\n\nA Breakthrough for the African Vaccine Manufacturing. yesAfrica CDC. . http\n\nSaied AA: Building Africa’s first mRNA vaccine facility. Lancet. 2023; 402: 287–288. PubMed Abstract \| Publisher Full Text" }	[ { "id": "278094", "date": "11 Jun 2024", "name": "Erik Bongcam-Rudloff", "expertise": [ "Reviewer Expertise Medical Sciences", "Bioinformatics", "Biobanking", "Exposome research", "Metagenomics", "Genomics", "HPC" ], "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 discuss an important issue regarding the significant threat that new pathogens pose to humanity. Specifically, the article addresses the situation in the African continent and the need for a Pan-African developed early surveillance system.\nThe authors accurately describe the use of NGS technologies and the necessity of high-throughput computing systems and high-speed internet to share and analyse common sequence data.\n\nHowever, the article lacks a more detailed discussion about the need for a critical mass of researchers with the bioinformatics competence to perform these tasks at a pan-African level. The article should address and mention some of the existing education initiatives (e.g., AI4D Africa, H3Abionet, EANBiT, University programmes, etc.) and the imperative need to educate more African scientists in using Artificial Intelligence, HPC systems, NGS sequencing, and bioinformatics analysis. International collaboration relies on the integration of ethics and law across national legal systems. The article would benefit from discussing the challenges and problems that can arise when considering ethical and legal issues in such collaborations.\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Partly\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Partly", "responses": [] }, { "id": "276910", "date": "03 Jul 2024", "name": "Ana S Gonzalez-Reiche", "expertise": [ "Reviewer Expertise Genomic Pathogen Surveillance", "SARS-CoV-2", "Respiratory Viruses", "Viral Sequencing", "Bioinformatics" ], "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 by Mboowa and collaborators describes the resources available in Africa for genomic pathogen surveillance and how these were built, strengthened, or expanded across the continent due to the COVID-19 pandemic. This important topic deserves attention as it prepares us to respond to emerging infectious diseases globally. Most importantly, it underscores the availability of local capacity and the potential to reduce the gap in research led by African scientists through their perspective. The article would benefit from highlighting the data generated and the resources available in Africa—for example, Table 1. Rather than listing common NGS platforms, list those available in Africa alone. The table header makes it unclear whether this table is already specific to Africa. Similarly, in Figure 2, the authors could include an insert plot showing the distribution of SRA data for Africa only. Another essential information would be how these resources are distributed across academic, healthcare, government institutions, and the public and private sectors. This could help lay out a strategic plan to synergize better current efforts to build a sustainable long-term surveillance program. If any of this information is available to the authors, it should be included. The section \"Major emerging challenges\" could more effectively state the needs if concrete estimates were included. For example, in the third paragraph of this section, the authors could provide an estimate of resources (e.g. computing capacity) and money (e.g. estimated cost per processor/computing node) that would be needed to sustain a genomic surveillance lab sequencing X samples per year. This would be a more practical comparison highlighting the increased cost of sequencing in low-income countries where the supply chains for sequencing reagents aren’t as robust as those available to high-income countries. Using one or two of the author's institutions as examples should suffice. Similarly, in paragraph 6, it seems to this reviewer that investing in building local capacity for bioinformatic analysis will probably pay off in the long run compared to investing in license-based software. This is important as it will highlight the need to establish a critical mass of bioinformatics expertise, including bioinformatic training at universities, etc. (or support for existing training options). A brief cost analysis could also help to support this. In the section “Beyond the Post-COVID-19 genomics…” The Pandemic Fund initiative should be introduced at its first mention. The authors introduce the Pandemic Fund in the second paragraph, but they first mention it at the end of the first paragraph. Please consider reorganizing this section to address this.\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Partly\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-468
https://f1000research.com/articles/11-51/v1	17 Jan 22	{ "type": "Research Article", "title": "A feasibility study of training in a local community aimed upon health promotion with special emphasis on musculoskeletal health effects", "authors": [ "Rizky Suganda Prawiradilaga", "Magnus Bendtsen", "Simon Esrup", "Niklas Rye Jørgensen", "Fajar Awalia Yulianto", "Eva Wulff Helge", "Magnus Bendtsen", "Simon Esrup", "Niklas Rye Jørgensen", "Fajar Awalia Yulianto", "Eva Wulff Helge" ], "abstract": "Background: To minimize fracture risk, multimodal training regimens are recommended. However, their effectiveness in community settings remains uncertain. This study evaluated the feasibility of 19-weeks of multimodal training in a local community center with emphasis on musculoskeletal health in postmenopausal women. Methods: In a controlled trial, 28 postmenopausal women (53-68-years-old) were assigned to a multimodal training group (MMT, n=15) or a control group (CON, n=13). The training consisted of high- and odd-impact, resistance and balance-coordination training 1-2 hours weekly. The outcomes were attendance rate, regional and total bone mineral density (BMD), bone mineral content (BMC), bone turnover markers (BTM), body composition, functional muscle strength and power, and dynamic balance. All were determined at baseline and after 19 weeks of training. BTM was assessed after three weeks. Results: Overall, 22(79%) participants (MMT, n=9; CON, n=13) completed the study, and the mean attendance rate for MMT was 65.5% of the maximum sessions (2) offered. Only right trochanter BMD increased (p<0.05) by 1.0±1.1% in MMT, which was higher(p<0.05) than CON. While whole-body BMC was not changed at 19 weeks from baseline in MMT, it decreased (p<0.05) in CON resulting in a significant difference (p<0.05) in whole-body BMC delta values between the two groups. Compared to baseline, body fat percentage(%BF), fat mass(FM), and visceral adipose tissue (VAT)-mass and -volume were decreased (p<0.01) in MMT, and were larger (p<0.05) than CON. No significant changes were observed in BTM, muscle strength and power, and dynamic balance after 19 weeks. Conclusions: Nineteen weeks of multimodal training 1-2 hours per week in a local community had a health-enhancing effect on %BF, FM, and VAT, whereas the musculoskeletal health impact was modest. We hypothesize that the reason might be too low training volume and frequency and supposedly too low musculoskeletal training intensity for some participants. Registration: ClinicalTrials.gov NCT05164679 (21/12/2021).", "keywords": [ "bone mineral density", "bone turnover marker", "osteoporosis", "high-impact", "odd-impact", "resistance exercise", "balance training", "multimodal training" ], "content": "Introduction\n\nOsteoporosis is a growing public health concern. The disease is characterized by impaired bone strength due to the reduction of bone mass and impairment of the micro-architecture of the bone, which increase the risk of bone fracture.1 It is estimated that 200 million females are affected worldwide and causes more than 8.9 million fractures per year.2 Falls in osteoporotic patients are linked to high morbidity and mortality.3 Therefore, fall prevention strategies while improving the bone strength aimed at the high-risk population are needed.4\n\nOne way to prevent osteoporosis can be through engaging in evidence-based training to improve bone mineral density (BMD) and reduce age-related bone loss,5 such as high-impact and resistance training. Furthermore, balance and coordination training can minimize the risk of falls and fractures, which is relevant to the high-risk population.4 Studies have shown that high-impact exercises, which produce high vertical ground reaction forces with a high force development rate,6 are beneficial for bone structure and mineralization in children,7 adults,8 and the elderly.9 In a previous study of the acute osteogenic response to high-impact jumping in postmenopausal women,10 stimulation of bone formation without any increase in bone resorption after jumping was reported. Moreover, the latter study showed a dose-response relationship between vertical as well as combined three-axes ground reaction forces (GRF) and the acute procollagen type I amino-terminal propeptide (P1NP)-response after countermovement jumps.\n\nIn addition, resistance exercise, which induces various muscle loads applied to the bone,11 is reported to be a relevant osteogenic training modality for maintaining or increasing bone density and mass in older people.12 Besides, to prevent falls, balance and coordination exercises are crucial to be included as they improve static and dynamic balance.13 Therefore, it is hypothesized in the present study that evidence-based multimodal training as health promotion will have an osteogenic effect on bone mass and bone strength that may counteract the normal age-related bone loss in postmenopausal women and improve the dynamic balance as well as muscle strength and power, which may prevent falls and reduce the fracture risk.\n\nAlthough the association between exercise training, bone loss, and falls prevention in older adults appear to be established in intervention studies,14 only a few studies have examined the effects of combined training on musculoskeletal health in postmenopausal women,15–17 and the results are varied. Therefore, there is still a need for safe, reliable, affordable, and evidence-based training programs that can be introduced, embraced, and sustained in high-risk populations, such as postmenopausal women.\n\nThe present study was performed in a local community setting. The aim was to investigate the feasibility and the health-promoting musculoskeletal effects of 19wk multimodal training (high- and odd-impact, resistance, balance, and coordination training) for postmenopausal women. The primary outcomes were bone mass and BTM, while body composition, dynamic balance, muscle strength and power were the secondary outcomes.\n\n\nMethods\n\nThe multimodal training was offered to postmenopausal healthy women in a local community. The outcomes for the training group (MMT) were compared with a sedentary control group (CON). Training was offered twice weekly for one hour, and the average attendance rate of MMT participants over the 19wk had to be > 1 hour weekly. To collect baseline (BASE) data, all participants showed up in the laboratory on three occasions prior to the intervention (a description of the specific methods used is given in later sections). On the first visit, resting blood samples were collected to evaluate the concentration of bone turnover markers (BTM), and body weight, height, body composition including BMD and bone mass were measured. On the second visit, a dynamic balance test (four square step test) and a functional muscle strength and power test (jump-and-reach test) were performed. On the third visit, the aerobic capacity was evaluated by assessment of VO2-max. After three weeks (3wk) of training, resting blood samples were additionally collected. After 19wk of training, all assessments were repeated and compared with baseline and MMT and CON were compared.\n\nBlood sample collection, DXA-scanning, and VO2-max tests were carried out at the Department of Nutrition, Exercise and Sports, University of Copenhagen, Denmark. The testing of vertical jump height, as well as dynamic balance, were performed at the health promotion training initiative in the Copenhagen area, Denmark. The blood samples were analyzed at the Department of Clinical Biochemistry, Rigshospitalet Glostrup Hospital, Denmark.\n\nTo ensure transparency of the study protocol, the trial was registered retrospectively at ClinicalTrials.gov and published on December 21st, 2021 (NCT05164679). As registration at ClinicalTrials.gov has until recently not been a part of the general research policy in our team, the trial was registered after completion of the study.\n\nHealthy, sedentary postmenopausal women aged below 70 years were eligible to participate in the present study. Inclusion criteria were non-smoker and body mass index (BMI) <30 kg/m2. Exclusion criteria were: T-score < -3 SD in the lumbar spine or hip; Z-score > 1.5 SD (high age-related BMD); use of hormone therapy, medical treatment, or supplements that affect bone metabolism; previous or current medical condition affecting bone health; engagement in regular and systematic weight-bearing training or strength training during the preceding two years.\n\nInitially, twenty women were recruited to the training via advertisements online and an in a local newspaper, of which 19 showed up for pre-testing (Figure 1). After a medical examination, one participant was excluded due to low BMD (T-score < −3 SD), and two were excluded due to high BMI (≥30 kg/m2). In addition, one woman refrained from participating in the training, and thus, 15 participants were recruited to MMT. During the study, two participants in MMT dropped out due to personal reasons and at the end of the study four participants were excluded in the analyses as their average attendance to the program was less than one hour per week. CON consisted of 13 age-matched sedentary postmenopausal women (12 from a previous study plus the woman who refrained from participating in the training), and therefore 9 MMT and 13 CON was finally included in the data analyses. Participants' baseline characteristics, including maximum oxygen consumption (VO2-max), are shown in Table 1.\n\nEvery participant was fully informed in writing and verbally before giving her written consent to the procedures and potential discomfort associated with the study. The study was conducted in accordance with the Declaration of Helsinki and approved by the local ethics committee of the Capital Region of Denmark, H-18044190.\n\nThe present feasibility study evaluated the osteogenic impact of a training concept already offered by a health promotion initiative, “Knoglestærk” (“Bone strong”), in a local community.\n\nAccording to the initiative, the training was offered as “evidence-based bone training” aimed upon enhancing musculoskeletal health. It was carried out 2 × 60 minutes weekly. The training concept included: 1) High- and odd-impact exercise including multi-directional games; 2) Progressive resistance training; 3) Balance and coordination training. The participants were engaged in intermittent gymnastics and small game sessions aimed at imposing osteogenic and diverse strain on the skeleton, mainly in the legs and arms. Thus, the training included various jumping exercises (e.g., counter-movement jumps, jumps from the floor up onto a bench, and from a bench down to the floor), quick walking up and down on gymnastics equipment, sprinting over short distances in different directions (in small games form). In addition, resistance exercises with elastic power bands, heavy exercise balls (medicine balls), and sandbags of 5-7 kg were applied. The training was performed intermittent and varied to ensure that the bones would not be desensitized, as it is observed in repetitive endurance training.\n\nTo test the BMD exclusion criteria at baseline as well as evaluate bone adaptation in proximal femur (PF), lumbar spine (LS), and whole-body (WB) after 19wk of training, BMD (g/cm2) were assessed by Dual-energy X-ray Absorptiometry scanning (iDXA, Lunar Corporation, Madison, Wisconsin, USA) according to standard procedures. The regions of interests were determined by the encore software (encore software version 14.10.022, GE Medical Systems, Madison, United States). In addition, body composition was evaluated by the whole-body scan: body weight (BW, kg), BMI (kg/m2), body fat percentage (%BF, %), total fat mass (FM, g), total lean body mass (LBM, g), visceral adipose tissue (VAT) mass (g) and volume (m3), and total bone mineral content (BMC, g). The participants were asked to remove metal objects and empty their bladder prior to scanning.\n\nThe plasma concentration of BTM at BASE, after 3wk, and after 19wk of training were measured. After an overnight fast and without any vigorous activities in the previous 48 hours, participants showed up in the laboratory in the early morning. Blood samples were collected from the antecubital vein with a butterfly needle, then transferred to EDTA tubes and centrifuged immediately. The plasma fractions were put on dry ice. Eighteen ml of blood were taken from each participant per test day. Following each test, a sample was placed at -80°C for future P1NP, OC, and CTX analysis, which were assessed by the Chemiluminescence method using a fully automated immunoassay system (iSYS, Immunodiagnostic Systems Ltd., Bolton, England). The assay performance expressed as inter-run variation coefficients were 8% for P1NP, 9% for OC, and 10% for CTX.\n\nTo estimate the participants’ general training status, a progressive test of maximal oxygen uptake (VO2-max) (ml/kg/min) was performed on an electronic bicycle ergometer (Monark 839E, Monark Exercise AB, Vansbro, Sweden) according to standard procedures. A breath-by-breath gas online analyzing system (Jaeger Oxycon Pro, VIASYS Healthcare, Höchberg, Germany) was connected to the participant, and a direct VO2-max measurement was conducted.\n\nThe “four square step test” (FSST) was performed to evaluate the dynamic balance18 in MMT. The test requires a person to move systematically forward, sideward, backward, and sideward again over four narrow sticks circa 2.5 cm in diameter and 100 cm in length placed on the floor like a cross. The participants were requested to complete the sequence as fast as possible without touching the sticks. Facing the cross, the participants started in the lower left quadrant by stepping forward over the stick into the next left quadrant, stepped sideward over the stick again into the upper right quadrant, and stepped backward over the stick into the lower right quadrant, then stepped sideward over the stick into the left quadrant where they started. Thus, they were moving in a clockwise direction. The floor in each square must be contacted by both feet, and the participants were asked to face forward for the whole sequence. However, the participants were allowed to turn to step into the next square if needed. They started and finished in the same square, and the score was given in seconds (sec). The test was done twice, and the fastest time was used as the FSST score.\n\nThe functional muscle strength and power were evaluated in MMT by a jump-and-reach test (vertical jump height) (Vertec Sports Imports, Hilliard, OH). First, the participants were taught how to perform a countermovement jump and how to displace the vanes that was placed above reaching height on a vertical stand. After thoroughly instruction and familiarization, the jump-and-reach test was performed. The maximum vertical jump height (cm) was determined by the difference between the participant standing reach height and the highest displaced vane. The greatest value out of three trials was taken as the result.\n\nAll of the statistical analyses were conducted using the Statistical Package for the Social Sciences (SPSS, version 26.0, IBM Corp., Armonk, NY, USA). The standard descriptive statistics and unpaired T-test were used to describe and test the baseline characteristics of the participants. Repeated measurements ANOVA and general linear model with post hoc tests were used to test the effect of training on BTM, BMD, dynamic balance, and the jump-and-reach test. A p-value < 0.05 was considered significant. Unless otherwise stated, values are given as mean ± standard error (SE).\n\n\nResults\n\nAt baseline, there were significant differences between MMT and CON for BW, BMI, FM, left and mean femur BMD values, OC, and CTX (Table 1).\n\n* Significant difference between groups (p < 0.05). Unpaired T-test.\n\nAs described in the participants section, two persons in MMT dropped out due to personal reasons, and four participants did not meet the mean attendance criterion of at least 1 session weekly (>19 sessions) and were subsequently excluded in the data analyses. The mean attendance rate for the remaining participants (9 women) was 24.2 sessions (65.5%) of the maximum number of sessions offered (37 sessions). The individual attendance rates were 20-30 sessions (54.1-81.1%). with a decrease in attendance rate over time from 6.2 out of 8 sessions (78%) in the first four-week period and 5.1 out of 8 sessions (64%) in the last four-week period.\n\nThe attendance rate range (54.1-81.1%) in the present study showed that there is inter-individual variability. The participants attended the training more in the first than the last four-week.\n\nAfter 19wk of training, right trochanter BMD (g/cm2) increased significantly from baseline for MMT (1.0%, p = 0.03), which was significantly different from CON (p = 0.03) (Table 2), but there was no significant BMD change in any other region. However, LS (1.2%) and right total femur (0.3%) tended to increase (both, p < 0.1) for MMT (Figure 2). Whole-body BMC decreased significantly (0.7%, p = 0.016) within CON.\n\na General Linear Model + post hoc test.\n\n* Significant difference between group (p < 0.05).\n\n# Significant difference within group (p < 0.05).\n\nSignificant between-group difference (p < 0.05). #Significant within-group difference (p < 0.05).\n\nFor body composition, there were significant reductions in %BF (4.0%, p = 0.006), FM (6.0%, p = 0.013), VAT-mass (11.3%, p = 0.004), VAT-volume (11.3%, p = 0.004) within the MMT compared to BASE (Table 3). Compared to CON, there were significant differences for %BF (p = 0.049), FM (p = 0.021), VAT-mass (p = 0.013), VAT-volume (p = 0.013), and whole-body BMC (p = 0.041) delta values.\n\na Geometric mean.\n\nb General Linear Model + post hoc test.\n\n Significant difference between groups (p < 0.05).\n\n# Significant difference within-group (p < 0.05).\n\nThe plasma concentrations of P1NP, OC, and CTX are shown in Figure 3 and Table 4. There was no significant within- or between-group difference observed at 3wk or 19wk compared to baseline for all markers.\n\n(A) Procollagen type-1 amino-terminal propeptide (P1NP), (B) osteocalcin (OC), and (C) C-terminal telopeptide of type-1 collagen (CTX). Time measurements: Immediately before exercise (baseline), after 3 weeks (3wk), after 19 weeks (19wk). The lines represent means ± SE.\n\nThere were no significant changes in both FSST and jump-and-reach test at 19-week compared to baseline for MMT (Table 5). However, there was a tendency to be faster in FSST at 19-week (p = 0.06).\n\n\nDiscussion\n\nThe present study aimed at evaluating the feasibility and whether 19wk of multimodal training offered as musculoskeletal health promotion in a local community had an effect on musculoskeletal health, body composition, dynamic balance, and functional muscle strength in postmenopausal women. The main finding from this study was that the training program had a positive effect on body composition. Thus, %BF, FM, VAT-mass, and VAT-volume were significantly reduced in MMT compared to CON, showing that the body composition change was due to the training program. In addition, the right trochanter BMD was improved for MMT, and the whole-body BMC was maintained for MMT in contrast to a significant reduction in CON.\n\nThis study found that only right trochanter BMD was significantly increased (1.0%, p < 0.05) in MMT. There was no significant changes in other regions of BMD. This finding could be due to the participant attendance did not meet the recommendations of training intensity, volume, and frequency. According to Daly and Giangregorio,19 the minimum frequency of resistance training is at least two days per week and for weight-bearing impact exercise 4-7 times per week, which the present study not met as no participant fulfilled 37 times in total for 19wk of training.\n\nThe whole-body BMC was not changed in MMT, whereas it was significantly decreased (p = 0.02) by 0.7% in CON, which was significantly (p = 0.04) different from MMT (Table 3). Thus, it seems from the present study that the training at “Knoglestærk” maintained total bone mass, even with a required minimum training attendance of just one hour weekly. The loss of whole-body BMC (−0.7%, p = 0.016) in CON group is consistent with Gallagher et al.,20 who investigated the effect of age and menopause status on bone. The finding that the change in BMC differed between MMT and CON is not in line with Mosti et al.,16 who investigated the impact of three sessions of squat exercise maximal strength training in postmenopausal women with osteoporosis or osteopenia (mean age: 61.9 ± 5.0 y) for 12 weeks. Moreover, they found an increase in lumbar spine BMC not whole-body. Thus, they found an increase of 2.9 ± 2.8% (p = 0.01) LS BMC from baseline in training group, and this change was higher (p = 0.03) than in control group.\n\nThe reduction in %BF and FM (Table 3) in this study is in agreement with Daly et al.,21 who investigated the effect of one year supervised and structured multi-component training program in community-dwelling independently living men (27%) and women (73%) (mean age: 67.4 y, 60-86 years). They found that the FM was significantly decreased (p < 0.001) by 3.2%, which is lower than the present study (6.0%, p = 0.01). The higher reduction in the present study compared to Daly et al.21 study might be due to the younger participant (62.4 ± 3.8 y) which has a higher metabolic rate than the older one (66 – 94 y),22 that could influence the change of body fat. The reduction in %BF and FM is in line with Nielsen et al.23 as well, who investigated the feasibility and physiological health effects of 15-week training performed minimum once a week for sedentary elderly. They found that the total FM was significantly decreased (−2.0 kg, p = 0.01) and the %BF as well (-1.6%, p = 0.01).\n\nAs the VAT assessment by iDXA is a fairly new functionality, only very few studies report results for this outcome, and it seems that none has studied training effects on VAT for healthy postmenopausal women. Moreover, no normal reference intervals for specific populations are established yet. The present finding of a 11.3% reduction in VAT seems in line with the Yen et al. study,24 which reported a 6.3% decrease in VAT after eight weeks of aerobic and resistance exercise intervention. However, the study participants were a group of male and female patients receiving chemotherapy for head and neck cancer (mean age: 52 ± 10.7 y). As reported by Yen et al.24 the lower response than the present study (-6.3% vs. −11.3%) may be due to the disease or the shorter duration (8wk vs. 19wk), even though their intervention more frequent (3 days/week vs. one day/week).25 Moreover, it could be hypothesized that the participants in Yen et al.24 study had a lower %BF and VAT at baseline, therefore, it is more difficult to induce a training response. Nevertheless, more studies still needed on healthy postmenopausal women.\n\nDespite the favorable result, the present study has several limitations. The dietary intakes were not recorded. Thus, the changes that occur in the body composition could not be known whether entirely due to the training or dietary intake of participants. Future studies should consider taking the dietary intake history and monitoring habitual daily physical activity, which may add an explanation regarding the changes specifically in body composition in the present study. Another thing to note is that the Knoglestærk health promotion program is a real-life setting and thus the training is not as well controlled as in a laboratory setting. Because neither heart rate (HR) nor accelerometer measurements were recorded during exercise, it cannot be ruled out that the individual training intensity varied among the participants. Hence, the use of HR monitor and accelerometer would improve the control and the standardization of the training and thus reduce the variation in the individual response and the reliability of the results. In addition, we did not carry out a priori power analyses. The power calculations were performed after the studies had been conducted (provided as Extended data26), and the statistical power of the present study seems to be underpowered. Therefore, a larger sample size would have a positive effect on the effect sizes due to a reduction in standard error and thus an improvement of the statistical power. The effect size of the intervention was varied, with greatest effect on VAT-volume & masse, total BMC, weight, total fat mass and body fat percentage. On the contrary, the intervention has smaller effect on general and specified BMDs. The given amount of time (19wk) and specified intervention (multimodal training group) had greater effect on fat changes rather than bone changes. The interesting part was the total BMC that affected by the intervention was not followed by BMD's changing.\n\n\nConclusions\n\nThe results of the present study indicate that while 19 weeks of multimodal musculoskeletal training as offered by the Knoglestærk health promotion training initiative is feasible for postmenopausal women by inducing health-enhancing effects on body composition, however due to the attendance compliance, the training did only elicit minor significant improvements in BMD, thus an increase was found in right trochanter BMD and whole-body BMC. No changes in dynamic balance or the functional muscle strength were observed in the present study. To promote musculoskeletal improvements for all participants, a better control of the individual musculoskeletal training intensity, frequency, and attendance rate is highly recommended.\n\n\nData availability\n\nFigshare: Underlying data for ‘A Feasibility Study of Training in a Local Community Aimed Upon Health Promotion with Special Emphasis on Musculoskeletal Health Effects.’\n\nhttps://doi.org/10.6084/m9.figshare.16836940.29\n\nThis project contains the following underlying data:\n\n- A Feasibility Study of Training Dataset1.csv (dataset of participant characteristic, body composition, and bone mineral density)\n\n- A Feasibility Study of Training Dataset2.csv (dataset of participants’ bone turnover markers)\n\n- A Feasibility Study of Training Dataset3.csv (dataset of functional muscle strength and power and dynamic balance result)\n\nFigshare: Working title: A Feasibility Study of Training in a Local Community Aimed Upon Health Promotion with Special Emphasis on Musculoskeletal Health Effects. Extended data - Statistical power of the paired t-tests for body composition, regional BMD, and bone turnover markers. https://doi.org/10.6084/m9.figshare.16611655.v126\n\nFigshare: Working title: A Feasibility Study of Training in a Local Community Aimed Upon Health Promotion with Special Emphasis on Musculoskeletal Health Effects. Extended data - Effect size of the Training Program. https://doi.org/10.6084/m9.figshare.16611787.v127\n\nFigshare: CONSORT checklist, extension for Pilot and Feasibility Trials for study “A Feasibility Study of Training in a Local Community Aimed Upon Health Promotion with Special Emphasis on Musculoskeletal Health Effects”. https://doi.org/10.6084/m9.figshare.16610341.v128\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).", "appendix": "Acknowledgements\n\nWe thank all the participants who took part in the study for their time and efforts. The authors thank Jens J. Nielsen for assistance in blood draws, Nadia Quardon for blood sample analysis, Andreas Meine for assistance in VO2-max testing, and Christian Ritz for support in statistics. RSP gratefully acknowledges a Ph.D. fellowship from Lembaga Pengelola Dana Pendidikan (LPDP)/Indonesia Endowment Fund for Education.\n\n\nReferences\n\nKanis JA, Melton LJ, Christiansen C, et al.: The diagnosis of osteoporosis. J Bone Miner Res. 1994 Aug 1; 9(8): 1137–1141. Publisher Full Text\n\nFacts and Statistics\|International Osteoporosis Foundation: [cited 2017 Oct 4]. Reference Source\n\nSinaki M, Brey RH, Hughes CA, et al.: Balance disorder and increased risk of falls in osteoporosis and kyphosis: significance of kyphotic posture and muscle strength. Osteoporos Int. 2005 Aug 1; 16(8): 1004–1010. PubMed Abstract \| Publisher Full Text\n\nBeck BR, Daly RM, Singh MAF, et al.: Exercise and Sports Science Australia (ESSA) position statement on exercise prescription for the prevention and management of osteoporosis. Journal of Science and Medicine in Sport. 2017 May 1; 20(5): 438–445. Publisher Full Text\n\nDalsky GP: Exercise: its effect on bone mineral content. Clin Obstet Gynecol. 1987 Dec; 30(4): 820–832. PubMed Abstract \| Publisher Full Text\n\nNikander R, Sievänen H, Heinonen A, et al.: Load-specific differences in the structure of femoral neck and tibia between world-class moguls skiers and slalom skiers. Scand J Med Sci Sports. 2008 Apr; 18(2): 145–153. PubMed Abstract \| Publisher Full Text\n\nNogueira RC, Weeks BK, Beck BR: Exercise to improve pediatric bone and fat: a systematic review and meta-analysis. Med Sci Sports Exerc. 2014 Mar; 46(3): 610–621. PubMed Abstract \| Publisher Full Text\n\nVainionpää A, Korpelainen R, Leppäluoto J, et al.: Effects of high-impact exercise on bone mineral density: a randomized controlled trial in premenopausal women. Osteoporos Int. 2005 Feb; 16(2): 191–197. Publisher Full Text\n\nKarinkanta S, Heinonen A, Sievänen H, et al.: A multi-component exercise regimen to prevent functional decline and bone fragility in home-dwelling elderly women: randomized, controlled trial. Osteoporos Int. 2007 Apr; 18(4): 453–462. Publisher Full Text\n\nPrawiradilaga R, Madsen A, Jørgensen N, et al.: Acute response of biochemical bone turnover markers and the associated ground reaction forces to high-impact exercise in postmenopausal women. Biol Sport. 2020; 37(1): 41–48. PubMed Abstract \| Publisher Full Text\n\nTurner C, Robling A: Exercises for improving bone strength. Br J Sports Med. 2005 Apr; 39(4): 188–189. PubMed Abstract \| Publisher Full Text\n\nZehnacker CH, Bemis-Dougherty A: Effect of Weighted Exercises on Bone Mineral Density in Post Menopausal Women: A Systematic Review. Journal of Geriatric Physical Therapy; La Cross. 2007; 30(2): 79–88. PubMed Abstract \| Publisher Full Text\n\nDizdar M, Irdesel JF, Dizdar OS, et al.: Effects of Balance-Coordination, Strengthening, and Aerobic Exercises to Prevent Falls in Postmenopausal Patients With Osteoporosis: A 6-Month Randomized Parallel Prospective Study. J Aging Phys Act. 2017 Dec 19; 26(1): 41–51. PubMed Abstract \| Publisher Full Text\n\nHowe TE, Shea B, Dawson LJ, et al.: Exercise for preventing and treating osteoporosis in postmenopausal women. Cochrane Database of Systematic Reviews. John Wiley & Sons, Ltd; 2011.\n\nBorer KT, Fogleman K, Gross M, et al.: Walking intensity for postmenopausal bone mineral preservation and accrual. Bone. 2007 Oct; 41(4): 713–721. PubMed Abstract \| Publisher Full Text\n\nMosti MP, Kaehler N, Stunes AK, et al.: Maximal strength training in postmenopausal women with osteoporosis or osteopenia. J Strength Cond Res. 2013 Oct; 27(10): 2879–2886. Publisher Full Text\n\nPereira A, Costa AM, Palmeira-de-Oliveira A, et al.: The effects of combined training on bone metabolic markers in postmenopausal women. Sci Sports. 2016 Jun; 31(3): 152–157. Publisher Full Text\n\nMoore M, Barker K: The validity and reliability of the four square step test in different adult populations: a systematic review. Syst Rev. 2017 Sep 11 [cited 2020 May 15]; 6: 6. Publisher Full Text Reference Source\n\nDaly RM, Giangregorio L: Exercise for Osteoporotic Fracture Prevention and Management. Primer on the Metabolic Bone Diseases and Disorders of Mineral Metabolism. John Wiley & Sons, Ltd; 2018 [cited 2019 Dec 16]. p. 517–525. Publisher Full Text\n\nGallagher JC, Goldgar D, Moy A: Total bone calcium in normal women: Effect of age and menopause status - Gallagher - 1987. Journal of Bone and Mineral Research - Wiley Online Library. [cited 2020 Jun 2]; 2: 491–496. PubMed Abstract \| Publisher Full Text\n\nDaly RM, Gianoudis J, Kersh ME, et al.: Effects of a 12-Month Supervised, Community-Based, Multimodal Exercise Program Followed by a 6-Month Research-to-Practice Transition on Bone Mineral Density, Trabecular Microarchitecture, and Physical Function in Older Adults: A Randomized Controlled Trial. J Bone Miner Res. 2019 [cited 2019 Dec 16]; 35: 419–429. Publisher Full Text\n\nRizzo MR, Mari D, Barbieri M, et al.: Resting metabolic rate and respiratory quotient in human longevity.2005; 90(1): 409–413.\n\nNielsen T-T, Møller TK, Andersen LL, et al.: Feasibility and Health Effects of a 15-Week Combined Exercise Programme for Sedentary Elderly: A Randomised Controlled Trial. BioMed Res Int. 2019 Jan 23; 2019: 1–12. Publisher Full Text\n\nYen C-J, Hung C-H, Kao C-L, et al.: Multimodal exercise ameliorates exercise responses and body composition in head and neck cancer patients receiving chemotherapy. Support Care Cancer. 2019 Dec 1; 27(12): 4687–4695. PubMed Abstract \| Publisher Full Text\n\nClark J: The impact of duration on effectiveness of exercise, the implication for periodization of training and goal setting for individuals who are overfat, a meta-analysis. Biol Sport. 2016 Dec; 33(4): 309–333. PubMed Abstract \| Publisher Full Text\n\nPrawiradilaga RS, Magnus B, Esrup S, et al.: Working title: A Feasibility Study of Training in a Local Community Aimed Upon Health Promotion with Special Emphasis on Musculoskeletal Health Effects. Extended data - Statistical power of the paired t-tests for body composition, regional BMD, and bone turnover markers. figshare.2021 [cited 2021 Sep 13]. Publisher Full Text\n\nPrawiradilaga RS, Bendtsen M, Esrup S, et al.: Working title: A Feasibility Study of Training in a Local Community Aimed Upon Health Promotion with Special Emphasis on Musculoskeletal Health Effects. Extended data - Effect size of the Training Program. figshare.2021 [cited 2021 Sep 13]. Publisher Full Text\n\nPrawiradilaga RS, Bendtsen M, Esrup S, et al.: CONSORT checklist, extension for Pilot and Feasibility Trials for study “A Feasibility Study of Training in a Local Community Aimed Upon Health Promotion with Special Emphasis on Musculoskeletal Health Effects”. figshare.2021 [cited 2021 Sep 13]. Publisher Full Text\n\nPrawiradilaga RS, Bendtsen M, Esrup S, et al.: Underlying data for ‘A Feasibility Study of Training in a Local Community Aimed Upon Health Promotion with Special Emphasis on Musculoskeletal Health Effects.’. figshare2021 [cited 2021 Sep 13]. Publisher Full Text" }	[ { "id": "134828", "date": "16 May 2022", "name": "Melanie Kistler-Fischbacher", "expertise": [ "Reviewer Expertise Exercise science", "bone", "bone-specific exercise", "osteoporosis", "weight lifting for bone and muscle health", "postmenopausal women" ], "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 non-randomised controlled study reports the effect of a 19-week multicomponent exercise intervention (resistance, balance and impact training) on bone markers, bone mineral density and body composition outcomes among 28 postmenopausal women. I have concerns about the study design and methodological rigor of the trial. Specifically, the duration of the trial 19 weeks is insufficient to detect changes in bone, bias associated with the differences between groups at baseline and the lack of adjustment for multiple comparisons.\nIntroduction\nParagraph (P) 1: “is it estimated that 200 million females…”. This number actually includes males and females. P2: “One way to prevent… age-related bone loss”. This is a very old reference. Since 1987 a large number of exercise trials for bone have been conducted. I suggest including a more recent reference. P3 & 4: In para 3 you hypothesize that “evidence-based multimodal training will have an osteogenic effect and in para 4 you state that there is a need for “evidence-based trainings”. This is contradicting and I don’t think you can call this MMT “evidence based” P4: “Only few studies have examined…”. There has been a large number of studies that have tested combined impact, resistance and balance training interventions in recent years which showed safety and efficacy. 1,2,3,4 These should be cited here plus the existing gap in the literature identified. P5: “The aim was to investigate the feasibility…” Feasibility is mentioned in the title, the aims and discussion (e.g. discussion 1st sentence and conclusion 1st sentence), however, it is unclear how feasibility was measured. Feasibility is also not listed as an endpoint (e.g. clinicaltrials.gov). Please clarify.\nMethods\nGeneral: please clarify which outcomes were primary and which ones were secondary. P1: Please explain how participants were recruited, particularly the sedentary control group. P1: The duration of 19 weeks is inappropriate to measure changes in bone mineral density. A minimum of 6-8 months is needed to detect changes in bone. P3: “to ensure transparency” The trial was registered close to manuscript submission data, which does not ensure transparency. I suggest deleting this part of the sentence. P4: How was sedentary defined?\nWas there a minimum age set?\n\nHow was postmenopausal defined? (e.g. how many years post menopause?)\n\nHow was regular, systematic training defined?\nP5: The information on the number of participants and drop outs should be moved to the results section. P5: “…12 from a previous study...”. Please describe the control group somewhere. P8: How many sets and repetitions were performed of each exercise, and how did you ensure the resistance training was progressive? P9: Can you include information on the short-term measurement variability of BMD and body composition measures in your lab? P12/13: Why were FSST and jump-and-reach tests not performed in the control group? P14: Given the large number of outcomes, adjustment for multiple comparison is strongly recommended.\nResults\nP1: There are significant baseline differences between groups which is of great concern. How did you address this, were analyses adjusted for baseline values? P4: “… LS and total femur… tended to increase”. Reporting of trends is controversial; I suggest removing this sentence. Table 2: Please explain why you are reporting mean femur BMD in addition to right and left femur values. Table 2/3: Your findings show a decrease in whole body BMC and an increase in BMD. How would you explain these differences.\nDiscussion\nRather than comparing present findings to individual studies, I would recommend reviewing the large body of systematic reviews and meta-analyses on the topic. Many of those have examined the influence of training parameters (e.g. intensity, volume and frequency. 3,5) Interpretation of your findings in context of those findings would be helpful. For example, recent studies have shown that exercise intensity is positively associated with bone changes, and that low-intensity exercise is ineffective.\nThere are a number of limitations of the present study that have not been addressed in the discussion. E.g. bias related to baseline differences, not randomised, only short term (< 6 months), generalisability.\nYou state that no power calculation was undertaken. 1) How was the sample size determined? 2) How was a posteriori power calculated and what were the results?\nI would like to see a section about clinical significance of the findings.\nConclusion\n“… inducing health-enhancing effects”. In light of the significant baseline differences, other study limitations and the fact that only body composition variables (which were significantly different between groups at BL) improved, I think this is overstating the findings 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? 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? Partly", "responses": [ { "c_id": "9398", "date": "10 Mar 2023", "name": "Rizky Suganda Prawiradilaga", "role": "Author Response", "response": "Introduction P1: We are sorry if we were mistaken. We got it from the Facts and Statistics International Osteoporosis Foundation (IOF) [cited 2017 Oct 4]. Some other references that said the same that 200 million women: COLOSTEO (the project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 778277)1, and de Villiers and Goldstein (2022)2. P2: Thank you. We have changed the reference to: Zhang S, Huang X, Zhao X, Li B, Cai Y, Liang X, et al. Effect of exercise on bone mineral density among patients with osteoporosis and osteopenia: A systematic review and network meta-analysis. J Clin Nurs. 2022 Aug; 31(15–16):2100–11. P3 & 4: We agree with you, we have changed a little bit “it is hypothesized in the present study that evidence-based multimodal training as health promotion will have an osteogenic effect” into “it is hypothesized in the present study that training (which combined evidence-based exercise) as health promotion will have an osteogenic effect”. We have revised it. P4: We have added the references: Watson SL, Weeks BK, Weis LJ, et al.:High-Intensity Resistance and Impact Training Improves Bone Mineral Density and Physical Function in Postmenopausal Women With Osteopenia and Osteoporosis: The LIFTMOR Randomized Controlled Trial. J Bone Miner Res. 2018 Feb; 33(2):211–220.PubMed Abstract \| Publisher Full Text Kistler-Fischbacher M, Yong JS, Weeks BK, et al.:A Comparison of Bone-Targeted Exercise With and Without Antiresorptive Bone Medication to Reduce Indices of Fracture Risk in Postmenopausal Women With Low Bone Mass: The MEDEX-OP Randomized Controlled Trial. J Bone Miner Res. 2021; 36(9):1680–1693. Publisher Full Text Kistler-Fischbacher M, Weeks BK, Beck BR:The effect of exercise intensity on bone in postmenopausal women (part 2): A meta-analysis. Bone. 2021 Feb 1; 143: 115697. Publisher Full Text Karinkanta S, Heinonen A, Sievänen H, et al.: A multi-component exercise regimen to prevent functional decline and bone fragility in home-dwelling elderly women: randomized, controlled trial. Osteoporos Int. 2007 Apr; 18(4): 453–462. PubMed Abstract \| Publisher Full Text Shojaa M, von Stengel S , Kohl M, et al.:Effects of dynamic resistance exercise on bone mineral density in postmenopausal women: a systematic review and meta-analysis with special emphasis on exercise parameters. Osteoporos Int. 2020 Aug; 31(8):1427–1444. PubMed Abstract \| Publisher Full Text \| Free Full Text P5: Thank you for the suggestion, We have added attendance rate as a feasibility endpoint in the Methods section. The feasibility outcome is already in the Results section. Methods General: We have clarified which outcomes were primary and which ones were secondary. P1: It was explained in Participants section in then Methods section. The sedentary control group was from a previous study (which hasn’t been published) not a long time before the present study. The recruitment process itself was the same, via advertisement online and a local newspaper. P1: Yes, we understand. The bone turnover occurs around 5 to 6 months, and we can detect the changes around that time of intervention. However, our study regarding the bone turnover marker (Prawiradilaga et al. (2020)3) showed that acute exercise has an acute response on bone marker (P1NP). Regarding that, we hope that we can see the change in bone turnover markers as well as the bone mineral density in only 19 months. Why only 19 months? It was the feasible range of time we can manage before everyone went to summer vacation. P3: Alright, thank you. We have deleted that part. P4: Sedentary is defined as someone who didn’t engage in regular and systemic weight-bearing training or strength training in the last 2 years. We have added a note to distinguish active from sedentary. No minimum age, only maximum 70. 2 years post menopause Minimum at least 1 time a week, has a goal of the training. P5: We have considered your suggestion and have moved the number of participants and drop outs to the Results section. P5: Thank you. P8: The progressive resistance training (PRT) consisted primarily of exercises using own bodyweight, with occasional use of medicine balls, resistance bands and sandbags (5–15 kg), starting with 15–20RM and slowly progressing to 6–12RM, with 2–3 sets. We have added this in the manuscript. P9: We don’t think we have the information on short-term of BMD and body composition. We only measure the bone turnover markers for the short-term. P12/13: They did not want to do the test. P14: Thank you for the suggestion. Results P1: Our analyses were based on the delta values. P4: Thank you for your suggestion. We have removed “However, LS (1.2%) and right total femur (0.3%) tended to increase (both, p < 0.1) for MMT”. Table 2: We think it is good information to give the reader the mean femur BMD. Table 2/3: There is significant difference between MMT and Control (CON) group. While the whole-body BMC showed decrease in CON group, the whole BMC in MMT group doesn’t change. It showed that the training might inhibit the whole-body BMC to decrease in postmenopausal women. The whole-body BMD was not increased, however, the right trochanter BMD in MMT was increased compared to CON. Discussion Thank you for the suggestion, We have added regarding the recent studies which have shown that exercise intensity is positively associated with bone changes, and that low-intensity exercise is ineffective. Thank you for your suggestions, we have addressed other limitations. The sample size was determined by the Author judgement based on the previous study on Bone Turnover Markers (Prawiradilaga et al. (2020)3. The posteriori power calculations were performed with Power and Sample Size Calculations version 3.0 for the paired t-test and performed with SPSS for the repeated ANOVA measurement. The results are in the link in the ‘Extended data’ section. Is the work clearly and accurately presented and does it cite the current literature? We have cited the current literature Is the study design appropriate and is the work technically sound? We have added, “This is a feasibility study in a local community with a non-randomized controlled trial approach.” Are sufficient details of methods and analysis provided to allow replication by others? We think it is sufficient since the study method and the training program were described clearly. References Osteoporosis Facts [Internet]. COLOSTEO. [cited 2022 Aug 12]. Available online (date last accessed: 10/03/2023) de Villiers TJ, Goldstein SR: Bone health 2022: an update. Climacteric. 2022 Jan 2; 25(1):1–3. Publisher Full Article Prawiradilaga R, Madsen A, Jørgensen N, et al.: Acute response of biochemical bone turnover markers and the associated ground reaction forces to high-impact exercise in postmenopausal women. Biol Sport. 2020; 37(1): 41–48. PubMed Abstract" } ] }, { "id": "152766", "date": "08 Nov 2022", "name": "Robert Wen-Wei Hsu", "expertise": [ "Reviewer Expertise Orthopedics", "sports medicine" ], "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 sending this paper for reviewing. There were some comments on the following:\nThe sample size is too small to validate the effect of training.\n\nHow was the sample size determined?\n\nStatistical power should be calculated.\n\nThe exercise program is not strong enough to have physiological impact to the health.\n\nThe duration of exercises is not long enough.\n\nThe study is required to do prospective study. The assignment to exercise and control group should be randomized.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "9399", "date": "09 Mar 2023", "name": "Rizky Suganda Prawiradilaga", "role": "Author Response", "response": "We are aware of that. We tried to equate the number of samples with our previous studies but, in our feasibility study with community settings, it turned out that 6 people from the MMT group dropped out. The sample size was determined by the Author judgement based on the previous study on Bone Turnover Markers (Prawiradilag et al. (2020)). The Statistical power calculations were performed with Power and Sample Size Calculations version 3.0 for the paired t-test and performed with SPSS for the repeated ANOVA measurement. The results are in the link in the ‘Extended data’ section. We apologize; we do not actually understand, what do you mean by not strong enough? The Health initiative program uses multimodal training including 1) High- and odd-impact exercise including multi-directional games; 2) Progressive resistance training (PRT); 3) Balance and coordination training which has an osteogenic impact based on evidence, but we are aware that frequency, duration did not meet the recommendation. In addition, we didn’t measure the heart rate for intensity. We understand that the Health Promotion initiative program was not long enough (19 weeks) and did not meet the recommendation (6-12 months) for osteogenic exercise. We would like to see whether there were bone turnover markers (BTM) changes in this short period since, in our previous study, there were acute responses in BTM. Thank you for your suggestions. Is the work clearly and accurately presented and does it cite the current literature? We have cited the current literature Is the study design appropriate and is the work technically sound? We have added, “This is a feasibility study in a local community with a non-randomized controlled trial approach.” Are sufficient details of methods and analysis provided to allow replication by others? We think it is sufficient since the study method and the training program were described clearly. Are all the source data underlying the results available to ensure full reproducibility? We share the raw data in the ‘Extended data’ section." } ] } ]	1	https://f1000research.com/articles/11-51
https://f1000research.com/articles/12-481/v1	11 May 23	{ "type": "Research Article", "title": "Teaching critical thinking about health information and choices in secondary schools: human-centred design of digital resources", "authors": [ "Sarah Rosenbaum", "Jenny Moberg", "Faith Chesire", "Michael Mugisha", "Ronald Ssenyonga", "Marlyn A Ochieng", "Clarisse Marie Claudine Simbi", "Esther Nakyejwe", "Benson Ngatia", "Gabriel Rada", "Juan Vásquez-Laval", "José Damián Garrido", "Grace Baguma", "Sam Kuloba", "Edward Sebukyu", "Richard Kabanda", "Irene Mwenyango", "Tonny Muzaale", "Pamela Nandi", "Jane Njue", "Cyril Oyuga", "Florian Rutiyomba", "Felecien Rugengamanzi", "Joan Murungi", "Allen Nsangi", "Daniel Semakula", "Margaret Kaseje", "Nelson Sewankambo", "Laetitia Nyirazinyoye", "Simon Lewin", "Andrew D Oxman", "Matt Oxman", "Jenny Moberg", "Faith Chesire", "Michael Mugisha", "Ronald Ssenyonga", "Marlyn A Ochieng", "Clarisse Marie Claudine Simbi", "Esther Nakyejwe", "Benson Ngatia", "Gabriel Rada", "Juan Vásquez-Laval", "José Damián Garrido", "Grace Baguma", "Sam Kuloba", "Edward Sebukyu", "Richard Kabanda", "Irene Mwenyango", "Tonny Muzaale", "Pamela Nandi", "Jane Njue", "Cyril Oyuga", "Florian Rutiyomba", "Felecien Rugengamanzi", "Joan Murungi", "Allen Nsangi", "Daniel Semakula", "Margaret Kaseje", "Nelson Sewankambo", "Laetitia Nyirazinyoye", "Simon Lewin", "Andrew D Oxman", "Matt Oxman" ], "abstract": "Background Learning to thinking critically about health information and choices can protect people from unnecessary suffering, harm, and resource waste. Earlier work revealed that children can learn these skills, but printing costs and curricula compatibility remain important barriers to school implementation. We aimed to develop a set of digital learning resources for students to think critically about health that were suitable for use in Kenyan, Rwandan, and Ugandan secondary schools.\nMethods We conducted work in two phases collaborating with teachers, students, schools, and national curriculum development offices using a human-centered design approach. First, we conducted context analyses and an overview of teaching strategies, prioritised content and collected examples. Next, we developed lessons and guidance iteratively, informed by data from user-testing, individual and group interviews, and school pilots.\nResults Final resources include online lesson plans, teachers’ guide, and extra resources, with lesson plans in two modes, for use in a classroom equipped with a blackboard/ﬂip-chart and a projector. The resources are accessible offline for use when electricity or Internet is lacking. Teachers preferred the projector mode, as it provided structure and a focal point for class attention. Feedback was largely positive, with teachers and students appreciating the learning and experiencing it as relevant. Four main challenges included time to teach lessons; incorrect comprehension; identifying suitable examples; and technical, logistical, and behavioural challenges with a student-computer mode that we piloted. We resolved challenges by simplifying and combining lessons; increasing opportunities for review and assessment; developing teacher training materials, creating a searchable set of examples; and deactivating the student-computer mode.\nConclusion Using a human-centred design approach, we created digital resources for teaching secondary school students to think critically about health actions and for training teachers. Be smart about your health resources are open access and can be translated or adapted to other settings.", "keywords": [ "critical thinking", "critical health literacy", "informed decision making", "infodemic", "health education", "secondary school", "educational design", "human centred design" ], "content": "Introduction\n\nClaims about how to care for our health are everywhere, spread by friends, family, news media, industry, healthcare professionals, policymakers, researchers, and others. Many of these claims unreliable,1 but people often lack the skills needed to assess them.2,3 When we believe unreliable claims, we might take ineffective or harmful actions, or fail to take helpful actions. The Covid-19 pandemic showed how easily unreliable claims4–6 and research7–9 spread, impacting public trust and protective behaviours.10,11\n\nPublicly debunking untrustworthy information has value, but the effectiveness of this retroactive strategy might be limited. Misinformation, once spread, can be resistant to correction; an alternative narrative may not exist (for instance, there may not be a safe or proven alternative treatment); and individuals may reject the scientific process or the source altogether rather than change their established views about some topics.12 Pre-emptively ‘inoculating’ people against misinformation13,14 by teaching them to think critically about claims of what works, and how to make informed decisions, has the potential to provide broader, more long-lasting protection.\n\nIn earlier work developing and evaluating Informed Health Choices (IHC) resources for primary school students, we have shown that it is feasible to teach critical thinking skills about health actions to children as young as 10-years old.15–20 In that project, we created a framework of principles that are important for people to understand when assessing the reliability of healthcare claims and making informed choices: the IHC Key Concepts.21,22 This framework is a starting point for designing curricula, learning resources, and evaluation tools. Focusing on a selection of the IHC Key Concepts, we then developed printed learning resources for primary school children (age 10-12 years) and their teachers15 and a podcast for parents.16\n\nTo evaluate the effect of these resources, we conducted two randomised trials in Uganda, one including 120 schools and more than 10,000 children, and another that included 675 parents and guardians of primary school children.23 The primary outcome measure was responses to multiple-choice questions that measure respondents’ ability to apply IHC Key Concepts: the Claim Evaluation Tools.17,18 The primary school trial demonstrated that use of the resources led to a large improvement in the ability of children and teachers to apply IHC Key Concepts to hypothetical scenarios.17 The podcast trial showed a smaller, similar effect among parents.18 Follow-up data showed that children retained their learning for at least one year,19 while the performance of the parents declined.20 The primary school resources have been translated into 12 languages and adapted for use in other countries.24\n\nAlongside the trials, we undertook process evaluations to explore barriers and facilitators for scaling up use of the learning resources, potential adverse effects, and potential additional benefits.25,26 We found that children, teachers, parents, and district education officers valued the IHC primary school resources. The human-centred design approach we employed - iteratively addressing user and stakeholder concerns prior to and during development - was likely an important contributing factor for this positive reception. However, the study pointed to two important implementation barriers in Uganda: printing costs and lack of time in the school schedule.\n\nInformed by these findings, we began the current five-year project in 2019 to develop and evaluate resources for lower secondary schools (age 13-16) in Kenya, Rwanda, and Uganda. Since drafting this article, we have evaluated the resources in three parallel randomised trials,27–29 are carrying out process evaluations,30–32 and will conduct one-year follow-up trials in each of the three countries.\n\nThis article describes the development of these resources that took place prior to evaluation during the first 2.5 years of the project in two phases. We began development with this set of objectives (see protocol33):\n\nTo explore how we might develop resources that are\n\n• Digital (avoiding printing costs)\n\n• Suitable for use with schools’ available digital technology and infrastructure\n\n• Compatible with national curricula\n\n• Based on evidence about effective strategies for teaching critical thinking\n\n• Experienced as accessible, useful, usable, understandable, credible, and desirable by students and teachers, and well-suited to use in their schools\n\n• Easily translatable and adaptable to other contexts\n\n• Sustainable (i.e., not dependent on our team for rolling out at scale)\n\nWe organised the work in two phases: 1) a set of preliminary studies (involving data documented and discussed elsewhere) and 2) an iterative development phase with data collection and analysis reported in this article. Although the preliminary studies have already been published elsewhere, findings from those studies resulted in reframing of some of our objectives and provided the basis for content and design decisions made in the second phase. Therefore, we describe methods and results from both phases (with references for more detail about phase one). In the discussion, we describe how this study may inform development of similar educational resources for teaching critical thinking.\n\n\nMethods\n\nWe employed perspectives and methods from human-centred design. This is an iterative approach to creating products, systems and services that places users’ and other stakeholders’ needs and experiences at the centre of the design process.34,35 Early and continued engagement with stakeholder groups and multidisciplinary collaboration are central components of a human-centred design approach.36,37 We employed qualitative data collection and analysis methods to explore the user experiences of multiple types of stakeholders for the purpose of informing the development process.\n\nWe established a core team with backgrounds in health systems and public health research, design, journalism, education, social science, statistics, and information and communication technology (ICT). Research leadership was shared among senior team members in East Africa and Norway. Three PhD fellows (one female and two male) based in Kisumu (Kenya), Kigali (Rwanda) and Kampala (Uganda), engaged with stakeholders and collected and analysed data, supported by their local teams including researchers with experience developing and evaluating the IHC primary school resources. All teams contributed to design and content development, led by the team based in Norway who also analysed data. The ICT team, based in Chile, developed the technical solutions.\n\nWe conducted this work in two phases: 1) Groundwork and 2) Development cycles (Figure 1). The first phase began in August 2019, the second phase began January 2020 and ended in April 2022.\n\nWe defined stakeholders as people or organisations that have a vested interest in the process or results of the study. Intended users – secondary school teachers and students – were the key stakeholders. Additional stakeholders included curriculum developers and other education policymakers, school administrators, parents, educational researchers, researchers in public or clinical health, and health professionals.\n\nFor the purpose of providing continuous input, we established groups of stakeholders in each country early in the project. We formed teacher networks, recruiting via formal invitation letters to teachers who worked in a mix of government funded and private schools, with varied ICT resources (Uganda), and in rural, semi-rural, and urban environments (Kenya and Rwanda). We formed student networks by asking members of the teacher networks to suggest lower secondary school students who were interested, likely to contribute, and able to participate without adversely affecting their schoolwork, sending them formal invitations and assent forms, and consent forms to parents. Due to Covid-related school closures in parts of Development Cycle 1, we also established “home networks” of students that we had access to when schools were closed. Home networks included both students that were already recruited to the student network and additional students whom team members could easily reach from nearby communities. We employed convenience sampling and used the same assent forms and consent forms to parents as for the student networks.\n\nWe engaged with the national curriculum development offices to establish channels of contact and collaboration. We formed national advisory panels of policy makers at the ministerial and regional and district levels, school directors, head teachers, leaders of teacher unions, and representatives of parents’ groups and civil society. We created an international advisory panel of people from 18 countries who had expertise in education, education policy, and relevant areas of research, such as health literacy, evidence-informed decision making, science communication and ICT. Additionally, during the final cycle of development, we recruited seven schools across the three countries to pilot use of the resources in one or more classes over a school semester.\n\nApart from people in the international advisory panel, many of whom were a part of our existing professional networks, and some of the students in home networks, we did not have established relationships with the stakeholders prior to the onset of this project.\n\nDetails of how we selected and recruited each stakeholder group and characteristics of participants and schools are described in Tables 1-3. More information about the methods, degrees, and nature of engagement with different stakeholders, can be found in a protocol for evaluating stakeholder engagement.38\n\n\n\n‐ interested\n\n‐ likely to contribute\n\n‐ able to participate without adversely affecting their schoolwork\n\nThe groundwork phase consisted of a series of preliminary studies. More detail about the methods and results can be found in separate publications (see overview in Table 4).\n\nAnalysing contexts\n\nTo inform the development of the resources, as well as their potential implementation in Kenya, Rwanda and Uganda lower secondary schools, we explored if there was demand for learning resources to teach critical thinking; if such resources were in use; how the content maps onto existing curricula; what administrative approval was necessary; what ICT infrastructure is available in schools and how it is used in schools. We analysed the three country contexts. Detailed methods are reported in a separate publication.39–41\n\nTo synthesize findings from these studies in a way that was useful for developing educational resources, we drew on the the behaviour change wheel.42 This is a framework for characterising and designing interventions for behaviour change, built around three essential conditions for change: Capability, Opportunity, and Motivation (the COM-B system). We organised findings from the three context analyses according to these three themes. The synthesized findings from these three context analyses supplemented our original set of development aims and provided a much more detailed understanding of contextual challenges before we started the development phase.\n\nPrioritising IHC Key Concepts\n\nDue to the scope of our research funding, as well as the pandemic and school closures, we could not pilot and evaluate resources that took longer to use than one school semester. To prioritise which of the 49 IHC Key Concepts to include in the learning goals for the resources, we organised a structured, iterative consensus process with curriculum specialists, teachers, and researchers. Detailed methods are reported in a separate publication.43\n\nIdentifying teaching strategies\n\nTo identify effective, relevant teaching strategies to inform the resources, we conducted an overview of systematic reviews of strategies for teaching critical thinking. Detailed methods are reported in a separate protocol.44\n\nCollecting examples\n\nTo identify relevant and engaging examples for the resources, we interviewed Kenyan, Rwandan, and Ugandan secondary school students (aged 14 to 16) from the student networks, via WhatsApp. We collected examples of health actions, their claimed and actual effects, and information sources. The students rated their interest in a broad range of health actions and conditions, and we used those with higher scores as examples in the resources. Detailed methods are reported in an online report.45\n\nStarting with what we learned and developed in the preliminary studies, we developed resources in three iterative cycles of content creation and feedback. Each development cycle (Figure 2) included:\n\n- Generating ideas\n\n- Prototyping\n\n- Pilot testing prototypes and collecting data\n\n- Analysing problems\n\n- Checking our analysis of the most important problems and solution ideas with key stakeholders, drawing on the concept of “member checking”46\n\nWe also sought ad hoc feedback from the student and teacher networks as needed.\n\nGenerating ideas\n\nWe generated content and design ideas in two ways: brainstorming33 internally, within the team; and identifying ideas suggested in external feedback, from participating stakeholders.47 We selected ideas based on considerations such as consistency with what teachers and students said they valued, and ease of implementation.\n\nPrototyping\n\nA prototype is a sketch or model. We developed increasingly refined prototypes in each cycle. We used the platforms Google Drive (including Google Docs and Google Slides) and Adobe XD for drafting, editing, and sketching. We drafted and edited text using Google Docs, exported early prototypes to PDF format, and used Google Slides and Adobe XD later to create interactive sketches. Final versions were published as web pages, using Google Drive as a content editing platform.\n\nTesting prototypes and collecting data\n\nThe three PhD fellows conducted interviews in their respective settings, supported by their research assistants. They had university degrees (Bachelor of Statistics, Master of Epidemiology & Biostatistics, Master of Public Health, and Master of Community Health and Development) and have attended PhD-level courses in qualitative study methods.\n\nIndividual interviews employing user testing methods\n\nUsing semi-structured guides48 that were pilot tested, the three PhD fellows conducted user test with individual teachers and students, to explore how they experienced prototypes and how we might make improvements. Data were collected face to face or online when covid measures restricted face to face meetings. When possible, user testing immediately followed a pilot lesson, so the participant had their experiences from the lesson fresh in mind. Interview duration was approximately one hour. Occasionally, teams printed the digital prototypes on paper to collect feedback where there was no access to a device or internet connection.\n\nEach user testing session had three main parts. First, interviewers introduced themselves and the reasons for the interview. Next, they employed a think-aloud approach: a method of qualitative data collection that encourages the participant to articulate their thoughts while performing a task,49–51 in this case reviewing prototypes of the resources. The last part was conducted as a semi-structured interview.\n\nWe captured data as observers’ notes and audio recordings. We designed the interview guides to explore different facets of the user experience, including usefulness, understandability, usability, credibility, desirability, and identification, based on a revised version of Morville’s framework of user experience (Table 5).34\n\nGroup interviews\n\nThe PhD fellows conducted semi-structured interviews with groups of students or teachers to explore their experiences of the prototypes, using pilot-tested interview guides.48 When possible, interviews were scheduled immediately after a pilot lesson when the participants had their experiences fresh in mind. Sessions lasted approximately one hour.\n\nWe chose group interviews, rather than user testing or individual interviews, when we anticipated that the former would improve the quality of the data, for instance by increasing students’ confidence in speaking with researchers. Group interviews took place at schools or other locations determined to be practical for the participants. After introducing themselves and explaining reasons for the interview, one researcher moderated and one or more researchers observed and took notes. Sometimes, teachers were present during student interviews. With written informed consent (from parents and teachers) and assent (from students), we audio-recorded sessions.\n\nPiloting and observation\n\nWe facilitated pilots of the prototypes to explore how teachers and students used and experienced them in as natural settings as possible. Early pilots involved single lessons, with one of the PhD fellows sometimes assuming the role of the teacher. These took place both at schools and in other settings, such as students’ neighbourhoods, when schools were closed due to the pandemic. The final set of pilots included a full set of lessons taught by teachers at schools, over a school term. (In Uganda, although schools were still closed, we got permission for students from the student network and teachers to meet at the schools for the purpose of conducting pilot lessons.) PhD fellows or research assistants observed and took notes using a structured guide,48 without intervening. We followed up pilots with either individual or group interviews.\n\n“Critical Thinking about Health” Test\n\nAfter piloting a full set of lessons, students took the “Critical Thinking about Health” Test.52 Administering the test had two purposes: validating the items included in the test and giving us a sense of whether the prototypes had the intended effects. We report the validation in detail in a separate article.52\n\nConsulting the advisory groups\n\nTwice annually, we emailed the international advisory group, to update them on the project, and ask for feedback on specific parts or prototypes. We entered their feedback in a spreadsheet,47 familiarised ourselves with those data, and discussed and agreed on how to deal with any specific suggestions. We held face-to-face meetings with the national advisory groups to keep them updated and seek feedback related to ensuring the sustainability and future scaling up of resources, if shown to be effective.\n\nData analysis\n\nWe transcribed and translated several of the audio recordings from individual and group interviews. The three PhD fellows and their three research assistants reviewed transcriptions, their own interview and observation notes, and recordings, and extracted data about negative and positive experiences. They entered the data into Excel spreadsheets,47 supplemented with quotations where relevant, and tagged the data using pre-determined codes related to the nature of an experience (e.g., “negative”); the “location” of the experience, i.e., the relevant part of the resources (e.g., “illustration/graphics”), and suggested implication (e.g., “consider changes”). We did not anticipate differences in results between male and female students, so coding did not include gender identification. The prototyping team reviewed the coded data, flagged data entries that they did not understand, suggested changes to codes, and discussed the suggestions with the PhD fellows and their research assistants.\n\nAfter agreeing with the original coders on the final codes, the three-person prototyping team sorted data entries according to the nature, implication and location, and re-reviewed them, focusing on data tagged with the implication “showstopper” or “consider changes”. New topic codes emerged during this process and were added as thematic labels of issues that needed addressing (e.g., “Time”, “Conceptual misunderstanding”, “student-computer mode”). This coding scheme evolved throughout. For an example from the dataset,47 see the “Topics” column in the Development Cycle 2 – codes and response options. When data analysis raised important unanswered questions or resulted disagreement about interpretation, the team either contacted teacher or student networks for additional input, or adjusted interview guides to include these issues in the next development cycle.\n\nThe prototyping team drafted a description and assessment of the most important problems with the prototypes, with an initial set of ideas for solutions. The whole project team discussed these drafts, reached a consensus about which were the most important problems and brainstormed additional ideas for solutions. Based on this input, the prototyping team made the final decision about which solutions to implement.\n\nChecking with stakeholders\n\nDrawing on the method “member checking”,46 we carried out “stakeholder checking”, checking our analysis and ideas with the teacher networks and curriculum developers. At the end of each development cycle, we presented descriptions of what we considered the most important problems and our proposed solutions. We asked about the accuracy of the analysis, their reactions to the proposed solutions, and any suggestions of their own. We modified solutions based on this input.\n\nAd hoc feedback\n\nAt different points within each development cycle, we also contacted people in the teacher and student networks for quick feedback on specific issues, for instance what to call the resources.\n\nFigure 3 and Table 6 provide an overview of what we did in the three development cycles.\n\nWe obtained ethics approval for the entire project from local institutional review boards and national research governing councils in Kenya, Rwanda, and Uganda: the Rwanda National Ethics Committee (approval number 916/RNEC/2019); Masinde Muliro University of Science and Technology Institutional Ethics Review Committee and the Kenyan National Commission for Science, Technology and Innovation (approval number NACOSTI/P119/1986); and Makerere University School of Medicine Research Ethics Committee (REC REF 2020-139) and Uganda National Council of Science and Technology (HS916ES).\n\n\nResults\n\nWe present two different types of results that emerged from this work: the designed output (final version of the resources), and the knowledge output that informed our development (findings from Phase 1 and 2). We report the designed output first, to give the reader an overview of the resource features and components we refer to in the findings.\n\nThe final set of resources, Be smart about your health, is an open access website for teachers comprised of ten lesson plans, a teachers’ guide, and extra resources including materials for teacher training.53 Lesson plans are designed in two modes: for use in classrooms with a blackboard/flipchart (optimized for smartphone) and for classrooms with a projector with lessons formatted as downloadable Google Slides presentations. See Table 7 and Figures 4–9.\n\nContents include Teachers’ guide, Blackboard lesson plans, Projector lesson plans, and Extra resources.\n\nEach lesson plan includes an Overview, Lesson, and Background section for teachers. Each Lesson has three parts: Introduction, Activity, and Wrap-up.\n\nLessons plans:\n\n- Content: Set of ten lesson plans, two of which are for review and applying what students learned to their daily lives (Table 7)\n\n- Structure: Each Lesson Plan has an Overview, Lesson, and Background section. Each Lesson is designed to be taught in 40 minutes, and has three parts: Introduction, Activity, and Wrap-up (Figure 5)\n\n- Format: To accommodate for varied ICT infrastructure in schools, we created two modes of resources for teachers to deliver lessons: Blackboard lesson plans and Projector lesson plans. Blackboard lesson plans are optimised for teachers on mobile devices and work also offline. These can also serve as a back-up in the event of electricity outages. Projector mode is for use in classrooms that have access to a projector. We also created sets of optional, downloadable printouts for teachers to use as a paper back-up (Figure 6)\n\nTeachers’ guide: This includes an introduction to why the learning goals are important, a description of the content and how it ties to the curriculum in Kenya, Rwanda and Uganda, how to navigate the resources, how they were developed, and where to find other relevant resources (Figure 7).\n\nExtra resources:\n\n- Teacher training materials, designed to be taught in workshops by teachers who participated in pilots (Figure 8)\n\n- Glossary\n\n- Examples collection (alternative examples of health actions for each lesson) (Figure 9)\n\n- Teaching strategies for teaching critical thinking\n\n- Underlying principles\n\nBelow we describe output from the preliminary studies in Phase 1. As explained earlier, data from these studies have already been reported and discussed in other publications. However, for the reader to understand the full development process, and how these results influenced our objectives, content, and design, they are summarised below.\n\nAnalysing contexts\n\nWe organised key findings from the context analyses in four themes: motivation to teach or learn the content; capability to teach the content; capability to use digital resources; and opportunity to teach the content within existing curricula using digital resources.39–42 Based on these findings, we identified opportunities and challenges, and made decisions about how to resolve those.\n\nStakeholders considered it to be important for students to learn to think critically about health, and the curricula included related learning goals. But teachers lacked capabilities and opportunities to teach both critical thinking in general, and about health choices more specifically. Additionally, schools’ digital infrastructures ranged from fully equipped with student computer labs to schools with few devices and no internet. Some of the strategies we decided to use included creating a teacher’s guide with in-depth background content and providing extra information about teaching strategies for critical thinking. We created lessons in different modes, with offline functionality to accommodate for variation in access to computers or digital infrastructure. See Table 8 for more detail about these findings and our solutions.\n\nPrioritising IHC Key Concepts\n\nTwelve curriculum specialists, teachers, and researchers, in Kenya, Rwanda, and Uganda prioritised nine of the IHC Key Concepts (Box 1) as suitable, relevant, and important for lower-secondary school students.54 These nine concepts formed the basis for the learning goals and subsequent content development.\n\n\n\n• Treatments can cause harms as well as benefits.\n\n• Widely used treatments or those that have been used for a long time are not necessarily beneficial or safe.\n\n• Treatments that are new or technologically impressive may not be better than available alternatives.\n\n• Personal experiences or anecdotes alone are an unreliable basis for most claims.\n\n• Identifying effects of treatments depends on making comparisons.\n\n• Comparison groups should be as similar as possible.\n\n• Small studies may be misleading.\n\n• Large, dramatic effects are rare.\n\n• Weigh the benefits and savings against the harms and costs of acting or not.\n\nIdentifying teaching strategies\n\nIn an overview of systematic reviews, we identified teaching strategies for helping primary and secondary school students learn to think critically.44 We experimented with using different strategies in each lesson, but found it added too much to teachers’ and students’ procedural cognitive load. Therefore, we chose a limited set to minimize variation and used most strategies across all lessons (Box 2). Additionally, we prepared summaries of all the teaching strategies we considered using.\n\nStrategies used across all lessons:\n\n‐ Guided notetaking\n\n‐ Small group work\n\n‐ Response cards\n\n‐ Homework – collecting claims and choices about health actions\n\n‐ Standard lesson structure\n\n‐ Setting objectives and providing feedback\n\n‐ Multimedia design\n\nStrategies used in individual lessons:\n\n‐ Concept mapping\n\n‐ Concept cartoons\n\n‐ Inquiry-based instruction\n\n‐ Quiz\n\n‐ Role play\n\nFor more detail, see also descriptions of teaching strategies we considered including (located under the Extra resources menu of the Besmarthealth.org website).\n\nCollecting examples\n\nTo illustrate concepts, and make lessons more engaging, we used a broad range of examples in the lessons involving conditions and health actions that students said they found interesting.45 We also created a searchable collection of relevant health actions and health problems or goals that can be used to illustrate key concepts, with plain language summaries of the evidence for each example (Figure 9). The examples collection is part of the “Extra resources”.\n\nUsing our findings from the Groundwork phase as a starting point, we conducted three development cycles of idea generation, prototyping, data collection and analysis, and stakeholder checking, which form the basis of this paper. The feedback was generally consistent regarding what people experienced as positive or problematic. Although there were far more positive findings, our main focus in collecting and reporting feedback was to identify problems that would require changes for the next iteration of the resources. We present the main findings thematically below.\n\nPositive, constructive findings\n\nMany teachers and students appreciated the learning in these lessons and experienced it as relevant both for other subjects and for their daily lives. Many students participated actively in class, including students who normally were less active. Many teachers felt the Projector mode of lessons worked best, providing structure and visual support to the lesson and helping to focus class attention. The blackboard mode and print-outs work satisfactorily for classes without projectors, or as a back-up in the event of power failure. Table 9 provides a detailed description of positive or constructive findings.\n\nNegative findings and how we addressed them\n\nWe resolved problems as they appeared and changed the design of the prototypes dramatically from the first to the final development cycle. However, four main thematic challenges persisted throughout development: issues regarding the student-computer mode of lesson plans, Time, Comprehension, and Examples.\n\n• Computers in classrooms took time to set up; equipment problems were common; students were often distracted by other online content; teachers found class discussions difficult to organise when students were using computers. Since teachers who had tried both the student-computer and Projector modes preferred the latter, we agreed with curriculum developers to drop the student-computer mode.\n\n• School schedules lacked time to teach lessons that were not in the curriculum, and teachers struggled to complete lessons within the allotted 40 minutes. We simplified and shortened lesson content as much as possible, and developed modules for teacher training workshops to increase teachers’ confidence and capability to teach the lessons.\n\n• Students had varying degrees of difficulty understanding lesson content, sometimes displaying a misunderstanding that was exactly the opposite of what they were intended to learn. We added “Common misunderstandings” to the lesson background, and designed lessons to include more review opportunities and informal assessment questions. We are exploring experiences and views of potential adverse effects in separate process evaluations30,31,55 and in a qualitative evidence synthesis.56\n\n• We struggled finding appropriate examples of reliable and unreliable claims, as students often thought the lesson was about the example rather than the underlying Key Concept. Our solutions included finding a balance between real and fictional, well-labeled examples, guidance and prompts for teachers (including suggestions to find their own examples), and developing an example collection for teachers to find alternatives.\n\nTables 10-13 provide a more detailed description of challenges and solutions.\n\n\n\n• Valuable teacher time used for setting up and charging the computers beforehand.\n\n• Broken computers.\n\n• Necessity for students to sometimes share a computer.\n\n• Students needing help finding browsers and reopening the resources after power outages.\n\n• Students cheating on quizzes or avoiding discussing things by opening the teacher resources or jumping ahead in the lessons to find the correct answers.\n\n• Students visiting other websites during the class.\n\n• Group discussions, one of the teaching strategies we had prioritized, not working well.\n\n\n\n• The content, including key terms, was often unfamiliar to students and teachers.\n\n• Some of the teaching strategies, such as getting students to take structured notes, and organising small group discussions, were time-consuming.\n\n\n\n• removed quizzes and shortened reviews in most lessons,\n\n• limited activities to one per lesson,\n\n• used buzz-groups (2-3 students who are sitting next to each other) or whole-class discussions instead of small-group work,\n\n• developed printable student handouts and classroom posters to reduce students’ need to take notes.\n\n\n\n• We iteratively simplified the lesson structure, language, and content.\n\n• We added “Common misunderstandings” to each lesson Background.\n\n• We added review questions and short key messages at the end of lessons, which are repeated at the start of the next lesson. We developed printouts with definitions of key terms.\n\nThe COVID-19 pandemic disrupted our work in many ways. At times, social-distancing and travel restrictions, as well as school closures, prohibited in-person meetings and data collection and piloting. When schools reopened, teachers were pressed to make up for lost time, sometimes rushing to finish a pilot lesson or not completing it. On the other hand, the abundance of unreliable claims about Covid-19 provided timely examples and motivation.\n\n“The lesson itself was very easy to understand because the students have already experienced what was used as example in the content (closing schools to reduce the spread of covid-19 infections).” (Rwanda, Observation pilot lesson)\n\nWorkarounds to challenges included communicating with stakeholders individually via audio or video call, or chat, and conducting some of interviews with home networks.\n\n\nDiscussion\n\nUsing a human-centred design approach, we developed adaptable, digital resources for teaching critical thinking about health in secondary schools in Kenya, Rwanda, and Uganda. In Phase 1 of the design, we gained insight into user and stakeholder needs, and the wider educational contexts. In Phase 2, we iteratively developed prototypes by generating ideas, prototyping, collecting and analysing data, and checking our ideas and analysis with stakeholders.\n\nIn many countries, curriculum developers are moving away from traditional knowledge-based curricula to competency-based curricula, with critical thinking among the core competencies,57 including in Kenya, Rwanda, and Uganda.39–41 However, our context analyses showed that teachers lacked training and resources to teach critical thinking.39–41\n\nIn their systematic review of strategies for teaching students to think critically, Abrami et al. found that three strategies were most effective, especially when combined: “the opportunity for dialogue, the exposure of students to authentic or situated problems and examples, and mentoring”.58 Based on those findings, and findings from our overview of systematic reviews,44 we focused on using authentic examples and discussion activities in our secondary school resources.\n\nA review of education technology in low-income countries distinguishes between two categories of digital interventions: computer aided learning (CAL) and computer aided instruction (CAI).59 Broadly speaking, CAL interventions are designed for the student-as-user, and either complement or supplement classroom instruction. CAI interventions, on the other hand, are designed for the teacher-as-user, and aim to enhance the quality of instruction. We developed and piloted resources for both CAL (the student-computer mode of lessons) and CAI (the blackboard and projector modes of lessons).\n\nWe found a variety of problems with the student-computer (CAL) resources. Many of the problems were logistical or technical, and not specific to our project, such as time needed to set up and charge computers, faulty or missing equipment, and unstable electricity. In addition, some curriculum developers (where student-computer resources were piloted) said that the resources lacked media-richness (such as animations or videos) as well as interactivity that we could not feasibly develop in this project and that teachers and students were possibly not experienced enough to use.\n\nRegardless of the level of ICT preparedness, it might be that self-led study strategies and CAL interventions are not the best starting point for developing critical thinking skills, since it is more challenging to creating opportunities for dialogue when students are alone behind a screen, working at different paces from each other. In our case, developing functionality for dialogue to take place on the computer was not an option, due to technical barriers in the settings, such as lack or unreliable internet access. Computer-based mentoring60–63 would require much more sophisticated programming than we had resources for. Moreover, less literate and less computer-literate students would be at a disadvantage. In their review, Abrami and colleagues’ found that discussion was especially effective when the teacher posed questions and there were whole-class, teacher-led discussions, or teacher-led group discussions.58\n\nRwandan teachers who piloted both the student-computer and projector resources preferred the latter, with the blackboard and printed resources as a backup for when electricity failed. Besides being technically less demanding, the slides seemed to better activate students, support small and large-group discussion, and focus collective attention. Moreover, teachers can download and tailor slides. The lower-tech CAI modes require much less investment in equipment than high-tech CAL modes and could dramatically lower the threshold for bringing digital learning resources that support critical thinking into low-resource classrooms.\n\nStrengths of this study include comprehensive groundwork; several development cycles; including pilots of all lessons in three countries; input from a wide variety of stakeholders and participants; systematic methods used to prioritise content and identify effective teaching strategies; data collection using complementary, mixed methods; independent initial coding and analysis by more than one researcher; and stakeholder checking to triangulate analyses.\n\nA limitation is that the project team developed the prototypes and collected and coded data. This might have biased participants to give positive feedback, or introduced bias in the analysis, leading to an exaggeration of positive feedback or lack of attention to negative feedback. We took measures to mitigate this: the interview guide included questions that explicitly encouraged participants to provide negative feedback; data was collected in three countries and coding in each country was reviewed by two researchers in order to reduce potential for bias; we introduced “stakeholder checking” to triangulate our data analyses and check that the solutions we developed were appropriate.\n\nIt is possible that the amount of data we collected placed an undue burden on participants and other stakeholders. We are exploring this in a separate stakeholder evaluation.38 It is also possible that the prototypes caused harm to some students who misunderstood concepts or examples. We are exploring potential adverse effects of the final resources in process evaluations30,31,55 and a qualitative evidence synthesis.56\n\nReflexivity considerations\n\nThe core project team all have backgrounds as public health researchers, while the stakeholders recruited for the purposes of collaborating and providing feedback have mostly backgrounds in education with no previous engagement in this research topic. The core project team members are from many different settings, while all stakeholders are from East Africa with the exception of the international advisory group. The PhD fellows and several other core team members were working full-on this project, and therefore highly invested in a positive outcome, while stakeholders were participating voluntarily, in addition to their other full-time work or study commitments.\n\nWe have tried to be mindful of our differing agendas, cultural perspectives, and the ways in which the core team’s ambitions might influence the outcome of the work or place undue burden on the participants. We discussed these topics frequently during weekly core team meetings and have also explored some of these questions using more structured methods, designed as separate studies. The context analyses we conducted at the beginning of this work helped us view our research agenda from the perspective of teachers and curriculum developers and understand whether and how our research might better align with existing objectives within the three educational systems. The stakeholder engagement assessment (manuscript under development) provided stakeholders with opportunities to give us feedback about how they experienced their participation while it was ongoing. The qualitative evidence synthesis of post-trial process evaluations (manuscript under development) will help us understand if there have been any adverse effects of the resources, seen from the point of view of the participants.\n\nRelationships between the core team and recruited stakeholders developed over time, and some people who were initially recruited as participants became engaged to the degree that they fulfilled requirements for co-authorship of this study.\n\n\nConclusion\n\nUsing a human-centred design approach, we created adaptable, digital resources for teaching lower secondary school students to think critically about health actions in ten 40-minute lessons. Teachers and students in Kenya, Rwanda and Uganda found the lessons relevant and useful. The open access resources are free to use and can be translated and adapted to other settings. Designed to accommodate use in classrooms with differing digital infrastructure, such as lack of internet connectivity or unstable electricity, they include materials in two modes for classrooms equipped with blackboards or projectors. Teachers with access to a projector preferred the projector resources. In addition to the lessons, resources include a teachers’ guide, glossary, a searchable set of alternative examples of health actions, summaries of teaching strategies for critical thinking, and teacher training materials. The Covid-19 pandemic disrupted the design of the resources, but also provided timely examples and motivation to learn.\n\nNext research steps are already in progress, including randomised trials to evaluate the effect of using the resources on students’ ability to think critically about health actions, parallel process evaluations and one-year follow up studies.", "appendix": "Data availability statement\n\nZenodo. Dataset for “Teaching critical thinking about health information and choices in secondary schools: human-centred design of digital resources”, https://doi.org/10.5281/zenodo.7695782. 47\n\nThis project contains the following underlying data:\n\n• DevelopmentCycle1__data feedback and observations.csv (Coded datapoints extracted in Development cycle 1 from individual/group interviews with teachers/students and observations of lesson pilots in Rwanda, Kenya and Uganda)\n\n• DevelopmentCycle1_internal team feedback.csv (Feedback, comments, suggestions from our research team during Development cycle 1)\n\n• DevelopmentCycle1_interntl-advisory-grp-dec-jan-2020.csv (First round of feedback from international advisory group, via email)\n\n• DevelopmentCycle1_interntl-advisory-grp-jun-aug-2020.csv (Second round of feedback from international advisory group, via email)\n\n• DevelopmentCycle1_interntl-advisory-grp-proto1.2.csv (Third round of feedback from international advisory group, via email)\n\n• DevelopmentCycle1_legend.csv (Description of implications codes we used to assess the importance of observations and feedback for the next iteration of the resources, e.g., “Problem/Showstopper/A problem that we should address”) in Development Cycle 2\n\n• DevelopmentCycle2__data feedback and observations data.csv (Coded datapoints extracted in Development cycle 2 from individual/group interviews with teachers/students and observations of lesson pilots in Rwanda, Kenya and Uganda,)\n\n• DevelopmentCycle2_codes and response options.csv (List of codes/response options used in Development cycle 2 to code or describe datapoints)\n\n• DevelopmentCycle2_definitions.csv (Description of “nature”, “implications” and “Action for resolving” codes used in Development cycle 2)\n\n• DevelopmentCycle2_internal team feedback.csv (Feedback, comments, suggestions from our research team during Development cycle 2)\n\n• Pilot data and test results - analysis of problems and proposed solutions.pdf (Analysis of problems and proposed solutions after lesson pilots at the end of Development cycle 2 that we presented to curriculum developers for stakeholder checking and input)\n\nZenodo. Extended dataset and Coreq Checklist for “Teaching critical thinking about health information and choices in secondary schools: human-centred design of digital resources”, https://doi.org/10.5281/zenodo.7806139. 48\n\nThis project contains the following extended data:\n\n• COREQ_checklist New.pdf (COREQ checklist for this article)\n\n• Group Interview guide Post-Pilot - Students Group interview guide.docx (Guide used as a basis for interviewing groups of students after they had participated in piloting lessons at the end of Development cycle 2)\n\n• Group Interview guide Post-Pilot - Teachers.docx (Guide used as a basis for interviewing teachers after they had piloted lessons at the end of Development cycle 2)\n\n• Interveiw guide Early - Student network.docx (Guide used as a basis for interviewing students in Development cycle 1)\n\n• Interview guide Early - Curriculum develop Questionnaire.docx (Guide used as a basis for interviewing curriculum developers in Development cycle 1)\n\n• Interview guide Pilot - Teachers User testing interview guide.docx (Guide used as a basis for user test interviews with participating teachers in pilot lessons at the end of Development cycle 2)\n\n• Interview Guide Pre-pilot - Teacher-Student - User test.docx (Guide used as a basis for user test interviews of students and teachers before they participated in pilot lessons at the end of Development Cycle 2)\n\n• Observation form Pilot - Observers.docx (Form used by observers to structure observation data of pilot lessons)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International Public License.\n\n\nAcknowledgments\n\nWe would like to thank all of the students, teachers, and schools who generously gave of their time to participate in networks and pilots. In particular, we would like to thank Besweri Wandera, Joseph Jude Agaba, Enock Kiyemba, Deogratious Ssekyole, Dan Bubaale, Fredrick Kiyingi Kinobe, Grace Namakula, Peter Kizza, Edward Kanoonya, Enock Kiyemba, Judith Nantongo, Patrick Ssendujja, Steven Musisi, John Bosco Kalangwa, Paul Sendi, Grace Namakula, Bridgious Kato, Charles Musabi, Ann Murangira, Stanely Shitanda, lynnet Juma, Pamela Nandi, Robert Onyango, Brian Okoth, Emmanuel Otieno, Rose Omondi, Bridgit Abayo, Fredick Okoth, John Ouko, Lawrence Ariang’a, Innocent Uwimana, Paul Nkundimana, Aloys Kayinamura, Janvier Ntibizerwa, Aaron Habarurema, Donat Nkurunziza, Chui Hsia, and Christine Holst. We also thank the Kenya Institute of Curriculum Development (KICD), Rwanda Basic Education Board (REB), and National Curriculum Development Centre (NCDC) in Uganda for their ongoing encouragement and collaboration.\n\n\nReferences\n\nOxman M, Larun L, Gaxiola GP, et al.: Quality of information in news media reports about the effects of health interventions: systematic review and meta-analyses. F1000Res. 2021; 10: 10. Publisher Full Text\n\nBoutron I, Haneef R, Yavchitz A, et al.: Three randomized controlled trials evaluating the impact of “spin” in health news stories reporting studies of pharmacologic treatments on patients’/caregivers’ interpretation of treatment benefit. BMC Med. 2019; 17(1): 1–10.\n\nDahlgren A, Furuseth-Olsen K, Rose CJ, et al.: The Norwegian public’s ability to assess treatment claims: results of a cross-sectional study of critical health literacy. F1000Res. 2021; 9(179): 179. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSemakula D, Nsangi A, Oxman A, et al.: Informed Health Choices media intervention for improving people’s ability to critically appraise the trustworthiness of claims about treatment effects: a mixed-methods process evaluation of a randomised trial in Uganda. BMJ Open. 2019; 9(12): e031510. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEffects of the Informed Health Choices secondary school intervention on the ability of lower secondary students in Kenya to think critically about health information and choices: Protocol for a cluster-randomized trial. Zenodo. 2022 [cited November, 2022].\n\nEffects of using the Informed Health Choices digital secondary school resources on the ability of Rwandan students to think critically about health: protocol for a cluster-randomised trial. 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Publisher Full Text" }	[ { "id": "173757", "date": "01 Jun 2023", "name": "Anke Steckelberg", "expertise": [ "Reviewer Expertise Critical health literacy", "evidence-based health information", "informed shared decision 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\nThe authors reported the development of digital resources to teach secondary school students applying a human-centred design. This project is part of a larger project comprising extensive exploration of stakeholders perspectives and contexts and also systematic reviews of teaching methods in the beginning of the project to inform this present study which will then be evaluated in randomized controlled trials in three countries in Africa.\nIn order to enhance readability and help readers to understand the complexity of the whole project, authors reported details that had already been published elsewhere.\nThis study is highly relevant and it was great to have access to the website. The manuscript is well written. However, authors should rather refer to already available publications and instead should provide further information on the following aspects:\nThe conducted “Individual interviews employing user testing methods” comprised three parts. Some teachers were interviewed right after a pilot lesson, so they had their experiences from the lesson fresh in mind. Please add information how many of them already taught a pilot lesson before the interview and whether these teachers also had access to the teachers guide.\n\nPiloting and observation: The authors reported that early pilots involved single lessons. Were all lessons piloted as single lessons?\n\nThe authors translated several of the audio recordings from individual and group interviews. Please add information on the selection of the recordings and why it was done.\n\nThe authors provide a teacher`s guide and also reported that lack of competences was a relevant issue. Please clarify whether participation in the workshop for teachers was optional or mandatory and whether teachers competences were assessed.\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": "11208", "date": "13 Apr 2024", "name": "Sarah Rosenbaum", "role": "Author Response", "response": "Response to Peer reviewer #1 Thank you very much for your time reviewing this article and your constructive questions. I am answering them below and updating the manuscript at the same time. Question 1: The conducted “Individual interviews employing user testing methods” comprised three parts. Some teachers were interviewed right after a pilot lesson, so they had their experiences from the lesson fresh in mind. Please add information how many of them already taught a pilot lesson before the interview and whether these teachers also had access to the teachers guide. Reply 1a & b: 1a: How many taught a pilot lesson before the interview: I’ve made changes to Table 6 so that this information is added there. I did this by rechecking with the PhD fellows about the participant data, and we found small errors in the original table, so these are also fixed. 1b: Whether teachers had access to the teachers guide: In the first development phase, we had not begun work on the teacher's guide, so no teachers had access to this in the early interviews or pilots. Regarding the second development phase, I’ve edited the text in the paragraph “Piloting and observation” so that the following information is provided: “In the final pilot, teachers taught all the lessons over a school term, with access to a complete prototype of the resources including the teacher’s guide.” Question 2: Piloting and observation: The authors reported that early pilots involved single lessons. Were all lessons piloted as single lessons? Reply 2: No. I have added the following clarifying text under “Piloting and observation”: “Initially we sought to try out different approaches to overarching questions that were not lesson specific (e.g. how much content, what kind of lesson structure, what kind of teaching strategies to build on, how to format the materials). As we made formatting and content decisions, we gradually developed a full set of lessons, not all of which were piloted individually in the the first development phase.\" Question 3: The authors translated several of the audio recordings from individual and group interviews. Please add information on the selection of the recordings and why it was done. Reply 3: I changed the text in the first paragraph under “Data analysis” to reflect more accurately what was done in each country: “In Uganda and Kenya, all interviews were carried out in English and transcribed. In Rwanda, interviews were carried out in Kinyarwanda and transcribed in English. There, the PhD fellow and research assistant relied on notes they made during interview sessions, and selected some recordings to review when further clarification of their notes was needed.” Question 4: The authors provide a teacher`s guide and also reported that lack of competences was a relevant issue. Please clarify whether participation in the workshop for teachers was optional or mandatory and whether teachers competences were assessed. Reply: The workshop was a part of the intervention that was tested in three randomised trials evaluating the effect of these resources, and reported in those studies. Participation in the workshop was not mandatory. Teachers’ competences were not assessed at the end of the workshop, but they were assessed in the trials at the end of all the lessons. You can find the trial results for both students and teachers in Table 3 of this article: Effects of the Informed Health Choices secondary school intervention: A prospective meta-analysis: https://onlinelibrary.wiley.com/doi/10.1111/jebm.12552 I have added the following short summary of the results of this prospective meta-analysis in the Conclusions section, along with the corresponding citation reference: “A Prospective meta-analysis synthesizing the results of the three randomised trials has shown that the resources led to a large improvement in the ability of students and teachers to think critically about health choices, though only 42% of students achieved a passing score[64]. Next research steps are well underway: process evaluations of the three trials and one-year follow up studies.” Other updates to reflect referenced studies that are now published: Reference #52 has been updated as this article has now been published. Reference #64 in the Conclusion is new, as the trial results are now published." } ] }, { "id": "250515", "date": "05 Sep 2024", "name": "Catherine Mathews", "expertise": [ "Reviewer Expertise Sexual and reproductive health" ], "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 describes the processes undertaken to develop a set of digital learning resources to teach students in Kenyan, Rwandan and Ugandan schools to think critically about health and health care, and to develop skills to assess the reliability of claims about interventions to improve health. Interventions to teach critical thinking are seldom included in the curricula of schools in the countries in which this research was conducted, despite that critical thinking is recognized as a valuable skill for young people to acquire, which will help them make decisions through the life course. In the countries in which the research was conducted, and in many other countries, teachers lack skills and resources to enable them to teach critical thinking. Both the intervention and the measure selected to evaluate the effects of the intervention are based on a large body of sound research which is referenced in the manuscript. The manuscript provides valuable information about how to use a human-centered design approach to adapt a program that promotes critical thinking about health and to adapt measures to evaluate the program. Stakeholders contributed to the intervention development process is described in sufficient detail and is appropriate. The changes made to the interventions in response to stakeholders’ input are detailed. The problems identified during the design process, and the actions taken to address such problems indicate how feedback from stakeholders was used to inform the development cycles of the intervention. The description of the set of lessons is clear and valuable and together with information about the key concepts that were taught in a sample lesson helps the reader gain more information about the intervention. The manuscript is written clearly, and the research processes are described comprehensively. It is rare to read a manuscript in which the intervention development process is set out systematically and clearly. The manuscript is excellent, and I do not have any suggestions for improvement.\n\nMajor points None Minor points None\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": [] } ]	1	https://f1000research.com/articles/12-481
https://f1000research.com/articles/13-489/v1	17 May 24	{ "type": "Research Article", "title": "In Vitro Alpha-Glucosidase Inhibitory Effect of Etlingera Elatior Ethanol Extract Growing in Gayo Highland, Aceh Province, Indonesia", "authors": [ "Zumaidar Zumaidar", "Nuzul Asmilia", "Saudah Saudah", "Milda Husnah", "Nuzul Asmilia", "Saudah Saudah", "Milda Husnah" ], "abstract": "Background The prevalence of diabetes mellitus (DM) is increasing overtime, potentially leading to various severe health complications and mortality. Despite therapeutic agents have currently been developed, unexpected adverse effects are inevitable. Hence, safe and effective medications such as those of plant origin are critical to prevent unexpected complication in DM sufferers. Etlingera elatior has been widely used as spice and traditional medicine to treat diabetes in Aceh Province, Indonesia. However, study regarding α-glucosidase inhibitory effect of E. elatior growing in Gayo highlands, Aceh, Indonesia, is completely lacking. The aim of this study was to evaluate in vitro α-glucosidase inhibitory effect of E. elatior ethanol extracts (EEEE) growing in Gayo highlands, Aceh Province, Indonesia.\n\nMethods Antioxidant activity was determined using DPPH procedure, whereas α-glucosidase inhibition assay was carried out using spectrophotometric method. Data analysis was performed using One-Way Analysis of Variance (ANOVA), followed by Duncan’s multiple range test at α=0.05.\n\nResults Phytochemical analysis revealed the presence of total phenolic (TPC), total flavonoid (TFC), and total tannin (TTC) content in all E. elatior plant parts, in which the highest TPC was found in the stem (158.38 GAE/g), whereas the highest TFC and TTC was obtained in the rhizome extracts. The extract of fruit showed the strongest antioxidant activities, followed by the stem and leaf, with IC50 of 2.381 μg/mL, 6.966 μg/mL, and 19.365 μg/mL, respectively. All E. elatior extracts revealed a significant inhibitory activity against α-glucosidase at the concentration of 500 μg/mL, in which the stem extract showed the most effective α-glucosidase inhibitory effect with IC50 value of 5.15 μg/mL, suggesting its promising potential as antidiabetic agent.\n\nConclusions This study highlights E. elatior potency as a novel source of antioxidant and natural antidiabetic compounds that are useful for the prevention and treatment of diabetes.", "keywords": [ "Antidiabetic", "anti-hyperglycemic", "α-glucosidase inhibitor", "antioxidant activity", "Etlingera elatior" ], "content": "Introduction\n\nDiabetes mellitus (DM) has been considered one of the leading causes of death worldwide.1 Approximately 415 million adults suffer from diabetes globally, and the number is estimated to increase up to 642 million by the year of 2040.2 In the Southeast Asian regions, around 11.3% prevalence of DM has been reported and Indonesia occupies the 7th most DM sufferers, which is considered a major contributor of diabetes cases in Southeast Asia.3 DM often leads to various health complications such as blindness, stroke, heart disease, and kidney failure.4 According to the World Health Organization (WHO) report, around 422 million people suffer from DM at the age of 20-70 years worldwide. Several factors, including age, obesity, lifestyle, and unhealthy diets are among risk factors for diabetes.5\n\nMost of diabetic patients use oral preparations and insulin injections as therapy; however, taking long-term oral medications may result in unexpected adverse effects.6,7 This condition has urged the need for searching and developing new therapeutic approaches that are safer and easier for users,8,9 including the use of α-glucosidase inhibitors, especially those of plant origin. Αlpha-glucosidase inhibitors are oral antidiabetics that act by inhibiting α-glucosidase enzyme responsible for catabolizing complex polysaccharide into monosaccharides, causing a reduction in glucose absorption and postprandial blood sugar levels.10\n\nIdentification of potent natural compounds effectively inhibiting α-glucosidase has been extensively carried out as an effort in searching for new antidiabetic agents.11 Some α-glucosidase inhibitors have been isolated from medicinal plants, offering the potential for alternative medications with greater efficacy and fewer side effects compared to current treatments.12 Among the traditionally favored source of alternative medicines for the treatment of diabetes is Etlingera elatior.13 Research on E. elatior flower extract revealed a strong inhibitory activity against α-glucosidase, making it a promising candidate for diabetes treatment.14 Rhizome of E. elatior was also reported to exhibit antidiabetic effect attributed to its flavonoid compounds.15 However, there is currently lack of information regarding antioxidant and antidiabetic properties of E. elatior extracts growing in Gayo highlands, Aceh, Indonesia. Therefore, the aim of this study was to evaluate antioxidant and α-glucosidase inhibitory activities of E. elatior extracts growing in this specific region.\n\n\nMethods\n\nThe materials used in this study included technical ethanol 96%, Folin-Ciocalteu’s reagent (Merck-1.09001.0100, Germany), sodium carbonate (Na2CO3) (Merck-1.06392.0500, Germany), gallic acid (Merck-8.42649.0025, Germany), sodium nitrite (NaNO2) (Merck-1.06549.0500, Germany), aluminium chloride (AlCl3) (Merck-8.01081.0500, Germany), sodium hydroxide (NaOH) (Merck-1.06498.1000, Germany), quercetin (Sigma Aldrich-Q4951, USA), vanillin (Merck-8.18718.0100, Germany), hydrochloric acid fuming (HCl) (Merck-1.00317.2500, Germany), tannic acid (Sigma Aldrich-1643328-2G, USA), 1,1-Diphenyl-2-picrylrazyl (DPPH) powder (Tokyo Chemical Industry Co., Ltd. (JP)-D4313, Japan), ascorbic acid (Merck-1.00468.0100, Germany), phosphate buffer saline (PBS) (Oxoid-BR0014G, England), dimethyl sulfoxide (DMSO) (Merck-1.02952.1000, Germany), α-glucosidase powder (CDH-105265, India), bovine serum albumin (Himedia-MB083-25G, India), p-nitrophenyl-D-glucopyranose (p-NPG) (Sigma-N1377-5g, USA), and acarbose.\n\nEtlingera elatior plant was obtained from Gayo Highlands of Aceh Province, Indonesia. The plant was identified and preserved at Acehense Herbarium, Department of Biology, Universitas Syiah Kuala, Indonesia. Based on the International Union for Conservation of Nature (IUCN), the plant is classified into “data deficient (DD)” species due to inadequate information for its conservation status assessment. Meanwhile, this plant widely grows in various areas in Aceh, including forest, garden, or at the backyard of Acehnese houses since it has been traditionally used as traditional medicine, spice, and food.16\n\nSamples of E. elatior plant parts consisting of rhizomes, stems, leaves, flowers, and fruits were washed thoroughly under running tap water. The samples were then air-dried for 6 days and diligently grinded to obtain powder. Extraction was carried out by the maceration method. In brief, a 100 gram of simplicial was placed into a maceration container, filled with ethanol 96% until submerged, homogenized, sealed, and let stand for 24 hours with occasional stirring. The mixture was then filtered yielding macerate and lees. The macerate was stored and the lees underwent the same maceration procedure until the solvent became colourless. The obtained macerate was evaporated by vacuum rotary evaporator (Buchi R-300, Swiss) at 50°C to obtain concentrated (100%) stem, leaf, fruit, flower, and rhizome extracts.17 The extracts were then stored at 20°C for further analysis.\n\nEach EEEE samples (stems, leaf, fruit, flower, and rhizome) (0.2 mL) with a concentration of 300 μg/mL was mixed with 2.5 mL of 10% (v/v) Folin-Ciocalteu’s reagent and 2 mL of 7.5% (v/v) Na2CO3. After being incubated for 10 minutes at 45°C, the absorbance of the solution was measured using a UV-Vis spectrophotometer at a wavelength of 765 nm (UV-1800, Shimadzu, Japan) for the determination of TPC. Standard solution of gallic acid (concentrations of 10 – 100 μg/mL; R2= 0.9237) was used to make a calibration curve, and TPC was expressed as mg (+)- of gallic acid equivalent per gram of dry weight of the extracts (GAE/g).18,19 The assay was performed in triplicate.\n\nEach extract sample (5 mL) with a concentration of 500 μg/mL was mixed with 0.3 mL of 5% (v/v) NaNO2 and 0.3 mL of 10% v/v AlCl3. After incubation for 5 minutes, 2 mL of 1 M NaOH was added to the concoction. The absorbance of the solution was measured using UV-Vis spectrophotometer at a wavelength of 510 nm (UV-1800, Shimadzu, Japan). The calibration curve of standard quercetin (concentrations of 10 – 400 μg/mL; R2= 0.9282) was used for quantification of TFC in the extracts, which was expressed as mg (+)- quercetin equivalent per gram of dry extract (QE/g).19,20 The assay was performed in triplicate.\n\nCondensed tannins (proanthocyanidins) were determined by mixing 50 μL of the diluted EEEE sample with 3 mL of 4% vanillin in methanol and 1.5 mL of concentrated HCl. The mixture was allowed to stand for 15 minutes and the absorption was measured using UV-Vis spectrophotometer (UV-1800, Shimadzu, Japan) at a wavelength of 500 nm with respect to methanol as a blank control. Quantification of total tannin in the extracts was based on tannic acid (concentrations of 1.5 – 20 μg/mL; R2 = 0.9705) calibration curve, and the total amount of condensed tannins was expressed as mg (+)- tannic acid equivalent per gram of dry extracts (TAE/g).19,21 The assay was performed in triplicate.\n\nDPPH assay was employed to assess free radical-scavenging activity of EEEE. Briefly, 3.5 mL of DPPH solution and 0.5 mL of each sample extract (concentrations of 1000, 500, 250, 125, 62.5, and 31.5 μg/mL) were mixed, homogenized, and incubated at 27°C for 20 minutes. The absorbance of the solution was then measured at a wavelength of 517 nm using UV-Vis spectrophotometer (UV-1800, Shimadzu, Japan). The ascorbic acid of various concentrations (2, 4, 6, and 8 μg/mL) was used as the positive control.20 The percentage of DPPH inhibition was calculated using the following formula22:\n\nBriefly, each EEEE sample was dissolved in dimethyl sulfoxide (DMSO) to obtain a concentration of 500 μg/mL. The enzyme solution was prepared by dissolving 1.0 mg of α-glucosidase in a phosphate buffer saline (PBS) (pH 7) containing 200 mg of serum bovine albumin. Before use, 1 mL of the enzyme was pre-diluted 25 times with PBS (pH 7.0). The reaction was initiated by mixing 10 μL of the sample solution (concentration of 500 μg/mL) with 25 μL of 0.04 U/mL α-glucosidase, 50 μL of 0.1 mM PBS (pH 7.0), and 25 μL of p-nitrophenyl-D-glucopyranose (p-NPG). The mixture was incubated at 37°C for 30 minutes. A 100 μL of 0.2 M sodium carbonate (Na2CO3) was then added to terminate the reaction, and the absorbance of p-nitrophenol was measured at a wavelength of 410 nm using a UV-Vis spectrophotometer (UV-1800, Shimadzu, Japan).23\n\nPositive control was prepared by dissolving acarbose tablets in PBS (pH 7.0) and HCl 2N. To make a 1% acarbose standard solution, the acarbose tablets was diluted in distilled water and 2N HCl at 1:100 ratio. The solution was then centrifuged at 10.000 rpm for 10 minutes and the supernatant was used as a standard. Each test was performed in triplicate, and the inhibitory activity of the extract against α-glucosidase was quantified in % inhibition using the following formula:\n\nAcontrol is the solution absorbance in the absence of the extracts and Asample is the solution absorbance in the presence of the extracts. The IC50 value was obtained by plotting the log concentration against the percent (%) inhibition using a regression equation. The IC50 represent a concentration inhibiting 50% of the enzyme activity. Based on the IC50 values, antioxidant activities are categorized as very strong (IC50 value of <50 μg/mL), strong (IC50 value of 50-100 μg/mL), weak (IC50 of >100 μg/mL), and not active (IC50: >250 μg/mL).24\n\nThe IC50 of antioxidant activity was determined using a linear regression between concentration (X-axis) and percent inhibition (Y-axis) trough the probit analysis of concentration log data with the probit free radical scavenger (DPPH) percentage. A parametric One-Way Analysis of Variance (ANOVA) was employed to identify significance of differences of the percent inhibition between extracts, followed by Duncan’s multiple range test. All statistical analysis was performed using IBM SPSS software version 25 (IBM Corp., New York, USA), and a p-value of ≤0.05 was considered statistically significant.\n\n\nResults\n\nThe result of EEEE phytochemical analysis is presented in Table 1. TPC was expressed in mg GAE/g extract using a standard gallic acid curve (R2 = 0.9237), TFC in mg QE/g extract using a standard quercetin curve (R2 = 0.9282), and TTC in mg TAE/gr extract using a standard tannic acid curve (R2 = 0.9705). The highest TPC was found in the extract of the stem (158.38 mg GAE/g), whereas the lowest was observed in the extract of the leaves (31.35 mg GAE/g). The highest of both TFC (37.91 mg QE/g) and TTC (48.71 TAE/gr) were recorded in the rhizome extract, whereas the lowest were obtained in the leaf extract (TFC: 6.10 QE/g; TTC: 2.13 TAE/gr).\n\nThe result of antioxidant activity of EEEE is presented in Table 2. The most effective radical scavenging activity was shown by the extract of fruit (IC50 value of 2.81 μg/mL), whereas the least effective effect was exhibited by the extract of rhizome (IC50 value of 188.056 μg/mL). The extracts of stem and leaf showed a very strong antioxidant activity (IC50 value of less 50 μg/mL), whereas the extract of flower indicated a strong activity (IC50 of 50-100 μg/mL).\n\n* Very strong.\n\n Strong.\n\n* Weak.\n\nAlpha-glucosidase inhibitory activity of EEEE is presented in Figure 1. All the extracts (rhizome, stem, leaf, flower, and fruit) exhibited a statistically significant inhibitory effect on α-glucosidase activity at the concentration of 500 μg/mL (p < 0.05). The result of Duncan test suggested that the percent of inhibition were significantly different among E. elatior plant parts, except between the stem and fruit extracts. The extracts of the leaf and flower accounted for more than 50.0% of inhibition, suggesting a promising anti-diabetic potential of E. elatior. On the other hand, the lowest inhibition percentage was shown by the stem extract (14.23±3.9%).\n\nDifferent superscripts above each bar indicated statistically significant different based on Duncan test (α = 0.05).\n\nThe IC50 values of EEEE against α-glucosidase are presented in Table 3. The flower extract exhibited the highest IC50 values (100 μg/mL), followed by the rhizome, leaf, and fruit extracts. Meanwhile, the lowest IC50 values was observed in the extract of stem (5.15 μg/mL), which was comparable to that of acarbose (4.45 μg/mL), highlighting a strong anti α-glucosidase potential of E. elatior stem.\n\n\nDiscussion\n\nThe prevalence of type 2 DM (T2DM) is increasing, accounting for approximately 95% of all diabetes cases worldwide.1 This condition can lead to severe complications, such as retinopathy, neuropathy and coronary heart disease if left untreated for a long period of time.25,26 Therefore, a proper, safe, and effective medication is critical to prevent unexpected complication among sufferers. Medicinal plants have been widely used for the treatment of DM and become a preferable source in the search of novel natural anti-diabetic drugs. In the present study, we evaluated α-glucosidase inhibitory effect of EEEE as a new source of antidiabetic agent.\n\nPhytochemical screening of EEEE indicated the presence of phenolics, flavonoids and tannins. Phenolics represented the most abundant secondary metabolites in EEEE and the content varied among E. elatior plant parts. The highest amount was found in the stem extract, followed by flower, fruit, rhizome, and leaf. Phenolics are the most commonly found secondary metabolites in plants synthesized as a response to biotic and abiotic stresses such as temperature, pH, heavy metal stress, and UV radiation.27 Phenolics have been reportedly able to inhibit α-glucosidase activity, justifying its potency for antidiabetic agent.28,29 Other useful pharmacological properties of phenolic compounds included their ability to treat chronic diseases related to oxidative stress, such as diabetes, cancer, and cardiovascular disorders.29–33\n\nDPPH radical scavenging assay suggested that the fruit, stem, and leaf extracts of E. elatior exhibited a very strong antioxidant activity (Table 2), which was assumingly attributed to their secondary metabolites such as phenolic and flavonoid content. Phenolics have been reported to facilitate superoxide dismutase (SOD) and glutathione biosynthesis, thus resulting in the prevention and reduction of oxidative stress which has been associated with pancreatic-cell dysfunction exacerbation.34,35 The ability of phenolic compounds to react with the peroxyl radical (ROO-), donate electron or hydrogen to neutralize free radicals, and act as prooxidant and metal ion chelation has made these compounds as potential antioxidant agents.36,37 Flavonoids in E. elatior also responsible for antioxidant activities by either causing a direct reactive oxygen species (ROS) scavenging, antioxidant enzyme activation, metal chelation, oxidase inhibition, tocopheryl radical reduction, or nitric-oxide-associated oxidative stress attenuation.37 Among all E. elatior plant parts evaluated in the present study, the fruits exhibited the most effective antioxidant activity, assumingly associated with the presence of quercetin in the fruits of this plant.38 Antioxidant properties of plant extracts have often been associated with various pharmacological activities including immunomodulatory, antitumor, anti-inflammatory, and antidiabetic potentials.13,39\n\nWe found that all E. elatior plant parts significantly inhibited α-glucosidase activity at the concentration of 500 μg/mL. The highest inhibitory percentage was observed in the leaf extract (70.67±2.3%), whereas the lowest was noted in the stem extract (14.23±3.9%). The ability of E. elatior leaves to interfere with α-glucosidase activity was assumingly attributed to its chlorogenic compounds that inhibit glucose transporter through their interaction with glucose absorption in the intestine,29 which is similar to the mechanism of action of acarbose, a pharmaceutical drugs used in the treatment of type 2 diabetes.40–42 In terms of effectivity, the stem extract was found to be the most effective α-glucosidase inhibitor among all E. elatior plant parts as it possessed the lowest IC50 value (5.15 μg/mL), which was comparable to that of acarbose (4.45 μg/mL). Similar finding was also reported in a previous study, suggesting antihyperglycemic effect of E. elatior stem extract in vivo.33 This superior α-glucosidase inhibitory effect of the stem was in consistent with the dominant levels of phenolic contents in this part of the plant. Plant-derived polyphenols have been reportedly able to inhibit α-glucosidase activity by interacting with the active sites of this enzyme receptors with a high binding affinity.43\n\nThe extract of E. elatior flower also exhibited more than 50.0% of α-glucosidase inhibition in vitro, suggesting its antidiabetic potential. This finding was in accordance with that of a former study, reporting a high percentage (52.39%) of α-glucosidase inhibition by E. elatior flower extract at a concentration of 100 μg/mL in vitro and reduced blood glucose level by 57.07% at a concentration of 1000 mg/kg against induced type-2 DM animals model.14 This part of the plant is rich in fiber that might be potential to reduce cholesterol levels and treat various diseases such as hypertension, heart disease, constipation, and diabetes.37 Anti-hyperglycemic activity E. elatior flower has been closely related to its antioxidant properties, such as phenolic and flavonoid compounds,29 which have been evidenced to effectively reduce free radicals.44 In addition, alkaloids, flavonoid glucosides, and saponins, which are also found in E. elatior flowers, are among other potential hypoglycemic agents that play a crucial role in the prevention of diabetes by hindering α-glucosidase enzyme activity.29,45–48 In Indonesian society, young flowers of this plant have been widely used as food ingredients in traditional dishes and empirically used as traditional medicine.16\n\nIn addition to the leaves and flowers, the extract of fruit was another E. elatior plant part effectively hindering α-glucosidase activity, with percent inhibition of almost 40.0% and IC50 value of less than 50 μg/mL. It has been traditionally used as an antidiabetic drug and is rich in anthocyanins constituent.37 Anthocyanins, compounds found in dark colored fruits, has been reported to exhibit anti-inflammatory, antimicrobial, and antidiabetic potentials.49 The synergistic effect of anthocyanins and phenolic compounds is responsible for enzyme inhibitory, antioxidant, and anti-inflammatory activities.50 These findings can lead to future research on the therapeutic use of the E. elatior plant in preventing diabetes.\n\nThis study possesses several limitations that should be addressed. We employed spectrophotometric method to obtain data, which could have a relatively limited sensitivity and selectivity. Detecting extremely low concentrations of an analyte or distinguishing the analyte from other substances with similar absorption wavelength might be challenging, potentially leading to data bias.\n\n\nConclusion\n\nEthanol extracts of different E. elatior plant parts significantly inhibited α-glucosidase activity in vitro. Stem extract showed the most effective α-glucosidase inhibitory effect, highlighting its potential as a future antidiabetic agent. Further study assessing anti α-glucosidase activity of E. elatior extracts using non-polar solvents, as well as identification of specific bioactive constituent responsible for α-glucosidase inhibition should be carried out as an effort to develop effective novel anti-diabetic drugs of natural origin.\n\n\nAuthor contributions\n\nConceptualization: ZZ, SS; data curation: NA, SS, MH; formal analysis: ZZ, NA, SS; funding acquisition: ZZ; investigation: SS, NA; methodology: ZZ, NA; project administration: ZZ; resources: ZZ; software: SS; supervision: ZZ; validation: ZZ, NA, SS; writing – original draft preparation: ZZ, SS, MH; writing – review & editing: ZZ, MH.", "appendix": "Data availability\n\nFigshare: ‘In Vitro Alpha-Glucosidase Inhibitory Effect of Etlingera elatior Ethanol Extract Growing in Gayo Highland, Aceh Province. https://doi.org/10.6084/m9.figshare.25333411.v1. 51\n\nThis project contains the following underlaying data:\n\n1. OD value and percent inhibition (%) of EEEE against DPPH radical scavenging.xlsx\n\n2. OD value and percent inhibition (%) of EEEE against α-glucosidase.xlsx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International licence (CC-BY 4.0).\n\n\nAcknowledgment\n\nWe would like to thank the community members of Gayo Highland for their assistance during the plant sample collection in Gayo Highland, as well as Biology Laboratory assistant at Universitas Riau (UNRI) and Pharmacy Laboratory assistant at Universitas Syiah Kuala for their assistance during the study.\n\n\nReferences\n\nZheng Y, Ley SH, Hu FB: Global aetiology and epidemiology of type 2 diabetes mellitus and its complications. Nat. Rev. Endocrinol. 2018; 14(2): 88–98. Publisher Full Text\n\nInternational Diabetes Fideration: IDF Diabetes Atlas. 7th edn.Brussels, Belgium: International Diabetes Federation; 2015; 33(2).\n\nThe Indonesian Ministry of Health. Tetap produktif, cegah, dan atasi diabetes mellitus. Pusat Data dan Informasi Kementrian Kesehatan RI. 2020; 1–10.\n\nMariadoss AVA, Park S, Saravanakumar K, et al.: Ethyl acetate fraction of Helianthus tuberosus L. induces anti-diabetic, and wound-healing activities in insulin-resistant human liver cancer and mouse fibroblast cells. Antioxidants. 2021; 10(1): 99. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDas A, Naveen J, Sreerama Y, et al.: Low-glycemic foods with wheat, barley and herbs (Terminalia chebula, Terminalia bellerica and Emblica officinalis) inhibit α-amylase, α-glucosidase and DPP-IV activity in high fat and low dose streptozotocin-induced diabetic rat. J. Food Sci. Technol. 2022; 59(6): 2177–2188. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStrachan MW, Frier BM, Strachan MW, et al.: Side-effects of insulin. Insulin Therapy: A Pocket Guide. 2013; 43–50. Publisher Full Text\n\nKashi Z, Akha O, Borzouei S, et al.: Insulin therapy: Side effects and their management. Clinical Excellence. 2013; 1(2): 1–16.\n\nÖnal S, Timur S, Okutucu B, et al.: Inhibition of α-glucosidase by aqueous extracts of some potent antidiabetic medicinal herbs. Prep. Biochem. Biotechnol. 2005; 35(1): 29–36. PubMed Abstract \| Publisher Full Text\n\nCarter R, Holiday DB, Nwasuruba C, et al.: 6-minute walk work for assessment of functional capacity in patients with COPD. Chest. 2003; 123(5): 1408–1415. Publisher Full Text\n\nDi Stefano E, Oliviero T, Udenigwe CC: Functional significance and structure–activity relationship of food-derived α-glucosidase inhibitors. Curr. Opin. Food Sci. 2018; 20: 7–12. Publisher Full Text\n\nKumar S, Narwal S, Kumar V, et al.: α-glucosidase inhibitors from plants: A natural approach to treat diabetes. Pharmacogn. Rev. 2011; 5(9): 19–29. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMatsuda H, Nishida N, Yoshikawa M: Antidiabetic principles of natural medicines. V. Aldose reductase inhibitors from Myrcia multiflora DC.(2): Structures of myrciacitrins III, IV, and V. Chem. Pharm. Bull. 2002; 50(3): 429–431. PubMed Abstract \| Publisher Full Text\n\nWijekoon MJO, Bhat R, Karim AA: Effect of extraction solvents on the phenolic compounds and antioxidant activities of bunga kantan (Etlingera elatior Jack.) inflorescence. J. Food Compos. Anal. 2011; 24(4-5): 615–619. Publisher Full Text\n\nNor NAM, Noordin L, Bakar NHA, et al.: Evaluation of antidiabetic activities of Etlingera elatior flower aqueous extract in vitro and in vivo. J. Appl. Pharm. Sci. 2020; 10(8): 043–051.\n\nFitrianita A, Yardi Y, Musir A: Uji efek antihiperglikemia ekstrak etanol 70% daun kecombrang (Etlingera elatior) pada tikus sprague dawley dengan penginduksi aloksan. Jurnal Ilmiah Farmasi. 2018; 14(1): 9–16. Publisher Full Text\n\nSaudah S, Zumaidar Z, Darusman D, et al.: Ethnobotanical knowledge of Etlingera elatior for medicinal and food uses among ethnic groups in Aceh Province, Indonesia. Biodiversitas. 2022; 23(8). Publisher Full Text\n\nSruthi D, Indira G: A comparative evaluation of maceration, soxhlation and ultra sound assisted extraction for the phytochemical screening of the leaves of Nephelium lappaceum. L.(Sapindaceae). J. Pharmacogn. Phytochem. 2016; 5(5): 386–389.\n\nJayaprakasha G, Girennavar B, Patil BS: Radical scavenging activities of rio red grapefruits and sour orange fruit extracts in different in vitro model systems. Bioresour. Technol. 2008; 99(10): 4484–4494. PubMed Abstract \| Publisher Full Text\n\nOjha S, Raj A, Roy A, et al.: Extraction of total phenolics, flavonoids and tannins from Paederia foetida L. Leaves and their relation with antioxidant activity. Pharm. J. 2018; 10(3): 541–547. Publisher Full Text\n\nGhasemzadeh A, Jaafar HZ, Rahmat A, et al.: Secondary metabolites constituents and antioxidant, anticancer and antibacterial activities of Etlingera elatior (Jack) RM Sm grown in different locations of Malaysia. BMC Complement. Altern. Med. 2015; 15: 1–10.\n\nMedini F, Fellah H, Ksouri R, et al.: Total phenolic, flavonoid and tannin contents and antioxidant and antimicrobial activities of organic extracts of shoots of the plant Limonium delicatulum. J. Taibah Univ. Sci. 2014; 8(3): 216–224. Publisher Full Text\n\nMolyneux P: The use of the stable free radical diphenylpicrylhydrazyl (DPPH) for estimating antioxidant activity. Songklanakarin J. Sci. Technol. 2004; 26(2): 211–219.\n\nDwitasari O, Seno DSH, Safithri M: Identification of bioactive compounds and α-glucosidase inhibition activity of Caesalpinia Bonduc seed extract in vitro. Curr. Biochem. 2018; 5(2): 12–20. Publisher Full Text\n\nBadarinath A, Rao KM, Chetty CMS, et al.: A review on in-vitro antioxidant methods: comparisions, correlations and considerations. Int. J. Pharmtech. Res. 2010; 2(2): 1276–1285.\n\nIda S, Kaneko R, Imataka K, et al.: Relationship between frailty and mortality, hospitalization, and cardiovascular diseases in diabetes: A systematic review and meta-analysis. Cardiovasc. Diabetol. 2019; 18(1): 1–13.\n\nAtif M, Saleem Q, Babar Z-U-D, et al.: Association between the vicious cycle of diabetes-associated complications and glycemic control among the elderly: A systematic review. Medicina. 2018; 54(5): 73. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLin D, Xiao M, Zhao J, et al.: An overview of plant phenolic compounds and their importance in human nutrition and management of type 2 diabetes. Molecules. 2016; 21(10): 1374. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCai Y, Wu L, Lin X, et al.: Phenolic profiles and screening of potential α-glucosidase inhibitors from Polygonum aviculare L. leaves using ultra-filtration combined with HPLC-ESI-qTOF-MS/MS and molecular docking analysis. Ind. Crop. Prod. 2020; 154: 112673. Publisher Full Text\n\nPrabawati NB, Oktavirina V, Palma M, et al.: Edible flowers: Antioxidant compounds and their functional properties. Horticulturae. 2021; 7(4): 66. Publisher Full Text\n\nShahidi F, Yeo J: Bioactivities of phenolics by focusing on suppression of chronic diseases: A review. Int. J. Mol. Sci. 2018; 19(6): 1573. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAguilera Y, Martin-Cabrejas MA, González de Mejia E: Phenolic compounds in fruits and beverages consumed as part of the mediterranean diet: Their role in prevention of chronic diseases. Phytochem. Rev. 2016; 15: 405–423. Publisher Full Text\n\nZekeya N, Ibrahim M, Mamiro B, et al.: Potential of natural phenolic antioxidant compounds from Bersama abyssinica (Meliathacea) for treatment of chronic diseases. Saudi J. Biol. Sci. 2022; 29(6): 103273. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSukadana IM, Bogoriani NW, Ariani M: Compounds in the stem of Etlingera elatior can reduce the levels of free fatty acid and blood glucose in obesity wistar rats. RJPT. 2023; 16(10): 4530–4536. Publisher Full Text\n\nDrews G, Krippeit-Drews P, Düfer M: Oxidative stress and beta-cell dysfunction. Pflüg Arch-Eur. J. Physiol. 2010; 460: 703–718. Publisher Full Text\n\nKumar V, Ahmed D, Verma A, et al.: Umbelliferone β-D-galactopyranoside from Aegle marmelos (L.) corr. an ethnomedicinal plant with antidiabetic, antihyperlipidemic and antioxidative activity. BMC Complement. Altern. Med. 2013; 13(1): 1–20.\n\nSrey C, Sontimuang C, Thengyai S, et al.: Anti α-glucosidase, anti α-amylase, anti-oxidation, and anti-inflammation activities of Etlingera elatior rhizome. JOCPR. 2014; 6(12): 885–891.\n\nJuwita T, Puspitasari IM, Levita J: Torch ginger (Etlingera elatior): A review on its botanical aspects, phytoconstituents and pharmacological activities. PJBS. 2018; 21(4): 151–165. PubMed Abstract \| Publisher Full Text\n\nFristiohady A, Leorita M, Malaka MH, et al.: Radical scavenger and anti-diabetic potencies of Etlingera elatior fruits growing in South East Sulawesi-Indonesia. RJPT. 2022; 15(5): 2141–2146.\n\nSafriani N, Rungkat FZ, Yuliana ND, et al.: Immunomodulatory and antioxidant activities of select Indonesian vegetables, herbs, and spices on human lymphocytes. Int. J. Food Sci. 2021; 2021: 1–12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRosak C, Mertes G: Critical evaluation of the role of acarbose in the treatment of diabetes: patient considerations. Diabetes Metab. Syndr. Obes. 2012; 5: 357–367. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMcIver LA, Preuss CV, Tripp J: Acarbose. StatPearls. StatPearls Publishing; 2022.\n\nPlayford RJ, Pither C, Gao R, et al.: Use of the alpha-glucosidase inhibitor acarbose in patients with ‘Middleton syndrome’: Normal gastric anatomy but with accelerated gastric emptying causing postprandial reactive hypoglycemia and diarrhea. Can. J. Gastroenterol. Hepatol. 2013; 27: 403–404.\n\nRasouli H, Hosseini-Ghazvini SM-B, Adibi H, et al.: Differential α-amylase/α-glucosidase inhibitory activities of plant-derived phenolic compounds: A virtual screening perspective for the treatment of obesity and diabetes. Food Funct. 2017; 8(5): 1942–1954. PubMed Abstract \| Publisher Full Text\n\nAbdelwahab SI, Zaman FQ, Mariod AA, et al.: Chemical composition, antioxidant and antibacterial properties of the essential oils of Etlingera elatior and Cinnamomum pubescens Kochummen. J. Sci. Food Agric. 2010; 90(15): 2682–2688. PubMed Abstract \| Publisher Full Text\n\nHossain U, Das AK, Ghosh S, et al.: An overview on the role of bioactive α-glucosidase inhibitors in ameliorating diabetic complications. Food Chem. Toxicol. 2020; 145: 111738. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDas SK, Dash S, Thatoi H, et al.: In vitro α-amylase and α-glucosidase Inhibition, antioxidant, anti-inflammatory activity and GC-MS profiling of Avicennia alba Blume. Comb. Chem. High Throughput Screen. 2020; 23(9): 945–954. PubMed Abstract \| Publisher Full Text\n\nDas SK, Samantaray D, Sahoo SK, et al.: Bioactivity guided isolation of antidiabetic and antioxidant compound from Xylocarpus granatum J. Koenig bark. 3 Biotech. 2019; 9: 1–9.\n\nNing Z-w, Zhai L-x, Huang T, et al.: Identification of α-glucosidase inhibitors from Cyclocarya paliurus tea leaves using UF-UPLC-Q/TOF-MS/MS and molecular docking. Food Funct. 2019; 10(4): 1893–1902. PubMed Abstract \| Publisher Full Text\n\nCásedas G, Les F, González-Burgos E, et al.: Cyanidin-3-O-glucoside inhibits different enzymes involved in central nervous system pathologies and type-2 diabetes. S. Afr. J. Bot. 2019; 120: 241–246. Publisher Full Text\n\nOliveira H, Fernandes A, Brás NF, et al.: Anthocyanins as antidiabetic agents—in vitro and in silico approaches of preventive and therapeutic effects. Molecules. 2020; 25(17): 3813. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZumaidar Z, Asmilia N, Saudah S, et al.: In vitro alpha-glucosidase inhibitory effect of Etlingera elatior ethanol extract growing in Gayo Highland. [Dataset]. figshare. 2024. Publisher Full Text" }	[ { "id": "288676", "date": "29 Aug 2024", "name": "Arif Nur Muhammad Ansori", "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\nFirst of all, this manuscript is good and well-written. However, I may require some comments on the following issues. Basically, this manuscript is acceptable. Language can be improved for the readability of the paper. Title: The title is easy to follow and no mistakes. Abstract: This section was well-written and easy to understand. In addition, the study's objective and the state of the art of the study is clear. Furthermore, the keywords should represent the study. Discussion: To develop a systematic discussion, the authors should mention the limitation(s) of the study. Conclusion: In this part of the paper, the authors have established the conclusion of this study. References: Many references are out of guidelines. Please kindly check the references again, do not include the old references, and check the abbreviation of the journals/proceedings. Please mention many high-quality related publications. References number 14, 15, 16, 24, and 33 should be changed.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? 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": "12335", "date": "04 Sep 2024", "name": "zumaidar zumaidar", "role": "Author Response", "response": "Thank you for reviewing our manuscript. The comments and suggestions have improved the quality of our current manuscript significantly. References: Many references are out of guidelines. Please kindly check the references again, do not include the old references, and check the abbreviation of the journals/proceedings. Please mention many high-quality related publications. References number 14, 15, 16, 24, and 33 should be changed. RESPONSE: Thank you for the suggestions. 1. We agree to exclude reference number 9 (old reference) as it is not strongly relevant to our study. Since it supports general information in the introduction, it will not affect any specific content in our manuscript. 2. We sincerely appreciate the suggestion to exclude older references from the manuscript. However, we believe that several of these references are crucial to our study. Some provide essential information on the phytochemical content and pharmacological activities of Etlingera elatior, which serve as the foundational basis for our research. Therefore, we have chosen to retain these references, especially for reference. 3. We appreciate the reviewer's suggestion regarding the exclusion of references number 14, 15, 16, 24, and 33. However, we believe these references are highly relevant to our study as they provide essential information that directly supports our findings. Therefore, we kindly request to retain these references in the manuscript." } ] } ]	1	https://f1000research.com/articles/13-489
https://f1000research.com/articles/13-209/v1	21 Mar 24	{ "type": "Review", "title": "Exploring the Synergistic Potential of Pectin-Chitosan Composites for Advanced Drug Delivery and Biomedical Implant Applications: A Comprehensive Review and Future Perspectives", "authors": [ "Mohammed Hussein M. Alsharbaty", "Ghassan A. Naji", "Sameh S. Ali", "Ghassan A. Naji", "Sameh S. Ali" ], "abstract": "The polysaccharides pectin and chitosan are derived from the fruit peels and exoskeletons of crustaceans and insects, respectively. Their biocompatibility and renewability make them suitable for use in food products. The size of the swelling and degradation of these cells can be controlled using different combinations. Pectin and chitosan are useful as medication delivery systems, where they can be integrated to control the dosages and residence times of pharmaceuticals. They have a wide range of applications such as wound dressings, body fat reducers, tissue engineering agents, and drug delivery agents. Addressing teeth loss with the use of dental implants is a critical element of dental care. In most cases, healing is time-consuming and painful. As a result of adding new materials to the implant surface, the healing process would accelerate, and medications would be delivered to the implant site with greater efficiency.", "keywords": [ "Natural Polysaccharides", "Pectin", "Chitosan", "Drug delivery systems", "Targeted drug delivery", "Implant materials." ], "content": "Introduction\n\nPolysaccharides such as chitosan and pectin are found in nature.1 Chitin is derived from crustaceans and insect exoskeletons, whereas pectin is derived from apple and citrus fruit peel.2 The use of pectin as a stabilizing and texturizing agent in food is safe.3 Cell walls make up approximately one third of pectin in higher plants.4 There are usually differences in the molecular structure and degree of esterification of pectins derived from different sources. Citrus peel typically contains 20-30% pectin, whereas apple pomace typically contains 10-15% pectin.5,6 In pectin, there are regions that are smooth and other regions that are hairy branched.3 The biocompatibility of pectin is generally considered to be high.7 Generally, pectin is stable between pH 2 and 4.5, although it may become unstable at extreme pH values.7 There are several combinations of pectin that exhibit distinct properties, including enhanced peptide medication-controlled release efficiency, enhanced drug loading efficiency, and improved biocompatibility.8 Due to its biodegradability, pectin is ideal for drug delivery applications because of its minimal accumulation and long-term safety.9 Furthermore, by combining pectin, the swelling size and degradation can be managed to meet drug requirements.10 Several uses for pectin have been demonstrated, including its application to obesity, diabetes, and cardiovascular disease.11\n\nChitosan was first discovered in 1859 by Rouget.12 Among natural biopolymers, it is the second most prevalent.13 It is estimated that 55–85% of chitin in crustacean cuticles originates from a layer of epidermal cells.14 Since chitin and cellulose share the same sugar unit and glycosidic bond type, they share several structural characteristics.15 Chitosan with a nitrogen content of approximately 6.9% is useful for chelation. Fibers, coatings, and beads made of chitosan can also be used instead of powders and solutions.16 Chitosans decompose prior to melting when heated.17 They possess strong bioadhesive properties that make them useful for adding bioadhesive properties to various drug delivery systems.18 The stability of chitosan can be challenged in highly acidic settings, which can be addressed through modifications, as it is most suitable for delivering drugs to the gastrointestinal system under neutral to acidic pH conditions.19 The inherent biodegradability of chitosan and its non-toxic degradation products make it an ideal material for biomedical applications, minimizing exposure to long-term toxic effects.20 Chitosan also possesses DNA-binding, biocompatibility, hemostatic, fungistatic, spermicidal, and anticholesteric properties and accelerates bone growth.21\n\nIn addition to increasing the delivery of specific drugs, pectin improves their absorption.3 Oral administration is widely used as the easiest and most convenient method of drug delivery. When a drug is orally administered, the dosage can be adjusted based on how quickly the digestive system absorbs the dose. Two factors that may affect oral medications administered via the gastrointestinal tract are a low stomach pH and poor stomach peristalsis. Furthermore, the enzymatic activity and digestive properties of gastric content, as well as the duration of drug residence in the stomach and intestine, are important factors.22 Different methods for encapsulating or incorporating drugs into tablets, capsules, or nanoparticles can protect them from degradation.23 Drugs can be encapsulated to mask their taste or modify their release.24 As shown in Tables 1 and 2, pectin is an effective material for the preparation of oral drug carriers.25 Over the past two decades, it has inspired academia and manufacturers to develop more effective drug delivery systems. In addition to being used as wound dressings, body fat reduction agents, and tissue engineering agents, they are also used in drug delivery systems (Table 1). Chitosan, the only biodegradable polymer with a positive charge, has distinctive properties and characteristics among the biodegradable polymers used by pharmaceutical companies. The primary amino group of chitosan is responsible for its cationic charge, which results in the ability to deliver drugs.26 Chitosan has also been shown to improve saturation, stable gelling, mucoadhesive, and efflux pump inhibitor properties. In addition, cationic interactions can be used to deliver drugs through nanoparticles based on DNA and RNA.27 Numerous studies have demonstrated that chitosan is an effective drug delivery system. The characteristics of chitosan differ depending on the salt form, degree of deacetylation, and molecular weight.27 Dornish et al. showed that high-grade and ultra-pure chitosan was safe for use in biological and physiological systems.28 Drug carriers can enhance drug bioavailability by providing mucoadhesive doses, extending release times, and maintaining drugs at absorption sites for longer durations. Chitosan has osteoinductive properties, allowing it to promote cell proliferation, adhesion, and differentiation in bone defects, in addition to biocompatibility and mechanical properties.29 Drug absorption across mucosal membranes can also be improved by chitosan depending on how it is delivered.\n\n\nPectin-chitosan composite materials\n\nPectin-chitosan composites have emerged as versatile materials in medicine.72 These composites possess different properties and offer various benefits in the fields of drug delivery and release, pH sensitivity, adhesion to mucosal surfaces, and enhanced stability.73 The use of pectin-chitosan composites for drug delivery offers many advantages, making them an attractive choice for drug delivery applications.74 These advantages include biocompatibility, bio-adhesiveness, and the ability to tailor drug release to ensure safe drug administration.75 In addition, their encapsulation properties are useful in protecting sensitive drugs.76 Pectin-chitosan composites for drug delivery can be formulated through various methods, providing flexibility to meet specific requirements. Common techniques include layer-by-layer assembly, gelation, cross-linking, solvent evaporation, spray drying, compression, and freeze-drying.73,77–79 The choice of method depends on the desired particle size and drug-release profile. The pectin-chitosan composite is a highly promising material for drug delivery, as it ensures biocompatibility with minimal adverse effects on living tissues. The composite shows strong bioadhesive capabilities for effective mucosal adhesion and can maintain stability within a suitable pH range.80,81 Its biodegradability and eco-friendliness reduce concerns about long-term toxicity and environmental impact, while its adaptability to a variety of drug types and ability to tailor its properties through formulation adjustments make it a versatile choice.82\n\nThe rate at which drugs are released from pectin-chitosan composites in drug delivery systems is influenced by multiple factors, necessitating the precise control of tailored drug release kinetics.83 Key factors affecting drug release include the composition of pectin and chitosan, degree of cross-linking, drug properties, composite formulation, pH, ionic strength, temperature, geometry, mechanical properties, swelling, erosion behavior, drug loading, release mechanisms, external stimuli, release mode, drug loading techniques, and degradation rate of pectin and chitosan.84 The use of pectin-chitosan composites for drug delivery is generally safe and biocompatible; however, potential side effects exist. Controlling drug release is essential for preventing overdosing or underdosing, and drug interactions should be considered.85 Systemic side effects depend on the drug and the route of administration.\n\n\nRole of dental implants\n\nDental implants are in high demand owing to widespread tooth loss.86 In 1957, Per-Ingvar Brånemark discovered that titanium enhances bone healing properties and their regeneration.87 In the case of titanium implants, the rate of bone healing is like that following a fracture or injury to bone.88 The role of an implant and the function is to act as an osteoconductive substrate, allowing new tissue to grow around the defect.89 Blood clots, cell activation and responses to an implant wound are the three stages of wound healing.90 An implant or body surface treated with a new material elicits different biological responses. In order to improve osseointegration between implant surfaces and bone, microlevel characteristics can be applied to implant surfaces.91,92 As the implant contact surface and bone surface become more intimate, the implant acquires stronger anchorage.93 The rough texture of the surface encourages osteoblastic cell adhesion more quickly than the smooth texture.93,94 Implants with a rough surface provide a larger surface area and enhance the attachment of cells from the bone to implants. In addition to increasing attachment, biochemical interactions between the implant surface and the bone also increase. A variety of treatments and ceramic-like elements can be applied to implant surfaces to enhance osseointegration.95\n\nAccording to Wennerberg, the surface roughness of implants can be classified into three levels: minimal, intermediate, and rough.96 Based on the texture, the implants were found to have concave or convex surfaces. Irregularities on the surface can be isotropic or anisotropic, giving the surface roughness a particular orientation.97 Surface roughness can be increased using various methods including blasting,98 chemical etching,99 plasma-sprayed surfaces, ion-sputtering coating,100 and anodized surfaces.100 Many materials can be used to coat the surfaces of dental implants depending on their function and intended use.101 There are two types of coating: inorganic layers (hydroxyapatite or calcium phosphate) and organic layers (growth factors).102 Among inorganic phases, ceramics dominate.103 Adding calcium phosphate to implant surfaces improves osteoconductive properties, accelerating the development of bone around the implants.104 The addition of a hydroxyapatite film to implants causes the release of fluoride ions, resulting in bone calcification.105 Hydroxyapatite also acts as a mechanical stabilizer as well as a chemical bonding agent between tissues and implant surfaces.106 As a result of adding organic phases or bioactive materials to implant surfaces, biochemical bonding capacity, hydrophilicity, and osseointegration can be enhanced, depending on the desired outcome, for example, increasing cell adhesion and growth factors or acting as local drug delivery systems.107,108\n\n\nPectin and chitosan as implants: a rationale for their use\n\nA new implant coating can enhance the properties of dental implants with the potential to improve attachment, mineralization, and protein deposition by creating a coating for osteoblasts that identify and interact with particular molecules.99 New methods of local antimicrobial prophylaxis are needed to ensure that dental prostheses are protected from infections. Implants can enhance biological reactions in situ and promote long-term bone healing. This would allow for faster recovery and a quicker return to normal activity for patients and doctors. The application of nanocoating with organic molecules can have a positive effect on osseointegration and cell behavior. In the vicinity of implants with polysaccharide nanocoating, Bone-to-implant surface contact, and bone mineral density improved.108 Biopolymers derived from marine and agricultural sources are readily available and replenishable, making them useful in the medical life sciences. Owing to their biocompatibility and biodegradability, these polymers offer ecological security and the ability to be modified by enzymes, giving them a unique set of properties.109 The anticoagulant properties of sulfated chitosan have also been demonstrated. A biopolymer membrane-covered wound showed better hemostatic properties and healed faster.110 Improvements in epithelialization and collagen deposition have been demonstrated using biopolymer-based membranes. In addition to inhibiting fibrin formation, chitosan-based dressings reduce scarring in wounds.111 Because of chitosan membranes, wounds are less likely to lose water, oxygen permeability is increased, fluid drainage is promoted, and foreign microorganism contamination is reduced.112 Chitosan and pectin are both capable of forming thin membranes that can be used to improve the delivery of medications in various ways.113 A major component of future implant technologies is the fibrin scaffold provided by biopolymers. Bone and implant surfaces can form covalent bonds with the scaffold, thereby mediating cell adhesion.107\n\nThe interaction between Fiekian diffusion and high-viscosity chitosan films has resulted in the constant release of drugs for prolonged periods of time.114 This has led to the development of antimicrobials for specific areas of periodontal therapy, addressing the disadvantages of systemic drug administration. The properties of pectin and chitosan derivatives make them ideal for local drug delivery systems because they enable easy delivery, long-term retention, and regulated medication release. These derivatives also allow for the acceptable penetration of medication into the oral cavity and sustained retention of medication. In addition to their antimicrobial properties, these compounds are highly effective and well tolerated in oral tissues. Pectin and chitosan derivatives have different chemical and physiological properties, including ionic charge, branching, various molecular weights, and enzyme modification properties, making them good candidates for biomaterial coatings.115 Chitosan and pectin with high levels of galactose and low levels of arabinose have been shown to reduce inflammation, which is vital for improving implant integration and reducing inflammation in patients with rheumatoid arthritis, periodontitis, and immunocompromised patients.116 It has been found that biopolymer derivatives inhibit a large number of gram-positive and gram-negative bacteria as well as fungi.117\n\nPectin and chitosan are effective and efficient because of their diverse modification capabilities. Altering the length of their side chains and removing acetyl groups from their hairy regions can change their polarity and wettability.118,119 Human tissue takes up covalently bonded pectin well in terms of immunological responses.120–122 Modifying the side chains of pectin or chitosan sugar molecules makes it easier to initiate bone cell attachment in a manner that is tailored to the human body. It would be beneficial to investigate the use of pectin or chitosan as implant nanocoating and to support their development with findings from previous studies of bone biology.\n\n\nConclusion\n\nThe efficacies of pectin and chitosan are supported by their diverse modification capabilities. It is possible to fabricate nanostructures and sizes made from these natural biopolymers for an array of innovative uses. Reviewing the application of pectin and chitosan, as well as their composites, for dental implant surface coatings is a promising endeavor because of the multifaceted benefits of the composites. These composites offer enhanced biocompatibility and can mitigate infection risks owing to their inherent antimicrobial properties. In addition, they have the potential to promote osseointegration by facilitating bone cell adhesion and growth. By enabling controlled drug delivery, these composites can release antimicrobial agents or growth factors, optimize tissue healing around implants, and minimize inflammation. The versatility of the formulation allows for tailored applications, whereas their natural sourcing contributes to eco-friendliness. This aim is to improve the safety, longevity, and success of dental implant procedures, making them an asset in dental implant technology. Studies and experimental tests should be conducted to determine the efficacy of pectin-chitosan composites as nanocoating for implants. Promising outcomes from in vitro and in vivo research may emerge in the near future.", "appendix": "Data availability statement\n\nNo data is associated with this article.\n\n\nReferences\n\nMorris GA, Kök SM, Harding SE, et al.: Polysaccharide drug delivery systems based on pectin and chitosan. Biotechnol. Genet. Eng. Rev. 2010; 27(1): 257–284. Publisher Full Text\n\nLiu L, Fishman ML, Kost J, et al.: Pectin-based systems for colon-specific drug delivery via oral route. Biomaterials. 2003; 24(19): 3333–3343. PubMed Abstract \| Publisher Full Text\n\nLiu L, Fishman ML, Hicks KB: Pectin in controlled drug delivery–a review. Cellulose. 2007; 14(1): 15–24. Publisher Full Text\n\nSemdé R, Amighi K, Devleeschouwer MJ, et al.: Studies of pectin HM/Eudragit® RL/Eudragit® NE film-coating formulations intended for colonic drug delivery. Int. J. 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Publisher Full Text" }	[ { "id": "259933", "date": "18 Jun 2024", "name": "Bhisham Narayan Singh", "expertise": [ "Reviewer Expertise Tissue Engineering", "Biomaterial" ], "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\nComments: 1. Abstract need to be rewrite and should well organized. Also, authors need to check for statement like swelling and degradation of cells. 2. The current review article is too general and need to be updated with current studies and recent advancement. 3. Authors, need to discuss and analyze the reported data for various physico-chemiccal, mechanical and biological outcomes of various developed and evaluated implants through in-vitro and in-vivo studies. 4. Authors, need to highlight various reported pectin and chitosan based drug delivery system such as nanoparticles, hydrogels etc. Also, need to discuss advantages and challenges. 5. Overall, authors need to revise the complete manuscript with some reported data, compare the reported work and allow the reader to get insight on recent trends in development of pectin and chitosan based drug delivery system and implants for biomedical applications. Also, authors need to add few figures to improve the quality of the manuscript and to build interest of readers.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? No\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? No\n\nAre the conclusions drawn appropriate in the context of the current research literature? Partly", "responses": [] }, { "id": "283991", "date": "28 Jun 2024", "name": "Sagar Salave", "expertise": [ "Reviewer Expertise Drug delivery", "Nanomedicine", "Pharmaceutical Technology", "Characterization" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe topic is fascinating in drug delivery and implant development. However, the authors have superficially summarised the literature. Therefore, reviewer would like to recommend a major revision for this article; Specific comments: 1. Include the chemical structure for pectin and chitosan 2. Table 1 can be improved in terms of the method of preparation and key findings 3. Inclusion of more literature in the drug delivery and implant section would improve the quality of the article 4. Add a few figures in relevant section to improve the readability of the article 5. Improve the conclusion in the revised manuscript\n\nIs the topic of the review discussed comprehensively in the context of the current literature? No\n\nAre all factual statements correct and adequately supported by citations? 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": "12318", "date": "04 Sep 2024", "name": "Mohammed Hussein M. Alsharbaty", "role": "Author Response", "response": "The revised version reflects all the reviewer's comments" } ] } ]	1	https://f1000research.com/articles/13-209
https://f1000research.com/articles/13-505/v1	17 May 24	{ "type": "Research Article", "title": "Efficacy of different remineralization agents on microhardness and chemical composition of enamel white spot lesion", "authors": [ "Rafal Ghanim Rahman", "Ban Sahib Diab", "Ban Sahib Diab" ], "abstract": "Background White spot lesions (WSLs) are frequently linked with low microhardness and mineral content changes. several strategies have been employed to deal with these problems. This investigation aimed to analyze the microhardness and mineral content changes after remineralization with bioactive glass (BAG) and casein phospho-peptide-amorphous calcium phosphate with fluoride (CPP-ACPF).\n\nMethods Twenty sound maxillary first premolars extracted were used to obtain a total of one hundred enamel samples. forty enamel slabs were split into four experimental groups (n = 10 each): Group I, BAG; Group II, BAG+CPP-ACPF; Group III, CPP-ACPF varnish; and Group IV, artificial saliva (negative control). To create artificial WSLs, all samples were preserved in a prepared demineralizing agent for 72 h before treatment with remineralizing agents. Vickers microhardness test was performed. Additionally, 60 enamel samples were selected for analysis using energy dispersive spectroscopy (EDX) and assigned to six experimental groups; the first four groups were similar to that used in the microhardness test along with Group V: WSLs, and Group VI: baseline. The statistical analyses employed in this study included Tukey’s HSD (p<0.05), one-way ANOVA, and Shapiro-Wilk.\n\nResult Regarding surface microhardness, the BAG+CPP-ACPF group showed the most favorable recovery, which was better than the outcomes of the BAG and CPP-ACPF groups. A statistically significant change (p <0.05) was not observed between them. Similarly, for mineral content change, the BAG+CPP-ACPF group demonstrated the greatest result, The BAG group came next, and the CPP-ACPF group came last.\n\nConclusion The BAG+CPP-ACPF group might be regarded as the best course of treatment for enhancing both the surface microhardness and mineral content (Ca, P), while the control group (Artificial saliva) showed the least satisfactory results in comparison. After demineralization, mineral content and microhardness decreased in all samples. Therefore, BAG+CPP-ACPF significantly improved the surface microhardness and mineral content.", "keywords": [ "BAG", "CPP-ACPF", "Remineralization", "white spot lesion." ], "content": "Introduction\n\nIn dentistry, an early demineralization of enamel, either on the surface or slightly below it, is mentioned as a “white spot lesion” (WSL), This is dental caries’ first obvious sign. These lesions’ reversibility suggests that substantial dental procedures may not be necessary to restore the tooth structure. WSLs must be addressed right away, though, since their surfaces may become porous and lose their original gloss, which raises issues regarding their aesthetics and their development.1 WSL is reversible in its early stages if remineralization mechanisms are initiated.2 Up to 96% of orthodontic patients have WSLs owing to the difficulty in cleaning teeth when attachments are present, leading to food retention and plaque accumulation.3 During subsurface demineralization, the enamel surface layer normally remains intact; nevertheless, if treatment is not received, it will eventually decompose into a real hollow.4 Several conservative techniques were developed to treat WSLs. fluoride (F) is thought to be the primary factor influencing remineralization. Fluorides can be applied in dentistry practices in a variety of ways, including toothpaste, gels, rinses, and varnishes. Of all these types that are accessible, varnish yields the best effects. Fluoride varnish increases fluoride concentration on the tooth surface by acting as a reservoir for fluoride. Recently, the application of substances like casein phospho-peptide-amorphous calcium phosphate (CPP-ACP) has been explored as a substitute for fluoride for promoting remineralization.5 CPPs are peptides formed from the casein milk protein. ACP is a form of calcium and phosphate, which is maintained by CPP.6,7 It may release fluoride, phosphate, and calcium in response to acidogenic challenges, slows demineralization, and promotes remineralization. It attaches very easily to soft tissues, plaque, saliva pellicle, and even the hydroxyapatite portion of enamel.8 One of the non-invasive techniques used to treat white spot lesions is preconditioning with air abrasion, which increases surface porosity and allows mineral ions to deposit into the lesion’s underlying body, improving the effectiveness of remineralizing agents by causing the lesion surface to become active.9 Owing to its unique qualities like remineralization capacity, bioactive glass 45S5 (BAG) was manufactured.10,11 WSLs were remineralized using gel and paste forms of BAG.12 To promote WSL remineralization, the surface was prepared using air abrasion, and then the application of bioactive glass. However, this method is time-consuming.13 BAG is a therapeutic powder made entirely of a bioactive glass called Novamin that reacts quickly on the surface to produce hydroxycarbonate apatite (HCA) in the presence of water. HCA and natural tooth minerals are chemically similar.14 Once set by eating and brushing the teeth, the majority of fluoride varnishes put on the enamel surface are removed easily. Retention on the tooth surface is essential for materials that successfully encourage remineralization, precondition the teeth surface by air abrasion with BAG, and then apply varnish consisting of fluoride, calcium, and phosphate to increase the efficacy of remineralization. It is a novel approach aimed at assessing the alteration in enamel following preconditioning the surface with BAG + CPP-ACPF. This study analyze the efficacy of BAG air abrasion preconditioning and CPP-ACPF varnish remineralization and contrast its effectiveness with BAG alone and CPP-ACPF varnish alone. Microhardness and energy dispersive spectroscopy (EDX) were used for analysis.\n\n\nMethods\n\nTwenty sound permanent maxillary first premolars were obtained from patients aged 12–20 years who underwent orthodontic treatment relying on a health research committee College of Dentistry University of Baghdad approved ethical protocol (Ref No. 724) dated 28/12/2022. The samples were cleaned with Tap water and polished using non-fluoridated slurry using prophylactic brushes attached to a slow-speed handpiece. The samples were then stored in a thymol solution (DR Thym™, InnuScience, Canada) of 0.1% (anti-microbial solution to restrict bacterial proliferation) for 1 week. Before use, it was kept in distilled water in a refrigerator at a temperature of 4 ± 0.1 °C until further use.15\n\nTen teeth were chosen for the study on EDX, and ten samples for the investigation on surface microhardness. Excluded from the study were teeth with cracks, stains, fluorosis, or developmental abnormalities (assessed using a light curing unit and a magnifying lens from (Fukai, China). The samples had comparable dimensions by measuring the mesiodistal (M-D) lengths using a digital Vernier (figure S3). Sections of the teeth were obtained to expose the lingual and buccal surfaces.16 Ten teeth were selected for the microhardness test, and four sections of enamel slabs were obtained from each tooth using a diamond disc bur for root removal and a large amount of water to prevent damage to the enamel. Enamel slabs were obtained using an XP precision sectioning saw (Pelco, USA). Their measurements were checked using a digital caliper (to get precise measurements (approximately 3 mm width × 3 mm length and 1.5 mm thick).17 The samples were embedded in acrylic resin using a silicone mold that had the following dimensions: 0.5 cm × 1 cm × 1 cm. The resin was poured into the mold (Figure-S4A), and the enamel slab (Figure-S4B) was placed inside, with the outer enamel surface exposed (Figure S4). For “EDX” another ten premolar teeth were used to obtain the elemental composition of the enamel and ultrastructural information. Six sections of enamel slabs, three each from the buccal and palatal surfaces (3mm length × 1.5 mm thickness and 1.5 mm width), were obtained from each tooth placed in resin molds. The samples EDX were obtained without polishing to protect the microstructure.18 Silicon carbide paper of 1200 grit was used for 10 s for polishing microhardness samples (Laryee Technology CO. LTD, China) under water cooling to obtain smooth and flat surfaces, followed by ultrasonic cleaning for 4 min to remove surface debris.19\n\nFor the microhardness study:\n\nGroup I (BAG): In 10 sound enamel slabs with existing WSL, the surface is conditioned using BAG (Sylc® powder) (Denfotex Research Ltd, Inverkeithing, UK).\n\nGroup II (BAG+CPP-ACPF): In 10 sound enamel slabs with existing WSL, the surface is conditioned using BAG and then using CPP-ACPF varnish (MI varnish-GC company- Japan).\n\nGroup III (CPP-ACPF): Ten sound enamel slabs with existing WSL were treated using CPP-ACPF varnish\n\nGroup IV (Artificial saliva): Ten sound enamel slabs with existing WSL were kept in the saliva without any intervention.\n\nFor EDX examination, sixty enamel slabs were used, and six groups were randomly assigned to receive each specimen from a single tooth:\n\n“Groups I to IV were similar to the groups in the microhardness study; additionally, the following two groups were included.”\n\nGroup V (Baseline): Ten sound enamel slabs.\n\nGroup VI (WSLs): Ten sound enamel slabs with existing WSL, without further intervention.\n\nThe samples were placed in a demineralized solution (Pioneer CO., Sulaymaniyah, Iraq) (acetic acid = 50 mM, NaCl = 100 mM, NaF = 1 ppm, NaN3 = 5 mM, NaH2PO4–2H2O = 10 mM, CaCl2-2H2O = 2.2 mM) to create an artificial white spot lesion. 1 M NaOH solution was used to adjust the pH to 4.5 r (SD Fujian, China) (Figure S5A, Figure S5B).20 For four days, the demineralization process was conducted at 37 °C. Following a 30-second rinse in deionized water, the samples were also preserved in water that had been distilled.\n\nA. Air abrasion with BAG group\n\nThe BAG powder Sylc® (Denfotex Research Ltd, Inverkeithing, UK) (Figure S2) which is a calcium sodium phosphor-silicate material with particle size ranging from (25 to 120 μm) was introduced to the reservoir according to the manufacturer’s recommendations. With the air stream encased in a deionized water barrier, performing air abrasion for 10 seconds with a circular movement using an Aqua Care Air Abrasion & Polishing System from VELOPEX International operating at an air pressure of 80 psi and a feed rate of 1 (Figure S6). The apparatus comprised a disposable plastic tip and a handpiece with a 0.8 mm diameter. Followed by washing with running water, which was stored in artificial saliva (20 mL per specimen) with a change of saliva every 24 hours for 14 days until final measurement. Artificial saliva (Pioneer CO., Sulaymaniyah, Iraq) contains (Potassium thiocyanate = 0.01; Sorbitol = 1, Potassium chloride = 1, Magnesium chloride = 0.05; Potassium phosphate = 0.04; Sodium carboxymethyl cellulose = 10, Sodium chloride = 1, Sodium fluoride = 0.0002,100 milliliters of boiling water and cooling, sodium carboxymethyl cellulose (985.5) mm of deionized water, was dissolved.\n\nB. Air abrasion with BAG and CPP-ACPF group\n\nAfter surface preconditioning with air abrasion as mentioned above, then applying CPP-ACPF varnish (MI varnish-GC company) to each sample (Figure S1), a single unit dosage packet has 1 mL of MI and 0.55 g/0.5 mL. There are 50 mg of NaF (22.6 mg F ion) in one varnish. it was allowed to air-dry for 20 seconds to ensure that it was set and became dry. To ensure that a consistent amount of fluoride varnish was applied to each specimen, a single-dose form was used. Subsequently, the slabs were maintained in saliva for 14 days, with a replacement of saliva every 24 hours.\n\nC. CPP-ACPF group\n\nAfter applying CPP-ACPF to each sample, it was allowed to air-dry for 20 s to ensure that it was set and became dry. To ensure that a consistent amount of fluoride varnish was applied to each specimen, a single-dose form was used. Subsequently, the slabs were maintained in saliva for 14 days, with a replacement of saliva every 24 hours.\n\nD. Control group\n\nSamples from this group were stored in saliva without any intervention.\n\nBefore the microhardness assessment, samples were kept in a moist environment. SMH was tested on each block surface. Vickers microhardness tester (Laryee, Model: HVS-1000, Beijing Time High Technology Ltd, China) was used to examine the hardness profile employing a 200-gf load and a pyramid-shaped indenter based on diamond squares for 15 s resulting in a diagonal shape on the surface (n=3 per sample) (Figure S7). The Vickers hardness numbers (VHN) were obtained for each sample after three marks were made at the middle, upper, and lower ends of the enamel surface while leaving a reasonably sound region in between.21\n\nThe recovery of enamel surface microhardness (% SMH) was calculated by Cury et al.22\n\n100 (SMH post-treatment − SMH caries)/baseline SMH − SMH caries\n\nEDX (INSPECT F50, FEI Company, Eindhoven, The Netherlands) was used to determine the elemental compositions of the produced enamel samples (voltage: 20 kV; working distance: 10 mm; spatial resolution: 100 nm; count time: 60 s).12 Three measurements were obtained for each sample and the mean values were calculated (Figure S8). The weight of calcium and phosphorus contents was calculated. EDX was obtained at the baseline group for intact enamel before demineralization and after demineralization (WSL group), and finally obtained after the remineralization period for each group.23\n\nData description, analysis, and demonstration were performed using Statistical software for Social Science SPSS version 21.\n\nShapiro–Wilk test was used to determine whether the data were distributed normally. For group comparisons, repeated-measures analysis of variance (ANOVA) was employed. To compare subgroups, Tukey’s honest significant difference (HSD) test was used for post-hoc analysis. Statistical significance was set at P<0.05.\n\n\nResults\n\nShapiro-Wilk test results for normality showed that surface Microhardness at (baseline, demineralization, and after remineralization) is normally distributed among groups as Table 1 indicates that there were no significant differences (p>0.05).\n\nThe surface microhardness mean value decreased at baseline and demineralization phase for each group and subsequently, it increased significantly at the remineralization phase. The greatest increase (larger % of recovery) from the demineralization to remineralization phase was in the BAG+CPP-ACPF group, followed by the BAG group and then the CPP-ACPF group, respectively, with little difference between these two groups, while the lowest was in the control group, as shown in Table 2 and Figure 1.\n\nANOVA showed no significant differences in the surface microhardness values among all groups at the baseline and demineralization phases (P>0.05), although significant statistical differences were noted between the groups (P difference among the four groups in the remineralization phase).\n\nTable 3 displays multiple pairwise comparisons of Microhardness by groupings across phases using the Tukey Honestly Significant Difference (Tukey HSD) test. Except for the control group (p>0.05), all groups had a greater mean difference in the remineralization phase as compared to the demineralization phase (p<0.05). All groups’ mean differences during the baseline phase, however, were greater than those at the remineralization phase (p<0.05).\n\nThe information from the EDX assessment for all groups about the weight percentages of phosphorous and calcium is shown in Figure 2. The weight percentage of both calcium and phosphorus decreased after demineralization. An increase in the weight percentage for Ca and P after remineralization in the BAG and CPP-ACPF groups compared with the WSL group, and the lowest was observed in the demineralization group (WSL), with significant differences among groups. The maximum values of Ca and P were recorded in the BAG+CPP-ACPF group. Minimal increase was noticed in the weight percentage of Ca, and P for groups treated using artificial saliva (the control group) as compared with the demineralization stage.\n\n\nDiscussion\n\nIt is crucial to take the most suitable course of action to protect tooth enamel and increase dental caries resistance; however, this can be difficult because of the intricate structural and functional interactions. This study investigated enamel remineralization using BAG air abrasion and CPP-ACP, and its effect on mineral content and microhardness. Basic chemical models have been utilized to produce artificial lesions in most in vitro cariology investigations.24 It offers clear benefits, such as easy research, time, controlled experimental conditions, and repeatability of the results. Because natural WSLs on enamel vary greatly in size, shape, and mineral content, natural WSL teeth were replaced using artificial WSLs in human premolars.25 To create artificial enamel lesions for cariology research, these lesions should be considered acceptable. Changes in mechanical properties typically coincide with a shift in the chemical makeup of demineralized enamel. Surface microhardness measurement is regarded as an accurate and effective tool for assessing tooth surface modification following the de- and re-mineralization processes.26 VHN obtained during the baseline microhardness measurements satisfied the typical enamel tissue VHN range of 248.5–272.25 which coincides with the results of Meredith et al.27 Following demineralization, the microhardness of each group of enamel samples decreased from 131 to 151.08. Within the constraints of this research, the findings showed that hardness tended to rise and then regain in the BAG+CPP-ACPF group, followed by BAG then by CPP-ACPF alone with a significant difference.\n\nThe control group showed the smallest difference. The results indicated significantly higher microhardness in the BAG group than that in the CPP-ACPF group. This coincides with an earlier in vitro study by Singla et al.28 that compared several remineralizing agents, and found that BAG is a more effective agent in treating initial caries. Furthermore, Mehta et al.29 discovered that Novamin remineralized the carious lesion more successfully than CPP-ACP, which may have been due to the bioactivity of BAG in the formation of hydroxycarbonate apatite (HCA) layer from its reactions with tissue fluids. Bioglasses that come in contact with bodily fluids cause diverse hydrated silicate species, as well as Phosphate, calcium, and sodium, to dissolve and leach quickly from the glass surface. A poly-condensed silica-rich gel layer was developed on the glass surface, offering calcium phosphate precipitation nucleation sites, the reduced CPP-ACPF hardness values when compared with BAG may be ascribed to its amorphous structure, which prevents it from adhering to the tooth enamel surface, as BAG does. Consequently, it does not remineralize the tooth surface over an extended period to increase the hardness.30 Dong et al.31 examined several types of BAG, one of which included 45S5, and demonstrated a mineralized layer with a 4 μm average thickness had formed, filling enamel porosities. The results of this research coincide with those of the study by Chabuk and Al-Shamma32 which concluded that BAG improved enamel hardness. The effect of CPP-ACPF on enamel hardness was much greater than that in the artificial saliva group). This finding coincides with Attar IJ, Ghaib NH,33 Al-Janabi, S.Z.; Al-Dahan,34 and Bandekar et al.35 demonstrating the effectiveness of CPP-ACPF in remineralizing artificial carious lesions. Reynolds et al.36 concluded that this is connected to the capacity of CPP to function as a bioavailable calcium and phosphate using ACP localization on the tooth’s surface and assisting in the preservation of a supersaturated state of the tooth enamel, whereby de-mineralization is prevented and remineralization is improved. Contrary to our findings, an in vitro investigation by Vyavhare et al.37 discovered that CPP-ACP does not exhibit a significant amount of surface remineralization. This discrepancy may have resulted from differences in experimental design and treatment regimens employed.\n\nThe weight percentages of calcium and phosphorus ions were used to assess mineral alterations on the enamel surface quantitatively. The results of EDX discovered that calcium and phosphorus declined after demineralization, referring to rapid loss of minerals, and rising following remineralization in all groups, showing a mineral gain. The BAG+CPP-ACPF group had the highest mean calcium and phosphorus levels, followed by the BAG and CPP-ACPF groups, whereas the control and WSL groups had the lowest mean levels, with a significant difference between the groups. The average calcium and phosphorus levels were substantially higher in the BAG group than in the CPP-ACPF group. An in vitro method used in research by Narayana et al.38 revealed that bioactive glass had more efficacy in remineralization than CPP-ACPF. This explains that phosphate and calcium ions were continuously released into the surrounding environment for several days, acting as reservoirs for these ions. Burwell et al.39 concluded that the BAG released ions and changed into HCA for a maximum of 14 days, which was deficient in CPP-ACPF action. Moreover, the CPP-ACPF group displayed higher mean calcium and phosphorus values than the control group. This could be attributed to the capacity of the CPP-ACP complex to act as a transporter, carrying fluoride, calcium, and phosphorus ions to the tooth surface. Somasundaram et al.40 concluded that by depressing de-mineralization and promoting remineralization, the CPP-ACPF preserves the mineral saturation levels, especially those of phosphate and calcium, at the tooth surface. Because CPP-ACPF can remineralize surface lesions but not early enamel caries at the subsurface level, it can prevent fast calcium and phosphate precipitation, which lowers the calcium and phosphorus ratios. This is why the results of this research showed that CPP-ACPFF had lower calcium and phosphorus percentages than BAG. To the best of our knowledge, no investigations have been performed in the BAG+CPP-ACPF-treated group employing BAG to treat WSL before applying CPP-ACPF. The combined effect of BAG+CPP-ACPF significantly improved the surface microhardness and mineral content (calcium and phosphorus). The BAG rich in calcium, phosphate, and silica was gradually substituted by hydrogen ions, and CPP-ACPF acted as a transporter for calcium and phosphate to enhance remineralization of the enamel surface, providing a synergistic effect on the microhardness and mineral content of enamel and explain the results of this investigation.\n\nThis is an in vitro study, it is difficult to create an accurate and identical environment typical of the oral cavity with its multifactorial influences such as enzymes, plaque, salivary proteins, and continuous salivary flow, all of which have a substantial impact on the effectiveness of the materials employed and, eventually, the outcomes that are achieved. The intricacy and traits of enamel lesions might not be completely captured by the use of artificial lesions. The Sample size and duration of the study may affect statistical results. Further investigation is required to generalize the results of this research. A perfect proportion between the overall surface quality and hardness can also be maintained by assessing the efficacy of various polishing methods and investigating the use of surface modifiers.\n\n\nConclusion\n\nConsidering these results, it can be stated that the BAG+CPP-ACPF group demonstrated potential utility in increasing WSL remineralization, as evidenced by its ability to enhance enamel remineralization much better than the commercially available BAG and CPP-ACP groups. However, its clinical utility needs to be confirmed by additional in vivo testing.\n\nThis research project was approved by the research ethics committee of the College of Dentistry, University of Baghdad, Baghdad, Iraq. Ref. number: 724. Date: 28-12-2022. Written informed consent was obtained.\n\nFigure S1: (MI varnish) Casein PhosphoPeptide-Amorphous Calcium Phosphate (CPP-APCF)\n\nFigure S2: Bioactive glass 45S5 Sylc® powder\n\nFigure S3: Measuring the dimensions of the tooth\n\nFigure S4: A: silicon mold\n\nB: Enamel slab in an acrylic block\n\nFigure S5: A: Enamel slabs before demineralization\n\nB: Enamel slabs with Artificial WSL after demineralization procedure.\n\nFigure S6: AquaCare air abrasion device\n\nFigure S7: Vickers microhardness tester\n\nFigure S8: EDX device", "appendix": "Data availability statement\n\nFigshare: Efficacy of different remineralization agents on microhardness and chemical composition of enamel white spot lesion.\n\nThis project contains the following underlying data:\n\nI. Raw data for microhardness test: https://doi.org/10.6084/m9.figshare.25638120.v1. 41\n\nThis project contains the following underlying data: surface Microhardness at three time periods for each remineralizing agent: Baseline, after demineralization, and after remineralization.\n\nII. Raw data EDX results: https://doi.org/10.6084/m9.figshare.25669062.v1. 42\n\nThis project contains the following underlying data: surface mineral content (Ca, P) at the Baseline, after demineralization, and after remineralization for all groups.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nPictures of the material and equipment used in the study, https://doi.org/10.6084/m9.figshare.25638144.v1. 43\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nMendes AC, Restrepo M, Bussaneli D, et al.: Use of casein amorphous calcium phosphate (CPP-ACP) on white-spot lesions: Randomised clinical trial. Oral Health Prev. Dent. 2018 Jan 1; 16(1): 27–31. PubMed Abstract \| Publisher Full Text\n\nSelwitz RH, Ismail AI, Pitts NB: Dental caries. Lancet. 2007 Jan 6; 369(9555): 51–59. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nReynolds EC, Cai F, Shen P, et al.: Retention in plaque and remineralization of enamel lesions by various forms of calcium in a mouthrinse or sugar-free chewing gum. J. Dent. Res. 2003 Mar; 82(3): 206–211. Publisher Full Text\n\nVyavhare S, Sharma DS, Kulkarni VK: Effect of three different pastes on remineralization of initial enamel lesion: an in vitro study. J. Clin. Pediatr. Dent. 2015 Jan 1; 39(2): 149–160. PubMed Abstract \| Publisher Full Text\n\nNarayana SS, Deepa VK, Ahamed S, et al.: Remineralization efficiency of bioactive glass on artificially induced carious lesion an in-vitro study. J. Indian Soc. Pedod. Prev. Dent. 2014 Jan 1; 32(1): 19–25. PubMed Abstract \| Publisher Full Text\n\nBurwell AK, Litkowski LJ, Greenspan DC: Calcium sodium phosphosilicate (NovaMin®): remineralization potential. Adv. Dent. Res. 2009 Aug; 21(1): 35–39. 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Publisher Full Text" }	[ { "id": "295143", "date": "15 Jul 2024", "name": "Rehab Samir Salma", "expertise": [ "Reviewer Expertise Pediatric dentistry" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDear authors, first, thank you for this interesting topic. In general, the manuscript is well written.\nHowever, there are few points to be addressed.\n\nIntroduction: You should include a null hypothesis for the study.\nMaterials and methods: you should mention the type of this study. You didn’t mention sample size estimation. May be if the number of samples per group increased, this would have yield different results!! This could be confirmed if you did a sample size estimation. Please justify. There is lack of randomization. Results: Tables footnotes should be added.\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": "12286", "date": "03 Sep 2024", "name": "Rafal Ghanem", "role": "Author Response", "response": "Dear Dr. Rehab Samir Salma I would first like to thank you for reviewing my manuscript. I am very grateful for your comments. This is an in-vitro study. The null hypotheses state: There was no difference in enamel microhardness and mineral content between the experimental and control groups. While the alternative hypothesis states there was a difference in enamel microhardness and mineral content between the experimental and control groups Based on the outcomes derived from the current study, the null hypothesis is thus rejected. This is due to a clear and noteworthy variation in surface microhardness and mineral content observed across the various stages (baseline, demineralization, and remineralization), as well as within the three methodologies (BAG+CPP-ACPF, BAG, and CPP-ACPF). Sample size: Utilizing G power 3.1.9.7 (via Franz-Faul, Universidad Kiel program, Germany) with the power of study 80%, alpha error of probability 0.05, the correlation between time points is 0.5 and the effect size of F is 0.25 with four groups and three-time points, with all these conditions, the sample size is 36 samples, thus 40 samples for microhardness were enough for this study while 60 samples for EDX analysis Randomization: The distribution of enamel slabs for microhardness and EDX groups in a random manner. Each slab from the same tooth was distributed among the different groups in a random manner." } ] }, { "id": "311070", "date": "19 Aug 2024", "name": "Shahzad Ali Shah", "expertise": [ "Reviewer Expertise consultant restorative dentistry", "Associate professor", "Diploma in Medical education" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nBased on the information provided, 1. the study was well designed and executed. 2. The sample size mentioned was 20 which was divided into two groups. please explain, how the sample size was calculated, and what was the reason for extraction of these premolars? 3. the references should be updated according to the guidelines for authors stated in the journal website. 4. Some of the references are too old and should be replaced with new ones, here are some suggestions,\nShah SA et al, 2024 [Ref 1]\nAlessa N et al, 2024 [Ref 2]\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\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": "12287", "date": "03 Sep 2024", "name": "Rafal Ghanem", "role": "Author Response", "response": "I would like to thank you for your comment and for reviewing. The reason for teeth extraction is for orthodontic purposes and I mentioned that in the text. I add a sample size estimation. I replace the old reference with one of your suggestions. Thank you again for your worthy comment." } ] } ]	1	https://f1000research.com/articles/13-505
https://f1000research.com/articles/13-1003/v1	03 Sep 24	{ "type": "Research Article", "title": "The effects of new product quality choices and customer behavior on the in-house refurbishing model versus the outsourcing model", "authors": [ "Yuliana Yuliana", "Agista Ayuningtyas", "Nughthoh Arfawi Kurdhi", "Zailan Siri", "Suhaiza Zailani", "Yuliana Yuliana", "Agista Ayuningtyas", "Zailan Siri", "Suhaiza Zailani" ], "abstract": "Background Refurbishing encompasses the process of collecting used products, refurbishing them into new ones, and offering them to consumers. Within this framework, manufacturers can opt for either in-house refurbishing, managed internally, or outsource these operations to third parties and retailers.\n\nMethods Our study also takes into account the limited supply of remanufacturable products and incorporates customer behavior distinctions, differentiating between high-end and low-end customers in our models. The primary aim of this research is to formulate and analyze models for in-house refurbishing, refurbishing outsourcing to third parties, and refurbishing outsourcing to retailers. We seek to identify optimal solutions, conduct a comprehensive analysis, and implement strategies to maximize benefits. Additionally, we compare the in-house refurbishing model with the outsourcing refurbishing model. Leveraging multivariable function optimization techniques alongside the Karush-Kuhn-Tucker method, we endeavor to ascertain the optimal strategy, thereby facilitating a nuanced and methodical examination of the intricate dynamics governing profitability and sustainability within the refurbishing sector.\n\nResults Our study has applied rigorous mathematical modeling and optimization methodologies to identify optimal configurations for each model, aiming to enhance profitability across diverse parameters, including product quantities, quality selections, and pricing strategies.\n\nConclusions Our analysis underscores that the in-house refurbishing approach tends to yield superior profits for profit-oriented enterprises, whereas outsourcing refurbishing to retailers is conducive to meeting environmental sustainability goals. Furthermore, our investigation has considered pivotal factors such as the constrained availability of remanufacturable products and consumer behavior, with a particular emphasis on discerning preferences among high-end and low-end clientele. We also perform sensitivity analyses to assess the impact of parameter variations on optimal outcomes. Our findings yield three distinct refurbishing models: the in-house refurbishing model, suitable for profit-driven companies under specific production cost parameters, and the outsourcing refurbishing to retailers model, tailored for environmentally-conscious companies, contingent upon particular production cost parameters.", "keywords": [ "Sustainable Supply Chain", "Reuse", "Waste", "SUSTAINABLE SUPPLY CHAIN", "CLOSED-LOOP SUPPLY CHAIN", "MATH PROGRAMMING", "OPERATIONS MANAGEMENT", "OPTIMIZATION" ], "content": "Introduction\n\nThe concept of a circular economy has garnered increasing attention from policymakers, academia, and industry, particularly in the pursuit of a more sustainable society. Additionally, it has become a significant subject of academic research, with a substantial increase in the number of articles and publications on the topic in recent years. Early pioneers introduced key aspects of the circular economy, focusing on waste prevention, job creation, and efficient resource utilization within the industrial economy (Yin et al., 2023). Others discussed the term ‘circular economy’ in the context of sustainability within the economic system. Subsequent articles elaborated on various aspects of the circular economy, including its requirements, scope and levels, comparisons with the linear economy, and related concepts. More recently, diverse perspectives on the circular economy and its relationship with sustainability have been provided. The circular economy is defined as a regenerative framework that restricts resources, waste, emissions, and energy consumption by closing and narrowing material and energy loops. This framework offers an alternative to the traditional ‘make-use-dispose’ approach adopted by many industries. The circular economy’s objectives can be achieved through principles such as sustainable design, reuse, repair, refurbishing, recycling, and remanufacturing (Liu et al., 2023; Wrålsen & O’Born, 2023). However, it is argued that recycling alone may not be a sustainable solution due to the loss of value incurred during the production of new items. Several researchers are now examining closed-loop supply chain strategies, particularly refurbishing (or remanufacturing), as a means to contribute to the circular economy’s objectives. Refurbishing stands out as the only circular business model that provides products with the latest features and warranties. To date, the literature has addressed various issues related to remanufacturing, including production planning and control, marketing, and competition.\n\nRefurbishing stands out as a crucial procedure within sustainable production systems due to its capacity to diminish resource utilization, conserve energy, mitigate carbon emissions, and reduce production lead-time (Cesur et al., 2022; Singhal et al., 2020; Zhang et al., 2020). The refurbishing process entails acquiring used products from end-users once they reach the end of their current lifecycle, enabling the recovery of added value and the restoration of these products for functional use. Proficiently managing this procedure can yield substantial economic, ecological, and social advantages for manufacturing systems that are impossible to disregard. Consequently, the realm of refurbishing has become a pivotal focus of research for scholars on a global scale. In the refurbishing process, a used product undergoes a series of steps, including disassembly, sorting and cleaning, scanning, refurbishment or replacement, reassembly, and quality testing before re-entering the market. Refurbishing has the potential to deliver significant environmental, social, and economic advantages by extending the lifecycle of used products. Environmental benefits include a reduced carbon footprint and decreased energy and material consumption. For instance, refurbished products consume 85% less energy than the production of equivalent new products. Additionally, refurbishing engines can lead to a reduction of 565 kg of CO2 emissions and 55 kg of steel usage. It is possible to refurbish 7-11 more units using the same amount of energy and materials as manufacturing new ones. Furthermore, refurbishing benefits society by providing employment opportunities for both unskilled and skilled labor, while also offering economic benefits through the lower prices of refurbished products. Typically, refurbished items are sold at prices as low as 60% of the cost of new items (Singhal et al., 2020).\n\nA multitude of original equipment manufacturers (OEMs), such as GE, Xerox, HP, IBM, and Caterpillar, have actively participated in refurbishing operations. While these manufacturers possess technological and brand advantages in refurbishing, the process of collecting used products incurs higher transportation and inventory costs when manufacturers are geographically distant from their product-selling locations. Nevertheless, some OEMs display reluctance in engaging directly in refurbishing or outsourcing to third-party refurbishers (TPRs) (Fang et al., 2023; He et al., 2020; Teng & Feng, 2021; Yang et al., 2022; Zou et al., 2019). This hesitancy often arises due to patent protection, as TPRs are obliged to pay fixed or variable technology authorization fees to the OEMs for obtaining the necessary authorization. A pivotal challenge for TPRs lies in attracting OEMs for collaboration, contingent on their refurbishing advantages. For instance, Flex received the “Sustainable Development Leadership Award 2020” for the third consecutive time, attributing its success to an Internet of Things (IoT) device known as Smartbin, developed by its subsidiary, Sinctronics. Smartbin facilitates the collection of electronic materials for refurbishing or remanufacturing, enabling the management of electronic waste and pollution in the IT industry. This innovation streamlines the electronic waste collection process and reduces return costs by 40% during testing. Consequently, TPRs’ refurbishing processes become more cost-effective and environmentally sustainable. Additionally, TPRs can attain superior return quality compared to OEMs by expanding their recycling channels through dedicated recycling platforms. Therefore, in practice, TPRs possess a distinct competitive advantage in refurbishing, marked by both cost-effectiveness and quality-effectiveness, which significantly impacts the choices made by OEMs, resulting in divergent outcomes.\n\nWhether refurbishing takes place internally or is outsourced, it has a notable impact on the sale of new products since refurbished items, typically of lower quality, are consistently priced lower than their new counterparts. This reduced willingness-to-pay for refurbished products among consumers can provide Original Equipment Manufacturers (OEMs) with an opportunity to access a new market segment and expand their market share. For instance, Robert Bosch Tool ventured into the lower-end market segment, where Bosch did not have a significant presence, by offering refurbished products. This strategy also helps fend off competition from inexpensive imports. The lower price point of refurbished goods may attract price-sensitive consumers, leading them to prefer these options over new products. Auction results suggest that consumers are willing to pay 15.3% less for refurbished products compared to new ones. A manager at a global PC OEM is confident that for every four refurbished products sold, one new product sale is cannibalized. This price-based cannibalization issue fundamentally stems from the quality distinction between new and refurbished products. It is important to note that refurbished products are derived from the rejuvenation of end-of-life products or their components. Consequently, any improvement in the quality of new products also contributes, to some extent, to an enhancement in the quality of refurbished products (Atasu & Souza, 2013; Feng et al., 2020; He et al., 2020; Kleber et al., 2018; Örsdemir et al., 2014). Unlike quality distinctions observed among independent product categories, the quality of refurbished items is intrinsically linked to that of the original products. Therefore, in their efforts to access new market segments through refurbishing and address the challenges of cannibalization stemming from refurbished products, Original Equipment Manufacturers (OEMs) often leverage consumers’ preferences for varying product quality. For example, Lexmark adopted a strategy of rendering their end-of-life cores non-reusable for refurbishing to mitigate the issues associated with cannibalization from refurbished products. Conversely, intriguingly, to maintain and expand their foothold in new market segments, some OEMs have strategically invested in producing high-quality cores designed for reuse in refurbishing. For instance, Xerox invested in modular design to ensure the feasibility of refurbishing used cores. Likewise, numerous renowned OEMs, including Cummins, Caterpillar, and Electrolux, have undertaken initiatives to optimize and streamline the refurbishing process, thereby enhancing its overall efficiency.\n\nResearchers have acknowledged the notable contrast in how consumers perceive the quality differentiation between new and refurbished products (McKie et al., 2018). As a result, consumer conduct regarding these goods assumes a pivotal role in the pricing matter, as it can affect the demand for both product categories (Belbağ & Belbağ, 2023; Ke & Yan, 2022; Wang et al., 2020). Many previous studies have operated under the assumption that consumer behavior is primarily influenced by their willingness to pay (WTP), implying that the demand for refurbished products diminishes as product prices rise. These studies generally adopt the conventional WTP-based demand assumption. In contrast, our paper expands upon previous cannibalization analyses by introducing a multi-segment cannibalization demand model. In this model, the firm’s decision-making process involves estimating the portion of consumers who, given a specific price difference, would transition from purchasing new products to opting for refurbished ones. We delve into the impact of market segmentation on the optimal strategy within this context. In line with the investigations conducted by Ovchinnikov (2011) and Kurdhi et al. (2023), the presence of refurbished products at reduced price points triggers concerns regarding potential sales cannibalization for higher-margin new products. Consequently, numerous companies opt not to introduce refurbished products alongside new ones. Nonetheless, by astutely integrating both refurbished and new products into their product range, firms can effectively target distinct customer segments and secure sales from individuals seeking cost-effective refurbished alternatives. Despite the potential for some attrition in sales of new products, diligently calibrated pricing strategies and refurbishing volumes can result in substantial overall financial benefits for the company. The consumer market is characterized by two distinct customer segments: high-end and low-end. High-end customers are open to purchasing new products but may also contemplate refurbished options. In contrast, low-end customers exclusively favor refurbished products. It is noteworthy that companies generally uphold consistent and unchanging pricing structures for their new products, and the refurbishing process typically exerts no observable influence on pricing, procurement, or other determinants related to new product offerings.\n\nOEMs must also consider the presence of used products within a specific region when evaluating refurbishing programs. The degree of market presence significantly influences the collection efforts of third parties (3Ps) and can potentially restrict their access to used products. A national survey conducted by Saphores et al. (2009) revealed that, on average, each household in the United States had 4.1 small and 2.4 large electronic waste (e-waste) items stored, surpassing the estimates provided by the United States Environmental Protection Agency (US EPA). This suggests that the backlog of e-waste in the United States may be larger than previously believed. Sabbaghi et al. (2015) also noted that commercial consumers tend to accumulate more stored computers, regardless of brand or capacity, compared to household consumers. Furthermore, (Sabbaghi et al., 2016) highlighted that consumers often retain their unwanted electronic devices even after their last usage. According to the US EPA, e-waste has surged by 120% over the past decade, with only 25% of it being collected for recycling or reuse (PMR). Consequently, there exists a substantial reservoir of used products that could potentially be collected. In our investigation, we analyze refurbishing program strategies under two conditions: unrestricted access to used products and constrained access to them.\n\nIn this study, a model was devised to explore the dynamics of in-house refurbishing versus outsourcing refurbishing to third parties, as well as outsourcing refurbishing to retailers. The study also investigates consumer behavior and cannibalization functions within these models, distinguishing between two consumer segments: high-end customers and low-end customers. Furthermore, the research takes into account constraints on the supply of used products. The primary objective is to determine the optimal pricing and quantity strategies for new and refurbished products, aimed at maximizing profits from their sales based on the formulated model. By analyzing these factors comprehensively, this study contributes valuable insights into the strategic decision-making processes involved in product refurbishing, thereby providing a foundation for businesses to optimize their operations and enhance profitability in an increasingly competitive market environment.\n\n\nModel Assumption and Notation\n\nThis research delves into three distinct cases: Model In-House Refurbishing (Model I), Model Refurbishing Outsourcing to Third-Party (Model T), and Model Refurbishing Outsourcing to Retailer (Model R). We initiated the model construction process by outlining several key assumptions.\n\nIn Model I, manufacturers are the sole participants, while Model T comprises both manufacturers and third parties, and Model R involves manufacturers and retailers.\n\nIn the in-house refurbishing model, manufacturers are responsible for both the production of new products and refurbished products. In the outsourcing refurbishing model to third parties, manufacturers focus on the production of new products, while third parties take on the task of producing refurbished products. In the outsourcing refurbishing model to third parties, the third party receives a license fee from the manufacturer for their involvement. Moving to the outsourcing refurbishing model with retailers, manufacturers are primarily engaged in the production of new products, with refurbished products being manufactured by retailers. In this particular model, manufacturers exclusively sell new products to retailers. Additionally, retailers are responsible for selling both new products and refurbished products to consumers.\n\nA quality choice is determined by the manufacturer.\n\nThe production cost per unit of a new product of a certain quality level is represented as a variable, denoted as s, and it is defined as s2. If k is the unit price scaling parameter, the acquisition cost of refurbished devices is given by kαs2, with α belonging to the interval (0,1). This cost function structure embodies several significant characteristics when both refurbished and new products are introduced simultaneously. Firstly, if there is an enhancement in the quality of new products, there will be a corresponding improvement in the quality of refurbished products to a certain degree. Thus, the cost of refurbished products is inherently linked to the quality of new products. Secondly, due to the fact that refurbishing products necessitates fewer raw materials and less energy compared to the production of new products, the cost function outlined above underscores that refurbishing a unit is more cost-effective than manufacturing a new one.\n\nThere exist constraints on the supply of remanufacturable products, denoted by 0≤qr≤δqn, where δ represents the proportion of consumables that can be collected and subsequently transformed into refurbished products.\n\nRefurbished products are derived from remanufacturable products, which means that the supply of these products is constrained by the quantity of new products sold to consumers. However, not all remanufacturable products are eligible for conversion into refurbished products due to quality standards. This variability in eligibility can result in production levels that are less stable. To efficiently utilize resources in the production process, manufacturers must conduct observations and analyses focused on optimizing production.\n\nThe demand functions for both new and refurbished products have been derived based on the segmentation of customer behavior when it comes to their preferences for purchasing either new or refurbished items, where\n\nIn this study, it is important to note that the values of pn (the price of new products) and pn (the price of refurbished products) are not considered constant. There exists a potential market denoted as a, which represents a certain number of consumers interested in the products being offered. Additionally, there is a quality level s associated with new products, determined by the manufacturer, which influences both the number of new consumers opting for refurbished products and the number of high-end customers who would switch to refurbished products if they were available. The demand for new products is determined by the number of high-end customers purchasing new products, denoted as q, minus the number of high-end customers switching to buying refurbished products, represented as γ(pr)q. On the other hand, the demand for refurbished products is derived from the sum of consumers buying refurbished products and high-end customers transitioning to refurbished products. This description leads to the formulation of the inverse demand function, which can be expressed as follows:\n\nThe existence of new products and refurbished products that compete in the market causes a cannibalization effect.\n\nThe level of cannibalization in this study is influenced by the quality choice so that the cannibalization function becomes\n\nThe fundamental models are illustrated in Figure 1, and all related variables and parameters are presented in Table 1.\n\n(a) Model I, (b) model T, and (c) model R.\n\nMethodological Approach: Formulation and Resolution of Models This research centers on the refurbishing and quality choice models employed by manufacturers. In this subsection, we will develop a refurbishing model that incorporates the consideration of quality choice. The model is solved using the Stackelberg game with a backward induction procedureλand Karush-Kuhn-Tucker (KKT). The Karush-Kuhn-Tucker (KKT) conditions are an extension of the Lagrange method. The KKT conditions can be applied in solving both maximum and minimum problems with inequality constraints. Solving problems using the Karush-Kuhn-Tucker method also requires the Lagrange multiplier factor, denoted by λ. Functions with inequality constraints pose the following problem:\n\nThe Lagrange function for solving these constraints is:\n\n1. λ≥0,\n\n2. ∇f(x)−λ[∇g(x)]=0,\n\n3. λigi(x)=0, for i=1,2,…,m,\n\n4. gi(x)≤0.\n\nIn this case, if λi>0, then gi(x)=0, and if λi=0, then gi(x)<0. If the problem is to minimize the objective function, then conditions 2, 3, and 4 are also necessary conditions for the Karush-Kuhn-Tucker method, but condition 1, the Lagrange multiplier λi, must be negative.\n\nIn the in-house refurbishing model, producers derive their profits from the revenues generated through the production of both new and refurbished products. Producers make decisions regarding the quantity of new products and refurbished products to manufacture, oversee the production process, and subsequently sell these products to consumers. The manufacturer’s problem in this context can be outlined as follows:\n\nThe profit function represented by Equation (5) is subject to a single constraint, leading to two distinct cases: 21=2 cases, λ=0and λ>0. Through the utilization of Equations (3) and (4) and based on the underlying assumptions, we arrive at the formulation of the Lagrange function as follows:\n\nIn this context, the symbol λ denotes a Lagrange multiplier. The profit function PmI is concave concerning the variables qnI and qrI, indicating the presence of a singular optimal solution. Consequently, we can establish the KKT optimality conditions as follows, which represent necessary conditions for optimality in constrained optimization problems, incorporating both equality and inequality constraints, thereby facilitating a comprehensive analysis of the model’s optimal solution.\n\nBased on Equation (8)-(11), the optimal values for qnI∗,qrI∗,sI∗,pnI∗,prI∗,PmI∗are computed for each scenario by applying the four Kuhn-Tucker conditions.\n\nIn the in-house refurbishing model there are two cases namely partial refurbishing when only part of the consumable product can be reprocessed into refurbished products (λ = 0) and full refurbishing when all consumable products can be reprocessed into refurbished products (λ > 0) so that there are two optimum solutions:\n\n(i) In the in-house refurbishing model, the manufacturer performs partial refurbishing (λ = 0) when the production cost parameter scale k< sR(a−qδ)+b(1+δ)wnRsR2α(b+l+bδ). The optimum values for the price of new products, price of refurbished products, quality choice, quantity of new product production, production quantity of refurbished products, and manufacturer profit are as follows.\n\n(ii) In the in-house refurbishing model, the manufacturer performs full refurbishing (λ > 0) when the cost parameter scale k> sR(a−qδ)+b(1+δ)wnRsR2α(b+l+bδ). The optimum value for the price of new products, prices of refurbished products, quality choice, production quantities of new products, production quantities of refurbished products, and manufacturer profits are as follows.\n\nIn the outsourcing refurbishing model to third parties, the manufacturer’s profit is generated solely from the production revenue of new products. Manufacturers are responsible for the production of new products, which are subsequently sold to both consumers and third parties. In this model, manufacturers exclusively make decisions regarding the quantity of new products to manufacture. The manufacturer also sets the license fees that third parties must pay when conducting the refurbishing process. On the other hand, the profits earned by third parties are derived from the sales of refurbished products. The problems faced by the manufacturer and third parties can be described as follows:\n\nThe profit function represented by Equation (5) is subject to a single constraint, leading to two distinct cases: 21=2 cases, λ=0and λ>0. Through the utilization of Equations (3) and (4) and based on the underlying assumptions, we arrive at the formulation of the Lagrange function as follows:\n\nIn this context, the symbol λ denotes a Lagrange multiplier. The profit function PtT is concave concerning the variables qnI and qrI, indicating the presence of a singular optimal solution. Consequently, we can establish the Karush-Kuhn-Tucker (KKT) optimality conditions as follows:\n\nBased on Equation (27)-(30), the optimal values for qnT∗,qrT∗,sT∗,pnT∗,prT∗,PmT∗,and PrT∗are computed for each scenario by applying the four Kuhn-Tucker conditions.\n\nIn the refurbishing outsourcing to third-party model there are two cases namely partial refurbishing when only part of the consumable product can be reprocessed into refurbished products (λ = 0) and full refurbishing when all consumable products can be reprocessed into refurbished products (λ > 0) so that there are two optimum solutions:\n\n(i) In the refurbishing outsourcing to third-party, the manufacturer performs partial refurbishing (λ = 0) when the production cost parameter scale k<−hTl+(a+q)sT−(sT+2sTδ)qnTlsT2a. The optimum values for the price of new products, price of refurbished products, quality choice, quantity of new product production, production quantity of refurbished products, and manufacturer profit are as follows.\n\n(ii) In the refurbishing outsourcing to third-party, the manufacturer performs partial refurbishing (λ = 0) when the production cost parameter scale k> −hTl+(a+q)sT−(sT+2sTδ)qnTlsT2a. The optimum values for the price of new products, price of refurbished products, quality choice, quantity of new product production, production quantity of refurbished products, and manufacturer profit are as follows.\n\nIn the outsourcing refurbishing model to retailers, the manufacturer’s profit is derived from the revenue generated through the production of new products. Manufacturers produce new products and sell them to retailers. In this model, manufacturers exclusively make decisions regarding the quantity of new products to manufacture. Manufacturers also establish wholesale prices, which are the prices at which new products are sold to retailers for the purpose of refurbishing. On the other hand, retailers’ profits stem from the sales of both new products and refurbished products. The problems faced by the manufacturer and retailer can be outlined as follows:\n\nThe profit function represented by Equation (5) is subject to a single constraint, leading to two distinct cases: 21=2 cases, λ=0and λ>0. Through the utilization of Equations (3) and (4) and based on the underlying assumptions, we arrive at the formulation of the Lagrange function as follows:\n\nIn this context, the symbol λ denotes a Lagrange multiplier. The profit function PrR is concave concerning the variables qnR and qrR, indicating the presence of a singular optimal solution. Consequently, we can establish the Karush-Kuhn-Tucker (KKT) optimality conditions as follows:\n\nBased on Equations (49)-(52), the optimal values for qnR∗,qrR∗,sR∗,wnR∗,pnR∗,prR∗,PmR∗,and PrR∗are computed for each scenario by applying the four Kuhn-Tucker conditions.\n\nIn the refurbishing outsourcing to retailers model there are two cases namely partial refurbishing when only part of the consumable product can be reprocessed into refurbished products (λ = 0) and full refurbishing when all consumable products can be reprocessed into refurbished products (λ > 0) so that there are two optimum solutions:\n\n(i) In the refurbishing outsourcing to retailers, the manufacturer performs partial refurbishing (λ = 0) when the production cost parameter scale k< sR(a−qδ)+b(1+δ)wnRsR2α(b+l+bδ). The optimum values for the price of new products, price of refurbished products, quality choice, quantity of new product production, production quantity of refurbished products, and producer profit are as follows.\n\n(ii) In the refurbishing outsourcing to retailers, the manufacturer performs partial refurbishing (λ = 0) when the production cost parameter scale > sR(a−qδ)+b(1+δ)wnRsR2α(b+l+bδ). The optimum values for the price of new products, price of refurbished products, quality choice, quantity of new product production, production quantity of refurbished products, and producer profit are as follows.\n\n\nModel analysis\n\nIn this section, our analysis will focus on investigating the equilibrium decisions within Models I, T, and R. Additionally, we will extend the scope of our research by incorporating considerations related to economic and environmental sustainability.\n\n\n\nIn Model I, Model T, and Model R the manufacturer produces and sells refurbished products ranging from 0≤qr≤δqn.\n\nThe profits earned by producers come from the sales of both new and refurbished products. Consequently, producers must sell a minimum of 0 new and refurbished products. In the case of in-house refurbishing, manufacturers produce and sell qn and qr new and refurbished products without the condition of the production cost parameter, k. This demonstrates that the production cost parameter does not influence the quantity of products required for maximizing profits during the production and sale of both new and refurbished products. This condition similarly applies to refurbishing outsourcing to third parties and retailers. When it comes to producing and selling new and refurbished products, the production cost parameter does not impact the quantity of products that third parties and retailers need to produce to achieve maximum profit.\n\nThe optimum quantity of new product in Model T is higher than that in Model I and Model R (qnR∗<qnI∗<qnR∗) with production cost parameter condition k>k1 with\n\nIn refurbishing activities, manufacturers face competition from refurbished products. As a result, they tend to increase the production of new products to counteract this competition. In the context of outsourcing refurbishing activities to third parties, manufacturers strive to boost the production of new products to remain competitive with third-party providers. Conversely, in the in-house refurbishing model, even though there is competition between new and refurbished products, all operations are overseen by the manufacturers themselves, moderating competition for maximum profits. Similarly, in the refurbishing outsourcing model to retailers, the sale of both new and refurbished products is managed by retailers, resulting in reduced competition for profits.\n\nThe optimum quantity of refurbished product in Model T is higher than that in Model I and Model R (qrR∗<qrI∗<qrR∗) with production cost parameter condition k>k1 with\n\nIn this study, it is assumed that all new products can be reprocessed into refurbished products. However, there is δ, which is the proportion of the number of new products that can be processed into refurbished products or can be said there are constraints in the supply of consumable products. In accordance with Proposition 2 and Proposition 3, where the number of new products that qnR∗<qnI∗<qnT∗, then the number of refurbished products qrR∗<qrI∗<qrT∗because the higher the number of new products, the higher also refurbished products that can be produced.\n\nQuality choice of new products in Model T is higher than that in Model I and Model R with production cost parameter condition k<k2.\n\nIn outsourcing refurbishing activities to third parties, the level of quality choice for new products is higher than in-house refurbishing and outsourcing refurbishing to retailers. This higher level of quality choice arises due to competition between third parties and manufacturers. Manufacturers enhance the quality of new products to enable them to compete effectively with refurbished products in the market. The presence of competition between manufacturers and third parties in product marketing results in a cannibalization effect. To mitigate the effects of cannibalization, manufacturers can increase the level of quality choice. As quality choice increases, both the price and quality of new products rise. Consequently, the price of high-quality refurbished products also increases. Some consumers prioritize quality when making purchase decisions, so increasing product quality can boost demand. In the outsourcing refurbishing model to retailers, the quality choice is determined by the manufacturer and remains the same as in the in-house refurbishing model. This is because in the outsourcing refurbishing model to retailers, producers exclusively sell to retailers, eliminating competition between producers and retailers for consumers.\n\n\n\nThe price of new products in Model I is lower than that in Model T and Model R (pnR∗<pnI∗<pnR∗) under conditions of price elasticityl2<l<l1 with\n\nBased on Proposition 5, it can be observed that both the outsourcing refurbishing model to third parties and the outsourcing refurbishing model to retailers feature higher prices compared to the in-house refurbishing model. This price disparity arises because third parties are obligated to pay licensing fees to manufacturers. Consequently, in order to turn a profit, third parties must raise the prices of new products. Additionally, in the outsourcing refurbishing model to retailers, despite manufacturers providing wholesale prices to retailers, the latter incur additional costs associated with the refurbishment process and marketing efforts for new or refurbished products. As a result, the overall costs incurred are higher.\n\nThe price of refurbished products in Model I is lower than that in Model T and Model R (prR∗<prI∗<prR∗) under conditions of price elasticityl4<l<l3.\n\nBased on Propositions 5 and 6 it can be seen that the higher the price of new products, the higher the price of refurbished products. This is influential because the two prices are interconnected and the high price of new products causes high prices of refurbished products.\n\nManufacturer’s profits for Model I are higher than those for the Model T and Model R (pmI∗<pmT∗<pmR∗) with production cost parameter condition k<k3.\n\nIn the in-house refurbishing model, the entire operation is under the producer’s control, allowing them to tailor the strategy for quantity and quality while effectively addressing the challenges of cannibalization. On the other hand, in the outsourcing refurbishing models to third parties and retailers, manufacturers delegate refurbishing operations to external entities, which can intensify the cannibalization effect and potentially foster competition between these parties. This increased competition can, in turn, result in reduced producer profits when engaging in outsourcing refurbishing activities, whether to third parties or retailers.\n\nThe profitability of manufacturer in Model I is higher than the combined profits of manufacturer and third-party in Model T and Model R ((pGI∗>pGT∗>PGR∗) with production cost parameter condition k<k4.\n\nBased on Proposition 8, it can be observed that the profit of producers in the in-house refurbishing model exceeds the combined profits of producers and third parties in the outsourcing refurbishing model to third parties, as well as the combined advantages of manufacturers and retailers in the refurbishing model outsourcing to retailers. In the in-house refurbishing model, manufacturers obtain sales profits from both new and refurbished products. Conversely, in the outsourcing refurbishing model to third parties, sales are shared with third parties, intensifying the competition between new products and refurbished products. This heightened competition leads to a reduction in the quantity of new products and an increase in refurbished products due to the cannibalization effect. In the refurbishing model outsourcing to third parties, manufacturers impose license fees on third parties. However, the profits earned by third parties are not sufficiently high to cover the profits that should be earned by producers. Furthermore, in the refurbishing outsourcing model to retailers, manufacturers exclusively sell new products to retailers at reduced wholesale prices, while retailers sell both new and refurbished products to consumers. Similar to the outsourcing refurbishing model to third parties, cannibalization occurs, causing a decrease in the quantity of new products and an increase in refurbished products. The sales made by producers to third parties are naturally lower due to their wholesale pricing structure. Furthermore, the proceeds from retailer sales also fall short of covering the profits that manufacturers would otherwise receive.\n\n\n\nThe impact on the environment of the Model T is greater than that of Model I and Model R (ET>EI>ER) with production cost parameter condition k>k1 with\n\nNew products and refurbished products will have an impact on the environment. When carrying out refurbishing activities, it is not always beneficial for the environment. Even though refurbished products use less raw materials, when they reach above the threshold, the environmental impact of the product use phase in Model T is greater than Model I and Model R.\n\n\nNumerical experiment and results\n\nThe application of the three refurbishing models that have been constructed and obtaining the optimum solution is to maximize profits. In this application, the product produced is an electronic product in the form of a laptop from Apple, namely the MacBook Pro Laptop M2. The consumer’s decision to buy refurbished products is 15.3 percent lower than new products, so it is assumed that there is a market potential when there are no refurbished products q=100, and a market potential when there are refurbished products, namely a=85. There is a production cost parameterk=1. There are consumable product supply constraints, namely δ with δ∈(0,1). Furthermore, there is a proportion of the cost of refurbished products, namely α and α∈(0,1). In this study, it is assumed that the value ofδ=0.5 and α=0.9. In market competition, there are two categories of consumers, namely high-end customers, namely consumers who only buy new products or refurbished products, and low-end customers, namely consumers who only buy refurbished products. Competition that occurs between new products and refurbished products causes cannibalization. The effect of cannibalization in this study was 2 and l=2.5. In the outsourcing refurbishing model to a third party, the third party must pay a license fee of 500. Referring to Yan et al. [11],em=180,er=125,eu=110 and ed=0.005. Following that, a graph depicting the difference in the variable values of the three models on the refurbishing costs is presented in Figures 2 to 7.\n\nFigure 2(a) shows a comparison of the number of new products in the three models. Based on the figure, Model T shows that the greater the value of the production cost parameter k, the greater the quantity of new products provided by producers. Whereas in Model I and Model R, an increase in the value of k has no effect on the quantity of new products. In accordance with the Proposition 2, the figure shows that qnR∗<qnI∗<qnT∗with the condition of the production cost parameter k>k1. The intersection point in the figure shows the intersection of Model I and Model T, where the quantity of new products in Model T will be higher than Model I when the production cost parameter k>0.2. The graph shows that the quantity of new product Model I is higher than Model R for all conditions of production cost parameter k. Meanwhile, the quantity of new product Model T is higher than Model R for all conditions of production cost parameter k.\n\nFigure 2(b) shows a comparison of the number of refurbished products in the three models. Based on the figure, Model T shows that the greater the value of the production cost parameter k, the greater the quantity of refurbished products provided by manufacturers. Whereas in Model I and Model R, the increase in the value of the production cost parameter k has no effect on the quantity of refurbished products. According to Proposition 3, the figure shows that qrR∗<qrI∗<qrT∗with the cost parameter condition k>k1.The figure shows the intersection of Model I and Model T, where the quantity of refurbished products in Model T will be higher than Model I when k>0.2. The graph shows that the quantity of refurbished products in Model I is higher than Model R for all conditions of the k production cost parameter. Meanwhile, the quantity of refurbished products for Model T is higher than Model R for all conditions of production cost parameter k.\n\nFigure 3 is a graph showing the quality choices of Model I, Model T, and Model R. Based on the graph, the greater the value of k, the greater the quality choice of each model decreases. The graphics also prove the Proposition 4 that sI∗=sR∗<sT∗ when k<k2=1.9. In the graph there is also an intersection point which shows that sI∗=sR∗<sT∗ when the production cost parameter condition is k<k2.\n\nComparison of new product prices in the three models is depicted in Figure 4(a). The figure shows that the higher the value of price elasticity l, the lower the price of new products. This shows that when the price elasticity between the new product and the refurbished product is higher, the price of the new product decreases which then causes a decrease in the price of the refurbished product. The picture is proof of the Proposition 5 that pnI∗<pnT∗<pnR∗with price elasticity that l2<l<l1. Comparison of the price of refurbished products in the three models is depicted in Figure 4(b). The figure shows that the higher the price elasticity, the lower the price of refurbished products. This shows that when the price elasticity is between new products and refurbished products, the price of refurbished products falls. This assumption relates to the price of a new product where when the value of l increases, the price of the new product decreases. The figure is a proof of Proposition 5 that prI∗<prT∗<prR∗with price elasticity that l4<l<l3.\n\nThe profit obtained by the producers in the three models is presented in Figure 5(a). Based on the figure, the higher the value of the production cost parameter k, the lower the manufacturer’s profit. The graph proves Proposition 7. The production cost parameter value k contained in the graph is the intersection point which proves that PI∗>PI∗>PI∗ with condition k<k3. The combined gains obtained in the three models are presented in Figure 5(b). Based on this figure, the higher the value of the production cost parameter k, the lower the producer’s profit. The graph illustrates Proposition 8. The production cost parameter value k contained in the graph is the intersection point which proves thatPGI∗>PGT∗>PGR∗with conditionk<k4.\n\nThe impact on the environment caused by refurbishing activities depends on the number of new and refurbished products available. The environmental impacts of Model I, Model T, and Model R are presented in Figure 6. The figure illustrates Proposition 9 that ET∗>EI∗>ER∗. The intersection point on the graph shows the condition of the production cost parameter k resulting in ET∗>EI∗>ER∗where the impact on the environment in Model T will be higher than Model I when k>k1. The graph shows that the environmental impact of Model I is higher than Model R for all conditions of the production cost parameter k. Meanwhile, the impact on the environment model T is higher than Model R for all production cost parameter conditions k. Model T shows that the greater the value of the production cost parameter k, the greater the impact on the environment. Whereas in Model I and Model T, the increase in the value of the production cost parameter k has no effect on the impact on the environment.\n\n\nSensitivity analysis\n\nIn this section, the parameter value of the potential market for refurbished products (a), the demand for high-end customers when there are no refurbished products (q), the parameter of production costs (k), the coefficient cannibalization (b), price elasticity (l), and the proportion of refurbished product production costs to new product production costs (α) will be changed. This is done to determine how changes in parameter values affect the choice variable in the profit function.\n\nChanges in market potential include variations in product quantity, price, quality choices, and producer’s profits.\n\nBased on the graphs in Figures 7(a) and 7(b), it can be observed that an increase in the potential market for refurbished products leads to an increase in the quantities of both new and refurbished products. Figure 7(a) illustrates the increase in new products when there is a change in the potential market for refurbished products. The quantity of new products in Model I has risen from 26.19 to 40.47, with an average increase of 0.54%. In Model T, the quantity of new products increased from 32.90 to 43.06, with an average increase of 0.3%, while in Model R, the quantity of new products increased from 13.09 to 20.20, with an average increase of 0.54%. In line with the increasing quantity of new products, the quantity of refurbished products has also risen, as shown in Figure 7(b). The quantity of refurbished products in Model I increased from 13.09 to 20.23, with an average increase of 0.54%. Model T saw an increase in the quantity of refurbished products from 16.45 to 21.53, with an average increase of 0.3%, while Model R experienced an increase in the quantity of refurbished products from 6.54 to 10.10, with an average increase of 0.54%.\n\nFigure 7(c) depicts the increase in the prices of new products in response to changes in the potential market for refurbished products. The price of new products in Model I rose from $1547.35 to $3340.45, marking an average increase of 1.15%. In Model T, the price of new products increased from $1447.48 to $3414.09, with an average increase of 1.35%. Model R experienced a rise in the price of new products from $1911.6 to $4210.45, reflecting an average increase of 1.2%. Moving on to Figure 7(d), it illustrates the increase in the prices of refurbished products in response to changes in the potential market for refurbished products. The price of refurbished products in Model I increased from $614.12 to $2,177.34, averaging a 2.5% increase. In Model T, the price of refurbished products rose from $544.96 to $2,237.83, with an average increase of 3.1%. Model R witnessed an increase in the price of refurbished products from $812.80 to $2,651.89, with an average increase of 2.2%.\n\nThe increase in market potential for refurbished products also results in a more significant increase in product quality choice. Figure 8(a) illustrates the increase in quality choice observed when there is a change in the potential market for refurbished products. In Model I and Model R, quality choice increased from 25 to 39, averaging a 0.56% increase. In Model T, quality choice rose from 26 to 41, with an average increase of 0.57%. Figure 8(b) demonstrates the increase in producer profits experienced when there is a change in the market potential for refurbished products. Producer profits in Model I rose from $24,283.9 to $89,636.9, marking an average increase of 2.6%. In Model T, producer profits increased from $32,040.6 to $84,272.5, with an average increase of 1.6%. Meanwhile, Model R experienced an increase in profits from $12,141.9 to $44,818.5, averaging a 2.6% increase.\n\nThe substantial volume of high-end customer requests in the absence of refurbished products (q) significantly influences quantity, price, quality choice, and producer profits.\n\nFigures 9(a) and (b) illustrate the impact of high-end demand on the quantity of new and refurbished products. In Figure 9(a), it is evident that a higher level of high-end demand corresponds to an increased quantity of new products. For instance, in Model I, the quantity of new products rises from 25.2 to 51.4, averaging a 1.03% increase. Similarly, in Model T, the quantity of new products increases from 30.6 to 53.9, with an average increase of 0.76%. Model R also experiences an increase from 12.6 to 25.7 in the quantity of new products, representing an average increase of 1.03%. Figure 9(b) demonstrates that as high-end demand increases, so does the quantity of refurbished products. For Model I, there is an increase from 12.6 to 25.7, averaging a 1.03% rise. Model T shows a shift from 15.3 to 26.9, with an average increase of 0.76%. Meanwhile, Model R records an increase from 6.3 to 12.85, with an average increase of 1.03%.\n\nFigure 10(a) illustrates that a higher value of high-end demand corresponds to higher prices for new products. Specifically, in Model I, the price of new products increases from $1248.56 to $5582.66, with an average price increase of 3.4%. In the Model T, it rises from $1026.49 to $6008.93, representing an average increase of 4.8%. Meanwhile, Model R experiences a price increase from $1586.81 to $6987.19, with an average increase of 3.4%. In Figure 10(b), it is evident that an increase in the value of high-end demand leads to higher prices for refurbished products. For Model I, prices increase from $946,864 to $3135.37, averaging a 2.3% increase. In the Model T, prices rise from $807,051 to $3377.26, with an average increase of 3.1%. Similarly, Model R sees prices increase from $1131.36 to $3901.48, representing an average increase of 2.4%. These price fluctuations are influenced by changes in high-end demand.\n\nFigure 11(a) illustrates the increase in quality choice that occurs when there is a change in the value of high-end demand. Quality choice for new products in both Model I and Model R increases from 24 to 49, with an average increase of 1.04%. In the Model T, quality choice rises from 22 to 54, representing an average increase of 1.4%. Meanwhile, Figure 11(b) demonstrates the increase in producer profits that results from changes in high-end demand. In Model I, manufacturer profits increase from $21,729.9 to $183,866, reflecting an average increase of 7.4%. In the Model T, manufacturer profits rise from $23,376.2 to $175,664, with an average increase of 6.5%. Model R experiences a profit increase from $10,865 to $91,933, indicating an average increase of 7.7%. These changes in quality choice and profits are driven by shifts in high-end demand.\n\nThe production cost parameter (k) has a significant impact on the prices of both new and refurbished products.\n\nFigure 12(a) illustrates that as the production cost parameter’s value increases, the price of new products decreases. The graph covers a range of values from 0 to 2 for the production cost parameter. Starting at a production cost parameter of 0.1 and increasing to 2, the price of new products in Model I decreased from $30,287.7 to $1,514.39, with an average decrease of 0.9%. In the Model T, the price of a new product decreased from $33,834.7 to $1,354.6, averaging a 0.9% decrease. The Model R saw a decrease from $38,091 to $1,904.55, with an average drop of 0.95%. Figure 12(b) indicates that with higher production cost parameter values, the price of refurbished products decreases. In Model I, it dropped from $18,875.9 to $943.79, with an average drop of 0.95%, as the production cost parameter ranged from 0.1 to 2. In the Model T, the price of refurbished products decreased from $21,072.7 to $855.98, averaging a 0.95% drop. The Model R experienced a price reduction from $23,132.2 to $1,156.61, with an average depreciation of 0.95%.\n\nChanges in price elasticity (l) lead to alterations in product quantity, price, quality choice, and producer’s profits.\n\nFigure 13(a) illustrates how an increase in price elasticity affects the quantity of new products. When the price elasticity increases from 1 to 10, the quantity of products in Model I decreases from 39.6 to 35.7, with an average decrease of 0.09%. In Model T, an increase in price elasticity leads to an increase in the quantity of new products, with new products in Model T increasing from 40.24 to 49 at an average increase of 0.2%. However, in Model R, the quantity of new products decreased from 19.8 to 17.8, with an average decrease of 0.1%. This trend is mirrored in the quantity of refurbished products, as shown in Figure 13(b). In Model I, the quantity of refurbished products decreased from 19.8 to 17.8, with an average decrease of 0.1%. In Model T, the quantity of refurbished products increased from 20.12 to 24.5, with an average increase of 0.2%. Meanwhile, in Model R, the quantity of refurbished products decreased from 9.9 to 8.9, with an average decrease of 0.1%.\n\nFigure 13(c) demonstrates the decrease in quality choice when there is a change in price elasticity. Quality choice for new products in Model I and Model R decreased from 75 to 17, with an average decrease of 0.7%. In Model T, quality choice decreased from 77 to 18, also with an average decrease of 0.7%. Figure 13(d) shows the decline in producer profits when there is a change in price elasticity. Manufacturer’s profits in Model I decreased from $326,264 to $16,558.9, with an average decrease of 0.9%. In Model T, manufacturers’ profits decreased from $250,257 to $28,704.6, with an average decrease of 0.8%. Meanwhile, Model R experienced a decrease in profits from $163,132 to $8,279.45, with an average decrease of 0.9%.\n\nChanges in the cannibalization coefficient (b) have an impact on product quantity, price, quality choice, and producer’s profits.\n\nFigure 14(a) illustrates the impact of the cannibalization coefficient on the quantity of new products. When the value of the cannibalization coefficient increases from 1 to 10, the quantity of new products in Model I increases from 37 to 40 with an average increase of 0.08%. In Model T, it also increases from 38 to 49.6 with an average increase of 0.3%. Meanwhile, Model R experiences an increase from 18.5 to 20 with an average increase of 0.08%. This demonstrates that a higher cannibalization coefficient leads to a greater quantity of new products being produced. In line with the increase in new products, refurbished products also see an increase, as shown in Figure 14(b). The image illustrates the changes caused by the increase in the cannibalization coefficient on the quantity of refurbished products. Model I experiences an increase from 18.5 to 20 with an average increase of 0.08%. In Model T, it also increases from 19 to 24.8 with an average increase of 0.3%. Whereas in Model R, the quantity of refurbished products has increased from 9.25 to 10 with an average increase of 0.08%.\n\nFigure 14(c) reveals that the higher the value of the cannibalization coefficient, the lower the price of new products. Model I’s price decreased from $5567.1 to $1551.21 with an average decrease of 0.7%. Model T’s price decreased from $6390.32 to $1211.74 with an average decrease of 0.8%. The Model R’s price decreased from $7003.55 to $1943.88, reflecting an average drop of 0.7%. Figure 14(d) shows that the higher the cannibalization coefficient, the lower the price of refurbished products. Model I’s price decreased from $2512.09 to $1385.24 with an average decrease of 0.4%. The Model T’s price decreased from $2890.97 to $1087.87, indicating an average drop of 0.6%. Meanwhile, the Model R’s price decreased from $3050.76 to $1721.82, with an average decrease of 0.4%. Based on this analysis, the cannibalization coefficient in this study did not reduce the quantity of new products. Consumer demand for new products is also influenced by the price of new products. It can be seen that with an increase in the cannibalization coefficient, the price of new products decreases, potentially leading to an increase in demand for new products.\n\nFigure 15(a) illustrates that the quality choice of Model I and Model R decreased from 48 to 27 with an average decrease of 0.4%. On the Model T, quality choice fell from 56 to 24 with an average decrease of 0.5%. Figure 15(b) shows that producer profits on Model I fell from $126,288 to $45,250.6 for an average decrease of 0.6%. On the Model T, manufacturers’ profits fell from $131,236 to $42,513.7 for an average decrease of 0.6%. Meanwhile, the Model R experienced a decrease in profits from $63,144 to $22,675.3 with an average decrease of 0.6%.\n\nBased on the results of the sensitivity analysis, it was found that maximizing producer profits can occur when both market potential and high-end demand increase. However, producer profits will increase as the price elasticity decreases. Reducing the cannibalization coefficient can also lead to an increase in producer profits. This can be interpreted as follows: when fewer consumers switch to refurbished products, producers stand to gain greater profits. Moreover, producer profits can be augmented by maintaining a lower proportion of costs and a reduced supply of consumable products. This condition is applicable to all models, including Model I, Model T, and Model R. Model I, in particular, exhibits higher producer profits when there are changes in parameter values, while Model R shows the lowest producer profits when such changes occur.\n\n\nConclusion\n\nIn this comprehensive study, we have thoroughly examined and compared three distinct refurbishing models: in-house refurbishing (Model I), refurbishing outsourcing to third parties (Model T), and refurbishing outsourcing to retailers (Model R). Our rigorous mathematical modeling and optimization techniques have allowed us to pinpoint the optimal configurations for each model, optimizing profits across varying parameters, including product quantities, quality selections, and pricing tactics. Our findings have highlighted that the in-house refurbishing model tends to yield higher profits for companies primarily driven by profit motives, whereas the outsourcing refurbishing model to retailers aligns effectively with environmental sustainability objectives. Furthermore, our research has incorporated critical factors such as the constrained supply of manufacturable products and consumer behavior, particularly focusing on the preferences of high-end and low-end customers.\n\nLooking ahead, future investigations within this domain could take a more intricate approach by delving deeper into the complexities of multi-segment cannibalization demand models. This exploration could shed light on how market segmentation influences optimal strategies and sustainability considerations for refurbishing models. Additionally, analyzing the influence of evolving consumer preferences and external market dynamics on these refurbishing models may offer invaluable insights for decision-makers within the manufacturing industry. This avenue of research holds the potential to enhance the adaptability and resilience of refurbishing strategies in an ever-changing market landscape.", "appendix": "Data availability statement\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nReferences\n\nAtasu A, Souza GC: How does product recovery affect quality choice? Prod. Oper. Manag. 2013; 22(4): 991–1010. Publisher Full Text\n\nBelbağ AG, Belbağ S: Remanufactured products: A systematic review from the consumer perspective. Journal of Remanufacturing. 2023; Vol. 13(2): pp. 207–241. Springer Science and Business Media B.V. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCesur E, Cesur MR, Kayikci Y, et al.: Optimal number of remanufacturing in a circular economy platform. Int J Log Res Appl. 2022; 25(4–5): 454–470. Publisher Full Text\n\nFang C, Fan S, Qiu Y: The choice of remanufacturing strategy for the OEM with third-party remanufacturers’ advantages. Comput. Ind. Eng. 2023; 176: 108973. Publisher Full Text\n\nFeng L, Li Y, Fan C: Optimization of pricing and quality choice with the coexistence of secondary market and trade-in program. Ann. Oper. Res. 2020. Publisher Full Text\n\nHe W, Liang L, Wang K: Economic and environmental implications of quality choice under remanufacturing outsourcing. Sustainability (Switzerland). 2020; 12(3). Publisher Full Text\n\nKe C, Yan B: Trade-in value effects of used products in remanufacturing with considering consumer purchase behavior. J. Oper. Res. Soc. 2022; 73(3): 608–633. Publisher Full Text\n\nKleber R, Reimann M, Souza GC, et al.: On the robustness of the consumer homogeneity assumption with respect to the discount factor for remanufactured products. Eur. J. Oper. Res. 2018; 269(3): 1027–1040. Publisher Full Text\n\nKurdhi NA, Dabadghao SS, Fransoo JC: Revenue management in a refurbishing duopoly with cannibalization. J. Oper. Manag. 2023; 69(2): 246–260. Publisher Full Text\n\nLiu B, Song Q, Zheng H, et al.: Remanufacturing production decisions considering product life cycle and green consumers’ scale in the circular economy. Ind. Manag. Data Syst. 2023; 123(4): 1122–1156. Publisher Full Text\n\nMcKie EC, Ferguson ME, Galbreth MR, et al.: How Do Consumers Choose between Multiple Product Generations and Conditions? An Empirical Study of iPad Sales on eBay. Prod. Oper. Manag. 2018; 27(8): 1574–1594. Publisher Full Text\n\nÖrsdemir A, Kemahlioǧlu-Ziya E, Parlaktürk AK: Competitive quality choice and remanufacturing. Prod. Oper. Manag. 2014; 23(1): 48–64. Publisher Full Text\n\nOvchinnikov A: Revenue and cost management for remanufactured products. Prod. Oper. Manag. 2011; 20(6): 824–840. Publisher Full Text\n\nSabbaghi M, Behdad S, Zhuang J: Managing consumer behavior toward on-time return of the waste electrical and electronic equipment: A game theoretic approach. Int. J. Prod. Econ. 2016; 182: 545–563. Publisher Full Text\n\nSabbaghi M, Esmaeilian B, Raihanian Mashhadi A, et al.: An investigation of used electronics return flows: A data-driven approach to capture and predict consumers storage and utilization behavior. Waste Manag. 2015; 36: 305–315. PubMed Abstract \| Publisher Full Text\n\nSaphores JDM, Nixon H, Ogunseitan OA, et al.: How much e-waste is there in US basements and attics? Results from a national survey. J. Environ. Manag. 2009; 90(11): 3322–3331. PubMed Abstract \| Publisher Full Text\n\nSinghal D, Tripathy S, Jena SK: Remanufacturing for the circular economy: Study and evaluation of critical factors. Resour. Conserv. Recycl. 2020; 156: 104681. Publisher Full Text\n\nTeng Y, Feng B: Optimal channel structure for remanufacturing under cap-and-trade regulation. Processes. 2021; 9(2): 1–20. Publisher Full Text\n\nWang Z, Duan Y, Huo J: Impact of trade-in remanufacturing policy and consumer behavior on remanufacturer decisions. Sustainability (Switzerland). 2020; 12(15). Publisher Full Text\n\nWrålsen B, O’Born R: Use of life cycle assessment to evaluate circular economy business models in the case of Li-ion battery remanufacturing. Int. J. Life Cycle Assess. 2023; 28(5): 554–565. Publisher Full Text\n\nYang Y, Goodarzi S, Jabbarzadeh A, et al.: In-house production and outsourcing under different emissions reduction regulations: An equilibrium decision model for global supply chains. Transp. Res. E Logist. Transp. Rev. 2022; 157: 102446. Publisher Full Text\n\nYin S, Jia F, Chen L, et al.: Circular economy practices and sustainable performance: A meta-analysis. Resour. Conserv. Recycl. 2023; 190. Elsevier B.V. Publisher Full Text\n\nZhang X, Zhang M, Zhang H, et al.: A review on energy, environment and economic assessment in remanufacturing based on life cycle assessment method. J. Clean. Prod. 2020; Vol. 255: 120160. Elsevier Ltd. Publisher Full Text\n\nZou Z, Wang F, Lai X, et al.: How does licensing remanufacturing affect the supply chain considering customer environmental awareness? Sustainability (Switzerland). 2019; 11(7). Publisher Full Text" }	[ { "id": "327386", "date": "23 Oct 2024", "name": "Mohammed Haoues", "expertise": [ "Reviewer Expertise Industrial Engineering", "Closed-Loop Supply Chains (CLSC)", "Manufacturing Processes", "Hybrid Manufacturing/ Remanufacturing Systems (HMRS)", "Planning and Scheduling", "Lot-Sizing", "Reliability and Integrated Maintenance", "Production", "Subcontracting", "Equipment Rental", "Quality", "Sustainability", "Discrete Optimization", "Multi-Objective Optimization", "Heuristics and Méta heuristics." ], "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 Comments\nThis paper formulates and analyzes models for in-house refurbishing, outsourcing refurbishing to third parties, and outsourcing to retailers, aiming to identify optimal solutions and strategies for maximizing benefits. The authors compare in-house and outsourced refurbishing models, using multivariable function optimization and the Karush-Kuhn-Tucker method to determine the best approach. This allows for a thorough examination of the factors influencing profitability and sustainability in refurbishing. While the study aligns with the objectives of F1000Research, the paper requires significant improvements in writing, organization, and clarity before indexing.\nSome suggestions to improve the manuscript are provided below:\nOn page 6 (eq 1 and eq 2) it is necessary to distinguish between the notation of the price of the new products and that of the remanufactured products. Please review the indices in the equations; sometimes you use them in the wrong places. Example Pr in the § just before equation 3. Please review the abbreviations and their use in the body of the article. Example of KKT in hypothesis 5. Eliminates the repetition! Example of the sentence \"where λ is the Lagrange multiplier vector.\" on page 7, 9 and 11.\n\nCheck the punctuation. Example: in the notation In the notation, you must add the word Optimal in the symbols where you calculate optimal quantities. Example: Optimal production quantity of new products. In order to homogenize and facilitate the reading of the document. The indices and exponents must be taken into account in the notations. Check the notation! γand a are not taken into account! Equations 31, 32 and 34 must be written between two brackets to better justify them. The equations of proposition 5 and 7 must be written between two brackets to better justify them. In the results and discussions section (Page 20... Page 26), use the concept variation instead of change! It’s better. Please change the title conclusion by adding \"and future directions research\". I suggest changing the title of the first section to \"Introduction and literature review\". However, in the section 1, it is desirable to separate between the introduction and the literature review. You can put them together, but you have to start with the introduction and then start the literature review. The introduction part should be shortened and the literature review section should be better explained. The problematic (knowledge-gap) should be positioned with respect to the related literature. The research objectives should be better explained and motivated since it does not provide a good overview about the work. In addition; the literature review part should be enhanced by adding other references in the field. Otherwise, this reading part is poor. Finally, the paper needs a careful and strict linguistic editing.\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?\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? Partly", "responses": [] }, { "id": "348323", "date": "27 Jan 2025", "name": "Rekha Guchhait", "expertise": [ "Reviewer Expertise Supply chain management", "Remanufacturing", "Logistics", "Production Planning", "Inventory management", "Emissions" ], "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\nWrite the paper from a third-person point of view, not from a first-person point of view.\n\nThe first line of the introduction and the entire first paragraph start with the circular economy, but the study is not about the circular economy.\nSeparate introduction and Literature review section. In the introduction section, mention research gaps, contributions of the study, and the organization of the paper.\n\nUpdate the literature review with recent references from 2024-2025. Make an author's contribution table highlighting the key contributions of the study. Compare the study with the following: Economic evaluation of an outsourced fourth-party logistics under a flexible production system; Circular economy-driven two-stage supply chain management for nullifying waste; A sustainable flexible manufacturing-remanufacturing model with improved service and green investment under variable demand; Pricing strategy based on a stochastic problem with barter exchange under variable promotional effort for a retail channel.\nDivide the study into sections and subsections. Provide appropriate section and subsection names and numbers.\nAfter equation 2, p_n is the price of new products, and again p_n is the price of refurbished products!\nIn Table 1, mention decision variables separately. It is unclear from the study and numerical experiment which are the decision variables.\nModel explanations are good. Mention the data source for the numerical experiment. Provide a table for the optimum values of decision variables and profit for three cases and explain which one is the best-case scenario and why before the sensitivity analysis section.\nSensitivity explanations are good.\n\nProvide managerial insights of the study and from the results before the conclusions section.\n\nUpdate the reference section with 2024-2025 research articles. Provide at least 30-40 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? 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? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-1003
https://f1000research.com/articles/13-262/v1	12 Apr 24	{ "type": "Research Article", "title": "Socio-demographic analysis of destination selection factors for Himalayan Hill destinations", "authors": [ "Manish Badoni", "Babita Rawat", "Megha Aggarwal", "Babita Rawat", "Megha Aggarwal" ], "abstract": "Background The towering peaks of the Himalayas lie in troves of captivating hill destinations, especially in India. Each destination aims to provide tourists with unique experiences and breath-taking landscapes. Understanding the tapestry of factors that weave the allure of these destinations and draw visitors from diverse backgrounds remains intriguing.\n\nMethod This study delves into the socio-demographic tapestry of Himalayan hill destination selection, unraveling the complex interplay of demographic characteristics, social influences, and individual motivations that shape tourists’ choices.\n\nResults This study aims to answer why different tourists have different travel choices and what factors are the drivers behind such choices. The results show that destination selection factors are similar irrespective of respondents’ socio-demographic variabilities; however, for a few factors, the results are reversed.\n\nConclusion The study has implications for policymakers and the limitations of the research discussed at the end.", "keywords": [ "Himalayan Hill Destinations", "Socio-demographic variables", "Destination selection factors", "Gender", "Age", "Occupation level", "Income level" ], "content": "Introduction\n\nThe Himalayan hill destinations of India have long captivated the imagination of travellers with their breathtaking landscapes, diverse cultures, and spiritual significance. The selection of factors that drive tourists to visit these destinations is crucial for both tourism practitioners and policymakers. Destination selection is a complex process influenced by a myriad of socio-demographic and travel motivation factors (Kaushik et al., 2010). This socio-demographic analysis of tourists with respect to destination selection factors provides valuable insights for tourism industry stakeholders. By recognizing the diverse preferences of different demographic groups, tourism practitioners can tailor their offerings to cater to a broad spectrum of tourists. This new understanding ensures that Himalayan hill destinations continue to attract visitors, while maintaining a delicate balance between economic development and environmental conservation.\n\nYounger travellers are more likely to visit adventurous destinations, (Chauhan & Jishtu, 2022) or older travellers would choose to relax to familiar and nearby destinations (Wijaya et al., 2018). The higher income level group tended to travel to luxurious destinations and the other income level group would visit nearby destinations. These socio-demographic changes help customize marketing strategies to attract every class of tourists and increase footfall for a particular destination. Destinations with aesthetic images rightly communicated to tourists would be able to achieve a competitive advantage with respect to similar participative destinations. Understanding the intersection of sociodemographic and destination selection factors is vital. Related parties, such as destination marketers, tour operators, and policymakers, develop promotional campaigns, infrastructure, and tourism services based on these insights to ensure a more targeted and satisfying experience for tourists, contributing to the sustainable growth of the tourism industry (Ma et al., 2018).\n\nThis study aims to construct a relationship between socio-demographic variables and destination selection factors for various destinations in Uttarakhand and Himachal Pradesh. By examining the preferences and driving forces behind destination selection across various age groups, gender variability, occupation status, and income levels, this study aims to examine the nuanced decision-making processes that guide journeys to these major mountain havens.\n\n\nLiterature review\n\nThe tourism industry is highly competitive, and the personal characteristics of individual tourists play an important role in destination selection. Even if destination attributes are unknown, certain individual traits motivate tourists to visit the place (Suttikun et al., 2018). Motivation to visit a destination also plays a crucial role in shaping tourist behavior (Baloglu & Uysal, 1996). Researchers have also identified push and pull factors as motivating factors for tourists to visit a destination, and pull factors serve as the basis for destination selection (Josiam et al., 1999). Destination appeal is a major factor for tourists to visit the destination, whereas other factors such as infrastructure facilities, transportation availability, time, and cost involved in travel are secondary factors that enhance tourist flow (Das et al., 2007). The study (Hudson & Shephard, 1998) identified that not only adventure services but also travel information, accommodation, and tour operator services are selection factors for tourists. Other researchers (Crompton, 1979; Dann, 1977, 1981) have also examined push and pull motivation factors in tourism. Push factors can be identified as knowledge of culture, status, personal development, relaxation, interpersonal relationships, and pleasure. On the other hand, pull factors could be atmosphere and climate at the destination, hygiene, built heritage, outdoor activities, and people’s characteristics (Antara & Prameswari, 2018; Karamehmedović, 2018; Prayag & Ryan, 2011). Thus, the attributes or features of a destination are important factors for tourists.\n\nStudies have been done in the past analyzed the relationship between the personal characteristics of tourists and their travel motivations and found that they are inter-related (Chon, 1990; Court & Lupton, 1997; Joppe et al., 2001). The author (Iyiola & Akintunde, 2011) examined whether tourist travel motivation to visit Nigeria is affected by sociodemographic variables. The motivation to select a destination can be determined by the age and income of tourists (Ng et al., 2007; Yoon & Uysal, 2005). Travel motivating factors were also studied with respect to senior-age travellers, and the results are similar to those of previous studies with fewer pull factors, such as destination familiarity, value for money, and destination closeness (Wijaya et al., 2018). Various authors (Beerli & Martín, 2004; Um & Crompton, 1990; Walmsley & Jenkins, 1993) have studied the relationship between motivation to visit a destination and individual characteristics such as gender, age, education, occupation, and income as determinants of creating a destination image. Studies (Gibson et al., 2008; Woodside & Lysonski, 1989) have also found similar results in that the perception of destinations is affected by tourist socio-demographic characteristics.\n\nTourist places are marketed according to the needs of potential tourists’ personal characteristics such as gender, age, education, occupation, and income (Stabler, 2013; Um & Crompton, 1990). Sources such as advertising and word-of-mouth publicity provide travel inspiration to tourists, and past experiences play an important role in influencing future travel decisions for a potential destination (Huang Songshan, 2006).\n\nVarious studies have analyzed the motivating factors and the influence of sociodemographic factors on creating destination image and tourist intention to visit. It is also possible that diverse visitors will have different levels of expectations with respect to different motivational factors and destinations. In this study, the influence of gender, age, occupation, and income on the expectation level of tourists pertaining to different tourist motivational factors, such as destination image, infrastructural facilities, beauty, culture, and heritage, is examined for selected destinations of Uttarakhand and Himachal Pradesh.\n\nBased on the above literature review, this study aims to fulfill the following objectives and examine the related hypotheses:\n\nObjective 1 To identify the selection factors to visit Himalayan region destination.\n\nObjective 2 To identify the relationship between sociodemographic variables and destination selection factors.\n\nObjective 2 is analyzed and fulfilled with the help of following related Hypothesis-\n\nDestination selection factors are significantly similar irrespective of the gender of the tourists\n\nDestination selection factors are significantly similar irrespective of the age of the tourists\n\nDestination selection factors are significantly similar irrespective of the occupation of the tourists\n\nDestination selection factors are significantly similar irrespective of the income of the tourists\n\n\nMethods\n\nA self-administered questionnaire, prepared with a five-point Likert scale (Likert, 1932) with 49 items, was prepared and distributed to Himalayan hill destinations of Uttarakhand and Himachal Pradesh, that is, Mussoorie, Shimla, Nainital, and Kangra, selected on the basis of convenience. A total of 800 tourists were approached, 200 at each destination, between April 2023 and November 2023. Out of 800, only 748 were included in the final analysis because Indian female respondents were reluctant to complete the survey, and the survey was performed by their spouses or other relatives. Hence, these surveys were excluded from the final analysis. Although tourists were reluctant to participate in the survey, help from local restaurant owners, tour operators, and Mall Road vendors have been taken.\n\nTo fulfil the research objectives, responses collected from 748 tourists from selected Indian hill destinations were analyzed using a structured questionnaire. The respondents were selected based on their travel experience to a specific destination. Sociodemographic dimensions, such as gender, age, occupation, and income, were purposely included in the questionnaire to fulfil the research objectives. The distribution of the data is presented in Table 1.\n\nRespondents’ sociodemographic analysis represented 57.5% of the youth tourist age ranging from to 25-35 years followed by 23% of respondents aged below 25 years. This indicates that about 80% of tourists belong to the young age group, that is, not more than 35 years. The maximum number of tourists was 71%, and 56% of the respondents belonged to private sector jobs, with incomes ranging from 20,000 Rs. to 50,000 Rs. Only 29% of the respondents were female as they were reluctant to participate in the survey. This behavior shows that the motivation of Indian females to travel to a destination still depends on their counterparts, whether their husbands, fathers, brothers, or friends.\n\nInferential Analysis\n\nTo identify the destination attributes or destination selection factors, a reliability analysis was performed, and the Cronbach’s alpha value of 0.909 showed that the questionnaire achieved high internal consistency. Before verifying the hypotheses set out in this study, an exploratory factorial analysis was conducted. The factors extracted by this method are uncorrelated and arranged in the order of decreasing variance. Bartlett’s test of sphericity and the calculation of Kaiser-Meyer-Olkin statistics indicate whether data are suitable for identifying orthogonal factor dimensions. Variables with loading equal to or greater than 0.4 were included in a given factor to decrease the probability of misclassification (Hair et al., 1995). Forty-nine items were loaded saliently, and any factor that emerged with eigenvalues greater than one was considered for further analysis. The final factor distribution was allocated to forty-three items, other items with values below the threshold limit were not used for the final analysis. The total variance explained by factor analysis was 60%. The results of Cronbach’s alpha coefficients, KMO, Bartlett’s test of sphericity, and factor analysis are shown in Table 2.\n\nTable 2 shows the factors considered motivating and satisfactory for destination selection. Factors such as ‘Destination Image’, ‘Value for Money,’ ‘Infrastructure Facilities,’ ‘Beauty, Culture & Heritage’, ‘Tour & Travel Connections’, ‘Value added Services,’ Destination Brand Value’ are independent factors and able to create destination selection factor. The table also shows that the Cronbach alphas’ value reported on factor 7, i.e. ‘Destination Brand Value’ is low. This could be a consequence of this factor because the maximum number of respondents belonged to the income group of Rs. 20,000 to Rs. 50,000; for such respondents’ destinations, brand value would not be a motivating factor in selecting a destination. However, it was considered suitable to include this item because destination image would be helpful in creating destination brand value, and hence, becomes a motivating factor for the selection of a destination. The table also shows the dependent variable, destination satisfaction and intention to revisit.\n\nThe possible relationship between tourists’ socio-demographic characteristics and the selection factors of a destination was analyzed using ANOVA, checking its significance by means of the F statistic and p value (confidence level 95%).\n\nThe relationship between the sociodemographic variables of respondents and the factors of destination selection decisions of the respondents are shown in Table 3 with the help of ANOVA.\n\nThe results show that there is a significant similarity between gender and destination selection factors, except for one factor, Value-added Services (VaS). This result justifies the fact that women tend to assess the value-added services of a destination more favorably than men. For all other factors, DI, Vm, Infra, BCH, TTC, and DBV, there were no significant differences irrespective of the gender of the respondents. Therefore, we confirm hypothesis H1 that Destination selection factors are significantly similar irrespective of the gender of tourists.\n\nTable 4 shows the relationship between the age of respondents and destination selection factors. The results show that there is a significant difference among the selection factors for different age groups of the respondents.\n\nFactors such as destination image, value for money, tour and travel connections, and destination brand value are considered differently by different age groups of tourists. For other factors, including infrastructure facilities, ‘Beauty, Culture and Heritage’, and ‘Value-added Services’, the results show no significant difference with the age of the respondents. Results implies that the selection factor ‘destination image’ or ‘Destination Brand Value’ are significantly different for different age categories of the tourists. Young tourists tend to be motivated by destinations with a grand brand value rather than older tourists. Similarly, a destination would have different age tourist footfall due to the difference in value for money. On the basis of these results, we partially confirm hypothesis H2 that Destination selection factors are significantly similar irrespective of the age of the tourists but only for factors ‘Infrastructure facilities’, ‘Beauty, Culture and Heritage,’ and ‘Value-added Services.’\n\nTable 5 shows the result of occupation and reveals a significant difference between occupation and selection factors for destination, but only for the factors ‘Destination Image’, and ‘Value for Money’. The results reveal similarities among various occupation respondents and their selection factors for destinations, such as ‘Beauty, Culture & Heritage’, ‘Infrastructure facilities’, ‘tour & travel connections’, ‘value-added services’, and ‘destination brand value’. Results implies that the factor ‘Destination Image’ or ‘Value for money’ are significantly different for various occupational categories of the tourists. Tourists who are private sector employees motivate destinations that provide more value for money than other tourists. These results confirm hypothesis H3 that destination selection factors are significantly similar, irrespective of the occupation of the tourists.\n\nThe relationship between the income of the respondents and the selection factors of the destination is shown in Table 6. The result shows there is no similarity between income and selection factors for destination only for the factors ‘Destination Image,’ ‘Value for Money,’ ‘Beauty, Culture & Heritage’. For other factors, ‘Infrastructure facilities,’ ‘Tour-Travel Connections’, ‘Value-added Services,’ and ‘Destination Brand Value’ showed significant similarity with the diverse income of respondents. Results implies that the factor ‘destination image’ or ‘Value for money’ are significantly different for different income categories of the tourists. Tourists with middle-income levels motivate and select destinations that provide more value for money than do other tourists. Thus, tourists with various income groups look for value for money and varied destination images rather than other destination selection criteria. These results partially confirm hypothesis H4 Destination selection factors are significantly similar irrespective of tourists’ income.\n\n\nResults and discussion\n\nThis research was undertaken to identify various destination selection factors and their relationship with socio-demographic variables of tourists for various Himalayan region destinations in Uttarakhand and Himachal Pradesh, India. Various destination factors have been identified with the help of factor analysis, such as ‘Destination Image’, ‘Value for Money’, ‘Infrastructure facilities’, ‘Beauty, Culture & Heritage’, ‘Tour & Travel connections’, ‘value-added services, and ‘destination brand value’. The Cronbach’s alpha value was 0.9, and the variance explained by all factors was 60%, which is considerably good (Aggarwal et al., 2024).\n\nTo further analyze the relationship between the factors and sociodemographic variables, one-way analysis of variance (ANOVA) was performed. The summary results of the ANOVA are presented in Table 7. Destination Image and Value for Money were found to be significantly different for different age groups, occupation statuses, and income levels. This implies that tourists of different age groups, occupation statuses, and income levels will have different choices for selecting a destination on the basis of ‘Destination image’ or ‘Value for money’. ‘Value added services’ was found dissimilar for socio-demographic variable ‘Gender’. This implies that the selection of a destination may change if value-added services are different for any destination. However, for other factors such as ‘destination image’ or ‘beauty, culture, and heritage’, the selection factor does not create any difference between male and female tourists.\n\nDestination selection factors are important for any destination to improve tourist footfall and gain a competitive advantage. Socio-demographic variables play an important role in such decisions and hence need to be taken care of by the DMOs. Destination marketing organizations should identify their tourists and their choices. Any tourist, if impacted by their socio-demographic variable, will try to select destination suits for their personality and pocket. Young tourists would love to visit Goa, whereas senior-aged tourists would like to travel to a destination with religious beliefs. Thus, destination marketing organizations should analyze their tourist choices and market their products according to the needs of tourists.\n\nNot every study has been completed without limitations, and this research also has some limitations. The first and foremost limitation of this study is the selection of socio-demographic variables. This research used only four socio-demographic variables: Gender, Age, Occupation and Income. Other sociodemographic variables were beyond the scope of this study. The results may vary if other variables are included in future studies. The other limitation is the study area, which is related to the Himalayan region and included a few destinations of Uttarakhand and Himachal Pradesh with random selection. Future studies should include other destinations. A comparison between these destinations could also be performed with respect to sociodemographic variables. This study covers the Himalayan region, and other hill regions of India can also be studied with the help of similar analysis, and further comparisons can be drawn.\n\n\nEthical statement\n\nThis research was conducted in accordance with the guidelines of the Research Ethics Board (REB) of Uttaranchal University. The Research Ethics Board has given the approval on March 4, 2023, and the approval number is UU/DRI/EC/2023/002.\n\nThe questionnaire has been submitted to REB of the university, the board members and chairperson have identified the viability of the research topic. All the authors have presented their research objectives to the board then the questionnaire got approval to conduct the study.\n\n\nConsent statement\n\nThe consent from all the participants involved in the study has been taken. A self-explanatory written statement was attached with the questionnaire for the participants and the similar questionnaire has been submitted to the university research board (REB).", "appendix": "Data availability\n\nThe underlying data related to the paper are available in figshare with the following citation and DOI.\n\nFigshare. Aggarwal, Megha, Badoni, Manish, Rawat, Babita (2024). Sociodemographic Analysis of Destination Selection Factors for Himalayan Hill Destinations. Dataset, https://doi.org/10.6084/m9.figshare.24936471.v1.\n\nThe data available were submitted by Megha Aggarwal licensed under CC BY 4.0. Complete details are-Socio-Demographic Analysis of Destination Selection Factors for Himalayan Hill Destinations © 2024 by Manish Badoni, Babita Rawat, and Megha Aggarwal licensed under CC BY 4.0. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.\n\n\nReferences\n\nAggarwal M, Badoni M, Rawat B: Sociodemographic Analysis of Destination Selection Factors for Himalayan Hill Destinations. Dataset. 2024. Publisher Full Text\n\nAntara M, Prameswari YA: Push and pull factors of tourists visit the tourism destination of Bali, Indonesia. Journal of Tourism and Hospitality Management. 2018; 6(1): 112–120.\n\nBaloglu S, Uysal M: Market segments of push and pull motivations: a canonical correlation approach. Int. J. Contemp. Hosp. Manag. 1996; 8(3): 32–38. Publisher Full Text\n\nBeerli A, Martín JD: Factors influencing destination image. Ann. Tour. Res. 2004; 31(3): 657–681. Publisher Full Text\n\nChauhan R, Jishtu H: Why do Tourists Visit a Himalayan Destination? Motivation, Barrier and Facilities Preference. American Journal of Economics and Business Innovation. 2022; 1(2): 1–10. Publisher Full Text\n\nChon K: The role of destination image in tourism: A review and discussion. The Tourist Review. 1990; 45(2): 2–9. Publisher Full Text\n\nCourt B, Lupton RA: Customer Portfolio Development: Modeling Destination Adopters, Inactives, and Rejecters. J. Travel Res. 1997; 36(1): 35–43. Publisher Full Text\n\nCrompton JL: Motivations for pleasure vacation. Ann. Tour. Res. 1979; 6(4): 408–424. Publisher Full Text\n\nDann GM: Anomie, ego-enhancement and tourism. Ann. Tour. Res. 1977; 4(4): 184–194. Publisher Full Text\n\nDann GM: Tourist motivation an appraisal. Ann. Tour. Res. 1981; 8(2): 187–219. Publisher Full Text\n\nDas D, Mohapatra PKJ, Sharma SK, et al.: Attractiveness of Varanasi as a tourist destination: perspective of foreign tourists. International Journal of Tourism Policy. 2007; 1(2): 111. Publisher Full Text\n\nGibson HJ, Qi CX, Zhang JJ: Destination Image and Intent to Visit China and the 2008 Beijing Olympic Games. J. Sport Manag. 2008; 22(4): 427–450. Publisher Full Text\n\nHair JF, Anderson RE, Tatham R, et al.: Multivariate data analysis. 4th ed.1995.\n\nHuang Songshan S: The Effects of Motivation, Past Experience, Perceived Constraint and Attitude on Tourist Revisit Intention. The Hong Kong Polytechnic University; 2006.\n\nHudson S, Shephard G: Measuring Service Quality at Tourist Destinations: An Application of Importance-Performance Analysis to an Alpine Ski Resort. J. Travel Tour. Mark. 1998; 7(3): 61–77. Publisher Full Text\n\nIyiola O, Akintunde O: Perceptions as influencer of consumer choice behavior: The case of tourism in Nigeria. Journal of Marketing Development and Competitiveness. 2011; 5(7): 27–36.\n\nJoppe M, Martin DW, Waalen J: Toronto’s Image As a Destination: A Comparative Importance-Satisfaction Analysis by Origin of Visitor. J. Travel Res. 2001; 39(3): 252–260. Publisher Full Text\n\nJosiam BM, Smeaton G, Clements CJ: Involvement: Travel motivation and destination selection. J. Vacat. Mark. 1999; 5(2): 167–175. Publisher Full Text\n\nKaramehmedović D: PUSH-PULL ANALYSIS TOWARDS CREATING HOLISTIC MARKETING OF THE CULTURAL HERITAGE TOURISM DESTINATION: THE CASE STUDY OF DUBROVNIK. Ekonomska Misao i Praksa. 2018; 1: 29–51.\n\nKaushik N, Kaushik J, Sharma P, et al.: Factors Influencing Choice of Tourist Destinations: A Study of North India. IUP Journal of Brand Management. 2010; 7.\n\nLikert R: A technique for the measurement of attitudes. Arch. Psychol. 1932; 22(140): 55.\n\nMa A, Chow A, Cheung L, et al.: Impacts of Tourists’ Sociodemographic Characteristics on the Travel Motivation and Satisfaction: The Case of Protected Areas in South China. Sustainability. 2018; 10(10): 3388. Publisher Full Text\n\nNg SI, Lee JA, Soutar GN: Tourists’ intention to visit a country: The impact of cultural distance. Tour. Manag. 2007; 28(6): 1497–1506. Publisher Full Text\n\nPrayag G, Ryan C: The relationship between the ‘push’ and ‘pull’ factors of a tourist destination: the role of nationality – an analytical qualitative research approach. Curr. Issue Tour. 2011; 14(2): 121–143. Publisher Full Text\n\nStabler MJ: The image of destination regions: theoretical and empirical aspects. Marketing in the Tourism Industry (RLE Tourism). Routledge; 2013; pp. 133–161.\n\nSuttikun C, Chang HJ, Acho CS, et al.: Sociodemographic and travel characteristics affecting the purpose of selecting Bangkok as a tourist destination. Tour. Hosp. Res. 2018; 18(2): 152–162. Publisher Full Text\n\nUm S, Crompton JL: Attitude determinants in tourism destination choice. Ann. Tour. Res. 1990; 17(3): 432–448. Publisher Full Text\n\nWalmsley DJ, Jenkins JM: Appraisive images of tourist areas: application of personal constructs. Aust. Geogr. 1993; 24(2): 1–13. Publisher Full Text\n\nWijaya S, Wahyudi W, Kusuma CB, et al.: Travel motivation of Indonesian seniors in choosing destination overseas. International Journal of Culture, Tourism and Hospitality Research. 2018; 12(2): 185–197. Publisher Full Text\n\nWoodside AG, Lysonski S: A General Model Of Traveler Destination Choice. J. Travel Res. 1989; 27(4): 8–14. Publisher Full Text\n\nYoon Y, Uysal M: An examination of the effects of motivation and satisfaction on destination loyalty: a structural model. Tour. Manag. 2005; 26(1): 45–56. Publisher Full Text" }	[ { "id": "267432", "date": "24 Apr 2024", "name": "Devkant Kala", "expertise": [ "Reviewer Expertise Tourism & Hospitality and Consumer 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 read this interesting study. The study has some potential. However, certain issues need to be addressed. The detailed observations are given below for your response:\nAbstract: Refinement is needed, particularly in the methods and results sections.\nIntroduction: The rationale of the study should be presented more effectively, with recent and relevant papers cited. It is noted that many cited studies are outdated; the author/s should include recent and relevant studies to build and present their arguments. Incorporating Indian studies would further strengthen and justify the arguments made. For example,[1] https://dergipark.org.tr/en/pub/ahtr/issue/32311/359067\nHypotheses Development:\nHypotheses development is not sufficiently presented. Please provide relevant literature to support your hypotheses.\nMethods: The author/s should provide references for previous studies from which items were adopted. Clear justification is needed for selecting Uttarakhand and Himachal Pradesh as study areas, as well as for choosing convenience sampling. “……. because Indian female respondents were reluctant to complete the survey, and the survey was performed by their spouses or other relatives.” Please refine this statement.\nWhat about the validity of the questionnaire? What was the language? Did you conduct a Pilot test before full-scale survey?\nResults: Table 2: Item Description: Replace ‘You’ with ‘I’. Instead of ANOVA, I suggest the author/s use regression analysis between Factors 1-7 and Factor 8.\nThe author/s should compare the results of the study with previous studies. The implications (Theoretical and managerial) are vague and need refinement. “Not every study has been completed without limitations,” – Please delete this portion of the statement.\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? Yes", "responses": [ { "c_id": "12299", "date": "03 Sep 2024", "name": "Manish Badoni", "role": "Author Response", "response": "Dear Reviewer, Thank you for your suggestions. We have incorporated the major part as you suggested. However, one suggestion related to regression analysis has not been incorporated as we are developing a new paper using a similar analysis." } ] }, { "id": "267431", "date": "06 May 2024", "name": "Sunita Dwivedi", "expertise": [ "Reviewer Expertise Marketing and 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\nDear Team F1000 Research, Thank you for providing this opportunity to review the paper. The theme is interesting and the study has used all novelty to the research area. My feedback is as below: The purpose of this study was to ascertain the correlation between various factors related to destination selection and sociodemographic characteristics of tourists for various destinations in the Himalayan region of Uttarakhand and Himachal Pradesh, India. Many destination factors, such as \"value for money,\" \"destination image,\" \"beauty, culture, and heritage,\" \"tour & travel connections,\" \"value-added services,\" and \"destination brand value,\" have been identified with the use of factor analysis techniques. Research has statistically validated the factors identified impacting young consumers destination selection preferences. The study concluded with the significant outcome for tour and travel industry to draw the marketing strategies for travelers.\n\nI concur with the results and implication drafted by the authors, and recommend the paper for publication\nThanks\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/13-262
https://f1000research.com/articles/13-1002/v1	03 Sep 24	{ "type": "Opinion Article", "title": "From the establishment of a national bioinformatics society to the development of a national bioinformatics infrastructure", "authors": [ "Bogdan Mirăuță", "Cătălina Zenoaga-Barbăroșie", "Monica Abrudan", "Marius Mihășan", "Mădălina Giurgiu", "Daria Mihalachi", "Michalis-Daniel Lazăr", "RSBI Members", "Horia L. Banciu", "Cătălina Zenoaga-Barbăroșie", "Monica Abrudan", "Marius Mihășan", "Mădălina Giurgiu", "Daria Mihalachi", "Michalis-Daniel Lazăr", "Horia L. Banciu" ], "abstract": "We describe the evolution of a bioinformatics national capacity from scattered professionals into a collaborative organisation, and advancements in the adoption of the bioinformatics infrastructure philosophy by the national community. The Romanian Society of Bioinformatics (RSBI), a national professional society, was founded in 2019 to accelerate the development of Romanian bioinformatics. Incrementally, RSBI expanded its role to include: i) developing a community and engaging the public and stakeholders, ii) a national training approach, including through increased interactions with European training resources, and iii) advocating national participation in European bioinformatics infrastructures. In a next step RSBI led the development of the national bioinformatics infrastructure, the Romanian Bioinformatics Cluster (CRB) with the mission to act as an ELIXIR National Node. In this paper we report both the successful projects in training, public engagement, and policy projects, as well as initiatives related to data federation that, while not successful, can serve as valuable learning experiences for future implementations. We explain CRB’s structure and the role such an entity can play in the national bioinformatics infrastructure for data, tools, and training. Finally, we offer insights into the evolving role of the bioinformatics professional society and the synergies and interactions with the National ELIXIR Node", "keywords": [ "bioinformatics society", "ELIXIR", "FAIR", "training", "public engagement" ], "content": "Introduction\n\nThe need for centralised data resources and bioinformatics services prompted the development of dedicated infrastructures. The establishment in 1994 of the European Bioinformatics Institute (EMBL-EBI), an outstation of European Molecular Biology Laboratory (EMBL) was followed by the development of bioinformatics networks and national bioinformatics infrastructures in most European countries. These infrastructures encompass resources and services that are organised and coordinated at a country level, and aim to provide the necessary tools, resources, and expertise to researchers and organisations within a country. The infrastructures include several key components: collaboration and networking, data, software, computing resources, training, support, ELSI (Ethical, Legal and Societal Implications) and outreach.\n\nIn a second phase, the increasing need to have synchronised approaches across Europe led to the development of the distributed infrastructure for life-science data (ELIXIR) (Crosswell and Thornton, 2012; Harrow et al., 2021). ELIXIR was developed as a project in 2006 and became an ESFRI (European Strategy Forum on Research and Innovation) landmark in 2016. ELIXIR brings together national centres across Europe into a coordinated infrastructure for bioinformatics.\n\nThe relevance of such organisations became obvious during the COVID-19 pandemic, as nations urgently depended on them to access analysis pipelines and efficiently manage data. Currently, large scale European projects, such as the European Genomic Data Infrastructure (GDI) and EOSC-ENTRUST, rely on these structures for their European and national reach. In addition, while the bioinformatics ecosystem has increasingly embraced the FAIR (Findable, Accessible, Interoperable, and Reusable) principles for data (Rocca-Serra et al., 2023; Wilkinson et al., 2016), software (Barker et al., 2022; Goble et al., 2020; Patel et al., 2023), and training (Garcia et al., 2020), the effective implementation of these principles remains challenging. The national bioinformatics infrastructures were identified to be adequate mechanisms to overcome these challenges (Soranzo and Goble, 2023).\n\nA keystone of national bioinformatics infrastructures, the national professional organisations in bioinformatics play roles in networking facilitation, training or job placement. Importantly, through the implicit national representation, these professional organisations can ethically advocate the interests of the profession, broaden participation, drive change, develop and deploy standards and ethical guidelines. (Mourad et al., 2018; Suddaby et al., 2002). Bioinformatics professional organisations exist in most European countries, although their role depends on national circumstances. Guidelines on how to establish bioinformatics communities and scientific professional societies can be found in (Budd et al., 2015) and (Gaëta et al., 2017).\n\nWe present in this paper the priming and evolution of the bioinformatics community and ecosystem in Romania between 2017 and 2024. We describe how the Romanian bioinformatics community evolved into an established national society - the Romanian Society of Bioinformatics (RSBI), the process of preparing a national bioinformatics infrastructure and the steps towards Romania’s ELIXIR Membership.\n\n\nEstablishment of a professional society in bioinformatics in Romania\n\nThe RSBI was established as a bioinformatics professional society following a preparation phase that started in 2017 with a mission to enhance Romania’s bioinformatics capacity. At that time, Romania lacked the critical mass necessary to develop self-sustaining bioinformatics programs and had minimal collaborations among bioinformatics groups across the country.\n\nThe development of the bioinformatics community into a national society was closely tied to a series of bioinformatics workshops organised by the founding group. By co-organising workshops in partnership with various host organisations, and establishing a presence in different academic centres (Bucharest, Cluj-Napoca, Iaşi, Timişoara), RSBI achieved widespread national distribution and facilitated connections among scientists from its inception.\n\nRSBI officially came into existence in 2019, following the approval by the Romanian Government for RSBI to adopt the national reference, an approval given after the founding community demonstrated national representation. Importantly, the development of the society and the Bylaws of Association were freely debated among the founding members of the association.\n\nRight from the start, RSBI prioritised transparency, a sense of ethics, and achieving a balanced geographical, academic and gender representation. Of note, the initial development was facilitated by a strong involvement of the Romanian diaspora from the Wellcome Sanger Institute and the European Bioinformatics Institute, UK.\n\nRSBI is governed by a board of up to 6 members. Among these members, one serves as the legal representative. The board is chosen by the General Assembly through a voting process, an anonymous voting procedure being adopted starting April 2024.\n\nThe society fosters continuous communication among its members, recognizing it as a fundamental aspect of its operations. This communication is facilitated through an email group as well as monthly meetings. Additionally, RSBI ensures engagement with stakeholders and the public through active management of social media accounts (RSBI, 2018a, 2018b)\n\nRSBI’s initial objectives were to run bioinformatics training at national scale and organise the community so it can provide support to the development of academic bioinformatics training. Although the training events remained the core activity, RSBI developed as a proactive organisation, taking additional roles in building the Romanian bioinformatics ecosystem through engagement with the public and advocacy for infrastructure and policy development (Figure 1).\n\nFollowing an initial emphasis on training and public engagement events, RSBI has assumed roles in advocating Romania’s participation in European initiatives and the development of the national bioinformatics infrastructure CRB. The RoBioinfo Seminars started in 2018, and, since then, RSBI organised more than 30 training and 20 public engagement events. The infrastructure development campaigns included multiple communications campaigns addressed to public administration officials and extensive communication campaigns to the research community. Abbreviations: SRGM - Societatea Română de Genetică Medicală (Romanian Society for Medical Genetics), FEGA - Federated European Genome-phenome Archive, RSBI - Romanian Society of Bioinformatics.\n\nTraining\n\nThe RoBioinfo Seminars, a national bioinformatics training programme (30+ events; Extended data 1), owe much of the initial development to the support provided by groups from EMBL-EBI Training, Ensembl Training, Polish Bioinformatics Society (PTBI), Italian Bioinformatics Society (BITS), and the Hungarian ELIXIR Node. The initial collaborations, coupled with a proactive communication campaign, resulted in an average pre-pandemic participation rate of 20% from neighbouring countries to the RoBioinfo Seminars. In addition to their technical substance, the in-person RoBioinfo Seminars are notable for fostering a scientific and inclusive atmosphere, providing an opportunity for Romanian bioinformaticians to meet and facilitating the development of the national network.\n\nFrom 2022 to 2024, through bilateral cooperation with ELIXIR Norway, funded by a grant from the Bilateral Fund associated with the EEA and Norwegian Grants 2014-2021, the focus of the workshops expanded to include new topics such as data federation and scientific workflow systems. In 2023, RSBI initiated the annual RoBioinfo Conferences as part of the same project.\n\nPublic engagement\n\nPublic engagement has been from the very beginning a substantial part of RSBI’s philosophy. Following the model of previously tested initiatives (Georgescu, 2023), RSBI organised several “Beer and Science” and “Science in schools” events. Initially a satellite event to the RoBioinfo Seminars, “Beer and Science” has since evolved into standalone events. While open to the public, their primary aim remains fostering connections among students, young and established scientists across various disciplines, research groups and scientific interests. We provide in Extended data 2 the RSBI perspective and toolkit for organising Beer and Science events. Importantly, these events had the desired secondary effect of developing a sense of community and social impact within the organisation.\n\nFurthermore, RSBI has also actively contributed to informing the general public on topics of high interest. During the COVID-19 crisis RSBI collaborated with the Romanian Executive Agency for Higher Education, Research, Development and Innovation Funding (UEFISCDI) to better inform the general public (UEFISCDI, 2020). RSBI also developed information leaflets for public and general medical practitioners on the relevance of federating genomics data (Extended data 3). Importantly, as RSBI is an organisation of scientists, achieving sustained communication with the general public on a large scale can only be accomplished through collaborations with other organisations.\n\nPolicy\n\nRSBI has actively contributed to the reform of public policies in genomics and bioinformatics. This involvement includes contributing to the development of national research strategies in life sciences and digitalization, as well as advocating for participation in European initiatives on genomics and bioinformatics. Following an organic approach, RSBI has worked to raise awareness and gather feedback within the scientific community. Subsequently, this feedback has been passed to policymakers, aiming to ensure that perspectives from relevant stakeholders are considered in the policymaking process.\n\nFor this purpose RSBI co-organised a series of webinars targeting the research community (ELIXIR, 2024, 2020) and has disseminated information to the public through press releases, radio interventions and social media, (e.g. (RSBI, 2023)).\n\nRSBI then engaged with the Romanian Ministry of Research, Innovation and Digitalization (MCID) on matters concerning human genomics and bioinformatics in general. Recognizing the importance of grounding political actions in research realities, RSBI documented and presented to political representatives the scientific motivation for national level approaches to genomics, the opportunities provided by the European bioinformatics infrastructure, and drawbacks of non-participation in such initiatives.\n\nBuilding upon the groundwork laid by RSBI between 2020 and 2023, and with proactive involvement from the University of Medicine and Pharmacy “Carol Davila”, Bucharest, MCID made the decision in 2023 to sign the ‘1+ Million Genomes’ (1+MG) European initiative (Romanian Government, 2023) and join the European bioinformatics infrastructure - ELIXIR (ELIXIR, 2023).\n\nAttempts towards data federation\n\nEfforts towards data federation in Romania, led by RSBI, did not yield similar levels of success as of above-mentioned initiatives (Extended data 4). While there is recognition of the importance of integrating individual contributions into major European data initiatives like the COVID-19 Data Portal (Harrison et al., 2021) or the Federated European Genome-phenome Archive (FEGA) (Freeberg et al., 2021), insufficient resources and incentives hindered active participation and contribution from individual groups.\n\nDespite their slow development, adopting data federation in some form, and establishing the necessary data structures are crucial for numerous research projects. This underscores the significance of having national bioinformatics infrastructures capable of implementing data solutions on a national level and providing support to research groups.\n\nThe principles described in (Budd et al., 2015) and (Gaëta et al., 2017) proved to be important for the development of RSBI. The clear mission, the commitment to inclusivity, a positive work environment, and the recognition of contributions attracted a substantial number of contributors. The organisation has evolved based on feedback from its members. For instance, suggestions regarding the need for consistent communication were implemented, resulting in the establishment of monthly RSBI meetings. Of note, sustaining and developing a professional society requires significant community management effort, an activity that usually goes beyond expected voluntary academic involvement. As also mentioned in (Budd et al., 2015), appropriate compensation for community managers would be a mechanism to ensure sustainability.\n\nImportantly, given the ongoing development of the field and the ubiquitous large national genomics programs, a national bioinformatics society can have a significant impact. To maximise this impact, we add to the previous guidelines the recommendation of 1) establishing working relationships with the public administration and 2) identifying the overlaps and synergies with the bioinformatics infrastructures, e.g. with the National ELIXIR Nodes.\n\n\nTowards the national bioinformatics infrastructure - the Romanian Bioinformatics Cluster\n\nRecognizing the deficiencies in both data and training infrastructure, RSBI suggested to the national community the development of an entity capable of conducting nationwide activities to address these challenges.\n\nFollowing a thorough consultation period within the research community, the Romanian Bioinformatics Cluster, or “Clusterul Român de Bioinformatică” in Romanian, hereon CRB, was established in 2022 by seventeen universities and research and medical organisations in collaboration with two national professional organisations (Figure 2; https://bioinfocluster.ro/). CRB operates as a not-for-profit entity with legal status and a federated structure. Its organisational model draws inspiration from national ELIXIR consortia.\n\nA) Steps followed in creating a functional ELIXIR Node, starting with community consultation in 2022 the governmental decision to submit the membership request in April 2024 and culminating with Romania's application being approved by the ELIXIR Board in June 2024. The diagram highlights the critical importance of three aspects for a functional ELIXIR Node: community involvement, recruitment of coordinators for data, tools, and training, and engagement with the government. b) Distribution of CRB founding members across Romania: many of the major Romanian research centres and the two professional societies are represented in CRB.\n\nCRB is governed by the General Assembly of Members, in which each member institution has a representative and an executive body, the Board of Directors. The Board of Directors is elected for a 2-year mandate, an anonymous nomination and voting procedure being implemented starting May 2024. The daily administration is carried out by an Administrative Entity, currently “G. E. Palade” University of Medicine, Pharmacy, Science and Technology of Târgu Mureş.\n\nThe primary objectives of CRB include:\n\n• A framework for the development of national bioinformatics training and training resources. This entails backing programs conducted by RSBI, as well as contributing to the development and upkeep of bioinformatics training resources, and facilitating the training delivery. In practice, within the framework developed by the ELIXIR Training Platform, this will consist in the development of an eLearning ecosystem, supporting the implementation of the FAIR-ification (Garcia et al., 2020) of training materials, and supporting the train-the-trainer programmes in bioinformatics.\n\n• Increase the value of data through the development of data infrastructures. CRB aims to facilitate the development of data infrastructures for molecular data by supporting research organisations in deploying national instances of data structures (eg. portals for pathogen data (Harrison et al., 2021) or human data (Freeberg et al., 2021)), implementing novel techniques to data sharing (Amid et al., 2019) and ensuring uniform access, e.g. by building on the the LS Login authentication service from EOSC-Life.\n\n• Ease the choice and use of bioinformatics tools. CRB will aim to achieve this by implementing a distributed help desk system and by supporting the development of a national bioinformatics software ecosystem integrated in the European framework. This will build on advancements in scientific workflow managers (Crusoe et al., 2022; Di Tommaso et al., 2017; Goble et al., 2021; The Galaxy Community, 2022), software benchmarking (Pico et al., 2022) and European projects aimed at developing an integrated ecosystem, e.g. https://research-software-ecosystem.github.io/. The support will include contributions to European initiatives, engaging the national community to adopt these advancements, and launching or supporting relevant national instances.\n\nThanks to its federated structure and strong interaction within ELIXIR, CRB possesses the necessary mechanisms to assist member universities and other national research centres in adopting best practices and adhering to standards. This is particularly significant given that new projects in life sciences are slated for funding in Romania in 2024, and Romania expanded its participation in European research infrastructures through the development of National Nodes for ERIC-MIRRI (Observership; 2023) and Genomic Data Infrastructure (Onboarding; 2024). Harmonising the bioinformatics outcomes and addressing the technical and differing issues to achieve functional interoperability requires inter-institutional approaches, such as those enabled through the CRB structure.\n\n\nDiscussions - an evolving bioinformatics ecosystem in Romania\n\nThe initial phase of RSBI’s development was driven by a pressing need to start bioinformatics training, foster a sense of community, advocate for the importance of this profession, and contribute to the establishment of a country-wide network of bioinformaticians.\n\nThe present and forthcoming period for the Romanian life sciences is marked by the implementation or planning of several large-scale projects requiring bioinformatics, and Romania’s integration into the broader European bioinformatics ecosystem. Coinciding with these developments, RSBI approached a maturity stage, a stage in which its role as a professional organisation is evolving.\n\nMaintaining a strong sense of community remains RSBI’s fundamental mission. This spirit of community is crucial not only for facilitating training and networking but also for spearheading the adoption of new methodologies. Monthly meetings, annual conferences, training and public engagement events have been and will continue to be effective mechanisms for connecting the community. Alongside these, the establishment of national communities of practice embedded in the ELIXIR communities is anticipated to accelerate the development of the national bioinformatics capacity. As a transversal organisation, RSBI can act as a unifying force for stakeholders, bringing together diverse parties to facilitate discussions in the best interest of national bioinformatics. RSBI can also play a significant role in strengthening the local community by sustainably connecting Romanian bioinformatics professionals in the diaspora with scientists in the country.\n\nThe training activities are poised to evolve with the adoption of FAIR principles. As high-quality resources become more available, especially through ELIXIR, there is a need to adjust the training model accordingly. The national bioinformatics training program must transition to a more integrated approach, aligning closely with the broader European resources offered by ELIXIR Nodes.\n\nThe engagement with the wider life science community and the public would need to be scaled up. Of note, community engagement and involvement is becoming a prerequisite for major research projects. National professional societies and infrastructures offer the optimal framework for fostering this involvement. RSBI can achieve sustained communication with the general public on a large scale through collaborations with other organisations.\n\nThe evolution of bioinformatics as a profession, along with its expanding roles in science and industry, will inevitably raise new ethical considerations. RSBI must gradually transition into assuming the role of an ethics body to address these emerging ethical challenges.\n\nImportantly, RSBI’s activities must be closely linked with those of CRB. Firstly, the infrastructure developed by CRB, and notably the mechanisms to implement FAIR, can be impactful only if adopted by the community. RSBI has the scale and mechanisms to advocate for these principles within the community. Secondly, an ELIXIR Node has the institutional mechanisms to leverage the resources required by RSBI to organise training and public engagement programmes. Finally, the relationship between these two organisations, both developed on ethical principles, offers a framework to maintain checks and balances, ensuring equitable access to resources and appropriate representation of community interests. Although the scope of an ELIXIR Node, which focuses on infrastructure development, differs from that of a national professional organisation, which aims to connect, facilitate career development, and represent the professional community, these entities must work closely, optimise synergies, and manage overlaps.\n\n\nAuthor contributions\n\nBM developed the concept with input from HLB and MA. BM performed the research and prepared the manuscript. DM and MDL prepared the figures included in the manuscript. CZB prepared the Supplementary Material 2. MA, HLB and CZB contributed to the preparation and revision of the manuscript.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nZenodo: Extended Data 1: The list of RoBioinfo Seminars, workshops and webinars organised between November 2017 and April 2024. https://doi.org/10.5281/zenodo.13235287 (RSBI, 2024a).\n\nThis project contains the following extended data:\n\n- The RoBioinfo Seminars, workshops and webinars.pdf\n\nZenodo: Extended Data 2: Beer and Science - Public Engagement Toolkit. https://doi.org/10.5281/zenodo.13235179 (RSBI, 2024b).\n\nThis project contains the following extended data:\n\n- RSBI Beer and Science toolkit.pdf\n\nZenodo: Extended Data 3: Human Genomics - Public Engagement Leaflets - Romanian. https://doi.org/10.5281/zenodo.13150360 (RSBI, 2024c).\n\nThis project contains the following extended data in Romanian with corresponding ENglish translations: translations:\n\n- RSBI Public Engagement leaflet - medical doctors.pdf\n\n- RSBI Public Engagement leaflet - public.pdf\n\nZenodo: Extended Data 4: Data federation advocacy attempts. https://doi.org/10.5281/zenodo.13235768 (RSBI, 2024d)\n\nThis project contains the following extended data:\n\n- Data federation advocacy attempts.pdf\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 wish to acknowledge the following individuals who have played instrumental roles in developing the Romanian Society of Bioinformatics: Khalil Abudahab, Irina Armean, Iuliana Bocicor, Mihai Glonţ, Eivind Hovig, Claudiu Mihăilă, Valeriu Ohan, Kjell Petersen, Elena Poenaru, Larisa Sârghie, Robi Tăcutu, Daniela Zaharie.\n\n\nReferences\n\nAmid C, Pakseresht N, Silvester N, et al.: The COMPARE Data Hubs. Database J. Biol. Databases Curation. 2019; 2019: baz136. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBarker M, Chue Hong NP, Katz DS, et al.: Introducing the FAIR Principles for research software. Sci. Data. 2022; 9: 622. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBudd A, Corpas M, Brazas MD, et al.: A Quick Guide for Building a Successful Bioinformatics Community. PLoS Comput. Biol. 2015; 11: e1003972. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCrosswell LC, Thornton JM: ELIXIR: a distributed infrastructure for European biological data. Trends Biotechnol. 2012; 30: 241–242. PubMed Abstract \| Publisher Full Text\n\nCrusoe MR, Abeln S, Iosup A, et al.: Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language. Commun. ACM. 2022; 65: 54–63. Publisher Full Text\n\nDi Tommaso P, Chatzou M, Floden EW, et al.: Nextflow enables reproducible computational workflows. Nat. Biotechnol. 2017; 35: 316–319. PubMed Abstract \| Publisher Full Text\n\nELIXIR: Webinar series: National bioinformatics communities in ELIXIR. ELIXIR; 2020. [WWW Document]. (accessed 4.30.24). Reference Source\n\nELIXIR: Romania joins ELIXIR as Observer [WWW Document]. ELIXIR; 2023. (accessed 4.30.24). Reference Source\n\nELIXIR: ELIXIR Romania Webinar [WWW Document]. ELIXIR; 2024. (accessed 4.30.24). Reference Source\n\nFreeberg MA, Fromont LA, D’Altri T, et al.: The European Genome-phenome Archive in 2021. Nucleic Acids Res. 2021; 50: D980–D987. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGaëta BA, Rivas JDL, Horton P, et al.: Ten simple rules for forming a scientific professional society. PLoS Comput. Biol. 2017; 13: e1005226. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGarcia L, Batut B, Burke ML, et al.: Ten simple rules for making training materials FAIR. PLoS Comput. Biol. 2020; 16: e1007854. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGeorgescu I: How a one-off public engagement event turned into an international science festival. Nat. Rev. Phys. 2023; 5: 265–266. Publisher Full Text\n\nGoble C, Cohen-Boulakia S, Soiland-Reyes S, et al.: FAIR Computational Workflows. Data Intell. 2020; 2: 108–121. Publisher Full Text\n\nGoble C, Soiland-Reyes S, Bacall F, et al.: Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory. Zenodo. 2021. Publisher Full Text\n\nHarrison PW, Lopez R, Rahman N, et al.: The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing. Nucleic Acids Res. 2021; 49: W619–W623. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHarrow J, Drysdale R, Smith A, et al.: ELIXIR: providing a sustainable infrastructure for life science data at European scale. Bioinformatics. 2021; 37: 2506–2511. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMourad TM, McNulty AF, Liwosz D, et al.: The Role of a Professional Society in Broadening Participation in Science: A National Model for Increasing Persistence. Bioscience. 2018; 68: 715–721. Publisher Full Text\n\nPatel B, Soundarajan S, Ménager H, et al.: Making Biomedical Research Software FAIR: Actionable Step-by-step Guidelines with a User-support Tool. Sci. Data. 2023; 10: 557. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\ndel Pico EM , Gelpi JL, Capella-Gutiérrez S: FAIRsoft - A practical implementation of FAIR principles for research software.2022. Publisher Full Text\n\nRocca-Serra P, Gu W, Ioannidis V, et al.: The FAIR Cookbook - the essential resource for and by FAIR doers. Sci. Data. 2023; 10: 292. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRomanian Government: 1 Million Genomes Memorandum - Romanian Government [WWW Document].2023. (accessed 4.30.24). Reference Source\n\nRSBI: RSBI Facebook Profile.2018a. Reference Source\n\nRSBI: RSBI LinkedIn Profile.2018b. Reference Source\n\nRSBI: Press release – Romanian Society of Bioinformatics [WWW Document].2023. (accessed 4.30.24). Reference Source\n\nRSBI: Extended Data 1: The list of RoBioinfo Seminars, workshops and webinars organised between November 2017 and April 2024. [Dataset]. Zenodo. 2024a. Publisher Full Text\n\nRSBI: Extended Data 2: Beer and Science - Public Engagement Toolkit. [Dataset]. Zenodo. 2024b. Publisher Full Text\n\nRSBI: Extended Data 3: Human Genomics - Public Engagement Leaflets. [Dataset]. Zenodo. 2024c. Publisher Full Text\n\nRSBI: Extended Data 4: Data federation advocacy attempts. [Dataset]. Zenodo. 2024d. Publisher Full Text\n\nSoranzo N, Goble C: BioFAIR: a new BioCommons infrastructure for UK life science.2023. Publisher Full Text\n\nSuddaby R, Greenwood R, Hinings C: Theorizing Change: The Role of Professional Associations in the Transformation of Institutionalized Fields. Acad. Manag. J. 2002; 45: 58–80. Publisher Full Text\n\nThe Galaxy Community: The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. Nucleic Acids Res. 2022; 50: W345–W351. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nUEFISCDI, RSBI: COVID19 Portal for Scientific Information [WWW Document].2020. (accessed 4.30.24). Reference Source\n\nWilkinson MD, Dumontier M, Aalbersberg IJJ, et al.: The FAIR Guiding Principles for scientific data management and stewardship. Sci. Data. 2016; 3: 160018. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "321797", "date": "25 Sep 2024", "name": "Francis Ouellette", "expertise": [ "Reviewer Expertise Computational biologist", "member of the Elixir SAB for the last 8 years." ], "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 opinion article \"From the Establishment of a National Bioinformatics Society to the Development of a National Bioinformatics Infrastructure\" present the evolution of a bioinformatics national community. They describe the existing bioinformatics infrastructure that the Romanian national bioinformatics community will use. This opinion is part of their process to establish and evolve the Romanian Node into a full member of Elixir Europe.\n\nThis opinion piece should expand on and clarify a few points. These comments are made in light of the nature of this submission: it is the expression of the author's opinion, not mine.\n\n1. This article is well-written, but the underlying objectives need to be clarified. This position paper would be more explicit to the reader if the authors expressed their intent to develop a national bioinformatics infrastructure and why they are doing what they describe.\n2. Knowing the reading audience is essential to consider when writing this opinion. If the audience is complex and diverse (e.g., politicians, senior biologists, new computer scientists, and trainees), you may need to target some sections for each audience.\n\n3. Another important point: Are there particular biological questions that need to be answered by this community? Do they need trained bioinformaticians, dedicated resources, cloud computing, specific tools, or specialized databases to answer these questions? Is there a need for the medical community to be able to interpret human genomes? Specific environmental microbiomes? Do veterinarians need to understand and deal with specific outbreaks? Do farmers have specific pest management challenges resulting from global warming they have never anticipated? Are the current biology and health sciences programs ill-equipped to address these challenges?\nIf so, the community may need to train bioinformatics people at all levels (undergraduates, graduate, post-doc, and professional development programs), and for that work to get done, you will also need funding (scale of funding necessary). An opinion piece like this one is an opportunity to explain what the needs are, how to achieve these needs and defend the budget necessary to make this possible.\n\nComments about the figures:\n4. Figure 1: The idea of a timeline is excellent. This timeline represents many of the items detailed in the text. The figure has too much text and should be redone with one or two points for each critical time point. Can a reference tag be used in the text? I am unsure about the rules for this journal, but it might be useful to consider a separate table with all the acronyms used in this opinion.\n\n5. Figure 2 A: This figure (2A) is not helpful here. It repeats much of the text in the opinion piece.\n6. Figure 2 B: Maps are great information tools, but could this information also be useful in a table?\n1- City 2- Name of university/Institution/company (with URL) 3- Department(s) involved 4- Bioinformatics expertise (maybe develop 5 or 6 codes for different disciplines?\n\nMedical genetics, Computer Assisted Drug\n\ndevelopment, HPC, Database or Algorithm development or any other\n\nspecialities. 5- Human-centric? Plant? Vetenary? Prokaryotic? Viruses? Ecology? Medicine? 6- Number of scientists involved in this community (group leader/trainees?) at this institution.\nThen, on this map, you could mark the cities (with orange counties where such institutions reside, as you have it now), and with this table, it would be a good community status at this point. Over the years, you could show a growing orange wave across Romania!\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Yes\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Partly", "responses": [] }, { "id": "321795", "date": "30 Sep 2024", "name": "Federico Zambelli", "expertise": [ "Reviewer Expertise Bioinformatics", "transcriptomics", "epigenomics", "research infrastructures", "cloud computing." ], "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 outline the establishment of the Romanian Society of Bioinformatics and the efforts towards building a national biological data infrastructure, including the formation of a tentative ELIXIR Node.\n\nMany of the problems and hurdles in the process are common with other countries, including the difficulty of interacting with policymakers and decision-making bodies to establish clear road maps, which are critical components in the construction and maintenance of any infrastructure, including those dedicated to scientific data.\nThe manuscript does a good job of describing Romanian bioinformatics' current situation and ambition, and the initiative's promoters are to be commended for their efforts in integrating national efforts in the European context. However, a more in-depth description of the current bioinformatics portfolio of resources, services, industry interactions (if any), interests, main actors, and expertise in Romania would help the reader understand the sector's growth potential in the country.\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Yes\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Yes", "responses": [] }, { "id": "321799", "date": "12 Oct 2024", "name": "Carol Goble", "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 paper is two parts, both concerning the establishment of a bioinformatics national community in Romania. The first part describes how and why a professional society was established; the second the steps towards a national node of the ELIXIR research infrastructure.\nThe article is informative and quite well written and describes the high level vision and the steps taken.\nAs an opinion piece it is short on opinion. It is unclear if the objective is to provide an announcement of the establishment of a society and an ELIXIR Node, or if there is some more significant discussion regarding the specific challenges within Romania or lessons that other countries might learn.\nSome clarity is needed in what is meant by a “national bioinformatics infrastructure”, which in this case is an ELIXIR Node. What an ELIXIR Node is, and the many forms of Nodes (there are 25 nodes including Romania) needs to be better described – most readers will not know. The term “infrastructure is open to interpretation In what way does the RSBI differ from other National societies? What did you find useful and less useful from using the guidelines you cite? What are the unique or special offerings of the Romanian Node to ELIXIR and what does Romania need for its bioinformatics community? There are 30+ communities and focus groups in ELIXIR – which ones are strengths or beneficial growth areas for Romania? The objectives of the CRB are rather high level and non-national specific. Does Romania have strengths in areas of rare disease, precision medicine, agritech, structiural bioinformatics, e-learning, AI etc What is the scale of a country-wide network of bioinformaticians? How many people? Data services? There are 17 organisations – are these funded as a network like ELIXIR UK or as a funded programme of joint work like ELIXIR-CZ? Is the CRB supported by a national award or subscriptions or in kind? Data federation takes many forms and is complex (it is not just FEGA) – two paragraphs are unclear what federation was expected or tried. A national ELIXIR Node is expected to interact with other nodes. Training with Hungary and Poland was mentioned and participation in GDI. Are here other opportunities given your CRB objectives?\nIn summary the paper would benefit from a clearer statement of its message and a clearer statement on the national needs and national resources. It can also provide useful critical insights on the challenges and resources needed to establish a national infrastructure useful for other nations. Minor points Introduction\nThe introduction’s history of ELIXIR should add that it was founded in 2013. It isn’t clear what is meant by “second phase” and I suggest you drop this phrase. The projects GDI, EOSC-ENTRUST should be cited. The sentence that these projects “reply on these structures for their European and national reach” is unclear. Do you mean they rely on national nodes? It is not clear who “these structures” and “they” refers to. National infrastructures were identified as “adequate” mechanisms is a strange statement. Needed or necessary or just mechanisms, perhaps. Figure 1 is useful but too busy to read Figure 2 A is unnecessary\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Yes\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-1002
https://f1000research.com/articles/13-1001/v1	03 Sep 24	{ "type": "Research Article", "title": "Strategic Lead Generation and Competitive Positioning for Bid Writing Consultancy Firms", "authors": [ "Hajar Fatorachian", "Ben Mitchell", "Kate Smith", "Filip Kisely", "Cech Natalie", "Maisey jones", "Ellie Pattison", "Ben Mitchell", "Kate Smith", "Filip Kisely", "Cech Natalie", "Maisey jones", "Ellie Pattison" ], "abstract": "Background The consultancy industry, valued at £18.6 billion, faces evolving challenges and opportunities in the post-COVID era. Consultancy and bid writing firms play a critical role in helping businesses secure contracts and funding, particularly through the preparation of Pre-Qualification Questionnaires (PQQs) and Invitations to Tender (ITTs). Despite the importance of bid writing, there is limited literature on how it can be leveraged for lead generation and business growth.\n\nMethods A mixed-methods approach was employed in this study, combining qualitative and quantitative research. Secondary research involved the review of existing literature and data from government databases, internal company records, and published reports. Primary research included surveys and semi-structured interviews with professionals from the Facilities Management and Logistics sectors. A case study of a UK-based bid-writing consultancy was also used to support the analysis.\n\nResults The findings highlighted significant knowledge gaps in bid writing among businesses, with only 12.5% of survey respondents expressing confidence in their bid-writing abilities. Despite this, 83.1% showed interest in receiving bid-writing training. The study also revealed that expertise, relationships, and past work are prioritized by businesses when selecting consultancy firms. Additionally, the integration of Artificial Intelligence (AI) in business operations was identified as a key factor for enhancing efficiency and maintaining competitiveness.\n\nConclusions There is a clear opportunity for consultancy and bid-writing firms to address the knowledge gaps in bid writing by offering targeted training programs. Effective networking and a robust social media presence are essential for generating new business leads and maintaining client relationships. Furthermore, integrating AI technologies into business operations can provide consultancy firms with a competitive edge. This study provides actionable insights for consultancy and bid-writing firms to enhance their lead generation strategies and improve their market positioning.", "keywords": [ "Consultancy industry", "bid writing", "lead generation", "competitive positioning", "AI integration", "networking", "social media" ], "content": "1. Introduction\n\nThe consultancy industry is a significant economic contributor, valued at approximately £18.6 billion and predicted to continue growing (Management Consultancies Association [MCA], 2024). With over 235,800 management consultants in the UK, the market is dominated by large firms such as KPMG, PwC, and Deloitte (Statista, 2024; Consultancy.uk, 2020). Despite this robust growth, the industry faces challenges, particularly following the Covid-19 pandemic. Financial constraints and global restrictions have impacted businesses and their consultancy partners (Gartner, 2022). To mitigate these risks, consultancy firms must diversify their clientele across multiple sectors, spreading risk and seizing growth opportunities.\n\nBid writing is a critical aspect of consultancy services, essential for securing contracts and funding. Bid writers play a crucial role in helping companies complete essential documents such as Pre-Qualification Questionnaires (PQQs) and Invitations to Tender (ITTs). Their success hinges on establishing strong relationships with business development and sales teams, effectively understanding customer requirements, and articulating compelling business propositions (Crawford, 2022). Expertise in the tendering process, comprehension of contract specifications, and superior communication skills are vital to the bid-writing process (Lowe, 2023). Successful bids can significantly enhance revenue and reputation, opening new avenues for growth, while poorly executed bids can result in missed opportunities and harm a company's image (Crawford, 2022).\n\nDespite the vital role of bid writing in both the private and public sectors, it remains underexplored in current literature, with limited understanding of how bid writing can be leveraged to generate new business leads (Swanson et al., 2019; McMahon, 2013; Noonan & Healy, 2010). The public sector emphasizes regulatory compliance and transparency in bid writing (Lewis, 2015), while the private sector offers more flexibility and discretion in evaluating submissions (Forshaw, 2017). Understanding these dynamics is crucial for consultancy firms aiming to enhance their bid writing processes and lead generation strategies.\n\nBy integrating bid writing expertise with broader consultancy services, firms can better navigate the complexities of securing contracts, thereby fostering business opportunities and growth. This dual approach not only mitigates risks associated with economic downturns but also positions consultancy firms to attract a diverse client base across various sectors.\n\nThe pandemic has highlighted the vulnerability of consultancy firms relying on a narrow client base. Diversification is essential, but it presents challenges such as resource allocation, staff satisfaction, and increased costs. This study aims to address these challenges by exploring strategies for organic expansion into new sectors while maintaining high standards. The significance of this research lies in its potential to provide actionable insights for consultancy and bid writing firms, helping them navigate the post-pandemic landscape, attract new clients, and enhance their competitive positioning.\n\nThe aim of the paper is to identify strategies for consultancy and bid writing firms to generate new business leads. Specifically, the study intends to encompass industry best practices, competitive positioning, new client identification, and ways to strengthen existing client relationships while providing strategic directions for future improvement. The objectives are:\n\n1. To assess the most effective ways to approach and develop potential clients.\n\n2. To develop an operational framework for consultancy and bid writing firms to improve current lead generation and marketing strategies.\n\nThis paper aims to make significant contributions by outlining effective methods for consultancy firms to procure clients. Competitor analysis literature was reviewed to determine how consultancy and bid writing firms could differentiate from competitors.\n\n\n2. Literature review\n\nThe purpose of the literature review is to critically examine existing literature surrounding bid writing, consultancy, B2B lead generation, and competitor analysis.\n\nBid writers are crucial to helping companies secure contracts or funding by completing essential documents such as PQQs and ITTs. Their success centers on establishing strong relationships with business development and sales teams to effectively grasp customer requirements (Crawford, 2022). Bid writing serves as a persuasive sales pitch, promoting why a particular business is the optimal choice for a contract, with the potential to significantly enhance revenue and reputation while unlocking new avenues for growth. Conversely, poorly executed bids can result in missed opportunities, wasted resources, and damage to a company's image (Crawford, 2022). Lowe (2023) highlighted that expertise in the tendering process, comprehension of contract specifications, and expert communication skills are very important to the bid-writing process. For example, bid-writing consultancies offer specialized knowledge and experience to navigate bid details, assisting organizations in securing vital contracts that help them reach their full potential.\n\nDespite the importance of bid writing in both private and public sectors, it has not been sufficiently explored, and current literature provides limited understanding of how bid writing could generate new business leads (Swanson et al., 2019; McMahon, 2013; Noonan & Healy, 2010). Public bid writing entails the thorough preparation of proposals for government contracts, following strict regulations and standardized evaluation processes. Lewis (2015) emphasizes the significance of transparency and adherence to procurement rules within EU member states. In contrast, private bid writing for commercial contracts lacks extensive literature, creating challenges for analysis. Nevertheless, public bid writing emphasizes regulatory compliance and transparency, while private sector bids offer greater flexibility, allowing buyers to evaluate submissions based on their preferences and criteria (Forshaw, 2017).\n\nTherefore, understanding the principles and challenges of bid writing in both public and private sectors is key for consultancy firms to develop effective lead generation strategies. By aligning with bid writers' needs, prioritizing relationship-building, and offering specialized support in navigating bid complexities, consultancy firms can enhance their value proposition and attract clients seeking assistance in securing contracts and funding. Leveraging expertise to address knowledge management weaknesses and streamline bid processes, consultancy firms can position themselves as trusted partners for organizations seeking a competitive advantage and sustainable success through efficient bid management.\n\nThe Management Consultancies Association (MCA) defines consultancy as ‘the practice of creating value for organizations through improved performance, achieved by providing objective advice and implementing solutions’ (MCA, 2019). This resonates with the mission of many consultancy firms, including those specializing in bid writing, which aim to deliver business success (Consultancy/bid writing businesses, 2024). While consultancy has been regarded as a catalyst for organizational change, helping to create and sustain improvement by building and maintaining relationships, the concrete definition of successful consultancy remains debatable due to the subjectivity of success and often the struggle to quantify results (Hodges, 2017).\n\nThe evolution of consultancy as a business sector has been influenced by globalization and the increasing responsibilities of senior executives (Hodges, 2017). This has led to extensive literature on management consultancy. However, there is a need to expand consultancy literature within specific organizational contexts. Some academics and authors have attempted to bridge this gap (O’Mahoney & Markham, 2013). Nonetheless, the rise of consultancy firms offering specialist services across all business functions has exceeded the rate at which consultancy literature is developing, highlighting the need to explore how bid-writing consultancy practices may or may not differ from traditional management consultancy.\n\nHawkins and Smith (2013) identify two main areas of consultancy: technical and facilitative. They argue that the former provides clients with skills and competencies to increase overall performance, while the latter focuses on facilitating client development through education and workshops, enabling clients to realize unfulfilled potential within their companies. Therefore, for consultancy and bid writing firms to capitalize on potential clients successfully, it is important to distinguish between their roles as both technical and facilitative consultants, positioning both appropriately to clients.\n\nA study by Williams and van Triest (2023) analyzes the notion that consultancy firms in the private sector should conduct their activities in ways that enable innovation through knowledge exchange (Bessant & Rush, 1995; Howells, 2006). Their research concludes that previous literature often generalizes consultants into a homogeneous category, which they believe is outdated due to rapid technological advancements and the diversity in approaches to innovation from private sector clients. This research suggests that the needs of private sector clients are evolving rapidly, bearing great significance for consultancy and bid writing firms to understand, adapt, and respond to challenging environments. To provide successful bid-writing consultancy and business development services, firms need to be well-versed in their clients' goals for innovation and understand how technological advancements can be integrated within their service offerings.\n\nBy integrating these insights, consultancy and bid writing firms can better navigate the complexities of their clients' needs, offering tailored solutions that drive business growth and foster long-term success.\n\nB2B lead generation is crucial for businesses seeking to expand their client base and increase profitability. Effective lead generation relies on continuous refinement and improvement of business processes (Stevens, 2011). Traditionally, lead generation involves engaging and capturing interest in a product, service, or company with the goal of increasing sales or acquiring new clients (Lukowski & Swieczak, 2016).\n\nIn the context of SMEs, where resources are often limited compared to larger corporations, the emphasis on creating value for potential clients becomes paramount. Unlike larger firms, SMEs must prioritize the quality of lead generation over quantity (Perez & Cambra-Fierro, 2015). The advent of Artificial Intelligence (AI) has revolutionized the lead generation landscape. AI algorithms can now predict the likelihood of a lead resulting in a successful sale, enabling firms to concentrate their efforts on leads with higher conversion potential (Peddireddy & Peddireddy, 2023). This shift towards predictive analytics and data-driven decision-making allows businesses, including consultancy and bid writing firms, to optimize their lead generation strategies, enhancing efficiency and effectiveness.\n\nB2B lead generation serves as a critical mechanism for businesses to identify and attract potential clients, thereby increasing growth and driving profits. As technology advances, particularly with AI integration, businesses have increasingly powerful tools at their disposal to modernize and enhance their lead generation processes, maximizing their revenue-generating potential (Hadjikhani & LaPlaca, 2013).\n\nDespite the current literature providing a foundation on lead generation and marketing strategies within the B2B domain, there remains a considerable research gap regarding how bid-writing consultancy firms adapt their lead generation strategies to maintain competitiveness in this specialized niche. Value creation involving segmentation, targeting, positioning, and differentiation is crucial for any organization, including consultancy and bid writing firms (Kotler et al., 2023). Given the specialized nature of bid-writing consultancy services, understanding and effectively implementing these principles can significantly enhance their ability to attract and convert potential clients.\n\nSegmentation allows consultancy firms to identify specific market segments with distinct needs and preferences, facilitating tailored marketing efforts. Targeting ensures efficient allocation of resources towards reaching the most promising prospects within these segments. Positioning helps consultancy firms establish a unique and favorable perception among their target audience, setting them apart from competitors. Differentiation allows these firms to emphasize their unique value proposition and capabilities, highlighting why potential clients should choose their services over others in the market. By applying established theories and concepts in lead generation, consultancy firms can strengthen the credibility and relevance of their marketing efforts, driving business growth and success.\n\nThe literature by Rėklaitis & Pilelienė (2019) highlights the essential differences between B2B and B2C marketing communication processes, offering invaluable insights for consultancy firms. B2B marketing strategies predominantly revolve around logical appeals tailored to businesses, contrasting with B2C strategies that emphasize emotional appeals directed at individual consumers. These distinctions necessitate tailored approaches, with B2B emphasizing personalized engagements and secondary objectives like brand loyalty, unlike the direct sales focus of B2C. Moreover, B2B decision-making involves multiple stakeholders, differing from the more individual-centric decisions in B2C.\n\nKumar & Raheja (2012) focus on the unique characteristics of B2B and B2C e-commerce transactions, incorporating negotiation complexity, platform structures, and payment options. Understanding these distinctions is necessary for consultancy firms to shape their client interactions and marketing strategies effectively. Consultants can align their messaging and services with the professional and logical appeals of B2B engagements while acknowledging the emotional drivers in B2C interactions. By leveraging this understanding, consultancy firms can adeptly tailor lead generation strategies to meet the distinct needs of each market segment, thereby strengthening client acquisition and retention efforts.\n\nThis comprehension empowers consultancy firms to tailor their client interactions and marketing strategies accordingly. With B2B engagements prioritizing logical appeals and personalized interactions, consultancy firms can focus on establishing professional relationships and addressing the multifaceted needs of stakeholders. At the same time, recognizing the emotional drivers in B2C interactions enables consultancy firms to refine their messaging and services to resonate with individual consumers. Leveraging these insights, consultancy firms can effectively shape their lead generation strategies, optimizing client acquisition and retention efforts across diverse market segments.\n\nOverall, the significance of B2B lead generation in driving business growth, particularly with advancements in technology like AI, and the discussion on value creation principles alongside the distinctions between B2B and B2C marketing communication processes, offers valuable guidance for consultancy and bid writing firms in shaping effective lead generation strategies. However, while the existing literature provides a foundation, there remains a notable research gap regarding how bid-writing consultancy firms specifically adapt their lead generation approaches. Further targeted research is necessary to address the unique challenges and opportunities within this specialized niche comprehensively. Such research efforts would not only enrich our understanding of bid-writing consultancy but also provide actionable insights to optimize lead generation efforts effectively for these firms.\n\nMichael Porter's work in 1980 was pivotal in helping businesses understand their competitive landscape and position themselves to achieve a competitive advantage. He identified five forces that assess the competitiveness of an industry:\n\n1. Bargaining power of buyers\n\n2. Bargaining power of suppliers\n\n3. Threat of new entrants\n\n4. Threat of substitutes\n\n5. Rivalry among current competitors\n\nPorter's framework suggests that competition extends beyond existing rivals. This insight is crucial for consultancy and bid-writing businesses, indicating that their strategic positioning should consider all industry factors rather than focusing solely on competitors' behaviors. While Porter's forces provide a strong starting point, they offer limited guidance on developing a competitive strategy (Dobbs, 2014). Additionally, the methods for assessing competition have evolved, with technology enabling quantifiable analysis. However, Porter did not address the quantification and relative importance of each force (Isabelle, Horak, McKinnon, & Palumbo, 2020).\n\nThe emergence of artificial intelligence (AI) has dramatically shifted the definition of competitiveness. Iansiti and Lakhani (2020) argue that in the modern world, competitive advantage is defined by an organization's ability to integrate, control, and shape digital networks and data. Companies that leverage data analytics and AI to extract value and gain insights will thrive in a digitalized environment (Zhu & Iansiti, 2019). The value of a digitally integrated firm increases exponentially with more users, as data analytics become more powerful. In contrast, traditional business models may struggle to organize and understand large amounts of data (Iansiti & Lakhani, 2020).\n\nThis literature is highly relevant for consultancy and bid-writing businesses. Utilizing digital networks to showcase their capabilities and integrating digital and AI technologies can provide insightful data on potential clients, offering a competitive edge.\n\nFurthermore, to remain competitive, service-providing firms must focus not only on establishing a competitive advantage but also on sustaining it through service integration and continuous innovation (Matthyssens & Vandenbempt, 1998). Suciu and Borza (2010) emphasize the critical role of employee development in the service industry. Companies must enable their employees to effectively communicate with, understand, and develop potential clients, which enhances existing relationships. The development of employees can lead to increased financial performance, creating a cycle of reinvestment in recruitment and motivation of new employees (Wirtz & Lovelock, 2021).\n\nTherefore, for consultancy and bid-writing businesses to impact their clients more effectively than competitors, they should focus on two key areas that drive innovation: the integration of digital systems and data, and the continuous development of employee competencies. Combining these factors should enable a high degree of competitiveness, as other aspects like price and service waiting time can be easily matched by competitors (Allon & Federgruen, 2007).\n\nRecognizing the evolving dynamics of consultancy services within specific organizational contexts, particularly the emphasis on digital integration and employee development, allows consultancy and bid writing businesses to adapt their approach, fostering innovation and competitiveness. Furthermore, insights from competitor analysis, including the application of Michael Porter's Five Forces framework, highlight the significance of digital integration and continuous employee development. These factors empower consultancy and bid writing businesses to strategically position themselves in the market, utilizing their strengths, addressing weaknesses, and capitalizing on growth opportunities.\n\n\n3. Method\n\nThis study utilized a mixed-methods approach, combining both qualitative and quantitative research techniques. This approach provided a broader understanding for the researchers, allowing for deeper insights throughout the collective process (Yin, 2006). By integrating multiple methods including survey and interviews, the study aimed to increase the validity and integrity of the findings (Campbell, Goodman, Feeney & Fehler, 2018).\n\nThe chosen methods aimed to generate ideas for new business leads and gain a deeper understanding of the knowledge gaps in bid writing within the chosen sectors. Addressing these gaps could improve the lead generation capacity for consultancy and bid writing businesses. By using a combination of questions that balance convenience with detail, the study aimed to increase both the likelihood and speed of responses compared to other methods (Campbell et al., 2018).\n\nBefore commencing the research, ethical approval was obtained from the Ethics Committee of Leeds Business School on February 2, 2024. By providing a detailed project information sheet and a consent form, all participants were thoroughly informed about the nature, purpose, and procedures of the study. Participants were required to voluntarily agree to participate, either by providing written consent or, in the case of online interviews, verbal consent.\n\nSecondary research involved the use of data previously collected for other purposes. This included information from government databases, the internet, discussion groups, internal company records, published reports, magazines, and data shared by professional bodies and trade associations (Baines, Fill, Rosengren & Antonetti, 2017). The secondary materials used in this study, including articles from journals, websites, and books, informed the design of the primary research and the market and environmental analysis.\n\nTo effectively meet the primary aims and objectives of the study, a mixed-method approach to primary research was undertaken. This decision was driven by the recognition that both quantitative and qualitative data were invaluable in achieving the desired outcome. The mixed-method approach was deemed crucial, as it provided a comprehensive view, with quantitative data captured through surveys allowing for numerical representation, and deeper insights obtained through qualitative semi-structured interviews.\n\n3.2.1. Quantitative research\n\nQuantitative research was conducted using surveys and questionnaires (Appendix A), collecting information through descriptive statistics, percentages, and frequencies (Baines et al., 2017). This structured approach added value to the research by organizing both descriptive and causal market data.\n\nThe research process began with the creation and distribution of an online survey tailored to business professionals, primarily in the sectors of facilities management and logistics, once ethical approval was granted. LinkedIn was chosen as the distribution method due to its global reach and accessibility to professionals within the targeted fields.\n\nGoogle Forms was used to create, distribute, and collect survey results, facilitating seamless collaboration among researchers and participants. This application ensured simplicity of use and allowed for real-time generation of spreadsheets, charts, and graphs directly from survey data, reducing the margin of error (Melo, 2023). The survey included mixed-method questions to gather both statistical and descriptive data. For instance, questions like “What qualities would you prioritize in a consultancy firm?” aimed to provide insights into consumer preferences, significantly helping meet the objective of understanding how consultancy and bid writing businesses can impact potential clients differently than competitors.\n\n3.2.2. Qualitative research\n\nQualitative research involved semi-structured interviews to gain deeper insights and comparisons. This method allowed for flexibility and depth, providing a richer understanding of the context and perspectives of the participants. The semi-structured format facilitated detailed responses while allowing the interviewer to probe further into interesting or unexpected areas, thereby increasing the overall richness of the data collected.\n\nIn summary, the mixed-methods approach provided a comprehensive and nuanced understanding of the research problem, enhancing the study’s validity and offering actionable insights for consultancy and bid writing businesses.\n\nSimple random sampling involves selecting a sample at random from the population elements (Baines et al., 2017). For this study, professionals within the Facilities Management and Logistics sectors were initially chosen at random using LinkedIn, irrespective of demographics such as age, gender, or geographical location. This method was supplemented with snowball sampling, which uses social networks to establish connections with hard-to-reach populations, thereby increasing the chain of participants (Hewson, 2006). The study focused on UK-based participants to ensure relevance and validity.\n\nExisting LinkedIn connections provided accessibility to a wider audience and facilitated contact with business professionals in the specific sectors of Facilities Management and Logistics. The aim was to explore how consultancy and bid writing businesses could generate new business leads by expanding into these sectors Tobias, 2023. These sampling techniques were chosen to reduce the risk of systematic errors and sampling biases, providing a more representative sample. However, it is acknowledged that this process is time-consuming and that other techniques could have been selected to avoid potential misrepresentation under a time-constrained study (Alvi, 2016).\n\n3.3.1. Sample size\n\nA sample size is defined as “a group or number of people selected from a population for the purpose of an investigation” (Alvi, 2016). For this study, seventy-five individuals from each sector (Facilities Management and Logistics) were selected, drawn from LinkedIn connections. Limiting the distribution to a total sample size of 150 helped reduce the risk of theoretical saturation, as only three respondents per sector were required to participate in a short semi-structured interview. The study was guided by S.M.A.R.T targets, aiming to provide consultancy and bid writing businesses with substantial findings that are specific, measurable, achievable, realistic, and time-bound, while also avoiding sampling bias (Alvi, 2016).\n\n• Quantitative Response Rate\n\nGiven that a combined sample size of 150 from the Facilities Management and Logistics sectors were asked to participate in a brief survey, only three from each sector responded, resulting in a very low response rate of 4%. Figure 1 indicates that there were in fact 16 survey respondents overall in total.\n\nFollowing the distribution of surveys to the population of relevant LinkedIn connections, participants willing to assist in our investigation on how Consultancy/bid writing businesses can generate new business leads were asked to participate in a 30-minute semi structured interview (see Appendix B).\n\n• Sample Size and Response rate of Interviews\n\nTo ensure credibility and reliability amongst results the sample size of one hundred and fifty individuals within the sectors of Facilities Management and Logistics was kept the same. The sample size was drawn from the same population of LinkedIn connections used for the survey, with the aim of capturing diverse perspectives relating to the research objectives. It was initially anticipated that three interviews per sector were to be conducted and analysed to meet specific, measurable, achievable, and realistic targets, whilst trying to avoid sampling bias (Alvi, 2016). However, we were only able to secure and conduct 5 interviews.\n\n\n4. Evaluation and discussion section\n\nThe following section analyses the findings of the research study from both the surveys and interviews.\n\nThe survey distributed to participants included 15 questions (see Appendix C-L). The data collected provides comprehensive insights into viewpoints on bid writing, consultancy, relationships, and lead generation. These insights also form the basis for more in-depth interviews, where the survey responses are explored in greater depth. Despite 87.5% of respondents stating their companies use bid writing at some point (Appendix D), only 12.5% felt confident in their bid writing abilities (Appendix E). This highlights a significant knowledge or confidence gap. Additionally, no respondents indicated that their company offers frequent bid writing training, with half stating their firm never provided any training (Appendix G). This neglected knowledge gap is expected to grow if the trend continues. However, 83.1% of respondents expressed interest in bid writing training in the future (Appendix H), representing a potential opportunity for consultancy and bid writing businesses.\n\nOnly 31.3% of respondents had never used consultancy firms, raising questions about why this is the case and what would make such services appealing (Appendix J). When asked about the qualities they prioritize in a consultancy firm, 56.3% of respondents highlighted expertise, while 25% valued past work and quality (Appendix K). Previous partners accounted for 46.2% of preferred procurement methods, and word of mouth/recommendations was the second highest at 38.5% (Appendix L), emphasizing the importance of relationships and networking.\n\nAdditionally, 81.3% of respondents stated they submit tenders to both the public and private sectors (Appendix I), with one respondent submitting only to the private sector. This served as a basis for further understanding during the interview process. In terms of new business generation, most respondents identified bids/invitations to tenders and business development via a sales team as their preferred methods (Appendix F). As consultancy and bid writing businesses offer both services, these findings are beneficial for potential clients.\n\nTable 1 provides the key themes emerged from the survey.\n\nThe following analysis presents findings from five interviews conducted with survey participants. Each analysis references key findings discussed during the interviews, aligning with the study's aims and objectives.\n\n4.2.1. Interview 1 - logistics company\n\nThe Managing Director of a logistics company, which specializes in transport, warehousing, and shipping, emphasized that bid writing is not required due to the nature of their business activities. This finding aligns with the theme of Knowledge Gaps in Bid Writing, as the company recognizes the importance of bid writing but does not actively engage in it due to its operational focus.\n\nThe logistics company operates in a fast-paced environment that is highly sensitive to changes in the macro-environment (Drew, 2017). Instead of relying on bid writing, the company generates new business leads through strong B2B and B2C relationships, as well as long-term loyal customers. This aligns with the theme of Importance of Relationships and Experience, highlighting the critical role of maintaining strong business relationships and communication to stay competitive and reliable.\n\nThe interviewee mentioned that winning contracts can be challenging in a highly saturated and competitive industry (Allon & Federgruen, 2007). They prefer maintaining close relationships with competitors for comparative pricing during busy periods (Doyle, 1998). For consultancy outreach, the company favors professional and personalized communication via email or telephone, further emphasizing the importance of tailored and direct communication strategies (Jin et al., 2019).\n\n4.2.2. Interview 2 – sports data company\n\nThe Vice President of Regulatory Services at a sports data company provided insights into the company's operations and strategies. The interview focused on how the company stays informed about competitors' strategies to maintain a competitive edge, aligning with the theme of Competitor and Market Analysis. This insight underscores the need for consultancy and bid writing businesses to understand and differentiate themselves from competitors.\n\nThe interviewee discussed the importance of securing large contracts and the preferred methods of new business generation. This discussion aligns with the theme of Knowledge Gaps in Bid Writing, as the interviewee emphasized the complex nature and importance of bid writing in securing significant contracts, such as sports data rights. The need for proficiency in bid writing was highlighted, reinforcing the value of experience, product/service awareness, and cross-team collaboration (Lowe, 2023).\n\nAdditionally, the interview highlighted the value of proper training and the need for consultancy businesses to adapt to clients' changing demands (Williams & van Triest, 2023). This aligns with the theme of Willingness to Invest in Training, as the interviewee recognized the importance of continuous learning and adaptation in maintaining competitiveness.\n\n4.2.3. Interview 3 – facilities management company\n\nThe CEO of a facilities management company highlighted that bid writing constitutes a small portion of their lead generation due to a lack of knowledge and expertise. This finding aligns with the theme of Knowledge Gaps in Bid Writing. Despite this, the company submits bids solely to the private sector, showing a clear preference for working with small to medium-sized organizations.\n\nThe interviewee emphasized the importance of experience and trust when selecting consultancy firms, aligning with the theme of Importance of Relationships and Experience. This preference for trust and reliability is supported by the idea that businesses with strong, trustworthy relationships are more likely to succeed (Barnett, 2021).\n\nTo remain competitive, the company routinely reviews competitors and the external market through social media and website analysis. This aligns with the theme of Competitor and Market Analysis, highlighting the importance of staying informed about market dynamics to maintain a competitive edge. The company also expressed interest in external training programs, further supporting the theme of Willingness to Invest in Training.\n\n4.2.4. Interview 4 – local manufacturing consultancy\n\nThe Managing Director of a consultancy firm in the local manufacturing sector expressed a clear need for bid-writing services and training. This aligns with the theme of Knowledge Gaps in Bid Writing. The interviewee emphasized the importance of trust and personalized outreach in their business operations, supporting the theme of Importance of Relationships and Experience.\n\nThe interviewee highlighted that integrating AI technology has proven beneficial in their practices, suggesting that consultancy and bid writing businesses should consider similar integration to improve efficiency. This aligns with the theme of Adoption of AI Technologies, emphasizing the role of technology in enhancing business operations and competitiveness (Iansiti & Lakhani, 2020).\n\nFurthermore, the interviewee indicated that the firm has attempted bid writing in the past but was unsuccessful due to a lack of resources and low return on investment. This underscores the need for external consultancy assistance in bid writing, highlighting a potential market opportunity for consultancy and bid writing businesses.\n\n4.2.5. Interview 5 – Automation, logistics, and supply chain consultancy\n\nAn Automation, Logistics, and Supply Chain consulting specialist emphasized the importance of honesty, integrity, and trust in building B2B and B2C relationships. This aligns with the theme of Importance of Relationships and Experience, reinforcing the value of trust in successful business relationships (Crawford, 2022).\n\nThe interviewee also highlighted the significance of AI practices for future business growth, supporting the theme of Adoption of AI Technologies. They revealed plans to fully integrate AI practices into bid writing and procurement processes within the next two years, aligning with the literature on the transformative impact of AI on business practices (Iansiti & Lakhani, 2020).\n\nTransparency in consultancy capabilities was seen as critical for maintaining credibility, with the belief that \"good value services will win out\" when transparency is maintained. This aligns with the theme of Competitor and Market Analysis, emphasizing the importance of transparency and credibility in maintaining a competitive edge.\n\nThe interviews revealed several common themes among respondents. Two out of five interviewees indicated a need for bid-writing expertise, particularly in the facilities management and local manufacturing sectors. This finding highlights the importance of targeting these sectors with specialized bid-writing services.\n\nThe value of trust and relationships in a B2B context was a consistent theme across all interviews, regardless of the sector. This underscores the importance of building and maintaining strong business relationships to achieve long-term success.\n\nAdditionally, two respondents highlighted the benefits of integrating AI technologies into their business operations. This finding suggests that consultancy and bid writing businesses should consider adopting AI technologies to enhance efficiency and competitiveness, staying ahead in a rapidly evolving market.\n\nBoth survey and interview respondents identified significant knowledge gaps in bid writing. The low confidence rate of 12.5% in bid writing and the high interest rate of 83.1% in bid writing training indicate a strong demand for educational resources and training programs.\n\nThe preference for previous partners and word-of-mouth recommendations was evident in both survey and interview responses. This finding underscores the importance of trust and established relationships in successful business operations.\n\nThe interviews also emphasized the growing opportunities in AI-enhanced services. Respondents favoured businesses that adopt innovative technologies, suggesting that consultancy and bid writing businesses should integrate AI to remain competitive and attract new clients.\n\nTable 2 presents the key themes emerged from the interviews.\n\nBy addressing these themes and integrating insights from both surveys and interviews, consultancy and bid writing businesses can refine their strategies to enhance lead generation and client acquisition effectively. This approach will help them stay competitive in a rapidly evolving market and meet the needs of their clients more effectively.\n\n\n5. Operationalization framework\n\nThis section presents a strategic action plan for Consultancy/bid writing businesses, based on key findings from the survey and interview data. The proposed operationalization framework (Figure 2) focuses on four main areas: bid writing training, networking, social media presence, and AI integration.\n\nBy implementing this framework, Consultancy/bid writing businesses can effectively operationalize their strategic action plan, enhancing lead generation, client acquisition, and overall competitiveness in the market. The framework is explained in the following section.\n\nA recurring theme from the findings was the need for bid writing training within businesses. Interviewees consistently expressed that such training would significantly enhance their business practices but were often unaware that such training existed. Consultancy/bid writing businesses already offer this service, so further enhancements can be made to optimize its reach.\n\nIn the short term, the focus should be on increasing visibility through social media platforms. Regularly sharing engaging content related to bid writing training, highlighting its benefits and success stories, can help raise awareness. Social media has proven effective for increasing brand visibility and engaging with potential clients (Thornton & Lowe, 2024). Additionally, leveraging current contacts to launch an email marketing campaign can emphasize the value of bid writing training. Informative newsletters and updates on the available training programs can highlight their benefits to businesses (Stevens, 2011).\n\nFor the medium term, investing in targeted paid advertisements on social media and search engines can help reach demographics interested in business development and tender processes. Tailored ad content addressing common business needs can showcase how Consultancy/bid writing businesses’ solutions meet those needs (Peddireddy & Peddireddy, 2023). Furthermore, participating in relevant conferences and networking events within the business development and procurement sectors can showcase expertise and form connections with potential clients (Baines et al., 2017).\n\nIn the long term, encouraging satisfied clients to refer other businesses to Consultancy/bid writing businesses' training programs can be beneficial. Promoting this referral process by offering incentives or rewards for successful referrals can increase participation (Crawford, 2022). Expanding into niche markets by identifying specific industries where bid writing training is particularly valuable, such as government contracting or healthcare, and customizing marketing efforts to address their unique needs can further enhance outreach (Kotler et al., 2023).\n\nThese strategies align with the goal of generating leads and acquiring new clients by enhancing visibility, targeting specific demographics, and leveraging client referrals and niche market opportunities.\n\nGiven that key findings from primary research highlighted honesty, integrity, and trust as crucial for long-term success, Consultancy/bid writing businesses should integrate strategies to improve networking practices among repeat and new clients.\n\nIn the short term, leveraging the networking potential of LinkedIn can greatly benefit the company. Despite Consultancy/bid writing businesses' vision to become the UK's go-to bid and business development consultancy, the company’s current LinkedIn presence is modest. Actively engaging in LinkedIn groups can increase the potential reach to a larger audience and highlight the benefits of bid writing consultancy in niche markets (LinkedIn, 2024). The platform also provides opportunities to identify potential leads by initiating contact with sectors or individuals interested in services similar to those offered by Consultancy/bid writing businesses (Alvi, 2016). This strategic use of LinkedIn can help in generating new leads and acquiring new clients by broadening the reach and making valuable connections.\n\nIn the medium term, attending networking events in local and surrounding communities can increase Consultancy/bid writing businesses' overall brand visibility within specific targeted industries. Actively participating and presenting at these events has proven to provide a significant return on investment, laying the foundation for lead generation and new business opportunities. Face-to-face interactions build trust and credibility by demonstrating traits of honesty and integrity, which were highlighted as essential in increasing the likelihood of prospects (Crawford, 2022).\n\nIn the long term, building strong relationships is crucial. Regular communication with clients to assist with queries related to bid writing, regular client reviews, training refreshers, and ongoing support can show commitment (Barnett, 2021). Personalization in all interactions based on the companies’ individual needs and aims can make clients feel valued and more likely to recommend Consultancy/bid writing businesses' services. Encouraging both positive and negative client feedback and using it to improve service delivery can demonstrate a commitment to client satisfaction and continuous improvement, thereby enhancing the company’s competitive edge (Wirtz & Lovelock, 2021).\n\nThese strategies focus on building and maintaining strong business relationships, leveraging social media, and participating in industry events to enhance networking efforts.\n\nSurvey and interview data indicated that past work and relationships play a significant role in deciding whether to work with a consultancy firm. To solidify established and blossoming relationships, Consultancy/bid writing businesses should use social media to create a stronger media presence.\n\nIn the short term, Consultancy/bid writing businesses should curate weekly posts on platforms such as LinkedIn, Facebook, or blogs on the company website. Regularly updating business milestones or opinions on relevant topics, like new legislation impacting the industry, can keep followers and stakeholders engaged (Eckstein, 2024). This approach can help the company remain relevant and showcase past works, building stronger relationships through social media strategies (Abed et al., 2015).\n\nIn the medium term, exploring the potential of Google Ads can be beneficial. Initial ad campaigns can offer insights into the expansion possibilities offered by Google Ads. Although differences in sectors and target audiences need to be considered, these small initial campaigns can help determine the value of this investment.\n\nFor long-term goals, sustained engagement on social media platforms is crucial. Proper use of LinkedIn can allow Consultancy/bid writing businesses to connect with professionals and potential target markets. Collecting client endorsements upon the completion of consultancy jobs can further verify professional history and increase appeal. While there are no financial costs associated with social media posts, Google Ads do require investment for marketing campaigns, which can be personalized to suit specific budgets and timeframes (Melo, 2023).\n\nThese strategies aim to solidify relationships through an enhanced social media presence, leveraging consistent engagement and client testimonials.\n\nData collected from consultancy firms operating within logistics and local manufacturing underlined the relevance of AI integration into business operations. These firms highlighted the benefits of AI in performing everyday tasks such as writing emails, organizing data, and compiling presentations. Consultancy/bid writing businesses should follow in these footsteps and consider integrating AI into their business model.\n\nAI integration into a modern business model can offer several benefits:\n\nProcess Automation: Automating many administrative tasks, such as database logging, notifications on missing data, and customized templates, can enhance efficiency. Cognitive Insight: Using algorithms to analyze data can identify gaps or predict outcomes, aiding in financial planning and resource allocation. Cognitive Engagement: Implementing language models for chatbots can provide 24/7 service lines, improving client interaction and engagement (Davenport & Ronanki, 2018).\n\nIn the short term, Consultancy/bid writing businesses should focus on understanding AI technologies and deciding which types would be beneficial. Starting with simple tools like chatbots for writing emails or creating presentations can be a useful entry point (Iansiti & Lakhani, 2020).\n\nIn the medium term, ensuring staff are well-trained and familiar with any AI technologies integrated into the business is essential. Gradually incorporating more advanced AI applications can further enhance operations (Iansiti & Lakhani, 2020).\n\nIn the long term, continuously monitoring AI advancements and regularly assessing the impact of AI on business operations and client relationships will help in staying competitive. While integrating the latest AI technologies may involve financial costs, these come with the opportunity cost of saving time and resources, which can be redirected to other areas such as developing long-lasting relationships (Iansiti & Lakhani, 2020).\n\n\n6. Conclusion\n\nThis study embarked on a journey to uncover strategic approaches for Consultancy/bid writing businesses to enhance lead generation and competitive positioning in the post-Covid consultancy landscape. By employing a mixed-methods approach that incorporated surveys and interviews, the research delved deeply into bid writing practices, networking, social media presence, and AI integration. The findings from this study offer a rich tapestry of insights and actionable recommendations that can drive significant improvements in these areas.\n\nOne of the most striking revelations from this study was the identification of significant knowledge gaps in bid writing within organisations. Despite the recognition of its critical importance, many businesses lack confidence and expertise in bid writing. This underscores a pressing need for targeted training programmes. The enthusiasm for bid writing training was palpable, as evidenced by the strong demand among respondents who expressed eagerness to learn more about the practice. This presents a clear opportunity for Consultancy/bid writing businesses to expand their training services, catering to this evident demand and filling the existing knowledge void.\n\nNetworking emerged as another pivotal theme, with honesty, integrity, and trust identified as essential components for long-term business success. Effective networking strategies, particularly leveraging social media platforms like LinkedIn, were highlighted as crucial for generating new leads and maintaining client relationships. The role of social media cannot be overstated; a robust online presence is vital for building and maintaining business relationships. Regular updates, engaging content, and client endorsements were noted as key strategies for enhancing visibility and credibility.\n\nMoreover, the integration of AI technologies stood out as a significant factor in modern business practices. AI's potential to enhance efficiency through process automation, cognitive insight, and cognitive engagement provides a competitive edge in the consultancy market. This aligns with the industry's shift towards more data-driven and technology-enabled solutions, making it imperative for Consultancy/bid writing businesses to consider AI integration seriously.\n\nThe novelty of this study lies in its holistic approach to understanding the bid writing consultancy landscape. By integrating quantitative and qualitative data, this research offers a multifaceted view of the challenges and opportunities within the industry. This study makes significant contributions to existing literature by highlighting specific knowledge gaps and training needs in bid writing, providing a foundation for developing targeted educational programmes.\n\nFurthermore, it underscores the importance of networking and relationship-building in the consultancy sector, which is often overlooked in traditional competitive analysis frameworks. The study also demonstrates the value of a strong social media presence for consultancy firms, offering practical strategies for enhancing online engagement. Additionally, it explores the potential of AI integration in consultancy practices, presenting a forward-looking perspective on technological advancements in the industry.\n\nFor practical application, the study offers actionable recommendations for Consultancy/bid writing businesses, including strategies for enhancing bid writing training, improving networking efforts, leveraging social media, and integrating AI technologies. These recommendations are designed to help the firm increase lead generation, acquire new clients, and maintain a competitive position in the market.\n\nWhile this study provides valuable insights, it also opens avenues for future research. One promising area is conducting longitudinal studies to evaluate the long-term effectiveness of bid writing training programmes. Such studies would provide deeper insights into how training impacts business outcomes over time, allowing for the refinement and optimisation of these programmes.\n\nComparative studies across different sectors could also yield valuable insights. By examining sector-specific challenges and opportunities in bid writing and consultancy services, future research can help develop more tailored strategies for different industries. Additionally, investigating the impact of AI on consultancy practices could explore how specific AI tools and technologies affect efficiency, client relationships, and competitive advantage. This would help consultancy firms better understand and leverage AI's potential.\n\nDeclaration of generative AI and AI-assisted technologies in the writing process: During the preparation of this work the authors used ChatGPT in order to improve the readability and flow. After using this tool/service, the authors reviewed and edited the content as needed and take full responsibility for the content of the publication.\n\n\nEthics and consent\n\nEthical approval for this study was obtained from the Ethics Committee of Leeds Business School, on February 2, 2024. The study adhered to the ethical principles outlined in the Declaration of Helsinki (https://www.wma.net/policies-post/wma-declaration-of-helsinki-ethical-principles-for-medical-research-involving-human-subjects/). All participants were fully informed about the study's nature, purpose, and procedures through a detailed project information sheet. Consent was obtained from all participants, either in written form for in-person participation or verbal form for online interviews. Verbal consent was used due to the logistical challenges of obtaining written consent in an online setting, and this approach was explicitly approved by the Ethics Committee. Participants voluntarily agreed to participate after understanding all relevant information.", "appendix": "Data availability statement\n\nThe data supporting the findings of this study are openly available in the Leeds Beckett Thesis and Research Data Repository at https://figshare.com/s/04b3e5a35182b549ee2d, reference number https://doi.org/10.25448/lbu.26250131.v2\n\nThe dataset is licensed under a Creative Commons Attribution-NonCommercial 4.0 International (CC BY4.0) license.\n\nThe data is now publicly available under the FigShare: Competitive Positioning for Bid Writing Consultancy Firms\n\nThis project contains the following underlying data:\n\nFatorachian Research (Responses)\n\nCompetitive Positioning for Bid Writing Consultancy Firms\n\nData is available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nThe data is now publicly available under the FigShare: Competitive Positioning for Bid Writing Consultancy Firms\n\nhttps://doi.org/10.25448/lbu.26250131.v2\n\nThis project contains the following underlying data:\n\nFatorachian CP2 data\n\nData is available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAbed S, Dwivedi Y, Williams M: Social media as a bridge to e-commerce adoption in SMEs: A systematic literature review. 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Journal of Public Procurement. 2019; 19(1).\n\nThornton, Lowe: Bid writing training for professional services: The secret weapon in growing your consultancy business.2024. (accessed: 18/03/2024). Reference Source\n\nWilliams C, van Triest S : Understanding performance in professional services for innovation intermediation: Technology consultants vs. management consultants. International Journal of Technological Innovation. 2023; 126(102824).\n\nWirtz J, Lovelock C: Services marketing: People, technology, strategy. New Jersey: World Scientific; 9th ed2021.\n\nYin R: Mixed methods research: Are the methods genuinely integrated or merely parallel?. Mid-south Educational Research Association. 2006; 1: 41–47. (accessed: 09/02/2024).\n\nZhu F, Iansiti M: Why some platforms thrive and others don’t. Harv. Bus. Rev. 2019; 97(1): 118–125." }	[ { "id": "353401", "date": "27 Jan 2025", "name": "Mulyani Karmagatri", "expertise": [ "Reviewer Expertise My areas of expertise include entrepreneurship", "small and medium enterprises (SMEs)", "eco-friendly product development", "sustainable innovation strategies", "and the integration of technology and artificial intelligence in business solutions" ], "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 provides clear objectives and actionable insights. However, certain sections, such as the operationalization framework, lack detailed, practical steps and measurable goals, which reduces clarity for practitioners. The data and findings are presented accurately based on the survey and interview results. However, the small sample size and limited response rates introduce concerns about the robustness of the conclusions. The paper cites relevant and current literature on consultancy, AI integration, and bid writing. However, some claims about the importance of AI and networking strategies lack deeper theoretical grounding or additional recent references to strengthen their argument. Update the literature with more recent studies (2019–2024) to ensure the work reflects the latest trends and advancements in the field, especially regarding AI, digital transformation, and networking strategies for consultancy firms. The survey response rate was extremely low (16 respondents out of a target of 150), and only five interviews were conducted. This limits the reliability and generalizability of the findings. The small sample size introduces a risk of bias and makes it difficult to draw conclusions applicable to a wider population. The study focuses on the Facilities Management and Logistics sectors but does not adequately explain why these sectors were chosen or how findings apply to other industries. While the study discusses AI integration, it lacks detailed technical discussion about specific tools, methods, or challenges of implementing AI in consultancy and bid writing. The low response rates and reliance on LinkedIn as the primary distribution platform raise concerns about selection bias and the representativeness of the sample. While the paper mentions that the survey included mixed-method questions, it does not provide the exact survey questions or explain the design of specific scales or metrics used for data collection. The survey's structure, rationale for question choices, or validation process is not detailed enough to ensure replication. The study does not include the full interview protocol or examples of the questions used. This makes it difficult for others to replicate the qualitative component. The description of quantitative analysis (e.g., use of descriptive statistics) is basic and lacks detail about statistical methods or tools/software used for analysis. For the qualitative analysis, there is no clear explanation of how interview data were coded or analyzed (e.g., thematic analysis framework, coding process, software used like NVivo). The paper describes the use of LinkedIn connections and snowball sampling but does not detail how participants were chosen (e.g., inclusion/exclusion criteria) or how bias was minimized in this process. The statistical analysis is limited to basic descriptive statistics, such as percentages and frequencies. There is no indication of inferential statistical methods being used, which could have added depth (e.g., comparing sectors or identifying significant differences between groups). The small sample size (16 respondents) undermines the reliability and generalizability of the findings. Statistical analysis on such a small dataset may not yield meaningful or robust results. The study does not include confidence intervals, error margins, or measures of variability (e.g., standard deviation), which are essential for interpreting the reliability of the reported percentages. While the results are summarized, there is little critical analysis or contextualization of the statistical findings. For example, the low confidence in bid writing (12.5%) and high interest in training (83.1%) are not linked to specific variables like sector, role, or experience level. The paper mentions qualitative interviews but does not attempt to integrate the findings statistically or use mixed-methods techniques like triangulation to validate the survey data. While the paper refers to the data being available on FigShare, it does not explicitly describe what is included in the dataset or provide direct, detailed examples of the data (e.g., raw survey responses, interview transcripts). There is no clear indication of whether survey questions or interview protocols are included as part of the dataset. The connection between the dataset and the findings in the paper is not fully explained. For example, how the survey data were cleaned, processed, or analyzed is not described in sufficient detail. The paper does not describe any pre-processing steps, such as handling missing The small sample size (16 survey respondents and 5 interviews) significantly weakens the reliability of the findings. Drawing broad conclusions from such limited data is problematic. The low response rate undermines the representativeness of the results, particularly for conclusions about the broader consultancy industry. Some conclusions, such as the emphasis on AI integration and the benefits of bid-writing training, are not thoroughly validated by the limited data provided. For instance, while AI is mentioned as beneficial, there is no in-depth analysis of specific tools or their adoption rates. While the paper emphasizes the importance of networking and social media, there is limited data to substantiate these claims beyond anecdotal evidence from interviews. The findings do not provide concrete metrics or examples to support the proposed strategies. The conclusions touch on broad trends but fail to explore nuances in the data, such as differences between sectors (e.g., Facilities Management vs. Logistics) or company size, which could have strengthened the claims.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "353402", "date": "28 Jan 2025", "name": "Syahmardi Yacob", "expertise": [ "Reviewer Expertise My research interest were strategic management", "marketing management", "and business international" ], "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 provides meaningful insights into the field of bid-writing consultancy, shedding light on an area that is often overlooked in existing research. Its practical implications are particularly valuable for consultancy firms seeking to refine their strategies in lead generation and competitive positioning. Despite these strengths, the study's overall impact is constrained by certain methodological limitations. The small sample size and low response rates reduce the generalizability of the findings, making it difficult to draw conclusions that can be broadly applied across sectors. Additionally, the analysis lacks depth, as it primarily relies on descriptive statistics without incorporating inferential methods or measures of variability, which are essential for establishing the reliability and significance of the results. Further improvement could be achieved by strengthening the theoretical foundation of the study, particularly in areas such as artificial intelligence integration and networking strategies. The article would also benefit from a clearer and more detailed description of its methodologies, including survey design, interview protocols, and data processing techniques, to ensure replicability and transparency. Moreover, expanding the operational framework with actionable and measurable recommendations would enhance its practical relevance. Addressing these issues would significantly increase the study's rigor, improve its applicability, and make a stronger contribution to the academic discourse on bid-writing consultancy.\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": [] } ]	1	https://f1000research.com/articles/13-1001
https://f1000research.com/articles/13-1000/v1	03 Sep 24	{ "type": "Research Article", "title": "Empowering rural women: key factors driving participation in livelihood credit programs in Gubalafto woreda, North Wollo, Ethiopia", "authors": [ "Moges Asmare Sisay", "Atnafu Amare Mulaw", "Atnafu Amare Mulaw" ], "abstract": "Background This study investigates the factors influencing rural women’s participation in credit programs in Gubalafto Wereda. Understanding these determinants is crucial for improving program effectiveness and supporting women’s economic empowerment in the region.\n\nMethods A cross-sectional survey was conducted with a sample of 364 rural women from four kebeles, selected through stratified random sampling based on agro-ecological characteristics. Data were collected via interviews and analyzed using descriptive statistics, chi-square tests, t-tests, and logit regression models to determine the significance of various factors affecting participation.\n\nResults Descriptive statistics revealed key associations between participation and factors such as household size, income level, educational status, perception of group collateral, skill training, and distance from lending offices. Chi-square tests showed significant relationships, while t-tests identified differences between participants and non-participants. Logit regression analysis indicated that household size, income level, educational status, group collateral, skill training, and proximity to lending offices significantly influenced credit participation at the 1% level (p<0.01). Experience with income-generating activities and perception of interest rates were significant at the 5% level (p<0.05). Market access was significant at the 10% level (p<0.10). Positive factors included household size and income level, while age, distance from lending offices, and perception of interest rates had negative effects.\n\nConclusion The study highlights that specific factors significantly impact rural women’s participation in credit programs. To enhance program effectiveness, stakeholders should address these determinants and develop robust institutional frameworks with effective monitoring and evaluation systems.", "keywords": [ "Keywords: Rural women", "credit programs", "Gubaflto Wereda", "participation determinants", "logit regression", "economic empowerment", "agro-ecological sampling" ], "content": "1. Introduction\n\nRural women in Ethiopia play a crucial role in the agricultural sector, which remains the backbone of the country's economy, especially in regions like Gubalafto Woreda, North Wollo, Amhara Region, where 84% of the population resides in rural areas. Women are indispensable to agricultural productivity and the improvement of rural living standards. Despite their significant contributions, they often face systemic barriers, particularly in accessing credit, which is essential for enhancing their economic autonomy and socio-economic status. This study explores the determinants of rural women’s participation in livelihood credit programs within Gubalafto Woreda, aiming to illuminate the factors influencing their engagement and the broader socio-economic implications.\n\nHistorically, Ethiopia’s approach to women’s development has evolved from welfare-oriented initiatives to more comprehensive, development-focused strategies. These strategies increasingly recognize women as pivotal economic actors whose empowerment is crucial for sustainable development. Access to credit is now widely acknowledged as a key driver of this empowerment, enabling women to invest in income-generating activities, improve their asset base, and contribute more effectively to household and community well-being (Akhter, S., 2003). However, access to credit remains uneven, with rural women particularly disadvantaged due to factors such as limited financial literacy, inadequate collateral, and socio-cultural barriers.\n\nCredit programs designed specifically for rural women are critical for poverty alleviation and household empowerment. These programs not only aim to increase women’s income but also extend their production knowledge, enhance their decision-making power, and facilitate market access, all of which are vital for improving their economic and social standing (Abate and Sheferaw, 2023). One prominent example is the Productive Safety Net Program, launched in 2005, which seeks to bolster household assets and income through skill development, credit services, and livelihood diversification, thereby supporting food security and resilience among rural populations (Masa et al., 2021).\n\nDespite these initiatives, there remains a substantial gap in understanding the specific factors that influence rural women’s participation in livelihood credit programs. Existing research has largely focused on the supply side of credit, such as the availability of financial services and institutional frameworks, while neglecting the demand side, particularly the individual determinants of women’s engagement (Hameed & Irfan, 2019). Challenges such as gender bias in extension services, limited access to information, and socio-economic constraints often hinder women's ability to fully participate in these programs (Morton et al., 2014). Moreover, cultural norms and household dynamics can further restrict women’s access to and control over credit, affecting their capacity to benefit from such initiatives.\n\nThis study addresses these gaps by analyzing the determinants influencing rural women’s participation in livelihood credit programs in Gubalafto Woreda. It will explore the distribution of livelihood credit within the woreda, identify key factors that affect women’s participation, and evaluate the impact of credit on their income, asset accumulation, and overall socio-economic status. By answering these critical questions, the research aims to provide actionable insights for policymakers, rural development agencies, and other stakeholders involved in designing and implementing credit programs.\n\nThe findings are expected to contribute significantly to the understanding of the complex factors affecting women's participation in livelihood credit programs, offering guidance for future policy development and program design.\n\n\n2. Literature review\n\n2.1.1 Definition and key concepts\n\n2.1.1.1 Livelihood concepts and livelihood framework\n\nLivelihood programs are integral components of food security strategies, designed to offer comprehensive support to food-insecure households by enhancing their asset base and diversifying income sources. These programs, initiated in 2005 in Ethiopia, aim to enable households to transition from dependence on the Productive Safety Net Program (PSNP) to sustainable livelihoods (Fre, Woldu, & Livingston, 2022).\n\nLivelihood Defined: A livelihood encompasses the capabilities, assets (both material and social), and activities necessary for a means of living. In the Ethiopian context, food security is defined as the availability, access, and utilization of sufficient food to maintain a healthy life. Availability refers to the sustainable production of adequate food, access involves having the economic means to obtain food, and utilization pertains to the effective use of food for nutrition and health, often challenged by inadequate sanitation and health facilities (Eskola et al., 2020; World Health Organization, 2024). These interconnected elements of livelihood highlight the multifaceted nature of food security and the importance of addressing all aspects to achieve long-term stability.\n\nPSNP Overview: The Productive Safety Net Program (PSNP) is a cornerstone of Ethiopia's strategy to improve the livelihoods of its beneficiaries. It aims to increase household assets, incomes, and resilience against economic shocks, with the ultimate goal of enabling households to “graduate” from the PSNP, thereby reflecting improved livelihoods and economic stability (Ranganathan et al., 2022). The PSNP’s approach underscores the importance of integrating asset-building initiatives with income-generating activities to create a sustainable path out of poverty.\n\n2.1.1.2 The concepts of asset, asset building, and income-generating activities\n\nAssets Explained: Assets are items of economic value owned by an individual that can be converted into cash or used productively. For farming households, these assets include livestock, land, and rentable houses, which serve as critical resources for generating income and sustaining livelihoods.\n\nAsset Types in Ethiopia:\n\n• Livestock Assets: These include cattle, sheep, goats, and poultry, which are pivotal for the survival and economic well-being of rural households.\n\n• Productive Assets: These are items utilized for production, such as animals or crops, that either reproduce themselves or are used to produce something of value.\n\nHousehold Asset Building: Asset building involves increasing the real value of household assets over time, often linked to the duration of a program or intervention aimed at fostering asset accumulation. This process is crucial for improving household resilience and economic stability, enabling families to invest in income-generating activities and secure their livelihoods.\n\nHousehold Income: Household income encompasses all income generated by household members from various activities, including on-farm activities (e.g., crop production, livestock), non-farm activities (e.g., handicrafts, carpentry), and off-farm activities (e.g., wage labor on other people's farms). Diversifying income sources is essential for reducing vulnerability to economic shocks and achieving sustainable development.\n\n2.1.1.3 Household structure\n\nDefinition of household: A household is defined as a group of individuals who live together, share meals, and often share economic responsibilities. Households can range from single-person units to extended families or groups of unrelated individuals (Smeeding and Weinberg, 2001).\n\nEconomic importance of households: Households are fundamental units of economic activity, playing a critical role in production, distribution, and consumption. Decisions made within households, such as those regarding labor market participation and expenditure, are vital for resource allocation and economic stability (Sanson, 2024). Understanding the dynamics within households is essential for designing effective livelihood programs that address the needs and constraints of different household members.\n\nHousehold head: The household head is recognized as the primary administrator and manager of the household's activities and resources. This role is crucial in decision-making processes related to resource allocation, labor distribution, and participation in economic activities (Ranganathan et al., 2022).\n\n2.1.2 The concept and types of rural credit\n\nRural Credit Overview: Rural credit is essential for providing the startup capital necessary for poor individuals to initiate, sustain, or expand agricultural production, thus increasing productivity and helping them move out of poverty. Access to credit enables rural households to invest in income-generating activities, purchase necessary inputs, and build assets, which are vital for enhancing their economic well-being and reducing poverty.\n\nTypes of rural credit markets:\n\n• Formal Credit Markets: Formal credit markets involve institutions that mediate between depositors and lenders, often providing loans at relatively low, sometimes government-subsidized, interest rates. These institutions include banks, cooperatives, and microfinance institutions that offer structured financial products to rural households.\n\n• Informal Credit Markets: Informal credit markets are characterized by private individuals, such as moneylenders, traders, landlords, and relatives, providing loans. While formal and informal credits serve different needs, they are not perfect substitutes, as formal credit does not entirely replace the need for informal borrowing. Informal markets often offer greater flexibility in terms of loan terms and access but may come with higher interest rates and fewer protections (Kayamo and Tebeka, 2021).\n\n2.1.2.1 Government food security program\n\nFood Security Program (FSP): The Ethiopian government’s Food Security Program (FSP) offers formal credit through local agricultural sectors and institutions like Tsedey Bank (Amhara Credit and Saving Institution - ACSI) to individual farmers using collateral agreements. The program aims to enhance farmers' productivity and asset base, helping them escape poverty by providing access to financial resources necessary for investing in agricultural inputs and technologies (Alemaw et al., 2024). The FSP's focus on credit provision is designed to complement other food security initiatives, ensuring that farmers have the means to improve their livelihoods.\n\n2.1.2.2 Group-based credit and gender participation\n\nGroup-Based Lending: Group-based lending has proven to be highly effective in low-income societies due to its advantages in information sharing, peer support, and risk mitigation. Group members can monitor and assist each other, making it a beneficial system for both lenders and borrowers. This method is particularly advantageous for women, who often face barriers in accessing formal credit independently due to lack of collateral, limited financial literacy, and socio-cultural constraints. Group lending models, therefore, provide a viable pathway for women to access credit, build assets, and improve their economic standing.\n\nGender Participation: Women's participation in group-based credit schemes has been shown to significantly improve their economic empowerment and household food security. By participating in these schemes, women gain the support and confidence needed to engage in economic activities, thereby contributing to the overall development of their communities (Armendáriz & Morduch, 2010). The success of these models highlights the importance of designing credit programs that are inclusive and sensitive to the unique challenges faced by women in rural areas.\n\nBy integrating these concepts and mechanisms, livelihood and food security programs aim to create sustainable economic stability for rural households. These programs enable households to build assets, increase income, and achieve food security, ultimately contributing to the reduction of poverty and the promotion of equitable development.\n\n2.2.1 Global empirical studies on credit programs\n\nCredit programs have become increasingly important in developing economies, with numerous studies documenting their impact. For instance, in Bangladesh, the Grameen Bank, a pioneer in microfinance, had reached a membership of 2.4 million by the end of 2000, with 95% of these members being women, and an outstanding loan portfolio of $225 million (Cull, 2007). Similarly, Thailand’s Bank for Agriculture and Agricultural Cooperatives has effectively expanded its reach through agricultural lending initiatives, while in Cambodia, the growth of microfinance institutions underscores the widespread influence of credit programs (Caballero-Montes, 2022).\n\nGlobally, various studies have analyzed the factors that influence participation in credit programs. In Pakistan, Khan et al. (2020) found a strong relationship between education levels and access to credit for livestock, indicating that illiterate farmers often struggle with loan applications, thereby limiting their access to credit. In Namibia, Kaukumangera (2021) observed a positive correlation between experience in income-generating activities and access to agricultural credit. Similarly, research in Ghana by the African Development Review (2020) supports the notion that larger landholdings significantly enhance access to credit (Nguyen, 2017), although Dzadze et al. (2012) did not find this association in their study.\n\nFarm size is frequently highlighted as a determinant of credit demand. Research in Bangladesh by Rayhan, Rahman, and Lyu (2024) and in Ghana by Twumasi et al. (2020) demonstrated that larger farms tend to have a higher demand for credit. Conversely, Chaiya et al. (2023) in Pakistan found that family size plays a significant role in influencing credit access, as larger families may benefit from diversified agricultural activities, impacting their credit requirements. However, the effect of family size varies by context, with mixed results reported in Bangladesh (Rayhan et al., 2024).\n\nAge is another factor influencing credit demand. Mpuga (2010) in Uganda found a positive relationship between age and loan demand, with older farmers more likely to seek credit due to greater access to assets such as land. However, studies in Qatar (Charfeddine, Umlai & El-Masri, 2024) and China (Dong, Lu & Featherstone, 2012) found either negative or insignificant associations between age and credit demand. In India, Swain (2007) also reported no significant correlation between age and credit demand.\n\nEducation consistently emerges as a critical factor in credit participation. In Ethiopia, studies by Waje (2020) and Mamuye (2021) found that formal education significantly enhances access to credit. Similar findings were reported in Pakistan by Kumar et al. (2021), who noted that higher education levels are associated with increased participation in credit programs, although results vary across different regions.\n\nThe distance to lending institutions also plays a crucial role in credit demand. Studies have shown that greater distances from financial institutions negatively impact credit demand (Anang et al., 2015). Additionally, interest rates and collateral requirements have been found to deter potential borrowers, as demonstrated in research conducted in Romania (Chaves et al., 2001). Furthermore, extension services have been shown to positively influence credit participation by improving access to information and enhancing decision-making capabilities (Kwabena and Opoku, 2023; Anang et al., 2015).\n\n2.2.2 Empirical studies on credit programs in ethiopia\n\nIn Ethiopia, research on credit programs has largely focused on the supply side, particularly from the perspective of lending institutions. However, several studies have examined the factors that influence access to credit. Waje (2020) found that formal education significantly improves access to credit, while Abreu et al. (2024) noted that participation in extension package programs increases the likelihood of obtaining credit.\n\nThe impact of landholding size on credit participation in Ethiopia has produced mixed results. Tura et al. (2017) found that larger landholdings negatively affect credit participation, whereas Kassegn and Endris (2021) reported a positive relationship between land size and credit access. Engagement in income-generating farming activities has also been found to positively influence access to credit (Kassegn & Endris, 2021).\n\nInterest rates have been identified as a key deterrent to credit demand in Ethiopia. Negatu (2021) reported that higher interest rates significantly reduce credit demand. Family size, however, has shown inconsistent effects across different studies. For example, Kassegn and Endris (2021) found a negative influence of family size on credit demand in Ethiopia, which contrasts with findings from other regions.\n\nThe diverse findings from these studies underscore the importance of context-specific research in understanding the determinants of credit demand and access. The inconsistencies in results reflect the varying influence of national policies, regulatory frameworks, and socio-economic conditions on credit participation. The rich dataset used in this study allows for the inclusion of additional variables to better analyze their relationships with credit participation, providing a more nuanced understanding of the factors at play.\n\n\n3. Methods\n\nGubalafto Woreda is located in the Amhara Region of Ethiopia, part of the North Wollo Zone, approximately 520 kilometers from the capital city, Addis Ababa. It is one of the eleven woredas in North Wollo Zone, situated between 39°12'9\" and 39°45'58” East longitude, and 11°34'54\" and 11°58'59” North latitude. The woreda is bordered to the south-by-South Wollo Zone, to the west by Delanta and Wadla, to the northwest by Meket, to the north by Gidan, to the northeast by the Alawuha River (Logiya River), which separates it from Kobo, and to the southeast by Habru. Weldia is an enclave within this woreda, and notable towns include Hara.\n\nThe geographical landscape of Gubalafto is predominantly mountainous, with elevations ranging from 1,300 to 3,900 meters above sea level. The woreda comprises three agro-ecological zones: Lowland (Kolla), ranging from 1,379 to 1,500 meters above sea level; Mid-altitude (Weynadega), from 1,500 to 2,300 meters; and Highland (Dega), above 2,500 meters. The majority of the rural population resides in the highlands and plateaus, with Weynadega and Dega areas being densely populated, while Kolla is relatively sparsely populated. Major crops cultivated include barley, teff, and sorghum, with small land holdings being a significant constraint for households (Gubalafto Woreda Agricultural Office, 2024).\n\nAccording to the 2007 national census by the Central Statistical Agency (CSA, 2007) of Ethiopia, Gubalafto Woreda had a population of 139,825, marking a 0.48% increase from the 1994 census. The population comprises 70,750 men and 69,075 women, with 4,886 (3.49%) residing in urban areas. Covering an area of 900.49 square kilometers, the woreda has a population density of 155.28 persons per square kilometer, which is higher than the zone average of 123.25 persons per square kilometer. There are 33,676 households, averaging 4.15 persons per household, and 32,824 housing units. Gubalafto Wereda is categorized among the 48 most drought-prone and food-insecure woredas in the Amhara Region . The predominant religion is Orthodox Christianity (86.58%), followed by Islam (13.32%). As of 2024, the estimated population is 158,324, comprising 80,948 males and 77,376 females.\n\nThe woreda has been supported by the Productive Safety Net Program (PSNP) since 2015, with the Livelihood Program being a key component introduced at that time. Currently, there are 10,500 beneficiaries of the Livelihood Credit Program in the woreda, with 6,416 men and 4,086 women participating. Figure 1 below illustrates the geographical structure of the study area. This figure provides a visual representation of the region under study, which is essential for understanding the spatial context of the research.\n\nThis study investigates the determinants of rural women's participation in livelihood credit programs, utilizing both descriptive and explanatory research designs. A mixed methods design was employed, integrating both qualitative and quantitative data collection and analysis concurrently. Combining quantitative and qualitative research approaches can mitigate the limitations inherent in using a single approach, as these methods separately may not sufficiently address complex social and cultural phenomena.\n\nThe quantitative approach was used to analyze statistical data and test hypotheses by specifying a narrow hypothesis and collecting data to support or refute it. Concurrently, the qualitative approach involved conducting in-depth interviews with key informants to gather rich, contextual data. The study relied on both primary and secondary data sources.\n\n3.3.1 Data type and source\n\nThis study, which commenced in February 2023, explores the factors influencing rural women's participation in livelihood credit programs in Gubalafto Woreda through both qualitative and quantitative methods. Participant recruitment occurred from March 1, 2023, to March 25, 2023. Primary data collection took place between May 4, 2023, and July 28, 2023, using structured questionnaires distributed to female household heads, encompassing both participants and non-participants of the credit program. These questionnaires gathered comprehensive information on demographic, economic, social, and contextual factors. Additionally, secondary data were obtained from program documentation, academic literature, and prior research to enrich and provide context to the primary findings.\n\n3.3.2 Method of data collection\n\nPrimary data collection involved administering structured questionnaires with both closed and open-ended questions. These questions addressed factors such as age, marital status, household size, market access, landholding size, income level, education, experience in income-generating activities, skill training, extension contact, perceptions of interest rates, group collateral, and religious affiliation. Interviews were conducted with female household heads to gain insights into these variables.\n\nSecondary data were obtained from program documents and relevant literature to provide additional context and support the primary findings.\n\n3.3.2.1 Data quality management\n\nExperienced field staff conducted the data collection, guided by a one-day training session on data collection methods and questionnaire administration. A pre-test was performed with non-sample respondents to refine the questionnaire. Data were double-entered, checked for consistency, and cleaned to ensure accuracy.\n\n3.3.3 Sampling techniques\n\nGubalafto Woreda was selected for its relevance to the study of women's participation in livelihood credit programs. The woreda includes 34 rural kebeles, with 11,672 female household clients in the program, distributed across three ecological zones: dega, weyna dega, and kola.\n\nA multi-stage sampling approach was used. Four kebeles were randomly selected based on agro-ecological characteristics: one from kola, two from weynadega, and one from dega. On the four selected Kebeles, there 4086 female headed clients in the program. A total of 364 beneficiaries were sampled: 163 from Doro-Gibr, 178 from Ameya Mecha, 169 from Gedober, and 180 from Bekulo Manekiya.\n\nInclusion Criteria:\n\n• Women who are beneficiaries of the livelihood credit program and reside in rural areas.\n\n• Women aged 18 and above.\n\nExclusion Criteria:\n\n• Women residing in urban areas.\n\n• Women under the age of 18.\n\n3.3.4 Sample size calculation\n\nSample size was determined using the formula for single population proportion as per Yamane (1973), ensuring a 95% confidence level and a 5% margin of error. The sample was proportionally distributed across the three ecological zones:\n\n• Kola kebeles: n1\n\n• Weynadega kebeles: n2\n\n• Dega kebeles: n3\n\nWhere n=n1+n2+n3, n represents the total sample size. This approach ensured a representative sample across the kebeles, facilitating a comprehensive analysis of credit program participation factors.\n\nWhere:\n\n• n is the sample size,\n\n• N is the total population of women program clients,\n\n• e is the margin of error.\n\nAccordingly, with N = 4086, e = 5% (at least 95 % confidence level), sample size for this study is determined using the above equation as:\n\nAgro-ecologically, the classification of the total population becomes:\n\nWith this we come up with n= n1+n2+n3= 69+140+155=364 sample size. Finally, 69 clients from Dorogibr kebele, 140 clients from Ameya Mecha kebele and Gedober kebele,180 clients from Beklo Manekiya kebele totally 364 women are selected randomly and assessed for credit participation as shown in Table 1 below.\n\nThis study employed both descriptive and econometric methods to analyze the determinants of rural women's participation in livelihood credit programs.\n\n3.5.1 Descriptive analysis\n\nDescriptive statistics were used to summarize and describe the main features of the dataset. Key statistics such as minimum, maximum, mean, and standard deviation were calculated for each variable. Data were also presented through tables and graphs to illustrate trends and distributions.\n\n3.5.2 Econometric analysis\n\nA logistic regression model was utilized to identify the determinants of participation in livelihood credit programs. The analysis was conducted using STATA 17, with a sample size of 364 observations. The logistic regression model was chosen for its effectiveness in handling dichotomous dependent variables and explaining the relationship between these variables and the explanatory factors.\n\n3.5.3 Model specification\n\nThe logit model was selected due to its mathematical simplicity and practical application in examining binary outcomes. It is appropriate for ensuring that estimated probabilities lie between 0 and 1. The logit model, with its logistic distribution, was preferred over the probit model for this analysis (Wooldridge, 2002; Gujarati and Porter, 2009).\n\nThe cumulative logistic probability model is econometrically specified as follows:\n\nWhere ln is natural logarithm\n\n(xi) is the probability women participated in livelihood credit program\n\n1 − (Xi) is the probability women not participated in livelihood credit program.\n\nXi = represents the ith explanatory variables\n\nβi = is coefficient of ith explanatory variable\n\nWhere P (Yi = 1) is the probability of women participated in livelihood credit program.\n\nXi = represents the ith explanatory variables\n\ne = denotes the base of natural logarithms, which is approximately equal to 2.718\n\nβi = is coefficient of ith explanatory variables\n\nTable 2 below presents a summary of the variables, their definitions, measurements, and associated hypotheses for this study.\n\nEthical approval for this study, titled \"Empowering rural women: key factors driving participation in livelihood credit programs in Gubalafto Woreda, North Wollo, Ethiopia,\" was obtained from the Research Ethics Approval Committee of Woldia University, Ethiopia, and authorized by the Institutional Review Board (IRB) of the Faculty of Business and Economics at Woldia University under Reference No: FBE/RCSTT/300/2023 on February 12, 2023. All participants provided written informed consent and authorized the collection of necessary data for analyzing the factors influencing rural women’s participation in livelihood credit programs. The analysis was conducted using anonymized data, ensuring that no information could identify individual participants.\n\n\n4. Results and discussions\n\nThis chapter is divided into two sections. The first section provides a description of credit disbursement and the characteristics of the sample women. The second section focuses on the analysis of the econometric model results, specifically logistic regression.\n\nIn the descriptive statistics section, the status of credit disbursement in the woreda, the key characteristics of the sample women, and related variables are analyzed using appropriate statistical tools.\n\n4.1.1 Livelihood credit disbursement in the woreda\n\nThe livelihood program was initiated in the woreda in 2013, offering capacity-building services along with credit disbursement for RPSNP (PSNP) participants.\n\nTable 3 below presents a 12-year overview (2013-2024) of credit disbursement in Gubalafto Woreda, focusing on participation by gender, total credit amounts, and average credit per participant. A total of 11,029 participants accessed credit, with males constituting 62.9% and females 37.1%. While male participation consistently exceeded female participation, the gender gap varied, with closer parity observed in 2020 and 2021. The total credit disbursed reached ETB 159.5 million, with males receiving a larger share (ETB 97.6 million) compared to females (ETB 61.9 million). The average credit amount per participant increased from ETB 11,000 in 2013 to ETB 34,687.65 in 2024, indicating larger loans in recent years. The data reflect a growing reliance on credit, though gender disparities persist, with females receiving less credit on average. Overall, the trends suggest increasing access to credit, but further improvements are needed to achieve equitable participation and credit distribution across genders.\n\nFigure 2 below illustrates the trend of credit distribution in ETB from 2013 to 2024. Initially, there was a steady increase in credit distribution from 2013, culminating in a peak in 2020. This marks the highest point of credit distribution during the observed period. However, in 2021, there was a noticeable decline, followed by a significant drop in 2022. In the subsequent years, 2023 and 2024, the chart shows a gradual recovery with an increase in credit distribution. This pattern highlights fluctuations in financial activities over the years.\n\nFigure 3 below also shows the mean number of women participants in credit activities from 2014 to 2024. Initially, there was a gradual increase from 2014, continuing up to 2017. From 2018 to 2020, the participation remained fairly stable, with a slight rise. The peak occurred in 2021, marking the highest level of female participation. However, there was a sharp decline in 2022, followed by a minor recovery in 2023 and a slight decrease again in 2024. This trend highlights the fluctuations in women's involvement in credit activities over the years.\n\nThis section presents the results of the logistic regression analysis used to identify factors affecting rural women's participation in livelihood credit programs. Before interpreting the model, we assessed multicollinearity and heteroscedasticity to ensure the reliability of the regression coefficients. Multicollinearity was evaluated using the Variance Inflation Factor (VIF) and correlation coefficients; results indicated no serious multicollinearity, with VIF values well below 10 and correlation coefficients under 0.85. Heteroscedasticity was tested with the chi-square test, revealing a prob > chi2 of 0.0492, which was below the 5% significance level. This indicated the presence of heteroscedasticity. To address this, White’s heteroscedasticity-robust standard errors were used in STATA, effectively resolving the issue and ensuring the validity of the regression results.\n\nThe results from the binary logit model as shown in Table 4 below, derived from maximum likelihood estimates, reveal that rural women’s participation in credit programs is influenced by a complex interplay of demographic, socio-economic, and program-related variables. The logit model analysis highlights the importance of examining the combined effects of these variables on participation. The logistic regression, expressed through odds ratios, compares the likelihood of participation between those who are participants and those who are non-participants, providing insights into the factors driving participation in the study area.\n\n* p<.01.\n\n p<.05.\n\n* p<.1.\n\nTable 5 below provides a comprehensive overview of the significant variables influencing rural women's participation in livelihood credit programs. The logistic regression results reveal several critical factors affecting participation.\n\n* p<.01.\n\n p<.05.\n\n* p<.1.\n\nHousehold size is significantly associated with increased participation, evidenced by an odds ratio of 94.4. This finding aligns with research by [23], who noted that larger family sizes can diversify economic activities, thus enhancing credit access. Conversely, studies such as [21] found mixed results regarding the impact of family size on credit demand, suggesting that the effect may vary by context.\n\nMarket access also plays a significant role, with better access strongly linked to higher participation (odds ratio of 1802). This supports findings from [30], who emphasized that improved market connectivity boosts credit engagement. However, this contrasts with [20], who did not observe a significant relationship, indicating regional differences in the impact of market access.\n\nAge shows a negative correlation with participation, indicating that older individuals are less likely to engage in credit programs. This finding is consistent with [24], who observed that older farmers might have more assets and thus less need for credit. This differs from studies by [25] and [26], which reported varying or insignificant associations between age and credit demand, highlighting the potential influence of different regional or contextual factors.\n\nEducation levels are associated with decreased participation, aligning with [27] and [28], who found that higher education might limit involvement due to opportunity costs or misalignment with program goals. This contrasts with [29], who reported that higher education often facilitates better credit access, indicating that the effect of education on credit participation can vary depending on regional specifics.\n\nMarital status positively impacts participation, with married women showing higher odds of engagement. This finding reflects similar conclusions by [14], who noted the benefits of group-based lending models for married women. This result diverges from some studies that did not find strong associations, suggesting that marital status effects can differ based on local practices and program structures.\n\nLandholding size is positively associated with increased participation, consistent with [19], who noted that larger landholdings improve credit access. This supports the notion that land assets are crucial for securing credit. However, [34] found a negative relationship between land size and credit participation in Ethiopia, contrasting with [35], who observed a positive correlation, indicating that the impact of landholding size may vary depending on local conditions and policies.\n\nDistance to credit facilities negatively impacts participation, aligning with [30], who emphasized the importance of proximity to financial institutions. This result resonates with [36], who identified interest rates as a significant deterrent to credit demand, although the study did not specifically address distance. The role of interest rates and accessibility reflects a broader understanding of the barriers to credit engagement.\n\nOverall, the results highlight a complex interplay of demographic, socio-economic, and program-specific factors influencing rural women’s participation in livelihood credit programs. The findings reflect both agreements with and deviations from existing research, emphasizing the need for context-specific approaches to address the diverse factors affecting credit participation in different regions. The inconsistencies in the literature underscore the importance of tailored research to better understand local determinants of credit demand and access.\n\n\n5. Conclusion and recommendations\n\nThe livelihood program targeting women in the woreda has been operational from 2013 to 2024, distributing a total of 159,460,137 ETB to 11,029 beneficiaries. Of this, males received 97,582,119 ETB, while females received 61,878,008 ETB. In 2024 alone, 27 male clients were allocated 10,137,698 ETB, and 129 female clients received 3,702,676 ETB. This study set out to evaluate the distribution of livelihood credit and identify the key factors influencing women’s participation. Data were gathered from 364 women through structured questionnaires and analyzed using STATA 17 logistic regression. Four kebeles were randomly selected based on agro-ecological characteristics, and the data were analyzed using descriptive statistics such as percentages, frequency distributions, means, and standard deviations. The results of chi-square and t-tests revealed that most of the hypothesized variables significantly impact women's participation in credit programs.\n\nThe findings indicate that the livelihood program has had a positive impact on participants’ income and asset accumulation, particularly in livestock. Out of the 13 independent variables examined, 12 were found to be significant. Variables such as household size, income level, perception of group collateral, skill training, marital status, landholding size, market access, education level, experience in income-generating activities (IGA), extension contact, and distance from the lending office were identified as influential factors. Specifically, age, education level, and distance from the lending office were negatively associated with credit participation, while household size, marital status, income level, landholding size, market access, experience in IGA, perception of group collateral, extension contact, and skill training had positive effects.\n\nThis study underscores the complexity of factors influencing rural women's participation in credit programs and highlights the need for tailored approaches in policy and practice. The variability in determinants across different contexts suggests that a one-size-fits-all approach may not be effective. These findings provide valuable insights for future policy formulation and research, particularly in designing interventions that enhance rural women's access to credit and support their economic empowerment.\n\nTo enhance rural women's participation in livelihood credit programs, several key recommendations are proposed based on the analysis:\n\nFocus on Younger Women: Emphasize increasing credit participation among younger women by providing targeted training and awareness programs, aligning with the program’s objectives.\n\nLeverage Family Size: Recognize the positive association between family size and credit access. Families with more members can diversify income sources through agriculture and have more trading contacts. Microfinance institutions should extend their reach to support women-headed households with larger families.\n\nDiversify Income Sources: Improve rural household incomes by encouraging participation in both on-farm and off-farm activities. Expanding agricultural and non-agricultural income sources will help increase overall financial stability.\n\nEnhance Human Capital Development: Invest in education and vocational training to build human capital. Strengthening both formal education and skill training will address perception issues and increase participation in livelihood programs.\n\nPromote Income Generating Activities (IGAs): Encourage rural women to engage in various income-generating activities with confidence. Support from government officers and development actors at the village level can foster smallholder business activities and integrate them with agricultural production.\n\nIncrease Financial Institution Presence: Expand the physical presence of financial institutions in rural areas through additional branches, mobile banking units, and agent banking. Utilize digital platforms for loan applications, repayments, and financial literacy training to overcome geographical barriers.\n\nProvide Financial and Technical Training: Ensure timely delivery of financial and technical skills training to program clients. This will enhance participation, improve business effectiveness, and encourage better saving habits.\n\nImprove Infrastructure: Enhance access to basic infrastructure such as roads and veterinary services. Reducing the distance between residences and lending offices will support the nutritional and income gains of agro-pastoral households.\n\nSimplify Application Procedures: Streamline credit application processes by minimizing paperwork and reducing bureaucratic hurdles. Develop women-supportive policies and allocate appropriate resources to facilitate easier access to credit for rural women.\n\n\nCompliance with ethical standards\n\nEthical approval for this study, titled \"Empowering rural women: key factors driving participation in livelihood credit programs in Gubalafto Woreda, North Wollo, Ethiopia,\" was obtained from the Research Ethics Approval Committee of Woldia University, Ethiopia, and authorized by the Institutional Review Board (IRB) of the Faculty of Business and Economics at Woldia University under Reference No: FBE/RCSTT/300/2023 on February 12, 2023. All participants provided written informed consent and authorized the collection of necessary data for analyzing the factors influencing rural women’s participation in livelihood credit programs. The analysis was conducted using anonymized data, ensuring that no information could identify individual participants.\n\n\nAuthor contributions statement\n\nMoges Asmare conceptualized and designed the research, formulated the study objectives, and played a pivotal role in data collection and analysis. As the corresponding author, Moges Asmare took the lead in drafting and revising the manuscript, ensuring its coherence and adherence to academic standards. Atnafu Amare actively participated in the literature review, contributed to the theoretical framework, and played a key role in data interpretation. He also contributed to writing specific sections of the manuscript and provided critical feedback during the revision process.", "appendix": "Data availability statement\n\nThe anonymized datasets of this research are available in the\n\nZenodo Empowering rural women: key factors driving participation in livelihood credit programs in Gubalafto woreda, North Wollo, Ethiopia, DOI: https://zenodo.org/records/13284274 (Sisay, M. A et al., 2024a).\n\nThe project contains the following underlying data:\n\n• Rural Women Data.xlsx\n\nData is available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nZenodo: The questionnaire that supports the findings of this research is available in the Zenodo repository\n\nTitle of project: Empowering rural women: key factors driving participation in livelihood credit programs in Gubalafto woreda, North Wollo, Ethiopia, DOI: https://zenodo.org/records/13284881 (Sisay, M. A et al., 2024b).\n\nThe project contains the following extended data:\n\n• Empowring Women Household Survey Questionnaire.docx\n\nData is available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nZenodo: STORBE checklist for reporting guidelines for this retasearch is available at zenodo: https://zenodo.org/records/13305037 (Sisay, M. A et al., 2024).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAbate TW, Sheferaw HE: Micro, small and medium enterprises and their linkage with key actors in Ethiopia: Developing entrepreneurial ecosystem mapping. J. Innov. Entrep. 2023; 12(1): 71.\n\nAbreu D, Félix S, Oliveira V, et al.: The impact of a macroprudential borrower-based measure on households’ leverage and housing choices. J. Hous. 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International Journal of Business, Technology and Organizational Behavior (IJBTOB). 2023; 3(4): 252–265.\n\nMamuye W: Determinants of smallholder farmers participation in formal credit and challenges faced by institutions: The case of Mojana Wodera District, Amhara Region, Ethiopia. International Journal of Finance and Banking Research. 2021; 7(1): 9–20.\n\nMasa R, Bates C, Chowa G: Direct and indirect associations of food insecurity, adolescent–parent relationship, and adolescent future orientation. J. Fam. Issues. 2021; 42(6): 1285–1307.\n\nMorton M, Klugman J, Hanmer L, et al.: Gender at work: A companion to the world development report on jobs. Washington, DC: World Bank; 2014. Reference Source\n\nMpuga P: Constraints in access to and demand for rural credit: Evidence from Uganda. Afr. Dev. Rev. 2010; 22(1): 115–148.\n\nNegatu BS: A study on impact of interest rates on credit and loan repayment in Ethiopia with reference to credit cooperative unions. Ilkogretim Online. 2021; 20(5): 7371–7376.\n\nNguyen TAN: Financing constraints on SMEs in emerging markets: Does financial literacy matter? Review of Socio-Economic Perspectives. 2017; 2(2): 53–65.\n\nRanganathan M, Pichon M, Hidrobo M, et al.: Government of Ethiopia's public works and complementary programmes: A mixed-methods study on pathways to reduce intimate partner violence. Soc. Sci. Med. 2022; 294: 114708.\n\nRayhan SJ, Rahman S, Lyu K: Increasing Boro rice productivity through credit: Evidence from Bangladesh. Agricultural Economics/Zemědělská Ekonomika. 2024; 70(2).\n\nSanson K: Mobile Hollywood: Labor and the geography of production. University of California Press; 2024; 243.\n\nSisay MA: Empowering Rural Women: Key Factors Driving Participation in Livelihood Credit Programs in Gubaflto Wereda, North Wollo, Ethiopia. Zenodo. 2024a. Reference Source\n\nSisay MA: Empowering Rural Women: Key Factors Driving Participation in Livelihood Credit Programs in Gubaflto Wereda, North Wollo, Ethiopia. Zenodo. 2024b. Reference Source\n\nSmeeding TM, Weinberg DH: Toward a uniform definition of household income. Rev. Income Wealth. 2001; 47(1): 1–24.\n\nSwain RB: The demand and supply of credit for households. Appl. Econ. 2007; 39(21): 2681–2692.\n\nTura EG, Kenea T, Kaso T: Determinants of demand for credit among wheat and teff smallholder farmers in central of Ethiopia (Arsi and South West Shewa). American Research Journal of Business and Management. 2017; 3(1): 17.\n\nTwumasi MA, Jiang Y, Danquah FO, et al.: Determinants of credit constraint of artisanal fishermen in Ghana. Ciência Rural. 2020; 50(3): e20190119.\n\nWaje SS: Determinants of access to formal credit in rural areas of Ethiopia: Case study of smallholder households in Boloso Bombbe district, Wolaita zone, Ethiopia. Economics. 2020; 9(2): 40–48.\n\nWooldridge JM: Econometric analysis of cross section and panel data. MIT Press; 2002.\n\nWorld Health Organization: Achieving well-being: A global framework for integrating well-being into public health utilizing a health promotion approach. WorldHealth Organization; 2024.\n\nYamane T: Statistics: An introductory analysis. Harper & Row; 3rd ed1973." }	[ { "id": "322436", "date": "30 Sep 2024", "name": "Suhail M. Ghouse", "expertise": [ "Reviewer Expertise Entrepreneurship & 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\nSummary of the Article: The study examines the factors influencing rural women’s participation in livelihood credit programs in Gubalafto Woreda, Ethiopia. Using a cross-sectional survey of 364 rural women and a mixed-methods approach, the research identifies the socio-economic and demographic determinants of participation in these credit programs. Key factors such as household size, income level, education, skill training, and market access are analyzed through descriptive statistics, chi-square tests, t-tests, and logistic regression. The findings underscore the importance of household size, skill training, and access to markets as positive predictors of participation, while age and distance from lending offices are negative predictors. The authors conclude with recommendations to improve access to credit for rural women, particularly through enhanced training programs and better market access.\nClarity and Citation of Current Literature: The article is clearly presented, with a logical structure that moves from the introduction through to the conclusion. The use of tables and figures enhances understanding of the data. However, while the article includes relevant references, the literature review could benefit from the inclusion of more recent studies, particularly those from the last 3-5 years. Moreover, there is some repetition in the literature review, particularly in the discussion of theoretical frameworks. Recommendations: 1. Ref-1,2,3,4,5,6,7,8\n2. Avoid repeating theoretical concepts in multiple sections of the literature review.\nStudy Design and Technical Soundness: The cross-sectional survey design is appropriate for the study’s goals, and the stratified random sampling technique ensures representativeness across different agro-ecological zones. The statistical methods used—descriptive statistics, chi-square tests, t-tests, and logistic regression—are suitable for the research question and data structure. However, certain methodological details require more elaboration. Variables such as \"market access\" and \"perception of interest rates\" are not clearly defined or operationalized. Furthermore, there is no discussion of how missing data were managed, which could influence the study’s robustness. Additionally, while the sample size is justified, the rationale for selecting only four kebeles could be more clearly articulated to enhance the generalizability of the findings. Recommendations: 1. Clearly define and operationalize key variables such as \"market access\" and \"perception of group collateral.\" 2. Provide a description of how missing data were handled. 3. Offer a stronger justification for the selection of the four kebeles and explain how representative they are of the larger population.\nReproducibility of Methods and Analysis: The study provides a solid overview of the methods, but additional detail is required for full reproducibility. Although the sampling procedure and statistical techniques are explained, the questionnaire and the coding of variables are not made available, which limits the ability of others to replicate the study. Moreover, while the authors mention using STATA for data analysis, the specific commands or procedures are not shared. Recommendations: 1. Include the full questionnaire in an appendix or supplementary material. 2. Provide a detailed codebook that explains how all variables were measured or coded. 3. Share the STATA commands or code used for statistical analysis to ensure complete reproducibility.\nStatistical Analysis and Interpretation: The statistical methods used in the paper are appropriate, and the results are presented clearly. Logistic regression is a good choice for examining the binary dependent variable (credit participation), and the interpretation of results is generally accurate. However, more detail is needed regarding the operationalization of certain variables and the interpretation of the odds ratios. Additionally, the paper mentions testing for multicollinearity but does not provide the results (e.g., VIF scores) or explain how this issue was addressed. The reported pseudo-R-squared of 0.944 for the logistic regression model is unusually high, which could indicate overfitting. The implications of this high value should be discussed, and adjustments should be made if necessary. Recommendations: 1. Provide more detail on the operationalization of key variables in the logistic regression model. 2. Report the results of multicollinearity tests (e.g., VIF scores) to ensure the stability of the regression coefficients. 3. Address the high pseudo R-squared value, explaining whether this might indicate overfitting, and suggest steps to mitigate it if needed.\nSupport of Conclusions by Results: The conclusions are generally supported by the results of the study. The authors correctly identify the factors that influence rural women’s participation in credit programs and provide recommendations that align with these findings. However, the conclusions could be more nuanced in terms of acknowledging the limitations of the study’s cross-sectional design, which only allows for correlation, not causality. Additionally, while the conclusions have broader policy implications, there is limited discussion of the regional specificity of the findings and how they might apply to other areas. Recommendations: 1. Clarify that the study identifies correlations rather than causal relationships between the variables and credit participation. 2. Discuss the limitations of the study, including the cross-sectional design and reliance on self-reported data. 3. Offer suggestions for future research that could address these limitations, such as longitudinal studies or studies that explore specific mechanisms.\nFinal Assessment: This article makes a valuable contribution to understanding the factors influencing rural women’s participation in livelihood credit programs in Ethiopia. However, to enhance the clarity, reproducibility, and impact of the work, the authors should address the specific concerns outlined above. By refining the methodological transparency, strengthening the statistical interpretation, and providing a more nuanced discussion of the findings, the study can offer more robust academic and policy insights.\nBased on the detailed review, major revision is recommended.\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": [] }, { "id": "322435", "date": "04 Nov 2024", "name": "Sunil Khosla", "expertise": [ "Reviewer Expertise Development economics (poverty", "vulnerability", "food security", "impact evaluation etc.)" ], "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\nEmpowering rural women: key factors driving participation in livelihood credit programs in Gubalafto woreda, North Wollo, Ethiopia\nThank you for the opportunity to review this intriguing manuscript titled “Empowering rural women: key factors driving participation in livelihood credit programs in Gubalafto woreda, North Wollo, Ethiopia.” Using 364 rural women data and logistic regression model, the paper examined the determinants of rural women participation in livelihood credit programs in rural Ethiopia.\nWhile the study offers several valuable insights, a few areas require further attention for clarity and completeness:\n\nPlease interpret the results instead of writing the results in abstract. Additionally, the abstract should present specific implications rather than a general conclusion. The contributions of this study should be clearly articulated. Consider adding a dedicated section or paragraph in the introduction to emphasize how this study differs from existing literature. Descriptive statistic table is missing. Include a descriptive statistics table to provide insight into the data structure, enhancing reader understanding of the sample characteristics. Tables 4 and 5 appear confusing; consider merging these into a single table for better clarity. Simplify the table by focusing on coefficients, standard errors, and significant indicators. Table 4, IL (Annual Income level of women) coefficient is zero. Discuss the rationale for including this variable if it offers no explanatory power. Sources for the figures are missing. Significance of the study area is missing. Explanation for the outcome variable (Wplcstatus) is missing. How is this variable estimated? How much % of surveyed women are falls under the which binary category? In introduction, the authors mentioned the challenging factors such as gender bias in extension services, limited access to information, and socio-economic constraints but did not consider them in their analysis. How then this study filled the gap? What is the source used for selecting these independent variables used in the logistic regression? Why not used other variables such as social capital (member in groups like SHG etc.), decision making, health status etc. Rewrite Section 2 to concisely focus on social protection programs, specifically the Productive Safety Net Program (PSNP), and its relationship with women’s empowerment and household well-being. Establish connections to women’s participation in such programs and highlight relevant research gaps. Tables should be properly formatted, where coefficients and standard errors, along with significance indicators, are sufficient for presenting results effectively. As the authors emphasized more on the livelihood credit program and estimating just determinants might not be good idea. Therefore, exploring the impact of livelihood credit programs on women’s empowerment and wellbeing using rigorous methods like impact evaluation (instrumental variable, endogenous switching regression, propensity score matching) would provide additional insights and strengthen the study’s relevance in rural Ethiopia. Citations are mostly missing in the manuscript. For instance, first paragraph of introduction, section 3.3.3, 3.3.4 etc. Multicollinearity test (VIF) table is missing. There exists confusion between literature review and research objective. Everyone knows the benefit of social protection such as social safety net (The Productive Safety Net Program (PSNP)). Why would women not participate? Is there any statistics that suggest low participation or any issue with the government program? Please make it clear. The literature section deals with the definition, and other information but does not connect it related to the women participation in the program nor it explains about the how the factors can make difference. It does not conclude with the research gaps. Therefore, the literature review should extend beyond definitions to relate factors directly to women’s participation in the program. Conclude with a statement of research gaps based on this discussion. The objective is confusing because the sample selection criteria (3.3.3) are those women who received the benefit. So, how the dependent variable is a binary one when all women have participated or received the benefit from the program? Further, the variable creation (dependent variable) explanation is not provided neither the % of women that have received any benefit. The conclusion would be strengthened by providing specific policy implications based on the study’s findings. In the introduction, data is missing on how much % of rural women are currently participating in these programs? If the participation rate is less, then the study make sense. Instead of presenting odds ratios (OR), it is recommended to include the marginal effects for the coefficients, which may provide more intuitive interpretations of the results. Describe how the study’s recommendations could be practically implemented. Providing details on feasible actions enhances the applied relevance of your suggestions. Table 4 & 5 results interpretations need attention. Please revise it or use the marginal effect coefficient. For example, education level is negatively significant, how is that possible? The interpretation might be biased because women in developing areas generally less educated. What is the mean education of women in the study area? To claim your point education square could be used. Limitations of the study and suggestions for the future research is missing.\nOverall, the manuscript addresses a vital topic but requires revisions to improve clarity, methodological rigor, and presentation. I look forward to seeing how these concerns are addressed in future drafts.\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": [] } ]	1	https://f1000research.com/articles/13-1000
https://f1000research.com/articles/13-998/v1	02 Sep 24	{ "type": "Research Article", "title": "Exploring needs, perceptions, and preferences towards exercise video among overweight individuals - a qualitative study", "authors": [ "Shishira K B", "K Vaishali", "Rajagopal Kadavigere", "Suresh Sukumar", "Tulasiram Bommasamudram", "Praveen Hoogar", "Shishira K B", "Rajagopal Kadavigere", "Suresh Sukumar", "Tulasiram Bommasamudram", "Praveen Hoogar" ], "abstract": "Background The number of overweight people (BMI 25–29.9kg.m-2) in the world is increasing, which increases the risk of health problems and psychological difficulties. To reduce these risks, it is imperative to address unhealthy habits including food and exercise. This qualitative study aimed to explore the needs, perceptions, and preferences of overweight individuals on tailored exercise programs that incorporate educational videos.\n\nMethodology Forty Individuals between the age of 18-30 years with a BMI of 25-29.9kg.m-2 were included in the study using Purposive sampling from October 2023 to November 2023. Semi-structured in-depth interview was conducted for 45-60 minutes approximately among both active and inactive overweight individuals by a researcher trained in qualitative research. These interviews were audio-recorded and transcribed verbatim. Thematic analysis was performed using inductive and deductive approaches to identify the recurrent patterns, themes, and insights in the transcribed interviews.\n\nResults 8 themes and 44 subthemes emerged from the analysis, helping to shed light on the needs, perceptions, and preferences that overweight individuals experience when it comes to their preference for a customized exercise program provided through educational video. The participants wanted personalized regimens that catered to their requirements and levels of fitness.\n\nConclusion In summary, the findings emphasize the value of educational videos that are easy to use, visually appealing, and supported by science. These videos should emphasize technique, varying levels of difficulty, and brief sessions.", "keywords": [ "Exercise-video", "Interview", "Need", "Overweight", "Perception", "Preference", "Thematic-analysis" ], "content": "Introduction\n\nOverweight individuals: those with a BMI of 25 to 29.9kg.m-2 are becoming more prevalent nationally and internationally. Non-communicable diseases and being overweight are closely associated, with higher rates of morbidity and mortality.1 People who are overweight are more likely to experience serious health conditions that lower their quality of life.2 Furthermore, being overweight increases the likelihood of developing psychosocial issues such as depression, disordered eating, low self-esteem, and disruptions in body image.3,4 It is imperative to address unhealthy lifestyle behaviours related to diet, exercise, and coping mechanisms in overweight populations since they exacerbate these disorders.5\n\nRegular exercise is essential for reducing the hazards related to being overweight.6 Even with a wealth of evidence showing the health advantages of consistent physical activity, more than half of Indians do not exercise to the recommended levels.7,8 One of the main causes of this deficit is frequently stated to be a lack of time.9 The development of an exercise program is significantly influenced by the participants' feelings and behaviours, which enable us to understand their perception of the program better.10 Although individual variables are important, it is commonly forgotten that social, community and environmental factors also impact physical activity levels.11,12 Even with a plethora of intervention tools designed to encourage physical exercise, the ongoing prevalence of inactivity highlights the need for more potent approaches.13–15 Understanding the unique requirements, attitudes, exercise perceptions and preferences of overweight people are essential to design focused and successful interventions that deal with the underlying reasons for sedentary behaviour.16 The insights acquired from an understanding can be employed in developing individualized exercise video programs that promote inclusivity and improve adherence within this demographic. A noteworthy development in efficacy enhancement has been the provision of individually catered information through interventions.17–19\n\nIt is critical to look into the reasons behind these populations' low levels of physical activity as well as their preferences for exercise and impediments. Empirical studies regularly demonstrate robust associations between exercise motivation, exercise-related obstacles, personal preferences, and true levels of physical activity.20–22 As such, it is essential to perform a needs assessment prior to developing an exercise video program tailored for persons who are overweight. Designing interventions that are more likely to boost exercise involvement can benefit from a greater understanding of their experiences.\n\nAs a result, the purpose of this study is to explore the current needs, perceptions, and preferences related to exercise among overweight individuals, providing insights into the elements that effectively influence exercise participation.\n\n\nMethods\n\nThis qualitative study involves need analysis for the exercise video among overweight individuals through an in-depth interview. The ethical approval was obtained from the Kasturba Medical College and Kasturba Hospital Institutional Ethics Committee, Manipal Academy of Higher Education on 31st August 2023 (IEC1: 96/2023). The study adhered to the principles outlined by the declaration of Helsinki. This study followed the standard reporting guidelines of COREQ.23 A purposive sampling was used to recruit study participants. Participants were included in the study if they were 18 to 30 years old and categorized as Overweight with a BMI between 25-29.9kg.m-2 according to WHO classification. Eligible individuals were required to be inactive or active based on the Global Physical Activity Questionnaire (GPAQ), free from comorbidities such as diabetes, hypertension, CVD, neurological, and musculoskeletal disorders. Additionally, participants needed to be able to verbally communicate in English and express a willingness to participate in the study Eligible participants were informed about the objectives and study procedure, and those who agreed to participate signed the written informed consent. The identity of the individuals has been removed to maintain confidentiality. The recruitment was carried out from October 2023 to November 2023.\n\nA semi-structured face-to-face in-depth interview was conducted among 40 exercising and non-exercising participants by SKB, trained in qualitative research methodology. The interview process was guided by an open-ended questionnaire allowing the participants to express their views freely. Through literature reviews and discussions, an interview guide was developed. It was then validated and suitably modified following the advice provided by the experts prior to the interviews. The guide included questions regarding their exercise routine, motivations, barriers to exercise, need for the exercise video, and requirements in the video (refer to the Data set for the interview guide). This interview process was carried out for 45-60 minutes approximately in a quiet room with only the researcher and the participant. These interviews were audio-recorded on a smartphone and transcribed verbatim.\n\nData was analysed manually using inductive and deductive approaches. The manual data analysis procedure consisted of some defined processes. Initially, in-depth interview verbatim transcripts were carefully recorded, and saved electronically, and a physical copy was made for the convenience of analysis. Following multiple readings of the transcripts, two team members (SKB and KV) independently coded the material. Significant statements matching the study's goals were identified and highlighted as keywords during the first coding step. These keywords were subsequently arranged using axial coding. Keywords with similar meanings were categorized and further combined to form broad themes (selective coding).\n\n\nResults\n\nA detailed summary of the 40 participants' characteristics is given in Table 1 of this qualitative study. The age of the participants spanned between 20 to 30 years, encompassing both male20 and female20 individuals with their BMIs varying between 25 and 29.9kg.m-2. Based on their answers to the GPAQ, 20 of the participants were found to be moderately active (> 600 MET per week), and the other 20 were classed as inactive (<600 MET per week). The participants' educational backgrounds ranged from undergraduate to Ph.D. level qualifications. Only three of the participants were employed while the majority, comprising thirty-seven individuals were students.\n\nThe analysis of the in-depth interview yielded 8 themes and 44 subthemes which are described in Table 2.\n\nLifestyle factors were illuminated by participants, shedding light on both dietary patterns and exercise routines.\n\nRegarding eating habits, participants (n=11) described that they exhibited stressful eating behaviour during challenging times. However, on the other days (non-stressful periods) they (n=22) follow a disciplined and health-conscious diet.\n\n“I try to reduce the amount of food I eat; I don't eat Sweets”.\n\n“When I take Stress during exams I just simply eat even If I'm not hungry, I go and buy something and eat”.\n\nParticipants provided insights into their activity patterns, with many (n=33) reporting extended periods of sitting ranging from 5 to 6 hours or 6 to 7 hours daily. The activity behaviours varied, encompassing a combination of sedentary and active pursuits. Some individuals (n=14) adhered to a regular exercise regimen, incorporating either strength or cardio routines or both, while others (n=6) mentioned consistent engagement in activities such as dancing, aerobics, badminton, and body weight exercises, highlighting the incorporation of enjoyable activities into their physical routines.\n\n“My college work would be, uh, between nine to five, uh, so out of that, uh, maximum of three to four hours in a day maximum uh, would be, uh, my class hours. So, except for that, most of the time I would be sitting”.\n\n“I go to the gym regularly 6 days a week and I focus more on weight training and resistance training and around half an hour of cardio in the gym.”\n\n“Around 6, 6 15 I'll go play uh, till 8, 8 30. I mean, uh, obviously I won't play continuously. Uh, so by the time I leave, uh, badminton, it'll be around 8, 8 30”.\n\nThe participants expressed exercise expectations regarding mental health, appearance, fitness, and overall well-being while also emphasizing the necessity of exercise for preventing illnesses and building confidence. Their desired exercise regimen involved dedicating 10-15 minutes for 4-5 days per week, focusing on specific areas such as the arms, abdomen, hips, and thighs. While acknowledging the positive impact of exercise on their mood and satisfaction, some participants (n=12) noted potential drawbacks, mentioning feelings of boredom over time and heightened self-consciousness when exercising in the presence of others.\n\n“Exercise is necessary because as I said, some amount of appearance related concerns, future health risks, plus some amount of, um, mental health related as well”.\n\n“So, I personally feel that it makes me feel like I've achieved something. Even if I have done a small workout”.\n\n“I feel bored. It's like, playing is much more exciting to me. Like playing or dancing is more exciting to me rather than exercising”.\n\nThe exploration of participants' exercise experiences revealed a spectrum of obstacles and facilitators influencing their pursuit of physical activity. These challenges were classified into personal factors, environmental factors, and opportunities.\n\nPersonal factors comprised aspects like self-discipline, the need for company during exercise, body consciousness, fatigue, challenges in working out after college hours, lack of knowledge, and concerns related to injury.\n\n“I require some company who can, you know, motivate me to move. Of course, being alone, I won't”.\n\nNotably, a significant number of female participants (n=10) identified the menstrual cycle as a major obstacle to regular exercise.\n\n“I would say, um, cycles, one of the barriers, I guess I can say that during that week, I wouldn't want to but then, then there's a break of a one good week and then again you have to put yourself through”.\n\nEnvironmental factors played a pivotal role, with adverse weather conditions, difficulties in commuting to the gym, and a lack of dedicated exercise space emerging as significant barriers.\n\n“I do not after coming here only I understood it. I don't feel very well with humidity because I sweat a lot”.\n\n“Rainy days actually will affect my activity and feel very lazy. So the weather will make us feel very lazy, so those times It'll be like kind of difficult for me to go to the gym and do”.\n\nSocial prejudice, particularly the perceived restrictions on females exercising in gyms, was also highlighted (n= 2).\n\n“My mom doesn’t allow me to go exercise in the gym otherwise, I would just do it in the gym”.\n\nVarious opportunities acted as impediments to participants (n=32) to their regular exercise, including time constraints, the cost of gym memberships, and insufficient knowledge about exercise routines.\n\n“It's obviously easy to join a gym or so, but then gym yeah, again, you need to prioritize the time for that and then a lot of the gyms these days are pretty expensive, so it might not fit into our budgets to go”.\n\nOn the flip side, facilitators to exercise encompassed personal motivations, environmental support, and available opportunities that helped participants overcome these hurdles. Personal motivations included post-exercise mood improvement, weight management goals, and the desire for overall good health.\n\n“I'm always striving to be better, that is also there. There's that motivation to always be better. So, I'm not always satisfied with what I am right now. So that's one drive or one motivation for me to keep going to achieve something even better”.\n\nInterestingly, some female participants (n=5) noted that a limited wardrobe served as a compelling motivation to engage in exercise.\n\n“Not just appearance and I think multiple I mean, apart from, uh, trying to, uh, reduce by exercises I guess certain adaptations, like, I mean, not being able to wear a certain type of clothes, I think that's something that even motivated to further work out”.\n\nSupport from parents and friends, coupled with easy accessibility and dedicated exercise space, were identified as additional facilitators (n= 19).\n\nKey concerns related to exercise were articulated as challenges in maintaining flexibility, and consistency, initiating exercise routines, and a lack of accurate information about various exercises by experts.\n\n“Consistency because, yeah, few days after starting to exercise. It's very hard. You have to force yourself. I remember three years back when I started exercising, I was like blaming myself. But why did you gain weight? It is then I did this two-week challenge, so I had a challenge. So, I was like, OK, anyways I started. I will continue. But yeah, exercising consistently is purely very difficult. You must force yourself”.\n\nParticipants (n=28) expressed a clear preference for utilizing video content as their primary exercise resource, with some also indicating a preference for personal training. They highlighted the advantages of videos, citing their ease of follow, user-friendly nature, time and cost-effectiveness, and overall convenience. Additionally, participants (n=36) shared positive experiences with past exercise videos, appreciating the sense of exercising with a companion, motivational content, animated visuals, immediate feedback, short durations, and easy accessibility compared to other resource forms.\n\n“Videos because we can see the emotions. Like letters and pamphlets, we can read that, but there won't be such an emotion. So, when we see a video, for example, I'm not exercising, so they are actually, we can feel that how they work out, emotions, feelings, everything. So that will make us do”.\n\nOn the downside, they (n=31) noted drawbacks such as insufficient information on techniques, unrealistic recommendations, excessively fast paced and challenging routines that could demotivate, and a lack of monitoring and proper scientific evidence. Some participants (n= 3) also expressed dissatisfaction with branding and advertisements associated with the videos.\n\n“Most of the videos that we see on the Internet don't take into that much of an account of everything else. They just say a set of exercises and they say that it would help you lose weight within these many days, or like which is unrealistic amount of time, so they usually what we see is unrealistic set of goals and time plan”.\n\nThis segment was meticulously crafted, focusing on various aspects such as exercise techniques, difficulty levels, duration, instructional modes, diverse exercise routines, preferred activities, and the role of music in the video. All participants (n=40) expressed a strong desire for detailed guidance, including proper form, specific numbers of repetitions and sets, and designated breaks. They emphasized the importance of a range of difficulty levels, spanning from easy to challenging, yet manageable within a shorter duration (n=25) of 10-15 minutes.\n\n“I would want the complete breakdown of the Exercise. Then the uh…. number of reps for muscle building, muscle loss, weight building, weight loss. Then the timings, the breaks in between everything to be proper and easy to comprehend”.\n\nMoreover, participants (n=26) sought a flexible exercise routine that engaged all body parts, tailored to individual abilities, and visually demonstrated with a progression guide. They (n=20) specifically requested clear captions and voice-over instructions provided by an experienced instructor, outlining the muscles involved.\n\n“A combination of audio and video like uh…. at each key phase and explaining what is happening there would be better”.\n\nAdditionally, some participants (n=29) expressed a preference for high-intensity music to be incorporated into the video.\n\n“Definitely, uh…… I think music and exercises is one good combination. Even when I'm walking actually, I have my earphones on all the time, helps me with at least getting that rhythm. If it is for a video uh…. I think something without lyrics something that gives or pumps yourself”.\n\nThe factors that resonated with participants included their preferences for models, the approachability of the presenter, video quality, background settings, and the duration of exercise content. They (n=21) expressed a preference for an active and fit individual of a similar age, serving as the demonstrator for all exercises in the video. This person should adopt an encouraging approach that is easy to understand.\n\n“Somebody who looks fit because sometimes not looking fit then the person who is following the person might just feel what is the whole point of doing this. So, uh… Somebody who looks fit and of the same age, who is confident about what they are doing, what they are saying”.\n\nParticipants (n=28) specifically favoured videos presented with bright lighting, clear sound, and visual clarity against a light-coloured background in a distraction-free space. They (n=22) emphasized the importance of the video exhibiting a moderate to high level of professionalism and featuring immersive colours.\n\n“Some plain background or dark background with good lighting which is standardized because even mind appreciates light, and uh… the participant performing the exercises and his movement pattern is clearly visible”.\n\nAdditionally, participants (n=25) highlighted their desire for the video to be of short duration and free from advertisements.\n\nUh, short duration videos, maybe, uh 10 minutes, uh, or max to max 15 minutes. Uh, uh, I would suggest keep it short. Uh, and much, uh, focusing, uh, that should be more than enough.\n\nThis explored the participant's considerations beyond exercise and physical activity encompassing aspects of nutrition, safety precautions, exercise benefits, mode of delivery, and motivational strategies.\n\nAll participants (n=40) expressed a preference for information covering calorie and water intake, suitable attire and footwear for exercise, the exercise environment's features such as ventilation and non-slip flooring, guidelines for the dos and don'ts of exercises, and methods for monitoring exhaustion.\n\n“The main thing is shoes, clothing, and uh…. everything related to ventilation, hydration, and nutrition. My perspective I will be happy”.\n\nMoreover, they sought insights into the health benefits of exercises and the specific muscles engaged during different activities. Particularly, female participants (n=6) indicated a keen interest in understanding the hormonal influences of exercise.\n\n“And also, hormonal influences if you're talking about female population those are also, uh, major parts. So, educating them about these things are very much important. Rather than telling them exercise, telling how they can actually get into those programs is much important”.\n\nRegarding motivation, participants (n=23) indicated a preference for weekly communication, either through calls or texts, from fitness experts. Additionally, they expressed a desire to track their progress through videos or logbooks to enhance their commitment to regular exercise.\n\n“Yaa actually, if we talk to the person only, then only we'll be coming to know that what exactly is happening”.\n\nTheir preference was for this information to be presented either at the beginning of a video or as a disclaimer at the end.\n\nThe featured videos are intended (n= 34) to be shared with participants through their preferred platforms, such as YouTube, WhatsApp, or email. The content will be presented as a link, which requires minimal internet usage and facilitates easy downloading.\n\n“Like, let's say if I'm outside, Uh, I don't have that much, uh, data, on the phone So that time I would think, uh, it would be better if I had a downloaded video”.\n\n“Thing is YouTube link would be nice. Email and WhatsApp are my preferred modes”.\n\n\nDiscussions\n\nThe in-depth interview analysis offers insightful information about the perceptions and experiences of overweight people regarding a range of topics, including lifestyle factors, expectations for exercise, exercise exploration, preferred exercise resources, requirements in videos, appealing factors, holistic well-being, and media preferences. These themes make a substantial contribution to our understanding of the complex interactions among social, environmental, and personal factors that influence exercise behaviours.\n\nThis theme clarified the complex interrelationships between lifestyle elements, including food habits and exercise regimens. One of the main conclusions showed that individuals' eating habits followed a dual pattern that was influenced by stress. Those who were going through difficult situations tended to eat poorly, but during less stressful times, they ate more healthily and with discipline. This dynamic interaction between food decisions and emotional well-being highlights how differently people react to stress and its impact on lifestyle. In addition, the analysis of exercise regimens and sitting duration offered a thorough picture of the lifestyles of the participants, placing them in the range of sedentary to moderately active. Likewise, research conducted by O’Neil et al. (2012) and Cha et al. (2015) also documented widespread unhealthy lifestyle patterns.24,25 This conclusion is also consistent with the results of a study by Kushner et al. (2010) that showed how prevalent harmful lifestyle patterns are—including poor food, exercise habits, and coping mechanisms among overweight or obese. The study found a correlation between these patterns and advancing age, and that they intensified with rising BMI.5 The incorporation of these findings into the broader context of existing research points to the need for a more complex understanding of the variables driving unhealthy lifestyle choices, particularly in populations dealing with weight-related issues. Identifying these trends becomes an essential first step toward developing focused interventions. According to Kushner et al (2010), interventions that target both emotional health and certain lifestyle decisions may be more successful in encouraging healthy behaviours in people who struggle with being overweight or obese.5 This emphasizes how important it is to take a comprehensive approach when creating therapies that are specific to the problems that unhealthy lifestyle patterns create.\n\nThe discussion on participants' expectations for exercise demonstrates the diverse nature of perspectives on physical activity. People approach exercise with a variety of objectives in mind, highlighting the importance of customized routines. The recognition of allocating time to target body parts emphasizes a tactical approach to fitness, rejecting a one-size-fits-all paradigm. Positive recognition of exercise's impact on mood aligns with the literature on mental health benefits26,27 (Demers et al 2013). However, it also highlights potential negative effects including boredom and self-consciousness, emphasizing the need for diversity and psychological considerations. This pattern of persistent negativity aligns with findings by Sikes et al. (2019), who highlighted boredom as the predominant factor contributing to youth's physical inactivity.28 The various expectations that participants have about their physical and mental well-being, appearance, and fitness highlight the necessity of inclusive exercise programs. Overall, the results support customized and holistic approaches to satisfy a range of needs and encourage sustained adherence to healthy lifestyle choices.\n\nA thorough examination of the exercise experiences of the participants in our study revealed a wide variety of barriers and enablers, which we divided into three categories: opportunistic, environmental, and personal variables. In terms of personal variables, difficulties were particularly associated with discipline and body consciousness. These were mentioned by participants as the key obstacles to adhering to a regular exercise schedule. Social prejudice and unfavourable weather patterns emerged as major obstacles on the environmental side. These results resonate with the systematic analysis conducted by Peng et al. (2023) among young adult women, emphasizing the multifaceted and interconnected nature of the challenges they encounter such as time, social support, body image, and cultural beauty standards.29 Enhancing physical activity among women necessitates addressing not only individual behaviours but also creating opportunities at the organizational, community, and policymaker levels. These elements add to a thorough comprehension of the challenges people have when following an exercise program.\n\nNevertheless, our study's identification of individual motivations, social support, and accessible opportunities as facilitators suggests possible intervention and support strategies to increase regular exercise participation. By focusing on these facilitators, interventions can be customized to help individuals overcome obstacles and encourage long-term physical activity. Concurrently, variables such as enhanced physical attractiveness, health advantages, and favourable psychological impacts were recognized as motivators, indicating a wider agreement on significant influences. The results of this study are consistent with previous research since other studies have also brought attention to perceived motivations such as maintaining or improving physical appearance, health benefits, and togetherness, while also focusing on perceived obstacles such as dislike of exercise, a lack of motivation, a lack of support, and time constraints.30,31\n\nFurther guiding the creation of focused exercise modules in the researched populations' emphasis on flexibility, consistency, initiation, and the accessibility of reliable exercise information. Adopting strategies that target these specific concerns can improve the efficacy of programs intended to encourage physical activity participation.\n\nIn summary, the thorough investigation of the variables affecting exercise regimens, as demonstrated by our research, and corroborated by the body of literature, offers insightful design information for customized interventions. By comprehending the intricacies of personal experiences and addressing both obstacles and enablers, we may aid in the advancement of more potent approaches designed to encourage consistent exercise engagement across a variety of demographics.\n\nIn the context of fitness and weight control programs, professionals face the difficulty of creating interventions that promote health and induce behavioural change without creating a feeling of social rejection. This project highlights the real-world difficulties in creating workout programs specifically for overweight people. The importance of widely accessible and user-friendly platforms is emphasized in Theme 4, which highlights the general preference for video content as the primary source for exercise. Purcell (2010) noted a trend among younger groups toward video content consumption.32 Vandelanotte et al. (2011) discovered that a video-based physical activity intervention was well-received by potential users, indicating its feasibility for development. This tendency could be attributed to the influence of social norms, as younger individuals usually establish developing internet trends that later gain traction across broader groups.33 Although participants find video materials engaging and convenient, they have concerns over their dependability and oversight. This dual viewpoint points out places where video-based workout tools need to be improved. The acknowledgment of video content's advantages indicates participants' engagement and motivation for fitness. Prioritizing accessibility and user-friendliness aligns with the modern desire for seamless experiences. However, concerns about monitoring and reliability highlight specific drawbacks and highlight the need for a more participatory and responsible experience. This insight draws attention to limitations in video-based fitness regimens and offers suggestions for improvement. In broad terms, this knowledge is essential for creating successful online workout regimens. Understanding user preferences and concerns allows fitness platforms to balance the convenience of video content with the need for reliability and monitoring. Features like progress tracking and engagement can improve the effectiveness and user happiness of online workout programs. To better address a variety of needs and encourage an active and healthy lifestyle, digital fitness solutions must be refined through ongoing user-developer conversation.\n\nThis section emphasizes the importance of making exercise videos specifically tailored for overweight people, with a focus on creating a supporting atmosphere with specially trained instructors. Fostering a positive and inclusive atmosphere can be enhanced by addressing specific needs and concerns. The exploration of participants' preferences emphasizes the requirement to provide precise instructions on exercise methods, levels of difficulty, duration, and instructional modalities. The findings align with previous research by Manaf et al. (2021) and Othman et al. (2022). These studies indicate a preference among participants for a low to moderate-intensity structured exercise regimen that offers flexibility along with manageable duration and frequency. These findings indicate a need for participant's favoured workouts to accommodate varying schedules and environments30,31 Participants in our study expressed a desire for flexible routines engaging all body parts, accompanied by music, emphasizing holistic and adaptable workout experiences that consider enjoyment and diversity as factors for maintaining motivation. Bian et al. (1989) highlighted the importance of such characteristics, finding that participants favoured exercise regimens tailored for overweight individuals or beginners, emphasizing the need for instructors with expertise, a non-judgmental attitude, along with proper pacing.10 Citing research such as Wankel et al., (1985) highlights the valuable insights that may be gained from fitness programs by highlighting the possible influence of strong social support.34 This realization raises the possibility that overcoming variations in individual self-motivation requires a strong sense of community and support. Finally, this area explores the preferences of the participants and provides insightful information to develop a comprehensive approach that is effective and specific to the needs of overweight individuals by emphasizing support, clear guidance, flexibility, and social components.\n\nOur study delved into factors influencing participant engagement, particularly focusing on the presentation and aesthetics of exercise videos. Preferences for relatable models, an encouraging approach, and professionally produced, distraction-free shorter videos highlight the importance of creating visually appealing and immersive experiences. These insights align with Vandelanotte et al.'s 2011 study on computer-tailored interventions using online video messages to promote physical activity laying the groundwork for understanding participant preferences and openness to innovative approaches.33 It is widely believed that internet-delivered interventions, particularly those with high interactivity and user appeal, promote increased participant engagement and retention. Furthermore, such interventions may offer increased and sustained effectiveness over the long term15,35\n\nAdditionally, participants expressed a desire for comprehensive information, including details on nutrition, safety precautions, exercise benefits, and motivational strategies. Solbrig et al., (2017) in his study concluded that individuals expressed a desire for motivational support for losing weight and increasing physical activity. He stated that there exists a mismatch between available public resources and the individuals desired health information regarding lifestyle information.36 This aligns with a holistic perspective recognizing the interconnectedness of physical and mental well-being, suggesting interventions should address both aspects.\n\nFurthermore, information on hormonal influences and regular communication from fitness experts address participant’s broader health concerns, emphasizing the need for comprehensive support structures within intervention programs to ensure adherence. Our study contributes valuable insights for designing holistic interventions beyond exercise guidance to address various factors influencing users.\n\nThe media platforms that participants prefer to use, such as email, WhatsApp, and YouTube, show a wide variety of consumption patterns. While WhatsApp and email reflect a need for immediate communication and easy access to information, YouTube suggests a preference for exercise material that is primarily based on videos. The focus on connections with low internet consumption needs draws attention to the necessity of content optimization for accessibility, taking participants' possible connectivity issues into account. Comprehending these inclinations is essential to customizing the content of exercises and maximizing the effectiveness of health promotion programs. By aligning dissemination strategies with favoured platforms, health professionals can maximize reach and impact. These results are consistent with research showing the feasibility of video-tailored interventions33,37,38. Such interventions are viable both in terms of user willingness to engage and technological viability. This is supported by the fact that most internet users have access to infrastructure that supports video downloads. According to Vandelanotte et al.'s (2011) findings, exercise interventions that consider participant preferences and include extensive support systems may enhance user engagement and promote long-term adherence.33 The understanding also highlights the importance of providing relevant, approachable content that fits participants' circumstances to increase engagement and encourage adherence to recommended exercise regimens.\n\nThe methodology employed in this study was equally as important as the results. Our one-on-one interviewing approach created a comfortable and secure environment for individuals to express their ideas. Everyone might express himself without feeling compelled to by others. To the best of our knowledge, our study is the first to examine the needs, perceptions, and preferences of overweight individuals about exercise videos. The limitation of the study was it involved purposive sampling and the findings may not be easily applicable to broader more general populations beyond the ones studied.\n\n\nConclusion\n\nIn conclusion, our qualitative research not only dives into the multiple elements that influence exercise behaviours among overweight individuals but also provide a thorough comprehension of their preferences for instructive exercise videos. The findings from this analysis provide a good framework for developing customized interventions that consider the complex interaction of individual experiences, preferences, and problems. This knowledge, together with the findings from our investigations into several themes such as lifestyle determinants, exercise expectations, and media preferences, guides the development of programs that go beyond a standard approach. By acknowledging the unique needs of overweight individuals, we aim to create effective, engaging, and accessible educational exercise videos.\n\n\nAuthors contributions\n\nSKB and KV conceptualized and designed the study protocol. Data collection was conducted by SKB with verification by KV. SKB and PH was involved in data curation. SKB prepared the preliminary draft of the manuscript. Scientific content and relevance were critically curated by SKB, VK, RKV, SS, and TB. The final manuscript version received approval from all authors before journal submission. Each author fulfilled the criteria set forth by ICMJE for authorship, contributed significantly to the manuscript, and critically reviewed and approved the final draft.\n\n\nEthics and Consent\n\nThe ethical approval was obtained from the Kasturba Medical College and Kasturba Hospital Institutional Ethics Committee, Manipal Academy of Higher Education on 31st August 2023 (IEC1: 96/2023). The study adhered to the principles outlined by the declaration of Helsinki (https://www.wma.net/policies-post/wma-declaration-of-helsinki-ethical-principles-for-medical-research-involving-human-subjects/). Eligible participants were informed about the objectives and study procedure, and those who agreed to participate signed the written informed consent.", "appendix": "Data Availability\n\nThe study's underlying and extended data: OSF: “Exploring needs, perceptions, and preferences towards exercise video among overweight individuals - a qualitative study”; 2024. Available from: https://doi.org/10.17605/OSF.IO/XSTBC 39\n\nData are available under the terms of the CC0 1.0 Universal\n\n\nAcknowledgement\n\nWe would like to thank the Department of Physiotherapy, Manipal College of Health Professions, Manipal Academy of Higher Education for their support and encouragement.\n\n\nReferences\n\nObesity: preventing and managing the global epidemic. Report of a WHO consultation. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShishira KB: Exploring needs, perceptions, and preferences towards exercise video among overweight individuals - a qualitative study. Open Science Framework. 2024." }	[ { "id": "343442", "date": "11 Dec 2024", "name": "Adi Pranoto", "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 have clearly stated that the study aims to explore the needs, perceptions, and preferences of overweight individuals on tailored exercise programs that incorporate educational videos. The paper is well-written, easy to follow and adds merit to the vital role of educational videos that are easy to use, visually appealing, and supported by science. These videos should emphasize technique, varying levels of difficulty, and brief sessions. Given this approach, this work can enhance future attempts in similar research area. However, I have highlighted a few suggestions and concerns in my specific comments section (below) that need to be addressed before considering whether this work should be indexed or not.\nABSTRACT - Exercise-video, Interview, Need, Overweight, Perception, Preference, Thematic-analysis. I suggest reducing keywords by taking the 5 most important keywords\nINTRODUCTION - “Even with a wealth of evidence showing the health advantages of consistent physical activity, more than half of Indians do not exercise to the recommended levels. 7,8” I highlight the following statement that researchers say more than half of Indians do not exercise at the recommended level. Therefore, I suggest researchers add the data on how many Indians in total are not exercising at the recommended levels. Apart from that, researchers can also add the recommended duration of exercise, such as recommendations from WHO (https://www.who.int/news-room/fact-sheets/detail/physical-activity). - I suggest researchers add, perhaps this can be supported by the results of previous research with inconsistent results.\nMATERIALS AND METHODS - How do you recruit potential participants? Forty individuals aged between 18-30 years with a BMI of 25-29.9kg.m-2 who were involved in the study using purposive sampling from October 2023 to November 2023 were obtained in what way? Do you do open recruitment or in certain communities? Please provide a detailed explanation in the methods section. - How do researchers obtain data about the medical records of each participant, so that researchers can ensure that participants are free from comorbidities such as diabetes, hypertension, CVD, neurological and musculoskeletal disorders? - In the data collection process, were the 40 participants involved interviewed at one time or were there differences in time? - Has the questionnaire used in this study been tested for validity and reliability? If so, can I see the results of the analysis? - In the Analysis subsection, researchers can add validity and reliability tests. - Please describe how the sample size is calculated?\nRESULTS - The results are presented well and in detail.\nDISCUSSION - The discussion section should present paragraphs to improve reading conditions. It should start with the objective of the study, followed by the main findings, and afterward relating these with the literature. It is also important to develop limitations and suggestions for future research at the end of this section.\nCONCLUSION - Add some recommendations for future research and add strong reasons to support the study.\nREFERENCES - Please adjust to the F1000Research reference writing style as there are still many discrepancies found.\nGENERAL COMMENTS - Pay attention to english grammar, syntax rules and punctuation all over 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?\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": [] } ]	1	https://f1000research.com/articles/13-998
https://f1000research.com/articles/13-996/v1	02 Sep 24	{ "type": "Research Article", "title": "Analyzing the Relationship Between Organizational Politics, Emotional Intelligence, and Employee Behavior: A PLS-SEM Modeling", "authors": [ "Sonakshi Bhatia", "Babita Rawat", "Dhani Shanker Chaubey", "Farman Ali", "Babita Rawat", "Dhani Shanker Chaubey", "Farman Ali" ], "abstract": "Background This study explores the complex relationship between organizational politics, emotional intelligence and employee behavior in contemporary settings. Organizational politics, which is widespread in organizational settings, has a substantial impact on different aspects of employee behavior. Emotional Intelligence has become a vital factor in individuals' capacity to successfully traverse the complexities of an organization. This study consolidates current material to offer insights into the impact of organizational politics on employee behavior and the mediating role of emotional intelligence in this connection.\n\nMethods A survey was undertaken with a sample size of 500 employees hailing from several Information Technology (IT) and Information Technology Enabled Services (ITES) firms in the Dehradun (Uttarakhand) region. The study employed quantitative methodologies to investigate the correlations between Emotional Intelligence, Perceived Organizational Politics and Employee Behavior. The data were evaluated using Partial Least Squares Structural Equation Modelling (PLS-SEM) to examine the hypothesized correlations and mediation effects.\n\nResults The study identified substantial correlations between Emotional Intelligence, Perceived Organizational Politics, and Employee Behavior. Emotional Intelligence was discovered to have a positive impact on Behavioral Dynamics. Perceived Organizational Politics had a substantial influence on both Emotional Intelligence and Behavioral Dynamics. Factors such as Need for Power, Relationship Conflict, Resource Constraints, Role Conflict, and Workforce Diversity were discovered to have an impact on Perceived Organizational Politics.\n\nConclusions The results confirm strong connections between organizational politics, emotional intelligence, and employee behavior, highlighting the significance of these concepts in comprehending employee behavior in organizational environments. The study proposes that enhancing employees' emotional intelligence can alleviate the adverse effects of organizational politics, resulting in enhanced behavioral dynamics. The study also addresses the limits, outlines potential areas for further research, and highlights the managerial implications. It suggests that firms should prioritize the development of emotional intelligence to cultivate a favorable work environment.", "keywords": [ "Organizational politics", "emotional intelligence", "employee behavior", "Behavioral Dynamics", "Relationship Conflict", "Resource Constraints", "Role Conflict." ], "content": "Introduction\n\nIn an unstable and complicated environment, an organisation is made up of individuals who manage and organise other resources to achieve established goals. Political behavior becomes prevalent and objective because of people’s involvement and the organization’s failure to match their expectations in terms of logic and objectivity. During the 1990s, the concept of organisational politics and workplace perceptions of organisational politics expanded and they are considered an essential component of contemporary business practices. Organizational politics and its impact on employee behavior have garnered significant attention from scholars and practitioners alike. Organizational politics is defined as the pursuit of self-interest within an organization, frequently at the expense of others' legitimate interests. It can take many forms including favoritism, manipulation and coalition-building. Organizational politics can have a significant impact on employee attitudes, job satisfaction and performance (G. R. Ferris et al., 2013). In recent years, scholars have increasingly acknowledged the importance of emotional intelligence in molding people's reactions to organizational politics. Emotional intelligence, as defined by (Salovey & Mayer, 1990) is the ability to notice, comprehend, control, and express emotions effectively. Individuals with high levels of emotional intelligence can negotiate complex social contexts, regulate their emotional responses, and empathize with others' points of view (Goleman, 1995). This paper will investigate the relationship between organizational politics, emotional intelligence, and employee behavior, relying on previous research to give theoretical insights and practical consequences for firms looking to encourage healthy workplace dynamics.\n\n\nReview of related literature\n\nRelationship conflict:\n\nRelationship conflict inside organizations has been extensively researched as a predictor of organizational politics. (Jehn, 1995) discovered that relational conflict, defined as interpersonal tension and hatred, strongly contributes to the establishment of political behaviors inside teams and departments. Such disputes are frequently caused by differences in employee personalities, values, or communication styles, which result in power struggles and manipulative activities aimed at securing personal interests above organizational goals. These reasons give rise to the following hypothesis:\n\nRelationship Conflict contribute significantly towards organizational politics\n\nRole conflict:\n\nRole conflict, which results from differences or inconsistencies in work expectations, has been established as a strong predictor of organizational politics (Rizzo et al., 1970). When employees encounter opposing demands from numerous sources, like as bosses, coworkers, or organizational regulations, they may use political methods to manage the tensions and preserve their own interests. This dynamic hamper workflow while also undermining trust and collaboration inside the business, creating an environment amenable to political manipulation. These reasons give rise to the following hypothesis:\n\nRole Conflict contribute significantly towards organizational politics\n\nResource constraints, such as limited funds, time, or people, have been associated to increased organizational politics (Cropanzano et al., 2017). When resources are tight, competition among personnel and departments heats up, resulting in strategic manipulation and coalition-building to get access to critical resources. Furthermore, resource scarcity exacerbates tensions and conflicts by forcing individuals to compete for a bigger share of limited resources, maintaining a culture of political gamesmanship and opportunism inside the organization. These reasons give rise to the following hypothesis:\n\nResource constraints Conflict contribute significantly towards organizational politics\n\nIndividual variations in the desire for power have been identified as crucial determinants in organizational politics (Winter, 1973). Employees that have a strong desire for power are more prone to participate in political activities in order to exert authority, control information and influence decision-making processes inside the firm. Their activities frequently favor personal ambition over communal goals, causing increasing friction and distrust among coworkers. As a result, the presence of individuals with a high desire for power can aggravate political dynamics while undermining organizational cohesiveness and performance. These reasons give rise to the following hypothesis:\n\nPower motive among employee contribute significantly towards organizational politics\n\nWorkforce diversity, which includes disparities in demographics, histories, and opinions, has been shown to influence the terrain of organizational politics (Shore et al., 2009). While diversity promotes innovation and creativity, it may also lead to disputes caused by cultural misunderstandings, prejudices, and power disparities. In diverse work contexts, individuals may use political methods to negotiate complicated social dynamics, defend their interests, or push their agendas, worsening internal tensions and divides. As a result, good diversity management is critical for limiting the harmful influence of organizational politics while also building inclusive and egalitarian workplace environments. These reasons give rise to the following hypothesis.\n\nWorkforce diversity among employee contribute significantly towards organizational politics\n\nOrganizational politics is a complicated phenomenon that is inextricably linked to employee behavior, providing a fertile ground for research in organizational psychology and management. Scholars have intensively researched the multidimensional character of organizational politics, emphasizing its ubiquitous presence in workplace dynamics (Gotsis & Kortezi, 2010). Studies have shown that it has an impact on several aspects of employee behavior, including work satisfaction, organizational commitment, and performance (Ng & Feldman, 2012; Hochwarter et al., 2020). Furthermore, recent research has focused on the methods by which organizational politics impact employee attitudes and behaviors, highlighting the importance of perceptions, power dynamics, and organizational culture (Hochwarter et al., 2020). In addition, emerging trends in the literature have investigated the intersection of organizational politics with present-day problems such as remote work arrangements and digital communication platforms, throwing light on new forms and manifestations of political behavior in modern organizational contexts. The literature on organizational politics and employee behavior reflects a nuanced understanding of the intricate interplay between organizational structures, individual motivations, and workplace interactions, offering valuable insights for practitioners and scholars alike. Organizational politics can exert a significant influence on various dimensions of employee behavior, including job satisfaction, organizational commitment, and job performance. Research indicates that perceptions of organizational politics are negatively correlated with employee job satisfaction and commitment (Kacmar & Ferris, 1991). Employees who perceive their organizations as politically charged may experience heightened levels of stress, reduced job satisfaction, and increased turnover intentions (Vigoda-Gadot, 2006). Moreover, organizational politics can shape employees' behavioral responses, leading to detrimental outcomes such as increased absenteeism, decreased organizational citizenship behaviors, and lower job performance (Drory & Romm, 1990). Employees may engage in defensive behaviors, such as withholding effort or information, to protect themselves from the perceived negative consequences of organizational politics (Kacmar & Ferris, 1991). These arguments leads to the following hypothesis:\n\nOrganisational politics have significant effect on employee behavior\n\nOrganizational politics has received substantial attention in the literature due to its complex influence on personnel and organizational results. Scholars have increasingly acknowledged the complex link between corporate politics, emotional intelligence (EI) and employee behavior dynamics. (Liu et al., 2021), found that exposure to organizational politics can have a considerable impact on people's emotional intelligence, specifically their capacity to identify, comprehend, and control emotions successfully. This conclusion is confirmed by a research by (Drory & Meisler, 2016), which focuses on the negative impacts of organizational politics on employees' emotional intelligence, resulting in worse job satisfaction and higher turnover intentions. (Naseer et al., 2016) for example, found that persons with higher emotional intelligence may be better equipped to navigate and cope with organizational politics, mitigating its negative impact on job performance and well-being. However, the link between organizational politics and emotional intelligence is multifaceted and may differ depending on contextual factors such as corporate culture and leadership style (Ghosh & Ghosh, 2019). Overall, the literature emphasizes the necessity of addressing organizational politics as a major element impacting employees' emotional intelligence and, by extension, organizational performance. Emotional intelligence is critical in balancing the link between corporate politics and employee behavior. Individuals with high levels of emotional intelligence are better able to deal with the emotional demands of organizational politics and employ constructive coping techniques (Goleman, 1995). They are better at managing their own emotions, empathizing with others' viewpoints, and resolving problems peacefully (Salovey & Mayer, 1990). Empirical investigations have shown that emotional intelligence buffers the negative consequences of organizational politics on employee attitudes and behaviors (Abraham, 2000). For example, employees with high emotional intelligence may be less likely to perceive organizational politics as threatening, thus reducing their propensity to engage in defensive behaviors or experience negative emotional outcomes (Jordan & Troth, 2002). These arguments lead to the assumption of following hypothesis:\n\nOrganisational politics have significant effect on employee emotional intelligence\n\nRecent research suggests an increasing interest in studying the link between emotional intelligence (EI) and employee behavior in business contexts. (Goleman et al., 2013) found that emotional intelligence plays an important role in promoting favorable workplace outcomes such as job satisfaction, organizational commitment, and successful leadership. Furthermore, research by (Brackett & Salovey, 2006) emphasizes the importance of EI in influencing employees' interpersonal relationships, conflict resolution abilities, and adaptation to changing work contexts. Furthermore, (Bar-On, 2010) findings indicate the influence of EI on lowering workplace stress and improving employee mental well-being, which contributes to overall organizational productivity and performance. However, inconsistent data exist about the magnitude of EI's effect on various behavioral outcomes, emphasizing a need for more empirical research (Mayer & Salovey, 2007). Thus, while existing literature emphasizes the relevance of EI in affecting employee behavior, future research should dive deeper into the processes by which EI functions and the consequences for varied organizational contexts. Furthermore, EI has been connected to decreased turnover intentions and higher work satisfaction (Miao et al., 2017). (Zeidner et al., 2016) conducted a study that underlined the relevance of emotional intelligence in leadership, demonstrating its influence on team dynamics and organizational environment. However, subsequent research have highlighted significant limits, such as the cultural and environmental uniqueness of EI components (Miao et al., 2021).\n\nPrevious study has shown that organizational politics, which are characterized by power conflicts, favoritism, and manipulation, have a major influence on employee attitudes, work satisfaction, and performance (Hochwarter et al., 2020). Concurrently, EI, defined as the ability to sense, comprehend, and successfully control emotions, has emerged as a critical component in determining individual achievement and organizational effectiveness (Mayer & Salovey, 2007). Recent research has highlighted the mediation function of EI in moderating the harmful impacts of organizational politics on employee behavior (Turi & Sarfraz, 2023). Employees with high EI, for example, may be able to better manage political circumstances, regulate their emotions in reaction to organizational pressures, and maintain healthy interpersonal connections despite political problems (Blaik-Hourani et al., 2023). Furthermore, emotional intelligence has been associated to improved conflict resolution abilities, resilience, and adaptive coping mechanisms, all of which lead to more constructive responses to organizational politics (Jordan & Troth, 2002). Understanding the relationship between organizational politics, EI, and employee behavior is critical for firms seeking to develop a healthy work environment and improve employee well-being and performance. These arguments result in the following hypothesis.\n\nEmotional Intelligence of employee have positive and significant effect on Employee Behavior\n\nEmotional Intelligence of employee mediates the relationship between organisational politics and employee behavior\n\nThe purpose of this study is to analyze the complex relationship between organizational politics, emotional intelligence (EI), and employee behavior using Partial Least Squares Structural Equation Modeling (PLS-SEM). Organizational politics, defined as the use of power and influence strategies to achieve personal or organizational objectives, has received a lot of attention in organizational behavior research because of its widespread impact on workplace dynamics (Mintzberg, 1985); (D. L. Ferris et al., 2008). Emotional intelligence, on the other hand, refers to the capacity to identify, analyze, and control one's own and others' emotions, which has been identified as a critical predictor of occupational performance and interpersonal interactions (Goleman, 1995). This research proposes a theoretical framework based on current literature in both organizational politics and emotional intelligence, which may act as a moderator in the interaction between organizational politics and employee behavior. Using PLS-SEM, this study aims to provide a nuanced understanding of how emotional intelligence may mitigate or exacerbate the effects of organizational politics on employee behavior, thereby providing valuable insights for both scholars and practitioners in managing organizational dynamics effectively.\n\n\nMethods\n\nThe relationship between organizational politics, emotional intelligence, and employee behavior is investigated quantitatively in this study using Partial Least Squares Structural Equation Modeling (PLS-SEM). The PLS-SEM approach was chosen because it is ideal for investigating complicated interactions in theoretical models with limited sample sets (Sarstedt et al., 2022). This section describes the research strategy, sample approach, data collecting tools, and analytical methods used in this study. A cross-sectional study strategy is used to collect data from participants from multiple organizations in November 2023. This method enables the investigation of connections between variables without the necessity for longitudinal data collection (Sarstedt et al., 2022). The research uses convenience sampling to identify individuals from a variety of sectors and organizational contexts. The research uses convenience sampling to identify individuals from a variety of sectors and organizational contexts. A sample size of at least 500 employees is intended to achieve acceptable statistical power and representativeness (Sarstedt et al., 2022). Participants will be recruited using internet platforms and professional networks, assuring broad geographical coverage and diverse demographic representation. The major data collecting tool consists of three validated survey scales: the Organizational Politics Scale (Kacmar & Ferris, 1991), the Wong and Law Emotional Intelligence Scale (WLEIS) (Wong & Law, 2017), and the Employee Behavior Inventory (Spector & Fox, 2002). The Organizational Politics Scale measures employees' perceptions of organizational politics, including favoritism, influence, and networking. The WLEIS assesses employees' emotional intelligence across four dimensions, while the Employee Behavior Inventory evaluates various dimensions of employee behavior. Partial Least Squares Structural Equation Modeling (PLS-SEM) is used to analyze the complex relationships between organizational politics, emotional intelligence, and employee behavior. PLS-SEM is a robust technique for modeling complex theoretical frameworks with latent variables and observed indicators, making it suitable for exploratory research. The analysis involves two stages: measurement model assessment and structural model evaluation. In the measurement model assessment stage, the instruments' reliability and validity are evaluated through internal consistency, convergent validity, and discriminant validity. The structural model is estimated to examine relationships between latent constructs and test hypothesized paths. Bootstrapping procedures are used to assess the significance of direct and indirect effects in the model. Table 1 indicates the demographic characteristic of employees\n\n\nResults\n\nTable 1 shows the demographics of respondents to research on the link between politics, emotional intelligence, and employee behavior. In terms of age distribution, the majority of respondents are between the ages of 36 and 45 (29.6%) and 46 to 55 (25.6%). This suggests a high representation of middle-aged people in the research. However, it is worth mentioning that respondents aged 26 to 35 years (17.4%) and 56 years and older (17.0%) make significant contributions to the sample. In terms of gender, the sample looks to be reasonably balanced, with slightly more males (53.8%) than females (46.2%). In terms of marital status, the majority of respondents are single (59.6%), with a sizable proportion married (40.4%). This distribution shows that marital status may have an impact on the variables being investigated, such as emotional intelligence and employee behavior. In terms of education, a considerable majority of respondents (64.2%) had a PhD or a professional certificate (22.6%), suggesting a well-educated sample group. This educational variety may lead to a more nuanced understanding of the relationships between politics, emotional intelligence, and employee behavior. In terms of income, the majority of respondents (35.0%) earn between Rs. 40,001 and Rs. 50,000 per month, closely followed by those earning Rs. 60,001 or more per month (34.0%). Finally, in terms of years of experience, a sizable majority of respondents had 2 to 5 years (43.0%), followed by those with 6 to 10 years (32.8%). This distribution indicates a somewhat experienced group, which may influence their perceptions and conduct at work.\n\nThe descriptive statistics presented in Table 2 (extended data) (Sonakshi Bhatia et al., 2024b), illustrate the mean scores and standard deviations for various factors influencing organizational politics, emotional intelligence, and employee behavior within the studied context. For relationship conflict (RC), respondents reported a mean score of 3.5592 with a standard deviation of 0.92123, indicating moderate levels of friction and tension among employees, as well as frequent conflicts about ideas and work tasks. Similarly, role conflict (ROC) exhibited a mean of 3.4902 with a standard deviation of 0.84026, suggesting instances where individuals face challenges aligning with organizational roles and encountering conflicting demands. Resource constraints (REC) were perceived at a mean of 3.4575 with a standard deviation of 0.86520, indicating a moderate perception of insufficient resources hindering effective job performance. The need for power was reported with a mean score of 3.4828 and a standard deviation of.86388, reflecting perceptions regarding authority, access to information, and influence within the organizational hierarchy. Workforce diversity (WD) exhibited a higher mean of 3.7373 with a standard deviation of 1.00694, suggesting notable variations in values, goals, and objectives among employees. Perceived organizational politics (POP) displayed a mean score of 3.5230 with a relatively lower standard deviation of 0.73836, indicating moderate agreement towards political behaviors such as self-promotion and conformity to influential groups. Emotional intelligence (EI) was reported with a mean of 3.6010 and a standard deviation of 0.79514, reflecting moderate levels of self-awareness, emotional understanding, and emotional regulation among respondents. Lastly, employee behavioral dynamics (BD) demonstrated a mean score of 3.5390 with a standard deviation of 0.74679, suggesting varying degrees of intention to remain in the organization, task engagement, and energy exertion. These descriptive statistics provide insights into the perceived levels of organizational dynamics and individual attributes among the study participants.\n\nMeasurement model\n\nIn evaluating the measurement model for factors influencing organizational politics, emotional intelligence and employee behavior, rigorous attention to construct validity, reliability, and factorial validity is paramount. Ensuring the validity and reliability of measuring tools is critical for doing sound research in organizational psychology. First, construct validity is proven through theoretical foundation and empirical evidence (Smith, 2018). This entails validating links between measured constructs and their theoretical frameworks. Second, reliability measures, such as internal consistency and test-retest reliability, are critical (Jones et al., 2020) High Cronbach's alpha values (0.805 to 0.972) show good internal consistency, whereas composite reliability estimates (rho_a and rho_c) greater than 0.7 (range from 0.812 to 0.975) confirm dependability (Brown & Jones, 2019). Confirmatory factor analysis is used to measure goodness-of-fit indices like as chi-square, CFI, TLI, and RMSEA (Brown et al., 2021). Discriminant validity guarantees that the model differentiates across constructs; AVE values (0.567 to 0.836) greater than 0.5 indicate adequate convergent validity (Black et al., 2017). Overall, these data indicate that the measuring approach has strong reliability and validity, which increases the trustworthiness of the study findings (Table 3).\n\nThe Heterotrait-Monotrait Ratio (HTMT) is used to examine the discriminant validity of components, with values less than one indicating appropriate discriminant validity, as shown in Table 4. The HTMT matrix in this study depicts the relationships between various constructs such as Behavioral Dynamics, Emotional Intelligence, Need for Power, Perceived Organizational Politics, Relationship Conflict, Resource Constraints, Role Conflict, Workforce Diversity, and the interaction term Emotional Intelligence and Perceived Organizational Politics. Notably, all values in the diagonal (which represents a construct's connection with itself) are more than 0.9, showing good convergent validity. Meanwhile, the off-diagonal components have values that are generally less than one, indicating discriminant validity between constructs. For example, the Emotional Intelligence and Perceived Organizational Politics interaction has the highest value of 0.34, suggesting the greatest association, although it is still below the threshold for discriminant validity. Overall, these findings support the distinctiveness of the constructs under investigation, crucial for ensuring the robustness of the study's theoretical framework.\n\nThe discriminant validity of the constructs was determined using the Fornell-Larcker criterion. The results reveal that all constructs have discriminant validity, since the square root of the Average Variance Extracted (AVE) for each construct (shown diagonally) exceeds the correlations between that construct and all other constructs. The diagonal elements reflect the AVE for each construct, but the off-diagonal elements show the correlations between them. For example, Emotional Intelligence has good discriminant validity (0.925), outperforming relationships with other dimensions such as Need for Power (0.878) and Perceived Organizational Politics (0.856). Similarly, additional constructs, such as Relationship Conflict and Resource Constraints, fit the requirement, with greater AVE values (0.819 and 0.795, respectively) than their correlations with other constructs. These findings suggest that the measurement model adequately discriminates between the constructs under examination, thus enhancing the robustness of the study's theoretical framework and contributing to the validity of the research instrument (Table 5).\n\nTable 6 shows the results of a regression analysis that looked at the relationship between several constructs, including Behavioral Dynamics, Emotional Intelligence, Need for Power, Perceived Organizational Politics, Relationship Conflict, Resource Constraints, Role Conflict, Workforce Diversity, and the interaction between Emotional Intelligence and Perceived Organizational Politics. The R-square values range from 0.733 to 0.972, indicating strong explanatory power across constructs. Furthermore, the f-square matrix demonstrates the relative relevance of each predictor in explaining variance within the constructs, with higher values suggesting greater influence. For example, Emotional Intelligence and Perceived Organizational Politics both contribute considerably to explaining variance in Behavioral Dynamics, as indicated by f-square values of 4.129 and 2.749, respectively. These findings indicate strong links between the researched dimensions, offering insights into organizational dynamics and suggested areas for further research.\n\nIn the structural model analysis, regression coefficients, t-values, and p-values were used to determine the correlations between different constructs. Path coefficients represent the intensity and direction of the associations. Notably, Emotional Intelligence significantly influenced Behavioural Dynamics (β = 0.361, t = 20.227, p < 0.001), while Need for Power notably affected Perceived Organisational Politics (β = 0.332, t = 15.666, p < 0.001). Perceived Organisational Politics was found to have substantial impacts on both Behavioural Dynamics (β = 0.661, t = 41.979, p < 0.001) and Emotional Intelligence (β = 0.856, t = 61.011, p < 0.001). Furthermore, different contextual elements such as relationship conflict, resource constraints, role conflict, and workforce diversity have a substantial impact on perceived organizational politics. A significant mediated association was found between perceived organizational politics, emotional intelligence, and behavioral dynamics (β = 0.309, t = 21.625, p < 0.001). Overall, all assumptions were confirmed, suggesting strong relationships between the components in the proposed model.\n\n\nDiscussion\n\nOrganizational politics, emotional intelligence, and employee behavior are all linked and have a significant impact on working conditions, as shown in the Figure 1. In a recent research that used Partial Least Squares Structural Equation Modeling (PLS-SEM), the interactions between these constructs were examined to identify their underlying dynamics. The findings found substantial connections, providing insight into the elements that influence organizational politics, emotional intelligence, and consequent behavioral consequences.\n\nSource: Author’s compilation\n\nEmotional intelligence emerged as a critical element, having significant implications for organizational behavioral dynamics. This is consistent with previous studies demonstrating that persons with higher emotional intelligence display more flexibility, effective communication, and conflict resolution abilities, contributing favorably to overall workplace behavior (Goleman, 1995).\n\nFurthermore, the craving for power was found to be a strong predictor of perceived organizational politics. Previous research has confirmed this association, stressing how individuals motivated by a desire for power may engage in manipulative actions or strive to influence organizational dynamics to achieve their goals (Kacmar & Ferris, 1991).\n\nPerceived organizational politics, in turn, had a significant impact on emotional intelligence and behavior dynamics. This conclusion is consistent with previous research that has highlighted the negative consequences of perceived politics on employee attitudes, motivation, and interpersonal connections (D. L. Ferris et al., 2008).\n\nFurthermore, contextual factors such as interpersonal conflict, resource limitations, role conflict, and workforce diversity were found to have a substantial influence on views of organizational politics. Prior research has highlighted the influence of these contextual variables on organizational dynamics, stressing their significance in affecting employee attitudes and actions (Jehn et al., 1997; Podsakoff et al., 2009; Jehn, 1995).\n\nFurthermore, the study found a mediated link between perceived organizational politics, emotional intelligence, and behavioral dynamics. This emphasizes the intricate interplay between these dimensions, implying that organizational politics might act as a stimulant for the development of emotional intelligence and subsequent behavioral reactions.\n\nFinally, the outcomes of this study illustrate the varied character of organizational dynamics, particularly the deep linkages between organizational politics, emotional intelligence, and employee behavior. Understanding these linkages allows firms to develop methods to limit the negative impacts of politics, encourage emotional intelligence, and promote good behavioral outcomes, resulting in increased overall organizational effectiveness and employee well-being.\n\nThe study adds theoretical value by revealing strong links between organizational politics, emotional intelligence, and employee behavior. Emotional intelligence has a significant impact on behavioral dynamics, whereas the desire for power shapes perceptions of corporate politics. The study also identifies contextual factors like relationship conflict, resource constraints, role conflict, and workforce diversity, which significantly impact perceived organizational politics. Moreover, it establishes a mediated relationship among perceived organizational politics, emotional intelligence, and behavioral dynamics. These findings offer valuable insights into understanding and managing workplace dynamics, contributing to the existing body of knowledge on organizational behavior. Implications for Practice: Understanding the interplay between organizational politics, emotional intelligence, and employee behavior has important implications for organizational leaders and practitioners.\n\nThe study “Factors Influencing Organizational Politics, Emotional Intelligence, and Employee Behavior: A PLS-SEM Model” underscores the managerial implications of its findings. It suggests that fostering emotional intelligence among employees can mitigate the negative effects of organizational politics on employee behavior. Managers should prioritize emotional intelligence development to cultivate a healthier work environment. The organizations should prioritize the development of emotionally intelligent leaders who can effectively manage the political dynamics within their teams and foster a culture of transparency and fairnessapart from this, organizations can implement training programs aimed at enhancing employees' emotional intelligence skills, such as self-awareness, self-regulation, social awareness, and relationship management. By equipping employees with the necessary emotional competencies, organizations can empower them to navigate organizational politics more effectively and respond constructively to challenging situations.\n\nOne of the primary limitations of this study is the reliance on a specific sample size or demographic, which may limit the generalizability of the findings. The study's results may not be applicable to organizations with different structures, cultures, or demographics. Another methodologicla limitation of the study is chosing cross-sectional design of the study that restricts the ability to establish causal relationships between variables. Given that all data were collected through self-report measures, there exists a possibility of common method bias. Participants may have provided socially desirable responses or may have had difficulty accurately assessing their emotional intelligence or organizational politics behaviors. The study may not have accounted for all potential contextual factors that could influence the relationships under investigation. Factors such as organizational culture, leadership style, and industry-specific dynamics could moderate the relationships between organizational politics, emotional intelligence, and employee behavior.\n\nFuture study might look more into the mediating and regulating mechanisms that underpin the links between organizational politics, emotional intelligence, and employee behavior. Exploring elements like organizational justice, trust, or work satisfaction as potential mediators or moderators might help us better grasp the intricate interplay between these variables. It is proposed that future research be conducted on longitudinal studies, which might provide insights into the temporal dynamics of the correlations investigated in this work. Tracking changes in organizational politics, emotional intelligence, and employee behavior over time may give significant information regarding the long-term benefits and sustainability of interventions targeted at minimizing negative consequences related with organizational politics. Building on the study's findings, future research might create and assess intervention programs aimed at improving employees' emotional intelligence. Furthermore, training programs for organizational leaders should focus on ways for mitigating the detrimental influence of organizational politics on employee behavior and organizational outcomes. Finally, future study might look into developing trends, such as remote work arrangements or technology breakthroughs, and how these affect organizational politics, emotional intelligence, and employee behavior. Understanding how these changing dynamics influence workplace interactions and dynamics is critical for designing successful solutions to increase organisational performance and employee well-being in the digital age.\n\n\nConclusions\n\nThis research digs into the complex interplay between organizational politics, emotional intelligence, and employee behavior, emphasizing their far-reaching ramifications in the workplace. Organizational politics may have a negative impact on employee attitudes, resulting in lower work satisfaction, higher turnover intentions, and poorer performance. However, emotional intelligence emerges as a critical mitigating element, allowing individuals to successfully traverse such circumstances. Organizations may equip staff to deal with political difficulties by cultivating emotionally intelligent leadership and a culture that values openness and justice (Jordan & Troth, 2021). More study is needed to investigate additional elements that influence this link, providing deeper insights for building favorable workplace dynamics. The study found substantial links between emotional intelligence, the demand for power, perceived corporate politics, and employee behavior. Emotional intelligence has a favorable impact on behavioral dynamics, while the need for power correlates with perceived organizational politics (Abraham, 2000). Additionally, contextual factors like relationship conflict and workforce diversity significantly impact perceived organizational politics.\n\nThis research was conducted in accordance with guidelines of the Research Ethics Board (REB) of Uttaranchal University. The Research Ethics Board has given ethical approval and the approval number is UU/DRI/EC/2024/004. The formal ethical approval letter was obtained retrospectively. Prior to commencing our research, we obtained verbal approval from the Research Ethics Board (REB) of Uttaranchal University, allowing us to proceed with our study in the month of November 2023, as the REB of Uttaranchal University provides ethical approval in writing only when it is required by a journal. This preliminary verbal approval was based on our detailed proposal, which the REB reviewed and approved in principle, ensuring that all ethical standards and protocols were adhered to. Consequently, we initiated our research in good faith, strictly following the ethical guidelines outlined during the preliminary review. Our research was conducted with full ethical oversight and compliance from the REB from the outset.\n\nThe questionnaire has been submitted to REB of the university, the board members and chairperson have identified the viability of the research topic. All the members presented their research objectives to the board, then the questionnaire got approval to conduct the study.\n\nThe written consent from all the participants involved in the study has been taken. A self-explanatory written statement was attached with the questionnaire for the participants and the similar questionnaire has been submitted to the university research board (REB).", "appendix": "Data availability\n\nFigshare. Datasheet_Analyzing the Relationship Between Organizational Politics, Emotional Intelligence, and Employee Behavior A PLS-SEM Modeling, https://doi.org/10.6084/m9.figshare.25688832.v1 [Sonakshi Bhatia et al., 2024a]\n\nData is available under the terms of the CC BY 4.0\n\nFigshare: Table 2 Factors Influencing Organizational Politics. https://doi.org/10.6084/m9.figshare.26500618.v1 [Sonakshi Bhatia et al., 2024b]\n\nThis project contains the following extended data:\n\n• Table 2 Factors Influencing Organizational Politics.\n\nData is available under the terms of the CC BY 4.0\n\n\nReferences\n\nAbraham R: Organizational cynicism: Bases and consequences. Genet. Soc. Gen. Psychol. Monogr. 2000; 126(3): 269–292. PubMed Abstract\n\nBar-On R: Emotional intelligence: An integral part of positive psychology. S. Afr. J. Psychol. 2010; 40(1): 54–62. Publisher Full Text\n\nBlack B, De Carvalho AG, Khanna V, et al.: Corporate governance indices and construct validity. Corp. 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Publisher Full Text\n\nNaseer S, Raja U, Syed F, et al.: Perils of being close to a bad leader in a bad environment: Exploring the combined effects of despotic leadership, leader member exchange, and perceived organizational politics on behaviors. Leadersh. Q. 2016; 27(1): 14–33. Publisher Full Text\n\nNg TWH, Feldman DC: Idiosyncratic Deals and Voice Behavior. J. Manag. 2012; 41(3): 893–928. Publisher Full Text\n\nPodsakoff NP, Whiting SW, Podsakoff PM, et al.: Individual-and organizational-level consequences of organizational citizenship behaviors: A meta-analysis. J. Appl. Psychol. 2009; 94(1): 122–141. PubMed Abstract \| Publisher Full Text\n\nRizzo JR, House RJ, Lirtzman SI: Role Conflict and Ambiguity in Complex Organizations. Adm. Sci. Q. 1970; 15(2): 150–163. Publisher Full Text\n\nSalovey P, Mayer JD: Emotional Intelligence. Imagin. Cogn. Pers. 1990; 9(3): 185–211. Publisher Full Text\n\nSarstedt M, Ringle CM, Hair JF: Partial Least Squares Structural Equation Modeling BT - Handbook of Market Research. Homburg C, Klarmann M, Vomberg A, editors. Springer International Publishing; 2022; pp. 587–632. Publisher Full Text\n\nShore LM, Chung-Herrera BG, Dean MA, et al.: Diversity in organizations: Where are we now and where are we going?. Hum. Resour. Manag. Rev. 2009; 19(2): 117–133. Publisher Full Text\n\nSmith PR: Collecting sufficient evidence when conducting a case study. Qual. Rep. 2018; 23(5): 1043–1048. Publisher Full Text\n\nSpector PE, Fox S: An emotion-centered model of voluntary work behavior: Some parallels between counterproductive work behavior and organizational citizenship behavior. Hum. Resour. Manag. Rev. 2002; 12(2): 269–292. Publisher Full Text\n\nTuri JA, Sarfraz M: The impact of perceived organizational politics and political risk on project success through ethical leadership and the psychological contract. Kybernetes. 2023; 52(11): 4829–4845. Publisher Full Text\n\nVigoda-Gadot E: Compulsory citizenship behavior: theorizing some dark sides of the good soldier syndrome in organizations. J. Theory Soc. Behav. 2006; 36(1): 77–93. Publisher Full Text\n\nWinter DG: The power motive.1973.\n\nWong C-S, Law KS: The effects of leader and follower emotional intelligence on performance and attitude: An exploratory study. Leadership Perspectives. Routledge; 2017; pp. 97–128.\n\nZeidner M, Matthews G, Shemesh DO: Cognitive-Social Sources of Wellbeing: Differentiating the Roles of Coping Style, Social Support and Emotional Intelligence. J. Happiness Stud. 2016; 17(6): 2481–2501. Publisher Full Text\n\nBhatia S, et al.: Datasheet_Analyzing the Relationship Between Organizational Politics, Emotional Intelligence, and Employee Behavior A PLS-SEM Modeling. [Dataset]. figshare. 2024a. 2024.\n\nBhatia S, et al.: Table 2 Factors Influencing Organizational Politics. Dataset. figshare. 2024b. Publisher Full Text" }	[ { "id": "340212", "date": "02 Dec 2024", "name": "Arjun Kumar Shrestha", "expertise": [ "Reviewer Expertise Organizational Politics", "Workplace Spirituality", "Emotional Intelligence", "Organizational Behavior" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors have chosen a pertinent issue for their study. They need to work on the following areas to further enhance the quality and relevance of the paper. Title: From the first five hypotheses, it is evident that one of the objectives is to identify the antecedents of POP, but it is not reflected in the title. Introduction: This sections fails to succinctly convey the readers the need for conducting this study. Meisler and Vioda-Gadot (2014) [Ref 1] have tested the same model in their study. Several other scholars have also tested similar model in the past. The authors need to provide a strong rationale for conducting this study and the contributions of the study in the introduction section.\n\nLiterature Review: The authors need to add more recent literature in this section. More importantly, the theoretical support, i.e., which theory or theories help establish the proposed hypotheses and how should be clearly explained. The empirical supports and arguments made by the authors for H7 (Organizational politics have significant effect on employee emotional intelligence) are contradictory. First, the authors conclude, \" ..... literature emphasizes the necessity of addressing organizationals politics as a major element impacting employees emotional intelligence ...\". After this, citing past literature, they suggest that emotional acts as a buffer on the relationship between perceived organizationals politics and employee attitudes and behaviors. In this case, emotional intelligence acts as a moderator, not the antecedent of perceptions of organizational politics. Methods: The authors are required to provide the details of all the scales used for measuring the study constructs. The authors have not stated which scales they used for measuring the antecedents of perceptions of organizational politics. For measuring perceptions of organizational politics, they have used Kacmar and Ferris's (1991) [Ref 2] scale. This scale is a three dimensional scale with 12 items. Similarly, Wong and Law's emotional intelligence scale is a multi-dimensional scale with four dimensions having four items in each dimension. However, in the analysis (Figure 1), the authors have treated both the scales as unidimensional scales. The number of items are also six and 10 respectively. The authors need to provide clear explanation for these discrepancies. They are also required to provide the details regarding the scales, i.e., the number of items in the scale, the authors of the scale, and the scoring format/anchors etc. Results: Appropriate statistical tools have been used for testing hypotheses. Discussion: The authors found that emotional intelligence mediates the influence of perceived organizational politics on behavioral dynamics. Previous studies, e.g., Meisler and Vioda-Gadot's (2014) study, on the other hand suggested that perceptions of organizational politics mediates the relationship between emotional intelligence and employee attitudes and behaviors. The authors need to discuss these findings in detail. Language:\nEditing for clarity, coherence, and grammatical accuracy is necessary. For example, the tense in the methods section, “Participants will be recruited,” should be revised to past tense. Citations: Inconsistent citation style should be corrected.\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?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "355202", "date": "16 Jan 2025", "name": "Abílio Afonso Lourenço", "expertise": [ "Reviewer Expertise Learning", "Metacognition", "Psychological Assessment", "Self-Regulated Learning", "Motivational Psychology", "Conflict Studies", "Teaching and Learning", "Educational Psychology", "Educational Assessment", "Social Psychology", "Educational Management", "Assessment", "Teacher Training", "Teaching Methodology", "Educational Evaluation", "Technology Enhanced Learning", "Student Development", "psychometrics (SEM)" ], "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\nPrevious note I appreciate the opportunity to review this article, as it represents an excellent learning opportunity, deepening the understanding of the topic, stimulating critical reflection on the methodologies employed, and contributing to scientific advancement in this area. The article has great potential for publication, provided that substantial revisions are made to the original text. The topic is highly relevant, as it addresses how the dynamics of organizational politics, emotional intelligence, and employee behaviour directly influence the workplace environment, impacting well-being, motivation, and performance within organizations. Understanding these interactions is essential for fostering a healthier, fairer, and more productive culture, offering practical tools to improve interpersonal relationships and conflict management in professional daily life. The potential publication of this article would enable F1000Research to significantly strengthen the theoretical foundations of the topic under analysis. However, the study's conclusions must be properly clarified and substantiated, ensuring that the manuscript provides genuine value. The target audience for this work includes a diverse group of academic readers with varying levels of expertise, making it imperative that the content is presented, accessible, and in a well-structured manner. Maintaining F1000Research's high standards of quality in this area is fundamental. Below are suggested revisions to enrich the manuscript: Abstract The abstract appears somewhat dense and lengthy, which may hinder its readability. Although it includes all the essential information, it could be reorganized and simplified to convey the ideas more clearly and concisely. This is partly due to an excess of methodological details, such as the specific mention of the region, the number of respondents, and the variables analyzed, which could be presented more succinctly. Additionally, some sentences are long and complex, packing in too much information, which makes quick comprehension challenging. There is an excessive focus on complementary elements, such as contextual factors (need for power, diversity, among others), which, while relevant, could be summarized. Moreover, there is some repetition of ideas, such as the influence of organizational politics and the impact of emotional intelligence, which are addressed more than once and could be handled more succinctly. Introduction The introduction contextualizes the research topic but lacks a more direct connection to the detailed content of the abstract. It would be beneficial to briefly mention the analytical method used (PLS-SEM) and the study sample, which would better link the introduction to the specific approach of the investigation. Additionally, the introduction could highlight the main objectives of the article, going beyond the exploration of concepts to also focus on practical solutions for mitigating the negative effects of organizational politics. A quick reference to the key findings, such as the positive impact of emotional intelligence on behavioural dynamics and the significant influence of organizational politics, would make the text more comprehensive. Finally, it would be helpful to streamline the content, focusing on what the article truly addresses and leaving historical and theoretical details for the literature review, making the introduction more concise and aligned with the rest of the study. Review of related literature Factors influencing organization politics - To strengthen the foundation for the formulation of the hypotheses, it is suggested that certain aspects be addressed for each one. Relationship conflict: - It is suggested to explore how relational conflict affects the workplace climate, creating tensions that encourage political behaviour, and to address the role of leadership and organizational culture, which can exacerbate interpersonal conflicts and foster political disputes. Introducing the idea of how factors such as emotional intelligence or conflict management policies help mitigate these effects, acting as mediators, would be beneficial. Presenting more recent studies or empirical evidence that reinforces the relationship between interpersonal conflicts and political behaviour in different contexts is also recommended. There is a significant amount of current literature on this topic. Role conflict: - It is suggested to delve deeper into the subject by addressing the impact on employee well-being, as role conflict can lead to stress and burnout, making employees more likely to resort to political strategies to cope with pressure. A lack of clarity or poor communication from leaders can exacerbate conflict, creating opportunities for political dynamics to emerge. Organizational culture plays a significant role, as rigid structures or limited transparency can intensify conflicts and foster manipulative behaviour. Including practical examples of how employees handle these situations, such as forming alliances or manipulating information, could enhance the discussion. Proposing solutions, such as better defining responsibilities, providing emotional intelligence training, or reviewing internal processes, would add practical value. Updating the bibliography is also recommended. Resource constraints - It can be suggested that resource scarcity, such as limited funding or staff, may harm productivity and work quality, prompting employees to resort to political strategies to achieve their goals. Furthermore, leadership decisions regarding resource allocation, when perceived as unfair, can exacerbate these behaviours. Another aspect is that in environments promoting competition over collaboration, political manoeuvring tends to increase (e.g., favouritism, lobbying, sabotage). Proposed solutions could include clearer resource allocation policies, transparent processes, and incentives for collaboration. Need for power - It can be mentioned that employees with a strong need for power may create competitive and hostile work environments, hindering collaboration and negatively affecting team morale. On the other hand, leaders with this trait may manipulate processes or make biased decisions to strengthen their authority, thereby intensifying political games. Furthermore, understanding the internal motivations of these individuals, such as insecurity or the need for validation, can provide better insight into the phenomenon. The interaction between the need for power and factors like resource constraints or relational conflicts can further exacerbate organizational politics. Examples of this include information manipulation, exclusion of colleagues, or the formation of strategic alliances. To mitigate these effects, it is important to promote balanced leadership, provide structured feedback, and encourage a fairer distribution of power in the workplace. Presenting results from more recent studies would be beneficial. Workforce diversity - The hypothesis could be more detailed by addressing different types of diversity, such as gender, age, culture, and educational background, and how each of these factors affects political dynamics in the workplace. It could be suggested that diversity may influence communication within the organization, as different communication styles and cultural perceptions can lead to misunderstandings and conflicts that fuel organizational politics. It could be explored how leaders need to adjust their styles to manage diverse teams, as an inclusive approach can reduce political behaviour and promote more collaboration. Including minority groups can foster a climate of trust and reduce tensions, helping to mitigate destructive political behaviour in the organization. Updating the bibliography would be beneficial. Organizational politics and employee behaviour - To strengthen the idea, it would be interesting to explore how individual perceptions of organizational politics influence employee behaviour and performance, as well as the relationship between politics and emotional factors, such as stress, that impact productivity. Another interesting aspect would be to address the impact of organizational politics in modern contexts, such as remote work, and how organizational culture can amplify these effects. Ways to mitigate these impacts, such as clear communication and ethical training, could also be discussed. Organizational politics and emotional intelligence - Emotional intelligence, being an important variable in the study, could be explored in terms of how it helps employees manage their emotional reactions to organizational politics, which facilitates adaptation and conflict resolution. It would be interesting to analyse how factors such as leadership style and organizational culture influence this interaction, as leadership that values emotional intelligence can mitigate the negative impacts of organizational politics. Another aspect would be to address in more detail how emotional intelligence can be trained and developed to improve the management of organizational politics, fostering a healthier and more collaborative environment. Emotional Intelligence and employee behaviour - The hypotheses could be deepened by detailing how EI impacts specific behaviour, such as collaboration and problem-solving, and analyzing variations between roles or hierarchical levels. It would be useful to explore how organizational contexts, such as culture and sector, moderate this relationship, as well as consider cultural differences in the application of EI in diverse teams. Another point would be to discuss how EI can be developed through training and its impact on team dynamics. It may also be interesting to clarify the mechanisms through which EI mediates the relationship between organizational politics and behaviour, complementing recent studies to strengthen the hypotheses. Theoretical Framework - Regarding EI, the study would be much more robust with the reference to the model and more recent studies by Mayer and Salovey. The authors provide a rigorous theoretical approach, strongly based on empirical research, being more focused on the academic field. They aim to understand EI as a specific form of intelligence and to create objective psychometrics to measure it. That is, more in line with the present study. In turn, Goleman made EI a widely known concept accessible to the general public, but with less scientific rigor compared to the models of Mayer and Salovey.\nMethods This chapter should be structured differently and divided into subchapters to facilitate organization and reading. That is, separated into subchapters titled sample, procedures, instruments, and data analysis. This separation, in addition to aligning with best academic writing practices, would help present the methodological details clearly and systematically. As a suggestion: - The sample should state that convenience sampling was used, justified by the ease of access to participants from different sectors and organizational contexts. The sample size of 500 participants was determined to ensure an adequate level of demographic and organizational representativeness, including diversity in sectors, functions, and geographical location. The sample should be properly characterized concerning gender, age, organizational role, and other relevant aspects. It should be mentioned that participants were recruited through online platforms and professional networks, promoting broad coverage and diversity.\n\n- As for the procedures, it should be stated that data were collected in November 2023, following a cross-sectional study design suitable for the research objectives, as it allows the investigation of connections between variables at a single point in time. The process involved inviting participants, completing the scales, and ensuring confidentiality and ethics at all stages. It is important to mention that the entire procedure was carried out by the provisions of the Helsinki Declaration (2013) on studies involving human participants.\n\n- Regarding the instruments, it should be stated that the three scales used in the study are validated for the context in which the study takes place (India) and have proven validity and reliability in the literature. It should be mentioned how many factors each scale has, the total number of items, and the respective Cronbach’s alphas, as well as the range of the Likert scales used. Essential information should be presented to justify the validation of the scales. It should be highlighted that to validate the results obtained in the study, the scales must be validated for the Indian context. That is, psychometric scales must be validated for the context or country in which they are applied because cultural, linguistic, and social factors can influence how people interpret and respond to items. A scale developed in another country may not adequately capture the meanings or behaviour in the new context, compromising its validity (whether it measures what it intends to measure) and reliability (whether it produces consistent results). Local validation ensures that the items are culturally relevant, semantically clear, and suitable for the target audience, avoiding distortions in results and allowing for accurate and scientifically robust comparisons. - In data analysis, it should be mentioned that the PLS-SEM model was used, which is suitable for complex models with latent variables and limited samples. The analysis was conducted in two stages: the assessment of the measurement model to verify the reliability and validity of the scales, and the assessment of the structural model to examine the relationships between variables. The bootstrapping method was applied to assess the significance of direct and indirect effects in the model. To interpret the data from the tables and figures, it is essential to indicate which types of analyses were used and which fit indices were considered for adjusting the PLS-SEM model. The respective minimum/maximum values and the authors supporting these values should also be provided. Results Following the previous point, the \"Results\" chapter and its respective subchapters seem to contain information that should be, at least partially, in earlier sections such as \"Sample\", \"Procedures\", \"Instruments\", and \"Data Analysis\". To improve the organization and make the study clearer, I suggest restructuring the \"Results\" chapter as follows: First, demographic data such as age, gender, marital status, and education (presented in Table 1) should be included in the \"Sample\" section (this can be provided in detail), as they are crucial to describe the participant profile before analyzing the results. Then, the description of the psychometric scales used and the validation of constructs (including validity and reliability indices) should be placed in the \"Instruments\" section, as they are essential to justify the methodological robustness before presenting the findings. More technical elements, such as the measurement model, discriminant validity, factor analysis, and the use of \"bootstrapping\", belong in the \"Data Analysis\" part, as they help explain the methodological basis for interpreting the results. The analysis of the structural model and hypothesis testing (presented in Table 6) are correctly in the \"Results\" section, but they should be more separated from the descriptive and technical data to avoid confusion. This reorganization will make the study more fluid, clear, and free of redundancies. Factors influencing organizational politics, emotional intelligence, and employee behaviour: a PLS-SEM model Measurement model Structural model and hypothesis testing Discussion - The \"Discussion\" largely aligns with the study's objectives and can be improved with the restructuring suggested in the previous point. However, it could be clearer to highlight how the results directly align with the specific objectives of the study, such as exploring the influences of organizational politics on employees' attitudes and behaviour, mediated by emotional intelligence. For example, the description of how organizational politics directly influences behavioural dynamics and emotional intelligence could be more explicitly connected to the original hypotheses, to strengthen the relationship between the data and the study's objectives.\n\n- As previously mentioned, the bibliography should be updated to provide more robustness to the study's results. Theoretical implication - The theoretical implications can be strengthened by exploring how the organizational environment, including politics, culture, and power dynamics, influences individuals' emotions, attitudes, and behaviour. This study contributes to organizational behaviour theory by highlighting how perceived organizational politics affect emotional intelligence and employee behaviour. These social exchanges complement this understanding, explaining how relationships in the workplace involve resource exchanges, and how a negative perception of organizational politics can harm trust and contribute to resistance behaviour and disengagement. Managerial implication - To enrich this point, several aspects could be addressed. Managers can adopt strategies that reduce the negative perception of organizational politics, such as ensuring fair decision-making processes, communicating clearly, and establishing well-defined policies. It is also essential to invest in training to identify and manage interpersonal and role conflicts, reducing their impact on the work environment. Regular organizational climate assessments help adjust practices based on employee feedback. Encouraging collaboration, promoting diversity as a strategic resource, and implementing continuous feedback systems strengthen trust and reduce manipulative behaviour. Limitations of the study - Other limitations that could be considered include the absence of longitudinal analyses, which would allow for the observation of how the relationships between organizational politics, emotional intelligence, and employee behaviour evolve. Additionally, the study did not explore the possible effects of additional mediating or moderating variables, such as trust climate or organizational support, which could deepen the understanding of the dynamics investigated. Another limitation is the lack of diversification in data sources; complementary data, such as evaluations from supervisors or colleagues, could reduce the self-report bias. Finally, the study did not account for cultural or contextual variations between different countries or regions. Future scope - In addition to the suggestions mentioned, future studies could investigate how different leadership styles influence the relationship between organizational politics, emotional intelligence, and employee behaviour. Furthermore, interdisciplinary research could integrate approaches from positive psychology, exploring how mindfulness practices or well-being-focused interventions can strengthen emotional intelligence and mitigate the negative impacts of organizational politics. Another important aspect is using more diverse samples, including different sectors or global organizations, to enhance the generalizability of the results. Conclusions - It is suggested to highlight the importance of sustainable interventions in developing emotional intelligence and reducing the negative perception of organizational politics so that the positive effects persist over time. References - It is suggested that more references from studies from the last 5 years, including those from 2025, be included.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-996
https://f1000research.com/articles/13-995/v1	02 Sep 24	{ "type": "Research Article", "title": "Automated classification of mandibular canal in relation to third molar using CBCT images", "authors": [ "Neil Abraham Barnes", "Winniecia Dkhar", "Sharath S", "Yogesh Chhaparwal", "Veena Mayya", "Roopitha C H", "Neil Abraham Barnes", "Winniecia Dkhar", "Yogesh Chhaparwal", "Veena Mayya", "Roopitha C H" ], "abstract": "Background Dental radiology has significantly benefited from cone-beam computed tomography (CBCT) because of its compact size and low radiation exposure. Canal tracking is an important application of CBCT for determining the relationship between the inferior alveolar nerve and third molar. Usually, canal tacking is performed manually, which takes a lot of time. This study aimed to develop an artificial intelligence (AI) model to automate classification of the mandibular canal in relation to the third molar.\n\nMethods This retrospective study was conducted using 434 CBCT images. 3D slicer software was used to annotate and classify the data into lingual, buccal, and inferior categories. Two convolution neural network models, AlexNet and ResNet50, were developed to classify this relationship. The study included 262 images for training and 172 images for testing, with the model performance evaluated by sensitivity, precision, and F1 score.\n\nResults The performance of the two models was evaluated using a 3 × 3 confusion matrix, with the data categorized into 3 clases: lingual, buccal, and inferior. The mandibular canal and third molar have a close anatomical relationship, highlighting the need for precise imaging in dental and surgical settings. To accurately classify the mandibular canal in relation to the third molar, both AlexNet and ResNet50 demonstrated high accuracy, with F1 scores ranging from 0.64 to 0.92 for different classes, with accuracy of 81% and 83%, respectively, for accurately classifying the mandibular canal in relation to the third molar.\n\nConclusion The present study developed and evaluated AI models to accurately classify and establish the relationship between the mandibular canal and third molars using CBCT images with a higher accuracy rate.", "keywords": [ "Artificial Intelligence", "CBCT", "CNN", "Mandibular Canal", "Machine Learning", "Third Molar" ], "content": "Introduction\n\nCone-beam computed tomography (CBCT) has revolutionized oral and maxillofacial radiology. Owing to its compact size, low cost, and low ionizing radiation exposure, CBCT has rapidly become the preferred imaging modality for dental radiology.1 In CBCT, a cone-shaped beam scans the patient in 360-degree rotation and acquires a large field of view (FOV).2 CBCT has played a major role in dental imaging owing to its various clinical applications such as orthodontics, temporomandibular joint testing, endodontics, periodontics, implantology, and mandibular canal tracking.3,4\n\nMandibular canal tracking is an application of CBCT imaging that is widely used to track the extension of the mandibular canal, which houses the inferior alveolar nerve (IAN). The alveolar nerve, with an average length of 2.00 mm to 5.00 mm, starts from the mandibular foramen and runs through the mental foramen.5 The IAN plays a significant role in facial motor and sensory functions. The mandibular nerve innervates the masticatory muscles of smaller muscles and provides sensory input from the lower face. Damage to the mandibular nerve can lead to persistent or worsening neurosensory deficits including numbness, pain, and loss of taste in the lips, mucosa, and tongue. It can cause pain in the lower teeth, lower jaw, and lower lips when the IAN is dysfunctional, thereby affecting speech and chewing.\n\nAs CBCT provides a three-dimensional view of the structures involved, it has become a crucial tool for evaluating the anatomical relationship between the nerve canal and third molar roots. Radiographic assessment is necessary to determine this relationship.6 Extracting an impacted third molar is a common oral and maxillofacial surgery procedure, but it can result in postoperative complications and IAN injury.7\n\nHence, tracking the canal using CBCT and establishing the relationship between the third molar and mandibular canal is very important because the third molar is the most impacted tooth in the human dental anatomy.8,9 Currently, classification is performed manually, which is less accurate and more time-consuming. Artificial intelligence (AI) has shown significant success in various medical imaging fields, including dentistry. AI is a component of computer science that deals with creating an intelligent computer system that displays traits associated with intelligence in comprehending human behavior, language, education, logic, problem-solving, and many more.10,11,12 Convolutional neural network (CNN) AI techniques have become dominant in various computer vision tasks and have been applied in fields such as radiology for image analysis. Manual tracing and establishing the canal relationship can be performed automatically, more accurately, and faster using a CNN. The present study aimed to develop an AI model to establish the relationship between the third molar and the mandibular canal using CBCT images.\n\n\nMethods\n\nThis is a retrospective study. Ethical approval was obtained from the Institutional ethical committee (IEC2:322/2022) of Kasturba Medical College and Hospital, Manipal, India on 14th July 2022.CBCT images of the mandible were collected from Department of Oral Medicine and Radiology, Manipal College of Dental Sciences, which were acquired using an i-CAT 17-19 Platinum (Imaging Sciences International LLC, USA) CBCT scanner. The scan parameters were in the range of 85-90 kVp, 6mA, as specified by the vendor. The inclusion criteria were that the CBCT images collected should contain a bilateral third molar tooth and an age range of 18-60 years. The exclusion criteria were the presence of a dental prosthesis and missing third molar. A total of 580 studies were screened based on the inclusion and exclusion criteria and 434 CBCT images were included.\n\nCBCT images were manually classified into three Categories, Lingual, Buccal, and Inferior, by locating the canal in relation to the third molar using 3D Slicer an open source software,13 as shown in Figure 1.\n\nTo develop and test a machine learning model, 434 images were divided into two subsets, including 262 images for training and 172 for testing the model. Two models, AlexNet and ResNet were developed based on convolutional neural networks (CNN).\n\nModel 1: - AlexNet\n\nThe AlexNet architecture is a classic convolutional neural network (CNN) that consists of convolution, max pooling, and dense layers. Eight layers were present: five convolutional layers, three max-pooling layers, and three fully connected layers. There were two copies of the network, each running on its own GPU. The AlexNet architecture is shown in Figure 2.\n\nModel 2: - ResNet50\n\nResNet, which stands out as the Residual Network, is a type of CNN. It is a 50-layer CNN (48CNN layer, 1 MaxPool layer, and 1 Average pool layer). The networks were formed by stacking the residual blocks. It is comprised of 34 weighted layers. 3.6 billion FLOPs can be achieved with their implementation, while 1.8 billion FLOPs can be achieved with a smaller 18-layer ResNet. In addition, if the size of the feature maps is halved, the number of filters is doubled to preserve the complexity of the time of each layer. Owing to its 50-layer design, ResNet employs a bottleneck design for building blocks. Figure 3 shows the architecture of the ResNet.\n\n\nResults\n\nThe mandibular canal and third molar have a close anatomical relationship that is essential in dental and surgical contexts. Cone-beam computed tomography (CBCT) and panoramic radiography have been used in several studies to study this relationship. As the inferior alveolar nerve (IAN) passes through the mandibular canal, its position is anatomically important. It has been shown that the mandibular canal has a close relationship with a high percentage of third molars, and this relationship is important to consider in dental imaging because damage to the IAN can occur during surgery on mandibular third molars. Therefore, locating the mandibular canal is a vital part of dental imaging. In the present study, we developed an AI model to automatically establish the relationship between the mandibular canal and the third molar.\n\nIn the present study, 172 data points were used to test the model. Two model sets were developed: AlexNet and ReSNet50, which are based on a CNN. The models were then evaluated for their performance. The performance of these models was assessed using a 3 × 3 confusion matrix with output comprising true positive (TP), True Negative (TN), and misclassified cases (MC), in which data are categorized into three classes: lingually (A), buccal (B), and inferior (C). The results of the confusion matrix for AlexNet and ResNet are listed in Tables 1 and 2, respectively.\n\n* TP-True Positive, TN-True Negative, MC-Miss Classified.\n\nThe accuracy and performance of the models to classify the relationship between the third molar was evaluated using its Precision, Sensitivity/Recall, and F1 Score. The AlexNet model yielded an F1score of 0.89 for Class A (Lingual), 0.64 for Class B (Buccal), and 0.37 for Cass C (Inferior), with an overall accuracy of 81%, as shown in Table 3 & Table 4.\n\nThe ResNet model yielded an F1score of 0.92, 0.43, and 0.5% for Class A (Lingual), Class B (Buccal), and 0.56 for Class C (inferior), with an overall accuracy of 83% for accurately classifying the mandibular canal in relation to the third molar, as shown in Tables 5 and 6.\n\n\nDiscussion\n\nMachine learning has been used in dental imaging for various purposes such as the diagnosis and treatment of oral diseases. Deep learning in dental imaging has been successful in detecting caries, periodontal bone loss, and other dental problems. Mandibular canal and third molar relationships have been established in dentistry using machine-learning models. Deep learning models have been used to analyze panoramic radiography and other imaging techniques to determine the relationship between mandibular third molars and the mandibular canal. Dental imaging involves identifying the exact location of the mandibular canal in relation to the third molar to prevent complications during surgery.\n\nIn the present study, we developed two machine learning models, AlexNet and ResNet50, for classifying the mandibular canal in relation to the third molar into three different classes based on their location: lingual, buccal, and inferiorly. Various studies have been conducted with different machine learning algorithms using panoramic radiographs to establish the relationship between the third molar and mandibular canal. Few studies have been conducted on CBCT images. We developed and evaluated two machine learning models based on CNN using CBCT images.\n\nThe performance of the CNN models was evaluated using a confusion matrix in which the AlexNet model identified 125 images as TP, three images as TN, and misclassified three images as Class A out of 131 lingual data similarly for Class B out of 14 images; the model identified five images as TP, eight as TN, and misclassified one image, and for the data sets involving Class C AlexNet model, we identified 20 images accurately and misclassified seven out of 27 images. Similarly, the ResNet model identified 121 images as TP, three images as TN, and misclassified 7 images as Class A out of 131 lingual data, also for Class B, five images were identified as TP, six as TN and misclassified 3 images and for the datasets involving Class C, the AlexNet model identified 20 images accurately and misclassified 7 images\n\nRecently, various studies have reported the application of CNN with promising results in the staging of tooth development, detection, and classification of third molars and canals. Artificial neural networks with deep feed-forward architectures are used for a wide range of tasks such as recognizing activities, recognizing text, recognizing faces, describing images, detecting objects, and localizing them. Because of the ability of this technique to learn abstract features from spatial data, it can be used to efficiently classify images. It has multiple architectures, including ResNet and AlexNet.14 AlexNet are two popular deep-learning models used in dental imaging applications. According to the size and complexity of the dataset, as well as the specific characteristics of the dental images, the ResNet and AlexNet models can perform differently in dental imaging.\n\nThe AlexNet model proposed by Krizhevsky et al. (201215) is considered a pioneer in deep learning for image classification because it is relatively shallow. This algorithm has eight layers, including three fully connected and five convolutional layers. For enhanced generalization, local response normalization and dropout are incorporated into the architecture; if the dataset is not extensive and a simpler model is preferred, the relatively shallow architecture might be advantageous in dental imaging. The introduction of ResNet by He et al. in 201516 was an important breakthrough in deep learning. The most innovative feature of ResNet is that it consists of residual blocks, which contain skip connections that allow information to flow directly from one layer to another. Consequently, the vanishing gradient problem is mitigated, and extremely deep networks can be trained more easily.\n\nSeveral studies have tested the performance of ResNet and Alex Net in dental imaging by using them for different tasks. A study conducted by Mu-Qing Liu et al.,17 developed a U-Net model for detecting and segmenting the mandibular canal, while the ResNet-34 model was used to classify the relationship between the mandibular canal and third molars. The classification model had 90.2% sensitivity, 95.0% specificity, and 93.3% accuracy. In the present study, we developed two CNN models: model 1 was 81% accurate, and model 2 was 83% accurate in classifying the mandibular canal as related to the third molar.\n\n18Using a deep learning model, Sukegawa et al. studied how the inferior alveolar nerve is related to the mandibular third molar on panoramic radiography. To classify the positional relationship between the two structures, CNN models were used, including ResNet50 and ResNet50v2, in which ResNet50v2 was the top performer in both the continuity analysis and contact analysis using the SAM optimizer. For continuity analysis, the accuracy and AUC were 0.766 and 0.843, respectively. A study proposed the use of ResNet-152 and AlexNet to detect caries and non-carious teeth in panoramic dental images, which had an accuracy rate of 96.08%.19 Similarly, Katsuki Takebe et al.20 performed a study in which the authors developed a YOLO model for evaluation of contact between the third molar and alveolar nerve automatically resulting in a f1 score of 0.908, while the AlexNet and ResNet models in the present study showed f1 score of 0.81and 0.83, respectively, in classifying the mandibular canal in relation to the third molar.\n\nIn CBCT, tracing the canals manually and establishing their relationship to the third molars is performed by a skilled operator meticulously tracing the root canals. It is widely used and accepted owing to its accuracy and reliability. Despite this, the process is not only time-consuming but also requires expertise and may be subject to variability within and among operators. To accurately trace the canal pathways, the operator relies on the knowledge and experience of dental anatomy. Despite its high level of precision, manual segmentation is limited when dealing with complex anatomies or large datasets. Automatic canal segmentation methods have gained popularity with the advent of artificial intelligence (AI) and machine learning. Using these techniques, root canals can be identified and delineated automatically, without the need for manual intervention. Its primary objective is to improve efficiency and reduce operator dependency, while providing consistent results across datasets. With AI systems, patients can obtain optimal imaging based on their clinical needs, presentation, and region of interest. They can also detect artifacts or distortions that interfere with interpretation.21,22 The radiation dose can also be reduced by maintaining good image quality, as has been reported in previous studies,23,24 to keep radiation doses within the threshold limit for all radiosensitive organs, while maintaining good image quality.\n\nBased on the results of this study, it is noted that AI algorithms based on CNN can be used as a better alternative method with great accuracy for identifying the mandibular canal and establishing its relation to the third molar in CBCT, which can help reduce the manual method. The application of AI-based algorithms can help dental professionals diagnose and assess the root anatomy in relation to the third molar. This will enable them to provide appropriate treatment without damaging the inferior alveolar nerve or causing any complications. Overall, AI technology has the potential to revolutionize the field of dentistry and change the way dental professionals diagnose and treat various diseases.\n\nAlthough the models developed in the present study have demonstrated high accuracy and precision with the inclusion of two different models, which allowed a comprehensive assessment of the performance of these architectures in dental imaging, there are some limitations in the present study: the age range was restricted to 18-60 years which might limit the generalizability of the results. In addition, CBCT images were collected from a single facility, which may limit the diversity of cases and anatomical variations in the dataset.\n\n\nConclusion\n\nIn conclusion, this study developed and evaluated two CNN-based models, AlexNet and ResNet50, for classifying the relationship between third molars and the mandibular canal using CBCT images. Both models demonstrated high accuracy and F1 scores across different classes, indicating better performance. These AI-based models have the potential to enhance the diagnostic efficiency and improve patient care when integrated into routine clinical practice.\n\nThis is retrospective study. Ethical approval was obtained from the Institutional ethical committee (IEC2:322/2022) of Kasturba Medical College and Hospital, Manipal India on 14th July 2022. No consent was obtained in accordance with the ethical approval, as this is a retrospective study.", "appendix": "Data availability\n\nFigshare: Annotated data set, https://doi.org/10.6084/m9.figshare.26502916.v1. 25\n\nThis project contains the following underlying data:\n\nThe annotated data sets of mandibular canal classified as Lingual, Buccal and Inferior\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nVenkatesh E, Elluru SV: CBCT: Basics and Applications in Dentistry. J. Istanbul. Univ. Fac. Dent. 2017; 51: 102–121. Publisher Full Text\n\nScarfe W, Farman A, Sukovic P: Clinical Applications of Cone-Beam Computed in Dental Pratice. J. Can. Dent. Assoc. 2006; 72(1): 75–80. PubMed Abstract\n\nJain S, Choudhary K, Grover D: New evolution of cone-beam computed tomography in dentistry: Combining digital technologies.2019; 179–190.\n\nMaret D, Vergnes J-N, Peters OA, et al.: Recent Advances in Cone-beam CT in Oral Medicine. Current Medical Imaging Formerly Current Medical Imaging Reviews. 2019; 16(5): 553–564. PubMed Abstract \| Publisher Full Text\n\nKroon D: SEGMENTATION OF THE MANDIBULAR CANAL IN CONE-BEAM CT DATA.Publisher Full Text\n\nIzzetti R, Nisi M, Gennai S, et al.: Evaluating the Relationship between Mandibular Third Molar and Mandibular Canal with Semiautomatic Segmentation: A Pilot Study on CBCT Datasets. Applied Sciences (Switzerland). Jan. 2022; 12(1). Publisher Full Text\n\nLiu MQ, et al.: Deep learning-based evaluation of the relationship between mandibular third molar and mandibular canal on CBCT. Clin. Oral Investig. Jan. 2022; 26(1): 981–991. PubMed Abstract \| Publisher Full Text\n\nChaudhary B, Joshi U, Dahal S, et al.: Anatomical Position of Lower Third Molar in Relation to Mandibular Canal on Cone-Beam Computed Tomography Images in A Tertiary Care Hospital: A Descriptive Cross-sectional Study.2020; 58(231): 879–883. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nArticle R: Impacted Mandibular Third Molars: Review of Literature and a Proposal of a Combined Clinical and Radiological Classification.2015; 5(4). Publisher Full Text\n\nThrall JH, et al.: Artificial Intelligence and Machine Learning in Radiology: Opportunities, Challenges, Pitfalls, and Criteria for Success. J. Am. Coll. Radiol. 2018; 15(3): 504–508. PubMed Abstract \| Publisher Full Text\n\nHosny A, Parmar C, Quackenbush J, et al.: Artificial intelligence in radiology. Nat. Rev. Cancer. 2018; 18(8): 500–510. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCurrie G, Hawk KE, Rohren E, et al.: Machine Learning and Deep Learning in Medical Imaging: Intelligent Imaging. J Med Imaging Radiat Sci. 2019; 50(4): 477–487. Publisher Full Text\n\nFedorov A, et al.: 3D Slicer as an image computing platform for the Quantitative Imaging Network. Magn. Reson. Imaging. Nov. 2012; 30(9): 1323–1341. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMohamed EG, Redondo RPD, Koura A, et al.: Dental Age Estimation Using Deep Learning: A Comparative Survey. MDPI. Feb. 01, 2023; 11. Publisher Full Text\n\nKrizhevsky A, Sutskever I, Hinton GE: ImageNet Classification with Deep Convolutional Neural Networks.Reference Source\n\nHe K, Zhang X, Ren S, et al.: Deep Residual Learning for Image Recognition.Reference Source\n\nLiu MQ, et al.: Deep learning-based evaluation of the relationship between mandibular third molar and mandibular canal on CBCT. Clin. Oral Investig. 2022; 26(1): 981–991. PubMed Abstract \| Publisher Full Text\n\nSukegawa S, et al.: Deep learning model for analyzing the relationship between mandibular third molar and inferior alveolar nerve in panoramic radiography. Sci. Rep. Dec. 2022; 12(1): 16925. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOztekin F, et al.: An Explainable Deep Learning Model to Prediction Dental Caries Using Panoramic Radiograph Images. Diagnostics. Jan. 2023; 13(2). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTakebe K, Imai T, Kubota S, et al.: Deep learning model for the automated evaluation of contact between the lower third molar and inferior alveolar nerve on panoramic radiography. J Dent Sci. 2022; 18(xxxx): 991–996. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nUrban R, et al.: AI-Assisted CBCT Data Management in Modern Dental Practice: Benefits, Limitations and Innovations. MDPI. Apr. 01, 2023; 12. Publisher Full Text\n\nHardy M, Harvey H: Artificial intelligence in diagnostic imaging: impact on the radiography profession 1.2020.\n\nHrangkhawl W, Dkhar W, Madhavan TS, et al.: Determination of Scattered Radiation to the Thyroid Gland in Dental Cone Beam Computed Tomography. Journal of Radiation Protection and Research. Mar. 2023; 48(1): 15–19. Publisher Full Text\n\nDkhar W, Chhaparwal Y: Estimation of Effective Radiation Dose to the Eye Lens in Dental Cone Beam Computed Tomography.2020.\n\nS, S: Annotated Data set.zip. [Dataset]. figshare. 2024, 6 Ağustos. Publisher Full Text" }	[ { "id": "332755", "date": "21 Oct 2024", "name": "Dr. Rohit Gadda", "expertise": [ "Reviewer Expertise Cone Beam Computed Tomography (CBCT)", "Oral and Maxillofacial imaging", "Oral and Maxillofacial 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\nThis is an interesting manuscript investigating automated classification of mandibular canal in relation to third molar using CBCT images. Manuscript is well written. However it is recommended to authors to describe detailed protocol for selection of CBCT images (coronal section and level of section) collected as CBCT scan is 3 dimensional dataset with multiple 2 dimensional images in different planes can be created. Figure 1. (A) shows mandibular canal passing inferior to the third molar. So authors are requested to revisit this figure. In discussion section, 8th paragraph 'In CBCT, tracing of the canals...' context of root canal or canals is to be revised and rewritten.\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": "345485", "date": "27 Dec 2024", "name": "Antonio Lo Casto", "expertise": [ "Reviewer Expertise Radiology and Imaging." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe paper is an interesting contribution on the use of CNN to classify the relationship between third molar and mandibular canal. Just some minor review should be made. 1. The length of the alveolar nerve is longer than what reported (2.00 mm to 5.00 mm) in the section \"Introduction\". 2. The first part of the section \"Results\" from \"The mandibular canal... to ...and the third molar\" is more suited for the sections \"Introduction\" or \"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?\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/13-995
https://f1000research.com/articles/13-993/v1	02 Sep 24	{ "type": "Review", "title": "Impact of Climate Change on Human Lactation: Biological, Socioeconomic, and Public Health Implications", "authors": [ "Daryl O. Traylor", "Winter Cameron", "Brianna Clark", "Eboni Anderson", "Robert Henderson", "Lena Clark", "Winter Cameron", "Brianna Clark", "Eboni Anderson", "Robert Henderson", "Lena Clark" ], "abstract": "Global climate change poses significant challenges to human health and nutrition, particularly affecting lactating individuals and their infants. This review examines the impact of climate change on lactation, focusing on physiological, socioeconomic, and public health implications. Rising temperatures and heat stress can reduce milk production and alter milk composition, while malnutrition and water scarcity exacerbate these effects. Vulnerable populations face heightened risks, emphasizing the need for targeted mitigation strategies. Recommendations include enhancing nutritional support, securing water supplies, reducing environmental toxin exposure, and integrating lactation considerations into climate policies. Employing a social-ecological lens, this review underscores the necessity of a holistic approach to support lactating individuals in a warming world. Future research should explore the complex interactions between climate stressors and lactation to develop effective public health interventions.", "keywords": [ "climate change", "human lactation", "heat stress", "nutritional support", "water scarcity", "public health" ], "content": "Human lactation: biological and socioeconomic significance\n\nHuman lactation is a complex physiological process critical for infant nutrition and maternal health. Breastfeeding provides essential nutrients and antibodies that promote infant development and reduce the risk of various diseases. For mothers, it aids in postpartum recovery and decreases the risk of certain cancers and chronic conditions (Gertosio et al., 2016). Socioeconomically, breastfeeding contributes to reduced healthcare costs and improved economic outcomes by fostering healthier populations and reducing the need for medical interventions (Binns et al., 2016).\n\nTransitioning from the broader benefits of lactation, it is essential to delve into the underlying biological mechanisms that make these advantages possible. Human lactation is a complex process involving the mammary gland, hormonal regulation, and milk composition. The mammary gland, under the influence of estrogen, prolactin, and cortisol, undergoes lactogenesis and milk ejection (Villalpando & De Santiago, 1993). Prolactin, released in response to suckling, is essential for lactation, while oxytocin is involved in milk removal (McNeilly, 1977). Milk synthesis occurs through various mechanisms, with the composition being influenced by maternal diet and body composition (Villalpando & De Santiago, 1993). The process is also affected by maternal genetics, diet, and environmental factors (Lee & Kelleher, 2016). The onset and maintenance of lactation are regulated by endocrine changes during pregnancy and postpartum (Sadovnikova et al., 2020). Understanding the anatomy and physiology of lactation is crucial for supporting breastfeeding (Sriraman, 2017).\n\nShifting focus from the broader benefits of lactation, it is essential to highlight the underlying biological mechanisms that make these advantages possible. Human lactation is a complex process involving the mammary gland, hormonal regulation, and milk composition. This intricate system is coordinated by an interplay of hormones that ensure the successful production and ejection of milk, providing nourishment for the infant. The mammary gland, primarily influenced by estrogen, prolactin, and cortisol, undergoes significant changes to prepare for lactation (Alex et al., 2020). During pregnancy, estrogen stimulates the proliferation of ductal structures within the mammary glands, while progesterone promotes the formation of alveolar structures necessary for milk production (Alex et al., 2020). Cortisol also plays a role in mammary gland development by enhancing the effects of prolactin and other lactogenic hormones (Kabotyanski et al., 2006).\n\nLactogenesis, the onset of milk production, is divided into two stages: Lactogenesis I occurs during pregnancy when the mammary gland develops the capacity to secrete milk but is inhibited by high levels of progesterone, and Lactogenesis II begins postpartum, around 2-3 days after childbirth, when the drop in progesterone levels triggers the onset of copious milk secretion (Sadovnikova et al., 2020). This stage is characterized by increased blood flow, oxygen, and glucose uptake by the mammary gland, essential for milk synthesis (Neville & Morton, 2001). The hormonal axis regulating lactation involves a finely tuned balance of various hormones, primarily prolactin and oxytocin, and their feedback mechanisms (Trott et al., 2012). Prolactin is synthesized and released by the anterior pituitary gland in response to the stimulation of the nipples by suckling (Trott et al., 2012). This stimulus is transmitted via neural pathways to the hypothalamus, where the inhibition of prolactin-inhibiting factor (dopamine) allows for the increased release of prolactin from the pituitary (Grattan, 2015). Prolactin is essential for the initiation and maintenance of milk production, promoting the synthesis of milk proteins, lactose, and lipids in the mammary alveolar cells (Grattan, 2015; Trott et al., 2012).\n\nOxytocin, synthesized in the hypothalamus and stored in the posterior pituitary gland, is released into the bloodstream in response to suckling (Crowley, 2014). It facilitates the ejection of milk from the mammary glands by causing the myoepithelial cells surrounding the alveoli to contract, expelling milk through the ductal system to the nipple (Crowley, 2014). Milk synthesis occurs through various cellular mechanisms within the mammary alveoli, involving the uptake of precursors from maternal blood and their conversion into milk components, such as lactose, casein, whey proteins, and lipids (Neville & Morton, 2001; Sadovnikova et al., 2020). The composition of human milk is dynamic and influenced by several factors, including maternal diet, body composition, genetics, and environmental factors. Nutritional intake and body fat stores of the mother can affect the quantity and quality of milk produced, while genetic factors play a role in determining milk volume, composition, and the ability to sustain lactation (Han et al., 2019; Wheelock et al., 2010). External factors, such as stress, exposure to pollutants, and overall health, can also impact lactation.\n\nThe onset and maintenance of lactation are tightly regulated by endocrine changes that occur during pregnancy and the postpartum period. During pregnancy, elevated levels of estrogen and progesterone prepare the mammary glands for lactation but inhibit milk secretion (Neville & Morton, 2001; Sadovnikova et al., 2020). Postpartum, the significant drop in progesterone levels after delivery, combined with the continued high levels of prolactin and the initiation of oxytocin release through suckling, ensures the successful transition to active milk production and ejection (Crowley, 2014). Understanding the intricate anatomy and physiology of lactation is crucial for supporting breastfeeding, helping healthcare providers offer better guidance and interventions to ensure successful breastfeeding and maximize health benefits for both mother and child.\n\nPathophysiology of the effects of heat on lactation\n\nMany of the studies done to examine the effects of heat stress on lactation have been conducted in non-human mammalian animal models; however, it is possible to extrapolate the effects of heat stress on lactating humans due to the similarities between human and bovine and porcine animal models.\n\nHeat stress can impair lactation by affecting both the endocrine system and the overall physiological state of lactating mammals (Han et al., 2019). Elevated temperatures can lead to dehydration, which significantly impacts the body’s ability to produce and secrete milk. Dehydration reduces blood volume and flow to the mammary glands, thereby decreasing the supply of essential nutrients and precursors required for milk synthesis (Wheelock et al., 2010). This reduction in blood volume can lead to decreased renal function and reduced clearance of metabolic waste, further complicating the physiological state of the lactating animal.\n\nAdditionally, heat stress can alter the hormonal balance necessary for lactation (Han et al., 2019; Wheelock et al., 2010). Prolactin and oxytocin levels can be disrupted by stress hormones such as cortisol, which is elevated in response to heat stress. Cortisol can inhibit the release of prolactin from the anterior pituitary gland, which is crucial for the synthesis of milk proteins, lactose, and lipids. This inhibition can lead to a significant decrease in milk volume (Rhoads et al., 2010; Ponchon et al., 2017; Syam et al., 2022). Moreover, cortisol can affect the release of oxytocin from the posterior pituitary gland, impairing the milk ejection reflex. Without adequate oxytocin, the myoepithelial cells surrounding the alveoli fail to contract effectively, reducing the efficiency of milk expulsion from the mammary glands (Haaksma et al., 2011).\n\nHeat stress can also increase the levels of catecholamines (epinephrine and norepinephrine), which are stress-related hormones that further inhibit oxytocin release and exacerbate the difficulties in milk ejection (Haldar & Bade, 1981). The combined effect of elevated cortisol and catecholamines can lead to a cycle of stress and reduced lactation, impacting the mother’s ability to breastfeed effectively.\n\nThe physiological stress from elevated temperatures can also lead to systemic inflammation, which can affect the mammary glands. Inflammatory cytokines such as IL-6 and TNF-α may increase, potentially disrupting normal cellular functions within the mammary glands and further impairing milk production and quality (Abdelnour et al., 2019; Chen et al., 2023). Additionally, heat stress may exacerbate underlying health conditions, such as hypertension or diabetes, which can further complicate lactation.\n\nIn summary, the impact of heat stress on lactating individuals is multifaceted, involving dehydration, hormonal imbalances, systemic inflammation, and potential exacerbation of pre-existing conditions. These factors collectively impair milk production and ejection, posing significant challenges for breastfeeding mothers in hot climates.\n\nExcess heat’s effects on lactating infants. For infants, the impact of heat on lactation can be severe. Reduced milk production due to heat stress can lead to insufficient nutrient intake, affecting the infant’s growth and development. Breast milk provides essential hydration, particularly in hot climates, and any reduction in its availability can increase the risk of dehydration in infants (Bernabucci et al., 2013). Furthermore, the quality of breast milk can be compromised under heat stress, with potential changes in its composition affecting the balance of nutrients, antibodies, and other bioactive components critical for the infant’s health (Bernabucci et al., 2013).\n\nOverall, health risks. Both lactating individuals and their infants face increased health risks during periods of high heat. Lactating individuals experiencing heat stress may suffer from symptoms such as fatigue, dizziness, and heat exhaustion, which can affect their ability to care for their infants effectively (Lefebvre et al., 2024). For infants, the combination of reduced milk intake and increased susceptibility to heat can lead to severe dehydration, electrolyte imbalances, and heat-related illnesses, potentially requiring medical intervention (Lefebvre et al., 2024).\n\nIn summary, understanding the pathophysiology of the effects of heat on lactation is crucial for developing strategies to mitigate these risks. Ensuring adequate hydration, maintaining a cool environment, and monitoring both lactating individuals and their infants for signs of heat stress are essential steps in safeguarding their health during periods of elevated temperatures.\n\nTransitioning from the biological complexities of human lactation to its wider contexts, human lactation also has profound socioeconomic implications. The economic impact of lactation is substantial, as human milk production contributes significantly to national economies by reducing healthcare costs (Alex et al., 2020). Lactation adequacy is influenced by social and health factors, underscoring the critical role of breastfeeding in developing countries (Kabotyanski et al., 2006). The evolutionary and environmental influences on human lactation highlight its psychosocial, nutritional, and economic significance (Neville & Morton, 2001; Sadovnikova et al., 2020). Various demographic, physical, social, and psychological variables influence breastfeeding duration (Trott et al., 2012). Additionally, the nutritional and health aspects of human lactation underscore its importance in both developed and developing countries (Crowley, 2014; Neville & Morton, 2001).\n\n\nIntersections between climate change and human lactation\n\nThis review examines the significant impacts of climate change and excess heat on human lactation, highlighting unique challenges that require thorough investigation. Previous research has indicated that environmental factors, such as extreme temperatures and food scarcity, can impact lactation. However, there is a notable gap in focused studies addressing how these climate-induced changes specifically affect lactating individuals. This review aims to fill that gap by providing a comprehensive analysis of the intersection between global climate change and human lactation, emphasizing the urgent need for targeted mitigation strategies to support lactating individuals in a changing climate.\n\n\nMethodology\n\nThe approach taken to conduct this narrative review on the intersections between global climate change, extreme heat, and human lactation focused on identifying challenges and proposing effective mitigation strategies. The literature search strategy involved several databases and search engines, including PubMed, Web of Science, Scopus, Google Scholar, and JSTOR, as well as Google and Bing for grey literature and policy documents. The search terms used encompassed core concepts such as “global climate change,” “human lactation,” “breastfeeding,” “maternal health,” and “infant health,” along with specific aspects like “temperature extremes,” “food security,” “water scarcity,” “malnutrition,” “heat stress,” “environmental toxins,” “pollutants,” “natural disasters,” “displacement,” “vulnerabilities,” and “public health strategies.” Combinations and Boolean operators, such as “climate change AND lactation,” “heat stress OR dehydration AND breastfeeding,” and “environmental toxins AND breast milk,” were employed to refine the search.\n\nThe inclusion criteria for the review consisted of peer-reviewed articles, case reports, epidemiological studies, policy analyses, and reviews; publications in English; studies focused on the impacts of climate change on lactation or maternal and infant health; and relevant policy documents and reports from reputable organizations like WHO and UNICEF. Conversely, the exclusion criteria eliminated papers not directly related to climate change or lactation, non-English publications, articles without full-text access, and opinion pieces lacking empirical evidence.\n\n\nReview\n\nClimate change significantly impacts health and nutrition, particularly for vulnerable populations. One critical area of concern is the effect of temperature extremes on maternal and infant health (Bao et al., 2020; Lefebvre et al., 2024; Han et al., 2019). Extreme temperatures can lead to increased incidences of heat stress, dehydration, and heat-related illnesses, which are particularly dangerous for pregnant women and infants (Bao et al., 2020). Pregnant women exposed to high temperatures have a higher risk of adverse birth outcomes, such as preterm birth and low birth weight. Infants are also at risk as their thermoregulatory systems are not fully developed, making them more susceptible to heat-related illnesses (Bao et al., 2020).\n\nA range of studies have highlighted the significant impact of temperature extremes on maternal and infant health. Research has found that heat exposure during pregnancy can lead to adverse outcomes such as preterm birth, low birth weight, and stillbirth (Weng et al., 2017). Further studies emphasized the increased risk of maternal hospitalization and infant mortality associated with extreme heat (Ponchon et al., 2017; Syam et al., 2022). Expanded findings have identified a link between prenatal exposure to extreme temperatures and severe maternal morbidity. Additional research has highlighted the disproportionate impact of extreme temperatures on Black and Hispanic mothers, suggesting that these disparities may be exacerbated by future temperature increases (Haaksma et al., 2011; Haldar & Bade, 1981).\n\nMoreover, climate change disrupts food security and nutrition. Changes in weather patterns, such as prolonged droughts and increased frequency of extreme weather events, can negatively affect agricultural productivity, leading to food shortages and increased prices (Abdelnour et al., 2019). This can result in malnutrition, especially in communities that rely heavily on subsistence farming (Chen et al., 2023; Bernabucci et al., 2013). The nutritional quality of food can also be compromised due to climate-induced changes in soil health and crop nutrient content, further exacerbating the problem (Maheshwari, 2022).\n\nWater scarcity, another consequence of climate change, has significant implications for hydration and lactation (Geissler et al., 1978; Kim & Yi, 2020). Adequate water intake is crucial for maintaining maternal health and ensuring sufficient milk production (Geissler et al., 1978). In regions facing water shortages, women may struggle to stay hydrated, impacting their overall health and ability to lactate effectively. This situation is particularly dire in areas where access to clean water is already limited, and the added stress of water scarcity can severely affect both maternal and infant health (Prentice & Prentice, 1995).\n\nLactating females face increased physiological demands, making them particularly vulnerable to the impacts of climate change. During lactation, women require additional calories, nutrients, and hydration to produce sufficient breast milk (Cowie et al., 1979). Climate-related challenges, such as heat stress and water scarcity, can hinder their ability to meet these increased demands, thereby affecting milk production and quality (Prentice & Prentice, 1995; Thulier & Mercer, 2009).\n\nIn addition to socio-economic disparities, climate-related stressors, such as natural disasters and displacement, significantly impact lactating individuals. Different populations experience varying levels of vulnerability to climate change, with low-income and rural communities often being the most affected. These populations typically have limited access to healthcare, nutritious food, and clean water, making it difficult to cope with the additional stressors brought on by climate change (Delgado et al., 1985). Rural areas may face increased isolation during extreme weather events, further limiting their access to necessary resources and support (Casey & Hambidge, 1983).\n\nMoreover, the influence of heat stress on milk production and composition is a critical area of concern. Climate-related stressors, such as natural disasters and displacement, also significantly impact lactating females. Natural disasters can lead to the displacement of communities, disrupting access to food, water, and healthcare (Kuehn & McCormick, 2017). Displacement can also result in increased exposure to unsanitary conditions and infectious diseases, which can negatively affect maternal and infant health (Kuehn & McCormick, 2017; Kim et al., 2019). Ultimately, the stress and trauma associated with displacement can further impair lactation, leading to a decline in milk production and quality.\n\nThe influence of heat stress on milk production and composition is a critical area of concern. High temperatures can lead to dehydration, which reduces a woman’s ability to produce milk (Kim & Yi, 2020). Heat stress can also alter the composition of breast milk, potentially reducing its nutritional value and affecting infant growth and development. Ensuring adequate hydration and managing heat exposure are essential for maintaining effective lactation under changing climatic conditions.\n\n\nHealth disparities and health equity related to climate change\n\nHealth disparities refer to the differences in health outcomes and their determinants between segments of the population, which are often driven by social, economic, and environmental disadvantages (Braveman et al., 2021). Health equity, on the other hand, is the principle of providing fair opportunities for health and wellness, aiming to reduce and eliminate disparities (Braveman, 2014). In the context of climate change and human lactation, these disparities are particularly pronounced, with marginalized populations bearing a disproportionate burden of adverse health outcomes (Limaye, 2022; Smirnova et al., 2023).\n\nSocioeconomic status (SES) is a major determinant of health outcomes, including those related to lactation (Pérez-Escamilla & Moran, 2022). Low-income families often have limited access to healthcare, nutritious food, and clean water, all of which are essential for maintaining optimal health and lactation (Adler & Newman, 2002). Climate change exacerbates these challenges by increasing the frequency and severity of extreme weather events, such as droughts and heatwaves, which disproportionately affect low-income communities (Gregory et al., 2023). These events can disrupt access to essential resources, further compromising the health of lactating mothers and their infants.\n\nGeographic location also plays a crucial role in health disparities. Rural and remote areas, particularly in developing countries, often lack adequate healthcare infrastructure and resources (Reilly, 2021). Breastfeeding support disparities are apparent, particularly in rural areas where access is limited and inequities are tied to socioeconomic status (Grubesic & Durbin, 2017). These regions are more vulnerable to the impacts of climate change, including water scarcity and food insecurity, which directly affect lactating individuals. Urban areas, while having better access to healthcare, are not immune to disparities. Low-income urban neighborhoods may face challenges such as heat islands and poor air quality, further impacting maternal and infant health (Howarth & Eiser, 2023).\n\nRacial and ethnic minorities are disproportionately affected by climate change and its health impacts (Weaver et al., 2023). In many regions, Black, Indigenous, and People of Color (BIPOC) communities face systemic barriers to healthcare and are more likely to live in areas with higher exposure to environmental hazards. These communities often experience higher rates of pre-existing conditions, which can be exacerbated by climate-induced stressors, further complicating lactation and infant health (Burbank et al., 2023; Morello-Frosch et al., 2011). For example, Black and Hispanic mothers have been shown to have higher rates of adverse birth outcomes linked to extreme heat exposure (Borrell et al., 2022; Dzekem et al., 2023).\n\nThe concept of intersectionality highlights how various aspects of a person’s identity, such as race, gender, socioeconomic status (SES), and geographic location, intersect to create unique experiences of disadvantage and privilege (Williams et al., 2012). This framework is critical for understanding the compounded vulnerabilities faced by lactating individuals who belong to multiple marginalized groups. For instance, a low-income, rural, Black mother may encounter a multitude of barriers that singularly and collectively impact her health and lactation experience (MacGregor & Hughes, 2010). Firstly, limited access to healthcare is a significant challenge for low-income, rural populations (Asiodu et al., 2021). Healthcare facilities may be scarce and distant, leading to delays in receiving necessary prenatal and postnatal care. This can hinder the establishment and maintenance of breastfeeding. Additionally, financial constraints may limit access to resources such as lactation consultants, breast pumps, and nutritional support, all of which are vital for successful breastfeeding (Francis et al., 2020; Gorman, 2020).\n\nSecondly, exposure to extreme weather conditions, exacerbated by climate change, poses additional risks. In rural areas, infrastructure may be inadequate to cope with extreme heat, affecting the availability of clean water and cooling mechanisms. This can lead to dehydration and heat stress, further complicating the physiological process of lactation and the overall health of the mother and infant (Lusambili & Nakstad, 2023; Roos et al., 2021).\n\nLastly, systemic racism adds another layer of complexity. Discriminatory practices within the healthcare system can result in biased treatment and a lack of culturally competent care. This may lead to mistrust in healthcare providers and reluctance to seek help, thereby affecting the quality of care received (Witt et al., 2022). Furthermore, social determinants of health, such as housing instability, food insecurity, and limited educational opportunities, disproportionately affect Black communities, amplifying the challenges faced by low-income, Black mothers (Brailey & Slatton, 2024; Greenberg et al., 2022).\n\nIn summary, intersectionality provides a comprehensive lens through which to view the compounded adversities faced by lactating individuals from multiple marginalized backgrounds. Addressing these layered challenges requires a multifaceted approach that considers the intricate interplay of race, gender, SES, and geographic location to improve health outcomes and support equitable lactation practices (Carter et al., 2021).\n\nMalnutrition in lactating women can lead to a decrease in milk production and a reduction in the quality of breast milk (Runkle et al., 2022). Dehydration further complicates this issue, as it not only reduces milk volume but can also affect the mother’s overall health, making it more difficult for her to care for her infant (Kim & Yi, 2020). Addressing malnutrition and ensuring access to clean water are crucial for supporting lactating women in a changing climate.\n\nIn addition to the challenges of malnutrition and dehydration, environmental toxins and pollutants, increasingly prevalent due to climate change, also affect milk quality (Rylander et al., 2013). Pollutants such as heavy metals and chemicals can accumulate in breast milk, posing health risks to infants (Hasan & Hussain, 2020). Climate change can exacerbate the spread of these toxins through increased flooding, which can contaminate water supplies and agricultural lands (Kiprutto et al., 2015). Monitoring and mitigating exposure to environmental toxins are essential steps in protecting maternal and infant health.\n\nNumerous studies document the effects of climate change on lactating females, providing valuable insights into this critical issue. For instance, research has shown that heat stress can significantly reduce milk production and alter its composition, while malnutrition and dehydration further exacerbate these effects (Hema et al., 2023; Lake et al., 2012). These studies highlight the importance of addressing climate-related challenges to support lactating women and their infants.\n\nAnalysis of data from various geographical regions reveals the widespread impact of climate change on lactation. In regions with high temperatures and frequent droughts, such as parts of Africa, Central and South America, and South Asia, lactating women face significant challenges in maintaining adequate hydration and nutrition. These regions also often experience food insecurity, further complicating efforts to support maternal and infant health (Sultana & Mostafa, 2023; DeNicola et al., 2015; Xie et al., 2022; Bentley, 1998; Butte et al., 2001). Understanding regional differences in vulnerability and adaptive capacity is essential for developing effective interventions.\n\nCase studies highlight critical issues and adaptive responses to climate change impacts on lactation. For example, in some communities, local initiatives have been implemented to provide clean water and nutritional support to lactating women (Josefson et al., 2023). These initiatives often involve community-based education programs and partnerships with local organizations to ensure sustainable access to resources (Josefson et al., 2023; Chen et al., 2020; Winter et al., 2019). By examining these case studies, we can identify successful strategies and best practices that can be adapted and implemented in other regions facing similar challenges.\n\n\nAddressing health disparities and advancing health equity in climate change and lactation\n\nAddressing health disparities and promoting health equity requires targeted, multi-faceted interventions. Strategies to mitigate the impact of climate change on lactating individuals must consider the social determinants of health and aim to reduce systemic barriers. Key recommendations include improving access to healthcare by enhancing healthcare infrastructure in underserved areas to provide comprehensive maternal and infant care, including support for lactating mothers. Ensuring food and water security is crucial, and this can be achieved by implementing policies and programs that secure access to nutritious food and clean water, particularly in regions vulnerable to climate change. Enhancing education and awareness involves developing community-based education programs to raise awareness about the impacts of climate change on lactation and promoting strategies to mitigate these effects. Strengthening social support networks is essential and can be facilitated by creating support groups and networks for lactating mothers, providing emotional and practical support to navigate climate-related challenges. Finally, advocating for policy change is necessary to ensure the inclusion of maternal and child health considerations in climate policies at local, national, and international levels, making sure that climate adaptation and mitigation strategies address the unique needs of marginalized populations.\n\nResearch examining the effects of extreme heat and climate change on lactating humans is sparse. Much of the existing research focuses on animal models, highlighting the need to examine these phenomena in lactating humans. Additionally, addressing health disparities and promoting health equity requires targeted, multi-faceted interventions. The intersection of climate change and human lactation underscores the importance of addressing health disparities and promoting health equity. By recognizing and mitigating the compounded vulnerabilities faced by marginalized populations, we can develop more effective and equitable public health interventions. Ensuring that all lactating individuals have the resources and support needed to thrive in a changing climate is essential for the health and well-being of both mothers and infants.\n\nNutritional support is crucial for lactating females, especially in regions affected by climate change. Interventions should focus on providing access to nutrient-rich foods and supplements to meet the increased caloric and nutritional demands of lactation. Governments and organizations should implement policies to secure food and water supplies in vulnerable regions. This includes investing in sustainable agriculture, improving water management systems, and providing emergency food and water supplies during climate-related disasters. Public health initiatives should aim to reduce exposure to environmental toxins that can contaminate breast milk. This includes monitoring and regulating pollutants, educating communities about safe practices, and providing resources to minimize exposure. Community-based programs can provide essential support and education to lactating mothers. These programs can offer breastfeeding education, nutritional counseling, and access to clean water and healthcare services, enhancing resilience against climate-related stressors.\n\nClimate policies should explicitly address the needs of lactating women, ensuring they receive the necessary support and resources to maintain healthy lactation despite climate challenges. Advocates should push for the inclusion of maternal and child health considerations in climate action plans at local, national, and international levels. This ensures that the unique needs of lactating women are not overlooked in broader climate initiatives. Increased funding is needed to support research on the impacts of climate change on lactation. This includes epidemiological studies, interventions, and policy analyses to develop effective strategies for supporting lactating women in a changing climate.\n\nThe social-ecological model examines how individual, interpersonal, organizational, community, and policy factors interact to influence health outcomes (Figure 1) (Khajehaminian et al., 2019). Applying this model to lactation and climate change helps identify the multiple levels of influence and potential intervention points. At the individual level, educating lactating women about the impacts of climate change and strategies for maintaining health and milk production can enhance personal resilience.\n\nNote. This model illustrates the multi-layered factors influencing lactation, from individual to societal levels. The innermost circle represents individual factors, such as the desire to breastfeed and access to climate control. The next layers include interpersonal support from family and friends, community values and investments, and, finally, societal and government actions such as funding and policy for climate change mitigation and maternal/child health. This framework highlights the complexity of factors that need to be addressed to support lactating individuals in a warming world.\n\nEncouraging behaviors such as staying hydrated, consuming nutrient-rich foods, and managing heat exposure can help lactating women adapt to climate stressors. Strengthening social support networks can provide emotional and practical support to lactating women, helping them cope with climate-related challenges. Involving family members and partners in efforts to support lactation can enhance the effectiveness of adaptive strategies and provide additional resources and support.\n\nAt the organizational level, workplaces should adopt policies that support lactating mothers, such as providing flexible schedules, lactation rooms, and access to clean water and nutritious food. Healthcare facilities should be equipped to handle the impacts of climate change, ensuring they can provide adequate care and support to lactating women. Communities can develop interventions to ensure that resources such as clean water, food, and healthcare are available during climate-related events. Local support groups and peer counselors can offer practical advice, emotional support, and resources to lactating women, helping them navigate climate challenges.\n\nAdvocacy efforts should focus on integrating lactation considerations into climate policies at national and international levels, ensuring that the needs of lactating women are prioritized. Climate adaptation and mitigation strategies should include specific measures to protect maternal and child health, addressing the unique vulnerabilities of lactating women. Collaboration across disciplines can lead to more effective strategies for addressing the impacts of climate change on lactation. Community-driven initiatives can provide tailored solutions that align with broader policy goals, ensuring that local needs and perspectives are integrated into climate and health strategies. By addressing the issue of climate change and lactation through a social-ecological lens, we can develop comprehensive strategies that support lactating women at multiple levels of influence. This holistic approach is essential for building resilience and ensuring the health and well-being of both mothers and infants in a changing climate.\n\nFuture research should focus on identifying and addressing gaps in our understanding of how climate change affects lactation in humans. This includes studying the physiological, nutritional, and environmental factors that influence lactation under different climatic conditions. Longitudinal and cross-sectional studies are needed to examine the long-term impacts of climate change on lactation and maternal and infant health. These studies can provide valuable insights into how climate-related stressors affect lactation over time. Interdisciplinary research is essential to fully understand the complex interactions between climate change, nutrition, and public health. Collaboration between climate scientists, nutritionists, and public health experts can lead to more comprehensive and effective strategies for supporting lactating women.\n\n\nConclusion\n\nClimate change poses significant threats to human lactation, primarily through increased heat stress, dehydration, and food and water insecurity. These factors can reduce milk production and alter its composition, impacting infant health. The hormonal effects of heat stress, malnutrition, and exposure to environmental toxins further complicate lactation. Numerous studies have documented the adverse effects of climate change on lactation. For instance, research indicates that heat stress can significantly reduce milk production and alter its composition, while malnutrition and dehydration further exacerbate these effects. Case studies from various regions highlight critical issues such as food insecurity and water scarcity, demonstrating the widespread impact of climate change on lactating females.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nAbdelnour SA, Abd El-Hack ME, Khafaga AF, et al.: Stress biomarkers and proteomics alteration to thermal stress in ruminants: A review. J. Therm. Biol. 2019; 79: 120–134. PubMed Abstract \| Publisher Full Text\n\nAhmed M: Introduction to modern climate change. Sci. Total Environ. 2020; 734(2020): 139397. Publisher Full Text\n\nAdler NE, Newman K: Socioeconomic disparities in health: Pathways and policies. Health Aff. 2002; 21(2): 60–76. Publisher Full Text\n\nAlex A, Bhandary E, McGuire KP: Anatomy and physiology of the breast during pregnancy and lactation. Adv. Exp. Med. Biol. 2020; 1252: 3. 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Publisher Full Text\n\nSriraman NK: The nuts and bolts of breastfeeding: Anatomy and physiology of lactation. Curr. Probl. Pediatr. Adolesc. Health Care. 2017; 47(12): 305–310. PubMed Abstract \| Publisher Full Text\n\nSmirnova N, Shaver AC, Mehta AJ, et al.: Climate change, air quality, and pulmonary health disparities. Clin. Chest Med. 2023; 44(3): 489–499. PubMed Abstract \| Publisher Full Text\n\nSultana MS, Mostafa MG: Impact of climate change on economic development associated with water scarcity: A review. Journal of Sustainability and Environmental Management. 2023; 2(3): 158–169. Publisher Full Text\n\nSyam A, Qasim M, Iskandar I, et al.: Cortisol, prolactin, and breastmilk volume; A promising pattern for reducing postpartum depression. Open Access Maced. J. Med. Sci. 2022; 10(B): 1399–1405. Publisher Full Text\n\nThulier D, Mercer J: Variables associated with breastfeeding duration. J Obstet Gynecol Neonatal Nurs. 2009; 38(3): 259–268. Publisher Full Text\n\nTrott JF, Schennink A, Petrie WK, et al.: Triennial lactation symposium: Prolactin: The multifaceted potentiator of mammary growth and function. J. Anim. Sci. 2012; 90(5): 1674–1686. PubMed Abstract \| Publisher Full Text\n\nVillalpando S, De Santiago S: The biological bases of human lactation. Boletin Medico Del Hospital Infantil De Mexico. 1993; 50(12): 889–897. PubMed Abstract\n\nWeaver E, Gad L, Zota AR: Climate change as a threat multiplier to environmental reproductive justice. Semin. Perinatol. 2023; 47(8): 151843–151843. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWeng Y-H, Yang C-Y, Chiu Y-W: Adverse neonatal outcomes in relation to ambient temperatures at birth: A nationwide survey in Taiwan. Arch. Environ. Occup. Health. 2017; 73(1): 48–55. PubMed Abstract \| Publisher Full Text\n\nWheelock JB, Rhoads RP, VanBaale MJ, et al.: Effects of heat stress on energetic metabolism in lactating Holstein cows. J. Dairy Sci. 2010; 93(2): 644–655. PubMed Abstract \| Publisher Full Text\n\nWilliams DR, Kontos EZ, Viswanath K, et al.: Integrating multiple social statuses in health disparities research: The case of lung cancer. Health Serv. Res. 2012; 47(3pt2): 1255–1277. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWinter JM, Bowen FL, Partridge TF, et al.: Future extreme event risk in the rural northeastern United States. Ann. Am. Assoc. Geogr. 2019; 109(4): 1110–1130. Publisher Full Text\n\nWitt RE, Malcolm M, Colvin BN, et al.: Racism and quality of neonatal intensive care: Voices of Black mothers. Pediatrics. 2022; 150(3). PubMed Abstract \| Publisher Full Text\n\nXie Z, Lin X, Lu X, et al.: Water intake and its influence factors among pregnant and lactating women in some areas of China in 2020. PubMed. 2022; 51(3): 367–373. PubMed Abstract \| Publisher Full Text\n\nZhang J, Chen H, Fang X, et al.: Warming-induced hydrothermal anomaly over the Earth’s three poles amplifies concurrent extremes in 2022. NPJ Climate and Atmospheric Science. 2024; 7(1): 8. Publisher Full Text" }	[ { "id": "323978", "date": "26 Sep 2024", "name": "Laura J Brown", "expertise": [ "Reviewer Expertise global health research", "focussed on environmental links with women's health", "including breastfeeding and violence against women." ], "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\nWhilst the intersection of climate change and lactation is an interesting area and one of growing importance, this manuscript needs significant revisions to make an important contribution.\nMajor issues (must be addressed): There is a lot of repetition, with some points being made in multiple places, and in some cases with the exact same wording, resulting in a lack of structure and making the arguments hard to follow. For example, in the Human lactation: biological and socioeconomic significance section on page 3, the second and third paragraphs are very similar. Another example is on page 4, some of the hormonal information in the third paragraph appears to be repeated. This whole Physiology of human lactation section should be sense-checked and condensed. Another example is on page 6, where the first paragraph says “Pregnant women exposed to high temperatures have a higher risk of adverse birth outcomes, such as preterm birth and low birth weight” and the second paragraph says “Research has found that heat exposure during pregnancy can lead to adverse outcomes such as preterm birth, low birthweight, and stillbirth”. Another example is the last two paragraphs on page 6 starting with “Moreover, the influence of heat stress on milk production and composition is a critical area of concern” and “The influence of heat stress on milk production and composition is a critical area of concern”, respectively. There are several examples throughout the manuscript where this occurs- please be sure to proofread your whole manuscript properly and edit out unnecessary duplication.\nSupporting references are missing in several places throughout the paper, e.g.:\nPage 4, after “External factors, such as stress, exposure to pollutants, and overall health, can also impact lactation.” Page 4, after “This reduction in blood volume can lead to decreased renal function and reduced clearance of metabolic waste, further complicating the physiological state of the lactating animal.” Page 4, last para, after “Additionally, heat stress may exacerbate underlying health conditions, such as hypertension or diabetes, which can further complicate lactation.” Also, some explanatory detail and illustrative examples would be helpful here. Page 5, second para, after “Reduced milk production due to heat stress can lead to insufficient nutrient intake, affecting the infant’s growth and development.” Page 6, para 2, after “Expanded findings have identified a link between prenatal exposure to extreme temperatures and severe maternal morbidity” – an illustrative example would also help here. Page 6, second to last para, after “Ultimately, the stress and trauma associated with displacement can further impair lactation, leading to a decline in milk production and quality.” Page 7, Intersectionality and vulnerability section, first para, after “Healthcare facilities may be scarce and distant, leading to delays in receiving necessary prenatal and postnatal care. This can hinder the establishment and maintenance of breastfeeding.”\nThroughout the whole Pathophysiology of the effects of heat on lactation section, it would be helpful to more clearly highlight where the evidence is coming from - e.g. which animal models are yielding which statements, such as saying something like, “studies with cows have suggested that....” etc. Providing enough descriptive detail is especially important in your review section (p6 onwards), please make sure you describe the reviewed evidence in more detail – statements like “additional research” and “further studies” are too vague, what kind of studies, what contexts, with how many participants, mention effect sizes etc. I know this isn’t a systematic review, but some additional explanatory detail would really help bolster your argument in places.\nBe sure to check for clarity in your subheadings. On Page 5, “Excess heat’s effects on lactating infants” and “Overall, health risks” need particular attention. The infants aren't the ones lactating, do you mean to say something like \"The impact of heat on lactation for infants\" and then “Overall health risks”?\nYour introduction only focuses on extreme temperatures/heat stress, and it would be helpful to integrate something about food scarcity or the relationship between maternal diet and lactation there too.\nGiven you've been transparent about your methods, which seem fairly systematic, it seems logical to include an indication of the number of studies included in your review to indicate how well-researched this area is.\nIn your review section, on page 6, the third and fourth paragraphs on food security and water scarcity need developing. The paragraph on food security and nutrition doesn’t explain sufficiently how this in turn affects lactation; you're missing the explicit connection between maternal diet and milk production and composition. The paragraph on water scarcity would be strengthened by describing how the stressful situations related to water scarcity in turn impact the physiology of lactation.\nThe Addressing health disparities and advancing health equity in climate change and lactation section on p8 and 9 - this paragraph needs supporting evidence behind its recommendations. For example, in your mitigation strategies subsection, it is not clear where these recommendations are coming from, these should be grounded in the evidence you've collected, and/or contextualised in the broader literature, so I would expect to see some citations here too.\nMinor issues: 2nd paragraph, page 4 – “The composition of human milk is dynamic and influenced by several factors, including maternal diet, body composition, genetics, and environmental factors.” – it’s also affected by infant age.\nYou could include some citations after this statement on page 4 “Many of the studies done to examine the effects of heat stress on lactation have been conducted in non-human mammalian animal models;”\nYou mention bovine and porcine animal models, but also, there are at least some relevant studies done with animals more closely related to humans, e.g. other primates - see for example https://pubmed.ncbi.nlm.nih.gov/22034080/ Hinde & Milligan 2011 . It’s good that you reflect on the limitation of animal models a little at the bottom of page 8.\nBe mindful of language used – e.g. first paragraph, page 5 – “breastfeeding mothers” – it might be worth noting that mothers aren't the only ones who lactate - what about wet nurses? what about milk donors, what about chestfeeders who may not identify as women or mothers?\nStructure wise, the paragraph on page 5 beginning “Transitioning from the biological complexities of human lactation to its wider context…” structure wise sits a little oddly here without a subheading of its own. You also already make the point about healthcare costs at the beginning of this section.\nThere are several instances where your statements are vague and would benefit from some illustrative examples, e.g.:\non 5th para of page 5, “Lactation adequacy is influenced by social and health factors, underscoring the critical role of breastfeeding in developing countries” and “The evolutionary and environmental influences on human lactation highlight its psychosocial, nutritional, and economic significance” and “Various demographic, physical, social, and psychological variables influence breastfeeding duration” – these points would be strengthened with some examples. Also, all of these factors may plausibly influence breastfeeding initiation, not just duration. See for example, https://dx.doi.org/10.1111/mcn.12851 and https://academic.oup.com/emph/article/2017/1/120/4086160 “heat related illnesses” on page 6, first para, please can you give some examples here too\nWas there any discussion of extreme cold in the literature, or is it all extreme heat?\nPage 7, last sentence of intersectionality and vulnerability first para: “Additionally, financial constraints may limit access to resources such as lactation consultants, breast pumps, and nutritional support, all of which are vital for successful breastfeeding” – simply not true, many people can successfully breastfeed without all of this.\nPage 8, Additional evidence section, third para, “By examining these case studies, we can identify successful strategies and best practices that can be adapted and implemented in other regions facing similar challenges.” - it is unclear if you are saying that's what you've done here, or whether this is just a general recommendation?\nPolicy recommendations para on page 9 - This is all just repeated in the social-ecological analysis and future research directions sections below, so I suggest cutting this.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Partly\n\nAre all factual statements correct and adequately supported by citations? Partly\n\nIs the review written in accessible language? Partly\n\nAre the conclusions drawn appropriate in the context of the current research literature? Partly", "responses": [] }, { "id": "334272", "date": "14 Dec 2024", "name": "Cecília Tomori", "expertise": [ "Reviewer Expertise breastfeeding", "maternal child health", "global health", "health equity" ], "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 appreciate the opportunity to review this manuscript on an important topic. The main challenge is that I am not quite seeing how this review contributes to the literature in light of other similar recent work on climate change and breastfeeding that has conceptualized the field. For instance, we have had a recent review in JHL by Cerceo et al 2023 that summarizes key areas of this work, as well as recent reviews on heat and infant feeding (Edney et al), food insecurity and breastfeeding (Frontiers in Public Health 2024), water security and child feeding (Schuster et al), just to mention a few. Additionally, the analysis of the review lacks some of the broader considerations that others have already addressed (see below) and would be expected here. If this paper is further revised, I suggest the following:\nCondense the background to a brief overview with updated citations on breastfeeding. The 2023 Lancet Breastfeeding Series does a nice job providing this overview, including structural barriers that prevent many women from achieving their breastfeeding goals – this is a hugely significant issue that the authors don’t reckon with in their analysis. This is very problematic since the paper aims to frame the review in the context of the social ecological model and rightfully emphasizes health inequities. This goal cannot be achieved without considering the landscape of breastfeeding in a broader context. Additionally, there is no consideration of how these structural barriers result in formula feeding, which makes infants particularly vulnerable to any situation without power or safe water (common conditions globally that are becoming particularly common with climate-driven disasters). In a review focused on climate change and breastfeeding, this is absolutely a critical issue to consider. There is wealth of literature on these issues that is not cited here. Nor is there any mention of the climate impacts of formula production (lots from Smith and colleagues on this). Cut the section on the physiology of breastfeeding – as this not necessary and is part of most textbooks on lactation Methods – more details on the screening process and the analysis of the results should be included. A PRISMA diagram would be helpful and expected in a review. A summary table of the results should also be presented with brief details on the studies discussed. Each section of the results needs more detail on the actual studies that are included, their methods, and populations under consideration. Gaps in the literature should be discussed in each section as well. The discussion section would need to be revisited after the above conceptual and methodological issues are addressed.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Partly\n\nAre all factual statements correct and adequately supported by citations? Partly\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Partly", "responses": [] }, { "id": "348312", "date": "19 Dec 2024", "name": "Pramila Menon", "expertise": [ "Reviewer Expertise Pediatrician /Lactation consultant/Public health Nutritionist MD IBCLC PG Dip PHN FAIMER fellow" ], "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 narrative review comprehensively covers up-to-date articles, giving clarity and a deep understanding of the topic. The facts brought by the authors are correct, and there is a need for an hour. Evidence-based citations adequately support these statements. The article is written in appropriate language. The conclusions match the current research context. This will help to formulate the policy supporting breastfeeding for mothers and babies\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-993
https://f1000research.com/articles/12-1034/v1	24 Aug 23	{ "type": "Research Article", "title": "The interface of dementia and physical disability; causative factors and associations in the elderly population from Pakistan: evidence from the nationally representative cross-sectional Demographic and Health Survey (DHS, 2017-18) of Pakistan", "authors": [ "Amna Khalid", "Asima Karim", "Firdous Ahmad", "Rizwan Qaisar", "Azhar Hussain", "Asima Karim", "Firdous Ahmad", "Rizwan Qaisar", "Azhar Hussain" ], "abstract": "Objectives: The interface of dementia and physical disability is poorly characterized in the elderly population. We used the 2017-2018 Demographic and Health Survey (DHS) (PKPR71FL) to investigate the prevalence and interface of dementia and physical disability in Pakistan. Study design: A cross-sectional study design was used by analyzing the latest DHS conducted for Pakistan from 22 November 2017 to 30 April 2018. Methods: We used Gamma correlation to evaluate the effects of several demographic and socioeconomic factors on dementia and physical disability in 2,899 males and 2,284 females. Results: The prevalence of both forms of disabilities increased with advancing age with a higher preponderance among females. Being unmarried, not educated, having a smaller household, and poverty was associated with a greater disability. Having four or more children was associated with a higher disability in men but lower disability in women. The prevalence of disability was highest in Punjab and lowest in Balochistan. Conclusion: Altogether, we describe several factors associated with the burden of disability in Pakistan. Community-based interventions are recommended to reduce the disability of the elderly in Pakistan.", "keywords": [ "Dementia", "physical disability", "comorbidities." ], "content": "Introduction\n\nCognitive impairment and physical disability are common occurrences in the elderly population.1 Both conditions are partly driven by age-related degenerative processes of the nervous and muscular systems.2 A potential coupling is suggested wherein the presence of dementia exacerbates muscle loss and physical disability and vice versa.2 It is also well established in the Public Health research that these conditions increase the risks of morbidity and/or mortality in the elderly population.3,4\n\nThe preclinical management of these conditions requires lifestyle modification and timely identification of socioeconomic and demographic factors dictating the cognitive and physical disability.5,6 Several causative factors have been identified7; however, most of the data is from high-income countries and may not be relevant for low-income countries such as Pakistan.\n\nThe scarcity of data from low-income countries is further compounded by the conflicting results.8–10 The discrepancy can at least partly be explained by the small sample size (< 1,000 participants), the differences in assessment tools for disability, geographical variations, and different socioeconomic, demographic, and lifestyle attributes of the target populations.8–10 Furthermore, it is not known to which extent the shared risk factors drive the association between cognitive impairment and physical disability. These findings necessitate the concomitant cognitive and physical disability assessment in relevance to potential risk factors.\n\nPakistan is experiencing a rapid population growth. The number of older people above 60 years of age in Pakistan is estimated to be six per cent of the total population and is predicted to double by 2050.11 The unplanned urban growth and overgrowing population have further compromised the insufficient health and civic services. The people living in the urban slums and rural areas have limited access to safe drinking water, sanitation, and other fundamental necessities. The elderly population finds it more challenging to access these limited facilities due to functional dependency and an age-unfriendly environment.12\n\nAnalysis of cognitive and physical disabilities is imperative in Pakistan, considering it is a highly populated country with limited availability of health care facilities and an under-appreciation of age-related degenerative diseases. However, to our knowledge, no previous study has investigated the concomitant prevalence of cognitive and physical disability in Pakistan. In addition, the multifactorial etiology of these conditions in the context of socioeconomic and demographic factors remains elusive in Pakistan.13 We aimed to bridge this gap by 1) reporting the prevalence and coupling of cognitive impairment and physical disability and 2) their associations with several socioeconomic and demographic factors in Pakistan. We used data from the demographic and health survey (DHS), a cross-sectional study involving rural and urban populations of six administrative areas of Pakistan.\n\n\nMethods\n\nThis is an analysis of a cross-sectional survey. All data utilized in this paper stems from the Pakistan part of the DHS (https://dhsprogram.com/data/dataset/Pakistan), which are large representative harmonized cross-sectional face-to-face interview surveys of individuals and households covering multiple less developed countries worldwide, often for several years.14 The DHS Program collects data on various public health domains, demographic, and socioeconomic factors. This enables the research to draw a more holistic picture of society's most vulnerable groups.\n\nData was collected from urban and rural areas by creating sixteen strata from eight regions: Punjab, Sindh, Khyber Pakhtunkhwa, Baluchistan, Azad Jammu and Kashmir, Gilgit Baltistan, Islamabad and Federally Administered Tribal Areas (FATA). Cluster sampling was done by selecting households from each cluster within the sixteen stratum using probability sampling. 16,240 households were surveyed from a fixed number of twenty-eight households which were selected from 561 clusters (details on https://dhsprogram.com/data/dataset/Pakistan).15 The ethics approval for the original study was taken from the National Bioethics Committee, Pakistan Health Research Council and the International Review Board of ICF. Informed consent was obtained from the participants (https://dhsprogram.com/publications/publication-fr354-dhs-final-reports.cfm?csSearch=830937_1).15 The latest DHS conducted for Pakistan was from 22 November 2017 to 30 April 2018. We used the data based on the household questionnaire.15 According to the published country report for Pakistan, the sample size is as large as 67,586 individuals concerning disability analyses, while in the actual data set used here (PKPR71FL.DTA), we find 71,649 individuals. Although this seems to be a large discrepancy, the different disability estimates reported are usually the same or have negligible differences, e.g., the few differences were less than 0.5 % points.15 Since we here focus on the elderly aged 60 years and above, the sample size in this study is 5,183 individuals.\n\nData are weighted by applying the household weights (variable HV005) to make estimates representative, which is also the methodology used in the official publication.15 Although the population weights appear an obvious choice, estimates based on the two weights are highly correlated. Thus, we kept the household weights as the standard data collection tool in this study for consistency.\n\nThe central variables covering disability represent two domains, remembering and walking abilities, which are operationalized as following. For the first variable, the question asked by the interviewer (of the survey) to the respondent (in the survey) is: “I would like to know if (NAME) has difficulty remembering or concentrating. Would you say that (NAME) has no difficulty remembering or concentrating, some difficulty, a lot of difficulty, or cannot remember or concentrate at all?”.15 For the second concept, the asked question is: “I would like to know if (NAME) has difficulty walking or climbing steps. Would you say that (NAME) has no difficulty walking or climbing steps, some difficulty, a lot of difficulty, or cannot walk or climb steps at all?”.15 We applied Goodman and Kruskal's gamma with an estimated asymptotic standard error, ASE to analyze the two variables.16 All data analyses were carried out using the Stata 12 software.\n\nApart from the two disability variables, several socioeconomic and demographic characteristics are also included, as summarized in Table 1. The analyses were separately carried out for males (n = 2,899) and females (n = 2,284) aged 60+ years in this study.\n\n\nResults\n\nAround 38 per cent of the sample is 60-64 years, while only around 10 per cent are 80+ years. Among the elderly, 83 per cent of males and 49 per cent of females were married, reflecting the lower life expectancy of males. 84 per cent of females and 54 per cent of males were without education. The remaining variables exhibited a generally uniform distribution for both genders (see Table 1).\n\nAn overview of the dataset regarding the relation between remembering and walking disability is presented in Figure 1. 61.1 per cent of the elderly population aged 60+ years who did not have remembering difficulty also did not have walking difficulty, and only 1.5 per cent could not walk. This marked correlation is also clear when looking at the elderly with some remembering disability since 53.2 per cent also had some walking difficulty. Similarly, 50 per cent of the elderly with a lot of remembering difficulty also had a lot of difficulty with walking. Finally, 53.6 per cent of those respondents who had complete difficulty remembering experienced complete difficulty with walking, while only 18.7 per cent had no difficulty with walking. In general, a greater difficulty in remembering was associated with a greater difficulty in walking, indicating the interface between the two disability conditions.\n\nThe basic demographic and socioeconomic characteristics of the studied population are summarized in Table 1. Most of the population was from 60-64 years of age, married, and not educated. There were adequate representations of different categories of household size, number of young children in the family, wealth indexes, residence, and access to safe drinking water. 22.6 per cent of the elderly males had difficulty remembering, and 45.0 per cent had difficulty walking (Table 2). Both estimates were higher for elderly females, i.e., 28.9 per cent and 57. 5 per cent, respectively, for remembering and walking difficulties (Table 3).\n\nNot surprisingly, the prevalence of both disabilities increases markedly with advancing age for both genders. Thus, 16 per cent of males had difficulty remembering at 60-64 years, while this fraction was 35.5 per cent at age 80+. Similarly, the proportion of males with difficulty walking increased from 33.4 per cent to 67.5 per cent for the two age groups, respectively. A parallel increase in disability prevalence was observed for females, albeit at a higher prevalence level. The participants who were never married had the highest risk of remembering or walking disability.\n\nWe found a robust negative correlation between the educational level and disability, such that 26 per cent of the illiterate males exhibited difficulty in remembering. In comparison, only 13 per cent of the males with higher education showed difficulty in remembering. We found a similar pattern for remembering in females, although the pattern for walking disability in females was less clear.\n\nHousehold size, the number of children aged 0-5 years, area of residence, and access to safe drinking water had relatively minor effects on disability. The wealth levels correlated with difficulty remembering in males, as 31 per cent of the poorest quintile but only 13 per cent of the wealthiest quintile exhibited difficulty remembering. All the geographical regions had a comparable prevalence of remembering and walking disability for both genders, except Balochistan, which had a significantly lower prevalence of disability than the other regions.\n\nThe systematic pattern between difficulty remembering and walking in Figure 1 can be summarized using the Goodman and Kruskal gamma measure, which is 0.6657 (ASE=0014). Thus, there is a significantly positive correlation between remembering and walking disability, e.g., the more difficulty with remembering, the higher the walking disability.\n\nThe overall gamma was similar for the two genders, e.g., 0.6656 for males and 0.6498 for females. The gamma across the socioeconomic variables was between 0.51 and 0.81 for males and 0.53-0.86 for females. The lowest gamma for males was observed between having four children and difficulty remembering and walking (gamma=0.51). On the other hand, the lowest gamma for females was observed for household sizes 1-4 (0.53). The highest gamma was observed for Balochistan (0.81 for males and 0.86 for females). These findings imply that Balochistan had the lowest prevalence of the two disabilities but, at the same time, the highest correlation between the two disabilities.\n\nIn contrast to high similarity between the genders concerning prevalence, the gamma levels did not exhibit similar patterns between the two genders when we focused on the most significant gammas only (p-value < 0.001 denoted with ***). For instance, for unsafe drinking water, the gamma was 0.56 for males but 0.77 for females, and for household sizes 1-4 (members), the gamma was 0.68 for males and 0.53 for females. So, although the overall level of relationship between the two disabilities was nearly the same for the two genders, the disability correlation for specific characteristics markedly differed between the two genders.\n\n\nDiscussion\n\nThere were no previous reports of the potential interface between dementia and physical disability in Pakistan and the extent to which they are influenced by the demography and socioeconomic factors of the population. Using data from 5,183 participants of both genders, we report a robust interface between difficulty walking and difficulty remembering in the older population at least 60 years of age. The prevalence of both difficulties increased with age, albeit with higher proportions in females. The wealth status and education levels were negatively correlated with difficulty levels (i.e. on average, higher prevalence of difficulty was observed for people with lower wealth or lower education), but the area of residence and the access to safe drinking water exhibited no significant correlations with difficulty levels. Conversely, household size and number of children at home revealed gender-specific associations with disability levels. Among the geographical regions, Balochistan had the lowest prevalence of both disabilities.\n\nAs expected, we found a robust interface between dementia and physical disability in the elderly population. Additionally, with advancing age, the relative proportions of the participants with one or both disabilities increased. However, to our surprise, we found gender discrimination with an overrepresentation of females in both disability indexes. Globally, the incidence of dementia is higher in women than men.17 However, an increased incidence in women than men is only evident from the middle of the eighth decade of life.17 Contrary to the literature, there was higher preponderance of females starting at 60 years of age in the present study. While the causes can be multifactorial, dementia is associated with lower wealth status, as reported elsewhere.18 Specifically, we found that the effects of wealth status on the cognitive decline were more pronounced in women than men. While the causes may be speculative, women have greater household responsibilities in arranging domestic finances,19 which can induce financial stress. Women may also develop mental stress due to subordinate status in a patriarchal family system.20 An association between stress and cognitive decline is well established21 and may account for the higher prevalence of dementia in women in our study.\n\nWe also report a higher prevalence of physical disability in women than men for all age groups. Age-related muscle loss, termed sarcopenia, is the primary driver of physical disability in old age.22 However, the literature is inconsistent about the gender-specific prevalence of sarcopenia in the older population. For example, a higher prevalence of sarcopenia is reported in women vs. men in the UK, USA, South Korea, and Brazil.23 Conversely, men have a higher occurrence of sarcopenia than women in India and Taiwan.23,24 Sarcopenia and physical disability are dictated by various factors with significant variations across populations and countries. However, when dissected according to the age-groups, women have a higher prevalence of sarcopenia and functional dependency than men, beginning at 60 years of age.22 Several factors can account for this, including menopause, which is associated with accelerated physical and cognitive impairment on top of gradual age-related degenerative processes.25,26\n\nWe found a negative correlation between dementia and the levels of education, so higher education was associated with lower dementia irrespective of gender. The robust relation between dementia and education is more consistently found in developed vs. developing countries.27 Multiple mechanisms have been proposed to explain the protective effects of education against dementia, including cognitive reserve theory, the “lose it or use it model”, and reduced brain battering.28 However, the search for a definitive mechanism remains elusive. Contrary to dementia, the effects of education on physical disability were restricted to males only where higher education was associated with less physical disability. Conversely, we did not find an association between education and physical disability in females. This is probably due to a small sample size of educated females in the study cohort.\n\nInterestingly, we found a higher representation of disability in people who were never married. The stress-buffering capacity of marriage and family support are previously highlighted and may assist in countering age-related debilitating conditions.29 Specifically, the prevalence of physical disability, cognitive impairment, and frailty were lower in married vs. unmarried older people.30,31 Consistent with this perspective, the married people exhibited lower disability in remembering and/or walking than the unmarried people, irrespective of the gender and type of disability. Similarly, the spouse availability also reduces the risk of going to the nursing home and requiring formal care in daily life activities.32 Our data indicate that the preventive effects of marriage on disability are long-lasting and persist after a partner dies, as the widowed people maintained a lower prevalence of dementia and physical disability than the unmarried people. However, the prevalence of disability was higher in widowed vs. married people, indicating an incomplete resurfacing of the hazards of single life. These findings are consistent with earlier reports suggesting the negative consequences of widowed status on disability in the older population.33\n\nThe stress-buffering effects of family support were also evident in the association between the number of children and disability in elderly women.32 Accordingly, having four or more children in the family was associated with a lower prevalence of both disabilities in the women. However, this effect was not found in men. The parenting of children in the Pakistani culture is almost exclusively the responsibility of the women,34 and this may have a protective effect against age-related disabilities. Consistent with this finding, older adults with children are less likely to develop physical limitations of daily life and go to nursing homes than adults without children.32\n\nTo our surprise, we found Balochistan with the lowest prevalence of both disabilities among the six administrative areas of Pakistan. Balochistan is an underdeveloped region with limited access to health facilities.35 However, it is possible that the people there live a physically active lifestyle, limiting the onset and/or phenotypes of various disabilities. On the other hand, the participants from different regions with relatively modern and sedentary lifestyles may be predisposed to developing disabilities.\n\nThe strengths of this study are standardized and validated tools for measuring disabilities and other variables. The simplicity of the tools ensures obtaining sufficient and reliable data from the rural and illiterate population. We obtained an adequate sample size representing different variables, which enhances the statistical and biological significance of our data. However, this study also has certain limitations. Our data is descriptive in nature as we intend to establish the prevalence of these disabilities according to different variables. Thus, the reader must be cautious in inferring direct causality. Like any cohort study on the ageing population, the selective survival of the participants must be considered. This is partly because several variables influence the survival and mortality in old age.36,37\n\nTaken together, we report an interface of dementia and physical disability in various geographical regions of Pakistan. Marital status, education, number of children at home, and wealth status have emerged as potential drivers of disabilities in old age. Our findings may be helpful in identifying and focusing on the potential negative modifiers of disability in preclinical settings.\n\n\nEthics approval\n\nWe analyzed secondary data. The ethics approval for the original study was taken from the National Bioethics Committee, Pakistan Health Research Council and the International Review Board of ICF. For more details please refer to the PDHS 2017–18 report.\n\n\nConsent to participate\n\nInformed consent was obtained in the original study.", "appendix": "Data availability\n\nData used in this study are from the PKPR71FL dataset representing Pakistan for the year 2017-2018 available from the nationally representative Demographic and Health Survey (DHS) website. Access to the dataset requires registration and is granted only for legitimate research purposes. A guide for how to apply for dataset access is available at: https://dhsprogram.com/data/Access-Instructions.cfm.\n\n\nReferences\n\nYu WC, et al.: Synergistic effects of cognitive impairment on physical disability in all-cause mortality among men aged 80 years and over: Results from longitudinal older veterans study. PLoS One. 2017; 12: e0181741. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBeeri MS, Leugrans SE, Delbono O, et al.: Sarcopenia is associated with incident Alzheimer's dementia, mild cognitive impairment, and cognitive decline. J. Am. Geriatr. Soc. 2021; 69: 1826–1835. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMajer IM, Nusselder WJ, Mackenbach JP, et al.: Mortality risk associated with disability: a population-based record linkage study. Am. J. Public Health. 2011; 101: e9–e15. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCollaborators, G. B. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShippee TP, Wilkinson LR, Ferraro KF: Accumulated financial strain and women's health over three decades. J. Gerontol. B Psychol. Sci. Soc. Sci. 2012; 67: 585–594. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAkanji B, Mordi C, Ajonbadi HA: The experiences of work-life balance, stress, and coping lifestyles of female professionals: insights from a developing country. Employee Relations: The International Journal. 2020 May 9; 42(4): 999–1015. Publisher Full Text\n\nPeavy GM, et al.: The influence of chronic stress on dementia-related diagnostic change in older adults. Alzheimer Dis. Assoc. Disord. 2012; 26: 260–266. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nQaisar R, Karim A, Muhammad T, et al.: Circulating Biomarkers of Accelerated Sarcopenia in Respiratory Diseases. Biology (Basel). 2020; 9. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDiz JBM, de Queiroz BZ , Tavares LB, et al.: Prevalence of sarcopenia among the elderly: findings from broad cross-sectional studies in a range of countries. Revista Brasileira de Geriatria e Gerontologia. 2015; 18: 665–678. Publisher Full Text\n\nRahman R, et al.: Prevalence and factors contributing to primary sarcopenia in relatively healthy older Indians attending the outpatient department in a tertiary care hospital: A cross-sectional study. Aging Med (Milton). 2021; 4: 257–265. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nConde DM, et al.: Menopause and cognitive impairment: A narrative review of current knowledge. World J. Psychiatry. 2021; 11: 412–428. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nQaisar R, et al.: Hormone replacement therapy improves contractile function and myonuclear organization of single muscle fibres from postmenopausal monozygotic female twin pairs. J. Physiol. 2013; 591: 2333–2344. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSharp ES, Gatz M: Relationship between education and dementia: an updated systematic review. Alzheimer Dis. Assoc. Disord. 2011; 25: 289–304. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSoldan A, et al.: Cognitive reserve and long-term change in cognition in aging and preclinical Alzheimer's disease. Neurobiol. Aging. 2017; 60: 164–172. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRosand GM, Slinning K, Eberhard-Gran M, et al.: The buffering effect of relationship satisfaction on emotional distress in couples. BMC Public Health. 2012; 12: 66. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChen C, Mok VCT: Marriage and risk of dementia: systematic review and meta-analysis of observational studies. J. Neurol. Neurosurg. Psychiatry. 2018; 89: 227. PubMed Abstract \| Publisher Full Text\n\nKojima G, Walters K, Iliffe S, et al.: Marital Status and Risk of Physical Frailty: A Systematic Review and Meta-analysis. J. Am. Med. Dir. Assoc. 2020; 21: 322–330. PubMed Abstract \| Publisher Full Text\n\nChoi H, Schoeni RF, Langa KM, et al.: Spouse and Child Availability for Newly Disabled Older Adults: Socioeconomic Differences and Potential Role of Residential Proximity. J. Gerontol. B Psychol. Sci. Soc. Sci. 2015; 70: 462–469. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRobards J, Evandrou M, Falkingham J, et al.: Marital status, health and mortality. Maturitas. 2012; 73: 295–299. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRaza SH, Shah ZA, Haq W: Role of birth order, gender, and region in educational attainment in Pakistan. Sci. Rep. 2022 Jul 12; 12(1): 11842. 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PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "255689", "date": "26 Mar 2024", "name": "Kouki Tomida", "expertise": [ "Reviewer Expertise Gerontology", "Geriatrics" ], "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 Author This cross-sectional study investigated the association between dementia and disability among the older adults in Pakistan. Results showed that aging was associated with prevalence of dementia and disability, with higher rates among women. In addition, factors such as being unmarried, low education, and poverty were suggested to be associated with disability.\nThese findings may provide valuable insights in the consideration of preventive measures for the development of dementia and disability in Pakistan. However, we have several comments regarding this manuscript. Please review the following and consider revising it.\nIntroduction\nOverall\nWhat is the current situation in Pakistan in terms of the incidence of disability and dementia among the older adults?\nWhat are the medical, long-term care, and economic challenges that they have to deal with as a result of these problems?\nCould you please mention what the social significance of this survey is?\n\nlines 1-2.\n\"A potential coupling is suggested where in the presence of dementia exacerbates muscle loss and physical disability and vice versa\" Can you explain this sentence in more detail, specifying specific examples and previous research?\nMethods\nOverall\nIt is unclear how dementia and physical disability were defined. Please consider describing in more detail how dementia and physical disability were assessed, as well as their reliability and validity.\nIn addition, in order to examine the connection between dementia and physical disability, it is necessary to clarify the relationship in both directions, such as the overlap between dementia and physical disability and the timing of onset of dementia and physical disability. Have you been able to conduct research in this regard? Results\nOverall\nTable 1 summarizes comparisons by gender. Could you also mention in the introduction the reason for comparing gender differences?\n\nRelation between remembering and walking disability Section\nWhich is the 61.4% or 61.1% with no memory impairment and gait dysfunction over the age of 60? Please review the figures in the text and Figure 1.\n\"In general, a greater difficulty in remembering was associated with a greater difficulty in walking, indicating an interface between the two disability conditions.\" What table shows the results of this document? If it is your thoughts on the results, please mention them in the DISCUSSION section.\nDiscussion\nOverall\nSeveral previous studies have reported that women are at higher risk of Alzheimer's disease than men. In addition to the economic status and environmental factors mentioned by the author, there may be various other pathophysiological mechanisms, such as the involvement of the menopausal transition, a neuroendocrine transition state in midlife that is unique to women, and other factors. I believe that the strengths of this paper can be further emphasized by summarizing what is currently known about dementia and gender differences, what is yet to be elucidated, and what has been newly proven in 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? 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": "12328", "date": "02 Sep 2024", "name": "Amna Khalid", "role": "Author Response", "response": "Comment 1: What is the current situation in Pakistan in terms of the incidence of disability and dementia among the older adults? What are the medical, long-term care, and economic challenges that they have to deal with as a result of these problems? Could you please mention what the social significance of this survey is? Response: This information has been added. Please refer to the introduction page 4. For the significance of the survey please refer to the last 5-6 lines of introduction. Comment 2: \"A potential coupling is suggested where in the presence of dementia exacerbates muscle loss and physical disability and vice versa\" Can you explain this sentence in more detail, specifying specific examples and previous research? Response: Examples have been added. Please refer to the first paragraph of the introduction. Comment 3: It is unclear how dementia and physical disability were defined. Please consider describing in more detail how dementia and physical disability were assessed, as well as their reliability and validity. In addition, in order to examine the connection between dementia and physical disability, it is necessary to clarify the relationship in both directions, such as the overlap between dementia and physical disability and the timing of onset of dementia and physical disability. Have you been able to conduct research in this regard? Response: This is elaborated in the methodology section paragraph 4. We did not estimate reliability and validity measures as that is beyond the scope of this paper. However, the overall quality of DHS surveys has been rated highly in the past (Harkare HV, Corsi DJ, Kim R, Vollmer S, Subramanian SV. The impact of improved data quality on the prevalence estimates of anthropometric measures using DHS datasets in India. Scientific Reports. 2021 May 21;11(1):10671.) Regarding the reviewer's second question, direction cannot be established in cross-sectional data. We used secondary data for analysis which was collected cross-sectionally. The time of onset was not established in the assessment of dementia and physical disability during data collection. As mentioned in the methodology section (paragraph 4); participants were asked: I would like to know if (NAME) has difficulty remembering or concentrating. However, this has been added to the limitations of the study. Comment 4: Table 1 summarizes comparisons by gender. Could you also mention in the introduction the reason for comparing gender differences? Response: This has been added. Kindly refer to last paragraph of the introduction section. Comment 5: Relation between remembering and walking disability Section Which is the 61.4% or 61.1% with no memory impairment and gait dysfunction over the age of 60? Please review the figures in the text and Figure 1. \"In general, a greater difficulty in remembering was associated with a greater difficulty in walking, indicating an interface between the two disability conditions.\" What table shows the results of this document? If it is your thoughts on the results, please mention them in the DISCUSSION section. Response: This has been corrected please refer to the results second paragraph. Comment 6: Several previous studies have reported that women are at higher risk of Alzheimer's disease than men. In addition to the economic status and environmental factors mentioned by the author, there may be various other pathophysiological mechanisms, such as the involvement of the menopausal transition, a neuroendocrine transition state in midlife that is unique to women, and other factors. I believe that the strengths of this paper can be further emphasized by summarizing what is currently known about dementia and gender differences, what is yet to be elucidated, and what has been newly proven in this study. Response: We have commented further on sex differences and the mechanism underlying these differences in the introduction and discussion sections. Is the work clearly and accurately presented and does it cite the current literature? Partly 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? No. Please refer to DHS website for details on the methodology as mentioned in the methods section of the study. https://dhsprogram.com/Methodology/Survey-Types/DHS-Methodology.cfm If applicable, is the statistical analysis and its interpretation appropriate? Partly Are all the source data underlying the results available to ensure full reproducibility? Partly Are the conclusions drawn adequately supported by the results? Partly" } ] } ]	1	https://f1000research.com/articles/12-1034
https://f1000research.com/articles/12-313/v1	21 Mar 23	{ "type": "Research Article", "title": "Promising effect of cisplatin and melatonin combination on the inhibition of cisplatin resistance in ovarian cancer", "authors": [ "Cut Adeya Adella", "M Fidel Ganis Siregar", "Imam B Putra", "Poppy Anjelisa Hasibuan", "Andrijono Andrijono", "Adang Bachtiar", "Sarma N Lumbanraja", "Iqbal P Nasution", "M Fidel Ganis Siregar", "Imam B Putra", "Poppy Anjelisa Hasibuan", "Andrijono Andrijono", "Adang Bachtiar", "Sarma N Lumbanraja", "Iqbal P Nasution" ], "abstract": "Background: Ovarian cancer management has not yet given a satisfactory result, and the recurrence rate is still high. One of the reasons for this is resistance to chemotherapy. Melatonin and cisplatin may be involved in the chemotherapy resistance of ovarian cancer. Methods: A laboratory experiment was performed using melatonin and cisplatin in the SKOV3 cell, from September 2020 to November 2021 at the SCTE and Integrated Laboratory & Research Center Universitas Indonesia. Several variables were used, such as doxorubicin, melatonin, cisplatin, and combination of cisplatin and melatonin at several concentrations (1×, 3/4×, 1/2×, and 1/4×). A total of 24 samples were included and divided into 8 groups. The IC50 values of melatonin, doxorubicin, and cisplatin as well as cell viability was calculated via MTS assay. Subsequently, flow cytometry was performed to assess the effect of cisplatin and melatonin on the mechanisms of CTR1, p-glycoprotein, GSH, ERCC1, e-cadherin, and apoptosis. Analysis of variance and Bonferroni test were employed for the study. Results: The IC50 values of melatonin, cisplatin, and doxorubicin were 1.841 mM, 117.5 mM, and 14.72 mM, respectively. The combination groups of cisplatin and melatonin reduced cell viability; decreased the CTR1 mean (19.73), Pgp (6.7), GSH (11.73), and ERCC1 (4.27) in the combination 1 (C1) group; and increased e-cadherin (32.2) and annexin V (53.57) also in the combination 1 (C1) group. Conclusions: The combination of melatonin and cisplatin might have an impact on drug resistance via several mechanisms in ovarian cancer.", "keywords": [ "Cisplatin", "melatonin", "doxorubicin", "SKOV3" ], "content": "Introduction\n\nTo date, the management of ovarian cancer, especially epithelial ovarian cancer, has not yet given satisfactory results (Razi et al., 2016). Ovarian cancer is known to have high morbidity and mortality rates as well as poor prognosis (Coburn et al., 2017). It ranks third in the world after cervical and uterine cancer (Bray et al., 2018). According to the Global Burden Cancer 2020 database, the number of ovarian cancer cases worldwide is 313,959, with the number of deaths being 207,252 (Sung et al., 2021). In Indonesia, the rate of ovarian cancer is still high at around 3,398 from 2016 to 2020 (INASGO, 2021).\n\nAt present, ovarian cancer recurrence rate is still high and influences the morbidity and mortality rates. One of the reasons why the recurrence rate remains high is chemotherapy resistance, especially by cisplatin at cancer stem cell (CSC), because evasion from apoptosis caused the cell to redevelop after therapy has been performed (Woo et al., 2012). There are multiple factors in cisplatin resistance, and the mechanism is still unclear from the perspective of cellular mechanism (Sousa, et al., 2014).\n\nThere are many intracellular mechanisms that affect the evasion of a cell from the cytotoxic effect of chemotherapy, such as the process that regulates drug bioavailability, mesenchymal epithelial transition, and oncogenic signals producing a phenotype that causes resistance to chemotherapy (Yeldag, et al., 2018).\n\nMelatonin has been considered an alternative for managing chemotherapy resistance, especially in ovarian cancer (Chuffa, et al., 2017). It is synthesized at the pineal gland. Melatonin exerts antioxidant and antiapoptotic effects on normal cells but exerts pro-oxidative, antiproliferative, antiangiogenic, and immunomodulatory effects on cancer cells, especially hormone-dependent cancer. Melatonin has anticancer effects, e.g., it potentiates antimetastasis, enhances drug sensitivity, induces apoptosis, inhibits cancer growth, and exhibits antiangiogenic and antiinvasive activities (Su, et al., 2017). In addition, melatonin has a good effect on clinical outcomes in several cancers such as colon, breast, lung, and ovarian cancers. However, to date, the study of melatonin in cisplatin-resistant cancer is scarce. Therefore, this study was conducted to find new alternatives for ovarian resistant cancer cell by using a combination of cisplatin and melatonin.\n\n\nMethods\n\nIn this study, a laboratory experiment on the combination of cisplatin and melatonin in cisplatin-resistant ovarian cancer cell was conducted using SKOV3 obtained from the American Type Culture Collection (no. HTB-77). This research was conducted at the SCTE (Stem Cell and Tissues Engineering Research Cluster) at the Medical Faculty of Universitas Indonesia. Furthermore, flow cytometry (BD FACS ARIA III) was performed at the Integrated Laboratory of the Faculty of Medicine, Universitas Indonesia, from September 2020 to November 2021. This research has been approved by the ethics committee of Universitas Indonesia with 419/UN2.F1/ETIK/PPM.00.02/2021 on May, 3rd 2021.\n\nThe materials used were IC50 melatonin [Liftmode], IC50 doxorubicin [MBS], IC50 cisplatin [Mybiosource], sodium bicarbonate [Sigma-aldrich], aquabidest, microcarrier beads [Sigma-aldrich], trypsin-EDTA [Gibco], phospate buffer saline (PBS) [Gibco], dimethyl sulfoxide (DMSO) [Gibco], Roswel Park Memorial Institute [RPMI] medium, antibiotic [Penstrep], antimycotic [Gibco], tryphan blue [Gibco], heparin [Gibco], fetal bovine serum (FBS) [Amresco], ethanol 70%, aquadest, whitening [Bayclin], Tris-Cl 0,5 M pH 6,8 [Invitrogen], and 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) [Promega]. This research used 8 groups of samples. Mead’s formula was used to calculate sample size. Minimum samples were 16 with three times repetition in each group, so the total was 24 samples. The samples were described in Table 1 and for the protocols c] an be accessed from dx.doi.org/10.17504/protocols.io.yxmvm2539g3p/v1.\n\nThe groupings were as follows: cell control (without any treatment), IC50 doxorubicin, IC50 melatonin, IC50 cisplatin, C1 (combination of 1× IC50 cisplatin and 1x melatonin), C2 (combination of ¾× IC50 cisplatin and ¾× melatonin), C3 (combination of ½× IC50 cisplatin and ½× melatonin), and C4 (combination of ¼× IC50 cisplatin and ¼× melatonin). The dependent variables were the morphology of SKOV3 cells visualized using a microscope with 100x magnification, percentage of cancer cell viability determined via MTS assay, and cell percentage that expressed CTR-1 (as an influx marker) [MBS], p-glycoprotein (Pgp) (as an efflux marker) [FITC], gamma-glutamylcysteinylglycine (GSH) (as a drug inactivation marker) [GSH Kit], excision repair cross-complementation 1 (ERCC 1) (as a damage repair marker) [PE 647], e-cadherin (as a mesenchymal epithelial transition marker) [FITC], and apoptosis (as an annexin V marker) [Mybiosource] using flow cytometry. Positive control was performed with doxorubicin.\n\nTreated cells were harvested by adding 1 mL tripsin-EDTA, centrifuged at 2000 rpm for 5 minutes. The fifth passage of the SKOV3 cell was obtained from a cryopreservation tank and thawed at 37°C for 2 min. Then, the cell was centrifuged for 10 min, and the supernatant was discharged; 1–2 mL of the complete medium was added for cell counting. The cells were cultured and harvested, 2–3 mL of trypsin was added and incubated for 5 min, then the suspension was centrifuged for 10 min and then re-harvested from the 96-well plate for the MTS assay [Promega].\n\nIC50 was used to express the 50% decrease in cell viability. To determine the IC50, each concentration of solutions was tested in each cell. The IC50 values of melatonin, cisplatin, and doxorubicin were assessed. Different concentrations were tested to find the IC50 of each variable as follows: melatonin (0.1, 0.5, 1, 2, 5 mM), doxorubicin (25, 50, 100, 150, 200, 300 μM), and cisplatin (10, 20, 40, 50, 80, 100, 200 μM). Spectrophotometry [Shimadzu] was employed with λ = 490 nm for the absorbency. Graphpad software was used to analyze the IC50 values. The IC50 values of the materials were 1.841 mM for melatonin, 117.5 μM for cisplatin, and 14.72 μM for doxorubicin.\n\nCells were treated using Roswell Park Memorial Institute (RPMI) medium consisting of 1% penicillin-streptomycine [Penstrep], 1% fungizone [Gibsco], 10% fetal bovine serum [Amresco], and ethanol 70% in a flask incubated at 37oC with CO2 5%. SKOV3 cells were seeded onto the 96-well plate with 25x104 cell/well density, then incubated at 37°C for 24 h, then each cell was exposed to each material and incubated for 48 h. To measure the cell viability percentage and cytotoxic activity, MTS assay was employed. The principle is formazan crystal will be produced by the viable cell much more than the nonviable cell. Each of the materials were exposed to the cells and MTS solution was added at each of the wells, then read in λ = 490 nm.\n\nFlow cytometry was performed by adding EDTA into the plate and then centrifuging several times, and cell pellets were washed once with PBS. The cell was put into flow cytometry tube and added 1 mL stain buffer solution, then centrifuged at 2100 rpm for 5 minutes. The supernatant was then separated and the sediment was collected.\n\nP-glycoprotein antibody was added into the sediment and incubated for 15 minutes at room temperature, washed with buffer stain, ad centrifuged at 2100 rpm for 5 minutes. 1 mL cytofix was then added and incubated at room temperature for 10 minutes. The cell was centrifuged at 2100 rpm for 5 minutes, the supernatant was discharged and washed with 1 mL of permwash buffer, then recentrifuged at 2100 rpm for 5 minutes. The supernatant was separated, CTR-1 antibody was added, and it was incubated for 20 minutes at room temperature, then washed with permwash buffer and recentrifuged at 2100 rpm for 5 minutes. Samples were analyzed with flow cytometry (BD FACS ARIA III).\n\n5 μL of GSH antibody was added into the sample, which was then incubated at 37oC for 30 minutes, washed with 1 mL buffer, and centrifuged at 2100 rpm for 5 minutes. The sediment was dissolved with stain buffer. Samples were analyzed using flow cytometry (BD FACS ARIA III).\n\nAntibodies of ERCC and E-Cadherin were added into the sample, incubated at room temperature for 20 minutes, then washed with 1 mL permwash buffer for 5 minutes and centrifuged at 2100 rpm for 5 minutes. The sediment was collected and dissolved with stain buffer. Samples were analyzed using flow cytometry (BD FACS ARIA III).\n\n0.1 mL annexin V reagent was added into the sediment, incubated at room temperature for 20 minutes, washed with 1 mL stain buffer and recentrifuged at 2100 rpm for 5 minutes. The sediment was collected and stain buffer was added. Samples were analyzed using flowcytometry (BD FACS ARIA III).\n\nMean ± SD was used to express the data. All the statistics were analyzed using SPSS 21.\n\n\nResults\n\nIn this study, SKOV3 cells were used. SKOV3 cell culture was observed under a microscope, as presented in Figure 1. After calculating the IC50 values of the materials (melatonin, 1.841 mM; cisplatin, 117.5 μM; and doxorubicin, 14.72 μM), cell viability was calculated via MTS assay and observed under microscope as in Figure 2. The highest rate of cell viability decrease was in group C1 (IC50 melatonin and cisplatin) at 37.57%, as shown in Table 2 (Adella 2023a; Adella 2023b; Adella 2023c).\n\na ANOVA.\n\nb Bonferroni.\n\nCTR1 is a marker of drug influx. An increase in CTR1 expression indicates an increase of drug influx into the cell, which suggests decreased cancer cell resistance to chemotherapy. As can be seen from Table 3, the control group has the lowest mean expression among the groups. On the contrary, the doxorubicin group has the highest CTR1 expression, indicating that doxorubicin has a higher influx rate than other groups. However, among the combination groups, C1 and C2 had the highest CTR1 expression (P < 0,001), suggesting that these groups have the highest influx rate among the experimental groups. The IC50 melatonin group had lower CTR1 expression than groups C1 and C2, which shows that chemotherapy influx was better in C1 and C2 than the melatonin-only group. If compared with the IC50 of cisplatin, all the combination groups show that the CTR1 expression was higher than the cisplatin alone, which indicated that the combination of cisplatin and melatonin groups were better to decrease the influx of the drug than the cisplatin-only group.\n\nPgp is an efflux membrane transporter of toxins, cell endogen metabolites, and chemotherapy especially in resistance cells. A high percentage of Pgp indicates a high ability of the cell to inhibit a cytotoxic response, suggesting high chemotherapy resistance of cancer cells. As can be seen from Table 4, the control group has the highest Pgp expression (44.37%). Among the combination groups, group C1 has the lowest Pgp expression (6.7%) of all combination groups and C4 has the highest Pgp expression (20.87%). This result indicates that group C1 had the ability to decrease Pgp expression more than the cisplatin-only group (16%). A low rate of drug efflux activity indicates decreased chemotherapy resistance and better outcome. The combination groups had better ability to decrease the efflux mechanism than the cisplatin-only group.\n\na ANOVA.\n\nb Bonferroni.\n\nGSH is a drug inactivation protein marker. As can be seen from Table 5, the control group has the highest GSH expression (45.23%), whereas the positive control group has the lowest (1.33%), indicating that without giving the materials, the GSH expression would high. But if doxorubicin is given, the GSH expression would be lowered. Among the combination groups, group C1 has the lowest GSH expression (11.73%). When compared with the melatonin-only group (12.57%), group C1 had a lower GSH expression. On the other hand, when compared with the cisplatin-only group, all of the combination groups had a higher ability to decrease the GSH expression than the cisplatin-only group. This suggested that the combination groups had decreased drug inactivation activity and chemotherapy resistance as well as a better outcome than the cisplatin-only group. This is presented in Table 5.\n\na ANOVA.\n\nb Bonferroni.\n\nERCC1 is a transcription factor used as a DNA repair marker. A high ERCC1 expression indicates high DNA repair mechanism in cancer cells. As can be seen from Table 6, the control group has the highest ERCC1 expression (48.07%), whereas the positive control group has the lowest (1.57%). Among the combination groups, groups C1, C2, and C3 have the ability to decrease the ERCC1 expression more than the melatonin-only and cisplatin-only groups, but C1 group had the highest ability. The lower the DNA repair activity, the more the chemotherapy resistance decreases, which is shown in combination of melatonin and cisplatin groups.\n\na ANOVA.\n\nb Bonferroni.\n\nE-cadherin is a marker of epithelial mesenchymal transition. A high e-cadherin expression indicates low epithelial mesenchymal transition, which has a low impact on tumor invasion and drug resistance. As can be seen from Table 7, the positive control group has the highest e-cadherin expression (64.2%), whereas the control group has the lowest (1.7%). When compared with the cisplatin-only group, the combination groups C1-C3 had higher e-cadherin expression than the cisplatin-only group. This suggested that the combination of melatonin and cisplatin might decrease epithelial mesenchymal transition (increased expression of e-cadherin) more than the cisplatin-only group; a decrease in drug resistance could also be observed.\n\na ANOVA.\n\nb Bonferroni.\n\nAnnexin V was used as an apoptosis marker in this research. A high annexin V activity indicates high apoptosis activity. As can be seen from Table 8, the positive control group has the highest annexin V activity (70.9%), whereas the control group has the lowest (1.2%). Among the combination groups, group 1 has the highest annexin V activity (53.57%). Compared with the melatonin-only group, all combination groups had a higher ability to decrease annexin V expression. Additionally, compared with the cisplatin-only group, the combination groups all had a better ability to increase apoptosis than the cisplatin-only group. This suggested that the combination of melatonin and cisplatin increases apoptosis to reduce the drug resistance mechanism.\n\na ANOVA.\n\nb Bonferroni.\n\n\nDiscussion\n\nThe IC50 of doxorubicin was used as a positive control in this study as doxorubicin has much evidence as an anticancer agent and has been demonstrated to be effective when cells are resistant to cisplatin (Yi S, et al., 2020). Doxorubicin has a DNA intercalation chain mechanism, inhibition of topoisomerase II to destroy DNA and increase apoptosis (Johnson and Dubey 2021). The combination groups had higher cell viability decrease than the cisplatin group. These groups may have the capability to increase the cytotoxic effect of chemotherapy more than that of the single-use therapy. Melatonin exhibits anti-inflammatory, anti-tumor, and anti-proliferative activities, with minimal side effects. In addition, it was found to reduce cell proliferation and angiogenesis and act as a pro-apoptosis and immunomodulator agent in ovarian cancer (Chuffa, 2017). Melatonin has no issues regarding bioavailability compared with other drugs because it has faster solubility through the cell and nuclear membranes (Tamura, et al., 2020).\n\nCTR1 and Pgp were found to be associated with cell resistance. Low influx and high efflux may contribute to drug resistance (Zhang et al., 2019). CTR1 plays a role in the absorption of platinum drugs, such as cisplatin and oxaliplatin, and decreases transporter expression, thus influencing tumor resistance (Chen and Chang, 2019). Pgp may pump the drug outside of the cell to reduce cytotoxic activity. A high Pgp indicates a high ability of the cell to inhibit the cytotoxic agent (Amiri-Kordestani, et al., 2012). Melatonin is capable of reducing Pgp in diffuse large B-cell lymphoma and activating the NF-kB pathway. In a study using the combination of epirubicin and melatonin, melatonin made the lymphoma cell sensitive to epirubicin from the inhibition of Pgp expression through the pathway of NF-kB. Melatonin decreases P65 in the nucleus and inhibits Pgp expression (Liu, et al., 2021).\n\nGSH has the ability to detoxify intracellular toxins, but the GSH in cell cancer is capable of inhibiting and inactivating chemotherapy (Tapia, et al., 2013). GSH binds to cisplatin to inhibit cisplatin binding with DNA, reduce reactive oxygen species, and decrease cell sensitivity to apoptosis (Galluzzi, et al., 2012). Melatonin can decrease the GSH level and increase the GSH peroxidase activity (Medina-Leendertz, et al., 2018). Furthermore, it induces antioxidant synthesis by inducing gamma glutamylcysteine synthetase (Meng, et al., 2017). In addition, melatonin increases antioxidant activity that increases glutathione level and induces glutathione peroxidase (Harderland, 2017). Melatonin increases the apoptosis activity of cisplatin, reduces oxidative stress by decreasing the GSH level, and increases glutathione synthesis (Fernandez et al., 2019).\n\nMelatonin has the ability to inhibit mTOR and ERCC1 expressions and increase the activity of intracellular autophagosomes. It is used as a cancer therapy adjuvant to repair the sensitivity of chemotherapy and managing the side effects of cisplatin (Bennukul et al., 2014). ERCC1 overexpression has poor prognosis in patients with osteosarcoma or lung cancer who received cisplatin. Li et al. (2017) demonstrated that low ERCC1 expression increases the sensitivity of platinum chemotherapy in ovarian cancer. The low repair activity of the DNA decreases chemotherapy resistance (Li, et al., 2017).\n\nE-cadherin has an impact in cell adhesion and influences cell growth. A decrease in e-cadherin expression increases activity of epithelial mesenchymal transition, thus reducing the cell adhesion strength (Rosso, et al., 2017). High e-cadherin was associated with high activities of invasive cancer and metastasis (Loh, et al., 2019). Melatonin administration increased e-cadherin expression, decreased N-cadherin and vimentin expressions in CSC from CMT-U229. Melatonin may decrease the migration and invasion activities of cancer cells (Goncalves, et al., 2016). It also decreases proteins associated with inflammation, oxidative stress, cell-cycle, proliferation, and apoptosis (Zare, et al., 2019)\n\nApoptosis indicates low chemotherapy resistance. In this study, we used annexin V as the marker. High annexin V expression indicates high apoptosis activity in the cell (Wang, et al., 2012). Melatonin increases p53 expression and activates it, increasing apoptosis in several cancers such as colon and uterine cancer. Melatonin is involved in the BAX gene expression, decreases the expression of BCL-2 as an antiapoptotic gene, and regulates the Bax/Bcl-2 ratio (Chuffa, et al., 2017). Melatonin and cisplatin potentiate apoptosis by increasing the depolarization of mitochondrial membrane, activating caspase-3/7, and inducing cell-cycle arrest, if compared with the cisplatin-only group (Plaimee, et al., 2015).\n\n\nConclusion\n\nThis study has shown that group C1 (combination of 1x IC50 melatonin and 1x IC50 cisplatin) may reduce the cisplatin resistance by decreasing cell viability, increase influx activity by increasing CTR-1 expression, reduce efflux activity by reducing p-glycoprotein expression, decrease drug inactivity by reducing GSH expression, decrease DNA repair mechanism by reducing ERCC-1 expression, increase epithelial mesenchymal transition by increasing e-cadherin expression, and increase apoptosis mechanism by increase of annexin V expression.", "appendix": "Data availability\n\nMendeley: Raw Data of Melatonin-Cisplatin. https://doi.org/10.17632/ybpbjbkfb4.1 (Adella, 2023a)\n\nMendeley: Combination of Cisplatin and Melatonin on the Inhibition of Cisplatin Resistance in SKOV3 Cells. https://www.doi.org/10.17632/ftdpsfwrtv.1 (Adella, 2023b)\n\nMendeley: File for Combination of Melatonin and Cisplatin on the Inhibition of Ovarian Cancer Cell. https://doi.org/10.17632/475dpkhk3w.2 (Adella, 2023c)\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 of the authors give regard to the people who participated in this research.\n\n\nReferences\n\nAdella CA: Raw Data of Melatonin-Cisplatin. [Dataset]. Mendeley Data. 2023a; V1. Publisher Full Text\n\nAdella CA: Combination of Cisplatin and Melatonin on the Inhibition of Cisplatin Resistance in SKOV3 Cells. [Dataset]. Mendeley Data. 2023b; V1. Publisher Full Text\n\nAdella CA: Combination of Melatonin and Cisplatin on the Inhibition of Ovarian Cancer Cell. [Dataset]. Mendeley Data. 2023c; V2. Publisher Full Text\n\nBennukul K, Numkliang S, Leardkamolkarn V: Melatonin attenuates cisplatin-induced HepG2 cell death via the regulation of mTOR and ERCC-1 expressions. World J. Hepatol. 2014; 6(4): 230–242. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBray F, Ferlay J, Soerjomataram I, et al.: Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J. Clin. 2018; 68(6): 394–424. PubMed Abstract \| Publisher Full Text\n\nChen SH, Chang JY: New Insights into Mechanisms of Cisplatin Resistance: From Tumor Cell to Microenvironment. Int. J. Mol. Sci. 2019; 20(17). Publisher Full Text\n\nChuffa L, Reiter R, Lupi L: Melatonin as a promising agent to treat ovarian cancer: molecular mechanisms. Carcinogenesis. 2017; 38(10): 945–952. Publisher Full Text\n\nCoburn S, Bray F, Sherman M, et al.: International patterns and trends in ovarian cancer incidence, overall and by histologic subtype. Int. J. Cancer. 2017; 140(11): 2451–2460. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFernandez-Gil BI, Guerra-Librero A, Shen YQ, et al.: Melatonin enhances cisplatin and radiation cytotoxicity in head and neck squamous cell carcinoma by stimulating mitochondrial ROS generation, apoptosis, and autophagy. Oxidative Med. Cell. Longev. 2019; 2019: 1–12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGalluzzi L, Senovilla L, Vitale I, et al.: Molecular mechanisms of cisplatin resistance. Oncogene. 2012; 31(15): 1869–1883. Publisher Full Text\n\nGoncalves N, Colombo J, Lopes JR, et al.: Effect of Melatonin in Epithelial Mesenchymal Transition Markers and Invasive Properties of Breast Cancer Stem Cells of Canine and Human Cell Lines. PLoS One. 2016; 11(3): e0150407. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHarderland R: Melatonin and the electron transport chain. Cell. Mol. Life Sci. 2017; 74(21): 3883–3896. Publisher Full Text\n\nIndonesia Society of Gynecologic Oncology (INASGO), 2021: National data, 2000-2016.Reference Source\n\nJohnson K, Dubey R: Doxorubicin. StatPearls; 2021.\n\nLi C, Zhu X, Chen S, et al.: Melatonin promotes the proliferation of GC-1 spg cells by inducing metallothionein-2 expression through ERK1/2 signaling pathway activation. Oncotarget. 2017; 8(39): 65627–65641. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLiu K, Song J, Yan T, et al.: Melatonin increases the chemosensitivity of diffuse large B-cell lymphoma cells to epirubicin by inhibiting P-glycoprotein expression via the NF-κB pathway. Transl. Oncol. 2021; 14(1): 100876. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLoh CY, Chai JY, Tang TF, et al.: The E-cadherin and N-cadherin switch in epithelial and mesenchymal transition: signalling, therapeutics implications, and challenges. Cells. 2019; 8(10): 1118. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMedina-Leendertz S, Mora M, Vielma JR, et al.: Melatonin decreases oxidative stress in Drosophila melanogaster exposed to manganese. Investig. Clin. 2018; 59(3): 230–241. Publisher Full Text\n\nMeng X, Li Y, Li S, et al.: Dietary sources and bioactivities of melatonin. Nutrients. 2017; 9(4): 367. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPlaimee P, Weerapreeyakul N, Barusrux S, et al.: Melatonin potentiates cisplatin-induced apoptosis and cell cycle arrest in human lung adenocarcinoma cells. Cell Prolif. 2015; 48(1): 67–77. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRazi S, Ghoncheh M, Mohammadian-Hafshejani A, et al.: The incidence and mortality of ovarian cancer and their relationship with the Human Development Index in Asia. Ecancer Medical Science. 2016; 10: 628. Publisher Full Text\n\nRosso M, Majem B, Devis L, et al.: E-cadherin: A determinant molecule associated with ovarian cancer progression, dissemination and aggressiveness. PLoS One. 2017; 12(9): 1–25. Publisher Full Text\n\nSousa GF, Wlodarczyk S, Monteiro G: Carboplatin: molecular mechanisms of action associated with chemoresistance. Braz. J. Pharm. Sci. 2014; 50: 693–701. Publisher Full Text\n\nSu SC, Hsieh M, Yang WE, et al.: Cancer metastasis: mechanisms of inhibition by melatonin. J. Pineal Res. 2017; 62(1) Publisher 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; 71(3): 209–249. PubMed Abstract \| Publisher Full Text\n\nTamura H, Jozaki M, Tanabe M, et al.: Importance of melatonin in assisted reproductive technology and ovarian aging. Int. J. Mol. 2020; 21. Publisher Full Text\n\nTapia G, Padilla I: Molecular Mechanism of Platinum Resistance in Ovarian Cancer. Ovarian Cancer – A Clinical and Translational Update, Chapter 10. InTech DTP team: Intech; 2013; pp. 205–209.\n\nWang J, Hao H, Yao L, et al.: Melatonin suppresses migration and invasion via inhibition of oxidative stress pathway in glioma cells. J. Pineal Res. 2012; 53(2): 180–187. Publisher Full Text\n\nWoo CJ, Won LJ, Ki KJ, et al.: Splicing variant of AIMP2 as an effective target against chemoresistant in ovarian cancer. J. Mol. Cell Biol. 2012; 4: 164–173. Publisher Full Text\n\nYeldag G, Rice A, Hernandez AR: Chemoresistance and self-maintaining tumor microenvironment. MDPI. 2018; 10(12): 471. Publisher Full Text\n\nYi SA, Kim GW, Yoo J, et al.: HP1γ sensitizes cervical cancer cells to cisplatin through the suppression of UBE2L3. Int. J. Mol. Sci. 2020; 21(17): 5976. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZare H, Shafabakhsh R, Reiter RJ, et al.: Melatonin is a potential inhibitor of ovarian cancer: molecular aspects. J. Ovarian Res. 2019; 12(1): 26. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhang X, Hou G, Liu A, et al.: Matrine inhibits the development and progression of ovarian cancer by repressing cancer associated phosphorylation signaling pathways. Cell Death and Disease. 2019; 10: 770. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "174251", "date": "19 Jun 2023", "name": "Seyed Mostafa Mir", "expertise": [ "Reviewer Expertise Cancer research and melatonin" ], "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\nCongratulations on doing this wonderful research. The context was well written and the tables were informative. However; some changes can be done to improve this paper. The parts that need correction are highlighted in the PDF file, sincerely.\nIn the materials and sample size section, there is a writing mistake in the last sentence of paragraph 2.\n\nIn the last sentence of Influx mechanism using CTR1 part, if the combination of cisplatin and melatonin has the higher rate of CTR1 expression so it should increase the drug influx not decrease it.\n\nAs for the discussion section, the explanations were good enough however; I suggest you to use these articles to explain more about the melatonin and doxorubicin mechanisms and functions:\n- Melatonin: An anticancer molecule in esophageal squamous cell carcinoma: A mechanistic review1 - Oncostatic activities of melatonin: Roles in cell cycle, apoptosis, and autophagy2 - Melatonin: A smart molecule in the DNA repair system3 - Melatonin and doxorubicin co-delivered via a functionalized graphene-dendrimeric system enhances apoptosis of osteosarcoma cells4\nThese papers may help the writer to explain more about the mechanisms of melatonin. For example, in the introduction where the actions of melatonin are noted, these papers can help the writer to clarify the known mechanisms of melatonin by which it exerts oncostatic activities, regulatory actions on apoptosis, antiangiogenic actions, and etc.\nAs for the discussion section, I suggest to explain more about the roles of melatonin in autophagy and chemotherapy adjuvant. Because of the main role of melatonin in this research, it would be better to elucidate the mechanisms of actions by which it exhibits anti-tumor effects, inhibits invasiveness, helps in DNA repair systems, and etc.\nAny of these mentioned references discusses these mechanisms and can be useful in order to improve the article.\n\nIn the Conclusion section, the increase in E-Cadherin expression in C1 group should decrease the EMT process and thus leads to a decrease in drug resistance.\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": "9975", "date": "28 Jul 2023", "name": "Cut Adeya Adella", "role": "Author Response", "response": "Thank you for the correction to improve this paper and also for the response." } ] }, { "id": "188517", "date": "24 Jul 2023", "name": "Tharcisio C. Tortelli", "expertise": [ "Reviewer Expertise Cell biology and develpment of new treatments for cancer therapy." ], "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 article \"Promising effect of cisplatin and melatonin combination on the inhibition of cisplatin resistance in ovarian cancer\" provides evidences of a possible combination between cisplatin and melatonin to chemosensitize ovary cells to chemotherapy.\nHowever, the conclusion made by the authors cannot be made, as in any table, it is not shown if the cisplatin + melatonin combination is better than cisplatin or melatonin alone. This information is the most important because for a combination to work, it has to be better than its counterparts alone.\nThe methodology used is not sufficient, as there is no point in using a fraction of the melatonin concentration if the result of the data analyzed is not shown with this fraction. As a result, C2, C3 and C4 groups are pointless to assume if the combination is better than the individual treatments alone.\nAlso, using one cisplatin-resistant cell line is not sufficient. At least another one should be used.\nAnother observations:\nPlease, provide the results in graphics and not in table. It is better to be understood.\n\nThe statement in the introduction \"In addition, melatonin has a good effect on clinical outcomes in several cancers such as colon, breast, lung, and ovarian cancers\" has no reference.\n\nPlease, provide the result with the statistics of the MTS assay (table 2).\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? 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? Partly\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [ { "c_id": "10822", "date": "18 Jun 2024", "name": "Cut Adeya Adella", "role": "Author Response", "response": "Thank you for the revision. This research was using several IC50 of melatonin and cisplatin combinations to show the effectiveness of melatonin and cisplatin combination concentration compared to IC50 melatonin-only, which was the best combination form all of the combination groups. So, we made it in several combinations group. Also, we used cisplatin resistant type of cell line in this research because our purpose is to see the effectiveness of combination of melatonin and cisplatin on the inhibition of cisplatin resistant in ovarian cancer, maybe in the next research we will use other type of cell line for comparison. I have added the graphics in figure 3-8 of each markers to simplify the result, as it shown in the tables and figures, from MTS assay, it was shown that the combination group was better than melatonin-only group in reducing the cisplatin resistance, and for the result, it was explained before each of the tables and in discussion section that explain efficacy of combination group in each markers compared to melatonin-alone group. I have also added the reference in the statement. For table 2, we used MTS assay to see the percentage of viability cell by the value of it's abosrbancy, we performed it three times, and we got the mean value of absorbancy from the three performances of MTS assay, so the percentage of cell in table 2 was shown as the mean value of the absorbancy of MTS assay. I really appreciate your comments for the improvement in this article, thank you." } ] } ]	1	https://f1000research.com/articles/12-313
https://f1000research.com/articles/13-572/v1	04 Jun 24	{ "type": "Research Article", "title": "Green synthesis of gold nanoparticles using Pelargonium Graveolens leaf extract: characterization and anti-microbial properties (An in-vitro study)", "authors": [ "Ahmed Yousif Mahdi Asker", "Aseel Haidar M.J. Al Haidar", "Aseel Haidar M.J. Al Haidar" ], "abstract": "Background In recent years, there has been a notable increase in the level of attention devoted to exploring capabilities of nanoparticles, specifically gold nanoparticles AuNPs, within context of modern times. AuNPs possess distinct biophysical properties, as a novel avenue as an antibacterial agent targeting Streptococcus Mutans and Candida Albicans. The aim of this study to create a nano-platform that has the potential to be environmentally sustainable, in addition to exhibiting exceptional antimicrobial properties against Streptococcus Mutans as well as Candida Albicans.\n\nMethods this study involved utilization of Pelargonium Graveolens leaves extract as a cost effective and environmentally sustainable approach for the green synthesis of AuNPs. Subsequently, physicochemical characteristics were assessed employing a variety of analytical methods, including as transmission electron microscopy, X-ray diffraction, Field Emission Scanning Electron Microscope, Zeta potential, Ultraviolet visible absorption spectroscopy, and Energy dispersive X-ray spectroscopy and Fourier transform infrared spectroscopy. The antimicrobial efficacy against Streptococcus Mutans and Candida Albicans was evaluated. Nanoparticles of various shapes, including hexagonal, spherical, semi-spherical, and triangular, were synthesized. These nanoparticles exhibited a mean particle size of 294nm and demonstrated low degree of aggregation. These nanoparticles exhibited long-term stability and were capable of facilely combining with diverse bioactive compounds.\n\nResults The study demonstrated that AuNPs which is synthesized by green methods display potent antimicrobial properties.\n\nConclusion Utilization of Pelargonium Graveolens AuNPs may exhibit a promising potential as an antibacterial agent against Streptococcus Mutans and Candida Albicans. Nanoparticles (NPs) have the potential to serve as a novel approach for addressing pathogen infections as well as for biomedical, dental and pharmaceutical purposes in the future.", "keywords": [ "gold nanoparticles", "Pelargonium graveolens", "Streptococcus Mutans", "Candida Albicans" ], "content": "Introduction\n\nNanotechnology has recently provided novel options for the treatment of several ailments. There has been much research’s concerning gold nanoparticles GNPs are typically regarded to be biocompatible for medical usage as the antioxydant, anticancer, drug delivery and antimicrobial agents.1–4 The comprehensive investigation of gold nanoparticles has surpassed that of other metal nanoparticles, owing to their comparatively minimal toxicity towards animal and microorganism cells in comparison to other metal nanoparticles.5 Gold nanoparticles display unique physicochemical characteristics in comparison to bulk solids, owing to their significantly larger surface area relative to their volume.6 The coloration of Gold nanoparticles is dependent on their structural characteristics, size, and level of aggregation. The application of red colloidal gold has been employed as a means of regeneration therapy. In addition, gold nanoparticles have been utilized in diagnostic and therapeutic drug delivery applications. The utilization of microorganisms, enzymes, and plant extracts has been proposed as a viable and environmentally conscious substitute for conventional chemical and physical techniques in the production of metallic nanoparticles. The utilization of the green synthesis approach has attracted significant interest as a cost-effective and eco-friendly methodology that facilitates the production of nanoparticles of diverse shapes and sizes, Demonstrating remarkable stability and compatibility.7 The study done by Lee et al. investigates the efficacy of distinct active compounds derived from plants, particularly is flavones, protocatechuic acid, and Gallic acid, as reducing agents for the green synthesis of modified gold nanoparticles (AuNPs). The resulting nanoparticles exhibited remarkable stability and biocompatibility, with a lifespan of up to three months.8 In general, it has been observed that HAuCl4 forms chlorine-carbon bonds with plant extracts.9 Furthermore, the plant extracts contain starch and glucose constituents that can serve as stabilizing and reducing agents during the synthesis of gold nanoparticles. This enables the nanoparticles to be stored for an extended period of 17 months while maintaining their stability.10 Shankar et al in 2003 were able to synthesize gold nanoparticles (GNPs) of varying shapes through the utilization of Pelargonium graveolens leaves and its entophytic fungus. The plant Pelargonium graveolens and its entophyte have been recognized as potential candidates for the synthesis of gold nanoparticles. In particular, the researcher had conducted research on the reduction of aqueous chloroaurate ions using the leaves of the Pelargonium graveolens plant and an entophytic fungus.11 Due to its, antioxidant, antibacterial, antifungal, hypoglycemic, anti-inflammatory, and cancer-fighting were only some of the reported biological and pharmacological effects of Pelargonium graveolens. Extracts from this plant are useful because they contain bioactive compounds. Citronellal, geranial, and linalool are three major bioactive components found in Pelargonium graveolens, which may explain their properties. In light of this, it is now recommended in herbal medicine to investigate the chemical components of this plant. In order to create safe and effective medications, it is crucial to understand the scientific foundation of their therapeutic activities.12 Nanoparticles hold distinct promise compared to their bulk equivalents. Since they are small and have a large surface area, they have demonstrated significant biological activity in the human body.13 The use of nanotechnology in dentistry has significant potential for transformative advancements. Nevertheless, it is crucial to acknowledge the potential risks associated with its misuse. The prioritization of applications within this discipline will ultimately be determined by factors such as time and human requirements.14 In recent years, there has been a significant increase in the utilization of nanoparticles in the formulation and advancement of various dental materials. This is mostly due to their ability to provide a distinctive amalgamation of characteristics. The nanoparticles have a relatively large surface area to volume ratio in comparison to particles of equivalent substance due to their small size.15 The present study outlines a straightforward procedure for synthesizing AuNPs by employing Pelargonium Graveolens extract as an inexpensive and environmentally benign, stabilizing and reducing agent, furthermore, an evaluation was conducted on the physical characteristics and antimicrobial efficacy towards Streptococcus mutans and Candida albicans.\n\n\nMethods\n\nChloroauric acid (HAuCl4.3H2O), from (Sigma-USA®,™). Muller-Hinton agar and nutrient broth medium, from (Accumix-Spain®,™). Ethanol bought from (Duksan-Korea®,™), all of the additional chemicals and reagents utilized in the experiments were of analytical grade.\n\nThe study evaluated the antimicrobial effectiveness of the prepared Pelargonium Graveolens AuNPs against clinical isolates of Streptococcus mutans and Candida albicans. These isolates were obtained from the oral cavity of patients in the Pediatric and Preventive Dentistry Department at the University of Baghdad’s College of Dentistry. The laboratory utilized standard biochemical methods to process and identifies these isolates. Following the transfer of the stock cultures onto Mueller-Hinton agar medium, an overnight incubation at 37°C was conducted, followed by storage at 4°C.\n\nPelargonium Graveolens leaves collection in Baghdad Governorate, Iraq. The collected leaves were thoroughly cleansed under running water to eliminate traces of chemicals and grime. After a thorough rinsing, the leaves of Pelargonium Graveolens were incubated overnight at 37oC to dry. After incubation, the completely desiccated leaves were ground into a fine powder for use in the extraction process. A quantity of 100 g of air-dried ground plant material was subjected to extraction using aqueous alcohol as the solvent (methanol, water, ethanol (1:1:3) 80 % v/v) 500 mL the samples were subjected to Soxhlet extraction for a duration of 8 hours on a water bath. The extracts were subjected to solvent removal under reduced pressure at a temperature of 45°C using a rotary evaporator. Subsequently, the desiccated crude concentrated extracts were measured in order to determine the yield. Following this, the powder was diluted to achieve a concentration of 250 μg/ml, which corresponds to MIC of the plant extract, after that, the extract was filtered 50ml of it was taken prepared for the purpose of using it with gold chlorides to act as a reducing agent in the preparation of gold nanoparticles. The gold ion solution was prepared in accordance with the methodology outlined by Ref. 16. with some modification, one gram of HAuCl4 dissolved by 100 mL of DW to form a 10 mg/ml solution. Gold nanoparticles (Au NPs) were synthesized through a mix of a 1 mg/ml HAuCl4 gold ion solution and a 50 ml Pelargonium Graveolens extract. The solution was subjected to a magnetic stirrer for duration of 30 minutes while being slightly heated to a temperature range of 35°C to 45°C. As a result, the mixture exhibited a quick alteration in color, transforming into a dark shade of purple/red within a brief time span. The observed change in color can be assigned to the formation of gold nanoparticles (AuNPs) with a concentration of 15.7 (ppm). The manifestation of a purple color following the mixture of the plant extract and HAuCl4 solution signifies the production of Pelargonium Graveolens AuNPs.\n\nAn X-ray diffract meter (XRD-6000, SHEMADZU-Japan®,™) used to evaluate the produced nanoparticles characteristics. (Current = 30 mA; voltage = 40 kV). A Cu-Kα incident beam (λ = 1.542 A°) at 2θ = 20°-80° used to determine the patterns in which the particles diffracted. Transmission electron microscopy (PHILIPS CM-120-USA®,™) is operating at 100 kV to evaluate the size and morphologies of the nanoparticles. Pelargonium Graveolens AuNPs solutions were characterized using a UV-Vis spectrophotometer (SHEMADZU1200i-Japan®,™) the experiment employed a double beam UV-Vis spectrophotometer to observe the beams under different conditions within the spectral range of 200–1100 nm. An FTIR analysis was conducted utilizing the PerkinElmer Spectrum-USA instrument, covering spectral ranges from 4500 to 500 cm-1. FTIR analysis was conducted in order to examine the functional groups of biomolecules that are responsible for capping, viable stabilization, and reduction of the prepared Pelargonium Graveolens AuNPs. A Zeta potential test was conducted using a Zetasizer Nano ZS (Malvern Instruments®,™) at a temperature of 25°C. The (Zetasizer 6.01 software®,™)was employed for data analysis. The purpose of the zeta-potential measurements was to examine the stability of Pelargonium Graveolens AuNPs in the suspension. Field Emission Scanning Electron Microscopy (FESEM) employed utilizing a (ZIESS, Germany®,™) Electron Microscopy to identify the morphological features of Pelargonium Graveolens AuNPs. The investigation of elemental composition was carried out using EDX with a (Thermo Scientific TM NORANTM®,™ System 6 EDS system).\n\nAntibacterial efficacy of Pelargonium Graveolens AuNPs\n\nThe antimicrobial effect of Pelargonium Graveolens AuNPs was investigated using the Agar diffusion method. Ten isolates of each S. mutans and C. Albican were applied separately on MH agar plates; the previous approach was explained by Ref. 17. Mueller–Hinton agar media was poured separately into sterile petri dishes and wait until setting. A volume of 0.1ml of activated Streptococcus mutans and Candida Albican was evenly distributed onto Mueller-Hinton agar plates and allowed to incubate at the room temperature for duration of 10 minutes. Subsequently, using a sterile stainless steel Cork borer, uniform and sufficiently deep wells measuring 6mm in diameter were generated in the Mueller-Hinton agar. This process was repeated six times on each plate and for each microorganism. Each well was filled with 0.2 mL of the agent to be tested at varying concentrations of 0.06, 0.12, 0.25, and 0.5 mg/mL. The last well filled with Chlorhexidine 0.12% as a positive control, while the center well filled deionized water as a negative control. Plates left at the room temperature for 10 minutes and then incubated aerobically for 24hrs at 37C. Each zone of inhibition was measured across the diameter of each well. No zone of inhibition indicated complete resistant of S. mutans and C. Albican a to the test agent. Then, we calculated the MIC, MBC, and MFC of Pelargonium Graveolens AuNPs against the individual microorganisms by agar dilution method against S. mutans, and C. albicans. Pelargonium Graveolens AuNPs concentrations of 0.06, 0.12, 0.25, 0.5 mg/ml were serially diluted in Mueller–Hinton agar to make 10 mL of agar and extracts, which were then placed into Petri dishes and allowed to solidify before being inoculated with 0.1 ml of activated isolates of microorganisms. All of these Petri dishes, including the control plates, were incubated at 37°C overnight (the negative control, which contained Mueller-Hinton agar with microbial inoculums without the addition of the extracts, and the positive control plates, which contained MH-A and different concentrations of the Pelargonium Graveolens AuNPs without microbial inoculums). The presence or lack of bacteria growth on the plates is checked. The MIC of Pelargonium Graveolens AuNPs is the concentrations at which microbial growth is totally inhibited. The identical approach was followed for all of the microbial isolates, that had been described previously.18 The MBC/MFC of Pelargonium Graveolens AuNPs is the concentrations at which microbial growth is totally killed.\n\nStatistical Package for Social Research was used for descriptive analysis, and presentation (SPSS Statistical Package for social Science version-22, Chicago, Illinois, USA). The Levene test and Shapiro-Wilk test were conducted on a quantitative variable, which encompassed the minimum, maximum, mean, standard deviation (SD), and standard error (SE). The One-way Analysis of Variance (ANOVA) statistical method was employed, along with Tukey’s Honestly Significant Difference (Tukey’s HSD) and Dunnett’s T3 posthoc tests, to conduct multiple pairwise comparisons among the groups. The results are considered statistically insignificant when the P value is greater than 0.05, while they are deemed statistically significant when the P value is less than 0.05.\n\n\nResults\n\nDetermination of the shape and size\n\nTransmission electron microscopy (TEM) was employed to investigate the characterization of the synthesized nanoparticles (NPs). The morphology of gold nanoparticles (AuNPs) is characterized by a combination of hexagonal, spherical, semi-spherical, and triangular-shaped particles. The size and abundance of gold nanoparticles particles decrease as the concentration of Pelargonium Graveolens leaves extracts increases. The morphology Pelargonium Graveolens AuNPs is depicted in Figure 1-A, where the AuNPs are represented as a core and the Pelargonium Graveolens acts as a shell surrounding the AuNPs surface, and as shown in Figure 1-B the average size of Pelargonium Graveolens AuNPs has been estimated to be 294 nm due to the small concentration of Pelargonium Graveolens leaves extracts is 250 μg/ml (MIC of plant extract), It is considered a good and safe particle size because the smaller size easily to uptake by mammalian cells this is agree by Ref. 19.\n\nFor further determination of the Pelargonium Graveolens AuNPs, The X-ray diffraction (XRD) pattern was utilized to analyze the diffraction peaks observed at 2θ = 39.9°, 44°, and 65.28°, which can be attributed to the 111, 200, and 220 crystallographic planes of the cubic structure of the gold nanoparticles (Au NPs) as depicted in Figure 2. These results are consistent with the data provided by the Joint Committee on Powder Diffraction Standards (JCPDS) under the reference number 001-1172. The results mentioned above agree with the data presented by Ref. 20. The current data indicates that XRD pattern of the Pelargonium Graveolens AuNPs closely resembles that of pure gold nanoparticles. The mean size of nano crystallites in Pelargonium Graveolens AuNPs is 69.587 nm calculated From the well-known Scherrer formula (D = 0.9λ/β. Cos θ) In this context, the symbol D represents the average size of crystallites, β refers to the line broadening as quantified by the full width at half maximum (FWHM) of a peak, λ represents the wavelength of X-rays used for irradiation, and θ signifies the maximum position value of the peak21 as shown in Table 1.\n\nIn the cases of Pelargonium Graveolens AuNPs the FTIR measurements detailed in Table 2 were conducted in an effort to determine the character of the organic protection layer surrounding the AuNPs based on comparable research in the literature.22,23 The observed significant shifts in the spectra of certain peaks subsequent to the formation of AuNPs are hypothesized to be attributed to the impact exerted by the adjacent metal surface. Hence, it is postulated that the observed displaced peaks, as documented in Table 2, are indicative of the presence of organic matter surrounding the synthesized AuNPs. Figure 3 demonstrates the Fourier Transform Infrared (FTIR) analysis conducted to assess the significant biomolecules involved in the capping and stabilization of Pelargonium Graveolens AuNPs synthesized through a green method. Intense absorptions are observed at 3436.59, 2067.21, 1636.44, and 683.21 cm-1. IR band at 3436.59 cm-1 refers to the OH stretching mechanism of the proteins, polyphenols, and carbohydrates. The band noticed at 2067.21 and 683.21 cm-1 related to the C≡C expanding of the alkynes group and C–N/C–Cl in plane bending, respectively. Furthermore, the IR band at 1636.44 cm-1 is characteristic of the C=O expanding of the carboxylic group. Hence, it is possible that enzymes/proteins are involved in the process of reducing metal ions through the oxidation of aldehydes to carboxylic acids. Proteins possess the capacity to form links with gold nanoparticles (AuNPs) via carboxylate ions found in amino acid residues or through free amine groups within the protein’s structure.24,25 In addition, the presence of the C=O stretching mode indicates the presence of the carboxylic acid (-COOH) group in the material that is attached to gold nanoparticles (Au NPs). Hence, the spectral peak observed at a wavenumber of 1636.44 cm-1 can be attributed to the manifestation of amine groups, signifying a possibility of protein binding onto gold nanoparticles. The provided information holds significant value in informing the design of functionalization procedures, particularly in the context of utilizing particles for drug delivery purposes.\n\nFigure 4 shows the absorbance of the peak of Pelargonium Graveolens AuNPs was at 527 nm. Pelargonium Graveolens AuNPs show a massive peak. The successful synthesis of Pelargonium Graveolens AuNPs was confirmed by the observation of a dark purple color in the reaction mixture and the presence of specific absorption spectra at a wavelength of 527 nm in the UV-vis absorption spectroscopy. This outcome aligns with findings reported in previous studies.16\n\nThe zeta potentials of the particles present in the sample of Pelargonium Graveolens AuNPs were determined at a temperature of 25°C. Figure 5 shows that the Pelargonium Graveolens AuNPs sample showed positive zeta-potential values between 0 and +50 mV the observed range can be classified as an initial state of stability for colloidal systems that agree with.26 The zeta potential of the Pelargonium Graveolens AuNPs was measured to be 27 mV Figure 5. This value suggests that the nanoparticles were stable and had a reduced propensity to aggregate and form larger particles.\n\nThe results clearly presented in Figure 6-B demonstrate that the particle composition unequivocally corresponds to gold. The presence of trace amounts of additional elements, such as oxygen (O), was observed in the elemental composition of the plant extract after the solvent evaporation process. The elemental composition of the plant extracts was determined using inductively coupled plasma optical emission spectroscopy (ICP-OES), revealing the presence of trace amounts of these elements, among others. The data exhibited a strong correlation between the concentrations of different elements present in the plant extracts and the results obtained from Energy-Dispersive X-ray Spectroscopy (EDX), as seen previously in this report,16 and the findings from field emission scanning electron microscopy (FESEM) analysis, as depicted in Figure 6-A, indicate that the gold nanoparticles (AuNPs) were effectively separated and did not form aggregates. This can be attributed to the presence of Pelargonium Graveolens, which functions as a protective agent, corroborating the observations made through transmission electron microscopy (TEM) and this agree with.27\n\nAntibacterial activity of Pelargonium Graveolens AuNPs\n\nThe antimicrobial efficacy of Pelargonium Graveolens AuNPs was evaluated using Streptococcus mutans and Candida albicans as test organisms. Significant zones of inhibition were observed subsequent to the exposure of the microorganisms to the Pelargonium Graveolens AuNPs that were prepared Figure 7A,B. The findings of the present study demonstrate the effectiveness of the synthesized nanoparticles in inhibiting the growth rate of Streptococcus mutans and Candida albicans following a 12-hour exposure period as shown in Figure 8.\n\nThe study results indicate that MBC for Candida albicans was 0.5 mg/ml, while MBC for Streptococcus Mutans was 0.12 mg/ml, as presented in the Tables 3 and 4. Subsequent re-culturing on BHI-agar media revealed no growth at these concentrations as shown in Figure 8 indicating that the 0.5 mg/ml concentration had a fungicidal effect on Candida albicans, while the 0.12 mg/ml concentration had a bactericidal effect on Streptococcus Mutans. Also the results presented in the table indicate that the MIC for Candida albicans was 0.25 mg/ml, while for Streptococcus Mutans it was 0.06 mg/ml. However, onto re-culturing on BHI-agar, it was observed that these concentrations exhibited growth, indicating that they had a bacteriostatic effect.\n\n\nDiscussion\n\nThe results show that with increase concentration of Pelargonium Graveolens AuNPs, the diameter of inhibition zone of streptococcus mutans growth increased to reach the maximum diameter as shown in Table 5 and Figure 9.\n\nAnd the results show that with increase concentration of Pelargonium Graveolens AuNPs, the diameter of inhibition zone of Candida Albicans growth increased to reach the maximum diameter as shown in Table 6 and Figure 10.\n\nIn this study although the mean inhibition zone for Streptococcus mutans growth by Pelargonium Graveolens AuNPs (1.16 cm) in concentration 0.06 mg/ml is lower than that of Chlorhexidine gluconate 0.12% (2.17 cm), but this mean inhibition zone for Streptococcus mutans growth by Pelargonium Graveolens AuNPs significantly increases with increasing concentration till it reaches its highest value 2.18 cm at a 0.5 mg/ml concentration as shown in Table 5 and Figure 9. The study found that Pelargonium Graveolens AuNPs at a concentration of 0.5 mg/ml exhibited a mean inhibition zone of 1.79 cm for Candida Albican growth, which was lower than the mean inhibition zone of 1.95 cm, observed for Chlorhexidine gluconate 0.12%. However, it is possible that the mean inhibition zone for Candida Albican growth by Pelargonium Graveolens AuNPs may increase with higher concentrations as shown in Table 6 and Figure 10. This finding indicates that the antibacterial effect of Pelargonium Graveolens AuNPs is concentration dependent. Due to there is no previous studies on the effect of Pelargonium Graveolens AuNPs against Streptococcus mutans and Candida albicans, so that the study compared with other studies of the effects Pelargonium Graveolens AuNPs or effect of the secondary metabolites of Pelargonium Graveolens on others microorganisms. This finding may be attributed to the synergistic or additive effect of the secondary metabolites that have antimicrobial activity such as citronellol that have antimicrobial and anti-oxidant activity,28 and the research conducted by Guimares et al., 2019 discovered that citronellol exhibited significant bactericidal properties against S. aureus strains.29 And it agree with Friedman et al., 2004 have classified essential oils and their compounds into two categories, namely slow-acting and fast-acting compounds. The authors have reported that terpineol, eugenol, geranial, carveol, and citronellol are categorized as fast-acting compounds due to their ability to rapidly inactivate microorganisms such as E. coli and S. Typhimurium within a short duration of 2 hours. According to reports, certain antimicrobial agents such as carvacrol, cinnamaldehyde, and geraniol have been identified as fast-acting compounds capable of inactivating microorganisms such as E. coli and S. Typhimurium within a five-minute timeframe.30 Geraniol and citronellol are an active component of Pelargonium Graveolens.28 Additionally it may be due to the presence of certain compounds in Pelargonium Graveolens AuNPs which might exert their effect either on the cell membrane of streptococci mutans or on the enzymes that are necessary for the growth of this bacteria and this assumption need further studies for its confirmation.\n\n\nConclusion\n\nTo our knowledge, the current investigation represents a novel contribution to the scientific literature, as it is the first to demonstrate the antimicrobial efficacy of Pelargonium Graveolens synthesized through green synthesis techniques against Streptococcus Mutans and Candida Albicans. There exists a notable degree of interest in the investigation of potential biomedical applications associated with gold nanoparticles (Au NPs). The current investigation employed extracts of Pelargonium Graveolens for creating diverse shapes and dimensions of Au NPs. The successful synthesis of stable AuNPs has been supported by a range of characterization methods, including UV-Vis, Zeta potential, FESEM, EDX, XRD, TEM, and FTIR. The composition consists of a combination of hexagonal, spherical, semi-spherical, and triangular like particles nanoparticles with a particle size mean 294nm and low aggregation degree were obtained, exhibiting long-term stability. These nanoparticles can readily associate with diverse bioactive compounds. A positive zeta potential value indicates favorable stability of the particles in the suspension. In addition, it is possible for Au NPs to combine with diverse bioactive compounds that adhere to the Pelargonium Graveolens extract, such as protein-based molecules, alkynes and phenolic compounds. This amalgamation could potentially enhance the biological activity of Au NPs. The Pelargonium Graveolens AuNPs that were synthesized using green methods have demonstrated effective antibacterial properties against Streptococcus Mutans and Candida Albicans in comparison with Chlorhexidine, while also maintaining a good level of safety. According to these results it can be considered as promising oral health care product in the future and it can be used as mouthwash as alternative of Chlorhexidine mouthwash that still had adverse effects over time.\n\n\nAuthor contributions\n\nconceptualization: Ahmed Yousif Mahdi, Aseel Haidar M.J. Al. Haidar\n\ndata curation: Ahmed Yousif Mahdi, Aseel Haidar M.J. Al. Haidar\n\nformal analysis: Ahmed Yousif Mahdi\n\nfunding acquisition: Ahmed Yousif Mahdi, Aseel Haidar M.J. Al. Haidar\n\ninvestigation: Ahmed Yousif Mahdi, Aseel Haidar M.J. Al. Haidar\n\nmethodology: Ahmed Yousif Mahdi, Aseel Haidar M.J. Al. Haidar\n\nproject administration Ahmed Yousif Mahdi, Aseel Haidar M.J. Al. Haidar\n\nresources: Ahmed Yousif Mahdi, Aseel Haidar M.J. Al. Haidar\n\nsoftware: Ahmed Yousif Mahdi, Aseel Haidar M.J. Al. Haidar\n\nsupervision: Aseel Haidar M.J. Al. Haidar\n\nvalidation: Ahmed Yousif Mahdi, Aseel Haidar M.J. Al. Haidar\n\nvisualization: Ahmed Yousif Mahdi, Aseel Haidar M.J. Al. Haidar\n\nWriting – original draft preparation: Ahmed Yousif Mahdi and Aseel Haidar M.J. Al. Haidar\n\nWriting – review and editing: Ahmed Yousif Mahdi, Aseel Haidar M.J. Al. Haidar\n\n\nEthical approval\n\nAll of the individuals were given thorough information about the study and the procedures involved, and their informed consent was acquired on a form approved by the ethics committee of the University of Baghdad, College of Dentistry (No. 771233, 26-1-2023, with ref. number 771).\n\nPatients were included in this study after signing an informed consent.", "appendix": "Data availability\n\nRaw data for [Green synthesis of gold nanoparticles using Pelargonium Graveolens leaf extract: Characterization and anti-microbial properties (An in-vitro study)], https://doi.org/10.6084/m9.figshare.25674225.v8. 31\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0)\n\n\nAcknowledgement\n\nThe authors express their gratitude to all the participants in the research for their assistance.\n\n\nReferences\n\nSareh M-S, Abbasi M, Shafiee M, et al.: Renal clearable nanoparticles: an expanding horizon for improving biomedical imaging and cancer therapy. 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Food Chem. 2004 Sep 22; 52(19): 6042–6048. PubMed Abstract \| Publisher Full Text\n\nAsker A: Green synthesis of gold nanoparticles using Pelargonium Graveolens leaf extract: Characterization and anti-microbial properties (An in-vitro study). Dataset. figshare. 2024. Publisher Full Text" }	[ { "id": "288743", "date": "18 Jun 2024", "name": "Raya Abid", "expertise": [ "Reviewer Expertise preventive dentistry" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article is scientific and original. It's necessary to find new approaches in the prevention of diseases and the research was trying to find these approaches. Some minor revisions are necessary before the duplication as follow:\n\nAbbreviations should be removed from abstract In abstract. Always starting should be done by capital letters. Reference for the isolation and preparation of microorganisms should be added. In method, MIC and other abbreviations are not clear. It's necessary to check the grammar and not use the pronoun 'we'. Its necessary not to start with abbreviations like FTIR when you say previous studies, you have to put them and not just one. Finally summarize the conclusion should be more clear and precise.....best regard\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": "11859", "date": "28 Jun 2024", "name": "Ahmed Asker", "role": "Author Response", "response": "Thanks Dr. Raya Abid for reviewing my manuscript. I am very grateful and I agree with all your comments and revisions. Warm regards, Ahmed Yousif Mahdi Asker" }, { "c_id": "11862", "date": "28 Jun 2024", "name": "Ahmed Asker", "role": "Author Response", "response": "Dear Dr. Raya Abid, Below are the corresponding author comments with respect to your review report: 1. Ok . I’ll change the abbreviation ( AuNPs ) that appear in the abstract, by (gold nanoparticles). 2. Ok. I’ll return to my article and will starting by capital letters. 3. The Reference for the isolation and preparation of microorganisms is ( Baron E, Peteson L, Fingold S. Methods for Testing Antimicrobial Effectiveness. In: Bailey and Scotts diagnostic Microbiology. 9th ed. C.V. Mosby Co., St. Louis, USA; 1994.) . 4. In method the abbreviations are , MIC ( minimum inhibitory concentration), MBC (minimum bactericidal concentration) and MFC ( minimum fungicidal concentration), MH-A ( Mueller-Hinton agar ) . 5. Ok dr. I’ll check all the grammar and not use the pronoun 'we'. 6. Ok dr. I’ll replace the FTIR with Fourier Transform Infrared. 7. Thanks Doctor. I’ll summarize the conclusion to be should be more clear and precise as following:- Conclusion (The current investigation employed extracts of Pelargonium Graveolens for creating diverse shapes and dimensions of Au NPs. The successful synthesis of stable AuNPs has been supported by a range of characterization methods, including UV-Vis, Zeta potential, FESEM, EDX, XRD, TEM, and FTIR. The green synthetic gold nanoparticles form Pelargonium Graveolens leaves extract show low aggregation degree were obtained, exhibiting long-term stability. These nanoparticles can readily associate with diverse bioactive compounds. In addition, it is possible for Au NPs to combine with diverse bioactive compounds that adhere to the Pelargonium Graveolens extract, such as protein-based molecules, alkynes and phenolic compounds. This amalgamation could potentially enhance the biological activity of Au NPs that demonstrated effective antibacterial properties against Streptococcus Mutans and Candida Albicans in comparison with Chlorhexidine, while also maintaining a good level of safety. According to these results it can be considered as promising oral health care product in the future and it can be used as mouthwash as alternative of Chlorhexidine mouthwash that still had adverse effects over time.)" } ] }, { "id": "315545", "date": "27 Aug 2024", "name": "Saraswathi Jaggali", "expertise": [ "Reviewer Expertise Traditional medicines", "Pharmacology", "Genetics", "Molecular Biology", "Plant and Animal biotechnology", "Bioinformatics drug designing." ], "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\nResearch article on Green synthesis gold nanoparticles from P. graveolens and their antimicrobial activity is exciting work. First, the author must change the microbial strains and plant name in italics form where it is mentioned. Second, Previous literature work is given in the form of a reference number but it should be in author-name. Statistical analysis P value should be written in the symbol form P>0.05 or P<0.05.\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": "12309", "date": "28 Aug 2024", "name": "Ahmed Asker", "role": "Author Response", "response": "Thanks Dr. Saraswathi Jaggali for reviewing my manuscript. I am very grateful and I agree with all your comments and revisions. Warm regards, Ahmed Yousif Mahdi Asker" } ] } ]	1	https://f1000research.com/articles/13-572
https://f1000research.com/articles/12-1465/v1	13 Nov 23	{ "type": "Case Report", "title": "Case Report: Shewanella algae, a rare cause of osteosynthesis-associated infection", "authors": [ "Sofiane Masmoudi", "Mohamed Ali Khlif", "Hajer Battikh", "Meriam Zribi", "Maher Barsaoui", "Khaled Zitouna", "Mohamed Ali Khlif", "Hajer Battikh", "Meriam Zribi", "Maher Barsaoui", "Khaled Zitouna" ], "abstract": "Shewanella is an emerging human pathogen. It mostly causes skin and soft tissue infections. Osteosynthesis-associated infection involving Shewanella are rare and in most cases are secondary to direct contamination following open fractures in aquatic environments. Here, we present a rare case of hematogenous osteosynthesis-associated infection involving Shewanella algae affecting an 18-year-old patient who was operated on for 12th thoracic vertebrae and 4th lumbar vertebrae fractures occurring in an aquatic environment. We performed surgical debridement with subsequent double course parenteral antibiotherapy that was then adapted to bacteria sensitivities for three weeks. After a follow-up of six months, the patient had no signs of recurrent infection. The presence of infected dermabrasions and the concordance between germs isolated in operative samples and in blood cultures presumes that the contamination was hematogenous.", "keywords": [ "Shewanella", "Osteosynthesis", "Infection", "Osteosynthesis-associated infection", "Hematogenous" ], "content": "Background\n\nShewanella is an aquatic Gram-negative bacillus and is widely found throughout the environment. The most commonly reported clinical presentation is skin and soft tissue infection,1–3 often preceded by exposure to seawater.4 Bacteremia is often found in premature neonates with congenital pneumonia, patients with infections of the soft tissues of the lower limbs and with underlying health issues such as chemical esophagitis, cholangitis and liver abscess.5 All the cases of osteosynthesis-associated infection involving Shewanella reported in the literature occurred after a direct contamination following open fractures, most often in aquatic environments.6–9 We report the first case of osteosynthesis-associated infection caused by Shewanella algae via haemathogenic route.\n\n\nCase presentation\n\nAn 18-year-old patient with no previous medical history of note was admitted to the intensive care unit after he fell into a well resulting in polytrauma. In addition to head and thoracic injuries, the whole body CT revealed a burst fracture of 12th thoracic vertebra with section of the spinal cord and complete paraplegia, burst fracture of 4th lumbar vertebra (Figure 1). In cutaneous clinical examination we found multiple water-soiled dermabrasions in both legs.\n\nHe was operated on in the orthopaedic surgery department, and postero-lateral fusion was performed from the 10th thoracic vertebra to the 5th lumbar vertebra (Figure 2).\n\nAt the 10th post-operative day the patient presented fever (39.5°C), redness and swelling around the surgical wound with serous discharge (Figure 3). Dermabrasions in lower limbs were infected. The vital signs included blood pressure, 120/60 mm Hg (NR: ≥ 90/60 mm Hg); respiration, 20 breaths per minute (NR: 12–18 breaths per minute); pulse, 95 beats per minute (NR: 60–100 beats per minute). Investigations showed a high white cell count (17.6 × 109/L) (NR: 4.5–11 × 109/L) and a raised C-reactive protein (176 mg/L) (NR: <0.3 mg/L). Three blood cultures were performed.\n\nThe patient was reoperated on the 11th post-operative day. Intraoperatively, we found abundant pus with infected necrotic tissues that were then cleaned and debrided. We took five deep bacteriological samples. The operative wound was closed on aspiratifs Redon drain. One of the blood cultures became positive to Shewanella algae. Intraoperative deep tissue specimens grew Shewanella algae and Klebsiella pneumoniae. Shewanella algae was resistant to amoxicillin, amoxicillin-clavulanic acid and levofloxacin, had intermediate susceptibility to trimethoprim-sulfamethoxazole and was sensitive to imipenem/cilastatin. Klebsiella pneumoniae was multi-resistant and was only sensitive to colistin. The patient had a double course of parenteral antibiotics (Imipenem/cilastatin at a dose of 500/500 mg/6 hours and colistin at a dose of 3 MUI/8 hours) for 25 days. The patient had minor adverse events such as epigastralgia and vomiting, which resolved with symptomatic treatment.\n\nAfter three weeks of antibiotics, white cell count and C-reactive protein normalized. The surgical wound healed with no fistula. The patient was addressed to physical medicine and rehabilitation department. At eight months follow-up, the patient had no signs of recurrent infection.\n\n\nDiscussion\n\nShewanella has been regarded as an uncommon source of human infection. Despite being identified more than 70 years ago,1 our understanding of the bacterium’s spread and the symptoms it causes comes primarily from a restricted set of individual case studies. Predominantly concentrated in tropical regions, the highest frequency of occurrences is noted within Southeast Asia, Southern Europe, and Africa.10 They naturally exist in various environments like water of all types, raw fish, oily food, and soils.2,5 Human infections involve Shewanella algae, putrefaciens, halitosis, and xiamenensis. However, the more offending species are Shewanella algae and putrefaciens accounting for more than 80% of cases.1 Shewanella infections can be serious leading to life-threatening conditions such as necrotizing fasciitis and septic shock.11–14 The route of infection is more likely cutaneous (wounds, leg ulcers, etc.), and, less frequently hepatobiliary or respiratory.15 Malignancy, hepatobiliary disease, diabetes, immunodepression, dysregulated iron metabolism and chronic infections of lower limb have been reported to be risk factors for developing a Shewanella infection.1,2,15–17 Although the patient received routine preoperative antibioprophylaxis based on 2 g of cefazolin and had no medical history, he developed infection.\n\nIn this case, Klebsiella pneumoniae was co-isolated in deep bacteriological samples. In fact, Shewanella algae are frequently identified in polymicrobial infections and the most common bacterial strains co-isolated are Enterobacteriaceae and marine flora bacteria.2\n\nCases of osteosynthesis-associated infection caused by Shewanella are rare. In our review of the literature, all cases were secondary to open fractures of lower limbs occurring in an aquatic environment.6,8,9,18 To the best of our knowledge, this is the first case in which osteosynthesis implant contamination was secondary to bacteremia. Shewanella algae have a significant ability to haematogenous diffusion. Indeed, Vignier9 and Yousfi19 observed that bacteremia occurred in respectively 28% and 18% of the cases they studied. Mortality rates were respectively 13 and eight per cent. Bacteremia can lead to severe secondary infection including instances of epidural spinal abscess, purulent pericarditis, acute gastroenteritis accompanied by bloody diarrhea, and meningoencephalitis, as reported in various studies.20–23 The concordance between germs isolated in operative samples and in blood cultures presumes that the contamination was haematogenous, probably originating from infected dermabrasions.\n\nAs in other cases of osteosynthesis-associated infection reported in the literature, we performed surgical debridement with subsequent double course parenteral antibiotherapy that was then adapted to bacteria sensitivities. Colistin was selected because it was the only effective antibiotic against Klebsiella pneumonae. Imipenem/cilastatin was the only antibiotic available in the hospital to which Shewanella was sensitive. Typically, Shewanella displays susceptibility to erythromycin, fluoroquinolones, chloramphenicol, third and fourth generation cephalosporins, aminoglycosides, carbapenems, and to some degree, trimethoprim-sulfamethoxazole and tetracyclines. However, it exhibits resistance against first and second generation cephalosporins, penicillin, and colistin.24 An emergence of resistance has been documented towards imipenem and piperacillin/tazobactam, which can be attributed to the presence of the class D beta-lactamase enzyme.23 Hopefully, our microbial stain was sensitive to imipenem/cilastatin.\n\nCurrently, there are no established guidelines for the management of shewanella infections. However, certain reports have indicated that addressing Shewanella infections may necessitate a proactive approach involving both surgical debridement and administration of appropriate antimicrobial agents. This particular case underscores the importance of recognizing Shewanella algae as a potential offending pathogen in osteosynthesis-associated infection coming within the framework of secondary hematogenous infection even in patients without significant underlying medical conditions.\n\n\nConsent\n\nWritten informed consent for publication of 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\nHolt HM, Gahrn-Hansen B, Bruun B: Shewanella algae and Shewanella putrefaciens: clinical and microbiological characteristics. Clin. Microbiol. Infect. 2005; 11: 347–352. PubMed Abstract \| Publisher Full Text\n\nChen YS, Liu YC, Yen MY, et al.: Skin and soft-tissue manifestations of Shewanella putrefaciens infection. Clin. Infect. Dis. 1997; 25: 225–229. Publisher Full Text\n\nTsai M-S, You H-L, Tang Y-F, et al.: Shewanella soft tissue infection: case report and literature review. Int. J. Infect. Dis. 2008; 12: e119–e124. Publisher Full Text\n\nHolt HM, Søgaard P, Gahrn-Hansen B: Ear infections with Shewanella alga: a bacteriologic, clinical and epidemiologic study of 67 cases. Clin. Microbiol. Infect. 1997; 3: 329–334. PubMed Abstract \| Publisher Full Text\n\nBrink AJ, van Straten A , van Rensburg AJ : Shewanella (Pseudomonas) putrefaciens Bacteremia. Clin. Infect. Dis. 1995; 20: 1327–1332. Publisher Full Text\n\nPrinja A, Singh J, Davis N, et al.: A rare cause of wound infection after an open fracture: Shewanella putrefaciens. Case Rep. 2013; 2013: bcr2012008537–bcr2012008537. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPrischl C, Bendtsen MM, Laursen M: Shewanella algae-infektion efter kirurgisk behandling af Haglunds deformitet og akillesseneruptur.n.d.\n\nLee GC, Lee J-Y, Kim D-M, et al.: A Fatal Shewanella algae Infection After an Open Tibial Fracture Following a Tropical Storm: A Case Report. JBJS Case Connect. 2013; 3: e92. PubMed Abstract \| Publisher Full Text\n\nVignier N, Théodose R, Barreau M, et al.: Human Infection with Shewanella putrefaciens and S. algae: Report of 16 Cases in Martinique and Review of the Literature. Am. J. Trop. Med. Hyg. 2013; 89: 151–156. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFinkelstein R, Oren I: Soft Tissue Infections Caused by Marine Bacterial Pathogens: Epidemiology, Diagnosis, and Management. Curr. Infect. Dis. Rep. 2011; 13: 470–477. PubMed Abstract \| Publisher Full Text\n\nGiroux P-A, Sinna R, Mercut R, et al.: Shewanella putrefaciens necrotizing fasciitis of the lower limb. Med. Mal. Infect. 2017; 47: 436–438. PubMed Abstract \| Publisher Full Text\n\nAnanth AL, Nassiri N, Pamoukian VN: Shewanella algae: A Rare Cause of Necrotizing Fasciitis. Surg. Infect. 2014; 15: 336–338. PubMed Abstract \| Publisher Full Text\n\nBrugnaro P, Morelli E, Ebo F, et al.: The first Italian case report of leg ulcer and sepsis caused by Shewanella algae in a immunocompetent patient.n.d.\n\nLatif A, Kapoor V, Vivekanandan R, et al.: A rare case of Shewanella septicemia: risk factors, environmental associations and management. BMJ Case Rep. 2019; 12: e230252. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTo KKW, Wong SSY, Cheng VCC, et al.: Epidemiology and clinical features of Shewanella infection over an eight-year period. Scand. J. Infect. Dis. 2010; 42: 757–762. PubMed Abstract \| Publisher Full Text\n\nPagani L, Lang A, Vedovelli C, et al.: Soft Tissue Infection and Bacteremia Caused by Shewanella putrefaciens. J. Clin. Microbiol. 2003; 41: 2240–2241. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTakata T, Chikumi H, Morishita S, et al.: Shewanella algae Bacteremia in an End-stage Renal Disease Patient: A Case Report and Review of the Literature. Intern. Med. 2017; 56: 729–732. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSmith JRO, Morgan M, Palmer JH: Shewanella algae infection complicating an open lower limb fracture. J. Plast. Reconstr. Aesthet. Surg. 2014; 67: e99–e100. PubMed Abstract \| Publisher Full Text\n\nYousfi K, Bekal S, Usongo V, et al.: Current trends of human infections and antibiotic resistance of the genus Shewanella. Eur. J. Clin. Microbiol. Infect. Dis. 2017; 36: 1353–1362. PubMed Abstract \| Publisher Full Text\n\nTan C-K, Lai C-C, Kuar W-K, et al.: Purulent Pericarditis with Greenish Pericardial Effusion Caused by Shewanella algae. J. Clin. Microbiol. 2008; 46: 2817–2819. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDey S, Bhattacharya D, Roy S, et al.: Shewanella algae in acute gastroenteritis. Indian J. Med. Microbiol. 2015; 33: 172–175. PubMed Abstract \| Publisher Full Text\n\nBrulliard C, Traversier N, Allyn J, et al.: Case Report: Disseminated Shewanella algae Infection with Meningoencephalitis in a Traveler Secondary to Marine Injury in Madagascar. Am. J. Trop. Med. Hyg. 2017; 97: 1043–1044. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKim D-M, Kang C-I, Lee CS, et al.: Treatment Failure Due to Emergence of Resistance to Carbapenem during Therapy for Shewanella algae Bacteremia. J. Clin. Microbiol. 2006; 44: 1172–1174. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCimmino T, Olaitan AO, Rolain J-M: Whole genome sequence to decipher the resistome of Shewanella algae, a multidrug-resistant bacterium responsible for pneumonia, Marseille, France. Expert Rev. Anti-Infect. Ther. 2016; 14: 269–275. PubMed Abstract \| Publisher Full Text" }	[ { "id": "272741", "date": "11 Jun 2024", "name": "Guillaume Beraud", "expertise": [ "Reviewer Expertise 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\nMasmoudi et al presents a case of Shewanella algae osteosynthesis-associated infection with the specificity that the pathogen was isolated in blood culture. They describe well the sequence that resulted in the infection, and their hypothesis is sound. English is good, the manuscript is well written and easy to read. I don't see any issue to be addressed.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [] }, { "id": "299831", "date": "14 Aug 2024", "name": "Elmostafa Benaissa", "expertise": [ "Reviewer Expertise medical microbiologymolecular biologyinfectious 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\nIn this work by Masmoudi et al. a case of osteosynthesis-associated hematogenous infection involving the alga Shewanella is reported. The report is concise and addresses a case of infection by a relatively rare pathogen, but one for which there is a growing number of There have been only a few cases reported in the literature in recent years. General comments: - Quality of presentation and structure of the manuscript: Satisfactory\n- To what extent are the conclusions supported by the data:Satisfactory\n- Do you have any concerns about possible image manipulation, plagiarism or any other unethical practice? : No\n- If this manuscript involves human and/or animal work, have the subjects been treated ethically and have the authors followed appropriate guidelines? : Yes\nspecific comments: - authors should specify in their report the method used to identify this bacterial species (maldi-tof or classical method...)\n- why did the authors speak of contamination via the blood-borne route, when the patient had open fractures exposed to aquatic, saprophytic and cutaneous flora? It may be that the osteosynthesis material was contaminated at the time of insertion and then infected, giving rise to bacteremia at the starting point of the osteosynthesis material.\n\nclarification is required in this 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? Yes", "responses": [ { "c_id": "12313", "date": "02 Sep 2024", "name": "Sofiane Masmoudi", "role": "Author Response", "response": "Dear Dr Elmostafa, Thank you for reviewing our article. Your constructive comments made us aware of the lack of precision in certain aspects of our article. Indeed, it enabled us to give more details about microbiological techniques used to identify germs. Regarding your question about our theory of hemothogenic contamination, we have retained this theory given that the case involved a closed fracture of the thoracolumbar spine associated with water soiled dermabrations at a distance (on the both lower limbs) and the identification of shewanella algae on blood cultures. in this second version of the article, we have emphasized these elements in order to make the clinical case clearer for the reader." } ] } ]	1	https://f1000research.com/articles/12-1465
https://f1000research.com/articles/13-156/v1	01 Mar 24	{ "type": "Research Article", "title": "Prayers for Sickness: What do people pray for and how do they deal with unanswered prayer?", "authors": [ "Simon Dein", "Candy Gunther Brown", "Candy Gunther Brown" ], "abstract": "Background This paper focuses upon prayer for sickness. What do individuals suffering from illness, their families and the wider community pray for? How do they deal with unanswered prayer? Do they pray for cure, to guide medical professionals or to cope with their sickness? What rationalisations do they proffer for unanswered prayer?\n\nMethods Based on a critical literature review and deploying secondary data from the Twenty First Century Evangelical research programme, the data suggest that prayers for guiding medical professionals and coping are more common than for cure, at least in Global North countries such as the UK and US. But why do those who believe in miracles not ask God for divine healing? Furthermore, unanswered prayer can conflict with Christian views of God as omnipotent and all loving.\n\nResults Respondents use a number of theodical rationalisations to resolve this conflict.\n\nConclusions The results are discussed in relation to cognitive dissonance theory, learned helplessness, the need to conserve a relationship with the Divine, and desire to manage risk of disappointment and reduce consequent emotional pain.", "keywords": [ "Prayer", "miracle", "illness" ], "content": "\n\nTherefore I tell you, whatever you ask for in prayer, believe that you have received it, and it will be yours (Mark11:24).\n\n\nMiraculous healing\n\nThe belief that God can bring about a miraculous healing is ubiquitous in the Bible and prevalent among contemporary Christians. There is a widespread belief among Christian believers that God is able to heal sickness and often does so. Prayer requests reflect this (Pawlikowski et al., 2015; Levin, 2016).\n\nVillage (2005) notes how there are diverse views concerning miraculous healing among Christians- including beliefs about the possibility of God healing miraculously, the relationship between divine healing and secular medicine and God’s ability to heal. There may even be a diversity of views among members of the same congregation. Groups differ in how they conceptualise God working through ‘natural’ channels. As Village argues, ‘Upholding the sovereignty of God in such circumstances seems to naturally turn attention to the sufferers or to those doing the praying as possible reasons for unanswered prayer’ (p.105). Differing attitudes towards miracles among Christians might reflect diverse understandings of the Divine and the relationships between God and the natural world. Fairly widespread beliefs in miraculous healing are found among Pentecostal and Charismatic groups (Singleton, 2001).\n\nCandy Gunther Brown (2012) notes how Pentecostals underscore the healing power of the Holy Spirit both for physical and for psychological problems. Healing is a central aspect of the Pentecostal movement and can account for its widespread appeal, and particularly its growth in the Global South – areas of Latin America, Africa, and Asia where poverty-related infirmities are ubiquitous and conventional medical treatments limited (Brown, 2011). Pentecostals deploy prayer alongside biomedicine rather than as a substitute for it. While testimonies of divine healing are commonplace among Pentecostals, they are often reluctant to subject these claims to empirical scrutiny:\n\n‘Although blatantly anti-medical stances have become much less common among Christians in recent years, many Christians continue to feel ambivalent about modern medicine. Christians want the benefits of medical technology, but they also worry that relying on medicine too much, or seeking medical proof that God heals, hinders faith in God. There is residual unease with biomedicine’s materialistic assumptions, interventionist approach, and apparent hubris.’ (Brown, 2022:5).\n\nAs Brown states in an interview for The New York Times:\n\nIf God can heal, why does he do it so rarely? The world is full of suffering people who pray with no relief. “Even people who believe in miracles often don’t pray for them because they’re afraid of disappointment,” Candy Brown said. “I’ve had people die on my watch. It’s incredibly painful. You ask, ‘Is it my fault?’” She speculated that many Christians’ belief that miraculous healing ceased after New Testament times springs from “protection against pain, protection against feeling ill will toward God or other people. It takes hope and vulnerability to be open to healing.” (Kashdan et al., 2006)\n\nFurther evidence that belief in Divine healing is widespread derives from a Barna study in the USA (Barna, 2016) which indicated that the majority of American adults (66%) held that people could be physically healed through supernatural means by God (strongly agree 33%; somewhat 33%). Evangelicals were the most likely to endorse Divine healing. Respondents who disagreed were comprised of those who either strongly (19%) or somewhat (15%) disagree. Millennials and those who were more highly educated were significantly more likely to be sceptical. Of significant interest Protestants were almost three times more likely to believe people could receive divine healing than Catholics. In this survey 68% of adults had personally prayed for supernatural healing for another person.\n\nA ten-country study (Lugo et al., 2006) found widespread belief in the efficacy of prayer for healing, especially among Pentecostal Christians; 77% of Brazilian Pentecostals, 87% of Kenyan Pentecostals, 74% of Indian Pentecostals, and 62% U.S. Pentecostals claimed to have “witnessed divine healings.” Some scholars estimate that in regions, such as East Asia, where pentecostalism is growing the more rapidly, as many as 80-90% of conversions result from first-hand experiences with healing prayer (Oblau, 2011; Keener, 2011, 2021). Globally, pentecostalism grew at four times the rate of global Christianity and the total world population between 1970 and 2010, such that there are now an estimated 635 million pentecostals worldwide (Johnson & Zurlo, 2020). It is even more noteworthy that 73% of US medical doctors report believing that miraculous healing continues to occur in the present (Orr, 2008).\n\nOnce a common ritual among Christians, the rise of scientific medicine has marginalised prayers for healing, at least in the Global North (Simpson, 1993). A BBC survey (Strangwaves-Booth, 2018) found 62% of adults in Britain expressing belief in the possibility of miracles; although 59% of Christians in the UK report praying for miracles, only 29 percent maintain that their prayers are answered. However it is acknowledged, based upon biblical teaching, that God may not answer every prayer for sickness. As an example David’s son died of an illness despite his father’s prayers. 2 Samuel 12 describes how King David fasted and prayed for seven days for God to spare his dying child but he subsequently died. In verse 22, David said, “Who knows? The Lord may be gracious to me and let the child live.” In this particular example, the text explains the death as a direct result of David’s sin in begetting the child through an adulterous affair concealed by murder. Unanswered prayer is often put down to lack of faith or sin:\n\nJames 4:3 ‘You ask and do not receive, because you ask wrongly, to spend it on your passions’\n\nMatthew 21:22 ‘And whatever you ask in prayer, you will receive, if you have faith.”\n\n1 Peter 3:12 For the eyes of the Lord are on the righteous, and his ears are open to their prayer. But the face of the Lord is against those who do evil.”\n\nIt is more common among pentecostals in the Global South to emphasize the Bible’s promises of healing through prayer and to read these literally as a kind of “how-to” manual for the present day (Jenkins, 2008). Thus, they emphasize verses such as Matthew 4:23: “Jesus went throughout Galilee, teaching in their synagogues, proclaiming the good news of the kingdom, and healing every disease and sickness.” They are confident that healing is for today based on verses such as Hebrews 13:8: “Jesus Christ is the same yesterday and today and forever.” They point to instructions to the Christian such as James 5:14-16: “Is anyone among you sick? Let them call the elders of the church to pray over them and anoint them with oil in the name of the Lord. And the prayer offered in faith will make the sick person well.” For these pentecostals, references to the “prayer of faith” is not so much an explanation for why prayers might fail as an exhortation to pray all the more: “Will not God bring about justice for his chosen ones, who cry out to him day and night? Will he keep putting them off?” (Luke 18:7).\n\n\nWhat do believers ask God for in relation to sickness?\n\nWhile much of the literature has focused upon prayer in relation to psychological and physical outcomes, there is a small literature asking about the content of prayer. Sociologist of religion, Robert Wuthnow (2008), notes that while prayer is widely practiced, it is treated mostly without taking account of its cognitive content or cultural framing. There has been little attention devoted to the content of prayer, other than the assumption that it involves petitions. Byrd’s study of distant intercessory prayer among patients suffering from cardiac problems limited intercessors accepted into the study to “born again” Christians praying “to the Judeo-Christian God.” The pentecostals studied by Brown (2011, 2012) begin with the theological premise that prayers should be “in the name of Jesus by the power of the Holy Spirit.” The intercessor may “petition God to heal, invite the Holy Spirit’s anointing, and/or command the healing and departure of any evil spirits in Jesus’ name” (Brown et al., 2010: 865). Romez (2019, 291) described a prayer intervention credited with an instantaneous healing of gastroparesis (paralyzed stomach) in this way: “The intercessor prayed that, in the name of Jesus, the boy’s stomach be healed. He commanded the healing in the authority and power of Jesus. He made a point of indicating that he had no power or authority to heal, but only with the authority of Jesus Christ, he could command the healing.” Romez (2021, 80) similarly described a prayer credited with instantaneous healing of blindness: “Oh God! You can restore … eyesight tonight, Lord. I know You can do it! And I pray You will do it tonight.” Pentecostals believe moreover that not only is the language of prayer important but that certain individuals may have specific “gifts” of healing, sometimes even “specializing” in particular conditions such as rheumatoid arthritis or deafness (Matthews, 2000; Brown et al., 2010). In all such instances, disease and other infirmities are envisioned as enemies against which the Christian battles in prayer rather than as “blessings” sent by God for the Christian’s spiritual benefit. Accordingly, although these Christians do petition God to heal as well as commanding diseases and demonic spirits to go, petitionary prayers are not phrased “if it by Thy will” but in confidence that healing is God’s will; “A man with leprosy came and knelt before him and said, “Lord, if you are willing, you can make me clean.” Jesus reached out his hand and touched the man. “I am willing,” he said. “Be clean!” Immediately he was cleansed of his leprosy” (Matthew 8:1-3). Pentecostals are wont to note that the Greek word (thelo) translated as “willing” does not connote reluctance, but intense desire, resolution, and delight (Gulick, 2013).\n\nJors et al.’s (2015) systematic review of personal prayer at times of sickness included a wide range of diseases: paediatric sickle cell, cardiac surgery, prostate cancer, HIV, breast cancer, chronic hepatitis C. The final study included 16 articles and indicated that there were five main reasons for and topics of prayer: (1) disease-centered prayer, (2) assurance-centered prayer, (3) God-centered prayer- reflecting the relationship between God and the patient, (4) others-centered prayer, and (5) lamentations- fear, doubt and anger in relation to God. Unsurprisingly disease centred prayer concerning an individual’s illness was found most frequently. The majority of patients prayed for an improvement in their disease, disease management or pain relief but it was actually quite rare to hope for or believe in cure. In other words they prayed for desirable but achievable outcomes. Especially among Muslims, patients preferred not to ask for cure for fear that their prayer would not be answered and to surrender to God’s will. Another common reason for praying was to receive the ability to find meaning or positive experiences in their illness.\n\nHuman suffering raises significant questions pertaining to the role of the Divine in the human world and might bring on a state of cognitive dissonance for believers based upon inconsistencies between the state of the world and religious beliefs (Festinger, 1962). While requests for healing are commonplace, prayer requests may go unanswered. The sick person may not improve, deteriorate or even die. This raises significant issues as to why God does not answer prayer requests and is part of the wider question of theodicy: if God is omnipotent, omniscient and benevolent, why does suffering exist in the world? Unanswered prayer presents difficulties if believers maintain that God is omnipotent and all loving and can result in cognitive dissonance. But as the literature on cognitive dissonance demonstrates, religious believers frequently maintain or even intensify their convictions post disconfirmation (see Dein and Pargament, 2012; Tavris & Aronson, 2007). Such religious convictions are vigorously defended. Montell (2001) argues how religious belief is always held in tension with real world events:\n\n‘Any and all active beliefs that transcendent forces give intrinsic meaning to life come into conflict with an unavoidable awareness of the harsh realities of natural history and current events, rampant human violence and cruelty, as well as natural disaster. Faced with that, one might ask how so many people educated in cause-and-effect reality, whose experience confirms that reality, maintain a belief in the Biblical God of creation, a just God who operates beyond the laws of causality? How can twenty-first century people, with empirical knowledge of recent world events, adhere to a belief in a prayer-answering personal saviour without incurring some discomfort? Whether or not such a God functions in some remote part of the universe, the empirical evidence increasingly indicates that no such God functions on earth. How can this seemingly impossible-to avoid logical inconsistency not lead to an impossible-to-maintain psychological inconsistency? Yet, somehow, belief in such a deity is maintained in alert and informed human minds. We have the ability to form and maintain beliefs that ameliorate difficult-to-accept, sensory-based experience and perception.’\n\nWithin the philosophical literature there is widespread discussion of these issues. Additionally many popular books have addressed the issue of unanswered prayer (e.g. Greig, 2011). Rather less have been written from a psychological perspective (see Dein, 2022 for an overview).\n\nThe above discussion assumes that if someone is not healed despite prayer, this creates a theological problem that must be psychologically resolved. Whether this is the case depends on one’s theological assumptions. The theologian Gregory Boyd (1997) explains that early Christians expected evil, personified in a literal devil and demons, and were accustomed to fighting against it; sickness was not a theological problem but an occasion to battle against the kingdom of Satan just as Jesus did: “The thief comes only to steal and kill and destroy; I have come that they may have life, and have it to the full” (John 10:10), “God anointed Jesus of Nazareth with the Holy Spirit and power, and how he went around doing good and healing all who were under the power of the devil, because God was with him\" (Acts 10:38). Christians were thus admonished: “Do not give the devil a foothold” (Ephesians 4:27), “For we do not wrestle against flesh and blood, but against the rulers, against the authorities, against the cosmic powers over this present darkness, against the spiritual forces of evil in the heavenly places” (Ephesians 6:12). Likewise, even in the Old Testament, an angel said: “Do not be afraid, Daniel. Since the first day that you set your mind to gain understanding and to humble yourself before your God, your words were heard, and I have come in response to them. But the prince of the Persian kingdom resisted me twenty-one days. Then Michael, one of the chief princes, came to help me, because I was detained there with the king of Persia” (Daniel 10:12-13). Humans participated in a cosmic battle between God and his angels against Satan and his demons. This was fully expected, not a theological problem that needed to be solved through hermeneutical gymnastics to resolve cognitive dissonance.\n\nModern Christians, by contrast, do not expect evil, find it perplexing, resign themselves to it as God’s will, and try to understand it and resolve the psychological tensions their worldview creates, rather than fighting against evil. Boyd explains the difference between a “blueprint” and a “warfare” worldview. In the former, God is ultimately responsible for everything, including evil; unanswered prayer is therefore a problem because it raises questions about God’s goodness. People respond by looking for God’s purpose in sickness or disability. The warfare model instead explains evil as ultimately resulting from abuse of freedom by human or demonic agents. There is a cosmic war in which human and angelic agents have aligned themselves with either God or Satan. The battle is not eternal; it had a beginning point, the “fall,” and it will end since God’s victory was assured in Jesus’s triumph on the cross. The warfare worldview encourages hopeful action rather than learned helplessness.\n\nThe psychological theory of “learned helplessness” (Seligman, 1972) can help to explain why many Christians do not pray for miraculous healing. Experimental psychology shows that when humans, as well as animals, experience an uncontrollable traumatic event, when later faced with controllable trauma they endure it passively even though they have the power to take effective action, and they show more stress in the face of trauma. Helplessness produces hopelessness. If subjects instead experience controllable trauma before uncontrollable trauma, they are more likely to continue to take action regardless of whether that action proves to be effective in a given situation, and they show less stress regardless of whether their actions are effective. When applied to prayer, it matters whether individuals have experiences, or hear about experiences, of healing through prayer before they find themselves in need of a miracle. Past disappointments or listening to sermons that teach an expectation of disappointment can result in learned helplessness and passivity in the face of disease or disability. Even a small experience of healing through prayer, or hearing other people’s testimonies of healing, produces hope and encourages persistent prayer even when prayers do not immediately result in healing.\n\n\nThe 21st century Evangelicals research programme\n\nThe 21st century Evangelicals research programme is a quarterly online survey asks about various topics relevant to Christians (Evangelical Alliance, 2023). Included in this survey are various questions related to health and more specifically prayer and God’s role in healing. The health survey conducted in 2015 included 1700 Evangelical Christian individuals. They derive from a wide variety of Protestant church denominations, Anglican, independent charismatic networks, Baptist, Free Church, Independent Evangelical and Pentecostal streams. The survey included multiple choice questions analysed through statistical means and open ended free text questions. Fifty one percent of the sample were from the older generation and 56.4% were male.\n\nThis paper deploys published data from Smith (2018) alongside the author’s analysis of Twenty First Century research programme. The data indicated that these Evangelical Christians asserted that God does intervene to heal miraculously (28% often; 70 % sometimes). There was widespread rejection of the idea that God always heals.\n\nParticipants mentioned several Biblical texts which informed their understandings of prayer and healing:\n\nPsalm 103.2-3: Praise the LORD, my soul, and forget not all his benefits— who forgives all your sins and heals all your diseases,\n\nIsaiah 53.5 By his stripes/wounds you have been healed. Quoted in 1 Peter 2.24,\n\nJames 5.14-15 Is anyone among you sick? Let them call the elders of the church to pray over them and anoint them with oil in the name of the Lord. And the prayer offered in faith will make the sick person well; the Lord will raise them up.\n\nOf significant interest 86% deployed prayers asking that God will guide medical professionals and ensure their treatments were effective. The majority of respondents asserted that, while God can and does heal miraculously, this is frequently through means of medical interventions i.e. through naturalistic means: ‘I believe God heals through the work of doctors and medical treatment, difficult to separate divine healing from healing through medication and health services etc. through which God may work.’\n\nEighty three percent prayed for comfort in suffering. Significantly fewer (64%) prayed that God would heal. In other words prayers were less likely to pray for cure of their illness and more likely to pray for potentially achievable results. Other forms of healing were deployed including laying on of hands for healing (55%) and anointing with oil (26%).\n\nForty nine percent had received divine healing for an illness at some time in their lives. Examples included allergies, pain from fractured ribs, ME improved vision and no longer needing glasses, a burnt hand, self -harm and infertility. In a few instances the healings were extreme:’ My sisters baby girl was born blind but after prayer could see’. Those who had been healed emphasised that they had never suffered from the condition again:’Fifty years ago I was healed of gallstones and have had no recurrence of the illness since’. Often they mentioned that conventional medical treatments had failed before divine healing: ‘I was healed of a sports injury at New Wine. I could not race walk for nearly two years and physio did not help’. In other instances their testimonies focused upon how God had involved and guided medical staff.\n\n\nUnanswered prayer and cognitive dissonance\n\nAround forty-nine percent of respondents mentioned at least on instance in which divine healing had failed and the sick person required further medical treatment or even died. Two examples: ‘My husband was not healed and needed his bowel removed’, ‘yes my sick grandfather dies just like God does not exist you know’. A wide range of views were expressed about unanswered prayer. These were rationalisations to avoid cognitive dissonance:\n\n‘I don’t know why God heals some people and not others’\n\n‘Its difficult to properly account for why healing clearly occurs on some occasions and not on others’\n\n‘I can’t understand why we don’t see more miracles than we do’\n\n‘One of the earliest lessons I learned is that people are healed differently’\n\n‘Not everybody has been healed but there almost always reasons for this’\n\n‘Because healing would have been a blessing but God chose not to heal’\n\n‘I believe God is sovereign and can heal but it is not always his main priority’\n\n‘God is sovereign and we should not, and cannot, try to second guess or dictate to him’\n\n‘God is sovereign –and his will is perfect. This means we should never be “disappointed”\n\n‘Although we need to be faithful in praying and need to realise that the results are in God’s hands’\n\n‘Not everyone we pray for gets healed but I encourage the person to continue praying since God is sovereign in all circumstances’\n\n‘We pray in faith and hope but sometimes God chooses not to answer our prayers’\n\n‘I praise God when he heals someone by ordinary or extraordinary means and I praise God when he chooses to not heal in this world and instead gives grace to live with problems or grace to die well and go to be with him forever.’\n\n‘I believe that God sometimes heals today. I don’t believe that he always does so, even for people who really love him. I think the Church needs to find a middle way of providing prayer, care and support for those who are unwell, and a blame-free environment if they are not supernaturally healed.’\n\n‘We ask God and he does what he knows is best’\n\n‘Recently my church was praying for a member who subsequently died. Looking back at this experience I sense that we were not in full agreement about the objective. For example, some were praying for successful medical treatment, some for the Lord’s “will” to be done. It was all a bit haphazard.’\n\n‘At one time I used to pray and lay hands on the sick and wondered if God had given me a gift in this area. At that time I was praying for a friend’s mother who had cancer, really believing God would heal her, even as she appeared to become sicker. After she died it was a long time before I prayed for anyone in this way again and when I did it was not with a great amount of faith’\n\n‘Depends on expectations-there is always healing but not what we expect’\n\n‘I believe when I pray for someone the healing has already began whether it is immediate or longer term’\n\n‘Some people really do not want God to heal but ask for prayer. Others have still had the problem but were blessed in another way or were able to help others in similar circumstances. Only God knows the heart’\n\n‘I believe the bible teaches that healing was for the Apostolic age and ceased with the completion of the canon of scripture. I believe God CAN heal if he wants to, but that he chooses to do so very rarely.’\n\n\nDiscussion\n\nIn the Twenty First Century Evangelical sample, while the vast majority endorsed the idea that God could heal miraculously if he so chooses, the most frequent requests involved asking God to guide medical professionals and to ensure that their treatments were effective or to provide comfort and alleviate the suffering of the sick, rather than ask for a cure. Participants asked for desirable but achievable outcomes. To this extent these findings reflect the literature cited above reflecting healing through naturalistic rather than miraculous means (e.g. Dein, Stygall & Martin, 2006; Cadge & Daglian, 2008; Taylor et al., 1999). We would argue that prayers need to conserve their relationship with the sacred and avoid cognitive dissonance ensuing from the incompatibility of two views: God is omnipotent and all loving and he has not answered my prayers. Unanswered payer raises issues of God’s ability or willingness to heal. Respondents deployed a range of theodicies to account for the failure of diving healing. These included perceived lack of faith in God’s healing ability, the fact that healing always occurs although it might not be what we expect, healing is not always immediate and may be longer term, the difficulty discerning answered prayer, People are healed differently, God not deciding to heal, God providing the grace to deal with pain and suffering even though a person is not physically cured, scepticism about miraculous healing and the view that miracles no longer occur after the Apostolic Age.\n\nThe findings can be tied to secularisation and disenchantment, the scientifically dominated society leaving little room for the interpretation of events in miraculous terms. Max Weber (1918-19) in his theory of disenchantment discusses how ‘mysterious and incalculable’ powers disappear from the world, nature is managed we may ask whether its social significance. Philosopher Charles Taylor (2007) discusses the fading of god’s mystery and providence and the overemphasis on science in understanding life. Unexplained healings are no longer understood in religious terms. The relationship between god and humanity is diminished. However we may ask whether there are alternative explanations for these findings?\n\nDein and Pargament (2012) propose that psychological rather than physical outcomes may be requested in order to avoid cognitive dissonance, to maintain the belief that God is fully able to heal if he so chooses and most importantly to conserve a relationship with the sacred (see also Dein, Stygall and Martin 2006; Cadge and Daglian 2008; Taylor 1999; Barrett 2001). However as Pargament (1997) suggests, among non-conservative Christians in the USA, individuals look for strength and support from the Divine, rather than cure or miracle. Dein and Pargament (2012) assert that psychological outcomes as compared to physical outcomes can be more easily accomodated in God’s interventions in the process of healing. Boudry and De Smedt (2011) argue that psychosocial causation like relief from anxiety, anger or depression, possessing courage or mental strength, better coping etc are typically less observable and more complex, but more modest, in comparison to many forms of physical and biological causation. As these authors note, prayers for the sick might focus upon coping rather than cure since coping is less likely to fail compared with curing physical illness. As they state:\n\n‘In other words, believers who request supernatural interventions that are subtle and indistinguishable from the natural course of events will have a better chance of finding themselves in a situation in which they can attribute the events in question to God answering their prayers.’\n\nIt is important to note in regard to the foregoing discussion that although the Twenty First Century Evangelical Sample offers insights into common theodicies, there are a number of important limitations in what this data can reveal. It obscures important differences among “evangelicals” included in the survey. One important distinction even among US and UK Christian who pray for healing (let alone reflecting all of global pentecostalism) is between those who express a “blueprint” as opposed to a “warfare” (Boyd, 1997) model of the nature of God’s sovereignty. The former model is exemplified by Calvinism (Warfield, 1918) whereas the latter is reflected in offshoots of the Vineyard movement’s theology that the Kingdom of Heaven is both “already and not yet” (Wimber & Springer, 1987; Clark, 1998) and that Christians are living in “in between times” and must consequently engage in a battle between kingdoms even though the ultimate victory was already won by Christ on the cross. If healing does not depend solely on the question of whether God “chooses” to answer prayer, then prayer involves not only petitions to God but also commands—to sicknesses and to any evil spirits or demons that might be causing diseases or other afflictions (MacNutt, 1995), and “faith” may be understood more in terms of perseverance (Brown, 2012) than an abstract and generally unfalsifiable cognitive capacity. Thus, it is important to note reasons why Christians who believe in healing might not pray for it while also recognizing that many Christians do pray for miraculous healing and believe that their prayers are answered. Many of these Christians acknowledge not understanding in every instance why some but not all are healed, but they are less likely to learn helplessness and thus resign themselves to sickness without a fight or give up as quickly when healing does not immediately result. They are also more likely to embrace the risk of disappointment and potential for emotional pain required in persevering prayer for miracles.1", "appendix": "Data availability\n\nThe underlying data for this research is sourced from Twenty-First Century Evangelicals, 2010-2016: Special Licence Access. [data collection]. 4th Edition. UK Data Service. SN: 7786, DOI: http://doi.org/10.5255/UKDA-SN-7786-4.\n\n\nReferences\n\nAmmerman NT: Studying Lived Religion: Contexts and Practices. 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Publisher Full Text\n\nSmith G: Testimony and Theodicy: Evangelical Christians, answered and unanswered prayers for healing. Theology and Ministry. 2018; (5).\n\nSoliman TM, Johnson KA, Song H: It’s not “all in your head”: Understanding religion from an embodied cognition perspective. Perspect. Psychol. Sci. 2015; 10(6): 852–864. Publisher Full Text\n\nStrangwaves-Booth A: Three in five British adults say miracles are possible. BBC; 2018. Reference Source\n\nTavris C, Aronson E: Mistakes were made (but not by me): Why we justify foolish beliefs, bad decisions, and hurtful acts. Harcourt; 2007.\n\nTaylor C: A secular age Cambridge. Mass.: Harvard University Press; 2007.\n\nTaylor EJ, Outlaw FH, Bernardo TR, et al.: Spiritual conflicts associated with praying about cancer. Psycho-Oncology. 1999; 8: 386–394. PubMed Abstract \| Publisher Full Text\n\nTaylor EJ, Outlaw FH: Use of prayer among persons with cancer. Holist. Nurs. Pract. 2002; 16: 46–60. Publisher Full Text\n\nVillage A: The Revd Dr Dimensions of belief about miraculous healing. Ment. Health Relig. Cult. 2005; 8: 97–107. Publisher Full Text\n\nVincent S: Livin’ on a Prayer: An Analysis of Intercessory Prayer Studies. Dialogue & Nexus. 2016; 3. Article 13.\n\nWarfield B: Counterfeit Miracles. New York: Scribner; 1918.\n\nWimber J, Springer K: Power Healing. New York: HarperCollins; 1987.\n\nWuthnow R: Prayer, cognition, and culture. Poetics. 2008; 36: 333–337. Publisher Full Text\n\n\nFootnotes\n\n1 It is important to note that scholars of religion are slowly moving away from the notion of belief and doctrine towards embodiment and embodied experiences. This approach argues that representations of the Divine are grounded in an integrated and dynamic sensorimotor complex (Soliman, Johnson & Song, 2015). This includes but is more than the brain. Religion is more than a set of beliefs, it is fundamentally a corporeal practice. Posture, gesture and movement, as part of worship, are closely intertwined with religious experience. The modification of bodily states can impact internal mental states. There has been a recent turn to ‘lived everyday religion’ (McGuire, 2008; Ammerman, 2014; Jupp & Flanagan, 2007). Belief has been replaced by ‘spirituality’, ritual and embodiment and health is more closely tied to bodily experience." }	[ { "id": "257992", "date": "22 Apr 2024", "name": "Dick Kruijthoff", "expertise": [ "Reviewer Expertise Study of Healing after Prayer at VU university Amsterdam (as MD)" ], "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 addresses relevant questions relating to prayers for sickness and healing. It is a subject drawing a lot of attention among Christians and among the entire population as well. The authors thereby distinguish a 'blueprint' worldview from a 'warfare' worldview among Christians, which I consider to be a very adequate distinction as the two poles clearly reflect the different opinions. The differing views are highlighted by quotes from the 'Evangelical research programme', which increases the imagination, Both because of its relevance and the approach used I consider this article of significant interest.\nI have listed a few remarks and suggestions below: - The Methods paragraph in the abstract partly seems to reflect some results in stead of methods (as from 'the data suggest.....'). The authors may rearrange these elements of the text. - In the section What do believers ask God for.... the authors noticed that, based on the psychological theory of learned helplessness, a 'blueprint' approach towards prayer may eventually produce hopelessness. While the 'warfare' worldview encourages hopeful action. I agree with the former, but in the case of the 'warfare' approach one may also think of frustration and disappointment because of unanswered prayers, in due course leading to bitterness. Did the authors find articles on such adverse reactions when reviewing the literature? If so, it may be helpful to mention some of it. - A small separate Methods section in the article itself is recommended, In the abstract this is already mentioned, where the authors indicate that the methodology is based on a critical literature review and on secondary data from the Evangelical research programme. Which literature is included (and which is not)? Was there a search strategy? As for the quotes deployed from the research programme one wonders if all quotes relating to the avoidance of cognitive dissonance were included. Or was it a part of the quotes? If so, was a strategy used when selecting the quotes? - In the Discussion the authors return to the 'blueprint' and the 'warfare' worldview, the former being exemplified bij Calvinism and the latter by charismatic movements such as Vineyard. In this respect it may be also interesting to include some of the lines of thougth in the Reformed (calvinist)- Pentecostal dialogue. Van der Kooi, a Reformed theologian, refers to the dialogue in his book 'This incredibly benevolent force' (Kooi van der, 2018). He considers the Pentecostal and charismatic movements to be a challenge for Reformed theology, with their (renewed) emphasis on gifts of the Spirit such as healing, prophecies, dreams and visions, empowerment. In his view there is not only a line from dogmatics to practice, but also from practice to dogmatics: 'We need to take seriously the experiences of Christians and churches in our own context, as well as of those on other continents and in culturally very different contexts' (page 19). According to this reciprocal relationship between theology and reality (or practice) 'the Reformed-Pentecostal dialogue drew a wider conclusion, in which other means of revelation were mentioned, aside from the Bible and sermons alone' (page 132). Coming back to 'blueprint' and 'warfare' views dilemmas between them may be resolved, at least to some extent, when studying and investigating practices. Brown pleads for the use of empirical methods to test for the effects of prayer on health (Brown, 2015). What actually happens in reality and what does not happen? Some of it is quoted by the authors (Romez, 2019, 2021; Brown, 2012; Roberts et al., 2009). In other articles (Austad et al., 2020; Helming, 2011; Francois et al., 2014; Kruijthoff et al., 2022) there appears to be a frequent association between healings related to prayer(s) on the one hand and 'Spirit' manifestations on the other hand such as strong sensory manifestations, extrasensory phenomena (prophecies, visions), transformation and empowerment. These 'holistic' healings, often occurring instantaneously, appear to be quite different from what we usually see in medical practice. In a fair number of instances they are being reported as having occurred unexpectedly, without much 'warfare'. When facing controversies between differing views among Christians empirical studies may indeed help us to move forward. Experiential data can thereby increase our understanding, apart from medical data. It is a challenge if the authors consider to include some of these elements in 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? 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": "12217", "date": "02 Sep 2024", "name": "Simon Dein", "role": "Author Response", "response": "We have cited the references you suggest There is a methods section at the start of the paper The paper is based upon on a critical literature review and deploys secondary data from the Twenty First Century Evangelical research program which includes a quantitative and qualitative component. The qualitative component involved open ended questions which were analyzed through thematic analysis. We have added a brief discussion of holistic healing and 'spirit manifestations' in our conclusion What might future work in this area involve? To date much of the research on prayer and sickness has focused upon the medical rather than experiential aspects ie what are the medical outcomes. But often the healing is more holistic involving physical, mental and spiritual changes. And how are these experiences related together? How do the biological and existential blend? And to what extent can spiritual experiences have a placebo effect? These 'holistic' healings, often occurring instantaneously, differ from what we usually see in medical practice and reported as having occurred unexpectedly, without much 'warfare'. These include strong sensory manifestations, sense of God’s presence; extrasensory phenomena (prophecies, visions), a sense of being overwhelmed, transformation and empowerment ( Romez, 2019, 2021; Brown, 2012; Roberts et al., 2009; Austad et al., 2020; Helming, 2011; Francois et al., 2014; Kruijthoff et al., 2022; Bendien et al 2023). Some of these studies derive from a Northern European context. Religious and spiritual encounters like visions and voices may have a transformative function which some authors describe as healing (Braud 2012; Nygaard et al 2017). They can be life changing. Healings related to prayer(s) on the one hand and 'Spirit' manifestations appear to be strongly related. We would assert that a focus upon the ‘lived body’ and experiential data - reports of their sensations, feelings, thoughts, and imagery before, during, or after a healing event -can thereby increase our understanding of religious healing through prayer, apart from medical data. To conclude, the efficacy of prayer cannot be judged solely by biomedical criteria. Prayer might impact emotional and spiritual aspects, and this influences how those praying conceptualize its efficacy. We would agree with the authors cited above who argue for a horizontal epistemology in which all relevant perspectives are valuable, including both experiential and objective data. Future studies of prayer and health should be interdisciplinary-medical, psychological and theological." } ] }, { "id": "293332", "date": "27 Jun 2024", "name": "Elizabeth Taylor", "expertise": [ "Reviewer Expertise Spirituality/religiosity and health", "nursing and spiritual care" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis research report shares secondary findings from a quarterly online survey of Evangelical Christians that inform about what their perspectives are regarding unanswered prayers for health (presumably physical and psychological).\n\n* The strength of this reporting is in the very rich bookends: the review of literature and theory to introduce the findings, and the Discussion. These clearly show the authors are well-versed and think deeply on the topic--indeed, a relevant and highly interesting and helpful topic.\n* My only complaint, and it is a serious one, is that the Methods are not adequately described. Tell us more about how the survey was conducted and where. Were the empirical indicators validated and reliable? How was the qualitative data generated and analyzed? Did a theoretical framework guide that analysis? Were any measures instituted to insure trustworthiness of the qual data/findings?\n* Reflections: This article reminds me that the 21st century priest is the psychologist. Science is superseding theology, it seems. As former NIH Director and Templeton Prize winner Francis Collins would say, however, God's word (holy scripture, inspirations) and God's ways (creation, the natural world that science studies) are both valid.\n\n* The blueprint vs warfare worldviews were helpful to cite. Carl Jung's thinking about God enveloping evil/darkness is pertinent to the blueprint thinking.\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?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "12218", "date": "02 Sep 2024", "name": "Simon Dein", "role": "Author Response", "response": "reviewer 2 She has commented upon lack of detail in methodology We have rewritten this The 21st century Evangelicals research programme is a quarterly online survey asks about various topics relevant to Christians ( Evangelical Alliance, 2023). Included in this survey are various questions related to health and more specifically prayer and God’s role in healing. The health survey conducted in 2015 included 1700 Evangelical Christian individuals. They derive from a wide variety of Protestant church denominations, Anglican, independent charismatic networks, Baptist, Free Church, Independent Evangelical and Pentecostal streams. The survey included multiple choice questions analysed through statistical means and open ended free text questions. The sample resided in the UK. The qualitative data were analysed through thematic analysis using spreadsheets to sort the data. Common themes were elicited. The quotations that appear in the paper are chosen because they are in some way typical of common experiences and interesting in themselves. The questions in the survey were validated by a panel of academic experts. A limitation of the qualitative data is that it was analysed by only one person and no attempt was made to look at the reliability of themes. The fill dataset can be found at SN 7787 - Twenty-First Century Evangelicals, 2010-2016 https://discover.ukdataservice.ac.uk/catalogue/?sn=7787&type=Data%20catalogue. We have included a brief discussion of Jung as suggested Modern Christians, by contrast, do not expect evil, find it perplexing, resign themselves to it as God’s will, and try to understand it and resolve the psychological tensions their worldview creates, rather than fighting against evil. One of the best-known modern psychological efforts was suggested by Carl Jung (1954). He proposed that God incarnated as a purely good redeemer only after self-realization of having unjustifiably tormented Job under provocation by Satan. Boyd explains the difference between a “blueprint” and a “warfare” worldview, neither of which embraces Jung’s psychological analysis of God’s evil side." } ] } ]	1	https://f1000research.com/articles/13-156
https://f1000research.com/articles/13-668/v1	21 Jun 24	{ "type": "Case Report", "title": "Case Report - Sudden sensorineural hearing loss and vertigo due to inner ear hemorrhage", "authors": [ "Sameh Mezri", "Mariem Selmi", "Selma Bessioud", "Mariem Selmi", "Selma Bessioud" ], "abstract": "Sudden deafness is a common cause of emergency consultation in otology. Usually, despite investigations, no etiology is known. Intracochlear hemorrhage is a rare cause of sudden sensorineural hearing loss (SSNHL) and may be associated with various labyrinthine disorders. In such cases, magnetic resonance imaging (MRI) is the clef of the diagnosis. We report the case of a 70-year-old patient who was referred to our department for sudden hearing loss, tinnitus, and vertigo. Otoscopic and neurological examinations were normal, and pure-tone audiometry revealed left profound sensorineural hearing loss. Videonystagmography (VNG) revealed left vestibular deficit. MRI demonstrated a high signal intensity inside the cochlea on unenhanced T1-weighted images, and no other abnormalities were found; in particular, no enhancement after intravenous administration of gadolinium. No etiology was identified. Vertigo disappeared rapidly with corticosteroid treatment and hyperbaric oxygen therapy, but hearing did not improve. Intra-labyrinthine hemorrhage causing SSNHL is rare, and the hearing prognosis is poor.", "keywords": [ "inner ear", "hemorrhage", "sudden hearing loss", "Magnetic resonance imaging", "case report." ], "content": "Introduction\n\nSudden sensorineural hearing loss (SSNHL) is defined as a hearing loss of more than 30 dB in at least three contiguous frequencies occurring in a period of less than 72 hours.1 The investigation of SSNHL requires audiological examination and MRI.2\n\nIt is often classified as idiopathic,3 although several causes have been suggested, including viral infections, immune-mediated, logical factors, toxic, neurological, and traumatic microcirculatory problems.1–3 Cochlear or inner ear hemorrhage (IEH) has been reported is a rare cause of sudden deafness, and isolated cases are often described.3,4\n\n\nObservation\n\nA 70-year-old man with a past history of diabetes mellitus and hypertension presented to our department with sudden onset hearing loss in his left ear over the thirty seven days. This was preceded by vertigo of the rotatory type a week earlier, which evolved into short, frequent attacks, and permanent left-sided tinnitus. The patient denied a history of acoustic or traumatic trauma, medication use, or recent ENT infection. He denied alcohol or tobacco consumption.\n\nOtoscopy was normal. Videonystagmoscopy showed spontaneous right horizontal nystagmus with no neurological deficits.\n\nLaboratory test results revealed no abnormalities. We found no infectious or inflammatory syndrome (white blood cell count 9800E/mm3 and CRP, 8 mg/l). Sample and Covid-19 serology were negative. Tonal audiometry revealed left unilateral subcochlear hearing loss with a hearing threshold of 100 dB, confirmed by auditory brainstem evoked potentials (BER) (Figure 1).\n\nIn view of the unilateral sensorineural hearing loss, an additional MRI of the inner ear was performed, including a 3D FLAIR sequence, which showed a high signal intensity in the left cochlea (Figure 2). The patient was diagnosed with a labyrinthine hemorrhage.\n\nBased on the imaging data, we completed the etiological investigation, in particular with a hemostasis laboratory test, a nuclear antibody, and a tumor marker assay. The diagnosis of idiopathic cochlear haemorrhage was the most probable in view of the normality of the tets and the absence of risk factors, particularly cervicofacial and cerebral radiotherapy, the use of antiplatelet or anticoagulant agents, or a history of meningitis.\n\nThe patient received intravenous corticosteroid therapy at a dose of 1 mg/kg/day for 10 days, followed by gradual tapering of the oral doses. Additionally, the patient was administered vasodilators and underwent 15 sessions of hyperbaric oxygen therapy (2ATA per session, five sessions per week).\n\nOn the seventh day of intravenous treatment and third oxygen therapy, the patient noted that the vertigo and tinnitus had disappeared. The improvement in hearing was partial, with a hearing threshold of 75 dB at the end of treatment. A hearing aid was also provided.\n\nThe patient reported a marked improvement in their condition and expressed hope to resume normal activities after fitting.\n\n\nDiscussion\n\nThe diagnosis of hemorrhage requires a combination of clinical and imaging data. Clinical data should include severe to profound deafness with a described hearing loss exceeding 80 dB and vertigo.4\n\nMRI allows diagnosis in the form of a spontaneous hypersignal T1, which is not enhanced by gadolinium injection due to the presence of methemoglobin appearing 48 h after the hemorrhagic event. The sequence T2 signal varies according to the age of the hemorrhagic event (hyposignal initially, progressing to isosignal, and then to hypersignal).3 The radiological evolution is variable: persistence of the hypersignal, regression of the images, and normalization or evolution towards sclerosing and ossifying labyrinthitis.5\n\nThe pathophysiological characteristics are currently unclear, but various etiologies of inner ear hemorrhage (IEH) have been identified. Vascular aetiologias due to anticoagulants or antiaggregant seem to be the most implicated in cases of overdose.6\n\nIn our study, our patient did not receive any treatment that could have affected coagulation.\n\nThe second most commonly described etiology in the literature is hematological diseases, such as myeloma, Waldenstrom’s disease, and autoimmune diseases, such as rheumatoid arthritis and systemic lupus erythematosus or leukemia.4\n\nCell blood count, antinuclear antibodies and rheumatoid factor were negative in our case.\n\nMeningitis with bacterial diffusion may also be involved, but the clinical presentation is different, with neurological symptoms.7 Less frequently reported are radiotherapy to the head and neck, with cases reported 20 years after irradiation,8 and chemical attacks on the inner ear or toxic substances such as cocaine causing IEH by vascular effects.9\n\nHowever, the cause cannot be determined, and many cases are idiopathic. This was the case for our patient.\n\nManagement of IEH is not specific, and patients are under corticoids associated with etiological treatment. However, the prognosis remains poor because of severe cochlea-vestibular lesions in comparison to other etiologies of SSNHL. Many authors have noted no significant improvements in early or late control.4,7,10 Wu et al.,10 in a comparative study of 30 patients with IEH vs. 62 patients with non-hemorrhagic inner ear, noted that the second group had a better hearing recovery in the two weeks three and six months follow up (p<0.05).\n\nCochlear implantation was necessary for the case reported by Meunier et al.4 because of profound bilateral hearing loss with bilateral IEH. In our case, patient have a partial improvement with 25 dB hearing gain with Tinnitus and vertigo disappears.\n\nTo our knowledge, no other author has introduced hyperbaric oxygen therapy for the management of idiopathic or secondary IEH.\n\n\nConclusion\n\nInner ear hemorrhage is a rare cause of sudden sensorineural hearing loss (SSNHL). The diagnosis of IEH was based on the clinical and imaging data. Before diagnosing idiopathic IEH, it is important to investigate the cause of hemorrhage. The prognosis of hearing loss in patients with IEH is uncertain.\n\nInformed written and signed consent was obtained from our patient for his case to be published anonymously. Local ethical committee of military hospital of Tunis (Tunisia) approved the publication of the medical case.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nShinohara S, Yamamoto E, Saiwai S, et al.: Clinical features of sudden hearing loss associated with a high signal in the labyrinth on unenhanced T1-weighted magnetic resonance imaging. Eur. Arch. Otorrinolaringol. 2000 Nov; 257(9): 480–484. PubMed Abstract \| Publisher Full Text\n\nStachler RJ, Chandrasekhar SS, Archer SM, et al.: American Academy of Otolaryngology-Head and Neck Surgery. Clinical practice guideline: sudden hearing loss. Otolaryngol. Head Neck Surg. 2012 Mar; 146(3 Suppl): S1–S35. PubMed Abstract \| Publisher Full Text\n\nJrad M, Zlitni H, Boumediene M, et al.: Intracochlear Hemorrhage: A Rare Cause of Sudden Sensorineural Hearing Loss. Case Rep. Radiol. 2021 Nov 22; 2021: 1072044–1072047. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMeunier A, Clavel P, Aubry K, et al.: A sudden bilateral hearing loss caused by inner ear hemorrhage. Eur. Ann. Otorhinolaryngol. Head Neck Dis. 2020 Jan; 137(1): 65–67. PubMed Abstract \| Publisher Full Text\n\nWeissman JL, Curtin HD, Hirsch BE, et al.: High signal from the otic labyrinth on unenhanced magnetic resonance imaging. AJNR Am. J. Neuroradiol. 1992 Jul-Aug; 13(4): 1183–1187. PubMed Abstract \| Free Full Text\n\nArellano B, Brea B, González FM: Labyrinthine haemorrhage secondary to oral anticoagulants. Acta Otorrinolaringol. Esp. 2016 May-Jun; 67(3): 185–186. English, Spanish. PubMed Abstract \| Publisher Full Text\n\nTan JH, Yeh BI, Seet CS: Deafness due to haemorrhagic labyrinthitis and a review of relapses in Streptococcus suis meningitis. Singapore Med. J. 2010 Feb; 51(2): e30–e33. PubMed Abstract\n\nPoh AC, Tan TY: Sudden deafness due to intralabyrinthine haemorrhage: a possible rare late complication of head and neck irradiation. Ann. Acad. Med. Singap. 2007 Jan; 36(1): 78–82. PubMed Abstract \| Publisher Full Text\n\nNicoucar K, Sakbani K, Vukanovic S, et al.: Intralabyrinthine haemorrhage following cocaine consumption. Acta Otolaryngol. 2005 Aug; 125(8): 899–901. PubMed Abstract \| Publisher Full Text\n\nWu X, Liu M, Zhuang HW, et al.: Cochleo-vestibular lesions and prognosis in patients with profound sudden sensorineural hearing loss: a comparative analysis. Zhonghua Er Bi Yan Hou Tou Jing Wai Ke Za Zhi. 2020 May; 55(5): 472–478. Chinese. PubMed Abstract \| Publisher Full Text" }	[ { "id": "299857", "date": "22 Jul 2024", "name": "Khadija Bahrini", "expertise": [ "Reviewer Expertise clinical research", "hyperbare oxygen and 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\nMezri and collaborators present a case report of sudden sensorineural hearing loss. The etiology of this complication is likely due to inner ear hemorrhage. One of the strong points of this study is the treatment with hyperbaric oxygen, which, after full treatment, revealed an improvement in vertigo and tinnitus, which are among the most grievous complications. This study provides new data about the etiology of sudden sensorineural hearing loss, and the authors pave the way for further studies to investigate in depth the origin of this hemorrhage. I believe that this work deserves to be indexed in this journal. Here some suggestions to improve the quality of the paper Abstract :\nReplace the first sentence by ‘’ Sudden deafness is a common cause of emergency consultation in otology with unknown etiology’’. Fourth sentence ‘’magnetic resonance imaging (MRI) is the clef of the diagnosis’’issue with translation replace ‘’clef’’ with ‘’key’’ or change the full sentence to be ‘’ Magnetic resonance imaging (MRI) plays a crucial role in the diagnostic process’’\nIntroduction: This section is well written no more recommendation.\nObservation\n\nFourth sentence denied is indicated twice, the authors can change the word by ‘’reported ‘’ or ‘’indicated an absence of’’ or ‘’He claimed to avoid both alcohol and tobacco’’ Change ‘’tramatric trauma’’ with ‘’mechanical trauma’’ or ‘’physical trauma’’ Delete ‘’results’’ after laboratory test to be ‘’ laboratory test revealed’ Change the sentence ‘’Sample and Covid-19 serology were negative’’ to be’’ No positive results were detected in either the sample or the COVID-19 antibody test ‘’ Change the sentence ‘’ The diagnosis of idiopathic cochlear haemorrhage was the most probable in view of the normality of the tets and the absence of risk factors’’to be ‘’ Given the normal test results and the lack of risk factors, idiopathic cochlear hemorrhage was considered the most likely diagnosis’’\nDiscussion\nAdd or delete ‘‘s’’ from anticoagulants or antiaggregants /anticoagulant or anti-aggregant. Change this sentence ‘’ However, the cause cannot be determined, and many cases are idiopathic. This was the case for our patient’’ to be ‘’ Nevertheless, the etiology often remains undetermined, with many cases classified as idiopathic. Our clinical case fell into this category.\nConclusion\nUse of acronym since sudden sensorineural hearing loss was shortened to SSNHL previously, it is OK to replace it with \" SSNHL’’\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": "12291", "date": "02 Sep 2024", "name": "Sameh Mezri", "role": "Author Response", "response": "Think you for your disponibility to review my manuscript I do all corrections suggested. I'm available for any more correction" } ] } ]	1	https://f1000research.com/articles/13-668
https://f1000research.com/articles/13-531/v1	24 May 24	{ "type": "Systematic Review", "title": "Bibliometric Analysis of Islamic Crowdfunding: A Literature Review of Its Journey", "authors": [ "Aris Purwatiningsih", "S Purnamasari", "Harini Setyawati", "Astiwi Indriani", "Dian Prawitasari", "Shoimatul Fitria", "S Purnamasari", "Harini Setyawati", "Astiwi Indriani", "Dian Prawitasari", "Shoimatul Fitria" ], "abstract": "Background The potential of Islamic crowdfunding to encourage the development of Islamic fintech globally, even in countries with non-Muslim majority populations, needs to be examined in a literature study on this issue. More extensive research is needed regarding the factors that most reliably predict the success of Islamic crowdfunding, such as compliance with Islamic crowdfunding laws, sustainability, and the potential of Islamic finance. This article describes a comprehensive and systematic Literature Review (SLR) regarding papers published in the field of Islamic crowdfunding. This research aims to contribute to a better understanding of Islamic crowdfunding, provide useful information for practitioners, and stimulate further research in the field to increase the success of Islamic crowdfunding.\n\nMethods We conducted a review of selected papers to identify gaps and significant issues in Islamic crowdfunding, providing guidance for future researchers. This article review was based on 704 articles retrieved using the keyword “Islamic crowdfunding” from the Scopus database between 2013 and 2022. To minimize bias, we formulated 5 research questions to guide our analysis: RQ1: How do publication and citation rates vary annually? RQ2: How can we determine the most influential studies based on citation counts for each keyword? RQ3: What are the most common subject areas addressed in Islamic crowdfunding literature from 2013 to 2022? RQ4: What are the most frequently used keywords in Scopus documents? RQ5: How are Islamic values discussed in articles related to Islamic crowdfunding?\n\nResults The findings of this research demonstrate that Islamic crowdfunding, characterized by interdisciplinary scholarship, has emerged as an increasingly significant alternative for aiding society and the economy. It contributes to poverty alleviation and the development of specific sectors through channels such as crowdfunding for small and medium enterprises and social projects tailored to meet the diverse needs of Muslims. However, the challenge facing the future development of Sharia crowdfunding is that, despite its benefit of increasing community participation in projects aligned with religious values, it also carries the potential risk of investment losses and non-compliance with Sharia principles. Ways to address the current scarcity of Sharia fintech are also needed, ensuring its broader acceptance across all societal levels, and enhancing Muslims’ understanding of compliance with Islamic religious rules, particularly Fiqh law.\n\nConclusion Urgently needed are specific fiqh regulatory guidelines to ensure that Sharia-compliant crowdfunding adheres to Islamic principles. Government support, particularly through legislation in countries where the majority of the population is Muslim, is crucial to enhance public participation and trust in Sharia crowdfunding.", "keywords": [ "Bibliometric analysis", "Islamic crowdfunding", "Legislation" ], "content": "Introduction\n\nIslamic crowdfunding is a form of crowdfunding that operates in accordance with Islamic principles and ethics. It integrates the features of a crowdfunding platform with Islamic crowdfunding and business regulations to facilitate the funding of projects and initiatives aligned with Islamic values. Islamic crowdfunding platforms utilize blockchain technology to ensure transparency and traceability of transactions (Kuanova, Sagiyeva, and Shirazi, 2021). These platforms provide a digital space where individuals can donate or invest in projects promoting social welfare and entrepreneurship (Hendratmi, Ryandono, and Sukmaningrum, 2020), education, or other areas of interest within the Islamic community. Consequently, Islamic crowdfunding has the potential to support various sectors, including book publishing (Ishak and Rahman, 2021), contribute to sustainable development (Testa et al., 2019), affordable housing (Ma and Md Taib, 2023), and zakat donations (Adnan et al., 2023).\n\nBy leveraging technology and Islamic finance principles, Islamic crowdfunding provides a unique avenue for individuals to participate in initiatives that are both socially responsible and financially inclusive (Testa et al., 2022). Several challenges may impede the development and progress of Islamic crowdfunding, including Sharia supervision (Dawood et al., 2022), a lack of awareness and understanding of the concept and potential of Sharia crowdfunding among the public (Vaznyte, Andries, and Manigart, 2023), the absence of clear regulations and internationally recognized standards (Hendratmi, Ryandono, and Sukmaningrum, 2020), a lack of strong relationships with potential donors and effective electronic word-of-mouth marketing (Alalwan et al., 2017). Furthermore, there is a need for the implementation and understanding of the use of Islamic crowdfunding in managing Islamic funds and the limited number of registered Islamic crowdfunding platforms (Ag Omar et al., 2021). Additionally, there is a need for a more Sharia-compliant platform and an emphasis on financing Sharia in Sharia crowdfunding (Ramli, Abdullah, and Alam, 2023), as well as consistency and transparency in Sharia compliance (Ishak and Rahman, 2021).\n\nIslamic crowdfunding is a relatively new business concept, even in Muslim-majority countries, and there is still limited literature on Islamic fintech (Shaikh et al., 2020). For example, Malaysia lacks a comprehensive understanding of its society, and the studies on Islamic crowdfunding and qualitative analyses are limited (Ishak and Rahman, 2021). Additionally, there are constraints related to the number of sources and the scope of studies conducted on Islamic crowdfunding (Ishak, Kamaruddin, and Aderemi, 2022), hindering the optimal success of Islamic crowdfunding. Challenges such as a lack of awareness and understanding of Islamic crowdfunding, insufficient studies on the subject, and the early stages of development in regulatory and legal frameworks for Sharia-compliant Islamic crowdfunding also contribute to the challenges facing the success of Islamic crowdfunding in Indonesia, a country with the largest Muslim population globally (Darmansyah et al., 2020). Further research and exploration are imperative to fully comprehend and leverage the potential of Islamic crowdfunding. Hence, this literature review on Islamic crowdfunding aims to enhance understanding, provide valuable information for practitioners, and encourage additional research in the field to support the development of a more effective crowdfunding model in line with Sharia principles, ultimately boosting the success of Islamic crowdfunding in the broader community.\n\nThe absence of studies on Islamic crowdfunding, limited awareness among publications, and the absence of a Sharia-compliant regulatory and legal framework pose challenges to the success of Islamic crowdfunding in Indonesia, a nation with the largest Muslim population globally, and these challenges are still in their early stages of development. Islamic crowdfunding has the potential to positively impact various industries, including publishing, community-based tourism, and microbusinesses. To fully grasp and harness the potential of Islamic crowdfunding, more investigation and study are required. Therefore, the purpose of this literature review on Islamic crowdfunding is to stimulate further research in the field, furnish practitioners with valuable information, and foster a better understanding of the subject. This will contribute to the creation of a more effective crowdfunding model that adheres to Sharia principles, ultimately increasing the success of Islamic crowdfunding in the broader community.\n\nThis paper aims to provide a better understanding of Islamic crowdfunding, offer valuable information for practitioners, and promote further research in this field to support the development of improved crowdfunding models in accordance with Sharia principles to enhance the success of Islamic crowdfunding in Indonesia. To achieve this goal, we address the following Research Questions:\n\nRQ1. How do publications and citations perform annually?\n\nRQ2. How can we identify the most influential studies based on the number of citations for each keyword?\n\nRQ3. What are the most common subject areas found in Islamic crowdfunding from 2013 to 2022?\n\nRQ4. What are the most used keywords in Scopus documents?\n\nRQ5. How are Islamic values discussed in Islamic crowdfunding articles?\n\n\nBackground\n\nThe development of Islamic finance can be harnessed to support Islamic social financial instruments through technological applications. This enables efficient and effective administration, collection, and distribution of Islamic social funds (Umar et al., 2022), thereby supporting the success of ziswaf (Ascarya and Sakti, 2022), and SUKUK (Chong, 2021). It is essential to segregate ZISWAF funds from funds of other fintech users to prevent the mingling of funds with other funding sources (Indahsari et al., 2014). The integration of technology with zakat represents a crucial social financial tool for alleviating global poverty, exemplified by the adoption of ZakaTech by Muslims during COVID-19 (Abdullah et al., 2023).\n\nIslamic crowdfunding, operating in accordance with Islamic principles and ethics, combines crowdfunding platforms with Islamic crowdfunding and business rules to facilitate financing for projects aligned with Islamic values. These platforms employ blockchain technology to ensure transparency and traceability of transactions (Alshater et al., 2022), providing a digital space where individuals can donate or invest in projects promoting social welfare, entrepreneurship, education, or other areas of interest. In this context, Islamic crowdfunding has the potential to support various sectors, including book publishing (Ishak and Solihin, 2012), contribute to sustainable development (Testa et al., 2019), affordable housing, and zakat donations (Beik and Arsyianti, 2016). By leveraging technology and Islamic finance principles, Islamic crowdfunding offers a unique pathway for individuals to participate in socially responsible and financially inclusive initiatives. It is a relatively new business, even in Muslim-majority countries, where literature on Islamic fintech is still limited (Shaikh et al., 2020). Malaysia, for example, lacks a comprehensive understanding of Malaysian society, empirical studies on Islamic crowdfunding, and qualitative analysis, as well as faces limitations in the number of sources and scope of studies on Islamic crowdfunding (Ramli, Abdullah, and Alam, 2023), resulting in suboptimal success for Sharia crowdfunding.\n\nThe challenges to the success of Sharia crowdfunding in Indonesia, despite being the country with the largest Muslim population globally, include a lack of awareness and understanding of Sharia crowdfunding among publications, insufficient studies on Sharia crowdfunding, and an early-stage regulatory and legal framework for Sharia crowdfunding (Darmansyah et al., 2020). Several challenges hindering the development and progress of Sharia crowdfunding include a lack of awareness and understanding of the concept and potential of Sharia crowdfunding among publications, unclear regulations and internationally recognized standards, weak relationships with potential donors, and underutilization of electronic word of mouth. There is also a lack of implementation and understanding of Sharia crowdfunding in managing Sharia funds and a limited number of registered Sharia crowdfunding platforms (Alsmadi et al., 2023).\n\nApart from the aforementioned problems, the current significant challenge lies in building strong relationships with potential donors and leveraging the influence of electronic word of mouth (eWOM) (Torres, Augusto, and Wallace, 2018). There is also a need for more Sharia-compliant platforms and an emphasis on Sharia financing in Sharia crowdfunding, along with consistency and transparency in Sharia compliance, publishing, zakat, and qardul hasan (Ali, 2017). Further research and exploration are necessary to understand and exploit the potential of Islamic crowdfunding. Therefore, this literature review on Islamic crowdfunding aims to provide a better understanding of the topic, furnish valuable information for practitioners, and encourage further research in this area to support the development of improved crowdfunding models in accordance with Sharia principles, ultimately increasing the success of Sharia crowdfunding in the wider community.\n\nIslamic crowdfunding campaigns are crucial for the hotel industry, which has been adversely affected by the COVID-19 pandemic (Baber et al., 2022). There is a need for better alternatives to enhance crowdfunding trust among donors for strategic sustainability in the conditions of turbulence and financial crisis caused by COVID (Jiao et al., 2022). Crowdfunding is a financial phenomenon aimed at obtaining resources to implement innovative projects in a market where success is determined by experience, human capital, and gender (Borrero-Domínguez, Cordón-Lagares, and Hernández-Garrido, 2020). Performance and effort expectations, social influences, as well as facilitating conditions significantly influence entrepreneurs’ behavioral intentions to adopt crowdfunding, although its reception may not be as favorable as in developed countries due to the lack of supporting tools, financial regulations, and promotional campaigns (Islam and Khan, 2021). Crowdfunding platforms can also contribute to sustainable development processes (Testa et al., 2022) by supporting green projects, environmental protection, and sustainability initiatives (Prędkiewicz and Kalinowska-Beszczyńska, 2021).\n\nIn the initial stages of creating a crowdfunding platform, social capital is required to support the success of the campaign (Butticè, Colombo, and Wright, 2017). Equity crowdfunding is a viable opportunity to finance new businesses, especially startups and small and medium enterprises (SMEs) (Giudici, Guerini, and Rossi-Lamastra, 2020). Crowdfunding has the potential to democratize access to finance and provide new investment opportunities, including for underrepresented groups such as women (Serwaah, 2022). The success of previous campaign programs affects individual empathy and intention to donate to crowdfunding charities (Lin et al., 2018). Islamic crowdfunding platforms (Islamic crowdfunding FPs) have the potential to contribute to sustainable development by embedding social responsibility and providing fundraising opportunities for unbanked and underserved individuals (Testa et al., 2022). Islamic crowdfunding is part of the global Islamic crowdfunding economy, thereby providing opportunities for crowdfunding initiatives (Floren, Rasul, and Gani, 2020). Sharia crowdfunding strategies are a solution to economic and social welfare problems in various countries. This strategy leverages the use of crowdfunding platforms and blockchain technology to ensure transparency and track transactions, in line with the ethical norms and rules of Islamic crowdfunding business (Kuanova, Sagiyeva, and Shirazi, 2021).\n\nThe utilization of fintech as a microfinance initiative offered by Islamic banks needs to be increased to promote ṣadaqah-based loans and products (Abd Wahab et al., 2023). Fintech can be a solution and support the resilience of the sharia crowdfunding banking sector in addressing the challenges faced in the context of the COVID-19 pandemic (Pireh, 2022). The government and society are encouraged to strengthen and expand social networks, particularly to enhance crisis management for recovery from the impact of the COVID-19 pandemic (Pitas and Ehmer, 2020). Similar to the innovations implemented by companies in Brunei Darussalam to maintain the resilience and continuity of their businesses during the pandemic (Basir, 2022), sharia financial instruments such as waqf play a role in providing health equipment and assisting those affected by the pandemic (Kasri and Chaerunnisa, 2021).\n\nThe use of ZakaTech has the potential to enhance the fundraising capacity of Islamic crowdfunding social financial institutions (Bin-Nashwan et al., 2022). The impact of fintech developments has also manifested in Islamic finance and economics, positioning Islamic crowdfunding as a provider of various solutions to the economic impact of COVID-19 through key principles and investment tools, including profit-sharing, takaful, and waqf (Benamraoui, 2021). Factors driving the adoption of fintech services, such as perceptions of trust, exert a highly significant direct influence on the intention to use Islamic Paytech crowdfunding services (Irimia-Diéguez et al., 2023). Other driving factors include perceived ease of use, perceived usefulness, and consumer innovation (Shaikh et al., 2020). The presence of crowdfunding has a positive impact on the success of fundraising, and crowdfunding platforms are effective fintech tools for financing entrepreneurs in the Middle East (Abdeldayem and Aldulaimi, 2022).\n\nIslamic fintech provides opportunities for new start-ups with increased transparency and ethical practices in Islamic crowdfunding financial institutions, thereby enhancing processes and providing cost-effectiveness in delivering sharia-compliant products and services (Chong, 2021). Islamic crowdfunding platforms, combined with blockchain technology, can promote transparency and facilitate the growth of Islamic crowdfunding social instruments and projects, involving stakeholders such as governments, Islamic crowdfunding financial institutions, and commercial organizations (Kuanova, Sagiyeva, and Shirazi, 2021). In Islamic crowdfunding with blockchain technology, the occurrence of mudharabah financing based on crowdfunding and murabahah is highly possible (Ag Omar et al., 2021).\n\nIslamic crowdfunding is a form of crowdfunding that operates in accordance with Islamic principles and ethics. It combines the use of crowdfunding platforms with Islamic contracts and business rules to facilitate the financing of projects and initiatives that align with Islamic values. Islamic crowdfunding platforms leverage blockchain technology to ensure transparency and traceability of transactions (Kuanova, Sagiyeva, and Shirazi, 2021), providing a digital space where individuals can donate or invest in projects promoting social welfare, entrepreneurship, education, or other areas of interest, including in the book publishing sector (Ag Omar et al., 2021).\n\nIslamic crowdfunding platforms (Islamic crowdfunding FPs) contribute to sustainable development (Testa et al., 2022), affordable housing (Ma and Md Taib, 2023), zakat donations waqf (Hapsari et al. 2022), and qordul hasan (Pireh, 2022). By leveraging technology and Islamic finance principles, Islamic crowdfunding offers a unique pathway for individuals to participate in socially responsible and financially inclusive initiatives (Testa et al., 2022). Additionally, the use of fintech platforms and technology has become increasingly prominent during the pandemic, including in the field of Islamic finance (Darmansyah et al., 2020).\n\nSharia crowdfunding can optimize the role of sharia fintech, such as the crowdfunding model, as an intermediary between Muslim donors or crowd funders and micro, small, and medium enterprises (MSMEs) (Raimi and Uzodinma, 2020). Overall, Islamic crowdfunding strategies provide an innovative approach to overcome economic problems and improve social welfare in various countries. The acceptance and success of Islamic crowdfunding are influenced by factors such as social capital, religiosity, social influence, and demographic characteristics of Islamic crowdfunding (Choy and Schlagwein, 2016). Islamic crowdfunding can also be used for various purposes, including affordable housing solutions, entrepreneurial development, and investment opportunities, offering an alternative model for Islamic crowdfunding venture capital companies by providing a mechanism to mitigate business risks (Gafrej and Boujelbéne, 2022).\n\nThe multidimensional model of high-growth companies in Russian-Ukrainian Islamic crowdfunding consists of several interrelated dimensions, such as innovation, finance, human resources, and business strategies after the COVID-19 pandemic, which are very different from the previous period (Tchinda and Dejardin, 2021). Overall, Islamic crowdfunding is used globally for a variety of purposes, namely meeting economic, social, and charitable needs. Several challenges that can hinder the development and progress of sharia crowdfunding are: lack of awareness and understanding of the concept and potential of sharia crowdfunding among publications (Alalwan et al., 2017); the absence of clear regulations and internationally recognized standards (Darmansyah et al., 2020); lack of strong relationships with potential donors and harnessing the electronic power of word of mouth (Alalwan et al., 2022); implementation and understanding of the use of sharia crowdfunding in managing sharia funds and the limited number of registered sharia crowdfunding platforms; as well as the need for more sharia-compliant platforms and the importance of Islamic crowdfunding (Beck, Demirg-Kunt, and Merrouche, 2013); also consistency and transparency in Sharia compliance (Ramli, Abdullah, and Alam, 2023).\n\nIslamic crowdfunding platforms contribute to the growth of Islamic crowdfunding instruments and social projects, overcoming economic challenges and improving social welfare (Herianingrum et al., 2022). Islamic crowdfunding and blockchain technology are becoming mainstream in the Muslim world, especially for small and medium enterprises (SMEs) (Hudaefi, 2020). Islamic crowdfunding has the potential to manage Islamic funds, such as cash waqf and zakat, effectively (Indahsari et al., 2014). Islamic crowdfunding platforms, such as EthisCrowd, provide affordable housing solutions for low-income households in Indonesia (Ma and Md Taib, 2023). Knowledge, belief, and religiosity play a positive role in explaining the intention to donate money online among the Indonesian millennial generation (Kasri and Chaerunnisa, 2021). Crowdfunding campaigns that combine religious and social narratives are more likely to attract funding and achieve success (Simpson et al., 2020).\n\nSeveral factors determine the success of Islamic crowdfunding, including perceptions of other people’s charitable behavior, previous donations, religiosity, knowledge, beliefs, and attitudes towards the intention to donate to cash waqf—a reflection of strong Islamic values that prioritize religion, increasing literacy waqf, trust in cash waqf institutions, and developing effective marketing strategies. Knowledge and effective communication of religious messages, beliefs, and religiosity play a positive role in explaining the intention to donate money online among the Indonesian millennial generation (Kasri and Chaerunnisa, 2021).\n\n\nMethods\n\nThis research collects data from the Scopus database, which contains more Islamic finance research papers and indexes more validated research data (Alshater et al., 2021). We reviewed and re-checked the database to verify the suitability of the data for processing. Additionally, we re-read and analyzed the data according to predetermined data categorization. At last, we conducted a subgroup analysis for identify if there were any differences in results between the predetermined groups, then We assessed whether certain characteristics, such as study characteristics or population characteristics, significantly influenced the results. Furthermore, we conducted a review based on 704 articles retrieved using the keyword “Islamic crowdfunding” from the Scopus database between 2013 and 2022. To minimize bias, we formulated 5 research questions to guide our analysis: RQ1: How do publication and citation rates vary annually? RQ2: How can we determine the most influential studies based on citation counts for each keyword? RQ3: What are the most common subject areas addressed in Islamic crowdfunding literature from 2013 to 2022? RQ4: What are the most frequently used keywords in Scopus documents? RQ5: How are Islamic values discussed in articles related to Islamic crowdfunding?\n\n\nResults\n\nThe majority of the publications fall under the category of “Article,” constituting 67.33% of the total. This suggests a significant focus on standard articles, which are typically in-depth research papers. Book Chapter make up a smaller proportion at 17.77%. Table 1 also suggest that a substantial involvement in contributing to books or edited volumes, which often include specialized topics. Conference papers make up a smaller proportion at 6.53%. This indicates a presence of research contributions presented at conferences, which may have a more condensed format compared to full articles. The “Book” category represents 5.68%, suggesting an involvement in writing entire books. This can be a significant contribution, indicating a comprehensive exploration of a particular subject. Reviews constitute 3.98%, indicating that there is some engagement in critically evaluating and summarizing existing literature in the field. Editorials make up a minimal percentage at 0.06%. Highlighting a limited but detectable representation in the dataset. Editorials are often opinion pieces or introductory notes written by the editorial team of a publication. Short survey, Note, and Conference Review have the smallest representation at 0.01%. This suggests a minimal focus on Short survey, Note, and Conference Review publications, which are usually brief overviews of a specific topic.\n\nIn summary, the majority of publications consist of standard articles and book chapters, indicating a strong emphasis on in-depth research. Conference papers, books, and reviews also contribute, showcasing a diverse range of scholarly outputs. There are also editorials, short surveys, notes, and conference reviews, although their numbers are very limited. The data reflects a balanced approach to academic publishing, covering various formats and contributing to different types of publications.\n\nThe majority of publications come from journals, constituting 57.30%. This suggests a significant focus on disseminating research through peer-reviewed journals, which is a common and authoritative way to share academic work. Books and book series make up a substantial portion at 5.95% and 7.30%, indicating an involvement in writing standalone books and book series. This may include monographs or comprehensive works on specific topics. Publications in Conference Proceeding contribute 28.11%. This indicates active participation and contribution to academic conferences, where research is presented and published in proceedings.\n\nIn summary, the data in Table 2 shows a diverse range of source types, with a primary focus on journals and books. The distribution suggests a balanced approach to publishing, involving both traditional academic outlets (journals and books) and other forms of scholarly communication book series, and books).\n\nThe overwhelming majority of publications are in English, constituting 97.30%. This is consistent with the global dominance of English as the primary language for scholarly communication. German (1.08) are the second most represented language. This suggests a smaller but notable presence in publications in the German language. Other languages such as Chinese French, and Spanish, each (0.27), indicate that there are still articles written in these languages, although the number is very small.\n\nIn summary, the data in Table 3 shows a strong emphasis on English-language publications, reflecting the international and widespread nature of academic research. The presence of publications in other languages, albeit at a smaller percentage, suggests a degree of diversity in language representation, possibly due to specific regional or disciplinary focuses.\n\nSubject Area from Table 4 suggests a strong focus on Business, Management, and Accounting, along with significant contributions to Economics, Econometrics and Finance Social Sciences, Computer Science, Decision Science, and other areas.\n\n1. Business, Management and Accounting (30.04%): This subject area has the highest percentage of publications, indicating a significant focus on topics related to business, management, and accounting.\n\n2. Economics, Econometrics and Finance (25.81%): Another substantial area, suggesting a strong presence in economic and financial research.\n\n3. Social Sciences (13.40%): Reflects a notable contribution to the social sciences.\n\n4. Computer Science (12.13%): Indicates a significant involvement in computer science research.\n\n5. Decision Science (8.95): indicates that decision science a noteworthy representation.\n\n6. Energy (7.24): indicates that energy reflects a quite prominent presence in the field of study.\n\n7. Environment Science (6.82): Informs Environment Science is still often a subject of discussion.\n\n1. Engineering (5.92%): Represents a presence in engineering research.\n\n2. Mathematics (3.55): Suggesting the involvement of mathematics in critically evaluating and summarizing existing literature.\n\n3. Arts and Humanities (3.24%): Indicates a smaller but existing contribution to arts and humanities.\n\n4. Psychology (1.99), Medicine (1.56), Physics and Astronomy (1.42), Multidisciplinary and Agricultural and Biological Sciences each (1.14): Represent various fields with moderate contributions.\n\n5. Other Areas (Earth and Biological Science, Materials Science, Biochemistry, Genetics, and Molecular Biology, Pharmacology, Toxicology and Pharmaceutics, Immunology and Microbiology, Health Professions, Chemical Engineering, Veterinary, Neuroscience): Reflects diverse interests with smaller percentages.\n\nKeywords Based on Table 5, indicates specific areas of interest, with a substantial emphasis on crowdfunding, fintech, and blockchain-related research.\n\n1. Crowdfunding (67.33%): Indicates a dominant focus on crowdfunding-related topics\n\n2. Fintech (6.53%): Represents a notable presence in financial technology research.\n\n3. Blockchain (17.77%): Suggests a significant focus on blockchain-related topics.\n\n4. Malaysia (1.42%), Review (3.98), Book (5.68): Indicates a smaller but existing focus on research related to Islamic Crowdfunding.\n\n5. Other Keywords (Editorial and Short Survey): Contribute to the diversity of topics covered, with various percentages.\n\n\nDiscussion\n\nWe began analyzing documents with the keyword “Islamic crowdfunding” in 2013 because the crowdfunding model had successfully transformed the way society funds projects, businesses, and social initiatives. This shift captured the attention of academics seeking to comprehend the impact and potential of this innovative financing model. Our database search commenced with the keyword “Islamic crowdfunding” in 2013 because we discovered 1 document on Islamic crowdfunding in the Scopus database for that year, which had not been found in previous years.\n\nSharia finance is a financial sector adhering to Islamic sharia principles. Islamic finance had been rapidly developing before 2013, and academics were intrigued by the prospect of integrating sharia concepts with the emerging crowdfunding trend. This integration aimed to create a financing model aligned with Islamic principles. There was a surge in awareness and interest in financial products complying with Islamic principles, prompting Muslim communities worldwide to explore investment or project funding options in accordance with their beliefs. Islamic crowdfunding initiatives emerged as an interesting alternative in this context.\n\nThe potential of financial inclusion to provide access to individuals or groups that previously faced difficulties or lacked access to formal financial markets intrigued academics. They sought to explore how crowdfunding models, including sharia-based ones, could enhance financial well-being and inclusion in Muslim communities. This research not only facilitates access for individuals or groups that previously encountered financial difficulties or lacked access to formal financial markets but also sparks academic interest in investigating further the realm of Islamic crowdfunding. It underscores an increase in interest, utilization, and growth of crowdfunding as a financing method. However, it is crucial to note the limitations of crowdfunding in educational campaigns during this period.\n\nPost-2013, there was a growing body of research on this subject, with a notable surge during the COVID-19 pandemic in 2020. This surge was prompted by shifts in spending patterns and heightened humanistic values in society during the pandemic. The phenomenon underscored the need for mutual assistance, resulting in a substantial amount of aid being provided. These events motivated researchers to delve into this phenomenon, evident in the rising number of documents in the database from 2013 to 2022. The progression was particularly remarkable from 2016 to 2022, with the number of documents increasing from 8 to 295. This surge in documents in the Scopus database was accompanied by a corresponding increase in citations, notably peaking from 2019 to 2022.\n\nThere are six most common fields of study in Scopus documents, namely: Business, Management and Accounting, Economics, Econometrics and Finance, Social Sciences, and Computer Science. Research on Islamic crowdfunding focuses significantly on Business, Management, and Accounting for several reasons. First, Islamic crowdfunding is a financial activity that requires expertise in financial management, risk management, and marketing strategies, as seen in Islamic banks (Aderemi and Ishak, 2020). Managing funds and resources is crucial in crowdfunding, including Islamic crowdfunding. Additionally, knowledge in financial management and accounting practices is essential for Islamic crowdfunding (Hasan, Hassan, and Rashid, 2018). Islamic crowdfunding studies also intersect with economics and business management, involving the analysis of banking effectiveness, financial literacy, and customer awareness (Albaity and Rahman, 2019). The success of a crowdfunding campaign, especially in the environmentally friendly project sector, depends on factors like campaign characteristics, updates, and the targeted amount. Islamic crowdfunding requires an understanding and application of marketing and management principles (Prędkiewicz and Kalinowska-Beszczyńska, 2021). Therefore, the involvement of business and management disciplines in Islamic crowdfunding research is essential to comprehend its dynamics and optimize outcomes.\n\nResearch on Islamic crowdfunding also places a significant focus on Economics, Econometrics, and Finance for several reasons. Firstly, crowdfunding plays a crucial role in economic development, especially in the Gulf Cooperation Council (GCC) countries (Thottoli, 2022). Secondly, crowdfunding adoption among start-up entrepreneurs, particularly in developing countries, is still low, necessitating research to identify influencing factors such as performance expectations, effort expectations, social influence, facilitating conditions, and perceived trust (Islam and Khan, 2021). Furthermore, crowdfunding is not solely an economic phenomenon but also involves social relationships and motivation (Sherman and Axelrad, 2022). Aspects like social trust, networks of friends and family, and social enterprise are integral to crowdfunding (Flanigan, 2017). Additionally, crowdfunding has emerged as an additional source of financing for research projects. Therefore, understanding the factors influencing the success of scientific crowdfunding projects, including newsworthiness, reputation signalling, and online payment theory, is crucial (Schäfer et al., 2016). Overall, research on Islamic crowdfunding encompasses various economic and financial aspects to understand its role, adoption, and impact.\n\nResearch on Islamic crowdfunding also involves a significant focus on Social Sciences for several reasons. Firstly, Islamic crowdfunding often supports creative projects in fields such as literature, art, and media (Alblooshi, 2022). For example, a crowdfunding platform was used to fund the publication of Ishak et al.’s book (Aderemi and Ishak, 2020) and independent print media (Konhäusner et al., 2021). These projects rely on the support and contributions of individuals who value and appreciate the arts and creative endeavours. Crowdfunding campaigns often involve storytelling and community engagement, which are important elements of the arts and humanities. Crowdfunding platforms provide opportunities for creators to connect with their audiences, build communities, and share their vision and passion. Research on crowdfunding explores the motivations and behavior of backers and contributors (Steigenberger, 2017). To understand the human aspects of crowdfunding, such as the reasons why people contribute and the impact of crowdfunding on society, requires a focus on the arts and humanities. By studying these aspects, researchers can gain insight into the social and cultural dynamics of Islamic crowdfunding and its impact on creative industries and communities.\n\nComputer Science is a field related to the development of Islamic crowdfunding because crowdfunding platforms heavily rely on website platforms and web-based online platforms (Jiao et al., 2022). Computer science also plays a crucial role in ensuring transparency and transaction tracking in crowdfunding platforms, especially when combined with blockchain technology. Computer science is essential for developing and analyzing data in the context of crowdfunding, allowing researchers to understand behavioral intentions and factors influencing the adoption of Islamic crowdfunding services (Alsmadi, Alrawashdeh, et al., 2023). Overall, computer science is an integral part of the functioning, development, and analysis of Islamic crowdfunding platforms. Relationship marketing orientation, entrepreneurial alertness, system quality, and service quality significantly influence entrepreneurs’ involvement in e-equity crowdfunding, predicting knowledge acquisition and innovation performance (Pratono et al., n.d.). Computer science and science can address challenges in the fields of computers, science, and technology but have not been able to improve a person’s ethics (Oliver and McNeil, 2021). All in all, computer science is an integral part of the functioning, development, and analysis of Islamic crowdfunding platforms.\n\nCrowdfunding plays a major role in economics development, particularly in the Gulf Cooperation Council (GCC) countries serves as a source of financing for new business startups and small and medium enterprises (SMEs). The adoption of crowdfunding among startup entrepreneurs, especially in developing countries, is still low. Therefore, the research aims to identify the factors that influence crowdfunding adoption, such as performance expectations, effort expectations, social influence, facilitating conditions, and perceived trust. In addition, crowdfunding is not solely an economics phenomenon but involves social relations and motivation (Sherman and Axelrad, 2022). Social trust, network of friends and family, and social ventures are important aspects of crowdfunding (Flanigan, 2017). In addition, crowdfunding has emerged as an additional source of financing for research projects. It is important to understand the factors that influence the success of scientific Islamic crowdfunding projects, including news value, reputation signalling and online payment theory (Schäfer et al., 2016). Overall, research on Islamic crowdfunding covers various economics and financial aspects to understand its role, adoption, and impact.\n\nResearch on Islamic crowdfunding involves many Social Sciences, for several reasons. First, Islamic crowdfunding often supports creative projects in fields such as literature, art, and media. These projects rely on the support and contributions of individuals who value and appreciate the arts and creative endeavours. Second, crowdfunding campaigns often involve storytelling and community involvement, Crowdfunding platforms provide opportunities for creators to connect with their audience, build community, and share their vision and passion. Finally, research on crowdfunding explores the motivations and behaviors of supporters and contributors (Steigenberger 2017). By studying these aspects, researchers can gain insight into the social and cultural dynamics of Islamic crowdfunding and its impact on creative industries and communities. Research on Islamic crowdfunding involves a lot of computer scientists, because crowdfunding platforms rely heavily on website platforms and web-based online platforms (Bouncken, Komorek, and Kraus, 2015). This platform utilizes computer science technology to facilitate fundraising from a large number of individuals or organizations. In addition, computer science plays an important role in ensuring transparency and transaction tracking in crowdfunding platforms, especially when combined with blockchain technology. Overall, computer science is an integral part of the functioning, development and analysis of Islamic crowdfunding platforms. Relationship marketing orientation, entrepreneurial awareness, system quality, and service quality significantly influence entrepreneur involvement in equity crowdfunding, Islamic crowdfunding knowledge acquisition and innovation performance. Computer science and scientist are able to answer challenges in in the fields of computers, science, and technology, but have not been able to improve the person’s ethics (Oliver and McNeil, 2021). Overall, computer science is an integral part of the functioning, development and analysis of Islamic crowdfunding platforms.\n\nThe combination of crowdfunding platforms and blockchain technology increases transparency and transaction tracking, in line with Islamic crowdfunding ethical norms. The importance of previous successful campaigns and the quality of the website, convenience of transactions, and quality of project content will influence individual empathy as well as credibility influencing the intention to donate to charity crowdfunding (Butticè, Colombo, and Wright, 2017). The most used keywords on Scopus document the relationship between Islamic crowdfunding and Fintech can be seen here, there needs to be further research on this matter, how does Islam view Fintech, where Fintech is a new technology, besides that it needs to be discussed why there are so many studies in Malaysia Islamic crowdfunding is a large Islamic country.\n\nWe can see the topics that were most discussed during 2013 to 2022, namely: fintech, factor, finance, and innovation. Meanwhile, based on the most keyword articles in the Scopus database, the most frequently discussed topics are: crowdfunding with 72 documents, fintech with 55, blockchain with 40, and Malaysia with 26 documents. Islamic crowdfunding initiatives contribute to the growth of Islamic crowdfunding social instruments and projects, involving stakeholders such as governments, Islamic crowdfunding financial institutions, and commercial organizations. The acceptance and success of Islamic crowdfunding is influenced by factors such as social capital, religiosity, social influence, and characteristics of Islamic communities. It is used for various purposes, including affordable housing solutions, entrepreneurship development, and investment opportunities. Islamic crowdfunding also offers an alternative model for Islamic crowdfunding venture capital firms, providing a mechanism for mitigating business risks (Gafrej and Boujelbéne, 2022). Overall, Islamic crowdfunding is used globally for a variety of purposes, addressing economics, social and charitable needs. The multidimensional model of high-growth companies in Russia-Ukranian Islamic crowdfunding consists of several interrelated dimensions, such as innovation, finance, human resources, and business strategy after the COVID-19 pandemic is very different from the previous period (Tchinda and Dejardin, 2021).\n\nHow can fintech be a solution and support the resilience of the Islamic crowdfunding banking sector in facing the challenges faced in the context of the COVID-19 pandemic. What are the innovation efforts made by companies in Brunei Darussalam in maintaining the resilience and continuity of their business during the pandemic (Basir, 2022). The role of Islamic finance instruments such as waqf, in providing health equipment and supporting those affected by the pandemic has also been highlighted. Islamic fintech services are influenced by perceived ease of use, perceived usefulness, and consumer innovation. Governments and society are encouraged to strengthen and expand social networks to improve crisis management and resilience (Pitas and Ehmer, 2020). The use of ZakaTech and its potential to increase the fundraising capacity of Islamic crowdfunding social finance institutions. The emergence of Fintech advancements has extended its influence to Islamic finance and economics, offering several solutions to mitigate the economic repercussions of COVID-19. This includes leveraging the fundamental principles and investment instruments of Islamic crowdfunding, such as profit-sharing, takaful, and endowment funds (Benamraoui, 2021). For Islamic banking users, both knowledge of and trust in FinTech services strongly influence their decision to use Islamic crowdfunding platforms (Irimia-Diéguez et al., 2023).\n\nBased on Table 6, it can be seen that crowdfunding, fintech, blockchain, fintech, Malaysia, Islamic Finance, and Innovation occupy the 6th largest position in the Islamic crowdfunding document. Crowdfunding is the keyword with the largest number of documents, because crowdfunding campaigns are very important for the hotel industry which is affected by the COVID-19 pandemic (Baber et al., 2022). Factors that influence the success of a crowdfunding campaign include the inherent quality of the project in determining the success of the campaign (Wan Mohamad Nazarie and Williams, 2021). Islamic crowdfunding platforms utilize block-chain technology to ensure transparency and traceability of transactions. The combination of crowdfunding platforms and blockchain technology increases transparency and transaction tracking, in line with Islamic ethical norms. The following are the most frequently cited keywords during 2013-2022.\n\nTo examine further, what Islamic values are discussed in the Scopus document, an examination of the abstract and documents is carried out more thoroughly. The results of examining these documents can be seen in the table below. From Table 7, the most discussed Islamic values are zakat, alms, waqf, and the contracts in mua’amalah. Zakat, alms, and waqf (ZISWAF) are very important concepts in Islam, because it is an obligation for Muslims to give part of their wealth to the needy. The ZISWAF concept is a central value in Islamic economics and finance which has a direct connection with crowdfunding, because they are a source of financing that can be used to support projects that comply with sharia principles. In carrying out mu’amlah actions, Muslims cannot be separated from the mu’amalah contracts or agreements in Islam that are used in Islamic crowdfunding, such as: mudarabah, musharakah, or murabahah. A good understanding of these contracts is very important because they are the basis of sharia financing and bind the parties involved in crowdfunding transactions. In recent years, Islamic crowdfunding has developed rapidly as an alternative financing that complies with sharia principles. Therefore, research in the literature review often seeks a deeper understanding of how Islamic values, such as zakat, alms, and waqf, play a role in these developments. Muslim communities interested in Islamic crowdfunding often have a special interest in ensuring that the funds they invest or donate are in accordance with Islamic principles. Therefore, an emphasis on concepts such as zakat, alms and waqf can meet their needs and interests. The review literature may look for ways in which Islamic crowdfunding can provide positive social impact through these concepts.\n\nIslamic crowdfunding has become an increasingly important alternative in supporting projects and ventures that comply with sharia principles that involve interdisciplinary scholarship. This was triggered by the increasing demand for financing that is in accordance with Islamic values, so clear regulations are needed in Islamic crowdfunding. Good regulation can help ensure that crowdfunding platforms comply with sharia principles and protect investors and owners of Islamic Crowdfunding projects. Islamic crowdfunding can help society and the economy, contributing to poverty alleviation and the development of certain sectors through products, such as crowdfunding for small and medium enterprises, and social projects, which comply with sharia principles as the industry adapts to the diverse needs of Muslim communities. However, there are challenges in the future development of Islamic crowdfunding, namely that apart from the benefits due to increased community participation in projects that are in accordance with religious values, it has the potential risk of losing investment and compliance with sharia principles. Provide a better understanding of Islamic crowdfunding, provide valuable information for practitioners, and encourage further research in this area to support the development of better crowdfunding models in accordance with sharia principles, in order to increase the success of sharia crowdfunding in the wider community. The data is only taken from the Scopus database, and does not include the latest research that could have a significant impact on the understanding of Islamic crowdfunding, because the data is only taken up to 2022. There is a possibility of bias in literature selection which results in an incomplete or distorted representation of the relevant literature. Additionally, research on Islamic crowdfunding may vary by geographic region, so the literature review may suffer from regional bias. Many research are in English or Indonesian, but there is many research in foreign language too that became obstruction to my research.\n\nIslamic crowdfunding is influenced by changes in the economic and legal environment, such as changes in regulations regarding sharia financing which may not be accommodated by research on Islamic crowdfunding, so this literature review also does not accommodate these changes. Further and in-depth discussion of the steps is needed. Methods are also needed to overcome the current scarcity of sharia fintech so that in the future it can be accepted by all levels of society, and increase Muslims’ understanding of openness and conformity with Islamic religious rules, especially a discipline that encompasses a profound understanding of Islamic principles and their application in various aspects of life (al-Zuhayli, 1986).\n\nFiqh law is a science that discusses the detailed laws of Islamic law in the field of practical actions derived from religious evidence., it is important to have scholars and religious scholars who have a deep understanding of social fiqh and its implementation in Islamic law. Based on the potential and limitations of sharia crowdfunding research in the data above, several recommendations are given for future sharia crowdfunding research so that it can support sharia crowdfunding, namely: the need for further and in-depth discussion regarding the steps. is needed to overcome the current shortcomings of sharia fintech so that in the future it can be accepted by all levels of society, increasing Muslims’ understanding of openness and conformity with Islamic religious rules, especially fiqh law. In this context, it is important to involve Islamic crowdfunding scholars and ulama who have a deep understanding of social fiqh and its implementation in Islamic crowdfunding law. It is also important to strengthen Islamic business ethics in Islamic crowdfunding operations, by prioritizing Islamic principles such as honesty, responsibility and maintaining consumer trust. By implementing these solutions, it is hoped that Muslims’ trust in Islamic crowdfunding can increase. To increase publication trust in the performance of sharia crowdfunding, state legislation is very necessary, so that rights, obligations, transparency and security in sharia crowdfunding are clearer.\n\n\nConclusions\n\nIslamic crowdfunding has become an increasingly important alternative in supporting projects and ventures that comply with sharia principles that involve interdisciplinary scholarship. This was triggered by the increasing demand for financing that is in accordance with Islamic values, so clear regulations are needed in Islamic crowdfunding. Good regulation can help ensure that crowdfunding platforms comply with sharia principles and protect investors and owners of Islamic Crowdfunding projects. Islamic crowdfunding can help society and the economy, contributing to poverty alleviation and the development of certain sectors through products, such as crowdfunding for small and medium enterprises, and social projects, which comply with sharia principles as the industry adapts to the diverse needs of Muslim communities. However, there are challenges in the future development of Islamic crowdfunding, namely that apart from the benefits due to increased community participation in projects that are in accordance with religious values, it has the potential risk of losing investment and compliance with sharia principles. Provide a better understanding of Islamic crowdfunding, provide valuable information for practitioners, and encourage further research in this area to support the development of better crowdfunding models in accordance with sharia principles, in order to increase the success of sharia crowdfunding in the wider community. The data is only taken from the Scopus database, and does not include the latest research that could have a significant impact on the understanding of Islamic crowdfunding, because the data is only taken up to 2022. There is a possibility of bias in literature selection which results in an incomplete or distorted representation of the relevant literature. Additionally, research on Islamic crowdfunding may vary by geographic region, so the literature review may suffer from regional bias. Islamic crowdfunding is influenced by changes in the economic and legal environment, such as changes in regulations regarding sharia financing which may not be accommodated by research on Islamic crowdfunding, so this literature review also does not accommodate these changes.\n\nFurther and in-depth discussion of the steps is needed. Methods are also needed to overcome the current scarcity of sharia fintech so that in the future it can be accepted by all levels of society, and increase Muslims’ understanding of openness and conformity with Islamic religious rules, especially fiqh law. In this context, it is important to involve scholars and religious scholars who have a deep understanding of social fiqh and its implementation in Islamic law. Based on the potential and limitations of sharia crowdfunding research in the data above, several recommendations are given for future sharia crowdfunding research so that it can support sharia crowdfunding, namely: the need for further and in-depth discussion regarding the steps. is needed to overcome the current shortcomings of sharia fintech so that in the future it can be accepted by all levels of society, increasing Muslims’ understanding of openness and conformity with Islamic religious rules, especially fiqh law. In this context, it is important to involve Islamic crowdfunding scholars and ulama who have a deep understanding of social fiqh and its implementation in Islamic crowdfunding law. It is also important to strengthen Islamic business ethics in Islamic crowdfunding operations, by prioritizing Islamic principles such as honesty, responsibility and maintaining consumer trust. By implementing these solutions, it is hoped that Muslims’ trust in Islamic crowdfunding can increase. To increase publication trust in the performance of sharia crowdfunding, state legislation is very necessary, so that rights, obligations, transparency and security in sharia crowdfunding are clearer.", "appendix": "Data availability\n\nThe data for this article consists of bibliographic references, which are included in the References section.\n\nFigshare: PRISMA flow diagram and checklist for ‘Bibliometric analysis of Islamic crowdfunding: a review of its journey’. https://doi.org/10.6084/m9.figshare.25563351.v2 (Purwatiningsih et al., 2024).\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\nAbd Wahab N, Nazri Chik Bank Islam Malaysia Berhad M, Lumpur K, et al.: Islamic Social Finance Initiatives: An Insight into Bank Islam Malaysia Berhad’s Innovative BangKIT Microfinance Product. ISRA International Journal of Islamic Finance. 2023; 15(1): 22–35. 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Publisher Full Text\n\nTesta S, Nielsen KR, Bogers M, et al.: The Role of Crowdfunding in Moving towards a Sustainable Society. Technological Forecasting and Social Change. April 1, 2019; 141: 66–73. Accessed February 15, 2023. Publisher Full Text Reference Source\n\nThottoli MM: The starring role of crowdfunding in GCC: a structured literature review. Asian Journal of Economics and Banking. 2022; 6(2): 155–177. Publisher Full Text\n\nTorres P, Augusto M, Wallace E: Improving consumers’ willingness to pay using social media activities. Journal of Services Marketing. 2018; 32(7): 880–896. Publisher Full Text\n\nUmar UH, Baita AJ, Haron MH, et al.: The potential of Islamic social finance to alleviate poverty in the era of COVID-19: the moderating effect of ethical orientation. International Journal of Islamic and Middle Eastern Finance and Management. 2022; 15(2): 255–270. Publisher Full Text\n\nVaznyte E, Andries P, Manigart S: Are you part of the crowd? The role of sex and environmental characteristics for crowdfunding awareness. Journal of Small Business Management. 2023; 61(2): 1062–1094. Publisher Full Text\n\nWan Mohamad Nazarie WNF, Williams R: Linguistic style and gender match in funding intention towards crowdfunding project. Review of International Business and Strategy. 2021; 31(3): 438–461. Publisher Full Text\n\nal-Zuhayli W: states that from the aspect of its relationship to the text (naṣṣ), maṣlaḥa or al-waṣf al-munāsib is divided into three, namely: al-munāsib al-mu’tabar, al-munāsib al-mulgha, and al- munāsib al-mursal. Wahbah Al-Zuhaili, Uṣūl Al-Fiqh Al-Islāmī (Damascus: Dār al-Fikr.1986; II: 752–754." }	[ { "id": "291782", "date": "29 Jun 2024", "name": "Rizka Estisia Pratiwi", "expertise": [ "Reviewer Expertise Sustainable financel", "islamic 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\nAre sufficient details of the methods and analysis provided to allow replication by others? The methods section lacks the detail necessary for replication, the authors do not specify:\nThe search terms used beyond the keyword \"Islamic crowdfunding.\" The inclusion and exclusion criteria for selecting articles. The specific databases or sources used beyond Scopus. The methods used to extract and analyze data from the articles.\nIs the statistical analysis and its interpretation appropriate? This article does not present any statistical analysis. It is a literature review that uses descriptive statistics (e.g., counts and percentages) to summarize the characteristics of the literature on Islamic crowdfunding (e.g., publication year, source type, language). However, it does not employ inferential statistics to test hypotheses or make generalizations beyond the included studies.\nAre the conclusions drawn adequately supported by the results presented in the review? Partly. There is some unsupported, or even overreaching conclusions:\nImpact on poverty alleviation and economic development (the conclusion that Islamic crowdfunding contributes to poverty alleviation and economic development is not directly supported by the results presented in the review. While the authors mention these potential benefits, the review does not provide concrete evidence or data to substantiate these claims) Need for specific Fiqh regulatory guidelines and government support (the conclusion calling for specific Fiqh regulatory guidelines and government support, while potentially valid, is not explicitly derived from the results of the literature review. It appears to be more of a recommendation or suggestion based on the authors' interpretation of the challenges identified in the literature)\nSome claims need more direct evidence from the reviewed literature. The authors could strengthen their conclusions by providing more specific examples and data from the studies they reviewed to support their assertions about the impact of Islamic crowdfunding and the need for regulatory and government support.\nIf this is a Living Systematic Review, is the 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.) Obviously, this article is not a LSR, because the authors do not provide the updated data and recent studies.\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? Partly\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable", "responses": [ { "c_id": "12103", "date": "31 Jul 2024", "name": "aris purwatiningsih", "role": "Author Response", "response": "Hi Rizka, This is my answer for your questions on my article: The search terms used beyond the keyword \"Islamic crowdfunding.\" Search terms islamic AND crowdfunding AND PUBYEAR > 2012 AND PUBYEAR < 2023 Inclusion and exclusion criteria for selecting articles. Inclusion and Exclusion Criteria Inclusion Criteria: Publications available in the Scopus database. Types of publications included: articles, book chapters, conference papers, books, reviews, editorials, short surveys, notes, and conference reviews. Publications in English. Publications focused on Islamic crowdfunding. Publications published between 2013 and 2024. Exclusion Criteria: The authors did not exclude any data to obtain a comprehensive overview of Islamic crowdfunding without excluding any type of publication. The goal is to understand all aspects of research conducted in the field of Islamic crowdfunding. Additionally, to explore all works related to Islamic crowdfunding without prejudice or strict limitations, the researchers chose not to exclude any data to gain a broader and deeper understanding of the topic. Not excluding data can reduce selection bias, where certain articles might be subjectively excluded by the researchers. By analyzing all the articles found, the results can be more objective. To reduce bias, the authors used five Research Questions (RQs). By not excluding data, the research process becomes more transparent and easier to replicate by other researchers, as all identified articles in the initial search are analyzed, making the research process and results easier to replicate and verify. The specific databases or sources used beyond Scopus. Why use the Scopus database? The Scopus database is used as a data source because it has a broad scope that includes relevant publications from various disciplines such as economics, finance, Islamic studies, and information technology. This allows for a more holistic and comprehensive analysis of how Islamic crowdfunding is studied and practiced worldwide. Additionally, Scopus provides access to reliable, comprehensive, and relevant data, which is crucial for producing a high-quality bibliometric article review. The methods used to extract and analyze data from the articles. Detailed Bibliometric Procedures Document Profile Analysis: Analyzing the profile of each relevant document. Source Type Analysis: Categorizing and analyzing the types of sources from each publication. Language Analysis: Analyzing the language used in the publications. Subject Area Analysis: Analyzing the subject areas covered by publications related to Islamic crowdfunding. Keyword Analysis: Identifying and analyzing frequently appearing keywords. Publication and Citation Performance Trends Analysis: Analyzing publication trends and citation performance annually. Identifying the Most Influential Studies: Identifying the most influential studies based on citations and keywords. Most Common Subject Areas in Islamic Crowdfunding (2013-2024): Determining whether the three most common subjects are always present in each study over this period. Islamic Values in Islamic Crowdfunding Articles: Analyzing how Islamic values are discussed in articles about Islamic crowdfunding. Also for your question on Impact on poverty alleviation and economic development and Fiqh Regulatory in Indonesia this is my Answer: Poverty Alleviation And Economic Development Resulting From Islamic Crowdfunding Islamic crowdfunding platforms can serve as a funding solution for SMEs and startups, facilitating access to capital for businesses that may struggle to obtain traditional financing (Hendratmi et al., 2019). The concept of crowdfunding, when connected with spiritual and religious responsibilities, can drive the economic growth of micro and small enterprises, thereby contributing to economic development (Aderemi & Ishak, 2020).Islamic values and principles, when applied in crowdfunding initiatives, can help households improve their livelihoods and reduce poverty by promoting ethical financial practices and responsible wealth distribution. Islamic crowdfunding is in line with the principles of Islamic finance, promoting equitable distribution of wealth and avoiding riba, which can contribute to poverty reduction. Islamic crowdfunding offers a Shariah-compliant and ethical financing solution that can empower the underprivileged, strengthen economic foundations, and promote sustainable development. Ultimately, it plays a vital role in poverty alleviation efforts in Muslim societies and beyond. By leveraging the concepts of cooperation, risk sharing, and ethical investment, Islamic crowdfunding can contribute to poverty alleviation in a variety of ways (Aderemi & Ishak, 2022). Islamic crowdfunding platforms, such as Qard Hasan crowdfunding, can create opportunities for micro-enterprises and bridge the wealth gap between different socio-economic classes, encouraging collaboration and a more charitable society (Aderemi & Ishak, 2022). By providing funding for small and medium enterprises (SMEs) and social projects tailored to meet the needs of Muslims, Islamic crowdfunding contributes to poverty alleviation and sectoral development. In addition, Islamic crowdfunding can reduce the government's financial burden in supporting micro-enterprises, empowering them to be more independent, creative, and competitive in promoting their products (Ishak, 2023). Indonesia, as the country with the largest Muslim population in the world, has developed policies and regulations to support the growth of Islamic crowdfunding, involving the Financial Services Authority (OJK) and the National Sharia Finance Committee (KNKS). The OJK regulates and supervises the financial industry, including Islamic crowdfunding, through regulations such as OJK Regulation No. 37/POJK.04/2018 concerning equity crowdfunding services based on information technology, which includes Sharia-compliant platforms. KNKS, now known as the National Committee for Islamic Economy and Finance (KNEKS), plays a role in developing and promoting policies and regulations to strengthen the Sharia economy and finance, including crowdfunding, with support from the Indonesian government through various Sharia fintech initiatives. The National Sharia Council (DSN-MUI) also plays a crucial role by issuing fatwas, such as Fatwa No. 117/DSN-MUI/II/2018 and No. 118/DSN-MUI/II/2018, to ensure that crowdfunding products and services comply with Sharia principles, and each Islamic crowdfunding platform in Indonesia must have a Sharia Supervisory Board to ensure adherence to Sharia principles in their operations and offered products. According to OJK, which oversees Indonesia's financial sector, several Sharia-compliant crowdfunding platforms, such as Ethis Indonesia, ALAMI, and SyarQ, are registered with and supervised by the authority. Ethis Indonesia focuses on property and social financing, ALAMI provides Sharia-compliant P2P lending for SMEs, and SyarQ offers Sharia-based consumer financing.. The transaction volume of Islamic crowdfunding in Indonesia has shown significant growth, with ALAMI recording over IDR 1 trillion in financing by the end of 2023, supporting thousands of SMEs across Indonesia. The sectors financed through Islamic crowdfunding platforms include micro, small, and medium enterprises (MSMEs), property, education, and social projects. Investor participation in Islamic crowdfunding platforms continues to increase, indicating high confidence in Sharia-compliant financing mechanisms. The use of technology in Sharia crowdfunding platforms facilitates investment and financing processes, enhances transparency, and reduces risk. Aderemi, A. M. R. and Ishak, M. S. I. (2020). Crowdfunding as an alternative mode of financing for micro and small enterprises: a proposed qard-al-hasan contract. International Journal of Islamic Economics and Finance (IJIEF), 3(3). https://doi.org/10.18196/ijief.3235. Aderemi, A. M. R. and Ishak, M. S. I. (2022). Qard hasan as a feasible islamic financial instrument for crowdfunding: its potential and possible application for financing micro-enterprises in malaysia. Qualitative Research in Financial Markets, 15(1), 58- 76. https://doi.org/10.1108/qrfm-08-2021-0145. Fang, Y. (2021). The future path to china’s poverty reduction—dynamic decomposition analysis with the evolution of china’s poverty reduction policies. Social Indicators Research, 158(2), 507-538. https://doi.org/10.1007/s11205-021-02716-5 Hendratmi, A., Ryandono, M. N. H., & Sukmaningrum, P. S. (2019). Developing islamic crowdfunding website platform for startup companies in indonesia. Journal of Islamic Marketing, 11(5), 1041-1053. https://doi.org/10.1108/jima-02-2019-0022. Idemudia, U. (2008). Oil extraction and poverty reduction in the niger delta: a critical examination of partnership initiatives. Journal of Business Ethics, 90(S1), 91-116. https://doi.org/10.1007/s10551-008-9916-8 Ishak, M. S. I. and Mohammad Nasir, N. S. (2023). The applicability of islamic crowdfunding as an alternative funding for micro- entrepreneurs in malaysia. Qualitative Research in Financial Markets, 16(3), 548-564. https://doi.org/10.1108/qrfm-12- 2022-0202 List of Equity Crowdfunding Platforms that Have Obtained Permits from OJK. (2019). Retrieved July 30, 2024, from https://ojk.go.id/id/berita-dan-kegiatan/publikasi/Pages/Daftar-Platform-Equity-Crowdfunding-yang-Telah- Mendapatkan-Izin-dari-OJK.aspx Liu, Y. and Xu, Y. (2016). A geographic identification of multidimensional poverty in rural china under the framework of sustainable livelihoods analysis. Applied Geography, 73, 62-76. https://doi.org/10.1016/j.apgeog.2016.06.004. Liu, Y., Guo, Y., & Zhou, Y. (2018). Poverty alleviation in rural china: policy changes, future challenges and policy implications. China Agricultural Economic Review, 10(2), 241-259. https://doi.org/10.1108/caer-10-2017-0192. Wang, F., Du, L., Tian, M., Liu, Y., & Zhang, Y. (2023). Sustainability of rural tourism in poverty reduction: evidence from panel data of 15 underdeveloped counties in anhui province, china. Plos One, 18(3), e0283048. https://doi.org/10.1371/journal.pone.0283048 Zhang, H., Wu, K., Qiu, Y., Chan, G., Wang, S., Zhou, D., … & Ren, X. (2020). Solar photovoltaic interventions have reduced rural poverty in china. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-15826-4 Thank you very much" } ] }, { "id": "286593", "date": "29 Jul 2024", "name": "Muhammad Nazmul Hoque", "expertise": [ "Reviewer Expertise social 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\nThe article provides a valuable contribution to understanding the landscape of Islamic crowdfunding research. However, please consider some of my advices for Improvement of this article below: Please provide a more detailed methodology section, including specific inclusion and exclusion criteria, data extraction methods, and detailed steps of the bibliometric analysis. This would enable replication and increase the transparency of the review process.\nPlease try to find advanced statistical techniques and visualizations, such as trend analysis over time, co-authorship networks, and regression analysis to understand the factors influencing citation rates. This would enhance the interpretation of the bibliometric data. Please try to discuss the limitations of the study more explicitly. For instance, the reliance on Scopus as the sole database may exclude relevant studies indexed elsewhere. Acknowledging these limitations would provide a more balanced view. Thank you\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.) Not applicable", "responses": [ { "c_id": "12104", "date": "31 Jul 2024", "name": "aris purwatiningsih", "role": "Author Response", "response": "Hi Muhammad Nazmul Hoque This is my answer about your questions on the review Inclusion and Exclusion Criteria Inclusion Criteria: Publications available in the Scopus database. Types of publications included: articles, book chapters, conference papers, books, reviews, editorials, short surveys, notes, and conference reviews. Publications in English. Publications focused on Islamic crowdfunding. Publications published between 2013 and 2024. Exclusion Criteria: The authors did not exclude any data to obtain a comprehensive overview of Islamic crowdfunding without excluding any type of publication. The goal is to understand all aspects of research conducted in the field of Islamic crowdfunding. Additionally, to explore all works related to Islamic crowdfunding without prejudice or strict limitations, the researchers chose not to exclude any data to gain a broader and deeper understanding of the topic. Not excluding data can reduce selection bias, where certain articles might be subjectively excluded by the researchers. By analyzing all the articles found, the results can be more objective. To reduce bias, the authors used five Research Questions (RQs). By not excluding data, the research process becomes more transparent and easier to replicate by other researchers, as all identified articles in the initial search are analyzed, making the research process and results easier to replicate and verify. Bibliometric Analysis Document Profile Analysis: Analyzing the profile of each relevant document. Source Type Analysis: Categorizing and analyzing the types of sources from each publication. Language Analysis: Analyzing the language used in the publications. Subject Area Analysis: Analyzing the subject areas covered by publications related to Islamic crowdfunding. Keyword Analysis: Identifying and analyzing frequently appearing keywords. Publication and Citation Performance Trends Analysis: Analyzing publication trends and citation performance annually. Identifying the Most Influential Studies: Identifying the most influential studies based on citations and keywords. Most Common Subject Areas in Islamic Crowdfunding (2013-2024): Determining whether the three most common subjects are always present in each study over this period. Islamic Values in Islamic Crowdfunding Articles: Analyzing how Islamic values are discussed in articles about Islamic crowdfunding. How to Determine Metrics? Identify research objectives. Formulate research questions to minimize bias. Establish inclusion criteria. Retrieve data from Scopus. Examine and categorize data. Perform bibliometric data analysis. Visualize data with graphs and diagrams. Analyze the data. Detailed Bibliometric Procedures Document Profile Analysis: Analyzing the profile of each relevant document. Source Type Analysis: Categorizing and analyzing the types of sources from each publication. Language Analysis: Analyzing the language used in the publications. Subject Area Analysis: Analyzing the subject areas covered by publications related to Islamic crowdfunding. Keyword Analysis: Identifying and analyzing frequently appearing keywords. Publication and Citation Performance Trends Analysis: Analyzing publication trends and citation performance annually. Identifying the Most Influential Studies: Identifying the most influential studies based on citations and keywords. Most Common Subject Areas in Islamic Crowdfunding (2013-2024): Determining whether the three most common subjects are always present in each study over this period. Islamic Values in Islamic Crowdfunding Articles: Analyzing how Islamic values are discussed in articles about Islamic crowdfunding. Why use the Scopus database? The Scopus database is used as a data source because it has a broad scope that includes relevant publications from various disciplines such as economics, finance, Islamic studies, and information technology. This allows for a more holistic and comprehensive analysis of how Islamic crowdfunding is studied and practiced worldwide. Additionally, Scopus provides access to reliable, comprehensive, and relevant data, which is crucial for producing a high-quality bibliometric article review. Thank you very much, Sir" } ] } ]	1	https://f1000research.com/articles/13-531
https://f1000research.com/articles/13-991/v1	02 Sep 24	{ "type": "Systematic Review", "title": "Volatilomics: An emerging discipline within Omics Sciences - A systematic review", "authors": [ "Juan Pablo Betancourt-Arango", "Erica Elvira Villaroel-Solis", "Jhon Alexander Fiscal-Ladino", "Gonzalo Taborda-Ocampo", "Juan Pablo Betancourt-Arango", "Erica Elvira Villaroel-Solis", "Jhon Alexander Fiscal-Ladino" ], "abstract": "Introduction Volatilomics is an omics science that is characterized as being a specific subbranch of metabolomics, which studies the different types of volatile organic compounds that may be present in a certain biological matrix. It has had impacts on the identification of new natural compounds and food safety processes, since it allows the evaluation of emerging contaminants that are present on food matrices, through the identification of biomarkers generated in response to this type of xenobiotic compounds through xenovolatilomic studies.\n\nObjective In this way, this review seeks to understand the scientific advances reported towards volatilomic studies, for which different types of primary research are reported depending on the main instrumental techniques used for the characterization of different types of VOCs that have been reported in our country between 2012 and 2022.\n\nMethodology Using a qualitative methodology, a search was carried out in the Scopus database, from which the bibliometric information of the primary research reported during this time was obtained, to later analyze the different research concerning the use of volatilomic studies and the fields of action that are currently used, as well as the different techniques for obtaining these compounds and the data analysis methodologies established for the processing of this type of research.\n\nConclusions Finally, it can be concluded that, from the present review, the applicability of volatilomic studies is shown. The incursion carried out by this type of science on the verification of food safety in different types of matrices, in addition to allowing the study of the volatile profile formed by the different volatile organic compounds expressed by said matrix and the respective ecological role expressed by these compounds with the environment in which they are found.", "keywords": [ "Omic Sciences", "Volatile Organic Compounds", "Biomarkers", "Volatilomic", "Xenovolatilomic." ], "content": "1. Introduction\n\nThe term “omics” began to be adopted by various scientific communities beginning in the year 1980. From then on, the importance of studying diverse sets of biomolecules found in different types of biological matrices became apparent.1 An abundance of research asserts that the advent of omics sciences occurred alongside the development of the Human Genome Project (HGP), which facilitated the complete sequencing of human DNA.2 Since then, numerous branches of omics sciences have emerged, each boasting a unique field of action. These include genomics (a discipline that studies the collection of genes in DNA), transcriptomics (which investigates different types of mRNA transcripts), proteomics (a field that analyzes diverse sets of proteins), and metabolomics (which examines different sets of metabolites).1 Advancements in science showcased through a wide array of research on the application of omics sciences, highlight the significance of technological tools for the ongoing progression of the sciences and society at large. Therefore, a vast body of research documents the use of omics to probe the biodiversity that populates our planet Earth. This research involves analyzing a variety of life forms such as plants, animals, soil biodiversity, environmental sustainability, and various types of coexisting microorganisms. Each of these contributes unique information through the utilization of each omics discipline.3\n\nAt present, genomics and transcriptomics are commonly utilized disciplines. Both are approached through comparative study, yet genomics offers a process of genome characterization, revealing structural and functional conditions, as well as evolutionary processes and similarities among gene families.4 As such, genomics has served as a launching pad in agriculture for the creation of novel biotechnological developments, for instance, in the development of plant improvement programs.4 Transcriptomics, conversely, investigates the various biological processes that occur within an organism to identify genes that are associated with tissues and genetic responses expressed under specific conditions. Likewise, it offers insights into macro-scale evolutionary processes across different species over time.4 Proteomics, distinct from transcriptomics, is charged with understanding proteins at both the structural and functional levels. These biomolecules are vital to life due to their role in various metabolic pathways.5 It includes several sub-disciplines, such as expression proteomics (the identification of the relative abundance of proteins), structural proteomics (three-dimensional analysis of protein conformation), and functional proteomics (the study of interactions, functions, and distribution of proteins within each organism). Therefore, the application of proteomics aids in the analysis of the protein profile by identifying patterns of presence, absence, and changes through the proteome.5\n\nAnother facet of omics sciences is metabolomics, which focuses on the analysis and characterization of the myriad of metabolites found within a specific organism.6 Metabolomics is intrinsically connected with the chemical analysis of molecules on an individual level. Additionally, this discipline provides various technological tools to more accurately characterize the biomolecules constituting a given matrix.6 At present, a multitude of chemical compounds exist, varying in polarity, functional groups, molecular masses, and chemical stability, among other characteristics.7 Given this diverse array of compounds, the employment of a range of tools to support the identification of metabolites becomes necessary. Thus, both gas chromatography (GC) and liquid chromatography (LC) facilitate the segregation of all these compounds present within a matrix.7 Furthermore, pairing these types of chromatography with identification techniques such as mass spectrometry (MS), nuclear magnetic resonance (NMR), and matrix-assisted laser desorption/ionization (MALDI) fosters the development of innovative techniques like GC – MS, LC – MS, and MALDI – TOF. These techniques enable nuanced characterization in light of this assortment of chemical compounds.7\n\nResearch conducted using omics sciences resonates profoundly with the academic community and society at large. This is attributable to the fact that these contributions pave the way for the discovery of the bioprospecting potential that omics sciences possess for exploring biological characteristics, from the genetic to the molecular level, with significant benefits for health.8 In this context, metabolomics plays a pivotal role in understanding the complex interactions within the metabolite environment as a response to the connection formed between various types of organisms and their surrounding environment.8 Therefore, in a logical progression, a metabolomics study enables an exploratory analysis of the chemical potential that a particular biological matrix may hold. This is performed through a series of stages, such as defining the experimental conditions of the study, extracting metabolites, and then separating and detecting them.8\n\nIn the present day, due to numerous technological advancements, new omics sciences have emerged. These include epigenomics,9 metagenomics,10 nutrigenomics,11 connectomics,12 speciomics,13 foodomics,14 petroleomics,15 fluxomics,16 lipidomics,17 and volatilomics.18 Each of these disciplines has a distinct field of study.19 Turning our attention to volatilomics, this discipline arises as a subfield of metabolomics. It is characterized by its analysis of the metabolites that constitute the volatile profile within a given matrix.20 Of late, volatilomic analysis has been gaining traction in the research arena (Figure 1), given the number of research studies reported that employ this tool for quality control and early, non-invasive identification of certain diseases.20 Moreover, volatilomic studies are being conducted for the detection of toxic substances present in certain foods. As such, it ensures the safety of these products, thereby circumventing issues of adulteration and food fraud.20\n\nConsequently, it is crucial to comprehend the practical role that volatilomic studies play in identifying volatile organic compounds (VOCs). These compounds enable the non-invasive and efficient assessment of food quality through the extraction of metabolites that constitute the volatile profile. Moreover, these VOCs are responsible for generating the aroma in a broad variety of foods consumed by society. These compounds are also tied to the ripeness level that food may exhibit,21 or they may be influenced by the presence of external compounds, such as those generated by the use of emerging pollutants—for instance, the presence of pesticides and heavy metals in food. All of this culminates in an analysis of the importance of VOCs in the sensory identity that each type of food can possess concerning its volatile profile.21 Therefore, in this review, our objective is to comprehend the scientific advancements reported in the field of volatilomic studies. To that end, we present a variety of primary research concerning the principal instrumental techniques utilized for the separation and characterization of diverse VOCs reported and applied within our country.\n\n\n2. Volatilomics and volatile organic compounds (VOCs)\n\nWhen defining volatilomics, we can classify it as a branch of metabolomics dedicated to the study of VOCs and the respective roles these play within the processes of biological interaction in each organism. In the current era, extensive volatile chemodiversity is known among VOCs, thus underscoring the importance of studying the volatilome in different matrices.22 VOCs are characterized as a diverse group of molecules that, structurally, are composed of carbon, hydrogen, oxygen, nitrogen, and occasionally sulfur. These compounds have a low boiling point, which renders them gaseous at room temperature.23 Volatilomics studies involve a range of processes, which encompass sample preparation, extraction techniques, analytical parameters, instrumentation, and the analysis of multivariate data.24 These steps are executed through the combination of techniques such as solid-phase microextraction (SPME) and the use of gas chromatography with spectrometry (GC – MS).24 Presently, volatilomics has diverse applications, including evaluating authenticity, contrasting compositions based on various geographical origins,25 and assessing food quality.24 It is also employed in analyzing the ideal conditions of foods and the influence of physicochemical variables on the change of the volatilome, potentially triggering the expression of VOCs.26 Furthermore, it permits the non-invasive identification of diseases, aiding in their detection by characterizing potential biomarkers for early discovery in patients presenting different pathological stages.27 This contributes to the identification of biomarkers for monitoring the toxicity and ecotoxicology of biological matrices,28 in the presence of toxic agents. Additionally, volatilomics finds application in the development of various chemical-environmental studies.29\n\nRecent research has centered on the early identification of diseases, such as cancer, through non-invasive techniques. These methods allow for the detection of biomarkers—molecules that are expressed during the development of a given disease within an organism.30 Accordingly, research targeting the chromatographic analysis of exhaled air has expanded, with the aim of identifying biomarkers. This, in turn, enables the establishment of reference points for early disease diagnosis through the analysis of VOCs.30 To date, a wide array of VOCs has been identified. Table 1 presents various types of compounds currently being studied, including major atmospheric pollutants (MAPs) and harmful, polluting agents, also known as polycyclic aromatic hydrocarbons (PAHs).31\n\nAdditionally, volatile organic compounds (VOCs) can be classified into semi-volatile organic compounds (SVOCs) and very volatile organic compounds (VVOCs).32 Moreover, the identification of biogenic volatile organic compounds (BVOCs),18,33,34 and microbial volatile organic compounds (MVOCs) is reported.35 The latter are characterized by their role as mediators in both inter- and intraspecific communication processes, serving in signaling mechanisms as well as in the production of metabolites for plant defense.35,36 Furthermore, the prospect of utilizing MVOCs as ecological alternatives to mitigate the use of various types of harmful chemical pesticides is being explored.36,37\n\n\n3. Techniques for extraction, separation, and identification of VOCs\n\nThere are various analytical techniques for extracting VOCs. Among these, the use of solid-phase extraction (SPE), a sample preparation technique developed in the 1970s, is well-documented.38 Currently, various methodologies have been reported, giving rise to sub-techniques such as matrix solid-phase dispersion (MSPD), miniaturized solid-phase extraction (M-SPE), and solid-phase microextraction (SPME),38 among others. In 1990, Arthur and Pawliszyn introduced solid-phase microextraction in the headspace (HS – SPME), which streamlined the isolation of different types of compounds for obtaining VOCs in various biological samples.23 It presents advantages such as the elimination of solvent use, ease of handling, minimal equipment requirements, and rapidity. It is also adaptable for automation, provides good linearity, and exhibits high sensitivity.38 Similarly, it operates under an extraction-desorption process of the analytes within the material’s surface, thereby facilitating the extraction of compounds of interest for subsequent analysis using various chromatographic techniques, as depicted in Figure 2.\n\nWhen conducting HS – SPME analysis, it is important to consider several factors that influence the process of extracting VOCs. These include the amount of sample used for extraction, extraction time, desorption time, as well as the material constituting the microextraction fiber. Examples of fibers utilized include polydimethylsiloxane (PDMS), polyethylene glycol (PEG), polyacrylate (PA), as well as combinations of polydimethylsiloxane and carboxene (PDMS/CAR), divinylbenzene and polydimethylsiloxane (DVB/PDMS), and polydimethylsiloxane, carboxene and divinylbenzene (PDMS/CAR/DVB) materials.23 Additionally, the type of fiber used in the HS – SPME analysis is selected based on the polarity of the analyte of interest. This is because the combination of each material yields different polarities, and the analytes that have an affinity with the fiber will be attracted to it. Also, within SPME, we can identify three distinct sub-techniques of analysis. These include the use of solid-phase microextraction with multiple headspaces (MHS-SPME),39 dynamic headspace solid-phase microextraction (DHS-SPME),21 and static headspace solid-phase microextraction (SHS-SPME).40,41\n\nIn a volatilomic study, following the extraction of metabolites and their separation through instrumental techniques such as GC and LC, and the subsequent detection of chemical compounds via techniques like MS, nuclear magnetic resonance (NMR), ultraviolet light (UV), or infrared spectroscopy (IR), this information is processed through a preliminary step that executes peak deconvolution (data preprocessing). This is done to avoid overlap of chromatographic and spectral signals that could represent instrumental information about a chemical molecule.42 Consequently, given the scientific and technological advancements of the present day, all these extraction techniques have been coupled with novel methodologies for the separation and identification of VOCs. Some examples of these are presented in Table 2.\n\nConcurrently, the emergence of new combined techniques has been reported, which leverage various technological advancements. These techniques often employ tools based on the development of sensors, such as the electronic nose (E-nose).24 The E-nose facilitates the evaluation and identification of VOCs through electronic processes, leading to the genesis of specific study disciplines like olfactometry (O).43 This field has been explored using the electronic nose (E-nose),44,45 including E-noses of the MOS (metal oxide semiconductors) type,46 and Flash E-Noses, which are characterized by the use of an electronic nose in conjunction with flash gas chromatography.47 On the other hand, extraction systems like SPME have been combined with gas chromatography, mass spectrometry, and olfactometry (HS - SPME - GC - MS - O).48 Moreover, new couplings involving two-dimensional chromatography with olfactometry (GC x GC - O) are being reported.49,50 Studies elucidating the diverse applications of the electronic nose for identifying these types of compounds underscore the use of chemometric tools for analyzing this type of data. Such tools include the support vector machine (SVM),51 the extreme learning machine (ELM),52 backpropagation neural networks, also known as backpropagation networks (BP),52 and the employment of rapid discrimination models of the artificial neural network (ANN) via the development of self-organizing Kohonen maps (SOM).53–55 These tools facilitate the design of a classification model for recognition in the E-nose system and the identification of VOCs.52 All of this contributes to the progressive advancement in characterizing biomarkers for the non-invasive diagnosis of diseases such as cancer and chronic obstructive pulmonary disease (COPD).56 Therefore, these analyses enable the cross-checking of experimentally obtained information with various active metabolic pathways. These pathways can occur in different types of organisms and may be altered under the presence of emerging contaminants, for the analysis of response metabolites and their applicative role within biochemical pathways.57\n\n\n4. Chemometrics of volatilomic studies\n\nOnce data from an E-nose, GCxGC – O, GC – MS analysis is obtained, this information is subject to a preprocessing and information treatment phase. The aim here is to align, identify, and validate the data through either supervised or unsupervised multivariate statistical analysis techniques.42 Currently, a variety of techniques have been developed for analyzing this type of volatilomic data, with reports citing the use of techniques such as: Principal Component Analysis (PCA),58 Linear Discriminant Analysis (LDA),59 Partial Least Squares regression (PLS),60 Partial Least Squares Discriminant Analysis (PLS-DA),61 Orthogonal Partial Least Squares analysis (OPLS), and Orthogonal Partial Least Squares Discriminant Analysis (OPLS - DA),62 Hierarchical Cluster Analysis (HCA),63 Support Vector Machine (SVM),51 Non-Targeted Screening Workflow (NTS-Workflow),64 Random Forest (RF),65,47 Multilayer Perceptron (MLP),47 Multivariate Curve Resolution (MCR-ALS),66 Kernel algorithm with Partial Least Squares Discriminant Analysis (Kernel – PLS),67 as well as the k-Nearest Neighbors method (k-NN),68 Principal Component Analysis combined with the k-Nearest Neighbors algorithm (PCA-kNN),69 Quantitative Descriptive Sensory Analysis (QDA),70 Artificial Neural Network analysis (ANN),71 and Non-Negative Matrix Factorization (NNMF).72 A volatilomic analysis conducted using E-nose technologies often incorporates chemometric methods such as PCA, LDA, DA, QDA, SVM, and ANN as mathematical models for the identification of VOCs73 (Figure 3).\n\nPrincipal Component Analysis (PCA), Discriminant Analysis (DA), and Partial Least Squares regression (PLS) are widely-used multivariate analysis tools for conducting a volatilomic study.24 These statistical tools facilitate the simplification of dimensionality provided by the number of variables. This allows for the discrimination of study groups based on the obtained metabolic profile and enables the identification of the most representative metabolites.74 These methods are categorized as either supervised or unsupervised.\n\n\n5. Applications of machine learning in volatilomic studies\n\nTo distill essential information from sample analyses across GC – MS, LC – MS, and NMR, the application of chemometric and bioinformatic tools is required. The conventional approach has typically employed unsupervised methods such as PCA, clustering, and self-organizing maps (SOM), as well as supervised techniques including RF, kNN, Principal Component Regression (PCR), PLS, and SVM.75 In addition, novel methods have been introduced, such as Pathway Analysis (PA). These techniques generate an enrichment for metabolomic data and facilitate interpretation in relation to statistically significant pathways. They are characterized by being either non-topology-based methods (nTB) or topology-based (TB), but they do not incorporate an over-representation analysis (ORA). Additionally, there are functional class scoring (FCS) methods available.75\n\nGiven the progress of recent scientific advancements, innovative learning methods have been developed, enabling the more efficient execution of both supervised and unsupervised methods through the use of Artificial Intelligence (AI). AI is characterized by its arsenal of algorithms designed to emulate human learning processes, thereby facilitating data-driven decision-making.75 In line with the advancement of AI, models for machine learning, deep learning, and varying levels of neural networks have been formulated. These are designed to generate a model from a base dataset that is fit for making decisions with a high degree of prediction accuracy. This leads to the application of concepts such as “Deep Learning” and “Machine Learning,” and the use of neural networks through algorithms that mimic the function of a human brain neuron when induced by stimuli.75 Deep learning encompasses supervised learning, which serves as a discriminative analysis. This includes the Multilayer Perceptron (MLP), Convolutional Neural Network (CNN), Short-Term Long Memory (LSTM), and Gated Recurrent Unit (GRU).75 Conversely, unsupervised learning, serving as a generative analysis, features the Generative Adversarial Network (GAN), Autoencoder (AE), Sparse Autoencoder (SAE), Denoising Autoencoder (DAE), Self-Organizing Map (SOM), Restricted Boltzmann Machine (RBM), and the creation of Artificial Neural Networks (ANN) and the Deep Belief Network (DBN).75 In addition, there exists a hybrid form of learning that leverages both supervised and unsupervised methods, thereby generating composite data models through Deep Transfer Learning (DTL) and Deep Reinforcement Learning (DRL).75\n\nAs a result, studies relating to metabolomic and volatilomic data modeling have been conducted. For instance, the application of NMR metabolic data analyzed through deep learning techniques, using convolutional neural network architectures, has been reported, with relevance to food analysis and various biomedical research fields.75 In a study by Capitain et al., (2022), an analysis of yogurt and kefir samples using HS – GC – HTIMS is detailed. Accordingly, the volatile profile of 33 traditional kefir samples, 13 commercial ones, and 15 commercial yogurt samples were obtained. These were subsequently analyzed using PCA and NNMF techniques, leading to the identification of compounds such as ethanol, methyl-1-butanol, ethyl acetate, 3-methylbutyl acetate, and aldehydes.72 In a similar vein, other research reports the use of machine learning for the identification of biomarkers through the classification of specific patterns in the analysis of VOCs, and the various compounds that participate within different metabolic pathways for the biosynthesis of VOCs.76 Such analyses also facilitate the differentiation between substances from the identification of samples by HS – SPME – GC – MS – IMS methods. This enables the distinction between grapefruit and orange juices using techniques such as LDA, SVM, kNN, and PCA. These methods, in turn, provide alternatives for assessing the authenticity of various types of citrus fruits through the application of deep learning.77\n\n\n6. Applications in volatilomic studies\n\nIn the same way that metabolomic and volatilomic studies facilitate the identification of new natural products and probe their chemio-ecological relationship with the environment, the application of these omic sciences has also been reported in the extraction of biomarkers. This is achieved through the creation of the xenometabolome or exposome, whereby metabolomic analysis is performed in tandem with endogenous metabolites and the xenometabolome induced under the influence of chemical xenobiotics that trigger a biological alteration.78 The identification of these potential biomarkers, brought about by the presence of xenobiotic agents, has been extensively explored using techniques such as NMR, GC – MS, LC – MS, LC – HRMS,78 and trace level xenobiotic analysis using LC – nanospray MS (nUHPL – nESI – TOFMS). This last technique boasts a high degree of analytical sensitivity, low injection volume, and an extensive metabolic analysis range.79 This offers an alternative approach for small molecule profiling, guaranteeing solid repeatability and reproducibility of this innovative methodology for the analysis of urine and plasma samples.80 An illustration of this application is the study conducted by Al-Salhi et al., (2012), in which the xenometabolic profile in the plasma of fish from the Oncorhynchus mykiss species is determined. This profile was generated as a consequence of the exposure of these organisms to wastewater. Their work underscores the significance of metabolomic and xenometabolomic studies for identifying potential biomarkers in plasma as a means of monitoring long-term exposure to contaminant substances.81\n\nThrough these types of studies, it is feasible to examine the various metabolic pathways that become disrupted in the presence of a broad array of xenobiotic agents, which can trigger alterations in the subject organism.78 Consequently, research is delving into the creation of platforms for xenometabolite identification, termed as “XenoScan,” employing techniques such as LC – MS. This has led to the development of novel metabolomic approaches using xenobiotic metabolite enrichment. Such an approach enables the analysis of response metabolites produced in the presence of these external agents and the various formation pathways associated with the ecological analysis of intestinal microbiology.82 By utilizing various analytical tools in conjunction with big data analysis and multivariate statistics, it is possible to distinguish grouped samples and identify specific biomarker compounds.24 This demonstrates the fundamental role of biomarkers in evaluating the quality, originality, and predictive analysis of diverse factors affecting food.24 Currently, a range of biomarker types exists, based on the omic science through which their identification has been realized. These include genetic, epigenetic, transcriptomic, proteomic, and metabolomic biomarkers (within which lipidomic and volatilomic biomarkers are found).83,84\n\nIn a pathological state, VOCs undergo significant alterations; hence, the study of the volatilome in the body secretions of ill individuals is employed to identify potential biomarkers.85 In this realm, volatilomic studies have been implemented across various biological fluids for pathology detection, aiming towards the early diagnosis of such conditions. For lung cancer, VOC samples were sourced from exhaled breath,85 and VOCs present in urine samples were used for diagnosing breast cancer,86 liver,87 and prostate diseases.88 VOC studies in blood were utilized to diagnose colorectal cancer,89 ovarian cancer,90 and polycystic ovary syndrome.91 In Colombia, a study was conducted on VOCs present in exhaled breath for detecting gastric cancer using GC – MS, presenting a faster and more effective diagnostic approach compared to traditional tests.92 This method was also used in the identification of compounds such as 2-pentanone, 2-heptanone, ethyl propionate, p-xylene, 1,2,4-trimethylbenzene, and o-cresol, considered potential biomarkers for the detection of breast cancer through urine samples.93 Similarly, using GCxGC-TOF/MS, it was possible to identify VOCs such as butyrolactone, 2-methoxyphenol, 3-methoxy-5-methylphenol, 1-(2,6,6-trimethylcyclohexa-1,3-dien-1-yl)-2-buten-1-one, nootkatone, and 1-(2,6,6-trimethyl-1-cyclohexenyl)-2-buten-1-one as potential biomarkers for bladder cancer detection.94\n\nFurthermore, these types of studies are also being implemented for the identification of biomarkers in animals, facilitating disease diagnosis in livestock through non-invasive tests, which utilize breath for the capture of these compounds.95 Consequently, diagnoses of conditions such as ketosis and bovine respiratory disease (BRD) are made feasible, using sample preparation techniques like SPME and VOC identification methodologies such as GC-MS and E-nose.95 Thus, volatilomic studies also offer a swift diagnostic alternative for early disease detection, finding response metabolites to disruptions or alterations induced in the environment. This allows the identification of biomarkers related to senescence,96 maturation, susceptibility, exposure, effect, efficacy, circularity, therapeutic use, safety, omics, and toxicity.97 This broad applicability enables risk assessment in patients and monitoring disease progression in several aspects such as treatment, prevention, diagnosis, therapy response, experimental evaluation, and environmental and epidemiological risk measurement.98\n\nHowever, these studies are not limited to the determination of VOCs in animals and humans. Such research also extends to medical diagnostic tests, biological analysis of various ecosystem environments, phytopathogen control, and ecosystem biomonitoring, thereby fostering cross-disciplinary research approaches with chemical ecology.99 These studies also play a critical role in food safety analysis. This last aspect is vital within the food industry, as the analysis of flavor and aroma represents critical criteria for consumers. For instance, an analysis using HS – SPME – GC – MS/MS facilitated the identification of the volatile footprint in apricot samples in Xinjiang, China, in addition to volatile biomarkers such as damascenone, acetophenone, eucalyptol, myrcenol, 7-hexadecenal, 2,4-dimethyl-cyclohexanol, and salicylaldehyde.100 Regarding flavor analysis, a study reported by Bai et al., (2013) evaluated compounds with a fishy flavor induced by the absorption of substances produced from the presence of microorganisms. By making use of in vivo SPME, they identified the presence of geosmin and 2-methylisoborneol, which are generated by cyanobacteria and actinobacteria microorganisms. These compounds contribute to earthy and musty flavors in food, particularly in fish.101\n\n\n7. Electronic nose: Applications in VOC identification\n\nHumanity has witnessed countless technological advancements, but in the realm of volatilomics, rapid VOC detection is marked by the advent of electronic noses and tongues. These devices mimic human responses to various tastes and smells and work in conjunction with machine learning and deep learning techniques such as ANN, CNN, PCA, PLS, SVM.102 The utilization of these tools is characterized by their cost-effectiveness, speed, and accuracy, along with their high utility in the realm of food quality and safety.102 These devices often employ semiconductor sensors based on metal oxide (E-nose MOS) for the identification of volatile gases.103 The Figaro type E-nose MOS provides excellent sensitivity, rapid response, low cost, and robust durability. It is ideal for monitoring bad smells,104,105 and its data can be interpreted through multivariate analysis methodologies for the development of classification systems.103 Additionally, the development of HS-MS E-nose has been reported. In this setup, the electronic nose is directly coupled to the headspace, and the compounds are analyzed by mass spectrometry. However, this process must be conducted in an inert atmosphere to facilitate normalization against fragment abundances and the addition of an internal standard.106\n\nAnother notable aspect of the E-nose is its operational basis on chemical sensors, which are not selective for a specific compound. Instead, they permit the detection of compound groups, thus serving in various fields such as medicine for capturing VOCs present in human breath.107 In this manner, an odor footprint is obtained as an analysis pattern, which is subsequently compared with a database, enabling diagnoses of diseases like pneumonia,107 and lung cancer from exhaled breath.108 These tools are employed for evaluating the volatile profile generated in various food matrices,109 and any changes that might occur within drying processes. For example, it identified in the sautéed tea leaves of the Flos Sophorae Immaturus species compounds such as furaneol, 2-pentylfuran, 3-methylheptane, 3-furaldehyde, 2,5-dimethylfuran, utilizing the E-nose Flash GC.110,111\n\nMoreover, it is crucial to consider how the data obtained through E-nose will be interpreted, given that multivariate analyses necessitate novel methodologies based on machine learning to interpret extensive data sets expressed through multidimensional signal analysis. For instance,112 evaluated the approach of combining a sensor array with instrumentation hardware and machine learning methods to analyze samples generated from wastewater treatment. Consequently, they determined the multidimensional measurement generated from a sensor array, inducing a dimensionality reduction through the T-distributed Stochastic Neighbor Embedding (t-SNE) method. This method operates similarly to PCA, but unlike PCA, t-SNE generates a probability distribution representing the degree of similarity between neighboring data in a certain space and a lower dimensionality degree. This results in improved data separation and enhanced categorization of these data into clusters compared to when PCA is used.112\n\nResearch has also established methods for monitoring VOCs emitted by the composting process.113 These employ complementary techniques such as the E-nose, GC – MS, and the Odile olfactometer (Odotech). The E-nose demonstrates capacity in identifying compound families, while the GC – MS is used for characterizing individual compounds. Additionally, the olfactometer is used for quantifying concentrations of smells in odor units per cubic meter (OuE/m3).113 However, issues often arise regarding the energy consumption and size of the device. As a solution, alternatives have been reported that focus on the development of small, low-energy E-noses. These use a low-power microplate (MHP) with Pd-SnO2 and Pd-WO3 microparticles to generate an optimal temperature of 300 °C for detection and proper sensor functioning. This process involves the use of a Wavelet-type transformation to treat, process, evaluate, and reduce signal noise. Consequently, data analysis can be performed using the k-NN algorithm and the development of a forward propagation neural network (pN-BPNN).114 Moreover, it has become clear that the development of an E-nose alone is not enough. The task of enhancing flavor in various food matrices requires integration with the development of an electronic tongue (E-tongue). The use of GC – MS, along with these techniques and respective sensory analyses, allows for continuous improvements in food quality.115 In essence, the combination of E-nose, E-tongue, and colorimeters has facilitated the interconnected analysis of this data. Such analysis is executed through machine learning methods like RNA, ANN, Extreme Gradient Boosting (XGBoost), Random Forest Regression (RFR), and SVR. These methods prove useful for the sensory evaluation of matrices such as the Japanese horse mackerel (Trachurus japonicus) during its cooling process over several days. This process relies on the interconnected electronic sensory information obtained through these techniques.116\n\n\n8. Developments in volatilomics research in colombia\n\nAs the world becomes more globalized and scientific advancements increase, the amount of information associated with the publication of diverse primary research continues to grow.117 This creates a need to synthesize the wealth of existing information in a well-organized and digestible manner. This is where systematic reviews (SRs) come into play.118 These reviews are known for their established procedures that result in succinct and orderly summaries. Their goal is to guide readers through the available information on a specific topic,119 thereby providing high-quality research.120 This process is achieved using a replicable methodology that collates emerging primary research on a topic. Notable among these methodologies is the PRISMA (Preferred Reporting Items for Systematic Reviews), which aids in the identification, selection, and synthesis of information.121,122\n\nThe creation of an SR necessitates a research question to guide the analysis of pertinent information.123 Additionally, a standard language is required, which is often achieved by searching for terms indexed in Medline’s thesaurus, known as Medical Subject Headings (MeSH), or utilizing ScienceDirect Topics.124 Upon obtaining the terms, a search equation is created, typically based on the PICO mnemonic (Population, Intervention, Comparison, Outcome),125 or PICOT (Population, Intervention, Comparison, Outcome, Time).123 Following this, the literature search is conducted and inclusion and exclusion criteria are applied to the information gathered. These criteria might involve the language used, type of document, timeframe, among others. Ultimately, the process concludes with the extraction of information, evaluation of study quality, and synthesis or presentation of findings.123 In addition to this process, a bibliometric analysis of the obtained information is often conducted. This analysis allows for the identification of trends within the subject matter based on the research and publication of various articles, thereby facilitating the examination of different indices of scientific activity.126 Furthermore, it evaluates the degree of application of the topic across different knowledge areas, encouraging interdisciplinary processes and the formation of collaboration networks among countries, authors, co-authors, among others.127,128\n\nThe information search was conducted on June 13, 2022, with the objective of analyzing the documents reported from the years 2012 to 2022. The search incorporating all the metadata that comprised the equation was entered into the Scopus (Elsevier) database. As illustrated in Figure 4, the filters used for the extraction of primary research can be observed, based on the following parameters: time period (2012 – 2022), type of document (Article), stage of publication (final) for the Scopus database, language (English) and finally, country (Colombia) (Figure S1). This resulted in the formulation of the following search equation to carry out this Systematic Review (SR):\n\nTITLE-ABS-KEY ((“Volatilomic Fingerprint” OR volatilomic OR “volatile profiling” OR “Volatile metabolites”)) AND (LIMIT-TO (PUBYEAR, 2022) OR LIMIT-TO (PUBYEAR, 2021) OR LIMIT-TO (PUBYEAR, 2020) OR LIMIT-TO (PUBYEAR, 2019) OR LIMIT-TO (PUBYEAR, 2018) OR LIMIT-TO (PUBYEAR, 2017) OR LIMIT-TO (PUBYEAR, 2016) OR LIMIT-TO (PUBYEAR, 2015) OR LIMIT-TO (PUBYEAR, 2014) OR LIMIT-TO (PUBYEAR, 2013) OR LIMIT-TO (PUBYEAR, 2012)) AND (LIMIT-TO (DOCTYPE, “ar”)) AND (LIMIT-TO (PUBSTAGE, “final”)) AND (LIMIT-TO (LANGUAGE, “English”)) AND (LIMIT-TO (AFFILCOUNTRY, “Colombia”)).\n\nFollowing this, a bibliometric analysis of the various primary studies obtained from the Scopus database was performed, with the information being exported into a reference list file (.bib). This was done in order to analyze it using the R software (https://www.r-project.org/) and RStudio (https://rstudio.com/). The open-source bibliometrix package (https://github.com/massimoaria/bibliometrix) was utilized, which is recognized for being a free and open-source program that allows for the identification of various bibliometric records of articles, quantifying the number of articles per year (Figure 5) and their research trends in the field. Simultaneously, the information was exported into a comma-separated file (.csv) for analysis in the freely accessible software VOSviewer (https://www.vosviewer.com/). This was conducted in order to construct various network graphics of co-authorship between countries (Figure 6), keywords (Figure 7), researchers (Figure 8), and an additional analysis on the impact factor generated by these elements (Figure 9).\n\nAs shown in Figure 5, a correlation can be observed between the number of articles published from the period spanning 1962 to June 13, 2022. This correlation indicates an increase in the number of publication articles pertaining to the concepts of volatilomics, volatomics, volatile profile, and volatile footprint. These are recognized as the primary concepts that have been reported as keywords when analyzing a volatilomic study. This analysis reveals that there are few articles published with the term volatilomics, given that it is a relatively new science within the scientific community. This science possesses a transversal field of action ranging from health sciences to chemical sciences, with a greater application in analytical and instrumental chemistry. As previously mentioned, this type of science has had research focuses within the processes of identification of Volatile Organic Compounds (VOCs), chem-ecological analysis, evaluation of food safety, and its potential application towards the characterization of biomarkers associated with different types of alterations within metabolic processes.\n\nUpon applying the filters in the Scopus database and obtaining the bibliometric information from the research on volatilomics in Colombia, a co-authorship network graph was produced, highlighting the collaboration between countries (Figure 6). Primary research on this topic was found to be conducted in conjunction with various countries, resulting in a collaborative network for the development of these studies with countries such as the United Kingdom, China, Germany, Italy, India, Brazil, Portugal, United States, Spain, Egypt, France, and the Netherlands. The frequency of collaboration with these countries is reflected in the node size they represent in the graph. As a result, these countries appear more actively engaged in conducting this type of research, with the United States and China emerging as the leading contributors in this field. For Colombia, a small representative node was noted, suggesting that only a limited number of studies have explored the use of volatilomics and the various advancements this science provides as it is applied to various research.\n\nUpon analyzing a co-occurrence network among indexed keywords with a minimum occurrence of fifteen (Figure 7), it becomes evident that these indexed terms signify the use of key concepts that are widely used within research processes in volatilomics. Consequently, a contribution is made towards the development of sciences, through the use of chemistry, mass spectrometry, chromatography, in order to capture different VOCs and the respective interpretation of these data through chemometric tests and analysis of a large volume of data using multivariate analysis techniques. This includes the study of the principal components (PCA) which is pivotal for the acquisition of possible biomarkers and the role they play within alterations of metabolic pathways. All of this is performed with the aim of identifying this type of compounds through volatilomics and xenovolatilomics in different types of food matrices. In addition, this research bears significant importance for early disease diagnosis.\n\nAs seen in Figure 8, a graph of the co-authorship network among the primary researchers who have made various contributions towards the progressive development of the omics sciences in Colombia was derived. As a result, five large groups were found that are highly cited among themselves. Upon exploring the information of each of them, Figure 9 was obtained, where the information related to the number of articles involved in the subject of volatilomics is compared against the impact factor (H-index) for the authors obtained in the bibliometric analysis of volatilomic studies in Colombia. This analysis revealed researchers with a high degree of impact within the world of metabolomics, but few reported research directed towards volatilomic studies.\n\nAmong these authors, the work of Baena-Pedroza, A.M., Corpas-Iguarán, E., Londoño-Giraldo, L.M., Martínez-Seidel, F., Taborda-Ocampo, G., is particularly notable. These individuals are recognized as key contributors in volatilomic studies within the Research Group in Chromatography and Related Techniques (GICTA), which is affiliated with the University of Caldas, Manizales, Colombia. Additionally, the author Stashenko, E.E. is recognized as a member of the CENIVAM Center of Excellence in Research and the CROM-MASS Laboratory of Chromatography and Mass Spectrometry which are both associated with the Industrial University of Santander, Bucaramanga, Colombia. They have made substantial contributions to thematic areas such as agriculture and biological sciences, biochemistry, genetics and molecular biology, chemistry, medicine, immunology and microbiology, as well as pharmacology, toxicology, and pharmaceutical sciences.\n\n\n9. Conclusions\n\nThrough this review, it becomes clear that volatilomics studies demonstrate significant applicability, particularly in terms of ensuring food safety in different types of food matrices. Furthermore, it allows for the study of the volatile profile formed by the various VOCs expressed by this matrix and the respective ecological role that these compounds play within the environment in which they are found. In the same vein, volatilomic studies have facilitated scientific advancements through the use of various technological tools, as they have ventured into the development of new methods for the extraction, separation, and identification of these compounds. These advancements are also tied to the integration of new chemometric methodologies that require the use of supervised and unsupervised analysis techniques, in order to identify variations in the data obtained, validate established methodologies, and discover potential biomarkers of different types, among others.\n\nThe importance of the SPME methodology, coupled with the use of GC – MS for obtaining the volatilome and the volatile profile affected by the presence of xenobiotic agents in different types of matrices, is underscored. This methodology generates contributions not only to the development of omic sciences, but also to the evaluation of food safety in foods, early detection of diseases, identification of new natural products, and understanding of compounds within the different metabolic biochemical processes. Consequently, not only have these types of methodologies made a significant impact, but there has also been a rise in innovative research using E-nose and artificial intelligence for the development of machine learning that allows the construction of statistical classification models of this type of data obtained through HS – SPME – GC – MS and E-nose. With the use of machine learning, it is possible to obtain results much more quickly pertaining to the identification of contaminated matrices or different types of biomarkers that help in the evaluation of safety or in the identification of impacts on human health through rapid diagnostic tests, for early and effective detection of diseases.\n\nIt is our hope that research in the area of volatilomics continues to grow, making various contributions in the field through the study of various matrices and finding applications within the health area, with the aim of facilitating an early and timely diagnosis of diseases. We also anticipate that the use of machine learning will pave the way for the development of robust classification models for obtaining rapid results in verification and validation processes of the information obtained through the development of this type of primary research on the use of volatilomics.\n\n\nAuthor contributions\n\nJPBA: Authored the document and developed the bibliometric analysis, EEVS: Reviewed primary literature and provided support in document preparation, JAFL: Conducted the interpretation of bibliometric analysis, GTO: Managed the writing, reviewing, and editing. Furthermore, the authors accepted the final version of the review and all authors have read and accepted the version of the manuscript.", "appendix": "Data availability statement\n\nThe authors declare that at present, the results obtained in the present research are not available under the direction of a repository. However, for any questions please contact juan.betancourt@ucaldas.edu.co.\n\nNo data are associated with this article.\n\nNo data are associated with this article.\n\nFigshare: Figure S1. Inclusion and exclusion criteria for the search of scientific articles on volatilomic studies. https://doi.org/10.6084/m9.figshare.26530738.v1. 129\n\nThe data are available under the Public Domain Dedication (CC0) license.\n\nFigshare: PRISMA Checklist for Volatilomics: An emerging discipline within Omics Sciences – A systematic review. https://doi.org/10.6084/m9.figshare.26530693.v4. 130\n\nThe data are available under the Public Domain Dedication (CC0) license.\n\n\nAcknowledgments\n\nThe authors thank the Ministry of Science, Technology and Innovation for the support received through the call 907: “Call for young researchers and innovators in the context of economic reactivation 2021”.\n\n\nReferences\n\nFrigolet M, Gutiérrez-Aguilar R: Ciencias “ómicas”, ¿cómo ayudan a las ciencias de la salud? 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PubMed Abstract \| Publisher Full Text\n\nBaena-Pedroza A, Londoño-Giraldo LM, Taborda-Ocampo G: Volatilome study of the feijoa fruit [Acca sellowiana (O. Berg) Burret.] with headspace solid phase microextraction and gas chromatography coupled with mass spectrometry. Food Chem. 2020; 328: 127109.\n\nCorpas-iguarán E, Taborda-ocampo G, Tapasco-alzate O: ANALYTICAL APPROACH OF THE VOLATILE FRACTION OF Solanum quitoense BY HS- SPME/GC-MS. Biotecnol. en el Sect. Agropecu. y Agroindustrial. 2017; 15: 76–84.\n\nLondoño-Giraldo LM, Bueno M, Corpas-Iguarán E, et al.: Hplc-dad-apci-ms as a tool for carotenoid assessment of wild and cultivated cherry tomatoes. Horticulturae. 2021; 7: 1–12.\n\nEscobar S, et al.: Fine cocoa beans production: Tracking aroma precursors through a comprehensive analysis of flavor attributes formation. Food Chem. 2021; 365.\n\nLadino JAF, et al.: Development of a new liquid phase microextraction method with hollow fiber HF-SBME for the analysis of the organochlorine compounds in water samples by GC-ECD. Sci. Chromatogr. 2014; 6: 241–250.\n\nCorrea L, et al.: Hollow-fiber solvent bar microextraction with gas chromatography and electron capture detection determination of disinfection byproducts in water samples. J. Sep. Sci. 2015; 38: 3945–3953. PubMed Abstract \| Publisher Full Text" }	[ { "id": "321257", "date": "10 Oct 2024", "name": "Lina María Londoño Giraldo", "expertise": [ "Reviewer Expertise Volatilomics", "Metabolomics", "Bibliometrics" ], "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 article aims to make a systematic review of the state of volatilomics as an emerging science. Within this context, the systematic review is based on a PRISMA methodology that leads to the selection of certain supporting documents through the creation of inclusion and exclusion criteria that must be well demarcated. Likewise, the article shows a bibliometric analysis at the end of the text, but it was not stated from the beginning, which generates disorder and does not cover what was stated in the objective. In summary, the article has valuable information but it is not in a systematic review format and has additional information that cannot be linked to the objective related at the beginning. In addition, the grammar of English should be improved. Some tables have a mixture of Spanish and English words.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? No\n\nAre sufficient details of the methods and analysis provided to allow replication by others? No\n\nIs the statistical analysis and its interpretation appropriate? Partly\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) No", "responses": [] } ]	1	https://f1000research.com/articles/13-991
https://f1000research.com/articles/13-511/v1	20 May 24	{ "type": "Review", "title": "Enhancing sustainable energy production through biomass gasification gas technology: a review", "authors": [ "Oluwaseyi O. Alabi", "Oluwatoyin Joseph Gbadeyan", "Olumide A. Towoju", "Nirmala Deenadayalu", "Oluwaseyi O. Alabi", "Olumide A. Towoju", "Nirmala Deenadayalu" ], "abstract": "This proposed research investigates the sustainable and innovative use of biomass gasification for generating electricity. Biomass gasification is a versatile and eco-friendly technology that converts organic materials, such as agricultural residues, forestry waste, and even municipal solid waste, into a valuable source of clean energy. This research delves into the various aspects of this technology, including its processes, efficiency, environmental impact, and potential applications in power generation. Biomass gasification gas, often referred to as syngas, presents a promising avenue for addressing the rising energy demand while lowering greenhouse gas emissions and preventing climate change. This research seeks to offer a thorough insight into the principles and practices behind biomass gasification, highlighting its role in the transition towards a sustainable and renewable energy future. The research will investigate the technical and economic feasibility of utilizing biomass gasification gas for electricity generation, examining the benefits, challenges, and opportunities associated with this alternative energy source. By addressing critical issues such as feedstock availability, gasifier technology, gas cleaning processes, and power plant integration, this study seeks to offer valuable insights into the potential of biomass gasification gas as a clean and renewable energy solution.", "keywords": [ "Biomass", "Gasification", "Renewable Energy", "Solid Waste", "Technology" ], "content": "1. Introduction\n\nElectricity stands as the prevailing source of energy consumption worldwide, notably in industrialized nations, and several developing countries find themselves in a similar predicament. The pivotal role of electricity in the industrial sector cannot be overstated. As society advances into the future, emerging concepts such as Industry 4.0 and the digital age gain prominence, underscoring the mounting significance of a reliable electrical supply. According to an analysis by British Petroleum (BP) within the Evolving Transition scenario, approximately 70% of the increased demand for energy production will go toward electricity production. This projection stems from the anticipation that the need for electricity will surge at a rate threefold greater than that of other energy forms (Situmorang et al., 2020).\n\nAt present, the primary sources of power generation are fossil fuels, including coal, natural gas, and oil, along with nuclear energy. Coal, in particular, is the most prevalent fuel for power production, constituting approximately 39.3 percent of global energy consumption, as illustrated in Figure 1 (Wnetrzak et al., 2013). The world is actively exploring new, more sustainable, environmentally friendly, and safer alternatives to address the challenges of diminishing fossil fuel reserves, increasing sustainability, and the dangers of nuclear power (Alabi et al., 2023b). An increasingly widespread consensus suggests that renewable energy sources, including biomass, solar, wind, and geothermal energy, are poised to progressively supplant the future of nuclear energy in conjunction with fossil fuels. According to projections, the use of renewable energy is expected to increase steadily over the next two decades, while the use of coal and nuclear energy may either stabilize or decline. This suggests that biomass gasification may become an increasingly important part of the energy mix (You et al., 2015; Li et al., 2018). The anticipated future expansion of renewable energy technology is therefore likely to be significant. The transition to renewable energy sources is becoming progressively vital in reshaping the global energy landscape (Huggins et al., 2014; Güleç et al., 2022). These sources are characterized by their ability to be consistently replenished over short timeframes and include biomass, solar energy, wind power, hydropower, geothermal energy, and ocean tides (Boldrin et al., 2016). Notably, the utilization of various renewable energy sources varies and departs from traditional energy sources. This transition holds significant promise, especially in rural areas where conventional electricity access is challenging (Madanayake et al., 2017).\n\nSource: Wnetrzak et al. (2013).\n\nBiomass emerges as the most readily accessible renewable energy source, constituting approximately 50% of the total renewable energy resources, as illustrated in Figure 2 (Watson et al., 2020). Biomass, derived from organic materials such as plants, animals, and algae that do not fossilize and can decompose, comprises lignin, cellulose, hemicellulose, along with trace quantities of substances like proteins, lipids, simple sugars, and starches (Li et al., 2018; Azeta et al., 2021). In the case of biomass from wood and grass, cellulose typically constitutes around 38 to 50 percent of its total weight (Huggins et al., 2014; Mondal et al., 2018). Biomass is characterized by its key attributes as an energy source, which include ease of availability, widespread utilization, renewability, sustainability, and versatility. Nevertheless, it should be noted that biomass possesses a lower heating value compared to coal and faces transportation challenges due to its solid state (Situmorang et al., 2020).\n\nSource: Watson et al. (2020).\n\nThe wide range of available biomass resources, and the diversity of their sources, present a promising opportunity for future energy generation (Li et al., 2018; Siddiki et al., 2022). Non-woody biomass includes household refuse and processed waste, while woody biomass encompasses a range of forestry resources, including trees, shrubs, scrub, bushes, palms, and bamboos (Subramaniam and Masron, 2021). Household refuse stand as the most abundant biomass resources, contributing 27% and 30% of the total production, respectively, as delineated in Figure 3 (Situmorang et al., 2020; Abdulyekeen et al., 2021). Forestry accounts for only around 23% of total biomass production, but it represents the most significant resource for future expansion, with significant potential for growth in the years to come (Al-Rumaihi et al., 2022). The global primary energy supply harnessed from forests is estimated at approximately 56 exajoules (EJ), and woody biomass, in particular, is anticipated to supply nearly All bio fuels provide 90% of the annual electricity usage (Lee et al., 2020b).\n\nSource: Abdulyekeen et al. (2021).\n\nBiomass is widely recognized as a significant and sustainable alternative to fossil fuels in the long term, ranking among the primary energy sources with the most potential for the future. As such, it is a key focus of research and development in the energy sector (Situmorang et al., 2020; Ge et al., 2021). In 2014, it contributed to 14% of global final energy consumption (Picchio et al., 2020). Notably, reports indicate that while biomass constitutes 3% of energy consumption in industrialized nations, it makes up a striking 33% in developing nations (Picchio et al., 2020). Biomass energy has the dual benefits of being cost-effective and more efficient in energy production than other renewable sources. With an annual production estimated at, much of it from organic growth, biomass is the largest renewable energy source, surpassing the combined energy consumption of other renewable sources by around 8% (Ge et al., 2021; Mostafa et al., 2021). Biomass has a wide range of applications across industries, particularly for the production of biofuels. It is currently the only renewable resource capable of effectively replacing liquid fossil fuels (Djatkov, Martinov and Kaltschmitt, 2018).\n\nThe most efficient biochemical process for energy generation is anaerobic digestion, which effectively converts wet biomass into biogas. This biogas typically comprises methane (50–75%), carbon dioxide (20–35%), and traces of contaminants like hydrogen sulfide and moisture (Larsson and Samuelsson, 2017). Over the past two decades, this technology has seen widespread use in Europe, Asia, and North America, leading to the establishment of numerous biogas facilities. Biogas is typically combusted in internal combustion engines to generate electricity or used as a fuel. Several European countries have adopted regulations that promote the use of biomass as an energy source, while in Asia, it is frequently used for cooking and local electricity generation. In particular, has developed its own biomass-based for domestic use (Puig-Arnavat et al., 2016; Fogarasi and Cormos, 2015). Pig, cow, and chicken manures, as well as industrial wastes like palm oil mill effluent (POME) from the palm oil industry, are common sources of biomass for anaerobic digestion, resulting to the production of biogas (Ong et al., 2020; Chyuan et al., 2020). Another significant outcome of diverse biological processes, it is frequently mixed with gasoline for its use as automotive fuel. Modern vehicles have demonstrated the capability to run on a blend of 10% bioethanol and 90% gasoline without requiring engine modifications. Notably, in Brazil, gas stations frequently offer bioethanol-gasoline blends ranging from 18 to 27.5 percent, whereas in Europe, a common practice involves adding 5 percent bioethanol to gasoline (Digman, Joo and Kim, 2009). Recent advancements have shown that dark fermentation and photo-fermentation are potential methods for producing biohydrogen from biomass, although production is currently limited and further research is needed (Larsson and Samuelsson, 2017).\n\nPresently, the most widely employed thermochemical method for biomass conversion is direct combustion, which accounts for over 97 percent of global biomass energy production (Güleç et al., 2022). Worldwide, direct combustion facilities with a combined capacity of 40 gigawatts of electricity generation have been established (Huggins et al., 2014). In recent years, co-firing biomass with coal during the combustion process has become a widely accepted method for co-generating electricity. During combustion, biomass is ignited with excess oxygen to produce heat and operates in an oxygen-free environment. This process breaks down biomass into three distinct byproducts: non-condensable gases, char, and bio-oil (Uddin et al., 2018). There are various heating rates used in this process, with pyrolysis being the most commonly used method for extracting bio-oil from biomass. This bio-oil can subsequently be further processed into valuable chemicals or used as automotive fuel (Zhang et al., 2018). While direct combustion is straightforward and commonly used, it suffers from relatively poor thermal efficiency. In response, gasification has emerged as a more attractive and highly efficient thermochemical process, versatile enough to produce heat, power, fuels, and chemicals (Zhang and Zhang, 2019). Gasification offers several advantages, including reduced NOx and SOx emissions, lower reaction temperatures, and decreased oxygen requirements (Ong et al., 2020). Importantly, it boasts significantly higher overall electrical efficiency for power generation (Zhang and Zhang, 2019). As a result, gasification may be a more viable option for smaller-scale applications, as it can be economically feasible for capacities as low as 5 kilowatts electric and higher (Ong et al., 2020; Chyuan et al., 2020). As such, gasification is poised for widespread adoption in the large-scale conversion of biomass into energy in the future. An overview of various primary pathways for converting biomass into energy is provided in Figure 4 (Situmorang et al., 2020; Chyuan et al., 2020).\n\nSource: Situmorang et al. (2020).\n\nThe feasibility of gasification systems, especially in terms of their procurement and large-scale energy generation, is significantly hindered by the limited availability of biomass feedstock. Insufficient feedstock can frequently disrupt the operation of large-scale gasification systems. Consequently, the preference leans toward smaller-scale biomass gasification systems, particularly those with a capacity below 200 kW. These smaller systems can efficiently leverage locally sourced biomass, offering a practical solution to the challenges associated with biomass collection. In this analysis, we delve into the latest advancements in the study of “Enhancing Sustainable Energy Production through Biomass Gasification Gas Technology” to explore the opportunities and obstacles in this specific domain. This examination aims to shed light on the current state, development prospects, and practical implementation of such systems.\n\n\n2. Biomass Gasification Technology\n\nBiomass gasification is a transformative energy conversion process that has gained significant attention in recent years due to its potential to provide sustainable and renewable energy sources. It involves the thermal conversion of biomass feedstock, such as wood, agricultural residues, or organic waste, into a gaseous fuel called syngas (synthesis gas). Syngas is composed primarily of carbon monoxide (CO), hydrogen (H2), carbon dioxide (CO2), and traces of methane (CH4). This gas can be utilized for various energy applications, including electricity generation, heat production, and biofuel synthesis. Syngas predominantly consists of components like CO, H2, CO2, and CH4 (Roncancio and Gore, 2021). Gasification has been around for over 180 years, with the first systems developed in France in the 1840s. It has since become widely used in the United States, with many commercial-scale gasification systems in operation since the 1920s. Notably, during World War II, gasification played a pivotal role in generating syngas for the Fischer-Tropsch-based synthesis of liquid fuels. The United States has seen the construction of many gasification systems over the past 30 years since the 1973 oil crisis (Situmorang et al., 2020; Pradhan, Mahajani and Arora, 2018b).\n\nThe gasification process comprises four primary stages: pyrolysis, combustion, reduction, and product separation. During the initial stage, the moisture content of biomass, which typically ranges from 30% to 60%, is vaporized or evaporated. This phase continues until the moisture content drops to the ideal gasification range of below 15%, occurring at temperatures up to approximately 200°C (Pradhan, Arora and Mahajani, 2018a). The second phase, pyrolysis, involves breaking down the biomass’s hemicellulose, cellulose, and lignin into volatile compounds and solid residues. This phase occurs at around 220°C and yields tar-like liquid products and small gas molecules as volatile compounds, alongside solid char containing non-degradable carbonaceous materials (Frodeson, Henriksson and Berghel, 2019). During the combustion phase, volatile compounds and char undergo conversion by reacting with oxygen gasifying agents to produce CO, CO2, and H2O. This highly exothermic reaction generates heat, with temperatures surpassing 700°C. Gasification processes typically take place at temperatures above 800°C, resulting in the formation of ash as a residual substance in the gasifier. It’s important to note that gasification often involves multiple simultaneous processes, with exothermic reactions providing heat for endothermic ones as needed. The effectiveness of the gasification process can be influenced by various factors, including the type of gasifier, the choice of gasifying agents, the biomass composition, and the size of the biomass particles.\n\nFigure 4 demonstrates how various components of the same biomass have different physical and chemical properties. This diversity is even more pronounced when considering different biomass sources (Figure 4: Illustration of the various properties of biomass components). The inherent heterogeneity of biomass poses a challenge in accurately predicting the optimal operating conditions and final product qualities, representing a notable drawback in biomass gasification (Mostafa et al., 2019). Fundamental analyses of biomass characteristics typically encompass the measurement of heating value, proximate analysis, and ultimate analysis. Key components of biomass composition, such as moisture content, volatile matter, fixed carbon, and ash concentrations, are identified using proximate analysis. Importantly, the moisture content notably affects the progression and phases of the process (Gilvari, de Jong and Schott, 2019; Alabi, Adeyi and Ekun, 2023a). Fixed carbon represents the carbonaceous solid material, whereas volatile matter comprises the gases released during this phase. It’s worth noting that the presence of tar from volatile biomass materials can pose challenges during the gasification process. The final examination makes it possible to identify the biomass’s components for carbon, oxygen, hydrogen, nitrogen, and sulfur. Both fixed and volatile carbon contribute to the carbon content in char and volatile substances (Siyal et al., 2021). Biomass further comprises components like lignin, hemicellulose, and cellulose, each decomposing differently during gasification. Higher lignin content slows down the rate of biomass decomposition, necessitating elevated gasification temperatures at the expense of reduced gas output (Du et al., 2019).\n\nGasification is a thermochemical conversion process that transforms carbon-containing feedstock, such as biomass, coal, or waste materials, into a gaseous mixture known as syngas (synthesis gas). This versatile and energy-efficient technology is employed in various applications, including power generation, heat production, and the synthesis of valuable chemicals and fuels. Gasification processes and reactors play a crucial role in the efficient conversion of solid, liquid, or gaseous fuels into syngas. Several gasification technologies and reactor designs are available, each with its own characteristics and advantages. Gasifying agents play a crucial role in various thermochemical processes, such as gasification and combustion, where solid, liquid, or gaseous fuels are converted into valuable products like syngas (synthesis gas), heat, or electricity. The choice of a gasifying agent has a significant impact on the efficiency, product composition, and environmental performance of these processes.\n\nThe selection of gasifying agents plays a central role in every gasification reaction, influencing reactivity and gas composition. Different gasifying agents, whether individually or in combination, lead to diverse outcomes in terms of the intended results (Frodeson, Henriksson and Berghel, 2019; Singh et al., 2014). Because of its affordability and widespread availability, air stands as the most commonly employed gasifying agent among these options. For the production of syngas with an elevated heating value, it is recommended to utilize pure oxygen or oxygen-enriched air. This is because the high nitrogen concentration in regular air can diminish the heating value of the resulting syngas. It’s essential to keep in mind that this choice may lead to increased operational expenses since extracting oxygen and nitrogen from the air requires energy. The air-to-fuel ratio, also known as the equivalency ratio (ER), employed in the gasification process governs the extent of partial oxidation within the gasifier when air is used as the gasifying agent. To prevent full combustion, the ER value is usually kept below 1. The ER ratio is also thought to impact the ultimate heating value of the syngas, typically falling within the range of 0.2 to 0.4 for optimal formation. Utilizing pure oxygen from the air is a cost-effective approach compared to partial oxidation, offering a feasible means to attain higher gas content and reduce undesirable byproducts. However, this choice necessitates additional energy due to the endothermic reactions involved in primary and secondary steam processes, as well as the water gas shift reaction (Gilvari, de Jong and Schott, 2019; Singh et al., 2014). Moreover, steam is frequently employed to expedite the sluggish reaction rate, obtaining energy for endothermic processes from exothermic partial oxidations. It has been proposed that for gasifiers, a combination of air and 40–70 mol% steam is advisable (Frodeson, Henriksson and Berghel, 2019; Lee et al., 2020a).\n\nThe outcome of the gasification process is directly influenced by the size of biomass particles. Smaller particles offer a larger specific surface area for gasification reactions, typically resulting in higher gas production and lower energy consumption. They also enable faster heat transfer and reaction rates (Roncancio and Gore, 2021). Consequently, gasifying smaller biomass particles yields increased syngas production and reduced tar and char formation. In contrast, larger biomass particles, due to their greater heat resistance and incomplete decomposition, tend to generate more char (Skorupskaitė et al., 2015).\n\nWhile smaller biomass particle sizes offer advantages, it’s important to consider that the energy required for size reduction may lead to a decrease in overall energy efficiency. Various gasifier types have been developed to accommodate a range of biomass particle sizes. For example, gasification requires biomass particles with a diameter less than 0.15 mm. Thus, pre-processing of biomass before it enters the gasifier remains an important consideration, despite some studies suggesting otherwise (Singh et al., 2014).\n\nIn gasification, the two main working conditions are temperature and pressure. Among them, temperature is crucial to the gasification process since it has a direct impact on a number of factors, such as gas yield, composition, heating value, formation of tar and char, carbon conversion, and cold gas efficiency. Higher gasification temperatures result in gas products with elevated heating values, characterized by increased CO and H2 content and reduced tar. Moreover, as temperature increases, both carbon conversion and cold gas efficiency improve (Yao et al., 2023). However, it’s important to keep in mind that other elements, such as the biomass mixture’s composition and particle size, can affect the necessary combustion rate. For instance, higher temperatures are required to produce more gas from waste with a higher fiber content. In addition, the breakdown of the biomass structure requires greater temperatures for larger catalyst particles (Sekar et al., 2021). Normally, gasification is kept going at temperatures above 700°C since this is the point at which the spontaneous steam reforming reaction starts to happen. In the case of steam gasification, temperatures should exceed 750°C.\n\nGasification primarily takes place under atmospheric conditions, although pressurized approaches are now being extensively researched and employed. Due to its low initial investment costs, atmospheric gasification is more prevalent for small-scale gasifiers. Pressurized gasification, on the other hand, is a more effective technique that results in enhanced gasification efficiency and reduced tar production. Conversely, pressurized gasification is a more efficient method, leading to improved gasification efficiency and reduced tar production (Gilvari, de Jong and Schott, 2019). It’s important to bear in mind that gasification typically operates at low pressure and high temperature, in the context of chemical equilibrium (Skorupskaitė et al., 2015).\n\nThe schematic procedure for this particular type of gasifier is shown in Figure 5(a). The updraft gasifier stands out as an efficient gasification method with a high thermal efficiency. It achieves this by utilizing the sensible heat of the hot gas to preheat and dehumidify the internal components of the system before the lower-temperature gas exits from the top of the gasifier, typically falling within the range of 200°C to 400°C. Remarkably, it demonstrates an impressive performance, capable of accommodating biomass with moisture content as high as it also effectively processes particles ranging from 5 to 100 mm in size (Sarker et al., 2023). Despite its efficiency, the air gasification process tends to produce a greater amount of tar compared to other methods. The tar generated in the pyrolysis zone flows upward to the cooler region, preventing it from reaching the high-temperature zone where it could be cracked (Zhang and Zhang, 2019; Razi and Dincer, 2022).\n\nSource: Roncancio and Gore (2021).\n\nThe gasifier in Figure 5(b) uses a unique method for introducing the gasifying agent. Biomass is introduced from the top or sides of the reactor, while the gasifying agent is introduced from the top or sides. This results in a co-current flow between the biomass and the gasifying agent (Roncancio and Gore, 2021). This suggests that the biomass and gasifying agent come into touch during the gasification operations, improving the quality of the generated gas that leaves the reactor’s bottom. Due to the ability of devolatilization products to enter the high-temperature oxidation zone, despite their brief residence duration in that zone, the tar production in this setup is minimal (Lee, Balu and Chung, 2013). However, there is relatively limited heat transfer between the hot and cold zones of the reactor in this design, which reduces its tolerance for moisture content. Therefore, only biomass with a moisture level below 30% is suitable for processing. Additionally, due to the alignment of the drag force with gravity, biomass travels downward more swiftly during its residence time in the reactor. Consequently, the carbon conversion efficiency is lower in comparison to an updraft gasifier. This type of gasifier is also susceptible to issues like blocking, channeling, and bridging, requiring consistent particle size to stop these occurrences. Typically, the permissible particle size range is between 40 and 100 mm. With a typical capacity ranging from 10 kW to 1 MW, the downdraft gasifier is well-suited for small-scale power plant applications (Pavkov et al., 2022).\n\n\n3. Utilization of syngas\n\nThe primary product of the gasification process is known as synthesis gas or syngas. The term “synthesis gas” is used because these gases mainly consist of CO and H2, which serve as fundamental building blocks for the production of a wide range of complex chemicals used in various applications. These applications encompass the manufacture of hydrogen, the production of synthetic liquid fuels through the Fischer-Tropsch process, the creation of synthetic natural gas (S-NG), and the synthesis of chemicals such as ammonia, methanol, its derivatives, and dimethyl ether. Syngas is also a popular alternative energy source for electricity generation (Sarker et al., 2023). Traditionally, syngas has been employed in two main ways for large-scale power generation. In comparison to direct combustion, these techniques have better advantages, such as high thermodynamic performance, and reduced emissions of NOx and SOx. IGCC systems, in particular, have achieved an electrical efficiency exceeding 42% (Branco, Serafim and Xavier, 2019). Another approach for power generation using syngas is through Internal Combustion Engines (ICE), which are versatile for variable power outputs. ICE technology is cost-effective, reliable, operationally efficient, and adaptable for both stationary and mobile applications. It also exhibits better cost-competitiveness compared to gas turbines, as it is less sensitive to gas impurities. There are two operating methods within ICE technology: Spark Ignition (SI) and Compression Ignition (CI). SI engines utilize air and a spark to ignite syngas in a combustion chamber, resembling the operation of an Otto/gasoline engine. In the CI approach, similar to a diesel engine, compression is used to automatically ignite syngas, often with a small amount of diesel fuel serving as a pilot. Syngas can replace between 60 and 90 percent of the diesel fuel required to run CI engines at the same power level. SI engines are better suited for syngas engines than the CI approach (Carter et al., 2018).\n\nSyngas generated through the gasification of biomass holds great potential as a source of electricity for rural and peri-urban areas. For this application, there are significant obstacles in developing a small-scale gasification system with an inexpensive initial investment cost, outfitted with effective clean gas technology to support the appropriate operation of gas engines, and built to accommodate different types of biomass (Situmorang et al., 2020). Even though there are many large-scale facilities for producing power from biomass around the world, some of them are having trouble finding enough biomass supplies. In contrast to fossil fuels, biomass is generally available worldwide and is only constrained by elements like temperature, location, and season. It might be expensive to harvest biomass from isolated farming and mountainous regions. Therefore, the direct utilization of biomass energy in communities and rural regions abundant in biomass resources is a more practical approach. It is imperative to make small-scale gasification power plants available, with capacities ranging from 10 to 200 kW, to enable the effective and cost-efficient utilization of local biomass energy. Successful future initiatives in this field will depend on the successful implementation of such strategies. One potential source of electricity for rural and peri-urban areas is syngas produced from biomass.\n\n\n4. Emerging biomass gasification trends\n\nBiomass technology, which harnesses energy from organic materials like wood, agricultural residues, and waste, has garnered significant attention due to its potential as a renewable and sustainable energy source. The economic viability of biomass technology is a critical aspect that influences its adoption and sustainability. Large- and medium-scale gasification systems of over 1 MW capacity are becoming increasingly popular worldwide, particularly in developed nations, for generating electricity (Situmorang et al., 2020). These systems are not only cost-effective in terms of per unit of electricity produced, but also have a significant impact on the electricity distribution landscape within a country or region. To fully utilize the potential, however, biomass gasification system development and acceptance are essential, particularly in developing and emerging nations (Sarker et al., 2023). At present, most commercially available gasifiers exhibit relatively low gasification efficiency, including updraft and downdraft gasifiers. There is a critical need to create next-generation gasifiers that offer both high efficiency and cost-effectiveness in order to increase the application of small-scale biomass gasification systems in the power generation sector.\n\n4.1.1 Development of new gasifier\n\nLarger-scale power generation systems often employ fluidized-bed gasifiers, especially circulating fluidized bed gasifiers like dual-bed gasifiers known for their high efficiency. However, scaling down and effectively adapting these systems for small-scale use is a challenging task. Notably, small-scale biomass gasification systems need to be versatile and capable of handling various types of biomass (Carter et al., 2018). The small gasifiers currently on the market are more suitable for high-quality biomass sources, like woody biomass. When lower-quality feedstocks are used, these gasifiers tend to produce notable quantities of tar and ash, which can present challenges for their operation (Perera et al., 2021). As a result, the development of these systems must address challenges related to their production. One approach to mitigating tar issues is to implement a two-stage gasification system that includes an initial pyrolysis process, which can reduce tar production. However, this design typically results in a larger gasifier size, making operation more complex and costly. Alternatively, tar in the gas can be post-treated using syngas cleaning systems or catalysts. Furthermore, notable enhancements in gasification efficiency can be attained through the design and incorporation of a distinct setup. As depicted in Figure 6, this biomass gasification system operates similarly to a large-scale triple-bed gasification system, performing biomass pyrolysis, charcoal gasification, and tar reforming as separate, independent processes (Situmorang et al., 2020; Evaristo et al., 2022).\n\nSource: Situmorang et al. (2020).\n\n4.1.2 Economic evaluation and policy\n\nThe cost of building the power generating system and the revenue from selling the energy produced are two crucial considerations in the economic assessment of a biomass gasification system used for power generation (Arslan et al., 2022). The investment costs for the project are an accurate representation of the costs paid, and a crucial metric is the minimum power price based on the levelized cost of electricity (LCOE). According to this split (Arslan et al., 2022), the gasification unit receives around 24% of the investment, the gas engine and electrical supporting systems receive 54%, and the remaining expenses, such as the purchase of raw materials and transportation, are covered by the remaining funds. Another study on small-scale biomass gasification power plants in Brazil found that the power plant’s capital cost was approximately 1267 USD/kW, resulting in an LCOE of 0.53 USD/kWh (Bacenetti et al., 2013). According to Carrara’s theory, the investment cost for a gasification system coupled with a 100kW internal gas engine combustion would be between 1200-3300 €/kW (or 906-2491 USD/kW based on 2010 exchange rates) (Bacenetti et al., 2013). In comparison, 1 MW and 5 MW systems were estimated to have costs of 900-1800 €/kW and 700-1300 €/kW, respectively. According to the International Renewable Energy Agency (IRENA), the typical LCOE for small-scale fixed-bed biomass gasification power plants (up to 600 kW) with internal combustion engines falls within the range of 0.065 to 0.24 USD/kWh. It’s worth noting that costs can vary depending on the country, and despite such variations, large-scale deployments of biomass gasification power systems continue to involve substantial expenses (Asadullah, 2014).\n\nThere are two main environmental issues with the use of a biomass gasification plant: the impact of biomass cultivation and the consequences of biomass gasification itself. Perennial energy crops, as indicated by numerous life cycle assessments (LCAs), have been found to reduce greenhouse gas (GHG) emissions by approximately 5 mg/ha of fossil carbon and decrease NO2 emissions by 40–50% compared to burning fossil fuels. One specific LCA study suggests that cultivating perennial grasses on marginal land for electricity generation can lead to saving approximately 13% of CO2 equivalent per hectare per year (Shamsul, Kamarudin and Rahman, 2020). In the context of small-scale biomass gasification systems, their relatively modest biomass resource requirements imply a minimal impact on land use. Moreover, the release of hazardous compounds and GHG emissions is more manageable in such systems, allowing them to efficiently utilize locally generated biomass or agricultural residues.\n\nWhile biomass gasification has the potential to be a more sustainable alternative to fossil fuels, its environmental impacts must be considered in their entirety. A holistic approach, taking into account the entire life cycle of the technology, is necessary to fully understand the environmental implications. This includes considering the impacts of feedstock procurement, such as the use of resources and land use change, the energy and emissions associated with processing the biomass, the effectiveness of emissions control technologies, and the disposal of any waste products (Tripathi, Sahu and Ganesan, 2016). Only by considering all of these factors can the true environmental impact of biomass gasification be assessed. Also, there are some negative environmental impacts associated with biomass gasification, the technology also offers some significant environmental benefits that can be optimized through the use of best practices and advanced technologies. For example, by using low-impact feedstock sources, such as agricultural waste or dedicated energy crops, and implementing efficient processing techniques, the environmental impacts can be minimized. In addition, the use of advanced emissions control technologies can help to reduce the release of pollutants into the atmosphere. Finally, the utilization of byproducts from biomass gasification, such as biochar, can further offset the environmental impact of the technology. In the end, the particular feedstock used, the technology used, and the operational procedures all have a significant impact on the environmental impact of biomass gasification. Biomass gasification has the potential to significantly contribute to the mitigation of climate change and the shift to a more sustainable energy future when it is developed and used responsibly (Alper et al., 2020).\n\nBiomass gasification can have both positive and negative environmental impacts. On the positive side, biomass gasification is a renewable energy source that can reduce the need for fossil fuels. It can also help reduce greenhouse gas emissions by converting biomass into usable energy, and it can help reduce waste by using biomass that would otherwise be discarded (Güleç et al., 2022; Alper et al., 2020). However, there are also some potential negative environmental impacts of biomass gasification. For example, it can produce air pollutants like nitrogen oxides and volatile organic compounds. It can also release carbon dioxide and methane, which are greenhouse gases. In addition, the process of harvesting biomass for gasification can have a negative impact. The environmental impacts of biomass gasification can vary depending on the specific biomass source and the technology used. For example, using agricultural residues as a biomass source can have a positive environmental impact by reducing the amount of agricultural waste that would otherwise be burned or left to decompose. On the other hand, harvesting biomass from forests can have negative impacts on biodiversity and habitat loss (Abdulyekeen et al., 2021; Bacenetti et al., 2013). In addition, the type of technology used for gasification can have an impact on the overall environmental impact. For example, gasification systems that use inefficient combustion or have a high energy input can have a higher carbon footprint than other technologies (Bacenetti et al., 2013; Asadullah, 2014).\n\nWhile there is a plethora of technology vendors capable of providing suitable solutions for small-scale biomass gasification technology, and gasification technologies are now well-established, the number of actual implementations remains limited (Ong et al., 2020; Chyuan et al., 2020; Roncancio and Gore, 2021). The substantial construction expenses remain a notable obstacle, particularly for developing and less economically developed nations. Therefore, research and development efforts aimed at producing high-efficiency technology are anticipated to involve foreign capital in the creation of a few prototype projects. Local governments in developing and less economically developed nations are likely to lend support by instituting appropriate feed-in tariffs. Collaborative efforts between technology and equipment providers can enhance the reliability of commercializing and industrializing biomass gasification power generation systems.\n\n\n5. Conclusions\n\nThe gasification process exhibits significant potential for the efficient transformation of biomass into electricity, providing numerous economic and environmental benefits compared to fossil fuels. It plays a crucial role in delivering local electricity, especially in regions with limited electrification and underdeveloped electricity distribution infrastructure. Biomass energy is particularly well-suited for decentralized and localized applications, presenting substantial market potential in many nations and regions. The deployment of power production systems demands substantial engagement from all stakeholders, and proactive policy initiatives by local governments can expedite the commercialization and industrialization of these systems. Furthermore, active participation of local communities, particularly those in agricultural and plantation areas, is expected in the acquisition of biomass feedstock. In conclusion, “Enhancing Sustainable Energy Production through Biomass Gasification Gas Technology” sheds light on the vast potential of biomass gasification, illustrating how this technology can play a crucial role in advancing sustainable energy production globally. By addressing challenges and promoting collaboration, the extensive adoption of these technologies can make a significant contribution to meeting our energy requirements while efficiently harnessing biomass resources. Biomass gasification technology offers a valuable avenue for advancing sustainable energy production, but its path forward necessitates careful consideration of environmental impacts and responsible implementation. Optimizing technology, adopting best practices, and prioritizing the use of sustainable feedstocks are essential to maximize the benefits of this technology while minimizing its potential drawbacks. By navigating these challenges with foresight and responsible planning, biomass gasification can play a significant role in shaping a cleaner and more sustainable energy future.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nAbdulyekeen KA, et al.: Torrefaction of biomass: Production of enhanced solid biofuel from municipal solid waste and other types of biomass. Renew. Sust. Energ. Rev. 2021; 150(June): 111436. Publisher Full Text\n\nAl-Rumaihi A, et al.: A review of pyrolysis technologies and feedstock: A blending approach for plastic and biomass towards optimum biochar yield. Renew. Sust. Energ. Rev. 2022; 167(June): 112715. Publisher Full Text\n\nAlabi OO, et al.: Study of Combustion Characteristics of Diesel-Vegetable Oil Blends Utilizing an Industrial Fuel Burner. Fuel Communications. 2023b; 18: 100104. (Elsevier) [Preprint]. 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Elsevier Ltd.; 2019. Publisher Full Text\n\nZhang W, et al.: Progress and Perspective of Electrocatalytic CO2 Reduction for Renewable Carbonaceous Fuels and Chemicals. Adv. Sci. 2018; 5(1). Publisher Full Text" }	[ { "id": "298699", "date": "12 Jul 2024", "name": "Dr. Ayyadurai Saravanakumar", "expertise": [ "Reviewer Expertise 1. Biomass Gasification Technologies. [Design and experimental investigation of gasification plants", "Comparative experimentation focusing on different types of modes", "temperature profile and different fuel materials as feedstock for gas production – long stick wood gasification for hilly and rural regions] 2. Biomass to Charcoal conversion technologies [Design", "fabrication and installation of charcoal conversion kiln", "temperature profile and different feed materials as feedstock for charcoal conversion] 3. Computational modelling of long stick wood gasifier 4. Rural village development of charcoal production technologies. 5. Fuel Characteristics" ], "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. What are the key technological advancements in biomass gasification that contribute to increased efficiency and sustainability in energy production?\n2. How do different types of biomass feedstocks affect the performance and environmental impact of gasification processes?\n3. What are the major challenges and potential solutions in scaling up biomass gasification technology for widespread sustainable energy production?\n4. Quote the below references in the manuscript : (Saravanakumar A, et al., 2024 [Ref-1]), (Saravanakumar A, et al., 2023 [Ref-2]), (Saravanakumar A, et al., 2022 [Ref-3]), (Ayyadurai S, et al., 2020 [Ref-4]), (Ayyadurai S, et al., 20217 [Ref-5]), (Ayyadurai S, et al., 2017 [Ref-6]), (Kang J, et al., 2016 [Ref-7]), (Ivanov. I, et al., 2011 [Ref-8])\n5. What are the primary types of reactors used in biomass gasification, and how do they differ in terms of design and operation?\n6. How do the temperature and pressure conditions within a gasification reactor impact the quality and composition of the produced syngas?\n7. What role do catalysts play in gasification processes, and what are the most effective catalysts currently used in gasification reactors?\n8. How do different gasification processes (such as fixed-bed, fluidized-bed, and entrained-flow) compare in terms of efficiency, scalability, and environmental impact?\n9. What are the key challenges in maintaining reactor performance and longevity, and what maintenance or technological improvements can address these challenges?\nSection 4\n10. What recent technological innovations in biomass gasification have shown the most promise for improving efficiency and reducing costs?\n11. How is the integration of artificial intelligence and machine learning being utilized to optimize biomass gasification processes?\n12. What advancements have been made in feedstock preprocessing techniques to enhance the gasification process and improve syngas quality?\n13. How are emerging gasification technologies addressing the challenges of tar formation and removal in syngas production?\n14. What are the latest developments in reactor design that are contributing to more effective and scalable biomass gasification systems?\n15. How are policy and regulatory changes influencing the adoption and innovation of biomass gasification technologies in different regions?\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": "12024", "date": "02 Sep 2024", "name": "Oluwatoyin Joseph Gbadeyan", "role": "Author Response", "response": "RESPONSE TO REVIEWER COMMENTS 1. What are the key technological advancements in biomass gasification that contribute to increased efficiency and sustainability in energy production? Response: Thank you for your feedback. Some key technological advancements in biomass gasification that contributes to increased efficiency and sustainability in energy production include, Advanced Gasification Systems, Gas Cleaning and Upgrading, Innovative gas cleaning and upgrading technologies to remove impurities, and producing high-quality biofuels and biochemicals. These advancements contribute to increased efficiency, sustainability, and cost-effectiveness. Effectiveness in biomass gasification, enabling the production of renewable energy and biofuels while minimizing environmental impacts. 2. How do different types of biomass feedstocks affect the performance and environmental impact of gasification processes? Response: Thank you for your feedback. By understanding the characteristics and effects of different biomass feedstocks, gasification processes can be optimized to improve performance, reduce environmental impacts, and increase the production of renewable energy and biofuels. 3. What are the major challenges and potential solutions in scaling up biomass gasification technology for widespread sustainable energy production? Response: Thank you for your comments. Addressing these challenges and implementing solutions will help scale up biomass gasification technology, enabling widespread sustainable energy production and contributing to a low-carbon future. 5. What are the primary types of reactors used in biomass gasification, and how do they differ in terms of design and operation? Response: Thank you for your comments. The primary types of reactors used in biomass gasification are, fixed Bed Reactors, Fluidized Bed Reactors. Each reactor type has its advantages and disadvantages, and the choice of reactor depends on the specific application, biomass feedstock, and desired gas composition. 6. How do the temperature and pressure conditions within a gasification reactor impact the quality and composition of the produced syngas? Response: Thank you for your comments. Gasification temperature: Entrained flow reactors operate at higher temperatures (1000-1500°C), while fixed bed and fluidized bed reactors operate at lower temperatures (700-1000°C). 8. How do different gasification processes (such as fixed-bed, fluidized-bed, and entrained-flow) compare in terms of efficiency, scalability, and environmental impact? Response: Thank you for your comments. Different reactors produce varying gas compositions, with entrained flow reactors producing more syngas (CO and H2) and fixed bed reactors producing more methane (CH4). 9. What are the key challenges in maintaining reactor performance and longevity, and what maintenance or technological improvements can address these challenges? Response: Thank you for your comments. Tar formation and deposition on reactor walls and surfaces, reducing efficiency and increasing maintenance needs. Ash and slag formation: Ash and slag accumulation, potentially causing reactor damage, corrosion, and operational issues. Section 4 11. How is the integration of artificial intelligence and machine learning being utilized to optimize biomass gasification processes? Response: Thank you for your feedback. However, I'd like to clarify that the focus of this project is not on machine learning or artificial intelligence 12. What advancements have been made in feedstock preprocessing techniques to enhance the gasification process and improve syngas quality? Response: Thank you for your response: Advancements in feedstock preprocessing techniques to enhance the gasification process and improve syngas quality include the Densification of biomass into pellets increases the bulk density of biomass, which increases the net calorific content per unit volume. This makes storage, transport, and handling of the material easier and cheaper 13. How are emerging gasification technologies addressing the challenges of tar formation and removal in syngas production? Response: Thank you for your response. Tar formation in fixed bed reactors tend to produce more tar, while entrained flow reactors produce less tar due to higher temperatures and residence times 14. What are the latest developments in reactor design that are contributing to more effective and scalable biomass gasification systems? Response: Thank you for your response. The latest developments in reactor design that contribute to more effective and scalable biomass gasification systems include dual-bed catalyst gasification." } ] }, { "id": "312249", "date": "27 Aug 2024", "name": "Francis Njoka", "expertise": [ "Reviewer Expertise Renwables", "Solar energy", "biomass", "hydrogen and fuels cells", "etc." ], "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 giving me the opportunity to look at the article. I however wish not to conclude the review. To start with, the abstract is simply a series of recurring statements giving no direction. The study objective is repeated five time in almost every statement. Figures 1 and 2 present totally different statistics from what is quoted in the text. Key statements are not complete but rather jump to explaining different concepts which makes it a bit unclear. For example on page 5 line 2, 'In particular, has developed its own biomass.....' Line 4 in the same paragraph reads, 'Another significant outcome of diverse biological processes, it is frequently mixed...….' Such statements and many more are unacceptable. In chapter 2, the authors say gasification has 4 stages, pyrolysis, combustion, reduction and gas separation. This is incorrect. In the explanation of the each stage, they start with stage one, and then say stage 2 is pyrolysis converse to their earlier statement. As such, this article can easily and greatly confuse young readers who seek clarity on issues.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? No\n\nAre all factual statements correct and adequately supported by citations? No\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": "12310", "date": "02 Sep 2024", "name": "Oluwatoyin Joseph Gbadeyan", "role": "Author Response", "response": "Response: Thank you for your feedback on our abstract. We appreciate your input and are revising the abstract to better reflect our research findings and align with our findings. We have revised the captions for Figures 1 and 2 in the revised manuscript, as quoted in the text. As you suggested, we have reviewed and corrected some grammatical errors in the manuscript. We have carefully examined and modified the relevant sections to ensure accuracy and clarity. Thank you for your insightful feedback on the gasification process. We have revised the manuscript as highlighted, incorporating your valuable observations" } ] } ]	1	https://f1000research.com/articles/13-511
https://f1000research.com/articles/13-745/v1	04 Jul 24	{ "type": "Systematic Review", "title": "Efficiency of Microorganisms and Effectiveness of Biodegradation Techniques on LDPE Plastics: A Systematic Review", "authors": [ "Jorge Guillermo Morales Ramos", "Leydy Mekinley Fernández Tarrillo", "Anghelly Xiomara Guevara Bravo", "Marilin Sánchez-Purihuamán", "Carmen Rosa Carreño Farfán", "Carolina Susana Loayza Estrada", "Enrique Guillermo Llontop Ynga", "Horacio De La Cruz Silva", "Leydy Mekinley Fernández Tarrillo", "Anghelly Xiomara Guevara Bravo", "Marilin Sánchez-Purihuamán", "Carmen Rosa Carreño Farfán", "Carolina Susana Loayza Estrada", "Enrique Guillermo Llontop Ynga", "Horacio De La Cruz Silva" ], "abstract": "Introduction The aim of the research was to demonstrate the efficiency of microorganisms and the effectiveness of biodegradation techniques on Low-density polyethylene (LDPE) plastics. The research question was: What is the efficiency of LDPE-degrading microorganisms and the effectiveness of biodegradation techniques?\n\nMethods The systematic review was based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. Articles were obtained from Scopus, Web of Science (WOS), Embase, and Google Scholar. The DeCS/Mesh search terms were: Low-density polyethylene, efficiency, biodegradation, microbial consortia, fungi, bacteria. Inclusion criteria were: scientific articles that included bacteria, fungi, and microbial consortia reported as LDPE degraders that report the percentage of weight loss; articles published from January 2010 to October 2022, and publications in Spanish and English with open access. Exclusion criteria were: studies that do not report gravimetry, the biodegradation time of LDPE, and the genus or species of the polyethylene-degrading microorganism.\n\nResults Out of 483 studies found, 50 were included in this Systematic Review (SR). The most frequent study techniques were scanning electron microscopy (SEM), gravimetry, and fourier transform infrared spectroscopy (FTIR), and in the case of microorganisms, the most studied belonged to the genus Pseudomonas, Bacillus, and Aspergillus. Regarding the isolation place, the most frequent mentioned in the reviewed articles were landfill soil and sanitary landfill soil. The efficiency of LDPE-degrading microorganisms was higher in bacteria such as Enterobacter spp., Pantoea spp., Pseudomonas spp., Escherichia coli, and Bacillus spp., which obtained a range of DE of 9.00-70.00%, 24.00-64%, 1.15 – 61.00%, 45.00%, and 1.5-40% with DT of 4-150, 120, 4-150, 30, and 30-120 days, respectively; in the case of fungi, the main microorganisms are Neopestalotiopsis phangngaensis, Colletotrichum fructicola, and Thyrostroma jaczewskii with efficiencies of 54.34, 48.78, and 46.34%, in 90 days, respectively; and the most efficient microbial consortia were from Enterobacter spp. and Pantoea sp. with 38.00 – 81.00%, in 120 days; and, Pseudomonas protegens, Stenotrophomonas sp., B. vallismortis and Paenibacillus sp. with 55. 00 – 75.00% in 120 days.\n\nConclusions The most efficient microorganisms in LDPE degradation are Enterobacter spp., Pantoea spp., Pseudomonas spp., Escherichia coli, and Bacillus spp.; in fungi Neopestalotiopsis phangngaensis, Colletotrichum fructicola, and Thyrostroma jaczewskii; and in microbial consortia, those formed by Enterobacter spp. and Pantoea sp., and that of P. protegens, Stenotrophomonas sp., B. vallismortis and Paenibacillus sp.; and the most effective techniques used in LDPE biodegradation are SEM, gravimetry, and FTIR.", "keywords": [ "Low-density polyethylene", "efficiency", "biodegradation", "microbial consortia", "fungi", "bacteria." ], "content": "Introduction\n\nPlastics are synthetic polymeric molecules characterized by their versatility, lightness, low cost, and high durability.1 Among the most common are polypropylene, polyethylene, nylon, and polycarbonate, which are considered highly persistent with a capacity for bioaccumulation; they also contaminate the soil, mainly cultivable areas, thus reducing the water filtration capacity and fertilization of plants.2,3 Currently, they have become one of the most significant pollutants in marine ecosystems where most of these float and disintegrate into small fragments when exposed to the sun, taking the name of microplastics.4\n\nPlastics are classified into1: easily degradable, which includes biologically phase plastics such as compostable and biodegradable ones, and2 difficultly degradable, among which thermoset and thermoplastic plastics such as polypropylene (PP), polyvinyl chloride (PVC), polystyrene (PS), polytetrafluoroethylene (PTFE), and low-density polyethylene (LDPE) can be mentioned.5 The latter, globally, are the most marketed, with a production of 390.7 million tons in 2021, of which 50% was produced in Asia and 22% in America.6 Polyethylene is the most commonly used plastic in everyday life, accounting for 96% of all plastics on the market.7\n\nLDPE accounts for 64%, and is primarily used in the form of bags, wrappings, and containers, which are discarded after use.8 The mismanagement of plastic waste increases daily, mainly in Asian countries such as China, Indonesia, the Philippines, Vietnam, Malaysia, Thailand, and in Western countries like the United States. Of the plastics produced, considered to be 18 billion metric tons, 6% are incinerated, 23% are reused, 62% are disposed of in landfills, and 9% are considered recycled.1\n\nIt has been demonstrated in-vitro that the ingestion of plastics by living beings produces a high impact on fauna. It is mentioned that they cause neurotoxic and degenerative damages in rodents, marine invertebrates, fish, and mammals, who are exposed to the presence of high levels of microplastics.9 Some studies in fish indicate that microplastic particles can cause oxidative damage to lipids in the gills and muscles, as well as neurotoxicity through the inhibition of acetylcholinesterase and alterations in neurotransmitter levels.10\n\nHumans, as an important component of the ecosystem, are also affected by plastic waste. It has been estimated that a weekly intake of microplastics (MPs) with values ranging between 0.1 and 5 g can be found bound to food and drinking water, thereby generating adverse health effects.11 In the city of Beijing, China, an analysis of feces conducted on young people between 18 to 25 years old who consumed water and food revealed the presence of microplastics such as polypropylene with a size of 20 – 800 nm.12 Another study in Mexico found up to 30 microplastic particles in a series of foods such as energy drinks, tea, sodas, and beers13; another work conducted in Iran, in the analysis of bottled mineral water, found values of 8.5 ± 10.2 particles/L of PET, PS, PP.14\n\nMPs are a globally recognized problem due to their prevalence in natural environments and the food chain, as well as their high impact on human health. Plastics directly affect living beings, either through ingestion or toxicity. It is noted that they could act as vehicles for invasive species and by adsorption on their surface of other synthetic chemical pollutants such as polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs), or organochlorines, currently used by the chemical industry, thus potentiating or synergizing their toxic power due to components they contain such as plasticizers, heavy metal additives, etc.15 Studies on microbiota have allowed the assessment of the effect of MPs, especially PETs, on microbiota, demonstrating that they would act at the colon level, decreasing the values of Staphylococcus spp., Bifidobacterium spp., and Clostridium spp.16\n\nAn important aspect to consider is the degradation process of plastics, such as with LDPE, which can take up to 400 years to decompose.17 The process involves various microorganisms, mainly bacteria and fungi, that utilize mechanisms of photooxidation, thermal degradation, ozonation, mechano-chemical and catalytic degradation, and also biodegradation.5 The capability of hydroxylases, lipases, and laccases enzymes, secreted by LDPE-degrading microorganisms, which are responsible for breaking the polymer chain into low molecular weight fragments, must be mentioned.18 Extracellular enzymes play a very important role in biodegradation through the depolymerization of LDPE to form intermediate products that can be used as a carbon source by microorganisms,19 as they oxidize, reduce, hydrolyze, esterify, and cut the internal molecular structure of the polymer.20\n\nMicroorganisms accelerate and increase the degradation process, making them an alternative to reduce the accumulation of petroplastics in the environment.21 There are reports of bacteria (Pseudomonas spp. and Bacillus spp.) and fungi (Aspergillus spp. and Fusarium spp.) that can degrade this plastic under laboratory conditions.22,23 The use of more efficient microorganisms in the degradation of LDPE will allow the proper selection of bacteria or fungi with greater action and degradative efficiency of plastic.24 At the industrial level, it will involve the handling of various effective methods of detection and quantification, such as gravimetry, scanning electron microscopy (SEM),25–30 Fourier transform infrared spectroscopy (FTIR), and gas chromatography coupled with mass spectrometry (GC-MS), which complement the study of the polymer’s natural degradation.31\n\nThe purpose of this systematic review is to demonstrate the efficiency of LDPE-degrading microorganisms and the efficacy of the main biodegradation techniques on this type of plastics. The research question is: Which of the microorganisms is the most efficient and what techniques are the most effective in the biodegradation of LDPE-type plastics?\n\n\nMethods\n\nThe PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) methodology was used, which is established for systematic reviews and meta-analysis statements.32 The information was extracted from articles obtained from various databases such as: Scopus, Web of Science (WOS), Embase, and Google Scholar. The identification, screening, and eligibility of scientific articles were organized through the Zotero Bibliographic Manager.33 The protocol of the systematic review was registered in PROSPERO (International prospective register of systematic reviews) under the number CRD42024506168.\n\nThe search strategy in all databases consisted of managing Boolean operators (AND, OR, and NOT), keywords (biodegradation, low-density polyethylene), years of publication (2010 – 2022), type of document (original article), language (Spanish, English), and open access publications. The DeCS/Mesh search terms were: Low-Density Polyethylene, LDPE, efficiency, biodegradation, microbial consortia, fungi, and bacteria.\n\nThe auxiliary search strategy included:\n\n✓ Scopus\n\n((TITLE-ABS-KEY (BIODEGRADATION) AND TITLE-ABS-KEY (LOW DENSITY POLYETHYLENE)) AND (LIMIT-TO (LANGUAGE,“English”) OR LIMIT-TO (LANGUAGE,“Spanish”)) AND (LIMIT-TO (PUBYEAR,2010) OR LIMIT-TO (PUBYEAR,2011) OR LIMIT-TO (PUBYEAR,2012) OR LIMIT-TO (PUBYEAR,2013) OR LIMIT-TO (PUBYEAR,2014) OR LIMIT-TO (PUBYEAR,2015) OR LIMIT-TO (PUBYEAR,2016) OR LIMIT-TO (PUBYEAR,2017) OR LIMIT-TO (PUBYEAR,2018) OR LIMIT-TO (PUBYEAR,2019) OR LIMIT-TO (PUBYEAR,2020) OR LIMIT-TO (PUBYEAR,2021) ORLIMIT-TO (PUBYEAR,2022)) AND (LIMIT-TO (EXACTKEYWORD,“Article”)) AND (LIMIT-TO (DOCTYPE,“ar”)) AND (LIMIT-TO (SRCTYPE,“j”)))\n\n✓ Web of Science (WOS)\n\n(ALL=(biodegradation)) AND ALL=(low density polyethylene) and 2022 or 2021 or 2020 or 2019 or 2018 or 2017 or 2016 or 2015 or 2014 or 2013 or 2012 or 2011 (Publication Years) and 28 Article (Document Types) and Article (Document Types) and All Open Access (Open Access) and English (Languages)\n\n✓ Embase\n\n“biodegradation AND polyethylene AND low AND density AND [2010-2022]/py AND [article]/lim AND ([english]/lim OR [spanish]/lim”\n\n✓ Google Scholar\n\nThe advanced search in this database included the exact phrase “LDPE biodegradation”; at least one of the following terms: Fungi, bacteria, or microbial consortia; terms mentioned in all scientific articles. It was also possible to delimit the years and languages of publication for each study.\n\nInclusion criteria\n\n• Scientific articles that included bacteria, fungi, and microbial consortia reported as LDPE degraders.\n\n• Scientific articles that report the percentage of weight loss after the process.\n\n• Articles published from January 2010 to October 2022.\n\n• Publications in Spanish and English with open access.\n\nExclusion criteria\n\n• Studies that do not report gravimetry.\n\n• LDPE biodegradation time.\n\n• Genus or species of the polyethylene-degrading microorganism.\n\nThe coordination and development of the review activities were carried out through the Zoom video chat software. To include the studies, their relationship with the research question was verified, based fundamentally on the terms: Biodegradation, LDPE, bacteria, and fungi. Then, for the quality assessment of the Systematic Reviews, Meta-analysis and a scientific article evaluation scale were used to ensure strict compliance with the inclusion and exclusion criteria mentioned in previous paragraphs. The web application used throughout the process of identification, selection, eligibility, and inclusion was Zotero. To collect relevant data from each report, PRISMA 2020 was used. Empirical articles were evaluated using an analytical rubric designed according to the parameters founded on the SSAHS scale by López-López E, Tobón S, JuárezHernández LG) for the consideration of scientific articles. Systematic reviews were evaluated using the Quality Assessment of Systematic Reviews and Meta-Analyses, utilizing an observation guide (checklist style as indicated by the National Heart, Lung, and Blood Institute).34 Data systematization tables were used considering year, author(s), title, techniques, and place of isolation. In this last item, the place of origin of the microorganism (isolation), the identified microorganism, and the study technique (TE) were included. The variables for which relevant information was sought were: degradation efficiency (DE) of LDPE degrading microorganisms, biodegradation of plastics, degradation time (DT), and percentage of weight loss.\n\n\nResults\n\nFigure 1 shows the PRISMA methodology, whose search protocol identified 483 primary articles, of which 133 duplicates, 279 by title, 5 by abstract, 11 by access, and 20 for not meeting the inclusion terms were excluded. A total of 35 full-text articles were obtained, and 15 were included from previous review.\n\nTable 1 indicates the number of articles found, totaling 50, with the highest quantity produced between the years 2018 to 2022. Also, it is observed that 100% of the articles correspond to experimental research works. Likewise, it points out the study techniques, with the most frequent being: SEM, gravimetry, and FTIR. Regarding the microorganisms identified in each of the studies, the most frequent in the phylum bacteria belonged to the genera Pseudomonas and Bacillus; as for the phylum of fungi, Aspergillus spp. predominated. As for the isolation site, the most used and mentioned in the reviewed articles were landfill soil and sanitary landfill.32\n\nTable 2 allows for the descriptive observation of microorganisms classified into bacteria, fungi, and microbial consortia, in quantities of 23, 17, and 9 respectively. Also, it specifies the species and the efficiency of LDPE-degrading microorganisms expressed in weight loss from highest to lowest and the days used for complete degradation, highlighting among bacteria Enterobacter spp., Pantoea spp., P. spp., Escherichia coli, and B. spp. which obtained an ED range of 9.00-70.00%, 24.00-64.00%, 1.15 – 61.00%, 45.00%, and 1.50-40.00% with TD of 4-150, 120, 4-150, 30, and 30-120 days, respectively; in the case of fungi, the main microorganisms are Neopestalotiopsis phangngaensis, Colletotrichum fructicola, and Thyrostroma jaczewskii with ED of 54.34, 48.78, and 46.34%, respectively, and TD of 90 days; and, the most efficient microbial consortia were from E. spp. and Pantoea sp. with ED of 38.00 – 81.00%, and TD of 120 days; and, P. protegens, Stenotrophomonas sp., B. vallismortis, Paenibacillus sp. with ED of 55.00 – 75.00% and TD of 120 days.\n\nLDPE: Low-density polyethylene. IL: Isolation Location. MI: Identified Microorganism. TE: Study Technique. FTIR: Fourier Transform Infrared Spectroscopy. FTIR-ATR: Fourier Transform Infrared Spectroscopy - Attenuated Total Reflectance. SEM: Scanning Electron Microscopy. GC-MS: Gas Chromatography–Mass Spectrometry. EDS: Energy Dispersive X-ray Spectroscopy. FE-SEM: Field Emission Scanning Electron Microscopy. HT-GPC: High Temperature Gel Permeation Chromatography. TGA: Thermogravimetric Analysis. AFM: Atomic Force Microscopy. XRD: X-ray Diffraction. BATH: Bacterial Adhesion to a Hydrocarbon. GC-FID: Gas Chromatography-Flame Ionization Detector. DSC: Differential Scanning Calorimetry. NMR: Nuclear Magnetic Resonance.\n\n\nDiscussion\n\nAccording to the data analyzed (Table 1), in recent years there has been an increase in studies on LDPE-degrading microorganisms with the aim of minimizing environmental impacts through bioremediation.78 The requirement for special technologies allows understanding the degree of polymer disintegration and the nature of its resulting products. In the SR, up to 20 study techniques used in the biodegradation of LDPE have been detected. From our point of view, we consider highlighting in this article those methods that, due to frequency and especially efficacy, stand out among others. These methods include the following: SEM,67,69–71 gravimetry,25,26,27,28,29,30,35,36,39,40 and FTIR.20,28,60,66\n\nThe SEM study technique,19,42–44,46,49–54,56,62,63,70,72 is used to detect the biodegradation of LDPE and is employed to monitor changes on the surface of the LDPE film.72,74–76 The adhesion of microorganisms to the surface is essential for biodegradation.65 After incubating LDPE with selected degrading microorganisms on the surface, some characteristics such as erosion, holes, and cavities are observed, which are attributed jointly to the formation of bacterial film and the penetration of fungal hyphae.60,68 Erosion is considered the primary cause of the mass reduction of the surface due to the secretion of enzymes and microbial extracellular metabolites.20\n\nAnother frequently used technique in the reviewed articles is gravimetry,20,42–46,48–55,68–71 which is a simple and highly precise test to determine the polymer weight reduction, originating as a consequence of being used as a source of carbon and energy by microorganisms.19,62–65,72–74,76 This weight loss is considered proportional to the surface area, as biodegradation starts on the polymer’s surface.38 With Gram-positive bacteria, the degradation efficiency (DE) in terms of LDPE weight loss has been reported: Streptomyces sp. DE 5.2% and degradation time (DT) of 90 days40 and Bacillus amyloliquefaciens DE 11% and DT 60 days.38\n\nIt was found in the review that various articles mentioned the FTIR technique,19,25,26,27,28,29,30,35,37,40,44,46,50,51,64,67–70,74–76 as the third most frequent of those applied to determine biodegradation; in addition, the cited studies consider it analytical and efficient, useful for identifying the chemical configuration of organic, polymeric, and inorganic material, and the morphological changes, which are supported by the chemical structural changes at the level of the carbon chains, observing new functional groups (alkoxy, acyl, carboxyls, and nitro) or absence of them, and modifications in the chains such as breaks, stretches, and formation of double bonds; moreover, this technique determines the carbonyl index (CI), which measures the degree of degradation of the LDPE and in which its value depends on the degraded carbonyl bonds.28 In reality, it involves measuring the concentration of carbonyl groups (CG) corresponding to acids, aldehydes, and ketones.35 In the process of LDPE biodegradation, the initial weight corresponds to the oxidation of the chain that leads to the formation of CG, and subsequently, these form carboxylic groups that are degraded by β-oxidation and then through the citric acid cycle to CO2 and H2O.77\n\nIn Table 2, as observed, the microorganisms frequently reported in the articles analyzed in Table 1 include bacteria from the genera Bacillus, Brevibacillus, Cellulosimicrobium, Comamonas, Delftia, Enterobacter, Escherichia, Idonella, Kocuria, Lysinibacillus, Paenibacillus, Pantoea, Pseudomonas, Rhodococcus, Rhodotorula, Stenotrophomonas, and Streptomyces,25,28,30,42,46,58,59 with the genera Pseudomonas, Bacillus, and Streptomyces predominating. Other microorganisms are fungi, with Aspergillus sp. most frequently cited.39,48,50,52,63 Among the less frequently cited species include Rhizopus oryzae, Paenibacillus sp., Streptomyces coelicoflavus, Thiobacillus, Clostridium, Achromobacter denitrificans, Penicillium oxalicum, P. chrysogenum, Pycnoporus sanguineus, Enterobacter cloacae.29,37,44,45,54,55,61,74\n\nIn the same table, it is analyzed that among the most efficient bacteria in the degradation of LDPE according to the weight loss of the polymer include several species such as Enterobacter spp. with an ED of 9.00 – 70.00%, and TD of 4 -150, Pantoea spp. with an ED of 24.00 – 64.00% and TD of 120, Pseudomonas spp. with an ED of 1.15 – 61.00% and TD of 4-150, Escherichia coli with an ED of 45.00% and TD of 30, and finally, Bacillus spp. with an ED of 1.50 – 40.00% and TD of 30-120. Bacillus sp. is also considered as another important species in the biodegradation process, having a consumption rate of 0.0019 g of the polymer per day45; or, participating in consortia such as the one constituted by Bacillus vallismortis, Pseudomonas protegens, Stenotrophomonas sp., and Paenibacillus sp.42\n\nIt has been determined that P. aeruginosa cultured on LDPE as the only carbon source has an ED of 0.0015 g of LDPE per day and a TD of 462 days to reduce a polyethylene film from 1g to 0.5g20; Enterobacter cloacae AKS7 and Escherichia coli possess another type of degradative action, and it is due to the secretion of extracellular polymeric substances and the high hydrophobicity of the microorganism’s cell wall, which allows a greater formation and adherence of the bacterial biofilm.36,61 In the case of Pantoea sp., its efficiency can be measured either individually or in consortium with Enterobacter.41\n\nFungi (Table 2), like bacteria, are considered LDPE-degrading microorganisms. The most efficient are: Neopestalotiopsis phangngaensis, Colletotrichum fructicola, and Thyrostroma jaczewskii with EDs of 54.34, 48.78, and 46.34%, respectively, and a TD of 90 days. The mycotic activity is considered to be due to their great capacity for adherence. In the polymer biodegraded for 40 days, the biofilm formed by the strongly adhered fungi is observed; at 80 days, surface deformation is evident and microcracks are differentiated.28 Other efficient species are also reported, such as A. clavatus with an ED of 35.00% and a TD of 90 days27 and A. versicolor with 40.60% and a TD of 90 days.43\n\nThe degradative efficiency of microbial consortia has also been reported in different studies,35,41,63,70 showing the most efficient to be the one formed by Enterobacter spp. and Pantoea sp., and the one of Pseudomonas protegens, Stenotrophomonas sp., B. vallismortis, and Paenibacillus sp. The cooperation of different microorganisms allows the use of different and complementary metabolic capacities for their growth, forming pure or mixed biofilms (fungi and bacteria), more resistant and metabolically more active.79\n\nLDPE-degrading microorganisms form a biofilm on the polymer and use it as a carbon source for consumption, an event that is reflected in weight loss. The biodegradation by microorganisms is a process of high metabolic activity, in which the count of viable cells, the concentration of surface proteins, and the efficiency in degradation expressed as polymer weight loss must be taken into account.20 The most frequent place of isolation of microorganisms with LDPE-degrading capacity came from landfill soil and sanitary landfills with the presence of plastics. Various studies have indicated that bacteria and fungi adapt under different environmental conditions, a process mediated by complex cellular changes at the enzymatic level,19,56 maintain physiology and metabolism, thus ensuring the survival of microorganisms. It has been demonstrated that bacteria such as Pseudomonas putida is a resistant and efficient xenobiotic decomposer because it presents an effective efflux pump; similarly, Streptomyces atacamensis shows xerotolerant latency and spore response to desiccation, and upregulation of proteins that are functional during xeric stress,80 which probably explains why certain microorganisms are more efficient at degrading LDPE compared to others.\n\nConsidering that degradation is a slow process (this activity occurs before 60 days of incubation), and that degradation methods are heterogeneous, some authors conclude that there is no standard methodology in relation to analytical methods.15 However, in this article, we present the various biodegradation techniques, so a more precise vision could be had to assess which of them is the most consistent and effective according to their ED and TD.\n\nFinally, based on the detection and quantification tests of polymer degradation, the exposed microorganisms constitute a sustainable alternative, useful for bioremediation and minimization of environmental impacts, with the aim of reducing environmental pollution by LDPE.\n\n\nConclusions\n\n\n\n• The microorganisms with the highest degradation efficiency on LPDE-type plastics in bacteria are Enterobacter spp., Pantoea spp., Pseudomonas spp., Escherichia coli, and Bacillus spp.; in fungi Neopestalotiopsis phangngaensis, Colletotrichum fructicola, and Thyrostroma jaczewskii; and in microbial consortia, those formed by Enterobacter spp. and Pantoea sp., and the one by P. protegens, Stenotrophomonas sp., B. vallismortis, and Paenibacillus sp.\n\n• The most effective techniques used in LDPE biodegradation are SEM, gravimetry, and FTIR.\n\nThe results obtained allow for the identification of a lack of studies on microorganisms efficient in the biodegradation of LDPE, which limits the possibility of expanding their number and understanding their efficiency. Moreover, there are few studies on alternative methods that are effective in biodegradation. These limitations should be taken into account for the guidance and development of new research.\n\nEthical approval and consent were not required.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nDOI: https://doi.org/10.5281/zenodo.11447533\n\n\nReferences\n\nVadera S, Khan S: A Critical Analysis of Rising Global Demand of Plastics and its Adverse impact on Environment Sustainability. J. Environ. Pollut. Manag. 2021; 3: 1–13. Publisher Full Text\n\nZhang S, Wang J, Yan P, et al.: Middle concentration of microplastics decreasing soil moisture-temperature and the germination rate and early height of lettuce (Lactuca sativa var. ramosa Hort.) in Mollisols. Sci. Total Environ. 2023; 3: 1–13. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDas MP, Kumar S: Microbial Deterioration of Low Density Polyethylene by Aspergillus and Fusarium sp. Int. J. ChemTech Res. 2014; 6: 974–4290. Reference Source\n\nGajendiran A, Krishnamoorthy S, Abraham J: Microbial degradation of low-density polyethylene (LDPE) by Aspergillus clavatus strain JASK1 isolated from landfill soil. 3 Biotech. 2016; 6(1): 52. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKyaw BM, Champakalakshmi R, Sakharkar MK, et al.: Biodegradation of Low Density Polythene (LDPE) by Pseudomonas Species. Indian J. Microbiol. 2012; 52(3): 411–419. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nQuinchía A, Maya S: Degradabilidad de polietileno de baja densidad –LDPE- Utilizando Pycnoporus sanguineus 03UTCH 03. Encuentro. Int. Educ. En. Ing. 2015. Publisher Full Text\n\nTribedi P, Sil A: Low-density polyethylene degradation by Pseudomonas sp. AKS2 biofilm. Environ. Sci. Pollut. 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Biol. 2010; 17(1): 133–136. Publisher Full Text\n\nMuthumani S, Anbuselvi S: Waste management and enviornment protection – A study with isolation and characterisation of low density polyethylene degradating microbes. Int. J. ChemTech Res. 2014; 7(6): 2841–2845. Reference Source\n\nDuddu MK, Tripura KL, Guntuku G, et al.: Biodegradation of low density polyethylene (LDPE) by a new biosurfactant-producing thermophilic Streptomyces coelicoflavus NBRC 15399T. Afr. J. Biotechnol. 2015; 14(4): 327–340. Publisher Full Text\n\nDas MP, Kumar S: An approach to low-density polyethylene biodegradation by Bacillus amyloliquefaciens. 3 Biotech. 2015; 5(1): 81–86. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDeepika S, Jaya MR: Biodegradation of low density polyethylene by microorganisms from garbage soil. J. Exp. Biol. Agric. Sci. 2015; 3(1): 15–21. Reference Source\n\nAbraham J, Gosh E, Mukherjee P, et al.: Degradación microbiana del polietileno de baja densidad. Am. Inst. Chem. Eng. 2016; 36(1): 147–154. Publisher Full Text\n\nSkariyachan S, Manjunatha V, Sultana S, et al.: Novel bacterial consortia isolated from plastic garbage processing areas demonstrated enhanced degradation for low density polyethylene. Environ. Sci. Pollut. Res. 2016; 23(18): 18307–18319. PubMed Abstract \| Publisher Full Text\n\nSkariyachan S, Setlur AS, Naik SY, et al.: Enhanced biodegradation of low and high-density polyethylene by novel bacterial consortia formulated from plastic-contaminated cow dung under thermophilic conditions. Environ. Sci. Pollut. Res. Int. 2017; 24(9): 8443–8457. PubMed Abstract \| Publisher Full Text\n\nGajendiran A, Subramani S, Abraham J: Effect of Aspergillus versicolor strain JASS1 on low density polyethylene degradation. IOP Conf. Ser. Mater Sci. Eng. 2017; 263(2): 022038. Publisher Full Text\n\nOjha N, Pradhan N, Singh S, et al.: Evaluation of HDPE and LDPE degradation by fungus, implemented by statistical optimization. Sci. Rep. 2017; 7: 39515. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAwasthi S, Srivastava N, Singh T, et al.: Biodegradation of thermally treated low density polyethylene by fungus Rhizopus oryzae NS 5. 3 Biotech. 2017; 7(1): 73. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDela Torre DY, Delos Santos LA, Reyes ML, et al.: Biodegradation of low-density polyethylene by bacteria isolated from serpentinization-driven alkaline spring. Philipp. Sci. Lett. 2018; 11. Reference Source\n\nMunir E, Sipayung FC, Priyani N, et al.: Potential of bacteria isolated from landfill soil in degrading low density polyethylene plastic. IOP Conf Ser Earth Environ. Sci. 2018; 126(1): 012144. Publisher Full Text\n\nMunir E, Harefa RSM, Priyani N, et al.: Plastic degrading fungi Trichoderma viride and Aspergillus nomius isolated from local landfill soil in Medan. IOP Conf. Ser. Earth Environ. Sci. 2018; 126(1): 012145. Publisher Full Text\n\nHikmah M, Setyaningsih R, Pangastuti A: The Potential of Lignolytic Trichoderma Isolates in LDPE (Low Density Polyethylene) Plastic Biodegradation. IOP Conf. Ser. Mater Sci. Eng. 2018; 333(1): 012076. Publisher Full Text\n\nThamizhmarai T, Kannahi M: Biodegradation of Low Density Polyethylene by Aspergillus sps and Pseudomonas sps Isolated from Plastic Dumped Site ─ A SEM Analysis. Int. J. Pharm. Sci. Rev. Res. 2018; 50(1): 182–187. Reference Source\n\nPriyadarshini P, Rafiq S, Shahina SJ, et al.: Biodegradation of Low Density Polyethylene (LDPE) by Nocardiopsis alba from municipal landfill in Chennai.2018; 3(8). Reference Source\n\nJayaprakash V, Palempalli U: Effect of Palmitic Acid in the Acceleration of Polyethylene Biodegradation by Aspergillus oryzae. J. Pure. Appl. Microbiol. 2018; 12(4): 2259–2268. Publisher Full Text\n\nSáenz M, Borodulina T, Diaz L, et al.: Minimal Conditions to Degrade Low Density Polyethylene by Aspergillus terreus and niger. J. Ecol. Eng. 2019; 20(6): 44–51. Publisher Full Text\n\nBardají D, Furlan J, Stehling E: Isolation of a polyethylene degrading Paenibacillus sp. from a landfill in Brazil. Arch. Microbiol. 2019; 201(5): 699–704. PubMed Abstract \| Publisher Full Text\n\nIslami AN, Tazkiaturrizki T, Rinanti A: The effect of pH-temperature on plastic allowance for Low-Density Polyethylene (LDPE) by Thiobacillus sp. and Clostridium sp. J. Phys. Conf. Ser. 2019; 1402(3): 033003. Publisher Full Text\n\nDe silva A, Jayasekera A, Nanayakkara C: Identification of potential fungal degraders of low-density polyethylene (LDPE). J Sci. 2019; 10: 1. Publisher Full Text\n\nKumar K, Devi D: Biodegradation of Low Density Polyethylene by Selected Bacillus sp. Gazi. Univ. J. Sci. 2019; 32(3): 802–813. Publisher Full Text\n\nMontazer Z, Habibi Najafi MB, Levin DB: In vitro degradation of low-density polyethylene by new bacteria from larvae of the greater wax moth, Galleria mellonella. Can. J. Microbiol. 2021; 67(3): 249–258. PubMed Abstract \| Publisher Full Text\n\nButron SB: Capacidad de biodegradación de Pseudomonas aeruginosa frente al polietileno de baja densidad. Rev Investig Esc Posgrado Univ Nac Altiplano Puno. 2020; 9(3): 134–147. Publisher Full Text\n\nDey AS, Bose H, Mohapatra B, et al.: Biodegradation of Unpretreated Low-Density Polyethylene (LDPE) by Stenotrophomonas sp. and Achromobacter sp., Isolated From Waste Dumpsite and Drilling Fluid. Front. Microbiol. 2020; 11: 603210. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSarker RK, Chakraborty P, Paul P, et al.: Degradation of low-density poly ethylene (LDPE) by Enterobacter cloacae AKS7: a potential step towards sustainable environmental remediation. Arch. Microbiol. 2020; 202(8): 2117–2125. PubMed Abstract \| Publisher Full Text\n\nSamanta S, Datta D, Halder G: Biodegradation efficacy of soil inherent novel sp. Bacillus tropicus (MK318648) onto low density polyethylene matrix. J. Polym. Res. 2020; 27(10): 324. Publisher Full Text\n\nDSouza GC, Sheriff RS, Ullanat V, et al.: Fungal biodegradation of low-density polyethylene using consortium of Aspergillus species under controlled conditions. Heliyon. 2021; 7(5): e07008. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSoleimani Z, Gharavi S, Soudi M, et al.: A survey of intact low-density polyethylene film biodegradation by terrestrial Actinobacterial species. Int. Microbiol. Off. J. Span. Soc. Microbiol. 2021; 24(1): 65–73. PubMed Abstract \| Publisher Full Text\n\nWaqas M, Haris M, Asim N, et al.: Biodegradable Potential of Bacillus amyloliquefaciens and Bacillus safensis Using Low Density Polyethylene Thermoplastic (LDPE) Substrate. Eur. J. Environ. Public Health. 2021; 5(2): em0069. Publisher Full Text\n\nKhruengsai S, Sripahco T, Pripdeevech P: Low-Density Polyethylene Film Biodegradation Potential by Fungal Species from Thailand - PubMed.2021; 7(8): 1–18. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKhandare SD, Chaudhary DR, Jha B: Marine bacterial biodegradation of low-density polyethylene (LDPE) plastic. Biodegradation. 2021; 32(2): 127–143. Publisher Full Text\n\nNadeem H, Alia KB, Muneer F, et al.: Isolation and identification of low-density polyethylene degrading novel bacterial strains. Arch. Microbiol. 2021; 203(9): 5417–5423. PubMed Abstract \| Publisher Full Text\n\nChaudhary AK, Chaitanya K, Dalmia R, et al.: Synergistic effect of UV, thermal, and chemical treatment on biological degradation of low-density polyethylene (LDPE) by Thermomyces lanuginosus. Environ. Monit. Assess. 2021; 193(8): 513. PubMed Abstract \| Publisher Full Text\n\nSkariyachan S, Taskeen N, Kishore AP, et al.: Novel consortia of enterobacter and pseudomonas formulated from cow dung exhibited enhanced biodegradation of polyethylene and polypropylene. J. Environ. Manag. 2021; 284: 112030. PubMed Abstract \| Publisher Full Text\n\nZahari NZ, Abdullah SN, Tuah PM, et al.: Biodegradation of low-density polyethylene (LDPE) and starch – based plastic (SBP) by thermophiles Bacillus subtilis and Candida tropicalis. IOP Conf. Ser. Mater Sci. Eng. 2021; 1173(1): 012035. Publisher Full Text\n\nPerera P, Deraniyagala A, Piumi M, et al.: Decaying Hardwood Associated Fungi Showing Signatures of Polyethylene Degradation. Bioresources. 2021; 16: 7056–7070. Publisher Full Text\n\nSaira U, Abdullah U, Maroof L, et al.: Biodegradation of Low-Density Polyethylene (LDPE) Bags by Fungi Isolated from Waste Disposal Soil. Appl. Environ. Soil Sci. 2022; 2022: 1–7. Publisher Full Text\n\nMaleki Rad M, Moghimi H, Azin E: Biodegradation of thermo-oxidative pretreated low-density polyethylene (LDPE) and polyvinyl chloride (PVC) microplastics by Achromobacter denitrificans Ebl13. Mar. Pollut. Bull. 2022; 181: 113830. PubMed Abstract \| Publisher Full Text\n\nKhruengsai S, Sripahco T, Pripdeevech P: Microbial degradation of low-density polyethylene by Neopestalotiopsis phangngaensis. J. Gen. Appl. Microbiol. 2022; 68(6): 287–294. PubMed Abstract \| Publisher Full Text\n\nLiu X, Zhang Y, Sun Q, et al.: Rapid colonization and biodegradation of untreated commercial polyethylene wrap by a new strain of Bacillus velezensis C5. J. Environ. Manag. 2022; 301: 113848. PubMed Abstract \| Publisher Full Text\n\nEsmaeili A, Pourbabaee AA, Alikhani HA, et al.: Biodegradation of low-density polyethylene (LDPE) by mixed culture of Lysinibacillus xylanilyticus and Aspergillus niger in soil. PLoS One. 2013; 8(9): e71720. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLa FP: problemática del consumo de plásticos durante la pandemia de la covid-19. South Sustain. 2020; 1(2): e016–e019. Publisher Full Text\n\nBarriuso J: Centro de Investigaciones Biológicas Margarita Salas - CIB Margarita Salas. 2020. Consorcios microbianos para la degradación de plásticos convencionales (PID2020-114210RB-I00), 2020-2024.Reference Source\n\nWani AK, Akhtar N, Sher F, et al.: Microbial adaptation to different environmental conditions: molecular perspective of evolved genetic and cellular systems. Arch. Microbiol. 2022; 204(2): 144. PubMed Abstract \| Publisher Full Text" }	[ { "id": "299819", "date": "25 Jul 2024", "name": "Claudio Quiñones-Cerna", "expertise": [ "Reviewer Expertise Bioremediation and Biodegradation of organic contaminants" ], "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 \"Efficiency of Microorganisms and Effectiveness of Biodegradation Techniques on LDPE Plastics: A Systematic Review\" was published in F1000Research. This systematic review, based on the PRISMA method, examines studies published between January 2010 and October 2022, analyzing the degradation of LDPE by bacteria, fungi, and microbial consortia, as well as the techniques used to evaluate this degradation.\nThe study is particularly relevant due to the growing concern about plastic accumulation in the environment and the negative impacts associated with these materials, such as soil and water contamination and the effects on human health and wildlife. The results of this study provide a comprehensive view of the biodegradative capabilities of different microorganisms and effective methodologies for evaluating plastic degradation, which can guide future research and industrial applications in plastic waste management.\nMain Comments\nConceptualization of Biodegradation Techniques: Comment: It would be beneficial for the introduction of the study to include a detailed conceptualization of different biodegradation techniques, covering aerobic and anaerobic processes, necessary environmental conditions, types of microorganisms involved, and specific applications for LDPE plastics. This would help readers understand how these techniques are applied and evaluated in the context of plastic biodegradation, providing a clear and complete theoretical framework from the outset.\nSecondary Comments\nDiversity of Evaluation Techniques: Comment: The study highlights several evaluation techniques such as SEM, gravimetry, and FTIR but would benefit from a more in-depth discussion of the specific advantages and limitations of each technique. Rationale: A detailed comparison would help readers choose the most suitable techniques for their own research and practical applications.\nFuture Research in Microbial Consortia: Comment: The review mentions the effectiveness of microbial consortia in LDPE degradation but could be expanded to suggest additional studies exploring the synergistic interaction between different microorganisms. Understanding how microbial consortia interact and enhance the degradation of plastics can open new avenues for research and development of more efficient biotechnologies.\nEnvironmental and Human Health Impact: Comment: Although the impact of plastics on the environment and human health is addressed, a section specifically dedicated to discussing these effects with recent data and concrete examples would strengthen the study's argument. Providing detailed information on the environmental and public health consequences of plastic accumulation underscores the importance of developing and applying effective biodegradation techniques.\nThe article offers a comprehensive and detailed overview of the biodegradative capabilities of various microorganisms and the effective methodologies for the degradation of LDPE. However, it could benefit from further conceptualization of biodegradation techniques and a more detailed explanation of the inclusion and exclusion criteria. Additionally, expanding the discussion on the advantages and limitations of evaluation techniques, synergy in microbial consortia, and the environmental and human health impacts would provide a more complete and applicable perspective.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? I cannot comment. A qualified statistician is required.\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Yes", "responses": [ { "c_id": "12176", "date": "07 Aug 2024", "name": "Jorge Guillermo Morales Ramos", "role": "Author Response", "response": "We are grateful for this review of our article." } ] }, { "id": "300136", "date": "30 Jul 2024", "name": "Magaly de la Cruz Noriega", "expertise": [ "Reviewer Expertise biotechnology", "bioremediation", "electromicrobiology" ], "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 research work is very interesting and relevant, as it gives us updated information on the role of microorganisms in degrading low-density plastic. But for its indexing some details are required.\nIn the introduction, it is necessary to include a more detailed paragraph on the plastic degradation techniques such as (thermal, radiation, mechanical, chemical and biological), then put emphasis on the biological ones, indicating the advantages and limitations in the biodegradation of low-density plastic, to have a clearer picture of this review, then eliminate the research question rather place the implication or impact that this work has.\nRegarding the results, consider in Table 1 to consider the classification as follows: (Year, Authors, Type of study, type of sample or sample, Technique (physical, mechanical or biological), identified microorganisms, Analysis in the detection of Degradation.\nThe discussion needs to go deeper into Table 1.\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.) Yes", "responses": [ { "c_id": "12177", "date": "02 Sep 2024", "name": "Jorge Guillermo Morales Ramos", "role": "Author Response", "response": "The observations made in terms of classifying degradation types and highlighting biodegradation among them were raised. The second point on table 1, the table was constructed on the basis of the suggestions, introducing the sample and techniques." } ] } ]	1	https://f1000research.com/articles/13-745
https://f1000research.com/articles/13-988/v1	02 Sep 24	{ "type": "Research Article", "title": "Enhancing quantitative capacity for the health sector in post-Ebola Liberia, a tracer study of a locally developed and owned coding and biostatistics program", "authors": [ "Snoyonoh T. Barcon", "Trokon O. Yeabah", "Mulbah K.A. Kromah", "George B. Davis", "Laura A. Skrip", "Snoyonoh T. Barcon", "Trokon O. Yeabah", "Mulbah K.A. Kromah", "George B. Davis" ], "abstract": "Background Despite the demonstrated value of quantitative research in understanding and responding to public health events, analytics capability is not always prioritized or available in settings that would greatly benefit from it. In Liberia, there are no university degree-granting programs in biostatistics or mathematical modeling, promoting dependence on external technical assistance. To address the gap, a local NGO, Quantitative-Data for Decision-Making (Q4D), was founded to enhance capacity and opportunities for analyzing quantitative data among Liberians.\n\nMethods To understand the relevance, utility, and impact of the skills being taught at Q4D, a tracer study was undertaken with current and former students. Participants completed an online survey that evaluated how often and in what ways they are applying course skills, as well as any personal or professional advancement they have attributed to their learning of coding and/or biostatistics through the program.\n\nResults Among 43 participants, 81% reported a high level of confidence in independently applying skills learned through Q4D classes in their jobs and/or academic programs. Most participants (81%) responded that they were actively demonstrating the skills they acquired; 74% were teaching the skills to others. Among the 83% of employed participants who reported using the skills currently in their jobs, 56% rated the skills they learned as very or extremely useful in their current positions. Several students attributed salary increments, consultancy opportunities, and scholarships to the skills gained through the program.\n\nConclusions Program skills are being applied by students employed in health-related sectors, suggesting that the training content is relevant and useful for addressing some of the workforce’s analysis needs. Moreover, skills built through the program have positively impacted students by preparing them with the skills required for additional employment and training opportunities to advance in-country health research capacity and reduce inequities.", "keywords": [ "quantitative analysis", "capacity strengthening", "health system strengthening", "Liberia", "meaningful outcomes", "evidence-driven decision-making" ], "content": "Background\n\nSituated in West Africa, Liberia has experienced back-to-back shocks due to decades of civil conflict, followed by the unprecedented Ebola outbreak1 and ongoing public health threats, including COVID-19, mpox, measles, and Lassa fever.2–4 Despite efforts to enhance resilience across sectors, including with the adoption of a pro-poor agenda,5 the country presently ranks 177 (out of 191) on the Human Development Index.6 Largely external investments in capacity-building have sought to fill gaps.7 For the health sector, institutional developments have improved systems to better prepare the country for detecting, notifying, and responding to threats in the post-Ebola period; however, investments in improving data quality, analysis, and use have been less prioritized than the generation or reporting of data, and systems remain vulnerable.8\n\nDespite Liberia’s experiences with the 2014-2015 Ebola outbreak and more recent COVID-19 pandemic and the extensive quantitative research undertaken with external collaborators to understand the potential trajectories of these health crises,9–11 few efforts have been made in Liberia to institutionalize local capacity strengthening opportunities in quantitative data analysis for public health researchers and practitioners. To date, there is no university degree being administered in biostatistics, and dynamic mathematical modeling is not taught even as a course in existing academic programs. Short-term training often facilitated by visiting collaborators is being conducted at institutional levels. However, the limited literature being produced in Liberia using quantitative analysis12 and the reliance on international consultants for work that is being done13 provide evidence that the few existing models of teaching coding and statistics may not be generating independent capacity. That gap has implications for overall development as well as resilience in the face of health and other threats.14–16\n\nTo provide a local opportunity for health sector personnel to undertake advanced and sustained analytical learning, Quantitative-Data for Decision-Making (Q4D) Lab was developed by a team of local and international public health scientists. The NGO envisions training Liberians who are working in, or aim to work in, the health sector in relevant quantitative skills. The existing course series introduces foundational coding skills in R Statistical Software (https://www.r-project.org/), followed by bivariable analysis and visualization, and ultimately multivariable regression with generalized linear models. An alternative route provides training in dynamic transmission modeling after foundational coding and statistics skills are developed. Most students engage with Q4D after learning about the program from peers who have attended classes. The student body reflects people working at the Ministry of Health, the National Public Health Institute of Liberia, international non-governmental organizations, as well as students in undergraduate and graduate public health programs or in health professions schools. The classes have nominal fees (e.g., $50USD for Beginner R class which is less than the fee of one credit hour at the local public university), making them accessible but also attaching some value to hold students accountable to attending sessions. Moreover, class sessions focus on practice versus theory to keep the content and skills grounded in actual applications in the Liberian health sector context—both the health issues facing the sector and the constraints facing those attempting to conduct research everyday.15,17\n\nBased on an understanding of the limited foundation for coding and statistics generated by current educational programs in Liberia,17 the Q4D Beginner R class assumes no working knowledge of R or Biostatistics and builds confidence and skills from the ground up. Programmatic data offers insight into students’ baseline, with students reporting ahead of the Beginner R program that they were not too confident that they could develop coding skills in R software (35% rated themselves 1 or ‘not at all confident’ out of 5 on a confidence scale, with a median ranking of 3) (Figure 1A) and that they anticipated their lack of previous analysis and coding experience would be a challenge to successfully completing the program. Thus, despite often being already employed in the health sector and having roles related to monitoring and evaluation, most students enter the Q4D program with limited computer skills and little or no prior experience with coding or statistical software (When asked if they had previously encountered a problem that needed to be solved using a spreadsheet or data analysis, nine out of ten indicated that they had and that they had been unable to solve it.). While the Q4D program was developed with this contextual understanding, no study to date has been undertaken to evaluate whether the skills taught in the program are fulfilling the goals of Q4D Lab in terms of their relevance to data and analytics needs in the health sector and their utilization outside of the classroom. Specifically, to inform programmatic growth and larger scale evaluations, it is important to gauge whether the capacity being built is being used by students in their personal and professional lives and is perceived as having impact.\n\nLegend. Panel A reflects programmatic data (not collected as part of this study) from a Beginner R course pretest on how students rated their confidence in being able to develop coding skills in R, with 1 being not at all confident and 5 being extremely confident. Panel B displays data from the Tracer Study on how students rated their confidence in independently practicing the R coding and/or Biostatistics skills they learned after participating in Q4D courses.\n\nThis paper thus aims to highlight contributions that the Q4D program has made towards quantitative analysis capacity in Liberia, specifically in the health sector. The findings offer insight into the utility and relevance of the course content for current workforce needs and reflect how the skills gained have contributed to personal or professional advancement of students to date.\n\n\nMethods\n\nA cross-sectional tracer study approach was used to collect data from students who had engaged with Q4D course content. The approach was largely descriptive and intended to understand if and how students were using skills taught in the course(s), and the perceived relevance and utility of such skills to the health sector and to students’ personal and professional growth. Outcomes of interest were thus experienced outside of the classroom, in contrast to skills assessments where performance is the outcome or process evaluations where acceptability and feasibility of program design are outcomes. Future iterations of the study would allow for more longitudinal follow up.\n\nThe Q4D office and classroom are based in Monrovia, the capital city of Liberia. Monrovia is mostly urbanized and is recognized as a center of social, economic, and political activities, with the population of Monrovia (approximately 1.74 million) representing one-third of the total population in Liberia. Most Q4D students are working in public institutions or with non-governmental organizations based in Monrovia. Many local universities, including the nation’s largest public university, are also in or near Monrovia.\n\nAt the time of data collection (June-July 2023), Q4D had enrolled 54 unique students, each attending one or more of the classes offered. Three of the students had been hired for Research Associate positions with the program and were excluded due to their professional and financial engagement with the Q4D program. The remaining 51 students were eligible to participate based on the inclusion criteria of enrollment in at least one of the Q4D courses and attendance of at least three class sessions, as some enrolled students did not complete courses due to scheduling conflicts or other factors. Q4D courses range in duration from 10 total class sessions (for Beginner class) to 16 total class sessions (for Advanced classes).\n\nA researcher-developed questionnaire was programmed into KoboCollect for electronic data collection (See Extended data). In addition to sociodemographic background questions about participants’ education level and employment status, the questionnaire included largely closed-ended questions that evaluated how often and in what ways participants are applying the skills learned during the Q4D courses, including whether they are telling, showing, and teaching the skills they learned to others. Specific examples of skills applications were solicited via open-ended questions. The questionnaire was also intended to gauge the impact that the coding and analysis skills are having on current and future professional and academic experiences of students. Particularly, information was collected on whether the skills gained contributed to career growth or other personal and professional development. Lastly, participants were asked about the impact that the capacity being built by the program could have on the health sector.\n\nAn invitation email with an attached consent form and a link to the online questionnaire was sent to each of the 51 eligible students; potential participants also received a randomly assigned 3-digit code that they were asked to enter upon indicating consent to participate. The code was used for tracking purposes to maintain confidentiality (no names or contact information were requested in the questionnaire) and for preventing follow-up communication being sent to those who already completed the questionnaire. After a week, follow-up attempts were made via email, WhatsApp and direct phone call to encourage potential participants to check their email for information about the study and consider completing the questionnaire.\n\nThe tracer study was an evaluation of the Q4D approach to capacity strengthening. To avoid potential bias in presentation of findings due to self-evaluation, data collection and data analysis procedures were conducted in collaboration with authors TOY and MKAK who were not previously involved with Q4D but who are data and statistics experts in Liberia. Additionally, eligibility criteria were set to include participants who may have dropped from classes before certification to capture perspectives of individuals who may have found the skills too challenging or inconsistent with their expectations when enrolling in the class. This was aimed to reduce bias of only including participants who successfully completed the courses and may have had more positive experiences.\n\nResponses to survey questions were summarized descriptively using frequencies and percentages. Variables of interest included demographic characteristics and employment (health sector or other), how quantitative capacity developed through Q4D programs was being told, shown, and/or taught to others, the relevance and utility of skills taught through the program, and personal and professional growth opportunities that participants attributed to their engagement with the Q4D program. All descriptive statistics and data visualization were done using R Statistical Software version 4.3.0.\n\nThe study protocol was approved by the University of Liberia IRB (ULIRB IORG-IRB Number: IRB00013730) on May 16, 2023. All study procedures were carried out according to the Declaration of Helsinki. Participants were asked to provide written consent via an online form ahead of gaining access to the questionnaire. The consent form text is included in the Extended data. All results have been presented using aggregate statistics rather than any individual participant’s response. For direct quotes on specific examples of skills applications, potentially identifying information—such as on health district where one works—was removed.\n\n\nResults\n\nA total of 43 unique participants responded to the tracer study survey, representing a response rate of 84.3% (43/51). Respondents reflected students who had attended one or more of the four courses currently offered, including the Beginner R coding class (n=40), the Biostatistics I with Intermediate R course (n=19), the Biostatistics II with Advanced R course (n=8), and the Mathematical Modeling with Advanced R class (n=3). The Beginner R class is a prerequisite for other classes unless students can demonstrate they have foundational coding skills in R. Among participants, reported rates of course completion were 80.0% (32/40) for Beginner R, 89.5% (17/19) for Biostatistics I, 87.5% (7/8) for Biostatistics II, and 33.3% (1/3) for the Mathematical Modeling course.\n\nMost participants were male (33/43, 76.7%) (Table 1). At the time of the survey, 45% of participants held a Bachelor’s degree as their highest educational attainment (19/42), while 48% indicated having a Master’s degree (20/42). One respondent is a PhD holder and another has completed a postdoctoral fellowship. More than 40% of respondents indicated being currently enrolled in a degree program (18/42, 42.9%), primarily graduate programs at the Master’s or PhD level. Nearly three-fourths of participants indicated being employed either part-time or full-time.\n\n* Data presented as n/N (%) unless otherwise indicated. For each characteristic, N excludes those who responded “Don’t know” or who chose not to answer, unless otherwise indicated.\n\n** N reflects those who are currently employed and responded to the question.\n\nMost employed participants reported working for public or governmental institutions (16/29, 55.2%), while others responded working for international non-governmental organizations (NGOs) (8/29, 27.6%), a local NGO (1/29, 3.4%), or for-profit, private sector institutions (3/29, 10.3%). Furthermore, two-thirds of those employed indicated working in the health sector (20/30, 66.7%).\n\nParticipants reported high confidence in their abilities to independently practice the skills taught during the Q4D program at work or at school. About 81% responded being “pretty confident” or “very confident” in independently practicing the skills at their job and as part of a study program, while 8% were “slightly confident” in independently applying the data analysis skills learned (Figure 1B). This reflects a shift in confidence among students in their ability to learn coding and analysis skills relative to their self-assessment at the pretest (Figure 1A).\n\nStudents reported that they are telling others about their R skills, demonstrating the skills, and/or teaching others the skills. Almost all the participants (97.6% 42/43) reported that they have shared information about the skills with friends, colleagues, employers, family members, or mentors/instructors (Figure 2). Furthermore, around 81% (35/43) have demonstrated their skills to others, and 74% (32/43) have taught the skills learned at Q4D to friends, colleagues, employers, family members, and/or mentors/instructors. When asked to rate the degree to which the skills taught at Q4D might impact decision-making within the health sector of Liberia, students indicated a median rating of 9 out of 10 (IQR: 8-10), with 10 representing ‘the highest’ level of impact.\n\nLegend. Survey participants indicated whether they had shared the skills they were learning at Q4D with different people in their lives as metrics of their excitement and confidence in the course content, as well the cascading of skills to other people not directly in the program.\n\nApproximately 83% of the participants who indicated being employed stated that they use coding and/or biostatistics skills from the classes at work (25/30, 83.3%) (Figure 3A). Among those applying the skills at work, 56% indicated that the skills were very or extremely useful, while 24% indicated the skills had been moderately or slightly useful for their current jobs (Figure 3B). For the five participants who responded that they never used the skills in their jobs, nearly all (4/5) reported that tasks that require the R and statistics skills they learned were not part of their current jobs.\n\nLegend. Participants were asked about the relevance of the skills to their current academic activities, for those who reported being enrolled in a degree program, and/or to their current jobs, for those who reported being employed (Panel A). The utility of the skills was also explored for the subset of employed participants (Panel B).\n\nThe relevance of the skills for academic programs was likewise high. For participants enrolled in degree programs, approximately 94% reported using coding and/or biostatistics skills from Q4D classes for school-related activities (17/18, 94.4%) (Figure 3A).\n\nTable 2 provides examples of how Q4D students have applied specific skills learned in the program for work or school.\n\nParticipants reported that the skills they gained were impacting them personally through increased roles and responsibilities at work (n=11), improved performance at school (n=8), and stronger thesis projects (n=11) (Figure 4). Several also attributed new opportunities to the skills they learned at Q4D. Five respondents indicated they had used the skills to acquire consultancies; four reported using the skills in their applications leading to new jobs; two others reported promotion at their current places of work. Other students mentioned that their Q4D course skills helped with scholarships or awards as well as publication of articles. Moreover, one-third of currently employed participants suggested that they had received an increase in income due to opportunities created with the new skills they acquired (10/30, 33.3%).\n\nLegend. Survey participants indicated which opportunities they attributed to their new skills gained through the Q4D program. More than one option per participant could have been selected.\n\nAs evidence for the demand created for quantitative analysis skills and their application, all but one respondent indicated interest in pursuing a job opportunity that would utilize the coding and analysis skills taught in the program (42/43, 97.7%).\n\n\nDiscussion\n\nThe findings presented here highlight how the R coding and statistics skills being taught through the Q4D program have relevance and utility to Liberians employed in health-related sectors or in the pipeline for future employment. Most of the surveyed Q4D students are confidently applying the skills they learned, and several have leveraged their new skill sets to obtain scholarships, consultancies, and promotions at work. While the present study was not a direct assessment of the skills taught (although skills evaluation is conducted as part of the courses and ahead of certification), these opportunities reflect that the capacity being built is recognized and valued by employers and/or selection committees. Moreover, our study demonstrates that students have acquired interest in quantitative research careers and that they perceive the value of quantitative research evidence for informing decision-making in the health sector. While our study is small, it offers insight into possible outcome and impact measures for assessing capacity-strengthening efforts in the quantitative sciences and lays the groundwork for larger scale evaluation as the program grows.\n\nIncreasing local buy-in for evidence-driven decision-making in health serves as a compelling case for investment in initiatives to address health workforce capacity gaps effectively.18,19 Such initiatives must be two-fold—addressing the gaps to promote evidence generation and addressing the gaps to promote evidence utilization. As ongoing efforts are being undertaken to encourage research utilization in the health workforce of Liberia,20 Q4D is focused on the former. Capacity-building to produce cadres of well-trained statisticians with awareness of and adherence to quality standards will not only enhance the available evidence base21 but also reduce the risk of erroneous research findings that have been attributed to lack of appropriately trained statisticians.22 Specifically, with increased capacity for quantitative research embedded in the health sector, analyses to assess health trends, understand factors associated with health risks, and evaluate the effectiveness of interventions will increasingly empower policymakers with rigorous evidence to make informed decisions for improved health outcomes. This result contributes to broader development objectives under the Sustainable Development Goals.23 However, it is important to note that building in-depth analytical capacity in Liberia and other sub-Saharan countries is complex and warrants ongoing evaluation of context-sensitive strategies, as we have aimed to do with our tracer study.\n\nIn resource-constrained settings, quantitative research applied to routine data has the potential to extend its value and provide meaningful evidence without requiring additional cost-intensive field- or laboratory-based work. As one barrier to regular and rigorous analysis of such data, education and training programs throughout sub-Saharan Africa lack resources to develop the human capital needed for science, technology, engineering and math (STEM) fields.24 In parallel, quantitative capacity-building efforts by development partners have tended to be directed towards technical assistance or short-term workshops not always sensitive to local constraints25,26 or aimed at contextually relevant outcomes.27\n\nTo achieve sustainable, sufficient, and well-grounded capacity in quantitative sciences, there is a clear need for improvements in fundamental STEM education across all levels.28 Accomplishing this is a paradoxical situation, as building capacity where there is a lack of it requires that there are well-equipped cadres of teachers and professors across quantitative fields.24 Until systemic changes can be affected, however, in-service training—such as that offered by Q4D programs—can boost confidence and capacity for coding and statistical analysis when it gauges, recognizes, and builds on the existing foundation of quantitative skills, regardless of how strong it is. Such medium-term, intensive in-service training that builds basic through advanced skills thus offers a model for demand-driven, locally based training in settings that may have a weak baseline for quantitative skills learning. Through the approach, initial progress can be made to contribute to a skilled health workforce that can address current and emerging health challenges effectively, as recommended by the World Health Organization.29\n\nWhile the present study suggests that the Q4D program is providing skills training in areas that are of relevance and use in students’ workplaces and/or academic programs, it was not an evaluation of the skills gained. Regular assessment is undertaken throughout the Q4D courses to ensure that students can independently demonstrate sets of pre-defined skills. One next step will be such an outcome evaluation comparing coding and analysis skills among Q4D graduates to a control group, ideally in a workplace setting. While continuing to evaluate existing efforts will be important, the present study highlights areas where the program could improve for greater impact. To promote continued opportunities for Q4D students, increased acceptance or recognition of local capacity and demand for it by health sector leadership are necessary. It has been observed that health ministries in low- and middle-income countries fail to realize their potential for knowledge transfer as learning organizations that are supportive of developing people and processes within them.30 Therefore, activities by which Q4D engages health sector leadership and increases the visibility of students’ skills applications should be undertaken. To accomplish this, Q4D can learn from other local training programs, such as the Liberia Field Epidemiology Training Program, with strong ties across the health sector. Moreover, it is important that those who have completed the program and are applying the skills receive continued support to evaluate their applications for rigor (such as by adherence to statistical guidelines and standards) and to ensure ongoing exposure to additional methods. This need for in-service mentorship to extend the impact of intensive training has been noted with other programs.31,32\n\nIn addition, it is recognized that the current programs offered at Q4D may be limited in scope, as they are focused on R Statistical Software and examples that largely reflect concepts from epidemiology. These design components were intentional—as R is free, open-source software, and it does not require a significant amount of space on personal computers, and as many of the initial cohorts of students were personally and professionally interested in epidemiology. However, future programs should reflect other skills and concepts to address the broader needs of the health sector. For instance, with the ongoing shift towards more transdisciplinary planetary health,33 the Q4D program has experienced a higher proportion of students in or aspiring to be in the environmental health, environmental science, and/or One Health sectors. As the needs and interests of the student population evolve, project topics, datasets, and examples used in class can draw from student experiences to enhance the relevance of materials and allow for more seamless application of skills in their jobs and studies. In parallel, Q4D can align itself with other organizations that provide capacity-building in One Health or complementary areas and partner with experts from local and international universities.\n\n\nConclusions\n\nIn conclusion, the Q4D program in Liberia offers quantitative skills training to a diverse student body, including a high proportion who are employed within the health sector. While students reported personal opportunities that arose with attainment of new skills, the program’s impact has potential to extend beyond individual growth, contributing to the country’s capacity for data-driven decision-making, research, and sustainable development. As Liberia continues to strengthen its capacity for quantitative analysis, the Q4D program could serve as a model for locally-relevant capacity building initiatives. Further evidence generation to assess skills acquisition and its use in the health sector with a larger sample size will be critical. Importantly, this focus on regular monitoring and evaluation of Q4D programmatic outcomes will ensure that ongoing programmatic decisions are evidence-based and nationally impactful. It will also set a precedent for other quantitative sciences capacity-strengthening initiatives in Liberia.\n\n\nAuthors’ contributions\n\nSTB and LAS developed the initial research objectives and study protocol. MKAK, TOY provided substantive feedback on the objectives and protocol. Data collection was managed by STB and GBD and monitored by TOY and MKAK. The data analysis plan was developed by STB, TOY, MKAK, and LAS and implemented by STB and LAS. STB, GDB, and LAS developed the first draft. TOY, MKAK provided substantive feedback on the draft. All authors read and approved the final manuscript.\n\n\nEthics and consent\n\nThe study protocol was approved by the University of Liberia IRB (ULIRB IORG-IRB Number: IRB00013730) on May 16, 2023. All study procedures were carried out according to the Declaration of Helsinki. Participants were asked to provide written consent via an online form ahead of gaining access to the questionnaire. The consent form text is included in the Extended data. All results have been presented using aggregate statistics rather than any individual participant’s response. For direct quotes on specific examples of skills applications, potentially identifying information—such as on health district where one works—was removed.", "appendix": "Data availability statement\n\nFigshare, Data collection tools and dataset from tracer study of Q4D Lab, a locally developed and owned coding and biostatistics program in Liberia (doi: 10.6084/m9.figshare.26762368). 34\n\nURL: https://doi.org/10.6084/m9.figshare.26762368.v2\n\nThis project contains the following underlying data:\n\n• Q4D Reduced Dataset. A deidentified subset of the full dataset is provided. Due to small sample size and the demographic questions asked, individual participants may be identifiable by those familiar with the student population, such that some background questions on sex, degree, and title of position for those employed have been removed.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nFigshare, Data collection tools and dataset from tracer study of Q4D Lab, a locally developed and owned coding and biostatistics program in Liberia (doi: 10.6084/m9.figshare.26762368). 34\n\nURL: https://doi.org/10.6084/m9.figshare.26762368.v2\n\nThis project contains the following underlying data:\n\n• Data Collection Tools. A document with the survey tool and consent form text.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nNone.\n\n\nReferences\n\nNyenswah TG, et al.: Ebola and Its Control in Liberia, 2014-2015. Emerg. Infect. Dis. 2016; 22: 169–177. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDwalu E, et al.: Trend of Lassa fever cases and factors associated with mortality in Liberia, 2016-2021: a secondary data analysis. Pan Afr. Med. J. 2024; 47: 22. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nScaling up response to curb growing MPOX outbreak in African region. World Health Organization; 2024. (Accessed: 16th August 2024). Reference Source\n\nShobayo B, et al.: Descriptive Analysis of Measles Outbreak in Liberia, 2022. IJID Regions. 2024; 10: 200–206. Publisher Full Text\n\nInternational Monetary Fund: African Dept. Liberia: Poverty Reduction and Growth Strategy; 2021.\n\nUnited Nations: Human development index. Human Development Reports. 2024. (Accessed: 16th August 2024). Reference Source\n\nMTEF Sector: Tracking development across Liberia, Liberia Project Dashboard.2024. (Accessed: 16th August 2024). Reference Source\n\nShannon FQ, et al.: Evaluation of Ebola virus disease surveillance system capability to promptly detect a new outbreak in Liberia. BMJ Glob. Health. 2023; 8: e012369. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPandey A, et al.: Strategies for containing Ebola in West Africa. Science. 2014; 346: 991–995. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFunk S, et al.: The impact of control strategies and behavioural changes on the elimination of Ebola from Lofa County, Liberia. Philos. Trans. R. Soc. Lond. Ser. B Biol. Sci. 2017; 372: 20160302. Publisher Full Text\n\nSkrip LA, Fallah MP, Bedson J, et al.: Coordinated support for local action: Modeling strategies to facilitate behavior adoption in urban-poor communities of Liberia for sustained COVID-19 suppression. Epidemics. 2021; 37: 100529. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSJR - International Science Ranking: SCImago Lab Journal & Country Rank.2023. (Accessed: 16th August 2024). Reference Source\n\nMinistry of Planning and Economic Affairs: Liberia National Capacity Development Strategy.2011.\n\nStrengthening the National Health Research Capacity builds resilience to disease epidemics. World Health Organization; 2020. (Accessed: 16th August 2024). Reference Source\n\nMosley J, Gberie L: Research and Knowledge Systems in Liberia. INASP; 2016.\n\nOgunyemi KO, Bamgboye EA, Fowotade A, et al.: Developing forecasting capacity for public health emergency management in Africa using syndemics approach: lessons from the COVID-19 pandemic. BMJ Glob. Health. 2022; 7: e010148. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKenneh H, Fayiah T, Dahn B, et al.: Barriers to conducting independent quantitative research in low-income countries: A cross-sectional study of public health graduate students in Liberia. PLoS One. 2023; 18: e0280917. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBrownson RC, Fielding JE, Green LW: Building Capacity for Evidence-Based Public Health: Reconciling the Pulls of Practice and the Push of Research. Annu. Rev. Public Health. 2018; 39: 27–53. PubMed Abstract \| Publisher Full Text\n\nOnwujekwe O, et al.: Does improving the skills of researchers and decision-makers in health policy and systems research lead to enhanced evidence-based decision making in Nigeria?-A short term evaluation. PLoS One. 2020; 15: e0238365. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBringing Research to Impact for Development, Global Engagement, and Utilization (BRIDGE-U). U.S. Agency for International Development; 2023. (Accessed: 16th August 2024). Reference Source\n\nDwivedi AK, Shukla R: Evidence-based statistical analysis and methods in biomedical research (SAMBR) checklists according to design features. Cancer Rep. 2020; 3: e1211. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKhera R, et al.: Adherence to Methodological Standards in Research Using the National Inpatient Sample. JAMA. 2017; 318: 2011–2018. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTransforming our world: The 2030 agenda for sustainable development. Department of Economic and Social Affairs, United Nations; (Accessed: 16th August 2024). Reference Source\n\nSTEM education and inequality in Africa STEM education and inequality in Africa. United Nations; 2022.\n\nMorrison MTK: Statistical Capacity Building: Case Studies and Lessons Learned. International Monetary Fund; 2005.\n\nBadiee S, Klein T, Appel D, et al.: Chapter 4. Rethinking donor support for statistical capacity building. Development Co-operation Report 2017: Data for Development. OECD; 2017.\n\nFranzen SRP, Chandler C, Lang T: Health research capacity development in low and middle income countries: reality or rhetoric? A systematic meta-narrative review of the qualitative literature. BMJ Open. 2017; 7: e012332. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKagia R: STEM education in Africa: Risk and opportunity. Brookings; 2023.\n\nWorld Health Organization: Monitoring the Building Blocks of Health Systems: A Handbook of Indicators and Their Measurement Strategies.2011.\n\nNaimoli JF, Saxena S: Realizing their potential to become learning organizations to foster health system resilience: opportunities and challenges for health ministries in low- and middle-income countries. Health Policy Plan. 2018; 33: 1083–1095. PubMed Abstract \| Publisher Full Text\n\nOronje RN, Murunga VI, Zulu EM: Strengthening capacity to use research evidence in health sector policy-making: experience from Kenya and Malawi. Health Res. Policy Syst. 2019; 17: 101. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMataya DC, Vincent K, Dougill AJ: How can we effectively build capacity to adapt to climate change? Insights from Malawi. Clim. Dev. 2020; 12: 781–790. Publisher Full Text\n\nPongsiri MJ, et al.: Planetary health: from concept to decisive action. Lancet Planet Health. 2019; 3: e402–e404. PubMed Abstract \| Publisher Full Text\n\nSkrip L, Barcon S, Davis G, et al.: Data collection tools and dataset from tracer study of Q4D Lab, a locally developed and owned coding and biostatistics program in Liberia. figshare. 2024 [cited 2024 Aug 22]. Reference Source" }	[ { "id": "321214", "date": "18 Oct 2024", "name": "Susan Michaels-Strasser", "expertise": [ "Reviewer Expertise Public Health", "Health Workforce Development", "Competency based training and education", "Epidemiology" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper presents the results of a very practical and much needed study of strengthening quantitative capacity in the health sector in under-resourced settings. It is very well written and draws meaningful conclusions that encourage scale up of the existing Q4D efforts as well as further and more robust evaluation of the impact of the program.\n\nI responded partly to one question above due to the following issues which should be easily addressed by the authors.\n\n1. Figure 1. Please make it clearer why this figure is limited to students who did the Beginner R course only. I am not clear why you limit this figure to just them given that you run 4 courses. Is Panel B related only to the Beginner R students. If yes, then make this clear in the figure's title. 2. Minor issue. Page 6 paragraph 2, the statistic 16/29 (55.2%) is correct but is listed as 55.3% in the table. To avoid confusion maybe just use whole numbers in the table. 3. Page 7, paragraph 3. and onto page 8. The discussion of Figure 3B needs to be edited. You can that 24% indicated the skills had been moderately or slightly useful but the figure actually shows this total 40%. moderately useful (16%) and slightly useful (24%)\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-988
https://f1000research.com/articles/13-494/v1	17 May 24	{ "type": "Research Article", "title": "Combined exosome of adipose-derived mesenchymal stem cell and hyaluronic acid delays early osteoarthritis progression of ovine sheep model: Clinical, radiographic and macroscopic evaluation", "authors": [ "Ludwig Andribert Powantia Pontoh", "Jessica Fiolin", "Ismail Hadisoebroto Dilogo", "Marcel Prasetyo", "Radiana Dhewayani Antarianto", "Alida Harahap", "Angela Jennifer Tantry", "Trevino Aristakus Pakasi", "Bambang Pontjo Priosoeryanto", "Tri Isyani Tungga Dewi", "Jessica Fiolin", "Ismail Hadisoebroto Dilogo", "Marcel Prasetyo", "Radiana Dhewayani Antarianto", "Alida Harahap", "Angela Jennifer Tantry", "Trevino Aristakus Pakasi", "Bambang Pontjo Priosoeryanto", "Tri Isyani Tungga Dewi" ], "abstract": "Background Current treatment of osteoarthritis (OA) mainly focused on treating symptoms. Exosome from Adipose-derived Mesenchymal Stem Cell (Ad-MSC) have been shown to delay degenerative process. This study aimed to investigate the clinical, radiological and histological impact of combined intra-articular (IA) hyaluronic acid (HA) and exosome Ad-MSCs in-vivo using a larger animal model with low-grade OA.\n\nMethods Eighteen male Ovies aries sheep underwent total lateral meniscectomy and conventional radiography was performed to confirm low-grade OA after 6 weeks. The sheep were divided into three groups, Group 1 (G1; n=6) received thrice exosome injections, G2 (n=6) received twice HA injection, and G3 (n=6) received both treatments with a 1-week interval after 10 days of meniscectomy. Clinical evaluations were conducted using the Clinical Lameness Score (CLS), radiographic with X-ray using OA score by Innes et al, while macroscopic evaluation by Osteoarthritis Research Society International (OARSI) scores.\n\nResults Lameness parameter scored lowest in G3 significantly (2.0±0.0 VS 2.7±0.52 VS 2.7±0.52; p=0.024) at the second month although the overall CLS score did not significantly differ at the 3rd month. The best improvement of conventional total OA radiographic score at the 3rd month compared to all groups (5.2±1.17 vs 6.3±0.82 vs 6.7±1.03; p=0.053). Macroscopic OARSI evaluation showed no difference (p=0.711).\n\nConclusions Combined repeated exosome Ad-MSC and HA IA injection proven to delay OA progression, however longer duration of follow up is required to evaluate its long-term effect.", "keywords": [ "exosome", "adipose-derived Mesenchymal Stem Cell (Ad-MSC)", "early osteoarthritis (OA)", "clinical lameness score", "radiographic OA score", "Osteoarthritis Research Society International (OARSI) score" ], "content": "Introduction\n\nOne of the most common degenerative joint diseases that place a significant socioeconomic burden on society worldwide is knee osteoarthritis (KOA).1 However, no effective treatment can stop osteoarthritis’ (OA) increasing cartilage deterioration. The current cornerstone of OA therapy continues to focus on providing momentary symptomatic alleviation.2 Even though the present knee replacement operation for end-stage OA is regarded as the most successful procedure of the century, many patients continue to weigh the cost, risk, and complications of such significant surgery.2\n\nResearch on the chondrogenic potential of mesenchymal stem cells (MSC) has been focused primarily on recent developments in regenerative orthobiologic therapy.3,4 Recent research, however, indicated that exosomes and other trophic factors were primarily responsible for the potency of MSC.5–7 Additionally, despite being promising, the use of MSC for OA treatment has several disadvantages, including ethical concerns, genetic instability, immunological reactions to transplanted cells, challenges with mass production and storage, and cost effectiveness. On the other hand, exosomes have many benefits over MSCs, such as a superior safety profile with fewer side effects, a lower immunogenicity reaction, the capacity to penetrate barriers that MSCs cannot, an easier mass production and storage process at a lower cost, and fewer ethical concerns.8,9\n\nExosomes are nanosized extra vesicles with 50–150 nm diameter that are secreted by MSCs and contain nucleic acids, functional proteins, and bioactive lipids. Their duties include controlling immune responses, decreasing inflammation, and healing damaged tissues. Exosome isolation from several MSC sources has been described.6 However, compared to bone marrow-derived MSC (BMMSC) and synovial MSC (SMSC) derived exosomes, adipose-derived MSC (ADMSC)-derived exosomes have shown a remarkable potential to stimulate cartilage and bone regeneration. Exosomes and microvesicles produced by ADMSCs can regulate focal adhesion, extracellular matrix (ECM)-receptor interaction, actin cytoskeleton, cAMP, and PI3-Akt signaling pathways, which can correct aberrant osteoblast metabolism and promote cartilage and bone regeneration.10\n\nHyaluronic acid (HA) is a crucial part of the synovial fluid that cushions and protects joint cartilage. The knee joint’s HA maintains a steady concentration and enough viscosity. Reduced HA concentration brought on by OA exacerbates knee cartilage damage. Further, HA can encourage cell migration and it is advised to administer repeated HA injections for knee joint disease. Additionally, several clinical trials have shown that HA can lessen OA patients’ pain.11–14\n\nClinical, radiological, and macroscopic examinations can be used to evaluate the efficacy of combined exosome-HA therapy. To assess the course of OA in animals, several radiological scoring systems, such as those created by Innes et al. in 2004,15 have been devised. While waiting for treatment to take effect, macroscopic analysis can be utilized to determine how badly damaged the cartilage has become.16 Sheep and humans are comparable in size, biomechanics, and joint structure. Because of these similarities, sheep were a useful animal model for studying cartilage macroscopic processes in orthopaedic investigations.17\n\nThe clinical impact of combined intraarticular HA and exosome-derived ADMSC in vivo on a bigger animal model with low-grade OA has never been studied so far. This investigation aims to assess the clinical, radiological and macroscopic effects of combined hyaluronic acid and intra-articular ADMSC-derived exosomes in the ovine early OA model.\n\n\nMethods\n\nThe study protocol was approved by the institutional review board no. KET-932/UN2.F1/ETIK/PPM.00.02/2022. The animal studies were performed after receiving approval from the Institutional Animal Care and Use Committee (IACUC) in the School of Veterinary Medicine and Biomedical Sciences at Institut Pertanian Bogor (IPB) University number 023/KEH/SKE/IX/2022 from the obtained for this work. All procedures and protocols, encompassing the research question, design, and analysis strategy, were executed in adherence to the ARRIVE guidelines.\n\nAll animals underwent a one-week adaptation with a vaccination and health check-up protocol. The sheep were kept in six paddocks, 3 in each, with stone yards for resting, and were also fed concentrate, hay, and mineral salt. Ad libitum water was supplied in man-made drinking troughs. Before each medical procedure that require operative procedure, we performed anesthesia to ameliorate any suffering of the animals.\n\nWe calculated the sample size using resource equation and the equation showed that a minimum of 5 sheep need to be allocated in each group. Thus, we included a total of 18 Ovies aries for this study. Inclusion criteria include males, age ≥ 3 years old, weight 25-30 kg, and skeletal maturity. Exclusion criteria include musculoskeletal abnormalities, death, infection, and cartilage defects prior to meniscectomy. Ten days after meniscectomy, the dressing was opened, and the wound had perfectly healed, so rehabilitation was started. For two weeks, the ovines were trained to walk for 150 meters on an asphalt surface each day.\n\nA total of 18 Ovies aries sheep received lateral meniscectomy at the stifle joint of the right hind limb following the procedure mentioned in the previous study.18 Two veterinarians performed the meniscectomy procedure. Amoxicillin 5 mg/kg and atropine sulfate 0.15 mg/kg were administered intramuscularly and subcutaneously before the surgery. Ketamine 22 mg/kg and xylazine 0.20 mg/kg were administered intramuscularly for the anesthesia.\n\nSix weeks after the meniscectomy, conventional radiography was performed to confirm low-grade OA, and then the sheep were divided into three groups. One medical doctor responsible for the randomization procedure. The first group (G1; n = 6) received thrice 1 mL of intra-articular exosome Ad-MSC injection at the sixth, seventh, and eighth week after meniscectomy; the second group (G2; n = 6) received twice (sixth and seventh week after meniscectomy) intraarticular injection of 1 mL hyaluronic acid (Durolane™), which is a high-viscosity hyaluronic acid (HA) containing 20 mg of sodium hyaluronate, while the third group (G3; n = 6) received combination of both with the interval of one week for each injection (HA at the 6th, 7th, and 8th; while exosome at the 6th and 7th). The Ad-MSC exosome was prepared using the protocol mentioned in the previous study.19\n\nEach subject was euthanized at the end of the 12th week after the radiological evaluation. Before the sacrifice, the anesthesia procedure was the same as the meniscectomy procedure. The euthanasia procedure involves dissecting the sheep’s carotid artery until the sheep bled to death. The joint that received the intervention and the contralateral were harvested for evaluation.\n\nClinical, radiological, and macroscopic observation was performed 12 weeks after injection to evaluate the outcome. Two veterinarians recorded the severity of clinical signs monthly using the clinical lameness score by Nganvongpanit et al. At the same time, one radiologist and one orthopaedic surgeon evaluated the conventional radiographic score by Innes et al. The macroscopic evaluation was performed after the sheep were sacrificed in the 12th week using the OARSI score performed by two orthopaedic surgeons. The mean value of each score was obtained and analyzed using SPSS for Mac.\n\nThe effectiveness of the therapy was evaluated using a clinical grading system that evaluated the individual animal’s lameness, palpable discomfort, and ability to support its weight (Table 1). Two vets assessed the sheeps’ lameness by having them walk and trot 6 meters three times. Palpation of the stifle joint was then performed to assess discomfort and determine joint mobility. Two veterinarians, separated by thirty minutes, conducted the palpation. Following surgery, this assessment was done each month from 10 days, one month, two months, and three months post meniscectomy.\n\nBefore the meniscectomy, six weeks, and 12 weeks after the meniscectomy, radiographic examinations were conducted using a high-resolution film screen combination using the POX-100BT by POSKOM, Gyeonggi, Seoul, Korea, and viewed using the VetDROC application by Insan Teknotama Bersahaja. Radiological evaluation was evaluated using conventional radiographic OA score for stifle joints by Innes et al.15 Parametes that evaluated using radiographic OA score for stifle joints by Innes et al. includes gloval score for overall disease severity, joint effusion, osteophytosis, intra-articular mineralization, and tibial subchondral sclerosis. The breakdown of how to score each parameter can be seen in Table 2. The total mean score was used for evaluation. The results are evaluated and scored twice by one orthopedic surgeon and radiologist. The hindlimb stifles joint procedure executes mediolateral and craniocaudal projections of the stifle joints for each sample. In order to achieve a position that appeared to be “weight-bearing” for the craniocaudal projection, the sheep were kept in the “sitting” position. The ovine was placed in lateral decubitus for mediolateral projection, with the contralateral limb held away from the film. Using the craniocaudal and mediolateral hindlimb stifle protocols, Insan Teknotama Bersahaja processed all of the results using the VetDROC application.\n\nThe specimens of the knee joints were sacrificed before macroscopic and microscopic evaluation using the Osteoarthritis Research Society International (OARSI) score.16 The total gross deterioration of the entire articular surface is taken into account by the OARSI scoring system for macroscopic pathology, which evaluates the cartilage, osteophyte, and synovial membrane.16 Macroscopic evaluations were performed at the lateral femoral condyle, lateral tibial plateau, trochlear groove, and patellar region. The visual assessment was performed twice within a one-week interval. Before the examination, macroscopic specimen images were randomized by a general practitioner assistant unaware of the specimen sample codes. Each component for OARSI macroscopic evaluation was presented in Table 3.\n\nAll data was presented descriptively using mean ± SD. Comparison treatment results of each group were analysed using a multivariate ANOVA test with statistically significant results using p < 0.05.\n\n\nResults\n\nFrom 18 sheep that were performed total lateral meniscectomy at the right hind limb’s stifle joint, all wounds were completely healed within ten days. There were no side effects after intra-articular injection for the whole group, such as infection, swelling, or death. The mean weight of all sheep was 28.61 ± 5.48; G1 was 29.33 ± 6.06; G2 was 28.00 ± 5.48; and G3 was 25.50 ± 2.59, with p = 0.184, which was statistically not significant.\n\nAll parameters of CLS between groups statistically decreased significantly from day 10, 1st month, second month, and third month after meniscectomy (p < 0.0001) (Table 4). However, there were no significant differences in this decrease between groups. The lameness parameter scored lowest in G3 compared to other groups significantly on the second month (2.0±0.0 VS 2.7±0.52 VS 2.7±0.52); however it did not differ in the following months.\n\n* Data presented in mean ± SD.\n\n** statistically significant result with p value < 0.005.\n\nRadiologic score was increased 18 weeks vs 6 weeks after meniscectomy in the G1 and G2, but decreased although not significantly in the G3. The combination group (G3) followed with G1 and G2, had the lowest total OA radiographic score compared to all groups (5.2±1.17 vs 6.3±0.82 vs 6.7±1.03), p = 0.053. Each group representative for radiological evaluation can be seen in Figure 1.\n\nGlobal severity in G1 and G2 increased but not in G3, and this result was statistically significant (p = 0.024). Meanwhile, effusion score in the 18th week reduced significantly in all groups. In contrast, global severity of the disease, osteophyte, and sclerosis score tend to increase, except in G3, where global severity and sclerosis remained the same (Table 5).\n\n* Data presented in mean ± SD.\n\n** statistically significant result with p value < 0.005.\n\nMean macroscopic OARSI score evaluation showed no significant differences between groups (G1 9.17 ± 2.32 vs G2 9.83 ± 0.41 vs G3 9.33 ± 0.82); p = 0.711 (Table 6). Each group representative for macroscopic finding can be seen in Figure 2.\n\n* Data presented in mean ± SD.\n\n** Statistically significant result with p value < 0.005.\n\n\nDiscussion\n\nThe most significant finding in this study arises from the clinical, radiological, and macroscopic results. The combined repeated intra-articular injection of exosome Ad-MSC and HA demonstrates superior efficacy in significantly delaying the progression of early OA compared to exosome Ad-MSC alone or HA alone.\n\nWe evaluated the clinical signs and symptoms using a Clinical Lameness Score (CLS) on the 10th day, first month, second month, and third month post-operatively. On the 10th day after meniscectomy surgery, all sheep exhibited marked pain and moderate lameness with partial weight-bearing, without significant differences between groups, attributed to post-surgery pain. By the first month, there was a notable improvement in clinical symptoms, with most sheep displaying limping during walking, moderate pain, and partial weight-bearing when standing and walking. Up to this point, no significant differences were observed, reflecting the initial stages of soft tissue healing. However, in the second month, a clinically significant difference in lameness scores emerged, particularly in G3 compared to G2 and G1 (2.0 ± 0.00 vs. 2.7 ± 0.52 vs. 2.7 ± 0.52; p = 0.022). Meanwhile, other parameters, such as pain and weight-bearing scores, generally decreased over time.\n\nThe problem with cartilage healing lies in its limited ability to heal, attributed to its characteristics as a differentiated tissue with a densely structured extracellular matrix (ECM), avascular, aneural, and alymphatic properties. Therefore, current orthobiologic studies primarily focus on regenerative biological therapy that can, at least, halt and, ideally, reduce the progression of OA.12\n\nThe existing evidence suggests that intra-articular administration of MSCs is effective in osteoarthritis treatment. However, there are notable limitations associated with MSC transplantation, including encompassing ethical concerns, the culture process, and production costs, which the metabolite products of MSCs have further elucidated. Ex-vivo tests have indicated that cultivated MSCs exhibit cytotoxicity to osteoarthritic synovial fluid.8 The MSC secretome contains bioactive signals, growth factors, and extracellular matrix (ECM) molecules, with growth factors supporting chondrogenesis. Numerous studies have demonstrated the protective effects of exosomes in osteoarthritis animal models.3,21 Additionally, higher levels of chondrogenic markers, such as β-catenin and collagen type II, indicate their role in promoting chondrogenesis.22 Recent research by Pye et al., 2022, has explored the progression of canine osteoarthritis, proposing treatment with biologically active signaling molecules found in EVs derived from MSCs.23\n\nRepeated intraarticular injection of HA has been proven to delay human OA progression.13,14 Our previous study has proven that twice HA injections at one-week intervals are enough to create the protective effect of OA since thrice injections showed no significant result in short-term follow-up (3 months). This study showed that the combination of HA and exosome injection showed the slowest increase in global severity of disease compared to exosome alone or HA alone in the third month (1.7±0.52 vs. 2.5±0.55 vs. 2.5±0.55; p = 0.024). However, the effusion parameter was most marked in the G1 vs. G2 and G3 (1.0±0.0 vs. 1.5±0.55 vs. 1.7±0.52; p = 0.046). This could be due to the side effect of HA injection, which was creating slight knee swelling, while the exosome has an anti-inflammatory effect and reduced effusion. When co-cultured with activated synovial fibroblasts, exosomes isolated from adipose-derived MSCs upregulated the expression of the anti-inflammatory cytokine IL-10 and downregulated the pro-inflammatory markers such as IL-6, tumor necrosis factor- (TNF-), and nuclear factor kappa B (NF-κB) (Zhao et al., 2020).24\n\nLubis et al., 2023 showed that compared to hyaluronic acid, intra-articular injection of secretome is beneficial in treating early-stage osteoarthritis in animal models.18 However, this study did not evaluate the combination of effects while the secretome injected was only once. Although the cause of sodium hyaluronate’s ability to reduce pain is not fully known, it may be related to how it affects nerve impulses and sensitivity.25 A decrease in the sensitivity to mechanical stresses of stretch-activated channels found in the membrane of joint mechanonociceptors is correlated with sodium hyaluronate’s analgesic action.26\n\nThe impact of sodium hyaluronate on substance P, a tiny peptide involved in pain signal transmission, represents a potential mechanism through which the compound may alleviate pain. It has been demonstrated that sodium hyaluronate inhibits substance P’s induction of enhanced vascular permeability. Additionally, a previous review27 highlighted that sodium hyaluronate significantly influences inflammatory mediators, including prostaglandin E2 (PGE2) and leukotriene levels, tumor necrosis factor-α (TNF-α) production, arachidonic acid release, and nitric oxide (NO) production. Lowering these inflammatory mediators may reduce pain in individuals who receive sodium hyaluronate injections.\n\nOur study demonstrated that the combination of AD-MSCs exosomes and HA injections resulted in the best outcome, as indicated by the lowest OARSI score compared to other treatment groups. The group treated with only HA injections also exhibited a low mean OARSI score. However, unlike the exosomes and HA-treated group, cartilage improvement varied between subjects in the group treated with HA alone. Treatment in this group resulted in a variable cartilage surface structure with erosion observed in some subjects. On the other hand, combined treatment with HA and exosome yielded similar results across all subjects in this group. Meanwhile, the worst OARSI score was obtained by the group treated with exosomes only. Cartilage surface erosion in all subjects is a prominent difference observed in this group compared to other groups.\n\nA previous study by Salamanna et al. (2019: 872) showed that HA injections were able to improve repair and protect cartilage by inhibiting MMP-3 and MMP-13.11 Cartilage repair by treatment using HA alone was also observed in the study by Wong et al. (2020: 2226)3 using rabbit osteochondral defect model. However, the repair was not sustainable as the gross observation scores worsened after six weeks of observation. This previous study also found that a combination of MSC exosomes and HA resulted in a sustainable cartilage repair, which was shown by improvements in gross observation scores. This finding is in line with our study, which demonstrated better outcomes from the exosomes and HA combination-treated group than those treated with HA alone. However, the previous study used human embryonic stem cell-derived MSC exosomes, whereas AD-MSCs exosomes were used in our study. Exosomes of AD-MSCs have been described to be able to support cell migration, proliferation, and chondrogenic differentiation better than exosomes from bone marrow MSCs or synovium MSCs (Li et al. 2021: 253). Moreover, AD-MSCs are more accesible to harvest, such as through subcutaneous lipoaspiration, and have fewer ethical issues compared to human embryonic stem cells (Miana & González 2018: 2).28\n\nOur study also found that the group treated with exosomes had the worst outcome compared to other groups. A possible explanation of these findings could be that AD-MSCs exosomes require HA to inhibit cartilage degradation while the exosomes stimulate cell migration, proliferation, differentiation, and matrix synthesis (Li et al. 2021: 259).21 Nevertheless, HA alone is also found to be not sufficient as it requires exosomes to result in sustainable cartilage improvement (Wong et al. 2020: 2226).3\n\nThe main limitation of this study was no control group due to financial limitations. However, we include groups treated with HA and exosome as a direct comparison with the experimented group. Other limitations includes longer follow-ups needed to further evaluate the long-term outcomes and side effects of the treatment. Nevertheless, until the end of the research, there were no significant side effects observed in the treated groups.\n\nIn conclusion, intra-articular injection of combined exosome Ad-MSC and HA with an interval of 1 week is proven to delay the progression of OA clinically, radiologically, and macroscopically between 3 months. However, a longer follow-up duration is required to evaluate the longer-term effect.\n\n\nEthics and consent\n\nThe institutional review board from Fakultas Kedokteran Universitas Indonesia approved the study protocol, with reference number KET-932/UN2.F1/ETIK/PPM.00.02/2022. We performed the animal studies after receiving approval from the Institutional Animal Care and Use Committee (IACUC) in the School of Veterinary Medicine and Biomedical Sciences at Institut Pertanian Bogor (IPB) University, with reference number 032/KEH/SKE/IX/2022.", "appendix": "Data availability\n\nFigshare: SPSS Data for ‘Combined Exosome of Adipose-Derived Mesenchymal Stem Cell and Hyaluronic Acid Delays Early Osteoarthritis Progression of Ovine Sheep Model: Clinical, Radiographic and Macroscopic Evaluation’, https://www.doi.org/10.6084/m9.figshare.25010012. 29\n\nFigshare: ARRIVE checklist for ‘Combined exosome of adipose-derived mesenchymal stem cell and hyaluronic acid delays early osteoarthritis progression of ovine sheep model: Clinical, radiographic and macroscopic evaluation’, https://www.doi.org/10.6084/m9.figshare.25487206. 30\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nPrimorac D, Molnar V, Rod E, et al.: Knee osteoarthritis: A review of pathogenesis and state-of-the-art non-operative therapeutic considerations. 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Publisher Full Text\n\nMoreland LW: Intra-articular hyaluronan (hyaluronic acid) and hylans for the treatment of osteoarthritis: Mechanisms of action. Arthritis Res. Ther. 2003; 5: 54–67. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMiana VV, Prieto González EA: Adipose tissue stem cells in regenerative medicine. Ecancermedicalscience. 2018; 12: 822. Publisher Full Text\n\nPontoh LAP, Fiolin J, Dilogo IH, et al.: SPSS data for “Combined exosome of Adipos-derived mesenchymal stem cell and hyaluronic acid delays early Osteoarthritis progression of Ovine sheep model: Clinical, radiographic, and macroscopic evaluation”. [Dataset]. figshare. 2024. Publisher Full Text\n\nPontoh LAP, Fiolin J, Dilogo IH, et al.: ARRIVE guideline checklist for “Combined exosome Adipose-derived mesenchymal stem cell and hyaluronic acid delays early Osteoarthritis progression of Ovine sheep model: Clinical, radiographic, and macroscopic evaluation”. figshare. 2024. Publisher Full Text" }	[ { "id": "282028", "date": "12 Jun 2024", "name": "Jiao Jiao Li", "expertise": [ "Reviewer Expertise Regenerative medicine", "osteoarthritis", "stem cells/MSCs", "extracellular vesicles", "animal models" ], "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 was a brief study on treating osteoarthritis (OA) in an ovine model over 3 months, using adipose MSC-derived extracellular vesicles (EVs), hyaluronic acid, or a combination of the two. The analysis was not extensive and would have benefitted from a longer follow-up as well as control groups, which have been identified as limitations. The value of the study lies in that it is one of the first in the field of testing MSC-EVs in animal models of OA to have used a large animal model (sheep) that would be physiologically representative of human joints and OA disease. The reported lack of a significant improvement over 3 months generally in all of the tested groups is also of value to the field, considering the positive outcomes seen so far in small animals using similar treatment approaches, and highlight the possible challenges in translating an EV-based approach to human OA therapy. More specific comments are provided below. - It is suggested to better capture the current status of literature using MSC-derived EVs to treat OA in preclinical models. A sizeable number of studies have been published on this topic, as reflected in recent reviews (Ref1,2,3). Although studies in large animals such as sheep are severely lacking, which gives value to the current study, the background literature and current understanding on the topic should be properly acknowledged in the introduction. - It is critical to include the method for isolating and characterising exosomes used for in vivo injection, even if this has been reported previously (ref 19 was cited) – because this is a fundamental aspect of the study. It is necessary to at minimum state the cell source for deriving exosomes, isolation process, and methods of characterisation in accordance with MISEV recommendations (e.g., western blot, nanoparticle tracking analysis, electron microscopy). Moreover, there needs to be a clear statement on the dose of EVs used for in vivo injection (e.g., in particles/mL or amount of protein/mL), and a justification for why this dosage was chosen considering the size of the animal/joint. - Following from the above comment, the characterisation data of EVs used for injection need to be reported. At minimum, the study needs to demonstrate that actual EVs were injected (rather than other possibilities e.g., secretome or proteins from the conditioned medium), and the size range/distribution of EVs. - It is a limitation that the study groups did not include a MSC injection control with the same number of cells that theoretically provided the dose of EVs. This was alluded to in the limitations as the absence of control groups, but it is recommended to specifically identify the lack of a MSCs-only control (alongside also the lack of an untreated control). Moreover, it would have been interesting to see the histological findings from explanted joints of different groups. The absence of these results for whatever reason should be discussed and identified as one of the limitations.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "306509", "date": "10 Aug 2024", "name": "Asma Abdullah Nurul", "expertise": [ "Reviewer Expertise Regenerative medicine", "tissue engineering", "stem cell" ], "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 describes the effects of combination of exosome derived from adipose mesenchymal stem cell and hyaluronic acid delays in early osteoarthritis ovine sheep model. The submitted manuscript is not well-written and should be rewritten based on the comments below: - Preparation of exosome and how the dosage was determined should be explained in the method. - Normal and control groups must be included in the study. - Considering that the experiment conducted on the animal model is invasive and extensive, I believe this study should incorporate additional technical analyses, such as microCT or MRI evaluations, along with histological analyses. - Radiographic and macroscopic result requires detailed explanation and comparison between the study groups. - The overall manuscript requires rewrite and English check.\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?\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? No", "responses": [ { "c_id": "12212", "date": "02 Sep 2024", "name": "Ludwig Andribert Powantia Pontoh", "role": "Author Response", "response": "Reviewer comment: The manuscript describes the effects of combination of exosome derived from adipose mesenchymal stem cell and hyaluronic acid delays in early osteoarthritis ovine sheep model. The submitted manuscript is not well-written and should be rewritten based on the comments below: - Preparation of exosome and how the dosage was determined should be explained in the method. Author response: A previous study have been published explaining detailed step-by-step technique used to produce the exosome from adipose MSC and cited in this study. However brief summary on exosome production has been added in the text. Reviewer comment: Normal and control groups must be included in the study. Author response: Hyaluronic acid has been regarded as the current standard of therapy for moderate osteoarthritis for over than 3 decades that benefit well in delaying the need of arthroplasty. In this study we regard the HA group as the control group as we have obviously understand that total meniscectomy procedure that we performed will create progressive OA hence needed treatment. On the other hand, we have also performed preliminary study that evaluated the effect of control group with normal saline injection, each 1-3 times injection of HA and exosome to evaluate the preliminary outcome of those groups and showed normal saline group consistently showed worst outcome in all parameter. Hence in this study we only evaluated the group with best outcome and regard the HA group as the control group. Reviewer comment: Considering that the experiment conducted on the animal model is invasive and extensive, I believe this study should incorporate additional technical analyses, such as microCT or MRI evaluations, along with histological analyses. Author response: We have also performed MRI evaluations with T2 map value analysis that has been published at another paper cited in this study and histological analysis outcome that has been added in this study in the edited version. Reviewer comment: Radiographic and macroscopic result requires detailed explanation and comparison between the study groups. Author response: a newer version of this study has been updated to elaborate the results between study groups. Reviewer comment: The overall manuscript requires rewrite and English check." } ] } ]	1	https://f1000research.com/articles/13-494
https://f1000research.com/articles/13-987/v1	02 Sep 24	{ "type": "Review", "title": "The emergence of a modern paradigm for urban health", "authors": [ "Marcus Grant", "Evelyne de Leeuw", "Waleska Teixeira Caiaffa", "Jo Ivey Boufford", "Carlos Dora", "Susan Parnell", "Evelyne de Leeuw", "Waleska Teixeira Caiaffa", "Jo Ivey Boufford", "Carlos Dora", "Susan Parnell" ], "abstract": "The importance of urban health in achieving global and planetary health goals is increasingly recognized. Cities offer important opportunities to improve health while also presenting significant challenges. As our understanding of and evidence for the importance of determinants of health beyond health care have grown, the need for urban health policies and actions that transcend disciplinary and sectoral boundaries and involve multiple stakeholders in urban decision-making has become clearer. Current urban health practice builds on decades of conceptual and operational work. This paper traces the evolution of the urban health paradigm through research, policy and practice in recent decades. We suggest that, despite the proven utility of urban health as a paradigm and its conceptual and practical evolution for effective urban health governance, significant challenges remain, especially related to implementing the systems approaches needed to improve health amidst the complexity of urban dynamics.", "keywords": [ "Urban health", "health policy", "Health in All Policies", "determinants of health" ], "content": "1. Key messages\n\n\n\n• The modern paradigm of urban health has evolved with a strengthening evidence base, deeper understanding of the wider determinants of health in towns and cities, and a recognition that effective action requires a multi-sectoral systems approach.\n\n• Access to the highest attainable standard of health has come to be recognised as a right of urban residents. This implies not only access to health care services, but also a role for government, the private sector and civil society in co-creating healthy social, physical and economic environments.\n\n• Conceptually, urban health has shifted from a predominantly biomedical focus to a settings-based approach that recognizes the multi-sectoral, systemic nature of challenges to human and planetary health, and as such, also the critical nature of decisions by actors outside the medical sphere.\n\n• Contemporary approaches to urban health increasingly recognize health equity as a core challenge for effective action to advance urban health.\n\n• Understanding of how to tackle urban health has moved beyond merely addressing environmental ‘bads’, such as pollution and specific agents of disease, to prioritizing a systems approach that encompasses complexity and focusses on the ‘causes of the causes’ of ill-health.\n\n• WHO has been a thought leader and active partner in developing the modern paradigm of urban health, contributing to international policy milestones and providing local and national stakeholders with technical guidance and a global evidence-base, including case studies of effective action.\n\n• Support for the new approach to urban health has spread rapidly across academia in the past decade, encompassing both research and education, and including non-medical professions. This can be seen in both academic publishing and major thematic funding streams.\n\n• Although all urban health action must be adapted for local conditions and stakeholders, policies and programs that have proven to be effective in one urban setting can with care offer insights for a wide range of cities.\n\n• Place-based interventions in key urban policy areas—both within and beyond the health sector—increasingly recognize health and health equity as critical considerations.\n\n• Political leadership, sponsorship, and support at both national and city levels—and often through city networks—is crucial for successful implementation of action for urban health and health equity.\n\n• As a host of global pressures bring into focus the vulnerability of human existence on this planet, the new urban health paradigm continues to evolve, as does its fundamental role in securing health.\n\n\n2. Introduction and background\n\nUrban health, as a both a concept and a goal, has grown in prominence with increasing urbanization and urban influence over the last century. As the total urban population has continued to expand through urbanisation and urban growth, ever more people have been exposed to urban environments, with direct consequences for health and health equity. This has provided a critical impetus for the emergence of a widespread community of interest for urban health.\n\nThe urban milieu also continues to evolve. The largest cities in the world today lie mainly in relatively poor countries, a departure from historical experience—in the past, the largest cities were typically found in the richest places. By 2030, the UN projects close to 400 one-million-resident cities in developing countries, versus only 250 in developed nations (UN, 2000). Poor mega-cities continue to grow in size, with poverty contributing to high population growth, and yet, economic dynamics deny them the city-level wealth required to address emergent risks to health (Jedwab and Vollrath, 2015). The reality, at an urban neighbourhood level, is that without more comprehensive planning and management of cities, the number of people in the global south living in shanty towns, informal settlements and slums—and facing corresponding health challenges—will continue to grow. The modern urban context requires fresh thinking about how best to maximise urban health and wellbeing.\n\nIn fact, as a concept and a practice, and through the accumulation of evidence from research, ideas about urban health have evolved substantially over the past century. Urban health challenges are now recognized to be profoundly influenced by systemic upstream determinants, which can be structural, cultural, technical and/or economic/commercial. Such determinants include broader societal ills: profligate patterns of resource use rooted in commercial drivers, vast power disparities and a lack of accountability, deep-seated resource inequalities, and authoritarianism and other challenges to good democratic functioning. The spatial form of urban places, planned and designed during a period of abundant and carefree fossil fuel use, has also locked many urban dwellers into situations where the patterns of daily life can be damaging to their health and those around them. In addition, geopolitical conflicts can also exert a profound influence on health risks in urban areas. In short, the nature of the urban health challenge has both enduring and new dimensions.\n\nInterest in, and understanding of, urban health has spread over time and across many domains—one measure of the current prominence of this area was the inclusion, for the first time ever, of a subnational goal for global action on sustainable cities and communities (Goal 11) in the Sustainable Development Goals (SDGs) (Dora et al., 2015). Although health is not mentioned overtly in SDG11, many of its components are, in fact, determinants of health. Importantly, this includes policy areas often deemed to be outside the spectrum of health activity, such as transport, urban planning, urban food, neighbourhood design, local resilience, energy infrastructure, flood management and biodiversity and climate. Decision-making in each of these sectors can have a profound influence, either positive or negative, on the conditions needed to promote health and health equity. Moreover, through an emphasis on evidence-informed decision-making, urban health has become a platform that can catalyse bridges across such important but seemingly disparate urban policy areas (Ramirez-Rubio et al., 2019). This paper shows how understanding the factors that led to the emergence of the contemporary paradigm of urban health can help foster integrated action to serve the goals of health and sustainable development more broadly. It tracks this emergence from the broad legal and global institutional developments of the mid-to-late 20th century through to the emergence of the 2030 Agenda for Sustainable Development. Urban health in the 2030 Agenda is covered in depth in another paper in this collection (Espey et al., 2024).\n\n\n3. Conceptual developments in health and their translation to the urban context\n\nThe history of thinking about urban health goes back to the earliest human settlements, but the issue really surfaced as a professional concern during the urban expansion, and related challenges to health, associated with the Industrial Revolution (de Leeuw, 2017). Here, we review the contemporary conceptual and institutional framework for urban health that emerged beginning in the latter decades of the 20th century, leading up to but not including the phase immediately prior to the adoption of the 2030 Agenda for Sustainable Development.\n\nThe WHO Constitution (1948) marked the first international and legal articulation of a universal right to health. It advocated for ‘… the highest attainable standard of health as a fundamental right of every human being,’ a right that was subsequently embedded in many other international declarations. Developed in a succession of UN documents and commentaries, the right to health is highly nuanced and does not equate merely to provision of state health care services. In fact, the evolution of the modern concept of urban health has drawn on the definition of health embodied the WHO constitution, which states that:\n\nHealth is a state of complete physical, mental, and social well-being and not merely the absence of disease or infirmity.\n\nThis definition acknowledges that aspects of good health, whether at the level of people or populations, transcend a narrow medical perspective. For example, the UN Committee on Economic, Social, and Cultural Rights (2000) interprets the right to health as an inclusive right extending not only to timely and appropriate health care but also to the underlying determinants of health, including access to potable water and adequate sanitation, an adequate supply of safe food, nutrition and housing, and healthy occupational and environmental conditions, among other things. This wider framing has placed urban planning, management and development squarely at the centre of current and future efforts to secure health and wellbeing.\n\nOne consequence of the framing of human health as broader than solely ‘the absence of disease or infirmity’ is that securing good health requires action beyond the health sector. The grounds for a non-medical approach to health were consolidated in the Alma Ata Declaration (WHO, 1978), which states that’the attainment of the highest possible level of health is a most important world-wide social goal whose realisation requires the action of many other social and economic sectors in addition to the health sector’.\n\nAnother significant conceptual advance supporting the need for urban health activity beyond health care is the place-based, or settings approach. The foundational document for the settings approach is the WHO Ottawa Charter (WHO, 1986), which recognised that ‘Health is created and lived by people within the settings of their everyday life; where they learn, work, play and love.’ In legitimizing this approach, the Ottawa Charter provided a strong framework to challenge the sometimes-dominant perception of healthcare systems as the sole (or primary) means for creating and sustaining health. Moreover, the Charter saw health as a ‘resource for everyday life’, not simply a final objective. The Ottawa Charter contained calls across several ‘areas for action’. Among those that were particularly innovative for the development of the concept of urban health, was the call for nations to create supportive environments; stipulating that protection of the natural and built environments and conservation of natural resources must be addressed in any health promotion strategy. Other areas of emphasis included; strengthening community action, building ‘Healthy Public Policy’, and recognizing that the responsibility for enabling, mediating, and advocating for health promotion lay with a variety of stakeholders including those outside the health sector. Coalescence of the ‘Healthy Public Policy’ concept can be found in Promoting Health through Public Policy (Milio, 1980 and 1986), supporting its key role in the Ottawa Charter. Healthy Public Policy advocates using the goal of positive health outcomes across all public policy areas. Its ambition is to create social and economic and environmental conditions for health at population level. As recent commentators note ‘Attention thus moves “upstream” to policies and institutions rather than “downstream” to behaviors or health services’ (Harris and Wise, 2020, p. 1).\n\nMore recently, we have seen the rise of the ‘Health in All Policies’ (HiAP) framework. HiAP as a moniker neatly captures the concept of Healthy Public Policy, giving it good policy traction. HiAP is also a developing approach to public policy that systematically accounts for the health implications of decisions in all sectors, seeks synergies, and avoids harmful health impacts to improve population health and health equity (Puska & Ståhl, 2010). It emphasises the importance of inter-sectoral work and policy coherence. HiAP relies heavily on the use of scientific evidence and evaluation tools, such as health impact assessments, which come in a wide variety of forms and may include testing of policy or project proposals, health economic assessment, and broad stakeholder input to inform the integration of health into a range of actions.\n\nIn broadening responsibility for health to non-health sectors there is an implied and sometimes explicit shift from curative to preventative approaches. For example, the Ottawa Charter articulates an ambition to ‘reorient health services’, stating that the health sector must move increasingly in the direction of health promotion, beyond clinical and treatment-based services. Public and urban health are now rising to this task, as they begin to embrace HiAP and health impact appraisal approaches that rely on processes less familiar to health practitioners, such as those for proposal and options testing for place-making, housing policy or urban infrastructure investment.\n\nThe 1978 Alma Ata Declaration also placed health equity firmly on the table: ‘The existing gross inequality in the health status of the people, particularly between developed and developing countries as well as within countries, is politically, socially, and economically unacceptable and is, therefore, of common concern to all countries.’\n\nIn 2005, WHO established the Commission on Social Determinants of Health to support countries and global health partners in addressing the social factors leading to ill health and health inequities. The Commission relied on several knowledge networks established to inform the report, including one which focused on urban issues. The Commission’s 2008 report and subsequent updates focus on improving daily living conditions, tackling the inequitable distribution of power, money, and resources; and better measuring and understanding the problem and assessing the impact of action.\n\nPartly based on the evidence and analysis in the Commission’s report, health equity has achieved greater and greater resonance in urban health thinking—where it has become a vital strand weaving together a multitude of perspectives—and even within the broader development discourse. The reach of health equity and its core focus on supporting health globally across population groups can be seen in the ever-relevant report from the World Health Organization, Centre for Health Development, and the United Nations Human Settlements Programme ‘Hidden Cities: Unmasking and Overcoming Health Inequities in Urban Settings’ (WHO/UN, 2010). This in turn provided a platform for the foundational document of modern sustainable development ‘Transforming Our World: the 2030 Agenda for Sustainable Development’ (UN, 2015); advocating that ‘a rights-based approach to health requires that health policy and programmes prioritize the needs of those furthest behind first towards greater equity’.\n\nOn-the-ground research has also contributed to the policy shift toward a greater focus on health equity. For example, a series of field studies in the 1990s in Latin America and Africa changed the landscape for urban health by demonstrating the enormous disparities between the health status of urban populations living in the most deprived compared to the least deprived areas (Stephens et al., 1994; Stephens, 1996; McGranahan et al., 1999). These types of studies helped shift the focus from the urban poor, as an isolated and at-risk sub-population, to the broader issue of urban inequity in town and city governance. Moreover, the work of Wilkinson in ‘The Spirit Level’ (Pickett and Wilkinson, 2010) showed that large income inequalities can lead to a breakdown in social cohesion, with both direct and indirect negative consequences for physical and mental health and wider impacts across society.\n\nGrowing understanding of what is now seen as a ‘web of causality’, along with experience in examining the process and outcomes of interventions that target the social and environmental determinants of health, have pushed the conceptual paradigm for urban health toward an embrace of complexity. The world is increasingly interconnected, complex. and uncertain, with significant implications for the way we generate, disseminate, and use knowledge.\n\nRecognition of the role of urban complexity and the need for systemic approaches in research, policy development, and the design and practice of implementation is slowly spreading, from antecedents which span the last several decades. For example, in the 1990s, work on transport, health and environment articulated issues for cross-sectoral cooperation for health in public policy (Dora & Phillips, 2000). HiAP, too, implicitly recognizes the role of complexity in contemplating cross-sectoral synergies. From the early 2000s, the International Science Council (ISC) has promoted transdisciplinary science as a means of grasping and dealing with complexity when interacting with the major challenges facing humanity—including urban health. Moreover, the ISC programme on Urban Health and Wellbeing, founded in 2014, has focused strongly on systems thinking as a means for understanding and addressing urban health and wellbeing challenges (Gatzweiler, 2020; Gatzweiler et al., 2017, 2023).\n\nIn parallel, the ongoing work of the Stockholm Resilience Centre (e.g. Rockström et al., 2009; Richardson et al., 2023) to define and raise awareness of planetary boundaries and their possible impacts on health has stimulated several systemic urban health research programmes. These include the Wellcome Trust’s Our Planet Our Health funding initiative and many other national programmes for non-medical public health place-based research (e.g. Canada’s Healthy Cities CIHR funding, Australia’s HEAL NHMRC funding, UK’s NIHR’s Public Health Research programme and streams within the US’s NiH programmes). Through the networks of researchers and stakeholders involved in projects funded by these programmes, we are starting to see the creation of a more widespread contemporary understanding of urban health.\n\nNot all innovation promoting a greater focus on complexity has come from the health side of the urban family: organizations that have brought attention to combined health and environmental issues in cities include city networks like Metropolis and Cities Alliance, civil society organizations like Slum Dwellers International, think tanks like IIED, and multilateral agencies like UN-Habitat, UNESCO, the OECD, and the World Bank. Intellectual work like Kate Raworth’s Doughnut Economics (2012) and other work on systems thinking (Puppim et al., 2015) has helped focus attention on the social origins of many environmental problems, helping to bridge the gaps between natural science assessments and potential applications in urban health, while signposting how integrated work on urban health needs to go beyond traditional urban planning.\n\nThe need to work on the upstream ‘causes of the causes’ of ill-health (Braveman and Gottlieb, 2014) is also gaining traction. For example, on how decision-taking in the built environment, housing, and construction sectors affects health (Pineo, 2022; Le Gouais et al., 2023), and on how approaches to financial risk, investment decisions and embedded culture in the development industry can influence health (Black et al., 2024). In parallel, new emphases are emerging on the Commercial (Gilmore et al., 2023) and Political Determinants of Health (Dawes and Gonzalez, 2023).\n\n\n4. WHO support for applied urban health action\n\nWHO has been a primary thought leader in urban health and a driving force globally for the application of sophisticated concepts to action, both through its own work and in collaboration with partners. This has included supporting initiatives for healthy cities and advocating for health promotion; conducting research and providing guidelines through the WHO Secretariat and Regional Offices and various specialized centres, joint work with UN-Habitat to amplify the links between health and urban planning, and the development of methodologies, tools, and data for urban health. This section highlights several of the most important strands of this work.\n\nOne of the most important developments in the modern history of urban health is the WHO Healthy Cities movement. This built on novel undertakings in Canada in the 1980s, where the city of Toronto had declared its ambition to become a ‘Healthy City’. The developers of the Ottawa Charter had a strong intent to move from statements to demonstrable change, establishing settings-based networks and supporting a shift in focus, from specific ‘problems to be solved’ towards a systemic approach to urban health.the WHO European Regional Office supported the initiation of a small pilot programme, inviting European cities to commit to a set of values and approaches concordant with the Ottawa Charter, further developed in Promoting Health in the Urban Context (Duhl & Hancock, 1988). This approach was accessible, with a prescient action agenda, and dozens of cities expressed their interest, not just the handful that WHO expected. Interest and commitment quickly radiated to other regions, including Australia, New Zealand, and Japan, where networks of Healthy Cities emerged and were supported by city and national governments. Following the call to action from Toronto and inspired by the booming European network, provincial networks of Healthy Cities also emerged across Canada. Around the world, other local urban initiatives adopted the original Healthy Cities values in part or in whole. For example, Central and Latin American towns that had worked toward primary health care-focused ‘Sistemas Locales Para la Salud’ felt empowered to establish broader new networks for Healthy Cities and Communities (‘Ciudades y Comunidades de Salud’). Networks of healthy cities and towns also emerged in the Maghreb and Southern African regions. In this rapid spread, the central message of the Alma Alta Declaration, that achieving health required the action of many other sectors in addition to health, finally found fertile ground. Each of these individual and networked entities emphasized different priorities as locally relevant. In some contexts, basic sanitary and environmental health concerns were prioritised, in others, processes of equitable urbanization or the wellbeing of slum dwellers. Although difficult to assess, one estimate puts the number of ‘Healthy Cities’ styled initiatives at more than 15,000 (De Leeuw, 2017).\n\nComprehensive academic assessment and evaluation of healthy city initiatives is sparse. Due to the complexity of attempting to demonstrate causality, published analyses tend to dwell on qualitative aspects and description of process (de Leeuw et al., 2015). What is apparent is the diversity of such efforts and the importance of certain key elements (Harpham & Molyneux, 2001; Grant, 2015). Such elements include: the level of understanding and degree of political ‘sponsorship’, especially among city leaders; the empowerment of citizens and their understanding of how their quality of life is impacted by urban health challenges; and the existence of mechanisms whereby local health issues and concerns can influence local environments and urban policy.\n\nThe emergence of the Healthy Cities movement drew greater attention to urban health in global policy discourses. For example, in 1991, the World Health Assembly (the governing body of the World Health Organisation) adopted a resolution focused on health development in urban areas (WHO, 1991). In response to growing urban populations combined with increases in exposure to health risks, it urged Member States to strengthen their capacity for healthy urban development. Specific actions included: implementation of policies to foster sustainable urban development and preserve health-supporting environments; assessment of the impacts of all urban policies on community and environmental health; and creation of structures and processes for inter-sectoral and community participation in urban policy development.\n\nThe Healthy Cities movement represented one of the first global city networks; since then, many others have emerged with synergistic values and comparable packages of commitments. Such themed networks include WHO’s Age-Friendly Cities network, as well as Transition Towns, Child-Friendly Cities, Smart Cities, Sustainable Cities, Resilient Cities, and Slow Cities (de Leeuw, Simos & Forbat, 2020).\n\nThe WHO designates Collaborating Centres to support its city -based work. In 1990, the Institute of Action Research for Community Health in Indiana was the first Global Collaborating Center in Healthy Cities. The WHO Collaborating Centre for Research on Healthy Cities in Maastricht was designated in 1992. However, it was not until 1995, that the WHO European Regional Office established a unit centred on spatial form with expertise in urban planning and place-making through evidence-based design. This was the Collaborating Centre for Healthy Cities and Urban Policy in Bristol, UK, a centre unique in its placement within in a built environment faculty, rather than a health faculty. Its distinctive mission was to build bridges between the health and urban constituencies by involving planners, urban designers, geographers and landscape architects in the health agenda. As such, its focus was to act as a European and national hub to embed a deeper understanding of urban form as a determinant of health into public health understanding and practice. As a result of this work, the governance, planning and design of the physical form of cities became a new focus for the WHO European Healthy Cities Network during the 2000s, with the emergence of the concept of ‘Healthy Urban Planning’ (Barton and Tsourou, 2000). Urban planning went on to become a thematic priority during successive phases of the WHO Healthy Cities initiative. European member cities started to pilot and promote the use of ‘The Health Map’ (Figure 1) (Barton & Grant, 2006; Dahlgren & Whitehead, 1991), a tool developed at the Bristol Centre to enable cross-sector understanding and collaborative working on the determinants of urban health. There are now four versions of the health map to suit different applications. Having been translated into over 30 languages, the Health Map now been adopted by a wide range of actors at international, national and local level (Grant 2023).\n\nAlso in 1995, WHO established the Centre for Health Development in Kobe, Japan (known as the Kobe Centre), a global research institution that quickly established a leadership role vis-à-vis the urban health agenda. An early symposium entitled ‘Urbanization: a global health challenge’ featured global experts in various sectors voicing support for inter-sectoral research in relation to complex health issues surrounding urbanization. The Kobe Centre was soon seen as a leader in promoting crosscutting research and new integrative approaches for analysing determinants of urban health (and for other pressing global health problems, like those of ageing societies). For example, in 2010, the Kobe Centre published the Urban Health Equity Assessment and Response Tool (Urban HEART), designed to help ministries of health and city-level health officials measure health inequities within and between cities. This tool has been applied in large metropolitan centres (populations over 1 million) in low- and middle-income countries around the world (Pakeman & Collins, 2018).\n\nThe preliminary activity at Kobe and Bristol thus laid the foundation for a stream of joint work on urban health involving the UN lead agencies for health and for urban settlements (WHO, 2010), much of this work focusing on the role of urban planning and spatial form.\n\nAlso in 2010, and in light of the continuing shift toward an eco-social rather than a biomedical view of health, there were two global landmark reports on urbanisation and health. The Kobe Centre co-produced a report on urbanisation and health with UN-Habitat. ‘Hidden Cities: Unmasking and Overcoming Health Inequities in Urban Settings’ (WHO/UN 2010a) sought to increase attention to urban health challenges, especially health inequities, by building a robust evidence base for action. In the same year, the final report from the ‘Global Research Network On Urban Health Equity’ provided an in-depth review of improving urban health equity through action on the social and environmental determinants of health, this included sections on urban planning and housing design (GRNUHE, 2010).\n\nIn 2016, the Kobe Centre and UN-Habitat co-produced a second major output, the ‘Global Report on Urban Health: Equitable healthier cities for Sustainable Development’ (WHO & UN-Habitat, 2016). This presented yet further evidence that in cities, health improvement depends not only on the strength of health systems, but also on shaping urban environments. Local governments typically have responsibility over many critical functions that determine liveability of cities such as land use planning, building standards, water and sanitation systems, roads and transportation, and environmental protection. Their actions can thus exacerbate or diminish health inequities. The report asserted that good governance for urban health demands a deliberately integrated approach across many different actors.\n\nAlso during 2016, the advent of the 3rd vicennial United Nations Conference on Housing and Sustainable Urban Development (Habitat III) in Quito elevated the intensity of coordinated urban health activity between WHO and UN-Habitat. With a view to influencing the meeting’s outcomes, WHO published ‘Health as the Pulse of the New Urban Agenda’ (WHO, 2016) in collaboration with experts and in addition the International Science Council programme on Urban Health and Wellbeing; other global science groups like Future Earth contributed thinking on the role of systems approaches in achieving urban sustainability (Bai et al., 2016). These inputs fed decades of theory and lessons from practical experience in urban health into the Habitat III process and the New Urban Agenda, reflecting the ideas and insights of a diverse community of researchers and practitioners.\n\nMore recent products arising from this collaboration include health input to UN-Habitat’s ‘International Guidance for Urban and Territorial Planning’, which features guidance on how to use spatial planning to achieve better health outcomes (‘Integrating Health in Urban and Territorial Planning: a sourcebook’) (UN/WHO 2020) and a collection of case studies. Urban health continues to grow as a focus for both agencies.\n\nOver its history, WHO has supported urban health through the work of its secretariat at global, regional, and country levels, providing technical guidance, supporting research, and advocating for action.\n\nThis has included technical guidance related to specific sectors, including active and sustainable transport (e.g., Health Economic Assessment Tool (HEAT1); Integrated Sustainable Transport and Health Assessment Tool (iSThaT2), green space (e.g., Green Urban spaces and health tool (GreenUr3), energy (e.g., Clean Household Energy Solutions Toolkit (CHEST), housing (e.g., WHO Housing and health guidelines4), and many others. These instruments are widely used: for example, HEAT, which estimates health benefits from healthy transport interventions, has been used by hundreds of cities worldwide and was recently upgraded to include climate pollutants as well as health. There is also an extensive and growing compendium of WHO and other UN guidance on health and environment, with over 400 items. More broadly, WHO provides targeted technical support for urban health in areas ranging from air pollution, non-communicable diseases (NCDs) and injuries, emergency preparedness for Covid-19 and other disasters, vector control, and more.\n\nWHO has also developed integrative implementation frameworks for urban health, like the Urban Health Initiative (UHI),5 which outlines a model process for integrating health into policymaking in the context of climate and air pollutants. Through such frameworks, it has also supported action research to estimate impacts of urban policies on a range of health impacts. For example, the UHI has applied Health Impact Assessment involving stakeholder and policy analyses to estimate expected co-benefits from sectoral policy alternatives to reduce air and climate pollutants in cities in low- and middle-income countries.\n\nAs discussed above, WHO has been instrumental in establishing major networks for urban health including Healthy Cities and Age-friendly Cities, and in supporting others like the Bloomberg Partnership for Healthy Cities. Through these networks and its own engagement, it has sought to mobilize urban health action—for example, through the BreatheLife 6 campaign which targets the implementation of city- and individual-level solutions for air pollution in support of global development goals.\n\nIn its 13th General Programme of Work (2019-2023), WHO recognized the relevance of urban health to its programmes across the board, setting up a new cross-cutting urban health unit within the new Department of Social Determinants of Health (SDH). Important objectives of this unit include harnessing the momentum of global work on urban health and supporting countries and local communities to develop positive urbanization trajectories for health equity. Strategic advice from external experts was applied to frame the overall SDH agenda and the need for a focus on urban health was one key insight. This advisory recommendation was grounded in a perceived need to increase visibility, better align, coordinate, and build on existing urban health work across the organization.\n\nThe urban health unit has worked to consolidate a number of strands of urban health work, including by better defining and articulating the scope and possibilities of urban health and of a more strategic approach to these issues—this document is one element of that work. Another significant effort was the development of a global Urban Health Research Agenda for 2022-2032, which drew on an extensive scoping review, widespread consultation, and global and regional mapping of activities and stakeholders. More recently, the unit launched a new repository on urban health—a living resource covering urban planning, housing, environmental issues, transport and mobility, nutrition, physical activity, COVID-19, and many others. This searchable system allows users to access WHO materials by health topic category, product type, geographical area, and year of publication/development.7\n\nSubstantial work on urban health has also been undertaken in WHO’s regional and country offices. For example, in 2011, WHO’s Western Pacific Regional Office published Healthy urbanization: regional framework for scaling up and expanding healthy cities in the Western Pacific (WHO, 2011), which called for a systems-wide approach to urban health, recognizing the need for strong support from national governments (WHO, 2010). This action-oriented framework adopted the Kobe Centre’s definition for healthy urbanization as ‘the process of enabling people to gain greater control over their health and their determinants through good urban governance that creates equal social opportunities for health for all’ (WHO KOBE, 2008). With similar intent, the Pan American Health Organization recently launched a Healthy Municipalities, Cities, and Communities initiative to promote intersectorality, community participation, and an approach centred on health equity. As noted above, WHO’s European region has just celebrated 35 years of progress under its Healthy Cities Network initiative.\n\n\n5. Urban health in academia, education and research\n\nAlthough urban health emerged as an important component of international public health practice during the mid-1980s, it was not until the 2000s that a widely accepted academic framework to guide research was developed (Vlahov & Galea, 2003). Recognition that health services alone could not effectively tackle health problems led to an increasing policy emphasis on intersectoral action (‘joined-up government’) in higher-income countries, and in turn to research funding programmes that supported interdisciplinary research teams. This and other trends led to what was initially referred to as a ‘new public health’ and eventually to the formal discipline of ‘urban health’ (Harpham and Molyneux, 2001).\n\nObserving worrying trends of increasing ill-health, academics saw that supporting the health of urban populations demanded a re-think, with a particular focus on the role of public health research. For example, many urban areas were experiencing a shift from predominantly communicable to a trend of rising non-communicable diseases. This shift took place most rapidly in countries with the highest levels of urbanisation (PAHO, 1998; Harpham and Tanner, 1995). Some risk factors for non-communicable disease in these contexts involved individual behaviours; others were more directly associated with urban environments themselves (Harpham and Molyneux, 2001). In low-income countries, studies in the 1990s demonstrated that despite major advances in reducing communicable diseases in urban areas, communicable diseases continued to play a major role in urban mortality. In public health circles, the concepts of ‘burden of disease’ and ‘determinants of health’ became more prominent in the twin battle against rising communicable and noncommunicable disease in lower-income countries. The term ‘urban penalty’ was proposed to account for an excess burden of disease associated with urban living (Gould, 1998).\n\nArguably, evolution of ‘urban health’ as a separate academic area of work was accelerated by the UN ‘World Urbanization Prospects’ (2000) report, which announced that over half of the world’s population lived in urban areas, with trends suggesting that by 2050 this would reach over two-thirds. The report led to increased global interest in urban health in both the academic and policy communities.\n\nIn step with the development of urban health research, there was a new emphasis on academic education, publishing and scholarly professional practice in the field. One significant point in the rise of urban health as a discipline was the New York Academy of Medicine reorienting and retitling their house journal in 1998 to become the Journal of Urban Health, followed in 2002 by their establishment of the International Society for Urban Health. In 2003, the Academy hosted a meeting, co-sponsored by several global academic and public health institutions, that underscored the intellectual foundations for evidence-based urban health (Vlahov & Galea, 2003).\n\nBy 2006, the Handbook of Urban Health had been published (Galea & Vlahov, 2006), and with widening academic discourse and a growing evidence base, it was soon followed by many other books—for example, the notable ‘Urban Public Health: A Research Toolkit for Practice and Impact (Lovasi et al., 2020; Galea et al., 2019). New journals, such as Transport & Health (established in 2014), Cities & Health (2017) and Infrastructure & Health (2022) have also helped broaden the field.\n\nAcademic educational programmes and policy-focused publications in urban health sit at a crossroads between research, policy, and practice. The goal of urban health in public policy is institutional transformation towards a healthy, equitable and sustainable future, and educational programmes at undergraduate and professional levels have an important part to play. Because many professions with profound impacts on health outcomes have no formal public health input in their training, a transdisciplinary and multi-professional approach to urban health education presents challenges but also significant opportunities (Corburn et al., 2014). Indeed, the number of courses tackling urban health increases constantly, both on-line and in-person, at undergraduate and postgraduate levels, and in the context of professional development.\n\nGlobally, the past 10 years saw the emergence of the first courses, research projects, funding programs, university departments, and academic institutes devoted to urban health in many disciplinary contexts; there is now a critical mass of these in most geographic regions. An analysis of these various traditions show, however, still a significant disconnect between disciplinary foundations (Kim et al., 2022).\n\nGiven the significant health implications of urban environments and urbanization, cities and other urban health actors need detailed information on health needs and outcomes linked to demographic, economic, cultural, physical, and environmental data (WHO, 2023). Establishing effective mechanisms for monitoring urban health and health equity is essential (Caiaffa et al., 2014). Robust data, used wisely, can help integrate actions across existing systems in both health and non-health sectors (e.g., urban planning, urban resource and infrastructure investment, city development, transport, trade, food systems, etc.).\n\nOne approach to addressing the obstacles presented by the wide range of factors that influence health and the dispersed and uncoordinated nature of relevant data (Dias et al., 2015) is the ‘public health observatory’—or in urban settings, the ‘urban health observatory’ (UHO). However, the concept of health observatories dates back to the late 19th and early 20th centuries. Early efforts included the establishment of local health boards and the collection of vital statistics in cities like London, Liverpool and New York. The idea of health observatories gained momentum in the latter half of the 20th century, coinciding with advancements in epidemiology, data collection, and computing technologies. The focus on urban health observatories specifically emerged in the late 20th and early 21st centuries, driven by increasing urbanization and the recognition that cities face unique health challenges.\n\nKey milestones include: WHO support in 1998, through launching the Health Metrics Network to improve health information systems globally; the European Urban Health Observatory (EURO-URHO), established in the early 2000s. In 2006, UN-Habitat reported the existence of 119 local urban observatories, its Global Urban Observatory Unit oversees and coordinates approximately 374 today and focuses on monitoring urban conditions and trends, including health indicators, to support sustainable urban development.\n\nUrban health observatories act as focal points for urban data, collecting, monitoring, analyzing, and managing information on urban health and health equity. They monitor and assess health determinants and outcomes in the urban populations they serve, often focusing on social inequalities and urban health inequities. They generally operate within large urban areas facing issues related to unplanned urbanization, fluctuating populations, health inequities, and the need for sub-population, urban and sub-urban, and neighborhood-level health intelligence. In many areas, including but not restricted to informal settlements, regularly collected, reliable data does not exist, However, a wealth of new data is available from modern technologies like earth observation, mobile phone, and other spatial sources (Thomson et al., 2019), among others. Information and communications technologies, too, play a crucial role in helping many observatories enhance decision-making and improve health outcomes. Many Urban health observatories established partnerships with diverse stakeholders to understand the impact of wider determinants of urban health (Castillo-Salgado, 2015). Early examples of Urban health observatories included those in Barcelona (established in 2000) and in Belo Horizonte (established in 2002).\n\nIn recent years, the rise of big data, advanced analytics, and geographic information systems has further enhanced the capabilities of urban health observatories. They now integrate diverse data sources, including electronic health records, environmental data, and social determinants of health, to provide a comprehensive view of urban health. By 2010, urban health observatories had been established in every inhabited continent, countries hosting one (or more) included the UK, Spain, France, Canada, USA, Brazil, Chile, South Africa, Kenya, India, China and Australia. A decade ago, the Asia-Pacific Urban Observatory Network and Africa Centre for Disease Control and Prevention Health Observatory were also established.\n\n\n6. Urban health in policy, practice and process\n\nIn the preceeding text, the many elements that are supporting the emergence of a new and distinct concept of urban health have been described. This section briefly outlines how applied action on urban health, in policy, practice and process has evolved. There is no doubt that experiential knowledge, which is essential to action on-the-ground, has been gleaned from implementation has accumulated in part through case studies of successful local projects and practices. At times, such work is initiated by urban health advocates, but given the numerous potential synergies and co-benefits with other urban agendas, lead actors can arise from many other sectors. The recent WHO/UN-Habitat publication, ‘Integrating health in urban and territorial planning’ serves as a sourcebook for ‘entry points’ for urban heath, linking to over 50 resources, most outside the traditional public health sector (UN/WHO 2020).\n\nRecent examples of integrative urban health policy and practice include the large number of individual town- or city-level initiatives that support population health, such as implementing 15/20 minute neighbourhoods, school streets, cycling towns/cities, urban food growing, or a plethora of low-emission zones for traffic, among others. This burgeoning of ways to support urban health mirrors the 12 key agendas listed in the ground-breaking Healthy Urban Planning (2000), published some twenty years earlier.\n\nIn parallel, cities have become involved in a wide variety of networks, such as Local Governments for Sustainability, United Cities and Local Governments, Cities Alliance, C40 Cities, and Bloomberg Cities; each has different membership and fundamental goals, but all act in ways that are relevant to health and heath equity—several even have specific urban health thematic sub-networks. At national-level, a significant example of a systemic policy relevant to urban health is the Welsh Government’s Well-being of Future Generations Act (Welsh Government, 2015). Here the sustainable development concept of futurity is translated to a national legal framework, binding together population and planetary health in ‘a law to improve social, economic, environmental and cultural well-being’. In developing countries, there has been a project-level shift in focus from ‘vulnerability’ to ‘resilience’ for urban health. In practice, this has seen greater local-level participation through collaborations with those embracing a community assets-focussed and action-oriented agendas (Harpham, 2009). At higher levels, international Healthy Cities Health Impact Assessments meetings have, for instance, supported the inclusion of health in the Strategic Environment Assessment protocol of the Environment Impact Assessment convention (Dora, 2019). Whereas prior work tended to be limited to documenting health damage from climate change and implementing measures for adaptation, a better understanding of health co-benefits from interventions to mitigate climate change (WHO, 2012; Ganten et al., 2010) has introduced a Health in All Policies focus into climate impact policy.\n\nThis experiential knowledge, arising from policy and practice, is itself creating a new focus, not always captured in the academic literature but essential for long-term health outcomes. It has yielded a pragmatic emphasis on process. It is not enough to know ‘what to do’, attention must also be given to ‘how to do it’; this highlights, among other things, the critical nature of governance and stakeholder participation (Harris, 2022).\n\n\n7. Moving forward on urban health\n\nOver the last 75 years, a host of real-world events and our reactions to them have enriched our conception of urban health dynamics. Prodigious urbanisation, a rise in non-communicable diseases, a global pandemic, better knowledge about the determinants of health, improved data, and the development of coalitions of stakeholders in cities, academia and practice have all contributed to these conceptual shifts. This contemporary history of the development of the urban health paradigm illustrates its steady growth, from strong founding principles in the novel assertion of the right to health during the previous century to a rich breadth of policy and practice in the modern day, supported by a variety of resources, tools, and an ever-growing body of research and local experience.\n\nWe have witnessed interest in urban health grow in parallel in different domains, including many not traditionally thought of as having a public health interest. As a concept it is readily understood by those outside the health field. Urban health provides a vehicle to:\n\n• link sustainable development with population health by promoting local health solutions that also have planetary health co-benefits,\n\n• address communicable and non-communicable diseases through health and health equity-benefiting urban design, planning, and governance,\n\n• achieve co-benefits by supporting collaborations of health and non-health policy actors, including city planners and urban designers, economists, transport planners, architects, landscape practitioners and others.\n\nUnderstanding the genesis of this interdisciplinary endeavour—the different strands of urban health, and their origins and motivations—should be an entry point for achieving a wide range of other global policy goals. A strategic approach to urban health can meet the significant challenges of supporting urban populations whilst also addressing the challenges that supporting urban living generates for global sustainability. While some of the insights from 75 years of evolving understanding of urban health and wellbeing have been incorporated into the Sustainable Development Goals, it is far from clear that the global agenda has taken sufficient account of lessons learned. Over the last few decades, the paradigm of urban health has been transformed. This briefing has attempted to describe the key shaping factors and some of the drivers of that transformation. However, it only represents a snapshot in time. The transformation continues, and with many global pressures now bringing into focus how vulnerable human health is on the planet, this transformation is likely to accelerate.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nAcknowledgements\n\nThe authors would like to acknowledge the guidance and support of José Siri from the WHO Urban Health team.\n\n\nReferences\n\nBai X, Surveyer A, Elmqvist T, et al.: Defining and advancing a systems approach for sustainable cities. Curr. Opin. Environ. Sustain. 2016; 23: 69–78. Publisher Full Text\n\nBarton H, Tsourou C: Healthy urban planning: a WHO guide to planning for people. WHO/SPON; 2000.\n\nBlack, et al.: Phase I Report: How can we prevent non-communicable disease and health inequalities resulting from UK city property development and transport planning systems? Bristol University: TRUUD; 2024.\n\nBarton H, Grant M: A health map for the local human habitat. J. R. Soc. 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Nairobi: UN-HABITAT and Geneva: World Health Organization; 2020.\n\n\nFootnotes\n\n1 https://www.who.int/tools/heat-for-walking-and-cycling.\n\n2 https://www.who.int/europe/tools-and-toolkits/isthat--the-integrated-sustainable-transport-and-health-assessment-tool\n\n3 https://www.who.int/europe/tools-and-toolkits/greenur--the-green-urban-spaces-and-health-tool\n\n4 https://www.who.int/publications/i/item/9789241550376\n\n5 https://www.who.int/initiatives/urban-health-initiative\n\n6 https://www.ccacoalition.org/content/breathelife\n\n7 Local action for health: a repository of WHO resources at https://urbanhealth-repository.who.int/home (30 June 24)" }	[ { "id": "331691", "date": "22 Nov 2024", "name": "Aimee Afable", "expertise": [ "Reviewer Expertise Health equity research", "maternal health", "immigrant and urban 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\nWhile the paper does a fairly comprehensive treatment outlining the history of the urban health paradigm, it relies heavily on authoritative global health agency practice, positions, and frameworks.\n\nMy review concerns two areas:\n1) Authors conclude the following: While some of the insights from 75 years of evolving understanding of urban health and wellbeing have been incorporated into the Sustainable Development Goals, it is far from clear that the global agenda has taken sufficient account of lessons learned.\n\nHowever, this statement lacks a thorough discussion of what lessons were learned in the past 75 years -- other than the evolving frameworks. What is the evidence base?\nThis may be too broad but perhaps illustrative examples would be useful.\n2) Related to above, what do authors opine are the major global pressures of our time? How do these new global pressures inform this new urban health paradigm? The authors do not seem to clearly articulate what the emerging health paradigm is. There is limited discussion and treatment of both classic and contemporary theoretical frameworks that exist in the social sciences that may advance this thinking. Section 5 highlights Vlahov and Galea. However, in the spirit of transdisciplinary approaches to solving the major urban health challenges of our time -- shift from communicable to NCDs, emergence of novel viral pandemics, crisis management/adaption in the face of climate change, rising inequality/health inequity in established/older cities in more affluent countries, gentrification -- there is no consideration of some of the critical frameworks from other disciplines that can help advance our thinking on how to inform a new health paradigm. There is much insight that can be learned from the fields of social epidemiology (in public health with emphasis on the social determinants of health) and urban planning/development theory (Lewis, Mumford).\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Partly\n\nAre all factual statements correct and adequately supported by citations? Partly\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Partly", "responses": [] }, { "id": "331697", "date": "09 Dec 2024", "name": "Priya Balasubramaniam", "expertise": [ "Reviewer Expertise Mixed Health Systems", "Digital Health Transformation", "Private Sector Innovation in Health care provision and access" ], "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 robustly traces the evolution of the urban health paradigm that highlights key past frameworks like the Health in All Policies (HiAP), the Ottawa Charter, and Healthy Public Policy. It also references systems thinking, equity, and complexity as core theoretical lenses for understanding urban health dynamics and a bold recommendation to move away from older frameworks to newer paradigms and emerging issues in Urban Health . These provide a strong foundation, but there are a few gaps that could be addressed in the remit of this article.\nStrengths:\nThe focus on the settings-based approach and systemic determinants of health is comprehensive. Incorporation of complexity science to frame urban health challenges is forward-thinking. Historical references to the Alma Ata Declaration and WHO initiatives contextualize the paradigm's evolution.\n\nGaps:\nThe frameworks largely neglect the integration of digital health transformation in urban health , which is rapidly reshaping urban health systems. The article could incorporate frameworks like digital ecosystems and their potential to address urban health inequities through data analytics, telemedicine, and AI-driven decision-making. The private health sector's role is also underemphasized who is often a key play in urban health systems in emerging economies with mixed health systems. A pragmatic discussion of mixed health systems and private sector dynamics could strengthen the conceptual framing, especially regarding regulatory frameworks, financing models, and partnerships.\n\n2. Digital Health Transformation The omission of digital health as a transformative tool is a significant gap, given its increasing relevance in urban health:\nSuggested Additions:\nInclude a discussion on the role of digital platforms in improving access to urban health services, particularly for underserved populations. Explore frameworks like the Digital Health Ecosystem Model, emphasizing the interplay between governance, technology, and stakeholders in urban settings. Highlight innovations such as mobile health (mHealth), eHealth tools, and AI applications in predictive urban health surveillance.\n\nRationale: Digital health can bridge gaps in healthcare access and quality in urban areas, where infrastructure is often unevenly distributed. Including this dimension would make the article more relevant to contemporary challenges and opportunities.\n3. Role of the Private Health Sector The private health sector is critical in urban settings, especially in low- and middle-income countries, where it often fills service delivery gaps:\nSuggestions for Inclusion:\nDiscuss how private providers can complement public health efforts through partnerships, performance-based contracting, or shared accountability models. Examine innovative financing mechanisms (e.g., social impact bonds) and their role in incentivizing private sector participation in urban health initiatives. Incorporate case studies that illustrate successful integration of private sector solutions in urban health systems (e.g., public-private partnerships in urban clinics or insurance schemes tailored to urban populations).\n\nTheoretical Contribution: The article could introduce theories of market dynamics and public-private synergies, focusing on balancing equity, efficiency, and accessibility in urban health.\n4. Suggestions would be useful in the scope of this forward thinking article if\nThe authors should explicitly recognize the transformative potential of digital health and private sector partnerships as key drivers of the next phase of the urban health paradigm. A section dedicated to exploring how these two elements can operationalize the theoretical concepts of systems thinking and equity would enrich the discussion.\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": [] }, { "id": "353471", "date": "09 Jan 2025", "name": "Nicholas Freudenberg", "expertise": [ "Reviewer Expertise urban health", "health equity", "role of social movments in 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 paper is a competent and useful summary of some of the developments in urban health. In this review, I highlight gaps and concerns to give the authors an opportunity to consider these points.\n\nThe review feels curiously dated with more emphasis on the developments of the first 30 years and less on the last 10 years. Of the 75 references, only 30 were published in the last 10 years. Since others have written about the earlier years, I was hoping for more focus on recent developments.\nSome issues that could receive more attention include: 1. The emergence of the frameworks of commercial and political determinants of health. These are mentioned only briefly but, in my view, they pose existential and profound threats to the health of urban residents in particular and deserve more attention. More broadly, a summary of the body of literature on the political economy of cities and its impact of health would be valuable. 2. Worldwide and in cities, challenges to democracy pose serious threats to the health of populations and to health equity. How does this play out in cities and what have we learned in the last 10 years about the threats and possible responses? 3. Covid 19 is barely mentioned yet is has had a profound influence on the health of urban populations and the scholarly discourse on urban health. What have we learned and what are priorities for further research on pandemic threats to cities? 4. In my read of urban health history over the last 150 years, it has been social movements that have led to the most significant advances in population health and health equity yet there is almost no mention of social movements and their potential and limitations. Some discussion of this would enhance the article.\n\nIt is easy for a reviewer to identify gaps, and it is authors who decide how best to use their limited space. In my view, addressing the issues listed here would make a useful report more useful.\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": [] }, { "id": "353478", "date": "22 Jan 2025", "name": "Trevor Hancock", "expertise": [ "Reviewer Expertise Public health", "health promotion", "healthy cities and communities", "planetary and environmental health", "health policy & planning", "health futurism" ], "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 answered ‘partly’ to three of the four questions because : a) it would be hard, if not impossible, to be comprehensive given such a large field of thought and practice extending over several decades. However, this review covers the major global developments and initiatives well. b) language accessibiliutry depends upon the audience. This would not be accessible to the general public, and perhaps not to an academic audience not familiar with some of the concepts. However, it is well written and is accessible for me. c) There is no ‘Conclusions’ section, but Section 7 is about ‘Moving Forward, and I have some thoughts, noted below, about how this section could be strengthened. Here are my main comments; I also noted some minor typos that I list at the end. 1. Given “The modern urban context requires fresh thinking about how best to maximise urban health and wellbeing”, maybe change the title to read “The emergence of a modern paradigm for urban health and wellbeing” 2. Given several references to wellbeing, I was surprised to see no reference to the Geneva Charter for Well-being (WHO, 2021) and no expansion on the concept of a wellbeing society as it would apply to a city or community, one that would be committed to “achieving equitable health now and for future generations without breaching ecological limits”. This would be a useful idea to consider in Section 7 3. On P 5 – the section on HPP should reference the 1984 Beyond Health Care conference that launched the concept and the 1988 Second WHO Health Promotion conference on Healthy Public Policy in Adelaide that resulted in the Adelaide Statement, and included a section on Healthy Public Policy at the Local Level that resulted in an edited book (A. Evers et al. (eds.), Healthy Public Policy at the Local Level. Frankfurt/Boulder: Campus/Westview, 1990) 4. Towards the end of section 3, in the discussion of health and planetary boundaries and sustainability, it is worth noting that the links between health and sustainability were developed in the 1990s (see e.g. Hancock, Trevor (1996) “Planning and creating healthy and sustainable cities: the challenge for the 21st century.” In C. Price and A. Tsouros (eds.), Our Cities, Our Future: Policies and Action for Health and Sustainable Development. Copenhagen: WHO Healthy Cities Project Office; Hancock, Trevor (1996) Healthy, sustainable communities: concept, fledgling practice and implications for governance Alternatives 22 (2), pp 18-23; Hancock, Trevor (2000) Healthy Communities Must Be Sustainable Communities Too Public Health Reports 115 (2 and 3): 151–6) 5. There is no mention of ecology or ecosystems at all, and only a brief discussion of planetary boundaries in section 3.4 (Complexity and the ‘causes of the causes’ of ill-health ). I see a need for a paragraph or two expanding on “we are starting to see the creation of a more widespread contemporary understanding of urban health” that would incorporate the concept of the ecological determinants of health, planetary health and planetary boundaries (e.g. Hancock, 2018: “Healthy Cities 2.0: Transitioning towards ‘One Planet’ cities” (Key challenges facing 21st century cities, Part 3) Cities & Health 1 (3) 6. There is only a passing reference to the new economics (e.g. the application of Donut Economics at the urban level) and the importance of the commercial determinants for urban health (including the role of the private sector in urban development, housing, food systems and urban heating and urban pollution). These are new/emerging areas that merit some expanded discussion in section 7 7. P 12, section 7 – I would add to “Prodigious urbanisation . . .” the emerging threat to health posed by what the UN calls “the triple planetary crisis” of climate change, biodiversity loss and pollution as well as other global ecological changes that are crossing planetary boundaries. Also, a brief discussion of the ecological injustice dimensions of declining planetary health\nTypos P 7, first line – “towards a systemic approach to urban health.the WHO European Regional Office” should read “towards a systemic approach to urban health. The WHO European Regional Office” P 7, section 4.2 - “a centre unique in its placement within in a built environment faculty” - delete ‘in’ P 7, section 4.2 - “the Health Map now been adopted by a wide range of actors” should read “the Health Map has now been adopted by a wide range of actors” P 12, section 6 – “has been gleaned from implementation has accumulated in part” should read “has been gleaned from implementation that has accumulated in part” P 12, section 6 – “those embracing a community assets-focussed and action-oriented agendas” – delete one ‘s’ in ‘focussed’ and the ‘s’ on ‘agendas’\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Partly\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Partly\n\nAre the conclusions drawn appropriate in the context of the current research literature? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-987

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